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Escherichia coli virulence genes and clonality in strains from diarrhoea in goat kids. Small Rumin Res 2023. [DOI: 10.1016/j.smallrumres.2023.106906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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2
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Petersen AM. Gastrointestinal dysbiosis and Escherichia coli pathobionts in inflammatory bowel diseases. APMIS 2022; 130 Suppl 144:1-38. [PMID: 35899316 PMCID: PMC9546507 DOI: 10.1111/apm.13256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andreas Munk Petersen
- Department of Gastroenterology and Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
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Zara ES, Vital PG. Phylogroup typing and carbapenem resistance of Escherichia coli from agricultural samples in Metro Manila, Philippines. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2022; 57:644-656. [PMID: 35852239 DOI: 10.1080/03601234.2022.2096988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Primary production environment is considered as reservoir of Escherichia coli contamination of produce. E. coli is classified into eight phylogroups which differ in ecological niches, evolutionary history, and phenotypic properties. To understand the population genetic structure and composition of E. coli in primary production environments in Metro Manila, Philippines, a total of 80 E. coli recovered from irrigation water, soil, vegetables, and feces of cat, carabao, chicken, dog, and goat were allocated into distinct phylogroups based on the presence and absence of genetic markers. Results showed that the most prevalent phylogroup was B1 (71.3%), followed by A (18.6%), D (6.3%), B2 (1.3%), E (1.3%), and an unknown phylogroup (1.3%). The most prevalent genetic marker was arpA, followed by TspE4.C2, yjaA, and chuA. The carbapenem resistance of 24 E. coli isolates representing different phylogroups was also evaluated. Intriguingly, all isolates exhibited uniform susceptibility. This is the first report to provide insights into the phylogroup structure and composition, as well as carbapenem resistance of E. coli from primary production in the Philippines, which highlights possible source of and solution for gastrointestinal and enteric diseases.
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Affiliation(s)
- Enrico S Zara
- Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Pierangeli G Vital
- Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City, Philippines
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Louge Uriarte EL, González Pasayo RA, Massó M, Carrera Paez L, Domínguez Moncla M, Donis N, Malena R, Méndez A, Morrell E, Giannitti F, Armendano JI, Faverin C, Centrón D, Parreño V, Odeón AC, Quiroga MP, Moreira AR. Molecular characterization of multidrug-resistant Escherichia coli of the phylogroups A and C in dairy calves with meningitis and septicemia. Microb Pathog 2022; 163:105378. [PMID: 34982979 DOI: 10.1016/j.micpath.2021.105378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/21/2021] [Accepted: 12/28/2021] [Indexed: 11/19/2022]
Abstract
Escherichia coli is an important cause of septicemia (SEPEC) and neonatal meningitis (NMEC) in dairy calves. However, the diversity of virulence profiles, phylogroups, antimicrobial resistance patterns, carriage of integron structures, and fluoroquinolone (FQ) resistance mechanisms have not been fully investigated. Also, there is a paucity of knowledge about the virulence profiles and frequency of potential SEPEC in feces from calves with or without diarrhea. This study aimed to characterize the virulence potential, phylogroups, antimicrobial susceptibility, integron content, and FQ-resistance mechanisms in Escherichia coli isolated from calves with meningitis and septicemia. Additionally, the virulence genes (VGs) and profiles of E. coli isolated from diarrheic and non-diarrheic calves were compared between them and together with NMEC and SEPEC in order to identify shared profiles. Tissue and fluid samples from eight dairy calves with septicemia, four of which had concurrent meningitis, were processed for bacteriology and histopathology. Typing of VGs was assessed in 166 isolates from diverse samples of each calf. Selected isolates were evaluated for antimicrobial susceptibility by the disk diffusion test. Phylogroups, integron gene cassettes cartography, and FQ-resistance determinants were analyzed by PCR, sequencing, and bioinformatic tools. Furthermore, 109 fecal samples and 700 fecal isolates from dairy calves with or without diarrhea were evaluated to detect 19 VGs by uniplex PCR. Highly diverse VG profiles were characterized among NMEC and SEPEC isolates, but iucD was the predominant virulence marker. Histologic lesions in all calves supported their pathogenicity. Selected isolates mainly belonged to phylogroups A and C and showed multidrug resistance. Classic (dfrA17 and arr3-dfrA27) and complex (dfrA17-aadA5::ISCR1::blaCTX-M-2) class 1 integrons were identified. Target-site mutations in GyrA (S83L and D87N) and ParC (S80I) encoding genes were associated with FQ resistance. The VGs detected more frequently in fecal samples included f17G (50%), papC (30%), iucD (20%), clpG (19%), eae (16%), and afaE-8 (13%). Fecal isolates displaying the profiles of f17 or potential SEPEC were found in 25% of calves with and without diarrhea. The frequency of E. coli VGs and profiles did not differ between both groups (p > 0.05) and were identical or similar to those found in NMEC and SEPEC. Overall, multidrug-resistant E. coli isolates with diverse VG profiles and belonging to phylogroups A and C can be implicated in natural cases of meningitis and septicemia. Their resistance phenotypes can be partially explained by class 1 integron gene cassettes and target-site mutations in gyrA and parC. These results highlight the value of antimicrobial resistance surveillance in pathogenic bacteria isolated from food-producing animals. Besides, calves frequently shed potential SEPEC in their feces as commensals ("Trojan horse"). Thus, these bacteria may be disseminated in the farm environment, causing septicemia and meningitis under predisposing factors.
