Defining the Clinical Significance of Alloscardovia omnincolens in the Urinary Tract

Abstract

The clinical significance of Alloscardovia omnincolens in the urinary tract has not been thoroughly evaluated. In this study, 15 patients with A. omnincolens present in their urine cultures were identified. A. omnincolens is only rarely associated with urinary tract symptoms and in some patients may play a commensal role.

INTRODUCTION

With the widespread adoption of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), bacteria are now identified with greater accuracy than with conventional phenotypic methods (1). This is particularly true for identification of bacteria that were difficult to distinguish or identify and would have been previously classified into broad categories such as urogenital flora. These organisms can now be identified to the species level with great accuracy. Although beneficial in most circumstances, the improved ability to rapidly identify most bacteria forces clinical microbiologists and infectious disease practitioners to interpret the clinical significance of unfamiliar organisms.

Alloscardovia omnincolens is one such organism. Prior to implementation of MALDI-TOF MS, this organism, a member of the Bifidobacteriaceae family, was difficult to identify in the absence of 16S rRNA sequencing (2). Appearing as small, pinpoint, alpha-hemolytic colonies on blood agar, A. omnincolens would have most likely been considered urogenital flora since it is a catalase- and oxidase-negative, Gram-positive rod that could not be accurately identified using phenotypic methods (2). This organism has been isolated and identified in urine, saliva, and blood specimens; however, its clinical significance is yet to be determined (3–6).

This study was prompted by the observation that A. omnincolens was being isolated from urine cultures in pure or predominant growth with unknown clinical presentations. To better understand the significance of this organism, both a 10-month retrospective review and prospective evaluation of >3,000 urine cultures were performed. In total, the laboratory results and clinical information of 15 patients with A. omnincolens were reviewed to assess the clinical significance and colonization frequency of this organism.

MATERIALS AND METHODS

Identification of isolates and cases.

This study consisted of both retrospective and prospective analyses. In the retrospective analysis, the laboratory information system was used to evaluate all urine cultures submitted to our laboratory between June 2013 and April 2014. This search was conducted to identify any culture that yielded significant growth of A. omnincolens. A threshold of 10⁴ CFU/ml was used to determine significant growth.

To establish the rate of colonization, a prospective analysis was performed between 12 August 2014 and 26 March 2015. In this analysis, 3,395 noncontinuous urine specimens submitted for routine bacterial culture were plated (0.01 ml) to 5% sheep blood (sBAP) and MacConkey agars; sBAPs were incubated for up to 48 h at 35°C in 5% CO₂ and prospectively examined for the growth of any amount of A. omnincolens. MacConkey agar plates were incubated in ambient air. Any colony appearing as a pinpoint, alpha-hemolytic colony on sBAP (Fig. 1A) was Gram stained. If a Gram-positive rod was detected (Fig. 1B), the organism was identified using the Bruker Biotyper MALDI-TOF MS (Bruker Daltonics, Billerica, MA). The performance of MALDI-TOF MS identification of A. omnincolens was validated against 16S rRNA gene sequencing and MALDI-TOF MS was shown to accurately identify Alloscardovia. 16S rRNA identification was performed by sequencing approximately 1,000 bp of the 16S rRNA gene.

FIG 1.

(A) Gram stain image (×100 magnification) of A. omnincolens taken from subculture growth on a 5% sheep blood agar growth. (B) 24-h growth of A. omnincolens subculture on 5% sheep blood agar plate.

Clinical significance.

A chart review was performed on all subjects from whom A. omnincolens was isolated. The patients' age, sex, temperature, white blood cell (WBC) count, colony count, urinalysis results, whether it was a pure culture, and whether it was the predominating organism were documented. Inpatient and outpatient notes were reviewed to determine the patient's past medical history, symptoms, and subsequent outcome. A urinalysis was considered positive if there were >5 WBC per high-powered field (HPF) or if small, medium, or large leukocyte esterase was present.

RESULTS

Between June 2013 and March 2015, a total of 15 patients had A. omnincolens isolated from their urine cultures. Nine patients were found during the retrospective review which took place from June 2013 to April 2014, and six additional cases were found during the prospective period from August 2014 to March 2015.

Clinical significance of A. omnincolens. (i) Retrospective study results.

Of the nine patients identified during the retrospective review, all but one was female, with ages ranging from 11 to 83 years (Table 1). Eight of the nine patients had an accompanying urinalysis, of which only one was positive (with 66 WBC per HPF), and moderate bacteria were seen. Of note, this was also the only patient who presented with a leukocytosis at 15.2 × 10⁹/liter. This patient had undergone a cystourethroscopy with laser lithotripsy and ureteral stent placement 1 week previously and was treated with antibiotics.

