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Kalalah AA, Koenig SSK, Feng P, Bosilevac JM, Bono JL, Eppinger M. Pathogenomes of Shiga Toxin Positive and Negative Escherichia coli O157:H7 Strains TT12A and TT12B: Comprehensive Phylogenomic Analysis Using Closed Genomes. Microorganisms 2024; 12:699. [PMID: 38674643 PMCID: PMC11052207 DOI: 10.3390/microorganisms12040699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 03/18/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Shiga toxin-producing Escherichia coli are zoonotic pathogens that cause food-borne human disease. Among these, the O157:H7 serotype has evolved from an enteropathogenic O55:H7 ancestor through the displacement of the somatic gene cluster and recurrent toxigenic conversion by Shiga toxin-converting bacteriophages. However, atypical strains that lack the Shiga toxin, the characteristic virulence hallmark, are circulating in this lineage. For this study, we analyzed the pathogenome and virulence inventories of the stx+ strain, TT12A, isolated from a patient with hemorrhagic colitis, and its respective co-isolated stx- strain, TT12B. Sequencing the genomes to closure proved critical to the cataloguing of subtle strain differentiating sequence and structural polymorphisms at a high-level of phylogenetic accuracy and resolution. Phylogenomic profiling revealed SNP and MLST profiles similar to the near clonal outbreak isolates. Their prophage inventories, however, were notably different. The attenuated atypical non-shigatoxigenic status of TT12B is explained by the absence of both the ΦStx1a- and ΦStx2a-prophages carried by TT12A, and we also recorded further alterations in the non-Stx prophage complement. Phenotypic characterization indicated that culture growth was directly impacted by the strains' distinct lytic phage complement. Altogether, our phylogenomic and phenotypic analyses show that these intimately related isogenic strains are on divergent Stx(+/stx-) evolutionary paths.
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Affiliation(s)
- Anwar A. Kalalah
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX 78249, USA
| | - Sara S. K. Koenig
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX 78249, USA
| | - Peter Feng
- U.S. Food and Drug Administration (FDA), College Park, MD 20740, USA
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - James L. Bono
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX 78249, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Weinroth MD, Clawson ML, Harhay GP, Eppinger M, Harhay DM, Smith TPL, Bono JL. Escherichia coli O157:H7 tir 255 T > A allele strains differ in chromosomal and plasmid composition. Front Microbiol 2023; 14:1303387. [PMID: 38169669 PMCID: PMC10758439 DOI: 10.3389/fmicb.2023.1303387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) O157:H7 strains with the T allele in the translocated intimin receptor polymorphism (tir) 255 A > T gene associate with human disease more than strains with an A allele; however, the allele is not thought to be the direct cause of this difference. We sequenced a diverse set of STEC O157:H7 strains (26% A allele, 74% T allele) to identify linked differences that might underlie disease association. The average chromosome and pO157 plasmid size and gene content were significantly greater within the tir 255 A allele strains. Eighteen coding sequences were unique to tir 255 A allele chromosomes, and three were unique to tir 255 T allele chromosomes. There also were non-pO157 plasmids that were unique to each tir 255 allele variant. The overall average number of prophages did not differ between tir 255 allele strains; however, there were different types between the strains. Genomic and mobile element variation linked to the tir 255 polymorphism may account for the increased frequency of the T allele isolates in human disease.
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Affiliation(s)
- Margaret D. Weinroth
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Michael L. Clawson
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Gregory P. Harhay
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Dayna M. Harhay
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Timothy P. L. Smith
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - James L. Bono
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
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Carter MQ, Quiñones B, He X, Pham A, Carychao D, Cooley MB, Lo CC, Chain PSG, Lindsey RL, Bono JL. Genomic and Phenotypic Characterization of Shiga Toxin-Producing Escherichia albertii Strains Isolated from Wild Birds in a Major Agricultural Region in California. Microorganisms 2023; 11:2803. [PMID: 38004814 PMCID: PMC10673567 DOI: 10.3390/microorganisms11112803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/02/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
Escherichia albertii is an emerging foodborne pathogen. To better understand the pathogenesis and health risk of this pathogen, comparative genomics and phenotypic characterization were applied to assess the pathogenicity potential of E. albertii strains isolated from wild birds in a major agricultural region in California. Shiga toxin genes stx2f were present in all avian strains. Pangenome analyses of 20 complete genomes revealed a total of 11,249 genes, of which nearly 80% were accessory genes. Both core gene-based phylogenetic and accessory gene-based relatedness analyses consistently grouped the three stx2f-positive clinical strains with the five avian strains carrying ST7971. Among the three Stx2f-converting prophage integration sites identified, ssrA was the most common one. Besides the locus of enterocyte effacement and type three secretion system, the high pathogenicity island, OI-122, and type six secretion systems were identified. Substantial strain variation in virulence gene repertoire, Shiga toxin production, and cytotoxicity were revealed. Six avian strains exhibited significantly higher cytotoxicity than that of stx2f-positive E. coli, and three of them exhibited a comparable level of cytotoxicity with that of enterohemorrhagic E. coli outbreak strains, suggesting that wild birds could serve as a reservoir of E. albertii strains with great potential to cause severe diseases in humans.
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Affiliation(s)
- Michelle Qiu Carter
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; (B.Q.); (A.P.); (D.C.); (M.B.C.)
| | - Beatriz Quiñones
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; (B.Q.); (A.P.); (D.C.); (M.B.C.)
| | - Xiaohua He
- Foodborne Toxin Detection and Prevention Research Unit, U.S. Department of Agriculture, Western Regional Research Center, Albany, CA 94710, USA;
| | - Antares Pham
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; (B.Q.); (A.P.); (D.C.); (M.B.C.)
| | - Diana Carychao
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; (B.Q.); (A.P.); (D.C.); (M.B.C.)
| | - Michael B. Cooley
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; (B.Q.); (A.P.); (D.C.); (M.B.C.)
| | - Chien-Chi Lo
- Biosecurity and Public Health Group, U.S. Department of Energy, Los Alamos National Laboratory, Santa Fe, NM 87545, USA; (C.-C.L.); (P.S.G.C.)
| | - Patrick S. G. Chain
- Biosecurity and Public Health Group, U.S. Department of Energy, Los Alamos National Laboratory, Santa Fe, NM 87545, USA; (C.-C.L.); (P.S.G.C.)
| | - Rebecca L. Lindsey
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA;
| | - James L. Bono
- Meat Safety and Quality Research Unit, U.S. Department of Agriculture, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA;
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Weinroth MD, Clawson ML, Arthur TM, Wells JE, Brichta-Harhay DM, Strachan N, Bono JL. Rates of evolutionary change of resident Escherichia coli O157:H7 differ within the same ecological niche. BMC Genomics 2022; 23:275. [PMID: 35392797 PMCID: PMC8991562 DOI: 10.1186/s12864-022-08497-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 03/23/2022] [Indexed: 11/25/2022] Open
Abstract
Background Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a pathogen known to reside in cattle feedlots. This retrospective study examined 181 STEC O157:H7 strains collected over 23 years from a closed-system feedlot. All strains were subjected to short-read sequencing, with a subset of 36 also subjected to long-read sequencing. Results Over 96% of the strains fell into four phylogenetically distinct clades. Clade membership was associated with multiple factors including stx composition and the alleles of a well-characterized polymorphism (tir 255 T > A). Small plasmids (2.7 to 40 kb) were found to be primarily clade specific. Within each clade, chromosomal rearrangements were observed along with a core phageome and clade specific phages. Across both core and mobile elements of the genome, multiple SNP alleles were in complete linkage disequilibrium across all strains within specific clades. Clade evolutionary rates varied between 0.9 and 2.8 SNP/genome/year with two tir A allele clades having the lowest evolutionary rates. Investigation into possible causes of the differing rates was not conclusive but revealed a synonymous based mutation in the DNA polymerase III of the fastest evolving clade. Phylogenetic trees generated through our bioinformatic pipeline versus the NCBI’s pathogen detection project were similar, with the two tir A allele clades matching individual NCBI SNP clusters, and the two tir T allele clades assigned to multiple closely-related SNP clusters. Conclusions In one ecological niche, a diverse STEC O157:H7 population exhibited different rates of evolution that associated with SNP alleles in linkage disequilibrium in the core genome and mobile elements, including tir 255 T > A. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08497-6.
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Affiliation(s)
- Margaret D Weinroth
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA.,Present address: U.S. Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Athens, GA, 30605, USA
| | - Michael L Clawson
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Terrance M Arthur
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - James E Wells
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Dayna M Brichta-Harhay
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Norval Strachan
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, Scotland, AB24 3UU, UK
| | - James L Bono
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA.
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Fitzgerald SF, Lupolova N, Shaaban S, Dallman TJ, Greig D, Allison L, Tongue SC, Evans J, Henry MK, McNeilly TN, Bono JL, Gally DL. Genome structural variation in Escherichia coli O157:H7. Microb Genom 2021; 7. [PMID: 34751643 PMCID: PMC8743559 DOI: 10.1099/mgen.0.000682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human zoonotic pathogen Escherichia coli O157:H7 is defined by its extensive prophage repertoire including those that encode Shiga toxin, the factor responsible for inducing life-threatening pathology in humans. As well as introducing genes that can contribute to the virulence of a strain, prophage can enable the generation of large-chromosomal rearrangements (LCRs) by homologous recombination. This work examines the types and frequencies of LCRs across the major lineages of the O157:H7 serotype. We demonstrate that LCRs are a major source of genomic variation across all lineages of E. coli O157:H7 and by using both optical mapping and Oxford Nanopore long-read sequencing prove that LCRs are generated in laboratory cultures started from a single colony and that these variants can be recovered from colonized cattle. LCRs are biased towards the terminus region of the genome and are bounded by specific prophages that share large regions of sequence homology associated with the recombinational activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that important virulence phenotypes such as Shiga-toxin production, type-3 secretion and motility can be affected by LCRs. In summary, E. coli O157:H7 has acquired multiple prophage regions over time that act to continually produce structural variants of the genome. These findings raise important questions about the significance of this prophage-mediated genome contingency to enhance adaptability between environments.
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Affiliation(s)
- Stephen F Fitzgerald
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Nadejda Lupolova
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Sharif Shaaban
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Timothy J Dallman
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - David Greig
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - Lesley Allison
- Scottish E. coli O157/VTEC Reference Laboratory, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - Sue C Tongue
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Judith Evans
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Madeleine K Henry
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Tom N McNeilly
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 OPZ, UK
| | - James L Bono
- United States Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, Nebraska, USA
| | - David L Gally
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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Amadio A, Bono JL, Irazoqui M, Larzábal M, Marques da Silva W, Eberhardt MF, Riviere NA, Gally D, Manning SD, Cataldi A. Genomic analysis of shiga toxin-containing Escherichia coli O157:H7 isolated from Argentinean cattle. PLoS One 2021; 16:e0258753. [PMID: 34710106 PMCID: PMC8553066 DOI: 10.1371/journal.pone.0258753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/04/2021] [Indexed: 11/19/2022] Open
Abstract
Cattle are the main reservoir of Enterohemorrhagic Escherichia coli (EHEC), with O157:H7 the distinctive serotype. EHEC is the main causative agent of a severe systemic disease, Hemolytic Uremic Syndrome (HUS). Argentina has the highest pediatric HUS incidence worldwide with 12–14 cases per 100,000 children. Herein, we assessed the genomes of EHEC O157:H7 isolates recovered from cattle in the humid Pampas of Argentina. According to phylogenetic studies, EHEC O157 can be divided into clades. Clade 8 strains that were classified as hypervirulent. Most of the strains of this clade have a Shiga toxin stx2a-stx2c genotype. To better understand the molecular bases related to virulence, pathogenicity and evolution of EHEC O157:H7, we performed a comparative genomic analysis of these isolates through whole genome sequencing. The isolates classified as clade 8 (four strains) and clade 6 (four strains) contained 13 to 16 lambdoid prophages per genome, and the observed variability of prophages was analysed. An inter strain comparison show that while some prophages are highly related and can be grouped into families, other are unique. Prophages encoding for stx2a were highly diverse, while those encoding for stx2c were conserved. A cluster of genes exclusively found in clade 8 contained 13 genes that mostly encoded for DNA binding proteins. In the studied strains, polymorphisms in Q antiterminator, the Q-stx2A intergenic region and the O and P γ alleles of prophage replication proteins are associated with different levels of Stx2a production. As expected, all strains had the pO157 plasmid that was highly conserved, although one strain displayed a transposon interruption in the protease EspP gene. This genomic analysis may contribute to the understanding of the genetic basis of the hypervirulence of EHEC O157:H7 strains circulating in Argentine cattle. This work aligns with other studies of O157 strain variation in other populations that shows key differences in Stx2a-encoding prophages.
