1
|
Moinet M, Rogers L, Biggs P, Marshall J, Muirhead R, Devane M, Stott R, Cookson A. High-resolution genomic analysis to investigate the impact of the invasive brushtail possum (Trichosurus vulpecula) and other wildlife on microbial water quality assessments. PLoS One 2024; 19:e0295529. [PMID: 38236841 PMCID: PMC10796070 DOI: 10.1371/journal.pone.0295529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/21/2023] [Indexed: 01/22/2024] Open
Abstract
Escherichia coli are routine indicators of fecal contamination in water quality assessments. Contrary to livestock and human activities, brushtail possums (Trichosurus vulpecula), common invasive marsupials in Aotearoa/New Zealand, have not been thoroughly studied as a source of fecal contamination in freshwater. To investigate their potential role, Escherichia spp. isolates (n = 420) were recovered from possum gut contents and feces and were compared to those from water, soil, sediment, and periphyton samples, and from birds and other introduced mammals collected within the Mākirikiri Reserve, Dannevirke. Isolates were characterized using E. coli-specific real-time PCR targeting the uidA gene, Sanger sequencing of a partial gnd PCR product to generate a gnd sequence type (gST), and for 101 isolates, whole genome sequencing. Escherichia populations from 106 animal and environmental sample enrichments were analyzed using gnd metabarcoding. The alpha diversity of Escherichia gSTs was significantly lower in possums and animals compared with aquatic environmental samples, and some gSTs were shared between sample types, e.g., gST535 (in 85% of samples) and gST258 (71%). Forty percent of isolates gnd-typed and 75% of reads obtained by metabarcoding had gSTs shared between possums, other animals, and the environment. Core-genome single nucleotide polymorphism (SNP) analysis showed limited variation between several animal and environmental isolates (<10 SNPs). Our data show at an unprecedented scale that Escherichia clones are shared between possums, other wildlife, water, and the wider environment. These findings support the potential role of possums as contributors to fecal contamination in Aotearoa/New Zealand freshwater. Our study deepens the current knowledge of Escherichia populations in under-sampled wildlife. It presents a successful application of high-resolution genomic methods for fecal source tracking, thereby broadening the analytical toolbox available to water quality managers. Phylogenetic analysis of isolates and profiling of Escherichia populations provided useful information on the source(s) of fecal contamination and suggest that comprehensive invasive species management strategies may assist in restoring not only ecosystem health but also water health where microbial water quality is compromised.
Collapse
Affiliation(s)
- Marie Moinet
- Hopkirk Research Institute, AgResearch, Palmerston North, New Zealand
| | - Lynn Rogers
- Hopkirk Research Institute, AgResearch, Palmerston North, New Zealand
| | - Patrick Biggs
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Jonathan Marshall
- School of Mathematical and Computational Sciences, Massey University, Palmerston North, New Zealand
| | | | - Megan Devane
- Institute of Environmental Science and Research Ltd. (ESR), Christchurch, New Zealand
| | - Rebecca Stott
- National Institute of Water and Atmospheric Research (NIWA), Hamilton, New Zealand
| | - Adrian Cookson
- Hopkirk Research Institute, AgResearch, Palmerston North, New Zealand
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| |
Collapse
|
2
|
De Silva PM, Bennett RJ, Kuhn L, Ngondo P, Debande L, Njamkepo E, Ho B, Weill FX, Marteyn BS, Jenkins C, Baker KS. Escherichia coli killing by epidemiologically successful sublineages of Shigella sonnei is mediated by colicins. EBioMedicine 2023; 97:104822. [PMID: 37806286 PMCID: PMC10579285 DOI: 10.1016/j.ebiom.2023.104822] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023] Open
Abstract
BACKGROUND Shigella sp. are enteric pathogens which causes >125 million cases of shigellosis annually. S. sonnei accounts for about a quarter of those cases and is increasingly prevalent in industrialising nations. Being an enteric pathogen, S. sonnei benefits from outcompeting gut commensals such as Escherichia coli to establish itself and cause disease. There are numerous mechanisms that bacterial pathogens use to outcompete its rivals including molecules called colicins. A Type 6 Secretion System (T6SS) was recently described as contributing to E. coli killing in S. sonnei. METHODS We used Bulk Phenotyping of Epidemiological Replicates (BPER) which combined bacterial Genome Wide Association Studies (bGWAS) and high throughput phenotyping on a collection of S. sonnei surveillance isolates to identify the genetic features associated with E. coli killing and explore their relationship with epidemiological behaviour. We further explored the presence of colicins and T6SS components in the isolates using genomics, laboratory experimentation, and proteomics. FINDINGS Our bGWAS analysis returned known and novel colicin and colicin related genes as significantly associated with E. coli killing. In silico analyses identified key colicin clusters responsible for the killing phenotype associated with epidemiologically successful sub-lineages. The killing phenotype was not associated with the presence of a T6SS. Laboratory analyses confirmed the presence of the key colicin clusters and that killing was contact-independent. INTERPRETATION Colicins are responsible for E. coli killing by S. sonnei, not a T6SS. This phenotype contributes to shaping the observed epidemiology of S. sonnei and may contribute to its increasing prevalence globally. BPER is an epidemiologically relevant approach to phenotypic testing that enables the rapid identification of genetic drivers of phenotypic changes, and assessment of their relevance to epidemiology in natural settings. FUNDING Biotechnology and Biological Sciences Research Council, Biotechnology and Biological Sciences Research Council Doctoral Training Partnership studentship, Wellcome Trust, Medical Research Council (UK), French National Research Agency.
Collapse
Affiliation(s)
- P Malaka De Silva
- Department of Clinical Infection, Microbiology, and Immunology, Institute for Infection, Veterinary, and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom
| | - Rebecca J Bennett
- Department of Clinical Infection, Microbiology, and Immunology, Institute for Infection, Veterinary, and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Patryk Ngondo
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Lorine Debande
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Elisabeth Njamkepo
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Brian Ho
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, UK
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Benoît S Marteyn
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Claire Jenkins
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, Colindale, London, UK
| | - Kate S Baker
- Department of Clinical Infection, Microbiology, and Immunology, Institute for Infection, Veterinary, and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom; Department of Genetics, University of Cambridge, Downing Place, Cambridge, UK.
| |
Collapse
|
3
|
García MD, Ruiz MJ, Medina LM, Vidal R, Padola NL, Etcheverria AI. Molecular and Genetic Characterization of Colicinogenic Escherichia coli Strains Active against Shiga Toxin-Producing Escherichia coli O157:H7. Foods 2023; 12:2676. [PMID: 37509768 PMCID: PMC10378606 DOI: 10.3390/foods12142676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/21/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
The objective of this work was to molecularly and genotypically characterize and test the inhibitory activity of six colicinogenic Escherichia coli strains (ColEc) and their partially purified colicins against STEC O157:H7 isolated from clinical human cases. Inhibition tests demonstrated the activity of these strains and their colicins against STEC O157:H7. By PCR it was possible to detect colicins Ia, E7, and B and microcins M, H47, C7, and J25. By genome sequencing of two selected ColEc strains, it was possible to identify additional colicins such as E1 and Ib. No genes coding for stx1 and stx2 were detected after analyzing the genome sequence. The inhibitory activity of ColEc against STEC O157:H7 used as an indicator showed that colicins are potent growth inhibitors of E. coli O157:H7, being a potential alternative to reduce the presence of pathogens of public health relevance.
Collapse
Affiliation(s)
- Mauro D García
- Laboratorio de Inmunoquímica y Biotecnología, Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET, CICPBA, Facultad de Ciencias Veterinarias, UNICEN-Campus Universitario, Tandil B7000, Argentina
| | - María J Ruiz
- Laboratorio de Inmunoquímica y Biotecnología, Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET, CICPBA, Facultad de Ciencias Veterinarias, UNICEN-Campus Universitario, Tandil B7000, Argentina
| | - Luis M Medina
- Food Science and Technology Department, Faculty of Veterinary Medicine, Universidad de Cordoba, 14071 Córdoba, Spain
| | - Roberto Vidal
- Instituto de Ciencias biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
| | - Nora L Padola
- Laboratorio de Inmunoquímica y Biotecnología, Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET, CICPBA, Facultad de Ciencias Veterinarias, UNICEN-Campus Universitario, Tandil B7000, Argentina
| | - Analía I Etcheverria
- Laboratorio de Inmunoquímica y Biotecnología, Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET, CICPBA, Facultad de Ciencias Veterinarias, UNICEN-Campus Universitario, Tandil B7000, Argentina
| |
Collapse
|
4
|
McMahon TC, Kingombe CB, Mathews A, Seyer K, Wong A, Blais BW, Carrillo CD. Microbial Antagonism in Food-Enrichment Culture: Inhibition of Shiga Toxin-Producing Escherichia coli and Shigella Species. Front Microbiol 2022; 13:880043. [PMID: 35814680 PMCID: PMC9259949 DOI: 10.3389/fmicb.2022.880043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial pathogens, such as Shiga toxin-producing Escherichia coli (STEC) and Shigella spp., are important causes of foodborne illness internationally. Recovery of these organisms from foods is critical for food safety investigations to support attribution of illnesses to specific food commodities; however, isolation of bacterial cultures can be challenging. Methods for the isolation of STEC and Shigella spp. from foods typically require enrichment to amplify target organisms to detectable levels. Yet, during enrichment, target organisms can be outcompeted by other bacteria in food matrices due to faster growth rates, or through production of antimicrobial agents such as bacteriocins or bacteriophages. The purpose of this study was to evaluate the occurrence of Shigella and STEC inhibitors produced by food microbiota. The production of antimicrobial compounds in cell-free extracts from 200 bacterial strains and 332 food-enrichment broths was assessed. Cell-free extracts produced by 23 (11.5%) of the strains tested inhibited growth of at least one of the five Shigella and seven STEC indicator strains used in this study. Of the 332 enrichment broths tested, cell-free extracts from 25 (7.5%) samples inhibited growth of at least one of the indicator strains tested. Inhibition was most commonly associated with E. coli recovered from meat products. Most of the inhibiting compounds were determined to be proteinaceous (34 of the 48 positive samples, 71%; including 17 strains, 17 foods) based on inactivation by proteolytic enzymes, indicating presence of bacteriocins. The cell-free extracts from 13 samples (27%, eight strains, five foods) were determined to contain bacteriophages based on the observation of plaques in diluted extracts and/or resistance to proteolytic enzymes. These results indicate that the production of inhibitors by food microbiota may be an important challenge for the recovery of foodborne pathogens, particularly for Shigella sonnei. The performance of enrichment media for recovery of Shigella and STEC could be improved by mitigating the impact of inhibitors produced by food microbiota during the enrichment process.
