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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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Creti R, Imperi M, Stanziale A, Giuliani G, Fazii P, Savini V. Group B streptococci (GBS) strains evading molecular diagnostics showed novel chromosomal deletions encompassing the CAMP-factor (cfb) encoding gene. Eur J Clin Microbiol Infect Dis 2023; 42:913-916. [PMID: 37160573 DOI: 10.1007/s10096-023-04620-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 05/03/2023] [Indexed: 05/11/2023]
Abstract
A highly conserved fragment adjacent to the cfb gene encoding the CAMP factor is the target of PCR-based molecular diagnostic systems for the identification of S. agalactiae (group B streptococci (GBS)). Six PCR-negative, culture-positive GBS strains were whole genome sequenced to assess why they escaped molecular diagnostics. GBS strains did not constitute a clonal cluster and presented variably sized chromosomal deletions (from 7 to 33 kb) which always included the cfb gene, a finding never described before. GBS strains that escape molecular diagnostics are considered rare; however, they can cause false-negative results using molecular diagnostics alone, affecting medical decisions.
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Affiliation(s)
- Roberta Creti
- Antibiotic Resistance and Special Pathogens Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena, 299 -, 00161, Rome, Italy.
| | - Monica Imperi
- Antibiotic Resistance and Special Pathogens Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena, 299 -, 00161, Rome, Italy
| | - Andrea Stanziale
- Clinical Microbiology and Virology, Spirito Santo Hospital, Via Fonte Romana 8, 65124, Pescara, Italy
| | - Giorgia Giuliani
- Clinical Microbiology and Virology, Spirito Santo Hospital, Via Fonte Romana 8, 65124, Pescara, Italy
| | - Paolo Fazii
- Clinical Microbiology and Virology, Spirito Santo Hospital, Via Fonte Romana 8, 65124, Pescara, Italy
| | - Vincenzo Savini
- Clinical Microbiology and Virology, Spirito Santo Hospital, Via Fonte Romana 8, 65124, Pescara, Italy
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Tsai IA, Su Y, Wang YH, Chu C. Alterations in Genes rib, scpB and Pilus Island Decrease the Prevalence of Predominant Serotype V, Not III and VI, of Streptococcus agalactiae from 2008 to 2012. Pathogens 2022; 11:pathogens11101145. [PMID: 36297202 PMCID: PMC9611264 DOI: 10.3390/pathogens11101145] [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] [Received: 08/10/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022] Open
Abstract
Streptococcus agalactiae (GBS) can infect newborns, pregnant women and immunocompromised or elderly people. This study aimed to investigate differences in three pilus genes and virulence genes pavA, cfb, rib and scpB and changes in predominant serotypes III, V and VI from 2008 to 2012. The susceptibilities to penicillin, ceftriaxone, azithromycin, erythromycin, clindamycin, levofloxacin and moxifloxacin of 145 GBS strains of serotype III, V and VI strains from 2008 and 2012 were determined using disc diffusion method. PCR identification of ST-17, the pilus genes and virulence genes; multilocus sequence typing (MLST); and conserved domain and phylogenetic analysis of scpB-1 and scpB-2 proteins were performed. A dramatic number reduction was observed in serotype V, not III and V, from 2008 to 2012. The rate of resistance to azithromycin, clindamycin and erythromycin was the highest in serotype V. ST-17 was only found in serotype III with pilus genes PI-1+PI-2b. The major pilus genotype was PI-1+PI-2a. Serotype V without the rib gene was reduced in number between two studied years. Compared to scpB-1, scpB-2 had a 128-bp deletion in a PA C5a-like peptidase domain and putative integrin-binding motif RGD. In conclusion, reduction in serotype V may be due to presence of scpB-2 or lack of genes scpB and rib.
