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Journal of Clinical Microbiology

Nanelle R Barash, Adam J Birkenheuer, Shelly L Vaden, Megan E Jacob
Bloodstream infections are a significant cause of morbidity and mortality in critically ill dogs, but due to cost and difficulties in sample acquisition, blood cultures are infrequently obtained. In ill dogs, urine cultures may be recommended as surrogates for blood cultures. In order to determine the outcome agreement between parallel urine and blood cultures, we retrospectively analyzed parallel blood and urine specimens submitted for culture from dogs at NC State Veterinary Hospital between 2011 and 2016...
July 11, 2018: Journal of Clinical Microbiology
Katherine Schultz, Emily Sickbert-Bennett, Ashley Marx, David J Weber, Lauren M DiBiase, Stacy Campbell-Bright, Lauren E Bode, Mike Baker, Tom Belhorn, Mark Buchanan, Sherie Goldbach, Jacci Harden, Emily Hoke, Beth Huenniger, Jonathan J Juliano, Michael Langston, Heather Ritchie, William A Rutala, Jason Smith, Shelley Summerlin-Long, Lisa Teal, Peter Gilligan
Healthcare facility-onset Clostridium difficile infections (HO-CDI) are an important national problem, causing increased morbidity and mortality, with longer and more costly hospital stays. HO-CDI is an important metric for the Center for Medicare and Medicaid Service's (CMS) performance measures. Hospitals that fall into the worst-performing quartile in preventing hospital acquired infections, including HO-CDI, may lose millions of dollars in reimbursement. Under pressure to reduce CDI and without a clear optimal method for C...
July 11, 2018: Journal of Clinical Microbiology
Tessa E LeCuyer, Barbara A Byrne, Joshua B Daniels, Dubraska V Diaz-Campos, G Kenitra Hammac, Claire B Miller, Thomas E Besser, Margaret A Davis
Escherichia coli is the most common cause of human and canine urinary tract infection (UTI). Clonal groups, often with high levels of antimicrobial resistance, are a major component of the E. coli population that causes human UTI. While little is known about the population structure of E. coli that causes UTI in dogs, there is evidence that dogs and humans can share fecal strains of E.coli and that human-associated strains can cause disease in dogs. In order to better characterize the E. coli that cause canine UTI, we analyzed 295 E...
July 11, 2018: Journal of Clinical Microbiology
Elisabetta Walters, Lesley Scott, Pamela Nabeta, Anne-Marie Demers, Gary Reubenson, Corné Bosch, Anura David, Marieke van der Zalm, Joshua Havumaki, Megan Palmer, Anneke C Hesseling, Jabulani Ncayiyana, Wendy Stevens, David Alland, Claudia Denkinger, Padmapriya Banada
The microbiological diagnosis of tuberculosis (TB) in children is challenging as it relies on the collection of relatively invasive specimens by trained healthcare workers, which is not feasible in many settings. Mycobacterium tuberculosis ( M.tb ) is detectable from the stools of children using molecular methods, but processing stool specimens is resource-intensive.We evaluated a novel, simple, centrifugation-free processing method for stool specimens for use on the Xpert MTB/RIF (Xpert), using two different stool masses: 0...
July 11, 2018: Journal of Clinical Microbiology
Stefan E Richter, Loren Miller, Daniel Z Uslan, Douglas Bell, Karol Watson, Romney Humphries, James A McKinnell
Infections due to colistin-resistant Gram-negative rods (ColR-GNR), and colistin-resistant Klebsiella pneumoniae (ColR-KP) in particular result in high associated mortality and poor treatment options. To determine risk factors for recovery on culture of ColR-GNR and ColR-KP, analyses were chosen to aid decisions at two separate time points, the first when only Gram stain results are available without any bacterial species information (corresponding to the ColR-GNR model), and the second when organism identification was performed, but prior to reporting of antimicrobial susceptibility results (corresponding to the ColR-KP model)...
July 5, 2018: Journal of Clinical Microbiology
Patricia J Simner, Heather B Miller, Florian P Breitweiser, Gabriel Pinilla Monsalve, Carlos A Pardo, Steven L Salzberg, Cynthia Sears, David L Thomas, Charles G Eberhart, Karen C Carroll
Background: The purpose of this study was to develop and optimize different processing, extraction, amplification and sequencing methods for metagenomic next-generation sequencing (mNGS) of CSF specimens. Methods: We applied mNGS to 10 CSF samples with known standard of care results (SoC; 8 positive and 2 negative). Each sample was subjected to 9 different methods by varying sample processing protocols (supernatant, pellet, neat CSF), sample pre-treatment (+/- bead-beating) and the requirement of nucleic acid amplification steps using DNASeq (+/- whole genome amplification [WGA]) and RNASeq methods...
