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A 16 th century Escherichia coli draft genome associated with an opportunistic bile infection. Commun Biol 2022; 5:599. [PMID: 35710940 PMCID: PMC9203756 DOI: 10.1038/s42003-022-03527-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/23/2022] [Indexed: 11/12/2022] Open
Abstract
Escherichia coli – one of the most characterized bacteria and a major public health concern – remains invisible across the temporal landscape. Here, we present the meticulous reconstruction of the first ancient E. coli genome from a 16th century gallstone from an Italian mummy with chronic cholecystitis. We isolated ancient DNA and reconstructed the ancient E. coli genome. It consisted of one chromosome of 4446 genes and two putative plasmids with 52 genes. The E. coli strain belonged to the phylogroup A and an exceptionally rare sequence type 4995. The type VI secretion system component genes appears to be horizontally acquired from Klebsiella aerogenes, however we could not identify any pathovar specific genes nor any acquired antibiotic resistances. A sepsis mouse assay showed that a closely related contemporary E. coli strain was avirulent. Our reconstruction of this ancient E. coli helps paint a more complete picture of the burden of opportunistic infections of the past. Ancient DNA from an Italian mummy’s gallstone provides insight into opportunistic E. coli infection.
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52
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Gophna U, Altman-Price N. Horizontal Gene Transfer in Archaea-From Mechanisms to Genome Evolution. Annu Rev Microbiol 2022; 76:481-502. [PMID: 35667126 DOI: 10.1146/annurev-micro-040820-124627] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Archaea remains the least-studied and least-characterized domain of life despite its significance not just to the ecology of our planet but also to the evolution of eukaryotes. It is therefore unsurprising that research into horizontal gene transfer (HGT) in archaea has lagged behind that of bacteria. Indeed, several archaeal lineages may owe their very existence to large-scale HGT events, and thus understanding both the molecular mechanisms and the evolutionary impact of HGT in archaea is highly important. Furthermore, some mechanisms of gene exchange, such as plasmids that transmit themselves via membrane vesicles and the formation of cytoplasmic bridges that allows transfer of both chromosomal and plasmid DNA, may be archaea specific. This review summarizes what we know about HGT in archaea, and the barriers that restrict it, highlighting exciting recent discoveries and pointing out opportunities for future research. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; ,
| | - Neta Altman-Price
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; , .,Department of Natural and Life Sciences, The Open University of Israel, Raanana, Israel
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53
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Yu D, Ryu K, Zhi S, Otto SJG, Neumann NF. Naturalized Escherichia coli in Wastewater and the Co-evolution of Bacterial Resistance to Water Treatment and Antibiotics. Front Microbiol 2022; 13:810312. [PMID: 35707173 PMCID: PMC9189398 DOI: 10.3389/fmicb.2022.810312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 05/09/2022] [Indexed: 12/30/2022] Open
Abstract
Antibiotic resistance represents one of the most pressing concerns facing public health today. While the current antibiotic resistance crisis has been driven primarily by the anthropogenic overuse of antibiotics in human and animal health, recent efforts have revealed several important environmental dimensions underlying this public health issue. Antibiotic resistant (AR) microbes, AR genes, and antibiotics have all been found widespread in natural environments, reflecting the ancient origins of this phenomenon. In addition, modern societal advancements in sanitation engineering (i.e., sewage treatment) have also contributed to the dissemination of resistance, and concerningly, may also be promoting the evolution of resistance to water treatment. This is reflected in the recent characterization of naturalized wastewater strains of Escherichia coli-strains that appear to be adapted to live in wastewater (and meat packing plants). These strains carry a plethora of stress-resistance genes against common treatment processes, such as chlorination, heat, UV light, and advanced oxidation, mechanisms which potentially facilitate their survival during sewage treatment. These strains also carry an abundance of common antibiotic resistance genes, and evidence suggests that resistance to some antibiotics is linked to resistance to treatment (e.g., tetracycline resistance and chlorine resistance). As such, these naturalized E. coli populations may be co-evolving resistance against both antibiotics and water treatment. Recently, extraintestinal pathogenic strains of E. coli (ExPEC) have also been shown to exhibit phenotypic resistance to water treatment, seemingly associated with the presence of various shared genetic elements with naturalized wastewater E. coli. Consequently, some pathogenic microbes may also be evolving resistance to the two most important public health interventions for controlling infectious disease in modern society-antibiotic therapy and water treatment.
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Affiliation(s)
- Daniel Yu
- School of Public Health, University of Alberta, Edmonton, AB, Canada
- Antimicrobial Resistance – One Health Consortium, Calgary, AB, Canada
| | - Kanghee Ryu
- School of Public Health, University of Alberta, Edmonton, AB, Canada
- Antimicrobial Resistance – One Health Consortium, Calgary, AB, Canada
| | - Shuai Zhi
- School of Medicine, Ningbo University, Ningbo, China
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
| | - Simon J. G. Otto
- School of Public Health, University of Alberta, Edmonton, AB, Canada
- Antimicrobial Resistance – One Health Consortium, Calgary, AB, Canada
- Human-Environment-Animal Transdisciplinary Antimicrobial Resistance Research Group, School of Public Health, University of Alberta, Edmonton, AB, Canada
- Healthy Environments, Centre for Health Communities, School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Norman F. Neumann
- School of Public Health, University of Alberta, Edmonton, AB, Canada
- Antimicrobial Resistance – One Health Consortium, Calgary, AB, Canada
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Ferrandis-Vila M, Tiwari SK, Mamerow S, Semmler T, Menge C, Berens C. Using unique ORFan genes as strain-specific identifiers for Escherichia coli. BMC Microbiol 2022; 22:135. [PMID: 35585491 PMCID: PMC9118744 DOI: 10.1186/s12866-022-02508-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 03/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial identification at the strain level is a much-needed, but arduous and challenging task. This study aimed to develop a method for identifying and differentiating individual strains among multiple strains of the same bacterial species. The set used for testing the method consisted of 17 Escherichia coli strains picked from a collection of strains isolated in Germany, Spain, the United Kingdom and Vietnam from humans, cattle, swine, wild boars, and chickens. We targeted unique or rare ORFan genes to address the problem of selective and specific strain identification. These ORFan genes, exclusive to each strain, served as templates for developing strain-specific primers. RESULTS Most of the experimental strains (14 out of 17) possessed unique ORFan genes that were used to develop strain-specific primers. The remaining three strains were identified by combining a PCR for a rare gene with a selection step for isolating the experimental strains. Multiplex PCR allowed the successful identification of the strains both in vitro in spiked faecal material in addition to in vivo after experimental infections of pigs and recovery of bacteria from faecal material. In addition, primers for qPCR were also developed and quantitative readout from faecal samples after experimental infection was also possible. CONCLUSIONS The method described in this manuscript using strain-specific unique genes to identify single strains in a mixture of strains proved itself efficient and reliable in detecting and following individual strains both in vitro and in vivo, representing a fast and inexpensive alternative to more costly methods.
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Affiliation(s)
- Marta Ferrandis-Vila
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Straße 96a, 07743, Jena, Germany
| | | | - Svenja Mamerow
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Straße 96a, 07743, Jena, Germany
| | | | | | - Christian Menge
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Straße 96a, 07743, Jena, Germany
| | - Christian Berens
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Straße 96a, 07743, Jena, Germany.
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55
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icaR
and
icaT
Are Ancient Chromosome Genes Encoding Substrates of the Type III Secretion Apparatus in Shigella flexneri. mSphere 2022; 7:e0011522. [PMID: 35582904 PMCID: PMC9241512 DOI: 10.1128/msphere.00115-22] [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] [Indexed: 11/20/2022] Open
Abstract
Shigella is an Escherichia coli pathovar that colonizes the cytosol of mucosal cells in the human large intestine. To do this, Shigella uses a Type III Secretion Apparatus (T3SA) to translocate several proteins into host cells. The T3SA and its substrates are encoded by genes of the virulence plasmid pINV or by chromosomal genes derived thereof. We recently discovered two chromosomal genes, which seem unrelated to pINV, although they are activated by MxiE and IpgC similarly to some of the canonical substrates of the T3SA. Here, we showed that the production of the corresponding proteins depended on the conservation of a MxiE box in their cognate promoters. Furthermore, both proteins were secreted by the T3SA in a chaperone-independent manner through the recognition of their respective amino-terminal secretion signal. Based on these observations, we named these new genes icaR and icaT, which stand for invasion chromosome antigen with homology for a transcriptional regulator and a transposase, respectively. icaR and icaT have orthologs in commensal and pathogenic E. coli strains belonging mainly to phylogroups A, B1, D and E. Finally, we demonstrated that icaR and icaT orthologs could be activated by the coproduction of IpgC and MxiE in strains MG1655 K-12 (phylogroup A) and O157:H7 ATCC 43888 (phylogroup E). In contrast, the coproduction of EivF and YgeG, which are homologs of MxiE and IpgC in the E. coli T3SS 2 (ETT2), failed to activate icaR and icaT. IMPORTANCEicaR and icaT are the latest members of the MxiE regulon discovered in the chromosome. The proteins IcaR and IcaT, albeit produced in small amounts, are nonetheless secreted by the T3SA comparably to canonical substrates. The high occurrence of icaR and icaT in phylogroups A, B1, D, and E coupled with their widespread absence in their B2 counterparts agree with the consensus E. coli phylogeny. The widespread conservation of the MxiE box among icaR and icaT orthologs supports the notion that both genes had already undergone coevolution with transcriptional activators ipgC and mxiE- harbored in pINV or a relative- in the last common ancestor of Shigella and of E. coli from phylogroups A, B1, D, and E. The possibility that icaR and icaT may contribute to Shigella pathogenesis cannot be excluded, although some of their characteristics suggest they are fossil genes.
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56
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Zooplankton as a Transitional Host for Escherichia coli in Freshwater. Appl Environ Microbiol 2022; 88:e0252221. [PMID: 35416683 PMCID: PMC9088391 DOI: 10.1128/aem.02522-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This study shows that Escherichia coli can be temporarily enriched in zooplankton under natural conditions and that these bacteria can belong to different phylogroups and sequence types (STs), including environmental, clinical, and animal isolates. We isolated 10 E. coli strains and sequenced the genomes of two of them. Phylogenetically, the two isolates were closer to strains isolated from poultry meat than to freshwater E. coli, albeit their genomes were smaller than those of the poultry isolates. After isolation and fluorescent protein tagging of strains ED1 and ED157, we show that Daphnia sp. can take up these strains and release them alive again, thus becoming a temporary host for E. coli. In a chemostat experiment, we show that this association does not prolong bacterial long-term survival, but at low abundances it also does not significantly reduce bacterial numbers. We demonstrate that E. coli does not belong to the core microbiota of Daphnia, suffers from competition by the natural Daphnia microbiota, but can profit from its carapax to survive in water. All in all, this study suggests that the association of E. coli with Daphnia is only temporary, but the cells are viable therein, and this might allow encounters with other bacteria for genetic exchange and potential genomic adaptation to the freshwater environment. IMPORTANCE The contamination of freshwater with feces-derived bacteria is a major concern regarding drinking water acquisition and recreational activities. Ecological interactions promoting their persistence are still very scarcely studied. This study, which analyses the survival of E. coli in the presence of zooplankton, is thus of ecological and water safety relevance.
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57
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Khedkar S, Smyshlyaev G, Letunic I, Maistrenko OM, Coelho LP, Orakov A, Forslund SK, Hildebrand F, Luetge M, Schmidt TSB, Barabas O, Bork P. Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes. Nucleic Acids Res 2022; 50:3155-3168. [PMID: 35323968 PMCID: PMC8989519 DOI: 10.1093/nar/gkac163] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/30/2022] [Accepted: 03/11/2022] [Indexed: 12/02/2022] Open
Abstract
Prokaryotic Mobile Genetic Elements (MGEs) such as transposons, integrons, phages and plasmids, play important roles in prokaryotic evolution and in the dispersal of cargo functions like antibiotic resistance. However, each of these MGE types is usually annotated and analysed individually, hampering a global understanding of phylogenetic and environmental patterns of MGE dispersal. We thus developed a computational framework that captures diverse MGE types, their cargos and MGE-mediated horizontal transfer events, using recombinases as ubiquitous MGE marker genes and pangenome information for MGE boundary estimation. Applied to ∼84k genomes with habitat annotation, we mapped 2.8 million MGE-specific recombinases to six operational MGE types, which together contain on average 13% of all the genes in a genome. Transposable elements (TEs) dominated across all taxa (∼1.7 million occurrences), outnumbering phages and phage-like elements (<0.4 million). We recorded numerous MGE-mediated horizontal transfer events across diverse phyla and habitats involving all MGE types, disentangled and quantified the extent of hitchhiking of TEs (17%) and integrons (63%) with other MGE categories, and established TEs as dominant carriers of antibiotic resistance genes. We integrated all these findings into a resource (proMGE.embl.de), which should facilitate future studies on the large mobile part of genomes and its horizontal dispersal.
