M e t h o d s i n M o l e c u l a r B i o l o g y

Series Editor John M. Walker School of Life and Medical Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK

For further volumes: http://www.springer.com/series/7651 Diagnostic Bacteriology

Methods and Protocols

Edited by Kimberly A. Bishop-Lilly

Germantown, MD, USA Editor Kimberly A. Bishop-Lilly Germantown, MD, USA

ISSN 1064-3745 ISSN 1940-6029 (electronic) Methods in Molecular Biology ISBN 978-1-4939-7035-3 ISBN 978-1-4939-7037-7 (eBook) DOI 10.1007/978-1-4939-7037-7

Library of Congress Control Number: 2017939131

© Springer Science+Business Media LLC 2017 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Cover illustration: Cover image credit to Heidi Bishop.

Printed on acid-free paper

This Humana Press imprint is published by Springer Nature The registered company is Springer Science+Business Media LLC The registered company address is: 233 Spring Street, New York, NY 10013, U.S.A. Preface

This volume in the Methods in Molecular Biology series is a comprehensive collection of protocols in molecular diagnostics of bacteria that will suit the needs of molecular biolo- gists, clinical laboratorians, and physician scientists alike. The benefits of applying a molecu- lar diagnostic approach for bacterial detection and identification are many—including reduced time (especially for difficult to culture or slow-growing organisms) and, in some cases, higher specificity (such as strain-level identification rather than species-level identifi- cation). In the case of high-throughput sequencing, one may even collect all the informa- tion one needs to know about a pathogen (such as genus-, species-, and strain-level identification along with virulence potential and antibiotic resistance potential) from a sin- gle reaction, rather than by applying several different highly specialized culture-based assays. With protocols that are specific for common bacterial pathogens as well as protocols that can be applied to diverse or even unknown pathogens, this volume is a valuable resource for anyone who wishes to delve into the molecular age of diagnostics. Topics included range from duplex real-time PCR to next-generation sequencing and the associated bioin- formatic analyses. The protocols contained within this book truly represent a range of assay types that are all on the cutting edge of diagnostic bacteriology.

Germantown, MD, USA Kimberly A. Bishop-Lilly

v Contents

Preface ...... v Contributors ...... ix

1 Whole-Genome Enrichment Using RNA Probes and Sequencing of Chlamydia trachomatis Directly from Clinical Samples ...... 1 Amanda Claire Brown and Mette T. Christiansen 2 Characterization of Sinus Microbiota by 16S Sequencing from Swabs . . . . 23 Thad W. Vickery, Jennifer M. Kofonow, and Vijay R. Ramakrishnan 3 Molecular Subtyping of Salmonella Typhimurium with Multiplex Oligonucleotide Ligation-PCR (MOL-PCR) ...... 39 Véronique Wuyts, Wesley Mattheus, Nancy H.C. Roosens, Kathleen Marchal, Sophie Bertrand, and Sigrid C.J. De Keersmaecker 4 Detection of Helicobacter pylori DNA in Formalin-Fixed Paraffin-­Embedded Gastric Biopsies Using Laser Microdissection and qPCR . 71 María Fernanda Loayza Villa, Valeria Liliana Herrera Sevilla, and Nicolás Vivar-Diaz 5 Mycobacterial Load Assay ...... 89 Stephen H. Gillespie, Wilber Sabiiti, and Katarina Oravcova 6 Defining Diagnostic Biomarkers Using Shotgun Proteomics and MALDI-TOF Mass Spectrometry ...... 107 Jean Armengaud 7 Detection and Typing of “Candidatus Phytoplasma” spp. in Host DNA Extracts Using Oligonucleotide-Coupled Fluorescent Microspheres . . 121 Edel Pérez-López, Christine Hammond, Chrystel Olivier, and Tim J. Dumonceaux 8 Detection of Helicobacter pylori in the Gastric Mucosa by Fluorescence In Vivo Hybridization ...... 137 Silvia Fontenete, Marina Leite, Ceu Figueiredo, Paul Cos, and Nuno F. Azevedo 9 Rapid Antibiotic Susceptibility Testing for Urinary Tract Infections . . . . 147 Anja Mezger, Mats Nilsson, and Dan I. Andersson 10 Detection and Differentiation of Lyme Spirochetes and Other Tick-Borne Pathogens from Blood Using Real-­Time PCR with Molecular Beacons . . . 155 Samantha Schlachter, Kamfai Chan, Salvatore A.E. Marras, and Nikhat Parveen 11 Methods for Real-Time PCR-Based Diagnosis of Chlamydia pneumoniae, Chlamydia psittaci, and Chlamydia abortus Infections in an Opened Molecular Diagnostic Platform 171 Onya Opota, René Brouillet, Gilbert Greub, and Katia Jaton

vii viii Contents

12 Real-Time PCR to Identify Staphylococci and Assay for Virulence from Blood ...... 183 Charles E. Okolie 13 Multiplex Peptide Nucleic Acid Fluorescence In Situ Hybridization (PNA-FISH) for Diagnosis of Bacterial Vaginosis ...... 209 Antonio Machado and Nuno Cerca 14 A Closed-tube Loop-Mediated Isothermal Amplification Assay for the Visual Endpoint Detection of Brucella spp. and Mycobacterium avium subsp. paratuberculosis ...... 221 Marcos D. Trangoni, Andrea K. Gioffré, and Silvio L. Cravero 15 Highly Specific Ligation-dependent Microarray Detection of Single Nucleotide Polymorphisms ...... 231 Noa Wolff and Ivan Barišicʹ 16 Multilocus Sequence Typing (MLST) for Cronobacter spp...... 241 Susan Joseph and Stephen Forsythe 17 Diagnostic Bacteriology: Raman Spectroscopy ...... 249 Rebecca L. Pavlicek, Nicole J. Crane, Meron Ghebremedhin, Katherine E. Cilwa, and Eric A. Elster

