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Breidenstein A, Lamy A, Bader CP, Sun WS, Wanrooij PH, Berntsson RPA. PrgE: an OB-fold protein from plasmid pCF10 with striking differences to prototypical bacterial SSBs. Life Sci Alliance 2024; 7:e202402693. [PMID: 38811160 PMCID: PMC11137577 DOI: 10.26508/lsa.202402693] [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: 03/05/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/31/2024] Open
Abstract
A major pathway for horizontal gene transfer is the transmission of DNA from donor to recipient cells via plasmid-encoded type IV secretion systems (T4SSs). Many conjugative plasmids encode for a single-stranded DNA-binding protein (SSB) together with their T4SS. Some of these SSBs have been suggested to aid in establishing the plasmid in the recipient cell, but for many, their function remains unclear. Here, we characterize PrgE, a proposed SSB from the Enterococcus faecalis plasmid pCF10. We show that PrgE is not essential for conjugation. Structurally, it has the characteristic OB-fold of SSBs, but it has very unusual DNA-binding properties. Our DNA-bound structure shows that PrgE binds ssDNA like beads on a string supported by its N-terminal tail. In vitro studies highlight the plasticity of PrgE oligomerization and confirm the importance of the N-terminus. Unlike other SSBs, PrgE binds both double- and single-stranded DNA equally well. This shows that PrgE has a quaternary assembly and DNA-binding properties that are very different from the prototypical bacterial SSB, but also different from eukaryotic SSBs.
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Affiliation(s)
- Annika Breidenstein
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- https://ror.org/05kb8h459 Wallenberg Centre for Molecular Medicine and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Anaïs Lamy
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- https://ror.org/05kb8h459 Wallenberg Centre for Molecular Medicine and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Cyrielle Pj Bader
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Wei-Sheng Sun
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- https://ror.org/05kb8h459 Wallenberg Centre for Molecular Medicine and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Paulina H Wanrooij
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Ronnie P-A Berntsson
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- https://ror.org/05kb8h459 Wallenberg Centre for Molecular Medicine and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
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2
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Al Mamun AAM, Kissoon K, Li YG, Hancock E, Christie PJ. The F plasmid conjutome: the repertoire of E. coli proteins translocated through an F-encoded type IV secretion system. mSphere 2024; 9:e0035424. [PMID: 38940509 PMCID: PMC11288057 DOI: 10.1128/msphere.00354-24] [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: 04/25/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024] Open
Abstract
Bacterial conjugation systems pose a major threat to human health through their widespread dissemination of mobile genetic elements (MGEs) carrying cargoes of antibiotic resistance genes. Using the Cre Recombinase Assay for Translocation (CRAfT), we recently reported that the IncFV pED208 conjugation system also translocates at least 16 plasmid-encoded proteins to recipient bacteria. Here, we deployed a high-throughput CRAfT screen to identify the repertoire of chromosomally encoded protein substrates of the pED208 system. We identified 32 substrates encoded by the Escherichia coli W3110 genome with functions associated with (i) DNA/nucleotide metabolism, (ii) stress tolerance/physiology, (iii) transcriptional regulation, or (iv) toxin inhibition. The respective gene deletions did not impact pED208 transfer proficiencies, nor did Group 1 (DNA/nucleotide metabolism) mutations detectably alter the SOS response elicited in new transconjugants upon acquisition of pED208. However, MC4100(pED208) donor cells intrinsically exhibit significantly higher SOS activation than plasmid-free MC4100 cells, and this plasmid carriage-induced stress response is further elevated in donor cells deleted of several Group 1 genes. Among 10 characterized substrates, we gained evidence of C-terminal or internal translocation signals that could function independently or synergistically for optimal protein transfer. Remarkably, nearly all tested proteins were also translocated through the IncN pKM101 and IncP RP4 conjugation systems. This repertoire of E. coli protein substrates, here termed the F plasmid "conjutome," is thus characterized by functions of potential benefit to new transconjugants, diverse TSs, and the capacity for promiscuous transfer through heterologous conjugation systems. IMPORTANCE Conjugation systems comprise a major subfamily of the type IV secretion systems (T4SSs) and are the progenitors of a second large T4SS subfamily dedicated to translocation of protein effectors. This study examined the capacity of conjugation machines to function as protein translocators. Using a high-throughput reporter screen, we determined that 32 chromosomally encoded proteins are delivered through an F plasmid conjugation system. The translocated proteins potentially enhance the establishment of the co-transferred F plasmid or mitigate mating-induced stresses. Translocation signals located C-terminally or internally conferred substrate recognition by the F system and, remarkably, many substrates also were translocated through heterologous conjugation systems. Our findings highlight the plasticity of conjugation systems in their capacities to co-translocate DNA and many protein substrates.