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Affiliation(s)
- I-An Tsai
- Ph.D. Program of Agriculture Science, College of Agriculture, National Chiayi University, Chiayi City 600, Taiwan
| | - Yaochi Su
- Ph.D. Program of Agriculture Science, College of Agriculture, National Chiayi University, Chiayi City 600, Taiwan
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chiayi University, Chiayi City 600, Taiwan
| | - Ying-Hsiang Wang
- Department of Pediatrics, Chang Gung Memorial Hospital, Puzi City 613, Taiwan
| | - Chishih Chu
- Department of Microbiology, Immunology and Biopharmaceuticals, College of Life Sciences, National Chiayi University, Chiayi City 600, Taiwan
- Correspondence: ; Tel.: +886-5-2717898
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Group B Streptococcus CAMP Factor Does Not Contribute to Interactions with the Vaginal Epithelium and Is Dispensable for Vaginal Colonization in Mice. Microbiol Spectr 2021; 9:e0105821. [PMID: 34908468 PMCID: PMC8672899 DOI: 10.1128/spectrum.01058-21] [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: 11/20/2022] Open
Abstract
The Gram-positive pathogen group B Streptococcus (GBS) is a leading cause of neonatal bacterial infections, preterm birth, and stillbirth. Although maternal GBS vaginal colonization is a risk factor for GBS-associated adverse birth outcomes, mechanisms promoting GBS vaginal persistence are not fully defined. GBS possesses a broadly conserved small molecule, CAMP factor, that is co-hemolytic in the presence of Staphylococcus aureus sphingomyelinase C. While this co-hemolytic reaction is commonly used by clinical laboratories to identify GBS, the contribution of CAMP factor to GBS vaginal persistence is unknown. Using in vitro biofilm, adherence and invasion assays with immortalized human vaginal epithelial VK2 cells, and a mouse model of GBS vaginal colonization, we tested the contribution of CAMP factor using GBS strain COH1 and its isogenic CAMP-deficient mutant (Δcfb). We found no evidence for CAMP factor involvement in GBS biofilm formation, or adherence, invasion, or cytotoxicity toward VK2 cells in the presence or absence of S. aureus. Additionally, there was no difference in vaginal burdens or persistence between COH1 and Δcfb strains in a murine colonization model. In summary, our results using in vitro human cell lines and murine models do not support a critical role for CAMP factor in promoting GBS vaginal colonization. IMPORTANCE Group B Streptococcus (GBS) remains a pervasive pathogen for pregnant women and their newborns. Maternal screening and intrapartum antibiotic prophylaxis to GBS-positive mothers have reduced, but not eliminated GBS neonatal disease, and have not impacted GBS-associated preterm birth or stillbirth. Additionally, this antibiotic exposure is associated with adverse effects on the maternal and neonatal microbiota. Identifying key GBS factors important for maternal vaginal colonization will foster development of more targeted, alternative therapies to antibiotic treatment. Here, we investigate the contribution of a broadly conserved GBS determinant, CAMP factor, to GBS vaginal colonization and find that CAMP factor is unlikely to be a biological target to control maternal GBS colonization.
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Increasing incidence of group B streptococcus neonatal infections in the Netherlands is associated with clonal expansion of CC17 and CC23. Sci Rep 2020; 10:9539. [PMID: 32533007 PMCID: PMC7293262 DOI: 10.1038/s41598-020-66214-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/15/2020] [Indexed: 01/19/2023] Open
Abstract
Group B streptococcus (GBS) is the leading cause of neonatal invasive disease worldwide. In the Netherlands incidence of the disease increased despite implementation of preventive guidelines. We describe a genomic analysis of 1345 GBS isolates from neonatal (age 0–89 days) invasive infections in the Netherlands reported between 1987 and 2016. Most isolates clustered into one of five major lineages: CC17 (39%), CC19 (25%), CC23 (18%), CC10 (9%) and CC1 (7%). There was a significant rise in the number of infections due to isolates from CC17 and CC23. Phylogenetic clustering analysis revealed that this was caused by expansion of specific sub-lineages, designated CC17-A1, CC17-A2 and CC23-A1. Dating of phylogenetic trees estimated that these clones diverged in the 1960s/1970s, representing historical rather than recently emerged clones. For CC17-A1 the expansion correlated with acquisition of a new phage, carrying gene encoding a putative cell-surface protein. Representatives of CC17-A1, CC17-A2 and CC23-A1 clones were identified in datasets from other countries demonstrating their global distribution.
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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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Guo D, Xi Y, Wang S, Wang Z. Is a positive Christie-Atkinson-Munch-Peterson (CAMP) test sensitive enough for the identification of Streptococcus agalactiae? BMC Infect Dis 2019; 19:7. [PMID: 30606123 PMCID: PMC6318942 DOI: 10.1186/s12879-018-3561-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/27/2018] [Indexed: 11/22/2022] Open
Abstract
Background For a long time, the Christie-Atkinson-Munch-Peterson (CAMP) test has been a standard test for the identification of Streptococcus agalactiae, and a positive result for S.agalactiae has been considered sensitive enough. Methods To confirm whether a positive CAMP test is a requirement for the identification of S.agalactiae, five suspected CAMP-negative S.agalactiae isolates from two hospitals, confirmed as Gram-positive and catalase-negative streptococci, were verified by the CAMP test in three batches of plates from two manufacturers and identified by the Phoenix system, MALDI-TOF MS, the PCR assay and the 16S rDNA gene sequencing. Results All five suspected strains were S.agalactiae, four of which were CAMP-negative and one of which was not S.agalactiae by the PCR assay. Conclusions A positive CAMP test was lacking sensitivity for the identification of S.agalactiae, and the question of whether the cfb gene is worthy of targeting should be further studied.
