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. 2023 Aug 29;18(8):e0290735. doi: 10.1371/journal.pone.0290735

Enterobacter cloacae infection characteristics and outcomes in battlefield trauma patients

William Bennett 1,2,*, Katrin Mende 1,3,4, Wesley R Campbell 5, Miriam Beckius 1, Laveta Stewart 3,4, Faraz Shaikh 3,4, Azizur Rahman 3,4, David R Tribble 3, Joseph M Yabes 1,2
Editor: Dona Benadof6
PMCID: PMC10464967  PMID: 37643169

Abstract

Enterobacter cloacae is a Gram-negative rod with multidrug-resistant potential due to chromosomally-induced AmpC β-lactamase. We evaluated characteristics, antibiotic utilization, and outcomes associated with battlefield-related E. cloacae infections (2009–2014). Single initial and serial E. cloacae isolates (≥24 hours from initial isolate from any site) associated with a clinical infection were examined. Susceptibility profiles of initial isolates in the serial isolation group were contrasted against last isolate recovered. Characteristics of 112 patients with E. cloacae infections (63 [56%] with single initial isolation; 49 [44%] with serial isolation) were compared to 509 patients with bacterial infections not attributed to E. cloacae. E. cloacae patients sustained more blast trauma (78%) compared to non-E. cloacae infections patients (75%; p<0.001); however, injury severity scores were comparable (median of 34.5 and 33, respectively; p = 0.334). Patients with E. cloacae infections had greater shock indices (median 1.07 vs 0.92; p = 0.005) and required more initial blood products (15 vs. 14 units; p = 0.032) compared to patients with non-E. cloacae infections. Although E. cloacae patients had less intensive care unit admissions (80% vs. 90% with non-E. cloacae infection patients; p = 0.007), they did have more operating room visits (5 vs. 4; p = 0.001), longer duration of antibiotic therapy (43.5 vs. 34 days; p<0.001), and lengthier hospitalizations (57 vs. 44 days; p<0.001). Patients with serial E. cloacae had isolation of infecting isolates sooner than patients with single initial E. cloacae (median of 5 vs. 8 days post-injury; p = 0.046); however, outcomes were not significantly different between the groups. Statistically significant resistance to individual antibiotics did not develop between initial and last isolates in the serial isolation group. Despite current combat care and surgical prophylaxis guidelines recommending upfront provision of AmpC-inducing antibiotics, clinical outcomes did not differ nor did significant antibiotic resistance develop in patients who experienced serial isolation of E. cloacae versus single initial isolation.

Introduction

The microbiology of infections associated with combat-related injuries have transitioned to a predominance of Gram-negative bacilli since the Vietnam War, as early wound debridement and anatomic site-directed empiric antibiotics have reduced the number of infections secondary to Gram-positive organisms [1]. In the U.S. Naval Hospital in DaNang, Vietnam, 52% of severe extremity wound cultures prior to debridement grew Gram-negative organisms and 20% of the entire wounded cohort developed Enterobacter spp. bacteremia by the fifth day of hospitalization [2]. During military operations in Afghanistan, there was a similar prevalence (56%) of Gram-negative organisms from mangled lower extremities on pre-operative wound cultures [3]. Both theaters of war saw wound cultures trend toward a Gram-negative predominance as hospitalization progressed [4]. As modern combat-related injuries have led to a surge in Gram-negative hospital-related infections, multidrug-resistant Gram-negative (MDRGN) infections have become an increasing threat [5].

Microbiology of wounds and wound infections among blast casualties injured in Iraq and Afghanistan has been described, and a higher prevalence of MDR organisms was found in polymicrobial infections compared to monomicrobial infections [6]. In that analysis, Enterobacter spp. was the second most commonly isolated Gram-negative organism from polymicrobial cultures and was noted to have a shorter time from injury to first infection. As polymicrobial infections among blast wound infections were more likely to produce MDR organisms and Enterobacter spp. infections have a potentially quicker onset, earlier identification and treatment of Enterobacter spp. infections may improve patient outcomes.

As MDRGN infections were being recognized as a worsening threat to patients in military hospitals, U.S. civilian hospitals saw a similar rise in these challenging infections. In the early 2000s, an epidemic of carbapenem-resistant Enterobacterales spread across the northeastern United States [7]. A subsequent analysis by the Veterans Health Administration from 2006–2015 indicated that Enterobacter cloacae was one of the emerging pathogens with dramatically increasing resistance rates largely secondary to AmpC β-lactamase induction [8]. E. cloacae is initially phenotypically susceptible to 3rd generation cephalosporins (e.g., cefotaxime, ceftriaxone, and ceftazidime) in vitro; however, as high as 19% of isolates developed β-lactam resistance during treatment [912]. Making matters more difficult, clinical laboratories do not typically test for AmpC production, and molecular testing is required to differentiate between chromosomally-induced or constitutively-expressed plasmid AmpC [9]. Third-generation cephalosporins are also not the only AmpC inducers, as amoxicillin / clavulanic acid, cefoxitin, 1st generation cephalosporins, and carbapenems are similarly potent inducers [13, 14].

Guidance surrounding the treatment of E. cloacae focuses primarily on bacteremia secondary to respiratory, urinary, intravascular, or intra-abdominal sources, but largely neglects wound infections [15, 16]. Due to concerns regarding potential delays in transport/medevac of combat casualties, the Department of Defense (DoD) Tactical Combat Casualty Care (TCCC) guidelines recommend use of ertapenem for care of open traumatic wounds in the field [17]. In addition, the DoD Joint Trauma System (JTS) clinical practice guidelines, as well as non-DoD guidelines, recommend cefazolin for post-injury prophylaxis [18, 19]. As both ertapenem and cefazolin may induce AmpC production, there is concern of increasing β-lactam resistance negatively affecting patient outcomes in infections where E. cloacae is the primary pathogen. Herein, we assessed the epidemiological characteristics of patients with E. cloacae infections, characterized the antibiotic prescribing patterns used in the treatment of these infections and their effects on developing resistance, and examined clinical outcomes compared to battlefield trauma patients who developed bacterial infections associated with organisms other than E. cloacae. We described clinical characteristics and outcome differences between patients with single initial isolation of E. cloacae and patients with serial isolation to assess for antimicrobial resistance development.

Materials and methods

Study population and definitions

Data and specimens were collected through the DoD–Veterans Affairs Trauma Infectious Disease Outcomes Study (TIDOS), which is an observational, longitudinal study of infectious outcomes among military personnel who were wounded in Iraq or Afghanistan (2009–2014) [20, 21]. Criteria for inclusion in TIDOS were being ≥18 years of age, active-duty personnel or DoD beneficiaries injured during deployment, and medically evacuated to Landstuhl Regional Medical Center in Germany with subsequent transfer to a participating military hospital in the United States. The participating U.S. military hospitals were Brooke Army Medical Center (BAMC) in San Antonio, TX, and Walter Reed National Military Medical Center in the National Capital Region (NCR) (prior to September 2011 it was National Naval Medical Center and Walter Reed Army Medical Center). Patients were included if they had E. cloacae isolation associated with a clinical infection diagnosis. Patients with a clinical diagnosis of a bacterial infection attributed to an organism(s) other than E. cloacae comprised the comparator population for the analysis. The Institutional Review Board (IRB) of the Uniformed Services University of the Health Sciences (USU, Bethesda, MD) approved this study. Data and specimens were collected from individuals who provided authorization through informed consent and HIPAA authorization processes, or through an IRB-approved waiver of consent for use of de-identified data not obtained through interaction or intervention with human subjects.

Demographics, injury characteristics, and early casualty care data were obtained from the DoD Trauma Registry (DoDTR). Infection-related data (e.g., infection syndromes, microbiology, and antibiotic management) were collected from the TIDOS Infectious Disease module of the DoDTR [22]. Data on use of ertapenem in the prehospital setting were not collected by the DoDTR. Tetracycline use was excluded from the analysis as doxycycline was prescribed to military personnel deployed to Afghanistan for antimalarial prophylaxis and continued for 28 days following departure from the country, per DoD guidelines.

Infections were identified using a combination of clinical (e.g., signs and symptoms from direct observations) and laboratory (e.g., microbiology) findings, and classified based on National Healthcare Safety Network definitions, as previously described [20, 23]. Isolates recovered during workups for clinical infection were classified as infecting. Inclusion criteria for the single initial E. cloacae isolate group required patients to have an infecting E. cloacae isolate collected from the initial culture (may be either monomicrobial or polymicrobial) with no isolation from subsequent cultures. For the serial E. cloacae isolate group, all patients with multiple non-colonizing E. cloacae isolates cultured at least one day apart were included, as prior studies have determined that E. cloacae may develop resistance to β-lactams after one day of therapy [10]. If multiple isolates were collected on the first day of E. cloacae isolation, the isolates collected from sterile body sites (more likely to be a true infection) or more proximal wound sites (wounds less likely to undergo early amputation) were given preference. In addition, all isolates must have been stored in the TIDOS specimen repository.

Laboratory analysis

Identification and susceptibility testing of the E. cloacae isolates were performed using the BD Phoenix Automated Microbiology System (NMIC/ID-308 and NMIC-311 panels, BD Diagnostics, Sparks, MD). Antimicrobial susceptibility testing results were interpreted in accordance with the Clinical Laboratory Standards Institute (CLSI M100 30th edition) breakpoints to construct an antibiogram [24]. Initial and last isolates cultured from patients in the serial isolate group were compared to assess the changing resistance patterns and we regarded any isolates with intermediate susceptibility as resistant. As molecular assays to assess for AmpC were not routinely conducted at the military hospitals during the study period, data on AmpC induction were not available.

