Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2

Ahmed, Sanaa A.; Awosika, Joy; Baldwin, Carson; Bishop-Lilly, Kimberly A.; Biswas, Biswajit; Broomall, Stacey; Chain, Patrick S.  G.; Chertkov, Olga; Chokoshvili, Otar; Coyne, Susan; Davenport, Karen; Detter, J. Chris; Dorman, William; Erkkila, Tracy H.; Folster, Jason P.; Frey, Kenneth G.; George, Matroner; Gleasner, Cheryl; Henry, Matthew; Hill, Karen K.; Hubbard, Kyle; Insalaco, Joseph; Johnson, Shannon; Kitzmiller, Aaron; Krepps, Michael; Lo, Chien-Chi; Luu, Truong; McNew, Lauren A.; Minogue, Timothy; Munk, Christine A.; Osborne, Brian; Patel, Mohit; Reitenga, Krista G.; Rosenzweig, C. Nicole; Shea, April; Shen, Xiaohong; Strockbine, Nancy; Tarr, Cheryl; Teshima, Hazuki; van Gieson, Eric; Verratti, Kathleen; Wolcott, Mark; Xie, Gary; Sozhamannan, Shanmuga; Gibbons, Henry S.

doi:10.1371/journal.pone.0048228

Title: Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2

Journal Article · Thu Nov 01 00:00:00 EDT 2012 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0048228· OSTI ID:1627555

Ahmed, Sanaa A. ^[1]; Awosika, Joy ^[2]; Baldwin, Carson ^[3]; Bishop-Lilly, Kimberly A. ^[2]; Biswas, Biswajit ^[2]; Broomall, Stacey ^[4]; Chain, Patrick S. G. ^[1]; Chertkov, Olga ^[1]; Chokoshvili, Otar ^[5]; Coyne, Susan ^[3]; Davenport, Karen ^[1]; Detter, J. Chris ^[1]; Dorman, William ^[3]; Erkkila, Tracy H. ^[1]; Folster, Jason P. ^[6]; Frey, Kenneth G. ^[2]; George, Matroner ^[2]; Gleasner, Cheryl ^[1]; Henry, Matthew ^[2]; Hill, Karen K. ^[1] more »

Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Naval Medical Research Center and Henry M. Jackson Foundation for Military Medicine, Frederick, MD (United States)
U.S. Army Research Inst. for Infectious Disease, Frederick, MD (United States)
U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD (United States)
National Center for Disease Control and Public Health, Tbilisi (Republic of Georgia). South Caucasus Field Epidemiology. Lab. Training Program
Centers for Disease Control and Prevention (CDC), Atlanta, GA (United States). Enteric Diseases Lab. Branch
U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD (United States); Excet Inc, Springfield, VA (United States)
U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD (United States); Science Applications International Corporation, Abingdon, MD (United States)
BioTeam, Inc., Middleton, MA (United States)
U.S. Army Research Inst. for Infectious Disease, Frederick, MD (United States); Team Ke’aki Tech, Frederick, MD (United States)
Defense Threat Reduction Agency, Alexandria, VA (United States)

In May of 2011, an enteroaggregative Escherichia coli O104:H4 strain that had acquired a Shiga toxin 2-converting phage caused a large outbreak of bloody diarrhea in Europe which was notable for its high prevalence of hemolytic uremic syndrome cases. Several studies have described the genomic inventory and phylogenies of strains associated with the outbreak and a collection of historical E. coli O104:H4 isolates using draft genome assemblies. We present the complete, closed genome sequences of an isolate from the 2011 outbreak (2011C–3493) and two isolates from cases of bloody diarrhea that occurred in the Republic of Georgia in 2009 (2009EL–2050 and 2009EL–2071). Comparative genome analysis indicates that, while the Georgian strains are the nearest neighbors to the 2011 outbreak isolates sequenced to date, structural and nucleotide-level differences are evident in the Stx2 phage genomes, the mer/tet antibiotic resistance island, and in the prophage and plasmid profiles of the strains, including a previously undescribed plasmid with homology to the pMT virulence plasmid of Yersinia pestis. In addition, multiphenotype analysis showed that 2009EL–2071 possessed higher resistance to polymyxin and membrane-disrupting agents. Finally, we show evidence by electron microscopy of the presence of a common phage morphotype among the European and Georgian strains and a second phage morphotype among the Georgian strains. The presence of at least two stx2 phage genotypes in host genetic backgrounds that may derive from a recent common ancestor of the 2011 outbreak isolates indicates that the emergence of stx2 phage-containing E. coli O104:H4 strains probably occurred more than once, or that the current outbreak isolates may be the result of a recent transfer of a new stx2 phage element into a pre-existing stx2-positive genetic background.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; Defense Threat Reduction Agency (DTRA)