Index ...... 263 Contributors

Dan I. Andersson • Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Jean Armengaud • CEA-Marcoule, DRF/JOLIOT/DMTS/SPI/Li2D, Laboratory “Innovative Technologies for Detection and Diagnostics”, Bagnols-sur-Cèze, France Nuno F. Azevedo • LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal Ivan Barisˇic´ • Molecular Diagnostics, AIT Austrian Institute of Technology, Vienna, Austria Sophie Bertrand • National Reference Centre for Salmonella and Shigella, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), , René Brouillet • Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Amanda Claire Brown • Oxford Gene Technology, Oxford, UK; Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA Nuno Cerca • CEB—Centre of Biological Engineering, LIBRO—Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal Kamfai Chan • AI Biosciences, Inc ., College Station, TX, USA Mette T. Christiansen • University College London, London, UK Katherine E. Cilwa • Department of Regenerative Medicine, Naval Medical Research Center, Silver Spring, MD, USA Paul Cos • Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium Nicole J. Crane • The Department of Surgery at Uniformed Services University of the Health Sciences & The Walter Reed National Military Medical Center, Bethesda, MD, USA Silvio L. Cravero • Institute of Biotechnology, Center for Research in Veterinary and Agronomic Sciences - National Institute of Agricultural Technology (INTA), Hurlingham, Buenos Aires, Argentina Sigrid C.J. De Keersmaecker • Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium Tim J. Dumonceaux • Agriculture and Agri-Food Canada Saskatoon Research Centre, Saskatoon, SK, Canada; Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada Eric A. Elster • The Department of Surgery atUniformed Services University of the Health Sciences & The Walter Reed National Military Medical Center, Bethesda, MD, USA Ceu Figueiredo • i3s Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; IPATIMUP, Institute of Molecular Pathology and Immunology of

ix x Contributors

the University of Porto, Porto, Portugal; FMUP, Faculty of Medicine of the University of Porto, Porto, Portugal Silvia Fontenete • LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal; i3s Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal; Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern , Odense M, Denmark; ICBAS, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal; Cancer Cell Biology Program, Epithelial Cell Biology Group, Spanish National Cancer Research Centre, Madrid, Spain Stephen Forsythe • Pathogen Research Group, School of Science & Technology, Nottingham Trent University, Nottingham, UK Meron Ghebremedhin • Department of Regenerative Medicine, Naval Medical Research Center, Silver Spring, MD, USA Stephen H. Gillespie • School of Medicine, University of St . Andrews, St . Andrews, UK Andrea K. Gioffré • Institute of Biotechnology, Center for Research in Veterinary and Agronomic Sciences - National Institute of Agricultural Technology (INTA), Hurlingham, Buenos Aires, Argentina; National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina Gilbert Greub • Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland Christine Hammond • Agriculture and Agri-Food Canada Saskatoon Research Centre, Saskatoon, SK, Canada Katia Jaton • Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland Susan Joseph • Institute of Dentistry, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, London, UK Jennifer M. Kofonow • Division of Infectious Disease, Department of Medicine, University of Colorado, Aurora, CO, USA Marina Leite • i3s Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal Antonio Machado • Microbiology Institute, Universidad San Francisco de Quito, Cumbayá, Quito, Ecuador Kathleen Marchal • Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; Department of Information Technology, Ghent University, IMinds, Ghent, Belgium Salvatore A.E. Marras • Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, NJ, USA Wesley Mattheus • National Reference Centre for Salmonella and Shigella, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium Anja Mezger • Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA Mats Nilsson • Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden Contributors xi

Charles E. Okolie • Department of Biological Sciences, Landmark University, Omu-Aran, Kwara State, Nigeria Chrystel Olivier • Agriculture and Agri-Food Canada Saskatoon Research Centre, Saskatoon, SK, Canada Onya Opota • Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland Katarina Oravcova • School of Medicine, University of St . Andrews, St . Andrews, UK Nikhat Parveen • Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, NJ, USA Rebecca L. Pavlicek • Naval Medical Research Center-Asia, Singapore, Singapore Edel Pérez-López • Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa, Veracruz, Mexico Valeria Liliana Herrera Sevilla • Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador Vijay R. Ramakrishnan • Department of Otolaryngology-Head and Neck Surgery, University of Colorado, Aurora, CO, USA Nancy H.C. Roosens • Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium Wilber Sabiiti • School of Medicine, University of St . Andrews, St . Andrews, UK Samantha Schlachter • Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, NJ, USA Marcos D. Trangoni • Institute of Biotechnology, Center for Research in Veterinary and Agronomic Sciences - National Institute of Agricultural Technology (INTA), Hurlingham, Buenos Aires, Argentina Thad W. Vickery • University of Colorado School of Medicine, Aurora, CO, USA Maria Fernanda Loayza Villa • Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador; Universidad de las Fuerzas Armadas ESPE, Sangolquí-Ecuador Nicolás Vivar-Díaz • Laboratorios NETLAB S .A ., Quito, Ecuador Noa Wolff • Molecular Diagnostics, AIT Austrian Institute of Technology, Vienna, Austria Véronique Wuyts • Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium