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Ryan MP, Carraro N, Slattery S, Pembroke JT. Integrative Conjugative Elements (ICEs) of the SXT/R391 family drive adaptation and evolution in γ-Proteobacteria. Crit Rev Microbiol 2024; 50:105-126. [PMID: 36634159 DOI: 10.1080/1040841x.2022.2161870] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023]
Abstract
Integrative Conjugative Elements (ICEs) are mosaics containing functional modules allowing maintenance by site-specific integration and excision into and from the host genome and conjugative transfer to a specific host range. Many ICEs encode a range of adaptive functions that aid bacterial survival and evolution in a range of niches. ICEs from the SXT/R391 family are found in γ-Proteobacteria. Over 100 members have undergone epidemiological and molecular characterization allowing insight into their diversity and function. Comparative analysis of SXT/R391 elements from a wide geographic distribution has revealed conservation of key functions, and the accumulation and evolution of adaptive genes. This evolution is associated with gene acquisition in conserved hotspots and variable regions within the SXT/R391 ICEs catalysed via element-encoded recombinases. The elements can carry IS elements and transposons, and a mutagenic DNA polymerase, PolV, which are associated with their evolution. SXT/R391 ICEs isolated from different niches appear to have retained adaptive functions related to that specific niche; phage resistance determinants in ICEs carried by wastewater bacteria, antibiotic resistance determinants in clinical isolates and metal resistance determinants in bacteria recovered from polluted environments/ocean sediments. Many genes found in the element hotspots are undetermined and have few homologs in the nucleotide databases.
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Affiliation(s)
- Michael P Ryan
- Department of Applied Sciences, Technological University of the Shannon, Limerick, Ireland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Shannon Slattery
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
| | - J Tony Pembroke
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
- Bernal Institute, University of Limerick, Ireland
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2
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Ojha D, Jaszczur MM, Sikand A, McDonald JP, Robinson A, van Oijen AM, Mak CH, Pinaud F, Cox MM, Woodgate R, Goodman MF. Host cell RecA activates a mobile element-encoded mutagenic DNA polymerase. Nucleic Acids Res 2022; 50:6854-6869. [PMID: 35736210 PMCID: PMC9262582 DOI: 10.1093/nar/gkac515] [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: 02/25/2022] [Revised: 05/23/2022] [Accepted: 05/31/2022] [Indexed: 12/24/2022] Open
Abstract
Homologs of the mutagenic Escherichia coli DNA polymerase V (pol V) are encoded by numerous pathogens and mobile elements. We have used Rum pol (RumA'2B), from the integrative conjugative element (ICE), R391, as a model mobile element-encoded polymerase (MEPol). The highly mutagenic Rum pol is transferred horizontally into a variety of recipient cells, including many pathogens. Moving between species, it is unclear if Rum pol can function on its own or requires activation by host factors. Here, we show that Rum pol biochemical activity requires the formation of a physical mutasomal complex, Rum Mut, containing RumA'2B-RecA-ATP, with RecA being donated by each recipient bacteria. For R391, Rum Mut specific activities in vitro and mutagenesis rates in vivo depend on the phylogenetic distance of host-cell RecA from E. coli RecA. Rum pol is a highly conserved and effective mobile catalyst of rapid evolution, with the potential to generate a broad mutational landscape that could serve to ensure bacterial adaptation in antibiotic-rich environments leading to the establishment of antibiotic resistance.
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Affiliation(s)
- Debika Ojha
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Malgorzata M Jaszczur
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Adhirath Sikand
- Department of Chemistry, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - John P McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew Robinson
- Molecular Horizons Institute and School of Chemistry and Biomolecular Science, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons Institute and School of Chemistry and Biomolecular Science, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Chi H Mak
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Department of Chemistry, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA.,Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Fabien Pinaud
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Department of Chemistry, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA.,Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 Wisconsin, USA
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Myron F Goodman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Department of Chemistry, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
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3
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LeGault KN, Hays SG, Angermeyer A, McKitterick AC, Johura FT, Sultana M, Ahmed T, Alam M, Seed KD. Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts. Science 2021; 373:eabg2166. [PMID: 34326207 PMCID: PMC9064180 DOI: 10.1126/science.abg2166] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/06/2021] [Indexed: 12/23/2022]
Abstract
Bacteriophage predation selects for diverse antiphage systems that frequently cluster on mobilizable defense islands in bacterial genomes. However, molecular insight into the reciprocal dynamics of phage-bacterial adaptations in nature is lacking, particularly in clinical contexts where there is need to inform phage therapy efforts and to understand how phages drive pathogen evolution. Using time-shift experiments, we uncovered fluctuations in Vibrio cholerae's resistance to phages in clinical samples. We mapped phage resistance determinants to SXT integrative and conjugative elements (ICEs), which notoriously also confer antibiotic resistance. We found that SXT ICEs, which are widespread in γ-proteobacteria, invariably encode phage defense systems localized to a single hotspot of genetic exchange. We identified mechanisms that allow phage to counter SXT-mediated defense in clinical samples, and document the selection of a novel phage-encoded defense inhibitor. Phage infection stimulates high-frequency SXT ICE conjugation, leading to the concurrent dissemination of phage and antibiotic resistances.