Statistical analysis

Patients with E. cloacae infections were analyzed against the comparator population of patients with non-E. cloacae infections. Characteristics of E. cloacae patients with single initial or serial isolates and characteristics were compared. Categorical variables were assessed using Χ2 and Fisher’s Exact Tests, where appropriate. Continuous variables were analyzed using Mann-Whitney U. Statistical analysis was performed using IBM SPSS Statistics 22 (Version 22 IBM, NY, 2013.). A p value of <0.05 was considered statistically significant.

Results

Population characteristics

A total of 112 patients with infections due to E. cloacae and 509 patients with non-E. cloacae infections met inclusion criteria for the analysis. The majority of patients were young males with median age of 24 years (interquartile range [IQR] 21–28) in the U.S. Army who suffered blast injuries from improvised explosive devices while on foot patrol in Afghanistan (Table 1). Patients diagnosed with E. cloacae infections sustained more blast injuries (89% vs 75%; p = 0.001) and burns (16% vs. 9%; p = 0.027), had higher first documented shock indices (1.07 vs 0.92; p = 0.005), received more blood products within the first 24 hours of injury (15 vs. 14 units; p = 0.032), and required a greater number of visits to the operating room (5 vs. 4; p<0.001; Table 1).

Table 1. Characteristics of patients with and without Enterobacter cloacae infection.

Characteristic, No. (%) Patients with E. cloacae infection (N = 112) Patients with non-E. cloacae infection (N = 509)a All Patients
(N = 621)
p-value
Age at injury, median (IQR) 23 (21–27) 24 (22–29) 24 (21–28) 0.065
Male 111 (99.1) 502 (98.6) 613 (98.7) 1.000
Branch of Service 0.449
    Air Force and Navy 5 (4.5) 36 (7.1) 41 (6.6)
    Army 68 (60.7) 298 (58.5) 366 (58.9)
    Marine 39 (34.8) 168 (33.0) 207 (33.3)
    Other 0 (0) 7 (1.4) 7 (1.1)
Combat Theater 0.069
    Afghanistan 108 (96.4) 460 (90.4) 568 (91.5)
    Iraq 4 (3.6) 31 (6.1) 35 (5.6)
    Non-theater 0 (0) 18 (3.5) 18 (2.9)
Combat Injury 108 (96.4) 476 (93.5) 584 (94.0) 0.239
Mechanism of Injury 0.001
    Blast 100 (89.3) 383 (75.2) 483 (77.8)
    Non-blast 12 (10.7) 126 (24.8) 138 (22.2)
Blast Type 0.410
    IED 93 (83.0) 346 (68.0) 439 (70.7)
    Non-IED 7 (6.2) 37 (7.2) 44 (7.1)
Injured on foot patrol 76 (67.9) 286 (56.2) 362 (58.3) 0.213
Burn 18 (16.1) 46 (9.0) 64 (10.3) 0.027
1st documented shock index, median (IQR) 1.07 (0.74–1.49) 0.92 (0.70–1.22) 0.93 (0.70–1.27) 0.005
1st 24 hour blood transfusion, median units (IQR) 15 (8–31) 14 (6–24) 14 (6–25) 0.032
Body Region of Injury 0.016
    Lower extremity 21 (18.7) 89 (17.5) 110 (17.7)
Upper extremity 7 (6.2) 26 (5.1) 33 (5.3)
    Both lower and upper extremity 82 (73.2) 334 (65.6) 416 (67.0)
    Non extremity 2 (1.8) 60 (11.8) 62 (10.0)
Injury severity score, median (IQR) 34.5 (24–45) 33 (24–43) 33 (24–43) 0.334
U.S. military hospital 0.004
    BAMC 36 (32.1) 94 (18.5) 130 (20.9)
    NCR 73 (65.2) 389 (76.4) 462 (74.4)
    Both BAMC and NCR 3 (2.7) 26 (5.1) 29 (4.7)
Mechanical ventilation 0.030
    LRMC only 16 (14.3) 126 (24.7) 142 (22.9)
    LRMC & U.S. hospital ≤1 week 55 (49.1) 242 (47.5) 297 (47.8)
    LRMC & U.S. hospital ≥2 weeks 3 (2.7) 4 (0.8) 7 (1.1)
    None 38 (33.9) 137 (26.9) 175 (28.2)
ICU admission 90 (80.4) 456 (89.6) 546 (87.9) 0.007
Number of operating room visits, median (IQR) 5 (4–6) 4 (3–6) 5 (3–6) <0.001
Hospitalization, median days (IQR) 57 (40.5–84.5) 44 (30–62) 45 (33–66) <0.001
Death 5 (4.5) 12 (2.4) 17 (2.7) 0.216

BAMC–Brooke Army Medical Center; ICU–intensive care unit; IED–improvised explosive device; IQR–interquartile range; LRMC–Landstuhl Regional Medical Center; NCR–National Capital Region

a Predominant non-E. cloacae infections include coagulase-negative staphylococci (13%), Pseudomonas aeruginosa (12%), Escherichia coli (10.5%), Acinetobacter calcoaceticus-baumannii complex (8%), and Enterococcus faecium (8%).

Ninety percent of the 621 patients in the population sustained extremity injuries with the patients with E. cloacae infections having a greater proportion compared to the non-E. cloacae infected patients (98% vs. 88%; p = 0.016; Table 1). Despite the higher initial shock indices and blood product requirements, there was no significant difference in the injury severity scores between E. cloacae and non-E. cloacae infected patients (35 vs. 33; p = 0.33). A higher proportion of patients admitted to BAMC developed a E. cloacae infection (32% vs 19% among patients with non-E. cloacae infections; p = 0.004). Although fewer patients with E. cloacae infections required mechanical ventilation (64% vs. 73%; p = 0.03) or intensive care unit (ICU) admission (80% vs. 90%; p = 0.007), they did have longer hospitalizations (57 vs. 44 days; p<0.001). Patients with E. cloacae infections received significantly more total days of antibiotic therapy (43.5 vs. 34 days p <0.001). These patients also were treated significantly more days with carbapenems, 1st generation cephalosporins, fluoroquinolones, and vancomycin (Table 2). There was no significant mortality difference between the groups and 97% of the total population survived (Table 1).

Table 2. Total duration of antibiotic use among patients with and without E. cloacae infectionsa.

Duration of Antibiotic Use, median days (IQR)
Antimicrobials Patients with E. cloacae infection (N = 112) Patients with non-E. cloacae infection (N = 509) All Patients (N = 621) p-value
Aminoglycoside 1 (0–7) 1 (0–4) 1 (0–4) 0.256
Carbapenem 12.5 (4–21.5) 9 (1–18) 9 (2–18) 0.003
Cephalosporin- 1st generation 8.5 (4–15) 7 (3–12) 7 (4–13) 0.018
Fluoroquinolone 9 (1.5–15.5) 5 (0–11) 5 (1–13) 0.003
Vancomycin 10 (2–27) 0 (0–0) 0 (0–0) <0.001
Total antibiotic durationb 43.5 (32.5–71.0) 34 (24–50) 36 (26–52) <0.001

IQR–interquartile range

a Antibiotics that were used for a median of zero days in both groups are not shown and include aminopenicillin, anti-pseudomonal penicillin, 2nd generation cephalosporin, 3rd generation cephalosporin, 4th generation cephalosporin, clindamycin, linezolid, macrolide, monobactam, penicillin, penicillinase-resistant penicillin, polymyxin, trimethoprim-sulfamethoxazole, and topical antibiotic therapy.

b Total antibiotic duration was calculated as the total number of days at least one antibiotic was administered. Any days on which no antibiotics were administered are not counted in this measure.

E. cloacae isolates were linked to 49 patients with serially infecting cultures and 63 patients with single initial infecting cultures. The patients with single initial and serial E. cloacae isolation were of similar median age (23 and 24 years, respectively), with the majority sustaining blast injuries (85.7% and 93.9%, respectively) resulting in a minority of burn wounds (15.9% and 16.3%, respectively) and a similar proportion of ICU admissions (81% and 79.6%, respectively; Table 3). There was a higher proportion of polymicrobial infections among the patients who had serial isolates compared to single initial isolates (86% and 67%, respectively; p = 0.021). Single initial vs serial isolation was not associated with a difference in number of operating room visits (median of 5 for both groups), length of hospitalization (median of 57 days for both groups), or death (5% and 4%, respectively; Table 3). Although there was not a significant difference in the duration of antibiotic therapy (median of 39 and 47 days for single initial and serial isolation respectively), there was a trend toward greater 1st generation cephalosporin utilization in patients who experienced serial isolation of E. cloacae (median of 11 vs. 7 days with single initial isolation; p = 0.052; Table 4); however, this does not control for duration of hospitalization and number of visits to the operating room, which would drive use of 1st generation cephalosporins in these trauma patients.

Table 3. Clinical characteristics of infected patients with single initial isolation of E. cloacae versus infected patients with serial isolation of E. cloacae.

