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Journal of Clinical Microbiology

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https://read.qxmd.com/read/31092597/looking-backwards-to-move-forward-the-utility-of-sequencing-historical-bacterial-genomes
#1
REVIEW
Rebecca J Bennett, Kate S Baker
Many pathogens which caused devastating disease throughout human history, such as Yersinia pestis , Mycobacterium tuberculosis and Mycobacterium leprae , remain problematic today. Historical bacterial genomes represent a unique source of genetic information and advancements in sequencing technologies have allowed unprecedented insights from this previously-understudied resource. This minireview brings together example studies which have utilised ancient DNA, individual historical isolates (both extant and dead) and collections of historical isolates...
May 15, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31092596/implications-of-bacteriophage-and-bacteriophage-component-based-therapies-for-the-clinical-microbiology-laboratory
#2
REVIEW
Katherine M Caflisch, Robin Patel
Treatment of bacterial infections is increasingly challenged by resistance to currently available antibacterial agents. Not only are such agents less likely to be active today than they were in the past, but their very use has selected for and continues to select for further resistance. Additional strategies for management of bacterial illness must be identified. In this review, bacteriophage-based therapies are presented as one promising approach. In anticipation of their potential expansion into clinical medicine, clinical microbiologists may wish to acquaint themselves with bacteriophages and their antibacterial components, and specifically with methods for testing them...
May 15, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31092595/comparison-of-the-novel-immunocatch%C3%A2-legionella-eiken-chemical-co-ltd-test-with-sofia%C3%A2-legionella-fia-assay-and-with-binaxnow%C3%A2-legionella-card-assay-for-the-detection-of-legionella-pneumophila-serogroup-1-antigen-in-urine-samples
#3
F Congestrì, M Morotti, R Vicari, M F Pedna, M Sparacino, A Torri, S Bertini, V Sambri
Legionnaires' disease (LD) refers to a serious form of acute pneumonia caused by Legionella species. LD can be difficult to diagnose because the signs and symptoms are non specific and therefore a rapid laboratory diagnosis is of paramount importance. In this study a recently introduced immunochromatographic test (IMMUNOCATCH™ Legionella (EIKEN CHEMICAL CO., LTD)) for Legionella pneumophila (Serogroup 1) urinary antigen detection was compared with Sofia Legionella FIA Quidel (routinely used in our laboratory) and with the widely used BinaxNOW Legionella Alere...
May 15, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31092594/detailed-analysis-of-the-characteristics-of-sample-volume-in-blood-culture-bottles
#4
Claes Henning, Nilsu Aygül, Patrik Dinnétz, Karin Wallgren, Volkan Özenci
Blood volume is the most important variable, for detection of microorganisms in blood cultures (BC). Most standards recommend 40-60 ml blood, collected in several BC bottles filled up to 10 ml. We measured blood volume in individual BC bottles, and analysed the association of hospital, bottle type, day of the week, daily sampling time, and age and gender of the patient, with sampling volume and BC result. The variation in blood volume per BC bottle was analysed in a mixed linear model using hospital, bottle type, weekday, sampling time, age and gender as fixed factors, and patient ID and episode as random factors to control for repetitive sampling of individual patients...
May 15, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31092593/the-new-new-daptomycin-breakpoint-for-enterococcus-spp
#5
Romney M Humphries
In 2019, the Clinical and Laboratory Standards Institute revised the daptomycin breakpoints for Enterococcus spp. twice in rapid succession. Analyses leading to these revisions included review of testing issues, murine and human in vivo pharmacodynamics, safety of off-label doses and treatment outcomes. The data review brought up a dilemma that is encountered with increasing frequency: the presence of a breakpoint suggested by pharmacokinetic/pharmacodynamic modeling that bisected the wild type E. faecium MIC distribution...