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Affiliation(s)
- Dacheng Guo
- Institute for Infectious Disease Control and Prevention, Henan Provincial Center for Disease Control and Prevention, Zhengzhou, China
| | - Yu Xi
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Shanmei Wang
- Department of Clinical Laboratory, Henan Provincial People's Hospital, Zhengzhou, China
| | - Zeyu Wang
- R&D Center, Autobio Diagnostics Co. Ltd, Zhengzhou, China.
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Kaindi DWM, Kogi-Makau W, Lule GN, Kreikemeyer B, Renault P, Bonfoh B, Otaru N, Schmid T, Meile L, Hattendorf J, Jans C. Colorectal cancer-associated Streptococcus infantarius subsp. infantarius differ from a major dairy lineage providing evidence for pathogenic, pathobiont and food-grade lineages. Sci Rep 2018; 8:9181. [PMID: 29907746 PMCID: PMC6003927 DOI: 10.1038/s41598-018-27383-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 05/25/2018] [Indexed: 02/07/2023] Open
Abstract
Streptococcus infantarius subsp. infantarius (Sii), a member of the Streptococcus bovis/Streptococcus equinus complex (SBSEC), predominates as dairy-adapted and non-adapted variants in fermented dairy products (FDP) in East and West Africa. Epidemiologic data suggest an association with colorectal cancer for most SBSEC members, including Sii from Kenyan patients. Phylogenetic relationships of East African human (EAH) isolates to those of dairy and pathogenic origin were analysed to better estimate potential health implications via FDP consumption. The MLST-derived population structure was also evaluated to provide host, disease, geography and dairy adaptation associations for 157 SBSEC isolates, including 83 novel Sii/SBSEC isolates of which 40 originated from Kenyan colonoscopy patients. Clonal complex (CC) 90 was delineated as potential pathogenic CC for Sii. Single EAH, West African dairy (WAD), food and animal Sii isolates clustered within CC-90, suggesting a potential link to pathogenic traits for CC-90. The majority of EAH and WAD Sii were clustered in a shared clade distinct from CC-90 and East African dairy (EAD) isolates. This indicates shared ancestry for the EAH and WAD clade and limitations to translate disease associations of EAH and CC-90 to EAD Sii, which could support the separation of pathogenic, pathobiont/commensal and food lineages.
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Affiliation(s)
| | - Wambui Kogi-Makau
- Department of Food Science, Nutrition and Technology, University of Nairobi, Nairobi, Kenya
| | | | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre Rostock, Rostock, Germany
| | - Pierre Renault
- Institut National de la Recherche Agronomique, UMR 1319 MICALIS, Jouy-en-Josas, France
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Adiopodoume, Ivory Coast
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nize Otaru
- Laboratory of Food Biotechnology, ETH Zurich, Zurich, Switzerland
| | - Thomas Schmid
- Laboratory of Food Biotechnology, ETH Zurich, Zurich, Switzerland
| | - Leo Meile
- Laboratory of Food Biotechnology, ETH Zurich, Zurich, Switzerland
| | - Jan Hattendorf
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Christoph Jans
- Laboratory of Food Biotechnology, ETH Zurich, Zurich, Switzerland.
