JOURNAL OF CLINICAL MICROBIOLOGY

JOURNAL OF CLINICAL MICROBIOLOGY Volume 47 April 2009 No. 4 GUEST COMMENTARY Sequence-Based Identification of Aspergillus, Fusarium, and Mucorales Species in the Clinical Mycology Laboratory: Where Are We and Where Should We Go from Here? S. A. Balajee, A. M. Borman, M. E. Brandt, J. Cano, M. CuencaEstrella, E. Dannaoui, J. Guarro, G. Haase, C. C. Kibbler, W. Meyer, K. O’Donnell, C. A. Petti, J. L. Rodriguez-Tudela, D. Sutton, A. Velegraki, and B. L. Wickes 877–884 BACTERIOLOGY Comparison of the Roll Plate Method to the Sonication Method To Diagnose Catheter Colonization and Bacteremia in Patients with Long-Term Tunnelled Catheters: a Randomized Prospective Study Distribution of Genes Encoding MSCRAMMs and Pili in Clinical and Natural Populations of Enterococcus faecium Nucleic Acid Amplification Tests for Diagnosis of Neisseria gonorrhoeae Oropharyngeal Infections Lennert Slobbe, Abdelilah el Barzouhi, Eric Boersma, and Bart J. A. Rijnders Jouko Sillanpa¨, Vittal P. Prakash, ¨a Sreedhar R. Nallapareddy, and Barbara E. Murray Laura H. Bachmann, Robert E. Johnson, Hong Cheng, Lauri E. Markowitz, John R. Papp, and Edward W. Hook III Mette Kusk Bøving, Lisbeth Nørum Pedersen, and Jens Kjølseth Møller S. Degrange, C. Cazanave, A. ´ Charron, H. Renaudin, C. Bebear, ´ ´ and C. M. Bebear ´ ´ Xiaohui Chen Nielsen, Ulrik Stenz Justesen, Rimtas Dargis, Michael Kemp, and Jens Jørgen Christensen Sidsel Bocher, Birgitte Tønning, ¨ Robert L. Skov, and Jørgen Prag Kathleen R. Jones, Young Min Joo, Sungil Jang, Yun-Jung Yoo, Hak Sung Lee, In-Sik Chung, Cara H. Olsen, Jeannette M. Whitmire, D. Scott Merrell, and Jeong-Heon Cha Azita Leavitt, Inna Chmelnitsky, Raul Colodner, Itzhak Ofek, Yehuda Carmeli, and Shiri NavonVenezia Christophe Ginevra, Marie Lopez, Francoise Forey, Monique Reyrolle, ¸ Helene Meugnier, Francois ¸ Vandenesch, Jerome Etienne, Sophie Jarraud, and Maelle ¨ Molmeret Rita M. Gander, Linda Byrd, Michael DeCrescenzo, Shaina Hirany, Michelle Bowen, and Judy Baughman 885–888 896–901 902–907 Eight-Plex PCR and Liquid-Array Detection of Bacterial and Viral Pathogens in Cerebrospinal Fluid from Patients with Suspected Meningitis Development of Multiple-Locus Variable-Number TandemRepeat Analysis for Molecular Typing of Mycoplasma pneumoniae Identification of Clinically Relevant Nonhemolytic Streptococci on the Basis of Sequence Analysis of 16S-23S Intergenic Spacer Region and Partial gdh Gene Staphylococcus lugdunensis, a Common Cause of Skin and Soft Tissue Infections in the Community Polymorphism in the CagA EPIYA Motif Impacts Development of Gastric Cancer 908–913 914–923 932–939 946–950 959–968 Ertapenem Resistance among Extended-Spectrum- Lactamase-Producing Klebsiella pneumoniae Isolates 969–974 Evaluation of a Nested-PCR-Derived Sequence-Based Typing Method Applied Directly to Respiratory Samples from Patients with Legionnaires’ Disease 981–987 Impact of Blood Cultures Drawn by Phlebotomy on Contamination Rates and Health Care Costs in a Hospital Emergency Department 1021–1024 Continued on following page Continued from preceding page Diagnosis of Streptococcus pneumoniae Infections in Adults with Bacteremia and Community-Acquired Pneumonia: Clinical Comparison of Pneumococcal PCR and Urinary Antigen Detection Michael D. Smith, Carmen L. Sheppard, Angela Hogan, Timothy G. Harrison, David A. B. Dance, Petra Derrington, and Robert C. George on behalf of the South West Pneumococcus Study Group Svea Sachse, Eberhard Straube, Marc Lehmann, Michael Bauer, Stefan Russwurm, and KarlHermann Schmidt Maitry S. Mehta, Suzanne M. Paule, Richard B. Thomson, Karen L. Kaul, and Lance R. Peterson S. Chatterjee, K. Ghosh, A. Raychoudhuri, G. Chowdhury, M. K. Bhattacharya, A. K. Mukhopadhyay, T. Ramamurthy, S. K. Bhattacharya, Karl E. Klose, and R. K. Nandy Paul P. Bourbeau and Brandi Lynn Swartz Ting-ting Qu, Jun-li Zhang, Jie Wang, Jing Tao, Yun-song Yu, Yagang Chen, Jian-ying Zhou, and Lan-juan Li Chien-Shun Chiou, Haruo Watanabe, You-Wun Wang, WanLing Wang, Jun Terajima, Kwai-Lin Thong, Dac Cam Phung, and Sheng Kai Tung Elizabeth Gladys Aarag Fredheim, Claus Klingenberg, Holger Rohde, Stephanie Frankenberger, Peter Gaustad, Trond Flægstad, and Johanna Ericson Sollid Tae Kyung Kim, Susan M. Thomas, Mengfei Ho, Shobha Sharma, Claudia I. Reich, Jeremy A. Frank, Kathleen M. Yeater, Diana R. Biggs, Noriko Nakamura, Rebecca Stumpf, Steven R. Leigh, Richard I. Tapping, Steven R. Blanke, James M. Slauch, H. Rex Gaskins, Jon S. Weisbaum, Gary J. Olsen, Lois L. Hoyer, and Brenda A. Wilson Richard L. Zuerner and David P. Alt Claudia Rodas, Volga Iniguez, Firdausi Qadri, Gudrun Wiklund, Ann-Mari Svennerholm, and Åsa Sjoling ¨ Rafał Gierczynski, Jolanta Szych, ´ Waldemar Rastawicki, Sebastian Wardak, and Marek Jagielski 1046–1049 Truncated Human Cytidylate-Phosphate-DeoxyguanylateBinding Protein for Improved Nucleic Acid Amplification Technique-Based Detection of Bacterial Species in Human Samples Identification of Staphylococcus Species Directly from Positive Blood Culture Broth by Use of Molecular and Conventional Methods Incidence, Virulence Factors, and Clonality among Clinical Strains of Non-O1, Non-O139 Vibrio cholerae Isolates from Hospitalized Diarrheal Patients in Kolkata, India 1050–1057 1082–1086 1087–1095 First Evaluation of the WASP, a New Automated Microbiology Plating Instrument Evaluation of Phenotypic Tests for Detection of Metallo- Lactamase-Producing Pseudomonas aeruginosa Strains in China Utility of Multilocus Variable-Number Tandem-Repeat Analysis as a Molecular Tool for Phylogenetic Analysis of Shigella sonnei 1101–1106 1136–1142 1149–1154 Biofilm Formation by Staphylococcus haemolyticus 1172–1180 Heterogeneity of Vaginal Microbial Communities within Individuals 1181–1189 Variable Nucleotide Tandem-Repeat Analysis Revealing a Unique Group of Leptospira interrogans Serovar Pomona Isolates Associated with California Sea Lions Development of Multiplex PCR Assays for Detection of Enterotoxigenic Escherichia coli Colonization Factors and Toxins Molecular Characterization of Human Clinical Isolates of Yersinia enterocolitica Bioserotype 1B/O8 in Poland: Emergence and Dissemination of Three Highly Related Clones 1202–1205 1218–1220 1225–1228 Continued on following page Continued from preceding page Predicting Clearance of Colonization with VancomycinResistant Enterococci and Methicillin-Resistant Staphylococcus aureus by Use of Weekly