Escalating threat of multidrug-resistant bacteria: Insights from a low-middle income country setting

Abstract

Background:

Infections due to multidrug-resistant bacteria have become a global threat, increasing morbidity, mortality and healthcare costs. The main drivers for antimicrobial resistance are indiscriminate antimicrobial use, poor drug quality and lack of antimicrobial stewardship programs.

Aim:

This one-year prospective study aimed to determine the prevalence of multidrug-resistant bugs among hospital-acquired infections (HAI) in a low-middle income country.

Methods:

Depending on the clinical suspicion, various samples were processed as per standard protocols. Multiple antibiotic resistance (MAR) index was calculated, and isolates were characterized into multi-/extensively/pan-drug resistant isolates (MDR/ XDR/ PDR).

Results:

Nosocomial bacterial infections were identified in 13% patients which yielded 165 isolates (85% Gram-negative). 89.6% of these GN isolates were MDR, 77.5% of which were XDR and 2.8% PDR.

Conclusion:

By prioritizing infection control measures, early detection and judicious empirical antimicrobial use, healthcare facilities can significantly reduce the risk of HAIs and ensure a safer environment for patients.

Introduction

Antimicrobial resistance (AMR) is now a major challenge for clinicians treating patients with infections or risk of infections. The alarming increase in antimicrobial resistance worldwide has led to AMR being listed as one of the top 10 threats to global health by the World Health Organization in 2019.[1] The emergence and rapid spread of multidrug resistant bacteria is attributed to limited antibiotic options, irrational drug use, poor drug quality, malnutrition, inadequate sanitation and health care systems, and lack of antibiotic stewardship programs. Infections resulting from antibiotic resistant bacteria are especially difficult to treat with the currently available antibiotics and lead to higher morbidity and mortality, imposing huge healthcare costs.[2] A high prevalence of multidrug resistant (MDR) strains has been reported worldwide, with special focus in low- and middle-income countries.[3] Infections acquired after 48 hours of hospital stay (hospital-acquired infections) are frequently MDR and the attributable mortality of patients with these infections is reported to be significantly higher.[2] This study provides evidence to guide rational antibiotic use, improving clinical outcomes while reducing antimicrobial resistance in both patients and the community.

Objectives

To study the prevalence of multidrug-resistant bugs in hospital-acquired infections.

Material and Methods

Study site and design

This was a laboratory-based prospective study conducted in the Department of Microbiology and surgical unit in north India. Over a period of one year, all patients with evidence of bacterial infection after 48 hours of admission were included in the study. The study was approved by the institutional ethical committee vide letter DMCH/P/2022/988-94 dated 13/09/2022.

Isolation, identification and antibiotic susceptibility testing

Various samples, depending on the clinical suspicion, were processed in the laboratory as per standard protocols. Urine, respiratory samples (sputum, endotracheal aspirate, bronchoalveolar lavage), pus, wound swabs, etc., for bacterial culture were inoculated on blood and MacConkey agar and incubated at 37ºC for 24-48 hours. Blood and body fluid specimens were inoculated in the BD BACTEC Fx (Becton Dickenson, USA) or BacT/Alert 3D (bioMerieux, France) automated culture systems for up to seven days. Bacterial identification and antibiotic susceptibility testing (AST) were done using the Vitek2 system and interpreted according to Clinical Laboratory Standards Institute (CLSI) 2022 guidelines. Colistin susceptibility testing was performed using the microbroth dilution test as per CLSI guidelines.[4,5] The isolates were then characterized into multi-/extensively/pan-drug resistant isolates (MDR/ XDR/ PDR).[6] Multiple antibiotic resistance (MAR) index was calculated for each isolate as the ratio of antimicrobial agents to which the isolate was resistant and the total number of antimicrobial agents tested.[7]

Data analysis

All relevant data from the cases included in the study were tabulated in Microsoft Excel 2010. Standard descriptive statistics were used to summarize data as percentage and rates as appropriate. The prevalence and antibiotic resistance rates of pathogens for selected antimicrobials were analyzed.

Results

Cases and samples

During the study period, a total of 1010 patients were admitted, of which 725 were admitted for longer than 48 hours. Of these, 132 patients developed infections (infection rate 13%) and formed the study group. The patients’ age ranged from 14 to 84 years (mean 49.7 years) and a male predominance (3:1) was noted. Majority of the patients were admitted through the emergency following trauma (28%). On admission, the mean APACHE II score was 14.77 ± 2.04 and the most common comorbidity was diabetes mellitus (31.8%) [Table 1].

Table 1.

Demographic details of patients with hospital acquired infections (n=132)

Characteristic		Value/patients
Mean age (years)		49.7
Male:Female		3:1
Apache 2 score on admission		14.77
Mean ICU stay (days)		9.95
Medical History:
Sepsis		63 (47.7%)
Diabetes mellitus Type 2		42 (31.8%)
Immobilisation		34 (25.8%)
Alcoholic		26 (19.7%)
Hypertension		24 (18.2%)
Elderly		16 (12.1%)
Smoker		11 (8.3%)
Chronic kidney disease		7 (5.3%)
Past tuberculosis		3 (2.3%)
Immunocompromised		2 (1.5%)
Coronary artery disease		2 (1.5%)
Type of infections:
Respiratory tract infections		55 (36.4%)
Body fluid infections		30 (19.9%)
Skin & soft tissue infections		29 (19.2%)
Bloodstream infections		21 (13.9%)
Urinary tract infections		16 (10.6%)
Outcome
Survived		81 (61.4%)
Expired		51 (38.6%)

Source of HAI and bacterial etiology

Among the 132 HAI patients, 112 patients had evidence of infection at single site and 19 at multiple sites, summing up to 151 bacterial infections. The most common source was respiratory tract infections (36.4%) followed by body fluid (19.9%) and bloodstream infections (19.1%). Of these, 137 infections were monomicrobial and 14 were polymicrobial (2 isolates each), thus yielding 165 isolates.

Gram-negative bacteria were predominant, accounting for 84.8% (140/165) as compared to Gram-positive bacteria (25/165, 15.2%). The prominent Gram-negative isolates included Klebsiella spp. (27.3%), Escherichia coli (22.4%), Acinetobacter baumannii (20%) and Pseudomonas aeruginosa (7.9%). Enterococcus spp. (7.2%) and coagulase-negative staphylococci (CoNS) (6.7%) accounted for majority of the Gram-positive isolates [Figure 1].

Figure 1.

Bacterial flora of HAI (n = 165)

Multidrug resistance

Out of 165 isolates, 148 (89.6%) were MDR (GN-90.7%, GP-79.2%) and 77.5% of these were XDR (GN-81.5%, GP-54.2%) while 4 isolates were PDR. The mean MAR index for all isolates was 0.718. The proportion of drug-resistant isolates was highest among A. baumannii (MAR index 0.84, 96.9% MDR and XDR), followed by K. pneumoniae (MAR index 0.77, 95.5% MDR, 91.1% XDR) and P. aeruginosa (MAR index 0.8, 92.3% MDR, 84.6% XDR) [Figure 2]. 100% E. coli and K. pneumoniae, 97% A. baumannii, and 82% P. aeruginosa isolates were extended-spectrum beta lactamase (ESBL) producers. The overall incidence of carbapenem-resistant Enterobacteriaceae (CRE) was 93.1%, carbapenem-resistant Klebsiella pneumoniae (CRKP) 77% while 100% A. baumannii and P. aeruginosa isolates were carbapenem-resistant.

Figure 2.

Distribution of MDR/ XDR/ PDR isolates

Antimicrobial resistance profile

MDR-Klebsiella spp. and MDR-E. coli showed nearly 100% resistance to cephalosporins and quinolones, and maximum sensitivity towards colistin (97.7 and 100%) and tigecycline (44.1 and 67.7%). Among the non-fermenters, considerable resistance was seen to almost all the antibiotics tested. MDR-A. baumannii isolates were most susceptible to colistin (93.3%) and minocycline (43.7%) followed by cefoperazone + sulbactam (28.1%). Colistin (85.7%) and cefoperazone + sulbactam (27.3%) were also the most effective antibiotics against MDR-Pseudomonas isolates. All isolates of Acinetobacter and Pseudomonas, 93.1% Klebsiella spp., and 71% E. coli isolates were carbapenem resistant [Figure 3].

Figure 3.

Susceptibility of MDR Gram-negative bacteria. (Ak- amikacin, Cot- cotrimoxazole, Tet- tetracycline, Min- minocycline, Cfm- cefixime, Cpm- cefepime, Ctr- ceftriaxone, Caz- ceftazidime, Cip- ciprofloxacin, Pip-taz- piperacillin- tazobactam, Cef-sul- cefoperazone- sulbactam, Amx-cla- amoxycillin- clavulanate, Imi- imipenem, Mer- meropenem, Ert- ertapenem, Tig- tigecycline, Col- colistin)

Among Gram-positive bacteria, MDR-Enterococcus isolates were susceptible to linezolid (91.7%), teicoplanin (58.3%) and vancomycin (50%) whereas they expressed high level of resistance to ciprofloxacin, tetracycline, cotrimoxazole (100%), erythromycin (91.7%), high-level gentamicin and penicillin (both 83.3%). Methicillin resistance was identified in 27.3% of CoNS isolates.

Discussion

A high prevalence of nosocomial infections attributable to MDR strains has been reported in countries worldwide. The incidence of HAIs varies from 2% to 49% as reported in recent studies, depending on the patient profile, healthcare processes, and factors such as device use.[8,9] The present study reports a nosocomial infection rate of 13% that is comparable with incidence rates of 11.97% and 17.7% reported by others but lower than the EPIC II study in which rates upto 51% have been reported.[8,10] The most HAIs (including device-associated) are pneumonia, surgical site infections, bloodstream infections and urinary tract infections. The most common infections in our study were respiratory tract infections (36.2%) followed by body fluid and bloodstream infections (19.7% and 19.1%). The increased use of non-invasive ventilation and non-ventilated hospital-acquired pneumonia is being emphasized in recent studies.[10,11,12,13] On the contrary, International Nosocomial Infection Control Consortium (INICC) involving seven Indian cities reported BSI as the most common HAI while another study from Saudi Arabia found UTI as the commonest HAI.[14,15] As the hospital conditions, local ecology and population characteristics differ, the microbial etiology also varies with Gram negative predominance in low- and middle-income countries.[16] Our study also provides evidence to support this with a higher frequency of Gram-negative isolates (84.8%) than Gram-positive. Analysis of data from our center revealed the prevalence of five common drug-resistant pathogens, namely, E. coli, K. pneumoniae, A. baumannii, P. aeruginosa, and Enterococcus spp. These bacteria are part of the notorious ESKAPE group of pathogens which are reported in HAIs worldwide.[1,8,11,17,18]

The patients admitted to the hospital are at a greater risk of MDR infections due to critical-illness related immunosuppression, extensive antibiotic use, and exposure to invasive devices.[19] The obtained results showed a high level of antibiotic resistance in both Gram-negative (MAR index 0.74) and Gram-positive organisms (MAR index 0.6), with a high prevalence of MDR-HAI infections (89.6%). This is significantly greater compared to previous studies by Choudhuri et al. (21.6%), Wang et al. (42.5%) and Karruli et al. (55.6%) from similar settings.[19,20,21] The high resistance rates support the trend of increasing prevalence of MDR and XDR strains observed in reports from India and abroad.[22,23,24,25] MAR index greater than 0.2 indicates a high-risk source of infection such as hospitals, where antibiotics are frequently used.[7]

The MDR-E. coli and MDR-K. pneumoniae isolates in the present study were mostly resistant to cephalosporins, β-lactam-β-lactamase inhibitor (BL-BLI) combinations, and quinolones, which indicates their unrestricted use. As majority of these were ESBL-producers and carbapenem-resistant, colistin and tigecycline have become the fallback option. The resistance pattern of MDR strains, especially to carbapenem, reiterates the precarious situation in developing countries as reported in studies by Saxena et al., Kaleem Ullah et al., and Verma et al.[22,23,26]

For non-fermenters, majority of the antibiotics including carbapenems, were ineffective with resistance rates varying from 72% to 100%. For Pseudomonas spp., resistance rates were lower than Acinetobacter spp., particularly for aminoglycosides and third-generation cephalosporins while good susceptibility was observed against colistin and minocycline (Acinetobacter spp. only). There are similar reports from other centers by Bannerjee et al., Gautam et al. and others, in which MDR isolates with resistance to all commonly used antibiotics except tigecycline and colistin have been observed, highlighting the magnitude of the problem.[3,9,18,23,27,28] The 100% resistance to imipenem is troubling and points to its overuse leading to selection of resistant strains in the hospital. The emergence of colistin-resistant Klebsiella, Acinetobacter, and Pseudomonas spp. is particularly distressing. As effective treatment options for HAIs continue to diminish, it is imperative to reserve colistin until the antimicrobial susceptibility report mandates its use. In addition, newer BL-BLI and other synergistic combinations need to be explored.

In the study, resistance of Enterococcus spp. to penicillin, fluoroquinolones, tetracycline, and cotrimoxazole ranged from 80% to 100%. VRE was reported in 50% of our isolates while rates ranging from 16.7% to 63% have been reported by Gautam et al. and Despotovic et al.[3,25]

The analysis of CoNS spp. revealed 50% methicillin resistance, comparable to Staphylococcus aureus and reports by Khan et al. (40%) and Ibrahim et al. (75%).[28,29] Such a scenario indicates poor hand hygiene practices, and underscores the importance of restricted access to vancomycin, which is a reserved drug for methicillin-resistant S. aureus (MRSA) infections.

The limitations of this study include data from a single center, which, though representative, may not be generalizable. Also, comparative evaluation of the effect of MDR infections on patient outcome could not be performed. However, these data-driven observations can be used to tailor antimicrobial prescription guidelines and empirical treatment protocols.

Conclusion

The alarming increase in multidrug resistant bacteria is becoming a global health challenge. In the present study, Gram negative isolates were predominant and showed high degree of resistance than Gram positive isolates. By prioritizing infection control measures and implementing antimicrobial stewardship programs, healthcare facilities in LMIC can significantly reduce the risk of HAIs and spread of MDR bugs, thus ensuring a safer environment for patients.

Conflicts of interest

There are no conflicts of interest.

Funding Statement

Nil.