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Lee E, Priutt E, Woods S, Quick A, King S, McLellan LK, Shields RC. Genomic analysis of conjugative and chromosomally integrated mobile genetic elements in oral streptococci. Appl Environ Microbiol 2024:e0136024. [PMID: 39254330 DOI: 10.1128/aem.01360-24] [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: 07/10/2024] [Accepted: 08/28/2024] [Indexed: 09/11/2024] Open
Abstract
This study aimed to investigate the diversity of conjugative and chromosomally integrated mobile genetic elements (cciMGEs) within six oral streptococci species. cciMGEs, including integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs), are stably maintained on the host cell chromosome; however, under certain conditions, they are able to excise, form extrachromosomal circles, and transfer via a conjugation apparatus. Many cciMGEs encode "cargo" functions that aid survival in new niches and evolve new antimicrobial resistance or virulence properties, whereas others have been shown to influence host bacterial physiology. Here, using a workflow employing preexisting bioinformatics tools, we analyzed 551 genomes for the presence of cciMGEs across six common health- and disease-associated oral streptococci. We identified 486 cciMGEs, 173 of which were ICEs and 233 of which were IMEs. The cciMGEs were diverse in size, cargo genes, and relaxase types. We identified several novel relaxase proteins and a widespread IME carrying a small multidrug resistance transporter. Additionally, we provide evidence that several of the bioinformatically predicted cciMGEs encoded within various Streptococcus mutans strains are capable of excision and circularization, a critical step for cciMGE conjugative transfer. These findings highlight the significance and potential impact of MGEs in shaping the genetic landscape, pathogenicity, and antimicrobial resistance profiles of the oral microbiota.IMPORTANCEOral streptococci are important players in the oral microbiome, influencing both health and disease states within dental bacterial communities. Evolutionary adaptation, shaped in a major part by the horizontal transfer of genes, is essential for their survival in the oral cavity and within new environments. Conjugation is a significant driver of horizontal gene transfer; however, there is limited information regarding this process in oral bacteria. This study utilizes publicly available genome sequences to identify conjugative and chromosomally integrated mobile genetic elements (cciMGEs) across several species of oral streptococci and presents the preliminary characterization of these elements. Our findings significantly enhance our understanding of the mobile genomic landscape of oral streptococci critical for human health, with valuable insights into how cciMGEs might influence the survival and pathogenesis of these bacteria in the oral microbiome.
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Affiliation(s)
- Erica Lee
- New York Institute of Technology College of Osteopathic Medicine, Jonesboro, Arkansas, USA
| | - Erin Priutt
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, USA
| | - Seth Woods
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, USA
| | - Allison Quick
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, USA
| | - Shawn King
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, USA
| | - Lisa K McLellan
- Department of Biological Sciences, Purdue University Fort Wayne, Fort Wayne, Indiana, USA
| | - Robert C Shields
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, USA
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Ares-Arroyo M, Coluzzi C, Moura de Sousa JA, Rocha EPC. Hijackers, hitchhikers, or co-drivers? The mysteries of mobilizable genetic elements. PLoS Biol 2024; 22:e3002796. [PMID: 39208359 PMCID: PMC11389934 DOI: 10.1371/journal.pbio.3002796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/11/2024] [Indexed: 09/04/2024] Open
Abstract
Mobile genetic elements shape microbial gene repertoires and populations. Recent results reveal that many, possibly most, microbial mobile genetic elements require helpers to transfer between genomes, which we refer to as Hitcher Genetic Elements (hitchers or HGEs). They may be a large fraction of pathogenicity and resistance genomic islands, whose mechanisms of transfer have remained enigmatic for decades. Together with their helper elements and their bacterial hosts, hitchers form tripartite networks of interactions that evolve rapidly within a parasitism-mutualism continuum. In this emerging view of microbial genomes as communities of mobile genetic elements many questions arise. Which elements are being moved, by whom, and how? How often are hitchers costly hyper-parasites or beneficial mutualists? What is the evolutionary origin of hitchers? Are there key advantages associated with hitchers' lifestyle that justify their unexpected abundance? And why are hitchers systematically smaller than their helpers? In this essay, we start answering these questions and point ways ahead for understanding the principles, origin, mechanisms, and impact of hitchers in bacterial ecology and evolution.
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Affiliation(s)
- Manuel Ares-Arroyo
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Charles Coluzzi
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Jorge A Moura de Sousa
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
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Hu W, Wang Y, Zhou L, Chu K, Jin P, Liang Q, Li J, Tan Z, Zhu F. Nasal Staphylococcus aureus Carriage and Antimicrobial Resistance Profiles Among Community-Dwelling Adults in Jiangsu, China. Infect Dis Ther 2024; 13:1215-1233. [PMID: 38700654 PMCID: PMC11128426 DOI: 10.1007/s40121-024-00969-4] [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: 03/05/2024] [Accepted: 03/27/2024] [Indexed: 05/28/2024] Open
Abstract
INTRODUCTION Persistent nasal carriage has been associated with Staphylococcus aureus infection. Previous S. aureus studies in Asia have primarily focused on clinical patients, providing limited information on persistent nasal carriage among the general adult population. METHODS This study examined 143 healthy adults in a community in Jiangsu, China. Nasal swab samples were collected 10 times. The colonization status was identified using SPA typing. We also determined antimicrobial susceptibility, genotype, and genomic characteristics of S. aureus. RESULTS The prevalence of S. aureus nasal carriage among the community individuals was on average 16.78%. The carriage rates of methicillin-resistant S. aureus and multidrug-resistant S. aureus were 6.29% and 7.69%, respectively. We identified 8.39% persistent carriers, 39.16% intermittent carriers, and 52.45% noncarriers. Furthermore, family members displayed concordance in terms of genotype and genomic characteristics. CONCLUSION Persistent nasal sampling captured intermittent carriers that were missed during short-term sampling, thus highlighting the necessity for regular community testing. SPA typing can serve as a rapid method for determining S. aureus colonization. The potential for intrafamilial transmission of S. aureus is evident, with persistent carriers being the most probable source of infection.
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Affiliation(s)
- Wenjing Hu
- School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Yang Wang
- Department of Science and Education, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Lu Zhou
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Kai Chu
- National Health Commission Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Innovation Center, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Pengfei Jin
- National Health Commission Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Innovation Center, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Qi Liang
- National Health Commission Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Innovation Center, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Jingxin Li
- National Health Commission Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Innovation Center, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Zhongming Tan
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China.
| | - Fengcai Zhu
- School of Public Health, Southeast University, Nanjing, Jiangsu, China.
- National Health Commission Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Innovation Center, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China.
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He J, Lu X, Yuan C, Zheng Y, Chen F, Luo J, Ma K, Yang F, Wang P, Zhou D, Wang L, Yin Z. Genetic Characteristics of Novel Inc pSE5381-aadB Plasmids, Integrative and Mobilizable Elements, and Integrative and Conjugative Elements in Pseudomonas aeruginosa. Infect Drug Resist 2024; 17:2053-2068. [PMID: 38813527 PMCID: PMC11135338 DOI: 10.2147/idr.s462670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 05/11/2024] [Indexed: 05/31/2024] Open
Abstract
Purpose Pseudomonas aeruginosa is a common causative bacteria in nosocomial infections. This study aims to describe the structure and evolutionary characteristics of mobile genetic elements (MGEs) carrying antibiotic resistance genes (ARGs) from P. aeruginosa and to conduct bioinformatics and comparative genomic analysis to provide a deeper understanding of the genetic characteristics and diversity of MGEs in P. aeruginosa. Methods Fifteen clinical isolates of P. aeruginosa from China were collected and sequenced in this study, and 15 novel MGEs were identified. Together with four MGEs from GenBank, a total of 19 MGEs were used to perform detailed modular structure dissection and sequence comparison. Then, the biological experiments were carried out to verify the biological characteristics of these isolates and MEGs. Results The novel MGEs identified in this study displayed diversification in modular structures, which showed complex mosaic natures. The seven types of 19 MGEs included in this study were divided into three groups: i) novel MGEs (firstly identified in this study): four IncpSE5381-aadB plasmids and three Tn7495-related integrative and mobilizable elements (IMEs); ii) newly defined MGEs (firstly designated in this study, but with previously determined sequences): four Tn7665-related IMEs; iii) novel transposons with reference prototypes identified in this study: two Tn6417-related integrative and conjugative elements (ICEs), two IS-based transposition units, two Tn501-related unit transposons, two Tn1403-related unit transposons. At least 36 ARGs involved in resistance to 11 different classes of antimicrobials and heavy metals were identified. Additionally, three novel blaOXA variants were identified. Antimicrobial susceptibility testing showed that these variants were resistant to some β-lactamase antibiotics and blaOXA-1204 was additionally resistant to cephalosporins. Conclusion The continuous evolution of ARG-carrying MGEs during transmission, leading to the emergence of novel MGEs or ARGs, which facilitates the spread of antibiotic resistance in P. aeruginosa and enhances the diversity of transmission modes of bacterial resistance.
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Affiliation(s)
- Jiaqi He
- Department of Clinical Laboratory, The First Affiliated Hospital of Henan University, Kaifeng, 475000, People’s Republic of China
| | - Xiuhui Lu
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, People’s Republic of China
| | - Chenchen Yuan
- Department of Clinical Laboratory, The First Affiliated Hospital of Henan University, Kaifeng, 475000, People’s Republic of China
| | - Yali Zheng
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, People’s Republic of China
| | - Fangzhou Chen
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, People’s Republic of China
| | - Jing Luo
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, People’s Republic of China
| | - Kejiao Ma
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, People’s Republic of China
| | - Fan Yang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, People’s Republic of China
| | - Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, People’s Republic of China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, People’s Republic of China
| | - Li Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Henan University, Kaifeng, 475000, People’s Republic of China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, People’s Republic of China
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Dechêne-Tempier M, de Boisséson C, Lucas P, Bougeard S, Libante V, Marois-Créhan C, Payot S. Virulence genes, resistome and mobilome of Streptococcus suis strains isolated in France. Microb Genom 2024; 10:001224. [PMID: 38536216 PMCID: PMC10995628 DOI: 10.1099/mgen.0.001224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/08/2024] [Indexed: 04/07/2024] Open
Abstract
Streptococcus suis is a leading cause of infection in pigs, causing extensive economic losses. In addition, it can also infect wild fauna, and can be responsible for severe infections in humans. Increasing antimicrobial resistance (AMR) has been described in S. suis worldwide and most of the AMR genes are carried by mobile genetic elements (MGEs). This contributes to their dissemination by horizontal gene transfer. A collection of 102 strains isolated from humans, pigs and wild boars in France was subjected to whole genome sequencing in order to: (i) study their genetic diversity, (ii) evaluate their content in virulence-associated genes, (iii) decipher the mechanisms responsible for their AMR and their association with MGEs, and (iv) study their ability to acquire extracellular DNA by natural transformation. Analysis by hierarchical clustering on principal components identified a few virulence-associated factors that distinguish invasive CC1 strains from the other strains. A plethora of AMR genes (n=217) was found in the genomes. Apart from the frequently reported erm(B) and tet(O) genes, more recently described AMR genes were identified [vga(F)/sprA, vat(D)]. Modifications in PBPs/MraY and GyrA/ParC were detected in the penicillin- and fluoroquinolone-resistant isolates respectively. New AMR gene-MGE associations were detected. The majority of the strains have the full set of genes required for competence, i.e for the acquisition of extracellular DNA (that could carry AMR genes) by natural transformation. Hence the risk of dissemination of these AMR genes should not be neglected.
