Archive for November 28, 2018

Evaluation of the Revised Ceftaroline Disk Diffusion Breakpoints When Testing a Challenge Collection of Methicillin-Resistant Staphylococcus aureus Isolates

Clin. Microbiol. December 2018 V.56 N.12

Helio S. Sader, Paul R. Rhomberg, Timothy B. Doyle, Robert K. Flamm and Rodrigo E. Mendes

We assessed ceftaroline disk diffusion breakpoints for Staphylococcus aureus when applying revised Clinical and Laboratory Standards Institute (CLSI) ceftaroline MIC breakpoints. Disk-MIC correlation was evaluated by testing a challenge collection (n = 158) of methicillin-resistant S. aureus (MRSA) isolates composed of 106 randomly selected isolates plus 52 isolates with decreased susceptibility to ceftaroline (MIC, 1 to 16 μg/ml). Disk diffusion was performed with 30-μg disks and Mueller-Hinton agar from 2 manufacturers each. Revised CLSI susceptible (S)/susceptible dose-dependent (SDD)/resistant (R) MIC breakpoints of ≤1/2 to 4/≥8 μg/ml were applied. The disk breakpoints that provided the lowest error rates were CLSI S/R breakpoints of ≥25 mm/≤19 mm, with no very major (VM) or major (Ma) errors and with minor (Mi) error rates of 0.0% for ≥2 doubling dilutions above the I or SDD (≥I + 2), 22.1% for I or SDD plus or minus 1 doubling dilution (I ± 1), and 2.3% for ≤2 doubling dilutions below the I or SDD ≤I − 2 (overall Mi error rate, 16.5%). No mutation in the penicillin-binding protein 2a (PBP2a) was observed in 5 of 15 isolates with a ceftaroline MIC of 2 μg/ml; 3 of 11 isolates with a ceftaroline MIC of 1 μg/ml exhibited mutations in the penicillin-binding domain (PBD; 1 isolate) or in the non-PBD (2 isolates). All isolates except 1, with a ceftaroline MIC of ≥4 μg/ml, showed ≥1 mutation in the PBD and/or non-PBD. In summary, results from the disk diffusion method showed a good correlation with those from the reference broth microdilution method. Our results also showed that the ceftaroline MIC distribution of isolates with no mutations in the PBP2a goes up to 4 μg/ml, and reference broth microdilution and disk diffusion methods do not properly separate wild-type from non-wild-type isolates.



November 28, 2018 at 3:14 pm

Improving the Diagnosis of Orthopedic Implant-Associated Infections: Optimizing the Use of Tools Already in the Box

Clin. Microbiol. December 2018 V.56 N.12

Shawn Vasoo

With the increasing number of prosthetic joints replaced annually worldwide, orthopedic implant-associated infections (OIAI) present a considerable burden. Accurate diagnostics are required to optimize surgical and antimicrobial therapy. Sonication fluid cultures have been shown in multiple studies to improve the microbiological yield of OIAIs, but uptake of sonication has not been widespread in many routine clinical microbiology laboratories. In this issue, M. Dudareva and colleagues (J Clin Microbiol 56:e00688-18, 2018, describe their unit’s experience with OIAI diagnosis using periprosthetic tissue inoculated into an automated blood culture system and sonication fluid culture.





Clin. Microbiol. December 2018 V.56 N.12

Sonication versus Tissue Sampling for Diagnosis of Prosthetic Joint and Other Orthopedic Device-Related Infections

Maria Dudareva, Lucinda Barrett, Mel Figtree, Matthew Scarborough, Masanori Watanabe, Robert Newnham, Rachael Wallis, Sarah Oakley, Ben Kendrick, David Stubbs, Martin A. McNally, Philip Bejon, Bridget A. Atkins, Adrian Taylor and Andrew J. Brent

