Commercial Identification Systems Research Articles

Caulobacter Species as a Cause of Postneurosurgical Bacterial Meningitis in a Pediatric Patient

Caulobacter species have been rarely found to be a cause of human infection. A case of probable Caulobacter species meningitis occurring postneurosurgery in a pediatric patient is reported in the present article. Gram stain and colony morphology of the isolate were not consistent with the identification provided by commercial phenotypic identification systems. The present case illustrates the need to reconcile conflicting phenotypic test results using 16S ribosomal DNA sequencing.

A simple xylose-based agar medium for the differentiation of Candida dubliniensis and Candida albicans

The utility of xylose-based agar medium for differentiation of Candida dubliniensis from Candida albicans is evaluated. All C. dubliniensis isolates failed to grow on this medium, while C. albicans isolates yielded good growth. This simple in-house medium offers an inexpensive alternative to commercial yeast identification systems for resource poor settings.

16S rRNA gene sequence analysis of a Brucella melitensis infection misidentified as Bergeyella zoohelcum

Misidentification of Brucella species from clinical specimens using commercial bacterial identification systems is a recurring problem. An isolate from a bacterimic patient was identified as Bergeyella zoohelcum by MicroScan Walk-Away (Siemens Healthcare Diagnostics Inc., West Sacramento, CA, USA) and as Brucella melitensis by Vitek 2 system (bioMérieuxInc., Durham, NC, USA). Because of this identification ambiguity by the two automated bacterial identification systems we performed 16S rRNA sequencing and serotyping of the isolate and confirmed it as a Brucella spp. Combining the sequence data with the Vitek 2 system data we conclude that the infection was caused by B. melitensis.

Characterization of Prototheca wickerhamii Isolated from Disseminated Algaemia of Kidney Transplant Patient from Malaysia

Prototheca wickerhamii isolated from blood of 61-year-old kidney transplant patient was described. Although it is classified as an alga (genus Chlorella), the disease, protothecosis, is included under mycoses because of its clinical pathological presentations. Colony characteristics of P. wickerhamii are indistinguishable from other yeast-like organisms like Cryptococcus and Candida. Fortunately, commercial identification system for yeast can be used to identify this organism to the species level. Electron microscopy demonstrated "morula" or daisy-like appearance of its endosporulating sporangia. The organism was sensitive to amphotericin B by E test method. Even though human protothecosis is uncommon, it cannot be ignored because it is emerging as an opportunistic infection in immunosuppressed individuals. To our knowledge, this is the first reported case of disseminated algaemia due to P. wickerhamii in Malaysia.

Escherichia fergusonii Bacteremia in a Diabetic Patient with Pancreatic Cancer

Although Escherichia fergusonii has been identified for decades, it has rarely been recovered from clinical specimens and its clinical significance remains unclear. We describe a case of E. fergusonii bacteremia in a diabetic patient with pancreatic cancer. The isolate was confirmed by three commercial identification systems and 16S rRNA gene sequence analysis. The patient's clinical condition gradually improved, and repeated blood cultures were negative after antibiotic treatment with an in vitro active agent (ceftriaxone).

Photorhabdus asymbiotica: Shedding Light on a Human Pathogenic Bioluminescent Bacterium

Photorhabdus asymbiotica is a gram-negative bacillus of the family Enterobacteriaceae. The bacterium displays the curious property of bioluminescence – the production of light without heat. It is recognized as a human pathogen in the United States and Australia, where it causes both locally invasive soft tissue infection and disseminated disease. In Australia, P. asymbiotica is vectored by the soil nematode Heterorhabditis gerrardi. The vector in the U.S. has not yet been identified, but it is likely to also be a Heterorhabditid nematode. Although it grows readily on conventional culture media, clinical microbiology laboratories may misidentify this pathogenic bacterium because of an over-reliance on commercial rapid identification systems.

Identification by 16S rRNA Gene Sequencing of Negativicoccus succinicivorans Recovered from the Blood of a Patient with Hemochromatosis and Pancreatitis

We describe a case of Negativicoccus succinicivorans bacteremia in an adult man with hemochromatosis and acute pancreatitis. Conventional phenotypic tests and commercial identification systems failed to definitively identify the tiny anaerobic Gram-negative coccus isolated from two sets of blood cultures. The bacterium was identified by 16S rRNA gene sequencing and analysis using the SmartGene Integrated Database Network System software. This is the first published report of the recovery of this organism from a patient with invasive infection.

