Vera Tesic

Evaluation of FilmArray and Verigene Systems for Rapid Identification of Positive Blood Cultures

ABSTRACT The Verigene tests for Gram-positive and Gram-negative organisms in blood culture and the FilmArray blood culture identification panel were assessed for their ability to identify pathogens from positive blood cultures. Both platforms correctly identified bacteria in 92% of monomicrobial cultures analyzed, with times to identification that were significantly shorter than those for identification from subcultures.

Alterations of lung microbiota in a mouse model of LPS-induced lung injury

Acute lung injury (ALI) and the more severe acute respiratory distress syndrome are common responses to a variety of infectious and noninfectious insults. We used a mouse model of ALI induced by intratracheal administration of sterile bacterial wall lipopolysaccharide (LPS) to investigate the changes in innate lung microbiota and study microbial community reaction to lung inflammation and barrier dysfunction induced by endotoxin insult. One group of C57BL/6J mice received LPS via intratracheal injection (n = 6), and another received sterile water (n = 7). Bronchoalveolar lavage (BAL) was performed at 72 h after treatment. Bacterial DNA was extracted and used for qPCR and 16S rRNA gene-tag (V3-V4) sequencing (Illumina). The bacterial load in BAL from ALI mice was increased fivefold (P = 0.03). The community complexity remained unchanged (Simpson index, P = 0.7); the Shannon diversity index indicated the increase of community evenness in response to ALI (P = 0.07). Principal coordinate analysis and analysis of similarity (ANOSIM) test (P = 0.005) revealed a significant difference between microbiota of control and ALI groups. Bacteria from families Xanthomonadaceae and Brucellaceae increased their abundance in the ALI group as determined by Metastats test (P < 0.02). In concordance with the 16s-tag data, Stenotrohomonas maltophilia (Xanthomonadaceae) and Ochrobactrum anthropi (Brucellaceae) were isolated from lungs of mice from both groups. Metabolic profiling of BAL detected the presence of bacterial substrates suitable for both isolates. Additionally, microbiota from LPS-treated mice intensified IL-6-induced lung inflammation in naive mice. We conclude that the morbid transformation of ALI microbiota was attributed to the set of inborn opportunistic pathogens thriving in the environment of inflamed lung, rather than the external infectious agents.

Rapid Identification of Positive Blood Cultures by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Using Prewarmed Agar Plates

ABSTRACT This study describes an inexpensive and straightforward method for identifying bacteria by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) directly from positive blood cultures using prewarmed agar plates. Different inoculation methods and incubation times were evaluated to determine the optimal conditions. The two methods using pelleted material from positive culture bottles performed best. In particular, the pellet streak method correctly identified 94% of the Gram negatives following 4 h of incubation and 98% of the Gram positives following 6 h of incubation.

Comparison of Cepheid Xpert® Flu/RSV XC and BioFire FilmArray® for detection of influenza A, influenza B, and respiratory syncytial virus

ABSTRACT The Xpert Flu/RSV XC was compared to the FilmArray respiratory panel for detection of influenza (Flu) A, Flu B, and respiratory syncytial virus (RSV), using 128 nasopharyngeal swabs. Positive agreements were 100% for Flu A and RSV and 92.3% for Flu B. The Xpert may be useful in clinical situations when extensive testing is not required and may serve an important role in laboratories already performing broader respiratory panel testing.

Prospective evaluation of the VITEK MS for the routine identification of bacteria and yeast in the clinical microbiology laboratory: assessment of accuracy of identification and turnaround time.

This study assessed the accuracy of bacterial and yeast identification using the VITEK MS, and the time to reporting of isolates before and after its implementation in routine clinical practice. Three hundred and sixty-two isolates of bacteria and yeast, consisting of a variety of clinical isolates and American Type Culture Collection strains, were tested. Results were compared with reference identifications from the VITEK 2 system and with 16S rRNA sequence analysis. The VITEK MS provided an acceptable identification to species level for 283 (78 %) isolates. Considering organisms for which genus-level identification is acceptable for routine clinical care, 315 isolates (87 %) had an acceptable identification. Six isolates (2 %) were identified incorrectly, five of which were Shigella species. Finally, the time for reporting the identifications was decreased significantly after implementation of the VITEK MS for a total mean reduction in time of 10.52 h (P<0.0001). Overall, accuracy of the VITEK MS was comparable or superior to that from the VITEK 2. The findings were also comparable to other studies examining the accuracy of the VITEK MS, although differences exist, depending on the diversity of species represented as well as on the versions of the databases used. The VITEK MS can be incorporated effectively into routine use in a clinical microbiology laboratory and future expansion of the database should provide improved accuracy for the identification of micro-organisms.

Use of the Accelerate Pheno System for Identification and Antimicrobial Susceptibility Testing of Pathogens in Positive Blood Cultures and Impact on Time to Results and Workflow

ABSTRACT The Accelerate Pheno system uses automated fluorescence in situ hybridization technology with morphokinetic cellular analysis to provide rapid species identification (ID) and antimicrobial susceptibility testing (AST) results for the most commonly identified organisms in bloodstream infections. The objective was to evaluate the accuracy and workflow of bacterial and yeast ID and bacterial AST using the Accelerate Pheno system in the clinical microbiology laboratory. The consecutive fresh blood cultures received in the laboratory were analyzed by the Accelerate Pheno system within 0 to 8 h of growth detection. ID/AST performance, the average times to results, and workflow were compared to those of the routine standard of care. Of the 232 blood cultures evaluated (223 monomicrobial and 9 polymicrobial) comprising 241 organisms, the overall sensitivity and specificity for the identification of organisms were 95.6% and 99.5%, respectively. For antimicrobial susceptibility, the overall essential agreement was 95.1% and categorical agreement was 95.5% compared to routine methods. There was one very major error and 3 major errors. The time to identification and the time to susceptibility using the Accelerate Pheno system were decreased by 23.47 and 41.86 h, respectively, compared to those for the standard of care. The reduction in hands on time was 25.5 min per culture. The Accelerate Pheno system provides rapid and accurate ID/AST results for most of the organisms found routinely in blood cultures. It is easy to use, reduces hands on time for ID/AST of common blood pathogens, and enables clinically actionable results to be released much earlier than with the current standard of care.