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Affiliation(s)
- Manon Dechêne-Tempier
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, BP53 22440 Ploufragan, France
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
| | - Claire de Boisséson
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, BP53 22440 Ploufragan, France
| | - Pierrick Lucas
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Génétique Virale et Biosécurité, BP53 22440 Ploufragan, France
| | - Stéphanie Bougeard
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Épidémiologie, santé et bien-être, BP53 22440 Ploufragan, France
| | | | - Corinne Marois-Créhan
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, BP53 22440 Ploufragan, France
| | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
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Ryan MP, Carraro N, Slattery S, Pembroke JT. Integrative Conjugative Elements (ICEs) of the SXT/R391 family drive adaptation and evolution in γ-Proteobacteria. Crit Rev Microbiol 2024; 50:105-126. [PMID: 36634159 DOI: 10.1080/1040841x.2022.2161870] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023]
Abstract
Integrative Conjugative Elements (ICEs) are mosaics containing functional modules allowing maintenance by site-specific integration and excision into and from the host genome and conjugative transfer to a specific host range. Many ICEs encode a range of adaptive functions that aid bacterial survival and evolution in a range of niches. ICEs from the SXT/R391 family are found in γ-Proteobacteria. Over 100 members have undergone epidemiological and molecular characterization allowing insight into their diversity and function. Comparative analysis of SXT/R391 elements from a wide geographic distribution has revealed conservation of key functions, and the accumulation and evolution of adaptive genes. This evolution is associated with gene acquisition in conserved hotspots and variable regions within the SXT/R391 ICEs catalysed via element-encoded recombinases. The elements can carry IS elements and transposons, and a mutagenic DNA polymerase, PolV, which are associated with their evolution. SXT/R391 ICEs isolated from different niches appear to have retained adaptive functions related to that specific niche; phage resistance determinants in ICEs carried by wastewater bacteria, antibiotic resistance determinants in clinical isolates and metal resistance determinants in bacteria recovered from polluted environments/ocean sediments. Many genes found in the element hotspots are undetermined and have few homologs in the nucleotide databases.
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Affiliation(s)
- Michael P Ryan
- Department of Applied Sciences, Technological University of the Shannon, Limerick, Ireland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Shannon Slattery
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
| | - J Tony Pembroke
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
- Bernal Institute, University of Limerick, Ireland
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Libante V, Dechêne-Tempier M, Leblond-Bourget N, Payot S. Detection and Quantification of Conjugative Transfer of Mobile Genetic Elements Carrying Antibiotic Resistance Genes. Methods Mol Biol 2024; 2815:79-91. [PMID: 38884912 DOI: 10.1007/978-1-0716-3898-9_7] [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] [Indexed: 06/18/2024]
Abstract
Multidrug resistance, due to acquired antimicrobial resistance genes, is increasingly reported in the zoonotic pathogen Streptococcus suis. Most of these resistance genes are carried by chromosomal Mobile Genetic Elements (MGEs), in particular, Integrative and Conjugative Elements (ICEs) and Integrative and Mobilizable Elements (IMEs). ICEs and IMEs frequently form tandems or nested composite elements, which make their identification difficult. To evaluate their mobility, it is necessary to (i) select the suitable donor-recipient pairs for mating assays, (ii) do PCR excision tests to confirm that the genetic element is able to excise from the chromosome as a circular intermediate, and (iii) evaluate the transfer of the genetic element by conjugation by doing mating assays. In addition to a dissemination of resistance genes between S. suis strains, MGEs can lead to a spreading of resistance genes in the environment and toward pathogenic bacteria. This propagation had to be considered in a One Health perspective.
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Affiliation(s)
| | - Manon Dechêne-Tempier
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- Anses, Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, Ploufragan, France
| | | | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, Nancy, France.
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Tokuda M, Shintani M. Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol 2024; 17:e14408. [PMID: 38226780 PMCID: PMC10832538 DOI: 10.1111/1751-7915.14408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Mobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini-review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.
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Affiliation(s)
- Maho Tokuda
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
| | - Masaki Shintani
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
- Research Institute of Green Science and TechnologyShizuoka UniversityHamamatsuJapan
- Japan Collection of MicroorganismsRIKEN BioResource Research CenterIbarakiJapan
- Graduate School of Integrated Science and TechnologyShizuoka UniversityHamamatsuJapan
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Colombini L, Santoro F, Tirziu M, Lazzeri E, Morelli L, Pozzi G, Iannelli F. The mobilome of Lactobacillus crispatus M247 includes two novel genetic elements: Tn 7088 coding for a putative bacteriocin and the siphovirus prophage ΦM247. Microb Genom 2023; 9:001150. [PMID: 38085804 PMCID: PMC10763512 DOI: 10.1099/mgen.0.001150] [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: 07/25/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Lactobacillus crispatus is a member of the vaginal and gastrointestinal human microbiota. Here we determined the complete genome sequence of the probiotic strain M247 combining Nanopore and Illumina technologies. The M247 genome is organized in one circular chromosome of 2 336 109 bp, with a GC content of 37.04 % and 2303 ORFs, of which 1962 could be annotated. Analysis of the M247 mobilome, which accounts for 14 % of the whole genome, revealed the presence of: (i) Tn7088, a novel 14 105 bp long integrative and mobilizable element (IME) containing 16 ORFs; (ii) ΦM247, a novel 42 510 bp long siphovirus prophage containing 52 ORFs; (iii) three clustered regularly interspaced short palindromic repeats (CRISPRs); and (iv) 226 insertion sequences (ISs) belonging to 14 different families. Tn7088 has a modular organization including a mobilization module encoding FtsK homologous proteins and a relaxase, an integration/excision module coding for an integrase and an excisionase, and an adaptation module coding for a class I bacteriocin and homologous to the listeriolysin S (lls) locus of Listeria monocytogenes. Genome-wide homology search analysis showed the presence of Tn7088-like elements in 12 out of 23 L. crispatus complete public genomes. Mobilization and integration/excision modules are essentially conserved, while the adaptation module is variable since it is the target site for the integration of different ISs. Prophage ΦM247 contains genes for phage structural proteins, DNA replication and packaging, lysogenic and lytic cycles. ΦM247-like prophages are present in seven L. crispatus complete genomes, with sequence variability mainly due to the integration of ISs. PCR and sequencing showed that the Tn7088 IME excises from the M247 chromosome producing a circular form at a concentration of 4.32×10-5 copies per chromosome, and reconstitution of the Tn7088 chromosomal target site occurred at 6.65×10-4 copies per chromosome. The ΦM247 prophage produces an excised form and a reconstituted target site at a level of 3.90×10-5 and 2.48×10-5 copies per chromosome, respectively. This study identified two novel genetic elements in L. crispatus. Tn7088 represents the first example of an IME carrying a biosynthetic gene cluster for a class I bacteriocin in L. crispatus.
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Affiliation(s)
- Lorenzo Colombini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Francesco Santoro
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Mariana Tirziu
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Elisa Lazzeri
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Lorenzo Morelli
- Università Cattolica del Sacro Cuore, Department of Food Science and Technologies for a Sustainable Agri-food Supply Chain (DiSTAS), University of Piacenza, 53100 Piacenza, Italy
| | - Gianni Pozzi
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Francesco Iannelli
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
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Chen F, Yu T, Yin Z, Wang P, Lu X, He J, Zheng Y, Zhou D, Gao B, Mu K. Uncovering the hidden threat: The widespread presence of chromosome-borne accessory genetic elements and novel antibiotic resistance genetic environments in Aeromonas. Virulence 2023; 14:2271688. [PMID: 37848422 PMCID: PMC10614715 DOI: 10.1080/21505594.2023.2271688] [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: 07/25/2023] [Accepted: 10/11/2023] [Indexed: 10/19/2023] Open
Abstract
The emergence of antibiotic-resistant Aeromonas strains in clinical settings has presented an escalating burden on human and public health. The dissemination of antibiotic resistance in Aeromonas is predominantly facilitated by chromosome-borne accessory genetic elements, although the existing literature on this subject remains limited. Hence, the primary objective of this study is to comprehensively investigate the genomic characteristics of chromosome-borne accessory genetic elements in Aeromonas. Moreover, the study aims to uncover novel genetic environments associated with antibiotic resistance on these elements. Aeromonas were screened from nonduplicated strains collected from two tertiary hospitals in China. Complete sequencing and population genetics analysis were performed. BLAST analysis was employed to identify related elements. All newly identified elements were subjected to detailed sequence annotation, dissection, and comparison. We identified and newly designated 19 chromosomal elements, including 18 integrative and mobilizable elements (IMEs) that could be classified into four categories: Tn6737-related, Tn6836-related, Tn6840-related, and Tn6844a-related IMEs. Each class exhibited a distinct pattern in the types of resistance genes carried by the IMEs. Several novel antibiotic resistance genetic environments were uncovered in these elements. Notably, we report the first identification of the blaOXA-10 gene and blaVEB-1 gene in clinical A. veronii genome, the first presence of a tetA(E)-tetR(E) resistance gene environment within the backbone region in IMEs, and a new mcr-3.15 resistance gene environment. The implications of these findings are substantial, as they provide new insights into the evolution, structure, and dissemination of chromosomal-borne accessory elements.
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Affiliation(s)
- Fangzhou Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ting Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiuhui Lu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jiaqi He
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yali Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bo Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Kai Mu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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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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12
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Wang L, Chen H, Liu W, Yang L, Xu Z, Chen D. Resistome and Genome Analysis of an Extensively Drug-Resistant Klebsiella michiganensis KMIB106: Characterization of a Novel KPC Plasmid pB106-1 and a Novel Cointegrate Plasmid pB106-IMP Harboring blaIMP-4 and blaSHV-12. Antibiotics (Basel) 2023; 12:1463. [PMID: 37760759 PMCID: PMC10525660 DOI: 10.3390/antibiotics12091463] [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: 07/14/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Klebsiella michiganensis is a recently emerging human pathogen causing nosocomial infections. This study aimed to characterize the complete genome sequence of a clinical Klebsiella michiganensis strain KMIB106 which exhibited extensive drug-resistance. The whole genome of the strain was sequenced using PacBio RS III systems and Illumina Nextseq 500. Annotation, transposable elements and resistance gene identification were analyzed by RAST, prokka and Plasmid Finder, respectively. According to the results, KMIB106 was resistant to multiple antimicrobials, including carbapenems, but it remained susceptible to aztreonam. The genome of KMIB106 consisted of a single chromosome and three predicted plasmids. Importantly, a novel KPC plasmid pB106-1 was found to carry the array of resistance genes in a highly different order in its variable regions, including mphA, msrE, mphE, ARR-3, addA16, sul1, dfrA27, tetD and fosA3. Plasmid pB106-2 is a typical IncFII plasmid with no resistant gene. Plasmid pB106-IMP consists of the IncN and IncX3 backbones, and two resistance genes, blaIMP-4 and blaSHV-12, were identified. Our study for the first time reported an extensively drug-resistant Klebsiella michiganensis strain recovered from a child with a respiratory infection in Southern China, which carries three mega plasmids, with pB106-1 firstly identified to carry an array of resistance genes in a distinctive order, and pB106-IMP identified as a novel IncN-IncX3 cointegrate plasmid harboring two resistance genes blaIMP-4 and blaSHV-12.
