Journal of Clinical Microbiology: 53 (7)

July 1, 2015; Volume 53,Issue 7

Photo Quiz

Photo Quiz
Photo Quiz: Mysterious Objects in a Pleural Biopsy Sample from a Patient with Recurrent Pleural Empyema
Jürgen Held, Kai Gräber, Gerhard Leubner-Metzger, Tim Kunkel, Christian Theilacker, Stefanie Kramme, Annette Schmitt-Graeff
Photo Quiz
Answer to July 2015 Photo Quiz
Jürgen Held, Kai Gräber, Gerhard Leubner-Metzger, Tim Kunkel, Christian Theilacker, Stefanie Kramme, Annette Schmitt-Graeff

Commentary

Free

Other
Commentary: Assessing Airway Microbiota in Cystic Fibrosis: What More Should Be Done?
John J. LiPuma

Minireview

Minireview
Standardization of Nucleic Acid Tests for Clinical Measurements of Bacteria and Viruses
Jernej Pavšič, Alison S. Devonshire, Helen Parkes, Heinz Schimmel, Carole A. Foy, Maria Karczmarczyk, Ion Gutiérrez-Aguirre, Isobella Honeyborne, Jim F. Huggett, Timothy D. McHugh, Mojca Milavec, Heinz Zeichhardt, Jana Žel

Bacteriology

Bacteriology
Streptococcus pyogenes emm Types and Clusters during a 7-Year Period (2007 to 2013) in Pharyngeal and Nonpharyngeal Pediatric Isolates
F. Koutouzi, A. Tsakris, P. Chatzichristou, E. Koutouzis, G. L. Daikos, E. Kirikou, N. Petropoulou, V. Syriopoulou, A. Michos
Free

Bacteriology
Rapid Detection of Emerging Pathogens and Loss of Microbial Diversity Associated with Severe Lung Disease in Cystic Fibrosis
William G. Flight, Ann Smith, Christopher Paisey, Julian R. Marchesi, Matthew J. Bull, Phillip J. Norville, Ken J. Mutton, A. Kevin Webb, Rowland J. Bright-Thomas, Andrew M. Jones, Eshwar Mahenthiralingam
Bacteriology
Implementation of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry in Routine Clinical Laboratories Improves Identification of Coagulase-Negative Staphylococci and Reveals the Pathogenic Role of Staphylococcus lugdunensis
Xavier Argemi, Philippe Riegel, Thierry Lavigne, Nicolas Lefebvre, Nicolas Grandpré, Yves Hansmann, Benoit Jaulhac, Gilles Prévost, Frédéric Schramm
Bacteriology
Molecular Assay for Detection of Genetic Markers Associated with Decreased Susceptibility to Cephalosporins in Neisseria gonorrhoeae
S. W. Peterson, I. Martin, W. Demczuk, A. Bharat, L. Hoang, J. Wylie, V. Allen, B. Lefebvre, G. Tyrrell, G. Horsman, D. Haldane, R. Garceau, T. Wong, M. R. Mulvey
Bacteriology
Population Structure of Klebsiella pneumoniae Causing Bloodstream Infections at a New York City Tertiary Care Hospital: Diversification of Multidrug-Resistant Isolates
Angela Gomez-Simmonds, Michelle Greenman, Sean B. Sullivan, Joshua P. Tanner, Madeleine G. Sowash, Susan Whittier, Anne-Catrin Uhlemann
Bacteriology
Cultures of Needleless Connectors Are Useful for Ruling Out Central Venous Catheter Colonization
María Guembe, María Jesús Pérez-Granda, Raquel Cruces, Pablo Martín-Rabadán, Emilio Bouza
Bacteriology
Comparative Profile of Heme Acquisition Genes in Disease-Causing and Colonizing Nontypeable Haemophilus influenzae and Haemophilus haemolyticus
Nurul I. Hariadi, Lixin Zhang, Mayuri Patel, Sara A. Sandstedt, Gregg S. Davis, Carl F. Marrs, Janet R. Gilsdorf
Bacteriology
Real-Time PCR Assay for Detection and Differentiation of Shiga Toxin-Producing Escherichia coli from Clinical Samples
Xuan Qin, Eileen J. Klein, Emmanouil Galanakis, Anita A. Thomas, Jennifer R. Stapp, Shannon Rich, Anne Marie Buccat, Phillip I. Tarr
Bacteriology
Efficient Detection of Carbapenemase Activity in Enterobacteriaceae by Matrix-Assisted Laser Desorption Ionization−Time of Flight Mass Spectrometry in Less Than 30 Minutes
Camille Lasserre, Luc De Saint Martin, Gaelle Cuzon, Pierre Bogaerts, Estelle Lamar, Youri Glupczynski, Thierry Naas, Didier Tandé
Bacteriology
Microbiological and Clinical Studies of Legionellosis in 33 Patients with Cancer
Xiang Y. Han, Andrea Ihegword, Scott E. Evans, Jiaqi Zhang, Li Li, Hongjing Cao, Jeffrey J. Tarrand, Omar El-Kweifi
Bacteriology
Identification of Haemophilus influenzae Type b Isolates by Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Viktor Månsson, Fredrik Resman, Markus Kostrzewa, Bo Nilson, Kristian Riesbeck
Bacteriology
Characterization of an Enterococcus gallinarum Isolate Carrying a Dual vanA and vanB Cassette
Alireza Eshaghi, Dea Shahinas, Aimin Li, Ruwandi Kariyawasam, Philip Banh, Marc Desjardins, Roberto G. Melano, Samir N. Patel
Bacteriology
Multicenter Clinical Evaluation of the Novel Alere i Strep A Isothermal Nucleic Acid Amplification Test
Daniel M. Cohen, Michael E. Russo, Preeti Jaggi, Jennifer Kline, William Gluckman, Amisha Parekh
Open Access

