Culture of Rectal Swab Specimens for Enteric Bacterial Pathogens Decreases Time to Test Result While Preserving Assay Sensitivity Compared to Bulk Fecal Specimens [Bacteriology]
In this study, we retrospectively reviewed 480 paired rectal swab and fecal specimens submitted for enteric culture to the Barnes-Jewish Hospital and St. Louis Children’s Hospital microbiology laboratories in St. Louis, MO, from 2002 to 2017. We report 32% positivity of paired specimens with an overall agreement of 93% and Cohen's of 0.84 (95% confidence interval, 0.78 to 0.89). Additionally, we evaluated the time to result from the time of patient presentation to the health care setting and demonstrate that rectal swabs have a significantly shorter time to an actionable result than bulk fecal specimens (median, 67.4...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Jean, S., Yarbrough, M. L., Anderson, N. W., Burnham, C.-A. D. Tags: Bacteriology Source Type: research

Factors That Influence Confirmation of Neisseria gonorrhoeae Positivity by Molecular Methods [Bacteriology]
The objective of this work was to assess N. gonorrhoeae confirmation in over 13,000 N. gonorrhoeae screen-positive samples representing various biospecimens and three separate screening assays, the Abbott RealTime CT/NG (Abbott Molecular, Inc., Des Plaines, IL), the Cobas CT/NG test (Roche Molecular Systems Inc., Alameda, CA), and the BD ProbeTec ET CT/GC amplified DNA assay (BD Diagnostics, Sparks, MD). Factors predictive of confirmation were determined via logistic regression involving sex, year, whether the sample was formally validated, and sample site. Level of confirmation varied according to screening assay (96.2%, ...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Cuschieri, K., Shepherd, J., Graham, C., Guerendiain, D., Templeton, K. E. Tags: Bacteriology Source Type: research

Diagnostic Accuracy of Stool Xpert MTB/RIF for Detection of Pulmonary Tuberculosis in Children: a Systematic Review and Meta-analysis [Epidemiology]
Invasive collection methods are often required to obtain samples for the microbiological evaluation of children with presumptive pulmonary tuberculosis (PTB). Nucleic acid amplification testing of easier-to-collect stool samples could be a noninvasive method of diagnosing PTB. We conducted a systematic review and meta-analysis to evaluate the diagnostic accuracy of testing stool with the Xpert MTB/RIF assay ("stool Xpert") for childhood PTB. Four databases were searched for publications from January 2008 to June 2018. Studies assessing the diagnostic accuracy among children of stool Xpert compared to a microbiolo...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: MacLean, E., Sulis, G., Denkinger, C. M., Johnston, J. C., Pai, M., Ahmad Khan, F. Tags: Epidemiology Source Type: research

Closing the Brief Case: Erysipelothrix Bacteremia and Endocarditis in a 59-Year-Old Immunocompromised Male on Chronic High-Dose Steroids [The Brief Case]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Jean, S., Lainhart, W., Yarbrough, M. L. Tags: The Brief Case Source Type: research

The Brief Case: Erysipelothrix Bacteremia and Endocarditis in a 59-Year-Old Immunocompromised Male on Chronic High-Dose Steroids [The Brief Case]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Jean, S., Lainhart, W., Yarbrough, M. L. Tags: The Brief Case Source Type: research

Phylogenetic Analysis of Mycobacterium tuberculosis Strains in Wales by Use of Core Genome Multilocus Sequence Typing To Analyze Whole-Genome Sequencing Data [Mycobacteriology and Aerobic Actinomycetes]
This study supports the use of a cgMLST method for standardized phylogenetic assignment of tuberculosis isolates and for outbreak resolution and provides the first insight into Welsh tuberculosis phylogenetics, identifying the presence of the Haarlem sublineage commonly associated with virulent traits. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Jones, R. C., Harris, L. G., Morgan, S., Ruddy, M. C., Perry, M., Williams, R., Humphrey, T., Temple, M., Davies, A. P. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Summary and Trends of the Russian Gonococcal Antimicrobial Surveillance Programme, 2005 to 2016 [Epidemiology]
The Russian Gonococcal Antimicrobial Surveillance Programme (RU-GASP) was established in 2004 and operated continuously during the years from 2005 to 2016. The aims of this study were to summarize the RU-GASP results over this 12-year period and evaluate the trends in Neisseria gonorrhoeae antimicrobial resistance in Russia. In total, 5,038 verified N. gonorrhoeae isolates from 40 participating regions were tested for susceptibility to six antimicrobials via an agar dilution method. DNA loci involved in antimicrobial resistance were identified via minisequencing or DNA microarray techniques. From 2005 to 2016, increasing s...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Kubanov, A., Solomka, V., Plakhova, X., Chestkov, A., Petrova, N., Shaskolskiy, B., Dementieva, E., Leinsoo, A., Gryadunov, D., Deryabin, D. Tags: Epidemiology Source Type: research