TABLE 1.

Characteristics of patients with A. omnincolens isolated from urine culture^a

Patient	Study period	Age (yr)	Gender	Temp (°C)	WBC count	Colony count (CFU/ml)	Pure growth	Predominant organism	Urinalysisb	Symptom(s)	Antibiotic treatment	Follow-up culture results	Past medical history
1	P	65	F	36.6	9.7	50,000	Yes	NA	Negative	Urinary frequency at night and chronic incontinence	None	Pure growth E. coli	ESRD secondary to polycystic kidney disease following renal transplant, HTN, high cholesterol, chronic UTIs, OA following left THA
2	P	80	F	36.3	NC	>100,000	No	Yes	Positivec	Abdominal pain, nausea, cramping, constipation	None	ND	Aortic stenosis, high cholesterol, HTN, urinary incontinence, OA, depression
3	P	68	F	NR	7.9	60,000	Yes	NA	Negative	Asymptomatic	None	Negative	CAD, DM2, pulmonary HTN, spinal stenosis, seizures, OSA, ITP, fibromyalgia
4	P	61	F	36.7	6	40,000	Yes	NA	Positive	Asymptomatic	None	ND	OA, AKI, PUD
5	P	47	F	36.5	10.8	1 colony	No	No	Positive	Asymptomatic	None	ND	Microangiopathic hemolytic anemia, HUS, HTN, seizure disorder
6	P	66	F	36.8	ND	20,000	Yes	NA	Negative	Dysuria, pelvic pressure, low back pressure	Ciprofloxacin	ND	HTN, DM, urge incontinence, chronic UTIs
7	R	36	F	36.8	15.2	>100,000	No	Yes	Positive	Abdominal pain, nausea, vomiting, diarrhea, chills	Keflex for 5 days	ND	Renal stones following laser lithotripsy and ureteral stent placement 8 days previously
8	R	83	F	36.4	7.8	60,000	No	No	Negative	Hypertensive urgency with exertional intolerance	None	ND	HTN, TIA, breast cancer, arthritis
9	R	36	F	NR	7.8	50,000	Yes	NA	Negative	Asymptomatic	Treated (antibiotics unknown)	ND	DM2, pregnant at the time
10	R	32	F	NR	7.2	>100,000	Yes	NA	Negative	Asymptomatic	None	Negative	Healthy, pregnant at the time
11	R	81	F	37	NC	25,000	No	No	Negative	Previous history of asymptomatic pyuria, recheck by primary care physician	None	Negative	HTN, chronic dizziness, HLD, breast cancer, allergic rhinitis, vitamin D deficiency.
12	R	11	F	39.4	0.6	>100,000	Yes	NA	Negative	Fever, fatigue, emesis	Ceftriaxone once, followed by 3 days of cefepime	Negative	Diamond-Blackfan anemia, autism, hypogammaglobinemia, scoliosis
13	R	31	F	NR	4.4	30,000	Yes	NA	Not done	Urinary frequency, fatigue, nausea (pregnant at the time)	None	Negative	Healthy, pregnant at the time
14	R	57	M	37.1	3	50,000	Yes	NA	Negative	Fatigue and abdominal distension (cirrhosis)	None	ND	HCV, cirrhosis with portal HTN, HCC, hepatic encephalopathy, GERD, cardiac dysrhythmias
15	R	79	F	36.7	6.5	>100,000	No	Yes	Negative	Left hip pain after fall	None	ND	HTN, DM, CAD

^aStudy period: P, prospective; R, retrospective. Gender: M, male; F, female. Temperature: NR, not recorded; ND, not done. WBC count: NC, no CBC. Predominant organism: NA, not applicable. Followup culture results: ND, not done. Past medical history: ESRD, end-stage renal disease; UTI, urinary tract infection; OA, osteoarthritis; THA, total hip arthroplasty; CAD, coronary artery disease; DM2, type 2 diabetes; ITP, idiopathic thrombocytopenia; AKI, acute kidney injury; PUD, peptic ulcer disease; HUS, hemolytic-uremic syndrome; DM, diabetes; TIA, transient ischemic accident; HCV, hepatitis C virus; GERD, gastroesophageal reflux disease; HCC, hepatocellular carcinoma.

^bA positive urinalysis was defined by 5 WBC per high-powered field (HPF) or if small, medium, or large leukocyte esterase was present.

^cPositive per note (results unavailable).

