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Journal of Clinical Microbiology

Ana Valero-Rello, Desiree Henares, Lesly Acosta, Mireia Jane, Iolanda Jordan, Pere Godoy, Carmen Muñoz-Almagro
Objectives: This study aimed to validate a comprehensive diagnostic protocol based on real-time PCR for the rapid detection and identification of B. pertussis , B. parapertussis and B. holmesii, as well as its implementation in the diagnostic routine of a reference children's hospital. Methods: The new algorithm included a triplex qPCR targeting IS 481 gene (in B. pertussis , B. holmesii and some B. bronchiseptica strains), pIS 1001 ( B. parapertussis -specific) and rnase P as human internal control. Two confirmatory singleplex for B...
November 7, 2018: Journal of Clinical Microbiology
Gabriela Echániz-Aviles, Soraia I Guerreiro, Catarina Silva-Costa, Catarina I Mendes, João André Carriço, María Noemí Carnalla-Barajas, Araceli Soto-Noguerón, Maria Elena Velazquez-Meza, José Melo-Cristino, Antonio Luévanos-Velazquez, Lucía Martínez-Medina, María Del Rosario Vázquez-Larios, Mário Ramirez
Streptococcus pneumoniae expressing serotype 3 have high virulence and case fatality ratio. Most studies of serotype 3 pneumococci have focused on a single lineage, the widespread ST180. To evaluate the serotype 3 lineages causing infections in Mexico we characterized 196 isolates recovered in 1994-2017. The isolates were mostly susceptible to all antimicrobials tested. A single meningitis isolate was resistant to penicillin and resistance to erythromycin was 5.2%. The isolates represented the widely disseminated clonal complex CC180 (n=140), the unusual CC4909 (n=42), CC260 (n=11), and a few singletons (n=3)...
November 7, 2018: Journal of Clinical Microbiology
Ihn Kyung Jang, Abby Tyler, Chris Lyman, Maria Kahn, Michael Kalnoky, John C Rek, Emmanuel Arinaitwe, Harriet Adrama, Maxwell Murphy, Mallika Imwong, Clare L Ling, Stephane Proux, Warat Haohankhunnatham, Melissa Rist, Annette M Seilie, Amelia Hanron, Glenda Daza, Ming Chang, Smita Das, Rebecca Barney, Andrew Rashid, Jordi Landier, David S Boyle, Sean C Murphy, James S McCarthy, François Nosten, Bryan Greenhouse, Gonzalo J Domingo
INTRODUCTION: Malaria rapid diagnostic tests (RDTs) detect primarily Plasmodium (P.) falciparum antigen histidine-rich protein 2 (HRP2) and the malaria-conserved antigen lactate dehydrogenase (LDH) for P. vivax and other malaria species. The performance of RDTs and their utility is dependent on circulating antigen concentration distributions in infected individuals in a malaria endemic population and the limit-of-detection of the RDT for the antigens. A multiplexed immunoassay for the quantification of HRP2, P...
November 7, 2018: Journal of Clinical Microbiology
Farzam Vaziri, Thomas A Kohl, Hasan Ghajavand, Mansour Kargarpour Kamakoli, Matthias Merker, Shima Hadifar, Sharareh Khanipour, Abolfazl Fateh, Morteza Masoumi, Seyed Davar Siadat, Stefan Niemann
The emergence and spread of multidrug resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains is a critical global health problem. Between 2014 and 2018, 606 MTBC strains were isolated from 13,892 suspected pulmonary tuberculosis (TB) patients in Tehran, Iran, including 16 MDR-TB (2.6%) cases. A combination of phenotypic and genotypic methods (whole genome sequencing), was employed for the identification of additional drug resistances and strain-to-strain genetic distances as a marker for recent transmission events...
November 7, 2018: Journal of Clinical Microbiology
B Leticia Fernández-Carballo, Tobias Broger, Romain Wyss, Niaz Banaei, Claudia M Denkinger
Detection of circulating free DNA (cfDNA) has transformed the field of oncology and prenatal diagnostics. Clinical application of cfDNA for disease diagnosis and monitoring, however, is relatively recent in the field of infectious disease. The potential of cfDNA as a non-invasive diagnostic and monitoring tool is especially promising for tuberculosis (TB) as it enables detection of both pulmonary and extrapulmonary TB from easily accessible urine and/or blood samples from any age group. However, despite the potential of cfDNA detection to identify TB, very few studies are described in the literature to date...
November 7, 2018: Journal of Clinical Microbiology
Aurélie Morand, Florent Cornu, Jean-Charles Dufour, Michel Tsimaratos, Jean-Christophe Lagier, Didier Raoult
The aim of this article is to review the human repertoire of bacteria already described by culture and metagenomic techniques in urine, and published in the literature. Our study led us to compare this repertoire with other human repertoires available.We followed automatic and manual bibliographical methods and found 562 bacterial species reported in the literature as part of the human urinary microbiota. Of the 562 species, 322 were described only by culture, 101 by both culture and metagenomics, and 139 only by metagenomic...