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Jans C, de Wouters T, Bonfoh B, Lacroix C, Kaindi DWM, Anderegg J, Böck D, Vitali S, Schmid T, Isenring J, Kurt F, Kogi-Makau W, Meile L. Phylogenetic, epidemiological and functional analyses of the Streptococcus bovis/Streptococcus equinus complex through an overarching MLST scheme. BMC Microbiol 2016; 16:117. [PMID: 27329036 PMCID: PMC4915170 DOI: 10.1186/s12866-016-0735-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 06/08/2016] [Indexed: 12/20/2022] Open
Abstract
Background The Streptococcus bovis/Streptococcus equinus complex (SBSEC) comprises seven (sub)species classified as human and animal commensals, emerging opportunistic pathogens and food fermentative organisms. Changing taxonomy, shared habitats, natural competence and evidence for horizontal gene transfer pose difficulties for determining their phylogeny, epidemiology and virulence mechanisms. Thus, novel phylogenetic and functional classifications are required. An SBSEC overarching multi locus sequence type (MLST) scheme targeting 10 housekeeping genes was developed, validated and combined with host-related properties of adhesion to extracellular matrix proteins (ECM), activation of the immune responses via NF-KB and survival in simulated gastric juice (SGJ). Results Commensal and pathogenic SBSEC strains (n = 74) of human, animal and food origin from Europe, Asia, America and Africa were used in the MLST scheme yielding 66 sequence types and 10 clonal complexes differentiated into distinct habitat-associated and mixed lineages. Adhesion to ECMs collagen I and mucin type II was a common characteristic (23 % of strains) followed by adhesion to fibronectin and fibrinogen (19.7 %). High adhesion abilities were found for East African dairy and human blood isolate branches whereas commensal fecal SBSEC displayed low adhesion. NF-KB activation was observed for a limited number of dairy and blood isolates suggesting the potential of some pathogenic strains for reduced immune activation. Strains from dairy MLST clades displayed the highest relative survival to SGJ independently of dairy adaptation markers lacS/lacZ. Conclusion Combining phylogenetic and functional analyses via SBSEC MLST enabled the clear delineation of strain clades to unravel the complexity of this bacterial group. High adhesion values shared between certain dairy and blood strains as well as the behavior of NF-KB activation are concerning for specific lineages. They highlighted the health risk among shared lineages and establish the basis to elucidate (zoonotic-) transmission, host specificity, virulence mechanisms and enhanced risk assessment as pathobionts in an overarching One Health approach. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0735-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Tomas de Wouters
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), KM 17 route de Dabou, Adiopodoumé Yopougon, Abidjan - 01B.P. 1303, Abidjan, Côte d'Ivoire
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Dasel Wambua Mulwa Kaindi
- Department of Food Science, Nutrition and Technology, College of Agriculture and Veterinary Sciences, University of Nairobi, P.O. Box 29053, Nairobi, Kenya
| | - Janine Anderegg
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Désirée Böck
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Sabrina Vitali
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Thomas Schmid
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Julia Isenring
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Fabienne Kurt
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Wambui Kogi-Makau
- Department of Food Science, Nutrition and Technology, College of Agriculture and Veterinary Sciences, University of Nairobi, P.O. Box 29053, Nairobi, Kenya
| | - Leo Meile
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.
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Carraro N, Libante V, Morel C, Charron-Bourgoin F, Leblond P, Guédon G. Plasmid-like replication of a minimal streptococcal integrative and conjugative element. MICROBIOLOGY-SGM 2016; 162:622-632. [PMID: 26825653 DOI: 10.1099/mic.0.000219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Integrative and conjugative elements (ICEs) are mobile genetic elements encoding their own excision from a replicon of their bacterial host, transfer by conjugation to a recipient bacterium and reintegration for maintenance. The conjugation, recombination and regulation modules of ICEs of the ICESt3 family are grouped together in a region called the ICE 'core region'. In addition to this core region, elements belonging to this family carry a highly variable region including cargo genes that could be involved in bacterial adaptation or in the maintenance of the element. Although ICEs are a major class of mobile elements through bacterial genomes, the functionality of an element encoding only its excision, transfer, integration and regulation has never been demonstrated experimentally. We engineered MiniICESt3, an artificial ICE derived from ICESt3, devoid of its cargo genes and thus only harbouring the core region. The functionality of this minimal element was assessed. MiniICESt3 was found to be able to excise at a rate of 3.1 %, transfer with a frequency of 1.0 × 10- 5 transconjugants per donor cell and stably maintain by site-specific integration into the 3' end of the fda gene, the same as ICESt3. Furthermore, MiniICESt3 was found in ∼10 copies per chromosome, this multicopy state likely contributing to its stability for >100 generations even in the absence of selection. Therefore, although ICEs were primarily assumed to only replicate along with the chromosome, our results uncovered extrachromosomal rolling-circle replicating plasmid-like forms of MiniICESt3.