The Pseudomonas aeruginosa Population among Cystic Fibrosis Patients in Quebec, Canada: a Disease Hot Spot without Known Epidemic Isolates [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Jeukens, J., Freschi, L., Kukavica-Ibrulj, I., Emond-Rheault, J.-G., Allard, C., Barbeau, J., Cantin, A., Charette, S. J., Deziel, E., Malouin, F., Milot, J., Nguyen, D., Popa, C., Boyle, B., Levesque, R. C. Tags: Letter To The Editor Source Type: research

Genotyping of Pneumocystis jirovecii by Use of a New Simplified Nomenclature System Based on the Internal Transcribed Spacer Regions and 5.8S rRNA Gene of the rRNA Operon [Mycology]
Genotyping based on internal transcribed spacer 1 (ITS1) and ITS2 of the rRNA operon has played an important role in understanding the transmission and epidemiology of Pneumocystis jirovecii, one of the major opportunistic pathogens in individuals with AIDS and other immunocompromised individuals. The widespread use of this typing system has resulted in several problems, including inconsistent genotype nomenclatures, difficult data transferability, and complicated interpretation of the length variation in multiple homopolymeric tracts. The aim of this study was to establish a new, simplified genotype nomenclature system fo...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Xue, T., Ma, Z., Liu, F., Du, W.-Q., He, L., Ma, L., An, C.-L. Tags: Mycology Source Type: research

Comparison of Three Nucleic Acid Amplification Tests and Culture for Detection of Group B Streptococcus from Enrichment Broth [Bacteriology]
Colonization of the gastrointestinal and genitourinary tracts of pregnant women with group B Streptococcus (GBS) can result in vertical transmission to neonates during labor/delivery. GBS infections in neonates can cause severe complications, such as sepsis, meningitis, and pneumonia. Accurate detection is critical because administration of intrapartum antibiotics can significantly reduce transmission. We compared the clinical sensitivities of three nucleic acid amplification tests (NAATs), the Hologic Panther Fusion GBS, Luminex Aries GBS, and Cepheid Xpert GBS LB assays, to that of the standard of care culture method rec...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Shin, J. H., Pride, D. T. Tags: Bacteriology Source Type: research

Societal Implications of the Internet of Pathogens [Commentary]
The growth of pathogen genomics shows no signs of abating. Whole-genome sequencing of clinical viral and bacterial isolates continues to grow in nearly exponential bounds. Reductions in cost driven by new technology have created a seamless environment for generating, sharing, and analyzing pathogen genomes. The high-resolution view of infectious disease transmission dynamics offered by analyzing whole genomes from pathogens, coupled with the genomicist ethic of widespread data sharing, has created a veritable Internet of pathogens, which inadvertently produces new threats to patient privacy and protected heath information....
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Greninger, A. L. Tags: Commentary Source Type: research

Ultrasensitive Detection of Clostridium difficile Toxins Reveals Suboptimal Accuracy of Toxin Gene Cycle Thresholds for Toxin Predictions [Commentary]
The use of nucleic acid amplification tests (NAATs) for the diagnosis of Clostridium (Clostridioides) difficile infection (CDI) leads to overdiagnosis. To improve the clinical specificity of NAATs, there has been a recent interest in using toxin gene cycle thresholds (CTs) to predict the presence and absence of toxins. Although there is an association between CT values and fecal toxin concentrations, the predictive accuracy of the former is suboptimal for use in clinical practice. Ultrasensitive toxin immunoassays to quantify free toxins in stool offer a novel option for high-sensitivity fecal toxin detection rather than u...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Sandlund, J., Wilcox, M. H. Tags: Commentary Source Type: research

Comparing Patient Risk Factor-, Sequence Type-, and Resistance Locus Identification-Based Approaches for Predicting Antibiotic Resistance in Escherichia coli Bloodstream Infections [Epidemiology]
Rapid diagnostic tests for antibiotic resistance that identify the presence or absence of antibiotic resistance genes/loci are increasingly being developed. However, these approaches usually neglect other sources of predictive information which could be identified over shorter time periods, including patient epidemiologic risk factors for antibiotic resistance and markers of lineage. Using a data set of 414 Escherichia coli isolates recovered from separate episodes of bacteremia at a single academic institution in Toronto, Ontario, Canada, between 2010 and 2015, we compared the potential predictive ability of three approac...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: MacFadden, D. R., Melano, R. G., Coburn, B., Tijet, N., Hanage, W. P., Daneman, N. Tags: Epidemiology Source Type: research