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Affiliation(s)
- Linjing Wang
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Haijun Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Wanting Liu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Ling Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Zhenbo Xu
- School of Food Science and Engineering, Research Institute for Food Nutrition and Human Health, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou 510640, China
- Department of Laboratory Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515141, China
| | - Dingqiang Chen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
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13
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Audrey B, Cellier N, White F, Jacques PÉ, Burrus V. A systematic approach to classify and characterize genomic islands driven by conjugative mobility using protein signatures. Nucleic Acids Res 2023; 51:8402-8412. [PMID: 37526274 PMCID: PMC10484663 DOI: 10.1093/nar/gkad644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/02/2023] Open
Abstract
Genomic islands (GIs) play a crucial role in the spread of antibiotic resistance, virulence factors and antiviral defense systems in a broad range of bacterial species. However, the characterization and classification of GIs are challenging due to their relatively small size and considerable genetic diversity. Predicting their intercellular mobility is of utmost importance in the context of the emerging crisis of multidrug resistance. Here, we propose a large-scale classification method to categorize GIs according to their mobility profile and, subsequently, analyze their gene cargo. We based our classification decision scheme on a collection of mobility protein motif definitions available in publicly accessible databases. Our results show that the size distribution of GI classes correlates with their respective structure and complexity. Self-transmissible GIs are usually the largest, except in Bacillota and Actinomycetota, accumulate antibiotic and phage resistance genes, and favour the use of a tyrosine recombinase to insert into a host's replicon. Non-mobilizable GIs tend to use a DDE transposase instead. Finally, although tRNA genes are more frequently targeted as insertion sites by GIs encoding a tyrosine recombinase, most GIs insert in a protein-encoding gene. This study is a stepping stone toward a better characterization of mobile GIs in bacterial genomes and their mechanism of mobility.
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Affiliation(s)
- Bioteau Audrey
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Frédérique White
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Vincent Burrus
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
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14
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Huang J, Dai X, Wu Z, Hu X, Sun J, Tang Y, Zhang W, Han P, Zhao J, Liu G, Wang X, Mao S, Wang Y, Call DR, Liu J, Wang L. Conjugative transfer of streptococcal prophages harboring antibiotic resistance and virulence genes. THE ISME JOURNAL 2023; 17:1467-1481. [PMID: 37369704 PMCID: PMC10432423 DOI: 10.1038/s41396-023-01463-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023]
Abstract
Prophages play important roles in the transduction of various functional traits, including virulence factors, but remain debatable in harboring and transmitting antimicrobial resistance genes (ARGs). Herein we characterize a prevalent family of prophages in Streptococcus, designated SMphages, which harbor twenty-five ARGs that collectively confer resistance to ten antimicrobial classes, including vanG-type vancomycin resistance locus and oxazolidinone resistance gene optrA. SMphages integrate into four chromosome attachment sites by utilizing three types of integration modules and undergo excision in response to phage induction. Moreover, we characterize four subtypes of Alp-related surface proteins within SMphages, the lethal effects of which are extensively validated in cell and animal models. SMphages transfer via high-frequency conjugation that is facilitated by integrative and conjugative elements from either donors or recipients. Our findings explain the widespread of SMphages and the rapid dissemination of ARGs observed in members of the Streptococcus genus.
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Affiliation(s)
- Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xingyang Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Xiao Hu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Junjie Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yijun Tang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanqiu Zhang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peizhao Han
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiaqi Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangjin Liu
- Key Lab of Animal Bacteriology, Ministry of Agriculture, OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoming Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Douglas R Call
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, 99164, USA
| | - Jinxin Liu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
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15
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Li X, Mu X, Chen F, Lu X, He J, Zheng Y, Zhou D, Yin Z, Wang P. Characterization of Three Novel IMP Metallo-β-Lactamases, IMP-89, IMP-91, and IMP-96, and Diverse blaIMP-Carrying Accessory Genetic Elements from Chinese Clinical Isolates. Microbiol Spectr 2023; 11:e0498622. [PMID: 37092959 PMCID: PMC10269577 DOI: 10.1128/spectrum.04986-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 03/17/2023] [Indexed: 04/25/2023] Open
Abstract
Three novel imipenemase (IMP)-type metallo-β-lactamases (MBLs), referred to as IMP-89, IMP-91, and IMP-96, were detected in three clinical isolates from China. Antimicrobial susceptibility tests indicated these novel enzymes were resistant to most β-lactams, and IMP-96 with a Ser262Gly mutation had higher activity against meropenem than its point mutant. We then collected sequence data on all 91 available IMP variants for phylogenetic analysis. To further analyze the genetic environment of blaIMP, an extensive comparison was applied to nine accessory genetic elements (AGEs), including six sequenced blaIMP-carrying AGEs in this study and three others from GenBank. These nine AGEs were divided into three groups: three IncpJBCL41 plasmids, Tn6417 and its two derivatives, and three Tn6879-related integrative and conjugative elements (ICEs). All blaIMP genes in this study were captured by class 1 integrons. In the integrons, blaIMP genes usually coexisted with other resistance genes, which further impeded clinical antibacterial treatment. The emergence of new IMP variants and the diversity and complexity of their genetic environment make the prevention and control of drug-resistant strains critical, requiring serious attention from clinical and public health management departments. IMPORTANCE The spread of IMP-type MBLs has increased dramatically in recent years. We discovered three novel IMP variants from three clinical isolates in China. We summarized the classification and evolutionary relationship of all available IMP variants. Moreover, we detailed the genetic characteristics of blaIMP-carrying accessory genetic elements in five clinical isolates. Given the risk of rapid and extensive spread of blaIMP genes, we suggest that continuous surveillance is crucial to combat the acquisition and transmission of blaIMP genes by bacteria, which can impede clinical therapy effectiveness.
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Affiliation(s)
- Xinyue Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaofei Mu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fangzhou Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiuhui Lu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jiaqi He
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yali Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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16
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Idola D, Mori H, Nagata Y, Nonaka L, Yano H. Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria. Mob DNA 2023; 14:7. [PMID: 37237359 DOI: 10.1186/s13100-023-00295-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND The strand-biased circularizing integrative elements (SEs) are putatively non-mobilizable integrative elements for transmitting antimicrobial resistance genes. The transposition mode and the prevalence of SEs in prokaryotes remain vague. RESULTS To corroborate the transposition mode and the prevalence of SEs, hypothetical transposition intermediates of an SE were searched for in genomic DNA fractions of an SE host. Then, the SE core genes were defined based on gene knockout experiments, and the synteny blocks of their distant homologs were searched for in the RefSeq complete genome sequence database using PSI-BLAST. A genomic DNA fractionation experiment revealed that SE copies are present in a double-stranded nicked circular form in vivo. Operonic structure of three conserved coding sequences (intA, tfp, intB) and srap located at the left end of SEs were identified as essential for attL × attR recombination. The synteny blocks of tfp and srap homologs were detected in 3.6% of the replicons of Gammaproteobacteria but not in other taxa, implying that SE movement is host-dependent. SEs have been discovered most frequently in the orders Vibrionales (19% of replicons), Pseudomonadales (18%), Alteromonadales (17%), and Aeromonadales (12%). Genomic comparisons revealed 35 new SE members with identifiable termini. SEs are present at 1 to 2 copies per replicon and have a median length of 15.7 kb. Three newly identified SE members carry antimicrobial resistance genes, like tmexCD-toprJ, mcr-9, and blaGMA-1. Further experiments validated that three new SE members possess the strand-biased attL × attR recombination activity. CONCLUSIONS This study suggested that transposition intermediates of SEs are double-stranded circular DNA. The main hosts of SEs are a subset of free-living Gammaproteobacteria; this represents a rather narrow host range compared to those of mobile DNA element groups discovered to date. As the host range, genetic organization, and movements are unique among the mobile DNA elements, SEs provide a new model system for host-mobile DNA element coevolution studies.
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Affiliation(s)
- Desmila Idola
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aobaku, Sendai, 980-8577, Japan
| | - Hiroshi Mori
- Department of Informatics, National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan
| | - Yuji Nagata
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aobaku, Sendai, 980-8577, Japan
| | - Lisa Nonaka
- Faculty of Human Life Sciences, Shokei University, 2-6-78 Kuhonji, Kumamoto, 862-8678, Japan
| | - Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aobaku, Sendai, 980-8577, Japan.
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, 4-2-1 Aobacho, Higashimurayama, Tokyo, 189-0002, Japan.
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17
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Zhu Z, Wu S, Zhu J, Wang T, Wen Y, Yang C, Lv J, Zhang H, Chen L, Du H. Emergence of Aeromonas veronii strain co-harboring blaKPC-2, mcr-3.17, and tmexC3.2-tmexD3.3-toprJ1b cluster from hospital sewage in China. Front Microbiol 2023; 14:1115740. [PMID: 37266015 PMCID: PMC10229833 DOI: 10.3389/fmicb.2023.1115740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/02/2023] [Indexed: 06/03/2023] Open
Abstract
Introduction The raise of multi-drug resistant bacteria involving carbapenem, colistin, or tigecycline resistance constitutes a threat to public health, which partly results from the transmission of corresponding mobile resistance genes, such as blaKPC and blaNDM for carbapenem, mcr for colistin, and tmexCD-toprJ gene cluster for tigecycline. Herein, we described the emergence of an Aeromonas veronii strain HD6454 co-harboring blaKPC-2, mcr-3.17, and tmexC3.2-tmexD3.3-toprJ1b gene cluster from hospital sewage. Methods Whole genome sequencing (WGS) was used to determine the genome sequence of HD6454, and the detailed genomic analysis of genetic elements or regions carrying key antimicrobial resistance genes (ARGs) from HD6454 were performed. Cloning experiment was conducted to confirm the function of key ARGs in mediating antimicrobial resistance. Conjugation experiment was conducted to determine the mobility of the plasmid. Results The results showed that this strain belonged to a novel sequence type (ST) variant ST1016, and carried 18 important ARGs. Among them, the blaKPC-2 was carried by non-self-transmissible IncP-6 plasmid, while tmexC3.2-tmexD3.3-toprJ1b gene cluster and mcr-3.17 were carried by integrative and mobilizable element (IME) or IME-related region in chromosome. The mcr-3.17, mcr-3.6, and mcr-3-like3 genes were further inferred to originate from IMEs of Aeromonas species. Additionally, for the first time, the mcr-3.17 was confirmed to confer low-level resistance to colistin under inducible expression, while tmexC3.2-tmexD3.3-toprJ1b gene cluster was confirmed to confer low-level resistance to tigecycline. Discussion This is the first report of a strain co-harboring blaKPC-2, mcr-3.17, and tmexC3.2-tmexD3.3-toprJ1b gene cluster. Although the resistance and/or mobility of these ARGs are limited in this strain, the emergence of this multiple important ARGs-carrying strain deserves further attention.
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Affiliation(s)
- Zhichen Zhu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Shuhua Wu
- Department of Geriatrics, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of General Practice, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Jie Zhu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Tao Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yicheng Wen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Chengcheng Yang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Jinnan Lv
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Haifang Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ, United States
- Hackensack Meridian School of Medicine, Seton Hall University, Nutley, NJ, United States
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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18
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Moura de Sousa J, Lourenço M, Gordo I. Horizontal gene transfer among host-associated microbes. Cell Host Microbe 2023; 31:513-527. [PMID: 37054673 DOI: 10.1016/j.chom.2023.03.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Horizontal gene transfer is an important evolutionary force, facilitating bacterial diversity. It is thought to be pervasive in host-associated microbiomes, where bacterial densities are high and mobile elements are frequent. These genetic exchanges are also key for the rapid dissemination of antibiotic resistance. Here, we review recent studies that have greatly extended our knowledge of the mechanisms underlying horizontal gene transfer, the ecological complexities of a network of interactions involving bacteria and their mobile elements, and the effect of host physiology on the rates of genetic exchanges. Furthermore, we discuss other, fundamental challenges in detecting and quantifying genetic exchanges in vivo, and how studies have contributed to start overcoming these challenges. We highlight the importance of integrating novel computational approaches and theoretical models with experimental methods where multiple strains and transfer elements are studied, both in vivo and in controlled conditions that mimic the intricacies of host-associated environments.