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Affiliation(s)
- Ariel Amadio
- Instituto de Investigación de la Cadena Láctea IDICaL (INTA-CONICET), Rafaela, Argentina
| | - James L. Bono
- U.S Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska, United States of America
| | - Matías Irazoqui
- Instituto de Investigación de la Cadena Láctea IDICaL (INTA-CONICET), Rafaela, Argentina
| | - Mariano Larzábal
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO)-CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
| | - Wanderson Marques da Silva
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO)-CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
| | | | - Nahuel A. Riviere
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO)-CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
| | - David Gally
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Shannon D. Manning
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Angel Cataldi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO)-CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
- * E-mail:
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8
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Franz E, Rotariu O, Lopes BS, Bono JL, Laing C, Gannon V, Van Hoek AHAM, Friesema I, French NP, George T, Biggs PJ, Jaros P, Rivas M, Chinen I, Campos J, Mellor GE, Chandry PS, Perez-Reche F, Forbes KJ, Strachan NJ. Reply to Baba and Kanamori. Clin Infect Dis 2020; 71:1353-1355. [PMID: 31711208 DOI: 10.1093/cid/ciz1102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Eelco Franz
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Ovidiu Rotariu
- School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Bruno S Lopes
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, Scotland, United Kingdom
| | - James L Bono
- United States (US) Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, Nebraska, USA
| | - Chad Laing
- National Centre for Animal Diseases, Canadian Food Inspection Agency, Lethbridge, Alberta, Canada
| | - Victor Gannon
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada
| | - Angela H A M Van Hoek
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Ingrid Friesema
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Nigel P French
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Tessy George
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patricia Jaros
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Marta Rivas
- Instituto Nacional de Enfermedades Infecciosas, Administracion Nacional del Laboratorios et Institutos de Salud "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Isabel Chinen
- Instituto Nacional de Enfermedades Infecciosas, Administracion Nacional del Laboratorios et Institutos de Salud "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Josefina Campos
- Instituto Nacional de Enfermedades Infecciosas, Administracion Nacional del Laboratorios et Institutos de Salud "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Glen E Mellor
- The Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Werribee, Australia
| | - P Scott Chandry
- The Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Werribee, Australia
| | - Francisco Perez-Reche
- Institute of Complex Systems and Mathematical Biology, Scottish Universities Physics Alliance, School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Ken J Forbes
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, Scotland, United Kingdom
| | - Norval Jc Strachan
- School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
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9
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Franz E, Rotariu O, Lopes BS, MacRae M, Bono JL, Laing C, Gannon V, Söderlund R, van Hoek AHAM, Friesema I, French NP, George T, Biggs PJ, Jaros P, Rivas M, Chinen I, Campos J, Jernberg C, Gobius K, Mellor GE, Chandry PS, Perez-Reche F, Forbes KJ, Strachan NJC. Phylogeographic Analysis Reveals Multiple International transmission Events Have Driven the Global Emergence of Escherichia coli O157:H7. Clin Infect Dis 2020; 69:428-437. [PMID: 30371758 DOI: 10.1093/cid/ciy919] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/28/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Shiga toxin-producing Escherchia coli (STEC) O157:H7 is a zoonotic pathogen that causes numerous food and waterborne disease outbreaks. It is globally distributed, but its origin and the temporal sequence of its geographical spread are unknown. METHODS We analyzed whole-genome sequencing data of 757 isolates from 4 continents, and performed a pan-genome analysis to identify the core genome and, from this, extracted single-nucleotide polymorphisms. A timed phylogeographic analysis was performed on a subset of the isolates to investigate its worldwide spread. RESULTS The common ancestor of this set of isolates occurred around 1890 (1845-1925) and originated from the Netherlands. Phylogeographic analysis identified 34 major transmission events. The earliest were predominantly intercontinental, moving from Europe to Australia around 1937 (1909-1958), to the United States in 1941 (1921-1962), to Canada in 1960 (1943-1979), and from Australia to New Zealand in 1966 (1943-1982). This pre-dates the first reported human case of E. coli O157:H7, which was in 1975 from the United States. CONCLUSIONS Inter- and intra-continental transmission events have resulted in the current international distribution of E. coli O157:H7, and it is likely that these events were facilitated by animal movements (eg, Holstein Friesian cattle). These findings will inform policy on action that is crucial to reduce the further spread of E. coli O157:H7 and other (emerging) STEC strains globally.
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Affiliation(s)
- Eelco Franz
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Ovidiu Rotariu
- School of Biological Sciences, The University of Aberdeen, United Kingdom
| | - Bruno S Lopes
- School of Medicine, Medical Sciences & Nutrition, The University of Aberdeen, United Kingdom
| | - Marion MacRae
- School of Medicine, Medical Sciences & Nutrition, The University of Aberdeen, United Kingdom
| | - James L Bono
- United States Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, Nebraska
| | - Chad Laing
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta
| | - Victor Gannon
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta
| | | | - Angela H A M van Hoek
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Ingrid Friesema
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Nigel P French
- Molecular EpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Tessy George
- Molecular EpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- Molecular EpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patricia Jaros
- Molecular EpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Marta Rivas
- Instituto Nacional de Enfermedades Infecciosas, Administracion Nacional del Laboratorios et Institutos de Salud "Dr Carlos G. Malbrán," Buenos Aires, Argentina
| | - Isabel Chinen
- Instituto Nacional de Enfermedades Infecciosas, Administracion Nacional del Laboratorios et Institutos de Salud "Dr Carlos G. Malbrán," Buenos Aires, Argentina
| | - Josefina Campos
- Instituto Nacional de Enfermedades Infecciosas, Administracion Nacional del Laboratorios et Institutos de Salud "Dr Carlos G. Malbrán," Buenos Aires, Argentina
| | - Cecilia Jernberg
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm
| | - Kari Gobius
- The Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Werribee, Victoria, Australia
| | - Glen E Mellor
- The Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Werribee, Victoria, Australia
| | - P Scott Chandry
- The Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Werribee, Victoria, Australia
| | - Francisco Perez-Reche
- Institute of Complex Systems and Mathematical Biology, SUPA, School of Natural and Computing Sciences, University of Aberdeen, United Kingdom
| | - Ken J Forbes
- School of Medicine, Medical Sciences & Nutrition, The University of Aberdeen, United Kingdom
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10
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Clawson ML, Schuller G, Dickey AM, Bono JL, Murray RW, Sweeney MT, Apley MD, DeDonder KD, Capik SF, Larson RL, Lubbers BV, White BJ, Blom J, Chitko-McKown CG, Brichta-Harhay DM, Smith TPL. Differences between predicted outer membrane proteins of genotype 1 and 2 Mannheimia haemolytica. BMC Microbiol 2020; 20:250. [PMID: 32787780 PMCID: PMC7424683 DOI: 10.1186/s12866-020-01932-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 07/29/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Mannheimia haemolytica strains isolated from North American cattle have been classified into two genotypes (1 and 2). Although members of both genotypes have been isolated from the upper and lower respiratory tracts of cattle with or without bovine respiratory disease (BRD), genotype 2 strains are much more frequently isolated from diseased lungs than genotype 1 strains. The mechanisms behind the increased association of genotype 2 M. haemolytica with BRD are not fully understood. To address that, and to search for interventions against genotype 2 M. haemolytica, complete, closed chromosome assemblies for 35 genotype 1 and 34 genotype 2 strains were generated and compared. Searches were conducted for the pan genome, core genes shared between the genotypes, and for genes specific to either genotype. Additionally, genes encoding outer membrane proteins (OMPs) specific to genotype 2 M. haemolytica were identified, and the diversity of their protein isoforms was characterized with predominantly unassembled, short-read genomic sequences for up to 1075 additional strains. RESULTS The pan genome of the 69 sequenced M. haemolytica strains consisted of 3111 genes, of which 1880 comprised a shared core between the genotypes. A core of 112 and 179 genes or gene variants were specific to genotype 1 and 2, respectively. Seven genes encoding predicted OMPs; a peptidase S6, a ligand-gated channel, an autotransporter outer membrane beta-barrel domain-containing protein (AOMB-BD-CP), a porin, and three different trimeric autotransporter adhesins were specific to genotype 2 as their genotype 1 homologs were either pseudogenes, or not detected. The AOMB-BD-CP gene, however, appeared to be truncated across all examined genotype 2 strains and to likely encode dysfunctional protein. Homologous gene sequences from additional M. haemolytica strains confirmed the specificity of the remaining six genotype 2 OMP genes and revealed they encoded low isoform diversity at the population level. CONCLUSION Genotype 2 M. haemolytica possess genes encoding conserved OMPs not found intact in more commensally prone genotype 1 strains. Some of the genotype 2 specific genes identified in this study are likely to have important biological roles in the pathogenicity of genotype 2 M. haemolytica, which is the primary bacterial cause of BRD.
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Affiliation(s)
- Michael L Clawson
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA.
| | - Gennie Schuller
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Aaron M Dickey
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - James L Bono
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | | | | | | | - Keith D DeDonder
- Veterinary and Biomedical Research Center, Inc, Manhattan, KS, USA
| | - Sarah F Capik
- Texas A&M AgriLife Research, Texas A&M University System, Amarillo, TX, USA
- Department of Veterinary Pathobiology, Texas A&M College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | | | | | | | - Jochen Blom
- Justus-Liebig-University Giessen, Giessen, Hesse, Germany
| | - Carol G Chitko-McKown
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Dayna M Brichta-Harhay
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Timothy P L Smith
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
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11
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Harhay DM, Weinroth MD, Bono JL, Harhay GP, Bosilevac JM. Rapid estimation of Salmonella enterica contamination level in ground beef - Application of the time-to-positivity method using a combination of molecular detection and direct plating. Food Microbiol 2020; 93:103615. [PMID: 32912587 DOI: 10.1016/j.fm.2020.103615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/21/2020] [Accepted: 07/31/2020] [Indexed: 11/28/2022]
Abstract
Little progress has been made in decreasing the incidence rate of salmonellosis in the US over the past decade. Mitigating the contribution of contaminated raw meat to the salmonellosis incidence rate requires rapid methods for quantifying Salmonella, so that highly contaminated products can be removed before entering the food chain. Here we evaluated the use of Time-to-Positivity (TTP) as a rapid, semi-quantitative approach for estimating Salmonella contamination levels in ground beef. Growth rates of 14 Salmonella strains (inoculated at log 1 to -2 CFU/g) were characterized in lean ground beef mTSB enrichments and time-to-detection was determined using culture and molecular detection methods. Enrichments were sampled at five timepoints and results were used to construct a prediction model of estimated contamination level by TTP (superscript indicates time in hours) defined as TTP4: ≥5 CFU/g; TTP6: ≤5, ≥1 CFU/g; TTP8: ≤1, ≥0.01 CFU/g; with samples negative at 8 h estimated ≤0.01 CFU/g. Model performance measures showed high sensitivity (100%) and specificity (83% and 93% for two detection methods) for samples with a TTP4, with false negative rates of 0%.
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Affiliation(s)
- Dayna M Harhay
- United States Department of Agriculture, Roman L. Hruska U.S. Meat Animal Research Center, Meat Safety and Quality Research Unit, Clay Center, NE, 68933, USA.
| | - Margaret D Weinroth
- United States Department of Agriculture, Roman L. Hruska U.S. Meat Animal Research Center, Meat Safety and Quality Research Unit, Clay Center, NE, 68933, USA
| | - James L Bono
- United States Department of Agriculture, Roman L. Hruska U.S. Meat Animal Research Center, Meat Safety and Quality Research Unit, Clay Center, NE, 68933, USA
| | - Gregory P Harhay
- United States Department of Agriculture, Roman L. Hruska U.S. Meat Animal Research Center, Meat Safety and Quality Research Unit, Clay Center, NE, 68933, USA
| | - Joseph M Bosilevac
- United States Department of Agriculture, Roman L. Hruska U.S. Meat Animal Research Center, Meat Safety and Quality Research Unit, Clay Center, NE, 68933, USA
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12
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Wells JE, Berry ED, Kim M, Bono JL, Oliver WT, Kalchayanand N, Wang R, Freetly HC, Means WJ. Determination of gastrointestinal tract colonization sites from feedlot cattle transiently shedding or super-shedding Escherichia coli O157:H7 at harvest. J Appl Microbiol 2020; 129:1419-1426. [PMID: 32350973 DOI: 10.1111/jam.14684] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 03/24/2020] [Accepted: 04/26/2020] [Indexed: 11/28/2022]
Abstract
AIMS The objective of the study was to determine levels of Escherichia coli O157:H7 colonization in the gastrointestinal tract (GIT) of naturally shedding cattle shedding the pathogen at low- or super-shedder levels. METHODS AND RESULTS Over 2 years, feedlot cattle were sampled multiple times for faecal shedding of E. coli O157:H7. Just prior to harvest (1-2 days), animals that were super-shedders (≥104 CFU per gram of faeces) were specifically identified, and based on the longer term screening data, pen cohorts that were low-shedders (years 1 and 2) or chronic-shedders (year 1) were also identified. At harvest, samples were collected from throughout the GIT, including the rectoanal junction (RAJ) for enumeration and enrichment of E. coli O157:H7. The mouth samples exhibited the greatest prevalence for the pathogen, and the abomasum and rumen exhibited the lowest prevalence (P < 0·05). Super-shedders had significantly greater prevalence for all GIT locations except the mouth and abomasum compared to low-shedders, but the super-shedders were the only animals with positive abomasum samples. Samples from the super-shedders were enumerable for most GIT locations, and the rectum and RAJ locations were the only locations that were significantly greater than other locations (P < 0·05). CONCLUSIONS Across all animals naturally exposed to E. coli O157:H7, the risk of ingestion is high, but rumen and abomasum are potential barriers to passage. In super-shedders, the passage through the GIT was greater, allowing colonization in the rectum and at the RAJ. SIGNIFICANCE AND IMPACT OF THE STUDY Escherichia coli O157:H7 low-shedding cattle had lower pathogen levels throughout the GIT, indicating intrinsic GIT factors to these cattle may reduce pathogen passage through the GIT, including the abomasum, and minimize risk of RAJ colonization.