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Affiliation(s)
- Abu Amar M. Al Mamun
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Kimberley Kissoon
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Yang Grace Li
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Erin Hancock
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, USA
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3
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Christi K, Hudson J, Egan S. Current approaches to genetic modification of marine bacteria and considerations for improved transformation efficiency. Microbiol Res 2024; 284:127729. [PMID: 38663232 DOI: 10.1016/j.micres.2024.127729] [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: 10/18/2023] [Revised: 02/25/2024] [Accepted: 04/15/2024] [Indexed: 05/26/2024]
Abstract
Marine bacteria play vital roles in symbiosis, biogeochemical cycles and produce novel bioactive compounds and enzymes of interest for the pharmaceutical, biofuel and biotechnology industries. At present, investigations into marine bacterial functions and their products are primarily based on phenotypic observations, -omic type approaches and heterologous gene expression. To advance our understanding of marine bacteria and harness their full potential for industry application, it is critical that we have the appropriate tools and resources to genetically manipulate them in situ. However, current genetic tools that are largely designed for model organisms such as E. coli, produce low transformation efficiencies or have no transfer ability in marine bacteria. To improve genetic manipulation applications for marine bacteria, we need to improve transformation methods such as conjugation and electroporation in addition to identifying more marine broad host range plasmids. In this review, we aim to outline the reported methods of transformation for marine bacteria and discuss the considerations for each approach in the context of improving efficiency. In addition, we further discuss marine plasmids and future research areas including CRISPR tools and their potential applications for marine bacteria.
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Affiliation(s)
- Katrina Christi
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia
| | - Jennifer Hudson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia.
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4
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Ma T, Xie N, Gao Y, Fu J, Tan CE, Yang QE, Wang S, Shen Z, Ji Q, Parkhill J, Wu C, Wang Y, Walsh TR, Shen J. VirBR, a transcription regulator, promotes IncX3 plasmid transmission, and persistence of bla NDM-5 in zoonotic bacteria. Nat Commun 2024; 15:5498. [PMID: 38944647 PMCID: PMC11214620 DOI: 10.1038/s41467-024-49800-1] [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: 10/12/2023] [Accepted: 06/18/2024] [Indexed: 07/01/2024] Open
Abstract
IncX3 plasmids carrying the New Delhi metallo-β-lactamase-encoding gene, blaNDM-5, are rapidly spreading globally in both humans and animals. Given that carbapenems are listed on the WHO AWaRe watch group and are prohibited for use in animals, the drivers for the successful dissemination of Carbapenem-Resistant Enterobacterales (CRE) carrying blaNDM-5-IncX3 plasmids still remain unknown. We observe that E. coli carrying blaNDM-5-IncX3 can persist in chicken intestines either under the administration of amoxicillin, one of the largest veterinary β-lactams used in livestock, or without any antibiotic pressure. We therefore characterise the blaNDM-5-IncX3 plasmid and identify a transcription regulator, VirBR, that binds to the promoter of the regulator gene actX enhancing the transcription of Type IV secretion systems (T4SS); thereby, promoting conjugation of IncX3 plasmids, increasing pili adhesion capacity and enhancing the colonisation of blaNDM-5-IncX3 transconjugants in animal digestive tracts. Our mechanistic and in-vivo studies identify VirBR as a major factor in the successful spread of blaNDM-5-IncX3 across one-health AMR sectors. Furthermore, VirBR enhances the plasmid conjugation and T4SS expression by the presence of copper and zinc ions, thereby having profound ramifications on the use of universal animal feeds.
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Affiliation(s)
- Tengfei Ma
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ning Xie
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yuan Gao
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jiani Fu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chun E Tan
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qiu E Yang
- College of Environment and Resources, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shaolin Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhangqi Shen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Quanjiang Ji
- School of Physical Science and Technology, Shanghai Tech University, Shanghai, China
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Congming Wu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yang Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China.
| | - Timothy R Walsh
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, Oxford, UK.
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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5
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Fraikin N, Couturier A, Lesterlin C. The winding journey of conjugative plasmids toward a novel host cell. Curr Opin Microbiol 2024; 78:102449. [PMID: 38432159 DOI: 10.1016/j.mib.2024.102449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 03/05/2024]
Abstract
Horizontal transfer of plasmids by conjugation is a fundamental mechanism driving the widespread dissemination of drug resistance among bacterial populations. The successful colonization of a new host cell necessitates the plasmid to navigate through a series of sequential steps, each dependent on specific plasmid or host factors. This review explores recent advancements in comprehending the cellular and molecular mechanisms that govern plasmid transmission, establishment, and long-term maintenance. Adopting a plasmid-centric perspective, we describe the critical steps and bottlenecks in the plasmid's journey toward a new host cell, encompassing exploration and contact initiation, invasion, establishment and control, and assimilation.
