skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Isolation and Whole-Genome Sequencing of Environmental Campylobacter

Abstract

As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter has a significant impact on human health. In the developed world, most campylobacteriosis cases are attributed to the consumption of undercooked, contaminated poultry; however, it has been shown that Campylobacter can be transmitted to humans through contaminated water and other types of food, including beef and milk. As such, high-resolution microbial source-tracking is essential for health department officials to determine the source(s) of Campylobacter outbreaks. For these reasons, this paper provides the techniques needed for isolation of Campylobacter from agricultural and environmental sources, as well as human clinical specimens. Additionally, we describe a simple method for preparing high-quality genomic DNA that can be used for whole-genome sequencing and downstream bioinformatics analyses of Campylobacter genotypes.

Authors:
 [1];  [2];  [2];  [2];  [1]
  1. Univ. of Tennessee, Knoxville, TN (United States). Dept. of Microbiology
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Univ. of Tennessee, Knoxville, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); ORNL Laboratory Directed Research and Development (LDRD) Program; Univ. of Tennessee Joint Directed Research and Development (JDRD) Program
OSTI Identifier:
1481691
Alternate Identifier(s):
OSTI ID: 1479577
Grant/Contract Number:  
AC05-00OR22725; R013318090
Resource Type:
Accepted Manuscript
Journal Name:
Current Protocols in Microbiology
Additional Journal Information:
Journal Volume: 51; Journal Issue: 1; Journal ID: ISSN 1934-8525
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Campylobacter; environmental isolation; whole-genome sequencing

Citation Formats

Kelley, Brittni R., Ellis, J. Christopher, Hyatt, Doug, Jacobson, Dan, and Johnson, Jeremiah. Isolation and Whole-Genome Sequencing of Environmental Campylobacter. United States: N. p., 2018. Web. doi:10.1002/cpmc.64.
Kelley, Brittni R., Ellis, J. Christopher, Hyatt, Doug, Jacobson, Dan, & Johnson, Jeremiah. Isolation and Whole-Genome Sequencing of Environmental Campylobacter. United States. doi:10.1002/cpmc.64.
Kelley, Brittni R., Ellis, J. Christopher, Hyatt, Doug, Jacobson, Dan, and Johnson, Jeremiah. Thu . "Isolation and Whole-Genome Sequencing of Environmental Campylobacter". United States. doi:10.1002/cpmc.64. https://www.osti.gov/servlets/purl/1481691.
@article{osti_1481691,
title = {Isolation and Whole-Genome Sequencing of Environmental Campylobacter},
author = {Kelley, Brittni R. and Ellis, J. Christopher and Hyatt, Doug and Jacobson, Dan and Johnson, Jeremiah},
abstractNote = {As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter has a significant impact on human health. In the developed world, most campylobacteriosis cases are attributed to the consumption of undercooked, contaminated poultry; however, it has been shown that Campylobacter can be transmitted to humans through contaminated water and other types of food, including beef and milk. As such, high-resolution microbial source-tracking is essential for health department officials to determine the source(s) of Campylobacter outbreaks. For these reasons, this paper provides the techniques needed for isolation of Campylobacter from agricultural and environmental sources, as well as human clinical specimens. Additionally, we describe a simple method for preparing high-quality genomic DNA that can be used for whole-genome sequencing and downstream bioinformatics analyses of Campylobacter genotypes.},
doi = {10.1002/cpmc.64},
journal = {Current Protocols in Microbiology},
number = 1,
volume = 51,
place = {United States},
year = {2018},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Genomic insights from whole genome sequencing of four clonal outbreak Campylobacter jejuni assessed within the global C. jejuni population
journal, December 2016


Exploiting Bacterial Whole-Genome Sequencing Data for Evaluation of Diagnostic Assays: Campylobacter Species Identification as a Case Study
journal, October 2016

  • Jansen van Rensburg, Melissa J.; Swift, Craig; Cody, Alison J.
  • Journal of Clinical Microbiology, Vol. 54, Issue 12
  • DOI: 10.1128/JCM.01522-16

Genetic Diversity of Campylobacter jejuni and Campylobacter coli Isolates from Conventional Broiler Flocks and the Impacts of Sampling Strategy and Laboratory Method
journal, February 2016

  • Vidal, A. B.; Colles, F. M.; Rodgers, J. D.
  • Applied and Environmental Microbiology, Vol. 82, Issue 8
  • DOI: 10.1128/AEM.03693-15

Distribution and numbers of Campylobacter in newly slaughtered broiler chickens and hens
journal, January 1992

  • Berndtson, Eva; Tivemo, Maria; Engvall, Anders
  • International Journal of Food Microbiology, Vol. 15, Issue 1-2
  • DOI: 10.1016/0168-1605(92)90134-O

Sensitivity of Direct Culture, Enrichment and PCR for Detection of Campylobacter jejuni and C. coli in Broiler Flocks at Slaughter
journal, October 2016

  • Rodgers, J. D.; Simpkin, E.; Lee, R.
  • Zoonoses and Public Health, Vol. 64, Issue 4
  • DOI: 10.1111/zph.12306

A longitudinal study of campylobacter infection of broiler flocks in Great Britain
journal, August 2000


Assessment of the Duration of Protection in Campylobacter jejuni Experimental Infection in Humans
journal, January 2010

  • Tribble, D. R.; Baqar, S.; Scott, D. A.
  • Infection and Immunity, Vol. 78, Issue 4
  • DOI: 10.1128/IAI.01021-09

Campylobacter jejuni transcriptome changes during loss of culturability in water
journal, November 2017