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Affiliation(s)
- Enrique L Louge Uriarte
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina.
| | - Ramón A González Pasayo
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Mariana Massó
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina
| | - Laura Carrera Paez
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina
| | - Manuel Domínguez Moncla
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina
| | - Nicolás Donis
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina
| | - Rosana Malena
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Alejandra Méndez
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Eleonora Morrell
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Federico Giannitti
- Instituto Nacional de Investigación Agropecuaria (INIA), Ruta 50 km 11, Estación Experimental La Estanzuela, Semillero, 70006, Colonia, Uruguay
| | - Joaquín I Armendano
- Departamento de Fisiopatología, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco s/n, Tandil, 7000, Argentina
| | - Claudia Faverin
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Daniela Centrón
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina
| | - Viviana Parreño
- Incuinta, Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Virología e Innovaciones Tecnológicas, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IVIT, INTA-CONICET), Castelar, 1712, Buenos Aires, Argentina
| | - Anselmo C Odeón
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - María Paula Quiroga
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina.
| | - Ana Rita Moreira
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
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Baquero F, Martínez JL, F. Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance. Clin Microbiol Rev 2021; 34:e0005019. [PMID: 34190572 PMCID: PMC8404696 DOI: 10.1128/cmr.00050-19] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.
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Affiliation(s)
- F. Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. L. Martínez
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - V. F. Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Central Bioinformatics Unit, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - J. Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. C. Galán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A. San Millán
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - R. Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - T. M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
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Phylogeny, recombination, and invasiveness of group B Streptococcus revealed by genomic comparisons of its global strains. Eur J Clin Microbiol Infect Dis 2020; 40:581-590. [PMID: 33067737 PMCID: PMC7567417 DOI: 10.1007/s10096-020-04067-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 10/09/2020] [Indexed: 11/26/2022]
Abstract
Capsular polysaccharide (CPS) genes and pilus islands encode important virulence factors for group B Streptococcus (GBS) genomes. This study aims to detect phylogenetic inconsistency in CPS genes and pilus islands in GBSs and to explore its relationship with invasiveness. A total of 1016 GBS genomes were downloaded from the NCBI public database. The multi-locus sequence typing (MLST) and Bayesian analysis of Population Structure (BAPS) analyses were both conducted for phylogeny construction. Serotyping and pilus typing were determined in silico using the genomic sequences. The CPS and pilus typing results were generally consistent with MLST and BAPS clustering. GBS isolates of serotype II and of the PI-1 + PI-2b and PI-2a types were more prone to phylogenetic inconsistency than the others. Isolates of serotype Ib and of PI-1 + PI-2a were more likely to appear as colonizing strains, whereas PI-2b was more likely to appear in invasive strains. For serotype V, phylogenetic inconsistency occurred more commonly in colonizing isolates, while for serotype III, the opposite occurred. The present study profiles for the first time the phylogenetic inconsistency of CPS genes and pilus islands in global GBS isolates, which is helpful for infection control and the development of new vaccines for the prevention of GBS occurrence.
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Hu D, Liu B, Wang L, Reeves PR. Living Trees: High-Quality Reproducible and Reusable Construction of Bacterial Phylogenetic Trees. Mol Biol Evol 2020; 37:563-575. [PMID: 31633785 DOI: 10.1093/molbev/msz241] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
An ideal bacterial phylogenetic tree accurately retraces evolutionary history and accurately incorporates mutational, recombination and other events on the appropriate branches. Current strain-level bacterial phylogenetic analysis based on large numbers of genomes lacks reliability and resolution, and is hard to be replicated, confirmed and reused, because of the highly divergent nature of microbial genomes. We present SNPs and Recombination Events Tree (SaRTree), a pipeline using six "living trees" modules that addresses problems arising from the high numbers and variable quality of bacterial genome sequences. It provides for reuse of the tree and offers a major step toward global standardization of phylogenetic analysis by generating deposit files including all steps involved in phylogenetic inference. The tree itself is a "living tree" that can be extended by addition of more sequences, or the deposit can be used to vary the programs or parameters used, to assess the effect of such changes. This approach will allow phylogeny papers to meet the traditional responsibility of providing data and analysis that can be repeated and critically evaluated by others. We used the Acinetobacter baumannii global clone I to illustrate use of SaRTree to optimize tree resolution. An Escherichia coli tree was built from 351 sequences selected from 11,162 genome sequences, with the others added back onto well-defined branches, to show how this facility can greatly improve the outcomes from genome sequencing. SaRTree is designed for prokaryote strain-level analysis but could be adapted for other usage.