May 15, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31092592/storage-of-sputum-in-cetylpyridinium-chloride-omnigenesputum-and-ethanol-is-compatible-with-molecular-tuberculosis-diagnostic-testing
#6
C N'Dira Sanoussi, Bouke C de Jong, Dissou Affolabi, Conor J Meehan, Mathieu Odoun, Leen Rigouts
We compared cetylpyridinium chloride (CPC), ethanol (ETOH) and OMNIgene.SPUTUM (OMNI) for 28-day storage of sputum at ambient temperature before molecular tuberculosis diagnostics.Three sputa were collected from 133 smear-positive TB patients (399 sputa). Each patient's sputum was stored with either CPC, ETOH or OMNI for 28 days at ambient temperature, with subsequent rpoB amplification, targeting a short fragment (81-bp, GeneXpert MTB/RIF (Xpert)) or a long fragment (1764-bp, in-house nested-PCR). For 36 patients, Xpert was also performed at baseline on all 108 fresh sputa...
May 15, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31068414/whole-genome-snp-analysis-applied-directly-to-stool-for-genotyping-shiga-toxin-producing-escherichia-coli-an-advanced-molecular-detection-method-for-foodborne-surveillance-and-outbreak-tracking
#7
Navjot Singh, Pascal Lapierre, Tammy M Quinlan, Tanya A Halse, Samantha Wirth, Michelle C Dickinson, Erica Lasek-Nesselquist, Kimberlee A Musser
Whole-genome sequencing (WGS) of pathogens from pure culture provides unparalleled accuracy and comprehensive results at a cost that is advantageous compared to traditional diagnostic methods. Sequencing pathogens directly from a primary clinical specimen would help circumvent the need for culture and in the process, substantially shorten the time to diagnosis and public health reporting. Unfortunately, this approach poses significant challenges because of the mixture of multiple sequences from a complex fecal biomass...
May 8, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31068413/-helicobacter-pylori-mutations-detected-by-next-generation-sequencing-in-formalin-fixed-paraffin-embedded-gastric-biopsies-are-associated-with-treatment-failure
#8
Behtash G Nezami, Mehul Jani, David Alouani, Daniel Rhoads, Navid Sadri
Helicobacter pylori ( H. pylori ) antibiotic-resistance is widespread and increasing worldwide. Routine detection of H. pylori mutations that invoke antimicrobial resistance may be a useful approach to guide antimicrobial therapy and possibly avert treatment failure. In this study, formalin-fixed paraffin-embedded (FFPE) gastric biopsy specimens from a cohort of individuals from northern Ohio in the United States were examined using a next-generation sequencing (NGS) assay to detect H. pylori mutations that are known to confer resistance to clarithromycin, levofloxacin, and tetracycline...
May 8, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31068412/the-effect-of-the-10-valent-pneumococcal-non-typeable-haemophilus-influenzae-protein-d-conjugate-vaccine-phid-cv-on-h-influenzae-in-healthy-carriers-and-middle-ear-infections-in-iceland
#9
Hildigunnur Sveinsdóttir, Jana Birta Björnsdóttir, Helga Erlendsdóttir, Martha Á Hjálmarsdóttir, Birgir Hrafnkelsson, Ásgeir Haraldsson, Karl G Kristinsson, Gunnsteinn Haraldsson
Vaccinations with the PHiD-CV pneumococcal vaccine started in Iceland in 2011. Protein D (PD) from H. influenzae , which is coded for by the hpd gene, is used as a conjugate in the vaccine, and can possibly provide protection against PD positive H. influenzae. We aimed to evaluate the effect of the PHiD-CV vaccination on H. influenzae in children, both in carriage and in acute otitis media (AOM). H. influenzae was isolated from nasopharyngeal swabs, collected from healthy children attending 15 day care centers in 2009 and 2012-2017, and from middle ear (ME) samples from children with AOM, collected from 2012-2017...
May 8, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31068411/a-taqman-probe-based-real-time-pcr-assay-for-the-rapid-identification-of-the-emerging-multidrug-resistant-candida-auris-on-the-bd-max%C3%A2-system
#10
Amorce Lima, Raymond Widen, Grant Vestal, Dominic Uy, Suzane Silbert
Candida auris is an emerging multidrug-resistant fungal pathogen that has been associated with nosocomial bloodstream and deep-wound infections causing a high mortality rate mainly in ICU patients. Laboratories currently rely on phenotypic testing using commercial automated systems for identification of yeasts; however, this technique has often leaded to misidentification of C. auris to other closely related species. We developed and validated a TaqMan-based real time-PCR assay on the BD MAX™ platform targeting the rDNA region nucleotide sequences to quickly and accurately test for C...