Evidence of Sharing of Klebsiella pneumoniae Strains between Healthy Companion Animals and Cohabiting Humans [Epidemiology]
This study aimed to characterize the fecal colonization and sharing of Klebsiella pneumoniae strains between companion animals and humans living in close contact. Fecal samples were collected from 50 healthy participants (24 humans, 18 dogs, and 8 cats) belonging to 18 households. Samples were plated onto MacConkey agar (MCK) plates with and without cefotaxime or meropenem supplementation. Up to five K. pneumoniae colonies per participant were compared by pulsed-field gel electrophoresis (PFGE) after XbaI restriction. K. pneumoniae strains with unique pulse types from each participant were characterized for antimicrobial s...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Marques, C., Belas, A., Aboim, C., Cavaco-Silva, P., Trigueiro, G., Gama, L. T., Pomba, C. Tags: Epidemiology Source Type: research

Evaluation of the Bio-Rad Geenius HIV 1/2 Assay as Part of a Confirmatory HIV Testing Strategy for Quebec, Canada: Comparison with Western Blot and Inno-Lia Assays [Immunoassays]
The rapid confirmatory Bio-Rad Geenius HIV 1/2 assay was evaluated as an alternative to the HIV-1 Western blot (WB) confirmatory assay. A total of 370 retrospective samples collected from 356 patients were tested. Sensitivity of the Geenius assay to detect HIV-1 and HIV-2 infections was 100% and 97%, respectively, and that of the WB assay was 86% and 39%, respectively. Geenius reduced the number of indeterminate results by 85% and exhibited a differentiation capacity for HIV-1 and HIV-2 of 100% and 89%, respectively. Three of 10 patients presenting with an early HIV infection (1 to 2 weeks before seroconversion by WB) were...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Serhir, B., Desjardins, C., Doualla-Bell, F., Simard, M., Tremblay, C., Longtin, J. Tags: Immunoassays Source Type: research

A Systematic Review and Meta-analysis of the Diagnostic Accuracy of Nucleic Acid Amplification Tests for Tuberculous Meningitis [Minireviews]
The diagnosis of tuberculous meningitis (TBM) is difficult and poses a significant challenge to physicians worldwide. Recently, nucleic acid amplification (NAA) tests have shown promise for the diagnosis of TBM, although their performance has been variable. We undertook a systematic review and meta-analysis to evaluate the diagnostic accuracy of NAA tests with cerebrospinal fluid (CSF) samples against that of culture as the reference standard or a combined reference standard (CRS) for TBM. We searched the Embase, PubMed, Web of Science, and Cochrane Library databases for the relevant records. The QUADAS-2 tool was used to ...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Pormohammad, A., Nasiri, M. J., McHugh, T. D., Riahi, S. M., Bahr, N. C. Tags: Minireviews Source Type: research

Development of Molecular Methods for Rapid Differentiation of Mycoplasma gallisepticum Vaccine Strains from Field Isolates [Clinical Veterinary Microbiology]
Mycoplasma gallisepticum is among the most economically significant mycoplasmas causing production losses in poultry. Seven melt-curve and agarose gel-based mismatch amplification mutation assays (MAMAs) and one PCR are provided in the present study to distinguish the M. gallisepticum vaccine strains and field isolates based on mutations in the crmA, gapA, lpd, plpA, potC, glpK, and hlp2 genes. A total of 239 samples (M. gallisepticum vaccine and type strains, pure cultures, and clinical samples) originating from 16 countries and from at least eight avian species were submitted to the presented assays for validation or in ...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Sulyok, K. M., Kreizinger, Z., Beko, K., Forro, B., Marton, S., Banyai, K., Catania, S., Ellis, C., Bradbury, J., Olaogun, O. M., Kovacs, A. B., Cserep, T., Gyuranecz, M. Tags: Clinical Veterinary Microbiology Source Type: research

Answer to June 2019 Photo Quiz [Photo Quiz]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Carretero, O., Recio, R., Silva, J. T., Panero, I., Gonzalez, C., Caso, O., San Juan, R., Lopez-Roa, P. Tags: Photo Quiz Source Type: research

Photo Quiz: An Unexpected Organism Isolated from an Intracranial Epidural Abscess [Photo Quiz]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Carretero, O., Recio, R., Silva, J. T., Panero, I., Gonzalez, C., Caso, O., San Juan, R., Lopez-Roa, P. Tags: Photo Quiz Source Type: research

GeneXpert MTB/RIF Is Superior to BBD Max MDR-TB for Diagnosis of Tuberculosis (TB) in a Country with Low Incidence of Multidrug-Resistant TB (MDR-TB) [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Mokaddas, E. M., Ahmad, S., Eldeen, H. S. Tags: Letter To The Editor Source Type: research

Epidemiological Cutoff Values: a Micro-Comic Strip [Editorial]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: McAdam, A. J. Tags: Editorial Source Type: research