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Affiliation(s)
- Jorge Moura de Sousa
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, 75015 Paris, France
| | - Marta Lourenço
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015 Paris, France
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande,6, Oeiras, Portugal.
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Ji B, Qin J, Ma Y, Liu X, Wang T, Liu G, Li B, Wang G, Gao P. Metagenomic analysis reveals patterns and hosts of antibiotic resistance in different pig farms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:52087-52106. [PMID: 36826766 DOI: 10.1007/s11356-023-25962-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
In actual production environments, antibiotic-resistant genes (ARGs) are abundant in pig manure, which can form transmission chains through animals, the environment, and humans, thereby threatening human health. Therefore, based on metagenomic analysis methods, ARGs and mobile genetic elements (MGEs) were annotated in pig manure samples from 6 pig farms in 3 regions of Shanxi Province, and the potential hosts of ARGs were analyzed. The results showed that a total of 14 ARG types were detected, including 182 ARG subtypes, among which tetracycline, phenol, aminoglycoside, and macrolide resistance genes were the main ones. ARG profiles, MGE composition, and microbial communities were significantly different in different regions as well as between different pig farms. In addition, Anaerobutyricum, Butyrivibrio, and Turicibacter were significantly associated with multiple ARGs, and bacteria such as Prevotella, Bacteroides, and the family Oscillospiraceae carried multiple ARGs, suggesting that these bacteria are potential ARG hosts in pig manure. Procrustes analysis showed that bacterial communities and MGEs were significantly correlated with ARG profiles. Variation partitioning analysis results indicated that the combined effect of MGEs and bacterial communities accounted for 64.08% of resistance variation and played an important role in ARG profiles. These findings contribute to our understanding of the dissemination and persistence of ARGs in actual production settings, and offer some guidance for the prevention and control of ARGs contamination.
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Affiliation(s)
- Bingzhen Ji
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Junjun Qin
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Yijia Ma
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Xin Liu
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, 100097, China
| | - Tian Wang
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, 100097, China
| | - Guiming Liu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Bugao Li
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Guoliang Wang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Pengfei Gao
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
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20
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Hochhauser D, Millman A, Sorek R. The defense island repertoire of the Escherichia coli pan-genome. PLoS Genet 2023; 19:e1010694. [PMID: 37023146 PMCID: PMC10121019 DOI: 10.1371/journal.pgen.1010694] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/21/2023] [Accepted: 03/06/2023] [Indexed: 04/08/2023] Open
Abstract
It has become clear in recent years that anti-phage defense systems cluster non-randomly within bacterial genomes in so-called "defense islands". Despite serving as a valuable tool for the discovery of novel defense systems, the nature and distribution of defense islands themselves remain poorly understood. In this study, we comprehensively mapped the defense system repertoire of >1,300 strains of Escherichia coli, the most widely studied organism for phage-bacteria interactions. We found that defense systems are usually carried on mobile genetic elements including prophages, integrative conjugative elements and transposons, which preferentially integrate at several dozens of dedicated hotspots in the E. coli genome. Each mobile genetic element type has a preferred integration position but can carry a diverse variety of defensive cargo. On average, an E. coli genome has 4.7 hotspots occupied by defense system-containing mobile elements, with some strains possessing up to eight defensively occupied hotspots. Defense systems frequently co-localize with other systems on the same mobile genetic element, in agreement with the observed defense island phenomenon. Our data show that the overwhelming majority of the E. coli pan-immune system is carried on mobile genetic elements, explaining why the immune repertoire varies substantially between different strains of the same species.
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Affiliation(s)
- Dina Hochhauser
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Millman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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21
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A New Integrative and Mobilizable Element Is a Major Contributor to Tetracycline Resistance in Streptococcus dysgalactiae subsp. equisimilis. Antibiotics (Basel) 2023; 12:antibiotics12030579. [PMID: 36978446 PMCID: PMC10044688 DOI: 10.3390/antibiotics12030579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/08/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
Tetracycline resistance in streptococci is mainly due to ribosomal protection mediated by the tet(M) gene that is usually located in the integrative and conjugative elements (ICEs) of the Tn916-family. In this study, we analyzed the genes involved in tetracycline resistance and the associated mobile genetic elements (MGEs) in Streptococcus dysgalactiae subsp. equisimilis (SDSE) causing invasive disease. SDSE resistant to tetracycline collected from 2012 to 2019 in a single hospital and from 2018 in three other hospitals were analyzed by whole genome sequencing. Out of a total of 84 SDSE isolates, 24 (28.5%) were resistant to tetracycline due to the presence of tet(M) (n = 22), tet(W) (n = 1), or tet(L) plus tet(W) (n = 1). The tet(M) genes were found in the ICEs of the Tn916-family (n = 10) and in a new integrative and mobilizable element (IME; n = 12). Phylogenetic analysis showed a higher genetic diversity among the strains carrying Tn916 than those having the new IME, which were closely related, and all belonged to CC15. In conclusion, tetracycline resistance in SDSE is mostly due to the tet(M) gene associated with ICEs belonging to the Tn916-family and a new IME. This new IME is a major cause of tetracycline resistance in invasive Streptococcus dysgalactiae subsp. equisimilis in our settings.
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22
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Michaelis C, Grohmann E. Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms. Antibiotics (Basel) 2023; 12:antibiotics12020328. [PMID: 36830238 PMCID: PMC9952180 DOI: 10.3390/antibiotics12020328] [Citation(s) in RCA: 68] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Most bacteria attach to biotic or abiotic surfaces and are embedded in a complex matrix which is known as biofilm. Biofilm formation is especially worrisome in clinical settings as it hinders the treatment of infections with antibiotics due to the facilitated acquisition of antibiotic resistance genes (ARGs). Environmental settings are now considered as pivotal for driving biofilm formation, biofilm-mediated antibiotic resistance development and dissemination. Several studies have demonstrated that environmental biofilms can be hotspots for the dissemination of ARGs. These genes can be encoded on mobile genetic elements (MGEs) such as conjugative and mobilizable plasmids or integrative and conjugative elements (ICEs). ARGs can be rapidly transferred through horizontal gene transfer (HGT) which has been shown to occur more frequently in biofilms than in planktonic cultures. Biofilm models are promising tools to mimic natural biofilms to study the dissemination of ARGs via HGT. This review summarizes the state-of-the-art of biofilm studies and the techniques that visualize the three main HGT mechanisms in biofilms: transformation, transduction, and conjugation.
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23
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A Glimpse at the Anti-Phage Defenses Landscape in the Foodborne Pathogen Salmonella enterica subsp. enterica serovar Typhimurium. Viruses 2023; 15:v15020333. [PMID: 36851545 PMCID: PMC9958689 DOI: 10.3390/v15020333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Bacteriophages, which specifically infect and kill bacteria, are currently used as additives to control pathogens such as Salmonella in human food (PhageGuard S®) or animal feed (SalmoFREE®, Bafasal®). Indeed, salmonellosis is among the most important zoonotic foodborne illnesses. The presence of anti-phage defenses protecting bacteria against phage infection could impair phage applications aiming at reducing the burden of foodborne pathogens such as Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) to the food industry. In this study, the landscape of S. Typhimurium anti-phage defenses was bioinformatically investigated in publicly available genomes using the webserver PADLOC. The primary anti-phage systems identified in S. Typhimurium use nucleic acid degradation and abortive infection mechanisms. Reference systems were identified on an integrative and conjugative element, a transposon, a putative integrative and mobilizable element, and prophages. Additionally, the mobile genetic elements (MGEs) containing a subset of anti-phage systems were found in the Salmonella enterica species. Lastly, the MGEs alone were also identified in the Enterobacteriaceae family. The presented diversity assessment of the anti-phage defenses and investigation of their dissemination through MGEs in S. Typhimurium constitute a first step towards the design of preventive measures against the spread of phage resistance that may hinder phage applications.
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24
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Luo X, Yin Z, Yu L, Zhang J, Hu D, Xu M, Wang P, Wang F, Feng J. Genomic analysis of chromosomal cointegrated bla NDM-1-carrying ICE and bla RSA-1-carrying IME from clinical multidrug resistant Aeromonas caviae. Front Cell Infect Microbiol 2023; 13:1131059. [PMID: 37033477 PMCID: PMC10076717 DOI: 10.3389/fcimb.2023.1131059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 03/14/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction The objective of this study is to thoroughly analyze the detailed genomic characteristics of clinical strain 211703 of Aeromonas caviae, which co-carrying bla RSA-1 and bla NDM-1 genes. 211703 was isolated from the patient's cerebrospinal fluid drainage sample in a Chinese tertiary hospital. Methods Carbapenemase NDM was detected by the immunocolloidal gold technique. The MIC values were determined by VITEK2. The whole genome sequence of 211703 was analyzed using phylogenetics, genomic comparison, and extensive dissection. Results This study revealed that 211703 only contained a single 4.78 Mb chromosome (61.8% GC content), and no plasmids were discovered in 211703. 15 different types of resistant genes were detected in the genome of 211703, including bla RSA-1 harbored on integrative and mobilizable element (IME) Tn7413a, and bla NDM-1 harbored on integrative and conjugative element (ICE). The ICE and IME were all carried on the chromosome of 211703 (c211703). Detailed comparison of related IMEs/ICEs showed that they shared similar conserved backbone regions, respectively. Comprehensive annotation revealed that bla RSA-1 was carried by the gene cassette of a novel integron In2148 on Tn7413a, and bla NDM-1 was captured by an insertion sequence ISCR14-like on the ICE of 211703. We speculated that mobile genetic elements (MGEs) such as ICE and IME facilitated the spread of resistance genes such as bla RSA-1 and bla NDM-1. Discussion In conclusion, this study provides an overall understanding of the genomic characterization of clinically isolated A. caviae 211703, and an in-depth discussion of multiple acquisition methods of drug resistance genes in Aeromonas. To the best of our knowledge, this is the first report of A. caviae carrying bla RSA-1 even both bla RSA-1 and bla NDM-1, and this is the first bacterium carrying bla RSA-1 isolated from the clinical setting.
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Affiliation(s)
- Xinhua Luo
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lianhua Yu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Jin Zhang
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Dakang Hu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Mengqiao Xu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fengling Wang
- Nanxiang Branch of Ruijin Hospital, Shanghai Jiaotong University, Shanghai, China
- *Correspondence: Jiao Feng, ; Fengling Wang,
| | - Jiao Feng
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
- *Correspondence: Jiao Feng, ; Fengling Wang,
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Palomino A, Gewurz D, DeVine L, Zajmi U, Moralez J, Abu-Rumman F, Smith RP, Lopatkin AJ. Metabolic genes on conjugative plasmids are highly prevalent in Escherichia coli and can protect against antibiotic treatment. THE ISME JOURNAL 2023; 17:151-162. [PMID: 36261510 PMCID: PMC9750983 DOI: 10.1038/s41396-022-01329-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 09/21/2022] [Accepted: 09/28/2022] [Indexed: 12/15/2022]
Abstract
Conjugative plasmids often encode antibiotic resistance genes that provide selective advantages to their bacterial hosts during antibiotic treatment. Previous studies have predominantly considered these established genes as the primary benefit of antibiotic-mediated plasmid dissemination. However, many genes involved in cellular metabolic processes may also protect against antibiotic treatment and provide selective advantages. Despite the diversity of such metabolic genes and their potential ecological impact, their plasmid-borne prevalence, co-occurrence with canonical antibiotic resistance genes, and phenotypic effects remain widely understudied. To address this gap, we focused on Escherichia coli, which can often act as a pathogen, and is known to spread antibiotic resistance genes via conjugation. We characterized the presence of metabolic genes on 1,775 transferrable plasmids and compared their distribution to that of known antibiotic resistance genes. We found high abundance of genes involved in cellular metabolism and stress response. Several of these genes demonstrated statistically significant associations or disassociations with known antibiotic resistance genes at the strain level, indicating that each gene type may impact the spread of the other across hosts. Indeed, in vitro characterization of 13 statistically relevant metabolic genes confirmed that their phenotypic impact on antibiotic susceptibility was largely consistent with in situ relationships. These results emphasize the ecological importance of metabolic genes on conjugal plasmids, and that selection dynamics of E. coli pathogens arises as a complex consequence of both canonical mechanisms and their interactions with metabolic pathways.