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Affiliation(s)
- Nicolas Carraro
- INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Virginie Libante
- INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Catherine Morel
- Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Florence Charron-Bourgoin
- Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Pierre Leblond
- Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Gérard Guédon
- Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
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11
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Abstract
Integrative and Conjugative Elements (ICEs) are bacterial mobile genetic elements that play a key role in bacterial genomes dynamics and evolution. ICEs are widely distributed among virtually all bacterial genera. Recent extensive studies have unraveled their high diversity and complexity. The present review depicts the general conserved features of ICEs and describes more precisely three major families of ICEs that have been extensively studied in the past decade for their biology, their evolution and their impact on genomes dynamics. First, the large SXT/R391 family of ICEs disseminates antibiotic resistance genes and drives the exchange of mobilizable genomic islands (MGIs) between many enteric pathogens such as Vibrio cholerae. Second, ICEBs1 of Bacillus subtilis is the most well understood ICE of Gram-positive bacteria, notably regarding the regulation of its dissemination and its initially unforeseen extrachromosomal replication, which could be a common feature of ICEs of both Gram-positive and Gram-negative bacteria. Finally, ICESt1 and ICESt3 of Streptococcus thermophilus are the prototypes of a large family of ICEs widely distributed among various streptococci. These ICEs carry an original regulation module that associates regulators related to those of both SXT/R391 and ICEBs1. Study of ICESt1 and ICESt3 uncovered the cis-mobilization of related genomic islands (CIMEs) by a mechanism called accretion-mobilization, which likely represents a paradigm for the evolution of many ICEs and genomic islands. These three major families of ICEs give a glimpse about ICEs dynamics and their high impact on bacterial adaptation.
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12
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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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13
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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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14
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Validation of absolute quantitative real-time PCR for the diagnosis of Streptococcus agalactiae in fish. J Microbiol Methods 2015; 119:168-75. [DOI: 10.1016/j.mimet.2015.10.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/26/2015] [Accepted: 10/26/2015] [Indexed: 11/24/2022]
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15
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Barnett TC, Cole JN, Rivera-Hernandez T, Henningham A, Paton JC, Nizet V, Walker MJ. Streptococcal toxins: role in pathogenesis and disease. Cell Microbiol 2015; 17:1721-41. [PMID: 26433203 DOI: 10.1111/cmi.12531] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/13/2015] [Accepted: 09/02/2015] [Indexed: 12/15/2022]
Abstract
Group A Streptococcus (Streptococcus pyogenes), group B Streptococcus (Streptococcus agalactiae) and Streptococcus pneumoniae (pneumococcus) are host-adapted bacterial pathogens among the leading infectious causes of human morbidity and mortality. These microbes and related members of the genus Streptococcus produce an array of toxins that act against human cells or tissues, resulting in impaired immune responses and subversion of host physiological processes to benefit the invading microorganism. This toxin repertoire includes haemolysins, proteases, superantigens and other agents that ultimately enhance colonization and survival within the host and promote dissemination of the pathogen.
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Affiliation(s)
- Timothy C Barnett
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Jason N Cole
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.,Department of Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Tania Rivera-Hernandez
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Anna Henningham
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.,Department of Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - James C Paton
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Victor Nizet
- Department of Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Mark J Walker
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
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16
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Carraro N, Burrus V. The dualistic nature of integrative and conjugative elements. Mob Genet Elements 2015; 5:98-102. [PMID: 26942046 PMCID: PMC4755238 DOI: 10.1080/2159256x.2015.1102796] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 09/26/2015] [Indexed: 11/23/2022] Open
Abstract
Integrative and conjugative elements (ICEs) are mobile genetic elements that play a key role in bacterial adaptation. Such elements are found in almost every bacterial genera and species, and often code for adaptive traits conferring selective advantages to their host. ICEs maintain by integrating into and replicating along with a replicon of the host genome. ICEs can propagate by conjugative transfer toward a recipient cell following excision from the replicon as a circular covalently-closed molecule. For a long time, the excised form of ICEs was assumed to be non-replicative. This assumption predicts that excised ICEs are sensitive to loss during cell division, unless they carry stabilization systems such as addiction modules or antibiotic resistance genes. Over the past few years, growing evidence have been presented that support conditional replication of the circular intermediate as an intrinsic feature of ICEs. We recently confirmed this feature in the large family of SXT/R391 ICEs, which thrive in several species of Enterobacteriaceae and Vibrionaceae. Furthermore, we demonstrated that SXT/R391 ICEs encode a functional plasmid-like type II partition system that enhances their stability, such systems being probably encoded by other ICEs. The lifecycle of ICEs is therefore much more complex than initially thought as many ICEs may use plasmid-like features to improve their stability and dissemination.