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Affiliation(s)
- Supriya Khedkar
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Georgy Smyshlyaev
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.,Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Ivica Letunic
- Biobyte solutions GmbH, Bothestr 142, 69117 Heidelberg, Germany
| | - Oleksandr M Maistrenko
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Askarbek Orakov
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Sofia K Forslund
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.,Max Delbrück Centre for Molecular Medicine, Berlin, Germany.,Experimental and Clinical Research Center, Charité-Universitätsmedizin and Max-Delbrück Center, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Falk Hildebrand
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Mechthild Luetge
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Thomas S B Schmidt
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Orsolya Barabas
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.,Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.,Max Delbrück Centre for Molecular Medicine, Berlin, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Yonsei Frontier Lab (YFL), Yonsei University, Seoul 03722, South Korea
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58
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Abstract
We hereby present the first descriptions of human-invasive infections caused by Escherichia marmotae, a recently described species that encompasses the former “Escherichia cryptic clade V.” We describe four cases, one acute sepsis of unknown origin, one postoperative sepsis after cholecystectomy, one spondylodiscitis, and one upper urinary tract infection. Cases were identified through unsystematic queries in a single clinical lab over 6 months. Through genome sequencing of the causative strains combined with available genomes from elsewhere, we demonstrate Es. marmotae to be a likely ubiquitous species containing genotypic virulence traits associated with Escherichia pathogenicity. The invasive isolates were scattered among isolates from a range of nonhuman sources in the phylogenetic analyses, thus indicating inherent virulence in multiple lineages. Pan genome analyses indicate that Es. marmotae has a large accessory genome and is likely to obtain ecologically advantageous traits, such as genes encoding antimicrobial resistance. Reliable identification might be possible by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), but relevant spectra are missing in commercial databases. It can be identified through 16S rRNA gene sequencing. Escherichia marmotae could represent a relatively common human pathogen, and improved diagnostics will provide a better understanding of its clinical importance. IMPORTANCEEscherichia coli is the most common pathogen found in blood cultures and urine and among the most important pathogenic species in the realm of human health. The notion that some of these isolates are not Es. coli but rather another species within the same genus may have implications for what Es. coli constitutes. We only recently have obtained methods to separate the two species, which means that possible differences in important clinical aspects, such as antimicrobial resistance rates, virulence, and phylogenetic structure, may exist. We believe that Es. marmotae as a common pathogen is new merely because we have not looked or bothered to distinguish between the thousands of invasive Escherichia passing through microbiological laboratories each day.
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59
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Dias D, Costa S, Fonseca C, Baraúna R, Caetano T, Mendo S. Pathogenicity of Shiga toxin-producing Escherichia coli (STEC) from wildlife: Should we care? THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:152324. [PMID: 34915011 DOI: 10.1016/j.scitotenv.2021.152324] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Shiga toxin-producing Escherichia coli (STEC) is one of the most frequent bacterial agents associated with food-borne outbreaks in Europe. In humans, the infection can lead to life-threatening diseases. Domestic and wild animals can harbor STEC, and ruminants are the main STEC reservoirs, although asymptomatic. In the present study we have characterized STEC from wildlife (wild boar (n = 56), red deer (n = 101), red fox (n = 37) and otter (n = 92)). Cultivable STEC (n = 52) were isolated from 17% (n = 49) of the faecal samples. All the isolates were non-O157 STEC encoding stx1 (n = 2; 4%) and/or stx2 genes (n = 51; 98%). Only one strain (2%) isolated from red fox had an antibiotic resistant phenotype. However, when the normalized resistance interpretation of epidemiological cutoffs (NRI ECOFFs) were used, 23% (n = 12) of the strains were non-wildtype to at least one of the antibiotics tested. After analysis by pulsed-field gel electrophoresis (PFGE), 20 strains were selected for whole genome sequencing and belonged to the following serotypes: O27:H30 (n = 15), O146:H28 (n = 2), O146:H21 (n = 1), O178:H19 (n = 1), and O103:H2 (n = 1). In addition to stx, all strains encode several virulence factors such as toxins, adhesins, fimbriae and secretion systems, among others. All sequenced genomes carried several mobile genetic elements (MGEs), such as prophages and/or plasmids. The core genome and the phylogenetic analysis showed close evolutionary relationships between some of the STEC recovered from wildlife and strains of clinical origin, highlighting their pathogenic potential. Overall, our results show the zoonotic potential of STEC strains originating from wildlife, highlighting the importance of monitoring their genomic characteristics following a One Health perspective, in which the health of humans is related to the health of animals, and the environment.
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Affiliation(s)
- Diana Dias
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Sávio Costa
- Centro de Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém, Brazil
| | - Carlos Fonseca
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal; ForestWISE - Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - Rafael Baraúna
- Centro de Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém, Brazil
| | - Tânia Caetano
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Sónia Mendo
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.
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60
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Genetic Characteristics of the Transmissible Locus of Stress Tolerance (tLST) and tLST Harboring Escherichia coli as Revealed by Large-Scale Genomic Analysis. Appl Environ Microbiol 2022; 88:e0218521. [PMID: 35285715 DOI: 10.1128/aem.02185-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The transmissible locus of stress tolerance (tLST) confers resistance to multiple stresses in E. coli. Utilizing 18,959 E. coli genomes available in the NCBI database, we investigated the prevalence, phylogenetic distribution, and configuration patterns of tLST, and correlations between tLST, and virulence and antimicrobial resistance (AMR) genes in E. coli. Four tLST variants were found in 2.7% of E. coli, with the most prevalent (77.1%) variant being tLST1 followed by tLST2 (8.3%), tLST3b (8.3%) and tLST3a (6.3%). The majority (93%) of those tLST were in E. coli belonging to phylogroup A in which the prevalence was 10.4%. tLST was also found in phylogroup B1 (0.5%) and C (0.5%) but not found in B2 or D-G. An additional 1% of the 18,959 E. coli genomes harbored tLST fragments to various extent. Phylogenetic analysis revealed both intra- and interspecies transmission of both chromosomal and plasmid-borne tLST, with E. coli showing a preference of chromosomal over plasmid-borne tLST. The presence of tLST and virulence genes in E. coli was overall negatively correlated, but tLST was found in all genomes of a subgroup of enterotoxigenic E. coli (ST2332). Of note, no Shiga toxin-producing E. coli (n = 3,492) harbored tLST. The prevalence of tLST and AMR genes showed different temporal trends over the period 1985 to 2019. However, a substantial fraction of tLST positive E. coli harbor AMR genes, posing a threat to public health. In conclusion, this study improves our understanding of the genetic characteristics of tLST and E. coli harboring tLST. IMPORTANCE This study, through a large-scale genomic analysis, demonstrated that the genomic island tLST related to multiple stress resistance (such as extreme heat resistance and oxidative stress tolerance) in E. coli is differentially present in subgroups of E. coli and is strongly associated with certain phylogenetic background of the host strain. The study also shows the transmission mechanisms of tLST in E. coli and other bacterial species. The overall negative association of tLST, and virulence genes and antimicrobial (AMR) genes suggest the selective pressures for the acquisition and transmission of these traits likely differ. Even so, the high prevalence of tLST in the enterotoxigenic E. coli clone ST2332 and co-occurrence of tLST and AMR genes in E. coli are concerning. Thus, the findings better our understanding of tLST evolution and provide information for risk assessment of tLST harboring bacteria.
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61
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Bong CW, Low KY, Chai LC, Lee CW. Prevalence and Diversity of Antibiotic Resistant Escherichia coli From Anthropogenic-Impacted Larut River. Front Public Health 2022; 10:794513. [PMID: 35356018 PMCID: PMC8960044 DOI: 10.3389/fpubh.2022.794513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Aquatic environments, under frequent anthropogenic pressure, could serve as reservoirs that provide an ideal condition for the acquisition and dissemination of antibiotic resistance genetic determinants. We investigated the prevalence and diversity of antibiotic-resistant Escherichia coli by focusing on their genetic diversity, virulence, and resistance genes in anthropogenic-impacted Larut River. The abundance of E. coli ranged from (estimated count) Est 1 to 4.7 × 105 (colony-forming units per 100 ml) CFU 100 ml−1 to Est 1 to 4.1 × 105 CFU 100 ml−1 with phylogenetic group B1 (46.72%), and A (34.39%) being the most predominant. The prevalence of multiple antibiotic resistance phenotypes of E. coli, with the presence of tet and sul resistance genes, was higher in wastewater effluents than in the river waters. These findings suggested that E. coli could be an important carrier of the resistance genes in freshwater river environments. The phylogenetic composition of E. coli and resistance genes was associated with physicochemical properties and antibiotic residues. These findings indicated that the anthropogenic inputs exerted an effect on the E. coli phylogroup composition, diversification of multiple antibiotic resistance phenotypes, and the distribution of resistance genes in the Larut River.
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Affiliation(s)
- Chui Wei Bong
- Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
- Institute of Ocean and Earth Sciences (IOES), Universiti Malaya, Kuala Lumpur, Malaysia
- *Correspondence: Chui Wei Bong ;
| | - Kyle Young Low
- Institute of Ocean and Earth Sciences (IOES), Universiti Malaya, Kuala Lumpur, Malaysia
- Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Lay Ching Chai
- Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
- Institute of Ocean and Earth Sciences (IOES), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Choon Weng Lee
- Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
- Institute of Ocean and Earth Sciences (IOES), Universiti Malaya, Kuala Lumpur, Malaysia
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van Dijk LR, Walker BJ, Straub TJ, Worby CJ, Grote A, Schreiber HL, Anyansi C, Pickering AJ, Hultgren SJ, Manson AL, Abeel T, Earl AM. StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities. Genome Biol 2022; 23:74. [PMID: 35255937 PMCID: PMC8900328 DOI: 10.1186/s13059-022-02630-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 02/09/2022] [Indexed: 01/21/2023] Open
Abstract
Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which deconvolves strain mixtures and characterizes component strains at the nucleotide level from short-read metagenomic sequencing with higher sensitivity and resolution than other tools. StrainGE is able to identify strains at 0.1x coverage and detect variants for multiple conspecific strains within a sample from coverages as low as 0.5x.
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Affiliation(s)
- Lucas R. van Dijk
- grid.66859.340000 0004 0546 1623Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142 USA ,grid.5292.c0000 0001 2097 4740Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE The Netherlands
| | - Bruce J. Walker
- grid.66859.340000 0004 0546 1623Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142 USA ,Applied Invention, Cambridge, MA USA
| | - Timothy J. Straub
- grid.66859.340000 0004 0546 1623Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Colin J. Worby
- grid.66859.340000 0004 0546 1623Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142 USA
| | - Alexandra Grote
- grid.66859.340000 0004 0546 1623Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142 USA
| | - Henry L. Schreiber
- grid.4367.60000 0001 2355 7002Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Women’s Infectious Disease Research (CWIDR), Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Christine Anyansi
- grid.5292.c0000 0001 2097 4740Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE The Netherlands
| | - Amy J. Pickering
- grid.47840.3f0000 0001 2181 7878Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA 94720 USA ,grid.429997.80000 0004 1936 7531Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA USA
| | - Scott J. Hultgren
- grid.4367.60000 0001 2355 7002Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Women’s Infectious Disease Research (CWIDR), Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Abigail L. Manson
- grid.66859.340000 0004 0546 1623Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142 USA
| | - Thomas Abeel
- grid.66859.340000 0004 0546 1623Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142 USA ,grid.5292.c0000 0001 2097 4740Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE The Netherlands
| | - Ashlee M. Earl
- grid.66859.340000 0004 0546 1623Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142 USA
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Thomson NM, Gilroy R, Getino M, Foster-Nyarko E, van Vliet AH, La Ragione RM, Pallen MJ. Remarkable genomic diversity among Escherichia isolates recovered from healthy chickens. PeerJ 2022; 10:e12935. [PMID: 35251780 PMCID: PMC8896058 DOI: 10.7717/peerj.12935] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/23/2022] [Indexed: 01/11/2023] Open
Abstract
The genus Escherichia has been extensively studied and it is known to encompass a range of commensal and pathogenic bacteria that primarily inhabit the gastrointestinal tracts of warm-blooded vertebrates. However, the presence of E. coli as a model organism and potential pathogen has diverted attention away from commensal strains and other species in the genus. To investigate the diversity of Escherichia in healthy chickens, we collected fecal samples from antibiotic-free Lohmann Brown layer hens and determined the genome sequences of 100 isolates, 81 of which were indistinguishable at the HC0 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing scheme. Despite initial selection on CHROMagar Orientation medium, which is considered selective for E. coli, in silico phylotyping and core genome single nucleotide polymorphism analysis revealed the presence of at least one representative of all major clades of Escherichia, except for E. albertii, Shigella, and E. coli phylogroup B2 and cryptic clade I. The most frequent phylogenomic groups were E. coli phylogroups A and B1 and E. ruysiae (clades III and IV). We compiled a collection of reference strains isolated from avian sources (predominantly chicken), representing every Escherichia phylogroup and species, and used it to confirm the phylogeny and diversity of our isolates. Overall, the isolates carried low numbers of the virulence and antibiotic resistance genes typically seen in avian pathogenic E. coli. Notably, the clades not recovered are ones that have been most strongly associated with virulence by other studies.
