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Mageiros L, Méric G, Bayliss SC, Pensar J, Pascoe B, Mourkas E, Calland JK, Yahara K, Murray S, Wilkinson TS, Williams LK, Hitchings MD, Porter J, Kemmett K, Feil EJ, Jolley KA, Williams NJ, Corander J, Sheppard SK. Genome evolution and the emergence of pathogenicity in avian Escherichia coli. Nat Commun 2021; 12:765. [PMID: 33536414 PMCID: PMC7858641 DOI: 10.1038/s41467-021-20988-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 01/04/2021] [Indexed: 01/30/2023] Open
Abstract
Chickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks.
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Affiliation(s)
- Leonardos Mageiros
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Sion C Bayliss
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
- MRC Cloud Infrastructure for Microbial Bioinformatics (CLIMB) Consortium, London, UK
| | - Johan Pensar
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Evangelos Mourkas
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Jessica K Calland
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Koji Yahara
- Antimicrobial Resistance Research Centre, National Institute of Infectious Diseases, Tokyo, Japan
| | - Susan Murray
- Uppsala University, Department for medical biochemistry and microbiology, Uppsala University, Uppsala, Sweden
| | - Thomas S Wilkinson
- Swansea University Medical School, Institute of Life Science, Swansea, SA2 8PP, UK
| | - Lisa K Williams
- Swansea University Medical School, Institute of Life Science, Swansea, SA2 8PP, UK
| | - Matthew D Hitchings
- Swansea University Medical School, Institute of Life Science, Swansea, SA2 8PP, UK
| | - Jonathan Porter
- National Laboratory Service, Environment Agency, Starcross, UK
| | - Kirsty Kemmett
- Department of Epidemiology and Population Health, Institute of Infection & Global Health, University of Liverpool, Leahurst Campus, Wirral, UK
| | - Edward J Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Keith A Jolley
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Nicola J Williams
- Department of Epidemiology and Population Health, Institute of Infection & Global Health, University of Liverpool, Leahurst Campus, Wirral, UK
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK.
- MRC Cloud Infrastructure for Microbial Bioinformatics (CLIMB) Consortium, London, UK.
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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Diversity of integron- and culture-associated antibiotic resistance genes in freshwater floc. Appl Environ Microbiol 2012; 78:4367-72. [PMID: 22467502 DOI: 10.1128/aem.00405-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clinically important antibiotic resistance genes were detected in culturable bacteria and class 1 integron gene cassettes recovered from suspended floc, a significant aquatic repository for microorganisms and trace elements, across freshwater systems variably impacted by anthropogenic activities. Antibiotic resistance gene cassettes in floc total community DNA differed appreciably in number and type from genes detected in bacteria cultured from floc. The number of floc antibiotic resistance gene cassette types detected across sites was positively correlated with total (the sum of Ag, As, Cu, and Pb) trace element concentrations in aqueous solution and in a component of floc readily accessible to bacteria. In particular, concentrations of Cu and Pb in the floc component were positively correlated with floc resistance gene cassette diversity. Collectively, these results identify suspended floc as an important reservoir, distinct from bulk water and bed sediment, for antibiotic resistance in aquatic environments ranging from heavily impacted urban sites to remote areas of nature reserves and indicate that trace elements, particularly Cu and Pb, are geochemical markers of resistance diversity in this environmental reservoir. The increase in contamination of global water supplies suggests that aquatic environments will become an even more important reservoir of clinically important antibiotic resistance in the future.
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Abstract
Antibiotic resistance in Gram-negative bacteria is often due to the acquisition of resistance genes from a shared pool. In multiresistant isolates these genes, together with associated mobile elements, may be found in complex conglomerations on plasmids or on the chromosome. Analysis of available sequences reveals that these multiresistance regions (MRR) are modular, mosaic structures composed of different combinations of components from a limited set arranged in a limited number of ways. Components common to different MRR provide targets for homologous recombination, allowing these regions to evolve by combinatorial evolution, but our understanding of this process is far from complete. Advances in technology are leading to increasing amounts of sequence data, but currently available automated annotation methods usually focus on identifying ORFs and predicting protein function by homology. In MRR, where the genes are often well characterized, the challenge is to identify precisely which genes are present and to define the boundaries of complete and fragmented mobile elements. This review aims to summarize the types of mobile elements involved in multiresistance in Gram-negative bacteria and their associations with particular resistance genes, to describe common components of MRR and to illustrate methods for detailed analysis of these regions.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The University of Sydney, Westmead Hospital, Sydney, NSW 2145, Australia.
