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Creti R, Imperi M, Khan UB, Berardi A, Recchia S, Alfarone G, Gherardi G. Emergence of High-Level Gentamicin Resistance in Streptococcus agalactiae Hypervirulent Serotype IV ST1010 (CC452) Strains by Acquisition of a Novel Integrative and Conjugative Element. Antibiotics (Basel) 2024; 13:491. [PMID: 38927158 PMCID: PMC11201010 DOI: 10.3390/antibiotics13060491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Streptococcus agalactiae (group B streptococci, GBS) is responsible for severe infections in both neonates and adults. Currently, empiric antimicrobial therapy for sepsis and meningitis is the combined use of penicillin and gentamicin due to the enhanced bactericidal activity. However, high-level gentamicin resistance (HLGR) abrogates the synergism. The rate of HLGR was investigated within a dataset of 433 GBS strains collected from cases of invasive disease in both adults and neonates as well as from pregnant carriers. GBS isolates (n = 20, 4.6%) presented with HLGR (gentamicin MIC breakpoint >1024 mg/L) that was differently diffused between strains from adults or neonates (5.2% vs. 2.8%). Notably, 70% of HLGR GBS strains (14 isolates) were serotype IV. Serotype IV HLGR-GBS isolates were susceptible to all antibiotics tested, exhibited the alpha-C/HvgA/PI-2b virulence string, and belonged to sequence type 1010 (clonal complex (CC) 452). The mobile element that harbored the HLGR aac(6')-aph(2)″ gene is a novel integrative and conjugative element (ICE) about 45 kb long, derived from GBS 515 ICE tRNALys. The clonal expansion of this HLGR hypervirulent serotype IV GBS CC452 sublineage may pose a threat to the management of infections caused by this strain type.
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Affiliation(s)
- Roberta Creti
- Dipartimento di Malattie Infettive, Reparto di Antibiotico-Resistenza e Patogeni Speciali, Istituto Superiore di Sanità, 00161 Rome, Italy; (M.I.); (S.R.); (G.A.); (G.G.)
| | - Monica Imperi
- Dipartimento di Malattie Infettive, Reparto di Antibiotico-Resistenza e Patogeni Speciali, Istituto Superiore di Sanità, 00161 Rome, Italy; (M.I.); (S.R.); (G.A.); (G.G.)
| | - Uzma Basit Khan
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK;
| | - Alberto Berardi
- Neonatal Intensive Care Unit, Department of Medical and Surgical Sciences of Mothers, Children and Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy;
| | - Simona Recchia
- Dipartimento di Malattie Infettive, Reparto di Antibiotico-Resistenza e Patogeni Speciali, Istituto Superiore di Sanità, 00161 Rome, Italy; (M.I.); (S.R.); (G.A.); (G.G.)
| | - Giovanna Alfarone
- Dipartimento di Malattie Infettive, Reparto di Antibiotico-Resistenza e Patogeni Speciali, Istituto Superiore di Sanità, 00161 Rome, Italy; (M.I.); (S.R.); (G.A.); (G.G.)
| | - Giovanni Gherardi
- Dipartimento di Malattie Infettive, Reparto di Antibiotico-Resistenza e Patogeni Speciali, Istituto Superiore di Sanità, 00161 Rome, Italy; (M.I.); (S.R.); (G.A.); (G.G.)
- Unità di Ricerca di Scienze Batteriologiche Applicate, Facoltà Dipartimentale di Medicina e Chirurgia, Università Campus Bio-Medico, 00128 Rome, Italy
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Alvarez Narvaez S, Sanchez S. Exploring the Accessory Genome of Multidrug-Resistant Rhodococcus equi Clone 2287. Antibiotics (Basel) 2023; 12:1631. [PMID: 37998833 PMCID: PMC10669575 DOI: 10.3390/antibiotics12111631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
Decades of antimicrobial overuse to treat respiratory disease in foals have promoted the emergence and spread of zoonotic multidrug-resistant (MDR) Rhodococcus equi worldwide. Three main R. equi MDR clonal populations-2287, G2106, and G2017-have been identified so far. However, only clones 2287 and G2016 have been isolated from sick animals, with clone 2287 being the main MDR R. equi recovered. The genetic mechanisms that make this MDR clone superior to the others at infecting foals are still unknown. Here, we performed a deep genetic characterization of the accessory genomes of 207 R. equi isolates, and we describe IME2287, a novel genetic element in the accessory genome of clone 2287, potentially involved in the maintenance and spread of this MDR population over time. IME2287 is a putative self-replicative integrative mobilizable element (IME) carrying a DNA replication and partitioning operon and genes encoding its excision and integration from the R. equi genome via a serine recombinase. Additionally, IME2287 encodes a protein containing a Toll/interleukin-1 receptor (TIR) domain that may inhibit TLR-mediated NF-kB signaling in the host and a toxin-antitoxin (TA) system, whose orthologs have been associated with antibiotic resistance/tolerance, virulence, pathogenicity islands, bacterial persistence, and pathogen trafficking. This new set of genes may explain the success of clone 2287 over the other MDR R. equi clones.
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Affiliation(s)
- Sonsiray Alvarez Narvaez
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Susan Sanchez
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
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3
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Lao J, Lacroix T, Guédon G, Coluzzi C, Payot S, Leblond-Bourget N, Chiapello H. ICEscreen: a tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. NAR Genom Bioinform 2022; 4:lqac079. [PMID: 36285285 PMCID: PMC9585547 DOI: 10.1093/nargab/lqac079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 11/23/2022] Open
Abstract
Mobile Genetic Elements (MGEs) are integrated in bacterial genomes and key elements that drive prokaryote genome evolution. Among them are Integrative and Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) which are important for bacterial fitness since they frequently carry genes participating in important bacterial adaptation phenotypes such as antibiotic resistance, virulence or specialized metabolic pathways. Although ICEs and IMEs are widespread, they are as yet almost never annotated in public bacterial genomes. To address the need of dedicated strategies for the annotation of these elements, we developed ICEscreen, a tool that introduces two new features to detect ICEs and IMEs in Firmicute genomes. First, ICEscreen uses an efficient strategy to detect Signature Proteins of ICEs and IMEs based on a database dedicated to Firmicutes and composed of manually curated proteins and Hidden Markov Models (HMM) profiles. Second, ICEscreen includes a new original algorithm that detects composite structures of ICEs and IMEs that are frequent in genomes of Firmicutes but are currently not resolved by any other tool. We benchmarked ICEscreen on experimentally supported elements and on a public dataset of 246 manually annotated elements including the genomes of 40 Firmicutes and demonstrate its efficiency to detect ICEs and IMEs.
