Journal of clinical microbiology (J Clin Microbiol)

Publications in this journal

• Article: Highly sensitive detection of hepatitis B virus surface antigen using a semi-automated immune complex transfer chemiluminescent enzyme immunoassay.

  Kazuhiko Takeda, Mari Maruki, Takahiro Yamagaito, Machiko Muramatsu, Yasuhiro Sakai, Hiroaki Tobimatsu, Hironori Kobayashi, Yoshiteru Mizuno, Yukio Hamaguchi
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  ABSTRACT: The performance of hepatitis B surface antigen (HBsAg) screening assays is continuously improved to reduce the risk of transfusion-associated hepatitis B. In this study, a semi-automated immune complex transfer chemiluminescence enzyme immunoassay (ICT-CLEIA) for the detection of HBsAg, which is as sensitive as hepatitis B virus (HBV)-DNA polymerase chain reaction (PCR), was developed; the ICT-CLEIA assay performance was compared with the performance of the Architect HBsAg QT assay and HBV-DNA PCR. The specificities in the initial assay and after retesting were 99.50% (1,988/1,998) and 99.95% (1,997/1,998), respectively. The analytical detection limit was determined to be 0.2 mIU/mL using the 2nd International WHO HBsAg standard, and the cutoff value (0.5 mIU/mL) of the ICT-CLEIA assay was 8.0 standard deviations (SD) above the mean of the HBsAg-negative specimens. The ICT-CLEIA assay could detect HBsAg even in the presence of anti-HBs antibodies and demonstrated a 23.6-day shorter window periods using commercially available HBsAg seroconversion panels when compared to the Architect HBsAg QT assay. Furthermore, the monitoring of the viral kinetics by the ICT-CLEA assay and the HBV-DNA PCR produced very similarly shaped curves during both the HBsAg seroconversion and reverse seroconversion periods. Therefore, the ICT-CLEIA assay may be useful not only for an earlier detection of HBV reactivation but also for the monitoring of hepatitis B patients.
  Journal of clinical microbiology 05/2013;
• Article: Multicenter evaluation of the VITEK MS MALDI-TOF mass spectrometry system for the identification of gram-positive aerobic bacteria.

  Jenna Rychert, Carey-Ann D Burnham, Maureen Bythrow, Omai B Garner, Christine C Ginocchio, Rebecca Jennemann, Michael A Lewinski, Ryhana Manji, A Brian Mochon, Gary W Procop, Sandra S Richter, Linda Sercia, Lars F Westblade, Mary Jane Ferraro, John A Branda
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  ABSTRACT: Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) is gaining momentum as a tool for bacterial identification in the clinical microbiology laboratory. Compared with conventional methods, this technology can more readily and conveniently identify a wide range of organisms. Here, we report the findings from a multi-center study to evaluate the VITEK MS v2.0 system (bioMérieux, Inc.) for the identification of aerobic gram-positive bacteria. A total of 1146 unique isolates, representing 13 genera and 42 species, were analyzed and compared to nucleic acid sequence-based identification as the reference method. For 1063 of 1146 isolates (92.8%), the VITEK MS provided a single identification that was accurate to the species level. For an additional 31 isolates (2.7%), multiple possible identifications were provided, all correct at the genus level. Mixed genera or single-choice incorrect identifications were provided for 18 isolates (1.6%). Although no identification was obtained for 33 isolates (2.9%), there was no specific bacterial species for which the VITEK MS consistently failed to provide identification. When a subset of 463 isolates representing commonly encountered, important pathogens was considered, 95% were accurately identified to the species-level and there were no misidentifications. Also, in all but one instance, the VITEK MS correctly differentiated S. pneumoniae from other viridans group streptococci. The findings demonstrate that the VITEK MS system is highly accurate for the identification of gram-positive aerobic bacteria in the clinical laboratory setting.
  Journal of clinical microbiology 05/2013;
• Article: Multi-Center Study Evaluating the VITEK MS for Identification of Medically Important Yeasts.

