Description

The Journal of Clinical Microbiology publishes the most current research on the microbiological aspects of human and animal infections and infestations, with emphasis on their etiologic agents, diagnosis, and epidemiology.

Publisher details

American Society for Microbiology

Publications in this journal

• A matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based method for discrimination between molecular types of Cryptococcus neoformans and Cryptococcus gattii

  Authors: Brunella Posteraro, Antonietta Vella, Massimo Cogliati, Elena De Carolis, Ada Florio, Patrizia Posteraro, Maurizio Sanguinetti, Anna Maria Tortorano

  Journal of Clinical Microbiology.

• A new loop-mediated isothermal amplification method for rapid, simple, and sensitive detection of Leptospira spp. in urine

  Authors: Nobuo Koizumi, Chie Nakajima, Tunehito Harunari, Tsutomu Tanikawa, Toshihiro Tokiwa, Eriko Uchimura, Tokujiro Furuya, Claro Mingala, Marvin Villanueva, Makoto Ohnishi, Yasuhiko Suzuki

  Journal of Clinical Microbiology.

  We developed a new loop-mediated isothermal amplification (LAMP) method to detect rrs, a 16S rRNA gene, of pathogenic Leptospira spp. in urine. The method enables detection of two leptospiral cellsWe developed a new loop-mediated isothermal amplification (LAMP) method to detect rrs, a 16S rRNA gene, of pathogenic Leptospira spp. in urine. The method enables detection of two leptospiral cells per reaction following boiling of urine specimens. The sensitivity of this method is higher than that of culture or of flaB-nested PCR.

• Use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for caspofungin susceptibility testing of Candida and Aspergillus species

  Authors: Elena De Carolis, Antonietta Vella, Ada R. Florio, Patrizia Posteraro, David S. Perlin, Maurizio Sanguinetti, and Brunella Posteraro

  Journal of Clinical Microbiology.

  MALDI-TOF MS was evaluated for testing susceptibility to caspofungin of wild-type and fks mutant isolates of Candida and Aspergillus. Complete essential agreement was observed with the CLSI referenceMALDI-TOF MS was evaluated for testing susceptibility to caspofungin of wild-type and fks mutant isolates of Candida and Aspergillus. Complete essential agreement was observed with the CLSI reference method, with categorical agreement for 94.1% of the Candida isolates tested. Thus, MALDI-TOF MS is a reliable and accurate method to detect fungal isolates with reduced caspofungin susceptibility.

• Use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for caspofungin susceptibility testing of Candida and Aspergillus species.

  Authors: De Carolis E, Vella A, Florio AR, Posteraro P, Perlin DS, Sanguinetti M

  Journal of Clinical Microbiology.

• Streptococcus pseudopneumoniae identification by pherotype: a method to assist the understanding of a potentially emerging or overlooked pathogen

  Authors: Leung M, Ling C, Ciesielczuk H, Lockwood J, Thurston S, Charalambous B.M, Gillespie S.H

  Journal of Clinical Microbiology.

  The recent identification of Streptococcus pseudopneumoniae (pseudopneumococcus) has complicated classification schemes within members of the "mitis" streptococcal group. Accurate differentiation ofThe recent identification of Streptococcus pseudopneumoniae (pseudopneumococcus) has complicated classification schemes within members of the "mitis" streptococcal group. Accurate differentiation of this species is necessary for understanding its disease potential and identification in clinical settings. This work described the use of competence-stimulatory peptide ComC sequence for identification of S. pseudopneumoniae. ComC sequences from clinical sources were determined for 17 strains of S. pseudopneumoniae, S. pneumoniae, and S. oralis. An aditional 58 ComC sequences from a range of sources were included to understand the diversity and suitability of this protein as a diagnostic marker for species identification. We identified three pherotypes for this species delineated CSP6.1 (10/14, 79%), CSP6.3 (3/14, 21%) and SK674 (1/14, 7%). Pseudopneumococcal ComC sequences formed a discrete cluster within those of other oral streptococci. This suggests that comC sequence could be used to identify S. Pseudopneumoniae, thus simplifying the study of the pathogenic potential of this organism. To avoid confusion between pneumococcal and pseudopneumococcal pherotypes, we have renamed the competence pherotype CSP6.1 formerly reported as an "atypical" pneumococcus to CSPps1 to reflect its occurrence in S. pseudopneumoniae.