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Affiliation(s)
| | | | - Gérard Guédon
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
| | - Charles Coluzzi
- Université Paris-Saclay, INRAE, MaIAGE, F-78350 Jouy-en-Josas, France,Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
| | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
| | | | - Hélène Chiapello
- To whom correspondence should be addressed. Tel: +33 1 34652884; Fax: +33 1 34652217;
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Laroussi H, Aoudache Y, Robert E, Libante V, Thiriet L, Mias-Lucquin D, Douzi B, Roussel Y, Chauvot de Beauchêne I, Soler N, Leblond-Bourget N. Exploration of DNA processing features unravels novel properties of ICE conjugation in Gram-positive bacteria. Nucleic Acids Res 2022; 50:8127-8142. [PMID: 35849337 PMCID: PMC9371924 DOI: 10.1093/nar/gkac607] [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: 11/30/2021] [Revised: 06/02/2022] [Accepted: 07/02/2022] [Indexed: 11/30/2022] Open
Abstract
Integrative and conjugative elements (ICEs) are important drivers of horizontal gene transfer in prokaryotes. They are responsible for antimicrobial resistance spread, a major current health concern. ICEs are initially processed by relaxases that recognize the binding site of oriT sequence and nick at a conserved nic site. The ICESt3/Tn916/ICEBs1 superfamily, which is widespread among Firmicutes, encodes uncanonical relaxases belonging to a recently identified family called MOBT. This family is related to the rolling circle replication initiators of the Rep_trans family. The nic site of these MOBT relaxases is conserved but their DNA binding site is still unknown. Here, we identified the bind site of RelSt3, the MOBT relaxase from ICESt3. Unexpectedly, we found this bind site distantly located from the nic site. We revealed that the binding of the RelSt3 N-terminal HTH domain is required for efficient nicking activity. We also deciphered the role of RelSt3 in the initial and final stages of DNA processing during conjugation. Especially, we demonstrated a strand transfer activity, and the formation of covalent DNA-relaxase intermediate for a MOBT relaxase.
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Affiliation(s)
- Haifa Laroussi
- Université de Lorraine, INRAE, DynAMic, F-54000, Nancy, France
| | - Yanis Aoudache
- Université de Lorraine, INRAE, DynAMic, F-54000, Nancy, France
| | - Emilie Robert
- Université de Lorraine, INRAE, DynAMic, F-54000, Nancy, France
| | | | - Louise Thiriet
- Université de Lorraine, INRAE, DynAMic, F-54000, Nancy, France
| | | | | | - Yvonne Roussel
- Université de Lorraine, INRAE, DynAMic, F-54000, Nancy, France
| | | | - Nicolas Soler
- Université de Lorraine, INRAE, DynAMic, F-54000, Nancy, France
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Lao J, Guédon G, Lacroix T, Charron-Bourgoin F, Libante V, Loux V, Chiapello H, Payot S, Leblond-Bourget N. Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of Streptococcus salivarius to the Environment. Genes (Basel) 2020; 11:genes11090999. [PMID: 32858915 PMCID: PMC7563491 DOI: 10.3390/genes11090999] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 01/15/2023] Open
Abstract
Streptococcus salivarius is a significant contributor to the human oral, pharyngeal and gut microbiomes that contribute to the maintenance of health. The high genomic diversity observed in this species is mainly caused by horizontal gene transfer. This work aimed to evaluate the contribution of integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) in S. salivarius genome diversity. For this purpose, we performed an in-depth analysis of 75 genomes of S. salivarius and searched for signature genes of conjugative and mobilizable elements. This analysis led to the retrieval of 69 ICEs, 165 IMEs and many decayed elements showing their high prevalence in S. salivarius genomes. The identification of almost all ICE and IME boundaries allowed the identification of the genes in which these elements are inserted. Furthermore, the exhaustive analysis of the adaptation genes carried by these elements showed that they encode numerous functions such as resistance to stress, to antibiotics or to toxic compounds, and numerous enzymes involved in diverse cellular metabolic pathways. These data support the idea that not only ICEs but also IMEs and decayed elements play an important role in S. salivarius adaptation to the environment.
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Affiliation(s)
- Julie Lao
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (T.L.); (V.L.); (H.C.)
| | - Gérard Guédon
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
| | - Thomas Lacroix
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (T.L.); (V.L.); (H.C.)
| | - Florence Charron-Bourgoin
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
| | - Virginie Libante
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
| | - Valentin Loux
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (T.L.); (V.L.); (H.C.)
| | - Hélène Chiapello
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (T.L.); (V.L.); (H.C.)
| | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
| | - Nathalie Leblond-Bourget
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
- Correspondence: ; Tel.: +33-3-72-74-51-46
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6
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Libante V, Sarica N, Mohamad Ali A, Gapp C, Oussalah A, Guédon G, Leblond-Bourget N, Payot S. Mobilization of IMEs Integrated in the oriT of ICEs Involves Their Own Relaxase Belonging to the Rep-Trans Family of Proteins. Genes (Basel) 2020; 11:genes11091004. [PMID: 32859088 PMCID: PMC7563843 DOI: 10.3390/genes11091004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 01/27/2023] Open
Abstract
Integrative mobilizable elements (IMEs) are widespread but very poorly studied integrated elements that can excise and hijack the transfer apparatus of co-resident conjugative elements to promote their own spreading. Sixty-four putative IMEs, harboring closely related mobilization and recombination modules, were found in 14 Streptococcus species and in Staphylococcus aureus. Fifty-three are integrated into the origin of transfer (oriT) of a host integrative conjugative element (ICE), encoding a MobT relaxase and belonging to three distant families: ICESt3, Tn916, and ICE6013. The others are integrated into an unrelated IME or in chromosomal sites. After labeling by an antibiotic resistance gene, the conjugative transfer of one of these IMEs (named IME_oriTs) and its host ICE was measured. Although the IME is integrated in an ICE, it does not transfer as a part of the host ICE (no cis-mobilization). The IME excises and transfers separately from the ICE (without impacting its transfer rate) using its own relaxase, distantly related to all known MobT relaxases, and integrates in the oriT of the ICE after transfer. Overall, IME_oriTs use MobT-encoding ICEs both as hosts and as helpers for conjugative transfer. As half of them carry lsa(C), they actively participate in the dissemination of lincosamide–streptogramin A–pleuromutilin resistance among Firmicutes.
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7
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Lannes-Costa PS, Baraúna RA, Ramos JN, Veras JFC, Conceição MVR, Vieira VV, de Mattos-Guaraldi AL, Ramos RTJ, Doran KS, Silva A, Nagao PE. Comparative genomic analysis and identification of pathogenicity islands of hypervirulent ST-17 Streptococcus agalactiae Brazilian strain. INFECTION GENETICS AND EVOLUTION 2020; 80:104195. [DOI: 10.1016/j.meegid.2020.104195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 01/09/2020] [Accepted: 01/14/2020] [Indexed: 11/29/2022]
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Liu M, Li X, Xie Y, Bi D, Sun J, Li J, Tai C, Deng Z, Ou HY. ICEberg 2.0: an updated database of bacterial integrative and conjugative elements. Nucleic Acids Res 2020; 47:D660-D665. [PMID: 30407568 PMCID: PMC6323972 DOI: 10.1093/nar/gky1123] [Citation(s) in RCA: 266] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 10/23/2018] [Indexed: 12/30/2022] Open
Abstract
ICEberg 2.0 (http://db-mml.sjtu.edu.cn/ICEberg/) is an updated database that provides comprehensive information about bacterial integrative and conjugative elements (ICEs). Compared with the previous version, three major improvements were made. First, with the aid of text mining and manual curation, it now recorded the details of 1032 ICEs, including 270 with experimental supports and 762 from bioinformatics prediction. Second, as increasing evidence has shown that ICEs frequently mobilize the so-called ‘hitchhikers’, such as integrative and mobilizable elements (IMEs) and cis-mobilizable elements (CIMEs), 83 known transfer interactions between 49 IMEs and 7 CIMEs with 19 ICEs taken from the literature were included and illustrated with visually intuitive directed graphs. An expanded collection of 260 chromosome-borne IMEs and 235 CIMEs was also added. At last, ICEberg 2.0 provides an online tool ICEfinder to predict ICEs or IMEs in bacterial genome sequences. It combines a similarity search for the integrase, relaxase and/or type IV secretion system and the co-localization of these corresponding homologous genes. With the recent updates, ICEberg 2.0 might provide better support for understanding the biological traits of ICEs, especially as their interaction with cognate mobilizable elements may further promote horizontal gene flow.
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Affiliation(s)
- Meng Liu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaobin Li
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yingzhou Xie
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Dexi Bi
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Jingyong Sun
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jun Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Cui Tai
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Chromosomal Conjugative and Mobilizable Elements in Streptococcus suis: Major Actors in the Spreading of Antimicrobial Resistance and Bacteriocin Synthesis Genes. Pathogens 2019; 9:pathogens9010022. [PMID: 31881744 PMCID: PMC7168690 DOI: 10.3390/pathogens9010022] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/10/2019] [Accepted: 12/20/2019] [Indexed: 12/30/2022] Open
Abstract
Streptococcus suis is a zoonotic pathogen suspected to be a reservoir of antimicrobial resistance (AMR) genes. The genomes of 214 strains of 27 serotypes were screened for AMR genes and chromosomal Mobile Genetic Elements (MGEs), in particular Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs). The functionality of two ICEs that host IMEs carrying AMR genes was investigated by excision tests and conjugation experiments. In silico search revealed 416 ICE-related and 457 IME-related elements. These MGEs exhibit an impressive diversity and plasticity with tandem accretions, integration of ICEs or IMEs inside ICEs and recombination between the elements. All of the detected 393 AMR genes are carried by MGEs. As previously described, ICEs are major vehicles of AMR genes in S. suis. Tn5252-related ICEs also appear to carry bacteriocin clusters. Furthermore, whereas the association of IME-AMR genes has never been described in S. suis, we found that most AMR genes are actually carried by IMEs. The autonomous transfer of an ICE to another bacterial species (Streptococcus thermophilus)-leading to the cis-mobilization of an IME carrying tet(O)-was obtained. These results show that besides ICEs, IMEs likely play a major role in the dissemination of AMR genes in S. suis.
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10
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Chen SL. Genomic Insights Into the Distribution and Evolution of Group B Streptococcus. Front Microbiol 2019; 10:1447. [PMID: 31316488 PMCID: PMC6611187 DOI: 10.3389/fmicb.2019.01447] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 06/11/2019] [Indexed: 01/31/2023] Open
Abstract
Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a bacteria with truly protean biology. It infects a variety of hosts, among which the most commonly studied are humans, cattle, and fish. GBS holds a singular position in the history of bacterial genomics, as it was the substrate used to describe one of the first major conceptual advances of comparative genomics, the idea of the pan-genome. In this review, I describe a brief history of GBS and the major contributions of genomics to understanding its genome plasticity and evolution as well as its molecular epidemiology, focusing on the three hosts mentioned above. I also discuss one of the major recent paradigm shifts in our understanding of GBS evolution and disease burden: foodborne GBS can cause invasive infections in humans.
