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Ratshilingano MT, du Plessis EM, Duvenage S, Korsten L. Characterization of Multidrug-Resistant Escherichia coli Isolated from Two Commercial Lettuce and Spinach Supply Chains. J Food Prot 2022; 85:122-132. [PMID: 34324673 DOI: 10.4315/jfp-21-125] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/24/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Leafy green vegetables have increasingly been reported as a reservoir of multidrug-resistant pathogenic Enterobacteriaceae, with Shiga toxin-producing Escherichia coli frequently implicated in disease outbreaks worldwide. This study examined the presence and characteristics of antibiotic resistance, diarrheagenic virulence genes, and phylogenetic groupings of E. coli isolates (n = 51) from commercially produced lettuce and spinach from farms, through processing, and at the point of sale. Multidrug resistance was observed in 33 (64.7%) of the 51 E. coli isolates, with 35.7% (10 of 28) being generic and 100% (23 of 23) being extended-spectrum β-lactamase/AmpC producing. Resistance of E. coli isolates was observed against neomycin (51 of 51, 100%), ampicillin (36 of 51, 70.6%), amoxicillin (35 of 51, 68.6%), tetracycline (23 of 51, 45%), trimethoprim-sulfamethoxazole (22 of 51, 43%), chloramphenicol (13 of 51, 25.5%), Augmentin (6 of 51, 11.8%), and gentamicin (4 of 51, 7.8%), with 100% (51 of 51) susceptibility to imipenem. Virulence gene eae was detected in two E. coli isolates from irrigation water sources only, whereas none of the other virulence genes for which we tested were detected. Most of the E. coli strains belonged to phylogenetic group B2 (25.5%; n = 13), B1 (19.6%; n = 10), and A (17.6%; n = 9), with D (5.9%; n = 3) less distributed. Although diarrheagenic E. coli was not detected, antibiotic resistance in E. coli prevalent in the supply chain was evident. In addition, a clear link between E. coli isolates from irrigation water sources and leafy green vegetables through DNA fingerprinting was established, indicating the potential transfer of E. coli from irrigation water to minimally processed leafy green vegetables. HIGHLIGHTS
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Affiliation(s)
- Muneiwa T Ratshilingano
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0002, South Africa
| | - Erika M du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0002, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0002, South Africa
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0002, South Africa
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, South Africa
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Kaczorowska J, Casey E, Lugli GA, Ventura M, Clarke DJ, van Sinderen D, Mahony J. In Vitro and In Vivo Assessment of the Potential of Escherichia coli Phages to Treat Infections and Survive Gastric Conditions. Microorganisms 2021; 9:1869. [PMID: 34576765 PMCID: PMC8472732 DOI: 10.3390/microorganisms9091869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 11/17/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) and Shigella ssp. infections are associated with high rates of mortality, especially in infants in developing countries. Due to increasing levels of global antibiotic resistance exhibited by many pathogenic organisms, alternative strategies to combat such infections are urgently required. In this study, we evaluated the stability of five coliphages (four Myoviridae and one Siphoviridae phage) over a range of pH conditions and in simulated gastric conditions. The Myoviridae phages were stable across the range of pH 2 to 7, while the Siphoviridae phage, JK16, exhibited higher sensitivity to low pH. A composite mixture of these five phages was tested in vivo in a Galleria mellonella model. The obtained data clearly shows potential in treating E. coli infections prophylactically.
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Affiliation(s)
- Joanna Kaczorowska
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland; (J.K.); (E.C.); (D.J.C.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
| | - Eoghan Casey
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland; (J.K.); (E.C.); (D.J.C.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
| | - Gabriele A. Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43121 Parma, Italy; (G.A.L.); (M.V.)
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43121 Parma, Italy; (G.A.L.); (M.V.)