Poor Immunogenicity, Not Vaccine Strain Egg Adaptation, May Explain the Low H3N2 Influenza Vaccine Effectiveness in 2012–2013

Abstract Background Influenza vaccination aims to prevent infection by influenza virus and reduce associated morbidity and mortality; however, vaccine effectiveness (VE) can be modest, especially for subtype A(H3N2). Low VE has been attributed to mismatches between the vaccine and circulating influenza strains and to the vaccine’s elicitation of protective immunity in only a subset of the population. The low H3N2 VE in the 2012–2013 season was attributed to egg-adaptive mutations that created antigenic mismatch between the actual vaccine strain (IVR-165) and both the intended vaccine strain (A/Victoria/361/2011) and the predominant circulating strains (clades 3C.2 and 3C.3). Methods We investigated the basis of low VE in 2012–2013 by determining whether vaccinated and unvaccinated individuals were infected by different viral strains and by assessing the serologic responses to IVR-165, A/Victoria/361/2011, and 3C.2 and 3C.3 strains in an adult cohort before and after vaccination. Results We found no significant genetic differences between the strains that infected vaccinated and unvaccinated individuals. Vaccination increased titers to A/Victoria/361/2011 and 3C.2 and 3C.3 representative strains as much as to IVR-165. These results are consistent with the hypothesis that vaccination boosted cross-reactive immune responses instead of specific responses against unique vaccine epitopes. Only approximately one-third of the cohort achieved a ≥4-fold increase in titer. Conclusions In contrast to analyses based on ferret studies, low H3N2 VE in 2012–2013 in adults does not appear to be due to egg adaptation of the vaccine strain. Instead, low VE might have been caused by low vaccine immunogenicity in a subset of the population.

Atypical favic invasion of the scalp by Microsporum canis: Report of a case and review of reported cases caused by Microsporum species

Favus is an uncommon pattern of dermatophytic infection of the scalp, glabrous skin and nails. We report the first documented case of favus of the scalp caused by Microsporum canis in an immunocompetent 8‐year‐old girl. The classic and various atypical clinical presentations of favus are discussed, as well as a brief review of the literature given.

Comparison of turnaround time and time to oseltamivir discontinuation between two respiratory viral panel testing methodologies

Respiratory infections contribute to many Emergency Department visits and hospitalizations, resulting in a high healthcare burden (Neuzil et al., 2003; Schull et al., 2005). Rapid detection of respiratory pathogens in patients presenting with symptoms of an upper respiratory tract infection is crucial for timely determination of optimal antimicrobial management, avoidance of unnecessary evaluations and implementation of transmission-reducing infection control practices. Rapid viral testing can also result in cost savings to the healthcare system through reduction in Emergency Department boarding time and decreased duration of empiric antiviral therapy (Schull et al., 2005). With increased emphasis on antimicrobial stewardship in hospitals to facilitate improved clinical and economic outcomes with antimicrobial therapy, the implementation of rapid diagnostics for laboratory identification of pathogens is of great interest (Bauer et al., 2014). Multiplex PCR is a highly sensitive molecular method for accurate detection of respiratory pathogens and provides a more rapid turnaround time (TAT) compared with other respiratory viral testing methodologies. Our microbiology laboratory switched from the Luminex xTAG respiratory viral panel (RVP) (http://www.luminexcorp.com), which detects 12 respiratory viruses with an assay time of 8.5 h, performed two to three times per week to the Biofire Diagnostics FilmArray respiratory panel (RP) (http://filmarray.com), which detects 17 respiratory viral and three bacterial targets with an assay time of 1.2 h, performed 24 h a day/7 days per week. We compared the TAT between the two RVPs performed at different frequencies and determined the time to discontinuation of empiric oseltamivir among patients testing negative for influenza. All adult patients with an RVP test result reported between 1 December 2011 and 28 February 2012 performed on Luminex xTAG RVP (two to three times per week) and 1 December 2012 and 28 February 2013 performed on FilmArray RP (24 h a day/7 days per week) were evaluated for mean TAT. The mean TAT for the Luminex xTAG RVP (two to three times per week) between 1 December 2011 and 28 February 2012 (n = 230 assays) was 46.4 h compared with a mean TAT of 3.1 h (P<0.001) for FilmArray RP (24 h a day/7 days per week) between 1 December 2012 and 28 February 2013 (n = 872 assays) (Fig. 1). The mean time to discontinuation of empiric oseltamivir amongst patients with an RVP negative for influenza was 4 and 2 days for the Luminex xTAG RVP (n = 42) and FilmArray RP (n = 75) groups, respectively (P<0.001). The reduction in mean time to discontinuation of empiric oseltamivir resulted in cost savings of ~US

The performance of Luminex ARIES ® Flu A/B & RSV and Cepheid Xpert ® Flu/RSV XC for the detection of influenza A, influenza B, and respiratory syncytial virus in prospective patient samples

34.16 per patient (using a wholesale acquisition cost for oseltamivir of US