Comparative Evaluation of Three Commercial Identification Systems Using Common and Rare Bloodstream Yeast Isolates

The commercial yeast identification systems API ID32C, Auxacolor, and Vitek were evaluated using 251 molecularly identified bloodstream isolates and 2 reference strains, representing a total of 35 species (6 common and 29 rare). Correct identification rates were higher for common species (Auxacolor, 95%; API ID32C, 94%; Vitek, 92%) than for rare species (Auxacolor, 43%; API ID32C, 56%; Vitek, 64%). All systems performed equally among the former, and Vitek performed best among the latter.

Streamlined Quality Control of Commercial Microbial Identification Systems

The Clinical and Laboratory Standards Institute issued an approved guideline (M50-A) in 2008 outlining what manufacturers and clinical microbiology laboratories had to do in order for laboratories to be eligible for streamlined quality control (QC) of commercial microbial identification systems. This article outlines the history behind this document, presents a description of the process for instituting streamlined QC, and discusses where the big three manufacturers are in helping laboratories reduce required quality control without compromising the reliability of results.

Genotypic relatedness and phenotypic characterization of Staphylococcus schleiferi subspecies in clinical samples from dogs

To assess the degree of biological similarity (on the basis of genotype determined via pulsed-field gel electrophoresis [PFGE]) between isolates of 2 Staphylococcus schleiferi subspecies (S schleiferi subsp coagulans and S schleiferi subsp schleiferi) in clinical samples obtained from dogs. 161 S schleiferi isolates from 160 canine patients. A commercial microbiology identification system was used to identify each isolate as S schleiferi. Isolates underwent slide and tube coagulase testing and antimicrobial susceptibility testing. A mecA PCR assay and a latex agglutination test for penicillin-binding protein 2a (PBP2a) were also performed on each isolate. Clonal clusters with a similarity cutoff value of 80% were identified via PFGE. Of the 161 isolates, 61 (38%), 79 (49%), and 21 (13%) were obtained from cutaneous sites, ears, and other sites, respectively; 110 (68%) were coagulase negative, and 51 (32%) were coagulase positive. Among the coagulase-negative and coagulase-positive isolates, 65% (71/110) and 39% (20/51) were oxacillin resistant, respectively. All oxacillin-resistant isolates yielded positive results via mecA PCR assay and PBP2a latex agglutination testing. Via PFGE, 15 major clusters and 108 individual pulsed-field profiles were identified. Oxacillin-resistant and oxacillin-susceptible isolates clustered separately. Clonal clusters were heterogeneous and contained representatives of both subspecies. Coagulase-positive and coagulase-negative isolates were not genotypically distinct and may represent a single S schleiferi sp with variable coagulase production, rather than 2 biologically distinct subspecies. Further studies are needed to characterize clinical or epidemiological differences associated with infections with coagulase-positive and coagulase-negative S schleiferi in dogs.

Aerobic bacteria from mucous membranes, ear canals, and skin wounds of feral cats in Grenada, and the antimicrobial drug susceptibility of major isolates

In a 2-year period 54 feral cats were captured in Grenada, West Indies, and a total of 383 samples consisting of swabs from rectum, vagina, ears, eyes, mouth, nose and wounds/abscesses, were cultured for aerobic bacteria and campylobacters. A total of 251 bacterial isolates were obtained, of which 205 were identified to species level and 46 to genus level. A commercial bacterial identification system (API/Biomerieux), was used for this purpose. The most common species was Escherichia coli (N=60), followed by Staphylococcus felis/simulans (40), S. hominis (16), S. haemolyticus (12), Streptococcus canis (9), Proteus mirabilis (8), Pasteurella multocida (7), Streptococcus mitis (7), Staphylococcus xylosus (7), S. capitis (6), S. chromogenes (4), S. sciuri (3), S. auricularis (2), S. lentus (2), S. hyicus (2), Streptococcus suis (2) and Pseudomonas argentinensis (2). Sixteen other isolates were identified to species level. A molecular method using 16S rRNA sequencing was used to confirm/identify 22 isolates. Salmonella or campylobacters were not isolated from rectal swabs. E. coli and S. felis/simulans together constituted 50% of isolates from vagina. S. felis/simulans was the most common species from culture positive ear and eye samples. P. multocida was isolated from 15% of mouth samples. Coagulase-negative staphylococci were the most common isolates from nose and wound swabs. Staphylococcus aureus, or S. intemedius/S. pseudintermedius were not isolated from any sample. Antimicrobial drug resistance was minimal, most isolates being susceptible to all drugs tested against, including tetracycline.