| | - David J. Clarke
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland; (J.K.); (E.C.); (D.J.C.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland; (J.K.); (E.C.); (D.J.C.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland; (J.K.); (E.C.); (D.J.C.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
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Rahmouni O, Vignal C, Titécat M, Foligné B, Pariente B, Dubuquoy L, Desreumaux P, Neut C. High carriage of adherent invasive E. coli in wildlife and healthy individuals. Gut Pathog 2018; 10:23. [PMID: 29946365 PMCID: PMC6001069 DOI: 10.1186/s13099-018-0248-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/23/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Adherent invasive Escherichia coli (AIEC) are suspected to be involved in the pathogenesis of inflammatory bowel diseases. Since AIEC was first described in 1999, despite important progress on its genomic and immune characterizations, some crucial questions remain unanswered, such as whether there exists a natural reservoir, or whether there is asymptomatic carriage. The ECOR collection, including E. coli strains isolated mainly from the gut of healthy humans and animals, constitutes an ideal tool to investigate AIEC prevalence in healthy condition. A total of 61 E. coli strains were examined for characteristics of AIEC. METHODS The adhesion, invasion and intramacrophage replication capabilities (AIEC phenotype) of 61 intestinal E. coli strains were determined. The absence of virulence-associated diarrheagenic E. coli pathotypes (EPEC, ETEC, EIEC, EHEC, DAEC, EAEC), and uropathogenic E. coli was checked. RESULTS Out of 61 intestinal strains, 13 (21%) exhibit the AIEC phenotype, 7 are from human origin and 6 are from animal origin. Prevalence of AIEC strains is about 24 and 19% in healthy humans and animals respectively. These strains are highly genetically diverse as they are distributed among the main described phylogroups. Among E. coli strains from the ECOR collection, we also detected strains able to detach I-407 cells. CONCLUSIONS Our study described for the first time AIEC strains isolated from the feces of healthy humans and animals.
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Affiliation(s)
- Oumaïra Rahmouni
- Lille Inflammation Research International Center, UMR 995 Inserm, Lille University, CHRU Lille, Lille, France
| | - Cécile Vignal
- Lille Inflammation Research International Center, UMR 995 Inserm, Lille University, CHRU Lille, Lille, France
| | - Marie Titécat
- Lille Inflammation Research International Center, UMR 995 Inserm, Lille University, CHRU Lille, Lille, France
- Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France
| | - Benoît Foligné
- Lille Inflammation Research International Center, UMR 995 Inserm, Lille University, CHRU Lille, Lille, France
| | - Benjamin Pariente
- Lille Inflammation Research International Center, UMR 995 Inserm, Lille University, CHRU Lille, Lille, France
- Service des Maladies de l’Appareil Digestif et de la Nutrition, Hôpital Claude Huriez, CHU Lille, 59037 Lille, France
| | - Laurent Dubuquoy
- Lille Inflammation Research International Center, UMR 995 Inserm, Lille University, CHRU Lille, Lille, France
| | - Pierre Desreumaux
- Lille Inflammation Research International Center, UMR 995 Inserm, Lille University, CHRU Lille, Lille, France
- Service des Maladies de l’Appareil Digestif et de la Nutrition, Hôpital Claude Huriez, CHU Lille, 59037 Lille, France
| | - Christel Neut
- Lille Inflammation Research International Center, UMR 995 Inserm, Lille University, CHRU Lille, Lille, France
- Laboratoire de Bactériologie, 3, Rue de Pr. Laguesse, B.P. 83, 59006 Lille Cedex, France
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Diarrheagenic Escherichia coli phylogroups are associated with antibiotic resistance and duration of diarrheal episode. ScientificWorldJournal 2015; 2015:610403. [PMID: 25811044 PMCID: PMC4355820 DOI: 10.1155/2015/610403] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 02/07/2015] [Accepted: 02/11/2015] [Indexed: 12/19/2022] Open
Abstract
Conventionally, in Escherichia coli, phylogenetic groups A and B1 are associated with commensal strains while B2 and D are associated with extraintestinal strains. The aim of this study was to evaluate diarrheagenic (DEC) and commensal E. coli phylogeny and its association with antibiotic resistance and clinical characteristics of the diarrheal episode. Phylogenetic groups and antibiotic resistance of 369 E. coli strains (commensal strains and DEC from children with or without diarrhea) isolated from Peruvian children <1 year of age were determined by a Clermont triplex PCR and Kirby-Bauer method, respectively. The distribution of the 369 E. coli strains among the 4 phylogenetic groups was A (40%), D (31%), B1 (21%), and B2 (8%). DEC-control strains were more associated with group A while DEC-diarrhea strains were more associated with group D (P < 0.05). There was a tendency (P = 0.06) for higher proportion of persistent diarrhea (≥14 days) among severe groups (B2 and D) in comparison with nonsevere groups (A and B1). Strains belonging to group D presented significantly higher percentages of multidrug resistance than the rest of the groups (P > 0.01). In summary, DEC-diarrhea strains were more associated with group D than strains from healthy controls.