Surveillance Cultures Charmaine M. Huckabee, W. Charles Huskins, and Patrick R. Murray 1229–1230 MYCOBACTERIOLOGY AND AEROBIC ACTINOMYCETES Sensitivity of PCR Targeting Mycobacterium ulcerans by Use of Fine-Needle Aspirates for Diagnosis of Buruli Ulcer R. O. Phillips, F. S. Sarfo, F. OseiSarpong, A. Boateng, I. Tetteh, A. Lartey, E. Adentwe, W. Opare, K. B. Asiedu, and M. WansbroughJones Bouke C. de Jong, Martin Antonio, Timothy Awine, Kunle Ogungbemi, Ype P. de Jong, Sebastien Gagneux, Kathryn DeRiemer, Thierry Zozio, Nalin Rastogi, Martien Borgdorff, Philip C. Hill, and Richard A. Adegbola Nick Mackenzie, David C. Alexander, Christine Y. Turenne, Marcel A. Behr, and Jeroen M. De Buck Hiyam H. El-Hajj, Salvatore A. E. Marras, Sanjay Tyagi, Elena Shashkina, Mini Kamboj, Timothy E. Kiehn, Michael S. Glickman, Fred Russell Kramer, and David Alland Cindy Hendry, Kim Dionne, Annie Hedgepeth, Karen Carroll, and Nicole Parrish 924–926 Use of Spoligotyping and Large Sequence Polymorphisms To Study the Population Structure of the Mycobacterium tuberculosis Complex in a Cohort Study of Consecutive Smear-Positive Tuberculosis Cases in The Gambia 994–1001 Genomic Comparison of PE and PPE Genes in the Mycobacterium avium Complex 1002–1011 Use of Sloppy Molecular Beacon Probes for Identification of Mycobacterial Species 1190–1198 Evaluation of a Rapid Fluorescent Staining Method for Detection of Mycobacteria in Clinical Specimens 1206–1208 MYCOLOGY Species-Specific Identification of a Wide Range of Clinically Relevant Fungal Pathogens by Use of Luminex xMAP Technology Bloodstream Infections Due to Trichosporon spp.: Species Distribution, Trichosporon asahii Genotypes Determined on the Basis of Ribosomal DNA Intergenic Spacer 1 Sequencing, and Antifungal Susceptibility Testing Development and Validation of a Microsphere-Based Luminex Assay for Rapid Identification of Clinically Relevant Aspergilli Identification of Candida nivariensis and Candida bracarensis in a Large Global Collection of Candida glabrata Isolates: Comparison to the Literature C. Landlinger, S. Preuner, B. Willinger, B. Haberpursch, Z. Racil, J. Mayer, and T. Lion Thomas C. Chagas-Neto, Guilherme M. Chaves, Analy S. A. Melo, and Arnaldo L. Colombo Kizee A. Etienne, Rui Kano, and S. Arunmozhi Balajee Shawn R. Lockhart, Shawn A. Messer, Michael Gherna, Justin A. Bishop, William G. Merz, Michael A. Pfaller, and Daniel J. Diekema 1063–1073 1074–1081 1096–1100 1216–1217 PARASITOLOGY Multiplexed Real-Time PCR Assay for Discrimination of Plasmodium Species with Improved Sensitivity for Mixed Infections Sandra E. Shokoples, Momar Ndao, Kinga Kowalewska-Grochowska, and Stephanie K. Yanow 975–980 Continued on following page Continued from preceding page VIROLOGY Comparison of the Abbott RealTime Human Immunodeficiency Virus Type 1 (HIV-1) Assay to the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test: Workflow, Reliability, and Direct Costs Highly Sensitive Detection of Dengue Virus Nucleic Acid in Samples from Clinically Ill Patients Cari R. Sloma, Jeffrey J. Germer, Tara M. Gerads, Jayawant N. Mandrekar, P. Shawn Mitchell, and Joseph D. C. Yao Jorge L. Munoz-Jordan, Cynthia S. ˜ ´ Collins, Edgardo Vergne, Gilberto A. Santiago, Lyle