Prevalent organisms on ostrich carcasses found in a commercial abattoir

The prevalent microbial growth on carcasses before and after overnight cooling in an ostrich abattoir and de-boning plant was investigated. The effect of warm or cold trimming of the carcasses was examined together with possible causes of contamination along the processing line. An attempt was made to link the prevalent microorganisms that were identified from carcasses to those from specific external contamination sources. Samples of carcasses and possible contaminants were collected in the plant, plated out and selected organisms were typed using a commercial rapid identification system. It was indicated that the cold trim (mainly of bruises) of carcasses was advantageous in terms of microbiological meat quality. Results indicated pooled water in the abattoir as the most hazardous vector for carcass contamination and that contaminants from this source are mostly Gram-negative pathogens. Pseudomonas and Shigella were frequently isolated from surface and air samples and indicated that the control of total plant hygiene is a requirement for producing ostrich meat that is safe to consume and has an acceptable shelf-life.

Respiratory infections by Achromobacter xylosoxidans in a cohort of Cystic Fibrosis patients: identification, antimicrobial susceptibility and molecular epidemiology

Pulmonary infections by Gram-negative bacteria such as Achromobacter xylosoxidans are recovered frequently in patients with Cystic Fibrosis. Aims of this study were to value the isolation frequency of A.xylosoxidans strains in a cohort of Cystic Fibrosis patients, to investigate their antimicrobial sensitivity and to establish possible clonal likeness among strains.A retrospective study was undertaken between January 2004 and December 2008 on 300 patients receiving care at the Regional Cystic Fibrosis Centre of “Federico II” University, Naples. Sputum samples were collected and selective media as well as commercial systems for bacterial identification were used. The activity of antimicrobial agents was determined using diffusion and micro-dilution methods. For DNA-fingerprinting, a genomic DNA macrorestriction followed by pulsed-field gel electrophoresis was carried out. A total of 238 strains from 51 patients were isolated. Strains were resistant to aztreonam, about half of these were resistant to gentamicin and trimethoprim-sulphamethoxazole. They were sensitive to piperacillin, piperacillin/tazobactam, and also to carbapenems, quinolones, cephalosporines. Macrorestriction analysis applied on some isolates showed substantial heterogeneity among strains.Actually, the prognostic role of A. xylosoxidans in Cystic Fibrosis is unclear, but this finding must imply difficulties on therapeutic approach. So, it is need to be on the look out regard such microorganisms. Preliminary results of DNA-fingerprinting indicate no evidence of clonal likeness and then of patient-to-patient spread.

Fatal Citrobacter farmeri Meningitis in a Patient with Nasopharyngeal Cancer

We describe the case of an adult male with nasopharyngeal carcinoma who had meningitis caused by Citrobacter farmeri. The isolate was confirmed as C. farmeri by two commercial identification systems and 16S rRNA gene analysis. The patient developed multiorgan failure and died despite antibiotic treatment with in vitro active agents (ceftriaxone and meropenem).

Accuracy of 6 commercial systems for identifying clinical Aeromonas isolates

We compared the accuracy of 6 commercial systems for Aeromonas identification by testing 87 clinical isolates in routine conditions, using partial rpoB gene sequencing as the reference standard. The systems were API-20E, API-32GN, the ID-GN card with the Vitek2 system (bioMérieux, Marcy l'Etoile, France), the identification portion of the NFC47 panel (MicroScan Walk/Away system; Siemens Healthcare, Sacramento, CA), ID69 (Phoenix system; BD Diagnostic Systems, Sparks, MD), and GN2 microplates (Omnilog system; Biolog, Hayward, CA), for which 67 (77.1%), 80 (91.9%), 72 (82.7%), 70 (80.5%), 64 (73.5%), and 59 (67.8%) isolates, respectively, were correctly identified at the genus and species level. Confusion with Vibrio affected 6.9% and 16.1% of results obtained with NFC47 and API-20E, respectively. Overall, the accuracy of identification for aeromonads was hampered by outdated databases and taxonomy, weak algorithms, and impractical additional tests. Commercial identification systems should be redesigned to make Aeromonas identification algorithms more robust and to cover infrequent clinical species of this genus.