November 7, 2018: Journal of Clinical Microbiology
Shannon Katiyo, Berit Muller-Pebody, Mehdi Minaji, David Powell, Alan P Johnson, Elizabeth De Pinna, Martin Day, Ross Harris, Gauri Godbole
Background: Non-typhoidal Salmonella (NTS) bacteraemia causes hospitalisation, and high morbidity and mortality. We linked Gastrointestinal Bacteria Reference Unit (GBRU) data to Hospital Episode Statistics (HES) to study the trends and outcomes of NTS bacteraemias in England between 2004 and 2015. Methods: All confirmed NTS isolates from blood from England submitted to GBRU between 1st January 2004 and 31st December 2015 were deterministically linked to HES records. Adjusted odds ratios (AOR), proportions and confidence intervals (CI) were calculated to describe differences in age, sex, antibiotic resistance patterns and serotypes over time...
October 31, 2018: Journal of Clinical Microbiology
Michelle Su, Sarah W Satola, Timothy D Read
Clinical microbiology has long relied on growing bacteria in culture to determine antimicrobial susceptibility profiles, but the use of whole genome sequencing for antibiotic susceptibility testing (WGS-AST) is now a powerful alternative. This review discusses the technologies that made this possible and presents results from recent studies to predict resistance based on genome sequences. We examine differences between calling antibiotic resistance profiles by simple presence or absence of previously known genes and SNPs against using approaches that deploy machine-learning and statistical models...
October 31, 2018: Journal of Clinical Microbiology
L Tang, Y Su, Z Gu, A M Caliendo, S Pounds, R T Hayden
Despite advances in standardization of quantitative DNAemia tests and efforts to better understand and characterize performance of reference materials in different assays, it remains unclear how the commutability performance of reference materials is related to intra- and inter-assay agreement. Building upon the previous work, we describe a comprehensive framework to determine the relationship of commutability with assay accuracy and agreement. The use of this framework is illustrated using previously generated data regarding the performance of four quantitative Epstein-Bar virus (EBV) PCR assays with the WHO and ABI standards as examples...
October 31, 2018: Journal of Clinical Microbiology
Yoko Kojima, Keiichi Furubayashi, Takuya Kawahata, Haruyo Mori, Jun Komano
Human treponematosis is caused by various pathogenic Treponema pallidum sub-species (subsp.), including pallidum (TPA), pertenue (TPE), endemicum (TEN), and carateum. The global prevalence of syphilis has been increasing since the 2000s. Men account for more than 90% of the cases, with the majority being men who have sex with men (MSM). In Japan, the increase in the number of syphilis patients began in 2011, a 10-year delay from the global trend. In 2017, a total of 5,829 syphilis cases (3,934 men and 1,895 women) were reported, with an outstanding increase in cases among young adult women; the number reported for women aged 15 to 20 years was 1100...
October 31, 2018: Journal of Clinical Microbiology
Patrice Nordmann, Laurent Poirel, Linda Mueller
The Rapid Fosfomycin/ Escherichia coli NP test was developed to detect fosfomycin resistance in E. coli isolates. It is based on glucose metabolization and therefore detection of bacterial growth in the presence of fosfomycin at 40 µg/ml. Bacterial growth is visually detectable by an orange-to-yellow color change of red phenol, a pH indicator. A total of 100 E. coli isolates, among which 22 were fosfomycin-resistant, were used to evaluate the test performance Its sensitivity and specificity were 100% and 98...
October 31, 2018: Journal of Clinical Microbiology
Norio Akuta, Fumitaka Suzuki, Hitomi Sezaki, Masahiro Kobayashi, Shunichiro Fujiyama, Yusuke Kawamura, Tetsuya Hosaka, Mariko Kobayashi, Satoshi Saitoh, Yoshiyuki Suzuki, Yasuji Arase, Kenji Ikeda, Hiromitsu Kumada
Little is known about the effects of virus- and host-related factors on hepatocarcinogenesis in patients who show viral clearance after HCV RNA eradication by direct-acting antivirals (DAAs). The subjects of this retrospective study were 1,922 patients with HCV genotype 1 or 2 (HCV-1 or HCV-2)-related chronic liver disease, who showed sustained virological response (SVR) (defined as negative HCV RNA at 12 weeks after cessation of all-oral DAAs). All patients were confirmed to be HCC-free before and during DAAs...
October 31, 2018: Journal of Clinical Microbiology
Catherine Hogan, Sara Tien, Madhukar Pai, Niaz Banaei
We report a significant increase in positivity rates among low-risk health care workers (HCW) undergoing annual TB testing at our health system after the 4th generation QuantiFERON-TB Gold Plus (QFT-Plus) assay replaced QuantiFERON-TB Gold (QFT).….
October 24, 2018: Journal of Clinical Microbiology
Mizue Kanai, Yuzo Arima, Shingo Nishiki, Ken Shimuta, Ichiro Itoda, Tamano Matsui, Kazunori Oishi, Makoto Ohnishi, Shu-Ichi Nakayama
In recent years, syphilis notifications have increased dramatically in Japan. We carried out molecular typing and macrolide resistance analyses of Treponema pallidum subsp . pallidum samples collected from patients at four clinics and a hospital in Tokyo and Osaka prefectures in 2017.The macrolide resistant strain type 14d/f (SS14-like clade) was found in significantly more cases of syphilis among heterosexuals than in those among men who have sex with men (MSM); i.e., 79% (31/39) of the strains from heterosexuals were 14d/f compared to 37% (7/19) of those from MSM (odds ratio (OR), 6...
