1
|
Lian ZJ, Phan MD, Hancock SJ, Nhu NTK, Paterson DL, Schembri MA. Genetic basis of I-complex plasmid stability and conjugation. PLoS Genet 2023; 19:e1010773. [PMID: 37347771 DOI: 10.1371/journal.pgen.1010773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/05/2023] [Indexed: 06/24/2023] Open
Abstract
Plasmids are major drivers of increasing antibiotic resistance, necessitating an urgent need to understand their biology. Here we describe a detailed dissection of the molecular components controlling the genetics of I-complex plasmids, a group of antibiotic resistance plasmids found frequently in pathogenic Escherichia coli and other Enterobacteriaceae that cause significant human disease. We show these plasmids cluster into four distinct subgroups, with the prototype IncI1 plasmid R64 subgroup displaying low nucleotide sequence conservation to other I-complex plasmids. Using pMS7163B, an I-complex plasmid distantly related to R64, we performed a high-resolution transposon-based genetic screen and defined genes involved in replication, stability, and conjugative transfer. We identified the replicon and a partitioning system as essential for replication/stability. Genes required for conjugation included the type IV secretion system, relaxosome, and several uncharacterised genes located in the pMS7163B leading transfer region that exhibited an upstream strand-specific transposon insertion bias. The overexpression of these genes severely impacted host cell growth or reduced fitness during mixed competitive growth, demonstrating that their expression must be controlled to avoid deleterious impacts. These genes were present in >80% of all I-complex plasmids and broadly conserved across multiple plasmid incompatibility groups, implicating an important role in plasmid dissemination.
Collapse
Affiliation(s)
- Zheng Jie Lian
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Minh-Duy Phan
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Steven J Hancock
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Nguyen Thi Khanh Nhu
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - David L Paterson
- The University of Queensland Centre for Clinical Research, Brisbane, Australia
| | - Mark A Schembri
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|
2
|
Das A, Doss K, Mandal J. CRISPR-cas heterogeneity and plasmid incompatibility types in relation to virulence determinants of Shigella. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Virulence factors (VFs) are the most potent weapon in the molecular armoury of
Shigella
. In bacteria, the mobile genetic elements (MGEs) are contributors to the evolution of different types of clustered regularly interspaced short palindromic repeats-CRISPR associated genes (CRISPR-cas) variants and plasmid incompatibility types. The present study explored the virulence potential of
Shigella
in relation to the CRISPR-cas pattern and incompatibility types among the isolates.
Hypothesis/Gap Statement. The profile of the CRISPR-cas systems among clinical isolates of
Shigella
in India has not been reported earlier. Limited knowledge is available on the pattern of plasmid incompatibility groups among clinical isolates
Shigella
. The bias is always towards studying the genetic elements associated with AMR, but the present study highlights CRISPR-cas and incompatibility types among
Shigella
in association with virulence.
Aim. We aimed to investigate the distribution of virulence factors, CRISPR-cas pattern followed by plasmid incompatibility types among
Shigella
isolates.
Methodology. Between 2012–2017, a total of 187 isolates of
Shigella
were included in the study. The virulence genes' distribution was carried out. CRISPR-cas profiling followed by analysis of the repeats and spacers was carried out. PCR-based replicon typing was used to determine the incompatibility types. The interplay was statistically determined using STATA.
Results. The distribution of virulence genes showed varied pattern with ipaH present in all the isolates followed by ompA (93.6 %), virF (66.8 %), ial and sen (60.4 %), set1A (39.6 %) and set1B (39 %). CRISPR 1, CRISPR 3 and Cas6-Cas5 region were dominantly conserved. Twenty-two types of spacers were identified. The CRISPR3 repeat appeared to have a highly conserved sequence. CRISPR2 being the least common CRISPR type showed a strong association with an array of virulence genes (ial-set1A-set1B-virF) while CRISPR1 being the most dominant showed the least association with virulence genes (sen-virF). The dominant plasmids were found to be belonging to the inc FII group. The incompatibility groups FII, IncIγ, U, FIIS, FIIK, K, A/C, I1alpha was found to be associated with a greater number of virulence genes.