Characteristic, No. (%) Patients with single initial E. cloacae isolation (N = 63) Patients with serial E. cloacae isolation (N = 49) Total Patients with E. cloacae isolation (N = 112) p-value
Age at injury, median (IQR) 22 (21–27) 24 (21–27) 23 (21–27) 0.343
Male 62 (98.4) 49 (100) 111 (99.1) 1.000
Branch of Service 0.403
    Air Force and Navy 2 (3.2) 3 (6.1) 5 (5.5)
    Army 36 (57.1) 32 (65.3) 68 (60.7)
    Marine 25 (39.7) 14 (28.6) 39 (34.8)
Combat Theater 0.441
    Afghanistan 60 (95.2) 48 (98.0) 108 (96.4)
    Iraq 3 (4.8) 1 (2.0) 4 (3.6)
Combat Injury 59 (93.6) 49 (100) 108 (96.4) 0.073
Mechanism of Injury 0.166
    Blast 54 (85.7) 46 (93.9) 100 (89.3)
    Non-blast 9 (14.3) 3 (6.1) 12 (10.7)
Blast Type 1.00
    IED 50 (79.4) 43 (87.7) 93 (83.0)
    Non-IED 4 (6.3) 3 (6.1) 7 (6.2)
Injured on foot patrol 40 (63.5) 36 (73.5) 76 (67.9) 0.322
Burn 10 (15.9) 8 (16.3) 18 (16.1) 0.948
1st documented shock index, median (IQR) 1.05 (0.70–1.48) 1.16 (0.83–1.51) 1.07 (0.74–1.49) 0.246
1st 24 hour blood transfusion, median (IQR) 15 (7–31) 14 (10–31) 15 (8–31) 0.930
Body Region of Injury 0.109
    Lower extremity 8 (12.7) 13 (26.5) 21 (18.7)
    Upper extremity 6 (9.5) 1 (2.0) 7 (6.2)
    Both lower and upper extremity 48 (76.2) 34 (69.4) 82 (73.2)
    Non extremity 1 (1.6) 1 (2.0) 2 (1.8)
Injury severity score, median (IQR) 34 (22–45) 36 (27–45) 34.5 (24–45) 0.516
U.S. military hospital 0.361
BAMC 19 (30.1) 17 (34.7) 36 (32.1)
NCR 41 (65.1) 32 (65.3) 73 (65.2)
Both BAMC and NCR 3 (4.8) 0 (0) 3 (2.7)
Mechanical ventilation 0.872
    LRMC only 9 (14.3) 7 (14.3) 16 (14.3)
    LRMC & U.S. hospital ≤1 week 32 (50.8) 23 (46.9) 55 (49.1)
    LRMC & U.S. hospital ≥ 2 weeks 1 (1.6) 2 (4.1) 3 (2.7)
    None 21 (33.3) 17 (34.7) 38 (33.9)
ICU admission 51 (81.0) 39 (79.6) 90 (80.4) 1.000
Number of operating room visits, median (IQR) 5 (4–7) 5 (4–6) 5 (4–6) 0.216
Polymicrobial infectiona 42 (66.7) 42 (85.7) 84 (75.0) 0.021
Hospitalization, median days (IQR) 57 (39–88) 57 (43–84) 57 (40.5–84.5) 0.904
Death 3 (4.8) 2 (4.0) 5 (4.5) 1.000

BAMC–Brooke Army Medical Center; ICU–intensive care unit; IED–improvised explosive device; IQR–interquartile range; LRMC–Landstuhl Regional Medical Center; NCR–National Capital Region

a Polymicrobial infection defined as a positive culture collected within ±3 days of the E. cloacae culture from the same anatomical site. Organisms predominantly isolated from polymicrobial infections were P. aeruginosa, E. faecium, E. coli, Acinetobacter calcoaceticus baumannii complex, Enterococcus faecalis, Aspergillus spp. and coagulase-negative staphylococci.

Table 4. Total duration of antibiotic use among patients with single initial isolation of E. cloacae versus patients with serial isolation of E. cloacaea.

Duration of Antibiotic Use, median days (IQR)
Antimicrobials Patients with single initial E. cloacae infection (N = 63) Patients with serial E. cloacae infection (N = 49) All Patients with E. cloacae isolation (N = 112) p-value
Aminoglycoside 1 (0–8) 1 (0–4) 1 (0–7) 0.153
Carbapenem 12 (5–20) 13 (4–22) 12.5 (4–21.5) 0.796
Cephalosporin- 1st generation 7 (3–15) 11 (6–15) 8.5 (4–15) 0.052
Fluoroquinolone 7 (0–15) 10 (3–16) 9 (1.5–15.5) 0.299
Vancomycin 12 (1–27) 9 (3–28) 10 (2–27) 0.911
Total antibiotic durationb 39 (30–63) 47 (35–72) 43.5 (32.5–71.0) 0.236

IQR–interquartile range

a Antibiotics that were used for a median of zero days in both groups are not shown and include aminopenicillin, anti-pseudomonal penicillin, 2nd generation cephalosporin, 3rd generation cephalosporin, 4th generation cephalosporin, clindamycin, linezolid, macrolide, monobactam, penicillin, penicillinase-resistant penicillin, polymyxin, trimethoprim-sulfamethoxazole, and topical antibiotic therapy.

b Total antibiotic duration was calculated as the total number of days at least one antibiotic was administered. Any days on which no antibiotics were administered are not counted in this measure.

Among the 84 patients with polymicrobial infections, Pseudomonas aeruginosa was the most frequently isolated (34.5%), followed by Enterococcus faecium (30%), Escherichia coli (26%), Acinetobacter calcoaceticus baumannii complex (17%), Enterococcus faecalis (15.5%), Aspergillus spp. (14%), coagulase-negative staphylococci (14%), Enterococcus spp. (11%), Klebsiella pneumoniae (9.5%), and Staphylococcus aureus (9.5%). When E. cloacae infections were examined based on whether the infections were polymicrobial (N = 84) or monomicrobial (N = 28), there was no difference in use of mechanical ventilation (68% and 61%, respectively; p = 0.583), ICU admission (83% and 71%; p = 0.170), number of operating room visits (median of 5 for both; p = 0.125), length of hospitalization (median of 56 and 58.5 days; p = 0.898), and death (5% and 4%; p = 1.00). Polymicrobial E. cloacae infections were further examined for 29 patients who had the combination of E. cloacae plus P. aeruginosa (with/without other pathogens). To evaluate a wider group of bacteria of high virulence, 49 patients with E. cloacae plus at least one bacterium of high virulence (i.e., P. aeruginosa, E. coli, K. pneumoniae, and/or S. aureus), with/without other pathogens, were assessed. All 29 patients from the E. cloacae plus P. aeruginosa combination group were also included in the 49 patients with E. cloacae plus bacteria of high virulence group. Use of mechanical ventilation (72% for patients with polymicrobial combination of E. cloacae plus P. aeruginosa, p = 0.183; and 73.5% for patients with polymicrobial combination of E. cloacae plus bacteria of high virulence, p = 0.327), ICU admission (90%, p = 0.081; and 86%, p = 0.128), length of hospitalization (median 71 days, p = 0.131; and median 67 days, p = 0.130), and death (10%, p = 0.612; and 8%, p = 0.612) were not significantly different compared to patients with monomicrobial E. cloacae infections. There was also no significant difference in the number of operating room visits between patients with monomicrobial E. cloacae infections and polymicrobial infections with E. cloacae plus P. aeruginosa (median of 5 and 6, respectively, p = 0.078); however, patients with the combination of E. cloacae plus bacteria of high virulence had a significantly higher number of operating room visits (median 5, IQR: 5–7) compared to those with monomicrobial infections (median of 5; IQR: 4–6; p = 0.034).

Enterobacter cloacae culture characteristics

All Enterobacter isolates were identified as E. cloacae (not E. cloacae complex). The majority of E. cloacae isolates were cultured from wounds (70%), followed by respiratory specimens (22%) and blood (6%) (Table 5). Seventy-five percent of the wound cultures were recovered from the lower extremities. Patients in the serial isolate group had a shorter duration from injury to E. cloacae isolation (median 5 days; IQR 3–13) than patients in the single initial isolate group (median 8 days; IQR 4–7; p = 0.046). For serial E. cloacae patients, the median number of days between the initial isolate and last isolate was 5 days (IQR: 2–20 days).

Table 5. Distribution of sources of initial E. cloacae isolates.

Sites of initial E. cloacae culture Initial Isolates (N = 112)
Wound a 78 (70%)
    Thigh 26 (33%)
    Lower leg 19 (24%)
    Pelvic, gluteal muscles, and genitalia 8 (10%)
    Knee 7 (9%)
    Foot and ankle 7 (9%)
    Upper arm and elbow 5 (6%)
    Forearm and hand 3 (4%)
    Head and neck 2 (3%)
    Abdomen 1 (1%)
Respiratory 25 (22%)
Blood 7 (6%)
Urine 1 (1%)
Intravascular Catheter Tip 1 (1%)

a The percentage for the specific wound sites is calculated using 78 as the denominator.

The comparative antibiogram between the initial and last E. cloacae isolates in the serial isolation group is shown in Fig 1. Amikacin, ceftazidime-avibactam, meropenem, and meropenem-vaborbactam retained 100% susceptibility between initial and last isolates. The last E. cloacae isolates were more resistant to almost all other antibiotics. The most notable decrease in susceptibility was noted for ceftriaxone, albeit not statistically significant (78% to 63% p = 0.121). All isolates were resistant to aminopenicillins, 1st generation cephalosporins, and cephamycins.