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Affiliation(s)
- Swaine L Chen
- Division of Infectious Diseases, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Infectious Diseases Group, Genome Institute of Singapore, Singapore, Singapore
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11
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Soler N, Robert E, Chauvot de Beauchêne I, Monteiro P, Libante V, Maigret B, Staub J, Ritchie DW, Guédon G, Payot S, Devignes MD, Leblond-Bourget N. Characterization of a relaxase belonging to the MOB T family, a widespread family in Firmicutes mediating the transfer of ICEs. Mob DNA 2019; 10:18. [PMID: 31073337 PMCID: PMC6499999 DOI: 10.1186/s13100-019-0160-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/11/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Conjugative spread of antibiotic resistance and virulence genes in bacteria constitutes an important threat to public health. Beyond the well-known conjugative plasmids, recent genome analyses have shown that integrative and conjugative elements (ICEs) are the most widespread conjugative elements, even if their transfer mechanism has been little studied until now. The initiator of conjugation is the relaxase, a protein catalyzing a site-specific nick on the origin of transfer (oriT) of the ICE. Besides canonical relaxases, recent studies revealed non-canonical ones, such as relaxases of the MOBT family that are related to rolling-circle replication proteins of the Rep_trans family. MOBT relaxases are encoded by ICEs of the ICESt3/ICEBs1/Tn916 superfamily, a superfamily widespread in Firmicutes, and frequently conferring antibiotic resistance. RESULTS Here, we present the first biochemical and structural characterization of a MOBT relaxase: the RelSt3 relaxase encoded by ICESt3 from Streptococcus thermophilus. We identified the oriT region of ICESt3 and demonstrated that RelSt3 is required for its conjugative transfer. The purified RelSt3 protein is a stable dimer that provides a Mn2+-dependent single-stranded endonuclease activity. Sequence comparisons of MOBT relaxases led to the identification of MOBT conserved motifs. These motifs, together with the construction of a 3D model of the relaxase domain of RelSt3, allowed us to determine conserved residues of the RelSt3 active site. The involvement of these residues in DNA nicking activity was demonstrated by targeted mutagenesis. CONCLUSIONS All together, this work argues in favor of MOBT being a full family of non-canonical relaxases. The biochemical and structural characterization of a MOBT member provides new insights on the molecular mechanism of conjugative transfer mediated by ICEs in Gram-positive bacteria. This could be a first step towards conceiving rational strategies to control gene transfer in these bacteria.
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Affiliation(s)
- Nicolas Soler
- Université de Lorraine, Inra, UMR1128 DynAMic, F-54000 Nancy, France
| | - Emilie Robert
- Université de Lorraine, Inra, UMR1128 DynAMic, F-54000 Nancy, France
| | | | - Philippe Monteiro
- Université de Lorraine, Inra, UMR1128 DynAMic, F-54000 Nancy, France
| | - Virginie Libante
- Université de Lorraine, Inra, UMR1128 DynAMic, F-54000 Nancy, France
| | - Bernard Maigret
- Université de Lorraine, CNRS, Inria, LORIA, F-54000 Nancy, France
| | - Johan Staub
- Université de Lorraine, Inra, UMR1128 DynAMic, F-54000 Nancy, France
| | - David W. Ritchie
- Université de Lorraine, CNRS, Inria, LORIA, F-54000 Nancy, France
| | - Gérard Guédon
- Université de Lorraine, Inra, UMR1128 DynAMic, F-54000 Nancy, France
| | - Sophie Payot
- Université de Lorraine, Inra, UMR1128 DynAMic, F-54000 Nancy, France
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Microevolution of Streptococcus agalactiae ST-261 from Australia Indicates Dissemination via Imported Tilapia and Ongoing Adaptation to Marine Hosts or Environment. Appl Environ Microbiol 2018; 84:AEM.00859-18. [PMID: 29915111 DOI: 10.1128/aem.00859-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/12/2018] [Indexed: 11/20/2022] Open
Abstract
Streptococcus agalactiae (group B Streptococcus [GBS]) causes disease in a wide range of animals. The serotype Ib lineage is highly adapted to aquatic hosts, exhibiting substantial genome reduction compared with terrestrial conspecifics. Here, we sequence genomes from 40 GBS isolates, including 25 isolates from wild fish and captive stingrays in Australia, six local veterinary or human clinical isolates, and nine isolates from farmed tilapia in Honduras, and compared them with 42 genomes from public databases. Phylogenetic analysis based on nonrecombinant core-genome single nucleotide polymorphisms (SNPs) indicated that aquatic serotype Ib isolates from Queensland were distantly related to local veterinary and human clinical isolates. In contrast, Australian aquatic isolates are most closely related to a tilapia isolate from Israel, differing by only 63 core-genome SNPs. A consensus minimum spanning tree based on core-genome SNPs indicates the dissemination of sequence type 261 (ST-261) from an ancestral tilapia strain, which is congruent with several introductions of tilapia into Australia from Israel during the 1970s and 1980s. Pangenome analysis identified 1,440 genes as core, with the majority being dispensable or strain specific, with non-protein-coding intergenic regions (IGRs) divided among core and strain-specific genes. Aquatic serotype Ib strains have lost many virulence factors during adaptation, but six adhesins were well conserved across the aquatic isolates and might be critical for virulence in fish and for targets in vaccine development. The close relationship among recent ST-261 isolates from Ghana, the United States, and China with the Israeli tilapia isolate from 1988 implicates the global trade in tilapia seed for aquaculture in the widespread dissemination of serotype Ib fish-adapted GBS.IMPORTANCEStreptococcus agalactiae (GBS) is a significant pathogen of humans and animals. Some lineages have become adapted to particular hosts, and serotype Ib is highly specialized to fish. Here, we show that this lineage is likely to have been distributed widely by the global trade in tilapia for aquaculture, with probable introduction into Australia in the 1970s and subsequent dissemination in wild fish populations. We report here the variability in the polysaccharide capsule among this lineage but identify a cohort of common surface proteins that may be a focus of future vaccine development to reduce the biosecurity risk in international fish trade.