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Li G, Kariyawasam S, Tivendale KA, Wannemuehler Y, Ewers C, Wieler LH, Logue CM, Nolan LK. tkt1, located on a novel pathogenicity island, is prevalent in avian and human extraintestinal pathogenic Escherichia coli. BMC Microbiol 2012; 12:51. [PMID: 22471764 PMCID: PMC3349570 DOI: 10.1186/1471-2180-12-51] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 04/03/2012] [Indexed: 12/04/2022] Open
Abstract
Background Extraintestinal pathogenic Escherichia coli are important pathogens of human and animal hosts. Some human and avian extraintestinal pathogenic E. coli are indistinguishable on the basis of diseases caused, multilocus sequence and phylogenetic typing, carriage of large virulence plasmids and traits known to be associated with extraintestinal pathogenic E. coli virulence. Results The gene tkt1 identified by a previous signature-tagged transposon mutagenesis study, was found on a 16-kb genomic island of avian pathogenic Escherichia coli (APEC) O1, the first pathogenic Escherichia coli strain whose genome has been completely sequenced. tkt1 was present in 39.6% (38/96) of pathogenic Escherichia coli strains, while only 6.25% (3/48) of E. coli from the feces of apparently healthy chickens was positive. Further, tkt1 was predominantly present in extraintestinal pathogenic E. coli belonging to the B2 phylogenetic group, as compared to extraintestinal pathogenic E. coli of other phylogenetic groups. The tkt1-containing genomic island is inserted between the metE and ysgA genes of the E. coli K12 genome. Among different extraintestinal pathogenic E. coli of the B2 phylogenetic group, 61.7% of pathogenic Escherichia coli, 80.6% of human uropathogenic E.coli and 94.1% of human neonatal meningitis-causing E. coli, respectively, harbor a complete copy of this island; whereas, only a few avian fecal E. coli strains contained the complete island. Functional analysis showed that Tkt1 confers very little transketolase activity but is involved in peptide nitrogen metabolism. Conclusion These results suggest tkt1 and its corresponding genomic island are frequently associated with avian and human ExPEC and are involved in bipeptide metabolism.
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Affiliation(s)
- Ganwu Li
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary medicine, Iowa State University, Ames, Iowa 50011, USA
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Smith A, van Rooyen JP, Argo E, Cash P. Proteomic analysis of Escherichia coli associated with urinary tract infections. Proteomics 2011; 11:2283-93. [DOI: 10.1002/pmic.201000626] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 02/27/2011] [Accepted: 03/07/2011] [Indexed: 11/09/2022]
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Pérez C, Gómez-Duarte OG, Arias ML. Diarrheagenic Escherichia coli in children from Costa Rica. Am J Trop Med Hyg 2010; 83:292-7. [PMID: 20682870 DOI: 10.4269/ajtmh.2010.09-0412] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
More than 5,000 diarrheal cases per year receive medical care at the National Children's Hospital of Costa Rica, and nearly 5% of them require hospitalization. A total of 173 Escherichia coli strains isolated from children with diarrhea were characterized at the molecular, serologic, and phenotypic level. Multiplex and duplex polymerase chain reactions were used to detect the six categories of diarrheagenic E. coli. Thirty percent (n = 52) of the strains were positive, indicating a high prevalence among the pediatric population. Enteropathogenic E. coli and enteroinvasive E. coli pathotypes were the most prevalent (21% and 19%, respectively). Pathogenic strains were distributed among the four E. coli phylogenetic groups A, B1, B2, and D, with groups A and B1 the most commonly found. This study used molecular typing to evaluate the prevalence of diarrheagenic E. coli reported in Costa Rica and demonstrated the importance of these pathotypes in the pediatric population.
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Affiliation(s)
- Cristian Pérez
- Laboratorio Clínico Hospital Nacional de Niños Dr. Carlos Sáenz Herrera, San José, Costa Rica.
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8
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Strand L, Jenkins A, Grude N, Allum AG, Mykland HC, Nowrouzian FL, Kristiansen BE. Emergence of fluoroquinolone-resistant clonal group A: clonal analysis of Norwegian and Russian E. coli isolates. APMIS 2010; 118:571-7. [PMID: 20666738 DOI: 10.1111/j.1600-0463.2010.02623.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We describe a study of urinary tract and intestinal isolates of Escherichia coli from Norway and Russia using automated ribotyping, single nucleotide polymorphism analysis for clonal group A (CgA) supplemented with phylogrouping, virulence gene profiling and resistance profiling. CgA comprised 19% of the Norwegian UTI isolates from 2001. Two highly multiresistant fluoroquinolone-resistant CgA isolates were found. Ribotypes clustered into four major and six minor groups (ribogroups). Fluoroquinolone-resistant isolates and phylogroups A and B1 were associated with ribogroup (R)A. Ribogroup (R)B predominated among Russian UTI isolates and was predominantly phylogroup A and depleted in P-fimbriae. Ribogroup (R)C predominated among Norwegian UTI isolates and was rich in virulence factors (S-fimbriae, haemagglutinin and haemolysin) and predominantly phylogroup B2 and D. Ribogroup (R)G was associated with CgA and predominantly phylogroup D. Ribogroups (R)D, (R)E and (R)F had too few members for statistical analysis. The correlation between ribotype and phylogenetic group was not as strong as reported in other studies.