July 5, 2018: Journal of Clinical Microbiology
Pascale Bémer, Julie Léger, Serge Milin, Chloé Plouzeau, Anne Sophie Valentin, Nathalie Stock, Anne Jolivet-Gougeon, Anne Moreau, Stéphane Corvec, Isabelle Quintin-Roue, Didier Tandé, Geneviève Héry-Arnaud, Marie-Christine Rousselet, Carole Lemarié, Marie Kempf, Patrick Michenet, Laurent Bret, Gonzague de Pinieux, Christophe Burucoa
Aims. No gold standard exists for histopathological diagnosis of a prosthetic-joint-infection (PJI). The historical criterion considers the presence of neutrophils (NG) infiltrate upon examination of periprosthetic tissue. Morawietz et al. proposed a classification of periprosthetic membrane and a more recently described classification with a new cut-off value of 23 NG in 10 High-Power Fields. We performed a multicenter prospective study which compared both methods for the diagnosis of PJI. Methods. All suspicions of PJI (n=264) were prospectively included between December 2010 and March 2012 in seven centers...
July 5, 2018: Journal of Clinical Microbiology
John P Dekker
Metagenomics approaches based on shotgun next generation sequencing hold promise for infectious disease diagnostics. Despite substantial challenges that remain, work done over the past few years justifies excitement about the potential for these approaches to transform how clinical pathogen identification and analysis are performed. In an article in this issue of the Journal of Clinical Microbiology , M. I. Ivy et al. (J. Clin Microbiol 56:e00402-18, 2018, have applied a shotgun metagenomics approach to the diagnosis of prosthetic joint infections directly from synovial fluid...
July 5, 2018: Journal of Clinical Microbiology
Adrien Fabre, Monica Oleastro, Alexandra Nunes, Andrea Santos, Elodie Sifré, Astrid Ducournau, Lucie Bénéjat, Alice Buissonnière, Pauline Floch, Francis Mégraud, Véronique Dubois, Philippe Lehours
A whole-genome sequencing (WGS) approach was conducted in order to identify the molecular determinants associated with antimicrobial resistance in 12 multidrug resistant Campylobacter jejuni and Campylobacter coli isolates, with a focus on aminoglycoside resistance determinants. Two variants of a new aminoglycoside phosphotransferase gene ( aph(2")-Ii1 and aph(2")-Ii2 ) putative associated with gentamicin resistance were found. In addition, new genes were identified for the first time in Campylobacter : A lincosamide nucleotidyltransferase ( lnu (G)), likely associated with lincomycin resistance, and two resistance enzymes encoded by spw and apmA genes, similar to those found in Staphylococcus aureus , which may confer spectinomycin and gentamicin resistance, respectively...
July 5, 2018: Journal of Clinical Microbiology
Adam L Bailey, Tom Armstrong, Hari-Prakash Dwivedi, Gerald A Denys, Janet Hindler, Shelley Campeau, Maria Traczewski, Romney Humphries, C A Burnham
Ceftolozane-tazobactam (C/T) is a novel beta-lactam/beta-lactamase inhibitor combination antibiotic approved by the USA Food and Drug Administration in 2014 for the treatment of complicated intra-abdominal infections (in combination with metronidazole) and complicated urinary tract infections. Here, we evaluated the performance of the C/T ETEST®, a gradient diffusion method. C/T ETEST® was compared to broth microdilution (BMD) for 51 Enterobacteriaceae challenge isolates and 39 Pseudomonas aeruginosa challenge isolates at three clinical sites...
July 5, 2018: Journal of Clinical Microbiology
Sarah van Alen, Britta Ballhausen, Ursula Kaspar, Robin Köck, Karsten Becker
Whereas the emergence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) clonal complex (CC) 398 in animal husbandry and its transmission to humans are well documented, less is known about factors driving the epidemic spread of this zoonotic lineage within the human population. One factor could be the bacteriophage phi3 , which is rarely detected in S. aureus isolates from animals, but commonly found among isolates from humans including those of the human-adapted methicillin-susceptible S...
July 5, 2018: Journal of Clinical Microbiology
Margaretha de Vos, Brigitta Derendinger, Tania Dolby, John Simpson, Paul D van Helden, John E Rice, Lawrence J Wangh, Grant Theron, Robin M Warren
Rationale: Most MDR-TB is never diagnosed (328300 of the ∼490000 cases in 2016 were missed). Xpert MTB/RIF detects resistance to only rifampicin despite ∼20% of rifampicin-resistant cases being susceptible to isoniazid (a critical first line drug). Consequently, many countries require further testing with GenoType MTBDR plus However, MTBDR plus is not recommended for use on smear-negative specimens and thus many specimens require culture-based drug susceptibility testing. Furthermore, MTBDR plus requires specialised expertise, lengthy hands-on time, significant laboratory infrastructure and interpretation is not automated...
July 5, 2018: Journal of Clinical Microbiology
Valentina Donà, Joost H Smid, Sara Kasraian, Dianne Egli-Gany, Ferah Dost, Fatime Imeri, Magnus Unemo, Nicola Low, Andrea Endimiani
Molecular methods are often used for Neisseria gonorrhoeae (NG) detection, but complete definition of antimicrobial resistance (AMR) patterns still requires phenotypic tests. We developed an assay that both identifies NG and detects AMR determinants in clinical specimens.We designed a mismatch amplification mutation assay (MAMA)-based SYBR Green real-time PCR targeting: one NG-specific region ( opa ); mosaic penA alleles (Asp345 deletion, Gly545Ser) associated with decreased susceptibility to cephalosporins; alterations conferring resistance to ciprofloxacin (GyrA: Ser91Phe), azithromycin (23S rRNA: A2059G and C2611T) and spectinomycin (16S rRNA: C1192T)...
