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Zhu L, Shuai X, Xu L, Sun Y, Lin Z, Zhou Z, Meng L, Chen H. Mechanisms underlying the effect of chlorination and UV disinfection on VBNC state Escherichia coli isolated from hospital wastewater. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127228. [PMID: 34547689 DOI: 10.1016/j.jhazmat.2021.127228] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
The occurrence of viable but non-culturable (VBNC) bacteria in the wastewater system poses a huge threat to environmental and public health, in particular in hospital wastewater treatment system (HWTS). HWTS-oriented studies have been conducted to assess the effectiveness of chlorination and UV disinfection using indigenous bacteria. Results revealed that the VBNC Escherichia coli and ARGs remained persistent even at high chlorination (12 mg/L for 2.5 h) and UV doses (1000 mJ/cm2). The molecular mechanisms underlying chlorination-/UV-induced VBNC state in E. coli were explored through the transcriptomics and results suggested that most energy-dependent physiological activities (e.g., metabolism) have been suppressed in VBNC E. coli, while the pathogenicity-related genes varied insignificantly compared to the culturable cells, indicating that the VBNC E. coli could potentially display pathogenicity. Further Galleria mellonella model experiment has confirmed that although the disinfection-induced VBNC state made cells less infectious, these cells could regain their pathogenicity after resuscitation. This in vitro study can be used as a reference for studies on infections from VBNC bacteria and highlights the health risk due to VBNC pathogens in hospital effluents. There is a need to develop effluent standards specifically for healthcare facilities, and a stricter downstream disinfection strategy should be considered for the removal of VBNC cells and ARGs in the effluent.
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Affiliation(s)
- Lin Zhu
- Department of Environmental Engineering, College of Environmental and Resource Sciences; Zhejiang University, Hangzhou 310058, China
| | - Xinyi Shuai
- Department of Environmental Engineering, College of Environmental and Resource Sciences; Zhejiang University, Hangzhou 310058, China
| | - Like Xu
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Yujie Sun
- Department of Environmental Engineering, College of Environmental and Resource Sciences; Zhejiang University, Hangzhou 310058, China
| | - Zejun Lin
- Department of Environmental Engineering, College of Environmental and Resource Sciences; Zhejiang University, Hangzhou 310058, China
| | - Zhenchao Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences; Zhejiang University, Hangzhou 310058, China
| | - Lingxuan Meng
- Department of Environmental Engineering, College of Environmental and Resource Sciences; Zhejiang University, Hangzhou 310058, China
| | - Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences; Zhejiang University, Hangzhou 310058, China.
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2
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Kolenda R, Burdukiewicz M, Wimonć M, Aleksandrowicz A, Ali A, Szabo I, Tedin K, Bartholdson Scott J, Pickard D, Schierack P. Identification of Natural Mutations Responsible for Altered Infection Phenotypes of Salmonella enterica Clinical Isolates by Using Cell Line Infection Screens. Appl Environ Microbiol 2021; 87:e02177-20. [PMID: 33127819 PMCID: PMC7783345 DOI: 10.1128/aem.02177-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/22/2020] [Indexed: 12/18/2022] Open
Abstract
The initial steps of Salmonella pathogenesis involve adhesion to and invasion into host epithelial cells. While well-studied for Salmonella enterica serovar Typhimurium, the factors contributing to this process in other, host-adapted serovars remains unexplored. Here, we screened clinical isolates of serovars Gallinarum, Dublin, Choleraesuis, Typhimurium, and Enteritidis for adhesion to and invasion into intestinal epithelial cell lines of human, porcine, and chicken origins. Thirty isolates with altered infectivity were used for genomic analyses, and 14 genes and novel mutations associated with high or low infectivity were identified. The functions of candidate genes included virulence gene expression regulation and cell wall or membrane synthesis and components. The role of several of these genes in Salmonella adhesion to and invasion into cells has not previously been investigated. The genes dksA (encoding a stringent response regulator) and sanA (encoding a vancomycin high-temperature exclusion protein) were selected for