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Schwan WR, Briska A, Stahl B, Wagner TK, Zentz E, Henkhaus J, Lovrich SD, Agger WA, Callister SM, DuChateau B, Dykes CW. Use of optical mapping to sort uropathogenic Escherichia coli strains into distinct subgroups. MICROBIOLOGY-SGM 2010; 156:2124-2135. [PMID: 20378655 PMCID: PMC3068680 DOI: 10.1099/mic.0.033977-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Optical maps were generated for 33 uropathogenic Escherichia coli (UPEC) isolates. For individual genomes, the NcoI restriction fragments aligned into a unique chromosome map for each individual isolate, which was then compared with the in silico restriction maps of all of the sequenced E. coli and Shigella strains. All of the UPEC isolates clustered separately from the Shigella strains as well as the laboratory and enterohaemorrhagic E. coli strains. Moreover, the individual strains appeared to cluster into distinct subgroups based on the dendrogram analyses. Phylogenetic grouping of these 33 strains showed that 32/33 were the B2 subgroup and 1/33 was subgroup A. To further characterize the similarities and differences among the 33 isolates, pathogenicity island (PAI), haemolysin and virulence gene comparisons were performed. A strong correlation was observed between individual subgroups and virulence factor genes as well as haemolysis activity. Furthermore, there was considerable conservation of sequenced-strain PAIs in the specific subgroups. Strains with different antibiotic-resistance patterns also appeared to sort into separate subgroups. Thus, the optical maps distinguished the UPEC strains from other E. coli strains and further subdivided the strains into distinct subgroups. This optical mapping procedure holds promise as an alternative way to subgroup all E. coli strains, including those involved in infections outside of the intestinal tract and epidemic strains with distinct patterns of antibiotic resistance.
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Pavlic M, Griffiths MW. Principles, Applications, and Limitations of Automated Ribotyping as a Rapid Method in Food Safety. Foodborne Pathog Dis 2009; 6:1047-55. [DOI: 10.1089/fpd.2009.0264] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Marin Pavlic
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Mansel W. Griffiths
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada
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Fouz B, Roig FJ, Amaro C. Phenotypic and genotypic characterization of a new fish-virulent Vibrio vulnificus serovar that lacks potential to infect humans. Microbiology (Reading) 2007; 153:1926-1934. [PMID: 17526849 DOI: 10.1099/mic.0.2006/005405-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Vibrio vulnificus is a bacterial species that is virulent for humans and fish. Human isolates are classified into biotypes 1 and 3 (BT1 and BT3) and fish isolates into biotype 2 (BT2). However, a few human infections caused by BT2 isolates have been reported worldwide (zoonosis). These BT2 human isolates belong to serovar E (SerE), which is also present in diseased fish. The aim of the present work was to characterize a new BT2 serovar [serovar A (SerA)], which emerged in the European fish-farming industry in 2000, by means of phenotypic, serological and genetic [plasmid profiling, ribotyping and random amplified polymorphic DNA (RAPD)] methodologies. The results confirmed that SerA constitutes a homogeneous O-serogroup within the species that shares plasmidic information with SerE. Like SerE, this new serogroup was resistant to fresh fish serum, as well as being highly virulent for fish. In contrast, it was sensitive to human serum and avirulent for mice, even after pretreatment with iron. The two serovars presented different biochemical profiles as well as specific patterns by ribotyping and RAPD analysis. In conclusion, SerA seems to constitute a different clonal group that has recently emerged within the species V. vulnificus, with pathogenic potential for fish but not for humans.