Bacteriology
Genomics Reveals the Worldwide Distribution of Multidrug-Resistant Serotype 6E Pneumococci
Andries J. van Tonder, James E. Bray, Lucy Roalfe, Rebecca White, Marta Zancolli, Sigríður J. Quirk, Gunnsteinn Haraldsson, Keith A. Jolley, Martin C. J. Maiden, Stephen D. Bentley, Ásgeir Haraldsson, Helga Erlendsdóttir, Karl G. Kristinsson, David Goldblatt, Angela B. Brueggemann
Bacteriology
Comparison of Inoculation with the InoqulA and WASP Automated Systems with Manual Inoculation
Antony Croxatto, Klaas Dijkstra, Guy Prod'hom, Gilbert Greub
Bacteriology
Coproduction of KPC-2 and IMP-10 in Carbapenem-Resistant Serratia marcescens Isolates from an Outbreak in a Brazilian Teaching Hospital
Kesia Esther Silva, Rodrigo Cayô, Cecilia Godoy Carvalhaes, Flávia Patussi Correia Sacchi, Fernanda Rodrigues-Costa, Ana Carolina Ramos da Silva, Julio Croda, Ana Cristina Gales, Simone Simionatto
Bacteriology
Optimized Protocol for Simple Extraction of High-Quality Genomic DNA from Clostridium difficile for Whole-Genome Sequencing
James Heng Chiak Sim, Victoria Anikst, Akshar Lohith, Nader Pourmand, Niaz Banaei
Bacteriology
Contamination of Ambient Air with Acinetobacter baumannii on Consecutive Inpatient Days
Luis A. Shimose, Yohei Doi, Robert A. Bonomo, Dennise De Pascale, Roberto A. Viau, Timothy Cleary, Nicholas Namias, Daniel H. Kett, L. Silvia Munoz-Price
Bacteriology
Assessment of Reproducibility of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Bacterial and Yeast Identification
Lars F. Westblade, Omai B. Garner, Karen MacDonald, Constance Bradford, David H. Pincus, A. Brian Mochon, Rebecca Jennemann, Ryhana Manji, Maureen Bythrow, Michael A. Lewinski, Carey-Ann D. Burnham, Christine C. Ginocchio
Bacteriology
Detection of Group A Streptococcus in Pharyngeal Swab Specimens by Use of the AmpliVue GAS Isothermal Helicase-Dependent Amplification Assay
Matthew L. Faron, Nathan A. Ledeboer, Paul Granato, Judy A. Daly, Kristina Pierce, Preeti Pancholi, Timothy S. Uphoff, Blake W. Buchan