  Lars F Westblade, Rebecca Jennemann, John A Branda, Maureen Bythrow, Mary Jane Ferraro, Omai B Garner, Christine C Ginocchio, Michael A Lewinski, Ryhana Manji, A Brian Mochon, Gary W Procop, Sandra S Richter, Jenna A Rychert, Linda Sercia, Carey-Ann D Burnham
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  ABSTRACT: Optimal management of fungal infections is correlated with timely organism identification. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is revolutionizing the identification of yeasts isolated from clinical specimens. We present a multi-center study assessing the performance of the VITEK MS system in identifying medically important yeasts. A collection of 852 isolates was tested, including 20 Candida species (626 isolates including: 58 C. albicans, 62 C. glabrata and 53 C. krusei), 35 Cryptococcus neoformans isolates, and 191 other clinically relevant yeast isolates; in total 31 different species were evaluated. Isolates were directly applied to a target plate followed by a formic acid overlay. Mass spectra were acquired using the VITEK MS and analyzed using the VITEK MS version 2.0 database. The gold standard for identification was sequence analysis of the D2 region of the 26S rRNA gene. In total, 823 isolates (96.6%) were identified to genus level and 819 isolates (96.1%) identified to species level. Twenty-four isolates (2.8%) were not identified, and five isolates (0.6%) were misidentified. Misidentified isolates included one isolate of C. albicans (n=58) identified as C. dubliniensis, one isolate of C. parapsilosis (n=73) identified as C. pelliculosa and three isolates of Geotrichum klebahnii (n=6) identified as G. candidum. Identification of clinically relevant yeasts using MS is superior to phenotypic identification systems currently employed in the clinical microbiology laboratory.
  Journal of clinical microbiology 05/2013;
• Article: Rapid, molecular detection of macrolide resistance in the Mycobacterium avium complex: Are we there yet?

  Sara Christianson, William Grierson, Joyce Wolfe, Meenu K Sharma
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  ABSTRACT: Macrolides are an important aspect in the treatment of Mycobacterium avium complex infections. Here, we evaluate the use of 23s rRNA gene sequencing for the rapid detection of macrolide resistance. Routine sequencing of the 23s rRNA gene is highly specific for macrolide resistance, but lacks in sensitivity.
  Journal of clinical microbiology 05/2013;
• Article: Rapid Molecular Microbiologic Diagnosis of Prosthetic Joint Infection.

  Charles Cazanave, Kerryl E Greenwood-Quaintance, Arlen D Hanssen, Melissa J Karau, Suzannah M Schmidt, Eric O Gomez Urena, Jayawant N Mandrekar, Douglas R Osmon, Lindsay E Lough, Bobbi S Pritt, James M Steckelberg, Robin Patel
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  ABSTRACT: We previously showed that culture of samples obtained by prosthesis vortexing and sonication was more sensitive than tissue culture for prosthetic joint infection (PJI) diagnosis. Despite improved sensitivity, culture-negative cases remained; furthermore, culture has a long turnaround-time.We designed a genus-/group-specific rapid PCR assay panel targeting PJI bacteria and applied it to samples obtained by vortexing and sonicating explanted hip and knee prostheses, comparing results to sonicate fluid and periprosthetic tissue culture obtained at revision or resection arthroplasty.We studied 434 subjects with knee (n=272) or hip (n=162) prostheses; using a standardized definition, 144 had PJI. Sensitivities of tissue culture, and sonicate fluid culture and PCR were 70.1, 72.9 and 77.1%, respectively. Specificities were 97.9, 98.3 and 97.9%, respectively. Sonicate fluid PCR was more sensitive than tissue culture (P=0.04).PCR of prosthesis sonication samples is more sensitive than tissue culture for the microbiologic diagnosis of prosthetic hip and knee infection, and provides same-day PJI diagnosis with definition of microbiology. High assay specificity suggests that typical PJI bacteria may not cause aseptic implant failure.
  Journal of clinical microbiology 05/2013;
• Article: Clinical bovine piroplasmosis by Babesia occultans, Italy.

  Nicola Decaro, Vittorio Larocca, Antonio Parisi, Michele Losurdo, Riccardo Paolo Lia, Maria Fiorella Greco, Antonio Miccolis, Gianpiero Ventrella, Domenico Otranto, Canio Buonavoglia
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  ABSTRACT: A clinical outbreak of bovine piroplasmosis is reported in Italy. The etiological agent was characterized as Babesia occultans, a parasite regarded as apathogenic and never detected before in continental Europe. This report paves the way for further studies to assess the occurrence of this tick-transmitted protozoan in other European regions.
  Journal of clinical microbiology 05/2013;
• Article: High genetic diversity of Newcastle disease virus in poultry in West and Central Africa: co-circulation of genotypes XIV and newly defined genotypes XVII and XVIII.