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Affiliation(s)
| | - Rachel Gilroy
- Quadram Institute Bioscience, Norwich, Norfolk, United Kingdom
| | - Maria Getino
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom,Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Ebenezer Foster-Nyarko
- Quadram Institute Bioscience, Norwich, Norfolk, United Kingdom,Department of Infection Biology, London School of Hygiene & Tropical Medicine, University of London, London, United Kingdom
| | - Arnoud H.M. van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Roberto M. La Ragione
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom,Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich, Norfolk, United Kingdom,Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, United Kingdom
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64
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Denamur E, Condamine B, Esposito-Farèse M, Royer G, Clermont O, Laouenan C, Lefort A, de Lastours V, Galardini M. Genome wide association study of Escherichia coli bloodstream infection isolates identifies genetic determinants for the portal of entry but not fatal outcome. PLoS Genet 2022; 18:e1010112. [PMID: 35324915 PMCID: PMC8946752 DOI: 10.1371/journal.pgen.1010112] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/21/2022] [Indexed: 11/19/2022] Open
Abstract
Escherichia coli is an important cause of bloodstream infections (BSI), which is of concern given its high mortality and increasing worldwide prevalence. Finding bacterial genetic variants that might contribute to patient death is of interest to better understand infection progression and implement diagnostic methods that specifically look for those factors. E. coli samples isolated from patients with BSI are an ideal dataset to systematically search for those variants, as long as the influence of host factors such as comorbidities are taken into account. Here we performed a genome-wide association study (GWAS) using data from 912 patients with E. coli BSI from hospitals in Paris, France. We looked for associations between bacterial genetic variants and three patient outcomes (death at 28 days, septic shock and admission to intensive care unit), as well as two portals of entry (urinary and digestive tract), using various clinical variables from each patient to account for host factors. We did not find any association between genetic variants and patient outcomes, potentially confirming the strong influence of host factors in influencing the course of BSI; we however found a strong association between the papGII operon and entrance of E. coli through the urinary tract, which demonstrates the power of bacterial GWAS when applied to actual clinical data. Despite the lack of associations between E. coli genetic variants and patient outcomes, we estimate that increasing the sample size by one order of magnitude could lead to the discovery of some putative causal variants. Given the wide adoption of bacterial genome sequencing of clinical isolates, such sample sizes may be soon available.
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Affiliation(s)
- Erick Denamur
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France
- Laboratoire de Génétique Moléculaire, Hôpital Bichat, AP-HP, Paris, France
| | | | - Marina Esposito-Farèse
- Département d’épidémiologie, biostatistiques et recherche clinique, Hôpital Bichat, AP-HP, Paris, France
| | - Guilhem Royer
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France
- LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Paris-Saclay, Evry, France
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, Créteil, France
| | | | - Cédric Laouenan
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France
- Département d’épidémiologie, biostatistiques et recherche clinique, Hôpital Bichat, AP-HP, Paris, France
| | - Agnès Lefort
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France
- Service de Médecine Interne, Hôpital Beaujon, AP-HP, Clichy, France
| | - Victoire de Lastours
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France
- Service de Médecine Interne, Hôpital Beaujon, AP-HP, Clichy, France
| | - Marco Galardini
- Institute for Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), Hannover, Germany
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65
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Halaji M, Fayyazi A, Rajabnia M, Zare D, Pournajaf A, Ranjbar R. Phylogenetic Group Distribution of Uropathogenic Escherichia coli and Related Antimicrobial Resistance Pattern: A Meta-Analysis and Systematic Review. Front Cell Infect Microbiol 2022; 12:790184. [PMID: 35281449 PMCID: PMC8914322 DOI: 10.3389/fcimb.2022.790184] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/26/2022] [Indexed: 12/20/2022] Open
Abstract
The phylogenetic classification of Escherichia coli isolates is of great importance not only for understanding the populations of E. coli but also for clarifying the relationship between strains and diseases. The present study aimed to evaluate the prevalence of phylogenetic groups, antibiotic susceptibility pattern, and virulence genes among uropathogenic E. coli (UPEC) isolated from different parts of Iran through a systematic review and meta-analysis. Several international electronic sources, including Web of Science, PubMed, Scopus, and Embase, were searched (2000–2020) in order to identify the studies compatible with our inclusion criteria. The meta-analysis was performed using the metaprop program in the STATA (version 11) software. Based on our comprehensive search, 28 studies meeting the eligibility criteria were included in the meta-analysis. The pooled prevalence of phylogroups B2, D, B1, and A was 39%, 26%, 18%, and 8%, respectively. In addition, there was a significant heterogeneity among different phylogroups. However, according to the results of Begg’s and Egger’s tests, there were no significant publication bias in phylogroups B2, D, B1, and A. This research provided the first comprehensive study on phylogroups of UPEC isolated in Iran. Our findings indicated that phylogroup B2 and group D were the most predominant phylogenetic groups among UPEC isolates in various regions of Iran. In addition, we observed that certain phylogenetic groups are more antibiotic resistant than the others. It was also observed that the dissemination of virulent phylogroup B2 and D should be controlled via comprehensive infection control measures. Additionally, certain strategies should be developed for monitoring the antibiotic therapy.
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Affiliation(s)
- Mehrdad Halaji
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Department of Microbiology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Amirhossein Fayyazi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Rajabnia
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Department of Microbiology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Donya Zare
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Abazar Pournajaf
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Department of Microbiology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
- *Correspondence: Reza Ranjbar,
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66
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Koh XP, Shen Z, Woo CF, Yu Y, Lun HI, Cheung SW, Kwan JKC, Lau SCK. Genetic and Ecological Diversity of Escherichia coli and Cryptic Escherichia Clades in Subtropical Aquatic Environments. Front Microbiol 2022; 13:811755. [PMID: 35250929 PMCID: PMC8891540 DOI: 10.3389/fmicb.2022.811755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli not only inhabit the large intestines of human and warm-blooded animals but could also persist in the external environment. However, current knowledge was largely based on host-associated strains. Moreover, cryptic Escherichia clades that were often misidentified as E. coli by conventional diagnostic methods were discovered. Failure to distinguish them from E. coli sensu stricto could lead to inaccurate conclusions about the population genetics of E. coli. Based on seven housekeeping genes, we determine the genetic and ecological diversity of E. coli and cryptic clades as they occupy aquatic habitats with different characteristics and human impact levels in subtropical Hong Kong. Contrary to previous reports, clade II was the most abundant cryptic lineage co-isolated with E. coli, being especially abundant in relatively pristine subtropical aquatic environments. The phylogenetically distinct cryptic clades and E. coli showed limited recombination and significant genetic divergence. Analyses indicated that these clade II strains were ecologically differentiated from typical E. coli; some may even represent novel environmental Escherichia clades that were closely related to the original clade II strains of fecal origins. E. coli of diverse origins exhibited clonality amidst divergent genotypes STs, echoing other studies in that recombination in housekeeping genes was insufficient to disrupt phylogenetic signals of the largely clonal E. coli. Notably, environmental E. coli were less diverse than fecal isolates despite contributing many new alleles and STs. Finally, we demonstrated that human activities influenced the distribution of E. coli and clade II in a small aquatic continuum. Moving from relatively pristine sites toward areas with higher human disturbance, the abundance of clade II isolates and new E. coli genotypes reduces, while E. coli bearing class I integrons and belonging to CCs of public health concern accumulates. Altogether, this work revealed the new genetic diversity of E. coli and cryptic clades embedded in selected subtropical aquatic habitats, especially relatively pristine sites, which will aid a more thorough understanding of the extent of their genetic and functional variations in relation to diverse habitats with varied conditions.
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Affiliation(s)
- Xiu Pei Koh
- Division of Environment and Sustainability, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Zhiyong Shen
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Chun Fai Woo
- Division of Environment and Sustainability, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Yanping Yu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Hau In Lun
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Sze Wan Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, Hong Kong SAR, China
| | - Joseph Kai Cho Kwan
- Division of Environment and Sustainability, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Stanley Chun Kwan Lau
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
- *Correspondence: Stanley Chun Kwan Lau,
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A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58. Nat Commun 2022; 13:683. [PMID: 35115531 PMCID: PMC8813906 DOI: 10.1038/s41467-022-28342-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 01/11/2022] [Indexed: 12/15/2022] Open
Abstract
Escherichia coli ST58 has recently emerged as a globally disseminated uropathogen that often progresses to sepsis. Unlike most pandemic extra-intestinal pathogenic E. coli (ExPEC), which belong to pathogenic phylogroup B2, ST58 belongs to the environmental/commensal phylogroup B1. Here, we present a pan-genomic analysis of a global collection of 752 ST58 isolates from diverse sources. We identify a large ST58 sub-lineage characterized by near ubiquitous carriage of ColV plasmids, which carry genes encoding virulence factors, and by a distinct accessory genome including genes typical of the Yersiniabactin High Pathogenicity Island. This sub-lineage includes three-quarters of all ExPEC sequences in our study and has a broad host range, although poultry and porcine sources predominate. By contrast, strains isolated from cattle often lack ColV plasmids. Our data indicate that ColV plasmid acquisition contributed to the divergence of the major ST58 sub-lineage, and different sub-lineages inhabit poultry, swine and cattle.
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68
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Nascimento JAS, Santos FF, Santos-Neto JF, Trovão LO, Valiatti TB, Pinaffi IC, Vieira MAM, Silva RM, Falsetti IN, Santos ACM, Gomes TAT. Molecular Epidemiology and Presence of Hybrid Pathogenic Escherichia coli among Isolates from Community-Acquired Urinary Tract Infection. Microorganisms 2022; 10:microorganisms10020302. [PMID: 35208757 PMCID: PMC8874565 DOI: 10.3390/microorganisms10020302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Urinary tract infections (UTI) affect community and healthcare patients worldwide and may have different clinical outcomes. We assessed the phylogenetic origin, the presence of 43 virulence factors (VFs) of diarrheagenic and extraintestinal pathogenic Escherichia coli, and the occurrence of hybrid strains among E. coli isolates from 172 outpatients with different types of UTI. Isolates from phylogroup B2 (46%) prevailed, followed by phylogroups A (15.7%) and B1 (12.2%), with similar phylogenetic distribution in symptomatic and asymptomatic patients. The most frequent VFs according to their functional category were fimA (94.8%), ompA (83.1%), ompT (63.3%), chuA (57.6%), and vat (22%). Using published molecular criteria, 34.3% and 18.0% of the isolates showed intrinsic virulence and uropathogenic potential, respectively. Two strains carried the eae and escV genes and one the aggR gene, which classified them as hybrid strains. These hybrid strains interacted with renal and bladder cells, reinforcing their uropathogenic potential. The frequency of UPEC strains bearing a more pathogenic potential in the outpatients studied was smaller than reported in other regions. Our data contribute to deepening current knowledge about the mechanisms involved in UTI pathogenesis, especially among hybrid UPEC strains, as these could colonize the host’s intestine, leading to intestinal infections followed by UTI.
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Affiliation(s)
- Júllia A. S. Nascimento
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, Brazil; (J.A.S.N.); (J.F.S.-N.); (L.O.T.); (M.A.M.V.); (A.C.M.S.)
| | - Fernanda F. Santos
- Laboratório Alerta, Disciplina de Infectologia, Departamento de Medicina, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04039-032, Brazil; (F.F.S.); (T.B.V.)
| | - José F. Santos-Neto
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, Brazil; (J.A.S.N.); (J.F.S.-N.); (L.O.T.); (M.A.M.V.); (A.C.M.S.)
| | - Liana O. Trovão
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, Brazil; (J.A.S.N.); (J.F.S.-N.); (L.O.T.); (M.A.M.V.); (A.C.M.S.)
| | - Tiago B. Valiatti
- Laboratório Alerta, Disciplina de Infectologia, Departamento de Medicina, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04039-032, Brazil; (F.F.S.); (T.B.V.)
| | - Isabel C. Pinaffi
- Laboratório Santa Cruz Medicina Diagnóstica, Mogi Guaçu 13840-052, Brazil; (I.C.P.); (I.N.F.)
| | - Mônica A. M. Vieira
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, Brazil; (J.A.S.N.); (J.F.S.-N.); (L.O.T.); (M.A.M.V.); (A.C.M.S.)
| | - Rosa M. Silva
- Laboratório de Enterobactérias, Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, Brazil;
| | - Ivan N. Falsetti
- Laboratório Santa Cruz Medicina Diagnóstica, Mogi Guaçu 13840-052, Brazil; (I.C.P.); (I.N.F.)
| | - Ana C. M. Santos
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, Brazil; (J.A.S.N.); (J.F.S.-N.); (L.O.T.); (M.A.M.V.); (A.C.M.S.)
| | - Tânia A. T. Gomes
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, Brazil; (J.A.S.N.); (J.F.S.-N.); (L.O.T.); (M.A.M.V.); (A.C.M.S.)