Fig 1. Comparative antibiogram of the E. cloacae isolates from the 49 patients in the serial isolation group.

Fig 1

Ordered by decreasing susceptibilities of the initial isolate.

Discussion

To the best of our knowledge, this study is the first to specifically characterize the significance that E. cloacae plays in battlefield trauma-related infections and broadly compare it against other bacterial infections. Battlefield trauma patients with E. cloacae infections more frequently presented with complex polytrauma resulting from blast injuries than patients with non-E. cloacae infection. Despite their critically-ill presentations, these patients did not require greater utilization of critical care, but they experienced lengthier hospitalizations, underwent a greater number of surgical interventions, and received longer durations of antimicrobial therapy. Secondarily, while patients who had serial E. cloacae isolates had a shorter duration from injury to 1st infecting isolate collection than those who had single initial isolates, there were no differences in characteristics or outcomes and no significant antibiotic resistance developed in the patients from whom E. cloacae was recovered multiple times. Although a large proportion of the E. cloacae infections were polymicrobial (75% of patients), there was no difference in outcomes (e.g., ICU admission, length of hospitalization, or death) when patients with polymicrobial and monomicrobial E. cloacae infections were compared, including when focused on specific polymicrobial combinations of clinical relevance (i.e., E. cloacae plus P. aeruginosa and E. cloacae plus bacteria of high virulence). The only significant difference between the patients with monomicrobial and polymicrobial infections was an increased number of operating visits among patients with the combination of E. cloacae plus bacteria of high virulence (i.e., P. aeruginosa, E. coli, K. pneumoniae, or S. aureus).

E. cloacae is the 4th most common Gram-negative organism causing bloodstream infections in over 200 medical centers in 45 different nations [25]. Notably, E. cloacae, as well as Klebsiella aerogenes and Citrobacter freundii have been found to be the most clinically relevant AmpC producers and AmpC’s conference of resistance to broad-spectrum β-lactams has been shown to produce significant adverse effects on clinical outcomes [26]. A 2002 study by Cosgrove et al. [27] evaluated health and economic outcomes for patients with a mean age of 63 years who had Enterobacter spp. infections cultured from several different anatomic sites that developed resistance to 3rd generation cephalosporins. Similar to other published reports [11, 12], they found that resistance developed in 10% of their population, producing an attributable longer hospital stay of 9 days, increased mortality relative risk of 5.02, and additional hospital cost of almost $30,000 [27].

In our study, compared to patients with non-E. cloacae infections, patients with E. cloacae had longer hospital stays (57 vs. 44 days) and required a significantly greater duration of antibiotic therapy (43.5 vs. 34 days); however, it should be noted that the duration of antibiotic therapy was the overall duration and not adjusted per length of hospitalization and number of operating room visits, which would impact antibiotic use (e.g., perioperative antibiotics). The comparison between patients with E. cloacae and non-E. cloacae infections did adjust for the occurrence of polymicrobial infections, including assessing clinically relevant combinations. A previous study using the TIDOS population identified that patients with P. aeruginosa infections had higher crude mortality compared to patients with infections attributed to other pathogens [28]. Therefore, we compared patients with monomicrobial E. cloacae infections to those with polymicrobial E. cloacae plus P. aeruginosa infections and there were no statistical differences in critical care or mortality between the groups. Among our total population, 17 (3% of 621) patients died and, without controlling for temporal relationship to infection or other potential factors that would potentially contribute to mortality, there was no significant mortality difference between those with and without E. cloacae infection (5% vs. 2%). In contrast to the 17% mortality reported by Cosgrove et al. [27], the low mortality in our patients is attributable to youth and overall better health prior to their battlefield wounds and E. cloacae infections.

It is noteworthy that 22% of our initial E. cloacae isolates were resistant to 3rd generation cephalosporins. Although this is lower than the prevalence of 36.4% that was seen in a national surveillance study that measured 3rd generation cephalosporin resistance amongst E. cloacae isolates cultured from American ICU patients [29], our study population’s baseline E. cloacae resistance to 3rd generation cephalosporins may have contributed to the comparatively adverse outcomes seen in the E. cloacae infection patients compared to those with a non-E. cloacae infection; although, analysis of that relationship was outside the scope of this study. Despite fewer admissions to the ICU and less need for mechanical ventilation (80% vs 90% and 66% vs. 73% between the E. cloacae and non-E. cloacae infection patients, respectively), patients with E. cloacae infections had higher first documented shock indices (1.07 vs. 0.92), received more blood products within the first 24 hours of care (15 vs. 14 units) and had more operating room visits (5 vs. 4), which may have been secondary to the fact that patients with E. cloacae infection suffered more blast injuries (89% vs. 75%) and burns (16% vs. 9%) resulting in greater fluid loss [30]. Also, the greater number of burns in the E. cloacae infection population contributed to their significantly higher admission rate to BAMC, as BAMC is the DoD’s only specialized burn center. As burns require frequent debridement, the greater number of burn injuries also potentially led to the higher number of operating room visits in the E. cloacae infection group.

Regarding specific antibiotic utilization, patients with E. cloacae infection received significantly more carbapenems, 1st generation cephalosporins, fluoroquinolones, and vancomycin (Table 2). Burn injury commonly results in infection with S. aureus, which has led to the empiric use of vancomycin [31]. Thus, the greater number of burn injuries in the E. cloacae infection group, as well as the high proportion of polymicrobial infections (75% of patients) likely contributed to their greater receipt of vancomycin.

As previously mentioned, E. cloacae has a chromosomal AmpC β-lactamase, which is strongly induced by β-lactams, such as carbapenems and 1st generation cephalosporins. Resistance development secondary to AmpC induction is of special interest to the U.S. Armed Forces as ertapenem is recommended to be carried on the battlefield by medics in the TCCC guidelines and cefazolin is recommended as post-trauma antibiotic prophylaxis in the JTS CPG [17, 19]. These recommendations provide the possibility for the development of harmful resistance, leading to poor patient outcomes when initial wound infections are due to E. cloacae. As a result of the resistance-inducing pressure of carbapenems, there has been significant interest in seeking out carbapenem-sparing therapies, such as piperacillin-tazobactam or cefepime [32]. Our population did not receive a significant amount of therapy with piperacillin-tazobactam nor cefepime and the most prescribed antibiotic therapy for patients who had an E. cloacae infection was a carbapenem. Cefepime has also garnered significant attention as a carbapenem-sparing agent when treating AmpC-producing organisms and was only recently recommended by the IDSA as first-line therapy against E. cloacae, as well as K. aerogenes and C. freundii when the minimum inhibitory concentration (MIC) is known to be ≤2 μg/mL [26]. In our study, approximately 85% of isolates were susceptible to cefepime (MIC ≤2 μg/mL) with the majority having a MIC ≤0.5 μg/mL, while the resistant isolates largely had a MIC >16 μg/mL. As infection site inevitably affects clinical outcome data, it is important to note that our isolates differed from those assessed in other studies, such as the MERINO trials which focused on bacteremia [33, 34], in that our isolates were largely collected from infected traumatic wounds and only 6% of initial isolates were blood cultures. A significant proportion of the patients with E. cloacae infection in our study sustained burn injuries (16%), and although Enterobacter spp. cause a minority of burn wound infections, the bacteriology of burn wound infection remains largely Gram-negative [35].

Despite the presumed high risk of AmpC induction and de-repression given our study population’s frequent receipt of carbapenems, no statistically significant resistance developed to any individual antibiotic in our study when examining serial isolates. Nevertheless, there was a non-significant trend toward resistance development against almost every β-lactam antibiotic tested except for ceftazidime-avibactam and meropenem (i.e., ceftolozane-tazobactam, imipenem, ertapenem, piperacillin-tazobactam, cefepime, aztreonam, ceftriaxone, and ceftazidime). The development of β-lactam resistance in our study is similar to prior burn wound infection literature that examined the incidence of general resistance phenotypes of Enterobacterales over time [36]. However, in the 2016 study by van Duin et al. [36], significant resistance developed over the course of weeks and in our study, the median interval between initial and last isolates was 5 days (IQR 2–20).

The lack of difference in clinical outcomes between the single initial and serial isolate groups in our study may be attributed to fast source control in both groups, as evidenced by the high number of visits to the operating room for surgical debridement. Patients in our serial E. cloacae group had a shorter duration to isolation after their injuries (5 vs. 8 days p = 0.046), and similar to the findings of a prior analysis of the TIDOS population [6], 75% of the E. cloacae infections in our analysis were associated with polymicrobial infections. Nevertheless, there was no difference in outcomes between patients in the E. cloacae single initial and serial isolate groups, as well as between the E. cloacae infection patients with polymicrobial and monomicrobial infections. Given that E. cloacae carries the greatest risk for AmpC derepression, our findings regarding resistance development and clinical outcomes may be generalizable to combat trauma infections with K. aerogenes, Serratia marcescens, C. freundii, Providencia stuartii, Morganella morganii [37]. The lack of difference in clinical outcomes between the single initial and serial isolate groups bolsters both the DoD’s current combat critical care and surgical prophylaxis guidelines with regard to AmpC induction and also supports prior literature that argued against the use of expanded Gram-negative antibiotic prophylaxis after combat trauma [17, 19, 38, 39].