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Lorenzo-Diaz F, Fernández-Lopez C, Douarre PE, Baez-Ortega A, Flores C, Glaser P, Espinosa M. Streptococcal group B integrative and mobilizable element IMESag-rpsI encodes a functional relaxase involved in its transfer. Open Biol 2017; 6:rsob.160084. [PMID: 27707895 PMCID: PMC5090054 DOI: 10.1098/rsob.160084] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022] Open
Abstract
Streptococcus agalactiae or Group B Streptococcus (GBS) are opportunistic bacteria that can cause lethal sepsis in children and immuno-compromised patients. Their genome is a reservoir of mobile genetic elements that can be horizontally transferred. Among them, integrative and conjugative elements (ICEs) and the smaller integrative and mobilizable elements (IMEs) primarily reside in the bacterial chromosome, yet have the ability to be transferred between cells by conjugation. ICEs and IMEs are therefore a source of genetic variability that participates in the spread of antibiotic resistance. Although IMEs seem to be the most prevalent class of elements transferable by conjugation, they are poorly known. Here, we have studied a GBS-IME, termed IMESag-rpsI, which is widely distributed in GBS despite not carrying any apparent virulence trait. Analyses of 240 whole genomes showed that IMESag-rpsI is present in approximately 47% of the genomes, has a roughly constant size (approx. 9 kb) and is always integrated at a single location, the 3′-end of the gene encoding the ribosomal protein S9 (rpsI). Based on their genetic variation, several IMESag-rpsI types were defined (A–J) and classified in clonal complexes (CCs). CC1 was the most populated by IMESag-rpsI (more than 95%), mostly of type-A (71%). One CC1 strain (S. agalactiae HRC) was deep-sequenced to understand the rationale underlying type-A IMESag-rpsI enrichment in GBS. Thirteen open reading frames were identified, one of them encoding a protein (MobSag) belonging to the broadly distributed family of relaxases MOBV1. Protein MobSag was purified and, by a newly developed method, shown to cleave DNA at a specific dinucleotide. The S. agalactiae HRC-IMESag-rpsI is able to excise from the chromosome, as shown by the presence of circular intermediates, and it harbours a fully functional mobilization module. Further, the mobSag gene encoded by this mobile element is able to promote plasmid transfer among pneumococcal strains, suggesting that MobSag facilitates the spread of IMESag-rpsI and that this spread would explain the presence of the same IMESag-rpsI type in GBS strains belonging to different CCs.
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Affiliation(s)
- Fabian Lorenzo-Diaz
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Av. Astrofísico Francisco Sánchez s/n, 38071 Santa Cruz de Tenerife, Spain Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | | | - Pierre-Emmanuel Douarre
- Institut Pasteur, Unité Ecologie et Evolution de la Résistance aux Antibiotiques, Paris CNRS UMR3525, France
| | - Adrian Baez-Ortega
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Carlos Flores
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Philippe Glaser
- Institut Pasteur, Unité Ecologie et Evolution de la Résistance aux Antibiotiques, Paris CNRS UMR3525, France
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The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems. Genes (Basel) 2017; 8:genes8110337. [PMID: 29165361 PMCID: PMC5704250 DOI: 10.3390/genes8110337] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022] Open
Abstract
Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements. Recent findings indicated that the main actors of conjugative transfer are not the well-known conjugative or mobilizable plasmids but are the integrated elements. This paper reviews current knowledge on “integrative and mobilizable elements” (IMEs) that have recently been shown to be highly diverse and highly widespread but are still rarely described. IMEs encode their own excision and integration and use the conjugation machinery of unrelated co-resident conjugative element for their own transfer. Recent studies revealed a much more complex and much more diverse lifecycle than initially thought. Besides their main transmission as integrated elements, IMEs probably use plasmid-like strategies to ensure their maintenance after excision. Their interaction with conjugative elements reveals not only harmless hitchhikers but also hunters that use conjugative elements as target for their integration or harmful parasites that subvert the conjugative apparatus of incoming elements to invade cells that harbor them. IMEs carry genes conferring various functions, such as resistance to antibiotics, that can enhance the fitness of their hosts and that contribute to their maintenance in bacterial populations. Taken as a whole, IMEs are probably major contributors to bacterial evolution.
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Diversity of Integrative and Conjugative Elements of Streptococcus salivarius and Their Intra- and Interspecies Transfer. Appl Environ Microbiol 2017; 83:AEM.00337-17. [PMID: 28432093 DOI: 10.1128/aem.00337-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/12/2017] [Indexed: 01/12/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are widespread chromosomal mobile genetic elements which can transfer autonomously by conjugation in bacteria. Thirteen ICEs with a conjugation module closely related to that of ICESt3 of Streptococcus thermophilus were characterized in Streptococcus salivarius by whole-genome sequencing. Sequence comparison highlighted ICE evolution by shuffling of 3 different integration/excision modules (for integration in the 3' end of the fda, rpsI, or rpmG gene) with the conjugation module of the ICESt3 subfamily. Sequence analyses also pointed out a recombination occurring at oriT (likely mediated by the relaxase) as a mechanism of ICE evolution. Despite a similar organization in two operons including three conserved genes, the regulation modules show a high diversity (about 50% amino acid sequence divergence for the encoded regulators and presence of unrelated additional genes) with a probable impact on the regulation of ICE activity. Concerning the accessory genes, ICEs of the ICESt3 subfamily appear particularly rich in restriction-modification systems and orphan methyltransferase genes. Other cargo genes that could confer a selective advantage to the cell hosting the ICE were identified, in particular, genes for bacteriocin synthesis and cadmium resistance. The functionality of 2 ICEs of S. salivarius was investigated. Autonomous conjugative transfer to other S. salivarius strains, to S. thermophilus, and to Enterococcus faecalis was observed. The analysis of the ICE-fda border sequence in these transconjugants allowed the localization of the DNA cutting site of the ICE integrase.IMPORTANCE The ICESt3 subfamily of ICEs appears to be widespread in streptococci and targets diverse chromosomal integration sites. These ICEs carry diverse cargo genes that can confer a selective advantage to the host strain. The maintenance of these mobile genetic elements likely relies in part on self-encoded restriction-modification systems. In this study, intra- and interspecies transfer was demonstrated for 2 ICEs of S. salivarius Closely related ICEs were also detected in silico in other Streptococcus species (S. pneumoniae and S. parasanguinis), thus indicating that diffusion of ICESt3-related elements probably plays a significant role in horizontal gene transfer (HGT) occurring in the oral cavity but also in the digestive tract, where S. salivarius is present.