• A matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based method for discrimination between molecular types of Cryptococcus neoformans and Cryptococcus gattii

  Authors: Brunella Posteraro, Antonietta Vella, Massimo Cogliati, Elena De Carolis, Ada Florio, Patrizia Posteraro, Maurizio Sanguinetti, Anna Maria Tortorano

  Journal of Clinical Microbiology.

• A Highly Specific Protease-Based Approach for the Detection of Porphyromonas gingivalis in the Diagnosis of Periodontitis

  Authors: Wendy Kaman, Fabiano Galassi, Hans de Soet, Sergio Bizzarro, Bruno Loos, Enno Veerman, Alex van Belkum, John Hays, Floris Bikker

  Journal of Clinical Microbiology. Paper #JCM05313-11R2.

• Major Mycobacterium tuberculosis Lineages Associate with Patient Country of Origin

  Authors: Michael B Reed, Victoria K Pichler, Fiona Mcintosh, Alicia Mattia, Ashley Fallow, Speranza Masala, Pilar Domenech, Alice Zwerling, Louise Thibert, Dick Menzies, Kevin Schwartzman, Marcel A Behr

  Journal of Clinical Microbiology. 47(103):1119--11282869.

  Over recent years, there has been an increasing acknowledgment of the diversity that exists among Myco-bacterium tuberculosis clinical isolates. To facilitate comparative studies aimed at decipheringOver recent years, there has been an increasing acknowledgment of the diversity that exists among Myco-bacterium tuberculosis clinical isolates. To facilitate comparative studies aimed at deciphering the relevance of this diversity to human disease, an unambiguous and easily interpretable method of strain classification is required. Presently, the most effective means of assigning isolates into a series of unambiguous lineages is the method of Gagneux et al. that involves the PCR-based detection of large sequence polymorphisms (LSPs). In this manner, isolates are classified into six major lineages, the majority of which display a high degree of geographic restriction. Here we describe an independent replicate of the Gagneux study carried out on 798 isolates collected over a 6-year period from mostly foreign-born patients resident on the island of Montreal, Canada. The original trends in terms of bacterial genotype and patient ethnicity are remarkably conserved within this Montreal cohort, even though the patient distributions between the two populations are quite distinct. In parallel with the LSP analysis, we also demonstrate that "clustered" tuberculosis (TB) cases defined through restriction fragment length poly-morphism (RFLP) analysis (for isolates with >6 IS6110 copies) or RFLP in combination with spoligotyping (for isolates with <6 IS6110 copies) do not stray across the LSP-defined lineage boundaries. However, our data also demonstrate the poor discriminatory power of either RFLP or spoligotyping alone for these low-IS6110-copy-number isolates. We believe that this independent validation of the LSP method should encourage researchers to adopt this system in investigations aimed at elucidating the role of strain variation in TB. Infection with Mycobacterium tuberculosis, the bacillus re-sponsible for tuberculosis (TB), still results in almost 2 million global deaths each year despite the availability of effective chemotherapy and a partially effective vaccine (ba-cillus Calmette-Guérin [Mycobacterium bovis BCG]) for well over half a century (43). Even though there have been real advances in our level of understanding of M. tuberculosis met-abolic pathways and in the identification of potential virulence-associated molecules since the advent of the "postgenomic era" (8), significant improvements with respect to treatment, diagnosis, and prevention of TB still remain elusive. Recent descriptions of variably expressed virulence factors and disease outcomes that are associated with particular lineages of M. tuberculosis further emphasize the layers of complexity that need to be overcome in our efforts to combat this devastating disease (6, 25, 31, 32, 38). While the fact that TB phenotypic diversity exists is no longer in dispute, there is heightened interest in epidemiolog-ical circles in establishing the relevance of this diversity to human disease. Of particular note are the recent publications

• Emergence of KPC-producing Pseudomonas aeruginosa in Trinidad and Tobago

  Authors: Akpaka PE, Swanston WH, Ihemere HN, Correa A, Torres JA, Tafur JD, Montealegre MC, Quinn JP, Villegas MV

  Journal of Clinical Microbiology.