Our study includes limitations inherent to retrospective studies. As our analysis was not a case-control study, the non-E. cloacae patients served as a comparator group rather than a control population, so matching was not applied. A potential confounder of clinical outcome differences is that a significant proportion of the patients infected with E. cloacae were hospitalized at BAMC, of whom, 16% were admitted for burn wound care, which likely led to prolonged hospitalizations [40]. Similar to other retrospective reports of emergence of resistance while on treatment [8, 27], we did not perform a molecular assessment to ascertain the likely mechanism for resistance observed. Even if using ceftriaxone resistance as a marker for AmpC or ESBL production, the difference in resistance between first and last isolates from the serial isolate population was not statistically significant (p = 0.121). As isolates did not undergo bacterial strain typing, we cannot directly state whether the initial and serial isolates were the same. Molecular or enzymatic characterization of β-lactamase production would likely have been useful if a significant difference in 3rd generation cephalosporin resistance between the initial and last isolates was detected. Lastly, the DoDTR did not capture antibiotics that were provided in the prehospital setting (e.g., ertapenem) at the time of injury, which may have limited the evaluation for β–lactam resistance development.

To the best of our knowledge, our study is the first to specifically evaluate E. cloacae’s role as a pathogen in infection secondary to modern combat trauma. Despite DoD combat care and surgical prophylaxis guidelines recommending upfront provision of AmpC-inducing antibiotics [41], we did not see worsened clinical outcomes or significant antibiotic resistance develop in patients who experienced serial isolation of E. cloacae versus single initial isolation. Carbapenems were the most frequently prescribed antibiotics for our combat trauma population with E. cloacae infections. As IDSA and DoD guidance changes regarding antibiotic utilization, future studies on clinical outcome surveillance coupled with molecular characterization of resistance mechanisms amongst combat trauma patients are needed to ensure optimal care and support antimicrobial stewardship efforts in the Military Health System.

Acknowledgments

We are indebted to the Infectious Disease Clinical Research Program Trauma Infectious Disease Outcomes Study team of clinical coordinators, microbiology technicians, data managers, clinical site managers, and administrative support personnel for their tireless hours to ensure the success of this project. We also wish to thank MAJ Jack Kiley for his support and guidance.

Data Availability

All relevant data are contained in the paper. Data for this study are available from the Infectious Disease Clinical Research Program (IDCRP), headquartered at the USU, Department of Preventive Medicine and Biostatistics. Review by the USU Institutional Review Board and approval of data sharing agreements are required for use of the data collected under this protocol. Data requests may be sent to: Address: 6270A Rockledge Drive, Suite 250, Bethesda, MD 20817. Email: contactus@idcrp.org.

Funding Statement

Support for this work (IDCRP-024) was provided by the Infectious Disease Clinical Research Program (IDCRP), a Department of Defense program executed through the Uniformed Services University of the Health Sciences, Department of Preventive Medicine and Biostatistics through a cooperative agreement with The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF). This project has been funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, https://www.niaid.nih.gov/, under Inter-Agency Agreement Y1-AI-5072 to DRT, the Defense Health Program, U.S. DoD, under award HU0001190002 to DRT, the Department of the Navy under the Wounded, Ill, and Injured Program (HU0001-10-1-0014) to DRT, and the Military Infectious Diseases Research Program, https://midrp.amedd.army.mil/ (HU0001-15-2-0045) to KM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Support in the form of salaries was provided by HJF for authors KM, LS, FS, AR; HJF did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.

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Decision Letter 0

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24 May 2023

PONE-D-23-05801Enterobacter cloacae infection characteristics and outcomes in battlefield trauma patientsPLOS ONE

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"Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized.

Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access.

We will update your Data Availability statement to reflect the information you provide in your cover letter.

Additional Editor Comments:

It is an interesting text, especially in the context that it refers to an area in which there is little literature, such as war wounds. I suggest reviewing the comments of the reviewers, and especially those of the microbiological field, since they are relevant to clarify possible confusions in the clinical field regarding patterns of susceptibility of microorganisms, relevance of the antimicrobials mentioned in the paper and resistance mechanisms of the microorganisms mentioned. I suggest review by a clinical microbiologist.And include the limitations sugested by reviewers.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

Reviewer #2: Partly

Reviewer #3: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: Yes

Reviewer #3: Yes

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: No

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Bennett and colleagues present a manuscript describing patients with E. cloacae infections after suffering battlefield trauma.

The subject of the manuscript is interesting and the authors are right when they stress the increasing relevance of infections due to MDR E. cloacae in different clinical settings, including trauma patients. However, there are a number of issues that require attention before publication.

Major comments:

1. In the introduction, the authors make the point of a possible causal effect between Enterobacter infections and the development of other "MDRGN infections". In the same line, it is suggested that "earlier identification and treatment of Enterobacter spp. infections may reduce the acquisition of secondary MDRGN infections". However, no data are provided this claim. I think throughout the manuscript there is a confusion between the possibility of developing resistance due to AmpC induction (that is in a same Enterobacter isolate previously exposed to the appropriate environmental conditions) and the risk of developing infections due to other MDR organisms. Also, the concept of 'induction' on resistance is never really addressed.

2. The Aim of the authors is to study “the epidemiological characteristics of patients with E. cloacae infections, characterized the antibiotic prescribing patterns used in the treatment of these infections and their effects on developing resistance, and examined clinical outcomes compared to battlefield trauma patients who developed bacterial infections associated with organisms other than E. cloacae. Also they “described clinical characteristics and outcome differences between patients with solitary isolation of E. cloacae and no known microbiological relapse and patients with serial isolation to assess for antimicrobial resistance development.” While all these questions are interesting, the study design has several problems that require attention. It is not clear to me how was infection defined, which is a major issue considering most of the cultures come from non-sterile sites such as wounds. Were all these cultures obtained from tissue under sterile conditions? Were swabs accepted? One example of the potential importance of this issue is that while coagulase negative staphylococci were the most frequent organisms in the non-Enterobacter group, the median days of vancomycin use for that group was 0. Moreover, the statement provided in lines 137-141 further emphasizes my point, where the authors conveniently chose isolates “more likely to be a true infection”. This is a fundamental issue that requires to be thoroughly addressed.

3. The definition of solitary is also confusing and sometimes blurred with monomicrobial vs. polymicrobial. Please clarify. How did you define relapse vs. persistent infection? Also, the fact that there is no molecular epidemiology studies precludes making any strong conclusion regarding subsequent isolates as there is no strong data proving isolates are actually the same (or even related)

4. After dealing with the issues of inclusion criteria stated above, the statistical analyses need to be improved to address possible confounding factors and assess the strength of the associations.

Minor comments:

1. Lines 70-75. Please italicize Enterobacteriaceae (ideally change to the updated taxonomical denomination of Enterobacterales). Also, please provide a reference for foe the statement ending in line 72.

2. Line 76. When you say “have been found to develop β-lactam resistance during treatment”, are you referring to 3rd gen cephalosporins? Please clarify and provide a reference.

3. Please rephrase lines 154-155.

Reviewer #2: Thank you for your submission. Please find below some comments about your manuscript.

1. It is important to harmonize if the isolates belong to Enterobacter cloacae complex. If so, please specify in all the manuscript E. cloacae complex.

2. Page 5 line 80. Please specify if it is amoxicillin/clavulanic acid as it seems separated by coma.

3. Please include the method used to identify the isolates. Was it MALDI TOF ? or just Phoenix 100 ?.

4. If there were not typing available to compare the first and subsequent isolates ( solitary vs serial ), it should be included as a limitation. There is a possibility of different isolates of E. cloacae in the same patient.

5. I suggest avoiding the report 0% of susceptibility for drugs with intrinsic resistance like cefoxitin, 1st and 2nd gen cephalosporins, amoxicillin/clavulanic, ampicillin, etc.

6. I suggest including also the IDSA guidance recommendations in the discussion. About the importance of E. cloacae along with C. freundii and K. aerogenes as derepression of AmpC may occur.

7. Please include or mention the 3rd generation cephalosporin used. Is it ceftriaxone?.

8. Page 22 line 385. Please change Enterobacteriaceae by Enterobacterales.

9. Please considering the reports, propose an antimicrobial stewardship strategy. For example include rapid ID diagnosis to switch from 1st gen cephalosporins to cefepime or ertapenem.

10. Please include the CLSI breakpoints used to interpret AST results. For example M100 33rd 2023.

11. In figure 1, I suggest to delete nitrofurantoin as the manuscript refers to soft tissue and bone infections. Also, cefuroxime should be deleted as is intrinsically resistant. Ceftaroline is not the preferred drug for E. cloacae. It may be removed also.

12. If possible, I suggest including MIC distributions for cefepime.

Reviewer #3: This is an interesting manuscript reporting infections due to Enterobacter claocae in patient with wounds acquired in battlefield. This is a retrospective, descriptive study. The authors compare mainly outcomes in this group of patients with E. cloacae infections and patient’s infections without E cloacae. Most of the infections are in wounds due to blast or burn. Most of the infections in both groups were polymicrobial.

This manuscript is well written. It follows the editorial guidelines. The title reflects the content. Abstract is correct. Introduction is too extensive. I recommend to shorter it. Methodology is of simple clinical series and with a comparator.

Results: since 75% of the infections are polymicrobial, I would like to have a better description of the combination of bacteria in both groups, in order to have a better understanding of the severity of infections and antibiotic treatments and outcomes. While 66.7 % of the patients in the E. cloacae group are polymicrobial, the role of E. cloacae is questionable in different outcomes, especially in wounds. In addition, severity of illness, complications and many interventions could be more related to the trauma injury rather the role of the infection. It is of interest to see how the susceptibility profile does not change much over time in these isolates of E. cloacae.

