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Journal of Clinical Microbiology

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https://www.readbyqxmd.com/read/28228494/an-evaluation-of-rgm-medium-for-isolation-of-nontuberculous-mycobacteria-from-respiratory-samples-from-patients-with-cystic-fibrosis-in-the-united-states
#1
Rongpong Plongla, Clair L Preece, John D Perry, Peter H Gilligan
A novel selective agar (RGM medium) has been advocated for the isolation of rapidly growing mycobacteria from the sputum of cystic fibrosis (CF) patients. The aim of this study was to compare RGM medium with Burkholderia cepacia selective agar (BCSA) and a standard AFB culture method for the isolation of nontuberculous mycobacteria (NTM) from patients with CF. The applicability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identification of NTM isolated on RGM was also assessed...
February 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28228493/hepatitis-e-virus-detection-and-quantification-by-an-rt-qpcr-assay-calibrated-to-the-world-health-organization-standard-for-hev-rna
#2
Jeffrey J Germer, Irina Ankoudinova, Yevgeniy S Belousov, Walt Mahoney, Chen Dong, Jihong Meng, Jayawant N Mandrekar, Joseph D Yao
Hepatitis E virus (HEV) has emerged as a cause of chronic hepatitis among immunocompromised patients. Molecular assays have become important tools for the diagnosis and management of these chronically-infected patients. A reverse transcription, real-time PCR (RT-qPCR) assay utilizing Pleiades probe chemistry and an RNA internal control for simultaneous detection and quantification of HEV RNA in human serum was developed based on adaptation of a previously described and broadly reactive primer set targeting the overlapping open reading frame (ORF) 2/3 nucleotide sequence of HEV...
February 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28228492/neisseria-gonorrhoeae-sequence-typing-for-antimicrobial-resistance-ng-star-a-novel-antimicrobial-resistance-multilocus-typing-scheme-for-tracking-the-global-dissemination-of-n-gonorrhoeae-strains
#3
W Demczuk, S Sidhu, M Unemo, D M Whiley, V G Allen, J R Dillon, M Cole, C Seah, E Trembizki, D L Trees, E N Kersh, A J Abrams, H J C de Vries, A P van Dam, I Medina, A Bharat, M R Mulvey, G Van Domselaar, I Martin
A curated web-based user-friendly sequence typing tool based on antimicrobial resistance determinants in Neisseria gonorrhoeae was developed and is publicly accessible at https://ngstar.canada.ca The N. gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) molecular typing scheme uses the DNA sequences of 7 genes (penA, mtrR, porB, ponA, gyrA, parC, 23S rRNA) associated with resistance to β-lactam antimicrobials, macrolides, or fluoroquinolones. NG-STAR uses the entire penA sequence combining the historical nomenclature for penA types I-XXXVIII with novel nucleotide sequence designations; the full mtrR sequence and a portion of its promoter region; portions of ponA, porB, gyrA and parC; and 23S rRNA sequences...
February 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28228491/maldi-tof-alone-versus-maldi-tof-combined-with-real-time-antimicrobial-stewardship-interventions-on-time-to-optimal-antimicrobial-therapy-in-patients-with-positive-blood-cultures
#4
Maya Beganovic, Michael Costello, Sarah M Wieczorkiewicz
Introduction: Matrix-assisted laser desorption ionization time of flight (MALDI-TOF) decreases time to organism identification and improves clinical and financial outcomes. The purpose of this study was to evaluate the impact of MALDI-TOF alone vs MALDI-TOF combined with real-time, pharmacist-driven, antimicrobial stewardship (AMS) intervention on patient outcomes.Methods: This single-center, pre-post quasi-experimental study evaluated hospitalized patients with positive blood cultures identified via MALDI-TOF combined with prospective AMS intervention, compared to a control cohort with MALDI-TOF identification without AMS intervention...
February 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28228490/short-read-whole-genome-sequencing-for-laboratory-based-surveillance-of-bordetella-pertussis
#5
Alex Marchand-Austin, Raymond S W Tsang, Jennifer L Guthrie, Jennifer H Ma, Gillian Lim, Natasha S Crowcroft, Shelley L Deeks, David J Farrell, Frances B Jamieson
Bordetella pertussis (BP) is a Gram-negative bacterium that causes respiratory infections in humans. Ongoing molecular surveillance of BP acellular vaccine (aP) antigens is critical for understanding the interaction between evolutionary pressures, disease pathogenesis, and vaccine effectiveness. Methods currently used to characterize aP components are relatively labour intensive and low throughput. To address this challenge, we sought to derive aP antigen genotypes from minimally processed short-read whole genome sequencing data generated from 40 clinical BP isolates and analyzed using the SRST2 bioinformatic package...