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Affiliation(s)
- Belén Fouz
- Department of Microbiology and Ecology, Faculty of Biology, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain
| | - Francisco J Roig
- Department of Microbiology and Ecology, Faculty of Biology, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain
| | - Carmen Amaro
- Department of Microbiology and Ecology, Faculty of Biology, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain
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Bielaszewska M, Dobrindt U, Gärtner J, Gallitz I, Hacker J, Karch H, Müller D, Schubert S, Alexander Schmidt M, Sorsa LJ, Zdziarski J. Aspects of genome plasticity in pathogenic Escherichia coli. Int J Med Microbiol 2007; 297:625-39. [PMID: 17462951 DOI: 10.1016/j.ijmm.2007.03.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Revised: 03/05/2007] [Accepted: 03/05/2007] [Indexed: 11/22/2022] Open
Abstract
The species Escherichia coli comprises not only non-pathogenic or commensal variants that belong to the normal intestinal flora of most mammals, but also various pathogenic strains causing diverse intestinal and extraintestinal infections in man and animals. Virulence factors and mechanisms involved in pathogenesis have been successfully analyzed for many years resulting in a wealth of knowledge about many E. coli pathotypes. However, our knowledge on the genome content, diversity and variability between pathogenic and also non-pathogenic subtypes is only slowly accumulating. Pathotypes have been largely defined by the presence or absence of particular DNA segments that in most cases appear to have been acquired via horizontal gene transfer events. As these regions are frequently subjected to excisions, rearrangements, and transfers they contribute to the previously unexpected and underestimated rapid evolution of E. coli variants resulting in the development of novel strains and even pathotypes. In these studies various novel aspects of genome diversity and plasticity in extraintestinal and intestinal pathogenic E. coli pathotypes have been addressed and the results have been directly applied for the improvement of diagnostic methods.
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Affiliation(s)
- Martina Bielaszewska
- Institut für Hygiene, Universitätsklinikum Münster, Robert-Koch-Str. 41, D-48149 Münster, Germany
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The taxonomy of Enterobacter sakazakii: proposal of a new genus Cronobacter gen. nov. and descriptions of Cronobacter sakazakii comb. nov. Cronobacter sakazakii subsp. sakazakii, comb. nov., Cronobacter sakazakii subsp. malonaticus subsp. nov., Cronobacter turicensis sp. nov., Cronobacter muytjensii sp. nov., Cronobacter dublinensis sp. nov. and Cronobacter genomospecies 1. BMC Evol Biol 2007; 7:64. [PMID: 17439656 PMCID: PMC1868726 DOI: 10.1186/1471-2148-7-64] [Citation(s) in RCA: 216] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Accepted: 04/17/2007] [Indexed: 02/05/2023] Open
Abstract
Background Enterobacter sakazakii is an opportunistic pathogen that can cause infections such as necrotizing enterocolitis, bacteraemia, meningitis and brain abscess/lesions. When the species was defined in 1980, 15 biogroups were described and it was suggested that these could represent multiple species. In this study the taxonomic relationship of strains described as E. sakazakii was further investigated. Results Strains identified as E. sakazakii were divided into separate groups on the basis of f-AFLP fingerprints, ribopatterns and full-length 16S rRNA gene sequences. DNA-DNA hybridizations revealed five genomospecies. The phenotypic profiles of the genomospecies were determined and biochemical markers identified. Conclusion This study clarifies the taxonomy of E. sakazakii and proposes a reclassification of these organisms.
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Bidet P, Metais A, Mahjoub-Messai F, Durand L, Dehem M, Aujard Y, Bingen E, Nassif X, Bonacorsi S. Detection and identification by PCR of a highly virulent phylogenetic subgroup among extraintestinal pathogenic Escherichia coli B2 strains. Appl Environ Microbiol 2007; 73:2373-7. [PMID: 17293507 PMCID: PMC1855671 DOI: 10.1128/aem.02341-06] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Closely related Escherichia coli B2 strains O1:K1, O2:K1, O18:K1, and O45:K1 constitute a major subgroup causing extraintestinal infections. A DNA pathoarray analysis was used to develop a PCR specific for this subgroup that was included in the multiplex phylogenetic-grouping PCR method. Our PCR may serve to identify this virulent subgroup among different ecological niches.
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Affiliation(s)
- Philippe Bidet
- Service de Microbiologie, Hôpital Robert Debré, 48 Bd Sérurier, 75395 Paris cedex 19, France.