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Affiliation(s)
- Dalong Hu
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China.,Tianjin Research Center for Functional Genomics and Biochip, Tianjin, People's Republic of China
| | - Lei Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China.,Ministry of Education, The Key Laboratory of Molecular Microbiology and Technology, Tianjin, People's Republic of China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, People's Republic of China.,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China
| | - Peter R Reeves
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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Gonzalez-Alba JM, Baquero F, Cantón R, Galán JC. Stratified reconstruction of ancestral Escherichia coli diversification. BMC Genomics 2019; 20:936. [PMID: 31805853 PMCID: PMC6896753 DOI: 10.1186/s12864-019-6346-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/28/2019] [Indexed: 12/15/2022] Open
Abstract
Background Phylogenetic analyses of the bacterial genomes based on the simple classification in core- genes and accessory genes pools could offer an incomplete view of the evolutionary processes, of which some are still unresolved. A combined strategy based on stratified phylogeny and ancient molecular polymorphisms is proposed to infer detailed evolutionary reconstructions by using a large number of whole genomes. This strategy, based on the highest number of genomes available in public databases, was evaluated for improving knowledge of the ancient diversification of E. coli. This staggered evolutionary scenario was also used to investigate whether the diversification of the ancient E. coli lineages could be associated with particular lifestyles and adaptive strategies. Results Phylogenetic reconstructions, exploiting 6220 available genomes in Genbank, established the E. coli core genome in 1023 genes, representing about 20% of the complete genome. The combined strategy using stratified phylogeny plus molecular polymorphisms inferred three ancient lineages (D, EB1A and FGB2). Lineage D was the closest to E. coli root. A staggered diversification could also be proposed in EB1A and FGB2 lineages and the phylogroups into these lineages. Several molecular markers suggest that each lineage had different adaptive trajectories. The analysis of gained and lost genes in the main lineages showed that functions of carbohydrates utilization (uptake of and metabolism) were gained principally in EB1A lineage, whereas loss of environmental-adaptive functions in FGB2 lineage were observed, but this lineage showed higher accumulated mutations and ancient recombination events. The population structure of E. coli was re-evaluated including up to 7561 new sequenced genomes, showing a more complex population structure of E. coli, as a new phylogroup, phylogroup I, was proposed. Conclusions A staggered reconstruction of E. coli phylogeny is proposed, indicating evolution from three ancestral lineages to reach all main known phylogroups. New phylogroups were confirmed, suggesting an increasingly complex population structure of E. coli. However these new phylogroups represent < 1% of the global E. coli population. A few key evolutionary forces have driven the diversification of the two main E. coli lineages, metabolic flexibility in one of them and colonization-virulence in the other.
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Affiliation(s)
- José Maria Gonzalez-Alba
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana, Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Juan Carlos Galán
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain. .,CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain. .,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana, Madrid, Spain.