February 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28202802/multi-laboratory-survey-to-evaluate-salmonella-prevalence-in-diarrheic-and-non-diarrheic-dogs-and-cats-in-the-usa-between-2012-and-2014
#6
Renate Reimschuessel, Michael Grabenstein, Jake Guag, Sarah M Nemser, Kyunghee Song, Junshan Qiu, Kristin A Clothier, Barbara A Byrne, Stanley L Marks, Kyran Cadmus, Kristy Pabilonia, Susan Sanchez, Sreekumari Rajeev, Steve Ensley, Timothy S Frana, Albert E Jergens, Kimberly H Chappell, Siddhartha Thakur, Beverly Byrum, Jing Cui, Yan Zhang, Matthew M Erdman, Shelley C Rankin, Russell Daly, Seema Das, Laura Ruesch, Sara D Lawhon, Shuping Zhang, Timothy Baszler, Dubraska Diaz-Campos, Faye Hartmann, Ogi Okwumabua
Eleven laboratories collaborated to determine the periodic prevalence of Salmonella in a population of dogs and cats in the USA visiting veterinary clinics. Fecal samples (2965) solicited from 11 geographically dispersed veterinary testing laboratories were collected in 36 states between January 2012 and April 2014 and tested using a harmonized method. The overall study prevalence of Salmonella in cats (3 of 542) was <1%. Prevalence in dogs (60 of 2422) was 2.5%. Diarrhea was present in only 55% of positive dogs; however 3...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28202801/molecular-epidemiology-and-strain-comparison-between-hepatitis-e-virus-in-human-sera-and-pig-livers-during-2014-2016-in-hong-kong
#7
Martin C W Chan, Kirsty Kwok, Tin-Nok Hung, Paul K S Chan
Hepatitis E virus (HEV) causes substantial morbidity and mortality in developing countries and is considered an emerging food-borne pathogen in previously non-endemic developed countries. To investigate genetic association between human HEV infection and HEV-contaminated high-risk food in Hong Kong, we compared local virus strains obtained from hepatitis E patient sera with those surveyed from high-risk food items during 2014-2016. Twenty-four cases of laboratory-confirmed human HEV infections were identified from January 2014 to March 2016 in our hospitals...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28202800/discovery-of-novel-pneumococcal-serotype-35d-a-natural-wcig-deficient-variant-of-serotype-35b
#8
K Aaron Geno, Jamil S Saad, Moon H Nahm
The pneumococcus (Streptococcus pneumoniae) remains a significant cause of morbidity and mortality, especially among those at the extremes of age. Its capsular polysaccharide is essential for systemic virulence. Over ninety serologically distinct pneumococcal capsular polysaccharides (serotypes) are recognized, but they are unequal in prevalence. Because antibodies against the capsule are protective, polysaccharide conjugate vaccines, which are constructed against the most prevalent serotypes, have made great reductions in pneumococcal disease caused by these serotypes...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28202799/clonal-complexity-in-mycobacterium-tuberculosis-can-hamper-diagnostic-procedures
#9
Laura Pérez-Lago, Marta Herranz, Yurena Navarro, María Jesús Ruiz Serrano, Pilar Miralles, Emilio Bouza, Darío García-de-Viedma
Clonal complexity is increasingly accepted in Mycobacterium tuberculosis infection, including mixed infections by ≥2 strains, which usually occur in settings with a high burden of tuberculosis and/or a high risk of overexposure to infected patients. Mixed infections can hamper diagnostic procedures: obtaining an accurate antibiogram is difficult when the susceptibility patterns of the strains differ. Here, we show how mixed infections can also prove challenging for other diagnostic procedures, even outside settings where mixed infections are traditionally expected...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28202798/high-prevalence-and-diversity-of-hepatitis-viruses-in-suspected-cases-of-yellow-fever-in-the-democratic-republic-of-congo
#10
Sheila Makiala-Mandanda, Frédéric Le Gal, Nadine Ngwaka-Matsung, Steve Ahuka-Mundeke, Richard Onanga, Berthold Bivigou-Mboumba, Elisabeth Pukuta-Simbu, Athenaïs Gerber, Jessica L Abbate, Dieudonné Mwamba, Nicolas Berthet, Eric Maurice Leroy, Jean-Jacques Muyembe-Tamfum, Pierre Becquart
The majority of patients with acute febrile jaundice (>95%) identified through a yellow fever surveillance program in the Democratic Republic of Congo (DRC) test negative for antibodies against yellow fever virus. However, no etiological investigation has ever been carried out on these patients. Here, we tested for hepatitis A (HAV), B (HBV), C (HCV), D (HDV) and E (HEV) viruses, all of which can cause acute febrile jaundice, in patients included in the yellow fever surveillance program in the DRC. On a total of 498 serum samples collected from suspected cases of yellow fever from January 2003 to January 2012, ELISA techniques were used to screen for antibodies against HAV (IgM) and HEV (IgM) and for antigens and antibodies against HBV (HBsAg and anti-HBc IgM), HCV and HDV...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28202797/the-epiquant-framework-for-computing-the-epidemiological-concordance-of-microbial-subtyping-data