Current guidelines recommend collection of multiple tissue samples for diagnosis of prosthetic joint infections (PJI). Sonication of explanted devices has been proposed as a potentially simpler alternative; however, reported microbiological yield varies. We evaluated sonication for diagnosis of PJI and other orthopedic device-related infections (DRI) at the Oxford Bone Infection Unit between October 2012 and August 2016. We compared the performance of paired tissue and sonication cultures against a “gold standard” of published clinical and composite clinical and microbiological definitions of infection. We analyzed explanted devices and a median of five tissue specimens from 505 procedures. Among clinically infected cases the sensitivity of tissue and sonication culture was 69% (95% confidence interval, 63 to 75) and 57% (50 to 63), respectively (P < 0.0001). Tissue culture was more sensitive than sonication for both PJI and other DRI, irrespective of the infection definition used. Tissue culture yield was higher for all subgroups except less virulent infections, among which tissue and sonication culture yield were similar. The combined sensitivity of tissue and sonication culture was 76% (70 to 81) and increased with the number of tissue specimens obtained. Tissue culture specificity was 97% (94 to 99), compared with 94% (90 to 97) for sonication (P = 0.052) and 93% (89 to 96) for the two methods combined. Tissue culture is more sensitive and may be more specific than sonication for diagnosis of orthopedic DRI in our setting. Variable methodology and case mix may explain reported differences between centers in the relative yield of tissue and sonication culture. Culture yield was highest for both methods combined.



November 28, 2018 at 3:12 pm

Blood Culture Results Reporting: How Fast Is Your Laboratory and Is Faster Better?

Clin. Microbiol. December 2018 V.56 N.12

Richard B. Thomson Jr. and Erin McElvania

Blood cultures are one of the most common and most important tests performed in clinical microbiology laboratories. Variables and technology that improve and speed the recovery of blood stream pathogens have been published in the Journal of Clinical Microbiology since its inception in 1975.

Blood cultures are one of the most common and most important tests performed in clinical microbiology laboratories. Variables and technology that improve and speed the recovery of blood stream pathogens have been published in the Journal of Clinical Microbiology since its inception in 1975. Despite the importance of blood cultures, little research has focused on the turnaround time of blood culture reports. In this issue of the Journal of Clinical Microbiology, Y. P. Tabak et al. (J Clin Microbiol 56:e00500-18, 2018, report the results of an investigation of Gram stain, organism identification, and susceptibility report turnaround times for 165,593 blood cultures from 13 laboratories. These data provide a starting point for clinical laboratories to establish targets for blood culture result reporting.




  1. Clin. Microbiol. December 2018 V.56 N.12

Blood Culture Turnaround Time in U.S. Acute Care Hospitals and Implications for Laboratory Process Optimization

Ying P. Tabak, Latha Vankeepuram, Gang Ye, Kay Jeffers, Vikas Gupta and Patrick R. Murray

The rapid identification of blood culture isolates and antimicrobial susceptibility test (AST) results play critical roles for the optimal treatment of patients with bloodstream infections. Whereas others have looked at the time to detection in automated culture systems, we examined the overall time from specimen collection to actionable test results. We examined four points of time, namely, blood specimen collection, Gram stain, organism identification (ID), and AST reports, from electronic data from 13 U.S. hospitals for the 11 most common, clinically significant organisms in septic patients. We compared the differences in turnaround times and the times from when specimens were collected and the results were reported in the 24-h spectrum. From January 2015 to June 2016, 165,593 blood specimens were collected, of which, 9.5% gave positive cultures. No matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry was used during the study period. Across the 10 common bacterial isolates (n = 6,412), the overall median (interquartile range) turnaround times were 0.80 (0.64 to 1.08), 1.81 (1.34 to 2.46), and 2.71 (2.46 to 2.99) days for Gram stain, organism ID, and AST, respectively. For all positive cultures, approximately 25% of the specimens were collected between 6:00 a.m. and 11:59 a.m. In contrast, more of the laboratory reporting times were concentrated between 6:00 a.m. and 11:59 a.m. for Gram stain (43%), organism ID (78%), and AST (82%), respectively (P < 0.001). The overall average turnaround times from specimen collection for Gram stain, organism ID, and AST were approximately 1, 2, and 3 days, respectively. The laboratory results were reported predominantly in the morning hours. Laboratory automation and work flow optimization may play important roles in reducing the microbiology result turnaround time.



November 28, 2018 at 3:11 pm

Outbreak of Tattoo-Associated Nontuberculous Mycobacterial Skin Infections.