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Affiliation(s)
- Alana Palomino
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA
| | - Danya Gewurz
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA
| | - Lela DeVine
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA
| | - Ujana Zajmi
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA
| | - Jenifer Moralez
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA
| | - Fatima Abu-Rumman
- grid.261241.20000 0001 2168 8324Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314 USA
| | - Robert P. Smith
- grid.261241.20000 0001 2168 8324Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314 USA ,grid.261241.20000 0001 2168 8324Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33314 USA
| | - Allison J. Lopatkin
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA ,grid.21729.3f0000000419368729Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027 USA ,grid.21729.3f0000000419368729Data Science Institute, Columbia University, New York, NY 10027 USA ,grid.21729.3f0000000419368729Department of Systems Biology, Columbia University, New York, NY 10027 USA ,grid.16416.340000 0004 1936 9174Department of Chemical Engineering, University of Rochester, Rochester, NY 14627 USA
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26
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Seshadri R, Roux S, Huber KJ, Wu D, Yu S, Udwary D, Call L, Nayfach S, Hahnke RL, Pukall R, White JR, Varghese NJ, Webb C, Palaniappan K, Reimer LC, Sardà J, Bertsch J, Mukherjee S, Reddy T, Hajek PP, Huntemann M, Chen IMA, Spunde A, Clum A, Shapiro N, Wu ZY, Zhao Z, Zhou Y, Evtushenko L, Thijs S, Stevens V, Eloe-Fadrosh EA, Mouncey NJ, Yoshikuni Y, Whitman WB, Klenk HP, Woyke T, Göker M, Kyrpides NC, Ivanova NN. Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes. CELL GENOMICS 2022; 2:100213. [PMID: 36778052 PMCID: PMC9903846 DOI: 10.1016/j.xgen.2022.100213] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 07/19/2022] [Accepted: 10/16/2022] [Indexed: 11/13/2022]
Abstract
The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%-50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences.
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Affiliation(s)
- Rekha Seshadri
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA,Corresponding author
| | - Simon Roux
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Katharina J. Huber
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dongying Wu
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Sora Yu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dan Udwary
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Lee Call
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Stephen Nayfach
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Richard L. Hahnke
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Rüdiger Pukall
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Neha J. Varghese
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Cody Webb
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | - Lorenz C. Reimer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Joaquim Sardà
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jonathon Bertsch
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | - T.B.K. Reddy
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Patrick P. Hajek
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Marcel Huntemann
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - I-Min A. Chen
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Alex Spunde
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Nicole Shapiro
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Zong-Yen Wu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zhiying Zhao
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Yuguang Zhou
- China General Microbiological Culture Collection Center, Beijing, China
| | - Lyudmila Evtushenko
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, All-Russian Collection of Microorganisms (VKM), Pushchino, Russia
| | - Sofie Thijs
- Center for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium
| | - Vincent Stevens
- Center for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium
| | - Emiley A. Eloe-Fadrosh
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nigel J. Mouncey
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido 060-8589, Japan
| | | | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany,Corresponding author
| | - Nikos C. Kyrpides
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia N. Ivanova
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA,Corresponding author
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27
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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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28
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de Lorenzo V. Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agents. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210395. [PMID: 35757882 PMCID: PMC9234819 DOI: 10.1098/rstb.2021.0395] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Contemporary synthetic biology-based biotechnologies are generating tools and strategies for reprogramming genomes for specific purposes, including improvement and/or creation of microbial processes for tackling climate change. While such activities typically work well at a laboratory or bioreactor scale, the challenge of their extensive delivery to multiple spatio-temporal dimensions has hardly been tackled thus far. This state of affairs creates a research niche for what could be called Environmental Galenics (EG), i.e. the science and technology of releasing designed biological agents into deteriorated ecosystems for the sake of their safe and effective recovery. Such endeavour asks not just for an optimal performance of the biological activity at stake, but also the material form and formulation of the agents, their propagation and their interplay with the physico-chemical scenario where they are expected to perform. EG also encompasses adopting available physical carriers of microorganisms and channels of horizontal gene transfer as potential paths for spreading beneficial activities through environmental microbiomes. While some of these propositions may sound unsettling to anti-genetically modified organisms sensitivities, they may also fall under the tag of TINA (there is no alternative) technologies in the cases where a mere reduction of emissions will not help the revitalization of irreversibly lost ecosystems. This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.
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Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid 28049, Spain
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29
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Atypical integrative element with strand-biased circularization activity assists interspecies antimicrobial resistance gene transfer from Vibrio alfacsensis. PLoS One 2022; 17:e0271627. [PMID: 35917316 PMCID: PMC9345347 DOI: 10.1371/journal.pone.0271627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
The exchange of antimicrobial resistance (AMR) genes between aquaculture and terrestrial microbial populations has emerged as a serious public health concern. However, the nature of the mobile genetic elements in marine bacteria is poorly documented. To gain insight into the genetic mechanisms underlying AMR gene transfer from marine bacteria, we mated a multidrug-resistant Vibrio alfacsensis strain with an Escherichia coli strain, and then determined the complete genome sequences of the donor and the transconjugant strains. Sequence analysis revealed a conjugative multidrug resistance plasmid in the donor strain, which was integrated into the chromosome of the recipient. The plasmid backbone in the transconjugant chromosome was flanked by two copies of a 7.1 kb unclassifiable integrative element harboring a β-lactamase gene. The 7.1 kb element and the previously reported element Tn6283 share four coding sequences, two of which encode the catalytic R-H-R-Y motif of tyrosine recombinases. Polymerase chain reaction and sequencing experiments revealed that these elements generate a circular copy of one specific strand without leaving an empty site on the donor molecule, in contrast to the movement of integron gene cassettes or ICE/IMEs discovered to date. These elements are termed SEs (strand-biased circularizing integrative elements): SE-6945 (the 7.1 kb element) and SE-6283 (Tn6283). The copy number and location of SE-6945 in the chromosome affected the antibiotic resistance levels of the transconjugants. SEs were identified in the genomes of other Vibrio species. Overall, these results suggest that SEs are involved in the spread of AMR genes among marine bacteria.
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30
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Zhang G, Cui Q, Li J, Guo R, Leclercq SO, Du L, Tang N, Song Y, Wang C, Zhao F, Feng J. The integrase of genomic island GIsul2 mediates the mobilization of GIsul2 and ISCR-related element CR2-sul2 unit through site-specific recombination. Front Microbiol 2022; 13:905865. [PMID: 35979485 PMCID: PMC9376610 DOI: 10.3389/fmicb.2022.905865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
In the worldwide health threat posed by antibiotic-resistant bacterial pathogens, mobile genetic elements (MGEs) play a critical role in favoring the dissemination of resistance genes. Among them, the genomic island GIsul2 and the ISCR-related element CR2-sul2 unit are believed to participate in this dissemination. However, the mobility of the two elements has not yet been demonstrated. Here, we found that the GIsul2 and CR2-sul2 units can excise from the host chromosomal attachment site (attB) in Shigella flexneri. Through establishing a two-plasmid mobilization system composed of a donor plasmid bearing the GIsul2 and a trap plasmid harboring the attB in recA-deficient Escherichia coli, we reveal that the integrase of GIsul2 can perform the excision and integration of GIsul2 and CR2-sul2 unit by site-specific recombination between att core sites. Furthermore, we demonstrate that the integrase and the att sites are required for mobility through knockout experiments. Our findings provide the first experimental characterization of the mobility of GIsul2 and CR2-sul2 units mediated by integrase. They also suggest a potential and unappreciated role of the GIsul2 integrase family in the dissemination of CR2-sul2 units carrying various resistance determinants in between.
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Affiliation(s)
- Gang Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qinna Cui
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Jianjuan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Ruiliang Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | | | - Lifeng Du
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Na Tang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yuqin Song
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Jie Feng
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Ott LC, Mellata M. Models for Gut-Mediated Horizontal Gene Transfer by Bacterial Plasmid Conjugation. Front Microbiol 2022; 13:891548. [PMID: 35847067 PMCID: PMC9280185 DOI: 10.3389/fmicb.2022.891548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The emergence of new antimicrobial resistant and virulent bacterial strains may pose a threat to human and animal health. Bacterial plasmid conjugation is a significant contributor to rapid microbial evolutions that results in the emergence and spread of antimicrobial resistance (AR). The gut of animals is believed to be a potent reservoir for the spread of AR and virulence genes through the horizontal exchange of mobile genetic elements such as plasmids. The study of the plasmid transfer process in the complex gut environment is limited due to the confounding factors that affect colonization, persistence, and plasmid conjugation. Furthermore, study of plasmid transfer in the gut of humans is limited to observational studies, leading to the need to identify alternate models that provide insight into the factors regulating conjugation in the gut. This review discusses key studies on the current models for in silico, in vitro, and in vivo modeling of bacterial conjugation, and their ability to reflect the gut of animals. We particularly emphasize the use of computational and in vitro models that may approximate aspects of the gut, as well as animal models that represent in vivo conditions to a greater extent. Directions on future research studies in the field are provided.
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Affiliation(s)
- Logan C. Ott
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
| | - Melha Mellata
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
- *Correspondence: Melha Mellata,
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Belloso Daza MV, Milani G, Cortimiglia C, Pietta E, Bassi D, Cocconcelli PS. Genomic Insights of Enterococcus faecium UC7251, a Multi-Drug Resistant Strain From Ready-to-Eat Food, Highlight the Risk of Antimicrobial Resistance in the Food Chain. Front Microbiol 2022; 13:894241. [PMID: 35814695 PMCID: PMC9262338 DOI: 10.3389/fmicb.2022.894241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/31/2022] [Indexed: 12/12/2022] Open
Abstract
The presence of multi-drug resistant (MDR) bacteria in ready-to-eat foods comprises a threat for public health due to their ability to acquire and transfer antibiotic-resistant determinants that could settle in the microbiome of the human digestive tract. In this study, Enterococcus faecium UC7251 isolated from a fermented dry sausage was characterized phenotypically and genotypically to hold resistance to multiple antibiotics including aminoglycosides, macrolides, β-lactams, and tetracyclines. We further investigated this strain following a hybrid sequencing and assembly approach (short and long reads) and determined the presence of various mobile genetic elements (MGEs) responsible of horizontal gene transfer (HGT). On the chromosome of UC7251, we found one integrative and conjugative element (ICE) and a conjugative transposon Tn916-carrying tetracycline resistance. UC7251 carries two plasmids: one small plasmid harboring a rolling circle replication and one MDR megaplasmid. The latter was identified as mobilizable and containing a putative integrative and conjugative element-like region, prophage sequences, insertion sequences, heavy-metal resistance genes, and several antimicrobial resistance (AMR) genes, confirming the phenotypic resistance characteristics. The transmissibility potential of AMR markers was observed through mating experiments, where Tn916-carried tetracycline resistance was transferred at intra- and inter-species levels. This work highlights the significance of constant monitoring of products of animal origin, especially RTE foodstuffs, to stimulate the development of novel strategies in the race for constraining the spread of antibiotic resistance.
