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Grünzweil OM, Palmer L, Cabal A, Szostak MP, Ruppitsch W, Kornschober C, Korus M, Misic D, Bernreiter-Hofer T, Korath ADJ, Feßler AT, Allerberger F, Schwarz S, Spergser J, Müller E, Braun SD, Monecke S, Ehricht R, Walzer C, Smodlaka H, Loncaric I. Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals. Int J Mol Sci 2021; 22:ijms22115905. [PMID: 34072783 PMCID: PMC8199236 DOI: 10.3390/ijms22115905] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023] Open
Abstract
Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene blaCMY (n = 51) was the predominant β-lactamase gene. In addition, blaTEM-1 (n = 38), blaSHV-33 (n = 8), blaCTX-M-15 (n = 7), blaOXA-1 (n = 7), blaSHV-11 (n = 3), and blaDHA-1 (n = 2) were detected. The most prevalent non-β-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.
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Affiliation(s)
- Olivia M. Grünzweil
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
| | - Lauren Palmer
- Marine Mammal Care Center, Los Angeles, CA 90731, USA;
| | - Adriana Cabal
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, 1090 Vienna, Austria; (A.C.); (W.R.); (F.A.)
| | - Michael P. Szostak
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, 1090 Vienna, Austria; (A.C.); (W.R.); (F.A.)
| | - Christian Kornschober
- Austrian Agency for Health and Food Safety (AGES), National Reference Centre for Salmonella, 8010 Graz, Austria;
| | - Maciej Korus
- Department of Functional Food Products Development, Faculty of Biotechnology and Food Science, Wroclaw University of Environmental and Life Sciences, 51-630 Wroclaw, Poland; (M.K.); (D.M.)
| | - Dusan Misic
- Department of Functional Food Products Development, Faculty of Biotechnology and Food Science, Wroclaw University of Environmental and Life Sciences, 51-630 Wroclaw, Poland; (M.K.); (D.M.)
| | - Tanja Bernreiter-Hofer
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
- Department for Farm Animals and Veterinary Public Health, University Clinic for Swine, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Anna D. J. Korath
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
| | - Andrea T. Feßler
- Centre for Infection Medicine, Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany; (A.T.F.); (S.S.)
| | - Franz Allerberger
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, 1090 Vienna, Austria; (A.C.); (W.R.); (F.A.)
| | - Stefan Schwarz
- Centre for Infection Medicine, Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany; (A.T.F.); (S.S.)
| | - Joachim Spergser
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
| | - Elke Müller
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Sascha D. Braun
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute for Medical Microbiology and Hygiene, Technical University of Dresden, 01307 Dresden, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Chris Walzer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, 1160 Vienna, Austria;
- Health Program, Wildlife Conservation Society, Bronx, New York City, NY 10460, USA
| | - Hrvoje Smodlaka
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766-1854, USA;
| | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
- Correspondence: ; Tel.: +43-125-077-2115
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Fashae K, Engelmann I, Monecke S, Braun SD, Ehricht R. Molecular characterisation of extended-spectrum ß-lactamase producing Escherichia coli in wild birds and cattle, Ibadan, Nigeria. BMC Vet Res 2021; 17:33. [PMID: 33461554 PMCID: PMC7814699 DOI: 10.1186/s12917-020-02734-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/22/2020] [Indexed: 01/24/2023] Open
Abstract
Background Antimicrobial resistance (AMR) is an increasing global health concern reducing options for therapy of infections and also for perioperative prophylaxis. Many Enterobacteriaceae cannot be treated anymore with third generation cephalosporins (3GC) due to the production of certain 3GC hydrolysing enzymes (extended spectrum beta-lactamases, ESBLs). The role of animals as carriers and vectors of multi-resistant bacteria in different geographical regions is poorly understood. Therefore, we investigated the occurrence and molecular characteristics of ESBL-producing Escherichia coli (E. coli) in wild birds and slaughtered cattle in Ibadan, Nigeria. Cattle faecal samples (n = 250) and wild bird pooled faecal samples (cattle egrets, Bubulcus ibis, n = 28; white-faced whistling duck, Dendrocygna viduata, n = 24) were collected and cultured on cefotaxime-eosin methylene blue agar. Antimicrobial susceptibility was determined by agar diffusion assays and all 3GC resistant isolates were genotypically characterised for AMR genes, virulence associated genes (VAGs) and serotypes using DNA microarray-based assays. Results All 3GC resistant isolates were E. coli: cattle (n = 53), egrets (n = 87) and whistling duck (n = 4); cultured from 32/250 (12.8%), 26/28 (92.9%), 2/24(8.3%), cattle, egrets and whistling duck faecal samples, respectively. blaCTX-M gene family was prevalent; blaCTX-M15 (83.3%) predominated over blaCTX-M9 (11.8%). All were susceptible to carbapenems. The majority of isolates were resistant to at least one of the other tested antimicrobials; multidrug resistance was highest in the isolates recovered from egrets. The isolates harboured diverse repositories of other AMR genes (including strB and sul2), integrons (predominantly class 1) and VAGs. The isolates recovered from egrets harboured more AMR genes; eight were unique to these isolates including tetG, gepA, and floR. The prevalent VAGs included hemL and iss; while 14 (including sepA) were unique to certain animal isolates. E. coli serotypes O9:H9, O9:H30 and O9:H4 predominated. An identical phenotypic microarray profile was detected in three isolates from egrets and cattle, indicative of a clonal relationship amongst these isolates. Conclusion Wild birds and cattle harbour diverse ESBL-producing E. coli populations with potential of inter-species dissemination and virulence. Recommended guidelines to balance public health and habitat conservation should be implemented with continuous surveillance.
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Affiliation(s)
- Kayode Fashae
- Department of Microbiology, University of Ibadan, Ibadan, Nigeria.
| | | | - Stefan Monecke
- InfectoGnostics Research Campus, Jena, Germany.,Leibniz Institute of Photonic Technology (Leibniz-IPHT), Jena, Germany.,Institut für Medizinische Mikrobiologie und Hygiene, Medizinische Fakultaet "Carl Gustav Carus", Technische Universitaet Dresden, Fiedlerstr 42, 01307, Dresden, Germany
| | - Sascha D Braun
- InfectoGnostics Research Campus, Jena, Germany.,Leibniz Institute of Photonic Technology (Leibniz-IPHT), Jena, Germany
| | - Ralf Ehricht
- InfectoGnostics Research Campus, Jena, Germany.,Leibniz Institute of Photonic Technology (Leibniz-IPHT), Jena, Germany.,Friedrich Schiller University Jena, Institute of Physical Chemistry, Jena, Germany
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Guerra JA, Zhang C, Bard JE, Yergeau D, Halasa N, Gómez-Duarte OG. Comparative genomic analysis of a Shiga toxin-producing Escherichia coli (STEC) O145:H25 associated with a severe pediatric case of hemolytic uremic syndrome in Davidson County, Tennessee, US. BMC Genomics 2020; 21:564. [PMID: 32807093 PMCID: PMC7437938 DOI: 10.1186/s12864-020-06967-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 08/03/2020] [Indexed: 12/02/2022] Open
Abstract
Background Shiga toxin-producing E. coli (STECs) are foodborne pathogens associated with bloody diarrhea and hemolytic uremic syndrome (HUS). Although the STEC O157 serogroup accounts for the highest number of infections, HUS-related complications and deaths, the STEC non-O157, as a group, accounts for a larger proportion of STEC infections and lower HUS cases. There is limited information available on how to recognize non-O157 serotypes associated with severe disease. The objectives of this study were to describe a patient with STEC non-O157 infection complicated with HUS and to conduct a comparative whole genome sequence (WGS) analysis among the patient’s STEC clinical isolate and STEC O157 and non-O157 strains. Results The STEC O145:H25 strain EN1I-0044-2 was isolated from a pediatric patient with diarrhea, HUS and severe neurologic and cardiorespiratory complications, who was enrolled in a previously reported case-control study of acute gastroenteritis conducted in Davidson County, Tennessee in 2013. The strain EN1I-0044-2 genome sequence contained a chromosome and three plasmids. Two of the plasmids were similar to those present in O145:H25 strains whereas the third unique plasmid EN1I-0044-2_03 shared no similarity with other STEC plasmids, and it carried 23 genes of unknown function. Strain EN1I-0044-2, compared with O145:H25 and O157 serogroup strains shared chromosome- and plasmid-encoded virulence factors, including Shiga toxin, LEE type III secretion system, LEE effectors, SFP fimbriae, and additional toxins and colonization factors. Conclusions A STEC O145:H25 strain EN1I-0044-2 was isolated from a pediatric patient with severe disease, including HUS, in Davidson County, TN. Phylogenetic and comparison WGS analysis provided evidence that strain EN1I-0044-2 closely resembles O145:H25, and confirmed an independent evolutionary path of STEC O145:H25 and O145:H28 serotypes. The strain EN1I-0044-2 virulence make up was similar to other O145:H25 and O157 serogroups. It carried stx2 and the LEE pathogenicity island, and additional colonization factors and enterotoxin genes. A unique feature of strain EN1I-0044-2 was the presence of plasmid pEN1I-0044-2_03 carrying genes with functions to be determined. Further studies will be necessary to elucidate the role that newly acquired genes by O145:H25 strains play in pathogenesis, and to determine if they may serve as genetic markers of severe disease.
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Affiliation(s)
- Julio A Guerra
- International Enteric Vaccine Research Program, Division of Infectious Diseases, Department of Pediatrics, University at Buffalo, The State University of New York (SUNY), Jacobs School of Medicine and Biomedical Sciences, 875 Ellicott St. Office 6090, Buffalo, NY, 14203, USA
| | - Chengxian Zhang
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jonathan E Bard
- UB Genomics and Bioinformatics Core, Center of Excellence in Bioinformatics, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Donald Yergeau
- UB Genomics and Bioinformatics Core, Center of Excellence in Bioinformatics, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Natasha Halasa
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Oscar G Gómez-Duarte
- International Enteric Vaccine Research Program, Division of Infectious Diseases, Department of Pediatrics, University at Buffalo, The State University of New York (SUNY), Jacobs School of Medicine and Biomedical Sciences, 875 Ellicott St. Office 6090, Buffalo, NY, 14203, USA. .,Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA.
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Barth SA, Weber M, Schaufler K, Berens C, Geue L, Menge C. Metabolic Traits of Bovine Shiga Toxin-Producing Escherichia Coli (STEC) Strains with Different Colonization Properties. Toxins (Basel) 2020; 12:toxins12060414. [PMID: 32580365 PMCID: PMC7354573 DOI: 10.3390/toxins12060414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/10/2020] [Accepted: 06/17/2020] [Indexed: 01/14/2023] Open
Abstract
Cattle harbor Shiga toxin-producing Escherichia coli (STEC) in their intestinal tract, thereby providing these microorganisms with an ecological niche, but without this colonization leading to any clinical signs. In a preceding study, genotypic characterization of bovine STEC isolates unveiled that their ability to colonize cattle persistently (STECper) or only sporadically (STECspo) is more closely associated with the overall composition of the accessory rather than the core genome. However, the colonization pattern could not be unequivocally linked to the possession of classical virulence genes. This study aimed at assessing, therefore, if the presence of certain phenotypic traits in the strains determines their colonization pattern and if these can be traced back to distinctive genetic features. STECspo strains produced significantly more biofilm than STECper when incubated at lower temperatures. Key substrates, the metabolism of which showed a significant association with colonization type, were glyoxylic acid and L-rhamnose, which were utilized by STECspo, but not or only by some STECper. Genomic sequences of the respective glc and rha operons contained mutations and frameshifts in uptake and/or regulatory genes, particularly in STECper. These findings suggest that STECspo conserved features leveraging survival in the environment, whereas the acquisition of a persistent colonization phenotype in the cattle reservoir was accompanied by the loss of metabolic properties and genomic mutations in the underlying genetic pathways.