Petersen, Wellington Sun, and Jeffrey M. Linnen Baochuan Lin, Anthony P. Malanoski, Zheng Wang, Kate M. Blaney, Nina C. Long, Carolyn E. Meador, David Metzgar, Christopher A. Myers, Samuel L. Yingst, Marshall R. Monteville, Magdi D. Saad, Joel M. Schnur, Clark Tibbetts, and David A. Stenger Roman Wolfel, Janusz T. Paweska, ¨ Nadine Petersen, Antoinette A. Grobbelaar, Patricia A. Leman, Roger Hewson, Marie-Claude Georges-Courbot, Anna Papa, Volker Heiser, Marcus Panning, Stephan Gunther, and Christian ¨ Drosten Carolina Garrido, Natalia Zahonero, Angelica Corral, Miguel ´ Arredondo, Vincent Soriano, and Carmen de Mendoza Aziza H. Kamel, Mohamed A. Ali, Hala G. El-Nady, Alexis de Rougemont, Pierre Pothier, and Gael Belliot ¨ Dean B. Everett, Kathy Baisley, John Changalucha, Andrew Vallely, Deborah Watson-Jones, Claire Cook, Louise Knight, David A. Ross, Kokugonza Mugeye, Sheena McCormack, Charles J. Lacey, Ute Jentsch, and Richard J. Hayes Marjorie Monleau, Celine ´ Montavon, Christian Laurent, Michel Segondy, Brigitte Montes, Eric Delaporte, Francois Boillot, ¸ and Martine Peeters Guillaume Besson and Mirdad Kazanji 889–895 927–931 Universal Detection and Identification of Avian Influenza Virus by Use of Resequencing Microarrays 988–993 Low-Density Macroarray for Rapid Detection and Identification of Crimean-Congo Hemorrhagic Fever Virus 1025–1030 Correlation between Human Immunodeficiency Virus Type 1 (HIV-1) RNA Measurements Obtained with Dried Blood Spots and Those Obtained with Plasma by Use of Nuclisens EasyQ HIV-1 and Abbott RealTime HIV Load Tests Predominance and Circulation of Enteric Viruses in the Region of Greater Cairo, Egypt 1031–1036 1037–1045 Suitability of Simple Human Immunodeficiency Virus Rapid Tests in Clinical Trials in Community-Based Clinic Settings 1058–1062 Evaluation of Different RNA Extraction Methods and Storage Conditions of Dried Plasma or Blood Spots for Human Immunodeficiency Virus Type 1 RNA Quantification and PCR Amplification for Drug Resistance Testing One-Step, Multiplex, Real-Time PCR Assay with Molecular Beacon Probes for Simultaneous Detection, Differentiation, and Quantification of Human T-Cell Leukemia Virus Types 1, 2, and 3 Using a Field Quantitative Real-Time PCR Test To Rapidly Identify Highly Viremic Rift Valley Fever Cases 1107–1118 1129–1135 M. Kariuki Njenga, Janusz Paweska, Rose Wanjala, Carol Y. Rao, Matthew Weiner, Victor Omballa, Elizabeth T. Luman, David Mutonga, Shanaaz Sharif, Marcus Panning, Christian Drosten, Daniel R. Feikin, and Robert F. Breiman 1166–1171 Continued on following page Continued from preceding page Nevirapine Resistance in Human Immunodeficiency Virus Type 1-Positive Infants Determined Using Dried Blood Spots Stored for Up to Six Years at Room Temperature Molecular Epidemiological Investigation of a Nosocomial Outbreak of Human Metapneumovirus Infection in a Pediatric Hemato-Oncology Patient Population Single-Point Mutations Causing More than 100-Fold Underestimation of Human Immunodeficiency Virus Type 1 (HIV-1) Load with the Cobas TaqMan HIV-1 Real-Time PCR Assay Julie A. E. Nelson, Amy M. Loftis, Deborah Kamwendo, Wafaie W. Fawzi, Taha E. Taha, Robert L. Goldenberg, and Susan A. Fiscus Sollip