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Zhao R, Hao J, Yang J, Tong C, Xie L, Xiao D, Zeng Z, Xiong W. The co-occurrence of antibiotic resistance genes between dogs and their owners in families. IMETA 2022; 1:e21. [PMID: 38868570 PMCID: PMC10989978 DOI: 10.1002/imt2.21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/18/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2024]
Abstract
The intimate relationship between humans and companion animals causes a unique and critical aspect of antimicrobial resistance in humans. However, a comprehensive analysis of antimicrobial resistance between companion animals and their owners is lacking. Here, we chose 13 owned dogs and 16 owners as well as 22 kennel dogs to analyze the effect of an intimate relationship between owned dogs and owners on their gut microbiome, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) and study the correlation of antimicrobial resistance between dogs and their owners in families by metagenomics. Dog gut microbiota had a higher abundance and diversity of ARGs while owners had a higher diversity of taxonomy. In the owned dog gut microbial community, ARG and MGE compositions were significantly more similar to the owner's gut microbiota than those of others. From the perspective of families, there was a strong correlation between macrolide resistance genes between dogs and their owners. In conclusion, our study demonstrated the correlation of ARGs between dogs and their owners at a community-wide level. These findings can alarm the use of antibiotics in companion animals, which implies the potential to harbor antimicrobial resistance and threaten public health.
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Affiliation(s)
- Ruonan Zhao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouGuangdongChina
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
| | - Jie Hao
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouGuangdongChina
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
| | - Jintao Yang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
| | - Cuihong Tong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouGuangdongChina
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
| | - Longfei Xie
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouGuangdongChina
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
| | - Danyu Xiao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouGuangdongChina
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouGuangdongChina
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouGuangdongChina
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
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Guédon G, Lao J, Payot S, Lacroix T, Chiapello H, Leblond-Bourget N. FirmiData: a set of 40 genomes of Firmicutes with a curated annotation of ICEs and IMEs. BMC Res Notes 2022; 15:157. [PMID: 35538580 PMCID: PMC9092696 DOI: 10.1186/s13104-022-06036-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/11/2022] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES 'Integrative and Conjugative Elements' (ICEs) and 'Integrative and Mobilizable Elements' (IMEs) are two classes of mobile genetic elements that are complex to detect and delineate. Therefore, they are yet poorly annotated in bacterial genomes. FirmiData provides to the scientific community of microbiologists and bioinformaticians a reference resource of annotated ICEs and of IMEs from Firmicutes. It illustrates their prevalence and their diversity but also gives information on their organization. FirmiData was designed to assist the scientific community in identifying and annotating these elements by using the sequences of these ICEs and IMEs for the identification of related elements in other genomes of Firmicutes. Therefore, Firmidata meets the needs of the scientific community. DATA DESCRIPTION Firmidata provides a manually curated annotation of 98 ICEs and 148 IMEs identified in 40 chromosomes of Firmicutes. The delineation at the nucleotide level of almost all of these elements allows for the characterization of the genes they carry.
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Affiliation(s)
- Gérard Guédon
- DynAMic, Université de Lorraine, INRAE, 54000 Nancy, France
| | - Julie Lao
- DynAMic, Université de Lorraine, INRAE, 54000 Nancy, France
- MaIAGE, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France
| | - Sophie Payot
- DynAMic, Université de Lorraine, INRAE, 54000 Nancy, France
| | - Thomas Lacroix
- MaIAGE, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France
| | - Hélène Chiapello
- MaIAGE, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France
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Guan J, Bao C, Wang P, Jing Y, Wang L, Li X, Mu X, Li B, Zhou D, Guo X, Yin Z. Genetic Characterization of Four Groups of Chromosome-Borne Accessory Genetic Elements Carrying Drug Resistance Genes in Providencia. Infect Drug Resist 2022; 15:2253-2270. [PMID: 35510160 PMCID: PMC9058013 DOI: 10.2147/idr.s354934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/20/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose The aim of this study was to gain a deeper genomics and bioinformatics understanding of diversification of accessory genetic elements (AGEs) in Providencia. Methods Herein, the complete genome sequences of five Providencia isolates from China were determined, and seven AGEs were identified from the chromosomes. Detailed genetic dissection and sequence comparison were applied to these seven AGEs, together with additional 10 chromosomal ones from GenBank (nine of them came from Providencia). Results These 17 AGEs were divided into four groups: Tn6512 and its six derivatives, Tn6872 and its two derivatives, Tn6875 and its one derivative, and Tn7 and its four derivatives. These AGEs display high-level diversification in modular structures that had complex mosaic natures, and particularly different multidrug resistance (MDR) regions were presented in these AGEs. At least 52 drug resistance genes, involved in resistance to 15 different categories of antimicrobials and heavy metal, were found in 15 of these 17 AGEs. Conclusion Integration of these AGEs into the Providencia chromosomes would contribute to the accumulation and distribution of drug resistance genes and enhance the ability of Providencia isolates to survive under drug selection pressure.
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Affiliation(s)
- Jiayao Guan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, 130122, People’s Republic of China
| | - Chunmei Bao
- Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, People’s Republic of China
| | - Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Ying Jing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Lingling Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Xinyue Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Xiaofei Mu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Boan Li
- Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, People’s Republic of China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Xuejun Guo
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, 130122, People’s Republic of China
- Xuejun Guo, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, 130122, People’s Republic of China, Tel +86-431-86985931, Email
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
- Correspondence: Zhe Yin, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China, Tel +86-10-66948557, Email
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Algarni S, Ricke SC, Foley SL, Han J. The Dynamics of the Antimicrobial Resistance Mobilome of Salmonella enterica and Related Enteric Bacteria. Front Microbiol 2022; 13:859854. [PMID: 35432284 PMCID: PMC9008345 DOI: 10.3389/fmicb.2022.859854] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/07/2022] [Indexed: 12/31/2022] Open
Abstract
The foodborne pathogen Salmonella enterica is considered a global public health risk. Salmonella enterica isolates can develop resistance to several antimicrobial drugs due to the rapid spread of antimicrobial resistance (AMR) genes, thus increasing the impact on hospitalization and treatment costs, as well as the healthcare system. Mobile genetic elements (MGEs) play key roles in the dissemination of AMR genes in S. enterica isolates. Multiple phenotypic and molecular techniques have been utilized to better understand the biology and epidemiology of plasmids including DNA sequence analyses, whole genome sequencing (WGS), incompatibility typing, and conjugation studies of plasmids from S. enterica and related species. Focusing on the dynamics of AMR genes is critical for identification and verification of emerging multidrug resistance. The aim of this review is to highlight the updated knowledge of AMR genes in the mobilome of Salmonella and related enteric bacteria. The mobilome is a term defined as all MGEs, including plasmids, transposons, insertion sequences (ISs), gene cassettes, integrons, and resistance islands, that contribute to the potential spread of genes in an organism, including S. enterica isolates and related species, which are the focus of this review.
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Affiliation(s)
- Suad Algarni
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, United States
| | - Steven L. Foley
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Jing Han
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- *Correspondence: Jing Han,
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37
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Morgado S, Vicente AC. Conjugative transfer of naturally occurring plasmid in Mycolicibacterium sp. FEMS Microbiol Lett 2022; 369:6554244. [PMID: 35333321 DOI: 10.1093/femsle/fnac035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/16/2022] [Accepted: 03/23/2022] [Indexed: 11/14/2022] Open
Abstract
Conjugation is considered the main horizontal gene transfer (HGT) mechanism in bacterial adaptation and evolution. In the Mycobacteriaceae family, Mycolicibacterium smegmatis has been used as the model organism for the conjugative transfer of hybrid plasmids. However, the natural conjugation process in any bacteria would involve the transfer of naturally occurring plasmids. Currently, there is a gap in this regard about this abundant environmental genus of Mycobacteriaceae. Here, we performed conjugation experiments between wild Mycolicibacterium sp. strains involving naturally occurring plasmids, and interestingly, evidence of conjugative transfer was obtained. Thus, it is likely that conjugation occurs in Mycolicibacterium in the natural environment, representing a source of diversification and evolution in this genus of bacteria.
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Affiliation(s)
- Sergio Morgado
- Laboratory of Molecular Genetics of Microorganisms, Institute Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ana Carolina Vicente
- Laboratory of Molecular Genetics of Microorganisms, Institute Oswaldo Cruz, Rio de Janeiro, Brazil
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Chen F, Wang P, Yin Z, Yang H, Hu L, Yu T, Jing Y, Guan J, Wu J, Zhou D. VIM-encoding Inc pSTY plasmids and chromosome-borne integrative and mobilizable elements (IMEs) and integrative and conjugative elements (ICEs) in Pseudomonas. Ann Clin Microbiol Antimicrob 2022; 21:10. [PMID: 35264204 PMCID: PMC8905914 DOI: 10.1186/s12941-022-00502-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 03/02/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The carbapenem-resistance genes blaVIM are widely disseminated in Pseudomonas, and frequently harbored within class 1 integrons that reside within various mobile genetic elements (MGEs). However, there are few reports on detailed genetic dissection of blaVIM-carrying MGEs in Pseudomonas. METHODS This study presented the complete sequences of five blaVIM-2/-4-carrying MGEs, including two plasmids, two chromosomal integrative and mobilizable elements (IMEs), and one chromosomal integrative and conjugative element (ICE) from five different Pseudomonas isolates. RESULTS The two plasmids were assigned to a novel incompatibility (Inc) group IncpSTY, which included only seven available plasmids with determined complete sequences and could be further divided into three subgroups IncpSTY-1/2/3. A detailed sequence comparison was then applied to a collection of 15 MGEs belonging to four different groups: three representative IncpSTY plasmids, two Tn6916-related IMEs, two Tn6918-related IMEs, and eight Tn6417-related ICEs and ten of these 15 MGEs were first time identified. At least 22 genes involving resistance to seven different categories of antibiotics and heavy metals were identified within these 15 MGEs, and most of these resistance genes were located within the accessory modules integrated as exogenous DNA regions into these MGEs. Especially, eleven of these 15 MGEs carried the blaVIM genes, which were located within 11 different concise class 1 integrons. CONCLUSION These blaVIM-carrying integrons were further integrated into the above plasmids, IMEs/ICEs with intercellular mobility. These MGEs could transfer between Pseudomonas isolates, which resulted in the accumulation and spread of blaVIM among Pseudomonas and thus was helpful for the bacteria to survival from the stress of antibiotics. Data presented here provided a deeper insight into the genetic diversification and evolution of VIM-encoding MGEs in Pseudomonas.
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Affiliation(s)
- Fangzhou Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.,Basic Medical College, Guizhou Medical University, Guiyang, 550025, China.,Guangzhou Medical University, Guangzhou, 511436, China
| | - Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ting Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ying Jing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Jiayao Guan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Jiahong Wu
- Basic Medical College, Guizhou Medical University, Guiyang, 550025, China.
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China. .,Guangzhou Medical University, Guangzhou, 511436, China.