- Correspondence: ; Tel.: +55-11-5576-4848
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Sacher-Pirklbauer A, Klein-Jöbstl D, Sofka D, Blanc-Potard AB, Hilbert F. Phylogenetic Groups and Antimicrobial Resistance Genes in Escherichia coli from Different Meat Species. Antibiotics (Basel) 2021; 10:antibiotics10121543. [PMID: 34943755 PMCID: PMC8698590 DOI: 10.3390/antibiotics10121543] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/03/2021] [Accepted: 12/14/2021] [Indexed: 12/02/2022] Open
Abstract
Escherichia coli isolated from meat of different animal species may harbour antimicrobial resistance genes and may thus be a threat to human health. The objectives of this study were to define antimicrobial resistance genes in E. coli isolates from pork, beef, chicken- and turkey meat and analyse whether their resistance genotypes associated with phylogenetic groups or meat species. A total number of 313 E. coli samples were isolated using standard cultural techniques. In 98% of resistant isolates, a dedicated resistance gene could be identified by PCR. Resistance genes detected were tet(A) and tet(B) for tetracycline resistance, strA and aadA1 for streptomycin resistance, sulI and sulII for resistance against sulphonamides, dfr and aphA for kanamycin resistance and blaTEM for ampicillin resistance. One stx1 harbouring E. coli isolated from pork harboured the tet(A) gene and belonged to phylogenetic group B2, whilst another stx1 positive isolate from beef was multi-resistant and tested positive for blaTEM,aphA, strA–B, sulII, and tet(A) and belonged to phylogenetic group A. In conclusion, the distribution of resistance elements was almost identical and statistically indifferent in isolates of different meat species. Phylogenetic groups did not associate with the distribution of resistance genes and a rather low number of diverse resistance genes were detected. Most E. coli populations with different resistance genes against one drug often revealed statistically significant different MIC values.
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Affiliation(s)
- Angelika Sacher-Pirklbauer
- Institute of Food Safety, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria; (A.S.-P.); (D.S.)
| | - Daniela Klein-Jöbstl
- Section of Herd Management, Clinic for Ruminats, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Dmitrij Sofka
- Institute of Food Safety, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria; (A.S.-P.); (D.S.)
| | - Anne-Béatrice Blanc-Potard
- Laboratory of Pathogen-Host Interactions (LPHI), Université Montpellier, 34095 Montpellier, France;
- CNRS, UMR 5235, 34095 Montpellier, France
| | - Friederike Hilbert
- Institute of Food Safety, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria; (A.S.-P.); (D.S.)
- Correspondence: ; Tel.: +43-125-0773-316
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Tan L, Zhang C, Liu F, Chen P, Wei X, Li H, Yi G, Xu Y, Zheng X. Three-compartment septic tanks as sustainable on-site treatment facilities? Watch out for the potential dissemination of human-associated pathogens and antibiotic resistance. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 300:113709. [PMID: 34547574 DOI: 10.1016/j.jenvman.2021.113709] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Improved sanitation is critical important to reduce the spread of human deposited pathogens and antibiotic resistance genes (ARGs). In the China's rural "Toilet Revolution", three-compartment septic tanks (SPTs) are widely used as household domestic sewage treatment facilities. The effluents of SPTs are encouraged to be used as fertilizer in agriculture. However, whether SPT could eliminate fecal pathogens and ARGs is still unrevealed which is crucial in risk assessment of SPT effluent utilization. Herein, we employed metagenomic sequencing to investigate the pathogens and ARGs in rural household SPTs from Tianjin, China. We found that rural household SPT effluents conserved pathogens comparable to that of the influents. A total of 441 ARGs conferring resistance to 26 antibiotic classes were observed in rural household SPTs, with the relative abundance ranging from 709 to 1800 ppm. Results of metagenomic assembly indicated that some ARG-MGE-carrying contigs were carried by pathogens, which may pose risk to human and animal health after being introduced to the environment. This study raises the question of SPTs as sustainable on-site treatment facilities for rural domestic sewage and underscores the need for more attention to the propagation and dissemination of antibiotic-resistant pathogens from SPT to the environments, animals, and humans.
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Affiliation(s)
- Lu Tan
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Chunxue Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Fang Liu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Peizhen Chen
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Xiaocheng Wei
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Houyu Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Gao Yi
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Yan Xu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
| | - Xiangqun Zheng
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
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Wan Y, Mills E, Leung RC, Vieira A, Zhi X, Croucher NJ, Woodford N, Jauneikaite E, Ellington MJ, Sriskandan S. Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom. Microb Genom 2021; 7:000702. [PMID: 34860151 PMCID: PMC8767348 DOI: 10.1099/mgen.0.000702] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Antimicrobial resistance in enteric or urinary Escherichia coli is a risk factor for invasive E. coli infections. Due to widespread trimethoprim resistance amongst urinary E. coli and increased bacteraemia incidence, a national recommendation to prescribe nitrofurantoin for uncomplicated urinary tract infection was made in 2014. Nitrofurantoin resistance is reported in <6% urinary E. coli isolates in the UK, however, mechanisms underpinning nitrofurantoin resistance in these isolates remain unknown. This study aimed to identify the genetic basis of nitrofurantoin resistance in urinary E. coli isolates collected from north west London and then elucidate resistance-associated genetic alterations in available UK E. coli genomes. As a result, an algorithm was developed to predict nitrofurantoin susceptibility. Deleterious mutations and gene-inactivating insertion sequences in chromosomal nitroreductase genes nfsA and/or nfsB were identified in genomes of nine confirmed nitrofurantoin-resistant urinary E. coli isolates and additional 11 E. coli isolates that were highlighted by the prediction algorithm and subsequently validated to be nitrofurantoin-resistant. Eight categories of allelic changes in nfsA, nfsB, and the associated gene ribE were detected in 12412 E. coli genomes from the UK. Evolutionary analysis of these three genes revealed homoplasic mutations and explained the previously reported order of stepwise mutations. The mobile gene complex oqxAB, which is associated with reduced nitrofurantoin susceptibility, was identified in only one of the 12412 genomes. In conclusion, mutations and insertion sequences in nfsA and nfsB were leading causes of nitrofurantoin resistance in UK E. coli. As nitrofurantoin exposure increases in human populations, the prevalence of nitrofurantoin resistance in carriage E. coli isolates and those from urinary and bloodstream infections should be monitored.
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Affiliation(s)
- Yu Wan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ewurabena Mills
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Rhoda C.Y. Leung
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Present address: Department of Microbiology, Queen Mary Hospital, Hong Kong S.A.R., PR China
| | - Ana Vieira
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Xiangyun Zhi
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Nicholas J. Croucher
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, Colindale, London, United Kingdom
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Matthew J. Ellington
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, Colindale, London, United Kingdom
| | - Shiranee Sriskandan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
- *Correspondence: Shiranee Sriskandan,
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72
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Genomic and Phenotypic Analysis of Heat and Sanitizer Resistance in Escherichia coli from Beef in Relation to the Locus of Heat Resistance. Appl Environ Microbiol 2021; 87:e0157421. [PMID: 34550750 DOI: 10.1128/aem.01574-21] [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: 01/21/2023] Open
Abstract
The locus of heat resistance (LHR) can confer heat resistance to Escherichia coli to various extents. This study investigated the phylogenetic relationships and the genomic and phenotypic characteristics of E. coli with or without LHR recovered from beef by direct plating or from enrichment broth at 42°C. LHR-positive E. coli isolates (n = 24) were subjected to whole-genome sequencing by short and long reads. LHR-negative isolates (n = 18) from equivalent sources as LHR-positive isolates were short-read sequenced. All isolates were assessed for decimal reduction time at 60°C (D60°C) and susceptibility to the sanitizers E-SAN and Perox-E. Selected isolates were evaluated for growth at 42°C. The LHR-positive and -negative isolates were well separated on the core genome tree, with 22/24 positive isolates clustering into three clades. Isolates within clade 1 and 2, despite their different D60°C values, were clonal, as determined by subtyping (multilocus sequence typing [MLST], core genome MLST, and serotyping). Isolates within each clade are of one serotype. The LHR-negative isolates were genetically diverse. The LHR-positive isolates had a larger (P < 0.001) median genome size by 0.3 Mbp (5.0 versus 4.7 Mbp) and overrepresentation of genes related to plasmid maintenance, stress response, and cryptic prophages but underrepresentation of genes involved in epithelial attachment and virulence. All LHR-positive isolates harbored a chromosomal copy of LHR, and all clade 2 isolates had an additional partial copy of LHR on conjugative plasmids. The growth rates at 42°C were 0.71 ± 0.02 and 0.65 ± 0.02 log(OD) h-1 for LHR-positive and -negative isolates, respectively. No meaningful difference in sanitizer susceptibility was noted between LHR-positive and -negative isolates. IMPORTANCE Resistant bacteria are serious food safety and public health concerns. Heat resistance conferred by the LHR varies largely among different strains of E. coli. The findings in this study show that genomic background and composition of LHR, in addition to the presence of LHR, play an important role in the degree of heat resistance in E. coli and that strains with certain genetic backgrounds are more likely to acquire and maintain the LHR. Also, caution should be exercised when recovering E. coli at elevated temperatures, as the presence of LHR may confer growth advantages to some strains. Interestingly, the LHR-harboring strains seem to have evolved further from their primary animal host to adapt to their secondary habitat, as reflected by fewer genes involved in virulence and epithelial attachment. The phylogenetic relationships among the isolates point toward multiple mechanisms for acquisition of LHR by E. coli, likely prior to its being deposited on meat.
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73
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Montero L, Irazabal J, Cardenas P, Graham JP, Trueba G. Extended-Spectrum Beta-Lactamase Producing- Escherichia coli Isolated From Irrigation Waters and Produce in Ecuador. Front Microbiol 2021; 12:709418. [PMID: 34671324 PMCID: PMC8521160 DOI: 10.3389/fmicb.2021.709418] [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: 05/13/2021] [Accepted: 09/13/2021] [Indexed: 11/25/2022] Open
Abstract
In cities across the globe, the majority of wastewater – that includes drug resistant and pathogenic bacteria among other contaminants – is released into streams untreated. This water is often subsequently used for irrigation of pastures and produce. This use of wastewater-contaminated streams allows antibiotic-resistant bacteria to potentially cycle back to humans through agricultural products. In this study, we investigated the prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from produce and irrigation water across 17 provinces of Ecuador. A total of 117 vegetable samples, 119 fruit samples, and 38 irrigation water samples were analyzed. Results showed that 11% of the samples were positive for E. coli including 11 irrigation water samples (29%), and samples of 13 vegetables (11%), and 11 fruits (9%). Among the 165 E. coli isolates cultured, 96 (58%) had the ESBL phenotype, and 58% of ESBL producing E. coli came from irrigation water samples, 11% from vegetables, and 30% from fruits. The blaCTX–M–55, blaCTX–M 65, and blaCTX–M 15 genes were the most frequently found gene associated with the ESBL phenotype and coincided with the blaCTX–M alleles associated with human infections in Ecuador. Three isolates had the mcr-1 gene which is responsible for colistin resistance. This report provides evidence of the potential role of irrigation water in the growing antimicrobial resistance crisis in Ecuador.
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Affiliation(s)
- Lorena Montero
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jorge Irazabal
- Agrocalidad, Agencia de Regulación y Control Fito y Zoosanitario, Quito, Ecuador
| | - Paul Cardenas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jay P Graham
- Environmental Health Sciences Division, University of California, Berkeley, Berkeley, CA, United States
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
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74
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Leclercq SO, Branger M, Smith DGE, Germon P. Lipopolysaccharide core type diversity in the Escherichia coli species in association with phylogeny, virulence gene repertoire and distribution of type VI secretion systems. Microb Genom 2021; 7. [PMID: 34586053 PMCID: PMC8715443 DOI: 10.1099/mgen.0.000652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli is a very versatile species for which diversity has been explored from various perspectives highlighting, for example, phylogenetic groupings and pathovars, as well as a wide range of O serotypes. The highly variable O-antigen, the most external part of the lipopolysaccharide (LPS) component of the outer membrane of E. coli, is linked to the innermost lipid A through the core region of LPS of which five different structures, denominated K-12, R1, R2, R3 and R4, have been characterized so far. The aim of the present study was to analyse the prevalence of these LPS core types in the E. coli species and explore their distribution in the different E. coli phylogenetic groups and in relationship with the virulence gene repertoire. Results indicated an uneven distribution of core types between the different phylogroups, with phylogroup A strains being the most diverse in terms of LPS core types, while phylogroups B1, D and E strains were dominated by the R3 type, and phylogroups B2 and C strains were dominated by the R1 type. Strains carrying the LEE virulence operon were mostly of the R3 type whatever the phylogroup while, within phylogroup B2, strains carrying a K-12 core all belonged to the complex STc131, one of the major clones of extraintestinal pathogenic E. coli (ExPEC) strains. The origin of this uneven distribution is discussed but remains to be fully explained, as well as the consequences of carrying a specific core type on the wider aspects of bacterial phenotype.