Conclusion. The isolates showed increasing diversity in their gene content that contributes to increasing heterogeneity among the isolates, which is a known virulence strategy among pathogens.
Collapse
Affiliation(s)
- Ankita Das
- Department of Microbiology, Jawaharlal Nehru Institute of Postgraduate Medical Institute and Research (JIPMER), Dhanvantri Nagar, Gorimedu, Pondicherry-605006, India
| | - Kamali Doss
- Jawaharlal Nehru Institute of Postgraduate Medical Institute and Research (JIPMER), Dhanvantri Nagar, Gorimedu, Pondicherry-605006, India
| | - Jharna Mandal
- Department of Microbiology, Jawaharlal Nehru Institute of Postgraduate Medical Institute and Research (JIPMER), Dhanvantri Nagar, Gorimedu, Pondicherry-605006, India
| |
Collapse
|
3
|
Pallares-Vega R, Macedo G, Brouwer MSM, Hernandez Leal L, van der Maas P, van Loosdrecht MCM, Weissbrodt DG, Heederik D, Mevius D, Schmitt H. Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains. Front Microbiol 2021; 12:656250. [PMID: 34349732 PMCID: PMC8326584 DOI: 10.3389/fmicb.2021.656250] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmid-mediated dissemination of antibiotic resistance among fecal Enterobacteriaceae in natural ecosystems may contribute to the persistence of antibiotic resistance genes in anthropogenically impacted environments. Plasmid transfer frequencies measured under laboratory conditions might lead to overestimation of plasmid transfer potential in natural ecosystems. This study assessed differences in the conjugative transfer of an IncP-1 (pKJK5) plasmid to three natural Escherichia coli strains carrying extended-spectrum beta-lactamases, by filter mating. Matings were performed under optimal laboratory conditions (rich LB medium and 37°C) and environmentally relevant temperatures (25, 15 and 9°C) or nutrient regimes mimicking environmental conditions and limitations (synthetic wastewater and soil extract). Under optimal nutrient conditions and temperature, two recipients yielded high transfer frequencies (5 × 10-1) while the conjugation frequency of the third strain was 1000-fold lower. Decreasing mating temperatures to psychrophilic ranges led to lower transfer frequencies, albeit all three strains conjugated under all the tested temperatures. Low nutritive media caused significant decreases in transconjugants (-3 logs for synthetic wastewater; -6 logs for soil extract), where only one of the strains was able to produce detectable transconjugants. Collectively, this study highlights that despite less-than-optimal conditions, fecal organisms may transfer plasmids in the environment, but the transfer of pKJK5 between microorganisms is limited mainly by low nutrient conditions.
Collapse
Affiliation(s)
- Rebeca Pallares-Vega
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
- Department Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Gonçalo Macedo
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Michael S. M. Brouwer
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Lucia Hernandez Leal
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
| | - Peter van der Maas
- Van Hall Larenstein, University of Applied Sciences, Leeuwarden, Netherlands
| | | | - David G. Weissbrodt
- Department Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Dick Heederik
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Dik Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Heike Schmitt
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
4
|
Neil K, Allard N, Rodrigue S. Molecular Mechanisms Influencing Bacterial Conjugation in the Intestinal Microbiota. Front Microbiol 2021; 12:673260. [PMID: 34149661 PMCID: PMC8213034 DOI: 10.3389/fmicb.2021.673260] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/10/2021] [Indexed: 12/26/2022] Open
Abstract
Bacterial conjugation is a widespread and particularly efficient strategy to horizontally disseminate genes in microbial populations. With a rich and dense population of microorganisms, the intestinal microbiota is often considered a fertile environment for conjugative transfer and a major reservoir of antibiotic resistance genes. In this mini-review, we summarize recent findings suggesting that few conjugative plasmid families present in Enterobacteriaceae transfer at high rates in the gut microbiota. We discuss the importance of mating pair stabilization as well as additional factors influencing DNA transfer efficiency and conjugative host range in this environment. Finally, we examine the potential repurposing of bacterial conjugation for microbiome editing.
Collapse
Affiliation(s)
- Kevin Neil
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Nancy Allard
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Sébastien Rodrigue
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| |
Collapse
|