• Evaluation of methods for rapid detection of resistance to isoniazid and rifampicin in Mycobacterium tuberculosis isolates collected in the Caribbean.

  Authors: Akpaka PE, Baboolal S, Clarke D, Francis L, Rastogi N

  Journal of Clinical Microbiology. 46(10):3426-3428.

• New Vitek 2 colorimetric GN Card for identification of gram-negative nonfermentative bacilli.

  Authors: David H Pincus

  Journal of clinical microbiology. 45(12):4094; author reply 4094-5.

• Detection of high-risk papillomavirus DNA with commercial invader-technology-based analyte-specific reagents following automated extraction of DNA from cervical brushings in ThinPrep media.

  Authors: Ted E Schutzbank, Charlene Jarvis, Nicole Kahmann, Katherine Lopez, Marlea Weimer, Aleta Yount

  Journal of clinical microbiology. 45(12):4067-9.

  We compared the performances of the Third Wave Technology Invader method and the Digene Hybrid Capture 2 assay to detect high-risk human papillomaviruses in 87 cervical brushing specimens submittedWe compared the performances of the Third Wave Technology Invader method and the Digene Hybrid Capture 2 assay to detect high-risk human papillomaviruses in 87 cervical brushing specimens submitted in Cytyc ThinPrep media. Two different methods for the extraction of DNA from squamous epithelial cells were also evaluated.

• Evaluation of the inoculation procedure using a 0.25 McFarland standard for the BD Phoenix automated microbiology system.

  Authors: J-L Donay, P Fernandes, P H Lagrange, J L Herrmann

  Journal of clinical microbiology. 45(12):4088-9.

• Rapid, standardized method for determination of Mycobacterium tuberculosis drug susceptibility by use of mycolic acid analysis.

  Authors: Nicole Parrish, Gerard Osterhout, Kim Dionne, Amy Sweeney, Nicole Kwiatkowski, Karen Carroll, Kenneth C Jost, James Dick

  Journal of clinical microbiology. 45(12):3915-20.

  Multidrug-resistant (MDR) Mycobacterium tuberculosis and extrensively drug-resistant (XDR) M. tuberculosis are emerging public health threats whose threats are compounded by the fact that currentMultidrug-resistant (MDR) Mycobacterium tuberculosis and extrensively drug-resistant (XDR) M. tuberculosis are emerging public health threats whose threats are compounded by the fact that current techniques for testing the susceptibility of M. tuberculosis require several days to weeks to complete. We investigated the use of high-performance liquid chromatography (HPLC)-based quantitation of mycolic acids as a means of rapidly determining drug resistance and susceptibility in M. tuberculosis. Standard susceptibility testing and determination of the MICs of drug-susceptible (n = 26) and drug-resistant M. tuberculosis strains, including MDR M. tuberculosis strains (n = 34), were performed by using the Bactec radiometric growth system as the reference method. The HPLC-based susceptibilities of the current first-line drugs, isoniazid (INH), rifampin (RIF), ethambutol (EMB), and pyrazinamide (PZA), were determined. The vials were incubated for 72 h, and aliquots were removed for HPLC analysis by using the Sherlock mycobacterial identification system. HPLC quantitation of total mycolic acid peaks (TMAPs) was performed with treated and untreated cultures. At 72 h, the levels of agreement of the HPLC method with the reference method were 99.5% for INH, EMB, and PZA and 98.7% for RIF. The inter- and intra-assay reproducibilities varied by drug, with an average precision of 13.4%. In summary, quantitation of TMAPs is a rapid, sensitive, and accurate method for antibiotic susceptibility testing of all first-line drugs currently used against M. tuberculosis and offers the potential of providing susceptibility testing results within hours, rather than days or weeks, for clinical M. tuberculosis isolates.

• Mycobacterium avium subspecies paratuberculosis infection in cases of irritable bowel syndrome and comparison with Crohn's disease and Johne's disease: common neural and immune pathogenicities.

  Authors: Antonio M Scanu, Tim J Bull, Sara Cannas, Jeremy D Sanderson, Leonardo A Sechi, Giuseppe Dettori, Stefania Zanetti, John Hermon-Taylor

  Journal of clinical microbiology. 45(12):3883-90.