Rapid identifcation and susceptibility testing of Gram-negative bacilli from blood cultures using the Vitek® 2 system

Providing rapid results for blood culture isolates is a critical function of clinical microbiology laboratories. This study evaluated the accuracy and turnaround time for identification and susceptibility testing of Gram-negative bacilli inoculated directly from positive blood cultures into the Vitek® 2 system. Direct inoculation was compared to conventional methods, which included biochemical tests, commercial identification systems and disc diffusion susceptibility testing. Two hundred and ninety-one of 327 isolates (89%) were correctly identified to at least genus level by the direct Vitek® method. Susceptibility test results were compared for 3,925 organism antibiotic combinations. The overall rate of categorical agreement of direct and conventional antimicrobial susceptibility testing was 92% with less than 3% very major and major errors combined. The mean turnaround time for identification and susceptibility testing was 7.5 hours (SD 3.0 hours) compared to a mean of 32.3 hours (SD 14.7 hours) for the conventional method. These results suggest that direct inoculation of the Vitek® 2 system from blood cultures provides accurate, reliable identification and antimicrobial susceptibility results for the majority of commonly occurring Gram-negative pathogens, while the significantly reduced turnaround time should benefit patients and permit earlier rationalisation of antibiotic therapy, with a reduction in the use of broad spectrum antibiotics. A suggested protocol for routine use is included.

First isolation and characterization of Lactococcus garvieae from Brazilian Nile tilapia, Oreochromis niloticus (L.), and pintado, Pseudoplathystoma corruscans (Spix & Agassiz)

Lactococcus garvieae infection in cultured Nile tilapia, Oreochromis niloticus (L.), and pintado, Pseudoplathystoma corruscans (Spix & Agassiz), from Brazil is reported. The commercial bacterial identification system, Biolog Microlog, confirmed the identity of L. garvieae. Infectivity trials conducted in Nile tilapia using Brazilian Nile tilapia L. garvieae isolates resulted in a median lethal dose-50 of 1.4 x 10(5) colony-forming units (CFU)/fish. This is the first evidence of the presence of this pathogen from Brazilian fish. In addition, this is the first report of L. garvieae infection in either Nile tilapia or pintado. Collectively, this evidence expands the geographical range of fish hosts, number of fish hosts harbouring L. garvieae and carbon source utilization by L. garvieae fish isolates. Furthermore, the Biolog system may be an alternative technique to polymerase chain reaction for the identification of L. garvieae and discrimination between closely related bacterial species.

Pulmonary Disease Due to Mycobacterium arosiense , an Easily Misidentified Pathogenic Novel Mycobacterium

Mycobacterium arosiense is a newly described species. After noticing it was misidentified as Mycobacterium intracellulare by the commercial identification system GenoType CM (Hein, Nehren, Germany), we detected 4 such strains among 33 that were previously misidentified as M. intracellulare. Three more strains were found among unidentified mycobacteria not tested previously with GenoType. The first case of pulmonary disease due to M. arosiense is reported here, and the novel species, of which so far only one strain had been investigated, is further characterized.

Microbiological and Epidemiological Features of Clinical Respiratory Isolates of Burkholderia gladioli

Burkholderia gladioli, primarily known as a plant pathogen, is involved in human infections, especially in patients with cystic fibrosis (CF). In the present study, the first respiratory isolates recovered from 14 French patients with CF and 4 French patients without CF, identified by 16S rRNA gene analysis, were tested for growth on B. cepacia selective media, for identification by commercial systems, and for their antimicrobial susceptibilities, and were compared by pulsed-field gel electrophoresis (PFGE). Patients' data were collected. All 18 isolates grew on oxidation-fermentation-polymyxin B-bacitracin-lactose medium and Pseudomonas cepacia agar, but only 13 grew on Burkholderia cepacia selective agar. API 20NE strips did not differentiate B. gladioli from B. cepacia, whereas Vitek 2 GN cards correctly identified 15 isolates. All isolates were susceptible to piperacillin, imipenem, aminoglycosides, and ciprofloxacin and were far less resistant to ticarcillin than B. cepacia complex organisms. Fifteen PFGE types were observed among the 18 isolates, but shared types were not identified among epidemiologically related patients. The microbiological follow-up of CF patients showed that colonization was persistent in 3 of 13 documented cases; B. gladioli was isolated from posttransplantation cultures of blood from 1 patient. Among the patients without CF, B. gladioli was associated with intubation (three cases) or bronchiectasis (one case). In summary, the inclusion of B. gladioli in the databases of commercial identification systems should improve the diagnostic capabilities of those systems. In CF patients, this organism is more frequently involved in transient infections than in chronic infections, but it may be responsible for complications posttransplantation; patient-to-patient transmission has not been demonstrated to date. Lastly, B. gladioli appears to be naturally susceptible to aminoglycosides and ciprofloxacin, although resistant isolates may emerge in the course of chronic infections.

Consensus Guidelines Developed for Streamlined Quality Control on Commercial Microbial Identification Systems

Consensus Guidelines Developed for Streamlined Quality Control on Commercial Microbial Identification Systems