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Sakata S, Ryu CS, Kitahara M, Sakamoto M, Hayashi H, Fukuyama M, Benno Y. Characterization of the genus Bifidobacterium by automated ribotyping and 16S rRNA gene sequences. Microbiol Immunol 2006; 50:1-10. [PMID: 16428867 DOI: 10.1111/j.1348-0421.2006.tb03762.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In order to characterize the genus Bifidobacterium, ribopatterns and approximately 500 bp (Escherichia coli positions 27 to 520) of 16S rRNA gene sequences of 28 type strains and 64 reference strains of the genus Bifidobacterium were determined. Ribopatterns obtained from Bifidobacterium strains were divided into nine clusters (clusters I-IX) with a similarity of 60%. Cluster V, containing 17 species, was further subdivided into 22 subclusters with a similarity of 90%. In the genus Bifidobacterium, four groups were shown according to Miyake et al.: (i) the Bifidobacterium longum infantis-longum-suis type group, (ii) the B. catenulatum-pseudocatenulatum group, (iii) the B. gallinarum-saeculare-pullorum group, and (iv) the B. coryneforme-indicum group, which showed higher than 97% similarity of the 16S rRNA gene sequences in each group. Using ribotyping analysis, unique ribopatterns were obtained from these species, and they could be separated by cluster analysis. Ribopatterns of six B. adolescentis strains were separated into different clusters, and also showed diversity in 16S rRNA gene sequences. B. adolescentis consisted of heterogeneous strains. The nine strains of B. pseudolongum subsp. pseudolongum were divided into five subclusters. Each type strain of B. pseudolongum subsp. pseudolongum and B. pseudolongum subsp. globosum and two intermediate groups, which were suggested by Yaeshima et al., consisted of individual clusters. B. animalis subsp. animalis and B. animalis subsp. lactis could not be separated by ribotyping using Eco RI. We conclude that ribotyping is able to provide another characteristic of Bifidobacterium strains in addition to 16S rRNA gene sequence phylogenetic analysis, and this information suggests that ribotyping analysis is a useful tool for the characterization of Bifidobacterium species in combination with other techniques for taxonomic characterization.
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Affiliation(s)
- Shinji Sakata
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan.
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Tankson JD, Fedorka-Cray PJ, Jackson CR, Headrick M. Genetic relatedness of a rarely isolated Salmonella: Salmonella enterica serotype Niakhar from NARMS animal isolates. J Antimicrob Chemother 2005; 57:190-8. [PMID: 16352736 DOI: 10.1093/jac/dki439] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND In the United States, Salmonella enterica serotype Niakhar is infrequently isolated. Between 1997 and 2000, the animal arm of the National Antimicrobial Resistance Monitoring System-Enteric Bacteria (NARMS) assayed a total of 22,383 Salmonella isolates from various animal sources (swine, cattle, chickens, turkeys, cats, horses, exotics and dogs) for antimicrobial susceptibility. Isolates originated from diagnostic and non-diagnostic submissions. OBJECTIVES To study the phenotypic and genotypic characteristics of Salmonella Niakhar. METHODS AND RESULTS Only five (0.02%) of the 22,383 isolates were identified as Salmonella Niakhar. Antimicrobial resistance testing indicated that three isolates were pan-susceptible, one isolate was resistant to ampicillin and one isolate was resistant to ampicillin, chloramphenicol, ciprofloxacin, kanamycin, nalidixic acid, streptomycin, sulfamethoxazole, tetracycline and trimethoprim/sulfamethoxazole. RAPD-PCR analysis, PFGE and ribotyping indicated that two pan-susceptible isolates were genetically similar, whereas the three remaining isolates were genetically different. The one Salmonella Niakhar isolate that was multiresistant harboured a class I integron, intI1 and two large plasmids. CONCLUSIONS This study represents the first report of a ciprofloxacin-resistant Salmonella isolate from the animal arm of NARMS.
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Affiliation(s)
- J D Tankson
- USDA/Agricultural Research Services, Bacterial and Epidemiology Antimicrobial Resistance Research Unit, 950 College Station Road, Athens, GA 30605, USA
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Hommais F, Pereira S, Acquaviva C, Escobar-Páramo P, Denamur E. Single-nucleotide polymorphism phylotyping of Escherichia coli. Appl Environ Microbiol 2005; 71:4784-92. [PMID: 16085876 PMCID: PMC1183324 DOI: 10.1128/aem.71.8.4784-4792.2005] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe a rapid and easily automated phylogenetic grouping technique based on analysis of bacterial genome single-nucleotide polymorphisms (SNPs). We selected 13 SNPs derived from a complete sequence analysis of 11 essential genes previously used for multilocus sequence typing (MLST) of 30 Escherichia coli strains representing the genetic diversity of the species. The 13 SNPs were localized in five genes, trpA, trpB, putP, icdA, and polB, and were selected to allow recovery of the main phylogenetic groups (groups A, B1, E, D, and B2) and subgroups of the species. In the first step, we validated the SNP approach in silico by extracting SNP data from the complete sequences of the five genes for a panel of 65 pathogenic strains belonging to different E. coli pathovars, which were previously analyzed by MLST. In the second step, we determined these SNPs by dideoxy single-base extension of unlabeled oligonucleotide primers for a collection of 183 commensal and extraintestinal clinical E. coli isolates and compared the SNP phylotyping method to previous well-established typing methods. This SNP phylotyping method proved to be consistent with the other methods for assigning phylogenetic groups to the different E. coli strains. In contrast to the other typing methods, such as multilocus enzyme electrophoresis, ribotyping, or PCR phylotyping using the presence/absence of three genomic DNA fragments, the SNP typing method described here is derived from a solid phylogenetic analysis, and the results obtained by this method are more meaningful. Our results indicate that similar approaches may be used for a wide variety of bacterial species.