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Affiliation(s)
- J E Wells
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, USA
| | - E D Berry
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, USA
| | - M Kim
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, USA
| | - J L Bono
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, USA
| | - W T Oliver
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, USA
| | - N Kalchayanand
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, USA
| | - R Wang
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, USA
| | - H C Freetly
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, USA
| | - W J Means
- Department of Animal and Range Science, University of Wyoming, Laramie, WY, USA
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13
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Nyong EC, Zaia SR, Allué-Guardia A, Rodriguez AL, Irion-Byrd Z, Koenig SSK, Feng P, Bono JL, Eppinger M. Pathogenomes of Atypical Non-shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive Phylogenomic Analysis Using Closed Genomes. Front Microbiol 2020; 11:619. [PMID: 32351476 PMCID: PMC7175801 DOI: 10.3389/fmicb.2020.00619] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/19/2020] [Indexed: 12/19/2022] Open
Abstract
The toxigenic conversion of Escherichia coli strains by Shiga toxin-converting (Stx) bacteriophages were prominent and recurring events in the stepwise evolution of enterohemorrhagic E. coli (EHEC) O157:H7 from an enteropathogenic (EPEC) O55:H7 ancestor. Atypical, attenuated isolates have been described for both non-sorbitol fermenting (NSF) O157:H7 and SF O157:NM serotypes, which are distinguished by the absence of Stx, the characteristic virulence hallmark of Stx-producing E. coli (STEC). Such atypical isolates either never acquired Stx-phages or may have secondarily lost stx during the course of infection, isolation, or routine subculture; the latter are commonly referred to as LST (Lost Shiga Toxin)-isolates. In this study we analyzed the genomes of 15 NSF O157:H7 and SF O157:NM strains from North America, Europe, and Asia that are characterized by the absence of stx, the virulence hallmark of STEC. The individual genomic basis of the Stx (-) phenotype has remained largely undetermined as the majority of STEC genomes in public genome repositories were generated using short read technology and are in draft stage, posing a major obstacle for the high-resolution whole genome sequence typing (WGST). The application of LRT (long-read technology) sequencing provided us with closed genomes, which proved critical to put the atypical non-shigatoxigenic NSF O157:H7 and SF O157:NM strains into the phylogenomic context of the stepwise evolutionary model. Availability of closed chromosomes for representative Stx (-) NSF O157:H7 and SF O157:NM strains allowed to describe the genomic basis and individual evolutionary trajectories underlying the absence of Stx at high accuracy and resolution. The ability of LRT to recover and accurately assemble plasmids revealed a strong correlation between the strains' featured plasmid genotype and chromosomally inferred clade, which suggests the coevolution of the chromosome and accessory plasmids. The identified ancestral traits in the pSFO157 plasmid of NSF O157:H7 strain LSU-61 provided additional evidence for its intermediate status. Taken together, these observations highlight the utility of LRTs for advancing our understanding of EHEC O157:H7/NM pathogenome evolution. Insights into the genomic and phenotypic plasticity of STEC on a lineage- and genome-wide scale are foundational to improve and inform risk assessment, biosurveillance, and prevention strategies.
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Affiliation(s)
- Emmanuel C. Nyong
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Sam R. Zaia
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Anna Allué-Guardia
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Armando L. Rodriguez
- Research Computing Support Group, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Zaina Irion-Byrd
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Sara S. K. Koenig
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | | | - James L. Bono
- United States Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture (ARS-USDA), Clay Center, NE, United States
| | - Mark Eppinger
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
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14
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Whitman KJ, Bono JL, Clawson ML, Loy JD, Bosilevac JM, Arthur TM, Ondrak JD. Genomic-based identification of environmental and clinical Listeria monocytogenes strains associated with an abortion outbreak in beef heifers. BMC Vet Res 2020; 16:70. [PMID: 32087722 PMCID: PMC7036198 DOI: 10.1186/s12917-020-2276-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 02/05/2020] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND In a beef cattle facility an outbreak of abortions occurred over a 36-day period and included samples from two aborted (non-viable) fetuses and 21 post-abortion clinical cases. There are numerous etiologies, including clinical listeriosis. At the species level, Listeria monocytogenes is ubiquitous in cattle production environments, including soil, feed, and occasionally water sources, and is a common enteric resident of cattle and other mammals. There are four genetically distinct lineages of L. monocytogenes (I-IV), with most lineage III and IV isolates obtained from ruminants. Definitive diagnosis of L. monocytogenes as a causative agent in disease outbreaks relies upon case identification, appropriate sample collection, and laboratory confirmation. Furthermore, clearly establishing a relationship between a pathogen source and clinical disease is difficult. RESULTS Of the two fetal and 21 clinical case submissions, 19 were positive for L. monocytogenes. Subsequent culture for L. monocytogenes from water and silage sources identified both as potential origins of infection. Using whole-genome sequencing and phylogenetic analyses, clinical, water and silage L. monocytogenes strains grouped into two of four lineages. All water and silage strains, plus 11 clinical strains placed in lineage III, with identical or nearly identical genomic sequences. The remaining eight clinical strains placed in lineage I, with seven having nearly identical sequences and one distinctly different. CONCLUSION Three genetically distinct strains within two lineages of L. monocytogenes caused the abortion outbreak. The etiology of abortion in 11 cases was directly linked to water and silage contamination from a lineage III L. monocytogenes strain. The source of infection for the remaining abortion cases with two different strains from lineage I is unknown. This is the first report of L. monocytogenes genomics being used as part of an outbreak investigation of cattle abortion.
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Affiliation(s)
- Katherine J Whitman
- University of Nebraska-Lincoln, School of Veterinary Medicine and Biomedical Sciences, Great Plains Veterinary Educational Center, Clay Center, NE, 68933, USA.
| | - James L Bono
- USDA ARS US Meat Animal Research Center, Clay Center, NE, 68933, USA.
| | - Michael L Clawson
- USDA ARS US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - John D Loy
- University of Nebraska-Lincoln, School of Veterinary Medicine and Biomedical Sciences, Nebraska Veterinary Diagnostic Center, Lincoln, NE, 68583-0907, USA
| | | | - Terrance M Arthur
- USDA ARS US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Jeff D Ondrak
- University of Nebraska-Lincoln, School of Veterinary Medicine and Biomedical Sciences, Great Plains Veterinary Educational Center, Clay Center, NE, 68933, USA
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15
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Miller WG, Yee E, Bono JL. Complete Genome Sequencing of Four Arcobacter Species Reveals a Diverse Suite of Mobile Elements. Genome Biol Evol 2020; 12:3850-3856. [PMID: 32011709 DOI: 10.1093/gbe/evaa014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2020] [Indexed: 11/13/2022] Open
Abstract
Arcobacter species are recovered from a wide variety of sources, including animals, food, and both fresh and marine waters. Several Arcobacter species have also been recovered from human clinical samples and are thus associated tentatively with food- and water-borne human illnesses. Genome sequencing of the poultry isolate Arcobacter cibarius H743 and the Arcobacter acticola, Arcobacter pacificus, and Arcobacter porcinus type strains identified a large number and variety of insertion sequences. This study presents an analysis of these A. acticola, A. cibarius, A. pacificus, and A. porcinus IS elements. The four genomes sequenced here contain 276 complete and degenerate IS elements, representing 13 of the current 29 prokaryotic IS element families. Expansion of the analysis to include 15 other previously sequenced Arcobacter spp. added 73 complete and degenerate IS elements. Several of these IS elements were identified in two or more Arcobacter species, suggesting movement by horizontal gene transfer between the arcobacters. These IS elements are putatively associated with intragenomic deletions and inversions, and tentative movement of antimicrobial resistance genes. The A. cibarius strain H743 megaplasmid contains multiple IS elements common to the chromosome and, unusually, a complete ribosomal RNA locus, indicating that larger scale genomic rearrangements, potentially resulting from IS element-mediated megaplasmid cointegration and resolution may be occurring within A. cibarius and possibly other arcobacters. The presence of such a large and varied suite of mobile elements could have profound effects on Arcobacter biology and evolution.
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Affiliation(s)
- William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California
| | - Emma Yee
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California
| | - James L Bono
- Meat Safety and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska
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16
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Harhay GP, Harhay DM, Bono JL, Capik SF, DeDonder KD, Apley MD, Lubbers BV, White BJ, Larson RL, Smith TPL. A Computational Method to Quantify the Effects of Slipped Strand Mispairing on Bacterial Tetranucleotide Repeats. Sci Rep 2019; 9:18087. [PMID: 31792233 PMCID: PMC6889271 DOI: 10.1038/s41598-019-53866-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 11/04/2019] [Indexed: 01/17/2023] Open
Abstract
The virulence and pathogenicity of bacterial pathogens are related to their adaptability to changing environments. One process enabling adaptation is based on minor changes in genome sequence, as small as a few base pairs, within segments of genome called simple sequence repeats (SSRs) that consist of multiple copies of a short sequence (from one to several nucleotides), repeated in series. SSRs are found in eukaryotes as well as prokaryotes, and length variation in them occurs at frequencies up to a million-fold higher than bacterial point mutations through the process of slipped strand mispairing (SSM) by DNA polymerase during replication. The characterization of SSR length by standard sequencing methods is complicated by the appearance of length variation introduced during the sequencing process that obscures the lower abundance repeat number variants in a population. Here we report a computational approach to correct for sequencing process-induced artifacts, validated for tetranucleotide repeats by use of synthetic constructs of fixed, known length. We apply this method to a laboratory culture of Histophilus somni, prepared from a single colony, and demonstrate that the culture consists of populations of distinct sequence phase and length variants at individual tetranucleotide SSR loci.
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Affiliation(s)
- Gregory P Harhay
- USDA ARS US Meat Animal Research Center, Clay Center, NE, United States.
| | - Dayna M Harhay
- USDA ARS US Meat Animal Research Center, Clay Center, NE, United States
| | - James L Bono
- USDA ARS US Meat Animal Research Center, Clay Center, NE, United States
| | - Sarah F Capik
- Texas A&M AgriLife Research, Amarillo, TX and the College of Veterinary Medicine & Biomedical Sciences, Texas A&M University System, College Station, TX, United States
| | - Keith D DeDonder
- Veterinary and Biomedical Research Center, Inc, Manhattan, KS, United States
| | - Michael D Apley
- Kansas State University, College of Veterinary Medicine, Manhattan, KS, United States
| | - Brian V Lubbers
- Kansas State University, College of Veterinary Medicine, Manhattan, KS, United States
| | - Bradley J White
- Kansas State University, College of Veterinary Medicine, Manhattan, KS, United States
| | - Robert L Larson
- Kansas State University, College of Veterinary Medicine, Manhattan, KS, United States
| | - Timothy P L Smith
- USDA ARS US Meat Animal Research Center, Clay Center, NE, United States
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17
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Fitzgerald SF, Beckett AE, Palarea-Albaladejo J, McAteer S, Shaaban S, Morgan J, Ahmad NI, Young R, Mabbott NA, Morrison L, Bono JL, Gally DL, McNeilly TN. Shiga toxin sub-type 2a increases the efficiency of Escherichia coli O157 transmission between animals and restricts epithelial regeneration in bovine enteroids. PLoS Pathog 2019; 15:e1008003. [PMID: 31581229 PMCID: PMC6776261 DOI: 10.1371/journal.ppat.1008003] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/25/2019] [Indexed: 02/06/2023] Open
Abstract
Specific Escherichia coli isolates lysogenised with prophages that express Shiga toxin (Stx) can be a threat to human health, with cattle being an important natural reservoir. In many countries the most severe pathology is associated with enterohaemorrhagic E. coli (EHEC) serogroups that express Stx subtype 2a. In the United Kingdom, phage type (PT) 21/28 O157 strains have emerged as the predominant cause of life-threatening EHEC infections and this phage type commonly encodes both Stx2a and Stx2c toxin types. PT21/28 is also epidemiologically linked to super-shedding (>103 cfu/g of faeces) which is significant for inter-animal transmission and human infection as demonstrated using modelling studies. We demonstrate that Stx2a is the main toxin produced by stx2a+/stx2c+ PT21/28 strains induced with mitomycin C and this is associated with more rapid induction of gene expression from the Stx2a-encoding prophage compared to that from the Stx2c-encoding prophage. Bacterial supernatants containing either Stx2a and/or Stx2c were demonstrated to restrict growth of bovine gastrointestinal organoids with no restriction when toxin production was not induced or prevented by mutation. Isogenic strains that differed in their capacity to produce Stx2a were selected for experimental oral colonisation of calves to assess the significance of Stx2a for both super-shedding and transmission between animals. Restoration of Stx2a expression in a PT21/28 background significantly increased animal-to-animal transmission and the number of sentinel animals that became super-shedders. We propose that while both Stx2a and Stx2c can restrict regeneration of the epithelium, it is the relatively rapid and higher levels of Stx2a induction, compared to Stx2c, that have contributed to the successful emergence of Stx2a+ E. coli isolates in cattle in the last 40 years. We propose a model in which Stx2a enhances E. coli O157 colonisation of in-contact animals by restricting regeneration and turnover of the colonised gastrointestinal epithelium. Enterohaemorrhagic E. coli (EHEC) O157 strains are found in cattle where they are asymptomatic, while human exposure can lead to severe symptoms including bloody diarrhoea and kidney damage due to the activity of Shiga toxin (Stx). The most serious symptoms in humans are associated with isolates that encode Stx subtype 2a. The advantage of these toxins in the animal reservoir is still not clear, however there is experimental evidence implicating Stx with increased bacterial adherence, immune modulation and suppression of predatory protozoa. In this study, the hypothesis that Stx2a is important for super-shedding and calf-to-calf transmission was tested by comparing excretion and transmission dynamics of E. coli O157 strains with and without Stx2a. While Stx2a did not alter excretion levels when calfs were orally challenge, it enabled colonisation of more in contact ‘sentinel’ animals in our transmission model. We show that Stx2a is generally induced more rapidly than Stx2c, resulting in increased levels of Stx2a expression. Both Stx2a and Stx2c were able to restrict cellular proliferation of epithelial cells in cultured bovine enteroids. Taken together, we propose that rapid production of Stx2a and its role in establishing E. coli O157 colonisation in the bovine gastrointestinal tract facilitate effective transmission and have led to its expansion in the cattle E. coli O157 population.