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Affiliation(s)
- Stefanie A. Barth
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany; (M.W.); (C.B.); (L.G.); (C.M.)
- Correspondence: ; Tel.: +49-3641-804-2270; Fax: +49-3641-804-2482
| | - Michael Weber
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany; (M.W.); (C.B.); (L.G.); (C.M.)
| | - Katharina Schaufler
- Free University Berlin, Institute of Microbiology and Epizootics, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany;
- University of Greifswald, Pharmaceutical Microbiology, Friedrich-Ludwig-Jahn-Str. 17, 17489 Greifswald, Germany
| | - Christian Berens
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany; (M.W.); (C.B.); (L.G.); (C.M.)
| | - Lutz Geue
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany; (M.W.); (C.B.); (L.G.); (C.M.)
| | - Christian Menge
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany; (M.W.); (C.B.); (L.G.); (C.M.)
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Wang LYR, Jokinen CC, Laing CR, Johnson RP, Ziebell K, Gannon VPJ. Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada. Microb Genom 2020; 6. [PMID: 32496181 PMCID: PMC7371104 DOI: 10.1099/mgen.0.000376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Verotoxigenic Escherichia coli (VTEC) are food- and water-borne pathogens associated with both sporadic illness and outbreaks of enteric disease. While it is known that cattle are reservoirs of VTEC, little is known about the genomic variation of VTEC in cattle, and whether the variation in genomes reported for human outbreak strains is consistent with individual animal or group/herd sources of infection. A previous study of VTEC prevalence identified serotypes carried persistently by three consecutive cohorts of heifers within a closed herd of cattle. This present study aimed to: (i) determine whether the genomic relatedness of bovine isolates is similar to that reported for human strains associated with single source outbreaks, (ii) estimate the rates of genome change among dominant serotypes over time within a cattle herd, and (iii) identify genomic features of serotypes associated with persistence in cattle. Illumina MiSeq genome sequencing and genotyping based on allelic and single nucleotide variations were completed, while genome change over time was measured using Bayesian evolutionary analysis sampling trees. The accessory genome, including the non-protein-encoding intergenic regions (IGRs), virulence factors, antimicrobial-resistance genes and plasmid gene content of representative persistent and sporadic cattle strains were compared using Fisher’s exact test corrected for multiple comparisons. Herd strains from serotypes O6:H34 (n=22), O22:H8 (n=30), O108:H8 (n=39), O139:H19 (n=44) and O157:H7 (n=106) were readily distinguishable from epidemiologically unrelated strains of the same serotype using a similarity threshold of 10 or fewer allele differences between adjacent nodes. Temporal-cohort clustering within each serotype was supported by date randomization analysis. Substitutions per site per year were consistent with previously reported values for E. coli; however, there was low branch support for these values. Acquisition of the phage-encoded Shiga toxin 2 gene in serotype O22:H8 was observed. Pan-genome analyses identified accessory regions that were more prevalent in persistent serotypes (P≤0.05) than in sporadic serotypes. These results suggest that VTEC serotypes from a specific cattle population are highly clonal with a similar level of relatedness as human single-source outbreak-associated strains, but changes in the genome occur gradually over time. Additionally, elements in the accessory genomes may provide a selective advantage for persistence of VTEC within cattle herds.
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Affiliation(s)
- Lu Ya Ruth Wang
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada
| | | | - Chad R Laing
- National Centre for Animal Disease, Canadian Food Inspection Agency, Lethbridge, Alberta, Canada
| | - Roger P Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Victor P J Gannon
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada
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The Occurrence and Characterization of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli Isolated from Clinical Diagnostic Specimens of Equine Origin. Animals (Basel) 2019; 10:ani10010028. [PMID: 31877788 PMCID: PMC7022413 DOI: 10.3390/ani10010028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/09/2019] [Accepted: 12/16/2019] [Indexed: 12/14/2022] Open
Abstract
Escherichia coli isolates were recovered from clinical specimens of equine patients admitted to the Texas A&M Veterinary Medical Teaching Hospital over a five-year period. Ceftiofur resistance was used as a marker for potential extended-spectrum beta-lactamase (ESBL)-activity, and of the 48 ceftiofur-resistant E. coli isolates, 27.08% (n = 13) were phenotypically ESBL-positive. Conventional PCR analysis followed by the large-scalebla Finder multiplex PCR detected the ESBL genes, CTX-M-1 and SHV, in seven out of the 13 isolates. Moreover, beta-lactamase genes of TEM-1-type, BER-type (AmpC), and OXA-type were also identified. Sequencing of these genes resulted in identification of a novel TEM-1-type gene, called blaTEM-233, and a study is currently underway to determine if this gene confers the ESBL phenotype. Furthermore, this report is the first to have found E. coli ST1308 in horses. This subtype, which has been reported in other herbivores, harbored the SHV-type ESBL gene. Finally, one out of 13 E. coli isolates was PCR-positive for the carbapenemase gene, blaIMP-1 despite the lack of phenotypically proven resistance to imipenem. With the identification of novel ESBL gene variant and the demonstrated expansion of E. coli sequence types in equine patients, this study underscores the need for more investigation of equines as reservoirs for ESBL-producing pathogens.
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Dias D, Caetano T, Torres RT, Fonseca C, Mendo S. Shiga toxin-producing Escherichia coli in wild ungulates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:203-209. [PMID: 30227290 DOI: 10.1016/j.scitotenv.2018.09.162] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/12/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens that live in the gastrointestinal tract of wildlife and cattle without causing disease. In humans, their colonization and infection lead to life-threatening disease. We investigated the occurrence of STEC in wild ungulates (wild boar, red deer and roe deer) inhabiting areas differently impacted by anthropogenic activities. STEC were detected in 9% (n = 6) of the samples and were recovered from the three species: 1 of wild boar, 4 of red deer and 1 of roe deer. All the isolates (n = 7) were non-O157 STEC encoding stx1 (n = 2; 29%) and/or stx2 genes (n = 6; 86%). O27:H30 was the most frequent serotype identified, followed by O146:H21 and O146:H28. Two STEC were O-untypable: ONT:H28 and ONT:H52. The phylo-groups identified were B1 (n = 3), E (n = 3) and F (n = 1). All the isolates recovered were susceptible to the different classes of antibiotics tested, although resistance genes were found in two strains. Apart from stx, all STEC encode many virulence factors (VF), particularly adhesins and/or other toxins. A strain with 13 VF collected from roe deer has a high enterohemorrhagic risk due to the presence of intimin, hemolysin and protease effectors genes. Enterohemorrhagic E. coli (EHEC) are implicated in the major cases of human infection and mortality, highlighting the zoonotic potential of wildlife-associated STEC. Wild ungulates are reservoirs of STEC potentially pathogenic to humans. Therefore, following the One Health concept, it is crucial to establish worldwide local monitoring programs that will benefit human, animal and environmental health.
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Affiliation(s)
- D Dias
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - T Caetano
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.
| | - R T Torres
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - C Fonseca
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - S Mendo
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
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Arais LR, Barbosa AV, Andrade JRC, Gomes TAT, Asensi MD, Aires CAM, Cerqueira AMF. Zoonotic potential of atypical enteropathogenic Escherichia coli (aEPEC) isolated from puppies with diarrhoea in Brazil. Vet Microbiol 2018; 227:45-51. [PMID: 30473351 DOI: 10.1016/j.vetmic.2018.10.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 10/10/2018] [Accepted: 10/23/2018] [Indexed: 02/02/2023]
Abstract
Recent studies point atypical enteropathogenic Escherichia coli (aEPEC) to be an important agent in childhood diarrhoea in Brazil. aEPEC are commonly found in various animal species, including dogs. Although the true zoonotic risk remains unknown, some strains recovered from dogs present the same serotypes and carry the same virulence genes implicated in human disease. In this study, we compared the virulence and genetic relationship among a set of aEPEC strains previously isolated from diarrheic faeces from companion dogs and humans. A total of 17 strains, 12 from puppies and five from children, were studied. The strains were assessed for: (i) presence of virulence-associated genes (a total of 31 genes) using PCR assays; (ii) genetic relationship by Random Amplified Polymorphic DNA (RAPD), Multilocus Sequence Typing (MLST) and Pulsed-field Gel Electrophoresis (PFGE); and (iii) adherence pattern in intestinal Caco-2 cells. The occurrence of virulence genes was similar between the canine and human isolates presenting the same serotype. The fimbrial genes ecpA and fimH were the most frequently detected, followed by hcpA, tccP, tccP2, lpfA1, lpfA2, astA and toxB genes. Several nle genes were also detected, with one canine strain (O156:H- / ST327) showing all PAI O-122 genes investigated (efa-1, nleB, nleE and ent/espL2). Canine and human strains of the same serotype were grouped into a single cluster by RAPD and PFGE, in which the ST10 and ST206 were identified. Additionally, most of the strains exhibited a localized adherence-like phenotype when interacting with Caco-2 cells. The results showed that some canine aEPEC strains share virulence genes commonly found in human pathogenic strains. Moreover, strains of the same serotype, isolated from dogs and children, share virulence genes and are phylogenetically close, suggesting a potential zoonotic risk.
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Affiliation(s)
- Lavicie R Arais
- Laboratório de Enteropatógenos, Microbiologia Veterinária e de Alimentos, Universidade Federal Fluminense, Professor Hernani Melo Street, 101, Niterói, RJ, 24210-130, Brazil
| | - André V Barbosa
- Laboratório de Enteropatógenos, Microbiologia Veterinária e de Alimentos, Universidade Federal Fluminense, Professor Hernani Melo Street, 101, Niterói, RJ, 24210-130, Brazil.
| | - João R C Andrade
- Faculdade de Ciências Médicas, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade do Estado do Rio de Janeiro. Prof., Manuel de Abreu Avenue, 444, Rio de Janeiro, RJ, 20550-170, Brazil
| | - Tânia A T Gomes
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Botucatu Street, 862, São Paulo, SP, 04023-062, Brazil
| | - Marise D Asensi
- Laboratório de Pesquisa em Infecção Hospitalar, Fundação Oswaldo Cruz, Brasil Avenue, 4365, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Caio A M Aires
- Laboratório de Pesquisa em Infecção Hospitalar, Fundação Oswaldo Cruz, Brasil Avenue, 4365, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Aloysio M F Cerqueira
- Laboratório de Enteropatógenos, Microbiologia Veterinária e de Alimentos, Universidade Federal Fluminense, Professor Hernani Melo Street, 101, Niterói, RJ, 24210-130, Brazil
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9
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Antimicrobial Resistance in Class 1 Integron-Positive Shiga Toxin-Producing Escherichia coli Isolated from Cattle, Pigs, Food and Farm Environment. Microorganisms 2018; 6:microorganisms6040099. [PMID: 30274159 PMCID: PMC6313391 DOI: 10.3390/microorganisms6040099] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 09/24/2018] [Accepted: 09/26/2018] [Indexed: 11/17/2022] Open
Abstract
The aim of this study was to investigate the presence of class 1 integrons in a collection of Shiga toxin-producing Escherichia coli (STEC) from different origins and to characterize pheno- and genotypically the antimicrobial resistance associated to them. A collection of 649 isolates were screened for the class 1 integrase gene (intI1) by Polymerase chain reaction The variable region of class 1 integrons was amplified and sequenced. Positive strains were evaluated for the presence of antimicrobial resistance genes with microarray and for antimicrobial susceptibility by the disk diffusion method. Seven out of 649 STEC strains some to serogroups, O26, O103 and O130 isolated from cattle, chicken burger, farm environment and pigs were identified as positive for intl1. Different arrangements of gene cassettes were detected in the variable region of class 1 integron: dfrA16, aadA23 and dfrA1-aadA1. In almost all strains, phenotypic resistance to streptomycin, tetracycline, trimethoprim/sulfamethoxazole, and sulfisoxazole was observed. Microarray analyses showed that most of the isolates carried four or more antimicrobial resistance markers and STEC strains were categorized as Multridrug-resistant. Although antimicrobials are not usually used in the treatment of STEC infections, the presence of Multridrug-resistant in isolates collected from farm and food represents a risk for animal and human health.