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Affiliation(s)
- Florence Hommais
- UMR 5122, Université Claude Bernard Lyon 1, 10 rue Dubois, 69622 Villeurbanne cedex, France.
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18
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Clermont O, Bonacorsi S, Bingen E. Characterization of an anonymous molecular marker strongly linked to Escherichia coli strains causing neonatal meningitis. J Clin Microbiol 2004; 42:1770-2. [PMID: 15071045 PMCID: PMC387582 DOI: 10.1128/jcm.42.4.1770-1772.2004] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An anonymous 14.9-kb rrn-containing HindIII fragment is strongly linked to Escherichia coli strains causing neonatal meningitis. We show in this report that this fragment does not encode new virulence factors but lacks arpA, a gene common in avirulent E. coli strains, and we developed a PCR test to detect this fragment.
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Affiliation(s)
- Olivier Clermont
- Laboratoire d'Etudes de Génétique Bactérienne dans les Infections de l'Enfant (EA3105), Université Denis Diderot-Paris 7, France
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Ren CP, Chaudhuri RR, Fivian A, Bailey CM, Antonio M, Barnes WM, Pallen MJ. The ETT2 gene cluster, encoding a second type III secretion system from Escherichia coli, is present in the majority of strains but has undergone widespread mutational attrition. J Bacteriol 2004; 186:3547-60. [PMID: 15150243 PMCID: PMC415751 DOI: 10.1128/jb.186.11.3547-3560.2004] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2003] [Accepted: 02/12/2004] [Indexed: 11/20/2022] Open
Abstract
ETT2 is a second cryptic type III secretion system in Escherichia coli which was first discovered through the analysis of genome sequences of enterohemorrhagic E. coli O157:H7. Comparative analyses of Escherichia and Shigella genome sequences revealed that the ETT2 gene cluster is larger than was previously thought, encompassing homologues of genes from the Spi-1, Spi-2, and Spi-3 Salmonella pathogenicity islands. ETT2-associated genes, including regulators and chaperones, were found at the same chromosomal location in the majority of genome-sequenced strains, including the laboratory strain K-12. Using a PCR-based approach, we constructed a complete tiling path through the ETT2 gene cluster for 79 strains, including the well-characterized E. coli reference collection supplemented with additional pathotypes. The ETT2 gene cluster was found to be present in whole or in part in the majority of E. coli strains, whether pathogenic or commensal, with patterns of distribution and deletion mirroring the known phylogenetic structure of the species. In almost all strains, including enterohemorrhagic E. coli O157:H7, ETT2 has been subjected to varying degrees of mutational attrition that render it unable to encode a functioning secretion system. A second type III secretion system-associated locus that likely encodes the ETT2 translocation apparatus was found in some E. coli strains. Intact versions of both ETT2-related clusters are apparently present in enteroaggregative E. coli strain O42.