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Lee IPA, Andam CP. Frequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis. Sci Rep 2022; 12:1515. [PMID: 35087075 PMCID: PMC8795270 DOI: 10.1038/s41598-022-04995-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/05/2022] [Indexed: 11/08/2022] Open
Abstract
Streptococcus consists of ecologically diverse species, some of which are important pathogens of humans and animals. We sought to quantify and compare the frequencies and characteristics of within-species recombination in the pan-genomes of Streptococcus agalactiae, Streptococcus pyogenes and Streptococcus suis. We used 1081, 1813 and 1204 publicly available genome sequences of each species, respectively. Based on their core genomes, S. agalactiae had the highest relative rate of recombination to mutation (11.5743) compared to S. pyogenes (1.03) and S. suis (0.57). The proportion of the species pan-genome that have had a history of recombination was 12.85%, 24.18% and 20.50% of the pan-genomes of each species, respectively. The composition of recombining genes varied among the three species, and some of the most frequently recombining genes are implicated in adhesion, colonization, oxidative stress response and biofilm formation. For each species, a total of 22.75%, 29.28% and 18.75% of the recombining genes were associated with prophages. The cargo genes of integrative conjugative elements and integrative and mobilizable elements contained genes associated with antimicrobial resistance and virulence. Homologous recombination and mobilizable pan-genomes enable the creation of novel combinations of genes and sequence variants, and the potential for high-risk clones to emerge.
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Affiliation(s)
| | - Cheryl P Andam
- University at Albany, State University of New York, New York, 12222, USA.
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40
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Goyal B, Verma N, Kharewal T, Gahlaut A, Hooda V. Structural effects of nanoparticles on their antibacterial activity against multi-drug resistance. INORG NANO-MET CHEM 2022. [DOI: 10.1080/24701556.2021.2025103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Bharti Goyal
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Neelam Verma
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Tannu Kharewal
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Anjum Gahlaut
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Vikas Hooda
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, India
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41
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Bottalico L, Charitos IA, Potenza MA, Montagnani M, Santacroce L. The war against bacteria, from the past to present and beyond. Expert Rev Anti Infect Ther 2021; 20:681-706. [PMID: 34874223 DOI: 10.1080/14787210.2022.2013809] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
INTRODUCTION The human defense against microorganisms dates back to the ancient civilizations, with attempts to use substances from vegetal, animal, or inorganic origin to fight infections. Today, the emerging threat of multidrug-resistant bacteria highlights the consequences of antibiotics inappropriate use, and the urgent need for novel effective molecules. METHODS AND MATERIALS We extensively researched on more recent data within PubMed, Medline, Web of Science, Elsevier's EMBASE, Cochrane Review for the modern pharmacology in between 1987 - 2021. The historical evolution included a detailed analysis of past studies on the significance of medical applications in the ancient therapeutic field. AREAS COVERED We examined the history of antibiotics development and discovery, the most relevant biochemical aspects of their mode of action, and the biomolecular mechanisms conferring bacterial resistance to antibiotics. EXPERT OPINION The list of pathogens showing low sensitivity or full resistance to most currently available antibiotics is growing worldwide. Long after the 'golden age' of antibiotic discovery, the most novel molecules should be carefully reserved to treat serious bacterial infections of susceptible bacteria. A correct diagnostic and therapeutic procedure can slow down the spreading of nosocomial and community infections sustained by multidrug-resistant bacterial strains.
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Affiliation(s)
- Lucrezia Bottalico
- Interdepartmental Research Center for Pre-Latin, Latin and Oriental Rights and Culture Studies (Cediclo), University of Bari, Bari, Italy
| | - Ioannis Alexandros Charitos
- Interdepartmental Research Center for Pre-Latin, Latin and Oriental Rights and Culture Studies (Cediclo), University of Bari, Bari, Italy.,Emergency/Urgent Department, National Poisoning Center, Riuniti University Hospital of Foggia, Foggia, Italy
| | - Maria Assunta Potenza
- Department of Biomedical Sciences and Human Oncology - Section of Pharmacology, School of Medicine, University of Bari "Aldo Moro," Policlinico University Hospital of Bari, Bari, Italy
| | - Monica Montagnani
- Department of Biomedical Sciences and Human Oncology - Section of Pharmacology, School of Medicine, University of Bari "Aldo Moro," Policlinico University Hospital of Bari, Bari, Italy
| | - Luigi Santacroce
- Department of Interdisciplinary Medicine, Microbiology and Virology Unit, School of Medicine,University of Bari "Aldo Moro", Bari, Italy
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The Facts and Family Secrets of Plasmids That Replicate via the Rolling-Circle Mechanism. Microbiol Mol Biol Rev 2021; 86:e0022220. [PMID: 34878299 DOI: 10.1128/mmbr.00222-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Plasmids are self-replicative DNA elements that are transferred between bacteria. Plasmids encode not only antibiotic resistance genes but also adaptive genes that allow their hosts to colonize new niches. Plasmid transfer is achieved by conjugation (or mobilization), phage-mediated transduction, and natural transformation. Thousands of plasmids use the rolling-circle mechanism for their propagation (RCR plasmids). They are ubiquitous, have a high copy number, exhibit a broad host range, and often can be mobilized among bacterial species. Based upon the replicon, RCR plasmids have been grouped into several families, the best known of them being pC194 and pUB110 (Rep_1 family), pMV158 and pE194 (Rep_2 family), and pT181 and pC221 (Rep_trans family). Genetic traits of RCR plasmids are analyzed concerning (i) replication mediated by a DNA-relaxing initiator protein and its interactions with the cognate DNA origin, (ii) lagging-strand origins of replication, (iii) antibiotic resistance genes, (iv) mobilization functions, (v) replication control, performed by proteins and/or antisense RNAs, and (vi) the participating host-encoded functions. The mobilization functions include a relaxase initiator of transfer (Mob), an origin of transfer, and one or two small auxiliary proteins. There is a family of relaxases, the MOBV family represented by plasmid pMV158, which has been revisited and updated. Family secrets, like a putative open reading frame of unknown function, are reported. We conclude that basic research on RCR plasmids is of importance, and our perspectives contemplate the concept of One Earth because we should incorporate bacteria into our daily life by diminishing their virulence and, at the same time, respecting their genetic diversity.
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Douglas GM, Shapiro BJ. Genic Selection Within Prokaryotic Pangenomes. Genome Biol Evol 2021; 13:6402011. [PMID: 34665261 PMCID: PMC8598171 DOI: 10.1093/gbe/evab234] [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] [Accepted: 10/14/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the evolutionary forces shaping prokaryotic pangenome structure is a major goal of microbial evolution research. Recent work has highlighted that a substantial proportion of accessory genes appear to confer niche-specific adaptations. This work has primarily focused on selection acting at the level of individual cells. Herein, we discuss a lower level of selection that also contributes to pangenome variation: genic selection. This refers to cases where genetic elements, rather than individual cells, are the entities under selection. The clearest examples of this form of selection are selfish mobile genetic elements, which are those that have either a neutral or a deleterious effect on host fitness. We review the major classes of these and other mobile elements and discuss the characteristic features of such elements that could be under genic selection. We also discuss how genetic elements that are beneficial to hosts can also be under genic selection, a scenario that may be more prevalent but not widely appreciated, because disentangling the effects of selection at different levels (i.e., organisms vs. genes) is challenging. Nonetheless, an appreciation for the potential action and implications of genic selection is important to better understand the evolution of prokaryotic pangenomes.
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Affiliation(s)
- Gavin M Douglas
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - B Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
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Oshkin IY, Danilova OV, But SY, Miroshnikov KK, Suleimanov RZ, Belova SE, Tikhonova EN, Kuznetsov NN, Khmelenina VN, Pimenov NV, Dedysh SN. Expanding Characterized Diversity and the Pool of Complete Genome Sequences of Methylococcus Species, the Bacteria of High Environmental and Biotechnological Relevance. Front Microbiol 2021; 12:756830. [PMID: 34691008 PMCID: PMC8527097 DOI: 10.3389/fmicb.2021.756830] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
The bacterial genus Methylococcus, which comprises aerobic thermotolerant methanotrophic cocci, was described half-a-century ago. Over the years, a member of this genus, Methylococcus capsulatus Bath, has become a major model organism to study genomic and metabolic basis of obligate methanotrophy. High biotechnological potential of fast-growing Methylococcus species, mainly as a promising source of feed protein, has also been recognized. Despite this big research attention, the currently cultured Methylococcus diversity is represented by members of the two species, M. capsulatus and M. geothermalis, while finished genome sequences are available only for two strains of these methanotrophs. This study extends the pool of phenotypically characterized Methylococcus strains with good-quality genome sequences by contributing four novel isolates of these bacteria from activated sludge, landfill cover soil, and freshwater sediments. The determined genome sizes of novel isolates varied between 3.2 and 4.0Mb. As revealed by the phylogenomic analysis, strains IO1, BH, and KN2 affiliate with M. capsulatus, while strain Mc7 may potentially represent a novel species. Highest temperature optima (45-50°C) and highest growth rates in bioreactor cultures (up to 0.3h-1) were recorded for strains obtained from activated sludge. The comparative analysis of all complete genomes of Methylococcus species revealed 4,485 gene clusters. Of these, pan-genome core comprised 2,331 genes (on average 51.9% of each genome), with the accessory genome containing 846 and 1,308 genes in the shell and the cloud, respectively. Independently of the isolation source, all strains of M. capsulatus displayed surprisingly high genome synteny and a striking similarity in gene content. Strain Mc7 from a landfill cover soil differed from other isolates by the high content of mobile genetic elements in the genome and a number of genome-encoded features missing in M. capsulatus, such as sucrose biosynthesis and the ability to scavenge phosphorus and sulfur from the environment.
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Affiliation(s)
- Igor Y. Oshkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Olga V. Danilova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Y. But
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia
| | - Kirill K. Miroshnikov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ruslan Z. Suleimanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Svetlana E. Belova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina N. Tikhonova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolai N. Kuznetsov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Valentina N. Khmelenina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia
| | - Nikolai V. Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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45
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Colombi E, Perry BJ, Sullivan JT, Bekuma AA, Terpolilli JJ, Ronson CW, Ramsay JP. Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium. Microb Genom 2021; 7. [PMID: 34605762 PMCID: PMC8627217 DOI: 10.1099/mgen.0.000657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Members of the Mesorhizobium genus are soil bacteria that often form nitrogen-fixing symbioses with legumes. Most characterised Mesorhizobium spp. genomes are ~8 Mb in size and harbour extensive pangenomes including large integrative and conjugative elements (ICEs) carrying genes required for symbiosis (ICESyms). Here, we document and compare the conjugative mobilome of 41 complete Mesorhizobium genomes. We delineated 56 ICEs and 24 integrative and mobilizable elements (IMEs) collectively occupying 16 distinct integration sites, along with 24 plasmids. We also demonstrated horizontal transfer of the largest (853,775 bp) documented ICE, the tripartite ICEMspSymAA22. The conjugation systems of all identified ICEs and several plasmids were related to those of the paradigm ICESym ICEMlSymR7A, with each carrying conserved genes for conjugative pilus formation (trb), excision (rdfS), DNA transfer (rlxS) and regulation (fseA). ICESyms have likely evolved from a common ancestor, despite occupying a variety of distinct integration sites and specifying symbiosis with diverse legumes. We found extensive evidence for recombination between ICEs and particularly ICESyms, which all uniquely lack the conjugation entry-exclusion factor gene trbK. Frequent duplication, replacement and pseudogenization of genes for quorum-sensing-mediated activation and antiactivation of ICE transfer suggests ICE transfer regulation is constantly evolving. Pangenome-wide association analysis of the ICE identified genes potentially involved in symbiosis, rhizosphere colonisation and/or adaptation to distinct legume hosts. In summary, the Mesorhizobium genus has accumulated a large and dynamic pangenome that evolves through ongoing horizontal gene transfer of large conjugative elements related to ICEMlSymR7A.