Detection of Campylobacter in Stool and Determination of Significance by Culture, Enzyme Immunoassay, and PCR in Developing Countries
journal, January 2014

  • Platts-Mills, J. A.; Liu, J.; Gratz, J.
  • Journal of Clinical Microbiology, Vol. 52, Issue 4
  • DOI: 10.1128/JCM.02935-13

Source Attribution of Human Campylobacter Isolates by MLST and Fla-Typing and Association of Genotypes with Quinolone Resistance
journal, November 2013


Increased Outbreaks Associated with Nonpasteurized Milk, United States, 2007–2012
journal, January 2015

  • Mungai, Elisabeth A.; Behravesh, Casey Barton; Gould, L. Hannah
  • Emerging Infectious Diseases, Vol. 21, Issue 1
  • DOI: 10.3201/eid2101.140447

Tracing the Source of Campylobacteriosis
journal, September 2008


Core Genome Multilocus Sequence Typing Scheme for Stable, Comparative Analyses of Campylobacter jejuni and C. coli Human Disease Isolates
journal, April 2017

  • Cody, Alison J.; Bray, James E.; Jolley, Keith A.
  • Journal of Clinical Microbiology, Vol. 55, Issue 7
  • DOI: 10.1128/JCM.00080-17

Detection of Campylobacter spp. in Ceca and Crops with and Without Enrichment
journal, June 2001

  • Musgrove, M. T.; Berrang, M. E.; Byrd, J. A.
  • Poultry Science, Vol. 80, Issue 6
  • DOI: 10.1093/ps/80.6.825

Sources of Campylobacter Colonization in Broiler Chickens
journal, August 2003


The PAS Domain-Containing Protein HeuR Regulates Heme Uptake in Campylobacter jejuni
journal, November 2016

  • Johnson, Jeremiah G.; Gaddy, Jennifer A.; DiRita, Victor J.
  • mBio, Vol. 7, Issue 6
  • DOI: 10.1128/mBio.01691-16

Cattle and sheep farms as reservoirs of Campylobacter
journal, May 2003


Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp.
journal, October 2015

  • Zhao, S.; Tyson, G. H.; Chen, Y.
  • Applied and Environmental Microbiology, Vol. 82, Issue 2
  • DOI: 10.1128/AEM.02873-15

Global Epidemiology of Campylobacter Infection
journal, June 2015

  • Kaakoush, Nadeem O.; Castaño-Rodríguez, Natalia; Mitchell, Hazel M.
  • Clinical Microbiology Reviews, Vol. 28, Issue 3
  • DOI: 10.1128/CMR.00006-15

Campylobacteriosis: the role of poultry meat
journal, February 2016

  • Skarp, C. P. A.; Hänninen, M. -L.; Rautelin, H. I. K.
  • Clinical Microbiology and Infection, Vol. 22, Issue 2
  • DOI: 10.1016/j.cmi.2015.11.019

Whole genome sequencing in clinical and public health microbiology
journal, April 2015


Environmental survival mechanisms of the foodborne pathogen Campylobacter jejuni
journal, April 2006


Comparison of three enrichment media for the isolation of Campylobacter spp. from foods
journal, November 2000


Real-Time Genomic Epidemiological Evaluation of Human Campylobacter Isolates by Use of Whole-Genome Multilocus Sequence Typing
journal, May 2013

  • Cody, A. J.; McCarthy, N. D.; Jansen van Rensburg, M.
  • Journal of Clinical Microbiology, Vol. 51, Issue 8
  • DOI: 10.1128/JCM.00066-13

Human Campylobacteriosis in Developing Countries
journal, March 2002


Colony Multiplex PCR Assay for Identification and Differentiation of Campylobacter jejuni, C. coli, C. lari, C. upsaliensis, and C. fetus subsp. fetus
journal, December 2002


Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms
journal, August 2014


Next-generation sequencing technologies and their application to the study and control of bacterial infections
journal, April 2018

  • Besser, J.; Carleton, H. A.; Gerner-Smidt, P.
  • Clinical Microbiology and Infection, Vol. 24, Issue 4
  • DOI: 10.1016/j.cmi.2017.10.013

Microbial contamination of drinking water and disease outcomes in developing regions
journal, May 2004


Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database
journal, March 2016

  • Allard, Marc W.; Strain, Errol; Melka, David
  • Journal of Clinical Microbiology, Vol. 54, Issue 8
  • DOI: 10.1128/JCM.00081-16

Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections
journal, August 2015

  • Dearlove, Bethany L.; Cody, Alison J.; Pascoe, Ben
  • The ISME Journal, Vol. 10, Issue 3
  • DOI: 10.1038/ismej.2015.149

Survival of Campylobacter jejuni on fresh spinach stored at 4 °C or 12 °C
journal, April 2015


Poultry as a Host for the Zoonotic Pathogen Campylobacter jejuni
journal, February 2012

  • Hermans, David; Pasmans, Frank; Messens, Winy
  • Vector-Borne and Zoonotic Diseases, Vol. 12, Issue 2
  • DOI: 10.1089/vbz.2011.0676

Campylobacter species in animal, food, and environmental sources, and relevant testing programs in Canada
journal, October 2015

  • Huang, Hongsheng; Brooks, Brian W.; Lowman, Ruff
  • Canadian Journal of Microbiology, Vol. 61, Issue 10
  • DOI: 10.1139/cjm-2014-0770

Campylobacter Genotyping to Determine the Source of Human Infection
journal, April 2009

  • Sheppard, Samuel K.; Dallas, John F.; Strachan, Norval J. C.
  • Clinical Infectious Diseases, Vol. 48, Issue 8
  • DOI: 10.1086/597402