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Baquero F, Lanza VF, Baquero MR, Del Campo R, Bravo-Vázquez DA. Microcins in Enterobacteriaceae: Peptide Antimicrobials in the Eco-Active Intestinal Chemosphere. Front Microbiol 2019; 10:2261. [PMID: 31649628 PMCID: PMC6795089 DOI: 10.3389/fmicb.2019.02261] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/17/2019] [Indexed: 12/31/2022] Open
Abstract
Microcins are low-molecular-weight, ribosomally produced, highly stable, bacterial-inhibitory molecules involved in competitive, and amensalistic interactions between Enterobacteriaceae in the intestine. These interactions take place in a highly complex chemical landscape, the intestinal eco-active chemosphere, composed of chemical substances that positively or negatively influence bacterial growth, including those originated from nutrient uptake, and those produced by the action of the human or animal host and the intestinal microbiome. The contribution of bacteria results from their effect on the host generated molecules, on food and digested food, and organic substances from microbial origin, including from bacterial degradation. Here, we comprehensively review the main chemical substances present in the human intestinal chemosphere, particularly of those having inhibitory effects on microorganisms. With this background, and focusing on Enterobacteriaceae, the most relevant human pathogens from the intestinal microbiota, the microcin’s history and classification, mechanisms of action, and mechanisms involved in microcin’s immunity (in microcin producers) and resistance (non-producers) are reviewed. Products from the chemosphere likely modulate the ecological effects of microcin activity. Several cross-resistance mechanisms are shared by microcins, colicins, bacteriophages, and some conventional antibiotics, which are expected to produce cross-effects. Double-microcin-producing strains (such as microcins MccM and MccH47) have been successfully used for decades in the control of pathogenic gut organisms. Microcins are associated with successful gut colonization, facilitating translocation and invasion, leading to bacteremia, and urinary tract infections. In fact, Escherichia coli strains from the more invasive phylogroups (e.g., B2) are frequently microcinogenic. A publicly accessible APD3 database http://aps.unmc.edu/AP/ shows particular genes encoding microcins in 34.1% of E. coli strains (mostly MccV, MccM, MccH47, and MccI47), and much less in Shigella and Salmonella (<2%). Some 4.65% of Klebsiella pneumoniae are microcinogenic (mostly with MccE492), and even less in Enterobacter or Citrobacter (mostly MccS). The high frequency and variety of microcins in some Enterobacteriaceae indicate key ecological functions, a notion supported by their dominance in the intestinal microbiota of biosynthetic gene clusters involved in the synthesis of post-translationally modified peptide microcins.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Val F Lanza
- Bioinformatics Unit, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Maria-Rosario Baquero
- Department of Microbiology, Alfonso X El Sabio University, Villanueva de la Cañada, Spain
| | - Rosa Del Campo
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Daniel A Bravo-Vázquez
- Department of Microbiology, Alfonso X El Sabio University, Villanueva de la Cañada, Spain
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10
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Dominguez JE, Faccone D, Tijet N, Gomez S, Corso A, Fernández-Miyakawa ME, Melano RG. Characterization of Escherichia coli Carrying mcr- 1-Plasmids Recovered From Food Animals From Argentina. Front Cell Infect Microbiol 2019; 9:41. [PMID: 30895173 PMCID: PMC6414435 DOI: 10.3389/fcimb.2019.00041] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 02/08/2019] [Indexed: 11/16/2022] Open
Abstract
In this study, we found mcr-1.1 and mcr-1.5 genes carried by IncI2 plasmids in a subset of Escherichia coli isolates recovered from commercial broiler farms in Argentina. The comparative analysis of the sequences of these plasmids with those described in human clinical isolates suggests that this replicon-type is one of the main mcr-disseminator sources in Argentina.
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Affiliation(s)
- Johana E Dominguez
- Laboratorio de Bacteriología General, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto de Patobiología, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Diego Faccone
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Servicio de Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) "Dr. C. Malbrán", Buenos Aires, Argentina
| | | | - Sonia Gomez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Servicio de Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) "Dr. C. Malbrán", Buenos Aires, Argentina
| | - Alejandra Corso
- Servicio de Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) "Dr. C. Malbrán", Buenos Aires, Argentina
| | - Mariano E Fernández-Miyakawa
- Laboratorio de Bacteriología General, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto de Patobiología, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Roberto G Melano
- Public Health Ontario Laboratory, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Sinai Health System, Mount Sinai Hospital, Toronto, ON, Canada
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11
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Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas. Front Microbiol 2018; 9:771. [PMID: 29765358 PMCID: PMC5938378 DOI: 10.3389/fmicb.2018.00771] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/05/2018] [Indexed: 12/17/2022] Open
Abstract
The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia, demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.
