Evaluation of the BD Phoenix Automated Microbiology System SMIC/ID panel for identification and antimicrobial susceptibility testing of Streptococcus spp

Association of Local Unit Sampling and Microbiology Laboratory Culture Practices With the Ability to Identify Causative Pathogens in Peritoneal Dialysis-Associated Peritonitis in Thailand

Introduction

This describes variations in facility peritoneal dialysis (PD) effluent (PDE) culture techniques and local microbiology laboratory practices, competencies, and quality assurance associated with peritonitis, with a specific emphasis on factors associated with culture-negative peritonitis (CNP).

Methods

Peritonitis data were prospectively collected from 22 Thai PD centers between May 2016 and October 2017 as part of the Peritoneal Dialysis Outcomes and Practice Patterns Study. The first cloudy PD bags from PD participants with suspected peritonitis were sent to local and central laboratories for comparison of pathogen identification. The associations between these characteristics and CNP were evaluated.

Results

CNP was significantly more frequent in local laboratories (38%) compared with paired PDE samples sent to the central laboratory (12%, P < 0.05). Marked variations were observed in PD center practices, particularly with respect to specimen collection and processing, which often deviated from International Society for Peritoneal Dialysis Guideline recommendations, and laboratory capacities, capabilities, and certification. Lower rates of CNP were associated with PD nurse specimen collection, centrifugation of PDE, immediate transfer of samples to the laboratory, larger hospital size, larger PD unit size, availability of an on-site nephrologist, higher laboratory capacity, and laboratory ability to perform aerobic cultures, undertake standard operating procedures in antimicrobial susceptibilities, and obtain local accreditation.

Conclusion

There were large variations in PD center and laboratory capacities, capabilities, and practices, which in turn were associated with the likelihood of culturing and correctly identifying organisms responsible for causing PD-associated peritonitis. Deviations in practice from International Society for Peritoneal Dialysis guideline recommendations were associated with higher CNP rates.

Identification of clinical isolates of α-hemolytic streptococci by 16S rRNA gene sequencing, matrix-assisted laser desorption ionization-time of flight mass spectrometry using MALDI Biotyper, and conventional phenotypic methods: a comparison

Fifty-six α-hemolytic streptococcal isolates were identified using MALDI Biotyper MS (Bruker Daltonics), API 20 Strep (bioMérieux), and BD Phoenix (Becton, Dickinson). The gold standard for identification was 16S rRNA gene sequence analysis with 16S-23S rRNA intergenic spacer sequencing. The following percentages of isolates were correctly identified to the species level: MALDI Biotyper, 46%; BD Phoenix, 35%; and API 20 Strep, 26%.

Phoenix 100 versus Vitek 2 in the identification of gram-positive and gram-negative bacteria: a comprehensive meta-analysis

Phoenix 100 and Vitek 2 (operating with the current colorimetric cards) are commonly used in hospital laboratories for rapid identification of microorganisms. The present meta-analysis aims to evaluate and compare their performance on Gram-positive and Gram-negative bacteria. The MEDLINE database was searched up to October 2010 for the retrieval of relevant articles. Pooled correct identification rates were derived from random-effects models, using the arcsine transformation. Separate analyses were conducted at the genus and species levels; subanalyses and meta-regression were undertaken to reveal meaningful system- and study-related modifiers. A total of 29 (6,635 isolates) and 19 (4,363 isolates) articles were eligible for Phoenix and colorimetric Vitek 2, respectively. No significant differences were observed between Phoenix and Vitek 2 either at the genus (97.70% versus 97.59%, P = 0.919) or the species (92.51% versus 88.77%, P = 0.149) level. Studies conducted with conventional comparator methods tended to report significantly better results compared to those using molecular reference techniques. Speciation of Staphylococcus aureus was significantly more accurate in comparison to coagulase-negative staphylococci by both Phoenix (99.78% versus 88.42%, P < 0.00001) and Vitek 2 (98.22% versus 91.89%, P = 0.043). Vitek 2 also reached higher correct identification rates for Gram-negative fermenters versus nonfermenters at the genus (99.60% versus 95.90%, P = 0.004) and the species (97.42% versus 84.85%, P = 0.003) level. In conclusion, the accuracy of both systems seems modified by underlying sample- and comparator method-related parameters. Future simultaneous assessment of the instruments against molecular comparator procedures may facilitate interpretation of the current observations.