  Mycobacterium avium subsp. paratuberculosis causes Johne's disease, a systemic infection and chronic inflammation of the intestine that affects many species, including primates. Infection isMycobacterium avium subsp. paratuberculosis causes Johne's disease, a systemic infection and chronic inflammation of the intestine that affects many species, including primates. Infection is widespread in livestock, and human populations are exposed. Johne's disease is associated with immune dysregulation, with involvement of the enteric nervous system overlapping with features of irritable bowel syndrome in humans. The present study was designed to look for an association between Mycobacterium avium subsp. paratuberculosis infection and irritable bowel syndrome. Mucosal biopsy specimens from the ileum and the ascending and descending colon were obtained from patients with irritable bowel syndrome attending the University of Sassari, Sassari, Sardinia, Italy. Crohn's disease and healthy control groups were also included. Mycobacterium avium subsp. paratuberculosis was detected by IS900 PCR with amplicon sequencing. Data on the potential risk factors for human exposure to these pathogens and on isolates from Sardinian dairy sheep were also obtained. Mycobacterium avium subsp. paratuberculosis was detected in 15 of 20 (75%) patients with irritable bowel syndrome, 3 of 20 (15%) healthy controls, and 20 of 23 (87%) people with Crohn's disease (P = 0.0003 for irritable bowel syndrome patients versus healthy controls and P = 0.0000 for Crohn's disease patients versus healthy controls). One subject in each group had a conserved single-nucleotide polymorphism at position 247 of IS900 that was also found in isolates from seven of eight dairy sheep. There was a significant association (P = 0.0018) between Mycobacterium avium subsp. paratuberculosis infection and the consumption of hand-made cheese. Mycobacterium avium subsp. paratuberculosis is a candidate pathogen in the causation of a proportion of cases of irritable bowel syndrome as well as in Crohn's disease.

• Molecular typing of a suspected cluster of Nocardia farcinica infections by use of randomly amplified polymorphic DNA, pulsed-field gel electrophoresis, and amplified fragment length polymorphism analyses.

  Authors: J S Kalpoe, K E Templeton, A M Horrevorts, H P Endtz, E J Kuijper, A T Bernards, C H W Klaassen

  Journal of clinical microbiology. 45(12):4048-50.

  Randomly amplified polymorphic DNA (RAPD), pulsed-field gelelectrophoresis (PFGE), and amplified fragment length polymorphism (AFLP) analyses were used to investigate a possible outbreak of NocardiaRandomly amplified polymorphic DNA (RAPD), pulsed-field gelelectrophoresis (PFGE), and amplified fragment length polymorphism (AFLP) analyses were used to investigate a possible outbreak of Nocardia farcinica. RAPD and PFGE analyses yielded irreproducible and unsatisfactory results, respectively. AFLP analysis seem to be a promising and welcome addition for molecular analysis of Nocardia isolates.

• Genotypic and phenotypic analysis of Enterobacter sakazakii strains from an outbreak resulting in fatalities in a neonatal intensive care unit in France.

  Authors: J Caubilla-Barron, E Hurrell, S Townsend, P Cheetham, C Loc-Carrillo, O Fayet, M F Prère, S J Forsythe

  Journal of clinical microbiology. 45(12):3979-85.

  In 1994, an outbreak of Enterobacter sakazakii infections occurred in a neonatal intensive care unit in France from 5 May to 11 July. During the outbreak, 13 neonates were infected with E. sakazakii,In 1994, an outbreak of Enterobacter sakazakii infections occurred in a neonatal intensive care unit in France from 5 May to 11 July. During the outbreak, 13 neonates were infected with E. sakazakii, resulting in 3 deaths. In addition, four symptomless neonates were colonized by E. sakazakii. The strains were subjected to 16S rRNA gene sequence analysis, genotyped using pulsed-field gel electrophoresis, and phenotyped for a range of enzyme activities. E. sakazakii was isolated from various anatomical sites, reconstituted formula, and an unopened can of powdered infant formula. A fourth neonate died from septic shock, attributed to E. sakazakii infection, during this period. However, 16S rRNA gene sequence analysis revealed that the organism was Enterobacter cloacae. There were three pulsotypes of E. sakazakii associated with infected neonates, and three neonates were infected by more than one genotype. One genotype matched isolates from unused prepared formula and unfinished formula. However, no pulsotypes matched the E. sakazakii strain recovered from an unopened can of powdered infant formula. One pulsotype was associated with the three fatal cases, and two of these isolates had extended-spectrum beta-lactamase activity. It is possible that E. sakazakii strains differ in their pathogenicities, as shown by the range of symptoms associated with each pulsotype.

• Isolation and characterization of a novel helicobacter species, "Helicobacter macacae," from rhesus monkeys with and without chronic idiopathic colitis.

  Authors: James G Fox, Samuel R Boutin, Laurence K Handt, Nancy S Taylor, Shilu Xu, Barry Rickman, Robert P Marini, Floyd E Dewhirst, Bruce J Paster, Sherri Motzel, Hilton J Klein

  Journal of clinical microbiology. 45(12):4061-3.

  Chronic idiopathic colitis is a common clinical entity in young captive rhesus monkeys. Eight isolates, cultured from five monkeys in colony 1 with endemic diarrhea and three from colony 2 withoutChronic idiopathic colitis is a common clinical entity in young captive rhesus monkeys. Eight isolates, cultured from five monkeys in colony 1 with endemic diarrhea and three from colony 2 without diarrhea, were grown under microaerobic conditions on selective agar and were classified by full 16S rRNA sequence, biochemical, and phenotypic analysis as a novel helicobacter, "Helicobacter macacae" (proposed name). All eight strains of H. macacae had 99.5% identical 16S rRNA sequences.

• Canine parvovirus types 2c and 2b circulating in North American dogs in 2006 and 2007.

  Authors: Sanjay Kapil, Emily Cooper, Cathy Lamm, Brandy Murray, Grant Rezabek, Larry Johnston, Gregory Campbell, Bill Johnson

  Journal of clinical microbiology. 45(12):4044-7.

  Parvovirus is the most common viral cause of diarrhea in young puppies. Based on the analysis of a partial VP2 sequence of 54 samples, canine parvovirus type 2c (CPV-2c) (n = 26), CPV-2b (n = 25),Parvovirus is the most common viral cause of diarrhea in young puppies. Based on the analysis of a partial VP2 sequence of 54 samples, canine parvovirus type 2c (CPV-2c) (n = 26), CPV-2b (n = 25), and CPV-2 (n = 3) were detected in the United States. The American CPV-2b isolates have unique codons (494 and 572) in VP2.

• Evaluation of a multiplexed PCR assay for detection of respiratory viral pathogens in a public health laboratory setting.

  Authors: David J Marshall, Erik Reisdorf, Gerda Harms, Edward Beaty, Michael J Moser, Wai-Ming Lee, James E Gern, Frederick S Nolte, Pete Shult, James R Prudent

  Journal of clinical microbiology. 45(12):3875-82.

  There are numerous viral and bacterial causes of respiratory disease. To enable rapid and sensitive detection of even the most prevalent causes, there is a need for more-simplified testing systemsThere are numerous viral and bacterial causes of respiratory disease. To enable rapid and sensitive detection of even the most prevalent causes, there is a need for more-simplified testing systems that enable researchers and clinicians to perform multiplexed molecular diagnostics quickly and easily. To this end, a new multiplexed molecular test called the MultiCode-PLx respiratory virus panel (PLx-RVP) was developed and then implemented in a public health laboratory setting. A total of 687 respiratory samples were analyzed for the presence of 17 viruses that commonly cause respiratory disease. As a comparator, the samples were also tested using a standard testing algorithm that included the use of a real-time influenza virus A and B reverse transcription-PCR test and routine viral culture identification. The standard testing algorithm identified 503 (73%) samples as positive and 184 as negative. Analyzing the same 687 samples, the PLx-RVP assay detected one or more targets in 528 (77%) samples and found 159 samples negative for all targets. There were 25 discordant results between the two systems; 14 samples were positive for viruses not routinely tested for by the Wisconsin State Laboratory of Hygiene, and 13 of these were confirmed by real-time PCR. When the results of the standard testing algorithm were considered "true positives," the PLx-RVP assay showed an overall sensitivity of 99% and an overall specificity of 87%. In total, the PLx-RVP assay detected an additional 40 viral infections, of which 11 were mixed infections.