Correction for Sakwinska et al., "Nasopharyngeal Microbiota in Healthy Children and Pneumonia Patients" [Author Correction]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Sakwinska, O., Bastic Schmid, V., Berger, B., Bruttin, A., Keitel, K., Lepage, M., Moine, D., Ngom Bru, C., Brüssow, H., Gervaix, A. Tags: Author Correction Source Type: research

Evaluation of the Liat Cdiff Assay for Direct Detection of Clostridioides difficile Toxin Genes within 20 Minutes [Bacteriology]
Clostridioides difficile is the main causative agent of antibiotic-associated diarrhea. Prompt diagnosis is required for initiation of timely infection control measures and appropriate adjustment of antibiotic treatment. The cobas Cdiff assay for use on the cobas Liat system enables a diagnostic result in 20 minutes. A total of 252 prospective (n = 150) and retrospective (n = 102) stool specimens from The Netherlands, France, and Switzerland were tested on the cobas Cdiff assay using the Xpert C. difficile assay as a reference method. The overall positive and negative percent agreement (PPA and NPA, respectively) of the co...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Hetem, D. J., Bos-Sanders, I., Nijhuis, R. H. T., Tamminga, S., Berlinger, L., Kuijper, E. J., Sickler, J. J., Claas, E. C. J. Tags: Bacteriology Source Type: research

Triazole Antifungal Susceptibility Patterns among Aspergillus Species in Quebec, Canada [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Cheng, M. P., Lawandi, A., Lee, T. C., Dufresne, P. J., Seidel, D., Verweij, P. E., Cornely, O. A., Sheppard, D. C. Tags: Letter To The Editor Source Type: research

Beyond Fever and Pain: Diagnostic Methods for Chikungunya Virus [Minireviews]
Chikungunya virus (CHIKV) is an alphavirus that is primarily transmitted by Aedes species mosquitoes. Though reports of an illness consistent with chikungunya date back over 200 years, CHIKV only gained worldwide attention during a massive pandemic that began in East Africa in 2004. Chikungunya, the clinical illness caused by CHIKV, is characterized by a rapid onset of high fever and debilitating joint pain, though in practice, etiologic confirmation of CHIKV requires the availability and use of specific laboratory diagnostics. Similar to infections caused by other arboviruses, CHIKV infections are most commonly detected w...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Natrajan, M. S., Rojas, A., Waggoner, J. J. Tags: Minireviews Source Type: research

Extragenital Screening Is Essential for Comprehensive Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in the Pediatric Population [Bacteriology]
Chlamydia trachomatis and Neisseria gonorrhoeae are the two most common causes of sexually transmitted disease in the United States. Studies in adults, mostly in men who have sex with men, have shown that the prevalence of C. trachomatis and N. gonorrhoeae infections is much higher in extragenital sources compared to urogenital sources. A similar large sample of data on the burden of C. trachomatis and N. gonorrhoeae infections by anatomic site is lacking in children. We retrospectively analyzed data from 655 patients tested for C. trachomatis (887 specimens) and N. gonorrhoeae (890 specimens) at the Children’s Hospi...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Uprety, P., Cardenas, A. M. Tags: Bacteriology Source Type: research

Beta-D-Glucan for Diagnosing Pneumocystis Pneumonia: a Direct Comparison between the Wako {beta}-Glucan Assay and the Fungitell Assay [Mycology]
Measuring serum beta-d-glucan (BDG) is a useful tool for supporting a quantitative PCR (qPCR)-based diagnosis of suspected Pneumocystis pneumonia (PCP) with bronchoalveolar lavage (BAL) fluid. Since the 2000s, the Fungitell assay was the only BDG assay which was FDA cleared and Conformité Européenne (CE) marked. However, the Wako β-glucan test was also recently CE marked and commercialized. We analyzed archived sera from 116 PCP cases (who were considered to have PCP based on compatible clinical and radiological findings plus a BAL fluid qPCR threshold cycle value of ≤28) and 114 controls (those with ...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Mercier, T., Guldentops, E., Patteet, S., Beuselinck, K., Lagrou, K., Maertens, J. Tags: Mycology Source Type: research

Evaluation of the ELITe InGenius PCR Platform for Detection of Mycoplasma pneumoniae [Bacteriology]
Mycoplasma pneumoniae is the leading cause of bacterial community-acquired pneumonia in persons of all ages. Due to the fastidious nature of this bacterium and the necessary specialized growth media, nucleic acid amplification testing is currently the most reliable means for patient diagnostics. Analytical sensitivity, specificity, reproducibility, and clinical performance of the ELITe InGenius automated PCR platform with its MGB Alert M. pneumoniae real-time PCR research use only reagents (ELITechGroup, Inc., Bothell, WA) were compared with those of a laboratory-developed real-time PCR assay targeting repMp1 for detection...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Totten, A. H., Leal, S. M., Ratliff, A. E., Xiao, L., Crabb, D. M., Waites, K. B. Tags: Bacteriology Source Type: research