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Affiliation(s)
- Stephen F. Fitzgerald
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
- Moredun Research Institute, Penicuik, United Kingdom
| | - Amy E. Beckett
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
- Moredun Research Institute, Penicuik, United Kingdom
| | | | - Sean McAteer
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
| | - Sharif Shaaban
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
| | - Jason Morgan
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
- Moredun Research Institute, Penicuik, United Kingdom
| | | | - Rachel Young
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
| | - Neil A. Mabbott
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
| | - Liam Morrison
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
| | - James L. Bono
- United States Department of Agriculture, Agricultural Research Service, Nebraska, United States of America
| | - David L. Gally
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
- * E-mail: (DLG); (TNM)
| | - Tom N. McNeilly
- Moredun Research Institute, Penicuik, United Kingdom
- * E-mail: (DLG); (TNM)
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18
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Berry ED, Wells JE, Durso LM, Friesen KM, Bono JL, Suslow TV. Occurrence of Escherichia coli O157:H7 in Pest Flies Captured in Leafy Greens Plots Grown Near a Beef Cattle Feedlot. J Food Prot 2019; 82:1300-1307. [PMID: 31310171 DOI: 10.4315/0362-028x.jfp-18-601] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Leafy greens are leading vehicles for Escherichia coli O157:H7 foodborne illness. Pest flies can harbor this pathogen and may disseminate it to produce. We determined the occurrence of E. coli O157:H7-positive flies in leafy greens planted up to 180 m from a cattle feedlot and assessed their relative risk to transmit this pathogen to leafy greens. The primary fly groups captured on sticky traps at the feedlot and leafy greens plots included house flies (Musca domestica L.), face flies (Musca autumnalis L.), stable flies (Stomoxys calcitrans L.), flesh flies (family Sarcophagidae), and blow flies (family Calliphoridae). E. coli O157:H7 carriage rates of house, face, flesh, and blow flies were similar (P > 0.05), ranging from 22.3 to 29.0 flies per 1,000 flies. In contrast, the carriage rate of stable flies was lower at 1.1 flies per 1,000 flies (P < 0.05). Differences in carriage rates are likely due to the uses of fresh bovine feces and manure by these different pest fly groups. E. coli O157:H7 carriage rates of total flies did not differ (P > 0.05) by distance (ranging from 0 to 180 m) from the feedlot. Most fly isolates were the same predominant pulsed-field gel electrophoresis types found in feedlot surface manure and leafy greens, suggesting a possible role for flies in transmitting E. coli O157:H7 to the leafy greens. However, further research is needed to clarify this role and to determine set-back distances between cattle production facilities and produce crops that will reduce the risk for pathogen contamination by challenging mechanisms like flies.
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Affiliation(s)
- Elaine D Berry
- 1 U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, P.O. Box 166, State Spur 18D, Clay Center, Nebraska 68933
| | - James E Wells
- 1 U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, P.O. Box 166, State Spur 18D, Clay Center, Nebraska 68933
| | - Lisa M Durso
- 2 U.S. Department of Agriculture, Agricultural Research Service, Agroecosystem Management Unit, 251 Filley Hall, UNL East Campus, Lincoln, Nebraska 68583
| | - Kristina M Friesen
- 2 U.S. Department of Agriculture, Agricultural Research Service, Agroecosystem Management Unit, 251 Filley Hall, UNL East Campus, Lincoln, Nebraska 68583
| | - James L Bono
- 1 U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, P.O. Box 166, State Spur 18D, Clay Center, Nebraska 68933
| | - Trevor V Suslow
- 3 Department of Plant Sciences, University of California, One Shields Avenue, Davis, California 95616, USA
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19
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Miller WG, Yee E, Bono JL. Complete Genome Sequences of the Arcobacter cryaerophilus Strains ATCC 43158 T and ATCC 49615. Microbiol Resour Announc 2018; 7:e01463-18. [PMID: 30533823 PMCID: PMC6256622 DOI: 10.1128/mra.01463-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/01/2018] [Indexed: 11/20/2022] Open
Abstract
Arcobacter cryaerophilus was originally recovered from aborted bovine and porcine fetuses, but it has been subsequently isolated from meat, water, and human clinical samples. This study describes the complete whole-genome sequences of two A. cryaerophilus strains, ATCC 43158T (=A 169/BT =LMG 24291T) and ATCC 49615 (=CDC D2610 =LMG 10829).
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Affiliation(s)
- William G. Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Emma Yee
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - James L. Bono
- Meat Safety and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska, USA
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20
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Miller WG, Yee E, Bono JL. Complete Genome Sequence of the Arcobacter suis Type Strain LMG 26152. Microbiol Resour Announc 2018; 7:e01307-18. [PMID: 30533764 PMCID: PMC6256499 DOI: 10.1128/mra.01307-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/10/2018] [Indexed: 11/25/2022] Open
Abstract
Arcobacter species are prevalent in pigs, and strains have been isolated from pig feces and pork meat; some Arcobacter strains may be porcine abortifacients. Arcobacter suis was recovered from pork meat in Spain. This study describes the whole-genome sequence of the A. suis type strain LMG 26152 (=F41T =CECT 7833T).
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Affiliation(s)
- William G. Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Emma Yee
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - James L. Bono
- Meat Safety and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska, USA
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21
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Miller WG, Yee E, Bono JL. Complete Genome Sequence of the Arcobacter molluscorum Type Strain LMG 25693. Microbiol Resour Announc 2018; 7:e01293-18. [PMID: 30533749 PMCID: PMC6256585 DOI: 10.1128/mra.01293-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 09/26/2018] [Indexed: 12/22/2022] Open
Abstract
As components of freshwater and marine microflora, Arcobacter spp. are often recovered from shellfish, such as mussels, clams, and oysters. Arcobacter molluscorum was isolated from mussels from the Ebro Delta in Catalonia, Spain. This article describes the whole-genome sequence of the A. molluscorum strain LMG 25693T (= F98-3T = CECT 7696T).
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Affiliation(s)
- William G. Miller
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Albany, California, USA
| | - Emma Yee
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Albany, California, USA
| | - James L. Bono
- U.S. Department of Agriculture, Meat Safety and Quality Research Unit, Agricultural Research Service, Clay Center, Nebraska, USA
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22
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Miller WG, Yee E, Bono JL. Complete Genome Sequence of the Arcobacter ellisii Type Strain LMG 26155. Microbiol Resour Announc 2018; 7:e01268-18. [PMID: 30533751 PMCID: PMC6256587 DOI: 10.1128/mra.01268-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 09/30/2018] [Indexed: 01/05/2023] Open
Abstract
Arcobacter spp. are highly prevalent in contaminated environmental waters and have been recovered from both freshwater and seawater, with several species isolated from shellfish. Arcobacter ellisii was recovered from mussels collected in Catalonia, Spain. This study describes the whole-genome sequence of the A. ellisii type strain LMG 26155 (=F79-6T =CECT 7837T).
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Affiliation(s)
- William G. Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Emma Yee
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - James L. Bono
- Meat Safety and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska, USA
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23
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Rotundo L, Boccia F, Fratamico PM, Xu A, Sommers CH, Liu Y, Bono JL, Pepe T. Draft Genome Sequences of Seven Strains of Shiga Toxin-Producing Escherichia coli O111 with Variation in Their Sensitivity to Novobiocin. Microbiol Resour Announc 2018; 7:e01030-18. [PMID: 30533630 PMCID: PMC6256608 DOI: 10.1128/mra.01030-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/15/2018] [Indexed: 11/20/2022] Open
Abstract
Inclusion of novobiocin as a selective agent for enrichment media and selective agars inhibits the growth of some Shiga toxin-producing Escherichia coli (STEC) strains, particularly non-O157 STEC, which can yield false-negative detection results. Here, we report the draft genomic sequences of seven STEC O111 isolates with different sensitivities to novobiocin.
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Affiliation(s)
- Luca Rotundo
- USDA, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, USA
| | - Federica Boccia
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Pina M. Fratamico
- USDA, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, USA
| | - Aixia Xu
- USDA, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, USA
| | - Christopher H. Sommers
- USDA, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, USA
| | - Yanhong Liu
- USDA, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, USA
| | - James L. Bono
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, Nebraska, USA
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
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24
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Allué-Guardia A, Koenig SSK, Quirós P, Muniesa M, Bono JL, Eppinger M. Closed Genome and Comparative Phylogenetic Analysis of the Clinical Multidrug Resistant Shigella sonnei Strain 866. Genome Biol Evol 2018; 10:2241-2247. [PMID: 30060169 PMCID: PMC6128377 DOI: 10.1093/gbe/evy168] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 01/10/2023] Open
Abstract
Shigella sonnei is responsible for the majority of shigellosis infections in the US with over 500,000 cases reported annually. Here, we present the complete genome of the clinical multidrug resistant (MDR) strain 866, which is highly susceptible to bacteriophage infections. The strain has a circular chromosome of 4.85 Mb and carries a 113 kb MDR plasmid. This IncB/O/K/Z-type plasmid, termed p866, confers resistance to five different classes of antibiotics including ß-lactamase, sulfonamide, tetracycline, aminoglycoside, and trimethoprim. Comparative analysis of the plasmid architecture and gene inventory revealed that p866 shares its plasmid backbone with previously described IncB/O/K/Z-type Shigella spp. and Escherichia coli plasmids, but is differentiated by the insertion of antibiotic resistance cassettes, which we found associated with mobile genetic elements such as Tn3, Tn7, and Tn10. A whole genome-derived phylogenetic reconstruction showed the evolutionary relationships of S. sonnei strain 866 and the four established Shigella species, highlighting the clonal nature of S. sonnei.
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Affiliation(s)
- Anna Allué-Guardia
- Department of Biology, University of Texas at San Antonio.,South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio
| | - Sara S K Koenig
- Department of Biology, University of Texas at San Antonio.,South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio
| | - Pablo Quirós
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Spain
| | - James L Bono
- Agricultural Research Service, United States Department of Agriculture, U.S. Meat Animal Research Center, Clay Center, Nebraska
| | - Mark Eppinger
- Department of Biology, University of Texas at San Antonio.,South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio
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25
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Nguyen SV, Harhay DM, Bono JL, Smith TPL, Fields PI, Dinsmore BA, Santovenia M, Wang R, Bosilevac JM, Harhay GP. Comparative genomics of Salmonella enterica serovar Montevideo reveals lineage-specific gene differences that may influence ecological niche association. Microb Genom 2018; 4:e000202. [PMID: 30052174 PMCID: PMC6159554 DOI: 10.1099/mgen.0.000202] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/05/2018] [Indexed: 01/01/2023] Open
Abstract
Salmonella enterica serovar Montevideo has been linked to recent foodborne illness outbreaks resulting from contamination of products such as fruits, vegetables, seeds and spices. Studies have shown that Montevideo also is frequently associated with healthy cattle and can be isolated from ground beef, yet human salmonellosis outbreaks of Montevideo associated with ground beef contamination are rare. This disparity fuelled our interest in characterizing the genomic differences between Montevideo strains isolated from healthy cattle and beef products, and those isolated from human patients and outbreak sources. To that end, we sequenced 13 Montevideo strains to completion, producing high-quality genome assemblies of isolates from human patients (n=8) or from healthy cattle at slaughter (n=5). Comparative analysis of sequence data from this study and publicly available sequences (n=72) shows that Montevideo falls into four previously established clades, differentially occupied by cattle and human strains. The results of these analyses reveal differences in metabolic islands, environmental adhesion determinants and virulence factors within each clade, and suggest explanations for the infrequent association between bovine isolates and human illnesses.