Kim, Heungsup Sung, Ho Joon Im, Soo-Jong Hong, and MiNa Kim Klaus Korn, Benedikt Weissbrich, Cornelia Henke-Gendo, Albert Heim, Christin Mariel Jauer, Ninon Taylor, and Josef Eberle 1209–1211 1221–1224 1238–1240 CLINICAL VETERINARY MICROBIOLOGY Identification of Spirochetes Associated with Contagious Ovine Digital Dermatitis G. Sayers, P. X. Marques, N. J. Evans, L. O’Grady, M. L. Doherty, S. D. Carter, and J. E. Nally 1199–1201 EPIDEMIOLOGY Presence and Molecular Epidemiology of Virulence Factors in Methicillin-Resistant Staphylococcus aureus Strains Colonizing and Infecting Soldiers Isolation, Antimicrobial Resistance, and Virulence Genes of Pasteurella multocida Strains from Swine in China Temporal Trends of Invasive Streptococcus pneumoniae Serotypes and Antimicrobial Resistance Patterns in Spain from 1979 to 2007 Major Mycobacterium tuberculosis Lineages Associate with Patient Country of Origin Michael W. Ellis, Matthew E. Griffith, James H. Jorgensen, Duane R. Hospenthal, Katrin Mende, and Jan E. Patterson Xibiao Tang, Zhanqin Zhao, Junyong Hu, Bin Wu, Xuwang Cai, Qigai He, and Huanchun Chen A. Fenoll, J. J. Granizo, L. Aguilar, M. J. Gimenez, L. Aragoneses´ Fenoll, G. Hanquet, J. Casal, and D. Tarrago ´ Michael B. Reed, Victoria K. Pichler, Fiona McIntosh, Alicia Mattia, Ashley Fallow, Speranza Masala, Pilar Domenech, Alice Zwerling, Louise Thibert, Dick Menzies, Kevin Schwartzman, and Marcel A. Behr Shannon D. Manning, A. Cody Springman, Erica Lehotzky, Maggi A. Lewis, Thomas S. Whittam, and H. Dele Davies Bogdan Luca-Harari, Jessica Darenberg, Shona Neal, Tuula Siljander, Lenka Strakova, Asha Tanna, Roberta Creti, Kim Ekelund, Maria Koliou, Panayotis T. Tassios, Mark van der Linden, Monica Straut, Jaana VuopioVarkila, Anne Bouvet, Androulla Efstratiou, Claes Schalen, Birgitta ´ Henriques-Normark, the StrepEURO Study Group, and Aftab Jasir Johann D. D. Pitout, Lorraine Campbell, Deirdre L. Church, Pauline W. Wang, David S. Guttman, and Daniel B. Gregson 940–945 951–958 1012–1020 1119–1128 Multilocus Sequence Types Associated with Neonatal Group B Streptococcal Sepsis and Meningitis in Canada 1143–1148 Clinical and Microbiological Characteristics of Severe Streptococcus pyogenes Disease in Europe 1155–1165 Using a Commercial DiversiLab Semiautomated Repetitive Sequence-Based PCR Typing Technique for Identification of Escherichia coli Clone ST131 Producing CTX-M-15 1212–1215 Continued on following page Continued from preceding page Prevalence of Community-Associated Methicillin-Resistant Staphylococcus aureus in Patients with Cystic Fibrosis Jennifer S. Goodrich, Tameaka N. Sutton-Shields, Alan Kerr, Joel P. Wedd, Melissa B. Miller, and Peter H. Gilligan Brigitte Lamy, Angeli Kodjo, the colBVH Study Group, and Frederic ´ ´ Laurent 1231–1233 Prospective Nationwide Study of Aeromonas Infections in France 1234–1237 CASE REPORTS Human Bocavirus in an Immunocompromised Child Presenting with Severe Diarrhea Jutte J. C. de Vries, Robbert G. M. Bredius, Patrick F. van Rheenen, Frans J. W. Smiers, Elisabeth H. Scholvinck, Ann C. T. M. Vossen, ¨ Eric C. J. Claas, and Hubert G. M. Niesters Zia U. Khan, Suhail Ahmad, Arnost Brazda, and Rachel Chandy S. Sunder, P. Lanotte, S. Godreuil, C. Martin, M. L. Boschiroli, and J. M. Besnier Y. N’Guyen, L. Andreoletti, M. Patey, C. Lecoq-Lafon, P. Cornillet, A. Leon, R. Jaussaud, C. Fieschi, ´ and C. Strady Kenneth L. Muldrew and Stephen C. Edberg Hila Elinav, Uzi Izhar, Shmuel Benenson, Dan Admon, Carlos Hidalgo-Grass, Itzhack Polacheck, and Maya Korem S. Rajeev, D. A. Sutton, B. L. Wickes, D. L. Miller, D. Giri, M. Van Meter, E. H. Thompson, M. G. Rinaldi, A. M. Romanelli, J. F. Cano, and J. Guarro J.