It's not easy being green: the viridans group streptococci, with a focus on pediatric clinical manifestations

The viridans group streptococci (VGS) are a heterogeneous group of organisms that can be human commensals, colonizing the gastrointestinal and genitourinary tracts in addition to the oral mucosa. VGS are generally considered to be of low pathogenic potential in immunocompetent individuals. However, in certain patient populations, VGS can cause invasive disease, such as endocarditis, intra-abdominal infection, and shock. Within the VGS, the rates and patterns of antimicrobial resistance vary greatly depending upon the species identification and the patient population. In general, Streptococcus mitis group organisms are resistant to more antimicrobial agents than the other VGS species. This review addresses current VGS taxonomy, in addition to the current methodologies being used in clinical microbiology laboratories for identification of VGS. Automated systems struggle overall with species level identification and susceptibility testing for VGS. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) identification is emerging as a potential alternative for organism identification. A review of recent pediatric-specific data regarding the clinical manifestations of VGS revealed that the Streptococcus anginosus group (SAG) organisms may be important pathogens in pediatric patients and that the VGS may contribute to disease in patients with cystic fibrosis. It also appears that rates of antimicrobial resistance in VGS in pediatric patients are surpassing those of the adult population.

Comparison of the automated Phoenix with the Vitek 2 for the identification of Streptococcus pneumoniae

Rapid and accurate identification of Streptococcus pneumoniae is a critical component in the optimal management of infected patients. The performance of the BD Phoenix Automated Microbiology System (BD Diagnostic Systems, Sparks, Md.) was evaluated for identification of S. pneumoniae (n = 311) and was compared to the Vitek 2 (bioMérieux, Marcy l'Etoile, France). Strains with discordant identification between methods were resolved with 16S rRNA gene sequencing as the gold standard. The Phoenix and the Vitek 2 correctly identified 96.8% (n = 301) and 95.2% (n = 296) of S. pneumoniae strains, respectively. Overall, there was no statistically significant difference in the performance of the 2 automated systems for the identification of S. pneumoniae in this study. The Vitek 2 mean time-to-results for all streptococcal identification was 1.5 h faster than that for the Phoenix. We conclude that the automated Phoenix and the Vitek 2 systems are comparable in their ability to identify S. pneumoniae and are preferable to the use of routine biochemical assays, which have delayed time-to-results and are not dependably accurate.

[Evaluation of the BD phoenix automated microbiology system SMIC/ID-2 panel for antimicrobial susceptibility testing of Streptococcus pneumoniae]

BACKGROUND

With the emergence of antimicrobial resistance among Streptococcus pneumoniae, a more accurate and automated antimicrobial susceptibility testing method is essential. We evaluated the BD Phoenix Automated Microbiology System (Becton Dickinson Diagnostic Systems, USA) SMIC/ID-2 panel for antimicrobial susceptibility testing of S. pneumoniae.

METHODS

A total of 113 clinical strains of S. pneumoniae (88 penicillin susceptible strains, 8 intermediate strains, and 17 resistant strains by 2008 CLSI criteria) were tested. Minimum inhibitory concentrations (MICs) for penicillin, cefotaxime, clindamycin, erythromycin, levofloxacin, trimethoprim/ sulfamethoxazole, tetracycline, and vancomycin were determined by Etest (AB Biodisk, Sweden) and Phoenix System. The results obtained by Phoenix system were compared to those obtained by Etest.

RESULTS

The overall essential agreement of MICs (within one dilution of MICs) defined by the Phoenix and Etest was 92.3%. Neither very major errors nor major errors were produced, and minor errors were 6.5%. Minor errors were frequently observed in susceptibility testings for penicillin (22.1%), cefotaxime (12.4%), and trimethoprim/sulfamethoxazole (11.5%).

CONCLUSIONS

The Phoenix SMIC/ID-2 panel provided a simple and rapid susceptibility testing for S. pneumoniae, and the results were in a good agreement with those of Etest. The Phoenix system appears to be an effective automated system in clinical microbiology laboratories.