October 24, 2018: Journal of Clinical Microbiology
Thomas Iftner, Klaus-Joachim Neis, Alejandra Castanon, Rebecca Landy, Barbara Holz, Astrid Woll-Herrmann, Angelika Iftner, Annette Staebler, Diethelm Wallwiener, Claus Hann von Weyhern, Felix Neis, Juliane Haedicke-Jarboui, Peter Martus, Sara Brucker, Melanie Henes, Peter Sasieni
Longitudinal data on the E6/E7 mRNA-based AHPV® HPV (AHPV) assay exceeding three years in comparison to the gold standard digene Hybrid Capture® 2 (HC2) test are not available. We previously reported the cross-sectional data of the German AHPV Screening Trial (GAST) where 10,040 women were recruited and tested by liquid-based cytology, the HC2 and the AHPV assay. 411 test-positive women were followed for up to six years. In addition, 3,295 triple-negative women were screened after a median time of six years...
October 24, 2018: Journal of Clinical Microbiology
Nicklas Sundell, Lars-Magnus Andersson, Robin Brittain-Long, Pär-Daniel Sundvall, Åsa Alsiö, Magnus Lindh, Lars Gustavsson, Johan Westin
The frequency of viral respiratory pathogens in asymptomatic subjects is poorly defined. The aim of this study was to explore the prevalence of respiratory pathogens in the upper airways of asymptomatic adults, as compared with a reference population of symptomatic patients sampled in the same centres during the same period. Nasopharyngeal (NP) swab samples were prospectively collected from adults with and without ongoing symptoms of respiratory tract infection (RTI) during 12 consecutive months, in primary care centres as well as hospital emergency departments, and analysed for respiratory pathogens by a PCR panel detecting 16 viruses and four bacteria...
October 24, 2018: Journal of Clinical Microbiology
Erik Skoglund, Casey Dempsey, Hua Chen, Kevin W Garey
Background : Blood culture contamination results in increased hospital costs and exposure to antimicrobials. We evaluated the potential clinical and economic benefits of an Initial Specimen Diversion Device® (ISDD®) when routinely utilized for blood culture collection in the emergency department (ED) of a quaternary care medical center. Methods : A decision analysis model was created to identify the cost benefit of use of the ISDD device in the ED. Probabilistic costs were determined from published literature and direct observation of pharmacy/microbiology staff...
October 24, 2018: Journal of Clinical Microbiology
Lin Wang, Xi Cao, Zhenzi Wang, Yuhua Gao, Juan Deng, Xueen Liu, Hui Zhuang
This study was to explore the correlation of serum hepatitis B core-related antigen (HBcrAg) with intrahepatic HBV covalently closed circular DNA (cccDNA) and HBV total DNA (tDNA) in HBeAg-positive chronic hepatitis B (CHB) patients. Serum HBcrAg and other parameters including HBV DNA, HBV RNA, HBeAg, HBsAg, anti-HBc, ALT, AST were quantitatively measured at baseline and follow-up time points. Intrahepatic HBV cccDNA and tDNA were quantitatively detected at baseline and 96-week. Grading of liver necroinflammation and staging of hepatic fibrosis were assessed at baseline and 96-week...
October 24, 2018: Journal of Clinical Microbiology
Ye Xu, Bin Liang, Chen Du, Xueshan Tian, Xingshan Cai, Yanjie Hou, Hui Li, Rongrong Zheng, Junlian Li, Yuqin Liu, Kaili Wang, Muhammad Ammar Athar, Yaoju Tan, Qingge Li
The sustained increase in nontuberculous mycobacteria (NTM) infection incidence and the difficulty in distinguishing these infections from tuberculosis constitute an urgent need for NTM species level identification. The MeltPro Myco assay is the first diagnostic system that identifies 19 clinically relevant mycobacteria in a single reaction based on multicolor melting curve analysis run on a real-time PCR platform. The assay was comprehensively evaluated regarding its analytical and clinical performances. The MeltPro Myco assay accurately identified 51 reference mycobacterial strains to the species/genus level and showed no cross-reactivity with 16 non-mycobacterial strains...
October 17, 2018: Journal of Clinical Microbiology
Shawn Vasoo
With the increasing number of prosthetic joints replaced annually worldwide, orthopedic implant-associated infections (OIAIs) present a considerable burden. Accurate diagnostics are required to optimize surgical and antimicrobial therapy. Sonication fluid cultures have been shown in multiple studies to improve the microbiologic yield OIAIs, but uptake of sonication has not been widespread in many routine clinical microbiology laboratories. In this issue M. Dudareva and colleagues (J Clin Microbiol 56:e00688-18, 2018, https://doi...
October 17, 2018: Journal of Clinical Microbiology
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