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10
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Variability in Characterizing Escherichia coli from Cattle Feces: A Cautionary Tale. Microorganisms 2018; 6:microorganisms6030074. [PMID: 30037096 PMCID: PMC6165469 DOI: 10.3390/microorganisms6030074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 11/17/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are diverse bacteria, with seven serogroups (O26, O45, O103, O111, O121, O145, O157; "Top 7") of interest due to their predominance in human disease. Confirmation of STEC relies on a combination of culturing, immunological and molecular assays, but no single gold standard for identification exists. In this study, we compared analysis of STEC between three independent laboratories (LAB) using different methodologies. In LAB A, colonies of Top 7 were picked after serogroup-specific immunomagnetic separation of feces from western-Canadian slaughter cattle. A fraction of each colony was tested by PCR (stx1, stx2, eae, O group), and Top 7 isolates were saved as glycerol stocks (n = 689). In LAB B, a subsample of isolates (n = 171) were evaluated for stx1 and stx2 using different primer sets. For this, approximately half of the PCR were performed using original DNA template provided by LAB A and half using DNA extracted from sub-cultured isolates. All Top 7 isolates were sub-cultured by LAB A and shipped to LAB C for traditional serotyping (TS) to determine O and H groups, with PCR-confirmation of virulence genes using a third set of primers. By TS, 76% of O groups (525/689) matched PCR-determined O groups. Lowest proportions (p < 0.05) of O group matches between PCR and TS (62.6% and 69.8%) occurred for O26 and O45 serogroups, respectively. PCR-detection of stx differed most between LAB A and LAB C. Excluding isolates where O groups by PCR and TS did not match, detection of stx1 was most consistent (p < 0.01) for O111 and O157:H7/NM. In contrast, for O45 and O103, stx1 was detected in >65% of isolates by LAB A and <5% by LAB C. Stx2 was only detected by LAB C in isolates of serogroups O121, O145, and O157:H7/NM. LAB B also detected stx2 in O26 and O157:H12/H29, while LAB A detected stx2 in all serogroups. Excluding O111 and O157:H7/NM, marked changes in stx detection were observed between initial isolation and sub-cultures of the same isolate. While multiple explanations exist for discordant O-typing between PCR and TS and for differences in stx detection across labs, these data suggest that assays for STEC classification may require re-evaluation and/or standardization.
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11
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Barth SA, Blome S, Cornelis D, Pietschmann J, Laval M, Maestrini O, Geue L, Charrier F, Etter E, Menge C, Beer M, Jori F. FaecalEscherichia colias biological indicator of spatial interaction between domestic pigs and wild boar (Sus scrofa) in Corsica. Transbound Emerg Dis 2018; 65:746-757. [DOI: 10.1111/tbed.12799] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Indexed: 01/17/2023]
Affiliation(s)
- S. A. Barth
- Institute of Molecular Pathogenesis; Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health; Jena Germany
| | - S. Blome
- Institute of Diagnostic Virology; Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health; Greifswald - Insel Riems Germany
| | - D. Cornelis
- CIRAD, UMR ASTRE, INRA; University Montpellier; Montpellier France
| | - J. Pietschmann
- Institute of Molecular Pathogenesis; Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health; Jena Germany
- Institute of Diagnostic Virology; Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health; Greifswald - Insel Riems Germany
| | - M. Laval
- Research Unit for Animal Husbandry Development (LRDE); INRA SAD; Corte Corsica France
| | - O. Maestrini
- Research Unit for Animal Husbandry Development (LRDE); INRA SAD; Corte Corsica France
| | - L. Geue
- Institute of Molecular Pathogenesis; Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health; Jena Germany
| | - F. Charrier
- Research Unit for Animal Husbandry Development (LRDE); INRA SAD; Corte Corsica France
| | - E. Etter
- CIRAD, UMR ASTRE, INRA; University Montpellier; Montpellier France
- Epidemiology Section; Department of Production Animals Studies; Faculty of Veterinary Science; University of Pretoria; Onderstepoort South Africa
| | - C. Menge
- Institute of Molecular Pathogenesis; Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health; Jena Germany
| | - M. Beer
- Institute of Diagnostic Virology; Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health; Greifswald - Insel Riems Germany
| | - F. Jori
- CIRAD, UMR ASTRE, INRA; University Montpellier; Montpellier France
- Department of Animal Science and Production; Botswana College of Agriculture; Gaborone Botswana
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12
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Wöchtl B, Gunzer F, Gerner W, Gasse H, Koch M, Bagó Z, Ganter M, Weissenböck H, Dinhopl N, Coldewey SM, von Altrock A, Waldmann KH, Saalmüller A, Zimmermann K, Steinmann J, Kehrmann J, Klein-Hitpass L, Blom J, Ehricht R, Engelmann I, Hennig-Pauka I. Comparison of clinical and immunological findings in gnotobiotic piglets infected with Escherichia coli O104:H4 outbreak strain and EHEC O157:H7. Gut Pathog 2017; 9:30. [PMID: 28559930 PMCID: PMC5445466 DOI: 10.1186/s13099-017-0179-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/17/2017] [Indexed: 11/26/2022] Open
Abstract
Background Shiga toxin (Stx) producing Escherichia coli (E. coli) (STEC) is the most frequent cause of diarrhoea-positive haemolytic uraemic syndrome (D + HUS) in humans. In 2011, a huge outbreak with an STEC O104:H4 strain in Germany highlighted the limited possibilities for causative treatment of this syndrome. The responsible STEC strain was found to combine Stx production with adherence mechanisms normally found in enteroaggregative E. coli (EAEC). Pathotypes of E. coli evolve and can exhibit different adhesion mechanisms. It has been shown previously that neonatal gnotobiotic piglets are susceptible for infection with STEC, such as STEC O157:H7 as well as for EAEC, which are considered to be the phylogenetic origin of E. coli O104:H4. This study was designed to characterise the host response to infection with the STEC O104:H4 outbreak strain in comparison to an STEC O157:H7 isolate by evaluating clinical parameters (scoring) and markers of organ dysfunction (biochemistry), as well as immunological (flow cytometry, assessment of cytokines/chemokines and acute phase proteins) and histological alterations (light- and electron microscopy) in a gnotobiotic piglet model of haemolytic uraemic syndrome. Results We observed severe clinical symptoms, such as diarrhoea, dehydration and neurological disorders as well as attaching-and-effacing lesions (A/E) in the colon in STEC O157:H7 infected piglets. In contrast, STEC O104:H4 challenged animals exhibited only mild clinical symptoms including diarrhoea and dehydration and HUS-specific/severe histopathological, haematological and biochemical alterations were only inconsistently presented by individual piglets. A specific adherence phenotype of STEC O104:H4 could not be observed. Flow cytometric analyses of lymphocytes derived from infected animals revealed an increase of natural killer cells (NK cells) during the course of infection revealing a potential role of this subset in the anti-bacterial activity in STEC disease. Conclusions Unexpectedly, E. coli O104:H4 infection caused only mild symptoms and minor changes in histology and blood parameters in piglets. Outcome of the infection trial does not reflect E. coli O104:H4 associated human disease as observed during the outbreak in 2011. The potential role of cells of the innate immune system for STEC related disease pathogenesis should be further elucidated.
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Affiliation(s)
- Bettina Wöchtl
- University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1220 Vienna, Austria
| | - Florian Gunzer
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Wilhelm Gerner
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1220 Vienna, Austria
| | - Hagen Gasse
- Institute of Anatomy, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Michaela Koch
- University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1220 Vienna, Austria
| | - Zoltán Bagó
- Institute for Veterinary Disease Control Mödling, Austrian Agency for Health and Food Safety, Robert-Koch-Gasse 17, 2340 Mödling, Austria
| | - Martin Ganter
- Clinic for Swine, Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Herbert Weissenböck
- Institute for Pathology and Forensic Veterinary Medicine, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1220 Vienna, Austria
| | - Nora Dinhopl
- Institute for Pathology and Forensic Veterinary Medicine, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1220 Vienna, Austria
| | - Sina M Coldewey
- Department of Anaesthesiology and Intensive Care Medicine, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany.,Centre for Innovation Competence (ZIK) Septomics, University Hospital Jena, Albert-Einstein-Strasse 10, 07745 Jena, Germany
| | - Alexandra von Altrock
- Clinic for Swine, Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Karl-Heinz Waldmann
- Clinic for Swine, Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Armin Saalmüller
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1220 Vienna, Austria
| | | | - Jörg Steinmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany
| | - Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany
| | - Ludger Klein-Hitpass
- Institute of Cell Biology, Medical Faculty, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, 35392 Gießen, Germany
| | - Ralf Ehricht
- Alere Technologies GmbH, Löbstedter Straße 103-105, 07749 Jena, Germany
| | - Ines Engelmann
- Alere Technologies GmbH, Löbstedter Straße 103-105, 07749 Jena, Germany
| | - Isabel Hennig-Pauka
- University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1220 Vienna, Austria
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13
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Genetic makeup of Shiga toxin-producing Escherichia coli in relation to clinical symptoms and duration of shedding: a microarray analysis of isolates from Swedish children. Eur J Clin Microbiol Infect Dis 2017; 36:1433-1441. [PMID: 28421309 PMCID: PMC5524872 DOI: 10.1007/s10096-017-2950-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 02/24/2017] [Indexed: 12/19/2022]
Abstract
Shiga toxin (Stx)-producing Escherichia coli (STECs) cause non-bloody diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome, and are the primary cause of acute renal failure in children worldwide. This study investigated the correlation of genetic makeup of STEC strains as revealed by DNA microarray to clinical symptoms and the duration of STEC shedding. All STEC isolated (n = 96) from patients <10 years of age in Jönköping County, Sweden from 2003 to 2015 were included. Isolates were characterized by DNA microarray, including almost 280 genes. Clinical data were collected through a questionnaire and by reviewing medical records. Of the 96 virulence genes (including stx) in the microarray, 62 genes were present in at least one isolate. Statistically significant differences in prevalence were observed for 21 genes when comparing patients with bloody diarrhea (BD) and with non-bloody stool (18 of 21 associated with BD). Most genes encode toxins (e.g., stx2 alleles, astA, toxB), adhesion factors (i.e. espB_O157, tir, eae), or secretion factors (e.g., espA, espF, espJ, etpD, nleA, nleB, nleC, tccP). Seven genes were associated with prolonged stx shedding; the presence of three genes (lpfA, senB, and stx1) and the absence of four genes (espB_O157, espF, astA, and intI1). We found STEC genes that might predict severe disease outcome already at diagnosis. This can be used to develop diagnostic tools for risk assessment of disease outcome. Furthermore, genes associated with the duration of stx shedding were detected, enabling a possible better prediction of length of STEC carriage after infection.