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Affiliation(s)
- Nicolas Carraro
- Laboratory of Bacterial Molecular Genetics; Département de Biologie; Université de Sherbrooke ; Sherbrooke, Canada
| | - Vincent Burrus
- Laboratory of Bacterial Molecular Genetics; Département de Biologie; Université de Sherbrooke ; Sherbrooke, Canada
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17
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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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18
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Pearce SL, Oakeshott JG, Pandey G. Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains. G3 (BETHESDA, MD.) 2015; 5:1081-94. [PMID: 25850427 PMCID: PMC4478539 DOI: 10.1534/g3.114.015933] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/29/2015] [Indexed: 11/18/2022]
Abstract
Hexachlorocyclohexane (HCH), a synthetic organochloride, was first used as a broad-acre insecticide in the 1940s, and many HCH-degrading bacterial strains have been isolated from around the globe during the last 20 years. To date, the same degradation pathway (the lin pathway) has been implicated in all strains characterized, although the pathway has only been characterized intensively in two strains and for only a single HCH isomer. To further elucidate the evolution of the lin pathway, we have biochemically and genetically characterized three HCH-degrading strains from the Czech Republic and compared the genomes of these and seven other HCH-degrading bacterial strains. The three new strains each yielded a distinct set of metabolites during their degradation of HCH isomers. Variable assembly of the pathway is a common feature across the 10 genomes, eight of which (including all three Czech strains) were either missing key lin genes or containing duplicate copies of upstream lin genes (linA-F). The analysis also confirmed the important role of horizontal transfer mediated by insertion sequence IS6100 in the acquisition of the pathway, with a stronger association of IS6100 to the lin genes in the new strains. In one strain, a linA variant was identified that likely caused a novel degradation phenotype involving a shift in isomer preference. This study identifies a number of strains that are in the early stages of lin pathway acquisition and shows that the state of the pathway can explain the degradation patterns observed.
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Affiliation(s)
| | | | - Gunjan Pandey
- CSIRO Ecosystem Sciences, Acton, ACT-2601, Australia
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19
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Puymège A, Bertin S, Guédon G, Payot S. Analysis of Streptococcus agalactiae pan-genome for prevalence, diversity and functionality of integrative and conjugative or mobilizable elements integrated in the tRNA(Lys CTT) gene. Mol Genet Genomics 2015; 290:1727-40. [PMID: 25832353 DOI: 10.1007/s00438-015-1031-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 03/17/2015] [Indexed: 11/27/2022]
Abstract
Streptococcus agalactiae is the first cause of invasive infections in human neonates and is also a major bovine and fish pathogen. High genomic diversity was observed in this species that hosts numerous mobile genetic elements, in particular elements transferable by conjugation. This works aims to evaluate the contribution of these elements to GBS genome diversity. Focusing on genomic islands integrated in the tRNA(Lys) (CTT) gene, a known hotspot of recombination, an extensive in silico search was performed on the sequenced genome of 303 strains of S. agalactiae isolated from different hosts. In all the isolates (except 9), whatever their origin (human, bovine, camel, dog, gray seal, dolphin, fish species or bullfrog), this locus carries highly diverse genomic islands transferable by conjugation such as integrative and conjugative elements (ICEs), integrative and mobilizable elements (IMEs), CIs-mobilizable elements (CIMEs) or composite elements. Transfer of an ICE from an ST67 bovine strain to a phylogenetically distant ST23 human isolate was obtained experimentally indicating that there was no barrier to ICE transfer between strains from different hosts. Interestingly, a novel family of putative IMEs that site-specifically integrate in the nic site of oriT of ICEs belonging to Tn916/ICESt3 superfamily was detected in silico. These elements carry an antibiotic resistance gene (lsa(C)) already described to confer cross-resistance to lincosamides, streptogramins A and pleuromutilins. Further work is needed to evaluate the impact of these IMEs on the transfer of targeted ICEs and the mobility and the dissemination of these IMEs.
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Affiliation(s)
- Aurore Puymège
- Faculté des Sciences et Technologies, INRA, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France.,Faculté des Sciences et Technologies, Université de Lorraine, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France
| | - Stéphane Bertin
- Faculté des Sciences et Technologies, INRA, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France.,Faculté des Sciences et Technologies, Université de Lorraine, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France
| | - Gérard Guédon
- Faculté des Sciences et Technologies, INRA, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France.,Faculté des Sciences et Technologies, Université de Lorraine, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France
| | - Sophie Payot
- Faculté des Sciences et Technologies, INRA, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France. .,Faculté des Sciences et Technologies, Université de Lorraine, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France.