further analyses, and we confirmed their roles in adhesion to and invasion into host cells. Furthermore, transcriptomic analyses were performed for S Enteritidis and S Typhimurium, with two highly infective and two marginally infective isolates for each serovar. Expression profiles for the isolates with altered infection phenotypes revealed the importance of type 3 secretion system expression levels in the determination of an isolate's infection phenotype. Taken together, these data indicate a new role in cell host infection for genes or gene variants previously not associated with adhesion to and invasion into the epithelial cells.IMPORTANCESalmonella is a foodborne pathogen affecting over 200 million people and resulting in over 200,000 fatal cases per year. Its adhesion to and invasion into intestinal epithelial cells represent one of the first and key steps in the pathogenesis of salmonellosis. Still, around 35 to 40% of bacterial genes have no experimentally validated function, and their contribution to bacterial virulence, including adhesion and invasion, remains largely unknown. Therefore, the significance of this study is in the identification of new genes or gene allelic variants previously not associated with adhesion and invasion. It is well established that blocking adhesion and/or invasion would stop or hamper bacterial infection; therefore, the new findings from this study could be used in future developments of anti-Salmonella therapy targeting genes involved in these key processes. Such treatment could be a valuable alternative, as the prevalence of antibiotic-resistant bacteria is increasing very rapidly.
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Affiliation(s)
- Rafał Kolenda
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- Institute of Biotechnology, Faculty Environment and Natural Sciences, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | | | - Marcjanna Wimonć
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Adrianna Aleksandrowicz
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Aamir Ali
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Istvan Szabo
- National Salmonella Reference Laboratory, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | | | - Josefin Bartholdson Scott
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, University of Cambridge Department of Medicine, Cambridge, United Kingdom
| | - Derek Pickard
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, University of Cambridge Department of Medicine, Cambridge, United Kingdom
| | - Peter Schierack
- Institute of Biotechnology, Faculty Environment and Natural Sciences, BTU Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences, Public Health Campus, Brandenburg, Germany
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3
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Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram. Int J Mol Sci 2020; 21:ijms21124310. [PMID: 32560350 PMCID: PMC7352166 DOI: 10.3390/ijms21124310] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 01/12/2023] Open
Abstract
Antimicrobial peptides (AMPs) are molecules widespread in all branches of the tree of life that participate in host defense and/or microbial competition. Due to their positive charge, hydrophobicity and amphipathicity, they preferentially disrupt negatively charged bacterial membranes. AMPs are considered an important alternative to traditional antibiotics, especially at the time when multidrug-resistant bacteria being on the rise. Therefore, to reduce the costs of experimental research, robust computational tools for AMP prediction and identification of the best AMP candidates are essential. AmpGram is our novel tool for AMP prediction; it outperforms top-ranking AMP classifiers, including AMPScanner, CAMPR3R and iAMPpred. It is the first AMP prediction tool created for longer AMPs and for high-throughput proteomic screening. AmpGram prediction reliability was confirmed on the example of lactoferrin and thrombin. The former is a well known antimicrobial protein and the latter a cryptic one. Both proteins produce (after protease treatment) functional AMPs that have been experimentally validated at molecular level. The lactoferrin and thrombin AMPs were located in the antimicrobial regions clearly detected by AmpGram. Moreover, AmpGram also provides a list of shot 10 amino acid fragments in the antimicrobial regions, along with their probability predictions; these can be used for further studies and the rational design of new AMPs. AmpGram is available as a web-server, and an easy-to-use R package for proteomic analysis at CRAN repository.