May 8, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31043468/don-t-get-wound-up-revised-fluoroquinolone-breakpoints-for-enterobacteriaceae-and-pseudomonas-aeruginosa
#11
REVIEW
Tam T Van, Emi Minejima, Chiao An Chiu, Susan M Butler-Wu
Fluoroquinolones remain one of the more commonly prescribed antimicrobial agents in the United States, despite the wide array of side effects reported that are associated with their use. In 2019, the Clinical Laboratories Standards Institute (CLSI) revised the fluoroquinolone antimicrobial susceptibility testing breakpoints for both Enterobacteriaceae and Pseudomonas aeruginosa This breakpoint revision was deemed necessary based on pharmacokinetic and pharmacodynamic (PK/PD) analyses suggesting that the previous breakpoints were too high, in addition to the inability of these previous breakpoints to detect low-level resistance to this antibiotic class...
May 1, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31043467/performance-of-three-common-hcv-genotyping-assays-for-identification-of-hcv-genotype-2-1-chimeras
#12
Kai-Henrik Peiffer, Lisa Kuhnhenn, Evelyn Stelzl, Julia Dietz, Simone Susser, Andrea Oliver Tal, Fabian Finkelmeier, Eli Zuckerman, Marcus Cornberg, Mira Barak, Valeria Piazzolla, Alessandra Mangia, Stefan Zeuzem, Harald H Kessler, Johannes Vermehren, Christoph Sarrazin
Besides six major HCV genotypes a number of inter-genotypic recombinant strains have been described. These so-called chimeras combine genetic characteristics of different HCV genotypes. However, correct genotype classification is important as choice and duration of direct-acting antivirals (DAA) treatment is mainly based on the viral genotype. Therefore, misclassification of chimeras might lead to suboptimal treatment of patients infected with these strains. For example, 2k/1b chimeras are typically described as HCV genotype 2 strains by commercially available hybridization-assays, but real-time PCR-based tests recognizing another HCV region might be more suitable for correct chimera detection...
May 1, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31043466/diagnosing-and-managing-sepsis-by-probing-the-host-response-to-infection-advances-opportunities-and-challenges
#13
REVIEW
Ian L Gunsolus, Timothy E Sweeney, Oliver Liesenfeld, Nathan A Ledeboer
Sepsis is a major source of mortality and morbidity globally. Accurately diagnosing sepsis remains challenging due to the heterogenous nature of the disease, and delays in diagnosis and intervention contribute to high mortality rates. Measuring the host response to infection enables more rapid diagnosis of sepsis than is possible through direct detection of the causative pathogen, and recent advances in host response diagnostics and prognostics hold promise for improving outcomes. The current review discusses recent advances in the technologies used to probe the host response to infection, particularly those based on transcriptomics...
May 1, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31043465/simple-assay-to-detect-central-asia-outbreak-clade-of-mycobacterium-tuberculosis-beijing-genotype
#14
Egor Shitikov, Anna Vyazovaya, Maja Malakhova, Andrei Guliaev, Julia Bespyatykh, Evgeniya Proshina, Oksana Pasechnik, Igor Mokrousov
Central Asia Outbreak (CAO) clade is a branch of the Mycobacterium tuberculosis Beijing genotype that is associated with multidrug-resistance, increased transmissibility and epidemic spread in parts of the former Soviet Union. Furthermore, migration flows bring these strains far beyond their areas of origin. We aimed to find a specific molecular marker of the Beijing CAO clade and develop a simple and affordable method of its detection. Based on the bioinformatics analysis of the large M. tuberculosis whole-genome sequencing (WGS) dataset (n=1398), we identified IS 6110 insertion in the Rv1359 - Rv1360 intergenic region as a specific molecular marker of the CAO clade...
May 1, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31018983/design-and-validation-of-transcription-mediated-amplification-nucleic-acid-amplification-tests-for-mycoplasma-genitalium
#15
Brett Kirkconnell, Barbara Weinbaum, Katherine Santos, Trisha Le Nguyen, Bryan Vinluan, Sabina Astete, Gwendolyn E Wood, Patricia A Totten, Damon K Getman
Mycoplasma genitalium is a sexually transmitted bacterium linked to adverse sexual and reproductive health outcomes in women and men. M. genitalium is difficult to culture, and in the absence of validated amplified molecular methods for diagnosis of infection, there is no reference standard available for use as a comparator for the validation of new M. genitalium diagnostic tests. We evaluated the analytical and clinical performance of three transcription-mediated amplification tests for M. genitalium , each targeting unique rRNA sequences, for use as a composite comparator for clinical validation of the Aptima® Mycoplasma genitalium (AMG) assay, an in vitro diagnostic (IVD) TMA test that targets 16s rRNA of M...