Collapse
Affiliation(s)
- Tanis C. McMahon
- Research and Development, Ottawa Laboratory (Carling), Ontario Laboratory Network, Canadian Food Inspection Agency, Ottawa, ON, Canada
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | | | - Amit Mathews
- Microbiology, Greater Toronto Area Laboratory, Ontario Laboratory Network, Canadian Food Inspection Agency, Toronto, ON, Canada
| | - Karine Seyer
- Microbiology (Food), St-Hyacinthe Laboratory, Eastern Laboratories Network, Canadian Food Inspection Agency, St-Hyacinthe, QC, Canada
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Burton W. Blais
- Research and Development, Ottawa Laboratory (Carling), Ontario Laboratory Network, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Catherine D. Carrillo
- Research and Development, Ottawa Laboratory (Carling), Ontario Laboratory Network, Canadian Food Inspection Agency, Ottawa, ON, Canada
- *Correspondence: Catherine D. Carrillo,
| |
Collapse
|
5
|
Parker JK, Davies BW. Microcins reveal natural mechanisms of bacterial manipulation to inform therapeutic development. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001175. [PMID: 35438625 PMCID: PMC10233263 DOI: 10.1099/mic.0.001175] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/17/2022] [Indexed: 12/20/2022]
Abstract
Microcins are an understudied and poorly characterized class of antimicrobial peptides. Despite the existence of only 15 examples, all identified from the Enterobacteriaceae, microcins display diversity in sequence, structure, target cell uptake, cytotoxic mechanism of action and target specificity. Collectively, these features describe some of the unique means nature has contrived for molecules to cross the 'impermeable' barrier of the Gram-negative bacterial outer membrane and inflict cytotoxic effects. Microcins appear to be widely dispersed among different species and in different environments, where they function in regulating microbial communities in diverse ways, including through competition. Growing evidence suggests that microcins may be adapted for therapeutic uses such as antimicrobial drugs, microbiome modulators or facilitators of peptide uptake into cells. Advancing our biological, ecological and biochemical understanding of the roles of microcins in bacterial interactions, and learning how to regulate and modify microcin activity, is essential to enable such therapeutic applications.
Collapse
Affiliation(s)
| | - Bryan William Davies
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
| |
Collapse
|
6
|
Snopková K, Dufková K, Chamrád I, Lenobel R, Čejková D, Kosina M, Hrala M, Holá V, Sedláček I, Šmajs D. Pyocin-mediated antagonistic interactions in Pseudomonas spp. isolated in James Ross Island, Antarctica. Environ Microbiol 2021; 24:1294-1307. [PMID: 34735036 DOI: 10.1111/1462-2920.15809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/15/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022]
Abstract
Interactions within bacterial communities are frequently mediated by the production of antimicrobial agents. Despite the increasing interest in research of new antimicrobials, studies describing antagonistic interactions among cold-adapted microorganisms are still rare. Our study assessed the antimicrobial interactions of 36 Antarctic Pseudomonas spp. and described the genetic background of these interactions in selected strains. The overall bacteriocinogeny was greater compared to mesophilic Pseudomonas non-aeruginosa species. R-type tailocins were detected on transmission electron micrographs in 16 strains (44.4%); phylogenetic analysis of the corresponding gene clusters revealed that the P. prosekii CCM 8878 tailocin was related to the Rp3 group, whereas the tailocin in Pseudomonas sp. CCM 8880 to the Rp4 group. Soluble antimicrobials were produced by eight strains (22.-2%); gene mining found pyocin L homologues in the genomes of P. prosekii CCM 8881 and CCM 8879 and pyocin S9-like homologues in P. prosekii CCM 8881 and Pseudomonas sp. CCM 8880. Analysis of secretomes confirmed the production of all S- and L-type pyocin genes. Our results suggest that bacteriocin-based inhibition plays an important role in interactions among Antarctic soil bacteria, and these native, cold-adapted microorganisms could be a promising source of new antimicrobials.
Collapse
Affiliation(s)
- Kateřina Snopková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
| | - Kristýna Dufková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
| | - Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, Olomouc-Holice, 779 00, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, Olomouc-Holice, 779 00, Czech Republic
| | - Darina Čejková
- Veterinary Research Institute, Hudcova 296/70, Brno, 621 00, Czech Republic
| | - Marcel Kosina
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
| | - Matěj Hrala
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
| | - Veronika Holá
- Faculty of Medicine, Institute for Microbiology, Masaryk University and St. Anne's University Hospital Brno, Pekařská 664/53, Brno, 656 91, Czech Republic
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
| |
Collapse
|
7
|
Administration of the Probiotic Escherichia coli Strain A0 34/86 Resulted in a Stable Colonization of the Human Intestine During the First Year of Life. Probiotics Antimicrob Proteins 2021; 12:343-350. [PMID: 31069717 DOI: 10.1007/s12602-019-09548-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Colinfant New Born (CNB) is an orally administered probiotic preparation containing the Escherichia coli strain A0 34/86, which is specially marketed for use in newborns and infants. Although the impact of different probiotics on the composition of the human gut microbiota has been previously described, the effects of E. coli probiotic consumption during infancy on the development of intestinal microbiota are not known. The effect of oral administration of CNB on the Enterobacteriaceae population was mapped using 16S rRNA gene sequencing in DNA samples isolated from the stools of one infant collected at 177 different time points during the first year of life. E. coli strains turnover was analyzed based on the detection of 26 genetic determinants, phylogroups, and pulsed-field gel electrophoresis (PFGE) analysis. Administration of CNB during the second and third month of life introduced the Escherichia genus to the infant's intestinal tract, and Escherichia became dominant among the Enterobacteriaceae family (p < 0.01). Genetic determinants, typical for probiotic E. coli A0 34/86 strain, were detected on the first day after application of CNB and persisted all year. In addition, nine transient E. coli strains were identified; these strains harbored different genetic determinants and showed different PFGE profiles. Transient strains were detected from 2 to 24 days in the stool samples. The first Escherichia colonizer originated from the application of the CNB probiotic preparation. Probiotic E. coli A0 34/86 successfully colonized the intestinal tract of an infant and became resident during the first year of life.
Collapse
|
8
|
Genomic and proteomic comparisons of bacteriocins in probiotic species Lactobacillus and Bifidobacterium and inhibitory ability of Escherichia coli MG 1655. ACTA ACUST UNITED AC 2021; 31:e00654. [PMID: 34258243 PMCID: PMC8254086 DOI: 10.1016/j.btre.2021.e00654] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 11/24/2022]
Abstract
The genomes and proteomes of 12 Bifidobacterium and 46 Lactobacillus were reviewed and then compared for bacteriocin identification. NCBI-Genome, UniProt-Proteome, Bactibase, and BAGL4 databases, as well as BLASTP, and Clustal Omega can be used for bacteriocin mining. Lactobacillus species have more diversity and abundance of bacteriocin compared to Bifidobacterium species. Notably, L. sakei, L. plamtarum, L. reuteri, L. fermentum, and L. casei had the highest pathogen inhibition (E. coli MG 1655); respectively. A set of Lactobacillus bacteria including L. sakei, L. reuteri, L. fermentum, and L. casei can be proposed as a biosecure and safe solution to control gastrointestinal pathogens.
Bacteriocins are a large family of bacterial peptides or proteins, ribosomally synthesized with antimicrobial activity against other bacteria. We investigated and compared the genomes and proteomes of 12 Bifidobacterium and 46 Lactobacillus species for bacteriocins using NCBI-Genome, UniProt-Proteome, Bactibase, and BAGL4 databases. Selected Lactobacillus species were examined for bile salt resistance, acid and pH resistance, pepsin and trypsin enzyme resistance, and antibiotic resistance. Also, the antimicrobial activity of selected Lactobacillus species was evaluated against E. coli MG 1655. Results showed that Lactobacillus species have more diversity and abundance of bacteriocin compared to Bifidobacterium species. Notably, L. sakei, L. plamtarum, L. reuteri, L. fermentum, and L. casei had the highest pathogen inhibition; respectively. Therefore, a combination of these Lactobacillus species can be suggested as a biochemical and safe solution to control gastrointestinal pathogens and suitable alternatives to antibiotics and chemicals in food technology.
Collapse
|
9
|
Lozica L, Repar J, Gottstein Ž. Longitudinal study on the effect of autogenous vaccine application on the sequence type and virulence profiles of Escherichia coli in broiler breeder flocks. Vet Microbiol 2021; 259:109159. [PMID: 34237496 DOI: 10.1016/j.vetmic.2021.109159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/16/2021] [Indexed: 11/26/2022]
Abstract
Colibacillosis is one of the most common problems in the poultry industry. Escherichia coli strains on farms are often genetically diverse and therefore commercial vaccines provide little protection to the flocks. Here, we investigated the effect of the autogenous E. coli vaccines on the prevalence of 84 virulence-associated genes in E. coli isolated from four and five consecutive flocks on two broiler breeder farms, respectively. 115 E. coli isolates were sequenced using Illumina technologies, and compared based on both their set of housekeeping genes and their virulence profiles, defined through the composition of virulence genes. Predominantly, phylogenetic analysis showed obvious distinction between the isolates originating from different farms suggesting spatial-dependent transmission of pathogenic strains. We detected 23 sequence types, while 52.58 % of the isolates belonged to two clonal complexes. Analysis of the virulence genes showed highest prevalence (>85 %) of feoB, uspA, uspB, uspG, uspE, fimH, ompA, astA, focA, hlyE, uspC, crl, csgA, ompT and iss, of which 50 % are toxin associated genes, demonstrating the importance of competition in the pathogenesis process. Interestingly, usp genes, which are primarily associated with uropathogenic E. coli strains, were detected in all investigated isolates. The heatmap analysis demonstrated that strains belonging to same phylogenetic groups often share similar virulence profiles, confirming the usefulness of quick tests for phylogenetic typing. However, our results suggest the need to update the list of the minimal predictors used for the identification of avian pathogenic strains. Overall results indicate that continuous application of autogenous vaccines led to lower genetic diversity of E. coli housekeeping genes, but not virulence genes.