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14
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Barth SA, Menge C, Eichhorn I, Semmler T, Pickard D, Geue L. Evaluation of applicability of DNA microarray–based characterization of bovine Shiga toxin–producing Escherichia coli isolates using whole genome sequence analysis. J Vet Diagn Invest 2017; 29:721-724. [DOI: 10.1177/1040638717700689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We assessed the ability of a commercial DNA microarray to characterize bovine Shiga toxin–producing Escherichia coli (STEC) isolates and evaluated the results using in silico hybridization of the microarray probes within whole genome sequencing scaffolds. From a total of 69,954 reactions (393 probes with 178 isolates), 68,706 (98.2%) gave identical results by DNA microarray and in silico probe hybridization. Results were more congruent when detecting the genoserotype (209 differing results from 19,758 in total; 1.1%) or antimicrobial resistance genes (AMRGs; 141 of 26,878; 0.5%) than when detecting virulence-associated genes (VAGs; 876 of 22,072; 4.0%). Owing to the limited coverage of O-antigens by the microarray, only 37.2% of the isolates could be genoserotyped. However, the microarray proved suitable to rapidly screen bovine STEC strains for the occurrence of high numbers of VAGs and AMRGs and is suitable for molecular surveillance workflows.
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Affiliation(s)
- Stefanie A. Barth
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany (Barth, Menge, Geue)
- Free University Berlin, Institute of Microbiology and Epizootics, Berlin, Germany (Eichhorn, Semmler)
- Robert Koch Institute, Berlin, Germany (Semmler)
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (Pickard)
| | - Christian Menge
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany (Barth, Menge, Geue)
- Free University Berlin, Institute of Microbiology and Epizootics, Berlin, Germany (Eichhorn, Semmler)
- Robert Koch Institute, Berlin, Germany (Semmler)
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (Pickard)
| | - Inga Eichhorn
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany (Barth, Menge, Geue)
- Free University Berlin, Institute of Microbiology and Epizootics, Berlin, Germany (Eichhorn, Semmler)
- Robert Koch Institute, Berlin, Germany (Semmler)
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (Pickard)
| | - Torsten Semmler
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany (Barth, Menge, Geue)
- Free University Berlin, Institute of Microbiology and Epizootics, Berlin, Germany (Eichhorn, Semmler)
- Robert Koch Institute, Berlin, Germany (Semmler)
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (Pickard)
| | - Derek Pickard
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany (Barth, Menge, Geue)
- Free University Berlin, Institute of Microbiology and Epizootics, Berlin, Germany (Eichhorn, Semmler)
- Robert Koch Institute, Berlin, Germany (Semmler)
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (Pickard)
| | - Lutz Geue
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany (Barth, Menge, Geue)
- Free University Berlin, Institute of Microbiology and Epizootics, Berlin, Germany (Eichhorn, Semmler)
- Robert Koch Institute, Berlin, Germany (Semmler)
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (Pickard)
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15
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Geue L, Menge C, Eichhorn I, Semmler T, Wieler LH, Pickard D, Berens C, Barth SA. Evidence for Contemporary Switching of the O-Antigen Gene Cluster between Shiga Toxin-Producing Escherichia coli Strains Colonizing Cattle. Front Microbiol 2017; 8:424. [PMID: 28377748 PMCID: PMC5359238 DOI: 10.3389/fmicb.2017.00424] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 02/28/2017] [Indexed: 11/13/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) comprise a group of zoonotic enteric pathogens with ruminants, especially cattle, as the main reservoir. O-antigens are instrumental for host colonization and bacterial niche adaptation. They are highly immunogenic and, therefore, targeted by the adaptive immune system. The O-antigen is one of the most diverse bacterial cell constituents and variation not only exists between different bacterial species, but also between individual isolates/strains within a single species. We recently identified STEC persistently infecting cattle and belonging to the different serotypes O156:H25 (n = 21) and O182:H25 (n = 15) that were of the MLST sequence types ST300 or ST688. These STs differ by a single nucleotide in purA only. Fitness-, virulence-associated genome regions, and CRISPR/CAS (clustered regularly interspaced short palindromic repeats/CRISPR associated sequence) arrays of these STEC O156:H25 and O182:H25 isolates were highly similar, and identical genomic integration sites for the stx converting bacteriophages and the core LEE, identical Shiga toxin converting bacteriophage genes for stx1a, identical complete LEE loci, and identical sets of chemotaxis and flagellar genes were identified. In contrast to this genomic similarity, the nucleotide sequences of the O-antigen gene cluster (O-AGC) regions between galF and gnd and very few flanking genes differed fundamentally and were specific for the respective serotype. Sporadic aEPEC O156:H8 isolates (n = 5) were isolated in temporal and spatial proximity. While the O-AGC and the corresponding 5' and 3' flanking regions of these aEPEC isolates were identical to the respective region in the STEC O156:H25 isolates, the core genome, the virulence associated genome regions and the CRISPR/CAS elements differed profoundly. Our cumulative epidemiological and molecular data suggests a recent switch of the O-AGC between isolates with O156:H8 strains having served as DNA donors. Such O-antigen switches can affect the evaluation of a strain's pathogenic and virulence potential, suggesting that NGS methods might lead to a more reliable risk assessment.
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Affiliation(s)
- Lutz Geue
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular PathogenesisJena, Germany
| | - Christian Menge
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular PathogenesisJena, Germany
| | - Inga Eichhorn
- Institute of Microbiology and Epizootics, Free University BerlinBerlin, Germany
| | - Torsten Semmler
- Institute of Microbiology and Epizootics, Free University BerlinBerlin, Germany
- Robert Koch InstituteBerlin, Germany
| | - Lothar H. Wieler
- Institute of Microbiology and Epizootics, Free University BerlinBerlin, Germany
- Robert Koch InstituteBerlin, Germany
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Pathogen GenomicsCambridge, UK
| | - Christian Berens
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular PathogenesisJena, Germany
| | - Stefanie A. Barth
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular PathogenesisJena, Germany
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16
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The Accessory Genome of Shiga Toxin-Producing Escherichia coli Defines a Persistent Colonization Type in Cattle. Appl Environ Microbiol 2016; 82:5455-64. [PMID: 27371579 DOI: 10.1128/aem.00909-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/23/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Shiga toxin-producing Escherichia coli (STEC) strains can colonize cattle for several months and may, thus, serve as gene reservoirs for the genesis of highly virulent zoonotic enterohemorrhagic E. coli (EHEC). Attempts to reduce the human risk for acquiring EHEC infections should include strategies to control such STEC strains persisting in cattle. We therefore aimed to identify genetic patterns associated with the STEC colonization type in the bovine host. We included 88 persistent colonizing STEC (STEC(per)) (shedding for ≥4 months) and 74 sporadically colonizing STEC (STEC(spo)) (shedding for ≤2 months) isolates from cattle and 16 bovine STEC isolates with unknown colonization types. Genoserotypes and multilocus sequence types (MLSTs) were determined, and the isolates were probed with a DNA microarray for virulence-associated genes (VAGs). All STEC(per) isolates belonged to only four genoserotypes (O26:H11, O156:H25, O165:H25, O182:H25), which formed three genetic clusters (ST21/396/1705, ST300/688, ST119). In contrast, STEC(spo) isolates were scattered among 28 genoserotypes and 30 MLSTs, with O157:H7 (ST11) and O6:H49 (ST1079) being the most prevalent. The microarray analysis identified 139 unique gene patterns that clustered with the genoserotypes and MLSTs of the strains. While the STEC(per) isolates possessed heterogeneous phylogenetic backgrounds, the accessory genome clustered these isolates together, separating them from the STEC(spo) isolates. Given the vast genetic heterogeneity of bovine STEC strains, defining the genetic patterns distinguishing STEC(per) from STEC(spo) isolates will facilitate the targeted design of new intervention strategies to counteract these zoonotic pathogens at the farm level. IMPORTANCE Ruminants, especially cattle, are sources of food-borne infections by Shiga toxin-producing Escherichia coli (STEC) in humans. Some STEC strains persist in cattle for longer periods of time, while others are detected only sporadically. Persisting strains can serve as gene reservoirs that supply E. coli with virulence factors, thereby generating new outbreak strains. Attempts to reduce the human risk for acquiring STEC infections should therefore include strategies to control such persisting STEC strains. By analyzing representative genes of their core and accessory genomes, we show that bovine STEC with a persistent colonization type emerged independently from sporadically colonizing isolates and evolved in parallel evolutionary branches. However, persistent colonizing strains share similar sets of accessory genes. Defining the genetic patterns that distinguish persistent from sporadically colonizing STEC isolates will facilitate the targeted design of new intervention strategies to counteract these zoonotic pathogens at the farm level.
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17
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Duan Z, Senchenkova SN, Guo X, Perepelov AV, Shashkov AS, Liu B, Knirel YA. Structure and gene cluster of the O-antigen of Escherichia coli O156 containing a pyruvic acid acetal. Carbohydr Res 2016; 430:24-28. [PMID: 27177202 DOI: 10.1016/j.carres.2016.04.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 11/27/2022]
Abstract
The lipopolysaccharide of Escherichia coli O156 was degraded under mild acidic and alkaline conditions and the resulting polysaccharides were studied by sugar analysis and (1)H and (13)C NMR spectroscopy. The following structure of the pentasaccharide repeating unit of the O-polysaccharide was established: where Rpyr indicates R-configurated pyruvic acid acetal. Minor O-acetyl groups also were present and tentatively localized on the Gal residues. The gene cluster for biosynthesis of the O-antigen of E. coli O156 was analyzed and shown to be consistent with the O-polysaccharide structure.
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Affiliation(s)
- Zhifeng Duan
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, 300457 Tianjin, China
| | - Sof'ya N Senchenkova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Xi Guo
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, 300457 Tianjin, China
| | - Andrei V Perepelov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Bin Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, 300457 Tianjin, China
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation.
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Ferdous M, Zhou K, de Boer RF, Friedrich AW, Kooistra-Smid AMD, Rossen JWA. Comprehensive Characterization of Escherichia coli O104:H4 Isolated from Patients in the Netherlands. Front Microbiol 2015; 6:1348. [PMID: 26696970 PMCID: PMC4667096 DOI: 10.3389/fmicb.2015.01348] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/16/2015] [Indexed: 11/25/2022] Open
Abstract
In 2011, a Shiga toxin-producing Enteroaggregative Escherichia coli (EAEC Stx2a+) O104:H4 strain caused a serious outbreak of acute gastroenteritis and hemolytic-uremic syndrome (HUS) in Germany. In 2013, E. coli O104:H4 isolates were obtained from a patient with HUS and her friend showing only gastrointestinal complaints. The antimicrobial resistance and virulence profiles of these isolates together with three EAEC Stx2a+ O104:H4 isolates from 2011 were determined and compared. Whole-genome sequencing (WGS) was performed for detailed characterization and to determine genetic relationship of the isolates. Four additional genomes of EAEC Stx2a+ O104:H4 isolates of 2009 and 2011 available on NCBI were included in the virulence and phylogenetic analysis. All E. coli O104:H4 isolates tested were positive for stx2a, aatA, and terD but were negative for escV. All, except one 2011 isolate, were positive for aggR and were therefore considered EAEC. The EAEC Stx2a+ O104:H4 isolates of 2013 belonged to sequence type (ST) ST678 as the 2011 isolates and showed slightly different resistance and virulence patterns compared to the 2011 isolates. Core-genome phylogenetic analysis showed that the isolates of 2013 formed a separate cluster from the isolates of 2011 and 2009 by 27 and 20 different alleles, respectively. In addition, only a one-allele difference was found between the isolate of the HUS-patient and that of her friend. Our study shows that EAEC Stx2a+ O104:H4 strains highly similar to the 2011 outbreak clone in their core genome are still circulating necessitating proper surveillance to prevent further outbreaks with these potentially pathogenic strains. In addition, WGS not only provided a detailed characterization of the isolates but its high discriminatory power also enabled us to discriminate the 2013 isolates from the isolates of 2009 and 2011 expediting the use of WGS in public health services to rapidly apply proper infection control strategies.