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Affiliation(s)
- Scott V. Nguyen
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Dayna M. Harhay
- USDA-ARS-US Meat Animal Research Center, Clay Center, NE 68933, USA
| | - James L. Bono
- USDA-ARS-US Meat Animal Research Center, Clay Center, NE 68933, USA
| | | | - Patricia I. Fields
- Enteric Disease Laboratory Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Blake A. Dinsmore
- Enteric Disease Laboratory Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Monica Santovenia
- Enteric Disease Laboratory Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Rong Wang
- USDA-ARS-US Meat Animal Research Center, Clay Center, NE 68933, USA
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26
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Abstract
Campylobacter sputorum is a nonthermotolerant campylobacter that is primarily isolated from food animals such as cattle and sheep. C. sputorum is also infrequently associated with human illness. Based on catalase and urease activity, three biovars are currently recognized within C. sputorum: bv. sputorum (catalase negative, urease negative), bv. fecalis (catalase positive, urease negative), and bv. paraureolyticus (catalase negative, urease positive). A multi-locus sequence typing (MLST) method was recently constructed for C. sputorum. MLST typing of several cattle-associated C. sputorum isolates suggested that they are members of a divergent C. sputorum clade. Although catalase positive, and thus technically bv. fecalis, the taxonomic position of these strains could not be determined solely by MLST. To further characterize C. sputorum, the genomes of four strains, representing all three biovars and the divergent clade, were sequenced to completion. Here we present a comparative genomic analysis of the four C. sputorum genomes. This analysis indicates that the three biovars and the cattle-associated strains are highly related at the genome level with similarities in gene content. Furthermore, the four genomes are strongly syntenic with one or two minor inversions. However, substantial differences in gene content were observed among the three biovars. Finally, although the strain representing the cattle-associated isolates was shown to be C. sputorum, it is possible that this strain is a member of a novel C. sputorum subspecies; thus, these cattle-associated strains may form a second taxon within C. sputorum.
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Affiliation(s)
- William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California
| | - Emma Yee
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California
| | - Mary H Chapman
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California
| | - James L Bono
- Meat Safety and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska
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27
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Miller WG, Yee E, Lopes BS, Chapman MH, Huynh S, Bono JL, Parker CT, Strachan NJC, Forbes KJ. Comparative Genomic Analysis Identifies a Campylobacter Clade Deficient in Selenium Metabolism. Genome Biol Evol 2017; 9:1843-1858. [PMID: 28854596 PMCID: PMC5570042 DOI: 10.1093/gbe/evx093] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2017] [Indexed: 12/19/2022] Open
Abstract
The nonthermotolerant Campylobacter species C. fetus, C. hyointestinalis, C. iguaniorum, and C. lanienae form a distinct phylogenetic cluster within the genus. These species are primarily isolated from foraging (swine) or grazing (e.g., cattle, sheep) animals and cause sporadic and infrequent human illness. Previous typing studies identified three putative novel C. lanienae-related taxa, based on either MLST or atpA sequence data. To further characterize these putative novel taxa and the C. fetus group as a whole, 76 genomes were sequenced, either to completion or to draft level. These genomes represent 26 C. lanienae strains and 50 strains of the three novel taxa. C. fetus, C. hyointestinalis and C. iguaniorum genomes were previously sequenced to completion; therefore, a comparative genomic analysis across the entire C. fetus group was conducted (including average nucleotide identity analysis) that supports the initial identification of these three novel Campylobacter species. Furthermore, C. lanienae and the three putative novel species form a discrete clade within the C. fetus group, which we have termed the C. lanienae clade. This clade is distinguished from other members of the C. fetus group by a reduced genome size and distinct CRISPR/Cas systems. Moreover, there are two signature characteristics of the C. lanienae clade. C. lanienae clade genomes carry four to ten unlinked and similar, but nonidentical, flagellin genes. Additionally, all 76 C. lanienae clade genomes sequenced demonstrate a complete absence of genes related to selenium metabolism, including genes encoding the selenocysteine insertion machinery, selenoproteins, and the selenocysteinyl tRNA.
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Affiliation(s)
- William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA
| | - Emma Yee
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA
| | - Bruno S Lopes
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, United Kingdom
| | - Mary H Chapman
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA
| | - Steven Huynh
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA
| | - James L Bono
- Meat Safety and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, NE
| | - Craig T Parker
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA
| | - Norval J C Strachan
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, United Kingdom
| | - Ken J Forbes
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, United Kingdom
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28
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Kim M, Kuehn LA, Bono JL, Berry ED, Kalchayanand N, Freetly HC, Benson AK, Wells JE. The impact of the bovine faecal microbiome on Escherichia coli O157:H7 prevalence and enumeration in naturally infected cattle. J Appl Microbiol 2017; 123:1027-1042. [PMID: 28736954 DOI: 10.1111/jam.13545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/05/2017] [Accepted: 07/10/2017] [Indexed: 12/24/2022]
Abstract
AIMS The objective of this study was to determine if the faecal microbiome has an association with Escherichia coli O157:H7 prevalence and enumeration. METHODS AND RESULTS Pyrosequencing analysis of faecal microbiome was performed from feedlot cattle fed one of three diets: (i) 94 heifers fed low concentrate (LC) diet, (ii) 142 steers fed moderate concentrate (MC) diet, and (iii) 132 steers fed high concentrate (HC) diet. A total of 322 585 OTUs were calculated from 2,411,122 high-quality sequences obtained from 368 faecal samples. In the LC diet group, OTUs assigned to the orders Clostridiales and RF39 (placed within the class Mollicutes) were positively correlated with both E. coli O157:H7 prevalence and enumeration. In the MC diet group, OTUs assigned to Prevotella copri were positively correlated with both E. coli O157:H7 prevalence and enumeration, whereas OTUs assigned to Prevotella stercorea were negatively correlated with both E. coli O157:H7 prevalence and enumeration. In both the MC diet group and the HC diet group, OTUs assigned to taxa placed within Clostridiales were both positively and negatively correlated with both E. coli O157:H7 prevalence and enumeration. However, all correlations were weak. In both the MC diet group and the HC diet group, stepwise linear regression through backward elimination analyses indicated that these OTUs were significantly correlated (P < 0·001) with prevalence or enumeration, explaining as much as 50% of variability in E. coli O157:H7 prevalence or enumeration. CONCLUSIONS Individual colonic bacterial species have little impact on E. coli O157:H7 shedding but collectively groups of bacteria were strongly associated with pathogen shedding. SIGNIFICANCE AND IMPACT OF THE STUDY Bacterial groups in the bovine colon may impact faecal shedding of the zoonotic pathogen E. coli O157:H7, and manipulation of the intestinal microbiota to alter these bacteria may reduce shedding of this pathogen and foodborne illnesses.
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Affiliation(s)
- M Kim
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - L A Kuehn
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - J L Bono
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - E D Berry
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - N Kalchayanand
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - H C Freetly
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - A K Benson
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - J E Wells
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
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Hales KE, Wells JE, Berry ED, Kalchayanand N, Bono JL, Kim M. The effects of monensin in diets fed to finishing beef steers and heifers on growth performance and fecal shedding of Escherichia coli O157:H7. J Anim Sci 2017; 95:3738-3744. [PMID: 28805884 DOI: 10.2527/jas.2017.1528] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Two experiments were conducted to study the effects of monensin dose on growth performance and O157:H7 shedding in finishing beef cattle. In Exp. 1, 198 heifers (298 ± 1.1 kg BW) were allocated to 1 of 2 treatments consisting of 1) 200 mg/heifer daily of monensin and 2) 400 mg/heifer daily of monensin and fed for 151 d. In Exp. 2, 199 steers (430 ± 1.9 kg BW) were stratified by BW and allocated to 1 of 2 treatments consisting of 1) 0 mg/steer daily of monensin and 2) 400 mg/steer daily of monensin and fed for 128 d. For both experiments, there were 4 pen replicates per treatment. For Exp. 1 and Exp. 2, the model included the fixed effect of treatment for growth performance measures and the fixed effects of treatment, time, and treatment × time interaction, respectively, for O157:H7 shedding. In Exp. 1, final BW was 1.9% greater for heifers fed 400 mg/d monensin than for heifers fed 200 mg/d monensin ( = 0.05). Furthermore, ADG was 4.9% greater ( = 0.05) and G:F was 3.1% greater ( = 0.04) when the heifers were fed 400 mg/d monensin vs. 200 mg/d monensin. Pen prevalence for O157:H7 ( = 0.96) and the percentage of animals in the pen shedding O157:H7 at enumerable levels ( = 0.82) did not differ between heifers fed 200 mg/d monensin and heifers fed 400 mg/d monensin over the 4 sampling periods. For Exp. 2, steers fed the supplement containing monensin had a 1.9% greater final BW ( = 0.04) and a 5.2% greater ADG ( = 0.02) than steers fed a control supplement without monensin. No differences in DMI or G:F were noted across the treatments ( ≥ 0.14). O157:H7 percentage of enumerable cattle within the pen was greater for the steers fed monensin than the control steers not fed monensin than the control steers not fed monensin ( = 0.02) over the 4 sampling periods. However, the percentage of animals in the pen shedding O157:H7 (prevalence positive) did not differ between treatments ( = 0.18), nor did the average fecal counts ( = 0.45). In conclusion, feeding a higher dose (400 mg/d) of monensin improved final BW and ADG compared with a low dose of monensin or a no-monensin control in steers and heifers across multiple years. The percentage of animals shedding O157:H7 at enumerable levels was greater for steers fed the monensin supplement than for steers fed the control supplement, yet the presence of monensin, irrespective of the dose, did not affect the percentage of animals in the pen shedding O157:H7.
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Shaaban S, Cowley LA, McAteer SP, Jenkins C, Dallman TJ, Bono JL, Gally DL. Evolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic Escherichia coli O157 by long-read sequencing. Microb Genom 2016; 2:e000096. [PMID: 28348836 PMCID: PMC5359411 DOI: 10.1099/mgen.0.000096] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/31/2016] [Indexed: 11/18/2022] Open
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) O157 is a zoonotic pathogen for which colonization of cattle and virulence in humans is associated with multiple horizontally acquired genes, the majority present in active or cryptic prophages. Our understanding of the evolution and phylogeny of EHEC O157 continues to develop primarily based on core genome analyses; however, such short-read sequences have limited value for the analysis of prophage content and its chromosomal location. In this study, we applied Single Molecule Real Time (SMRT) sequencing, using the Pacific Biosciences long-read sequencing platform, to isolates selected from the main sub-clusters of this clonal group. Prophage regions were extracted from these sequences and from published reference strains. Genome position and prophage diversity were analysed along with genetic content. Prophages could be assigned to clusters, with smaller prophages generally exhibiting less diversity and preferential loss of structural genes. Prophages encoding Shiga toxin (Stx) 2a and Stx1a were the most diverse, and more variable compared to prophages encoding Stx2c, further supporting the hypothesis that Stx2c-prophage integration was ancestral to acquisition of other Stx types. The concept that phage type (PT) 21/28 (Stx2a+, Stx2c+) strains evolved from PT32 (Stx2c+) was supported by analysis of strains with excised Stx-encoding prophages. Insertion sequence elements were over-represented in prophage sequences compared to the rest of the genome, showing integration in key genes such as stx and an excisionase, the latter potentially acting to capture the bacteriophage into the genome. Prophage profiling should allow more accurate prediction of the pathogenic potential of isolates.
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Affiliation(s)
- Sharif Shaaban
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
| | - Lauren A. Cowley
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, London NW9 5EQ, UK
| | - Sean P. McAteer
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, London NW9 5EQ, UK
| | - Timothy J. Dallman
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, London NW9 5EQ, UK
| | - James L. Bono
- U.S. Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, NE 68933-0166, USA
| | - David L. Gally
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
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Clawson ML, Murray RW, Sweeney MT, Apley MD, DeDonder KD, Capik SF, Larson RL, Lubbers BV, White BJ, Kalbfleisch TS, Schuller G, Dickey AM, Harhay GP, Heaton MP, Chitko-McKown CG, Brichta-Harhay DM, Bono JL, Smith TPL. Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes. BMC Genomics 2016; 17:982. [PMID: 27894259 PMCID: PMC5127058 DOI: 10.1186/s12864-016-3316-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/18/2016] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Mannheimia haemolytica typically resides in cattle as a commensal member of the upper respiratory tract microbiome. However, some strains can invade their lungs and cause respiratory disease and death, including those with multi-drug resistance. A nucleotide polymorphism typing system was developed for M. haemolytica from the genome sequences of 1133 North American isolates, and used to identify genetic differences between isolates from the lungs and upper respiratory tract of cattle with and without clinical signs of respiratory disease. RESULTS A total of 26,081 nucleotide polymorphisms were characterized after quality control filtering of 48,403 putative polymorphisms. Phylogenetic analyses of nucleotide polymorphism genotypes split M. haemolytica into two major genotypes (1 and 2) that each were further divided into multiple subtypes. Multiple polymorphisms were identified with alleles that tagged genotypes 1 or 2, and their respective subtypes. Only genotype 2 M. haemolytica associated with the lungs of diseased cattle and the sequence of a particular integrative and conjugative element (ICE). Additionally, isolates belonging to one subtype of genotype 2 (2b), had the majority of antibiotic resistance genes detected in this study, which were assorted into seven combinations that ranged from 1 to 12 resistance genes. CONCLUSIONS Typing of diverse M. haemolytica by nucleotide polymorphism genotypes successfully identified associations with diseased cattle lungs, ICE sequence, and antibiotic resistance genes. Management of cattle by their carriage of M. haemolytica could be an effective intervention strategy to reduce the prevalence of respiratory disease and supplemental needs for antibiotic treatments in North American herds.