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Stokes HW, Gillings MR. Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens. FEMS Microbiol Rev 2011; 35:790-819. [PMID: 21517914 DOI: 10.1111/j.1574-6976.2011.00273.x] [Citation(s) in RCA: 372] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Antibiotics were one of the great discoveries of the 20th century. However, resistance appeared even in the earliest years of the antibiotic era. Antibiotic resistance continues to become worse, despite the ever-increasing resources devoted to combat the problem. One of the most important factors in the development of resistance to antibiotics is the remarkable ability of bacteria to share genetic resources via Lateral Gene Transfer (LGT). LGT occurs on a global scale, such that in theory, any gene in any organism anywhere in the microbial biosphere might be mobilized and spread. With sufficiently strong selection, any gene may spread to a point where it establishes a global presence. From an antibiotic resistance perspective, this means that a resistance phenotype can appear in a diverse range of infections around the globe nearly simultaneously. We discuss the forces and agents that make this LGT possible and argue that the problem of resistance can ultimately only be managed by understanding the problem from a broad ecological and evolutionary perspective. We also argue that human activities are exacerbating the problem by increasing the tempo of LGT and bacterial evolution for many traits that are important to humans.
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Affiliation(s)
- Hatch W Stokes
- The i3 Institute, University of Technology, Broadway 2007, Sydney, NSW, Australia.
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Abstract
Horizontal gene transfer (HGT) has been responsible for the dissemination of numerous antimicrobial-resistance determinants throughout diverse bacterial species. The rapid and broad dissemination of resistance determinants by HGT, and subsequent selection for resistance imposed by the use of antimicrobials, threatens to undermine the usefulness of antimicrobials. However, vigilant surveillance of the emerging antimicrobial resistance in clinical settings and subsequent studies of resistant isolates create a powerful system for studying HGT and detecting rare events. Two of the most closely monitored phenotypes are resistance to beta-lactams and resistance to fluoroquinolones. Studies of resistance to these antimicrobials have revealed that (1) transformation occurs between different species of bacteria including some recipient species that were not previously known to be competent for natural transformation; (2) transduction may be playing an important role in generating novel methicillin-resistant Staphylococcus aureus (MRSA) strains, although the details of transferring the SCCmec element are not yet fully understood; (3) Resistance genes are probably moving to plasmids from chromosomes more rapidly than in the past; and (4) Resistance genes are aggregating upon plasmids. The linkage of numerous resistance genes on individual plasmids may underlie the persistence of resistance to specific antimicrobials even when use of those antimicrobials is discontinued. Further studies of HGT and methods for controlling HGT may be necessary to maintain the usefulness of antimicrobials.
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Toleman MA, Walsh TR. Evolution of the ISCR3 group of ISCR elements. Antimicrob Agents Chemother 2008; 52:3789-91. [PMID: 18663029 PMCID: PMC2565877 DOI: 10.1128/aac.00479-08] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Revised: 06/15/2008] [Accepted: 07/20/2008] [Indexed: 11/20/2022] Open
Abstract
The ISCR elements ISCR3, ISCR4, ISCR5, ISCR14, and ISCR16 all share a percent G+C of 68 to 69%. They also share between 75% and 97% identity in their transposase open reading frames. Furthermore, with the exception of ISCR5, they are all found adjacent to sections of groEL that display the highest identity to the same gene from Xanthomonas spp. The combined information is consistent with the descent from an ancestral ISCR element in a Xanthomonas-like organism.
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Affiliation(s)
- Mark A Toleman
- School of Medicine, Department of Medical Microbiology, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom.
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