Advances in molecular serotyping and subtyping of Escherichia coli

Fratamico, Pina M.; DebRoy, Chitrita; Liu, Yanhong; Needleman, David S.; Baranzoni, Gian Marco; Feng, Peter

doi:10.3389/fmicb.2016.00644

Title: Advances in molecular serotyping and subtyping of Escherichia coli

Journal Article · Tue May 03 00:00:00 EDT 2016 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2016.00644· OSTI ID:1257610

Fratamico, Pina M. ^[1]; DebRoy, Chitrita ^[2]; Liu, Yanhong ^[1]; Needleman, David S. ^[1]; Baranzoni, Gian Marco ^[1]; Feng, Peter ^[3]

U.S. Dept. of Agriculture, Wyndmoor, PA (United States)
Pennsylvania State Univ., University Park, PA (United States)
U.S. Food and Drug Administration, College Park, MD (United States)

Escherichia coli plays an important role as a member of the gut microbiota; however, pathogenic strains also exist, including various diarrheagenic E. coli pathotypes and extraintestinal pathogenic E. coli that cause illness outside of the GI-tract. E. coli have traditionally been serotyped using antisera against the ca. 186 O-antigens and 53 H-flagellar antigens. Phenotypic methods, including bacteriophage typing and O- and H- serotyping for differentiating and characterizing E. coli have been used for many years; however, these methods are generally time consuming and not always accurate. Advances in next generation sequencing technologies have made it possible to develop genetic-based subtyping and molecular serotyping methods for E. coli, which are more discriminatory compared to phenotypic typing methods. Furthermore, whole genome sequencing (WGS) of E. coli is replacing established subtyping methods such as pulsedfield gel electrophoresis, providing a major advancement in the ability to investigate food-borne disease outbreaks and for trace-back to sources. Furthermore, a variety of sequence analysis tools and bioinformatic pipelines are being developed to analyze the vast amount of data generated by WGS and to obtain specific information such as O- and H-group determination and the presence of virulence genes and other genetic markers.

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Research Organization:: Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-06OR23100

OSTI ID:: 1257610

Journal Information:: Frontiers in Microbiology, Vol. 7; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 69 works

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Virulence gene profiling of enterohemorrhagic (EHEC) and enteropathogenic (EPEC) Escherichia coli strains: a basis for molecular risk assessment of typical and atypical EPEC strains Bugarel, Marie; Martin, Annett; Fach, Patrick BMC Microbiology, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2180-11-142	journal	January 2011
Genetical and functional investigation of fliC genes encoding flagellar serotype H4 in wildtype strains of Escherichia coli and in a laboratory E. coli K-12 strain expressing flagellar antigen type H48 Beutin, Lothar; Strauch, Eckhard; Zimmermann, Sonja BMC Microbiology, Vol. 5, Issue 1, p. 4 https://doi.org/10.1186/1471-2180-5-4	journal	January 2005
Food Reservoir forEscherichia coliCausing Urinary Tract Infections Giufrè, Maria; Graziani, Caterina; Accogli, Marisa Emerging Infectious Diseases, Vol. 16, Issue 6 https://doi.org/10.3201/eid1606.100158	journal	June 2010

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Fourier transform infrared spectroscopy: unlocking fundamentals and prospects for bacterial strain typing Novais, Ângela; Freitas, Ana R.; Rodrigues, Carla European Journal of Clinical Microbiology & Infectious Diseases, Vol. 38, Issue 3 https://doi.org/10.1007/s10096-018-3431-3	journal	November 2018
Multiplex real-time PCR assay for detection of Escherichia coli O157:H7 and screening for non-O157 Shiga toxin-producing E. coli Li, Baoguang; Liu, Huanli; Wang, Weimin BMC Microbiology, Vol. 17, Issue 1 https://doi.org/10.1186/s12866-017-1123-2	journal	November 2017
The relationship between phylogenetic classification, virulence and antibiotic resistance of extraintestinal pathogenic Escherichia coli in İzmir province, Turkey Bozcal, Elif; Eldem, Vahap; Aydemir, Sohret PeerJ, Vol. 6 https://doi.org/10.7717/peerj.5470	journal	January 2018
Construction of a Pan-Genome Allele Database of Salmonella enterica Serovar Enteritidis for Molecular Subtyping and Disease Cluster Identification Liu, Yen-Yi; Chen, Chih-Chieh; Chiou, Chien-Shun Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.02010	journal	December 2016
Escherichia coli Bloodstream Infections in Patients at a University Hospital: Virulence Factors and Clinical Characteristics Daga, Ana Paula; Koga, Vanessa Lumi; Soncini, João Gabriel Material Frontiers in Cellular and Infection Microbiology, Vol. 9 https://doi.org/10.3389/fcimb.2019.00191	journal	June 2019
Variability in Characterizing Escherichia coli from Cattle Feces: A Cautionary Tale Stanford, Kim; Reuter, Tim; Hallewell, Jennyka Microorganisms, Vol. 6, Issue 3 https://doi.org/10.3390/microorganisms6030074	journal	July 2018
Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure Cookson, Adrian L.; Biggs, Patrick J.; Marshall, Jonathan C. Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-00890-6	journal	April 2017
Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective Rumore, Jillian; Tschetter, Lorelee; Kearney, Ashley BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-5243-3	journal	December 2018
O-serogroups, virulence genes, antimicrobial susceptibility, and MLST genotypes of Shiga toxin-producing Escherichia coli from swine and cattle in Central China Peng, Zhong; Liang, Wan; Hu, Zizhe BMC Veterinary Research, Vol. 15, Issue 1 https://doi.org/10.1186/s12917-019-2177-1	journal	November 2019
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