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20
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Jans C, Meile L, Lacroix C, Stevens MJA. Genomics, evolution, and molecular epidemiology of the Streptococcus bovis/Streptococcus equinus complex (SBSEC). INFECTION GENETICS AND EVOLUTION 2014; 33:419-36. [PMID: 25233845 DOI: 10.1016/j.meegid.2014.09.017] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/10/2014] [Accepted: 09/11/2014] [Indexed: 02/07/2023]
Abstract
The Streptococcus bovis/Streptococcus equinus complex (SBSEC) is a group of human and animal derived streptococci that are commensals (rumen and gastrointestinal tract), opportunistic pathogens or food fermentation associates. The classification of SBSEC has undergone massive changes and currently comprises 7 (sub)species grouped into four branches based on sequences identities: the Streptococcus gallolyticus, the Streptococcus equinus, the Streptococcus infantarius and the Streptococcus alactolyticus branch. In animals, SBSEC are causative agents for ruminal acidosis, potentially laminitis and infective endocarditis (IE). In humans, a strong association was established between bacteraemia, IE and colorectal cancer. Especially the SBSEC-species S. gallolyticus subsp. gallolyticus is an emerging pathogen for IE and prosthetic joint infections. S. gallolyticus subsp. pasteurianus and the S. infantarius branch are further associated with biliary and urinary tract infections. Knowledge on pathogenic mechanisms is so far limited to colonization factors such as pili and biofilm formation. Certain strain variants of S. gallolyticus subsp. macedonicus and S. infantarius subsp. infantarius are associated with traditional dairy and plant-based food fermentations and display traits suggesting safety. However, due to their close relationship to virulent strains, their use in food fermentation has to be critically assessed. Additionally, implementing accurate and up-to-date taxonomy is critical to enable appropriate treatment of patients and risk assessment of species and strains via recently developed multilocus sequence typing schemes to enable comparative global epidemiology. Comparative genomics revealed that SBSEC strains harbour genomics islands (GI) that seem acquired from other streptococci by horizontal gene transfer. In case of virulent strains these GI frequently encode putative virulence factors, in strains from food fermentation the GI encode functions that are pivotal for strain performance during fermentation. Comparative genomics is a powerful tool to identify acquired pathogenic functions, but there is still an urgent need for more physiological and epidemiological data to understand SBSEC-specific traits.
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Affiliation(s)
- Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Leo Meile
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Marc J A Stevens
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
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21
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Conjugative transfer of ICESde3396 between three β-hemolytic streptococcal species. BMC Res Notes 2014; 7:521. [PMID: 25115242 PMCID: PMC4266954 DOI: 10.1186/1756-0500-7-521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 07/31/2014] [Indexed: 12/02/2022] Open
Abstract
Background Integrative conjugative elements (ICEs) are mobile genetic elements (MGEs) that possess all genes necessary for excision, transfer and integration into recipient genome. They also carry accessory genes that impart new phenotypic features to recipient strains. ICEs therefore play an important role in genomic plasticity and population structure. We previously characterised ICESde3396, the first ICE identified in the β-hemolytic Streptococcus dysgalactiae subsp equisimilis (SDSE) and demonstrated its transfer to single isolates of Streptococcus pyogenes (group A streptococcus, GAS) and Streptococcus agalactiae (group B streptococcus, GBS). While molecular studies found the ICE in multiple SDSE and GBS isolates, it was absent in all GAS isolates examined. Results Here we demonstrate that ICESde3396:km is transferable from SDSE to multiple SDSE, GAS and GBS isolates. However not all strains of these species were successful recipients under the same growth conditions. To address the role that host factors may have in conjugation we also undertook conjugation experiments in the presence of A549 epithelial cells and DMEM. While Horizontal Gene Transfer (HGT) occurred, conjugation efficiencies were no greater than when similar experiments were conducted in DMEM. Additionally transfer to GAS NS235 was successful in the presence of DMEM but not in Todd Hewitt Broth suggesting that nutritional factors may also influence HGT. The GAS and GBS transconjugants produced in this study are also able to act as donors of the ICE. Conclusion We conclude that ICEs are major sources of interspecies HGT between β-hemolytic streptococci, and by introducing accessory genes imparting novel phenotypic characteristics, have the potential to alter the population structure of these species.
