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Kalalah AA, Koenig SSK, Bono JL, Bosilevac JM, Eppinger M. Pathogenomes and virulence profiles of representative big six non-O157 serogroup Shiga toxin-producing Escherichia coli. Front Microbiol 2024; 15:1364026. [PMID: 38562479 PMCID: PMC10982417 DOI: 10.3389/fmicb.2024.1364026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Shiga toxin (Stx)-producing Escherichia coli (STEC) of non-O157:H7 serotypes are responsible for global and widespread human food-borne disease. Among these serogroups, O26, O45, O103, O111, O121, and O145 account for the majority of clinical infections and are colloquially referred to as the "Big Six." The "Big Six" strain panel we sequenced and analyzed in this study are reference type cultures comprised of six strains representing each of the non-O157 STEC serogroups curated and distributed by the American Type Culture Collection (ATCC) as a resource to the research community under panel number ATCC MP-9. The application of long- and short-read hybrid sequencing yielded closed chromosomes and a total of 14 plasmids of diverse functions. Through high-resolution comparative phylogenomics, we cataloged the shared and strain-specific virulence and resistance gene content and established the close relationship of serogroup O26 and O103 strains featuring flagellar H-type 11. Virulence phenotyping revealed statistically significant differences in the Stx-production capabilities that we found to be correlated to the strain's individual stx-status. Among the carried Stx1a, Stx2a, and Stx2d phages, the Stx2a phage is by far the most responsive upon RecA-mediated phage mobilization, and in consequence, stx2a + isolates produced the highest-level of toxin in this panel. The availability of high-quality closed genomes for this "Big Six" reference set, including carried plasmids, along with the recorded genomic virulence profiles and Stx-production phenotypes will provide a valuable foundation to further explore the plasticity in evolutionary trajectories in these emerging non-O157 STEC lineages, which are major culprits of human food-borne disease.
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Affiliation(s)
- Anwar A. Kalalah
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
| | - Sara S. K. Koenig
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
| | - James L. Bono
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
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Chase-Topping M, Dallman TJ, Allison L, Lupolova N, Matthews L, Mitchell S, Banks CJ, Prentice J, Brown H, Tongue S, Henry M, Evans J, Gunn G, Hoyle D, McNeilly TN, Fitzgerald S, Smith-Palmer A, Shaaban S, Holmes A, Hanson M, Woolhouse M, Didelot X, Jenkins C, Gally DL. Analysis of Escherichia coli O157 strains in cattle and humans between Scotland and England & Wales: implications for human health. Microb Genom 2023; 9:001090. [PMID: 37672388 PMCID: PMC10569735 DOI: 10.1099/mgen.0.001090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023] Open
Abstract
For the last two decades, the human infection frequency of Escherichia coli O157 (O157) in Scotland has been 2.5-fold higher than in England and Wales. Results from national cattle surveys conducted in Scotland and England and Wales in 2014/2015 were combined with data on reported human clinical cases from the same time frame to determine if strain differences in national populations of O157 in cattle could be associated with higher human infection rates in Scotland. Shiga toxin subtype (Stx) and phage type (PT) were examined within and between host (cattle vs human) and nation (Scotland vs England and Wales). For a subset of the strains, whole genome sequencing (WGS) provided further insights into geographical and host association. All three major O157 lineages (I, II, I/II) and most sub-lineages (Ia, Ib, Ic, IIa, IIb, IIc) were represented in cattle and humans in both nations. While the relative contribution of different reservoir hosts to human infection is unknown, WGS analysis indicated that the majority of O157 diversity in human cases was captured by isolates from cattle. Despite comparable cattle O157 prevalence between nations, strain types were localized. PT21/28 (sub-lineage Ic, Stx2a+) was significantly more prevalent in Scottish cattle [odds ratio (OR) 8.7 (2.3-33.7; P<0.001] and humans [OR 2.2 (1.5-3.2); P<0.001]. In England and Wales, cattle had a significantly higher association with sub-lineage IIa strains [PT54, Stx2c; OR 5.6 (1.27-33.3); P=0.011] while humans were significantly more closely associated with sub-lineage IIb [PT8, Stx1 and Stx2c; OR 29 (4.9-1161); P<0.001]. Therefore, cattle farms in Scotland were more likely to harbour Stx2a+O157 strains compared to farms in E and W (P<0.001). There was evidence of limited cattle strain migration between nations and clinical isolates from one nation were more similar to cattle isolates from the same nation, with sub-lineage Ic (mainly PT21/28) exhibiting clear national association and evidence of local transmission in Scotland. While we propose the higher rate of O157 clinical cases in Scotland, compared to England and Wales, is a consequence of the nationally higher level of Stx2a+O157 strains in Scottish cattle, we discuss the multiple additional factors that may also contribute to the different infection rates between these nations.