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Affiliation(s)
- Nathan Fraikin
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007 Lyon, France
| | - Agathe Couturier
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007 Lyon, France
| | - Christian Lesterlin
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007 Lyon, France.
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6
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Liu Z, Gao Y, Wang M, Liu Y, Wang F, Shi J, Wang Z, Li R. Adaptive evolution of plasmid and chromosome contributes to the fitness of a blaNDM-bearing cointegrate plasmid in Escherichia coli. THE ISME JOURNAL 2024; 18:wrae037. [PMID: 38438143 PMCID: PMC10976473 DOI: 10.1093/ismejo/wrae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/08/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Large cointegrate plasmids recruit genetic features of their parental plasmids and serve as important vectors in the spread of antibiotic resistance. They are now frequently found in clinical settings, raising the issue of how to limit their further transmission. Here, we conducted evolutionary research of a large blaNDM-positive cointegrate within Escherichia coli C600, and discovered that adaptive evolution of chromosome and plasmid jointly improved bacterial fitness, which was manifested as enhanced survival ability for in vivo and in vitro pairwise competition, biofilm formation, and gut colonization ability. From the plasmid aspect, large-scale DNA fragment loss is observed in an evolved clone. Although the evolved plasmid imposes a negligible fitness cost on host bacteria, its conjugation frequency is greatly reduced, and the deficiency of anti-SOS gene psiB is found responsible for the impaired horizontal transferability rather than the reduced fitness cost. These findings unveil an evolutionary strategy in which the plasmid horizontal transferability and fitness cost are balanced. From the chromosome perspective, all evolved clones exhibit parallel mutations in the transcriptional regulatory stringent starvation Protein A gene sspA. Through a sspA knockout mutant, transcriptome analysis, in vitro transcriptional activity assay, RT-qPCR, motility test, and scanning electron microscopy techniques, we demonstrated that the mutation in sspA reduces its transcriptional inhibitory capacity, thereby improving bacterial fitness, biofilm formation ability, and gut colonization ability by promoting bacterial flagella synthesis. These findings expand our knowledge of how cointegrate plasmids adapt to new bacterial hosts.
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Affiliation(s)
- Ziyi Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- College of Animal Science and Technology & College of Veterinary medicine, Zhejiang Agriculture and Forestry University, Hangzhou, 311300 Zhejiang Province, People's Republic of China
| | - Yanyun Gao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
| | - Mianzhi Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
| | - Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
| | - Fulin Wang
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 Jiangsu Province, People's Republic of China
| | - Jing Shi
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 Jiangsu Province, People's Republic of China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Institute of Agricultural Science and Technology Development, Yangzhou, 225009 Jiangsu Province, People's Republic of China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
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7
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Wang B, Finazzo M, Artsimovitch I. Machine Learning Suggests That Small Size Helps Broaden Plasmid Host Range. Genes (Basel) 2023; 14:2044. [PMID: 38002987 PMCID: PMC10670969 DOI: 10.3390/genes14112044] [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: 10/15/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Plasmids mediate gene exchange across taxonomic barriers through conjugation, shaping bacterial evolution for billions of years. While plasmid mobility can be harnessed for genetic engineering and drug-delivery applications, rapid plasmid-mediated spread of resistance genes has rendered most clinical antibiotics useless. To solve this urgent and growing problem, we must understand how plasmids spread across bacterial communities. Here, we applied machine-learning models to identify features that are important for extending the plasmid host range. We assembled an up-to-date dataset of more than thirty thousand bacterial plasmids, separated them into 1125 clusters, and assigned each cluster a distribution possibility score, taking into account the host distribution of each taxonomic rank and the sampling bias of the existing sequencing data. Using this score and an optimized plasmid feature pool, we built a model stack consisting of DecisionTreeRegressor, EvoTreeRegressor, and LGBMRegressor as base models and LinearRegressor as a meta-learner. Our mathematical modeling revealed that sequence brevity is the most important determinant for plasmid spread, followed by P-loop NTPases, mobility factors, and β-lactamases. Ours and other recent results suggest that small plasmids may broaden their range by evading host defenses and using alternative modes of transfer instead of autonomous conjugation.