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Affiliation(s)
- Chuan-Peng Ren
- Bacterial Pathogenesis and Genomics Unit, Division of Immunity and Infection, Medical School, University of Birmingham, Birmingham B15 2TT, United Kingdom
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Escobar-Páramo P, Sabbagh A, Darlu P, Pradillon O, Vaury C, Denamur E, Lecointre G. Decreasing the effects of horizontal gene transfer on bacterial phylogeny: the Escherichia coli case study. Mol Phylogenet Evol 2004; 30:243-50. [PMID: 15022774 DOI: 10.1016/s1055-7903(03)00181-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phylogenetic reconstructions of bacterial species from DNA sequences are hampered by the existence of horizontal gene transfer. One possible way to overcome the confounding influence of such movement of genes is to identify and remove sequences which are responsible for significant character incongruence when compared to a reference dataset free of horizontal transfer (e.g., multilocus enzyme electrophoresis, restriction fragment length polymorphism, or random amplified polymorphic DNA) using the incongruence length difference (ILD) test of Farris et al. [Cladistics 10 (1995) 315]. As obtaining this "whole genome dataset" prior to the reconstruction of a phylogeny is clearly troublesome, we have tested alternative approaches allowing the release from such reference dataset, designed for a species with modest level of horizontal gene transfer, i.e., Escherichia coli. Eleven different genes available or sequenced in this work were studied in a set of 30 E. coli reference (ECOR) strains. Either using ILD to test incongruence between each gene against the all remaining (in this case 10) genes in order to remove sequences responsible for significant incongruence, or using just a simultaneous analysis without removals, gave robust phylogenies with slight topological differences. The use of the ILD test remains a suitable method for estimating the level of horizontal gene transfer in bacterial species. Supertrees also had suitable properties to extract the phylogeny of strains, because the way they summarize taxonomic congruence clearly limits the impact of individual gene transfers on the global topology. Furthermore, this work allowed a significant improvement of the accuracy of the phylogeny within E. coli.
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Affiliation(s)
- Patricia Escobar-Páramo
- INSERM E0339, IFR 02, Faculté de Médecine Xavier Bichat, 16 rue Henri Huchard, Paris 75018, France
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Abstract
Mapping, and ultimately preventing, the dissemination of infectious agents is an important topic in public health. Newly developed molecular-microbiological methods have contributed significantly to recent advances in the efficient tracking of the nosocomial and environmental spread of microbial pathogens. Not only has the application of novel technologies led to improved understanding of microbial epidemiology, but the concepts of population structure and dynamics of many of the medically significant microorganisms have advanced significantly also. Currently, genetic identification of microbes is also within the reach of clinical microbiology laboratory professionals including those without specialized technology research interests. This review summarizes the possibilities for high-throughput molecular-microbiological typing in adequately equipped medical microbiology laboratories from both clinical and fundamental research perspectives. First, the development and application of methods for large-scale comparative typing of serially isolated microbial strains are discussed. The outcome of studies employing these methods allows for long-term epidemiologic surveillance of infectious diseases. Second, recent methods enable an almost nucleotide-by-nucleotide genetic comparison of smaller numbers of strains, thereby facilitating the identification of the genetic basis of, for instance, medically relevant microbiological traits. Whereas the first approach provides insights into the dynamic spread of infectious agents, the second provides insights into intragenomic dynamics and genetic functionality. The current state of technology is summarized, and future perspectives are sketched.
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Affiliation(s)
- A van Belkum
- Erasmus MC, Department of Medical Microbiology & Infectious Diseases, Rotterdam, The Netherlands.
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Cordevant C, Tang JS, Cleland D, Lange M. Characterization of members of the Legionellaceae family by automated ribotyping. J Clin Microbiol 2003; 41:34-43. [PMID: 12517822 PMCID: PMC149609 DOI: 10.1128/jcm.41.1.34-43.2003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to implement a new and reliable method for characterizing different species of Legionella, a genetic fingerprinting study with an automated ribotyping system (RiboPrinter) was completed with members of this genus which were deposited at the American Type Culture Collection. The RiboPrinter examined the different patterns of EcoRI digestion fragments from the rRNA operons of 110 strains, representing 48 of the 49 described Legionella species as well as 70 serogroups of those species. Distinctive and consistent patterns were obtained for the type strains of the 48 species investigated. Legionella pneumophila subsp. fraseri and L. pneumophila subsp. pascullei each generated a specific pattern, whereas L. pneumophila subsp. pneumophila produced six different fingerprint patterns. No correlation seemed to exist between the ribotypes obtained and the 15 serotypes of L. pneumophila. For the other species, those with two known serogroups presented two distinctive patterns with the RiboPrinter with the exception of L. hackeliae and L. quinlivanii, which yielded only one pattern. We also encountered ribotypes for strains which were not identified to the species level. The ribotypes generated for these strains with the RiboPrinter did not match those generated for known type strains, suggesting the putative description of new serogroups or species. Although the automated system did not have sufficient discriminatory ability to serve as an epidemiological tool in a clinical setting, it appeared to be a powerful tool for general genomic analysis of the Legionella isolates (e.g., determination of new species) and assessment of the interrelationship among Legionella strains through the RiboPrinter database connection.
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