Discussion is also too extensive. A shorter discussion would be better. In discussion the authors state that there were no differences when compared monomicrobial with polymicrobial infections. This information is not in the results. Also, it is not clear if the comparison is in the E. cloacae infections group or in the when compared with non E. cloacae infections.

Table 1 and figure 1 are fine. Table 2 and 3 are not necessary since the outcomes are not relevant. Duration of antibiotics, in spite there are differences, is not relevant, since the duration of treatment is not prolonged in most patients. References are fine.

In summary, the manuscript is well written, methods are fine. The results are reliable since are based in microbiological and clinical feature. In addition, the conclusion is based in the results. However, most of the infections are polymicrobial, and the role of E. cloacae in these infections is not clear and are of not enough interest. A better description of the polymicrobial infections and the combination of treatment is needed to have a better understanding and see the importance of this study. In addition, these missing data could help to understand why they study E. cloacae, in step of S. aureus or Pseudomonas aeruginosa, or other specific bacteria in these infections. This data could help to support the study and see the role of E. cloacae in these infections. Finally, this manuscript could fit better as a brief report.

**********

6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

**********

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While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PLoS One. 2023 Aug 29;18(8):e0290735. doi: 10.1371/journal.pone.0290735.r002

Author response to Decision Letter 0


5 Jul 2023

RESPONSE TO REVIEWERS

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

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Author Response: The manuscript has been formatted per PLOS ONE’s style requirements, including file naming.

2. Please provide additional details regarding participant consent. In the ethics statement in the Methods and online submission information, please ensure that you have specified what type you obtained (for instance, written or verbal, and if verbal, how it was documented and witnessed). If your study included minors, state whether you obtained consent from parents or guardians. If the need for consent was waived by the ethics committee, please include this information.

Author Response. The following information is included as the last sentence of the 1st paragraph of the Methods section and in the online submission form: ‘Data and specimens were collected from individuals who provided authorization through informed consent and HIPAA authorization processes, or through an IRB-approved waiver of consent for use of de-identified data not obtained through interaction or intervention with human subjects.’

3. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability.

"Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized.

Author Response: All relevant data are included in the manuscript and tables/figures. Per our organization’s Institutional Review Board, we do have restrictions on making the data publicly available. As such, we have modified the Data Availability statement to the following:

‘Data for this study are available from the Infectious Disease Clinical Research Program (IDCRP), headquartered at the USU, Department of Preventive Medicine and Biostatistics. Review by the USU Institutional Review Board and approval of data sharing agreements are required for use of the data collected under this protocol. Data requests may be sent to: Address: 6270A Rockledge Drive, Suite 250, Bethesda, MD 20817. Email: contactus@idcrp.org.’

Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access.

We will update your Data Availability statement to reflect the information you provide in your cover letter.

Author Response: There are restrictions placed on making the data publicly available per our Institutional Review Board and requests for use must be reviewed by them.

Additional Editor Comments:

It is an interesting text, especially in the context that it refers to an area in which there is little literature, such as war wounds. I suggest reviewing the comments of the reviewers, and especially those of the microbiological field, since they are relevant to clarify possible confusions in the clinical field regarding patterns of susceptibility of microorganisms, relevance of the antimicrobials mentioned in the paper and resistance mechanisms of the microorganisms mentioned. I suggest review by a clinical microbiologist. And include the limitations suggested by reviewers.

Author Response: Thank you for your comments. We have reviewed the comments from the peer reviewers and revised the manuscript accordingly, including adding an additional statement to the limitations section. One of the co-authors is a microbiologist and she had comprehensively reviewed the reviewer comments and worked with the lead authors on the revision of the manuscript.

REVIEWER COMMENTS’

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

Reviewer #2: Partly

Reviewer #3: Yes

________________________________________

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: Yes

Reviewer #3: Yes

________________________________________

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: No

________________________________________

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

________________________________________

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

REVIEWER #1:

Bennett and colleagues present a manuscript describing patients with E. cloacae infections after suffering battlefield trauma. The subject of the manuscript is interesting and the authors are right when they stress the increasing relevance of infections due to MDR E. cloacae in different clinical settings, including trauma patients. However, there are a number of issues that require attention before publication.

Major comments:

1. In the introduction, the authors make the point of a possible causal effect between Enterobacter infections and the development of other "MDRGN infections". In the same line, it is suggested that "earlier identification and treatment of Enterobacter spp. infections may reduce the acquisition of secondary MDRGN infections". However, no data are provided this claim. I think throughout the manuscript there is a confusion between the possibility of developing resistance due to AmpC induction (that is in a same Enterobacter isolate previously exposed to the appropriate environmental conditions) and the risk of developing infections due to other MDR organisms. Also, the concept of 'induction' on resistance is never really addressed.

Author Response: Thank you for your comments. We have revised the text in the Introduction to remove the language suggesting that Enterobacter spp. infections may have contributed to acquisition of secondary MDRGN infections. The revised text (lines 59-64) reads ‘In that analysis, Enterobacter spp. was the second most commonly isolated Gram-negative organism from polymicrobial cultures and was noted to have a shorter time from injury to first infection. As polymicrobial infections among blast wound infections were more likely to produce MDR organisms and Enterobacter spp. infections have a potentially quicker onset, earlier identification and treatment of Enterobacter spp. infections may improve patient outcomes.’

Regarding your comments about AmpC induction, we agree that there may have been more mention of AmpC induction in the Introduction than needed, considering that we were unable to directly report on it in the Results. As it is an important mechanism related to resistance of E. cloacae, we did not remove the topic from the Introduction, but we revised the text to reduce its mention (deleted two sentences and revised text on lines 78-80). The sentence on lines 84-86 was also revised to indicate that the focus is more on increasing beta-lactam resistance versus AmpC induction. A sentence was also added to the end of the Laboratory Analysis section of the Methods (lines 142-144) to state that ‘As molecular assays to assess for AmpC were not routinely conducted at the military hospitals during the study period, data on AmpC induction were not available.’

While we do not have data from the molecular assays, we have addressed the concept of AmpC induction on resistance in the Discussion to our best ability via assessment of the initial and final isolates’ antibiograms (lines 431-433). The revised text reads ‘Even if using ceftriaxone resistance as a marker for AmpC or ESBL production, the difference in resistance between first and last isolates from the serial isolate population was not statistically significant (p=0.121). As isolates did not undergo bacterial strain typing, we cannot directly state whether the initial and serial isolates were the same. Molecular or enzymatic characterization of β-lactamase production would likely have been useful if a significant difference in 3rd generation cephalosporin resistance between the initial and last isolates was detected.’

2. The Aim of the authors is to study “the epidemiological characteristics of patients with E. cloacae infections, characterized the antibiotic prescribing patterns used in the treatment of these infections and their effects on developing resistance, and examined clinical outcomes compared to battlefield trauma patients who developed bacterial infections associated with organisms other than E. cloacae. Also they “described clinical characteristics and outcome differences between patients with solitary isolation of E. cloacae and no known microbiological relapse and patients with serial isolation to assess for antimicrobial resistance development.” While all these questions are interesting, the study design has several problems that require attention. It is not clear to me how was infection defined, which is a major issue considering most of the cultures come from non-sterile sites such as wounds. Were all these cultures obtained from tissue under sterile conditions? Were swabs accepted? One example of the potential importance of this issue is that while coagulase negative staphylococci were the most frequent organisms in the non-Enterobacter group, the median days of vancomycin use for that group was 0. Moreover, the statement provided in lines 137-141 further emphasizes my point, where the authors conveniently chose isolates “more likely to be a true infection”. This is a fundamental issue that requires to be thoroughly addressed.

Author Response: Thank you for your questions. Infections were defined using standardized criteria from the CDC National Healthcare Safety Network, as described on lines 121-124. Isolates were classified as infecting if they were collected from clinical work-ups per suspicion of infection.

Regarding your question if swabs were collected, the majority were operative cultures. As E. cloacae was the focus of this paper, sterile body sites were considered to be a reliable source for cultures for infecting isolates when multiple isolates were available from the first day of isolation from different sources. This is substantiated by the findings of Pien et al. (Am J Med. 2010;123(9):819-828), which evaluated 2,669 isolates from 2,273 positive blood cultures and determined that 51% of those isolates represented true infections. Among the E. cloacae isolates identified in the Pien et al. study, 93% were considered true bloodstream infections. In our study, there was a low occurrence of patients with multiple E. cloacae isolates collected on the first day of isolation and from those patients, 8 of the selected E. cloacae isolates were cultured from sterile body sites.

3. The definition of solitary is also confusing and sometimes blurred with monomicrobial vs. polymicrobial. Please clarify. How did you define relapse vs. persistent infection? Also, the fact that there is no molecular epidemiology studies precludes making any strong conclusion regarding subsequent isolates as there is no strong data proving isolates are actually the same (or even related)

Author Response: Thank you for your comments and we agree that the term ‘solitary’ may be confusing. We have revised the text throughout to replace ‘solitary’ with ‘single initial’ and clarified that the definition refers only to the isolation of E. cloacae and does not preclude the cultures being polymicrobial. The revised text on lines 124-127 reads ‘Inclusion criteria for the single initial E. cloacae isolate group required patients to have an infecting E. cloacae isolate collected from the initial culture (may be either monomicrobial or polymicrobial) with no isolation from subsequent cultures.’