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22
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Fléchard M, Gilot P. Physiological impact of transposable elements encoding DDE transposases in the environmental adaptation of Streptococcus agalactiae. Microbiology (Reading) 2014; 160:1298-1315. [DOI: 10.1099/mic.0.077628-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We have referenced and described Streptococcus agalactiae transposable elements encoding DDE transposases. These elements belonged to nine families of insertion sequences (ISs) and to a family of conjugative transposons (TnGBSs). An overview of the physiological impact of the insertion of all these elements is provided. DDE-transposable elements affect S. agalactiae in a number of aspects of its capability to adapt to various environments and modulate the expression of several virulence genes, the scpB–lmB genomic region and the genes involved in capsule expression and haemolysin transport being the targets of several different mobile elements. The referenced mobile elements modify S. agalactiae behaviour by transferring new gene(s) to its genome, by modifying the expression of neighbouring genes at the integration site or by promoting genomic rearrangements. Transposition of some of these elements occurs in vivo, suggesting that by dynamically regulating some adaptation and/or virulence genes, they improve the ability of S. agalactiae to reach different niches within its host and ensure the ‘success’ of the infectious process.
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Affiliation(s)
- Maud Fléchard
- Biochimie et Génétique Moléculaire Bactérienne, Institut des Sciences de la Vie, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Philippe Gilot
- INRA, UMR1282 Infectiologie et Santé Publique, F-37380 Nouzilly, France
- Université de Tours, UMR1282 Infectiologie et Santé Publique, Bactéries et Risque Materno-Foetal, F-37032 Tours, France
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23
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Bellanger X, Payot S, Leblond-Bourget N, Guédon G. Conjugative and mobilizable genomic islands in bacteria: evolution and diversity. FEMS Microbiol Rev 2014; 38:720-60. [DOI: 10.1111/1574-6976.12058] [Citation(s) in RCA: 223] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/15/2013] [Accepted: 12/19/2013] [Indexed: 11/28/2022] Open
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Gyles C, Boerlin P. Horizontally Transferred Genetic Elements and Their Role in Pathogenesis of Bacterial Disease. Vet Pathol 2013; 51:328-40. [DOI: 10.1177/0300985813511131] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
This article reviews the roles that laterally transferred genes (LTG) play in the virulence of bacterial pathogens. The features of LTG that allow them to be recognized in bacterial genomes are described, and the mechanisms by which LTG are transferred between and within bacteria are reviewed. Genes on plasmids, integrative and conjugative elements, prophages, and pathogenicity islands are highlighted. Virulence genes that are frequently laterally transferred include genes for bacterial adherence to host cells, type 3 secretion systems, toxins, iron acquisition, and antimicrobial resistance. The specific roles of LTG in pathogenesis are illustrated by specific reference to Escherichia coli, Salmonella, pyogenic streptococci, and Clostridium perfringens.
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Affiliation(s)
- C. Gyles
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - P. Boerlin
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
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Abstract
Streptococcus agalactiae (group B streptococcus [GBS]) is a Gram-positive bacterium that was first recognized as a causative agent of bovine mastitis. S. agalactiae has subsequently emerged as a significant cause of human diseases. Here, we report the draft genome sequence of S. agalactiae PR06, which was isolated from a septicemic patient in a local hospital in Malaysia.
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Conjugative transfer and cis-mobilization of a genomic island by an integrative and conjugative element of Streptococcus agalactiae. J Bacteriol 2012; 195:1142-51. [PMID: 23275243 DOI: 10.1128/jb.02199-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Putative integrative and conjugative elements (ICEs), i.e., genomic islands which could excise, self-transfer by conjugation, and integrate into the chromosome of the bacterial host strain, were previously identified by in silico analysis in the sequenced genomes of Streptococcus agalactiae (M. Brochet et al., J. Bacteriol. 190:6913-6917, 2008). We investigated here the mobility of the elements integrated into the 3' end of a tRNA(Lys) gene. Three of the four putative ICEs tested were found to excise but only one (ICE_515_tRNA(Lys)) was found to transfer by conjugation not only to S. agalactiae strains but also to a Streptococcus pyogenes strain. Transfer was observed even if recipient cell already carries a related resident ICE or a genomic island flanked by attL and attR recombination sites but devoid of conjugation or recombination genes (CIs-Mobilizable Element [CIME]). The incoming ICE preferentially integrates into the 3' end of the tRNA(Lys) gene (i.e., the attR site of the resident element), leading to a CIME-ICE structure. Transfer of the whole composite element CIME-ICE was obtained, showing that the CIME is mobilizable in cis by the ICE. Therefore, genomic islands carrying putative virulence genes but lacking the mobility gene can be mobilized by a related ICE after site-specific accretion.
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