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Affiliation(s)
- Mithila Ferdous
- Department of Medical Microbiology, University Medical Center Groningen, University of GroningenGroningen, Netherlands
| | - Kai Zhou
- Department of Medical Microbiology, University Medical Center Groningen, University of GroningenGroningen, Netherlands
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesHangzhou, China
| | - Richard F. de Boer
- Department of Medical Microbiology, Certe-Laboratory for Infectious DiseasesGroningen, Netherlands
| | - Alexander W. Friedrich
- Department of Medical Microbiology, University Medical Center Groningen, University of GroningenGroningen, Netherlands
- *Correspondence: Alexander W. Friedrich,
| | - Anna M. D. Kooistra-Smid
- Department of Medical Microbiology, University Medical Center Groningen, University of GroningenGroningen, Netherlands
- Department of Medical Microbiology, Certe-Laboratory for Infectious DiseasesGroningen, Netherlands
| | - John W. A. Rossen
- Department of Medical Microbiology, University Medical Center Groningen, University of GroningenGroningen, Netherlands
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Krüger A, Lucchesi PMA, Sanso AM, Etcheverría AI, Bustamante AV, Burgán J, Fernández L, Fernández D, Leotta G, Friedrich AW, Padola NL, Rossen JWA. Genetic characterization of Shiga toxin-producing Escherichia coli O26:H11 strains isolated from animal, food, and clinical samples. Front Cell Infect Microbiol 2015; 5:74. [PMID: 26539413 PMCID: PMC4612136 DOI: 10.3389/fcimb.2015.00074] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/05/2015] [Indexed: 11/16/2022] Open
Abstract
The Shiga-toxin producing Escherichia coli (STEC) may cause serious illness in human. Here we analyze O26:H11 strains known to be among the most reported STEC strains causing human infections. Genetic characterization of strains isolated from animal, food, and clinical specimens in Argentina showed that most carried either stx1a or stx2a subtypes. Interestingly, stx2a-positive O26:H11 rarely isolated from cattle in other countries showed to be an important proportion of O26:H11 strains circulating in cattle and food in our region. Seventeen percent of the isolates harbored more than one gene associated with antimicrobial resistance. In addition to stx, all strains contained the virulence genes eae-β, tir, efa, iha, espB, cif, espA, espF, espJ, nleA, nleB, nleC, and iss; and all except one contained ehxA, espP, and cba genes. On the other hand, toxB and espI genes were exclusively observed in stx2-positive isolates, whereas katP was only found in stx1a-positive isolates. Our results show that O26:H11 STEC strains circulating in Argentina, including those isolated from humans, cattle, and meat products, present a high pathogenic potential, and evidence that cattle can be a reservoir of O26:H11 strains harboring stx2a.
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Affiliation(s)
- Alejandra Krüger
- Laboratorio de Inmunoquímica y Biotecnología, Facultad de Ciencias Veterinarias, Centro de Investigación Veterinaria de Tandil, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, Universidad Nacional del Centro de la Provincia de Buenos Aires Tandil, Argentina
| | - Paula M A Lucchesi
- Laboratorio de Inmunoquímica y Biotecnología, Facultad de Ciencias Veterinarias, Centro de Investigación Veterinaria de Tandil, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, Universidad Nacional del Centro de la Provincia de Buenos Aires Tandil, Argentina
| | - A Mariel Sanso
- Laboratorio de Inmunoquímica y Biotecnología, Facultad de Ciencias Veterinarias, Centro de Investigación Veterinaria de Tandil, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, Universidad Nacional del Centro de la Provincia de Buenos Aires Tandil, Argentina
| | - Analía I Etcheverría
- Laboratorio de Inmunoquímica y Biotecnología, Facultad de Ciencias Veterinarias, Centro de Investigación Veterinaria de Tandil, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, Universidad Nacional del Centro de la Provincia de Buenos Aires Tandil, Argentina
| | - Ana V Bustamante
- Laboratorio de Inmunoquímica y Biotecnología, Facultad de Ciencias Veterinarias, Centro de Investigación Veterinaria de Tandil, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, Universidad Nacional del Centro de la Provincia de Buenos Aires Tandil, Argentina
| | - Julia Burgán
- Laboratorio de Inmunoquímica y Biotecnología, Facultad de Ciencias Veterinarias, Centro de Investigación Veterinaria de Tandil, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, Universidad Nacional del Centro de la Provincia de Buenos Aires Tandil, Argentina
| | - Luciana Fernández
- Laboratorio de Inmunoquímica y Biotecnología, Facultad de Ciencias Veterinarias, Centro de Investigación Veterinaria de Tandil, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, Universidad Nacional del Centro de la Provincia de Buenos Aires Tandil, Argentina
| | - Daniel Fernández
- Laboratorio de Inmunoquímica y Biotecnología, Facultad de Ciencias Veterinarias, Centro de Investigación Veterinaria de Tandil, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, Universidad Nacional del Centro de la Provincia de Buenos Aires Tandil, Argentina
| | - Gerardo Leotta
- Línea Seguridad Alimentaria, Instituto de Genética Veterinaria Ing. F.N. Dulout, Consejo Nacional de Investigaciones Científicas y Técnicas La Plata, Argentina
| | - Alexander W Friedrich
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Nora L Padola
- Laboratorio de Inmunoquímica y Biotecnología, Facultad de Ciencias Veterinarias, Centro de Investigación Veterinaria de Tandil, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, Universidad Nacional del Centro de la Provincia de Buenos Aires Tandil, Argentina
| | - John W A Rossen
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
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20
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Barth S, Geue L, Hinsching A, Jenckel M, Schlosser J, Eiden M, Pietschmann J, Menge C, Beer M, Groschup M, Jori F, Etter E, Blome S. Experimental Evaluation of Faecal Escherichia coli and Hepatitis E Virus as Biological Indicators of Contacts Between Domestic Pigs and Eurasian Wild Boar. Transbound Emerg Dis 2015; 64:487-494. [PMID: 26190581 DOI: 10.1111/tbed.12389] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Indexed: 11/30/2022]
Abstract
Domestic pigs and Eurasian wild boar (Sus scrofa) share several important viral and bacterial pathogens. Therefore, direct and indirect contacts between domestic pigs and wild boar present a risk of pathogen spillover and can lead to long-term perpetuation of infection. Biological indicators could be a powerful tool to understand and characterize contacts between wild boar and domestic pigs. Here, faecal Escherichia coli and Hepatitis E virus (HEV) were explored as potential biological indicators under experimental conditions. The data gained in our pilot study suggest that faecal E. coli can be used as biological indicator of contact between wild boar and domestic pig. For HEV, faecal transmission was also confirmed. However, molecular studies on full-genome basis did not reveal markers that would allow tracing of transmission direction. Based on these promising results, future field studies will especially target the practicability of E. coli microbiome molecular typing as surrogate of contacts at the wildlife-livestock interface.
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Affiliation(s)
- S Barth
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Jena, Germany
| | - L Geue
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Jena, Germany
| | - A Hinsching
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Jena, Germany
| | - M Jenckel
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - J Schlosser
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - M Eiden
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - J Pietschmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - C Menge
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Jena, Germany
| | - M Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - M Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - F Jori
- Department of Environment and Society, UPR AGIRS, CIRAD, Montpellier, France.,Department of Animal Science and Production, Botswana College of Agriculture, Gaborone, Botswana
| | - E Etter
- Department of Environment and Society, UPR AGIRS, CIRAD, Montpellier, France.,Department of Production Animals Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - S Blome
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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Herrero-Fresno A, Larsen I, Olsen JE. Genetic relatedness of commensal Escherichia coli from nursery pigs in intensive pig production in Denmark and molecular characterization of genetically different strains. J Appl Microbiol 2015; 119:342-53. [PMID: 25963647 DOI: 10.1111/jam.12840] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 04/29/2015] [Accepted: 04/29/2015] [Indexed: 12/01/2022]
Abstract
AIMS To determine the genetic relatedness and the presence of virulence and antibiotic resistance genes in commensal Escherichia coli from nursery pigs in Danish intensive production. METHODS AND RESULTS The genetic diversity of 1000 E. coli strains randomly picked (N = 50 isolates) from cultured faecal samples (N = 4 pigs) from five intensive Danish pigs farms was analysed by repetitive extragenic palindromic-PCR (REP-PCR) and 42 unique REP-profiles were detected (similarity <92%). One profile was dominant (67.2% of strains) but farms differed significantly in the diversity of commensal E. coli: between eight and 21 different profiles per farm were detected. One to three strains representing each REP-profile were characterized by multilocus typing scheme-typing, as well as for presence of antimicrobial and virulence genes and serogrouping through microarray analysis. The 42 REP-profiles were classified into 22 different sequence types (ST) with ST10 being the most common, encompassing 10 REP-profiles. Resistance and virulence genes were detected in most of the isolates. Genes encoding AmpC-β-lactamases and quinolone resistance were found in one and three isolates, respectively. Toxin-producing genes were observed in 20 isolates. CONCLUSIONS A low genetic diversity was found in commensal gut E. coli from nursery pigs in Denmark. No correlation was observed between REP-profiles, ST-types and resistance/virulence patterns. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study analysing in depth the genetic variability of commensal E. coli from pigs in Danish intensive pig production. A tendency for higher diversity was observed with in nursery pigs that were treated with zinc oxide only, in absence of other antimicrobials. Strains with potential to disseminate virulence and antibiotic resistance genes to pathogenic subgroups of E. coli were found to be wide-spread.
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Affiliation(s)
- A Herrero-Fresno
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - I Larsen
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - J E Olsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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22
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Gwida M, Hotzel H, Geue L, Tomaso H. Occurrence of Enterobacteriaceae in Raw Meat and in Human Samples from Egyptian Retail Sellers. INTERNATIONAL SCHOLARLY RESEARCH NOTICES 2014; 2014:565671. [PMID: 27379312 PMCID: PMC4897388 DOI: 10.1155/2014/565671] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/09/2014] [Accepted: 10/10/2014] [Indexed: 11/24/2022]
Abstract
The present study was performed to assess the presence of Enterobacteriaceae in raw meat and handlers in Egypt using cultivation and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). A total of 100 raw meat samples (chicken and beef meat, 50 each) were randomly purchased from butchers and local meat retailers located at Mansoura city, Egypt. Fifty human samples were collected from meat handlers (hand swabs and stool specimens, 25 each). 228 bacterial isolates were recovered from these samples. Unidentified isolates were characterized by partial 16S rRNA gene sequencing. Escherichia coli isolates were further typed using a DNA microarray system. Proteus spp. (60.0%) were found to be the most abundant followed by Escherichia coli (38.7%), Klebsiella spp. (17.3%), and Citrobacter spp. (13.3%). The presence of different Enterobacteriaceae in locally produced retail raw meat demonstrates the risk of infection of people through consumption of raw or undercooked meat and the risk for cross-contamination of other food products. Harmonized and concerted actions from veterinary and public health authorities are needed to reduce the risk of infection.