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Affiliation(s)
| | - Maxime Branger
- UMR ISP, INRAE, Université François Rabelais de Tours, F-37380 Nouzilly, France
| | - David G E Smith
- Institute for Biological Chemistry, Biophysics and Bioengineering (IB3), Riccarton Campus, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Pierre Germon
- UMR ISP, INRAE, Université François Rabelais de Tours, F-37380 Nouzilly, France
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75
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Colquhoun RM, Hall MB, Lima L, Roberts LW, Malone KM, Hunt M, Letcher B, Hawkey J, George S, Pankhurst L, Iqbal Z. Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs. Genome Biol 2021; 22:267. [PMID: 34521456 PMCID: PMC8442373 DOI: 10.1186/s13059-021-02473-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 08/19/2021] [Indexed: 12/21/2022] Open
Abstract
We present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the accessory genome, methods which analyze SNPs in just the core genome have unsatisfactory limitations. Pandora approximates a sequenced genome as a recombinant of references, detects novel variation and pan-genotypes multiple samples. Using a reference graph of 578 Escherichia coli genomes, we compare 20 diverse isolates. Pandora recovers more rare SNPs than single-reference-based tools, is significantly better than picking the closest RefSeq reference, and provides a stable framework for analyzing diverse samples without reference bias.
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Affiliation(s)
- Rachel M Colquhoun
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Michael B Hall
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Leandro Lima
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Leah W Roberts
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Kerri M Malone
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Martin Hunt
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Brice Letcher
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia
| | - Sophie George
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Louise Pankhurst
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Zoology, University of Oxford, Mansfield Road, Oxford, UK
| | - Zamin Iqbal
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.
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76
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Petitjean M, Condamine B, Burdet C, Denamur E, Ruppé E. Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes. Microb Genom 2021; 7. [PMID: 34435947 PMCID: PMC8549366 DOI: 10.1099/mgen.0.000489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Escherichia coli is a ubiquitous bacterium that has been widely exposed to antibiotics over the last 70 years. It has adapted by acquiring different antibiotic-resistance genes (ARGs), the census of which we aim to characterize here. To do so, we analysed 70 301 E. coli genomes obtained from the EnteroBase database and detected 1 027 651 ARGs using the AMRFinder, Mustard and ResfinderFG ARG databases. We observed a strong phylogroup and clonal lineage specific distribution of some ARGs, supporting the argument for epistasis between ARGs and the strain genetic background. However, each phylogroup had ARGs conferring a similar antibiotic class resistance pattern, indicating phenotypic adaptive convergence. The G+C content or the type of ARG was not associated with the frequency of the ARG in the database. In addition, we identified ARGs from anaerobic, non-Proteobacteria bacteria in four genomes of E. coli, supporting the hypothesis that the transfer between anaerobic bacteria and E. coli can spontaneously occur but remains exceptional. In conclusion, we showed that phylum barrier and intra-species phylogenetic history are major drivers of the acquisition of a resistome in E. coli.
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Affiliation(s)
| | | | - Charles Burdet
- IAME, INSERM, Université de Paris, F-75018 Paris, France.,Département d'Epidémiologie, Biostatistique et Recherche Clinique, Hôpital Bichat, APHP, F-75018 Paris, France
| | - Erick Denamur
- IAME, INSERM, Université de Paris, F-75018 Paris, France.,Laboratoire de Génétique Moléculaire, Hôpital Bichat, APHP, F-75018 Paris, France
| | - Etienne Ruppé
- IAME, INSERM, Université de Paris, F-75018 Paris, France.,Laboratoire de Bactériologie, Hôpital Bichat, APHP, F-75018 Paris, France
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77
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Clermont O, Condamine B, Dion S, Gordon DM, Denamur E. The E phylogroup of Escherichia coli is highly diverse and mimics the whole E. coli species population structure. Environ Microbiol 2021; 23:7139-7151. [PMID: 34431197 DOI: 10.1111/1462-2920.15742] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/16/2021] [Accepted: 08/22/2021] [Indexed: 12/11/2022]
Abstract
To get a global picture of the population structure of the Escherichia coli phylogroup E, encompassing the O157:H7 EHEC lineage, we analysed the whole genome of 144 strains isolated from various continents, hosts and lifestyles and representative of the phylogroup diversity. The strains possess 4331 to 5440 genes with a core genome of 2771 genes and a pangenome of 33 722 genes. The distribution of these genes among the strains shows an asymmetric U-shaped distribution. E phylogenetic strains have the largest genomes of the species, partly explained by the presence of mobile genetic elements. Sixty-eight lineages were delineated, some of them exhibiting extra-intestinal virulence genes and being virulent in the mouse sepsis model. Except for the EHEC lineages and the reference EPEC, EIEC and ETEC strains, very few strains possess intestinal virulence genes. Most of the strains were devoid of acquired resistance genes, but eight strains possessed extended-spectrum beta-lactamase genes. Human strains belong to specific lineages, some of them being virulent and antibiotic-resistant [sequence type complexes (STcs) 350 and 2064]. The E phylogroup mimics all the features of the species as a whole, a phenomenon already observed at the STc level, arguing for a fractal population structure of E. coli.
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Affiliation(s)
- Olivier Clermont
- Université de Paris, IAME, UMR 1137, INSERM, Paris, F-75018, France
| | | | - Sara Dion
- Université de Paris, IAME, UMR 1137, INSERM, Paris, F-75018, France
| | - David M Gordon
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Erick Denamur
- Université de Paris, IAME, UMR 1137, INSERM, Paris, F-75018, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat-Claude Bernard, Paris, F-75018, France
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78
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Antimicrobial Resistance of Escherichia coli in Dairy Calves: A 15-Year Retrospective Analysis and Comparison of Treated and Untreated Animals. Animals (Basel) 2021; 11:ani11082328. [PMID: 34438785 PMCID: PMC8388469 DOI: 10.3390/ani11082328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/02/2021] [Accepted: 08/05/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary In dairy production, antimicrobial resistance (AMR) is both a health and economic issue that may lead to treatment failures and the spread of multidrug-resistant pathogens. Epidemiological and farm data on AMR are instrumental for selecting the appropriate therapy. However, such data are not always available. We investigated the AMR profile of 2612 Escherichia coli strains isolated from cases of calf diarrhea over a 15-year period (2002–2016). Furthermore, the AMR profiles and major virulence genes of 505 E. coli strains isolated from 1-week- and 2-week-old calves were examined, with a comparison made between those treated with antimicrobials (n = 406) and not treated (n = 99) as well as between the two age groups to evaluate the potential effects of treatments on AMR and pathogenicity. Resistance to tetracycline was the most common, followed by resistance to sulfamethoxazole/trimethoprim and flumequine. Treated calves showed a higher rate of AMR and virulence genes. These results highlight the risk of the frequent use of antimicrobials on calf microflora in leading to potentially ineffective treatments. A higher resistance to amoxicillin/clavulanic acid, enrofloxacin, and florfenicol was found in 1-week-old calves, suggesting the environment as a possible AMR source. In conclusion, measures such as improved hygiene in the calving pen, antimicrobial stewardship, and monitoring for resistant pathogens in manure should be promoted to prevent the spread of AMR. Abstract The health problem of antimicrobial resistance (AMR) involves several species. AMR surveillance is essential to identify its development and design control strategies; however, available data are still limited in some contexts. The AMR profiles of 2612 E. coli strains isolated over a period of 15 years (2002–2016) from calf enteric cases were analyzed to determine the presence of resistance and their temporal dynamics. Furthermore, the AMR profiles and the presence of the major virulence genes of 505 E. coli strains isolated from 1-week- and 2-week-old calves, 406 treated with antimicrobials and 99 untreated, were analyzed and compared to investigate the potential effects of treatment on AMR and strain pathogenicity. Resistance to tetracycline (90.70%) was the most common, followed by resistance to sulfamethoxazole/trimethoprim (77.70%) and flumequine (72.10%). The significantly higher percentage of AMR and virulence gene expression recorded in treated calves, combined with the statistically higher resistance to sulfamethoxazole/trimethoprim in E. coli with K99, corroborates the notion of resistance being induced by the frequent use of antimicrobials, leading to treatments potentially becoming ineffective. The significantly higher resistance to amoxicillin/clavulanic acid, enrofloxacin, and florfenicol in isolates from 1-week-old calves suggests the role of the environment as a source of contamination that should be investigated further.
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79
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Redondo-Salvo S, Bartomeus-Peñalver R, Vielva L, Tagg KA, Webb HE, Fernández-López R, de la Cruz F. COPLA, a taxonomic classifier of plasmids. BMC Bioinformatics 2021; 22:390. [PMID: 34332528 PMCID: PMC8325299 DOI: 10.1186/s12859-021-04299-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/12/2021] [Indexed: 11/10/2022] Open
Abstract
Background Plasmids are mobile genetic elements, key in the dissemination of antibiotic resistance, virulence determinants and other adaptive traits in bacteria. Obtaining a robust method for plasmid classification is necessary to better understand the genetics and epidemiology of many pathogens. Until now, plasmid classification systems focused on specific traits, which limited their precision and universality. The definition of plasmid taxonomic units (PTUs), based on average nucleotide identity metrics, allows the generation of a universal plasmid classification scheme, applicable to all bacterial taxa. Here we present COPLA, a software able to assign plasmids to known and novel PTUs, based on their genomic sequence. Results We implemented an automated pipeline able to assign a given plasmid DNA sequence to its cognate PTU, and assessed its performance using a sample of 1000 unclassified plasmids. Overall, 41% of the samples could be assigned to a previously defined PTU, a number that reached 63% in well-known taxa such as the Enterobacterales order. The remaining plasmids represent novel PTUs, indicating that a large fraction of plasmid backbones is still uncharacterized. Conclusions COPLA is a bioinformatic tool for universal, species-independent, plasmid classification. Offered both as an automatable pipeline and an open web service, COPLA will help bacterial geneticists and clinical microbiologists to quickly classify plasmids. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04299-x.
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Affiliation(s)
- Santiago Redondo-Salvo
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Roger Bartomeus-Peñalver
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Luis Vielva
- Departamento de Ingeniería de las Comunicaciones, Universidad de Cantabria, Santander, Spain
| | - Kaitlin A Tagg
- Centers for Disease Control and Prevention, Atlanta, USA.,WDS, Inc., Atlanta, USA
| | - Hattie E Webb
- Centers for Disease Control and Prevention, Atlanta, USA.,WDS, Inc., Atlanta, USA
| | - Raúl Fernández-López
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain.
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80
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Genomic evolution of antimicrobial resistance in Escherichia coli. Sci Rep 2021; 11:15108. [PMID: 34301966 PMCID: PMC8302606 DOI: 10.1038/s41598-021-93970-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/05/2021] [Indexed: 11/09/2022] Open
Abstract
The emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.
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81
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Saraceno M, Gómez Lugo S, Ortiz N, Gómez BM, Sabio Y García CA, Frankel N, Graziano M. Unraveling the ecological processes modulating the population structure of Escherichia coli in a highly polluted urban stream network. Sci Rep 2021; 11:14679. [PMID: 34282205 PMCID: PMC8289912 DOI: 10.1038/s41598-021-94198-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 07/07/2021] [Indexed: 02/06/2023] Open
Abstract
Escherichia coli dynamics in urban watersheds are affected by a complex balance among external inputs, niche modulation and genetic variability. To explore the ecological processes influencing E. coli spatial patterns, we analyzed its abundance and phylogenetic structure in water samples from a stream network with heterogeneous urban infrastructure and environmental conditions. Our results showed that environmental and infrastructure variables, such as macrophyte coverage, DIN and sewerage density, mostly explained E. coli abundance. Moreover, main generalist phylogroups A and B1 were found in high proportion, which, together with an observed negative relationship between E. coli abundance and phylogroup diversity, suggests that their dominance might be due to competitive exclusion. Lower frequency phylogroups were associated with sites of higher ecological disturbance, mainly involving simplified habitats, higher drainage infrastructure and septic tank density. In addition to the strong negative relationship between phylogroup diversity and dominance, the occurrence of these phylogroups would be associated with increased facilitated dispersal. Nutrients also contributed to explaining phylogroup distribution. Our study proposes the differential contribution of distinct ecological processes to the patterns of E. coli in an urban watershed, which is useful for the monitoring and management of fecal pollution.
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Affiliation(s)
- Martín Saraceno
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), CONICET - Universidad de Buenos Aires, 1428, Buenos Aires, Argentina
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428, Buenos Aires, Argentina
| | - Sebastián Gómez Lugo
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428, Buenos Aires, Argentina
| | - Nicolás Ortiz
- Instituto Nacional del Agua, 1804, Ezeiza, Argentina
| | | | - Carmen A Sabio Y García
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428, Buenos Aires, Argentina
| | - Nicolás Frankel
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET - Universidad de Buenos Aires, 1428, Buenos Aires, Argentina
| | - Martín Graziano
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), CONICET - Universidad de Buenos Aires, 1428, Buenos Aires, Argentina.