Collapse
Affiliation(s)
- Liča Lozica
- Department of Poultry Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia
| | - Jelena Repar
- Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Željko Gottstein
- Department of Poultry Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia.
| |
Collapse
|
10
|
Alonso CA, de Toro M, de la Cruz F, Torres C. Genomic Insights into Drug Resistance and Virulence Platforms, CRISPR-Cas Systems and Phylogeny of Commensal E. coli from Wildlife. Microorganisms 2021; 9:999. [PMID: 34063152 PMCID: PMC8148099 DOI: 10.3390/microorganisms9050999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/30/2022] Open
Abstract
Commensal bacteria act as important reservoirs of virulence and resistance genes. However, existing data are generally only focused on the analysis of human or human-related bacterial populations. There is a lack of genomic studies regarding commensal bacteria from hosts less exposed to antibiotics and other selective forces due to human activities, such as wildlife. In the present study, the genomes of thirty-eight E. coli strains from the gut of various wild animals were sequenced. The analysis of their accessory genome yielded a better understanding of the role of the mobilome on inter-bacterial dissemination of mosaic virulence and resistance plasmids. The study of the presence and composition of the CRISPR/Cas systems in E. coli from wild animals showed some viral and plasmid sequences among the spacers, as well as the relationship between CRISPR/Cas and E. coli phylogeny. Further, we constructed a single nucleotide polymorphisms-based core tree with E. coli strains from different sources (humans, livestock, food and extraintestinal environments). Bacteria from humans or highly human-influenced settings exhibit similar genetic patterns in CRISPR-Cas systems, plasmids or virulence/resistance genes-carrying modules. These observations, together with the absence of significant genetic changes in their core genome, suggest an ongoing flow of both mobile elements and E. coli lineages between human and natural ecosystems.
Collapse
Affiliation(s)
- Carla Andrea Alonso
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, 26006 Logroño, Spain;
- Servicio de Microbiología, Hospital San Pedro, 26006 Logroño, Spain
| | - María de Toro
- Plataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain;
| | - Fernando de la Cruz
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (Universidad de Cantabria-CSIC), 39011 Santander, Spain;
| | - Carmen Torres
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, 26006 Logroño, Spain;
| |
Collapse
|
11
|
Qiu XQ, Cao KF, Zhang XF, Tong CY, Ma HL, Xu HM, Ma Y, Zou Z, Zhang XL, Li RQ. Defending the homeland: microbiome molecules provide protection to their vertebrate hosts. Future Microbiol 2020; 15:1697-1712. [PMID: 33350865 DOI: 10.2217/fmb-2020-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Aim: The resident bacterial microbiome may shape and protect the health of vertebrate host. An array of molecules secreted by microbiome may contribute to the ecological stability of the microbiome itself. Material & methods: ELISA, radioactivity, immunofluorescence and cytokines measurements were used to observe the bioactivity and stability of colicin Ia level in oviparous and viviparous animal circulation. Results: Colicin Ia, a protein antimicrobial produced by Escherichia coli, is not present in animals at birth, but increases in concentration with the establishment of a stable gut microbiome and drops when the microbiome is experimentally disrupted. Colicin introduced in vivo is transported to tissues at concentrations able to prevent or eliminate bacterial infection. Conclusion: Our findings suggest an unexpected benefit provided by the presence of a resident microbiome in the form of active, circulating, bacterially-synthesized antimicrobial molecules.
Collapse
Affiliation(s)
- Xiao-Qing Qiu
- Laboratory of Biomembrane & Membrane Protein, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ke-Fu Cao
- Laboratory of Biomembrane & Membrane Protein, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiao-Feng Zhang
- Laboratory of Biomembrane & Membrane Protein, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Chong-Yi Tong
- Laboratory of Biomembrane & Membrane Protein, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hong-Lung Ma
- Laboratory of Biomembrane & Membrane Protein, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hui-Min Xu
- Laboratory of Biomembrane & Membrane Protein, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yue Ma
- National Center for Antimicrobial Resistance, National Institute of Food & Drug Inspection, Beijing, 100050, China
| | - Zhen Zou
- Department of Biochemistry & Molecular Biology, Peking Union Medical College, Tsinghua University, Beijing, 100005, China
| | - Xiang-Li Zhang
- Laboratory of Biomembrane & Membrane Protein, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Rong-Qi Li
- Laboratory of Biomembrane & Membrane Protein, West China Hospital, Sichuan University, Chengdu, 610041, China
| |
Collapse
|
12
|
Meza-Segura M, Zaidi MB, Vera-Ponce de León A, Moran-Garcia N, Martinez-Romero E, Nataro JP, Estrada-Garcia T. New Insights Into DAEC and EAEC Pathogenesis and Phylogeny. Front Cell Infect Microbiol 2020; 10:572951. [PMID: 33178627 PMCID: PMC7593697 DOI: 10.3389/fcimb.2020.572951] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/09/2020] [Indexed: 11/13/2022] Open
Abstract
Diarrheagenic E. coli can be separated into six distinct pathotypes, with enteroaggregative (EAEC) and diffusely-adherent E. coli (DAEC) among the least characterized. To gain additional insights into these two pathotypes we performed whole genome sequencing of ten DAEC, nine EAEC strains, isolated from Mexican children with diarrhea, and one EAEC plus one commensal E. coli strains isolated from an adult with diarrhea and a healthy child, respectively. These genome sequences were compared to 85 E. coli genomes available in public databases. The EAEC and DAEC strains segregated into multiple different clades; however, six clades were heavily or exclusively comprised of EAEC and DAEC strains, suggesting a phylogenetic relationship between these two pathotypes. EAEC strains harbored the typical virulence factors under control of the activator AggR, but also several toxins, bacteriocins, and other virulence factors. DAEC strains harbored several iron-scavenging systems, toxins, adhesins, and complement resistance or Immune system evasion factors that suggest a pathogenic paradigm for this poorly understood pathotype. Several virulence factors for both EAEC and DAEC were associated with clinical presentations, not only suggesting the importance of these factors, but also potentially indicating opportunities for intervention. Our studies provide new insights into two distinct but related diarrheagenic organisms.
Collapse
Affiliation(s)
- Mario Meza-Segura
- Molecular Biomedicine Department, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Mussaret B Zaidi
- Infectious Diseases Research Unit, Hospital General O'Horan, Mérida, Mexico.,Department of Epidemiology and Biostatistics, Michigan State University, Lansing, MI, United States
| | | | - Nadia Moran-Garcia
- Molecular Biomedicine Department, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | | | - James P Nataro
- Department of Pediatrics, University of Virginia, Charlottesville, VI, United States
| | - Teresa Estrada-Garcia
- Molecular Biomedicine Department, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| |
Collapse
|
13
|
Bosák J, Hrala M, Micenková L, Šmajs D. Non-antibiotic antibacterial peptides and proteins of Escherichia coli: efficacy and potency of bacteriocins. Expert Rev Anti Infect Ther 2020; 19:309-322. [PMID: 32856960 DOI: 10.1080/14787210.2020.1816824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION The emergence and spread of antibiotic resistance among pathogenic bacteria drives the search for alternative antimicrobial therapies. Bacteriocins represent a potential alternative to antibiotic treatment. In contrast to antibiotics, bacteriocins are peptides or proteins that have relatively narrow spectra of antibacterial activities and are produced by a wide range of bacterial species. Bacteriocins of Escherichia coli are historically classified as microcins and colicins, and, until now, more than 30 different bacteriocin types have been identified and characterized. AREAS COVERED We performed bibliographical searches of online databases to review the literature regarding bacteriocins produced by E. coli with respect to their occurrence, bacteriocin role in bacterial colonization and pathogenicity, and application of their antimicrobial effect. EXPERT OPINION The potential use of bacteriocins for applications in human and animal medicine and the food industry includes (i) the use of bacteriocin-producing probiotic strains, (ii) recombinant production in plants and application in food, and (iii) application of purified bacteriocins.
Collapse
Affiliation(s)
- Juraj Bosák
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Matěj Hrala
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Micenková
- Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| |
Collapse
|
14
|
Mazurek-Popczyk J, Pisarska J, Bok E, Baldy-Chudzik K. Antibacterial Activity of Bacteriocinogenic Commensal Escherichia coli against Zoonotic Strains Resistant and Sensitive to Antibiotics. Antibiotics (Basel) 2020; 9:E411. [PMID: 32679778 PMCID: PMC7400030 DOI: 10.3390/antibiotics9070411] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/05/2020] [Accepted: 07/13/2020] [Indexed: 12/23/2022] Open
Abstract
Antibiotic resistance concerns various areas with high consumption of antibiotics, including husbandry. Resistant strains are transmitted to humans from livestock and agricultural products via the food chain and may pose a health risk. The commensal microbiota protects against the invasion of environmental strains by secretion of bacteriocins, among other mechanisms. The present study aims to characterize the bactericidal potential of bacteriocinogenic Escherichia coli from healthy humans against multidrug-resistant and antibiotic-sensitive strains from pigs and cattle. Bacteriocin production was tested by the double-layer plate method, and bacteriocin genes were identified by the PCR method. At least one bacteriocinogenic E. coli was detected in the fecal samples of 55% of tested individuals, adults and children. Among all isolates (n = 210), 37.1% were bacteriocinogenic and contained genes of colicin (Col) Ib, ColE1, microcin (Mcc) H47, ColIa, ColM, MccV, ColK, ColB, and single ColE2 and ColE7. Twenty-five E. coli carrying various sets of bacteriocin genes were further characterized and tested for their activity against zoonotic strains (n = 60). Strains with ColE7 (88%), ColE1-ColIa-ColK-MccH47 (85%), MccH47-MccV (85%), ColE1-ColIa-ColM (82%), ColE1 (75%), ColM (67%), and ColK (65%) were most active against zoonotic strains. Statistically significant differences in activity toward antibiotic-resistant strains were shown by commensal E. coli carrying MccV, ColK-MccV, and ColIb-ColK. The study demonstrates that bacteriocinogenic commensal E. coli exerts antagonistic activity against zoonotic strains and may constitute a defense line against multidrug-resistant strains.