Regarding relapse vs persistent infection, we did not differentiate relapse vs persistent infection; however, our underlying hypothesis of differing clinical characteristics between patients with serial vs single initial E. cloacae isolation was based on the fact that patients with single initial E. cloacae isolation did not have known “relapse” or “persistent infection” on the basis of repeated culture.

We agree that the lack of molecular analysis is a limitation of the study and have added a sentence to the limitations paragraph in the Discussion (lines 433-435) to read ‘As isolates did not undergo bacterial strain typing, we cannot directly state whether the initial and serial isolates were the same.’

4. After dealing with the issues of inclusion criteria stated above, the statistical analyses need to be improved to address possible confounding factors and assess the strength of the associations.

Author Response: Thank you for your suggestion. However, we feel that our inclusion criteria are appropriate to the analysis (please see the responses above). The potential of confounding from polymicrobial infections among the patients with E. cloacae infections is addressed in the Results text with expanded analysis included per the comments from Reviewer #3. As the purpose of the analysis was to delineate the epidemiology of E. cloacae infections in battlefield trauma, we feel that the univariate analyses included in the Results are appropriate for the study. Based on the findings in the study, multivariate modeling to identify risk factors for infections or predictors of poor outcomes may be warranted, but that is outside the scope of this study.

Minor comments:

1. Lines 70-75. Please italicize Enterobacteriaceae (ideally change to the updated taxonomical denomination of Enterobacterales). Also, please provide a reference for foe the statement ending in line 72.

Author Response: Thank you for the suggestion. Enterobacteriaceae has been changed to Enterobacterales and italicized in the text. A reference (new #7) was added to the statement per you indicated.

2. Line 76. When you say “have been found to develop β-lactam resistance during treatment”, are you referring to 3rd gen cephalosporins? Please clarify and provide a reference.

Author Response: Thank you for your question. The sentence has been revised to be ‘E. cloacae is initially phenotypically susceptible to 3rd generation cephalosporins (e.g., ceftriaxone and ceftazidime) in vitro; however, as high as 19% of isolates developed β-lactam resistance during treatment [9-12].’

3. Please rephrase lines 154-155.

Author Response: Thank you for the suggestion. The sentence was revised to the following: ‘Categorical variables were assessed using �2 and Fisher’s Exact Tests, where appropriate.’

REVIWER #2

Thank you for your submission. Please find below some comments about your manuscript.

1. It is important to harmonize if the isolates belong to Enterobacter cloacae complex. If so, please specify in all the manuscript E. cloacae complex.

Author Response: Thank you for the question. The BD Phoenix Automated Microbiology System used in this analysis does have the option to identify isolates as E. cloacae complex; however, all the isolates included in our study were specifically identified as E. cloacae. A new sentence (line 281) was added to the Enterobacter Cloacae Culture Characteristics section of the Results to state ‘All Enterobacter isolates were identified as E. cloacae (not E. cloacae complex).’

2. Page 5 line 80. Please specify if it is amoxicillin/clavulanic acid as it seems separated by comma.

Author Response: Thank you for catching that typo. The text was revised to amoxicillin/clavulanic acid.

3. Please include the method used to identify the isolates. Was it MALDI TOF ? or just Phoenix 100 ?.

Author Response: Thank you for the question. The method used to identify the isolates was the BD Phoenix Automated Microbiology System. The first sentence in the Methods Laboratory Analysis section was revised to clarify this point. It now reads ‘Identification and susceptibility testing of the E. cloacae isolates were performed using the BD Phoenix Automated Microbiology System (NMIC/ID-308 and NMIC-311 panels, BD Diagnostics, Sparks, MD).’

4. If there were not typing available to compare the first and subsequent isolates ( solitary vs serial ), it should be included as a limitation. There is a possibility of different isolates of E. cloacae in the same patient.

Author Response: Thank you for the suggestion and we agree that this is a limitation of our analysis and have added a statement to the limitations paragraph in the Discussion (lines 433-435) to read ‘As isolates did not undergo bacterial strain typing, we cannot directly state whether the initial and serial isolates were the same.’.

5. I suggest avoiding the report 0% of susceptibility for drugs with intrinsic resistance like cefoxitin, 1st and 2nd gen cephalosporins, amoxicillin/clavulanic, ampicillin, etc.

Author Response: Thank you for the suggestion. The statement in the legend of Figure 1 reporting the 0% susceptibility for the antibiotics with intrinsic resistance has been deleted.

6. I suggest including also the IDSA guidance recommendations in the discussion. About the importance of E. cloacae along with C. freundii and K. aerogenes as derepression of AmpC may occur.

Author Response: Thank you for the suggestion. The sentence on lines 323-326 in the Discussion has been revised to state ‘Notably, E. cloacae, as well as Klebsiella aerogenes and Citrobacter freundii have been found to be the most clinically relevant AmpC producers and AmpC’s conference of resistance to broad-spectrum β-lactams has been shown to produce significant adverse effects on clinical outcomes.’ In addition, we have also revised the sentence on lines 384-387 to read ‘Cefepime has also garnered significant attention as a carbapenem-sparing agent when treating AmpC-producing organisms and was only recently recommended by the IDSA as first-line therapy against E. cloacae, as well as K. aerogenes and C. freundii when the minimum inhibitory concentration (MIC) is known to be ≤2 µg/mL.’

7. Please include or mention the 3rd generation cephalosporin used. Is it ceftriaxone?.

Author Response: Thank you for the question. However, we do not have further specificity with regard to the 3rd generation cephalosporin as that is how it was recorded and both ceftriaxone and ceftazidime were options available through the DoD. Resistance amongst initial E. cloacae isolates was 22% to both ceftriaxone and ceftazidime with 63% and 67% resistance in the last isolate group, respectively.

8. Page 22 line 385. Please change Enterobacteriaceae by Enterobacterales.

Author Response: Thank you for the suggestion. We have made that change in the text.

9. Please considering the reports, propose an antimicrobial stewardship strategy. For example include rapid ID diagnosis to switch from 1st gen cephalosporins to cefepime or ertapenem.

Author Response: Thank you for the suggestion. The purpose of this study was not to develop recommendations or propose practice changes for the DoD, but to characterize the epidemiology of these infections. We also feel that our findings at this time do not justify making direct recommendations as there were no statistically significant differences in outcomes identified between the patients who had single initial isolation versus serial isolation of E. cloacae. Nevertheless, antimicrobial stewardship is an important priority for the Military Health System and our findings will be shared with individuals focused on improving antimicrobial stewardship at clinical sites. The last sentence (lines 446-449) in the conclusions was revised to incorporate the need to support antimicrobial stewardship efforts in the Military Health System and reads ‘As IDSA and DoD guidance changes regarding antibiotic utilization, future studies on clinical outcome surveillance coupled with molecular characterization of resistance mechanisms amongst combat trauma patients are needed to ensure optimal care and support antimicrobial stewardship efforts in the Military Health System.’

10. Please include the CLSI breakpoints used to interpret AST results. For example M100 33rd 2023.

Author Response: Thank you for the question. The AST results were interpreted using the most updated BD Phoenix software at that time which was in concordance with the CLSI M100-S30 Performance Standards for Antimicrobial Susceptibility Testing - 30th Info Supplement – 2020. The sentence in the Results Laboratory Analysis section was revised to clarify that point and the CLSI volume is included as citation #24. The sentence now reads ‘Antimicrobial susceptibility testing results were interpreted in accordance with the Clinical Laboratory Standards Institute (CLSI M100 30th edition) breakpoints to construct an antibiogram [24].’

11. In figure 1, I suggest to delete nitrofurantoin as the manuscript refers to soft tissue and bone infections. Also, cefuroxime should be deleted as is intrinsically resistant. Ceftaroline is not the preferred drug for E. cloacae. It may be removed also.

Author Response: Thank you for the suggestion. As this is a descriptive study and colonization by these organisms may predispose to other mechanisms of infection, we would prefer to keep all the antimicrobials in Figure 1 so it is a broad-ranging antibiogram.

12. If possible, I suggest including MIC distributions for cefepime.

Author Response: Thank you for the suggestion. A statement was added to the Discussion on lines 387-389 that reads ‘In our study, approximately 85% of isolates were susceptible to cefepime (MIC ≤2 µg/mL) with the majority having a MIC ≤0.5 µg/mL, while the resistant isolates largely had a MIC >16 µg/mL.’

REVIWER #3:

This is an interesting manuscript reporting infections due to Enterobacter claocae in patient with wounds acquired in battlefield. This is a retrospective, descriptive study. The authors compare mainly outcomes in this group of patients with E. cloacae infections and patient’s infections without E cloacae. Most of the infections are in wounds due to blast or burn. Most of the infections in both groups were polymicrobial.

This manuscript is well written. It follows the editorial guidelines. The title reflects the content. Abstract is correct. Introduction is too extensive. I recommend to shorter it. Methodology is of simple clinical series and with a comparator.

Author Response: Thank you for your comments. We feel that the information included in the Introduction was important for a reader to understand the relevance regarding why our study was needed; however, we do see your point and have revised the text to slightly shorten it.

Results: since 75% of the infections are polymicrobial, I would like to have a better description of the combination of bacteria in both groups, in order to have a better understanding of the severity of infections and antibiotic treatments and outcomes. While 66.7 % of the patients in the E. cloacae group are polymicrobial, the role of E. cloacae is questionable in different outcomes, especially in wounds. In addition, severity of illness, complications and many interventions could be more related to the trauma injury rather the role of the infection. It is of interest to see how the susceptibility profile does not change much over time in these isolates of E. cloacae.