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Affiliation(s)
- Mayada Gwida
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743 Jena, Germany
| | - Lutz Geue
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, 07743 Jena, Germany
| | - Herbert Tomaso
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743 Jena, Germany
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23
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Badura A, Luxner J, Feierl G, Reinthaler FF, Zarfel G, Galler H, Pregartner G, Riedl R, Grisold AJ. Prevalence, antibiotic resistance patterns and molecular characterization of Escherichia coli from Austrian sandpits. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2014; 194:24-30. [PMID: 25089889 DOI: 10.1016/j.envpol.2014.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/25/2014] [Accepted: 07/03/2014] [Indexed: 06/03/2023]
Abstract
The aim was to determine the prevalence of E. coli and coliform bacteria in playground sand of all public children's sandpits in Graz (n = 45), Austria, and to assess the frequency of antimicrobial resistance in E. coli. Molecular characterization included the discrimination of O-serotypes and H-antigens and the determination of virulence and resistance genes, using a microarray technology. E. coli isolates were tested for susceptibility to a set of antibiotics by VITEK2 system and disk diffusion method. In total, 22 (49%) and 44 (98%) sandpits were positive for E. coli and coliform bacteria. Median concentrations of E. coli and coliform bacteria in the sand samples were: 2.6 × 10(4) CFU/100 g and 3.0 × 10(5) CFU/100 g. Resistance rates were: ampicillin, 12.5%; piperacillin, 10.4%; amoxicillin/clavulanic acid, 9.4%; cotrimoxazole, 6.3%; tetracycline, 6.3%; piperacillin/tazobactam, 5.2%. No ESBL- or carbapenemase-producing isolates were found. The most prevalent serogroups were O15, O6 and O4. Isolates harbored 0 up to 16 different virulence genes.
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Affiliation(s)
- Alexandra Badura
- Institute of Hygiene, Microbiology and Environmental Medicine; Medical University of Graz, Universitaetsplatz 4, A-8010 Graz, Austria.
| | - Josefa Luxner
- Institute of Hygiene, Microbiology and Environmental Medicine; Medical University of Graz, Universitaetsplatz 4, A-8010 Graz, Austria
| | - Gebhard Feierl
- Institute of Hygiene, Microbiology and Environmental Medicine; Medical University of Graz, Universitaetsplatz 4, A-8010 Graz, Austria
| | - Franz F Reinthaler
- Institute of Hygiene, Microbiology and Environmental Medicine; Medical University of Graz, Universitaetsplatz 4, A-8010 Graz, Austria
| | - Gernot Zarfel
- Institute of Hygiene, Microbiology and Environmental Medicine; Medical University of Graz, Universitaetsplatz 4, A-8010 Graz, Austria
| | - Herbert Galler
- Institute of Hygiene, Microbiology and Environmental Medicine; Medical University of Graz, Universitaetsplatz 4, A-8010 Graz, Austria
| | - Gudrun Pregartner
- Institute for Medical Informatics, Statistics and Documentation; Medical University of Graz, Austria
| | - Regina Riedl
- Institute for Medical Informatics, Statistics and Documentation; Medical University of Graz, Austria
| | - Andrea J Grisold
- Institute of Hygiene, Microbiology and Environmental Medicine; Medical University of Graz, Universitaetsplatz 4, A-8010 Graz, Austria
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Development of a rapid microarray-based DNA subtyping assay for the alleles of Shiga toxins 1 and 2 of Escherichia coli. J Clin Microbiol 2014; 52:2898-904. [PMID: 24899022 DOI: 10.1128/jcm.01048-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In this study, we developed a new rapid, economic, and automated microarray-based genotyping test for the standardized subtyping of Shiga toxins 1 and 2 of Escherichia coli. The microarrays from Alere Technologies can be used in two different formats, the ArrayTube and the ArrayStrip (which enables high-throughput testing in a 96-well format). One microarray chip harbors all the gene sequences necessary to distinguish between all Stx subtypes, facilitating the identification of single and multiple subtypes within a single isolate in one experiment. Specific software was developed to automatically analyze all data obtained from the microarray. The assay was validated with 21 Shiga toxin-producing E. coli (STEC) reference strains that were previously tested by the complete set of conventional subtyping PCRs. The microarray results showed 100% concordance with the PCR results. Essentially identical results were detected when the standard DNA extraction method was replaced by a time-saving heat lysis protocol. For further validation of the microarray, we identified the Stx subtypes or combinations of the subtypes in 446 STEC field isolates of human and animal origin. In summary, this oligonucleotide array represents an excellent diagnostic tool that provides some advantages over standard PCR-based subtyping. The number of the spotted probes on the microarrays can be increased by additional probes, such as for novel alleles, species markers, or resistance genes, should the need arise.
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25
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Quantification and characterization of mucosa-associated and intracellular Escherichia coli in inflammatory bowel disease. Inflamm Bowel Dis 2013; 19:2326-38. [PMID: 23989750 DOI: 10.1097/mib.0b013e3182a38a92] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Mucosa-associated Escherichia coli are abundant in inflammatory bowel disease (IBD), but whether these bacteria gain intracellular access within the mucosa is uncertain. If E. coli does gain intracellular access, the contribution of bacterial pathogenicity to this requires further elucidation. This study aimed to quantify and characterize mucosa-associated and intracellular E. coli in patients with IBD and in healthy control subjects (HC). METHODS Mucosal biopsies from 30 patients with Crohn's disease (CD), 15 with ulcerative colitis (UC), and 14 HC were cultured with or without gentamicin protection to recover intracellular or mucosa-associated E. coli, respectively. Overall, 40 strains (CD: n = 24, UC: n = 9, and HC: n = 7) were characterized by phylogenetic typing, adhesion and invasion assays, detection of virulence factors, antimicrobial resistance genes, and proteomic analysis. RESULTS Mucosa-associated E. coli were more abundant in CD and UC than in HC (2750 versus 1350 versus 230 median colony-forming units per biopsy; P = 0.01). Intracellular E. coli were more prevalent in CD (90%) than in UC (47%) or HC mucosal biopsies (0%) (P < 0.001). Of 24 CD strains, 2 were adherent and invasive, but there were no unifying pathogenicity determinants that could distinguish most CD strains from UC or HC strains, or intracellular isolates from mucosa-associated isolates. CONCLUSIONS Intracellular E. coli are more common in CD than in UC and not identified in HC. Most intracellular E. coli did not have characterizing pathogenic features, suggesting a significant role for defects in mucosal immunity or barrier dysfunction in their ability to gain intracellular access.
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Wu G, Day MJ, Mafura MT, Nunez-Garcia J, Fenner JJ, Sharma M, van Essen-Zandbergen A, Rodríguez I, Dierikx C, Kadlec K, Schink AK, Wain J, Helmuth R, Guerra B, Schwarz S, Threlfall J, Woodward MJ, Woodford N, Coldham N, Mevius D. Comparative analysis of ESBL-positive Escherichia coli isolates from animals and humans from the UK, The Netherlands and Germany. PLoS One 2013; 8:e75392. [PMID: 24086522 PMCID: PMC3784421 DOI: 10.1371/journal.pone.0075392] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/12/2013] [Indexed: 11/26/2022] Open
Abstract
The putative virulence and antimicrobial resistance gene contents of extended spectrum β-lactamase (ESBL)-positive E. coli (n=629) isolated between 2005 and 2009 from humans, animals and animal food products in Germany, The Netherlands and the UK were compared using a microarray approach to test the suitability of this approach with regard to determining their similarities. A selection of isolates (n=313) were also analysed by multilocus sequence typing (MLST). Isolates harbouring blaCTX-M-group-1 dominated (66%, n=418) and originated from both animals and cases of human infections in all three countries; 23% (n=144) of all isolates contained both blaCTX-M-group-1 and blaOXA-1-like genes, predominantly from humans (n=127) and UK cattle (n=15). The antimicrobial resistance and virulence gene profiles of this collection of isolates were highly diverse. A substantial number of human isolates (32%, n=87) did not share more than 40% similarity (based on the Jaccard coefficient) with animal isolates. A further 43% of human isolates from the three countries (n=117) were at least 40% similar to each other and to five isolates from UK cattle and one each from Dutch chicken meat and a German dog; the members of this group usually harboured genes such as mph(A), mrx, aac(6’)-Ib, catB3, blaOXA-1-like and blaCTX-M-group-1. forty-four per cent of the MLST-typed isolates in this group belonged to ST131 (n=18) and 22% to ST405 (n=9), all from humans. Among animal isolates subjected to MLST (n=258), only 1.2% (n=3) were more than 70% similar to human isolates in gene profiles and shared the same MLST clonal complex with the corresponding human isolates. The results suggest that minimising human-to-human transmission is essential to control the spread of ESBL-positive E. coli in humans.
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Affiliation(s)
- Guanghui Wu
- Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), Addlestone, United Kingdom
- * E-mail:
| | | | - Muriel T. Mafura
- Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), Addlestone, United Kingdom
| | - Javier Nunez-Garcia
- Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), Addlestone, United Kingdom
| | - Jackie J. Fenner
- Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), Addlestone, United Kingdom
| | - Meenaxi Sharma
- Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), Addlestone, United Kingdom
| | - Alieda van Essen-Zandbergen
- Department of Bacteriology and TSEs, Central Veterinary Institute (CVI) of Wageningen, Lelystad, the Netherlands
| | - Irene Rodríguez
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Cindy Dierikx
- Department of Bacteriology and TSEs, Central Veterinary Institute (CVI) of Wageningen, Lelystad, the Netherlands
| | - Kristina Kadlec
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Anne-Kathrin Schink
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - John Wain
- Public Health England, London, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Reiner Helmuth
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Beatriz Guerra
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | | | - Martin J. Woodward
- Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), Addlestone, United Kingdom
| | | | - Nick Coldham
- Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), Addlestone, United Kingdom
| | - Dik Mevius
- Department of Bacteriology and TSEs, Central Veterinary Institute (CVI) of Wageningen, Lelystad, the Netherlands
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Lee YJ, van Nostrand JD, Tu Q, Lu Z, Cheng L, Yuan T, Deng Y, Carter MQ, He Z, Wu L, Yang F, Xu J, Zhou J. The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. ISME JOURNAL 2013; 7:1974-84. [PMID: 23765101 DOI: 10.1038/ismej.2013.88] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 04/10/2013] [Accepted: 04/20/2013] [Indexed: 12/21/2022]
Abstract
Pathogens present in the environment pose a serious threat to human, plant and animal health as evidenced by recent outbreaks. As many pathogens can survive and proliferate in the environment, it is important to understand their population dynamics and pathogenic potential in the environment. To assess pathogenic potential in diverse habitats, we developed a functional gene array, the PathoChip, constructed with key virulence genes related to major virulence factors, such as adherence, colonization, motility, invasion, toxin, immune evasion and iron uptake. A total of 3715 best probes were selected from 13 virulence factors, covering 7417 coding sequences from 1397 microbial species (2336 strains). The specificity of the PathoChip was computationally verified, and approximately 98% of the probes provided specificity at or below the species level, proving its excellent capability for the detection of target sequences with high discrimination power. We applied this array to community samples from soil, seawater and human saliva to assess the occurrence of virulence genes in natural environments. Both the abundance and diversity of virulence genes increased in stressed conditions compared with their corresponding controls, indicating a possible increase in abundance of pathogenic bacteria under environmental perturbations such as warming or oil spills. Statistical analyses showed that microbial communities harboring virulence genes were responsive to environmental perturbations, which drove changes in abundance and distribution of virulence genes. The PathoChip provides a useful tool to identify virulence genes in microbial populations, examine the dynamics of virulence genes in response to environmental perturbations and determine the pathogenic potential of microbial communities.