April 24, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31018982/epidemiology-and-antifungal-susceptibility-profile-of-aspergillus-species-comparison-between-environmental-and-clinical-isolates-from-patients-with-hematologic-malignancies
#16
Sung-Yeon Cho, Dong-Gun Lee, Won-Bok Kim, Hye-Sun Chun, Chulmin Park, Jun-Pyo Myong, Yeon-Joon Park, Jae-Ki Choi, Hyo-Jin Lee, Si-Hyun Kim, Sun Hee Park, Su-Mi Choi, Jung-Hyun Choi, Jin-Hong Yoo
Global data on the epidemiology and susceptibility of Aspergillus are crucial in management of invasive aspergillosis. Here, we aimed to determine the characteristics of clinical and environmental Aspergillus isolates, focusing mainly on hematologic malignancy patients. We prospectively collected all consecutive cases and clinical isolates of culture-positive proven/probable invasive aspergillosis patients from January 2016 to April 2018 and sampled the air inside and outside the hospital. The cryptic species-level identification of Aspergillus , antifungal susceptibilities, and cyp51s sequencing were performed, and clinical data were analyzed...
April 24, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31018981/molecular-bacterial-load-assay-mbla-concurs-with-culture-on-the-naoh-induced-mycobacterium-tuberculosis-loss-of-viability
#17
Bariki Mtafya, Wilber Sabiiti, Issa Sabi, Joseph John, Emanuel Sichone, Nyanda E Ntinginya, Stephen H Gillespie
Effective methods to detect viable Mycobacterium tuberculosis (Mtb), the main causative agent of tuberculosis (TB) are urgently needed. To date, cultivation of Mtb is the gold standard which depends on initial sample processing with N-Acetyl-L-Cysteine/Sodium hydroxide (NALC/NaOH), chemicals that compromise Mtb viability and, consequently the performance of downstream tests. We applied culture and the novel Molecular bacterial load assay (MBLA) to measure the loss of Mtb viability following NALC/NaOH treatment of Mtb H37Rv pure culture and clinical sputa from pulmonary TB patients...
April 24, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/31018980/evaluation-of-a-novel-aspergillus-antigen-elisa
#18
Karl Dichtl, Ulrich Seybold, Steffen Ormanns, Heidi Horns, Johannes Wagener
Invasive aspergillosis (IA) is a life-threatening infection that mainly occurs in immunocompromised patients. Here, we compared the novel Aspergillus -specific galactomannoprotein ELISA (GP; EUROIMMUN Medizinische Labordiagnostika AG) to the established Platelia Aspergillus galactomannan ELISA (GM; Bio-Rad Laboratories) for the detection of IA. Forty-five cases of proven and 4 episodes of probable IA according to EORTC/MSG criteria with a total of 267 serum samples and 156 sera from patients without evidence of IA were tested...
April 24, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/30995993/beyond-fever-and-pain-diagnostic-methods-for-chikungunya-virus
#19
REVIEW
Muktha S Natrajan, Alejandra Rojas, Jesse J Waggoner
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 cause 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...
April 17, 2019: Journal of Clinical Microbiology
https://read.qxmd.com/read/30995992/cim-city-the-game-continues-for-a-better-carbapenemase-test
#20
Romney M Humphries
The Clinical and Laboratory Standards Institute and European Committee on Antimicrobial Susceptibility Testing agree that carbapenemase testing is not necessary for clinical care, provided the laboratory is up to date with current breakpoints. Nonetheless, publication on the development and modification of carbapenemase tests continues, as is the case in this issue of the Journal of Clinical Microbiology (R.W. Beresford and M. Maley, J Clin Microbiol, In press, 2019, doi: 10.1128/JCM.01852-18). This commentary explores modifications to the carbapenem inactivation method - but is this the right focus for clinical laboratories?...
April 17, 2019: Journal of Clinical Microbiology
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