Xpert MTB/RIF Ultra for Detection of Mycobacterium tuberculosis in Cerebrospinal Fluid [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Chin, J. H., Musubire, A. K., Morgan, N., Pellinen, J., Grossman, S., Bhatt, J. M., Wadda, V., Ssengooba, W. Tags: Letter To The Editor Source Type: research

Pigment Visibility on Rectal Swabs Used To Detect Enteropathogens: a Prospective Cohort Study [Epidemiology]
We describe the test characteristics of rectal swabs with and without pigment in children with gastroenteritis. Between December 2014 and September 2017, children (age,
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Xie, J., Tarr, G. A. M., Ali, S., Chui, L., Pang, X.-L., Lee, B. E., Vanderkooi, O. G., Tarr, P. I., Zhuo, R., Parsons, B., Berenger, B. M., Kim, K., Freedman, S. B., on behalf of the Alberta Provincial Pediatric EnTeric Infection TEam (APPETITE) and Pedi Tags: Epidemiology Source Type: research

Comparative Evaluation of Enteric Bacterial Culture and a Molecular Multiplex Syndromic Panel in Children with Acute Gastroenteritis [Bacteriology]
Although enteric multianalyte syndromic panels are increasingly employed, direct comparisons with traditional methods and the inclusion of host phenotype correlations are limited. Luminex xTAG gastrointestinal pathogen panel (GPP) and culture results are highly concordant. However, phenotypic and microbiological confirmatory testing raises concerns regarding the accuracy of the GPP, especially for Salmonella spp. A total of 3,089 children with gastroenteritis submitted stool specimens, rectal swab specimens, and clinical data. The primary outcome was bacterial pathogen detection agreement for shared targets between culture...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Kellner, T., Parsons, B., Chui, L., Berenger, B. M., Xie, J., Burnham, C.-A. D., Tarr, P. I., Lee, B. E., Nettel-Aguirre, A., Szelewicki, J., Vanderkooi, O. G., Pang, X.-L., Zelyas, N., Freedman, S. B., on behalf of the Alberta Provincial Pediatric EnTeri Tags: Bacteriology Source Type: research

Understanding and Addressing CLSI Breakpoint Revisions: a Primer for Clinical Laboratories [Minireviews]
The Clinical and Laboratory Standards Institute (CLSI) has revised several breakpoints since 2010 for bacteria that grow aerobically. In 2019, these revisions include changes to the ciprofloxacin and levofloxacin breakpoints for the Enterobacteriaceae and Pseudomonas aeruginosa, daptomycin breakpoints for Enterococcus spp., and ceftaroline breakpoints for Staphylococcus aureus. Implementation of the revisions is a challenge for all laboratories, as not all systems have FDA clearance for the revised (current) breakpoints, compounded by the need for laboratories to perform validation studies and to make updates to laboratory...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Humphries, R. M., Abbott, A. N., Hindler, J. A. Tags: Minireviews Source Type: research

hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus [Bacteriology]
Haemophilus influenzae exclusively colonizes the human nasopharynx and can cause a variety of respiratory infections as well as invasive diseases, including meningitis and sepsis. A key virulence determinant of H. influenzae is the polysaccharide capsule, of which six serotypes are known, each encoded by a distinct variation of the capsule biosynthesis locus (cap-a to cap-f). H. influenzae type b (Hib) was historically responsible for the majority of invasive H. influenzae disease, and its prevalence has been markedly reduced in countries that have implemented vaccination programs targeting this serotype. In the postvaccin...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Watts, S. C., Holt, K. E. Tags: Bacteriology Source Type: research

Methodology for Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Isolates in a Routine Hospital Microbiology Laboratory [Bacteriology]
There is growing evidence for the value of bacterial whole-genome sequencing in hospital outbreak investigations. Our aim was to develop methods that support efficient and accurate low-throughput clinical sequencing of methicillin-resistant Staphylococcus aureus (MRSA) isolates. Using a test panel of 25 MRSA isolates previously associated with outbreak investigations, we devised modifications to library preparation that reduced the processing time by 1 hour. We determined the maximum number of isolates that could be sequenced per run using an Illumina MiniSeq platform and a 13-hour (overnight) run time, which equated to 21...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Raven, K. E., Blane, B., Leek, D., Churcher, C., Kokko-Gonzales, P., Pugazhendhi, D., Fraser, L., Betley, J., Parkhill, J., Peacock, S. J. Tags: Bacteriology Source Type: research