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Coluzzi C, Guédon G, Devignes MD, Ambroset C, Loux V, Lacroix T, Payot S, Leblond-Bourget N. A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins. Front Microbiol 2017; 8:443. [PMID: 28373865 PMCID: PMC5357655 DOI: 10.3389/fmicb.2017.00443] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/03/2017] [Indexed: 12/22/2022] Open
Abstract
Recent analyses of bacterial genomes have shown that integrated elements that transfer by conjugation play an essential role in horizontal gene transfer. Among these elements, the integrative and mobilizable elements (IMEs) are known to encode their own excision and integration machinery, and to carry all the sequences or genes necessary to hijack the mating pore of a conjugative element for their own transfer. However, knowledge of their prevalence and diversity is still severely lacking. In this work, an extensive analysis of 124 genomes from 27 species of Streptococcus reveals 144 IMEs. These IMEs encode either tyrosine or serine integrases. The identification of IME boundaries shows that 141 are specifically integrated in 17 target sites. The IME-encoded relaxases belong to nine superfamilies, among which four are previously unknown in any mobilizable or conjugative element. A total of 118 IMEs are found to encode a non-canonical relaxase related to rolling circle replication initiators (belonging to the four novel families or to MobT). Surprisingly, among these, 83 encode a TcpA protein (i.e., a non-canonical coupling protein (CP) that is more closely related to FtsK than VirD4) that was not previously known to be encoded by mobilizable elements. Phylogenetic analyses reveal not only many integration/excision module replacements but also losses, acquisitions or replacements of TcpA genes between IMEs. This glimpse into the still poorly known world of IMEs reveals that mobilizable elements have a very high prevalence. Their diversity is even greater than expected, with most encoding a CP and/or a non-canonical relaxase.
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Affiliation(s)
- Charles Coluzzi
- UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Gérard Guédon
- UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Marie-Dominique Devignes
- UMR7503 Laboratoire Lorrain de Recherche en Informatique et ses Applications, Centre National de la Recherche Scientifique, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Chloé Ambroset
- UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Valentin Loux
- UR1404 Mathématiques et Informatique Appliquées du Génome à l'Environnement, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Thomas Lacroix
- UR1404 Mathématiques et Informatique Appliquées du Génome à l'Environnement, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sophie Payot
- UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Nathalie Leblond-Bourget
- UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France
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Teatero S, Lemire P, Dewar K, Wasserscheid J, Calzas C, Mallo GV, Li A, Athey TBT, Segura M, Fittipaldi N. Genomic Recombination Leading to Decreased Virulence of Group B Streptococcus in a Mouse Model of Adult Invasive Disease. Pathogens 2016; 5:pathogens5030054. [PMID: 27527222 PMCID: PMC5039434 DOI: 10.3390/pathogens5030054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 07/21/2016] [Accepted: 08/01/2016] [Indexed: 01/06/2023] Open
Abstract
Adult invasive disease caused by Group B Streptococcus (GBS) is increasing worldwide. Whole-genome sequencing (WGS) now permits rapid identification of recombination events, a phenomenon that occurs frequently in GBS. Using WGS, we described that strain NGBS375, a capsular serotype V GBS isolate of sequence type (ST)297, has an ST1 genomic background but has acquired approximately 300 kbp of genetic material likely from an ST17 strain. Here, we examined the virulence of this strain in an in vivo model of GBS adult invasive infection. The mosaic ST297 strain showed intermediate virulence, causing significantly less systemic infection and reduced mortality than a more virulent, serotype V ST1 isolate. Bacteremia induced by the ST297 strain was similar to that induced by a serotype III ST17 strain, which was the least virulent under the conditions tested. Yet, under normalized bacteremia levels, the in vivo intrinsic capacity to induce the production of pro-inflammatory cytokines was similar between the ST297 strain and the virulent ST1 strain. Thus, the diminished virulence of the mosaic strain may be due to reduced capacity to disseminate or multiply in blood during a systemic infection which could be mediated by regulatory factors contained in the recombined region.
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Affiliation(s)
- Sarah Teatero
- Public Health Ontario Laboratory, 661 University Avenue, Suite 17-100, Toronto, ON M5G 1M1, Canada.
| | - Paul Lemire
- Laboratory of Immunology, Faculty of Veterinary Medicine, University of Montreal, 3200 Sicotte Street, Saint-Hyacinthe, QC J2S 2M2, Canada.
| | - Ken Dewar
- McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfield Avenue Rm 7104, Montreal, QC H3A 0G1, Canada.
| | - Jessica Wasserscheid
- McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfield Avenue Rm 7104, Montreal, QC H3A 0G1, Canada.
| | - Cynthia Calzas
- Laboratory of Immunology, Faculty of Veterinary Medicine, University of Montreal, 3200 Sicotte Street, Saint-Hyacinthe, QC J2S 2M2, Canada.
| | - Gustavo V Mallo
- Public Health Ontario Laboratory, 661 University Avenue, Suite 17-100, Toronto, ON M5G 1M1, Canada.