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Affiliation(s)
- Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Luz E Ochoa-Sánchez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas, Zaragoza, Spain.,Fundación Agencia Aragonesa para la Investigacion y el Desarrollo (ARAID), Zaragoza, Spain
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12
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Landscape-Scale Factors Affecting the Prevalence of Escherichia coli in Surface Soil Include Land Cover Type, Edge Interactions, and Soil pH. Appl Environ Microbiol 2018. [PMID: 29523546 DOI: 10.1128/aem.02714-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli is deposited into soil with feces and exhibits subsequent population decline with concomitant environmental selection. Environmentally persistent strains exhibit longer survival times during this selection process, and some strains have adapted to soil and sediments. A georeferenced collection of E. coli isolates was developed comprising 3,329 isolates from 1,428 soil samples that were collected from a landscape spanning the transition from the grasslands to the eastern deciduous forest biomes. The isolate collection and sample database were analyzed together to discover how land cover, site characteristics, and soil chemistry influence the prevalence of cultivable E. coli in surface soil. Soils from forests and pasture lands had equally high prevalences of E. coli Edge interactions were also observed among land cover types, with proximity to forests and pastures affecting the likelihood of E. coli isolation from surrounding soils. E. coli is thought to be more prevalent in sediments with high moisture, but this was observed only in grass- or crop-dominated lands in this study. Because differing E. coli phylogroups are thought to have differing ecology profiles, isolates were also typed using a novel single-nucleotide polymorphism (SNP) genotyping assay. Phylogroup B1 was the dominant group isolated from soil, as has been reported in all other surveys of environmental E. coli Although differences were small, isolates belonging to phylogroups B2 and D were associated with wooded areas, slightly more acidic soils, and soil sampling after rainfall events. In contrast, isolates from phylogroups B1 and E were associated with pasture lands.IMPORTANCE The consensus is that complex niches or life cycles should select for complex genomes in organisms. There is much unexplained biodiversity in E. coli, and its cycling through complex extrahost environments may be a cause. In order to understand the evolutionary processes that lead to adaptation for survival and growth in soil, an isolate collection that associates soil conditions and isolate genome sequences is required. An equally important question is whether traits selected in soil or other extrahost habitats can be transmitted to E. coli residing in hosts via gene flow. The new findings about the distribution of E. coli in soil at the landscape scale (i) enhance our capability to study how extrahost environments influence the evolution of E. coli and other bacteria, (ii) advance our knowledge of the environmental biology of this microbe, and (iii) further affirm the emerging scientific consensus that E. coli in waterways originates from nonpoint sources not associated with human activity or livestock farming.
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13
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Vila J, Sáez-López E, Johnson JR, Römling U, Dobrindt U, Cantón R, Giske CG, Naas T, Carattoli A, Martínez-Medina M, Bosch J, Retamar P, Rodríguez-Baño J, Baquero F, Soto SM. Escherichia coli: an old friend with new tidings. FEMS Microbiol Rev 2018; 40:437-463. [PMID: 28201713 DOI: 10.1093/femsre/fuw005] [Citation(s) in RCA: 180] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/23/2015] [Accepted: 02/04/2016] [Indexed: 12/16/2022] Open
Abstract
Escherichia coli is one of the most-studied microorganisms worldwide but its characteristics are continually changing. Extraintestinal E. coli infections, such as urinary tract infections and neonatal sepsis, represent a huge public health problem. They are caused mainly by specialized extraintestinal pathogenic E. coli (ExPEC) strains that can innocuously colonize human hosts but can also cause disease upon entering a normally sterile body site. The virulence capability of such strains is determined by a combination of distinctive accessory traits, called virulence factors, in conjunction with their distinctive phylogenetic background. It is conceivable that by developing interventions against the most successful ExPEC lineages or their key virulence/colonization factors the associated burden of disease and health care costs could foreseeably be reduced in the future. On the other hand, one important problem worldwide is the increase of antimicrobial resistance shown by bacteria. As underscored in the last WHO global report, within a wide range of infectious agents including E. coli, antimicrobial resistance has reached an extremely worrisome situation that ‘threatens the achievements of modern medicine’. In the present review, an update of the knowledge about the pathogenicity, antimicrobial resistance and clinical aspects of this ‘old friend’ was presented.
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Affiliation(s)
- J Vila
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - E Sáez-López
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - J R Johnson
- VA Medical Center, Minneapolis, MN, USA, and University of Minnesota, Minneapolis, MN, USA
| | - U Römling
- Karolinska Institute, Stockholm, Sweden
| | - U Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - R Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - C G Giske
- Karolinska Institute, Stockholm, Sweden
| | - T Naas
- Hôpital de Bicêtre, Université Paris Sud, Le Kremlin-Bicêtre, France
| | - A Carattoli
- Department of infectious, parasitic and immune-mediated diseases, Istituto Superiore di Sanità, Rome, Italy
| | - M Martínez-Medina
- Laboratory of Molecular Microbiology, Department of Biology, University of Girona, Girona, Spain
| | - J Bosch
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
| | - P Retamar
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, Departamento de Medicina, Universidad de Sevilla, Seville, Spain
| | - J Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, Departamento de Medicina, Universidad de Sevilla, Seville, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - F Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - S M Soto
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
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14
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Tijet N, Faccone D, Rapoport M, Seah C, Pasterán F, Ceriana P, Albornoz E, Corso A, Petroni A, Melano RG. Molecular characteristics of mcr-1-carrying plasmids and new mcr-1 variant recovered from polyclonal clinical Escherichia coli from Argentina and Canada. PLoS One 2017; 12:e0180347. [PMID: 28678874 PMCID: PMC5498056 DOI: 10.1371/journal.pone.0180347] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/14/2017] [Indexed: 11/18/2022] Open
Abstract
We have characterized nine mcr-1-harboring plasmids from clinical Escherichia coli isolates previously described in Argentina and Canada. Three of these plasmids carried a mcr-1-variant called here mcr-1.5. All these E. coli isolates were not clonally related and were recovered in different years and locations. However, their mcr-1-harboring plasmids showed high identity among them and to others characterized in other countries, which strongly suggests that this plasmid-type is playing an important role in spreading this mechanism of resistance to polymyxins.