Collapse
Affiliation(s)
- Justyna Mazurek-Popczyk
- Department of Microbiology and Molecular Biology, Collegium Medicum, University of Zielona Góra, 65-417 Zielona Góra, Poland; (J.P.); (E.B.); (K.B.-C.)
| | | | | | | |
Collapse
|
15
|
Whole Genome Sequencing Analysis of Porcine Faecal Commensal Escherichia coli Carrying Class 1 Integrons from Sows and Their Offspring. Microorganisms 2020; 8:microorganisms8060843. [PMID: 32512857 PMCID: PMC7355456 DOI: 10.3390/microorganisms8060843] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/03/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022] Open
Abstract
Intensive pig production systems often rely on the use of antimicrobials and heavy metal feed additives to maintain animal health and welfare. To gain insight into the carriage of antimicrobial resistance genes (ARGs) in the faecal flora of commercially reared healthy swine, we characterised the genome sequences of 117 porcine commensal E. coli that carried the class 1 integrase gene (intI1+). Isolates were sourced from 42 healthy sows and 126 of their offspring from a commercial breeding operation in Australia in 2017. intI1+ E. coli was detected in 28/42 (67%) sows and 90/126 (71%) piglets. Phylogroup A, particularly clonal complex 10, and phylogroup B1 featured prominently in the study collection. ST10, ST20, ST48 and ST361 were the dominant sequence types. Notably, 113/117 isolates (96%) carried three or more ARGs. Genes encoding resistance to -lactams, aminoglycosides, trimethoprim, sulphonamides, tetracyclines and heavy metals were dominant. ARGs encoding resistance to last-line agents, such as carbapenems and third generation cephalosporins, were not detected. IS26, an insertion sequence noted for its ability to capture and mobilise ARGs, was present in 108/117 (92%) intI1+ isolates, and it played a role in determining class 1 integron structure. Our data shows that healthy Australian pig faeces are an important reservoir of multidrug resistant E. coli that carry genes encoding resistance to multiple first-generation antibiotics and virulence-associated genes.
Collapse
|
16
|
Kohoutova D, Forstlova M, Moravkova P, Cyrany J, Bosak J, Smajs D, Rejchrt S, Bures J. Bacteriocin production by mucosal bacteria in current and previous colorectal neoplasia. BMC Cancer 2020; 20:39. [PMID: 31948419 PMCID: PMC6966821 DOI: 10.1186/s12885-020-6512-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/02/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Optimal therapy for colorectal carcinoma (CRC), a frequently diagnosed malignancy, does not exist. Some of colicins and microcins, ribosomally synthesized peptides by gramnegative bacteria, have shown significant biological activity specifically against different cancer cells in vitro and in vivo conditions. The aim of this prospective study was to evaluate natural colicin and microcin production by large intestinal mucosal bacteria in each stage of colorectal neoplasia and in those with a history of colorectal neoplasia. METHODS A total of 21 patients with non-advanced adenoma (non-a-A; 16/21 with current and 5/21 with history of non-a-A), 20 patients with advanced colorectal adenoma (a-A; 11/20 with current and 9/20 with history of a-A), 22 individuals with CRC (9/22 with current and 13/22 with history of CRC) and 20 controls were enrolled. Mucosal biopsies from the caecum, transverse colon and the rectum were taken during colonoscopy in each individual. Microbiological culture followed. Production of colicins and microcins was evaluated by PCR methods. RESULTS A total of 239 mucosal biopsies were taken. Production of colicins and microcins was significantly more frequent in individuals with non-a-A, a-A and CRC compared to controls. No significant difference in colicin and microcin production was found between patients with current and previous non-a-A, a-A and CRC. Significantly more frequent production of colicins was observed in men compared to women at the stage of colorectal carcinoma. A later onset of increased production of microcins during the adenoma-carcinoma sequence has been observed in males compared to females. CONCLUSIONS Strains isolated from large intestinal mucosa in patients with colorectal neoplasia produce colicins and microcins more frequently compared to controls. Bacteriocin production does not differ between patients with current and previous colorectal neoplasia. Fundamental differences in bacteriocin production have been confirmed between males and females.
Collapse
Affiliation(s)
- Darina Kohoutova
- 2nd Department of Internal Medicine Gastroenterology, Charles University, Faculty of Medicine in Hradec Kralove, University Hospital, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
- The Royal Marsden Hospital NHS Foundation Trust, Fulham Road, Chelsea, London, SW3 6JJ UK
| | - Miroslava Forstlova
- Department of Clinical Microbiology, Charles University, Faculty of Medicine in Hradec Kralove, University Hospital, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| | - Paula Moravkova
- 2nd Department of Internal Medicine Gastroenterology, Charles University, Faculty of Medicine in Hradec Kralove, University Hospital, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| | - Jiri Cyrany
- 2nd Department of Internal Medicine Gastroenterology, Charles University, Faculty of Medicine in Hradec Kralove, University Hospital, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| | - Juraj Bosak
- Department of Biology, Masaryk University, Faculty of Medicine, University Campus at Bohunice, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - David Smajs
- Department of Biology, Masaryk University, Faculty of Medicine, University Campus at Bohunice, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Stanislav Rejchrt
- 2nd Department of Internal Medicine Gastroenterology, Charles University, Faculty of Medicine in Hradec Kralove, University Hospital, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| | - Jan Bures
- 2nd Department of Internal Medicine Gastroenterology, Charles University, Faculty of Medicine in Hradec Kralove, University Hospital, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| |
Collapse
|
17
|
da Cruz Campos AC, Cavallo FM, Andrade NL, van Dijl JM, Couto N, Zrimec J, Lo Ten Foe JR, Rosa ACP, Damasco PV, Friedrich AW, Chlebowicz-Flissikowska MA, Rossen JWA. Determining the Virulence Properties of Escherichia coli ST131 Containing Bacteriocin-Encoding Plasmids Using Short- and Long-Read Sequencing and Comparing Them with Those of Other E. coli Lineages. Microorganisms 2019; 7:E534. [PMID: 31698849 PMCID: PMC6920910 DOI: 10.3390/microorganisms7110534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/29/2019] [Accepted: 11/01/2019] [Indexed: 01/17/2023] Open
Abstract
Escherichia coli ST131 is a clinical challenge due to its multidrug resistant profile and successful global spread. They are often associated with complicated infections, particularly urinary tract infections (UTIs). Bacteriocins play an important role to outcompete other microorganisms present in the human gut. Here, we characterized bacteriocin-encoding plasmids found in ST131 isolates of patients suffering from a UTI using both short- and long-read sequencing. Colicins Ia, Ib and E1, and microcin V, were identified among plasmids that also contained resistance and virulence genes. To investigate if the potential transmission range of the colicin E1 plasmid is influenced by the presence of a resistance gene, we constructed a strain containing a plasmid which had both the colicin E1 and blaCMY-2 genes. No difference in transmission range was found between transformant and wild-type strains. However, a statistically significantly difference was found in adhesion and invasion ability. Bacteriocin-producing isolates from both ST131 and non-ST131 lineages were able to inhibit the growth of other E. coli isolates, including other ST131. In summary, plasmids harboring bacteriocins give additional advantages for highly virulent and resistant ST131 isolates, improving the ability of these isolates to compete with other microbiota for a niche and thereby increasing the risk of infection.
Collapse
Affiliation(s)
- Ana Carolina da Cruz Campos
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil; (A.C.d.C.C.); (N.L.A.); (A.C.P.R.)
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Francis M. Cavallo
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Nathália L. Andrade
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil; (A.C.d.C.C.); (N.L.A.); (A.C.P.R.)
| | - Jan Maarten van Dijl
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Jan Zrimec
- Department of biology and Biological Engineering, Chalmers University of Technology, Chalmersplatsen 4, 412 96 Göteborg, Sweden;
| | - Jerome R. Lo Ten Foe
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Ana C. P. Rosa
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil; (A.C.d.C.C.); (N.L.A.); (A.C.P.R.)
| | - Paulo V. Damasco
- Departamento de Doenças Infecciosas e Parasitárias, Universidade Federal do Estado do Rio de Janeiro, Rua Voluntário da Patria, 21, Rio de Janeiro 941-901107, Brazil;
| | - Alex W. Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Monika A. Chlebowicz-Flissikowska
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - John W. A. Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| |
Collapse
|
18
|
Colicin Z, a structurally and functionally novel colicin type that selectively kills enteroinvasive Escherichia coli and Shigella strains. Sci Rep 2019; 9:11127. [PMID: 31366939 PMCID: PMC6668396 DOI: 10.1038/s41598-019-47488-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/16/2019] [Indexed: 01/14/2023] Open
Abstract
Colicin production in Escherichia coli (E. coli) strains represents an important trait with regard to microbial survival and competition in the complex intestinal environment. A novel colicin type, colicin Z (26.3 kDa), was described as a product of an original producer, extraintestinal E. coli B1356 strain, isolated from the anorectal abscess of a 17 years-old man. The 4,007 bp plasmid (pColZ) was completely sequenced and colicin Z activity (cza) and colicin Z immunity (czi) genes were identified. The cza and czi genes are transcribed in opposite directions and encode for 237 and 151 amino acid-long proteins, respectively. Colicin Z shows a narrow inhibitory spectrum, being active only against enteroinvasive E. coli (EIEC) and Shigella strains via CjrC receptor recognition and CjrB- and ExbB-, ExbD-mediated colicin translocation. All tested EIEC and Shigella strains isolated between the years 1958–2010 were sensitive to colicin Z. The lethal effect of colicin Z was found to be directed against cell wall peptidoglycan (PG) resulting in PG degradation, as revealed by experiments with Remazol Brilliant Blue-stained purified peptidoglycans and with MALDI-TOF MS analyses of treated PG. Colicin Z represents a new class of colicins that is structurally and functionally distinct from previously studied colicin types.