  Chantal J Snoeck, Ademola A Owoade, Emmanuel Couacy-Hymann, Bello R Alkali, Mbah P Okwen, Adeniyi T Adeyanju, Giscard F Komoyo, Emmanuel Nakouné, Alain Le Faou, Claude P Muller
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  ABSTRACT: Despite rampant Newcastle disease virus (NDV) outbreaks in Africa since decades, the information about the genetic characteristics of the virulent strains circulating in West and Central Africa is still scarce. In this study, 96 complete NDV fusion gene sequences were obtained from poultry sampled in Cameroon, Central African Republic, Côte d'Ivoire and Nigeria between 2006 and 2011. Based on rational criteria recently proposed for the classification of NDV strains into classes, genotypes and sub-genotypes, we revisited the classification of virulent strains in particular from West and Central Africa, leading to their grouping into genotypes XIV and newly defined genotypes XVII and XVIII, each with two sub-genotypes. Phylogenetic analyses revealed that several (sub-)genotypes are found in almost every country. In Cameroon, most strains were related to vaccine strains, but a single genotype XVII strain was also found. Only three highly similar genotype XVII strains were detected in Central African Republic. Sub-genotypes XVIIa, XVIIIa and XVIIIb co-circulated in Côte d'Ivoire, while sub-genotypes XIVa, XIVb, XVIIa, XVIIb and XVIIIb were found in Nigeria. While these genotypes are so far geographically restricted, local and international trade of domestic and exotic birds may lead to their spread beyond West and Central Africa. A high genetic diversity, mutations in important neutralizing epitopes paired with suboptimal vaccination, various levels of clinical response of poultry and wild birds to virulent strains, strains with new cleavage site and other genetic modifications found in these genotypes tend to undermine and complicate NDV management in Africa.
  Journal of clinical microbiology 05/2013;
• Article: Helicobacter cinaedi and H. fennelliae transmission in a hospital from 2008 to 2012.

  Emiko Rimbara, Shigetarou Mori, Hyun Kim, Mari Matsui, Satowa Suzuki, Shunji Takahashi, Satoshi Yamamoto, Masaya Mukai, Keigo Shibayama
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  ABSTRACT: Forty-six Helicobacter cinaedi isolates from the same hospital were analyzed by multilocus sequence typing. Most H. cinaedi exhibited clonal complex 9 and were mainly isolated from immunocompromised patients in the same ward. Three H. fennelliae were isolated from the same ward and exhibited the same pulsed gel electrophoresis patterns. All isolates were resistant to clarithromycin and ciprofloxacin. H. cinaedi and H. fennelliae must be carefully monitored to prevent nosocomial infection.
  Journal of clinical microbiology 05/2013;
• Article: Ward-specific nasal co-colonization rates with methicillin-susceptible and -resistant Staphylococcus spp. and the potential impact on molecular MRSA screening tests.

  Sophie Trouillet-Assant, Jean-Philippe Rasigade, Sebastien Lustig, Yannick Lhoste, Florent Valour, Claude Guerin, Frederic Aubrun, Sylvestre Tigaud, Frederic Laurent
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  ABSTRACT: We report that the rates of nasal co-colonization with methicillin-susceptible Staphylococcus aureus and methicillin-resistant coagulase-negative staphylococci can vary widely between patients admitted to different wards within a single hospital. Such co-colonization can greatly influence the performance of molecular MRSA screening tests depending on the methods used and targets selected.
  Journal of clinical microbiology 05/2013;
• Article: Use of Luminex MagPlex(R) Magnetic Microspheres for High-Throughput Spoligotyping of M. tuberculosis Isolates in Port-au-Prince, Haiti.