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 27 King's College Circle, Toronto, ON M5S 1A1, Canada.
| | - Aimin Li
- Public Health Ontario Laboratory, 661 University Avenue, Suite 17-100, Toronto, ON M5G 1M1, Canada.
| | - Taryn B T Athey
- Public Health Ontario Laboratory, 661 University Avenue, Suite 17-100, Toronto, ON M5G 1M1, Canada.
| | - Mariela Segura
- Laboratory of Immunology, Faculty of Veterinary Medicine, University of Montreal, 3200 Sicotte Street, Saint-Hyacinthe, QC J2S 2M2, Canada.
| | - Nahuel Fittipaldi
- Public Health Ontario Laboratory, 661 University Avenue, Suite 17-100, Toronto, ON M5G 1M1, Canada.
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 27 King's College Circle, Toronto, ON M5S 1A1, Canada.
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Ambroset C, Coluzzi C, Guédon G, Devignes MD, Loux V, Lacroix T, Payot S, Leblond-Bourget N. New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration. Front Microbiol 2016; 6:1483. [PMID: 26779141 PMCID: PMC4701971 DOI: 10.3389/fmicb.2015.01483] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 12/08/2015] [Indexed: 12/30/2022] Open
Abstract
Recent genome analyses suggest that integrative and conjugative elements (ICEs) are widespread in bacterial genomes and therefore play an essential role in horizontal transfer. However, only a few of these elements are precisely characterized and correctly delineated within sequenced bacterial genomes. Even though previous analysis showed the presence of ICEs in some species of Streptococci, the global prevalence and diversity of ICEs was not analyzed in this genus. In this study, we searched for ICEs in the completely sequenced genomes of 124 strains belonging to 27 streptococcal species. These exhaustive analyses revealed 105 putative ICEs and 26 slightly decayed elements whose limits were assessed and whose insertion site was identified. These ICEs were grouped in seven distinct unrelated or distantly related families, according to their conjugation modules. Integration of these streptococcal ICEs is catalyzed either by a site-specific tyrosine integrase, a low-specificity tyrosine integrase, a site-specific single serine integrase, a triplet of site-specific serine integrases or a DDE transposase. Analysis of their integration site led to the detection of 18 target-genes for streptococcal ICE insertion including eight that had not been identified previously (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG, and ebfC). It also suggests that all specificities have evolved to minimize the impact of the insertion on the host. This overall analysis of streptococcal ICEs emphasizes their prevalence and diversity and demonstrates that exchanges or acquisitions of conjugation and recombination modules are frequent.
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Affiliation(s)
- Chloé Ambroset
- DynAMic, Faculté des Sciences et Technologies, Université de Lorraine, UMR 1128Vandœuvre-lès-Nancy, France; DynAMic, Institut National de la Recherche Agronomique, UMR 1128Vandœuvre-lès-Nancy, France
| | - Charles Coluzzi
- DynAMic, Faculté des Sciences et Technologies, Université de Lorraine, UMR 1128Vandœuvre-lès-Nancy, France; DynAMic, Institut National de la Recherche Agronomique, UMR 1128Vandœuvre-lès-Nancy, France
| | - Gérard Guédon
- DynAMic, Faculté des Sciences et Technologies, Université de Lorraine, UMR 1128Vandœuvre-lès-Nancy, France; DynAMic, Institut National de la Recherche Agronomique, UMR 1128Vandœuvre-lès-Nancy, France
| | - Marie-Dominique Devignes
- Laboratoire Lorrain de Recherche en Informatique et ses Applications, Faculté des Sciences et Technologies, Université de Lorraine, UMR 7503Vandœuvre-lès-Nancy, France; CNRS, Laboratoire Lorrain de Recherche en Informatique et ses Applications, UMR 7503Vandśuvre-lès-Nancy, France
| | - Valentin Loux
- UR 1404 Mathématiques et Informatique Appliquées du Génome à l'Environnement, Institut National de la Recherche Agronomique Jouy-en-Josas, France
| | - Thomas Lacroix
- UR 1404 Mathématiques et Informatique Appliquées du Génome à l'Environnement, Institut National de la Recherche Agronomique Jouy-en-Josas, France
| | - Sophie Payot
- DynAMic, Faculté des Sciences et Technologies, Université de Lorraine, UMR 1128Vandœuvre-lès-Nancy, France; DynAMic, Institut National de la Recherche Agronomique, UMR 1128Vandœuvre-lès-Nancy, France
| | - Nathalie Leblond-Bourget
- DynAMic, Faculté des Sciences et Technologies, Université de Lorraine, UMR 1128Vandœuvre-lès-Nancy, France; DynAMic, Institut National de la Recherche Agronomique, UMR 1128Vandœuvre-lès-Nancy, France
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Douarre PE, Sauvage E, Poyart C, Glaser P. Host specificity in the diversity and transfer of lsa resistance genes in group B Streptococcus. J Antimicrob Chemother 2015; 70:3205-13. [PMID: 26410170 DOI: 10.1093/jac/dkv277] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 08/12/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES In group B Streptococcus (GBS), cross-resistance to lincosamides, streptogramin A and pleuromutilins (LSAP) is mediated by the acquisition of lsa genes. Here, we characterized the diversity, mobility and ecology of lsa genes in this species. METHODS lsa variants were systematically identified by BLAST searches in the genomes of 531 GBS strains from different hosts and geographical origins. The associated phenotypes were determined by a microdilution MIC method. Acquisition of resistance genes was deduced from comparative genomics and phylogeny. Their mobility was tested by conjugation experiments. RESULTS lsa(E) and three variants of lsa(C) were identified in GBS strains. Two lsa(C) variants had not been previously reported. All four variants conferred LSAP phenotypes. lsa(E) was located in a multiresistance gene cluster of a single human strain. This gene was transferred by a high-frequency recombination-type mechanism between GBS strains. Two lsa(C) variants are carried in six unrelated human strains by two similar elements specifically integrated in the oriT site of four different classes of integrative and conjugative elements (ICEs). Strikingly, the acquisition of the resistance gene always occurred by the integration of the element into a resident ICE. The third lsa(C) variant was located at the same site in the core genome of 11 genetically distant bovine strains and was likely propagated by horizontal transfer of the corresponding chromosomal region. CONCLUSIONS lsa genes in GBS show distinct host specificities and modes of transfer. In general, their dissemination is mediated by recombination rather than by the transfer of conjugative elements.