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428, Buenos Aires, Argentina.
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82
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Haudiquet M, Buffet A, Rendueles O, Rocha EPC. Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae. PLoS Biol 2021; 19:e3001276. [PMID: 34228700 PMCID: PMC8259999 DOI: 10.1371/journal.pbio.3001276] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/07/2021] [Indexed: 01/01/2023] Open
Abstract
Mobile genetic elements (MGEs) drive genetic transfers between bacteria using mechanisms that require a physical interaction with the cellular envelope. In the high-priority multidrug-resistant nosocomial pathogens (ESKAPE), the first point of contact between the cell and virions or conjugative pili is the capsule. While the capsule can be a barrier to MGEs, it also evolves rapidly by horizontal gene transfer (HGT). Here, we aim at understanding this apparent contradiction by studying the covariation between the repertoire of capsule genes and MGEs in approximately 4,000 genomes of Klebsiella pneumoniae (Kpn). We show that capsules drive phage-mediated gene flow between closely related serotypes. Such serotype-specific phage predation also explains the frequent inactivation of capsule genes, observed in more than 3% of the genomes. Inactivation is strongly epistatic, recapitulating the capsule biosynthetic pathway. We show that conjugative plasmids are acquired at higher rates in natural isolates lacking a functional capsular locus and confirmed experimentally this result in capsule mutants. This suggests that capsule inactivation by phage pressure facilitates its subsequent reacquisition by conjugation. Accordingly, capsule reacquisition leaves long recombination tracts around the capsular locus. The loss and regain process rewires gene flow toward other lineages whenever it leads to serotype swaps. Such changes happen preferentially between chemically related serotypes, hinting that the fitness of serotype-swapped strains depends on the host genetic background. These results enlighten the bases of trade-offs between the evolution of virulence and multidrug resistance and caution that some alternatives to antibiotics by selecting for capsule inactivation may facilitate the acquisition of antibiotic resistance genes (ARGs). A study of how the complex interaction between capsules and mobile genetic elements shapes gene flow in populations of Klebsiella pneumoniae reveals that capsule inactivation by phage pressure facilitates its subsequent re-acquisition by conjugation, and this loss and re-gain process influences the gene flow towards other lineages whenever it leads to serotype changes.
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Affiliation(s)
- Matthieu Haudiquet
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
- Ecole Doctoral FIRE–Programme Bettencourt, CRI, Paris, France
- * E-mail:
| | - Amandine Buffet
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
| | - Olaya Rendueles
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
| | - Eduardo P. C. Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
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83
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Diversity and Adaptations of Escherichia coli Strains: Exploring the Intestinal Community in Crohn's Disease Patients and Healthy Individuals. Microorganisms 2021; 9:microorganisms9061299. [PMID: 34203637 PMCID: PMC8232093 DOI: 10.3390/microorganisms9061299] [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: 05/18/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/17/2022] Open
Abstract
Crohn's disease (CD) is characterized by a chronic, progressive inflammation across the gastrointestinal tract with a series of exacerbations and remissions. A significant factor in the CD pathogenesis is an imbalance in gut microbiota composition, particularly the prevalence of Escherichia coli. In the present study, the genomes of sixty-three E. coli strains from the gut of patients with CD and healthy subjects were sequenced. In addition, eighteen E. coli-like metagenome-assembled genomes (MAGs) were reconstructed from the shotgun-metagenome sequencing data of fecal samples. The comparative analysis revealed the similarity of E. coli genomes regardless of the origin of the strain. The strains exhibited similar genetic patterns of virulence, antibiotic resistance, and bacteriocin-producing systems. The study showed antagonistic activity of E. coli strains and the metabolic features needed for their successful competition in the human gut environment. These observations suggest complex bacterial interactions within the gut which may affect the host and cause intestinal damage.
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84
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Díaz-Gavidia C, Álvarez FP, Munita JM, Cortés S, Moreno-Switt AI. Perspective on Clinically-Relevant Antimicrobial Resistant Enterobacterales in Food: Closing the Gaps Using Genomics. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.667504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance is one of the most important public health concerns—it causes 700,000 deaths annually according to the World Health Organization (WHO). Enterobacterales such as E. coli and Klebsiella pneumoniae, have become resistant to many relevant antimicrobials including carbapenems and extended spectrum cephalosporins. These clinically relevant resistant Enterobacterales (CRRE) members are now globally distributed in the environment including different food types (meats, produce, dairy). Unlike known foodborne pathogens, CRRE are not usually part of most food surveillance systems. However, numerous reports of CRRE highlight the importance of these bacteria in food and have been shown to contribute to the overall crisis of antimicrobial resistance. This is especially important in the context of carriage of these pathogens by immuno-compromised individuals. CRRE infections upon consumption of contaminated food could colonize the human gastrointestinal tract and eventually be a source of systemic infections such as urinary tract infections or septicemia. While different aspects need to be considered to elucidate this, whole genome sequencing along with metadata could be used to understand genomic relationships of CRRE obtained from foods and humans, including isolates from clinical infections. Once robust scientific data is available on the role of CRRE in food, countries could move forward to better survey and control CRRE in food.
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85
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Royer G, Darty MM, Clermont O, Condamine B, Laouenan C, Decousser JW, Vallenet D, Lefort A, de Lastours V, Denamur E. Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period. Genome Med 2021; 13:77. [PMID: 33952335 PMCID: PMC8097792 DOI: 10.1186/s13073-021-00892-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/22/2021] [Indexed: 11/12/2022] Open
Abstract
Background Escherichia coli is the leading cause of bloodstream infections, associated with a significant mortality. Recent genomic analyses revealed that few clonal lineages are involved in bloodstream infections and captured the emergence of some of them. However, data on within sequence type (ST) population genetic structure evolution are rare. Methods We compared whole genome sequences of 912 E. coli isolates responsible for bloodstream infections from two multicenter clinical trials that were conducted in the Paris area, France, 12 years apart, in teaching hospitals belonging to the same institution (“Assistance Publique-Hôpitaux de Paris”). We analyzed the strains at different levels of granularity, i.e., the phylogroup, the ST complex (STc), and the within STc clone taking into consideration the evolutionary history, the resistance, and virulence gene content as well as the antigenic diversity of the strains. Results We found a mix of stability and changes overtime, depending on the level of comparison. Overall, we observed an increase in antibiotic resistance associated to a restricted number of genetic determinants and in strain plasmidic content, whereas phylogroup distribution and virulence gene content remained constant. Focusing on STcs highlighted the pauci-clonality of the populations, with only 11 STcs responsible for more than 73% of the cases, dominated by five STcs (STc73, STc131, STc95, STc69, STc10). However, some STcs underwent dramatic variations, such as the global pandemic STc131, which replaced the previously predominant STc95. Moreover, within STc131, 95 and 69 genomic diversity analysis revealed a highly dynamic pattern, with reshuffling of the population linked to clonal replacement sometimes coupled with independent acquisitions of virulence factors such as the pap gene cluster bearing a papGII allele located on various pathogenicity islands. Additionally, STc10 exhibited huge antigenic diversity evidenced by numerous O:H serotype/fimH allele combinations, whichever the year of isolation. Conclusions Altogether, these data suggest that the bloodstream niche is occupied by a wide but specific phylogenetic diversity and that highly specialized extra-intestinal clones undergo frequent turnover at the within ST level. Additional worldwide epidemiological studies overtime are needed in different geographical and ecological contexts to assess how generalizable these data are. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00892-0.
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Affiliation(s)
- Guilhem Royer
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Paris-Saclay, Evry, France.,Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000, Créteil, France
| | - Mélanie Mercier Darty
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000, Créteil, France
| | - Olivier Clermont
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France
| | | | - Cédric Laouenan
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,Département d'épidémiologie, biostatistiques et recherche clinique, Hôpital Bichat, AP-HP, F-75018, Paris, France
| | - Jean-Winoc Decousser
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000, Créteil, France
| | - David Vallenet
- LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Paris-Saclay, Evry, France
| | - Agnès Lefort
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,Service de Médecine Interne, Hôpital Beaujon, AP-HP, F-92100, Clichy, France
| | - Victoire de Lastours
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,Service de Médecine Interne, Hôpital Beaujon, AP-HP, F-92100, Clichy, France
| | - Erick Denamur
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France. .,Laboratoire de Génétique Moléculaire, Hôpital Bichat, AP-HP, F-75018, Paris, France.
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86
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Kauter A, Epping L, Ghazisaeedi F, Lübke-Becker A, Wolf SA, Kannapin D, Stoeckle SD, Semmler T, Günther S, Gehlen H, Walther B. Frequency, Local Dynamics, and Genomic Characteristics of ESBL-Producing Escherichia coli Isolated From Specimens of Hospitalized Horses. Front Microbiol 2021; 12:671676. [PMID: 33936023 PMCID: PMC8085565 DOI: 10.3389/fmicb.2021.671676] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 03/23/2021] [Indexed: 12/04/2022] Open
Abstract
Previous research identified veterinary clinics as hotspots with respect to accumulation and spread of multidrug resistant extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (EC). Therefore, promoting the prudent use of antibiotics to decrease selective pressure in that particular clinical environment is preferable to enhance biosecurity for animal patients and hospital staff. Accordingly, this study comparatively investigated the impact of two distinct perioperative antibiotic prophylaxis (PAP) regimens (short-term versus prolonged) on ESBL-EC carriage of horses subjected to colic surgery. While all horses received a combination of penicillin/gentamicin (P/G) as PAP, they were assigned to either the “single-shot group” (SSG) or the conventional “5-day group” (5DG). Fecal samples collected on arrival (t0), on the 3rd (t1) and on the 10th day after surgery (t2) were screened for ESBL-EC. All isolates were further investigated using whole genome sequences. In total, 81 of 98 horses met the inclusion criteria for this study. ESBL-EC identified in samples available at t0, t1 and t2 were 4.8% (SSG) and 9.7% (5DG), 37% (SSG) and 47.2% (5DG) as well as 55.6% (SSG) and 56.8% (5DG), respectively. Regardless of the P/G PAP regimen, horses were 9.12 times (95% CI 2.79–29.7) more likely to carry ESBL-EC at t1 compared to t0 (p < 0.001) and 15.64 times (95% CI 4.57–53.55) more likely to carry ESBL-EC at t2 compared to t0 (p < 0.001). ESBL-EC belonging to sequence type (ST) 10, ST86, ST641, and ST410 were the most prevalent lineages, with blaCTX–M–1 (60%) being the dominant ESBL gene. A close spatio-temporal relationship between isolates sharing a particular ST was revealed by genome analysis, strongly indicating local spread. Consequently, hospitalization itself has a strong impact on ESBL-EC isolation rates in horses, possibly masking differences between distinct PAP regimens. The results of this study reveal accumulation and spread of multi-drug resistant ESBL-EC among horses subjected to colic surgery with different P/G PAP regimens, challenging the local hygiene management system and work-place safety of veterinary staff. Moreover, the predominance of particular ESBL-EC lineages in clinics providing health care for horses needs further investigation.
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Affiliation(s)
- Anne Kauter
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany
| | - Lennard Epping
- Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Fereshteh Ghazisaeedi
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Antina Lübke-Becker
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Silver A Wolf
- Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Dania Kannapin
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Sabita D Stoeckle
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Torsten Semmler
- Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | | | - Heidrun Gehlen
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Birgit Walther
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany
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87
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Shaw LP, Chau KK, Kavanagh J, AbuOun M, Stubberfield E, Gweon HS, Barker L, Rodger G, Bowes MJ, Hubbard ATM, Pickford H, Swann J, Gilson D, Smith RP, Hoosdally SJ, Sebra R, Brett H, Peto TEA, Bailey MJ, Crook DW, Read DS, Anjum MF, Walker AS, Stoesser N. Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae. SCIENCE ADVANCES 2021; 7:eabe3868. [PMID: 33837077 PMCID: PMC8034854 DOI: 10.1126/sciadv.abe3868] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/22/2021] [Indexed: 05/07/2023]
Abstract
Escherichia coli and other Enterobacteriaceae are diverse species with "open" pangenomes, where genes move intra- and interspecies via horizontal gene transfer. However, most analyses focus on clinical isolates. The pangenome dynamics of natural populations remain understudied, despite their suggested role as reservoirs for antimicrobial resistance (AMR) genes. Here, we analyze near-complete genomes for 827 Enterobacteriaceae (553 Escherichia and 274 non-Escherichia spp.) with 2292 circularized plasmids in total, collected from 19 locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30-km radius at three time points over a year. We find different dynamics for chromosomal and plasmid-borne genes. Plasmids have a higher burden of AMR genes and insertion sequences, and AMR-gene-carrying plasmids show evidence of being under stronger selective pressure. Environmental niche and local geography both play a role in shaping plasmid dynamics. Our results highlight the importance of local strategies for controlling the spread of AMR.