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Affiliation(s)
- Nathalie Tijet
- Public Health Ontario Laboratory, Toronto, Ontario, Canada
| | - Diego Faccone
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Melina Rapoport
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Christine Seah
- Public Health Ontario Laboratory, Toronto, Ontario, Canada
| | - Fernando Pasterán
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Paola Ceriana
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Ezequiel Albornoz
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Alejandra Corso
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Alejandro Petroni
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Roberto G. Melano
- Public Health Ontario Laboratory, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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15
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Rocha IV, Andrade CADN, Campos TDL, Rezende AM, Leal NC, Vidal CFDL, Xavier DE. Ciprofloxacin-resistant and extended-spectrum β-lactamase-producing Escherichia coli ST410 strain carrying the mcr-1 gene associated with bloodstream infection. Int J Antimicrob Agents 2017; 49:655-656. [DOI: 10.1016/j.ijantimicag.2017.03.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/02/2017] [Indexed: 11/28/2022]
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16
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Michael GB, Kaspar H, Siqueira AK, de Freitas Costa E, Corbellini LG, Kadlec K, Schwarz S. Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates collected from diseased food-producing animals in the GERM-Vet monitoring program 2008-2014. Vet Microbiol 2017; 200:142-150. [PMID: 27634182 DOI: 10.1016/j.vetmic.2016.08.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 08/22/2016] [Accepted: 08/31/2016] [Indexed: 11/19/2022]
Abstract
The aim of this study was to identify extended-spectrum β-lactamase (ESBL)-producing Escherichia coli collected from diseased food-producing animals in Germany. A total of 6849 E. coli isolates, collected from diseased cattle, pigs and poultry in the German national monitoring program GERM-Vet (2008-2014), were characterized by antimicrobial susceptibility testing and screened for the ESBL phenotype. ESBL genes were identified by PCR and sequencing. The isolates were further characterized by PCR-based phylotyping. The 419/6849 (6.1%) ESBL-producers identified included 324/2896 (11.2%) isolates from cattle, 75/1562 (4.8%) from pigs and 20/2391 (0.8%) from poultry. The ESBL genes detected were: blaCTX-M-1 (69.9%), blaCTX-M-15 (13.6%), blaCTX-M-14 (11.7%), blaTEM-52 (1.9%), blaSHV-12 (1.4%), blaCTX-M-3 (1.0%), and blaCTX-M-2 (0.5%). The phylogroup A was the dominant phylogroup (57.0%) followed by phylogroups D (23.4%), B1 (17.9%), and B2 (1.7%). Bovine isolates belonged predominantly to the phylogroups A and D, whereas the porcine and avian isolates mainly belonged to A and B1. The majority of the ESBL-producing isolates found in each phylogroup were from animals suffering from gastrointestinal infections. In 399/419 isolates (95.2%), additional resistance to non-β-lactam antibiotics was seen. Multidrug-resistance [resistance to aminoglycosides, fluoro(quinolones), sulphonamides, tetracyclines, and trimethoprim] was seen in 369/419 (88.1%) isolates, which may facilitate the co-selection of ESBL genes, when located on the same mobile genetic element as the others resistance genes, and may compromise the therapeutic options.
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Affiliation(s)
- Geovana Brenner Michael
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany.