Chlamydiology and Rickettsiology

Chlamydiology and Rickettsiology
Global Multilocus Sequence Type Analysis of Chlamydia trachomatis Strains from 16 Countries
Björn Herrmann, Jenny Isaksson, Martin Ryberg, Jeanette Tångrot, Isam Saleh, Bart Versteeg, Kirsten Gravningen, Sylvia Bruisten
and on behalf of The Chlamydia trachomatis MLST Study Group

Mycobacteriology and Aerobic Actinomycetes

Mycobacteriology and Aerobic Actinomycetes
A Novel Reporter Phage To Detect Tuberculosis and Rifampin Resistance in a High-HIV-Burden Population
Max R. O'Donnell, Alexander Pym, Paras Jain, Vanisha Munsamy, Allison Wolf, Farina Karim, William R. Jacobs, Michelle H. Larsen
Mycobacteriology and Aerobic Actinomycetes
Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples
Amanda C. Brown, Josephine M. Bryant, Katja Einer-Jensen, Jolyon Holdstock, Darren T. Houniet, Jacqueline Z. M. Chan, Daniel P. Depledge, Vladyslav Nikolayevskyy, Agnieszka Broda, Madeline J. Stone, Mette T. Christiansen, Rachel Williams, Michael B. McAndrew, Helena Tutill, Julianne Brown, Mark Melzer, Caryn Rosmarin, Timothy D. McHugh, Robert J. Shorten, Francis Drobniewski, Graham Speight, Judith Breuer
Mycobacteriology and Aerobic Actinomycetes
Comparison of Sample Preparation Methods, Instrumentation Platforms, and Contemporary Commercial Databases for Identification of Clinically Relevant Mycobacteria by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Craig B. Wilen, Allison R. McMullen, Carey-Ann D. Burnham
Mycobacteriology and Aerobic Actinomycetes
Rapid Detection of Acquired and Inducible Clarithromycin Resistance in Mycobacterium abscessus Group by a Simple Real-Time PCR Assay
Robert F. Luo, Cheyenne Curry, Nathan Taylor, Indre Budvytiene, Niaz Banaei
Open Access

Mycobacteriology and Aerobic Actinomycetes
Mycobacterium abscessus Complex Identification with Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Theofano Panagea, David H. Pincus, Dorothy Grogono, Melissa Jones, Josephine Bryant, Julian Parkhill, R. Andres Floto, Peter Gilligan
Mycobacteriology and Aerobic Actinomycetes
In Vivo IS6110 Profile Changes in a Mycobacterium tuberculosis Strain as Determined by Tracking over 14 Years
María Isabel Millán-Lou, Isabel Otal, María Luisa Monforte, María Asunción Vitoria, María José Revillo, Carlos Martín, Sofía Samper