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Affiliation(s)
- Michael L. Clawson
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| | | | | | | | - Keith D. DeDonder
- Kansas State University, Manhattan, KS USA
- Veterinary and Biomedical Research Center, Inc, Manhattan, KS USA
| | | | | | | | | | | | - Gennie Schuller
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - Aaron M. Dickey
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - Gregory P. Harhay
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - Michael P. Heaton
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - Carol G. Chitko-McKown
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - Dayna M. Brichta-Harhay
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - James L. Bono
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - Timothy P. L. Smith
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
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32
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Cowley LA, Dallman TJ, Fitzgerald S, Irvine N, Rooney PJ, McAteer SP, Day M, Perry NT, Bono JL, Jenkins C, Gally DL. Short-term evolution of Shiga toxin-producing Escherichia coli O157:H7 between two food-borne outbreaks. Microb Genom 2016; 2:e000084. [PMID: 28348875 PMCID: PMC5320650 DOI: 10.1099/mgen.0.000084] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/08/2016] [Indexed: 01/21/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a public health threat and outbreaks occur worldwide. Here, we investigate genomic differences between related STEC O157:H7 that caused two outbreaks, eight weeks apart, at the same restaurant. Short-read genome sequencing divided the outbreak strains into two sub-clusters separated by only three single-nucleotide polymorphisms in the core genome while traditional typing identified them as separate phage types, PT8 and PT54. Isolates did not cluster with local strains but with those associated with foreign travel to the Middle East/North Africa. Combined long-read sequencing approaches and optical mapping revealed that the two outbreak strains had undergone significant microevolution in the accessory genome with prophage gain, loss and recombination. In addition, the PT54 sub-type had acquired a 240 kbp multi-drug resistance (MDR) IncHI2 plasmid responsible for the phage type switch. A PT54 isolate had a general fitness advantage over a PT8 isolate in rich medium, including an increased capacity to use specific amino acids and dipeptides as a nitrogen source. The second outbreak was considerably larger and there were multiple secondary cases indicative of effective human-to-human transmission. We speculate that MDR plasmid acquisition and prophage changes have adapted the PT54 strain for human infection and transmission. Our study shows the added insights provided by combining whole-genome sequencing approaches for outbreak investigations.
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Affiliation(s)
- Lauren A Cowley
- 1Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - Timothy J Dallman
- 1Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - Stephen Fitzgerald
- 2Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG Roslin, UK
| | - Neil Irvine
- 3Public Health Agency, 12-22 Linenhall St, BT2 8BS Belfast, Northern Ireland
| | - Paul J Rooney
- 4Microbiology Laboratory, Royal Victoria Hospital, BT12 6BA Belfast, Northern Ireland
| | - Sean P McAteer
- 2Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG Roslin, UK
| | - Martin Day
- 1Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - Neil T Perry
- 1Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - James L Bono
- 5U.S. Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska 68933-0166, USA
| | - Claire Jenkins
- 1Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - David L Gally
- 2Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG Roslin, UK
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Beier RC, Franz E, Bono JL, Mandrell RE, Fratamico PM, Callaway TR, Andrews K, Poole TL, Crippen TL, Sheffield CL, Anderson RC, Nisbet DJ. Disinfectant and Antimicrobial Susceptibility Profiles of the Big Six Non-O157 Shiga Toxin-Producing Escherichia coli Strains from Food Animals and Humans. J Food Prot 2016; 79:1355-70. [PMID: 27497123 DOI: 10.4315/0362-028x.jfp-15-600] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The disinfectant and antimicrobial susceptibility profiles of 138 non-O157 Shiga toxin-producing Escherichia coli strains (STECs) from food animals and humans were determined. Antimicrobial resistance (AMR) was moderate (39.1% of strains) in response to 15 antimicrobial agents. Animal strains had a lower AMR prevalence (35.6%) than did human strains (43.9%) but a higher prevalence of the resistance profile GEN-KAN-TET. A decreasing prevalence of AMR was found among animal strains from serogroups O45 > O145 > O121 > O111 > O26 > O103 and among human strains from serogroups O145 > O103 > O26 > O111 > O121 > O45. One animal strain from serogroups O121 and O145 and one human strain from serogroup O26 had extensive drug resistance. A high prevalence of AMR in animal O45 and O121 strains and no resistance or a low prevalence of resistance in human strains from these serogroups suggests a source other than food animals for human exposure to these strains. Among the 24 disinfectants evaluated, all strains were susceptible to triclosan. Animal strains had a higher prevalence of resistance to chlorhexidine than did human strains. Both animal and human strains had a similar low prevalence of low-level benzalkonium chloride resistance, and animal and human strains had similar susceptibility profiles for most other disinfectants. Benzyldimethylammonium chlorides and C10AC were the primary active components in disinfectants DC&R and P-128, respectively, against non-O157 STECs. A disinfectant FS512 MIC ≥ 8 μg/ml was more prevalent among animal O121 strains (61.5%) than among human O121 strains (25%), which may also suggest a source of human exposure to STEC O121 other than food animals. Bacterial inhibition was not dependent solely on pH but was correlated with the presence of dissociated organic acid species and some undissociated acids.
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Affiliation(s)
- Ross C Beier
- U.S. Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, Texas 77845, USA.
| | - Eelco Franz
- Laboratory for Zoonoses and Environmental Microbiology, Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | - James L Bono
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, USA
| | - Robert E Mandrell
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California 94710, USA
| | - Pina M Fratamico
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania 19038, USA
| | - Todd R Callaway
- U.S. Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, Texas 77845, USA
| | - Kathleen Andrews
- U.S. Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, Texas 77845, USA
| | - Toni L Poole
- U.S. Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, Texas 77845, USA
| | - Tawni L Crippen
- U.S. Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, Texas 77845, USA
| | - Cynthia L Sheffield
- U.S. Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, Texas 77845, USA
| | - Robin C Anderson
- U.S. Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, Texas 77845, USA
| | - David J Nisbet
- U.S. Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, Texas 77845, USA
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Dickey AM, Loy JD, Bono JL, Smith TPL, Apley MD, Lubbers BV, DeDonder KD, Capik SF, Larson RL, White BJ, Blom J, Chitko-McKown CG, Clawson ML. Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with infectious bovine keratoconjunctivitis versus the deep nasopharynx of asymptomatic cattle. Vet Res 2016; 47:31. [PMID: 26872821 PMCID: PMC4752781 DOI: 10.1186/s13567-016-0316-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/22/2016] [Indexed: 11/25/2022] Open
Abstract
Moraxella bovoculi is a recently described bacterium that is associated with infectious bovine keratoconjunctivitis (IBK) or “pinkeye” in cattle. In this study, closed circularized genomes were generated for seven M. bovoculi isolates: three that originated from the eyes of clinical IBK bovine cases and four from the deep nasopharynx of asymptomatic cattle. Isolates that originated from the eyes of IBK cases profoundly differed from those that originated from the nasopharynx of asymptomatic cattle in genome structure, gene content and polymorphism diversity and consequently placed into two distinct phylogenetic groups. These results suggest that there are genetically distinct strains of M. bovoculi that may not associate with IBK.
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Affiliation(s)
- Aaron M Dickey
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center (USMARC), State Spur 18D, Clay Center, NE, 68933, USA.
| | - John D Loy
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0907, USA.
| | - James L Bono
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center (USMARC), State Spur 18D, Clay Center, NE, 68933, USA.
| | - Timothy P L Smith
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center (USMARC), State Spur 18D, Clay Center, NE, 68933, USA.
| | - Mike D Apley
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA.
| | - Brian V Lubbers
- Kansas State Diagnostic Laboratory, Kansas State University, Manhattan, KS, 66506, USA.
| | - Keith D DeDonder
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA.
| | - Sarah F Capik
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA.
| | - Robert L Larson
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA.
| | - Brad J White
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA.
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392, Giessen, Germany.
| | - Carol G Chitko-McKown
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center (USMARC), State Spur 18D, Clay Center, NE, 68933, USA.
| | - Michael L Clawson
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center (USMARC), State Spur 18D, Clay Center, NE, 68933, USA.
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Wang R, Kalchayanand N, Bono JL. Sequence of Colonization Determines the Composition of Mixed Biofilms by Escherichia coli O157:H7 and O111:H8 Strains. J Food Prot 2015; 78:1554-9. [PMID: 26219370 DOI: 10.4315/0362-028x.jfp-15-009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bacterial biofilms are one of the potential sources of cross-contamination in food processing environments. Shiga toxin-producing Escherichia coli (STEC) O157:H7 and O111:H8 are important foodborne pathogens capable of forming biofilms, and the coexistence of these two STEC serotypes has been detected in various food samples and in multiple commercial meat plants throughout the United States. Here, we investigated how the coexistence of these two STEC serotypes and their sequence of colonization could affect bacterial growth competition and mixed biofilm development. Our data showed that E. coli O157:H7 strains were able to maintain a higher cell percentage in mixed biofilms with the co-inoculated O111:H8 companion strains, even though the results of planktonic growth competition were strain dependent. On solid surfaces with preexisting biofilms, the sequence of colonization played a critical role in determining the composition of the mixed biofilms because early stage precolonization significantly affected the competition results between the E. coli O157:H7 and O111:H8 strains. The precolonizer of either serotype was able to outgrow the other serotype in both planktonic and biofilm phases. The competitive interactions among the various STEC serotypes would determine the composition and structure of the mixed biofilms as well as their potential risks to food safety and public health, which is largely influenced by the dominant strains in the mixtures. Thus, the analysis of mixed biofilms under various conditions would be of importance to determine the nature of mixed biofilms composed of multiple microorganisms and to help implement the most effective disinfection operations accordingly.
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Affiliation(s)
- Rong Wang
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, P.O. Box 166, State Spur 18D, Clay Center, Nebraska 68933-0166, USA.
| | - Norasak Kalchayanand
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, P.O. Box 166, State Spur 18D, Clay Center, Nebraska 68933-0166, USA
| | - James L Bono
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, P.O. Box 166, State Spur 18D, Clay Center, Nebraska 68933-0166, USA
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36
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Griffing SM, MacCannell DR, Schmidtke AJ, Freeman MM, Hyytiä-Trees E, Gerner-Smidt P, Ribot EM, Bono JL. Canonical Single Nucleotide Polymorphisms (SNPs) for High-Resolution Subtyping of Shiga-Toxin Producing Escherichia coli (STEC) O157:H7. PLoS One 2015; 10:e0131967. [PMID: 26132731 PMCID: PMC4488506 DOI: 10.1371/journal.pone.0131967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 06/08/2015] [Indexed: 01/09/2023] Open
Abstract
The objective of this study was to develop a canonical, parsimoniously-informative SNP panel for subtyping Shiga-toxin producing Escherichia coli (STEC) O157:H7 that would be consistent with epidemiological, PFGE, and MLVA clustering of human specimens. Our group had previously identified 906 putative discriminatory SNPs, which were pared down to 391 SNPs based on their prevalence in a test set. The 391 SNPs were screened using a high-throughput form of TaqMan PCR against a set of clinical isolates that represent the most diverse collection of O157:H7 isolates from outbreaks and sporadic cases examined to date. Another 30 SNPs identified by others were also screened using the same method. Two additional targets were tested using standard TaqMan PCR endpoint analysis. These 423 SNPs were reduced to a 32 SNP panel with the almost the same discriminatory value. While the panel partitioned our diverse set of isolates in a manner that was consistent with epidemiological data and PFGE and MLVA phylogenies, it resulted in fewer subtypes than either existing method and insufficient epidemiological resolution in 10 of 47 clusters. Therefore, another round of SNP discovery was undertaken using comparative genomic resequencing of pooled DNA from the 10 clusters with insufficient resolution. This process identified 4,040 potential SNPs and suggested one of the ten clusters was incorrectly grouped. After its removal, there were 2,878 SNPs, of which only 63 were previously identified and 438 occurred across multiple clusters. Among highly clonal bacteria like STEC O157:H7, linkage disequilibrium greatly limits the number of parsimoniously informative SNPs. Therefore, it is perhaps unsurprising that our panel accounted for the potential discriminatory value of numerous other SNPs reported in the literature. We concluded published O157:H7 SNPs are insufficient for effective epidemiological subtyping. However, the 438 multi-cluster SNPs we identified may provide the additional information required.