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Affiliation(s)
- Liam P Shaw
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK.
| | - Kevin K Chau
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - James Kavanagh
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Emma Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - H Soon Gweon
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
- School of Biological Sciences, University of Reading, Reading RG6 6AS, UK
| | - Leanne Barker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Gillian Rodger
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Mike J Bowes
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Alasdair T M Hubbard
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Hayleah Pickford
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Jeremy Swann
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford OX4 9DU, UK
| | - Daniel Gilson
- Department of Epidemiological Sciences, The Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Richard P Smith
- Department of Epidemiological Sciences, The Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Sarah J Hoosdally
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Sema4, a Mount Sinai venture, 333 Ludlow Street, North Tower, 8th floor, Stamford, CT 06902, USA
| | - Howard Brett
- Thames Water Utilities, Clearwater Court, Vastern Road, Reading RG1 8DB, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford OX4 9DU, UK
| | - Mark J Bailey
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford OX4 9DU, UK
| | - Daniel S Read
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford OX4 9DU, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK.
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
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Reshadi P, Heydari F, Ghanbarpour R, Bagheri M, Jajarmi M, Amiri M, Alizade H, Badouei MA, Sahraei S, Adib N. Molecular characterization and antimicrobial resistance of potentially human-pathogenic Escherichia coli strains isolated from riding horses. BMC Vet Res 2021; 17:131. [PMID: 33766016 PMCID: PMC7992949 DOI: 10.1186/s12917-021-02832-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/10/2021] [Indexed: 11/29/2022] Open
Abstract
Background Transmission of antimicrobial resistant and virulent Escherichia coli (E. coli) from animal to human has been considered as a public health concern. This study aimed to determine the phylogenetic background and prevalence of diarrheagenic E. coli and antimicrobial resistance in healthy riding-horses in Iran. In this research, the genes related to six main pathotypes of E. coli were screened. Also, genotypic and phenotypic antimicrobial resistance against commonly used antibiotics were studied, then phylo-grouping was performed on all the isolates. Results Out of 65 analyzed isolates, 29.23 % (n = 19) were determined as STEC and 6.15 % (n = 4) as potential EPEC. The most prevalent antimicrobial resistance phenotypes were against amoxicillin/clavulanic acid (46.2 %) and ceftriaxone (38.5 %). blaTEM was the most detected resistance gene (98.4 %) among the isolates and 26.15 % of the E. coli isolates were determined as multi-drug resistant (MDR). Three phylo-types including B1 (76.92 %), A (13.85 %) and D (3.08 %) were detected among the isolates. Conclusions Due to the close interaction of horses and humans, these findings would place emphasis on the pathogenic and zoonotic potential of the equine strains and may help to design antimicrobial resistance stewardship programs to control the dissemination of virulent and multi-drug resistant E. coli strains in the community.
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Affiliation(s)
- Pouya Reshadi
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Fatemeh Heydari
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Reza Ghanbarpour
- Molecular Microbiology Research Group, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mahboube Bagheri
- Department of Food Science and Technology, Bardsir Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maziar Jajarmi
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Mohadese Amiri
- Mashhad Branch, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Mashhad, Iran
| | - Hesam Alizade
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mahdi Askari Badouei
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Shademan Sahraei
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Nasrin Adib
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
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89
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Baquero F, Coque TM, Galán JC, Martinez JL. The Origin of Niches and Species in the Bacterial World. Front Microbiol 2021; 12:657986. [PMID: 33815348 PMCID: PMC8010147 DOI: 10.3389/fmicb.2021.657986] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 02/23/2021] [Indexed: 12/15/2022] Open
Abstract
Niches are spaces for the biological units of selection, from cells to complex communities. In a broad sense, "species" are biological units of individuation. Niches do not exist without individual organisms, and every organism has a niche. We use "niche" in the Hutchinsonian sense as an abstraction of a multidimensional environmental space characterized by a variety of conditions, both biotic and abiotic, whose quantitative ranges determine the positive or negative growth rates of the microbial individual, typically a species, but also parts of the communities of species contained in this space. Microbial organisms ("species") constantly diversify, and such diversification (radiation) depends on the possibility of opening up unexploited or insufficiently exploited niches. Niche exploitation frequently implies "niche construction," as the colonized niche evolves with time, giving rise to new potential subniches, thereby influencing the selection of a series of new variants in the progeny. The evolution of niches and organisms is the result of reciprocal interacting processes that form a single unified process. Centrifugal microbial diversification expands the limits of the species' niches while a centripetal or cohesive process occurs simultaneously, mediated by horizontal gene transfers and recombinatorial events, condensing all of the information recovered during the diversifying specialization into "novel organisms" (possible future species), thereby creating a more complex niche, where the selfishness of the new organism(s) establishes a "homeostatic power" limiting the niche's variation. Once the niche's full carrying capacity has been reached, reproductive isolation occurs, as no foreign organisms can outcompete the established population/community, thereby facilitating speciation. In the case of individualization-speciation of the microbiota, its contribution to the animal' gut structure is a type of "niche construction," the result of crosstalk between the niche (host) and microorganism(s). Lastly, there is a parallelism between the hierarchy of niches and that of microbial individuals. The increasing anthropogenic effects on the biosphere (such as globalization) might reduce the diversity of niches and bacterial individuals, with the potential emergence of highly transmissible multispecialists (which are eventually deleterious) resulting from the homogenization of the microbiosphere, a possibility that should be explored and prevented.
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Affiliation(s)
- Fernando Baquero
- Division of Biology and Evolution of Microorganisms, Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
| | - Teresa M Coque
- Division of Biology and Evolution of Microorganisms, Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
| | - Juan Carlos Galán
- Division of Biology and Evolution of Microorganisms, Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
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90
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Ingle DJ, Howden BP, Duchene S. Development of Phylodynamic Methods for Bacterial Pathogens. Trends Microbiol 2021; 29:788-797. [PMID: 33736902 DOI: 10.1016/j.tim.2021.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 11/30/2022]
Abstract
Phylodynamic methods have been essential to understand the interplay between the evolution and epidemiology of infectious diseases. To date, the field has centered on viruses. Bacterial pathogens are seldom analyzed under such phylodynamic frameworks, due to their complex genome evolution and, until recently, a paucity of whole-genome sequence data sets with rich associated metadata. We posit that the increasing availability of bacterial genomes and epidemiological data means that the field is now ripe to lay the foundations for applying phylodynamics to bacterial pathogens. The development of new methods that integrate more complex genomic and ecological data will help to inform public heath surveillance and control strategies for bacterial pathogens that represent serious threats to human health.
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Affiliation(s)
- Danielle J Ingle
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia; National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia; Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia; Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia; Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
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91
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Rousset F, Cabezas-Caballero J, Piastra-Facon F, Fernández-Rodríguez J, Clermont O, Denamur E, Rocha EPC, Bikard D. The impact of genetic diversity on gene essentiality within the Escherichia coli species. Nat Microbiol 2021; 6:301-312. [PMID: 33462433 DOI: 10.1038/s41564-020-00839-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 11/20/2020] [Indexed: 01/28/2023]
Abstract
Bacteria from the same species can differ widely in their gene content. In Escherichia coli, the set of genes shared by all strains, known as the core genome, represents about half the number of genes present in any strain. Although recent advances in bacterial genomics have unravelled genes required for fitness in various experimental conditions, most studies have focused on single model strains. As a result, the impact of the species' genetic diversity on core processes of the bacterial cell remains largely under-investigated. Here, we have developed a CRISPR interference platform for high-throughput gene repression that is compatible with most E. coli isolates and closely related species. We have applied it to assess the importance of ~3,400 nearly ubiquitous genes in three growth conditions in 18 representative E. coli strains spanning most common phylogroups and lifestyles of the species. Our screens revealed extensive variations in gene essentiality between strains and conditions. Investigation of the genetic determinants for these variations highlighted the importance of epistatic interactions with mobile genetic elements. In particular, we have shown how prophage-encoded defence systems against phage infection can trigger the essentiality of persistent genes that are usually non-essential. This study provides broad insights into the evolvability of gene essentiality and argues for the importance of studying various isolates from the same species under diverse conditions.
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Affiliation(s)
- François Rousset
- Synthetic Biology, Department of Microbiology, Institut Pasteur, Paris, France.,Sorbonne Université, Collège Doctoral, Paris, France
| | | | | | | | | | - Erick Denamur
- Université de Paris, IAME, INSERM UMR1137, Paris, France.,AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France.
| | - David Bikard
- Synthetic Biology, Department of Microbiology, Institut Pasteur, Paris, France.
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92
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Horesh G, Blackwell GA, Tonkin-Hill G, Corander J, Heinz E, Thomson NR. A comprehensive and high-quality collection of Escherichia coli genomes and their genes. Microb Genom 2021; 7:000499. [PMID: 33417534 PMCID: PMC8208696 DOI: 10.1099/mgen.0.000499] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/07/2020] [Indexed: 01/25/2023] Open
Abstract
Escherichia coli is a highly diverse organism that includes a range of commensal and pathogenic variants found across a range of niches and worldwide. In addition to causing severe intestinal and extraintestinal disease, E. coli is considered a priority pathogen due to high levels of observed drug resistance. The diversity in the E. coli population is driven by high genome plasticity and a very large gene pool. All these have made E. coli one of the most well-studied organisms, as well as a commonly used laboratory strain. Today, there are thousands of sequenced E. coli genomes stored in public databases. While data is widely available, accessing the information in order to perform analyses can still be a challenge. Collecting relevant available data requires accessing different sources, where data may be stored in a range of formats, and often requires further manipulation and processing to apply various analyses and extract useful information. In this study, we collated and intensely curated a collection of over 10 000 E. coli and Shigella genomes to provide a single, uniform, high-quality dataset. Shigella were included as they are considered specialized pathovars of E. coli. We provide these data in a number of easily accessible formats that can be used as the foundation for future studies addressing the biological differences between E. coli lineages and the distribution and flow of genes in the E. coli population at a high resolution. The analysis we present emphasizes our lack of understanding of the true diversity of the E. coli species, and the biased nature of our current understanding of the genetic diversity of such a key pathogen.
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Affiliation(s)
- Gal Horesh
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1RQ, UK
| | - Grace A. Blackwell
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1RQ, UK
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Gerry Tonkin-Hill
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1RQ, UK
| | - Jukka Corander
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1RQ, UK
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology (HIIT), University of Helsinki, Helsinki, Finland
| | - Eva Heinz
- Department of Vector Biology and Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Nicholas R. Thomson
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1RQ, UK
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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93
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Nowicki S, deLaurent ZR, de Villiers EP, Githinji G, Charles KJ. The utility of Escherichia coli as a contamination indicator for rural drinking water: Evidence from whole genome sequencing. PLoS One 2021; 16:e0245910. [PMID: 33481909 PMCID: PMC7822521 DOI: 10.1371/journal.pone.0245910] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/09/2021] [Indexed: 12/12/2022] Open
Abstract
Across the water sector, Escherichia coli is the preferred microbial water quality indicator and current guidance upholds that it indicates recent faecal contamination. This has been challenged, however, by research demonstrating growth of E. coli in the environment. In this study, we used whole genome sequencing to investigate the links between E. coli and recent faecal contamination in drinking water. We sequenced 103 E. coli isolates sampled from 9 water supplies in rural Kitui County, Kenya, including points of collection (n = 14) and use (n = 30). Biomarkers for definitive source tracking remain elusive, so we analysed the phylogenetic grouping, multi-locus sequence types (MLSTs), allelic diversity, and virulence and antimicrobial resistance (AMR) genes of the isolates for insight into their likely source. Phylogroup B1, which is generally better adapted to water environments, is dominant in our samples (n = 69) and allelic diversity differences (z = 2.12, p = 0.03) suggest that naturalised populations may be particularly relevant at collection points with lower E. coli concentrations (<50 / 100mL). The strains that are more likely to have originated from human and/or recent faecal contamination (n = 50), were found at poorly protected collection points (4 sites) or at points of use (12 sites). We discuss the difficulty of interpreting health risk from E. coli grab samples, especially at household level, and our findings support the use of E. coli risk categories and encourage monitoring that accounts for sanitary conditions and temporal variability.