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Affiliation(s)
- Margo Chase-Topping
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Timothy J. Dallman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Gastrointestinal Bacteria Reference Unit, Public Health England, London NW9 5HT, UK
| | - Lesley Allison
- Scottish E. coli O157/STEC Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Nadejda Lupolova
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Louise Matthews
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Sonia Mitchell
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Christopher J. Banks
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Jamie Prentice
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Helen Brown
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Sue Tongue
- Epidemiology Research Unit, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - Madeleine Henry
- Epidemiology Research Unit, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - Judith Evans
- Epidemiology Research Unit, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - George Gunn
- Epidemiology Research Unit, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - Deborah Hoyle
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Tom N. McNeilly
- Moredun Research Institute, Pentlands Science Park, Penicuik EH26 0PZ, UK
| | - Stephen Fitzgerald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Moredun Research Institute, Pentlands Science Park, Penicuik EH26 0PZ, UK
| | | | - Sharif Shaaban
- Scottish E. coli O157/STEC Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Anne Holmes
- Scottish E. coli O157/STEC Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Mary Hanson
- Scottish E. coli O157/STEC Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh EH9 3DL, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Warwick CV4 7AL, UK
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit, Public Health England, London NW9 5HT, UK
| | - David L. Gally
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
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Charity OJ, Acton L, Bawn M, Tassinari E, Thilliez G, Chattaway MA, Dallman TJ, Petrovska L, Kingsley RA. Increased phage resistance through lysogenic conversion accompanying emergence of monophasic Salmonella Typhimurium ST34 pandemic strain. Microb Genom 2022; 8:mgen000897. [PMID: 36382789 PMCID: PMC9836087 DOI: 10.1099/mgen.0.000897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) comprises a group of closely related human and animal pathogens that account for a large proportion of all Salmonella infections globally. The epidemiological record of S. Typhimurium in Europe is characterized by successive waves of dominant clones, each prevailing for approximately 10-15 years before replacement. Succession of epidemic clones may represent a moving target for interventions aimed at controlling the spread and impact of this pathogen on human and animal health. Here, we investigate the relationship of phage sensitivity and population structure of S. Typhimurium using data from the Anderson phage typing scheme. We observed greater resistance to phage predation of epidemic clones circulating in livestock over the past decades compared to variants with a restricted host range implicating increased resistance to phage in the emergence of epidemic clones of particular importance to human health. Emergence of monophasic S. Typhimurium ST34, the most recent dominant multidrug-resistant clone, was accompanied by increased resistance to phage predation during clonal expansion, in part by the acquisition of the mTmII prophage that may have contributed to the fitness of the strains that replaced ancestors lacking this prophage.
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Affiliation(s)
- Oliver J. Charity
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK,University of East Anglia, Norwich NR4 7TJ, UK
| | - Luke Acton
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK,University of East Anglia, Norwich NR4 7TJ, UK
| | - Matt Bawn
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK,Earlham Institute, Norwich, NR4 7UZ, UK
| | - Eleonora Tassinari
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK,University of East Anglia, Norwich NR4 7TJ, UK
| | - Gaёtan Thilliez
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Marie A. Chattaway
- Gastrointestinal Bacteria Reference Unit, UK Health Security Agency (UKHSA), London, NW9 5EQ, UK
| | - Timothy J. Dallman
- Gastrointestinal Bacteria Reference Unit, UK Health Security Agency (UKHSA), London, NW9 5EQ, UK
| | - Liljana Petrovska
- Animal & Plant Health Agency (APHA), Weybridge, London, KT15 3NB, UK
| | - Robert A. Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK,University of East Anglia, Norwich NR4 7TJ, UK,*Correspondence: Robert A. Kingsley,