  Oksana Ocheretina, Yves Mary Merveille, Marie-Marcelle Mabou, Vincent E Escuyer, Sherry A Dunbar, Warren D Johnson, Jean W Pape, Daniel W Fitzgerald
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  ABSTRACT: Genotyping of Mycobacterium tuberculosis strains became indispensable for understanding tuberculosis transmission dynamics and designing measures to combat the disease. Unfortunately, typing involves sophisticated laboratory analysis, is expensive, and requires a high level of technical expertise, which limited its use in resource poor countries where the majority of tuberculosis cases occur.Spoligotyping is a PCR-based Mycobacterium tuberculosis complex genotyping method with advantages of technical simplicity, numerical output and high reproducibility. It is based on presence or absence of 43 distinct "spacers" separating insertion element in the direct repeat region of the Mycobacterium tuberculosis genome. Spoligotyping assay involves reverse hybridization of PCR products to the capture spacers attached to nitrocellulose membranes or to microspheres. Here we report modification of the classic 43-spacer method using the new generation of Luminex multiplexing technology with magnetic microspheres.The method was successfully established and validated on strains with known spoligotypes in our laboratory in Haiti. Distribution of spoligotypes determined in a collection of 764 recent Mycobacterium tuberculosis isolates was in accordance with previous data for Haitian isolates in the SITWITWEB international database, which were obtained with traditional membrane-based method. In the present form, spoligotyping may be suitable as a high-throughput, first-line tool for genotyping of Mycobacterium tuberculosis in countries with limited resources.
  Journal of clinical microbiology 05/2013;
• Article: Rapid and reliable identification of Staphylococcus aureus capsular serotypes by means of artificial neural network-assisted Fourier-Transform Infrared Spectroscopy.

  Tom Grunert, Mareike Wenning, María Sol Barbagelata, Martina Fricker, Daniel O Sordelli, Fernanda R Buzzola, Monika Ehling-Schulz
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  ABSTRACT: Staphylococcus aureus capsular polysaccharides (CP) are important virulence factors and represent putative targets for vaccine development. Therefore the purpose of this study was to develop a high-throughput method to identify and discriminate the clinically important S. aureus capsular serotypes 5, 8 and NT (non-typeable). A comprehensive set of clinical isolates derived from different origins and control strains, representative for each serotype, were used to establish a CP typing system based on Fourier-transform infrared (FTIR) spectroscopy and chemometric techniques. By combining FTIR spectroscopy with artificial neuronal network (ANN) analysis a system was successfully established, allowing a rapid identification and discrimination of all three serotypes. The overall accuracy of the ANN-assisted FTIR spectroscopy CP typing system was 96.7% for the internal validation and 98.2% for the external validation, respectively. One isolate in the internal and one isolate in the external validation failed in the classification procedure but none of the isolates was incorrectly classified. The present study demonstrates that ANN-assisted FTIR spectroscopy allows a rapid and reliable discrimination of S. aureus capsular serotypes. It is suitable for diagnostic as well as large scale epidemiologic surveillance of S. aureus capsule expression and provides useful information with respect to chronicity of infection.
  Journal of clinical microbiology 05/2013;
• Article: Targeting the treponemal microbiome of digital dermatitis infections by high-resolution phylogenetic analyses and comparison with fluorescent in situ hybridization.

  Kirstine Klitgaard, Antoni Foix Bretó, Mette Boye, Tim K Jensen
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  ABSTRACT: Modern pyrosequencing technology allows for a more comprehensive approach than traditional Sanger sequencing when elucidating the aetiology of bovine digital dermatitis. We sought to describe the composition and diversity of treponemes in digital dermatitis lesions using deep sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene coupled with species-level, taxonomic identification. Treponema-specific 16S rRNA gene PCR and pyrosequencing were performed on biopsies originating from 10 different Catalan dairy herds (n=36) with digital dermatitis, and this analysis yielded 75 297 sequences. We identified 20 different taxa, including a potential novel phylotype that displayed 95% sequence identity to members of the T. denticola/T. pedis-like bacteria. Species frequencies and abundances that were obtained by pyrosequencing analysis were highly correlated with results that applied fluorescence in situ hybridisation using phylotype-specific oligonucleotide probes. In a limited number of animals from a single geographic region, we detected most of the Treponema phylotypes that were described in previous investigations of digital dermatitis. Additionally, we identified a number of phylotypes that mapped to oral treponemes of humans and canines that had not been reported in digital dermatitis lesions. The results presented here support previous observations of a polytreponemal infection aetiology, which contained T. phagedenis-like, T. medium/T. vincentii-like, and T. denticola/T. pedis-like phylotypes, being highly associated with disease. Using this new approach, it has now become feasible to study large herds and their surrounding environment, which could provide a basis for further understanding of the pathogenesis of this disease.
  Journal of clinical microbiology 05/2013;
• Article: Update of pneumococcal "PCR-serotyping" for detection of a commonly occurring type 19F wzy variant in Brazil.