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Affiliation(s)
- Saskia Nowicki
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
| | - Zaydah R. deLaurent
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Etienne P. de Villiers
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Department of Public Health, Pwani University, Kilifi, Kenya
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Katrina J. Charles
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
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94
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Perrin A, Rocha EPC. PanACoTA: a modular tool for massive microbial comparative genomics. NAR Genom Bioinform 2021; 3:lqaa106. [PMID: 33575648 PMCID: PMC7803007 DOI: 10.1093/nargab/lqaa106] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/10/2020] [Accepted: 12/01/2020] [Indexed: 02/06/2023] Open
Abstract
The study of the gene repertoires of microbial species, their pangenomes, has become a key part of microbial evolution and functional genomics. Yet, the increasing number of genomes available complicates the establishment of the basic building blocks of comparative genomics. Here, we present PanACoTA (https://github.com/gem-pasteur/PanACoTA), a tool that allows to download all genomes of a species, build a database with those passing quality and redundancy controls, uniformly annotate and then build their pangenome, several variants of core genomes, their alignments and a rapid but accurate phylogenetic tree. While many programs building pangenomes have become available in the last few years, we have focused on a modular method, that tackles all the key steps of the process, from download to phylogenetic inference. While all steps are integrated, they can also be run separately and multiple times to allow rapid and extensive exploration of the parameters of interest. PanACoTA is built in Python3, includes a singularity container and features to facilitate its future development. We believe PanACoTa is an interesting addition to the current set of comparative genomics tools, since it will accelerate and standardize the more routine parts of the work, allowing microbial genomicists to more quickly tackle their specific questions.
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Affiliation(s)
- Amandine Perrin
- Microbial Evolutionary Genomics, CNRS, UMR3525, Institut Pasteur, 28, rue Dr Roux, Paris 75015, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, CNRS, UMR3525, Institut Pasteur, 28, rue Dr Roux, Paris 75015, France
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95
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Abstract
Escherichia coli is a clinically important bacterial species implicated in human- and livestock-associated infections worldwide. The bacterium is known to reside in the guts of humans, livestock, and wild animals. Escherichia coli is a common bacterial species in the gastrointestinal tracts of warm-blooded animals and humans. Pathogenicity and antimicrobial resistance in E. coli may emerge via host switching from animal reservoirs. Despite its potential clinical importance, knowledge of the population structure of commensal E. coli within wild hosts and the epidemiological links between E. coli in nonhuman hosts and E. coli in humans is still scarce. In this study, we analyzed the whole-genome sequencing data of a collection of 119 commensal E. coli strains recovered from the guts of 55 mammal and bird species in Mexico and Venezuela in the 1990s. We observed low concordance between the population structures of E. coli isolates colonizing wild animals and the phylogeny, taxonomy, and ecological and physiological attributes of the host species, with distantly related E. coli strains often colonizing the same or similar host species and distantly related host species often hosting closely related E. coli strains. We found no evidence for recent transmission of E. coli genomes from wild animals to either domesticated animals or humans. However, multiple livestock- and human-related virulence factor genes were present in E. coli of wild animals, including virulence factors characteristic of Shiga toxin-producing E. coli (STEC) and atypical enteropathogenic E. coli (aEPEC), where several isolates from wild hosts harbored the locus of enterocyte effacement (LEE) pathogenicity island. Moreover, E. coli isolates from wild animal hosts often harbored known antibiotic resistance determinants, including those against ciprofloxacin, aminoglycosides, tetracyclines, and beta-lactams, with some determinants present in multiple, distantly related E. coli lineages colonizing very different host animals. We conclude that genome pools of E. coli colonizing the guts of wild animals and humans share virulence and antibiotic resistance genes, underscoring the idea that wild animals could serve as reservoirs for E. coli pathogenicity in human and livestock infections. IMPORTANCEEscherichia coli is a clinically important bacterial species implicated in human- and livestock-associated infections worldwide. The bacterium is known to reside in the guts of humans, livestock, and wild animals. Although wild animals are recognized as potential reservoirs for pathogenic E. coli strains, the knowledge of the population structure of E. coli in wild hosts is still scarce. In this study, we used fine resolution of whole-genome sequencing to provide novel insights into the evolution of E. coli genomes from a small yet diverse collection of strains recovered within a broad range of wild animal species (including mammals and birds), the coevolution of E. coli strains with their hosts, and the genetics of pathogenicity of E. coli strains in wild hosts in Mexico. Our results provide evidence for the clinical importance of wild animals as reservoirs for pathogenic strains and highlight the need to include nonhuman hosts in the surveillance programs for E. coli infections.
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96
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Galardini M, Clermont O, Baron A, Busby B, Dion S, Schubert S, Beltrao P, Denamur E. Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study. PLoS Genet 2020; 16:e1009065. [PMID: 33112851 PMCID: PMC7592755 DOI: 10.1371/journal.pgen.1009065] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/20/2020] [Indexed: 11/18/2022] Open
Abstract
The genus Escherichia is composed of several species and cryptic clades, including E. coli, which behaves as a vertebrate gut commensal, but also as an opportunistic pathogen involved in both diarrheic and extra-intestinal diseases. To characterize the genetic determinants of extra-intestinal virulence within the genus, we carried out an unbiased genome-wide association study (GWAS) on 370 commensal, pathogenic and environmental strains representative of the Escherichia genus phylogenetic diversity and including E. albertii (n = 7), E. fergusonii (n = 5), Escherichia clades (n = 32) and E. coli (n = 326), tested in a mouse model of sepsis. We found that the presence of the high-pathogenicity island (HPI), a ~35 kbp gene island encoding the yersiniabactin siderophore, is highly associated with death in mice, surpassing other associated genetic factors also related to iron uptake, such as the aerobactin and the sitABCD operons. We confirmed the association in vivo by deleting key genes of the HPI in E. coli strains in two phylogenetic backgrounds. We then searched for correlations between virulence, iron capture systems and in vitro growth in a subset of E. coli strains (N = 186) previously phenotyped across growth conditions, including antibiotics and other chemical and physical stressors. We found that virulence and iron capture systems are positively correlated with growth in the presence of numerous antibiotics, probably due to co-selection of virulence and resistance. We also found negative correlations between virulence, iron uptake systems and growth in the presence of specific antibiotics (i.e. cefsulodin and tobramycin), which hints at potential “collateral sensitivities” associated with intrinsic virulence. This study points to the major role of iron capture systems in the extra-intestinal virulence of the genus Escherichia. Bacterial isolates belonging to the genus Escherichia can be human commensals but also opportunistic pathogens, with the ability to cause extra-intestinal infection. There is therefore the need to identify the genetic elements that favour extra-intestinal virulence, so that virulent bacterial isolates can be identified through genome analysis and potential treatment strategies be developed. To reduce the influence of host variability on virulence, we have used a mouse model of sepsis to characterize the virulence of 370 strains belonging to the genus Escherichia, for which whole genome sequences were also available. We have used a statistical approach called Genome-Wide Association Study (GWAS) to show how the presence of genes that encode for iron scavenging are significantly associated with the propensity of a bacterial isolate to cause extra-intestinal infections. Taking advantage of previously generated growth data on a subset of the strains and its correlation to virulence we generated hypothesis on the relationship between iron scavenging and growth in the presence of various antimicrobials, which could have implications for developing new treatment strategies.
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Affiliation(s)
- Marco Galardini
- EMBL-EBI, Wellcome Genome Campus, Cambridge, United Kingdom
- * E-mail: (MG); (ED)
| | | | | | - Bede Busby
- Genome Biology Unit, EMBL, Heidelberg, Germany
| | - Sara Dion
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
| | - Sören Schubert
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Germany
| | - Pedro Beltrao
- EMBL-EBI, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Erick Denamur
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
- * E-mail: (MG); (ED)
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97
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Teelucksingh T, Thompson LK, Cox G. The Evolutionary Conservation of Escherichia coli Drug Efflux Pumps Supports Physiological Functions. J Bacteriol 2020; 202:e00367-20. [PMID: 32839176 PMCID: PMC7585057 DOI: 10.1128/jb.00367-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Bacteria harness an impressive repertoire of resistance mechanisms to evade the inhibitory action of antibiotics. One such mechanism involves efflux pump-mediated extrusion of drugs from the bacterial cell, which significantly contributes to multidrug resistance. Intriguingly, most drug efflux pumps are chromosomally encoded components of the intrinsic antibiotic resistome. In addition, in terms of xenobiotic detoxification, bacterial efflux systems often exhibit significant levels of functional redundancy. Efflux pumps are also considered to be highly conserved; however, the extent of conservation in many bacterial species has not been reported and the majority of genes that encode efflux pumps appear to be dispensable for growth. These observations, in combination with an increasing body of experimental evidence, imply alternative roles in bacterial physiology. Indeed, the ability of efflux pumps to facilitate antibiotic resistance could be a fortuitous by-product of ancient physiological functions. Using Escherichia coli as a model organism, we here evaluated the evolutionary conservation of drug efflux pumps and we provide phylogenetic analysis of the major efflux families. We show the E. coli drug efflux system has remained relatively stable and the majority (∼80%) of pumps are encoded in the core genome. This analysis further supports the importance of drug efflux pumps in E. coli physiology. In this review, we also provide an update on the roles of drug efflux pumps in the detoxification of endogenously synthesized substrates and pH homeostasis. Overall, gaining insight into drug efflux pump conservation, common evolutionary ancestors, and physiological functions could enable strategies to combat these intrinsic and ancient elements.
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Affiliation(s)
- Tanisha Teelucksingh
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Laura K Thompson
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Georgina Cox
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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98
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Devane ML, Moriarty E, Weaver L, Cookson A, Gilpin B. Fecal indicator bacteria from environmental sources; strategies for identification to improve water quality monitoring. WATER RESEARCH 2020; 185:116204. [PMID: 32745743 DOI: 10.1016/j.watres.2020.116204] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 07/13/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
In tropical to temperate environments, fecal indicator bacteria (FIB), such as enterococci and Escherichia coli, can persist and potentially multiply, far removed from their natural reservoir of the animal gut. FIB isolated from environmental reservoirs such as stream sediments, beach sand and vegetation have been termed "naturalized" FIB. In addition, recent research suggests that the intestines of poikilothermic animals such as fish may be colonized by enterococci and E. coli, and therefore, these animals may contribute to FIB concentrations in the aquatic environment. Naturalized FIB that are derived from fecal inputs into the environment, and subsequently adapted to maintain their population within the non-host environment are termed "naturalized enteric FIB". In contrast, an additional theory suggests that some "naturalized" FIB diverged from enteric FIB many millions of years ago and are now normal inhabitants of the environment where they are referred to as "naturalized non-enteric FIB". In the case of the Escherichia genus, the naturalized non-enteric members are identified as E. coli during routine water quality monitoring. An over-estimation of the health risk could result when these naturalized, non-enteric FIB, (that is, not derived from avian or mammalian fecal contamination), contribute to water quality monitoring results. It has been postulated that these environmental FIB belonging to the genera Escherichia and Enterococcus can be differentiated from enteric FIB by genetic methods because they lack some of the genes required for colonization of the host intestine, and have acquired genes that aid survival in the environment. Advances in molecular tools such as next generation sequencing will aid the identification of genes peculiar or "enriched" in particular habitats to discriminate between enteric and environmental FIB. In this appraisal, we have reviewed the research studying "naturalized" FIB, and discussed the techniques for their differentiation from enteric FIB. This differentiation includes the important distinction between enteric FIB derived from fresh and non-recent fecal inputs, and those truly non-enteric environmental microbes, which are currently identified as FIB during routine water quality monitoring. The inclusion of tools for the identification of naturalized FIB (enteric or environmental) would be a valuable resource for future studies assessing water quality.
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Affiliation(s)
- Megan L Devane
- Institute of Environmental Science and Research Ltd., 27 Creyke Rd, Ilam, Christchurch, New Zealand.
| | - Elaine Moriarty
- Institute of Environmental Science and Research Ltd., 27 Creyke Rd, Ilam, Christchurch, New Zealand
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd., 27 Creyke Rd, Ilam, Christchurch, New Zealand
| | - Adrian Cookson
- AgResearch Ltd., Hopkirk Research Institute, Massey University, Palmerston North, New Zealand; mEpiLab, School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
| | - Brent Gilpin
- Institute of Environmental Science and Research Ltd., 27 Creyke Rd, Ilam, Christchurch, New Zealand
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99
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Breckell G, Silander OK. Complete Genome Sequences of 47 Environmental Isolates of Escherichia coli. Microbiol Resour Announc 2020; 9:e00222-20. [PMID: 32943554 PMCID: PMC7498420 DOI: 10.1128/mra.00222-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022] Open
Abstract
Escherichia coli is commonly considered a host-associated bacterium. However, there is evidence that some strains occupy environmental (non-host-associated) niches. Here, we report the complete genomes of 47 Escherichia coli environmental isolates. These will be useful for understanding the dynamics of plasmids, phages, and other repetitive genetic elements.
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Affiliation(s)
- Georgia Breckell
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Olin K Silander
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
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100
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Abstract
Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes that represent groups of strains with specific pathogenic characteristics have been described based on heterogeneous and complex criteria. The democratization of whole-genome sequencing has led to an accumulation of genomic data that render possible a population phylogenomic approach to the emergence of virulence. Few lineages are responsible for the pathologies compared with the diversity of commensal strains. These lineages emerged multiple times during E. coli evolution, mainly by acquiring virulence genes located on mobile elements, but in a specific chromosomal phylogenetic background. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome.
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