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Affiliation(s)
- Yong-Jin Lee
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
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Etcheverría AI, Padola NL. Shiga toxin-producing Escherichia coli: factors involved in virulence and cattle colonization. Virulence 2013; 4:366-72. [PMID: 23624795 PMCID: PMC3714128 DOI: 10.4161/viru.24642] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) cause hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS) in humans. Outbreaks are linked to bovine food sources. STEC O157:H7 has been responsible for the most severe outbreaks worldwide. However, non-O157 serotypes have emerged as important enteric pathogens in several countries. The main virulence factor of STEC is the production of Shiga toxins 1 and 2. Additional virulence markers are a plasmid-encoded enterohemolysin (ehxA), an autoagglutinating adhesin (Saa), a catalase-peroxidase (katP), an extracellular serine protease (espP), a zinc metalloprotease (stcE), a subtilase cytotoxin (subAB), among others. Other virulence factors are intimin and adhesins that had a roll in the adherence of STEC to bovine colon. This review focuses on the virulence traits of STEC and especially on those related to the adhesion to bovine colon. The known of the interaction between STEC and the bovine host is crucial to develop strategies to control cattle colonization.
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Affiliation(s)
- Analía Inés Etcheverría
- Laboratorio de Imunoquímica y Biotecnología, Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CICPBA, Facultad de Ciencias Veterinarias, UNCPBA, Tandil, Argentina.
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29
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Blum SE, Leitner G. Genotyping and virulence factors assessment of bovine mastitis Escherichia coli. Vet Microbiol 2013; 163:305-12. [PMID: 23374653 DOI: 10.1016/j.vetmic.2012.12.037] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 12/23/2012] [Accepted: 12/24/2012] [Indexed: 11/18/2022]
Abstract
Escherichia coli is a major agent of bovine mastitis worldwide. However, specific E. coli virulence factors associated to pathogenicity during intra-mammary infections are yet unknown and this pathotype remains uncharacterized. The objectives of the present work were to assess the presence of a wide range of known virulence factors in a large set of E. coli strains isolated from bovine mastitis (mastitis set) and to study the genotypic distribution of strains in the mastitis set in comparison to a set of strains isolated from cows' environment in dairy farms (environmental set). Virulence factors were assessed by DNA hybridization microarray. The three most prevalent virulence factors found in the mastitis set were lpfA (long polar fimbriae), iss (increased serum resistance) and astA (enteroaggregative E. coli heat-stable enterotoxin 1). None, however, characterized the majority of these strains. Genotyping was assessed by ECOR phylogenetic grouping, multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Strains in the mastitis and environmental sets were differentially distributed into ECOR phylogenetic groups; groups A and B1 being the most prevalent ones. Multiple MLST strain types were found in the two sets of strains, but only a few were common to both, and diversity was higher in the environmental set. A variety of PFGE patterns were found in the mastitis and environmental sets. Two clusters comprising mostly highly similar mastitis strains were identified. The results confirm that mastitis E. coli strains mostly lack known E. coli virulence factors. In addition, it is shown that the genotypic diversity of mastitis strains does not reflect the diversity found in the environmental E. coli population.
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Affiliation(s)
- Shlomo E Blum
- Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, Rehovot, 76100, Israel.
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Braun SD, Ziegler A, Methner U, Slickers P, Keiling S, Monecke S, Ehricht R. Fast DNA serotyping and antimicrobial resistance gene determination of salmonella enterica with an oligonucleotide microarray-based assay. PLoS One 2012; 7:e46489. [PMID: 23056321 PMCID: PMC3464306 DOI: 10.1371/journal.pone.0046489] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 09/04/2012] [Indexed: 01/21/2023] Open
Abstract
Salmonellosis caused by Salmonella (S.) belongs to the most prevalent food-borne zoonotic diseases throughout the world. Therefore, serotype identification for all culture-confirmed cases of Salmonella infection is important for epidemiological purposes. As a standard, the traditional culture method (ISO 6579:2002) is used to identify Salmonella. Classical serotyping takes 4–5 days to be completed, it is labor-intensive, expensive and more than 250 non-standardized sera are necessary to characterize more than 2,500 Salmonella serovars currently known. These technical difficulties could be overcome with modern molecular methods. We developed a microarray based serogenotyping assay for the most prevalent Salmonella serovars in Europe and North America. The current assay version could theoretically discriminate 28 O-antigens and 86 H-antigens. Additionally, we included 77 targets analyzing antimicrobial resistance genes. The Salmonella assay was evaluated with a set of 168 reference strains representing 132 serovars previously serotyped by conventional agglutination through various reference centers. 117 of 132 (81%) tested serovars showed an unique microarray pattern. 15 of 132 serovars generated a pattern which was shared by multiple serovars (e.g., S. ser. Enteritidis and S. ser. Nitra). These shared patterns mainly resulted from the high similarity of the genotypes of serogroup A and D1. Using patterns of the known reference strains, a database was build which represents the basis of a new PatternMatch software that can serotype unknown Salmonella isolates automatically. After assay verification, the Salmonella serogenotyping assay was used to identify a field panel of 105 Salmonella isolates. All were identified as Salmonella and 93 of 105 isolates (88.6%) were typed in full concordance with conventional serotyping. This microarray based assay is a powerful tool for serogenotyping.
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31
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Naseer U, Olsson-Liljequist BE, Woodford N, Dhanji H, Cantón R, Sundsfjord A, Lindstedt BA. Multi-locus variable number of tandem repeat analysis for rapid and accurate typing of virulent multidrug resistant Escherichia coli clones. PLoS One 2012; 7:e41232. [PMID: 22859970 PMCID: PMC3407997 DOI: 10.1371/journal.pone.0041232] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 06/19/2012] [Indexed: 11/18/2022] Open
Abstract
One hundred E. coli isolates from Norway
(n = 37), Sweden (n = 24), UK
(n = 20) and Spain (n = 19), producing
CTX-M-type - (n = 84), or SHV-12
(n = 4) extended spectrum β-lactamases, or the plasmid
mediated AmpC, CMY-2 (n = 12), were typed using multi-locus
sequence typing (MLST) and multi-locus variable number of tandem repeat analysis
(MLVA). Isolates clustered into 33 Sequence Types (STs) and 14 Sequence Type
Complexes (STCs), and 58 MLVA-Types (MTs) and 25 different MLVA-Type Complexes
(MTCs). A strong agreement between the MLST profile and MLVA typing results was
observed, in which all ST131-isolates (n = 39) and most of
the STC-648 (n = 10), STC-38 (n = 9),
STC-10 (n = 9), STC-405 (n = 8) and
STC-23 (n = 6) isolates were clustered distinctly into
MTC-29, -36, -20, -14, -10 and -39, respectively. MLVA is a rapid and accurate
tool for genotyping isolates of globally disseminated virulent multidrug
resistant E. coli lineages, including ST131.
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Affiliation(s)
- Umaer Naseer
- Research Group for Host-Microbe Interactions, Department of Medical Biology, University of Tromsø, Tromsø, Norway.
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Schilling AK, Hotzel H, Methner U, Sprague LD, Schmoock G, El-Adawy H, Ehricht R, Wöhr AC, Erhard M, Geue L. Zoonotic agents in small ruminants kept on city farms in southern Germany. Appl Environ Microbiol 2012; 78:3785-93. [PMID: 22447607 PMCID: PMC3346384 DOI: 10.1128/aem.07802-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 03/05/2012] [Indexed: 11/20/2022] Open
Abstract
Sheep and goats are popular examples of livestock kept on city farms. In these settings, close contacts between humans and animals frequently occur. Although it is widely accepted that small ruminants can carry numerous zoonotic agents, it is unknown which of these agents actually occur in sheep and goats on city farms in Germany. We sampled feces and nasal liquid of 48 animals (28 goats, 20 sheep) distributed in 7 city farms and on one activity playground in southern Germany. We found that 100% of the sampled sheep and 89.3% of the goats carried Shiga toxin-producing Escherichia coli (STEC). The presence of Staphylococcus spp. in 75% of both sheep and goats could be demonstrated. Campylobacter spp. were detected in 25% and 14.3% of the sheep and goats, respectively. Neither Salmonella spp. nor Coxiella burnetii was found. On the basis of these data, we propose a reasonable hygiene scheme to prevent transmission of zoonotic agents during city farm visits.
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Affiliation(s)
- Anna-Katarina Schilling
- Ludwig-Maximilians-Universität Munich, Faculty of Veterinary Medicine, Department of Veterinary Sciences, Munich, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Ulrich Methner
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Lisa D. Sprague
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Gernot Schmoock
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Hosny El-Adawy
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | | | - Anna-Caroline Wöhr
- Ludwig-Maximilians-Universität Munich, Faculty of Veterinary Medicine, Department of Veterinary Sciences, Munich, Germany
| | - Michael Erhard
- Ludwig-Maximilians-Universität Munich, Faculty of Veterinary Medicine, Department of Veterinary Sciences, Munich, Germany
| | - Lutz Geue
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Wusterhausen, Germany
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33
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Wu G, Ehricht R, Mafura M, Stokes M, Smith N, Pritchard GC, Woodward MJ. Escherichia coli isolates from extraintestinal organs of livestock animals harbour diverse virulence genes and belong to multiple genetic lineages. Vet Microbiol 2012; 160:197-206. [PMID: 22766078 DOI: 10.1016/j.vetmic.2012.05.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 05/20/2012] [Accepted: 05/22/2012] [Indexed: 11/26/2022]
Abstract
Escherichia coli, the most common cause of bacteraemia in humans in the UK, can also cause serious diseases in animals. However the population structure, virulence and antimicrobial resistance genes of those from extraintestinal organs of livestock animals are poorly characterised. The aims of this study were to investigate the diversity of these isolates from livestock animals and to understand if there was any correlation between the virulence and antimicrobial resistance genes and the genetic backbone of the bacteria and if these isolates were similar to those isolated from humans. Here 39 E. coli isolates from liver (n=31), spleen (n=5) and blood (n=3) of cattle (n=34), sheep (n=3), chicken (n=1) and pig (n=1) were assigned to 19 serogroups with O8 being the most common (n=7), followed by O101, O20 (both n=3) and O153 (n=2). They belong to 29 multi-locus sequence types, 20 clonal complexes with ST23 (n=7), ST10 (n=6), ST117 and ST155 (both n=3) being most common and were distributed among phylogenetic group A (n=16), B1 (n=12), B2 (n=2) and D (n=9). The pattern of a subset of putative virulence genes was different in almost all isolates. No correlation between serogroups, animal hosts, MLST types, virulence and antimicrobial resistance genes was identified. The distributions of clonal complexes and virulence genes were similar to other extraintestinal or commensal E. coli from humans and other animals, suggesting a zoonotic potential. The diverse and various combinations of virulence genes implied that the infections were caused by different mechanisms and infection control will be challenging.