June 27, 2018: Journal of Clinical Microbiology
Daiana de Lima-Morales, Helena Ávila, Tatiana Soldi, Tanise Vendruscolo Dalmolin, Larissa Lutz, Valério Aquino, Alexandre Prehn Zavascki, Afonso Luís Barth
The aim of this study was to evaluate the two rapid colorimetric methods (CNPt-Direct and Blue-Carba) for the detection of carbapenemase production directly from blood culture in a routine microbiology laboratory. The methods were initially evaluated on spiked blood cultures with 61 carbapenemase-positive isolates. Afterwards they were used in blood cultures (314 samples were evaluated) obtained from patients in a routine microbiology laboratory, during a period of 6 months. The colorimetric methods were compared to the conventional culture of blood...
June 27, 2018: Journal of Clinical Microbiology
Sohei Harada, Yohei Doi
Hypervirulent Klebsiella pneumoniae strains have higher potential to cause more severe and disseminated infections compared with classic K. pneumoniae strains. While initially reported from East Asian countries, cases have now been identified worldwide, sometimes in conjunction with extensive drug resistance. In this issue of the Journal of Clinical Microbiology, Russo et al. validated the diagnostic accuracy of biomarkers that differentiate hypervirulent K. pneumoniae strains from classic strains. This represents a major step forward in building a consensus definition and designing international studies aimed at elucidating the global epidemiology, clinical features and outcome of this important pathogen...
June 27, 2018: Journal of Clinical Microbiology
François Caméléna, Aurélie Cointe, Vincent Mathy, Claire Hobson, Catherine Doit, Béatrice Bercot, Dominique Decré, Isabelle Podglajen, Laurent Dortet, Audrey Monjault, Philippe Bidet, Stéphane Bonacorsi, André Birgy
The dissemination of carbapenemase-producing Enterobacteriaceae (CPE) is a major threat to public health. Rapid and accurate detection of CPE is essential to initiate appropriate antimicrobial treatment and to establish infection control measures. The carbapenem inactivation method (CIM) was recently described with good sensitivity and specificity but a detection time of 20 hours. In this study, we evaluated the performances of a new version, the CIMplus that allows the detection of carbapenemase in 8 hours and the characterization of the carbapenemase classes, according to Ambler classification, in 20 hours...
June 27, 2018: Journal of Clinical Microbiology
Alana Sterkel, Allen Bateman, Ann Valley, David Warshauer
Candida spp. are the most common cause of fungal infections worldwide and the fifth most common cause of nosocomial infections (1).….
June 27, 2018: Journal of Clinical Microbiology
Luke R Green, Jay Lucidarme, Neelam Dave, Hannah Chan, Stephen Clark, Ray Borrow, Christopher D Bayliss
A recombinant NadA protein is one of the four major protective antigens of 4C-MenB (Bexsero®), a vaccine developed for serogroup B Neisseria meningitidis (MenB). The Meningococcal Antigen Typing System (MATS) is utilised as a high throughput assay for assessing the invasive MenB strain coverage of 4C-MenB. Where present, the nadA gene is subject to phase variable changes in transcription due to a 5'TAAA repeat tract located in a regulatory region. The promoter-containing intergenic region sequences (IGR) and 5'TAAA repeat numbers were determined for 906 invasive meningococcal disease isolates possessing the nadA gene...
June 27, 2018: Journal of Clinical Microbiology
Daniel Perez-Risco, David Rodriguez-Temporal, Ivan Valledor-Sanchez, Fernando Alcaide
The rapid detection of Mycobacterium tuberculosis complex (MTUBC) in clinical samples is essential for successful treatment. New techniques such as Real-Time PCR have been developed in order to facilitate rapid diagnosis, but their sensitivity is low in extrapulmonary specimens, due to the low bacillary load in such samples. A next-generation assay has recently been developed to try to overcome this limitation. The aim of this study was to analyze the effectiveness of the Xpert MTB/RIF Ultra (GX-Ultra) for the detection of MTUBC DNA in 108 smear-negative extrapulmonary specimens that were MTUBC culture-positive...
June 27, 2018: Journal of Clinical Microbiology
Kristen A Davenport, Clare E Hoover, Nathaniel D Denkers, Candace K Mathiason, Edward A Hoover
Chronic wasting disease (CWD), a fatal neurodegenerative prion disease of cervids, has spread across North America and has been detected in The Republic of Korea, Finland and Norway. CWD appears to spread by horizontal transmission, and prions shed in saliva, feces and urine are thought to contribute. However, studies investigating the rapid spread of CWD have been hampered by assay inhibitors and a lack of consistent and sensitive means to detect the relatively low levels of prions in these samples. Here we show that saliva frequently contains an inhibitor of the real-time quaking-induced conversion assay (RT-QuIC), and that the inhibitor is a member of the mucin family...
June 27, 2018: Journal of Clinical Microbiology
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