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Affiliation(s)
- Sean M. Griffing
- PulseNet Next Generation Subtyping Methods Unit, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Duncan R. MacCannell
- PulseNet Next Generation Subtyping Methods Unit, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Amber J. Schmidtke
- PulseNet Next Generation Subtyping Methods Unit, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Molly M. Freeman
- PulseNet Next Generation Subtyping Methods Unit, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Eija Hyytiä-Trees
- PulseNet Next Generation Subtyping Methods Unit, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Peter Gerner-Smidt
- PulseNet Next Generation Subtyping Methods Unit, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Efrain M. Ribot
- PulseNet Next Generation Subtyping Methods Unit, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - James L. Bono
- United States Meat Animal Research Center, United States Department of Agriculture, Agricultural Research Service, Clay Center, Nevada, United States of America
- * E-mail:
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Yan X, Fratamico PM, Bono JL, Baranzoni GM, Chen CY. 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. BMC Microbiol 2015; 15:83. [PMID: 25887577 PMCID: PMC4393859 DOI: 10.1186/s12866-015-0413-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 03/12/2015] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Various H-serotypes of the Shiga toxin-producing Escherichia coli (STEC) O104, including H4, H7, H21, and H¯, have been associated with sporadic cases of illness and have caused food-borne outbreaks globally. In the U.S., STEC O104:H21 caused an outbreak associated with milk in 1994. However, there is little known on the evolutionary origins of STEC O104 strains, and how genotypic diversity contributes to pathogenic potential of various O104 H-antigen serotypes isolated from different ecological niches and/or geographical regions. RESULTS Two STEC O104:H21 (milk outbreak strain) and O104:H7 (cattle isolate) strains were shot-gun sequenced, and the genomes were closed. The intimin (eae) gene, involved in the attaching-effacing phenotype of diarrheagenic E. coli, was not found in either strain. Examining various O104 genome sequences, we found that two "complete" left and right end portions of the locus of enterocyte effacement (LEE) pathogenicity island were present in 13 O104 strains; however, the central portion of LEE was missing, where the eae gene is located. In O104:H4 strains, the missing central portion of the LEE locus was replaced by a pathogenicity island carrying the aidA (adhesin involved in diffuse adherence) gene and antibiotic resistance genes commonly carried on plasmids. Enteroaggregative E. coli-specific virulence genes and European outbreak O104:H4-specific stx2-encoding Escherichia P13374 or Escherichia TL-2011c bacteriophages were missing in some of the O104:H4 genome sequences available from public databases. Most of the genomic variations in the strains examined were due to the presence of different mobile genetic elements, including prophages and genomic island regions. The presence of plasmids carrying virulence-associated genes may play a role in the pathogenic potential of O104 strains. CONCLUSIONS The two strains sequenced in this study (O104:H21 and O104:H7) are genetically more similar to each other than to the O104:H4 strains that caused an outbreak in Germany in 2011 and strains found in Central Africa. A hypothesis on strain evolution and pathogenic potential of various H-serotypes of E. coli O104 strains is proposed.
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Affiliation(s)
- Xianghe Yan
- USDA, Agricultural Research Service, Eastern Regional Research Center, 600 E. Mermaid Lane, 19038, Wyndmoor, PA, USA.
- U.S. Department of Agriculture, Eastern Regional Research Center, Agricultural Research Service, 600 East Mermaid Lane, 19038, Wyndmoor, PA, USA.
| | - Pina M Fratamico
- USDA, Agricultural Research Service, Eastern Regional Research Center, 600 E. Mermaid Lane, 19038, Wyndmoor, PA, USA.
| | - James L Bono
- USDA, Agricultural Research Service, Meat Animal Research Center, Clay Center, NE, 68933, USA.
| | - Gian Marco Baranzoni
- USDA, Agricultural Research Service, Eastern Regional Research Center, 600 E. Mermaid Lane, 19038, Wyndmoor, PA, USA.
| | - Chin-Yi Chen
- USDA, Agricultural Research Service, Eastern Regional Research Center, 600 E. Mermaid Lane, 19038, Wyndmoor, PA, USA.
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Norman KN, Clawson ML, Strockbine NA, Mandrell RE, Johnson R, Ziebell K, Zhao S, Fratamico PM, Stones R, Allard MW, Bono JL. Comparison of whole genome sequences from human and non-human Escherichia coli O26 strains. Front Cell Infect Microbiol 2015; 5:21. [PMID: 25815275 PMCID: PMC4356229 DOI: 10.3389/fcimb.2015.00021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/21/2015] [Indexed: 11/13/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) O26 is the second leading E. coli serogroup responsible for human illness outbreaks behind E. coli O157:H7. Recent outbreaks have been linked to emerging pathogenic O26:H11 strains harboring stx 2 only. Cattle have been recognized as an important reservoir of O26 strains harboring stx 1; however the reservoir of these emerging stx 2 strains is unknown. The objective of this study was to identify nucleotide polymorphisms in human and cattle-derived strains in order to compare differences in polymorphism derived genotypes and virulence gene profiles between the two host species. Whole genome sequencing was performed on 182 epidemiologically unrelated O26 strains, including 109 human-derived strains and 73 non-human-derived strains. A panel of 289 O26 strains (241 STEC and 48 non-STEC) was subsequently genotyped using a set of 283 polymorphisms identified by whole genome sequencing, resulting in 64 unique genotypes. Phylogenetic analyses identified seven clusters within the O26 strains. The seven clusters did not distinguish between isolates originating from humans or cattle; however, clusters did correspond with particular virulence gene profiles. Human and non-human-derived strains harboring stx 1 clustered separately from strains harboring stx 2, strains harboring eae, and non-STEC strains. Strains harboring stx 2 were more closely related to non-STEC strains and strains harboring eae than to strains harboring stx 1. The finding of human and cattle-derived strains with the same polymorphism derived genotypes and similar virulence gene profiles, provides evidence that similar strains are found in cattle and humans and transmission between the two species may occur.
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Affiliation(s)
- Keri N. Norman
- U.S. Meat Animal Research Center, United States Department of Agriculture, Agricultural Research ServiceClay Center, NE, USA
| | - Michael L. Clawson
- U.S. Meat Animal Research Center, United States Department of Agriculture, Agricultural Research ServiceClay Center, NE, USA
| | - Nancy A. Strockbine
- Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and PreventionAtlanta, GA, USA
| | - Robert E. Mandrell
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research ServiceAlbany, CA, USA
| | - Roger Johnson
- Laboratory for Foodborne Zoonoses, Public Health Agency of CanadaGuelph, ON, Canada
| | - Kim Ziebell
- Laboratory for Foodborne Zoonoses, Public Health Agency of CanadaGuelph, ON, Canada
| | - Shaohua Zhao
- Division of Animal and Food Microbiology, Center for Veterinary Medicine, Food and Drug AdministrationLaurel, MD, USA
| | - Pina M. Fratamico
- Eastern Regional Research Center, United States Department of Agriculture, Agricultural Research ServiceWyndmoor, PA, USA
| | - Robert Stones
- Food and Environment Research AgencySand Hutton, York, UK
| | - Marc W. Allard
- Division of Microbiology, Center for Food Safety and Applied Nutrition, Office of Regulatory Science, Food and Drug AdministrationCollege Park, MD, USA
| | - James L. Bono
- U.S. Meat Animal Research Center, United States Department of Agriculture, Agricultural Research ServiceClay Center, NE, USA
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Koren S, Harhay GP, Smith TPL, Bono JL, Harhay DM, Mcvey SD, Radune D, Bergman NH, Phillippy AM. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biol 2015; 14:R101. [PMID: 24034426 PMCID: PMC4053942 DOI: 10.1186/gb-2013-14-9-r101] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 08/22/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem. RESULTS To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads. CONCLUSIONS Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.
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Miller WG, Yee E, Chapman MH, Smith TPL, Bono JL, Huynh S, Parker CT, Vandamme P, Luong K, Korlach J. Comparative genomics of the Campylobacter lari group. Genome Biol Evol 2014; 6:3252-66. [PMID: 25381664 PMCID: PMC4986449 DOI: 10.1093/gbe/evu249] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The Campylobacter lari group is a phylogenetic clade within the epsilon subdivision of the Proteobacteria and is part of the thermotolerant Campylobacter spp., a division within the genus that includes the human pathogen Campylobacter jejuni. The C. lari group is currently composed of five species (C. lari, Campylobacter insulaenigrae, Campylobacter volucris, Campylobacter subantarcticus, and Campylobacter peloridis), as well as a group of strains termed the urease-positive thermophilic Campylobacter (UPTC) and other C. lari-like strains. Here we present the complete genome sequences of 11 C. lari group strains, including the five C. lari group species, four UPTC strains, and a lari-like strain isolated in this study. The genome of C. lari subsp. lari strain RM2100 was described previously. Analysis of the C. lari group genomes indicates that this group is highly related at the genome level. Furthermore, these genomes are strongly syntenic with minor rearrangements occurring only in 4 of the 12 genomes studied. The C. lari group can be bifurcated, based on the flagella and flagellar modification genes. Genomic analysis of the UPTC strains indicated that these organisms are variable but highly similar, closely related to but distinct from C. lari. Additionally, the C. lari group contains multiple genes encoding hemagglutination domain proteins, which are either contingency genes or linked to conserved contingency genes. Many of the features identified in strain RM2100, such as major deficiencies in amino acid biosynthesis and energy metabolism, are conserved across all 12 genomes, suggesting that these common features may play a role in the association of the C. lari group with coastal environments and watersheds.
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Affiliation(s)
- William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California
| | - Emma Yee
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California
| | - Mary H Chapman
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California
| | - Timothy P L Smith
- Meat Safety and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska
| | - James L Bono
- Meat Safety and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska
| | - Steven Huynh
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California
| | - Craig T Parker
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Khai Luong
- Pacific Biosciences, Menlo Park, California
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Kim M, Kim J, Kuehn LA, Bono JL, Berry ED, Kalchayanand N, Freetly HC, Benson AK, Wells JE. Investigation of bacterial diversity in the feces of cattle fed different diets. J Anim Sci 2013; 92:683-94. [PMID: 24352967 DOI: 10.2527/jas.2013-6841] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The objective of this study is to investigate individual animal variation of bovine fecal microbiota including as affected by diets. Fecal samples were collected from 426 cattle fed 1 of 3 diets typically fed to feedlot cattle: 1) 143 steers fed finishing diet (83% dry-rolled corn, 13% corn silage, and 4% supplement), 2) 147 steers fed late growing diet (66% dry-rolled corn, 26% corn silage, and 8% supplement), and 3) 136 heifers fed early growing diet (70% corn silage and 30% alfalfa haylage). Bacterial 16S rRNA gene amplicons were determined from individual fecal samples using next-generation pyrosequencing technology. A total of 2,149,008 16S rRNA gene sequences from 333 cattle with at least 2,000 sequences were analyzed. Firmicutes and Bacteroidetes were dominant phyla in all fecal samples. At the genus level, Oscillibacter, Turicibacter, Roseburia, Fecalibacterium, Coprococcus, Clostridium, Prevotella, and Succinivibrio were represented by more than 1% of total sequences. However, numerous sequences could not be assigned to a known genus. Dominant unclassified groups were unclassified Ruminococcaceae and unclassified Lachnospiraceae that could be classified to a family but not to a genus. These dominant genera and unclassified groups differed (P < 0.001) with diets. A total of 176,692 operational taxonomic units (OTU) were identified in combination across all the 333 cattle. Only 2,359 OTU were shared across 3 diet groups. UniFrac analysis showed that bacterial communities in cattle feces were greatly affected by dietary differences. This study indicates that the community structure of fecal microbiota in cattle is greatly affected by diet, particularly between forage- and concentrate-based diets.
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Affiliation(s)
- M Kim
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933
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Beier RC, Poole TL, Brichta-Harhay DM, Anderson RC, Bischoff KM, Hernandez CA, Bono JL, Arthur TM, Nagaraja TG, Crippen TL, Sheffield CL, Nisbet DJ. Disinfectant and antibiotic susceptibility profiles of Escherichia coli O157:H7 strains from cattle carcasses, feces, and hides and ground beef from the United States. J Food Prot 2013; 76:6-17. [PMID: 23317851 DOI: 10.4315/0362-028x.jfp-12-253] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The disinfectant and antibiotic susceptibility profiles of 344 Escherichia coli O157:H7 strains from cattle carcasses, feces, and hides and ground beef from the United States were determined. A low prevalence of antibiotic resistance was observed (14%). The highest prevalences of resistance were to sulfisoxazole (10.5%), tetracycline (9.9%), streptomycin (7%), and chloramphenicol (4.9%). Four strains were resistant to eight antibiotics (two strains from ground beef and one strain each from hide and preevisceration carcass swabs of cull cattle at harvest). Pulsed-field gel electrophoresis analysis of the E. coli O157:H7 strains revealed two major groups (designated 1 and 2) composed of 17 and 20 clusters, respectively. Clusters 1A, 1B, 1C, and 1G.1 were associated with multidrug-resistant strains. There was no observed correlation between disinfectant resistance and antibiotic resistance. Sixty-nine (20%) of the 344 strains were resistant to chlorhexidine or benzalkonium chloride or the MICs of benzyldimethyldodecylammonium chloride were elevated. Inducible resistance was observed at elevated concentrations of antibiotics (1.4%) and disinfectants (6.1%). The highest rate of disinfectant inducible resistance was to OdoBan, quaternary ammonium chlorides, and the surface disinfectants F25, FS512, and MG, which are used in dairies, restaurants, and food processing plants. High MICs (1,024 to 4,096 m g/ml) of acetic, lactic, and citric acids were found. The decreasing order of acid potency based on molar MICs (MICs(molar)) was acetic, citric, and lactic acid. The correlation of the concentration of dissociated organic acids and MICs(molar) strongly suggests that the observed inhibition of E. coli O157:H7 was primarily due to dissociated forms of the acids.