#11
Benjamin M Hetman, Steven K Mutschall, James E Thomas, Victor P J Gannon, Clifford G Clark, Frank Pollari, Eduardo N Taboada
A fundamental assumption in the use and interpretation of microbial subtyping results for public health investigations is that isolates that appear to be related based on molecular subtyping data are expected to share commonalities with respect to their origin, history and distribution. Critically, no approach currently exists for systematically assessing the underlying epidemiology of subtyping results. Our aim was to develop a method for directly quantifying the similarity between bacterial isolates using basic sampling metadata and to develop a framework for computing the epidemiologic concordance of microbial typing results...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28202796/evaluation-of-genotypic-and-phenotypic-protease-virulence-tests-for-dichelobacter-nodosus-infection-in-sheep
#12
Andrew S McPherson, Om P Dhungyel, Richard J Whittington
Dichelobacter nodosus is a fastidious, strictly anaerobic bacterium, an obligate parasite of the ruminant hoof and the essential causative agent of virulent ovine footrot. The clinical disease results from a complex interplay between pathogen, environment and host. Sheep flocks diagnosed with virulent but not benign footrot in Australia may be quarantined and required to undergo a compulsory eradication program, with costs met by the farmer. Virulence of D. nodosus is at least partially dependent on elaboration of a protease coded by aprV2 and manifest as elastase activity...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28202795/tuberculosis-outbreak-in-an-educational-institution-in-norway
#13
Gunnstein Norheim, Siri Seterelv, Trude M Arnesen, Anne Torunn Mengshoel, Tone Tønjum, Janne O Rønning, Vegard Eldholm
Within one week in April 2013, three cases of pulmonary tuberculosis (TB) were reported among students attending training sessions at an educational institution in Oslo, Norway. By the end of October 2013, a total of nine epidemiologically linked cases had been reported. The outbreak encompassed a total of 24 cases in the period 2009-14, among which all of the 22 Mycobacterium tuberculosis isolates available had identical MIRU-VNTR profile (MtbC15-9 code 10287-189), belonging to the Beijing lineage. Whole genome sequencing (WGS) of the M...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28202794/evaluation-of-the-toxoplasma-elite-mgb%C3%A2-real-time-pcr-assay-for-the-diagnosis-of-toxoplasmosis
#14
Florence Robert-Gangneux, Marie-Pierre Brenier-Pinchart, Hélène Yera, Sorya Belaz, Emmanuelle Varlet-Marie, Patrick Bastien
Molecular diagnosis of congenital toxoplasmosis or disseminated toxoplasmosis is mainly based on PCR. The repeated DNA element rep529 has become the main DNA target used in most, whether laboratory-developed or commercial, PCR methods. In this multicenter study, we evaluated the Toxoplasma ELITe MGB® (Elitech®) commercial kit, by comparison with three reference quantitative PCR assays (RA) used in routine in three proficient laboratories of the French National Reference Center for Toxoplasmosis network, using Toxoplasma calibrated suspensions diluted to obtain a range of concentrations from 0...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28202793/the-new-aptima-hbv-quant-real-time-tma-assay-accurately-quantifies-hepatitis-b-virus-dna-from-genotypes-a-to-f
#15
Stéphane Chevaliez, Claude Dauvillier, Fabienne Dubernet, Jean-Dominique Poveda, Syria Laperche, Christophe Hézode, Jean-Michel Pawlotsky
Sensitive and accurate hepatitis B virus (HBV) DNA detection and quantification are essential to diagnose HBV infection, establish the prognosis of HBV-related liver disease, guide the decision to treat and monitor the virological response to antiviral treatment and the emergence of resistance. Currently available HBV DNA platforms and assays are generally designed for batching multiple specimens within an individual run and require at least one full day of work to complete the analyses. The aim of this study was to evaluate the ability of the newly developed, fully automated, one-step Aptima HBV Quant assay to accurately detect and quantify HBV DNA in a large series of patients infected with different HBV genotypes...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28202792/towards-a-new-strategy-for-the-diagnosis-of-congenital-trypanosoma-cruzi-infection
#16