-M. Dot, A. Debourgogne, J. Champigneulle, Y. Salles, M. Brizion, J. M. Puyhardy, J. Collomb, F. Plenat, and M. Machouart ´ 1241–1243 Mucor circinelloides as a Cause of Invasive Maxillofacial Zygomycosis: an Emerging Dimorphic Pathogen with Reduced Susceptibility to Posaconazole Human-to-Human Transmission of Tuberculosis Caused by Mycobacterium bovis in Immunocompetent Patients Fatal Epstein-Barr Virus Primo Infection in a 25-Year-Old Man Treated with Azathioprine for Crohn’s Disease 1244–1248 1249–1251 1252–1254 Growth of Adenocarcinoma on Routine Microbiological Media Inoculated with Fluid from a Pleural Effusion in an 82-Year-Old Female Invasive Scytalidium dimidiatum Infection in an Immunocompetent Adult 1255–1258 1259–1263 Isolation and Characterization of a New Fungal Species, Chrysosporium ophiodiicola, from a Mycotic Granuloma of a Black Rat Snake (Elaphe obsoleta obsoleta) 1264–1268 Molecular Diagnosis of Disseminated Adiaspiromycosis Due to Emmonsia crescens 1269–1273 LETTERS TO THE EDITOR Molecular Diagnosis of Polymicrobial Sepsis Nicasio Mancini, Silvia Carletti, Nadia Ghidoli, Paola Cichero, Cristina M. Ossi, Rossella Ieri, Elena Poli, Roberto Burioni, and Massimo Clementi Frederic Barbut, Mylena Braun, ´ ´ Beatrice Burghoffer, Valerie ´ ´ Lalande, and Catherine Eckert Letter: Carita Savolainen-Kopra, Soile Blomqvist, Teemu Smura, Merja Roivainen, Tapani Hovi. Reply: David Kiang, Ishmeet Kalra, Shigeo Yagi, Janice K. Louie, Homer Boushey, John Boothby, and David P. Schnurr 1274–1275 Rapid Detection of Toxigenic Strains of Clostridium difficile in Diarrheal Stools by Real-Time PCR 5 Noncoding Region Alone Does Not Unequivocally Determine Genetic Type of Human Rhinovirus Strains 1276–1277 1278–1280 Continued on following page Continued from preceding page Identification of Acinetobacter Genomic Species 13TU by Sequence Analysis of the 16S-23S rRNA Gene Spacer Region Letter: Raffaele Zarrilli, Maria Giannouli, Anna Di Popolo, Federica Tomasone, Yiu-Wai Chu. Reply: Mario Vaneechoutte, Lenie Dijkshoorn, and Tsung Chain Chang* 1281–1282 ERRATA Predominance of Mycobacterium tuberculosis EAI and Beijing Lineages in Yangon, Myanmar Evaluation of an Immunochromatographic Assay Kit for Rapid Identification of Mycobacterium tuberculosis Complex in Clinical Isolates Sabai Phyu, Ruth Stavrum, Thandar Lwin, Øyvind S. Svendsen, Ti Ti, and Harleen M. S. Grewal Mi Young Park, Young Jin Kim, Sang Hyun Hwang, Hyoung Hoi Kim, Eun Yup Lee, Seok Hoon Jeong, and Chulhun L. Chang 1283 1284 AUTHOR’S CORRECTION Novel Light-Upon-Extension Real-Time PCR Assays for Detection and Quantification of Genogroup I and II Noroviruses in Clinical Specimens Johan Nordgren, Filemon Bucardo, ´ Olaf Dienus, Lennart Svensson, and Per-Eric Lindgren 1285