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Affiliation(s)
- Pierre-Emmanuel Douarre
- Unité de Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur, 28 Rue du Dr Roux, 75724, Paris, France CNRS, UMR3525, Paris, France
| | - Elisabeth Sauvage
- Unité de Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur, 28 Rue du Dr Roux, 75724, Paris, France CNRS, UMR3525, Paris, France
| | - Claire Poyart
- Unité de Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur, 28 Rue du Dr Roux, 75724, Paris, France Centre National de Référence des Streptocoques, Groupe Hospitalier Paris Centre Cochin-Hôtel Dieu-Broca, Paris, France Institut Cochin, Université Sorbonne Paris Descartes, Paris, France INSERM, U1016, Paris, France
| | - Philippe Glaser
- Unité de Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur, 28 Rue du Dr Roux, 75724, Paris, France CNRS, UMR3525, Paris, France
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Chuzeville S, Dramsi S, Madec JY, Haenni M, Payot S. Antigen I/II encoded by integrative and conjugative elements of Streptococcus agalactiae and role in biofilm formation. Microb Pathog 2015; 88:1-9. [PMID: 26232503 DOI: 10.1016/j.micpath.2015.07.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 07/13/2015] [Accepted: 07/20/2015] [Indexed: 10/23/2022]
Abstract
Streptococcus agalactiae (i.e. Group B streptococcus, GBS) is a major human and animal pathogen. Genes encoding putative surface proteins and in particular an antigen I/II have been identified on Integrative and Conjugative Elements (ICEs) found in GBS. Antigens I/II are multimodal adhesins promoting colonization of the oral cavity by streptococci such as Streptococcus gordonii and Streptococcus mutans. The prevalence and diversity of antigens I/II in GBS were studied by a bioinformatic analysis. It revealed that antigens I/II, which are acquired by horizontal transfer via ICEs, exhibit diversity and are widespread in GBS, in particular in the serotype Ia/ST23 invasive strains. This study aimed at characterizing the impact on GBS biology of proteins encoded by a previously characterized ICE of S. agalactiae (ICE_515_tRNA(Lys)). The production and surface exposition of the antigen I/II encoded by this ICE was examined using RT-PCR and immunoblotting experiments. Surface proteins of ICE_515_tRNA(Lys) were found to contribute to GBS biofilm formation and to fibrinogen binding. Contribution of antigen I/II encoded by SAL_2056 to biofilm formation was also demonstrated. These results highlight the potential for ICEs to spread microbial adhesins between species.
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Affiliation(s)
- Sarah Chuzeville
- INRA, UMR1128 DynAMic, F-54506 Vandoeuvre-lès-Nancy, France; Université de Lorraine, UMR1128 DynAMic, F-54506 Vandoeuvre-lès-Nancy, France; ANSES Site de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Shaynoor Dramsi
- Institut Pasteur, Unité de Biologie des Bactéries Pathogènes à Gram-Positif, Paris, France; CNRS ERL3526, Paris, France
| | - Jean-Yves Madec
- ANSES Site de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marisa Haenni
- ANSES Site de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Sophie Payot
- INRA, UMR1128 DynAMic, F-54506 Vandoeuvre-lès-Nancy, France; Université de Lorraine, UMR1128 DynAMic, F-54506 Vandoeuvre-lès-Nancy, France.
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Kingston AW, Roussel-Rossin C, Dupont C, Raleigh EA. Novel recA-Independent Horizontal Gene Transfer in Escherichia coli K-12. PLoS One 2015; 10:e0130813. [PMID: 26162088 PMCID: PMC4498929 DOI: 10.1371/journal.pone.0130813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 05/27/2015] [Indexed: 01/19/2023] Open
Abstract
In bacteria, mechanisms that incorporate DNA into a genome without strand-transfer proteins such as RecA play a major role in generating novelty by horizontal gene transfer. We describe a new illegitimate recombination event in Escherichia coli K-12: RecA-independent homologous replacements, with very large (megabase-length) donor patches replacing recipient DNA. A previously uncharacterized gene (yjiP) increases the frequency of RecA-independent replacement recombination. To show this, we used conjugal DNA transfer, combining a classical conjugation donor, HfrH, with modern genome engineering methods and whole genome sequencing analysis to enable interrogation of genetic dependence of integration mechanisms and characterization of recombination products. As in classical experiments, genomic DNA transfer begins at a unique position in the donor, entering the recipient via conjugation; antibiotic resistance markers are then used to select recombinant progeny. Different configurations of this system were used to compare known mechanisms for stable DNA incorporation, including homologous recombination, F'-plasmid formation, and genome duplication. A genome island of interest known as the immigration control region was specifically replaced in a minority of recombinants, at a frequency of 3 X 10(-12) CFU/recipient per hour.
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Affiliation(s)
- Anthony W. Kingston
- New England Biolabs, Ipswich, Massachusetts, 01938, United States of America
| | | | - Claire Dupont
- New England Biolabs, Ipswich, Massachusetts, 01938, United States of America
| | - Elisabeth A. Raleigh
- New England Biolabs, Ipswich, Massachusetts, 01938, United States of America
- * E-mail:
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