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Affiliation(s)
- Guanghui Wu
- Epidemiology, Surveilance and Risk Group, Animal Health and Veterinary Laboratories Agency, New Haw, Addlestone, Surrey KT15 3NB, UK.
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34
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Stokes MO, Cottell JL, Piddock LJV, Wu G, Wootton M, Mevius DJ, Randall LP, Teale CJ, Fielder MD, Coldham NG. Detection and characterization of pCT-like plasmid vectors for blaCTX-M-14 in Escherichia coli isolates from humans, turkeys and cattle in England and Wales. J Antimicrob Chemother 2012; 67:1639-44. [PMID: 22514265 DOI: 10.1093/jac/dks126] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES To detect and characterize Escherichia coli strains and pCT-like plasmids implicated in the dissemination of the CTX-M-14 gene in animals and humans, in England and Wales. METHODS UK CTX-M-14-producing E. coli (n=70) from cattle (n=33), turkeys (n=9), sheep (n=2) and humans (n=26) were screened using multiplex PCR for the detection of a previously characterized plasmid, pCT. Isolates found to be carrying two or more pCT genetic markers were further analysed using PFGE. Their antimicrobial-resistance genes and virulence genes were also determined. These plasmids were transferred to Salmonella enterica serotype Typhimurium 26R and further examined for incompatibility type, genetic environment of the bla(CTX-M-14) gene, size, restriction fragment length polymorphism (RFLP) and nikB sequence. RESULTS The 25 E. coli isolates carrying pCT genetic markers generated 19 different PFGE profiles, and 23 isolates had different virulence and antimicrobial-resistance gene patterns. One isolate from cattle was a verotoxigenic E. coli ('VTEC'); the rest were commensal or extra-intestinal pathogenic E. coli. pCT-like plasmids with similar molecular characteristics (size, replicon type, RFLP pattern, pCT markers and genetic environment of the bla(CTX-M-14) gene) were detected in 21/25 of the field isolates, which comprised those from cattle (n=9), turkeys (n=8) and humans (n=4). All pCT-like plasmids were conjugative, and most were IncK (n=21) and had the same local genetic environment flanking the bla(CTX-M-14) gene (n=23). RFLP analysis demonstrated ≥ 75% similarity among most plasmids (n=22). CONCLUSIONS pCT-like plasmids were common vectors for horizontal dissemination of 30% of the bla(CTX-M-14) genes to different E. coli isolates from humans, cattle and turkeys.
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Affiliation(s)
- M O Stokes
- Department of Bacteriology, Animal Health and Veterinary Laboratories Agency, Addlestone, UK.
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35
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Schnee C, Schulsse S, Hotzel H, Ayling RD, Nicholas RAJ, Schubert E, Heller M, Ehricht R, Sachse K. A novel rapid DNA microarray assay enables identification of 37 Mycoplasma species and highlights multiple Mycoplasma infections. PLoS One 2012; 7:e33237. [PMID: 22479374 PMCID: PMC3315567 DOI: 10.1371/journal.pone.0033237] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 02/06/2012] [Indexed: 12/02/2022] Open
Abstract
Mycoplasmas comprise a conglomerate of pathogens and commensals occurring in humans and animals. The genus Mycoplasma alone contains more than 120 species at present, and new members are continuously being discovered. Therefore, it seems promising to use a single highly parallel detection assay rather than develop separate tests for each individual species. In this study, we have designed a DNA microarray carrying 70 oligonucleotide probes derived from the 23S rRNA gene and 86 probes from the tuf gene target regions. Following a PCR amplification and biotinylation step, hybridization on the array was shown to specifically identify 31 Mycoplasma spp., as well as 3 Acholeplasma spp. and 3 Ureaplasma spp. Members of the Mycoplasma mycoides cluster can be recognized at subgroup level. This procedure enables parallel detection of Mollicutes spp. occurring in humans, animals or cell culture, from mono- and multiple infections, in a single run. The main advantages of the microarray assay include ease of operation, rapidity, high information content, and affordability. The new test's analytical sensitivity is equivalent to that of real-time PCR and allows examination of field samples without the need for culture. When 60 field samples from ruminants and birds previously analyzed by denaturing-gradient gel electrophoresis (DGGE) were tested by the microarray assay both tests identified the same agent in 98.3% of the cases. Notably, microarray testing revealed an unexpectedly high proportion (35%) of multiple mycoplasma infections, i.e., substantially more than DGGE (15%). Two of the samples were found to contain four different Mycoplasma spp. This phenomenon deserves more attention, particularly its implications for epidemiology and treatment.
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Affiliation(s)
- Christiane Schnee
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-lnstitut (Federal Research Institute for Animal Health), Jena, Germany
| | - Samuel Schulsse
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-lnstitut (Federal Research Institute for Animal Health), Jena, Germany
| | - Helmut Hotzel
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-lnstitut (Federal Research Institute for Animal Health), Jena, Germany
| | - Roger D. Ayling
- Department of Bacteriology, Animal Health and Veterinary Laboratories Agency Mycoplasma Group, Addlestone, United Kingdom
| | - Robin A. J. Nicholas
- Department of Bacteriology, Animal Health and Veterinary Laboratories Agency Mycoplasma Group, Addlestone, United Kingdom
| | - Evelyn Schubert
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-lnstitut (Federal Research Institute for Animal Health), Jena, Germany
| | - Martin Heller
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-lnstitut (Federal Research Institute for Animal Health), Jena, Germany
| | | | - Konrad Sachse
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-lnstitut (Federal Research Institute for Animal Health), Jena, Germany
- * E-mail:
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Economic high-throughput-identification of influenza A subtypes from clinical specimens with a DNA-oligonucleotide microarray in an outbreak situation. Mol Cell Probes 2011; 26:6-10. [PMID: 22019422 DOI: 10.1016/j.mcp.2011.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 09/06/2011] [Accepted: 10/09/2011] [Indexed: 11/23/2022]
Abstract
Influenza A surface proteins H (haemagglutinin) and N (neuraminidase) occur in sixteen and nine distinct genotypes, respectively. The need for a timely production of vaccinations in case of pandemics or seasonal epidemics requires rapid typing methods for the determination of these alleles. The aim of the present study was to develop and improve a rapid and economic assay for determining H and N subtypes of influenza A from patient samples. The assay is based on the hybridisation of labelled amplicons from H and N reverse transcriptase-PCRs using consensus primer pairs to subtype-specific probes on microtiterstripe-mounted DNA-microarrays. An algorithm for semi-automatic data interpretation of raw data and assignment to H and N subtypes was proposed. Altogether, 191 samples were genotyped. This included 134 patient and 44 reference samples as well as controls. Under routine conditions sensitivity and specificity proved to be comparable to conventional nested or real-time PCRs. At least 130 out of 147 array-positive samples were unambiguously assignable. This included all sixteen variants of H as well as all nine variants of N. Furthermore, eighty-two samples from the 2009/2010 "novel H1N1/swine flu" (SF)-outbreak were correctly identified.
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37
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Presence of enterohemorrhagic Escherichia coli ST678/O104:H4 in France prior to 2011. Appl Environ Microbiol 2011; 77:8784-6. [PMID: 22003010 DOI: 10.1128/aem.06524-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two isolates of enterohemorrhagic Escherichia coli (EHEC) O104:H4 were isolated in France in 2004 and 2009. Both were characterized and compared to the strain which caused the German outbreak in 2011 and to other O104:H4 strains. This suggests that different O104:H4 EHEC strains were present several years prior to the 2011 outbreak.
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38
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Döpfer D, Geue L, Schares S, Mintel B, Hoffmann B, Fischer EAJ. Dynamics of shiga-toxin producing Escherichia coli (STEC) and their virulence factors in cattle. Prev Vet Med 2011; 103:22-30. [PMID: 21920615 DOI: 10.1016/j.prevetmed.2011.08.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 08/18/2011] [Accepted: 08/22/2011] [Indexed: 10/17/2022]
Abstract
Starting at birth, twenty Holstein calves were housed individually, in groups of five and finally in one large freestall while fecal samples were collected weekly for 25 weeks. From each sample, twenty isolates of Escherichia coli were screened for 6 virulence markers including shiga-toxin 1, 2, intimin, enterohemolysin, the fimbrial antigen efa1 and the adhesin saa. Dynamic models of transmission of E. coli were used to model the transmission of different virulotypes between calves and the loss of the same virulotypes from the calves. It was found that, once E. coli encoding shiga-toxins in combination with enterohemolysin were transmitted and established in a calf, they tended to be eliminated less efficiently compared to E. coli without this combination of virulence markers. It was concluded that the presence of certain combinations of virulence markers coincided with persistence of E. coli in the bovine gastrointestinal tract. In addition, the combinations of stx with either eae or ehxA in E. coli have a greater impact on the loss rates than on the transmission rates.
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Affiliation(s)
- D Döpfer
- Central Veterinary Institute, Wageningen UR, P.O. Box 65, 8200 AB Lelystad, The Netherlands.
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39
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High-resolution genotyping of Chlamydia trachomatis by use of a novel multilocus typing DNA microarray. J Clin Microbiol 2011; 49:2838-43. [PMID: 21697318 DOI: 10.1128/jcm.00883-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Typing of Chlamydia trachomatis is important to understanding its epidemiology. Currently used methods such as DNA sequencing of the ompA gene and multilocus sequence typing (MLST) either offer limited epidemiological resolution or are laborious and expensive, or both. DNA microarray technology using the ArrayStrip format is an affordable alternative for genotyping. In this study, we developed a new multilocus typing (MLT) DNA microarray, based on the target regions of a high-resolution MLST system as well as software for easy analysis. Validation of the array was done by typing 80 previously MLST-typed clinical specimens from unselected adolescents in school. The MLT array showed 100% specificity and provided 2.4-times-higher resolution than ompA sequencing, separating the commonly predominating ompA E/Bour genotype into 7 MLT array genotypes. The MLT array reproduced epidemiological findings revealed by the MLST system and showed sufficient sensitivity to work with clinical specimens. Compared to MLST analysis, the expenses needed for testing a sample with the MLT array are considerably lower. Moreover, testing can be completed within 1 working day rather than 3 or 4 days, with data analysis not requiring highly specialized personnel. The present MLT array represents a powerful alternative in C. trachomatis genotyping.
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Determination of serotypes of Shiga toxin-producing Escherichia coli isolates by intact cell matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 2010; 77:896-905. [PMID: 21115707 DOI: 10.1128/aem.01686-10] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) isolates representing the serotypes O165:H25, O26:H11/H32, and O156:H25 were analyzed by matrix-assisted laser desorption/ionization (MALDI) mass spectra of whole cells, a procedure also known as intact cell mass spectrometry (ICMS or IC-MALDI MS) or MALDI-typing. We demonstrate that within the given species the three serotypes can be well discriminated by ICMS. Conditions for the construction of serotype-specific prototypic mass spectra were systematically optimized by filtering out masses that do not contribute to the discrimination of the serotypes. Binary distances between prototypic spectra and sample spectra were used to determine serotypes of unknown samples. With parameters optimized, only 0.7% of the assignments were incorrect compared to 31% when distances were calculated from alignments of unfiltered mass spectra. Within the different serotypes, clusters of genetically related E. coli most probably originating from single clones could be distinguished by restriction fragment length polymorphism analysis. Since ICMS did not reproduce these clusters, we conclude that the power of ICMS is just sufficient to discriminate E. coli serotypes under certain conditions but fails for the differentiation of E. coli below this level.
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