  Ana Paula de O Menezes, Joice Neves Reis, Yves Mauro Ternes, Ana Lúcia Andrade, Fabiana C Pimenta, Maria da Gloria Carvalho, Bernard Beall
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  ABSTRACT: In this era of effective pneumococcal conjugate vaccines, simple and inexpensive methods are desirable for determining capsular serotype (st) distributions.…
  Journal of clinical microbiology 05/2013;
• Article: Asymptomatic Carriage of ST398, spa type t571 Methicillin-Susceptible Staphylococcus aureus in an Urban Jail: A Newly Emerging, Transmissible Pathogenic Strain.

  Michael Z David, Jane Siegel, Franklin D Lowy, Diana Zychowski, Alexis Taylor, Caroline J Lee, Susan Boyle-Vavra, Robert S Daum
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  ABSTRACT: ST398 Staphylococcus aureus, frequently carried by livestock, has caused severe human infections and often carries transmissible antibiotic resistance genes. Among methicillin-susceptible S. aureus isolates colonizing Dallas Jail detainees, 13.2% were ST398, spa type t571, and were genetically similar to human colonization isolates from New York, Chicago, and the Dominican Republic.
  Journal of clinical microbiology 05/2013;
• Article: Fluoroquinolone and macrolide resistance-associated mutations in Mycoplasma genitalium.

  Kaitlin A Tagg, Neisha J Jeoffreys, Deborah L Couldwell, Jennifer A Donald, Gwendolyn L Gilbert
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  ABSTRACT: Mycoplasma genitalium is a significant sexually transmitted pathogen, causing up to 25% of cases of non-gonococcal urethritis in men and is strongly associated with cervicitis and pelvic inflammatory disease in women. Currently, the usual first-line treatment is with the macrolide antibiotic, azithromycin, but an increasing incidence of treatment failure over the last five years suggests emergence of resistance. Mutations responsible for macrolide resistance have been found in the 23S rRNA gene (23S rDNA) in numerous M. genitalium populations. A second-line antibiotic, the fluoroquinolone moxifloxacin, was thought to be a reliable alternative when azithromycin failed, but recent studies have identified mutations in the genes, parC and gyrA, that may confer fluoroquinolone resistance.The aim of this study was to determine the prevalence of antibiotic resistance in M. genitalium in Sydney, Australia, by detection of relevant mutations in 23S rDNA, parC and gyrA. M. genitalium-positive DNA extracts of specimens, collected from patients attending sexual health clinics in Sydney, were tested by PCR amplification and DNA sequence alignment. The 186 specimens tested included 143 initial patient specimens, and 43 second, or subsequent, specimens from 24 patients. We identified known macrolide resistance-associated mutations in 23S rDNA of 43%, and mutations potentially associated with fluoroquinolone resistance in parC or gyrA sequences of 15%, of initial patient samples. These findings support anecdotal clinical reports of azithromycin and moxifloxacin treatment failures in Sydney. Our results indicated that further surveillance is needed and testing and treatment protocols for M. genitalium infections may need to be reviewed.
  Journal of clinical microbiology 05/2013;
• Article: Identification of blaOXA-51-like, blaOXA-58, blaDIM-1 and blaVIM Carbapenemase Genes in Hospital Enterobacteriaceae Isolates from Sierra Leone

  Tomasz A. Leski, Umaru Bangura, David H. Jimmy, Rashid Ansumana, Stephen E. Lizewski, Robert W. Li, David A. Stenger, Chris R. Taitt, Gary J. Vora
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  ABSTRACT: We describe the results of a molecular epidemiological survey of 15 carbapenemase-encoding genes from a recent collection of clinical isolates from Mercy Hospital in Bo, Sierra Leone. The most salient findings revealed that (i) 60% of the isolates harbored multiple carbapenemase genes, (ii) the blaDIM-1 gene that has only been reported in The Netherlands is also circulating in this environment and (iii) blaOXA-51-like and blaOXA-58 genes, which were thought to reside exclusively in Acinetobacter species, can also be found in members of the Enterobacteriaceae.
  Journal of clinical microbiology 05/2013;