• Bivalvular Bartonella henselae prosthetic valve endocarditis.

  Authors: Holenarasipur R Vikram, A Kirstin Bacani, Patrick A DeValeria, Scott A Cunningham, Franklin R Cockerill

  Journal of clinical microbiology. 45(12):4081-4.

  Prosthetic valve endocarditis is an uncommon manifestation of infection with Bartonella species. Herein, we report a case of Bartonella henselae endocarditis involving prosthetic mitral and aorticProsthetic valve endocarditis is an uncommon manifestation of infection with Bartonella species. Herein, we report a case of Bartonella henselae endocarditis involving prosthetic mitral and aortic valves. The patient had a favorable outcome with combined medical and surgical therapy. Concomitant crescentic glomerulonephritis led to an initial mistaken diagnosis of Wegener's granulomatosis.

• Trends in prescribing beta-lactam antibiotics for treatment of community-associated methicillin-resistant Staphylococcus aureus infections.

  Authors: Kalpana Gupta, Ann MacIntyre, Gary Vanasse, Louise-Marie Dembry

  Journal of clinical microbiology. 45(12):3930-4.

  Rates of prescribing of beta-lactam antibiotics as initial empirical therapy for patients with skin and soft tissue infections (SSTIs) caused by molecularly and epidemiologically characterizedRates of prescribing of beta-lactam antibiotics as initial empirical therapy for patients with skin and soft tissue infections (SSTIs) caused by molecularly and epidemiologically characterized community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) isolates were assessed over a 3-year period. A prospectively developed database was used to calculate the prevalence of CA-MRSA SSTIs from 2004 to 2006. Molecular characterization of the MRSA isolate and medical record review for assessment of initial antimicrobial therapy were performed on a subset of patients. Among 2,636 patients with S. aureus SSTIs, the prevalence of CA-MRSA was 9% in 2004, 16% in 2005, and 21% in 2006 (P < 0.0001, chi-square test for trend). Seventy-five percent of CA-MRSA isolates tested were of the USA 300 or 400 clone type. Ninety-two percent of CA-MRSA isolates tested were positive for Panton-Valentine leukocidin, of which 90% carried staphylococcal chromosomal cassette mec type IV. The rate of use of a beta-lactam antibiotic as initial empirical therapy for patients with CA-MRSA SSTIs was 86%, 77%, and 60% in 2004, 2005, and 2006, respectively (P = 0.04, chi-square test for trend). Thirty percent of beta-lactam-treated patients had a documented risk factor for CA-MRSA infection. The use of a beta-lactam antibiotic as initial empirical therapy for CA-MRSA SSTIs has decreased significantly over the past 3 years. However, even as the prevalence of CA-MRSA SSTIs approaches 25%, the majority of patients are still receiving inactive antimicrobial therapy. Further evaluation of the outcomes associated with discordant therapy for CA-MRSA SSTIs is needed.

• Microevolution of Helicobacter pylori type IV secretion systems in an ulcer disease patient over a ten-year period.

  Authors: Ayesha Alvi, S Manjulata Devi, Irshad Ahmed, M Abid Hussain, Mohammed Rizwan, Hérve Lamouliatte, Francis Mégraud, Niyaz Ahmed

  Journal of clinical microbiology. 45(12):4039-43.

  Helicobacter pylori cagA and vacA genotypes have been used for almost a decade as stable entities to link the severity of gastritis and ulcer disease. We describe here microevolution of the twoHelicobacter pylori cagA and vacA genotypes have been used for almost a decade as stable entities to link the severity of gastritis and ulcer disease. We describe here microevolution of the two genomic islands, cag pathogenicity island (cagPAI; 40 kb) and tfs3 (16 kb) from isolates obtained at inclusion (one subclone) and after a 10-year period (two subclones) from a duodenal ulcer patient. Our results indicate microevolution in cagA, cagE, and cag7 genes of the cagPAI and open reading frames G, P, and L in tfs3, which possibly leads to inactivation or pseudogenization of these genes. Interestingly, no significant reduction in the severity of gastroduodenal pathology was found. These results point to an obvious difficulty in correlating the continuously evolving virulence factors such as the cagPAI genes with disease characteristics that appear to remain stable.