Molecular Typing of Mycoplasma pneumoniae Strains in Sweden from 1996 to 2017 and the Emergence of a New P1 Cytadhesin Gene, Variant 2e [Bacteriology]
Mycoplasma pneumoniae causes respiratory infections, such as community-acquired pneumonia (CAP), with epidemics recurring every 3 to 7 years. In 2010 and 2011, many countries experienced an extraordinary epidemic peak. The cause of these recurring epidemics is not understood, but decreasing herd immunity and shifts in the strains’ antigenic properties have been suggested as contributing factors. M. pneumoniae PCR-positive samples were collected between 1996 and 2017 from four neighboring counties inhabited by 12% of Sweden’s population. A total of 578 isolates were characterized directly from 624 clinical sampl...
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Gullsby, K., Olsen, B., Bondeson, K. Tags: Bacteriology Source Type: research

Methicillin-Resistant Staphylococcus aureus Harboring mecC Still Eludes Us in East London, United Kingdom [Bacteriology]
Reports of methicillin-resistant Staphylococcus aureus (MRSA) harboring the mecC gene have increased in the UK since first being described. To our diagnostic S. aureus multiplex PCR, a mecC primer set was designed and implemented, and then the prevalence in our patient population was investigated. Fewer than 1% of the clinical isolates possessed the mecC gene, confirming that mecA remains the dominant genetic determinant of MRSA in East London. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Authors: Ciesielczuk, H., Xenophontos, M., Lambourne, J. Tags: Bacteriology Source Type: research

Editorial Board [Masthead]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 24, 2019 Category: Microbiology Tags: Masthead Source Type: research

Development of a Multiplexed Assay for Detection of Leishmania donovani and Leishmania infantum Protein Biomarkers in Urine Samples of Patients with Visceral Leishmaniasis [Parasitology]
Visceral leishmaniasis (VL) is a serious and fatal disease caused by the parasites Leishmania infantum and Leishmania donovani. The gold standard diagnostic test for VL is the demonstration of parasites or their DNA in spleen, lymph node, or bone marrow aspirates. Serological tests exist but cannot distinguish active VL from either prior exposure to the parasites or previously treated VL disease. Using mass spectroscopy, we have previously identified three L. infantum protein biomarkers (Li-isd1, Li-txn1, and Li-ntf2) in the urine of VL patients and developed a sensitive and specific urine-based antigen detection assay for...
Source: Journal of Clinical Microbiology - April 26, 2019 Category: Microbiology Authors: Abeijon, C., Alves, F., Monnerat, S., Wasunna, M., Mbui, J., Viana, A. G., Bueno, L. L., Siqueira, W. F., Carvalho, S. G., Agrawal, N., Fujiwara, R., Sundar, S., Campos-Neto, A. Tags: Parasitology Source Type: research

Candida auris Isolates of the Southern Asian and South African Lineages Exhibit Different Phenotypic and Antifungal Susceptibility Profiles In Vitro [Mycology]
Candida auris is a serious nosocomial health risk, with widespread outbreaks occurring in hospitals worldwide. Sequence analyses of outbreak isolates revealed that C. auris has simultaneously emerged as four distinct continentally restricted clonal lineages. We previously reported multiple independent introductions of C. auris isolates from at least three of these lineages (the Southern Asia, South African, and Japanese/Korean lineages) into hospitals across the United Kingdom and that isolates circulating in the United Kingdom displayed two different cell phenotypes which correlated with differences in virulence in Galler...
Source: Journal of Clinical Microbiology - April 26, 2019 Category: Microbiology Authors: Szekely, A., Borman, A. M., Johnson, E. M. Tags: Mycology Source Type: research

A Simple Microfluidic Assay for Diagnosing Tuberculous Meningitis in HIV-Uninfected Patients [Mycobacteriology and Aerobic Actinomycetes]
We evaluated the diagnostic performance of a simple and label-free pathogen enrichment method using homobifunctional imidoesters (HI) and a microfluidic system, called the SLIM assay, followed by real-time PCR from cerebrospinal fluid (CSF) in human immunodeficiency virus (HIV)-uninfected patients with suspected tuberculous meningitis (TBM). Patients with suspected TBM were prospectively enrolled in a tertiary hospital in an intermediate tuberculosis (TB)-burden country during a 30-month period. TBM was classified according to the uniform case definition. Definite and probable TBM were regarded as the reference standards f...
Source: Journal of Clinical Microbiology - April 26, 2019 Category: Microbiology Authors: Park, J. H., Jin, C. E., Koo, B., Kwon, J.-S., Cha, H. H., Kim, J. Y., Noh, G. S., Koo, Y. S., Jeon, S.-B., Lee, S.-A., Shin, Y., Kim, S.-H. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Evaluation of the Aries Bordetella Assay for Detection and Identification of Bordetella pertussis in Nasopharyngeal Swab Specimens [Bacteriology]
The objective of this study was to evaluate the performance of the Aries BA in comparison to that of the BioFire FilmArray respiratory panel (RP). The Aries BA was evaluated using retrospective, remnant nasopharyngeal swabs (NPS), previously tested by FilmArray RP. Performance characteristics evaluated included positive percent agreement (PPA) and negative percent agreement (NPA) with the FilmArray RP. Discordant analysis was performed using bidirectional sequencing. A time and motion study was performed to compare the laboratory workflow of the two tests. Three hundred samples were included in the study. There were no sam...
Source: Journal of Clinical Microbiology - April 26, 2019 Category: Microbiology Authors: McMillen, T., Chow, H. Y., Das, S., Dunbar, S. A., Babady, N. E. Tags: Bacteriology Source Type: research