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Affiliation(s)
- Elena Colombi
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia.,Curtin Medical School, Curtin University, Perth, WA, Australia
| | - Benjamin J Perry
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Amanuel A Bekuma
- Centre for Rhizobium Studies, Food Futures Institute, Murdoch University, Perth, WA, Australia, Murdoch University, Perth, WA, Australia.,Present address: Western Australian Department of Primary Industries and Regional Development, Research and Industry Innovation, South Perth, WA, Australia
| | - Jason J Terpolilli
- Centre for Rhizobium Studies, Food Futures Institute, Murdoch University, Perth, WA, Australia, Murdoch University, Perth, WA, Australia
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Joshua P Ramsay
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia.,Curtin Medical School, Curtin University, Perth, WA, Australia
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Durand R, Deschênes F, Burrus V. Genomic islands targeting dusA in Vibrio species are distantly related to Salmonella Genomic Island 1 and mobilizable by IncC conjugative plasmids. PLoS Genet 2021; 17:e1009669. [PMID: 34415925 PMCID: PMC8409611 DOI: 10.1371/journal.pgen.1009669] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/01/2021] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
Salmonella Genomic Island 1 (SGI1) and its variants are significant contributors to the spread of antibiotic resistance among Gammaproteobacteria. All known SGI1 variants integrate at the 3’ end of trmE, a gene coding for a tRNA modification enzyme. SGI1 variants are mobilized specifically by conjugative plasmids of the incompatibility groups A and C (IncA and IncC). Using a comparative genomics approach based on genes conserved among members of the SGI1 group, we identified diverse integrative elements distantly related to SGI1 in several species of Vibrio, Aeromonas, Salmonella, Pokkaliibacter, and Escherichia. Unlike SGI1, these elements target two alternative chromosomal loci, the 5’ end of dusA and the 3’ end of yicC. Although they share many features with SGI1, they lack antibiotic resistance genes and carry alternative integration/excision modules. Functional characterization of IMEVchUSA3, a dusA-specific integrative element, revealed promoters that respond to AcaCD, the master activator of IncC plasmid transfer genes. Quantitative PCR and mating assays confirmed that IMEVchUSA3 excises from the chromosome and is mobilized by an IncC helper plasmid from Vibrio cholerae to Escherichia coli. IMEVchUSA3 encodes the AcaC homolog SgaC that associates with AcaD to form a hybrid activator complex AcaD/SgaC essential for its excision and mobilization. We identified the dusA-specific recombination directionality factor RdfN required for the integrase-mediated excision of dusA-specific elements from the chromosome. Like xis in SGI1, rdfN is under the control of an AcaCD-responsive promoter. Although the integration of IMEVchUSA3 disrupts dusA, it provides a new promoter sequence and restores the reading frame of dusA for proper expression of the tRNA-dihydrouridine synthase A. Phylogenetic analysis of the conserved proteins encoded by SGI1-like elements targeting dusA, yicC, and trmE gives a fresh perspective on the possible origin of SGI1 and its variants. We identified integrative elements distantly related to Salmonella Genomic Island 1 (SGI1), a key vector of antibiotic resistance genes in Gammaproteobacteria. SGI1 and its variants reside at the 3’ end of trmE, share a large, highly conserved core of genes, and carry a complex integron that confers multidrug resistance phenotypes to their hosts. Unlike members of the SGI1 group, these novel genomic islands target the 5’ end dusA or the 3’ end of yicC, lack multidrug resistance genes, and seem much more diverse. We showed here that, like SGI1, these elements are mobilized by conjugative plasmids of the IncC group. Based on comparative genomics and functional analyses, we propose a hypothetical model of the evolution of SGI1 and its siblings from the progenitor of IncA and IncC conjugative plasmids via an intermediate dusA-specific integrative element through gene losses and gain of alternative integration/excision modules.
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Affiliation(s)
- Romain Durand
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Florence Deschênes
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Vincent Burrus
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
- * E-mail:
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Durand R, Huguet KT, Rivard N, Carraro N, Rodrigue S, Burrus V. Crucial role of Salmonella genomic island 1 master activator in the parasitism of IncC plasmids. Nucleic Acids Res 2021; 49:7807-7824. [PMID: 33834206 PMCID: PMC8373056 DOI: 10.1093/nar/gkab204] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 12/26/2022] Open
Abstract
IncC conjugative plasmids and the multiple variants of Salmonella Genomic Island 1 (SGI1) are two functionally interacting families of mobile genetic elements commonly associated with multidrug resistance in the Gammaproteobacteria. SGI1 and its siblings are specifically mobilised in trans by IncC conjugative plasmids. Conjugative transfer of IncC plasmids is activated by the plasmid-encoded master activator AcaCD. SGI1 carries five AcaCD-responsive promoters that drive the expression of genes involved in its excision, replication, and mobilisation. SGI1 encodes an AcaCD homologue, the transcriptional activator complex SgaCD (also known as FlhDCSGI1) that seems to recognise and activate the same SGI1 promoters. Here, we investigated the relevance of SgaCD in SGI1's lifecycle. Mating assays revealed the requirement for SgaCD and its IncC-encoded counterpart AcaCD in the mobilisation of SGI1. An integrative approach combining ChIP-exo, Cappable-seq, and RNA-seq confirmed that SgaCD activates each of the 18 AcaCD-responsive promoters driving the expression of the plasmid transfer functions. A comprehensive analysis of the activity of the complete set of AcaCD-responsive promoters of SGI1 and the helper IncC plasmid was performed through reporter assays. qPCR and flow cytometry assays revealed that SgaCD is essential to elicit the excision and replication of SGI1 and destabilise the helper IncC plasmid.
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Affiliation(s)
- Romain Durand
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Kévin T Huguet
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Nicolas Rivard
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Nicolas Carraro
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Vincent Burrus
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
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48
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Dechêne-Tempier M, Marois-Créhan C, Libante V, Jouy E, Leblond-Bourget N, Payot S. Update on the Mechanisms of Antibiotic Resistance and the Mobile Resistome in the Emerging Zoonotic Pathogen Streptococcus suis. Microorganisms 2021; 9:microorganisms9081765. [PMID: 34442843 PMCID: PMC8401462 DOI: 10.3390/microorganisms9081765] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022] Open
Abstract
Streptococcus suis is a zoonotic pathogen causing important economic losses in swine production. The most commonly used antibiotics in swine industry are tetracyclines, beta-lactams, and macrolides. Resistance to these antibiotics has already been observed worldwide (reaching high rates for macrolides and tetracyclines) as well as resistance to aminoglycosides, fluoroquinolones, amphenicols, and glycopeptides. Most of the resistance mechanisms are encoded by antibiotic resistance genes, and a large part are carried by mobile genetic elements (MGEs) that can be transferred through horizontal gene transfer. This review provides an update of the resistance genes, their combination in multidrug isolates, and their localization on MGEs in S. suis. It also includes an overview of the contribution of biofilm to antimicrobial resistance in this bacterial species. The identification of resistance genes and study of their localization in S. suis as well as the environmental factors that can modulate their dissemination appear essential in order to decipher the role of this bacterium as a reservoir of antibiotic genes for other species.
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Affiliation(s)
- Manon Dechêne-Tempier
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, F-22440 Ploufragan, France; (M.D.-T.); (C.M.-C.); (E.J.)
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (V.L.); (N.L.-B.)
| | - Corinne Marois-Créhan
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, F-22440 Ploufragan, France; (M.D.-T.); (C.M.-C.); (E.J.)
| | - Virginie Libante
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (V.L.); (N.L.-B.)
| | - Eric Jouy
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, F-22440 Ploufragan, France; (M.D.-T.); (C.M.-C.); (E.J.)
| | | | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (V.L.); (N.L.-B.)
- Correspondence:
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49
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Smith TJ, Tian R, Imanian B, Williamson CHD, Johnson SL, Daligault HE, Schill KM. Integration of Complete Plasmids Containing Bont Genes into Chromosomes of Clostridium parabotulinum, Clostridium sporogenes, and Clostridium argentinense. Toxins (Basel) 2021; 13:473. [PMID: 34357945 PMCID: PMC8310154 DOI: 10.3390/toxins13070473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022] Open
Abstract
At least 40 toxin subtypes of botulinum neurotoxins (BoNTs), a heterogenous group of bacterial proteins, are produced by seven different clostridial species. A key factor that drives the diversity of neurotoxigenic clostridia is the association of bont gene clusters with various genomic locations including plasmids, phages and the chromosome. Analysis of Clostridium sporogenes BoNT/B1 strain CDC 1632, C. argentinense BoNT/G strain CDC 2741, and Clostridium parabotulinum BoNT/B1 strain DFPST0006 genomes revealed bont gene clusters within plasmid-like sequences within the chromosome or nested in large contigs, with no evidence of extrachromosomal elements. A nucleotide sequence (255,474 bp) identified in CDC 1632 shared 99.5% identity (88% coverage) with bont/B1-containing plasmid pNPD7 of C. sporogenes CDC 67071; CDC 2741 contig AYSO01000020 (1.1 MB) contained a ~140 kb region which shared 99.99% identity (100% coverage) with plasmid pRSJ17_1 of C. argentinense BoNT/G strain 89G; and DFPST0006 contig JACBDK0100002 (573 kb) contained a region that shared 100% identity (99%) coverage with the bont/B1-containing plasmid pCLD of C. parabotulinum Okra. This is the first report of full-length plasmid DNA-carrying complete neurotoxin gene clusters integrated in three distinct neurotoxigenic species: C. parabotulinum, C. sporogenes and C. argentinense.
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Affiliation(s)
- Theresa J. Smith
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (T.J.S.); (C.H.D.W.)
| | - Renmao Tian
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL 60501, USA; (R.T.); (B.I.)
| | - Behzad Imanian
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL 60501, USA; (R.T.); (B.I.)
- Food Science and Nutrition, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Charles H. D. Williamson
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (T.J.S.); (C.H.D.W.)
| | - Shannon L. Johnson
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (S.L.J.); (H.E.D.)
| | | | - Kristin M. Schill
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Bedford Park, IL 60501, USA
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50
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Morgado SM, Paulo Vicente AC. Genomics of Atlantic Forest Mycobacteriaceae strains unravels a mobilome diversity with a novel integrative conjugative element and plasmids harbouring T7SS. Microb Genom 2021; 6. [PMID: 32496186 PMCID: PMC7478629 DOI: 10.1099/mgen.0.000382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mobile genetic elements (MGEs) are agents of bacterial evolution and adaptation. Genome sequencing provides an unbiased approach that has revealed an abundance of MGEs in prokaryotes, mainly plasmids and integrative conjugative elements. Nevertheless, many mobilomes, particularly those from environmental bacteria, remain underexplored despite their representing a reservoir of genes that can later emerge in the clinic. Here, we explored the mobilome of the Mycobacteriaceae family, focusing on strains from Brazilian Atlantic Forest soil. Novel Mycolicibacterium and Mycobacteroides strains were identified, with the former ones harbouring linear and circular plasmids encoding the specialized type-VII secretion system (T7SS) and mobility-associated genes. In addition, we also identified a T4SS-mediated integrative conjugative element (ICEMyc226) encoding two T7SSs and a number of xenobiotic degrading genes. Our study uncovers the diversity of the Mycobacteriaceae mobilome, providing the evidence of an ICE in this bacterial family. Moreover, the presence of T7SS genes in an ICE, as well as plasmids, highlights the role of these mobile genetic elements in the dispersion of T7SS.
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