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Allué-Guardia A, Koenig SSK, Martinez RA, Rodriguez AL, Bosilevac JM, Feng† P, Eppinger M. Pathogenomes and variations in Shiga toxin production among geographically distinct clones of Escherichia coli O113:H21. Microb Genom 2022; 8. [PMID: 35394418 PMCID: PMC9453080 DOI: 10.1099/mgen.0.000796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Infections with globally disseminated Shiga toxin-producing Escherichia coli (STEC) of the O113:H21 serotype can progress to severe clinical complications, such as hemolytic uremic syndrome (HUS). Two phylogeographically distinct clonal complexes have been established by multi locus sequence typing (MLST). Infections with ST-820 isolates circulating exclusively in Australia have caused severe human disease, such as HUS. Conversely, ST-223 isolates prevalent in the US and outside Australia seem to rarely cause severe human disease but are frequent contaminants. Following a genomic epidemiology approach, we wanted to gain insights into the underlying cause for this disparity. We examined the plasticity in the genome make-up and Shiga toxin production in a collection of 20 ST-820 and ST-223 strains isolated from produce, the bovine reservoir, and clinical cases. STEC are notorious for assembly into fragmented draft sequences when using short-read sequencing technologies due to the extensive and partly homologous phage complement. The application of long-read technology (LRT) sequencing yielded closed reference chromosomes and plasmids for two representative ST-820 and ST-223 strains. The established high-resolution framework, based on whole genome alignments, single nucleotide polymorphism (SNP)-typing and MLST, includes the chromosomes and plasmids of other publicly available O113:H21 sequences and allowed us to refine the phylogeographical boundaries of ST-820 and ST-223 complex isolates and to further identify a historic non-shigatoxigenic strain from Mexico as a quasi-intermediate. Plasmid comparison revealed strong correlations between the strains' featured pO113 plasmid genotypes and chromosomally inferred ST, which suggests coevolution of the chromosome and virulence plasmids. Our pathogenicity assessment revealed statistically significant differences in the Stx2a-production capabilities of ST-820 as compared to ST-223 strains under RecA-induced Stx phage mobilization, a condition that mimics Stx-phage induction. These observations suggest that ST-820 strains may confer an increased pathogenic potential in line with the strain-associated epidemiological metadata. Still, some of the tested ST-223 cultures sourced from contaminated produce or the bovine reservoir also produced Stx at levels comparable to those of ST-820 isolates, which calls for awareness and for continued surveillance of this lineage.
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Affiliation(s)
- Anna Allué-Guardia
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, USA
| | - Sara S. K. Koenig
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, USA
| | - Ricardo A. Martinez
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, USA
| | - Armando L. Rodriguez
- University of Texas at San Antonio, Research Computing Support Group, San Antonio, TX, USA
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Peter Feng†
- U.S. Food and Drug Administration (FDA), College Park, MD, USA
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, USA
- *Correspondence: Mark Eppinger,
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Pinto G, Sampaio M, Dias O, Almeida C, Azeredo J, Oliveira H. Insights into the genome architecture and evolution of Shiga toxin encoding bacteriophages of Escherichia coli. BMC Genomics 2021; 22:366. [PMID: 34011288 PMCID: PMC8136144 DOI: 10.1186/s12864-021-07685-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 05/07/2021] [Indexed: 11/18/2022] Open
Abstract
Background A total of 179 Shiga toxin-producing Escherichia coli (STEC) complete genomes were analyzed in terms of serotypes, prophage coding regions, and stx gene variants and their distribution. We further examined the genetic diversity of Stx-converting phage genomes (Stx phages), focusing on the lysis-lysogeny decision and lytic cassettes. Results We show that most STEC isolates belong to non-O157 serotypes (73 %), regardless the sources and geographical regions. While the majority of STEC genomes contain a single stx gene (61 %), strains containing two (35 %), three (3 %) and four (1 %) stx genes were also found, being stx2 the most prevalent gene variant. Their location is exclusively found in intact prophage regions, indicating that they are phage-borne. We further demonstrate that Stx phages can be grouped into four clusters (A, B, C and D), three subclusters (A1, A2 and A3) and one singleton, based on their shared gene content. This cluster distribution is in good agreement with their predicted virion morphologies. Stx phage genomes are highly diverse with a vast number of 1,838 gene phamilies (phams) of related sequences (of which 677 are orphams i.e. unique genes) and, although having high mosaicism, they are generally organized into three major transcripts. While the mechanisms that guide lysis–lysogeny decision are complex, there is a strong selective pressure to maintain the stx genes location close to the lytic cassette composed of predicted SAR-endolysin and pin-holin lytic proteins. The evolution of STEC Stx phages seems to be strongly related to acquiring genetic material, probably from horizontal gene transfer events. Conclusions This work provides novel insights on the genetic structure of Stx phages, showing a high genetic diversity throughout the genomes, where the various lysis-lysogeny regulatory systems are in contrast with an uncommon, but conserved, lytic system always adjacent to stx genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07685-0.
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Affiliation(s)
- Graça Pinto
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.,INIAV, IP-National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Marta Sampaio
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Oscar Dias
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Carina Almeida
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.
| | - Hugo Oliveira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.
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