Antimicrobial Stewardship Opportunities in Patients with Bacteremia Not Identified by BioFire FilmArray [Bacteriology]
A subset of bacteremia cases are caused by organisms not detected by a rapid-diagnostics platform, BioFire blood culture identification (BCID), with unknown clinical characteristics and outcomes. Patients with ≥1 positive blood culture over a 15-month period were grouped by negative (NB-PC) versus positive (PB-PC) BioFire BCID results and compared with respect to demographics, infection characteristics, antibiotic therapy, and outcomes (length of hospital stay [LOS] and in-hospital mortality). Six percent of 1,044 positive blood cultures were NB-PC. The overall mean age was 65 ± 22 years, 54% of the patients were...
Source: Journal of Clinical Microbiology - April 26, 2019 Category: Microbiology Authors: Ny, P., Ozaki, A., Pallares, J., Nieberg, P., Wong-Beringer, A. Tags: Bacteriology Source Type: research

Impact of Early Antiretroviral Therapy on Detection of Cell-Associated HIV-1 Nucleic Acid in Blood by the Roche Cobas TaqMan Test [Virology]
The Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test, v2.0 (the CAP/CTM assay), was used to quantify cell-associated HIV-1 (CAH) nucleic acid in peripheral blood mononuclear cells (PBMC) from well-characterized clinical specimens from HIV-1-infected individuals on antiretroviral therapy (ART). Chronically infected individuals on ART with no detectable plasma HIV-1 RNA demonstrated average CAH burdens of 3.2 HIV-1 log10 copies/million cells. Assay sensitivity and specificity were 98.9% and 100%, respectively, with the positive and negative predictive values being 100% and 98.6%, respectively. The CAH burden was also measured a...
Source: Journal of Clinical Microbiology - April 26, 2019 Category: Microbiology Authors: Jagodzinski, L. L., Manak, M. M., Hack, H. R., Liu, Y., Malia, J. A., Freeman, J., Phanuphak, N., de Souza, M., Kroon, E. D., Colby, D. J., Chomchey, N., Lally, M. A., Michael, N. L., Ananworanich, J., Peel, S. A., on behalf of the RV254/SEARCH010 Study T Tags: Virology Source Type: research

Development of an Enzyme-Linked Immunosorbent Assay To Detect Antibodies Targeting Recombinant Envelope Protein 2 of Mayaro Virus [Virology]
Mayaro virus (MAYV) is a neglected arthropod-borne virus (arbovirus) antigenically clustered into the Semliki Forest complex group of Alphavirus genus (Togaviridae family), maintained in an unclear zoonotic cycle involving mosquitoes from Haemagogus genus as the main vector. The genome is composed of a positive single-stranded RNA of 11.5 kb in length, which contains two genes that encode four nonstructural (nsP1 to nsP4) and five structural (C, E3, E2, 6K, and E1) proteins. In the present study, we have developed an enzyme-linked immunosorbent assay (ELISA) using as antigen the recombinant envelope protein 2 of MAYV produ...
Source: Journal of Clinical Microbiology - April 26, 2019 Category: Microbiology Authors: Fumagalli, M. J., de Souza, W. M., Romeiro, M. F., de Souza Costa, M. C., Slhessarenko, R. D., Figueiredo, L. T. M. Tags: Virology Source Type: research

New Variant of Vibrio cholerae O139 in Odisha, India [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - April 26, 2019 Category: Microbiology Authors: Pal, B. B., Mohanty, A., Biswal, B., Nayak, S. R. Tags: Letter To The Editor Source Type: research