All but one patient was afebrile. The febrile patient was a child with Diamond-Blackfan anemia who presented with febrile neutropenia and was treated with antibiotics. No other sources for the fever were identified. In six of the nine retrospective cases, A. omnincolens was the only isolate found and in four patients the colony count was >100,000 CFU/ml. The remaining five cultures yielded between 25,000 and 60,000 CFU/ml.

Three of the nine patients identified during the retrospective review received antibiotic treatment. Only four of the cases had follow up cultures, all of which were negative. Interestingly, three of the follow-up cultures were from patients who had not received any antibiotic treatment for the initial positive urine culture. Only one patient experienced urinary tract symptoms (frequency), but none complained of dysuria, flank pain, or hematuria.

(ii) Prospective study results.

Retrospective analyses were limited in that only those cultures in which A. omnincolens was present in significant quantities could be identified. To determine whether A. omnincolens is present in low quantities, as might be expected for urogenital flora, we conducted a prospective analysis over an 8-month period from August 2014 to March 2015. In total, 3,395 urine cultures from 47 noncontinuous days were prospectively screened for the presence of any amount of A. omnincolens; of these cultures, six cases of A. omnincolens were identified.

All patients were female with ages ranging from 47 to 80 years old. Four had recorded temperatures at the time of visit, and none were febrile. Complete blood cell counts were obtained on four of them, and none had a leukocytosis. Four of six cultures yielded pure growth of A. omnincolens in amounts ranging from 20,000 CFU/ml to >100,000 CFU/ml (Table 1).

All cultures had corresponding urinalyses, three of which were deemed positive. Only one patient had acute symptoms consistent with urinary tract infection and that was the only patient who was treated with antibiotics (Table 1). This patient had atrophic vaginitis and urgent incontinence with complaints of burning with urination with pelvic and low back pain. Although afebrile during her visit, she reported having fevers at home. Her urinalysis was negative for leukocyte esterase and nitrite but positive for moderate blood. The culture grew 20,000 CFU/ml of A. omnincolens in pure culture.

Despite prospectively reviewing 3,395 cultures for the presence of any amount of A. omnincolens, only one culture was identified to contain fewer than 20,000 CFU/ml. This culture contained a single colony among predominating growth of urogenital flora. As in the retrospective analyses, prospective study also failed to identify a single case of confirmed A. omnincolens urinary tract infection. Interestingly though, with one exception, A. omnincolens was only identified in quantities exceeding 20,000 CFU/ml. The significance of this finding will be discussed below.

DISCUSSION

Very little is known about A. omnincolens. It is thought to be a commensal of the oral cavity and gastrointestinal tracts; however, its clinical significance when isolated from the urinary tract is unclear (3, 4, 6). The peer-reviewed literature offers little information on the role of A. omnincolens in infection. One of the few manuscripts to address its clinical significance is by Mahlen et al., who identified five urine cultures with A. omnincolens. For one case, no clinical data were available. In another patient, the isolate was listed as a possible cause of urinary tract infection; however, the urinalysis was normal, and the patient was not treated. Two of the positive cultures were thought to represent true urinary tract infections with significant pyuria on urinalysis; these two cultures were obtained from the same patient 2 months apart. This patient also had underlying bladder cancer. In a fourth patient, the urinalysis was normal, and A. omnincolens was not thought to be associated with urinary tract infection. With the exception of the first case with no available data, A. omnincolens colony counts were all >100,000 CFU/ml.

The results from our study were similarly mixed, but we can make the following conclusions. From our prospective analysis, we can conclude that A. omnincolens is rarely encountered in clinical specimens, but when it is found, it is usually in women. In reviewing the four patients in our study with positive UA results, we believe one patient (patient 7) had probable A. omnincolens urinary tract infection (UTI) and two patients (patients 2 and 4) had possible infections (Table 2). Patient 2 complained of abdominal pain, nausea, cramping, dysuria, pelvic pressure, and constipation that ultimately resolved without intervention. According to the report, her urinalysis was positive, but treatment was withheld while awaiting culture results and the patient's symptoms improved within 2 days. Her symptoms were likely related to constipation and cessation of vaginal estrogen therapy. Thus, she was categorized as possibly having infection.

TABLE 2.