• Changing antimicrobial susceptibility epidemiology of Helicobacter pylori strains in Japan between 2002 and 2005.

  Authors: Intetsu Kobayashi, Kazunari Murakami, Mototsugu Kato, Seiichi Kato, Takeshi Azuma, Shin'ichi Takahashi, Naomi Uemura, Tsutomu Katsuyama, Yoshihiro Fukuda, Ken Haruma, Masaru Nasu, Toshio Fujioka

  Journal of clinical microbiology. 45(12):4006-10.

  Surveillance of Helicobacter pylori antimicrobial susceptibility reflecting the general population in Japan is limited. The antimicrobial susceptibilities of 3,707 H. pylori strains isolated fromSurveillance of Helicobacter pylori antimicrobial susceptibility reflecting the general population in Japan is limited. The antimicrobial susceptibilities of 3,707 H. pylori strains isolated from gastric mucosa samples of previously untreated patients diagnosed with gastroduodenal diseases at 36 medical facilities located throughout Japan between October 2002 and September 2005 were evaluated. Using an agar dilution method for antimicrobial susceptibility testing of H. pylori, the MIC distributions and trends during the study period for clarithromycin, amoxicillin, and metronidazole were studied. While the MIC(50) and MIC(90) for clarithromycin did not change during the 3-year period, the MIC(80) showed a 128-fold increase. Furthermore, the rate of resistance increased yearly from 18.9% (2002 to 2003) to 21.1% (2003 to 2004) and 27.7% (2004 to 2005). With a resistance rate of 19.2% among males compared to 27.0% among females, a significant gender difference was observed (P < 0.0001). Our study shows that in Japan, there is an evolving trend towards increased resistance to clarithromycin with geographical and gender differences as well as between clinical disease conditions. No significant changes in resistance were observed for amoxicillin and metronidazole during the period. While the benefit of H. pylori antimicrobial susceptibility testing has been debated in Japan, current empirical regimens are not based on susceptibility data representative of the general population. The development of an effective H. pylori eradication regimen in Japan will require continued resistance surveillance as well as a better understanding of the epidemiology of resistance.

• Characterization of a new sensitive PCR assay for quantification of viral DNA isolated from patients with hepatitis B virus infections.

  Authors: Vincent Thibault, Christian Pichoud, Carolyn Mullen, James Rhoads, Jane B Smith, Alain Bitbol, Sven Thamm, Fabien Zoulim

  Journal of clinical microbiology. 45(12):3948-53.

  Sensitive and accurate quantification of hepatitis B virus (HBV) DNA is necessary for monitoring patients with chronic hepatitis receiving antiviral therapy in order to determine treatment responseSensitive and accurate quantification of hepatitis B virus (HBV) DNA is necessary for monitoring patients with chronic hepatitis receiving antiviral therapy in order to determine treatment response and to adapt therapy in case of inadequate virologic control. The development of quantitative PCR assays has been crucial in meeting these needs. The objective of this study was to compare the performance of a new real-time PCR assay (Abbott RealTime) for HBV DNA with that of three other commercial assays for the detection of HBV DNA. These were the Versant 3.0 branched-chain DNA assay, the Cobas Amplicor HBV Monitor test, and the Cobas AmpliPrep-Cobas TaqMan hepatitis B virus assay (CAP-CTM). HBV DNA was measured in blood samples taken from two cohorts of patients with chronic hepatitis. HBV DNA levels measured with the Abbott RealTime assay were highly correlated with those measured with the other three tests over their respective dynamic ranges (r, 0.88 to 0.96). The sensitivity (detection limit, 10 IU/ml) and dynamic range of the Abbott RealTime assay (10(1) to 10(9) IU/ml) was superior to that of the Versant assay. The RealTime assay recognized both HBV strains belonging to genotypes A to G and those bearing polymerase gene mutations equivalently. In conclusion, this study demonstrates the utility of the Abbott RealTime assay for monitoring HBV DNA levels in patients with chronic hepatitis B. Its sensitivity and wide dynamic range should allow optimal monitoring of antiviral therapy and timely treatment adaptation.

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