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4
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Awan AB, Schiebel J, Böhm A, Nitschke J, Sarwar Y, Schierack P, Ali A. Association of biofilm formation and cytotoxic potential with multidrug resistance in clinical isolates of Pseudomonas aeruginosa. EXCLI JOURNAL 2019; 18:79-90. [PMID: 30956641 PMCID: PMC6449682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/23/2019] [Indexed: 11/01/2022]
Abstract
Multidrug resistant (MDR) Pseudomonas aeruginosa having strong biofilm potential and virulence factors are a serious threat for hospitalized patients having compromised immunity. In this study, 34 P. aeruginosa isolates of human origin (17 MDR and 17 non-MDR clinical isolates) were checked for biofilm formation potential in enriched and minimal media. The biofilms were detected using crystal violet method and a modified software package of the automated VideoScan screening method. Cytotoxic potential of the isolates was also investigated on HepG2, LoVo and T24 cell lines using automated VideoScan technology. Pulse field gel electrophoresis revealed 10 PFGE types in MDR and 8 in non-MDR isolates. Although all isolates showed biofilm formation potential, strong biofilm formation was found more in enriched media than in minimal media. Eight MDR isolates showed strong biofilm potential in both enriched and minimal media by both detection methods. Strong direct correlation between crystal violet and VideoScan methods was observed in identifying strong biofilm forming isolates. High cytotoxic effect was observed by 4 isolates in all cell lines used while 6 other isolates showed high cytotoxic effect on T24 cell line only. Strong association of multidrug resistance was found with biofilm formation as strong biofilms were observed significantly higher in MDR isolates (p-value < 0.05) than non-MDR isolates. No significant association of cytotoxic potential with multidrug resistance or biofilm formation was found (p-value > 0.05). The MDR isolates showing significant cytotoxic effects and strong biofilm formation impose a serious threat for hospitalized patients with weak immune system.
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Affiliation(s)
- Asad Bashir Awan
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Juliane Schiebel
- Institute for Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Alexander Böhm
- Institute for Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Jörg Nitschke
- Institute for Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Yasra Sarwar
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Peter Schierack
- Institute for Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Aamir Ali
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
- Institute for Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
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5
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Ovine Mannheimia haemolytica isolates from lungs with and without pneumonic lesions belong to similar genotypes. Vet Microbiol 2018; 219:80-86. [DOI: 10.1016/j.vetmic.2018.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/07/2018] [Accepted: 04/07/2018] [Indexed: 11/22/2022]
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6
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Liebsch C, Rödiger S, Böhm A, Nitschke J, Weinreich J, Fruth A, Roggenbuck D, Lehmann W, Schedler U, Juretzek T, Schierack P. Solid-phase microbead array for multiplex O-serotyping of Escherichia coli. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2088-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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7
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Wyrsch ER, Roy Chowdhury P, Chapman TA, Charles IG, Hammond JM, Djordjevic SP. Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis. Front Microbiol 2016; 7:843. [PMID: 27379026 PMCID: PMC4908116 DOI: 10.3389/fmicb.2016.00843] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/22/2016] [Indexed: 11/18/2022] Open
Abstract
Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance.
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Affiliation(s)
- Ethan R Wyrsch
- The ithree Institute, University of Technology Sydney, Sydney NSW, Australia
| | - Piklu Roy Chowdhury
- The ithree Institute, University of Technology Sydney, SydneyNSW, Australia; NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, SydneyNSW, Australia
| | - Toni A Chapman
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Sydney NSW, Australia
| | - Ian G Charles
- Institute of Food Research, Norwich Research Park Norwich, UK
| | - Jeffrey M Hammond
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Sydney NSW, Australia
| | - Steven P Djordjevic
- The ithree Institute, University of Technology Sydney, Sydney NSW, Australia
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8
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Sánchez del Rey V, Fernández-Garayzábal JF, Domínguez L, Gottschalk M, Vela AI. Screening of virulence-associated genes as a molecular typing method for characterization of Streptococcus suis isolates recovered from wild boars and pigs. Vet J 2015; 209:108-12. [PMID: 26831161 DOI: 10.1016/j.tvjl.2015.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 11/11/2015] [Accepted: 11/12/2015] [Indexed: 11/24/2022]
Abstract
Streptococcus suis is an important zoonotic pathogen associated with a wide range of diseases in pigs, but has also been isolated from wild animals such as rabbits and wild boars. In the current study, 126 S. suis isolates recovered from pigs (n = 85) and wild boars (n = 41) were tested by polymerase chain reaction (PCR) for the presence of nine virulence-associated genes. S. suis isolates from wild boars were differentiated by the lower detection rates of the epf, sly, mrp, sao and dltA genes (0%, 2.4%, 2.4%, 4.8% and 21.9%, respectively) compared with the isolates from pigs (56.5%, 75.3%, 56.5%, 88.2.0% and 88.2%, respectively). The differences in the content of these virulence-associated genes were statistically significant (P < 0.05). There was a correlation between the variants saoM and saoL and serotypes 2 and 9, respectively (P < 0.05). Isolates were classified into 31 virulence-associated gene profiles (VPs). Ten VPs were detected among wild boar isolates and 22 VPs among pig isolates, with only two VPs common to wild boars and pigs. The predominant VPs among isolates from wild boars (VP1, VP7) were different from those observed in pig isolates (VP16 and VP26). VP16 was detected exclusively in clinical pig isolates of serotype 9 and VP26 was detected in 71.4% of the serotype 2 clinical pig isolates. Further multilocus sequence typing (MLST) analysis showed a significant correlation association between certain VPs and STs (VP16 and VP17 with ST123 and ST125 and VP26 with ST1). In conclusion, the current study showed that combination of virulence-associated gene profiling and MLST analysis may provide more information of the relatedness of the S. suis strains from different animal species that could be useful for epidemiological purposes.
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Affiliation(s)
- Verónica Sánchez del Rey
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain
| | - José F Fernández-Garayzábal
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain; Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
| | - Lucas Domínguez
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain
| | - Marcelo Gottschalk
- Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculté de Médecine, Vétérinaire, Université de Montréal, 3200 Sicotte, St.-Hyacinthe, Québec, J2S 2M2, Canada
| | - Ana I Vela
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain; Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain.
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9
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Spitzer F, Speiser S, Vahjen W, Zentek J. Effect of different feed ingredients and additives on IPEC-J2 cells challenged with an enterotoxigenic Escherichia coli strain. Cytotechnology 2015; 68:1463-71. [PMID: 26275434 DOI: 10.1007/s10616-015-9905-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 07/27/2015] [Indexed: 01/19/2023] Open
Abstract
The intestinal porcine epithelial cell line IPEC-J2 was used as an in vitro model to assess effects of additives on the adhesion and cell toxic effects of a F4-positive (ETEC) and a F4-negative Escherichia coli (DSM 2840) strain. Bacterial adhesion was examined using flow cytometry in IPEC-J2 cells infected with bacteria stained with 5,6-carboxymethyl fluorescein diacetate succinimidyl ester. Measurement of transepithelial electrical resistance (TEER) was performed to characterize the impact on IPEC-J2 monolayer integrity. The feed additives were prepared as aqueous extract and tested in different dilutions and incubation times. The F4-positive ETEC strain had a high adhesion to IPEC-J2 cells and reduced TEER shortly after the in vitro infection. The nonpathogenic E. coli strain DSM 2840 showed only low adhesion capacity and no TEER impairment. Infection with ETEC with added test extracts showed a reduction of bacterial adhesion to IPEC-J2 cells by an autolyzed yeast product (p < 0.05). Bovine colostrum, an additive containing thyme extract and an organic acid mix did not interfere with the ETEC adherence. The TEER decrease of the IPEC-J2 monolayer after ETEC infection was not affected by the added substances. In conclusion, interference with epithelial adhesion might be a protective mechanism of the tested yeast extract, indicating that the cell culture model might be suitable as screening tool to complement in vivo challenge trials with piglets.
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Affiliation(s)
- F Spitzer
- Department of Veterinary Medicine, Institute of Animal Nutrition, Freie Universität Berlin, Königin-Luise-Str. 49, 14195, Berlin, Germany
| | - S Speiser
- Department of Veterinary Medicine, Institute of Animal Nutrition, Freie Universität Berlin, Königin-Luise-Str. 49, 14195, Berlin, Germany
| | - W Vahjen
- Department of Veterinary Medicine, Institute of Animal Nutrition, Freie Universität Berlin, Königin-Luise-Str. 49, 14195, Berlin, Germany.
| | - J Zentek
- Department of Veterinary Medicine, Institute of Animal Nutrition, Freie Universität Berlin, Königin-Luise-Str. 49, 14195, Berlin, Germany
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10
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Matter LB, Spricigo DA, Tasca C, Vargas ACD. Invasin gimB found in a bovine intestinal Escherichia coli with an adherent and invasive profile. Braz J Microbiol 2015; 46:875-8. [PMID: 26413073 PMCID: PMC4568875 DOI: 10.1590/s1517-838246320140621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/19/2014] [Indexed: 11/22/2022] Open
Abstract
The invasin gimB (genetic island associated with human newborn
meningitis) is usually found in ExPEC (Extraintestinal Pathogenic Escherichia
coli) such as UPEC (uropathogenic E. coli), NMEC
(neonatal meningitis E. coli) and APEC (avian pathogenic E.
coli). In NMEC, gimB is associated with the invasion
process of the host cells. Due to the importance of E. coli as a
zoonotic agent and the scarce information about the frequency of
gimB-carrying strains in different animal species, the aim of
this study was to investigate the presence of gimB in isolates from
bovine, swine, canine and feline clinical samples. PCR was conducted on 196 isolates
and the identity of the amplicons was confirmed by sequencing. Of the samples tested,
only E. coli SB278/94 from a bovine specimen was positive (1/47) for
gimB, which represents 2.1% of the bovine isolates. The ability
of SB278/94 to adhere to and invade eukaryotic cells was confirmed by adherence and
gentamicin-protection assays using HeLa cells. This is the first study that
investigates for gimB in bovine, canine and feline E.
coli isolates and shows E. coli from the
intestinal-bovine samples harboring gimB.
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Affiliation(s)
- Letícia B Matter
- Laboratório de Bacteriologia, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Denis A Spricigo
- Laboratório de Bacteriologia, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Caiane Tasca
- Laboratório de Bacteriologia, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Agueda C de Vargas
- Laboratório de Bacteriologia, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
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11
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Smati M, Clermont O, Bleibtreu A, Fourreau F, David A, Daubié AS, Hignard C, Loison O, Picard B, Denamur E. Quantitative analysis of commensal Escherichia coli populations reveals host-specific enterotypes at the intra-species level. Microbiologyopen 2015; 4:604-15. [PMID: 26033772 PMCID: PMC4554456 DOI: 10.1002/mbo3.266] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/14/2015] [Accepted: 04/17/2015] [Indexed: 12/26/2022] Open
Abstract
The primary habitat of the Escherichia coli species is the gut of warm-blooded vertebrates. The E. coli species is structured into four main phylogenetic groups A, B1, B2, and D. We estimated the relative proportions of these phylogroups in the feces of 137 wild and domesticated animals with various diets living in the Ile de France (Paris) region by real-time PCR. We distinguished three main clusters characterized by a particular abundance of two or more phylogroups within the E. coli animal commensal populations, which we called “enterocolitypes” by analogy with the enterotypes defined in the human gut microbiota at the genus level. These enterocolitypes were characterized by a dominant (>50%) B2, B1, or A phylogroup and were associated with different host species, diets, and habitats: wild and herbivorous species (wild rabbits and deer), domesticated herbivorous species (domesticated rabbits, horses, sheep, and cows), and omnivorous species (boar, pigs, and chickens), respectively. By analyzing retrospectively the data obtained using the same approach from 98 healthy humans living in Ile de France (Smati et al. 2013, Appl. Environ. Microbiol. 79, 5005–5012), we identified a specific human enterocolitype characterized by the dominant and/or exclusive (>90%) presence of phylogroup B2. We then compared B2 strains isolated from animals and humans, and revealed that human and animal strains differ regarding O-type and B2 subgroup. Moreover, two genes, sfa/foc and clbQ, were associated with the exclusive character of strains, observed only in humans. In conclusion, a complex network of interactions exists at several levels (genus and intra-species) within the intestinal microbiota.
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Affiliation(s)
- Mounira Smati
- INSERM, IAME, UMR 1137, F-75018, Paris, France.,Univ Paris Nord, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.,APHP, Hôpitaux Universitaires Paris Seine Saint-Denis, Hôpital Avicenne, Service de Bactériologie-Virologie-Hygiène, Bobigny, France
| | - Olivier Clermont
- INSERM, IAME, UMR 1137, F-75018, Paris, France.,Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France
| | - Alexandre Bleibtreu
- INSERM, IAME, UMR 1137, F-75018, Paris, France.,Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France
| | - Frédéric Fourreau
- APHP, Hôpitaux Universitaires Paris Seine Saint-Denis, Hôpital Avicenne, Service de Bactériologie-Virologie-Hygiène, Bobigny, France
| | - Anthony David
- INSERM, IAME, UMR 1137, F-75018, Paris, France.,Univ Paris Nord, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.,Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France
| | - Anne-Sophie Daubié
- INSERM, IAME, UMR 1137, F-75018, Paris, France.,APHP, Hôpitaux Universitaires Paris Seine Saint-Denis, Hôpital Avicenne, Service de Bactériologie-Virologie-Hygiène, Bobigny, France.,Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France
| | - Cécile Hignard
- Univ Paris Diderot, Station d'Ecologie Forestière, Sorbonne Paris Cité, Fontainebleau, France
| | - Odile Loison
- Univ Paris Diderot, Station d'Ecologie Forestière, Sorbonne Paris Cité, Fontainebleau, France
| | - Bertrand Picard
- INSERM, IAME, UMR 1137, F-75018, Paris, France.,Univ Paris Nord, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.,APHP, Hôpitaux Universitaires Paris Seine Saint-Denis, Hôpital Avicenne, Service de Bactériologie-Virologie-Hygiène, Bobigny, France
| | - Erick Denamur
- INSERM, IAME, UMR 1137, F-75018, Paris, France.,Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France
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12
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Bok E, Mazurek J, Stosik M, Wojciech M, Baldy-Chudzik K. Prevalence of virulence determinants and antimicrobial resistance among commensal Escherichia coli derived from dairy and beef cattle. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015; 12:970-85. [PMID: 25607605 PMCID: PMC4306905 DOI: 10.3390/ijerph120100970] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/22/2014] [Indexed: 01/30/2023]
Abstract
Cattle is a reservoir of potentially pathogenic E. coli, bacteria that can represent a significant threat to public health, hence it is crucial to monitor the prevalence of the genetic determinants of virulence and antimicrobial resistance among the E. coli population. The aim of this study was the analysis of the phylogenetic structure, distribution of virulence factors (VFs) and prevalence of antimicrobial resistance among E. coli isolated from two groups of healthy cattle: 50 cows housed in the conventional barn (147 isolates) and 42 cows living on the ecological pasture (118 isolates). The phylogenetic analysis, identification of VFs and antimicrobial resistance genes were based on either multiplex or simplex PCR. The antimicrobial susceptibilities of E. coli were examined using the broth microdilution method. Two statistical approaches were used to analyse the results obtained for two groups of cattle. The relations between the dependent (VFs profiles, antibiotics) and the independent variables were described using the two models. The mixed logit model was used to characterise the prevalence of the analysed factors in the sets of isolates. The univariate logistic regression model was used to characterise the prevalence of these factors in particular animals. Given each model, the odds ratio (OR) and the 95% confidence interval for the population were estimated. The phylogroup B1 was predominant among isolates from beef cattle, while the phylogroups A, B1 and D occurred with equal frequency among isolates from dairy cattle. The frequency of VFs-positive isolates was significantly higher among isolates from beef cattle. E. coli from dairy cattle revealed significantly higher resistance to antibiotics. Some of the tested resistance genes were present among isolates from dairy cattle. Our study showed that the habitat and diet may affect the genetic diversity of commensal E. coli in the cattle. The results suggest that the ecological pasture habitat is related to the increased spreading rate of the VFs, while the barn habitat is characterised by the higher levels of antimicrobial resistance among E. coli.
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Affiliation(s)
- Ewa Bok
- Department of Molecular Biology, Faculty of Biological Sciences, University of Zielona Góra, Monte Cassino St. 21b, 65-561 Zielona Góra, Poland.
| | - Justyna Mazurek
- Department of Molecular Biology, Faculty of Biological Sciences, University of Zielona Góra, Monte Cassino St. 21b, 65-561 Zielona Góra, Poland.
| | - Michał Stosik
- Department of Molecular Biology, Faculty of Biological Sciences, University of Zielona Góra, Monte Cassino St. 21b, 65-561 Zielona Góra, Poland.
| | - Magdalena Wojciech
- Department of Mathematical Statistics and Econometrics, Faculty of Mathematics, Computer Science and Econometrics, University of Zielona Góra, Prof. Z. Szafrana St. 4a, 65-516 Zielona Góra, Poland.
| | - Katarzyna Baldy-Chudzik
- Department of Molecular Biology, Faculty of Biological Sciences, University of Zielona Góra, Monte Cassino St. 21b, 65-561 Zielona Góra, Poland.
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Semmler T, Eichhorn I, Bethe A, Bauerfeind R, Pickard D, Kingsley RA, Dougan G, Wieler LH. Genome Sequence of Porcine Escherichia coli Strain IMT8073, an Atypical Enteropathogenic E. coli Strain Isolated from a Piglet with Diarrhea. GENOME ANNOUNCEMENTS 2013; 1:e00573-13. [PMID: 23908298 PMCID: PMC3731852 DOI: 10.1128/genomea.00573-13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 07/03/2013] [Indexed: 11/23/2022]
Abstract
Escherichia coli is a highly diverse bacterial species, with atypical enteropathogenic E. coli (aEPEC) causing intestinal disease in both human and animal hosts. Here, we report the first complete genome sequence of an aEPEC strain of sequence type ST794 and serotype Ont:H7, isolated from a diseased piglet.
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Affiliation(s)
- Torsten Semmler
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Inga Eichhorn
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Astrid Bethe
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Rolf Bauerfeind
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Derek Pickard
- Pathogen Genomics, the Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Robert A. Kingsley
- Pathogen Genomics, the Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Gordon Dougan
- Pathogen Genomics, the Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Lothar H. Wieler
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
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14
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Adhesion of human and animal Escherichia coli strains in association with their virulence-associated genes and phylogenetic origins. Appl Environ Microbiol 2013; 79:5814-29. [PMID: 23872574 DOI: 10.1128/aem.01384-13] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Intestinal colonization is influenced by the ability of the bacterium to inhabit a niche, which is based on the expression of colonization factors. Escherichia coli carries a broad range of virulence-associated genes (VAGs) which contribute to intestinal (inVAGs) and extraintestinal (exVAGs) infection. Moreover, initial evidence indicates that inVAGs and exVAGs support intestinal colonization. We developed new screening tools to genotypically and phenotypically characterize E. coli isolates originating in humans, domestic pigs, and 17 wild mammal and avian species. We analyzed 317 isolates for the occurrence of 44 VAGs using a novel multiplex PCR microbead assay (MPMA) and for adhesion to four epithelial cell lines using a new adhesion assay. We correlated data for the definition of new adhesion genes. inVAGs were identified only sporadically, particularly in roe deer (Capreolus capreolus) and the European hedgehog ( Erinaceus europaeus). The prevalence of exVAGs depended on isolation from a specific host. Human uropathogenic E. coli isolates carried exVAGs with the highest prevalence, followed by badger (Meles meles) and roe deer isolates. Adhesion was found to be very diverse. Adhesion was specific to cells, host, and tissue, though it was also unspecific. Occurrence of the following VAGs was associated with a higher rate of adhesion to one or more cell lines: afa-dra, daaD, tsh, vat, ibeA, fyuA, mat, sfa-foc, malX, pic, irp2, and papC. In summary, we established new screening methods which enabled us to characterize large numbers of E. coli isolates. We defined reservoirs for potential pathogenic E. coli. We also identified a very broad range of colonization strategies and defined potential new adhesion genes.
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