Mycology

Mycology
Quick Detection of FKS1 Mutations Responsible for Clinical Echinocandin Resistance in Candida albicans
Catiana Dudiuk, Soledad Gamarra, Cristina Jimenez-Ortigosa, Florencia Leonardelli, Daiana Macedo, David S. Perlin, Guillermo Garcia-Effron
Mycology
Improved Standardization of the Bio-Rad Platelia Aspergillus Galactomannan Antigen Sandwich Enzyme Immunoassay Using the DS2 (Dynex) Enzyme-Linked Immunosorbent Assay (ELISA) Processing System
R. L. Gorton, P. L. White, E. Bagkeris, D. Cotterall, R. Desai, T. McHugh, C. C. Kibbler
Mycology
Dual Invasive Infection with Phaeoacremonium parasiticum and Paraconiothyrium cyclothyrioides in a Renal Transplant Recipient: Case Report and Comprehensive Review of the Literature of Phaeoacremonium Phaeohyphomycosis
Marie-Alice Colombier, Alexandre Alanio, Blandine Denis, Giovanna Melica, Dea Garcia-Hermoso, Bénédicte Levy, Marie-Noëlle Peraldi, Denis Glotz, Stéphane Bretagne, Sébastien Gallien
Mycology
Aspergillus-Specific Lateral-Flow Device and Real-Time PCR Testing of Bronchoalveolar Lavage Fluid: a Combination Biomarker Approach for Clinical Diagnosis of Invasive Pulmonary Aspergillosis
Gemma L. Johnson, Shah-Jalal Sarker, Francesco Nannini, Arianna Ferrini, Emma Taylor, Cornelia Lass-Flörl, Wolfgang Mutschlechner, Stephen A. Bustin, Samir G. Agrawal
Mycology
Analytical and Clinical Evaluation of the PathoNostics AsperGenius Assay for Detection of Invasive Aspergillosis and Resistance to Azole Antifungal Drugs during Testing of Serum Samples
P. Lewis White, Raquel B. Posso, Rosemary A. Barnes
Mycology
Impact of Mucorales and Other Invasive Molds on Clinical Outcomes of Polymicrobial Traumatic Wound Infections
Tyler E. Warkentien, Faraz Shaikh, Amy C. Weintrob, Carlos J. Rodriguez, Clinton K. Murray, Bradley A. Lloyd, Anuradha Ganesan, Deepak Aggarwal, M. Leigh Carson, David R. Tribble
and on behalf of the Infectious Disease Clinical Research Program Trauma Infectious Disease Outcomes Study Group
Mycology
High-Level Pan-Azole-Resistant Aspergillosis
Jakko van Ingen, Henrich A. L. van der Lee, Antonius J. M. M. Rijs, Eveline Snelders, Willem J. G. Melchers, Paul E. Verweij

Parasitology

Parasitology
Development of Conventional and Real-Time Quantitative PCR Assays for Diagnosis and Monitoring of Scabies
Samson S. Y. Wong, Rosana W. S. Poon, Sandy Chau, Sally C. Y. Wong, Kelvin K. W. To, Vincent C. C. Cheng, Kitty S. C. Fung, K. Y. Yuen
Parasitology
Simple Real-Time PCR and Amplicon Sequencing Method for Identification of Plasmodium Species in Human Whole Blood
Martina I. Lefterova, Indre Budvytiene, Johanna Sandlund, Anna Färnert, Niaz Banaei
Parasitology
Molecular Diagnosis of Abdominal Armillifer grandis Pentastomiasis in the Democratic Republic of Congo
Dennis Tappe, Mihály Sulyok, Lajos Rózsa, Birgit Muntau, Alexandra Haeupler, Imre Bodó, Richard Hardi

Virology

Virology
Genotype- and Subtype-Independent Full-Genome Sequencing Assay for Hepatitis C Virus
Charlotte Hedskog, Krishna Chodavarapu, Karin S. Ku, Simin Xu, Ross Martin, Michael D. Miller, Hongmei Mo, Evguenia Svarovskaia
Virology
Comparison of Onclarity Human Papillomavirus (HPV) Assay with Hybrid Capture II HPV DNA Assay for Detection of Cervical Intraepithelial Neoplasia Grade 2 and 3 Lesions
F. Bottari, M. Sideri, C. Gulmini, S. Igidbashian, A. Tricca, C. Casadio, S. Carinelli, S. Boveri, D. Ejegod, J. Bonde, M. T. Sandri
Virology
Naturally Occurring Resistance-Associated Variants of Hepatitis C Virus Protease Inhibitors in Poor Responders to Pegylated Interferon-Ribavirin
Sylvie Larrat, Sophie Vallet, Sandra David-Tchouda, Alban Caporossi, Jennifer Margier, Christophe Ramière, Caroline Scholtes, Stéphanie Haïm-Boukobza, Anne-Marie Roque-Afonso, Bernard Besse, Elisabeth André-Garnier, Sofiane Mohamed, Philippe Halfon, Adeline Pivert, Hélène LeGuillou-Guillemette, Florence Abravanel, Matthieu Guivarch, Vincent Mackiewicz, Olivier Lada, Thomas Mourez, Jean-Christophe Plantier, Yazid Baazia, Sophie Alain, Sebastien Hantz, Vincent Thibault, Catherine Gaudy-Graffin, Dorine Bouvet, Audrey Mirand, Cécile Henquell, Joel Gozlan, Gisèle Lagathu, Charlotte Pronier, Aurélie Velay, Evelyne Schvoerer, Pascale Trimoulet, Hervé Fleury, Magali Bouvier-Alias, Etienne Brochot, Gilles Duverlie, Sarah Maylin, Stéphanie Gouriou, Jean-Michel Pawlotsky, Patrice Morand
Virology
Characterization of Full-Length Genomes of Hepatitis B Virus Quasispecies in Sera of Patients at Different Phases of Infection
Zhi-Tao Yang, Su-Yuan Huang, Li Chen, Feng Liu, Xiao-Hui Cai, Yang-Fan Guo, Ming-Jie Wang, Yue Han, De-Min Yu, Jie-Hong Jiang, Dong-Hua Zhang, Qi-Ming Gong, Guo-Qing Zhang, Guo-Qing Zang, Zhong-Hua Lu, Li-Hua Huang, Xin-Xin Zhang
Virology
Evaluation of Unbiased Next-Generation Sequencing of RNA (RNA-seq) as a Diagnostic Method in Influenza Virus-Positive Respiratory Samples
Nicole Fischer, Daniela Indenbirken, Thomas Meyer, Marc Lütgehetmann, Heinrich Lellek, Michael Spohn, Martin Aepfelbacher, Malik Alawi, Adam Grundhoff
Virology
Direct Detection of Influenza A and B Viruses in Less Than 20 Minutes Using a Commercially Available Rapid PCR Assay
Matthew J. Binnicker, Mark J. Espy, Cole L. Irish, Emily A. Vetter
Free

Virology
Use of the FilmArray System for Detection of Zaire ebolavirus in a Small Hospital in Bo, Sierra Leone
Tomasz A. Leski, Rashid Ansumana, Chris R. Taitt, Joseph M. Lamin, Umaru Bangura, Joseph Lahai, George Mbayo, Mohamed B. Kanneh, Ben Bawo, Alfred S. Bockarie, Matt Scullion, Cynthia L. Phillips, Cynthia P. Horner, Kathryn H. Jacobsen, David A. Stenger

Immunoassays

Immunoassays
Detection of Group A Streptococcus from Pharyngeal Swab Samples by Bacterial Culture Is Challenged by a Novel mariPOC Point-of-Care Test
Jukka Vakkila, Janne O. Koskinen, Annika Brandt, Anna Muotiala, Viivi Liukko, Sari Soittu, Siiri Meriluoto, Marika Vesalainen, Pentti Huovinen, Kerttu Irjala
Immunoassays
Competitive Homogeneous Immunoassay for Rapid Serodiagnosis of Hantavirus Disease
Satu Hepojoki, Juuso Rusanen, Jussi Hepojoki, Visa Nurmi, Antti Vaheri, Åke Lundkvist, Klaus Hedman, Olli Vapalahti
Immunoassays
Changes in MMP-9 and TIMP-1 Concentrations in Cerebrospinal Fluid after 1 Week of Treatment of Childhood Bacterial Meningitis
Irmeli Roine, Tuula Pelkonen, Anneli Lauhio, Maija Lappalainen, Manuel Leite Cruzeiro, Luis Bernardino, Taina Tervahartiala, Timo Sorsa, Heikki Peltola

Clinical Veterinary Microbiology

Clinical Veterinary Microbiology
Epizootiological Investigation of Getah Virus Infection among Racehorses in Japan in 2014
Hiroshi Bannai, Manabu Nemoto, Akihiro Ochi, Takuya Kikuchi, Minoru Kobayashi, Koji Tsujimura, Takashi Yamanaka, Takashi Kondo
Open Access

Clinical Veterinary Microbiology
Performance of a Noninvasive Test for Detecting Mycobacterium bovis Shedding in European Badger (Meles meles) Populations
Hayley C. King, Andrew Murphy, Phillip James, Emma Travis, David Porter, Jason Sawyer, Jennifer Cork, Richard J. Delahay, William Gaze, Orin Courtenay, Elizabeth M. Wellington
Clinical Veterinary Microbiology
Molecular Basis of Resistance to Selected Antimicrobial Agents in the Emerging Zoonotic Pathogen Streptococcus suis
Mamata Gurung, Migma Dorji Tamang, Dong Chan Moon, Su-Ran Kim, Jin-Ha Jeong, Geum-Chan Jang, Suk-Chan Jung, Yong-Ho Park, Suk-Kyung Lim

Epidemiology

Open Access

Epidemiology
Extensive Within-Host Diversity in Fecally Carried Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli Isolates: Implications for Transmission Analyses
N. Stoesser, A. E. Sheppard, C. E. Moore, T. Golubchik, C. M. Parry, P. Nget, M. Saroeun, N. P. J. Day, A. Giess, J. R. Johnson, T. E. A. Peto, D. W. Crook, A. S. Walker
and the Modernizing Medical Microbiology Informatics Group
Epidemiology
Mixed Infections and Rifampin Heteroresistance among Mycobacterium tuberculosis Clinical Isolates
Chao Zheng, Song Li, Zhongyue Luo, Rui Pi, Honghu Sun, Qingxia He, Ke Tang, Mei Luo, Yuqing Li, David Couvin, Nalin Rastogi, Qun Sun
Open Access

Epidemiology
Genome-Based Characterization of Emergent Invasive Neisseria meningitidis Serogroup Y Isolates in Sweden from 1995 to 2012
Bianca Törös, Sara T. Hedberg, Magnus Unemo, Susanne Jacobsson, Dorothea M. C. Hill, Per Olcén, Hans Fredlund, Holly B. Bratcher, Keith A. Jolley, Martin C. J. Maiden, Paula Mölling

Case Reports

CASE REPORTS
Unanticipated Multiplex PCR-Based Identification of Polymicrobial Blood Culture Resulting in Earlier Isolation, Determination of Susceptibilities, and Optimization of Clinical Care
Tristan Timbrook, M. Sean Boger, Lisa L. Steed, John M. Hurst
CASE REPORTS
Two Rapidly Growing Mycobacterial Species Isolated from a Brain Abscess: First Whole-Genome Sequences of Mycobacterium immunogenum and Mycobacterium llatzerense
Alexander L. Greninger, Charles Langelier, Gail Cunningham, Chris Keh, Michael Melgar, Charles Y. Chiu, Steve Miller
CASE REPORTS
Sepsis Due to a Novel Urease-Positive Helicobacter Species in a Young Man
Nobuaki Mori, Narito Kagawa, Akiko Higuchi, Yasuko Aoki, Kiyofumi Ohkusu
CASE REPORTS
Pulmonary Fungal Infection Caused by Neoscytalidium dimidiatum
Brandon Dionne, Luke Neff, Samuel A. Lee, Deanna A. Sutton, Nathan P. Wiederhold, Jonathan Lindner, Hongxin Fan, Bernadette Jakeman
CASE REPORTS
Definitive Identification of Laribacter hongkongensis Acquired in the United States
Hope A. Beilfuss, David Quig, Mary Ann Block, Paul C. Schreckenberger

Letters to the Editor

LETTERS TO THE EDITOR
Rapid Genotyping of Shigella sonnei by Use of Multiplex High-Resolution Melting
Waleed Mazi, Vartul Sangal, Amir Saeed, Gunnar Sandstrom, François-Xavier Weill, Jun Yu
LETTERS TO THE EDITOR
Effects of Frozen Storage on Detection of Intermediate Vancomycin Susceptibility and Heteroresistance in Methicillin-Resistant Staphylococcus aureus Blood Isolates
K. Riederer, S. Iyer, S. Shemes, V. Dejaeghere, M. Sharma, S. Szpunar, R. Khatib

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Table of Contents

Photo Quiz

Commentary

Minireview

Bacteriology

Chlamydiology and Rickettsiology

Mycobacteriology and Aerobic Actinomycetes

Mycology

Parasitology

Virology

Immunoassays

Clinical Veterinary Microbiology

Epidemiology

Case Reports

Letters to the Editor

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