Author Response: Thank you for your comments. We agree that it is challenging to determine the impact of specific bacteria isolated from polymicrobial cultures on outcomes. After identifying differences in outcomes between patients with E. cloacae infections versus those with non-E. cloacae infection, we did further analysis of the E. cloacae group to try and better delineate the role of E. cloacae with regard to outcomes. Specifically, we compared requirements for mechanical ventilation, ICU admission, number of operating room visits, length of hospitalization, and death between patients with monomicrobial E. cloacae infections and polymicrobial E. cloacae infections and identified no significant differences between the groups (please see lines 229-234 in the Results text).

We thank you for your suggestion to further examine the polymicrobial combinations. In a previous study using the TIDOS population, we examined characteristics of patients with Pseudomonas aeruginosa infections and identified that those patients had significantly higher crude mortality compared to patients with infections attributed to other pathogens (Ford et al. Mil Med. 2022; 187(3/4):426-434). Based on that finding and similar observations in the literature, as well as the high frequency of patients with P. aeruginosa isolated in the polymicrobial infections, we assessed characteristics of 29 patients with the polymicrobial combination of E. cloacae plus P. aeruginosa, as well as 49 patients with the combination of E. cloacae plus bacteria of high virulence (i.e., P. aeruginosa, E. coli, K. pneumoniae, and/or S. aureus), and compared characteristics against those of the patients with monomicrobial E. cloacae infections. Similar to the findings from the comparison with the overall polymicrobial group, there were no significant differences in the characteristics between the patients with monomicrobial E. cloacae infections and the polymicrobial combination of E. cloacae plus P. aeruginosa. When patients with the polymicrobial combination of E. cloacae plus bacteria of high virulence were compared to monomicrobial infections, the only significant difference was that the polymicrobial patients had a greater number of operating room visits. These findings have been added to the Results text on lines 234-251 and also incorporated into the Discussion on lines 316-321 and lines 337-344.

While the frequently identified organisms from polymicrobial infections are listed as footnotes with Tables 1 and 3, we have added a new sentence (lines 225-229) to provide the distribution of other organisms isolated from patients with the polymicrobial infections. The sentence reads ‘Among the 84 patients with polymicrobial infections, Pseudomonas aeruginosa was the most frequently isolated (34.5%), followed by Enterococcus faecium (30%), Escherichia coli (26%), Acinetobacter calcoaceticus baumannii complex (17%), Enterococcus faecalis (15.5%), Aspergillus spp. (14%), coagulase-negative staphylococci (14%), Enterococcus spp. (11%), Klebsiella pneumoniae (9.5%), and Staphylococcus aureus (9.5%).’

Discussion is also too extensive. A shorter discussion would be better. In discussion the authors state that there were no differences when compared monomicrobial with polymicrobial infections. This information is not in the results. Also, it is not clear if the comparison is in the E. cloacae infections group or in the when compared with non E. cloacae infections.

Author Response: Thank you for your comments. We have made revisions to shorten the Discussion slightly.

The comparison of monomicrobial and polymicrobial infections is specific to the individuals with E. cloacae infections. The text in the Results section comparing the monomicrobial and polymicrobial E. cloacae infections can be found on lines 229-234. The text reads ‘When E. cloacae infections were examined based on whether the infections were polymicrobial (N=84) or monomicrobial (N=28), there was no difference in use of mechanical ventilation (68% and 61, respectively; p=0.583), ICU admission (83% and 71%; p=0.170), number of operating room visits (median of 5 for both; p=0.125), length of hospitalization (median of 56 and 58.5 days; p=0.898), and death (5% and 4%; p=1.00).’ Per your suggestion, we have also added data from further examination of the E. cloacae polymicrobial combinations and a statement with data on the distribution of other organisms in the polymicrobial E. cloacae infections (see response above and lines 234-251 and 225-229 in the revised manuscript).

Regarding the sentence in the Discussion (lines 413-416), to clarify that the monomicrobial and polymicrobial comparisons were within the E. cloacae infection group, the sentence was revised to the following: ‘Nevertheless, there was no difference in outcomes between patients in the E. cloacae single initial and serial isolate groups, as well as between the E. cloacae infection patients with polymicrobial and monomicrobial infections.’

Table 1 and figure 1 are fine. Table 2 and 3 are not necessary since the outcomes are not relevant. Duration of antibiotics, in spite there are differences, is not relevant, since the duration of treatment is not prolonged in most patients. References are fine.

Author Response: Thank you for your comments. We feel that the data included in Tables 2 and 3 are valuable for the reader. While the duration of treatment was not prolonged, we believe that readers would like to know details on the duration of treatment as it potentially relates to changes in susceptibility with the serial isolates. We also feel that it is important to have Table 3 to show that there were no statistical differences between patients who had only single initial versus serial isolation of E. cloacae as prolonged isolation of other pathogens have been attributed to worsened clinical status and outcomes.

In summary, the manuscript is well written, methods are fine. The results are reliable since are based in microbiological and clinical feature. In addition, the conclusion is based in the results. However, most of the infections are polymicrobial, and the role of E. cloacae in these infections is not clear and are of not enough interest. A better description of the polymicrobial infections and the combination of treatment is needed to have a better understanding and see the importance of this study. In addition, these missing data could help to understand why they study E. cloacae, in step of S. aureus or Pseudomonas aeruginosa, or other specific bacteria in these infections. This data could help to support the study and see the role of E. cloacae in these infections. Finally, this manuscript could fit better as a brief report.

Author Response: Thank you for your comments. We agree that the description of the polymicrobial infections is very important to our conclusions and we do have data in the text comparing characteristics between the patients with E. cloacae monomicrobial and polymicrobial infections (lines 229-234). Per your suggestion, we have expanded the text to compare patients with monomicrobial E. cloacae infections to those with specific polymicrobial combinations (i.e., E. cloacae plus P. aeruginosa and E. cloacae plus bacteria of high virulence; please see response above and lines 234-251 and 225-229 in the text).

Attachment

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Decision Letter 1

Dona Benadof

8 Aug 2023

PONE-D-23-05801R1Enterobacter cloacae infection characteristics and outcomes in battlefield trauma patientsPLOS ONE

Dear Dr. William Bennett

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

==============================

ACADEMIC EDITOR:You have done a good job with the suggestions and changes of manuscript.

 I suggest a minor change that implies taking the reviewer's suggestion that I indicate below: "In figure 1, I suggest to delete nitrofurantoin as the manuscript refers to soft tissue and bone infections. Also, cefuroxime should be deleted as is intrinsically resistant. Ceftaroline is not the preferred drug for E. cloacae. It may be removed also."  Despite the fact that you indicate and justify it as a broad-spectrum antibiogram, in reality clinical microbiology should inform the antibiogram according to the identified microorganism and the site of infection. I think that this figure can be an element of confusion for the reader.==============================

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Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

PLoS One. 2023 Aug 29;18(8):e0290735. doi: 10.1371/journal.pone.0290735.r004

Author response to Decision Letter 1


11 Aug 2023

ACADEMIC EDITOR:

You have done a good job with the suggestions and changes of manuscript.

Author Response: Thank you very much.

I suggest a minor change that implies taking the reviewer's suggestion that I indicate below:

"In figure 1, I suggest to delete nitrofurantoin as the manuscript refers to soft tissue and bone infections. Also, cefuroxime should be deleted as is intrinsically resistant. Ceftaroline is not the preferred drug for E. cloacae. It may be removed also."

Despite the fact that you indicate and justify it as a broad-spectrum antibiogram, in reality clinical microbiology should inform the antibiogram according to the identified microorganism and the site of infection. I think that this figure can be an element of confusion for the reader.

Author Response: Thank you for your suggestion. Figure 1 has been modified per your comments and ceftaroline has been removed from the sentence on lines 399-403.

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Author Response: Thank you. The reference list has been reviewed and it is complete. There was a change for the URL for reference #19, which was updated in the revised version. Reference #26 was also updated to reflect the current version available for that document. The rest of the references are correct. None of the papers cited have been retracted.

Attachment

Submitted filename: Response to Reviewers.docx

Decision Letter 2

Dona Benadof

15 Aug 2023

Enterobacter cloacae infection characteristics and outcomes in battlefield trauma patients

PONE-D-23-05801R2

Dear Dr.William Bennet

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Dona Benadof, M.D

Academic Editor

PLOS ONE

Acceptance letter

Dona Benadof

21 Aug 2023

PONE-D-23-05801R2

Enterobacter cloacae infection characteristics and outcomes in battlefield trauma patients

Dear Dr. Bennett:

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org.

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Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Dona Benadof

Academic Editor

PLOS ONE

Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    Attachment

    Submitted filename: Response to Reviewers.docx

    Attachment

    Submitted filename: Response to Reviewers.docx

    Data Availability Statement

    All relevant data are contained in the paper. Data for this study are available from the Infectious Disease Clinical Research Program (IDCRP), headquartered at the USU, Department of Preventive Medicine and Biostatistics. Review by the USU Institutional Review Board and approval of data sharing agreements are required for use of the data collected under this protocol. Data requests may be sent to: Address: 6270A Rockledge Drive, Suite 250, Bethesda, MD 20817. Email: contactus@idcrp.org.


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