Laser-induced fluorescence-capillary electrophoresis and fluorescence microplate reader measurement: two methods to quantify the effect of antibiotics

Putative antibiotic drugs have to be classified according to their bactericidal potential. Two new methods by means of fluorescence spectroscopy (FS) using a fluorescence microplate reader (FMR) and laser-induced fluorescence capillary electrophoresis (LIF-CE), respectively, were developed for the assessment of the bactericidal efficiency using the LIVE/DEAD BacLight viability kit composed of the two fluorescent nucleic acid stains, SYTO9 (stains all cells green) and propidium iodide (stains cells with damaged membrane red). By correlation of the ratio of green and red fluorescence with the percentage of live cells by employing FS and LIF-CE, respectively, dose response curves of drug-treated Pseudomonas spp. and Streptococcus spp. samples were calculated, which allowed for the assessment of ED50 values. Both methods led to similar results which were in agreement with the minimum inhibitory concentrations (MICs) obtained by conventional broth microdilution. The application of the BacLight viability kit on drug-treated bacteria cultures presents a rapid method of assessing the antibiotic potency which is of great importance for high throughput screening in the development of new antibiotics. Additionally, the new LIF-CE method, which based on the use of a second unlabeled bacteria injection as a stacking front, allowed drawing conclusions from the electrophoretic profile about the constitution of the bacterial population. Thus, the tendency of bacterial chain formation and alterations in the live/dead ratio of the bacterial composition can be directly observed in the presence of different antibiotics.

Drug susceptibility testing of clinical isolates of streptococci and enterococci by the Phoenix automated microbiology system

Background

Drug resistance is an emerging problem among streptococcal and enterococcal species. Automated diagnostic systems for species identification and antimicrobial susceptibility testing (AST) have become recently available. We evaluated drug susceptibility of clinical isolates of streptococci and enterococci using the recent Phoenix system (BD, Sparks, MD). Diagnostic tools included the new SMIC/ID-2 panel for streptococci, and the PMIC/ID-14 for enterococci. Two-hundred and fifty isolates have been investigated: β-hemolytic streptococci (n = 65), Streptococcus pneumoniae (n = 50), viridans group streptococci (n = 32), Enterococcus faecium (n = 40), Enterococcus faecalis (n = 43), other catalase-negative cocci (n = 20). When needed, species ID was determined using molecular methods. Test bacterial strains were chosen among those carrying clinically-relevant resistance determinants (penicillin, macrolides, fluoroquinolones, glycopeptides). AST results of the Phoenix system were compared to minimal inhibitory concentration (MIC) values measured by the Etest method (AB Biodisk, Solna, Sweden).

Results

Streptococci: essential agreement (EA) and categorical agreement (CA) were 91.9% and 98.8%, respectively. Major (ME) and minor errors (mE) accounted for 0.1% and 1.1% of isolates, respectively. No very major errors (VME) were produced. Enterococci: EA was 97%, CA 96%. Small numbers of VME (0.9%), ME (1.4%) and mE (2.8%) were obtained. Overall, EA and CA rates for most drugs were above 90% for both genera. A few VME were found: a) teicoplanin and high-level streptomycin for E. faecalis, b) high-level gentamicin for E. faecium. The mean time to results (± SD) was 11.8 ± 0.9 h, with minor differences between streptococci and enterococci.

Conclusion

The Phoenix system emerged as an effective tool for quantitative AST. Panels based on dilution tests provided rapid and accurate MIC values with regard to clinically-relevant streptococcal and enterococcal species.

Use of the Phoenix automated system for identification of Streptococcus and Enterococcus spp

The Phoenix system (Becton Dickinson Diagnostic Systems, Sparks, MD) was evaluated for identification (ID) to the species level of streptococci and enterococci. Two hundred clinical isolates were investigated: beta-hemolytic streptococci (n = 50), Streptococcus pneumoniae organisms (n = 46), viridans group streptococci (n = 31), Enterococcus faecium (n = 36), Enterococcus faecalis (n = 25), and other catalase-negative cocci (n = 12). The API system (bioMérieux, Marcy l'Etoile, France) was used as a comparator. Molecular methods (sequencing of 16S rRNA and zwf and gki genes and ddl gene amplification) were used to investigate discordant results. Upon resolution of discrepancies, correct species ID was achieved by the Phoenix system for 121/129 (93.8%) streptococci and 63/70 (90.0%) enterococci. Excellent results were obtained for S. pneumoniae (45/45) and beta-hemolytic streptococci (49/50). With regard to viridans streptococci, the accuracy of the Phoenix system was 83.9%. Among the latter organisms, the best performance was obtained with isolates of the Streptococcus sanguinis group and Streptococcus anginosus group; problems were instead encountered with the Streptococcus mitis group. Four E. faecium and three E. faecalis isolates were misidentified as Enterococcus casseliflavus/Enterococcus gallinarum or Enterococcus durans. Thus, these isolates were identified only at the genus level. Compared with commercially available systems, the Phoenix system appears a reliable diagnostic tool for identifying clinically relevant streptococci and enterococci. The SMIC/ID-2 panel proved particularly effective for beta-hemolytic streptococci and pneumococci.