Evaluation of Mass Spectrometry-Based Detection of Panfungal Serum Disaccharide for Diagnosis of Invasive Fungal Infections: Results from a Collaborative Study Involving Six European Clinical Centers [Mycology]
A mass spectrometry (MS) method that detects a serum disaccharide (DS) (MS-DS) was recently described for the diagnosis of invasive fungal infections (IFI). We carried out a European collaborative study to evaluate this assay. Patients with the following IFI were selected according to the availability of sera obtained at about the time that IFI was documented: invasive candidiasis (IC; n = 26 patients), invasive aspergillosis (IA; n = 19), and mucormycosis (MM; n = 23). Control sera originated from 20 neutropenic patients and 20 patients with bacteremia. MS-DS was carried out in blind manner for the diagnosis of IFI. A dia...
Source: Journal of Clinical Microbiology - April 26, 2019 Category: Microbiology Authors: Cornu, M., Sendid, B., Mery, A., Francois, N., Malgorzata, M., Letscher-Bru, V., De Carolis, E., Damonti, L., Titecat, M., Bochud, P.-Y., Alanio, A., Sanguinetti, M., Viscoli, C., Herbrecht, R., Guerardel, Y., Poulain, D. Tags: Mycology Source Type: research

Evaluation of the MicroScan Colistin Well and Gradient Diffusion Strips for Colistin Susceptibility Testing in Enterobacteriaceae [Bacteriology]
Many laboratories are unable to perform colistin susceptibility testing. Diffusion-based antimicrobial susceptibility testing methods are not recommended, and not all laboratories have the capacity to perform broth microdilution (BMD). Using a multistep tiered approach, we investigated whether the adapted use of the MicroScan colistin well (4 μg/ml) could enhance laboratory capacity for the detection and subsequent molecular characterization of colistin-resistant Enterobacteriaceae. For the MicroScan colistin well, categorical agreement with BMD was 92.7%, and the very major error rate was 10.7%. For gradient diffusion ...
Source: Journal of Clinical Microbiology - April 26, 2019 Category: Microbiology Authors: Lutgring, J. D., Kim, A., Campbell, D., Karlsson, M., Brown, A. C., Burd, E. M. Tags: Bacteriology Source Type: research

Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance [Minireviews]
Foodborne pathogen surveillance in the United States is transitioning from strain identification using restriction digest technology (pulsed-field gel electrophoresis [PFGE]) to shotgun sequencing of the entire genome (whole-genome sequencing [WGS]). WGS requires a new suite of analysis tools, some of which have long histories in academia but are new to the field of public health and regulatory decision making. Although the general workflow is fairly standard for collecting and analyzing WGS data for disease surveillance, there are a number of differences in how the data are collected and analyzed across public health agen...
Source: Journal of Clinical Microbiology - April 26, 2019 Category: Microbiology Authors: Timme, R. E., Strain, E., Baugher, J. D., Davis, S., Gonzalez-Escalona, N., Sanchez Leon, M., Allard, M. W., Brown, E. W., Tallent, S., Rand, H. Tags: Minireviews Source Type: research

Development of the TypeSeq Assay for Detection of 51 Human Papillomavirus Genotypes by Next-Generation Sequencing [Virology]
We have developed a new human papillomavirus (HPV) genotyping assay for detection of 51 HPV genotypes by next-generation sequencing (NGS). The TypeSeq assay consists of 3 PCR steps that equalize viral load and each type’s amplicon copies prior to genotyping by NGS, thereby maximizing multiple-type sensitivity with minimal sequencing reads. The analytical sensitivity of the TypeSeq assay is 10 copies per reaction for 49 of the 51 types, including 13 high-risk (HR) types. We tested 863 clinical cervical specimens previously evaluated with the Roche Linear Array HPV genotyping test (LA). TypeSeq achieved 94.4% positive ...
Source: Journal of Clinical Microbiology - April 26, 2019 Category: Microbiology Authors: Wagner, S., Roberson, D., Boland, J., Yeager, M., Cullen, M., Mirabello, L., Dunn, S. T., Walker, J., Zuna, R., Schiffman, M., Wentzensen, N. Tags: Virology Source Type: research

EDTA-Modified Carbapenem Inactivation Method: a Phenotypic Method for Detecting Metallo-{beta}-Lactamase-Producing Enterobacteriaceae [Bacteriology]
The increase in the prevalence and impact of infections caused by carbapenemase-producing Enterobacteriaceae is a global health concern. Therefore, rapid and accurate methods to detect these organisms in any clinical microbiology laboratory, including those in resource-limited settings, are essential to prevent and contain their spread. It is also important to differentiate between serine- and metal-dependent carbapenemases elaborated by carbapenemase-producing isolates for epidemiologic, infection control and prevention, and therapeutic purposes. Here, we describe the development and evaluation of the EDTA-modified carbap...
Source: Journal of Clinical Microbiology - April 26, 2019 Category: Microbiology Authors: Sfeir, M. M., Hayden, J. A., Fauntleroy, K. A., Mazur, C., Johnson, J. K., Simner, P. J., Das, S., Satlin, M. J., Jenkins, S. G., Westblade, L. F. Tags: Bacteriology Source Type: research