Alba Abras, Carmen Muñoz, Cristina Ballart, Pere Berenguer, Teresa Llovet, Mercedes Herrero, Silvia Tebar, María-Jesús Pinazo, Elizabeth Posada, Carmen Martí, Victoria Fumadó, Jordi Bosch, Oriol Coll, Teresa Juncosa, Gemma Ginovart, Josep Armengol, Joaquim Gascón, Montserrat Portús, Montserrat Gállego
The immigration of Latin American women of childbearing age has spread the congenital transmission of Chagas disease to non-endemic areas, and the disease is now a worldwide problem. Some European health authorities have implemented screening programs to prevent vertical transmission, but the lack of a uniform protocol calls for the urgent establishment of a new strategy, common for all laboratories. Our aims were (i) to analyze the trend of passive IgG antibodies in the newborn by means of five serological tests for the diagnosis and follow-up of congenital Trypanosoma cruzi infection, (ii) to assess the utility of these techniques for diagnosing a congenital transmission, and (iii) to propose a strategy for a prompt, efficient and cost-effective diagnosis of T...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28202791/establishment-and-use-of-epidemiological-cutoff-values-for-molds-and-yeasts-using-the-clinical-and-laboratory-standards-institute-m57-standard
#17
Shawn R Lockhart, Mahmoud A Ghannoum, Barbara D Alexander
Breakpoints are used to predict whether an antifungal agent will be clinically effective against a particular fungal isolate. They are based on a combination of MIC values, pharmacokinetic/pharmacodynamic values and clinical outcome data. For many fungus/antifungal combinations this data will never be available. For these combinations Epidemiological Cutoff Values (ECVs) provide a methodology to categorize isolates as either wild type or non-wild type. This review defines ECVs, explains how they are generated using the CLSI methodology in standard M57, and describes how they can be used in clinical practice...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28202790/reactivity-of-anti-pedv-structural-protein-antibodies-to-porcine-enteric-coronaviruses-diagnostic-implications
#18
Luis Gabriel Gimenez-Lirola, Jianqiang Zhang, Jose Antonio Carrillo-Avila, Qi Chen, Ronaldo Magtoto, Korakrit Poonsuk, David H Baum, Pablo Piñeyro, Jeffrey Zimmerman
The development of porcine epidemic diarrhea virus (PEDV) antibody-based assays is important for detecting infected animals, confirming previous virus exposure, and monitoring sow herd immunity. However, the potential cross-reactivity among porcine coronaviruses is a major concern for the development of pathogen-specific assays. In this study, we used serum samples (n = 792) from pigs of precisely known infection status and a multiplex fluorescent microbead-based immunoassay and/or enzyme-linked immunoassay platform to characterize the antibody response against PEDV whole-virus (WV) particles and recombinant polypeptides derived from the four PEDV structural proteins, i...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28202789/use-of-multiplex-real-time-pcr-to-diagnose-scrub-typhus
#19
Wiwit Tantibhedhyangkul, Ekkarat Wongsawat, Saowaluk Silpasakorn, Duangdao Waywa, Nuttawut Saenyasiri, Jintapa Suesuay, Wilawan Thipmontree, Yupin Suputtamongkol
Scrub typhus, caused by Orientia tsutsugamushi, is a common cause of acute undifferentiated febrile illness in the Asia--Pacific region. However, its non-specific clinical manifestation often prevents early diagnosis. We propose the use of PCR and serologic tests as diagnostic tools. Here, we developed a multiplex real-time PCR assay using hydrolysis (Taqman) probes targeting O. tsutsugamushi47-kDa, groEL, and human IFNB genes to improve early diagnosis of scrub typhus. The amplification efficiency was higher than 94%, and the lower detection limit was 10 copies per reaction...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28179407/calprotectin-as-a-biomarker-for-melioidosis-disease-progression-and-management
#20
Mohan Natesan, Enoka Corea, Shivankari Krishnananthasivam, Harindra Darshana Sathkumara, Jennifer L Dankmeyer, Beverly K Dyas, Kei Amemiya, Aruna Dharshan De Silva, Robert G Ulrich
Melioidosis is a neglected tropical disease that is caused by the bacterium Burkholderia pseudomallei, and is underreported in many endemic countries. A long and costly administration of antibiotics is required to clear infections, and there is an unmet need for biomarkers to guide antibiotic treatment and increase the number of patients that complete therapy. We identified calprotectin as a lead biomarker of Burkholderia pseudomallei infections, and examined correlations between this serum protein and antibiotic treatment outcomes of melioidosis patients...
February 8, 2017: Journal of Clinical Microbiology
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