Contributing Organization:: Threat Characterization Consortium

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1627555

Journal Information:: PLoS ONE, Vol. 7, Issue 11; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance Ahn, Tae-Hyuk; Chai, Juanjuan; Pan, Chongle Bioinformatics, Vol. 31, Issue 2 https://doi.org/10.1093/bioinformatics/btu641	journal	September 2014
MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples Zolfo, Moreno; Tett, Adrian; Jousson, Olivier Nucleic Acids Research, Vol. 45, Issue 2 https://doi.org/10.1093/nar/gkw837	journal	September 2016
Shiga toxins and stx phages: highly diverse entities Krüger, Alejandra; Lucchesi, Paula M. A. Microbiology, Vol. 161, Issue 3 https://doi.org/10.1099/mic.0.000003	journal	March 2015
Genome sequencing and comparative genomics provides insights on the evolutionary dynamics and pathogenic potential of different H-serotypes of Shiga toxin-producing Escherichia coli O104 Yan, Xianghe; Fratamico, Pina M.; Bono, James L. BMC Microbiology, Vol. 15, Issue 1 https://doi.org/10.1186/s12866-015-0413-9	journal	April 2015
E. coli diversity: low in colorectal cancer Tang, Le; Zhou, Yu-Jie; Zhu, Songling BMC Medical Genomics, Vol. 13, Issue 1 https://doi.org/10.1186/s12920-020-0704-3	journal	April 2020
MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data Caboche, Ségolène; Even, Gaël; Loywick, Alexandre Genome Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s13059-017-1367-z	journal	December 2017
Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences Lanza, Val F.; de Toro, María; Garcillán-Barcia, M. Pilar PLoS Genetics, Vol. 10, Issue 12 https://doi.org/10.1371/journal.pgen.1004766	journal	December 2014
When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes Gardner, Shea N.; Hall, Barry G. PLoS ONE, Vol. 8, Issue 12 https://doi.org/10.1371/journal.pone.0081760	journal	December 2013
DNA microarray-based assessment of virulence potential of Shiga toxin gene-carrying Escherichia coli O104:H7 isolated from feedlot cattle feces Shridhar, Pragathi B.; Patel, Isha R.; Gangiredla, Jayanthi PLOS ONE, Vol. 13, Issue 4 https://doi.org/10.1371/journal.pone.0196490	journal	April 2018
Comparative Genomic and Phylogenetic Analysis of a Shiga Toxin Producing Shigella sonnei (STSS) Strain Sváb, Domonkos; Bálint, Balázs; Vásárhelyi, Bálint Frontiers in Cellular and Infection Microbiology, Vol. 7 https://doi.org/10.3389/fcimb.2017.00229	journal	May 2017
Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis Wyrsch, Ethan R.; Roy Chowdhury, Piklu; Chapman, Toni A. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00843	journal	June 2016
Klebsiella pneumoniae Asparagine tDNAs Are Integration Hotspots for Different Genomic Islands Encoding Microcin E492 Production Determinants and Other Putative Virulence Factors Present in Hypervirulent Strains Marcoleta, Andrés E.; Berríos-Pastén, Camilo; Nuñez, Gonzalo Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00849	journal	June 2016
Predominance of CTX-M-15 among ESBL Producers from Environment and Fish Gut from the Shores of Lake Victoria in Mwanza, Tanzania Moremi, Nyambura; Manda, Elizabeth V.; Falgenhauer, Linda Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.01862	journal	December 2016
Public Health Research Resulting from One of the World’s Largest Outbreaks Caused by Entero-Hemorrhagic Escherichia coli in Germany 2011: A Review Köckerling, Elena; Karrasch, Laura; Schweitzer, Aparna Frontiers in Public Health, Vol. 5 https://doi.org/10.3389/fpubh.2017.00332	journal	December 2017
Development and Validation of a Microtiter Plate-Based Assay for Determination of Bacteriophage Host Range and Virulence Xie, Yicheng; Wahab, Laith; Gill, Jason Viruses, Vol. 10, Issue 4 https://doi.org/10.3390/v10040189	journal	April 2018
The moron comes of age Cumby, Nichole; Davidson, Alan R.; Maxwell, Karen L. Bacteriophage, Vol. 2, Issue 4 https://doi.org/10.4161/bact.23146	journal	October 2012

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viral genomics
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Title: Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2

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