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Affiliation(s)
- Kristen N LeGault
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Stephanie G Hays
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Angus Angermeyer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Amelia C McKitterick
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Fatema-Tuz Johura
- icddr,b, formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Marzia Sultana
- icddr,b, formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Tahmeed Ahmed
- icddr,b, formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Munirul Alam
- icddr,b, formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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4
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Bhandari M, Jennison AV, Rathnayake IU, Huygens F. Evolution, distribution and genetics of atypical Vibrio cholerae - A review. INFECTION GENETICS AND EVOLUTION 2021; 89:104726. [PMID: 33482361 DOI: 10.1016/j.meegid.2021.104726] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 01/07/2021] [Accepted: 01/15/2021] [Indexed: 12/21/2022]
Abstract
Vibrio cholerae is the etiological agent of cholera, a severe diarrheal disease, which can occur as either an epidemic or sporadic disease. Cholera pandemic-causing V. cholerae O1 and O139 serogroups originated from the Indian subcontinent and spread globally and millions of lives are lost each year, mainly in developing and underdeveloped countries due to this disease. V. cholerae O1 is further classified as classical and El Tor biotype which can produce biotype specific cholera toxin (CT). Since 1961, the current seventh pandemic El Tor strains replaced the sixth pandemic strains resulting in the classical biotype strain that produces classical CT. The ongoing evolution of Atypical El Tor V. cholerae srains encoding classical CT is of global concern. The severity in the pathophysiology of these Atypical El Tor strains is significantly higher than El Tor or classical strains. Pathogenesis of V. cholerae is a complex process that involves coordinated expression of different sets of virulence-associated genes to cause disease. We are yet to understand the complete virulence profile of V. cholerae, including direct and indirect expression of genes involved in its survival and stress adaptation in the host. In recent years, whole genome sequencing has paved the way for better understanding of the evolution and strain distribution, outbreak identification and pathogen surveillance for the implementation of direct infection control measures in the clinic against many infectious pathogens including V. cholerae. This review provides a synopsis of recent studies that have contributed to the understanding of the evolution, distribution and genetics of the seventh pandemic Atypical El Tor V. cholerae strains.
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Affiliation(s)
- Murari Bhandari
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia; Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Amy V Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Irani U Rathnayake
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Flavia Huygens
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia.
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Sato JL, Fonseca MRB, Cerdeira LT, Tognim MCB, Sincero TCM, Noronha do Amaral MC, Lincopan N, Galhardo RS. Genomic Analysis of SXT/R391 Integrative Conjugative Elements From Proteus mirabilis Isolated in Brazil. Front Microbiol 2020; 11:571472. [PMID: 33193168 PMCID: PMC7606855 DOI: 10.3389/fmicb.2020.571472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022] Open
Abstract
Integrative conjugative elements (ICEs) are widespread in many bacterial species, often carrying antibiotic resistance determinants. In the present work, we screened a collection of Proteus mirabilis clinical isolates for the presence of type 1 SXT/R391 ICEs. Among the 76 isolates analyzed, 5 of them carry such elements. The complete sequences of these elements were obtained. One of the isolates carried the CMY-2 beta-lactamase gene in a transposon and is nearly identical to the element ICEPmiJpn1 previously described in Japan, and later shown to be present in other parts of the world, indicating global spread of this element. Nevertheless, the Brazilian isolate carrying ICEPmiJpn1 is not clonally related to the other lineages carrying the same element around the world. The other ICEs identified in this work do not carry known antibiotic resistance markers and are diverse in variable gene content and size, suggesting that these elements may be responsible for the acquisition of other advantageous traits by bacteria. Some sequences carried by these elements in Brazilian strains were not previously found in other SXT/R391 variants.
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Affiliation(s)
- Juliana L Sato
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marina R B Fonseca
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Louise T Cerdeira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Maria C B Tognim
- Department of Basic Health Sciences, State University of Maringá, Maringá, Brazil
| | - Thais C M Sincero
- Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, Brazil
| | | | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rodrigo S Galhardo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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6
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Isolation, nucleotide sequencing and genomic comparison of a Novel SXT/R391 ICE mobile genetic element isolated from a municipal wastewater environment. Sci Rep 2020; 10:8716. [PMID: 32457296 PMCID: PMC7251087 DOI: 10.1038/s41598-020-65216-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
Integrative Conjugative Elements (ICE’s) of the SXT/R391 family have largely been detected in clinical or environmental isolates of Gammaproteobacteria, particularly Vibrio and Proteus species. As wastewater treatment plants accumulate a large and diverse number of such species, we examined raw water samples taken from a municipal wastewater treatment plant initially using SXT/R391 family integrase gene-specific PCR probes to detect the presence of such elements in a directed approach. A positive amplification occurred over a full year period and a subsequent Restriction Fragment Length Polymorphism (RFLP) analysis revealed a very limited diversity in the treatment plant examined. Samples demonstrating positive amplification were cultured using Vibrio and Proteus selective media and PCR amplification tracking was utilized to monitor SXT/R391-ICE family containing strains. This screening procedure resulted in the isolation and identification of a Proteus mirabilis strain harbouring an ICE. Whole-genome sequencing of this ICE containing strain using Illumina sequencing technology revealed a novel 81 kb element that contained 75 open reading frames on annotation but contained no antibiotic or metal resistance determinants. Comparative genomics revealed the element contained a conserved ICE core with one of the insertions containing a novel bacteriophage defence mechanism. This directed isolation suggests that ICE elements are present in the environment without apparent selective pressure but may contain adaptive functions allowing survival in particular environments such as municipal wastewater which are reservoirs for large bacterial phage populations.
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