| | - Heike Kaspar
- Federal Office of Consumer Protection and Food Safety (BVL), Berlin, Germany
| | - Amanda Keller Siqueira
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Eduardo de Freitas Costa
- Laboratory of Veterinary Epidemiology, Faculty of Veterinary Medicine, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Luís Gustavo Corbellini
- Laboratory of Veterinary Epidemiology, Faculty of Veterinary Medicine, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Kristina Kadlec
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
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17
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Shamsi H, Mardani K, Ownagh A. Phylogenetic analysis of Escherichia coli isolated from broilers with colibacillosis based on gyrA gene sequences. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2017; 81:28-32. [PMID: 28154459 PMCID: PMC5220591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 07/21/2016] [Indexed: 06/06/2023]
Abstract
Escherichia coli isolates from chickens with colibacillosis were assigned to phylogenetic groups based on multiplex polymerase chain reaction (PCR) and antibacterial resistance of E. coli belonging to these groups was examined. Furthermore, the gyrA gene of isolates was sequenced and a phylogenetic tree was generated. A total of 84 E. coli isolates were grouped using multiplex PCR of TSPE4.C2, chuA, yjaA, and gadA molecular markers. Four phylogenetic groups were identified with strains divided as follows: 16 in group A (19.05%), 17 in group B1 (20.24%), 23 in group B2 (27.38%), and 28 in group D (33.33%). Escherichia coli isolates belonging to phylogenetic groups B2 and D were resistant to Soltrim and Flumequine unlike the majority of E. coli isolates that belonged to groups A and B1, and which were susceptible to these antibiotics. The phylogenetic results based on gyrA gene sequences from multiplex PCR revealed that E. coli phylogenetic grouping was in accordance with the clusters obtained in the phylogenetic tree. In conclusion, the comparative sequence analysis of gyrA sequences provides a firm framework for an accurate classification of E. coli and related taxa and may constitute a pertinent phylogenetic marker for E. coli.
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Affiliation(s)
| | - Karim Mardani
- Address all correspondence to Dr. Karim Mardani; telephone: +98 44 3194 2618; fax: +98 44 3277 1926; e-mail:
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18
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Keane OM. Genetic diversity, the virulence gene profile and antimicrobial resistance of clinical mastitis-associated Escherichia coli. Res Microbiol 2016; 167:678-684. [PMID: 27404459 DOI: 10.1016/j.resmic.2016.06.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/27/2016] [Accepted: 06/29/2016] [Indexed: 12/27/2022]
Abstract
Escherichia coli is a common cause of bovine mastitis, particularly around parturition and early lactation when the host is immunosuppressed. Isolates (n = 37) recovered from cases of clinical mastitis in Ireland were characterised with respect to genotypic diversity, phylogenetic group, virulence gene profile and antimicrobial susceptibility. The isolates were genotypically diverse, belonging to 19 different sequence types. However, the majority (86%) belonged to phylogenetic groups A or B1, groups commonly associated with commensal E. coli. The isolates encoded few virulence genes with iss (increased serum survival, 41%), lpfA (long polar fimbriae, 19%) and astA (enteroaggregative heat-stable toxin, 14%) among the most common virulence genes detected. The only virulence gene to differ in frequency between the phylogenetic groups was lpfA, found exclusively in B1. Resistance to at least one antimicrobial was detected in 16% of isolates. Three isolates were multidrug-resistant, with one resistant to seven antibiotics. There was no relationship between antimicrobial resistance and phylogenetic group. These results indicate that many cases of clinical E. coli mastitis in Ireland may be caused by opportunistic commensal organisms lacking specific virulence genes. However, the organisms represent a reservoir of antimicrobial resistance determinants with the potential to disseminate determinants to other organisms.
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Affiliation(s)
- Orla M Keane
- Animal & Bioscience Research Department, Teagasc, Grange, Dunsany, Co. Meath, Ireland.
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19
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Bromberg R, Grishin NV, Otwinowski Z. Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer. PLoS Comput Biol 2016; 12:e1004985. [PMID: 27336403 PMCID: PMC4918981 DOI: 10.1371/journal.pcbi.1004985] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 05/10/2016] [Indexed: 01/20/2023] Open
Abstract
Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz. Due to their lack of distinct morphological features, bacteria and archaea were extremely difficult to classify until technology was developed to obtain their DNA sequences; these sequences could then be compared to estimate evolutionary relationships. Now, due to technological advances, there is a flood of available sequences from a wide variety of organisms. These advances have spurred the development of algorithms which can estimate evolutionary relationships using whole genomes, in contrast to the more traditional methods which used single genes earlier and now typically use groups of conserved genes. However, there are many challenges when attempting to infer evolutionary relationships, in particular horizontal gene transfer, where DNA is transferred from one organism to another, resulting in an organism’s genome containing DNA that does not reflect its evolution by descent. We developed a new whole-genome method for estimating evolutionary distances which identifies and corrects for horizontal transfer. We found that for SlopeTree and all other whole-genome methods we applied, horizontal transfer causes some evolutionary distances to be grossly underestimated, and that our correction corrects for this.
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Affiliation(s)
- Raquel Bromberg
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Nick V. Grishin
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Zbyszek Otwinowski
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
- * E-mail:
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20
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Falgenhauer L, Imirzalioglu C, Ghosh H, Gwozdzinski K, Schmiedel J, Gentil K, Bauerfeind R, Kämpfer P, Seifert H, Michael GB, Schwarz S, Pfeifer Y, Werner G, Pietsch M, Roesler U, Guerra B, Fischer J, Sharp H, Käsbohrer A, Goesmann A, Hille K, Kreienbrock L, Chakraborty T. Circulation of clonal populations of fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST410 in humans and animals in Germany. Int J Antimicrob Agents 2016; 47:457-65. [PMID: 27208899 DOI: 10.1016/j.ijantimicag.2016.03.019] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/23/2016] [Accepted: 03/28/2016] [Indexed: 12/14/2022]
Abstract
Multidrug-resistant Escherichia coli encoding CTX-M-type extended-spectrum β-lactamases (ESBLs) are isolated in increasing numbers from humans, companion animals and livestock, raising concern regarding the exchange and spread of isolates in these populations. In this study, whole-genome sequencing of CTX-M-15-producing E. coli isolates recently sampled from humans, companion animals, livestock and farm environments was performed. In total, 26 different sequence types (STs) were detected, of which ST410 was the most frequent and was the only ST present in all populations studied. Five clades (designated A-E) were detected within the ST410 isolates. In particular, isolates of clade B were present in all four populations and had core genomes that differed by less than 70 single nucleotide polymorphisms (SNPs). Isolates of clades B and C were also clonally marked, exhibiting identical chromosomal insertions of blaCTX-M-15 at distinct loci. These data provide strong evidence for the clonal dissemination of specific clades of CTX-M-15-producing E. coli ST410 in human and animal populations.
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Affiliation(s)
- Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Hiren Ghosh
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Konrad Gwozdzinski
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Judith Schmiedel
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Katrin Gentil
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Rolf Bauerfeind
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus Liebig University Giessen, Giessen, Germany
| | - Harald Seifert
- German Center for Infection Research (DZIF), Braunschweig, Germany; Institute for Medical Microbiology, Immunology, and Hygiene, University of Cologne, Cologne, Germany
| | - Geovana Brenner Michael
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Yvonne Pfeifer
- Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Michael Pietsch
- Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Uwe Roesler
- Institute for Animal Hygiene and Environmental Health, Free University Berlin, Berlin, Germany
| | - Beatriz Guerra
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Jennie Fischer
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Hannah Sharp
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Annemarie Käsbohrer
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Alexander Goesmann
- Institute of Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Katja Hille
- Institute for Biometry, Epidemiology, and Information Processing, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Lothar Kreienbrock
- Institute for Biometry, Epidemiology, and Information Processing, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany.
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Dale AP, Woodford N. Extra-intestinal pathogenic Escherichia coli (ExPEC): Disease, carriage and clones. J Infect 2015; 71:615-26. [PMID: 26409905 DOI: 10.1016/j.jinf.2015.09.009] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/16/2015] [Indexed: 10/23/2022]
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) have a complex phylogeny, broad virulence factor (VF) armament and significant genomic plasticity, and are associated with a spectrum of host infective syndromes ranging from simple urinary tract infection to life-threatening bacteraemia. Their importance as pathogens has come to the fore in recent years, particularly in the context of the global emergence of hyper-virulent and antibiotic resistant strains. Despite this, the mechanisms underlying ExPEC transmission dynamics and clonal selection remain poorly understood. Large-scale epidemiological and clinical studies are urgently required to ascertain the mechanisms underlying these processes to enable the development of novel evidence-based preventative and therapeutic strategies. In the current review, we provide a concise summary of the methods utilised for ExPEC phylogenetic delineation before exploring in detail the associations between ExPEC VFs and site-specific disease. We then consider the role of ExPEC as an intestinal colonist and outline known associations between ExPEC clonal variation, specific disease syndromes and antibiotic resistance.
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Affiliation(s)
- Adam P Dale
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, South Academic Block, Tremona Road, Southampton SO16 6YD, UK.
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Reference Microbiology Services, Public Health England, London NW9 5EQ, UK; The NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0HS, UK
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22
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First Report of OXA-181-Producing Escherichia coli in China and Characterization of the Isolate Using Whole-Genome Sequencing. Antimicrob Agents Chemother 2015; 59:5022-5. [PMID: 26014927 DOI: 10.1128/aac.00442-15] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/17/2015] [Indexed: 02/05/2023] Open
Abstract
We report the first OXA-181-producing strain in China. blaOXA-181 was found in sequence type 410 (ST410) Escherichia coli strain WCHEC14828 from a Chinese patient without recent travel history. Genome sequencing and conjugation experiments were performed. blaOXA-181 was carried on a 51-kb self-transmissible IncX3 plasmid and was linked with qnrS1, a quinolone resistance gene. blaOXA-181 was introduced onto the IncX3 plasmid from a ColE2-type plasmid, and IncX3 plasmids have the potential to mediate the dissemination of blaOXA-181.
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