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:
-
- Univ. of Tennessee, Knoxville, TN (United States). Dept. of Microbiology
- 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); 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:https://doi.org/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:https://doi.org/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}
}
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
- Clark, Clifford G.; Berry, Chrystal; Walker, Matthew
- BMC Genomics, Vol. 17, Issue 1
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
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
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
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
A longitudinal study of campylobacter infection of broiler flocks in Great Britain
journal, August 2000
- Evans, S. J.; Sayers, A. R.
- Preventive Veterinary Medicine, Vol. 46, Issue 3
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
Campylobacter jejuni transcriptome changes during loss of culturability in water
journal, November 2017
- Bronowski, Christina; Mustafa, Kasem; Goodhead, Ian
- PLOS ONE, Vol. 12, Issue 11
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
Source Attribution of Human Campylobacter Isolates by MLST and Fla-Typing and Association of Genotypes with Quinolone Resistance
journal, November 2013
- Kittl, Sonja; Heckel, Gerald; Korczak, Bożena M.
- PLoS ONE, Vol. 8, Issue 11
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
Tracing the Source of Campylobacteriosis
journal, September 2008
- Wilson, Daniel J.; Gabriel, Edith; Leatherbarrow, Andrew J. H.
- PLoS Genetics, Vol. 4, Issue 9
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
Prevalence of Campylobacter spp., Escherichia coli, and Salmonella Serovars in Retail Chicken, Turkey, Pork, and Beef from the Greater Washington, D.C., Area
journal, December 2001
- Zhao, C.; Ge, B.; De Villena, J.
- Applied and Environmental Microbiology, Vol. 67, Issue 12
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
Sources of Campylobacter Colonization in Broiler Chickens
journal, August 2003
- Newell, D. G.; Fearnley, C.
- Applied and Environmental Microbiology, Vol. 69, Issue 8
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
Cattle and sheep farms as reservoirs of Campylobacter
journal, May 2003
- Stanley, K.; Jones, K.
- Journal of Applied Microbiology, Vol. 94, Issue s1
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
Global Epidemiology of Campylobacter Infection
journal, June 2015
- Kaakoush, Nadeem O.; Castaño-Rodríguez, Natalia; Mitchell, Hazel M.
- Clinical Microbiology Reviews, Vol. 28, Issue 3
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
Whole genome sequencing in clinical and public health microbiology
journal, April 2015
- Kwong, J. C.; Mccallum, N.; Sintchenko, V.
- Pathology, Vol. 47, Issue 3
Environmental survival mechanisms of the foodborne pathogen Campylobacter jejuni
journal, April 2006
- Murphy, C.; Carroll, C.; Jordan, K. N.
- Journal of Applied Microbiology, Vol. 100, Issue 4
Comparison of three enrichment media for the isolation of Campylobacter spp. from foods
journal, November 2000
- Baylis, C. L.; MacPhee, S.; Martin, K. W.
- Journal of Applied Microbiology, Vol. 89, Issue 5
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
Human Campylobacteriosis in Developing Countries
journal, March 2002
- Coker, Akitoye O.
- Emerging Infectious Diseases, Vol. 8, Issue 3
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
- Wang, G.; Clark, C. G.; Taylor, T. M.
- Journal of Clinical Microbiology, Vol. 40, Issue 12
Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms
journal, August 2014
- Kaas, Rolf S.; Leekitcharoenphon, Pimlapas; Aarestrup, Frank M.
- PLoS ONE, Vol. 9, Issue 8
The use of membrane filters applied directly to the surface of agar plates for the isolation of campylobacter jejuni from feces
journal, January 1984
- Steele, Trevor W.; McDermott, S. N.
- Pathology, Vol. 16, Issue 3
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
Microbial contamination of drinking water and disease outcomes in developing regions
journal, May 2004
- Ashbolt, Nicholas John
- Toxicology, Vol. 198, Issue 1-3
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
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
Survival of Campylobacter jejuni on fresh spinach stored at 4 °C or 12 °C
journal, April 2015
- Guévremont, Evelyne; Lamoureux, Lisyanne; Ward, Pierre
- Food Control, Vol. 50
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
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
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
Blood-free selective medium for isolation of Campylobacter jejuni from feces.
journal, January 1984
- Bolton, F. J.; Hutchinson, D. N.; Coates, D.
- Journal of Clinical Microbiology, Vol. 19, Issue 2
PCR detection, identification to species level, and fingerprinting of Campylobacter jejuni and Campylobacter coli direct from diarrheic samples.
journal, January 1997
- Linton, D.; Lawson, A. J.; Owen, R. J.
- Journal of clinical microbiology, Vol. 35, Issue 10
Indicator medium for isolation of Campylobacter pylori.
journal, January 1987
- Queiroz, D. M.; Mendes, E. N.; Rocha, G. A.
- Journal of Clinical Microbiology, Vol. 25, Issue 12
Works referencing / citing this record:
The Human Cytomegalovirus Chemokine vCXCL-1 Modulates Normal Dissemination Kinetics of Murine Cytomegalovirus In Vivo
journal, June 2019
- Jackson, Joseph W.; Hancock, Trevor J.; LaPrade, Ellen
- mBio, Vol. 10, Issue 3
A Chaperone for the Stator Units of a Bacterial Flagellum
journal, August 2019
- Ribardo, Deborah A.; Kelley, Brittni R.; Johnson, Jeremiah G.
- mBio, Vol. 10, Issue 4