Collapse
|
19
|
Bosák J, Hrala M, Pirková V, Micenková L, Čížek A, Smola J, Kučerová D, Vacková Z, Budinská E, Koláčková I, Šmajs D. Porcine pathogenic Escherichia coli strains differ from human fecal strains in occurrence of bacteriocin types. Vet Microbiol 2019; 232:121-127. [PMID: 31030835 DOI: 10.1016/j.vetmic.2019.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 04/04/2019] [Accepted: 04/05/2019] [Indexed: 01/09/2023]
Abstract
Enterotoxigenic and Shiga-toxigenic Escherichia coli (i.e., ETEC and STEC) are important causative agents of human and animal diseases. In humans, infections range from mild diarrhea to severe life-threating conditions, while infections of piglets result in lower weight gain and higher pig mortality with the accompanying significant economic losses. In this study, frequencies of four phylogenetic groups, fourteen virulence- and thirty bacteriocin determinants were analyzed in a set of 443 fecal E. coli isolates from diseased pigs and compared to a previously characterized set of 1283 human fecal E. coli isolates collected in the same geographical region. In addition, these characteristics were compared among ETEC, STEC, and non-toxigenic porcine E. coli isolates. Phylogenetic group A was prevalent among porcine pathogenic E. coli isolates, whereas the frequency of phylogroup B2, adhesion/invasion (fimA, pap, sfa, afaI, ial, ipaH, and pCVD432) and iron acquisition (aer and iucC) determinants were less frequent compared to human fecal isolates. Additionally, porcine isolates differed from human isolates relative to the spectrum of produced bacteriocins. While human fecal isolates encoded colicins and microcins with a similar prevalence, porcine pathogenic E. coli isolates produced predominantly colicins (94% of isolates); especially colicins B (42.6%), M (40.1%), and Ib (34.0%), which are encoded on large conjugative plasmids. The observed high prevalence of these colicin determinants suggests the importance of large colicinogenic plasmids and/or the importance of colicin production in intestinal inflammatory conditions.
Collapse
Affiliation(s)
- Juraj Bosák
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Matěj Hrala
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Viktória Pirková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Micenková
- Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Alois Čížek
- Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Jiří Smola
- Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | | | | | - Eva Budinská
- Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
| |
Collapse
|
20
|
Kurnick SA, Mannion AJ, Feng Y, Madden CM, Chamberlain P, Fox JG. Genotoxic Escherichia coli Strains Encoding Colibactin, Cytolethal Distending Toxin, and Cytotoxic Necrotizing Factor in Laboratory Rats. Comp Med 2019; 69:103-113. [PMID: 30902120 PMCID: PMC6464076 DOI: 10.30802/aalas-cm-18-000099] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/13/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023]
Abstract
Although many Escherichia coli strains are considered commensals in mammals, strains encoding the cyclomodulin genotoxins are associated with clinical and subclinical disease in the urogenital and gastrointestinal tracts, meningitis, and inflammatory disorders. These genotoxins include the polyketide synthase (pks) pathogenicity island, cytolethal distending toxin (cdt), and hemolysin-associated cytotoxic necrotizing factor (cnf). E. coli strains are not excluded from rodents housed under SPF conditions in academic or vendor facilities. This study isolated and characterized genotoxin-encoding E. coli from laboratory rats obtained from 4 academic institutions and 3 vendors. A total of 69 distinct E. coli isolates were cultured from feces, rectal swab, nares, or vaginal swab of 52 rats and characterized biochemically. PCR analysis for cyclomodulin genes and phylogroup was performed on all 69 isolates. Of the 69 isolates, 45 (65%) were positive for pks, 20/69 (29%) were positive for cdt, and 4 (6%) were positive for cnf. Colibactin was the sole genotoxin identified in 21 of 45 pks+ isolates (47%), whereas cdt or cnf was also present in the remaining 24 isolates (53%); cdt and cnf were never present together or without pks. All genotoxin-associated strains were members of pathogen-associated phylogroup B2. Fisher exact and χ² tests demonstrated significant differences in genotoxin prevalence and API code distribution with regard to vendor. Select E. coli isolates were characterized by HeLa cell in vitro cytotoxicity assays, serotyped, and whole-genome sequenced. All isolates encoding cyclomodulins induced megalocytosis. Serotypes corresponded with vendor origin and cyclomodulin composition, with the cnf+ serotype representing a known human uropathogen. Whole-genome sequencing confirmed the presence of complete pks, cdt, and hemolysin-cnf pathogenicity islands. These findings indicate that genotoxin-encoding E. coli colonize laboratory rats from multiple commercial vendors and academic institutions and suggest the potential to contribute to clinical disease and introduce confounding variables into experimental rat models.
Collapse
Affiliation(s)
- Susanna A Kurnick
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Anthony J Mannion
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Yan Feng
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Carolyn M Madden
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Paul Chamberlain
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts;,
| |
Collapse
|
21
|
Tanhaeian A, Damavandi MS, Mansury D, Ghaznini K. Expression in eukaryotic cells and purification of synthetic gene encoding enterocin P: a bacteriocin with broad antimicrobial spectrum. AMB Express 2019; 9:6. [PMID: 30617751 PMCID: PMC6323060 DOI: 10.1186/s13568-018-0729-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/31/2018] [Indexed: 01/13/2023] Open
Abstract
Due to the emergence of multidrug-resistant bacteria, treatment options for infectious diseases are decreasing. Bacteriocins are small antimicrobial peptides produced by numerous bacteria that offer alternative therapeutic strategies to combat multidrug-resistant bacterial infections. We evaluated the cloning, functional expression, and antimicrobial activities of enterocin P (EntP), a class II bacteriocin member, in Chinese hamster ovary (CHO) cells. A synthetic gene matching CHO cell codon usage was designed from the known mature amino acid sequence of EntP and cloned into the protein expression vector pcDNA™3.1(+). CHO cells were transformed with the recombinant plasmid and cultured, and the recombinant protein was purified by affinity chromatography. Antimicrobial activities of the recombinant EntP were evaluated on Gram-positive, Gram-negative, and multidrug-resistant pathogens. Recombinant EntP inhibited growth of a variety of bacteria, including pathogenic species known to cause nosocomial infections, often with multidrug-resistant strains. In addition, recombinant EntP demonstrated broad antimicrobial activities in both high salt medium and human plasma and was stable at high temperatures. The broad antimicrobial activity and stability of EntP make it an attractive therapeutic candidate, particularly for treatment of multidrug-resistant bacterial infections.
Collapse
|
22
|
Askari N, Ghanbarpour R. Molecular investigation of the colicinogenic Escherichia coli strains that are capable of inhibiting E. coli O157:H7 in vitro. BMC Vet Res 2019; 15:14. [PMID: 30616623 PMCID: PMC6323730 DOI: 10.1186/s12917-018-1771-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 12/28/2018] [Indexed: 11/23/2022] Open
Abstract
Background Escherichia coli O157:H7 is a highly virulent human pathogen with severe consequences following infection, which claims many lives worldwide. A suggested method for controlling this bacterium is the competitive elimination through using probiotic bacteria that prevent its colonization. Some nonpathogenic E. coli strains that produce antibacterial colicins are among these probiotic bacteria. We aimed to isolate and characterize the colicinogenic E. coli strains from diarrheic and healthy sheep that inhibit E. coli O157:H7, which could be used as possible probiotic sources. A total of 292 E. coli isolates (146 from each diarrheic and healthy sheep) were screened for the presence of colicin and virulence genes. The phylogenetic group/subgroup determination was performed by PCR. In vitro evaluation of inhibitory effect of colicinogenic isolates on E. coli O157:H7 was done phenotypically. Results The frequency of diarrhea associated colicinogenic E. coli isolates was significantly higher than those isolated from healthy sheep. An association between ETEC and the genes coding for colicin-V & colicin-Iab in diarrheic E. coli isolates was observed. Moreover, there was an association between ipaH and Colicin-V encoding genes. Furthermore, E. coli isolates showing bacteriocinogeny while possessing no virulence genes had a frequency of 97.67 and 11.94% in healthy and diarrheic isolates, respectively. Of these strains, five isolates (3.42%) from diarrheic and twenty-five isolates (17.12%) from healthy sheep inhibited O157:H7 strain. Additionally, colicin E1 and colicin Iab genes were more prevalent in B1 phylogroup. Conclusions These results signified that healthy sheep could be considered as a potential source for anti-O175:H7 bacterial isolates.
Collapse
Affiliation(s)
- Nasrin Askari
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Reza Ghanbarpour
- Molecular Microbiology Research Group, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran.
| |
Collapse
|
23
|
Bosák J, Micenková L, Hrala M, Pomorská K, Kunova Bosakova M, Krejci P, Göpfert E, Faldyna M, Šmajs D. Colicin F Y inhibits pathogenic Yersinia enterocolitica in mice. Sci Rep 2018; 8:12242. [PMID: 30115964 PMCID: PMC6095899 DOI: 10.1038/s41598-018-30729-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/06/2018] [Indexed: 12/26/2022] Open
Abstract
Yersiniosis belongs to the common foodborne diseases around the world, and frequently manifests as diarrhea that can be treated with probiotics. Colicin FY is an antibacterial agent produced by bacteria and it is capable of specific growth inhibition of Yersinia enterocolitica, the causative agent of gastrointestinal yersiniosis. In this study, recombinant E. coli producing colicin FY were constructed, using both known probiotic strains EcH22 and EcColinfant, and the newly isolated murine strains Ec1127 and Ec1145. All E. coli strains producing colicin FY inhibited growth of pathogenic Y. enterocolitica during co-cultivation in vitro. In dysbiotic mice treated with streptomycin, E. coli strains producing colicin FY inhibited progression of Y. enterocolitica infections. This growth inhibition was not observed in mice with normal gut microflora, likely due to insufficient colonization capacity of E. coli strains and/or due to spatial differences in intestinal niches. Isogenic Y. enterocolitica producing colicin FY was constructed and shown to inhibit pathogenic Y. enterocolitica in mice with normal microflora. Evidence of in vivo antimicrobial activity of colicin FY may have utility in the treatment of Y. enterocolitica infections.
