Diagnostic Bacteriology: Methods and Protocols

265 Pages·2017·5.7 MB·English

by  Kimberly A. Bishop-Lilly (eds.)

Methods in
Molecular Biology 1616
Kimberly A. Bishop-Lilly Editor
Diagnostic
Bacteriology
Methods and Protocols
M M B
ethods in olecular iology
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
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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, Sweden
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), Brussels, Belgium
rené BrouIllet • Institute of Microbiology, University Hospital Center, University of
Lausanne, Lausanne, Switzerland
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 Denmark,
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