Urine culture history for patients with A. omnincolens positive culture and positive urinalysis

Patient	Colony count (CFU/ml)	Pure culture	Predominant organism	UA result(s)	Symptom(s)	Antibiotic received	Previously positive urine culture or UA within 1 yr	Results/date	Follow-up culture	Follow-up UA	Alloscardovia infection
2	>100,000	No: mixed urogenital flora	Yes	NAa	Abdominal pain, nausea, cramping, constipation	None	Yes	Days prior to culture: 210; culture result: >100,000 CoNSc; UA result: LE, small; microscopy, 3 WBC/HPF	No	No	Possible
4	40,000	Yes	NA	LE,b moderate; nitrite, negative; microscopy, 22 WBC/HPF	Asymptomatic	None	No	NA	No	Days following culture: 194; UA result: LE, trace; microscopy, 3 WBC/HPF	Possible
5	1 colony	No: mixed urogenital flora	No	LE, small; nitrite, negative; microscopy, 13 WBC/HPF	Asymptomatic	None	No	NA	No	No	Unlikely
7	>100,000	No: <10,000 Klebsiella pneumoniae	Yes	LE, small; nitrite, negative; microscopy, 66 WBC/HPF	Abdominal pain, nausea, vomiting, diarrhea, chills	Keflex (5 days)	Yes	Days prior to culture: 10; culture result: no culture; UA result: LE, none; microscopy, 1 WBC/HPF	No	No	Probable

^aPositive per note. The results are unavailable.

^bLE, leukocyte esterase.

^cCoNS, coagulase-negative staphylococci.

The patient (patient 7) with probable infection had undergone recent urologic instrumentation for urinary calculi. She presented with complaints of fevers, abdominal pain, nausea, and vomiting with a positive urinalysis. Her culture yielded pure growth of >100,000 CFU/ml of A. omnincolens. We identified a third patient with possible infection but who had a negative urinalysis. This patient, patient 12, had symptoms consistent with UTI, responded to therapy, and was neutropenic which may explain the negative UA result. Thus, we conclude that this organism is capable of causing true infection in some circumstances but that further studies are needed to elucidate the role of A. omnincolens as a lower-urinary-tract pathogen. A detailed discussion of the 10 patients deemed not to have A. omnincolens infection follows.

From the remaining 10 identified cases, urine samples were obtained from three patients (patients 10, 11, and 13) as part of routine prenatal care. These patients had no dysuria and negative urinalyses and thus were determined not to have UTI. Urine samples were obtained from patients 3, 9, 14, and 15 as a matter of routine care and not for symptoms thought to be secondary to urinary tract infection. None of these patients had pyuria on urinalysis. Given these findings, the urine culture results are probably not representative of urinary tract infections. Patient 1 presented with complaints of increased nighttime urinary frequency and incontinence which were chronic and unchanged from baseline. She had no dysuria or inflammatory response, as seen on urinalysis, so she was not treated. One could argue she was on immunosuppressive agents due to renal transplant and may not have been able to mount an inflammatory response. However, on follow-up 3 months later, the patient had new onset fever with worsening urinary frequency. At that follow-up visit her urinalysis was positive for pyuria and urine culture grew Escherichia coli; she subsequently received antibiotics.

Lastly, patient 6 had a history of chronic mixed urinary incontinence and overactive bladder. She presented with symptoms consistent with urinary tract infection, including fever, dysuria, and low back pain. However, her urinalysis was negative, and the complaint of dysuria may have actually been pain associated with incontinence dermatitis which she was noted to have on exam. The patient was seen 2 weeks later by urogynecology for her continued symptoms despite receiving antibiotic treatment. Upon further evaluation, her symptoms were attributed to chronic, mixed urinary incontinence and an overactive bladder which some authors have suggested may have an infectious etiology (4). She was referred for pelvic physical therapy and has not had further urinary complaints at subsequent visits.

In our study, 14 of the 15 patients identified to have A. omnincolens in their culture, had growth that exceeded 10,000 CFU/ml, which may indicate that the presence of A. omnincolens is a marker of a condition other than infection. In a study by Pearce et al. (4), the urinary microbiome of women with urgency urinary incontinence was compared to that of asymptomatic women. Distinct differences in the microbiome composition were found. Women with urgency urinary incontinence were more likely to have Gardnerella and less likely to have Lactobacillus. As expected, the genera of women with urgency urinary incontinence were more likely to contain at least one pathogenic species. Alloscardovia was isolated in both groups with no statistically significant difference in frequency and, as a result, did not appear to contribute to urgency urinary incontinence.

These findings, taken together, suggest that A. omnincolens is a possible human pathogen that is rarely encountered in the urine of women and even more rarely in men. Clinical microbiologists should be alerted to the fact that this organism may be present in pure growth in significant quantities and still not represent true infection. Further studies are warranted to better define the clinical significance of this organism in UTI, but at this time we believe that urinalysis and clinical presentation should be considered carefully, along with culture results, prior to determining clinical significance. For the clinical microbiologist, we recommend paying special attention to cultures that yield significant and pure amounts of small alpha-hemolytic growth. A simple Gram stain revealing Gram-positive rods (Fig. 1) can be used to determine whether A. omnincolens is a possibility.