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Affiliation(s)
- Ross C Beier
- U.S. Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, Texas 77845, USA.
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Wang R, Bono JL, Kalchayanand N, Shackelford S, Harhay DM. Biofilm formation by Shiga toxin-producing Escherichia coli O157:H7 and Non-O157 strains and their tolerance to sanitizers commonly used in the food processing environment. J Food Prot 2012; 75:1418-28. [PMID: 22856565 DOI: 10.4315/0362-028x.jfp-11-427] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Shiga toxin-producing Escherichia coli (STEC) strains are important foodborne pathogens. Among these, E. coli O157:H7 is the most frequently isolated STEC serotype responsible for foodborne diseases. However, the non-O157 serotypes have been associated with serious outbreaks and sporadic diseases as well. It has been shown that various STEC serotypes are capable of forming biofilms on different food or food contact surfaces that, when detached, may lead to cross-contamination. Bacterial cells at biofilm stage also are more tolerant to sanitizers compared with their planktonic counterparts, which makes STEC biofilms a serious food safety concern. In the present study, we evaluated the potency of biofilm formation by a variety of STEC strains from serotypes O157:H7, O26:H11, and O111:H8; we also compared biofilm tolerance with two types of common sanitizers, a quaternary ammonium chloride-based sanitizer and chlorine. Our results demonstrated that biofilm formation by various STEC serotypes on a polystyrene surface was highly strain-dependent, whereas the two non-O157 serotypes showed a higher potency of pellicle formation at air-liquid interfaces on a glass surface compared with serotype O157:H7. Significant reductions of viable biofilm cells were achieved with sanitizer treatments. STEC biofilm tolerance to sanitization was strain-dependent regardless of the serotypes. Curli expression appeared to play a critical role in STEC biofilm formation and tolerance to sanitizers. Our data indicated that multiple factors, including bacterial serotype and strain, surface materials, and other environmental conditions, could significantly affect STEC biofilm formation. The high potential for biofilm formation by various STEC serotypes, especially the strong potency of pellicle formation by the curli-positive non-O157 strains with high sanitization tolerance, might contribute to bacterial colonization on food contact surfaces, which may result in downstream product contamination.
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Affiliation(s)
- Rong Wang
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, USA.
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Durso LM, Wells JE, Harhay GP, Rice WC, Kuehn L, Bono JL, Shackelford S, Wheeler T, Smith TPL. Comparison of bacterial communities in faeces of beef cattle fed diets containing corn and wet distillers' grain with solubles. Lett Appl Microbiol 2012; 55:109-14. [PMID: 22583366 DOI: 10.1111/j.1472-765x.2012.03265.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
AIM The mammalian intestinal microflora has been shown to impact host physiology. In cattle, intestinal bacteria are also associated with faecal contamination of environmental sources and human illness via foodborne pathogens. Use of wet distillers' grains with solubles (WDGS) in cattle feed creates a gastrointestinal environment where some bacterial species are enriched. Here, we examine if a diet containing 40% WDGS results in fundamentally different microbial community structures. METHODS AND RESULTS The 20,002 16S r-RNA gene sequences from 20 beef cattle were analysed using Sanger sequencing methods. At the genus level, Prevotella (Gram negative) and Anaerobacter (Gram positive) were the most frequently occurring bacteria in our beef cattle faecal samples. Diet-associated differences in prevalence were noted for Prevotella but not Anaerobacter. CONCLUSIONS Diet affects community structure. Faecal communities of co-housed beef cattle are not identical. SIGNIFICANCE AND IMPACT OF THE STUDY It is known that a diet of 40% corn-based WDGS increases the generic Escherichia coli in the faeces and enriches E. coli O157:H7. The results from the current study suggest that in addition to previously observed changes in E. coli, the entire bacterial community structure is different for animals fed 40% corn-based WDGS compared to a traditional corn-finishing diet.
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Affiliation(s)
- L M Durso
- USDA, ARS, Agroecosystem Management Resource Unit, Lincoln, NE 68583, USA.
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Bono JL, Smith TPL, Keen JE, Harhay GP, McDaneld TG, Mandrell RE, Jung WK, Besser TE, Gerner-Smidt P, Bielaszewska M, Karch H, Clawson ML. Phylogeny of Shiga toxin-producing Escherichia coli O157 isolated from cattle and clinically ill humans. Mol Biol Evol 2012; 29:2047-62. [PMID: 22355013 PMCID: PMC3408066 DOI: 10.1093/molbev/mss072] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cattle are a major reservoir for Shiga toxin-producing Escherichia coli O157 (STEC O157) and harbor multiple genetic subtypes that do not all associate with human disease. STEC O157 evolved from an E. coli O55:H7 progenitor; however, a lack of genome sequence has hindered investigations on the divergence of human- and/or cattle-associated subtypes. Our goals were to 1) identify nucleotide polymorphisms for STEC O157 genetic subtype detection, 2) determine the phylogeny of STEC O157 genetic subtypes using polymorphism-derived genotypes and a phage insertion typing system, and 3) compare polymorphism-derived genotypes identified in this study with pulsed field gel electrophoresis (PFGE), the current gold standard for evaluating STEC O157 diversity. Using 762 nucleotide polymorphisms that were originally identified through whole-genome sequencing of 189 STEC O157 human- and cattle-isolated strains, we genotyped a collection of 426 STEC O157 strains. Concatenated polymorphism alleles defined 175 genotypes that were tagged by a minimal set of 138 polymorphisms. Eight major lineages of STEC O157 were identified, of which cattle are a reservoir for seven. Two lineages regularly harbored by cattle accounted for the majority of human disease in this study, whereas another was rarely represented in humans and may have evolved toward reduced human virulence. Notably, cattle are not a known reservoir for E. coli O55:H7 or STEC O157:H− (the first lineage to diverge within the STEC O157 serogroup), which both cause human disease. This result calls into question how cattle may have originally acquired STEC O157. The polymorphism-derived genotypes identified in this study did not surpass PFGE diversity assessed by BlnI and XbaI digestions in a subset of 93 strains. However, our results show that they are highly effective in assessing the evolutionary relatedness of epidemiologically unrelated STEC O157 genetic subtypes, including those associated with the cattle reservoir and human disease.
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Affiliation(s)
- James L Bono
- United States Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, Nebraska, USA
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Durso LM, Harhay GP, Smith TPL, Bono JL, DeSantis TZ, Clawson ML. Bacterial community analysis of beef cattle feedlots reveals that pen surface is distinct from feces. Foodborne Pathog Dis 2011; 8:647-9. [PMID: 21214381 DOI: 10.1089/fpd.2010.0774] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The surface of beef cattle feedlot pens is commonly conceptualized as being packed uncomposted manure. Despite the important role that the feedlot pen may play in the transmission of veterinary and zoonotic pathogens, the bacterial ecology of feedlot surface material is not well understood. Our present study characterized the bacterial communities of the beef cattle feedlot pen surface material using 3647 full-length 16S rDNA sequences, and we compared the community composition of feedlot pens to the fecal source material. The feedlot surface composite was represented by members of the phylum Actinobacteria (42%), followed by Firmicutes (24%), Bacteroidetes (24%), and Proteobacteria (9%). The feedlot pen surface material bacterial communities were clearly distinct from those of the feces from animals in the same pen. Comparisons with previously published results of feces from the animals in the same pen reveal that, of 139 genera identified, only 25 were present in both habitats. These results indicate that, microbiologically, the feedlot pen surface material is separate and distinct from the fecal source material, suggesting that bacteria that originate in cattle feces face different selection pressures and survival challenges during their tenure in the feedlot pen, as compared to their residence in the gastrointestinal tract.
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Affiliation(s)
- Lisa M Durso
- U.S. Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska, USA.
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Durso LM, Harhay GP, Bono JL, Smith TPL. Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach. J Microbiol Methods 2010; 84:278-82. [PMID: 21167876 DOI: 10.1016/j.mimet.2010.12.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 12/07/2010] [Accepted: 12/07/2010] [Indexed: 11/25/2022]
Abstract
The bovine fecal microbiota impacts human food safety as well as animal health. Although the bacteria of cattle feces have been well characterized using culture-based and culture-independent methods, techniques have been lacking to correlate total community composition with community function. We used high throughput sequencing of total DNA extracted from fecal material to characterize general community composition and examine the repertoire of microbial genes present in beef cattle feces, including genes associated with antibiotic resistance and bacterial virulence. Results suggest that traditional 16S sequencing using "universal" primers to generate full-length sequence may under represent Acitinobacteria and Proteobacteria. Over eight percent (8.4%) of the sequences from our beef cattle fecal pool sample could be categorized as virulence genes, including a suite of genes associated with resistance to antibiotic and toxic compounds (RATC). This is a higher proportion of virulence genes found in Sargasso sea, chicken cecum, and cow rumen samples, but comparable to the proportion found in Antarctic marine derived lake, human fecal, and farm soil samples. The quantitative nature of metagenomic data, combined with the large number of RATC classes represented in samples from widely different habitats indicates that metagenomic data can be used to track relative amounts of antibiotic resistance genes in individual animals over time. Consequently, these data can be used to generate sample-specific and temporal antibiotic resistance gene profiles to facilitate an understanding of the ecology of the microbial communities in each habitat as well as the epidemiology of antibiotic resistant gene transport between and among habitats.
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Affiliation(s)
- Lisa M Durso
- USDA, ARS, Agroecosystem Mangagement Research Unit, UNL-East Campus, Lincoln, NE 68983, USA.
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Durso L, Maguire H, Cronquist A, Bono JL. Outbreak investigation: STEC O157. MLO Med Lab Obs 2010; 42:42. [PMID: 20384003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Lisa Durso
- U.S. Department of Agriculture, Agricultural Research Service, Lincoln, NE, USA
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Abstract
Escherichia coli are ubiquitous in the world, and for the most part are non-pathogenic and part of the normal lower gastrointestinal tract in mammals. However, some pathogenic isolates can cause severe disease that range from meningitis to hemorrhagic colitis (HC). In recent years, Shiga toxin-containing E. coli (STEC) have been a major cause of food borne and environmental cases of HC and hemolytic uremic syndrome. One STEC serotype, O157:H7, has been responsible for numerous food-associated outbreaks and recalls worldwide. The protocols in this unit will allow the reader to use real-time polymerase chain reaction genotyping to identify isolates that are more likely to cause disease in humans. The genotyping assay targets a single-nucleotide polymorphism (SNP) in the tir gene. The tir gene is located in a virulence operon called the locus for enterocyte effacement and functions as a receptor for the tight adherence of E. coli O157:H7 to epithelial cells. As more genomes are sequenced, informative SNPs that associate with phenotypes will be identified. Identifying isolates not only by their genus and species, but also by using other informative genomic traits will increase the general knowledge about their genetic diversity.
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Affiliation(s)
- James L Bono
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska, USA
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Bosilevac JM, Arthur TM, Bono JL, Brichta-Harhay DM, Kalchayanand N, King DA, Shackelford SD, Wheeler TL, Koohmaraie M. Prevalence and enumeration of Escherichia coli O157:H7 and Salmonella in U.S. abattoirs that process fewer than 1000 head of cattle per day. J Food Prot 2009; 72:1272-8. [PMID: 19610339 DOI: 10.4315/0362-028x-72.6.1272] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A significant portion (15 to 20%) of beef in the United States is produced in small beef processing plants that harvest fewer than 1000 cattle per day. However, there are little data on the prevalence and levels of Escherichia coli O157:H7 and Salmonella in these processing plants. To address this lack of data, hides (n=1995) and carcasses (n=1995) of cattle at seven small processing plants located across the United States were analyzed for E. coli O157:H7 and Salmonella. Across all plants, hide prevalence of E. coli O157:H7 and Salmonella was 71 and 91%, respectively. Twelve percent of hides had E. coli O157:H7 at enumerable levels (> or =40 CFU/100 cm2), while 36% of hides had Salmonella at enumerable levels. Across all plants, the prevalence of E. coli O157:H7 on preevisceration carcasses was 33%, with 2% at an enumerable level (> or = 0.8 CFU/ 100 cm2). Across all plants, Salmonella prevalence on preevisceration carcasses was 58%, with 8% at an enumerable level. Significant plant-to-plant variations in levels and prevalence of pathogens on carcasses were detected. Reduced levels of pathogens on carcasses were noted among small processors that had incorporated a hide-directed intervention. The results obtained are comparable to those observed previously for larger processors, showing that smaller beef processors face and address the same challenges as do larger beef processors.
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Affiliation(s)
- Joseph M Bosilevac
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Nebraska 68933-0166, USA.
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