Collapse
Affiliation(s)
- Juraj Bosák
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Micenková
- Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Matěj Hrala
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Katarína Pomorská
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | | | - Pavel Krejci
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | | | | | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
| |
Collapse
|
24
|
Escherichia coli isolates from patients with inflammatory bowel disease: ExPEC virulence- and colicin-determinants are more frequent compared to healthy controls. Int J Med Microbiol 2018; 308:498-504. [PMID: 29735381 DOI: 10.1016/j.ijmm.2018.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 04/04/2018] [Accepted: 04/30/2018] [Indexed: 12/12/2022] Open
Abstract
A set of 178 Escherichia coli isolates taken from patients with inflammatory bowel disease (IBD) was analyzed for bacteriocin production and tested for the prevalence of 30 bacteriocin and 22 virulence factor determinants. Additionally, E. coli phylogenetic groups were also determined. Pulsed-field gel electrophoresis (PFGE) was used for exclusion of clonal character of isolates. Results were compared to data from a previously published analysis of 1283 fecal commensal E. coli isolates. The frequency of bacteriocinogenic isolates (66.9%) was significantly higher in IBD E. coli compared to fecal commensal E. coli isolates (54.2%, p < 0.01). In the group of IBD E. coli isolates, a higher prevalence of determinants for group B colicins (i.e., colicins B, D, Ia, Ib, M, and 5/10) (p < 0.01), including a higher prevalence of the colicin B determinant (p < 0.01) was found. Virulence factor determinants encoding fimbriae (fimA, 91.0%; pap, 27.5%), cytotoxic necrotizing factor (cnf1, 11.2%), aerobactin synthesis (aer, 43.3%), and the locus associated with invasivity (ial, 9.0%) were more prevalent in IBD E. coli (p < 0.05 for all five determinants). E. coli isolates from IBD mucosal biopsies were more frequently bacteriocinogenic (84.6%, p < 0.01) compared to fecal IBD isolates and fecal commensal E. coli. PFGE analysis revealed clusters specific for IBD E. coli isolates (n = 11), for fecal isolates (n = 13), and clusters containing both IBD and fecal isolates (n = 10). ExPEC (Extraintestinal Pathogenic E. coli) virulence and colicin determinants appear to be important characteristics of IBD E. coli isolates, especially the E. coli isolates obtained directly from biopsy samples.
Collapse
|
25
|
Grillová L, Sedláček I, Páchníková G, Staňková E, Švec P, Holochová P, Micenková L, Bosák J, Slaninová I, Šmajs D. Characterization of four Escherichia albertii isolates collected from animals living in Antarctica and Patagonia. J Vet Med Sci 2017; 80:138-146. [PMID: 29249728 PMCID: PMC5797873 DOI: 10.1292/jvms.17-0492] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Escherichia albertii is a recently discovered species with a limited number of well characterized strains. The aim of this study was to characterize four of the E. albertii strains, which were among 41 identified Escherichia strains isolated from the feces of living animals on James Ross Island, Antarctica, and Isla Magdalena, Patagonia. Sequencing of 16S rDNA, automated ribotyping, and rep-PCR were used to identify the four E. albertii isolates. Phylogenetic analyses based on multi-locus sequence typing showed these isolates to be genetically most similar to the members of E. albertii phylogroup G3. These isolates encoded several virulence factors including those, which are characteristic of E. albertii (cytolethal distending toxin and intimin) as well as bacteriocin determinants that typically have a very low prevalence in E. coli strains (D, E7). Moreover, E. albertii protein extracts caused cell cycle arrest in human cell line A375, probably because of cytolethal distending toxin activity.
Collapse
Affiliation(s)
- Linda Grillová
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00, Brno, Czech Republic
| | - Ivo Sedláček
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Gabriela Páchníková
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00, Brno, Czech Republic
| | - Eva Staňková
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Pavel Švec
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Pavla Holochová
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Lenka Micenková
- Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Juraj Bosák
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00, Brno, Czech Republic
| | - Iva Slaninová
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00, Brno, Czech Republic
| |
Collapse
|
26
|
Feng Y, Mannion A, Madden CM, Swennes AG, Townes C, Byrd C, Marini RP, Fox JG. Cytotoxic Escherichia coli strains encoding colibactin and cytotoxic necrotizing factor (CNF) colonize laboratory macaques. Gut Pathog 2017; 9:71. [PMID: 29225701 PMCID: PMC5718112 DOI: 10.1186/s13099-017-0220-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 11/21/2017] [Indexed: 02/06/2023] Open
Abstract
Background Many Escherichia coli strains are considered to be a component of the normal flora found in the human and animal intestinal tracts. While most E. coli strains are commensal, some strains encode virulence factors that enable the bacteria to cause intestinal and extra-intestinal clinically-relevant infections. Colibactin, encoded by a genomic island (pks island), and cytotoxic necrotizing factor (CNF), encoded by the cnf gene, are genotoxic and can modulate cellular differentiation, apoptosis and proliferation. Some commensal and pathogenic pks+ and cnf+ E. coli strains have been associated with inflammation and cancer in humans and animals. Results In the present study, E. coli strains encoding colibactin and CNF were identified in macaque samples. We performed bacterial cultures utilizing rectal swabs and extra-intestinal samples from clinically normal macaques. A total of 239 E. coli strains were isolated from 266 macaques. The strains were identified biochemically and selected isolates were serotyped as O88:H4, O25:H4, O7:H7, OM:H14, and OM:H16. Specific PCR for pks and cnf1 gene amplification, and phylogenetic group identification were performed on all E. coli strains. Among the 239 isolates, 41 (17.2%) were pks+/cnf1−, 19 (7.9%) were pks−/cnf1+, and 31 (13.0%) were pks+/cnf1+. One hundred forty-eight (61.9%) E. coli isolates were negative for both genes (pks−/cnf1−). In total, 72 (30.1%) were positive for pks genes, and 50 (20.9%) were positive for cnf1. No cnf2+ isolates were detected. Both pks+ and cnf1+ E. coli strains belonged mainly to phylogenetic group B2, including B21. Colibactin and CNF cytotoxic activities were observed using a HeLa cell cytotoxicity assay in representative isolates. Whole genome sequencing of 10 representative E. coli strains confirmed the presence of virulence factors and antibiotic resistance genes in rhesus macaque E. coli isolates. Conclusions Our findings indicate that colibactin- and CNF-encoding E. coli colonize laboratory macaques and can potentially cause clinical and subclinical diseases that impact macaque models. Electronic supplementary material The online version of this article (10.1186/s13099-017-0220-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yan Feng
- Division of Comparative Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 16-825, Cambridge, MA 02139 USA
| | - Anthony Mannion
- Division of Comparative Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 16-825, Cambridge, MA 02139 USA
| | - Carolyn M Madden
- Division of Comparative Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 16-825, Cambridge, MA 02139 USA
| | - Alton G Swennes
- Division of Comparative Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 16-825, Cambridge, MA 02139 USA.,Present Address: Center for Comparative Medicine, Baylor College of Medicine, Houston, TX USA
| | - Catherine Townes
- Division of Comparative Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 16-825, Cambridge, MA 02139 USA
| | - Charles Byrd
- Division of Comparative Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 16-825, Cambridge, MA 02139 USA.,Present Address: North Powers Animal Hospital, Colorado Springs, CO USA
| | - Robert P Marini
- Division of Comparative Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 16-825, Cambridge, MA 02139 USA
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 16-825, Cambridge, MA 02139 USA
| |
Collapse
|
27
|
Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models. PLoS Comput Biol 2017; 13:e1005652. [PMID: 28715501 PMCID: PMC5536347 DOI: 10.1371/journal.pcbi.1005652] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 07/31/2017] [Accepted: 06/21/2017] [Indexed: 11/28/2022] Open
Abstract
Bacteria exploit an arsenal of antimicrobial peptides and proteins to compete with each other. Three main competition systems have been described: type six secretion systems (T6SS); contact dependent inhibition (CDI); and bacteriocins. Unlike T6SS and CDI systems, bacteriocins do not require contact between bacteria but are diffusible toxins released into the environment. Identified almost a century ago, our understanding of bacteriocin distribution and prevalence in bacterial populations remains poor. In the case of protein bacteriocins, this is because of high levels of sequence diversity and difficulties in distinguishing their killing domains from those of other competition systems. Here, we develop a robust bioinformatics pipeline exploiting Hidden Markov Models for the identification of nuclease bacteriocins (NBs) in bacteria of which, to-date, only a handful are known. NBs are large (>60 kDa) toxins that target nucleic acids (DNA, tRNA or rRNA) in the cytoplasm of susceptible bacteria, usually closely related to the producing organism. We identified >3000 NB genes located on plasmids or on the chromosome from 53 bacterial species distributed across different ecological niches, including human, animals, plants, and the environment. A newly identified NB predicted to be specific for Pseudomonas aeruginosa (pyocin Sn) was produced and shown to kill P. aeruginosa thereby validating our pipeline. Intriguingly, while the genes encoding the machinery needed for NB translocation across the cell envelope are widespread in Gram-negative bacteria, NBs are found exclusively in γ-proteobacteria. Similarity network analysis demonstrated that NBs fall into eight groups each with a distinct arrangement of protein domains involved in import. The only structural feature conserved across all groups was a sequence motif critical for cell-killing that is generally not found in bacteriocins targeting the periplasm, implying a specific role in translocating the nuclease to the cytoplasm. Finally, we demonstrate a significant association between nuclease colicins, NBs specific for Escherichia coli, and virulence factors, suggesting NBs play a role in infection processes, most likely by enabling pathogens to outcompete commensal bacteria. Bacteria deploy a variety of antimicrobials to kill competing bacteria. Nuclease bacteriocins are a miscellaneous group of protein toxins that target closely related species, cleaving nucleic acids in the cytoplasm. It has proved difficult to establish how widespread bacteriocins are in bacterial populations due to the high diversity of bacteriocin-encoding genes. Here, we describe an in silico approach to identify nuclease bacteriocin genes in bacterial genomes and to distinguish them from other competition toxins. Bacteria that contain nuclease bacteriocin genes are found in many different types of environment but are prevalent in niches where interbacterial competition is likely to be high. Nuclease bacteriocins are found exclusively in γ-proteobacteria and are particularly abundant in the Enterobacteriaceae and Pseudomonadaceae families. Although the sequences we identify are indeed diverse (<20% sequence identity between protein families) we show that all nuclease bacteriocins contain an invariant motif, usually within a common structural scaffold, that is implicated in translocating the cytotoxic nuclease to the cytoplasm. Finally, we show that nuclease bacteriocins in pathogenic E. coli are strongly associated with virulence factors suggesting they play a role in pathogenicity mechanisms.
Collapse
|
28
|
The therapeutic potential of bacteriocins as protein antibiotics. Emerg Top Life Sci 2017; 1:65-74. [PMID: 33525816 PMCID: PMC7243282 DOI: 10.1042/etls20160016] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 03/14/2017] [Accepted: 03/16/2017] [Indexed: 02/07/2023]
Abstract
The growing incidence of antibiotic-resistant Gram-negative bacterial infections poses a serious threat to public health. Molecules that have yet to be exploited as antibiotics are potent protein toxins called bacteriocins that are produced by Gram-negative bacteria during competition for ecological niches. This review discusses the state of the art regarding the use for therapeutic purposes of two types of Gram-negative bacteriocins: colicin-like bacteriocins (CLBs) and tailocins. In addition to in vitro data, the potency of eight identified CLBs or tailocins has been demonstrated in diverse animal models of infection with no adverse effects for the host. Although the characteristics of bacteriocins will need further study, results obtained thus far regarding their in vivo potency, immunogenicity and low levels of resistance are encouraging. This leads the way for the development of novel treatments using bacteriocins as protein antibiotics.