Clinical Infectious Diseases

Isabel Griffin, MPH  Ann Schmitz, DVM  Christine Oliver  Scott Pritchard, MPH Guoyan Zhang, MD, MPH  Edhelene Rico, MPH  Emily Davenport  Anthoni Llau, PhD Emily Moore, MPH  Danielle Fernandez, MPH 


On April 29, 2015, the Florida Department of Health in Miami-Dade County (DOH-Miami-Dade) was notified by a local dermatologist of three patients with suspect nontuberculous mycobacterial (NTM) infection after receiving tattoos at a local tattoo studio.


DOH-Miami-Dade conducted interviews and offered testing, described below, to tattoo studio clients reporting rashes. Culture of clinical isolates and identification were performed at the Florida Bureau of Public Health Laboratories (BPHL). Characterization of NTM was performed by the Centers for Disease Control and Prevention (CDC) and the United States Food and Drug Administration (FDA), respectively. Whole-genome sequencing (WGS) and single-nucleotide polymorphism (SNP) analyses were used to construct a phylogeny among 21 Mycobacterium isolates at FDA.


Thirty-eight of 226 interviewed clients were identified as outbreak-associated cases. Multivariate logistic regression revealed individuals who reported grey tattoo ink in their tattoos were 8.2 times as likely to report a rash [95% CI: 3.07—22.13]. Multiple NTM species were identified in clinical and environmental specimens. Phylogenetic results from environmental samples and skin biopsies indicated that two M. fortuitum isolates (greywash ink and a skin biopsy) and 11 M. abscessus isolates (five from the implicated bottle of greywash tattoo ink, two from tap water, and four from skin biopsies) were indistinguishable. In addition, M. chelonae was isolated from five unopened bottles of greywash ink provided by two other tattoo studios in Miami-Dade County.


WGS and SNP analyses identified the tap water and the bottle of greywash tattoo ink as the sources of the NTM infections.



November 28, 2018 at 8:19 am

Multi-Drug resistant Enterobacter bugandensis species isolated from the International Space Station and comparative genomic analyses with human pathogenic strains.

BioMed Central Microbiology 2018 V.18 P.175

Nitin K. Singh†, Daniela Bezdan†, Aleksandra Checinska Sielaff, Kevin Wheeler, Christopher E. Mason and Kasthuri Venkateswaran


The antimicrobial resistance (AMR) phenotypic properties, multiple drug resistance (MDR) gene profiles, and genes related to potential virulence and pathogenic properties of five Enterobacter bugandensis strains isolated from the International Space Station (ISS) were carried out and compared with genomes of three clinical strains. Whole genome sequences of ISS strains were characterized using the hybrid de novo assembly of Nanopore and Illumina reads. In addition to traditional microbial taxonomic approaches, multilocus sequence typing (MLST) analysis was performed to classify the phylogenetic lineage. Agar diffusion discs assay was performed to test antibiotics susceptibility. The draft genomes after assembly and scaffolding were annotated with the Rapid Annotations using Subsystems Technology and RNAmmer servers for downstream analysis.


Molecular phylogeny and whole genome analysis of the ISS strains with all publicly available Enterobacter genomes revealed that ISS strains were E. bugandensis and similar to the type strain EB-247T and two clinical isolates (153_ECLO and MBRL 1077). Comparative genomic analyses of all eight E. bungandensis strains showed, a total of 4733 genes were associated with carbohydrate metabolism (635 genes), amino acid and derivatives (496 genes), protein metabolism (291 genes), cofactors, vitamins, prosthetic groups, pigments (275 genes), membrane transport (247 genes), and RNA metabolism (239 genes). In addition, 112 genes identified in the ISS strains were involved in virulence, disease, and defense. Genes associated with resistance to antibiotics and toxic compounds, including the MDR tripartite system were also identified in the ISS strains. A multiple antibiotic resistance (MAR) locus or MAR operon encoding MarA, MarB, MarC, and MarR, which regulate more than 60 genes, including upregulation of drug efflux systems that have been reported in Escherichia coli K12, was also observed in the ISS strains.


Given the MDR results for these ISS Enterobacter genomes and increased chance of pathogenicity (PathogenFinder algorithm with > 79% probability), these species pose important health considerations for future missions. Thorough genomic characterization of the strains isolated from ISS can help to understand the pathogenic potential, and inform future missions, but analyzing them in in-vivo systems is required to discern the influence of microgravity on their pathogenicity.



November 28, 2018 at 8:18 am


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