Collapse
|
29
|
Micenková L, Beňová A, Frankovičová L, Bosák J, Vrba M, Ševčíková A, Kmeťová M, Šmajs D. Human Escherichia coli isolates from hemocultures: Septicemia linked to urogenital tract infections is caused by isolates harboring more virulence genes than bacteraemia linked to other conditions. Int J Med Microbiol 2017; 307:182-189. [DOI: 10.1016/j.ijmm.2017.02.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/17/2017] [Accepted: 02/24/2017] [Indexed: 12/24/2022] Open
|
30
|
Kaczmarek A, Skowron K, Budzyńska A, Grudlewska K, Gospodarek-Komkowska E. Virulence genes and antimicrobial susceptibility of lactose-negative and lactose-positive strains of Escherichia coli isolated from pregnant women and neonates. Folia Microbiol (Praha) 2017; 62:363-371. [PMID: 28236177 PMCID: PMC5579066 DOI: 10.1007/s12223-017-0506-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/10/2017] [Indexed: 11/25/2022]
Abstract
Escherichia coli can cause serious infections in the neonates and pregnant women. Although E. coli is widely studied, E. coli lactose-negative (lac−) strains have been rarely described before. So, the aim of this study was to compare lac− and lactose-positive (lac+) E. coli strains in respect of antimicrobial susceptibility and the frequency of virulence genes (VGs). The study included 58 lac+ and 58 lac− E. coli strains isolated from pregnant women and neonates. Culture and the results of biochemical reactions were conducted for lac− and lac+ E. coli identification and differentiation. Disc diffusion test was performed to study the antimicrobial susceptibility of the isolates, and PCR was used to detect VGs. Resistance to at least one of the tested antibiotics was found among 14 (25.9%) E. coli lac+ and in 26 (44.9%) E. coli lac− strains. Both lac+ and lac− E. coli strains were mostly resistant to ampicillin (22.4 and 39.7%) and ticarcillin (20.7 and 39.7%). None of the tested strains produced extended-spectrum β-lactamases (ESBLs). Genes fimH, fimA, iutA, sfa/foc, neuC, ibeA, and hlyF were detected, respectively, in 96.6, 82.8, 32.8, 24.1, 22.4, 12.1, and 6.9% of lac+ E. coli strains and in 94.8, 86.2, 48.3, 19.0, 8.6, 8.6, and 1.7% of lac− strains. The antimicrobial susceptibility and the pathogenic potential of both tested groups of E. coli strains are similar. Therefore, omitting E. coli lac− strains as a potential etiological agent of infections may pose a threat to the health and life of both mothers and neonates.
Collapse
Affiliation(s)
- Agnieszka Kaczmarek
- Department of Microbiology, Nicolaus Copernicus University in Torun, Ludwik Rydygier Collegium Medicum, 9 M. Skłodowskiej-Curie Street, 85-094, Bydgoszcz, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Nicolaus Copernicus University in Torun, Ludwik Rydygier Collegium Medicum, 9 M. Skłodowskiej-Curie Street, 85-094, Bydgoszcz, Poland.
| | - Anna Budzyńska
- Department of Microbiology, Nicolaus Copernicus University in Torun, Ludwik Rydygier Collegium Medicum, 9 M. Skłodowskiej-Curie Street, 85-094, Bydgoszcz, Poland
| | - Katarzyna Grudlewska
- Department of Microbiology, Nicolaus Copernicus University in Torun, Ludwik Rydygier Collegium Medicum, 9 M. Skłodowskiej-Curie Street, 85-094, Bydgoszcz, Poland
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Nicolaus Copernicus University in Torun, Ludwik Rydygier Collegium Medicum, 9 M. Skłodowskiej-Curie Street, 85-094, Bydgoszcz, Poland
| |
Collapse
|
31
|
Micenková L, Bosák J, Vrba M, Ševčíková A, Šmajs D. Human extraintestinal pathogenic Escherichia coli strains differ in prevalence of virulence factors, phylogroups, and bacteriocin determinants. BMC Microbiol 2016; 16:218. [PMID: 27646192 PMCID: PMC5028950 DOI: 10.1186/s12866-016-0835-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 09/13/2016] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The study used a set of 407 human extraintestinal pathogenic E. coli strains (ExPEC) isolated from (1) skin and soft tissue infections, (2) respiratory infections, (3) intra-abdominal infections, and (4) genital smears. The set was tested for bacteriocin production, for prevalence of bacteriocin and virulence determinants, and for phylogenetic typing. Results obtained from the group of ExPEC strains were compared to data from our previously published analyses of 1283 fecal commensal E. coli strains. RESULTS The frequency of bacteriocinogeny was significantly higher in the set of ExPEC strains (63.1 %), compared to fecal E. coli (54.2 %; p < 0.01). Microcin producers and microcin determinants dominated in ExPEC strains, while colicin producers and colicin determinants were more frequent in fecal E. coli (p < 0.01). Higher production of microcin M and lower production of microcin B17, colicin Ib, and Js was detected in the set of ExPEC strains. ExPEC strains had a significantly higher prevalence of phylogenetic group B2 (52.6 %) compared to fecal E. coli strains (38.3 %; p < 0.01). CONCLUSIONS Human ExPEC strains were shown to differ from human fecal strains in a number of parameters including bacteriocin production, prevalence of several bacteriocin and virulence determinants, and prevalence of phylogenetic groups. Differences in these parameters were also identified within subgroups of ExPEC strains of diverse origin. While some microcin determinants (mM, mH47) were associated with virulent strains, other bacteriocin types (mB17, Ib, and Js) were associated with fecal flora.
Collapse
Affiliation(s)
- Lenka Micenková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic
| | - Juraj Bosák
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic
| | - Martin Vrba
- Department of Clinical Microbiology, Faculty Hospital Brno, Jihlavská 20, 625 00 Brno, Czech Republic
| | - Alena Ševčíková
- Department of Clinical Microbiology, Faculty Hospital Brno, Jihlavská 20, 625 00 Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic
| |
Collapse
|
32
|
Bosák J, Micenková L, Doležalová M, Šmajs D. Colicins U and Y inhibit growth of Escherichia coli strains via recognition of conserved OmpA extracellular loop 1. Int J Med Microbiol 2016; 306:486-494. [PMID: 27510856 DOI: 10.1016/j.ijmm.2016.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/28/2016] [Accepted: 07/31/2016] [Indexed: 01/04/2023] Open
Abstract
Interactions of colicins U and Y with the OmpA (Outer membrane protein A) receptor molecule were studied using site-directed mutagenesis and colicin binding assay. A systematic mutagenesis of the colicin-susceptible OmpA sequence from Escherichia coli (OmpAEC) to the colicin-resistant OmpA sequence from Serratia marcescens (OmpASM) was performed in regions corresponding to extracellular OmpA loops 1-4. Susceptibility to colicins U and Y was significantly affected by the OmpA mutation in loop 1. As with functional analysis, a decrease in binding capacity of His-tagged colicin U was found for recombinant OmpA with a mutated segment in loop 1 compared to control OmpAEC. To verify the importance of the identified amino acid residues in OmpA loop 1, we introduced loop 1 from OmpAEC into OmpASM, which resulted in the substantial increase of susceptibility to colicins U and Y. In addition, colicins U and Y were tested against a panel of 118 bacteriocin non-producing strains of four Escherichia species, including E. coli (39 strains), E. fergusonii (10 strains), E. hermannii (42 strains), and E. vulneris (27 strains). A majority (82%) of E. coli strains was susceptible to colicins U and Y. Interestingly, colicins U and Y also inhibited all of the 30 tested multidrug-resistant E. coli O25b-ST131 isolates. These findings, together with the fact that OmpA loop 1 is important for bacterial virulence and is evolutionary conserved, offer the potential of using colicins U and Y as specific anti-OmpA loop 1 directed antibacterial proteins.
Collapse
Affiliation(s)
- Juraj Bosák
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic
| | - Lenka Micenková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic
| | - Magda Doležalová
- Department of Environment Protection Engineering, Faculty of Technology, Tomas Bata University in Zlín, T. G. Masaryk square 275, Zlín, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic.
| |
Collapse
|
33
|
Micenková L, Bosák J, Štaudová B, Kohoutová D, Čejková D, Woznicová V, Vrba M, Ševčíková A, Bureš J, Šmajs D. Microcin determinants are associated with B2 phylogroup of human fecal Escherichia coli isolates. Microbiologyopen 2016; 5:490-8. [PMID: 26987297 PMCID: PMC4906000 DOI: 10.1002/mbo3.345] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/22/2016] [Accepted: 02/03/2016] [Indexed: 12/30/2022] Open
Abstract
Escherichia coli strains are classified into four main phylogenetic groups (A, B1, B2, and D) and strains of these phylogroups differ in a number of characteristics. This study tested whether human fecal E. coli isolates belonging to different phylogroups differ in prevalence of bacteriocinogenic isolates and prevalence of individual bacteriocinogenic determinants. A set of 1283 fecal E. coli isolates from patients with different diseases was tested for the presence of DNA regions allowing classification into E. coli phylogroups and for the ability to produce bacteriocins (23 colicins and 7 microcins). Of the isolates tested, the most common was phylogroup B2 (38.3%) followed by phylogroups A (28.3%), D (26.3%) and B1 (7.2%). Altogether, 695 bacteriocin producers were identified representing 54.2% of all tested isolates. The highest prevalence of bacteriocin producers was found in group B2 (60.3%) and the lowest in group B1 (44.6%). Determinants encoding colicins E1, Ia, and microcin mV were most common in phylogroup A, determinants encoding microcins mM and mH47 were most common in phylogroup B2, and determinant encoding mB17 was most common in phylogroup D. The highest prevalence of bacteriocinogeny was found in phylogroup B2, suggesting that bacteriocinogeny and especially the synthesis of microcins was associated with virulent and resident E. coli strains.
Collapse
Affiliation(s)
- Lenka Micenková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic
| | - Juraj Bosák
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic
| | - Barbora Štaudová
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic
| | - Darina Kohoutová
- 2nd Department of Internal Medicine - Gastroenterology, Charles University in Prague, Faculty of Medicine at Hradec Králové, University Teaching Hospital, Sokolská 581, 500 05, Hradec Králové, Czech Republic
| | - Darina Čejková
- Department of Immunology, Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic
| | - Vladana Woznicová
- Department of Microbiology, Faculty of Medicine, Masaryk University and St. Anne's University Hospital, Pekarˇská 53, 656 91, Brno, Czech Republic
| | - Martin Vrba
- Department of Clinical Microbiology, Faculty Hospital Brno, Jihlavská 20, 625 00, Brno, Czech Republic
| | - Alena Ševčíková
- Department of Clinical Microbiology, Faculty Hospital Brno, Jihlavská 20, 625 00, Brno, Czech Republic
| | - Jan Bureš
- 2nd Department of Internal Medicine - Gastroenterology, Charles University in Prague, Faculty of Medicine at Hradec Králové, University Teaching Hospital, Sokolská 581, 500 05, Hradec Králové, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic
| |
Collapse
|
34
|
Murphy SF, Thumbikat P. The importance of the "V"-Factor: Escherichia coli bacteremia and sepsis. Virulence 2016; 6:107-8. [PMID: 25831399 DOI: 10.1080/21505594.2014.1000766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Stephen F Murphy
- a Urology and Pathology; Urology and Pathology ; Chicago , IL USA
| | | |
Collapse
|
35
|
Štaudová B, Micenková L, Bosák J, Hrazdilová K, Slaninková E, Vrba M, Ševčíková A, Kohoutová D, Woznicová V, Bureš J, Šmajs D. Determinants encoding fimbriae type 1 in fecal Escherichia coli are associated with increased frequency of bacteriocinogeny. BMC Microbiol 2015; 15:201. [PMID: 26445407 PMCID: PMC4594643 DOI: 10.1186/s12866-015-0530-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 09/25/2015] [Indexed: 01/03/2023] Open
Abstract
Background To screen whether E. coli strains encoding type 1 fimbriae, isolated from fecal microflora, produce bacteriocins more often relative to fimA-negative E. coli strains of similar origin. Methods PCR assays were used to detect presence of genes encoding 30 bacteriocin determinants (23 colicin- and 7 microcin-encoding genes) and 18 virulence determinants in 579 E. coli strains of human and animal origin isolated from hospitals and animal facilities in the Czech and Slovak Republic. E. coli strains were also classified into phylogroups (A, B1, B2 and D). Results fimA-negative E. coli strains (defined as those possessing none of the 18 tested virulence determinants) were compared to fimA-positive E. coli strains (possessing fimA as the only detected virulence determinant). Strains with identified bacteriocin genes were more commonly found among fimA-positive E. coli strains (35.6 %) compared to fimA-negative E. coli strains (21.9 %, p < 0.01) and this was true for both colicin and microcin determinants (p = 0.02 and p < 0.01, respectively). In addition, an increased number of strains encoding colicin E1 were found among fimA-positive E. coli strains (p < 0.01). Conclusions fimA-positive E. coli strains produced bacteriocins (colicins and microcins) more often compared to fimA-negative strains of similar origin. Since type 1 fimbriae of E. coli have been shown to mediate adhesion to epithelial host cells and help colonize the intestines, bacteriocin synthesis appears to be an additional feature of colonizing E. coli strains. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0530-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Barbora Štaudová
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic.
| | - Lenka Micenková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic.
| | - Juraj Bosák
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic.
| | - Kristýna Hrazdilová
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1/3, 612 42, Brno, Czech Republic. .,CEITEC - Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1/3, 612 42, Brno, Czech Republic.
| | - Eva Slaninková
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1/3, 612 42, Brno, Czech Republic.
| | - Martin Vrba
- Department of Clinical Microbiology, Faculty Hospital Brno, Jihlavská 20, 625 00, Brno, Czech Republic.
| | - Alena Ševčíková
- Department of Clinical Microbiology, Faculty Hospital Brno, Jihlavská 20, 625 00, Brno, Czech Republic.
| | - Darina Kohoutová
- 2nd Department of Internal Medicine - Gastroenterology, Charles University in Praha, Faculty of Medicine at Hradec Kralové, University Teaching Hospital, Sokolská 581, Hradec Kralové, 500 05, Czech Republic.
| | - Vladana Woznicová
- Department of Microbiology, Faculty of Medicine, Masaryk University and St. Anne's University Hospital, Pekařská 53, 656 91, Brno, Czech Republic.
| | - Jan Bureš
- 2nd Department of Internal Medicine - Gastroenterology, Charles University in Praha, Faculty of Medicine at Hradec Kralové, University Teaching Hospital, Sokolská 581, Hradec Kralové, 500 05, Czech Republic.
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic.
| |
Collapse
|
36
|
Cavera VL, Arthur TD, Kashtanov D, Chikindas ML. Bacteriocins and their position in the next wave of conventional antibiotics. Int J Antimicrob Agents 2015; 46:494-501. [PMID: 26341839 DOI: 10.1016/j.ijantimicag.2015.07.011] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 07/10/2015] [Accepted: 07/15/2015] [Indexed: 12/13/2022]
Abstract
Micro-organisms are capable of producing a range of defence mechanisms, including antibiotics, bacteriocins, lytic agents, protein exotoxins, etc. Such mechanisms have been identified in nearly 99% of studied bacteria. The multiplicity and diversity of bacteriocins and the resultant effects of their interactions with targeted bacteria on microbial ecology has been thoroughly studied and remains an area of investigation attracting many researchers. However, the incorporation of bacteriocins into drug delivery systems used in conjunction with, or as potential alternatives to, conventional antibiotics is only a recent, although rapidly expanding, field. The extensive array of bacteriocins positions them as one of the most promising options in the next wave of antibiotics. The goal of this review was to explore bacteriocins as novel antimicrobials, alone and in combination with established antibiotics, and thus position them as a potential tool for addressing the current antibiotic crisis.
Collapse
Affiliation(s)
- Veronica L Cavera
- Department of Biochemistry and Microbiology, Rutgers State University, 76 Lipman Drive, New Brunswick, NJ 08901, USA
| | - Timothy D Arthur
- Department of Biochemistry and Microbiology, Rutgers State University, 76 Lipman Drive, New Brunswick, NJ 08901, USA
| | - Dimitri Kashtanov
- School of Environmental and Biological Sciences, Rutgers State University, 65 Dudley Road, New Brunswick, NJ 08901, USA
| | - Michael L Chikindas
- School of Environmental and Biological Sciences, Rutgers State University, 65 Dudley Road, New Brunswick, NJ 08901, USA.
| |
Collapse
|
37
|
Micenková L, Sišková P, Bosák J, Jamborová I, Cernohorská L, Smajs D. Characterization of human uropathogenic ESBL-producing Escherichia coli in the Czech Republic: spread of CTX-M-27-producing strains in a university hospital. Microb Drug Resist 2015; 20:610-7. [PMID: 24959675 DOI: 10.1089/mdr.2014.0013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AIMS The purpose of this study was to characterize the extended-spectrum β-lactamase (ESBL)-producing uropathogenic Escherichia coli (UPEC) strains isolated in the South Moravia region of the Czech Republic. RESULTS Out of 109 ESBL-producing UPEC isolates, the CTX-M-15-producing E. coli O25b-ST131 was detected in 55 (50.5%) and the CTX-M-27-producing E. coli O25b-ST131 in 40 isolates (36.7%). Most isolates were distributed among three pulsed-field gel electrophoresis clusters and were characterized by low variability relative to antibiotic resistance patterns, in E. coli phylogroups and by the prevalence of virulence and bacteriocin determinants. Despite this, 14 groups of identical isolates (comprising a total of 41 isolates) were identified when all tested parameters of E. coli were combined. CONCLUSIONS Since the occurrence of E. coli B2-O25b-ST131 CTX-M-27 was only recently described in Asia, the frequent isolation of this lineage among patients in South Moravia suggests an efficient transfer of this clone from Asian countries. The limited variability of detected parameters of ESBL-producing UPEC strains is consistent with a common origin of the analyzed isolates, in which there is an ongoing process of genetic diversification.
Collapse
Affiliation(s)
- Lenka Micenková
- 1 Department of Biology, Faculty of Medicine, Masaryk University , Brno, Czech Republic
| | | | | | | | | | | |
Collapse
|
38
|
Abstract
Developments in the use of genomics to guide natural product discovery and a recent emphasis on understanding the molecular mechanisms of microbiota-host interactions have converged on the discovery of small molecules from the human microbiome. Here, we review what is known about small molecules produced by the human microbiota. Numerous molecules representing each of the major metabolite classes have been found that have a variety of biological activities, including immune modulation and antibiosis. We discuss technologies that will affect how microbiota-derived molecules are discovered in the future and consider the challenges inherent in finding specific molecules that are critical for driving microbe-host and microbe-microbe interactions and understanding their biological relevance.
Collapse
Affiliation(s)
- Mohamed S Donia
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Michael A Fischbach
- Department of Bioengineering and Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
39
|
Kamalov AA, Khodyreva LA, Dudareva AA, Nizov AN. Risk factors causing the development of infection and inflammation of the lower urinary tract. VESTNIK DERMATOLOGII I VENEROLOGII 2015. [DOI: 10.25208/0042-4609-2015-91-2-63-67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Persistence as well as high survival rate and resistance of microorganisms belong to the key reasons promoting symptoms of lower urinary tract diseases. They can stay active for a long time and can substantially deteriorate the life quality of patients suffering from chronic infections and inflammations in the wall of the urinary bladder even after the eradication of the pathogen. Recent studies in the field of clinical microbiology reflect serious qualitative and quantitative changes in the infection incidence structure, which is mainly related to changes in the bacterial pathogenicity. Pathogenicity island genes control the synthesis of different adhesins, invasins, hemolysins and toxins (hemolysin, cytotoxic necrotizing factor type 1, etc.) as well as iron ion absorption system, which are essential for the pathogen propagation and activity in tissues. The determination of genetic determinants will provide a new insight into the bacterial evolution process and will help to understand the reason of prompt formation and propagation of virulent strains as well as fast development of the infection and inflammation in the lower urinary tract, which may explain different severity of the pathology and symptoms of the lower urinary tract.
Collapse
|