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Affiliation(s)
- Bing Wang
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA;
| | | | - Irina Artsimovitch
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA;
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8
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Li YG, Kishida K, Ogawa-Kishida N, Christie PJ. Ligand-displaying Escherichia coli cells and minicells for programmable delivery of toxic payloads via type IV secretion systems. mBio 2023; 14:e0214323. [PMID: 37772866 PMCID: PMC10653926 DOI: 10.1128/mbio.02143-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 08/17/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE The rapid emergence of drug-resistant bacteria and current low rate of antibiotic discovery emphasize the urgent need for alternative antibacterial strategies. We engineered Escherichia coli to conjugatively transfer plasmids to specific E. coli and Pseudomonas aeruginosa recipient cells through the surface display of cognate nanobody/antigen (Nb/Ag) pairs. We further engineered mobilizable plasmids to carry CRISPR/Cas9 systems (pCrispr) for the selective killing of recipient cells harboring CRISPR/Cas9 target sequences. In the assembled programmed delivery system (PDS), Nb-displaying E. coli donors with different conjugation systems and mobilizable pCrispr plasmids suppressed the growth of Ag-displaying recipient cells to significantly greater extents than unpaired recipients. We also showed that anucleate minicells armed with conjugation machines and pCrispr plasmids were highly effective in killing E. coli recipients. Together, our findings suggest that bacteria or minicells armed with PDSs may prove highly effective as an adjunct or alternative to antibiotics for antimicrobial intervention.
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Affiliation(s)
- Yang Grace Li
- Department of Microbiology and Molecular Genetics, McGovern School of Medicine, University of Texas Health Science Center, Houston, Texas, USA
| | - Kouhei Kishida
- Department of Microbiology and Molecular Genetics, McGovern School of Medicine, University of Texas Health Science Center, Houston, Texas, USA
| | - Natsumi Ogawa-Kishida
- Department of Microbiology and Molecular Genetics, McGovern School of Medicine, University of Texas Health Science Center, Houston, Texas, USA
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics, McGovern School of Medicine, University of Texas Health Science Center, Houston, Texas, USA
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9
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Li YG, Kishida K, Ogawa-Kishida N, Christie PJ. Ligand-Displaying E. coli Cells and Minicells for Programmable Delivery of Toxic Payloads via Type IV Secretion Systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.553016. [PMID: 37609324 PMCID: PMC10441419 DOI: 10.1101/2023.08.11.553016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Bacterial type IV secretion systems (T4SSs) are highly versatile macromolecular translocators and offer great potential for deployment as delivery systems for therapeutic intervention. One major T4SS subfamily, the conjugation machines, are well-adapted for delivery of DNA cargoes of interest to other bacteria or eukaryotic cells, but generally exhibit modest transfer frequencies and lack specificity for target cells. Here, we tested the efficacy of a surface-displayed nanobody/antigen (Nb/Ag) pairing system to enhance the conjugative transfer of IncN (pKM101), IncF (F/pOX38), or IncP (RP4) plasmids, or of mobilizable plasmids including those encoding CRISPR/Cas9 systems (pCrispr), to targeted recipient cells. Escherichia coli donors displaying Nb's transferred plasmids to E. coli and Pseudomonas aeruginosa recipients displaying the cognate Ag's at significantly higher frequencies than to recipients lacking Ag's. Nb/Ag pairing functionally substituted for the surface adhesin activities of F-encoded TraN and pKM101-encoded Pep, although not conjugative pili or VirB5-like adhesins. Nb/Ag pairing further elevated the killing effects accompanying delivery of pCrispr plasmids to E. coli and P. aeruginosa transconjugants bearing CRISPR/Cas9 target sequences. Finally, we determined that anucleate E. coli minicells, which are clinically safer delivery vectors than intact cells, transferred self-transmissible and mobilizable plasmids to E. coli and P. aeruginosa cells. Minicell-mediated mobilization of pCrispr plasmids to E. coli recipients elicited significant killing of transconjugants, although Nb/Ag pairing did not enhance conjugation frequencies or killing. Together, our findings establish the potential for deployment of bacteria or minicells as Programmed Delivery Systems (PDSs) for suppression of targeted bacterial species in infection settings. IMPORTANCE The rapid emergence of drug-resistant bacteria and current low rate of antibiotic discovery emphasize an urgent need for alternative antibacterial strategies. We engineered Escherichia coli to conjugatively transfer plasmids to specific E. coli and Pseudomonas aeruginosa recipient cells through surface display of cognate nanobody/antigen (Nb/Ag) pairs. We further engineered mobilizable plasmids to carry CRISPR/Cas9 systems (pCrispr) for selective killing of recipient cells harboring CRISPR/Cas9 target sequences. In the assembled Programmed Delivery System (PDS), Nb-displaying E. coli donors with different conjugation systems and mobilizable pCrispr plasmids suppressed growth of Ag-displaying recipient cells to significantly greater extents than unpaired recipients. We also showed that anucleate minicells armed with conjugation machines and pCrispr plasmids were highly effective in killing of E. coli recipients. Together, our findings suggest that bacteria or minicells armed with PDSs may prove highly effective as an adjunct or alternative to antibiotics for antimicrobial intervention.
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Affiliation(s)
- Yang Grace Li
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, Texas 77030
| | - Kouhei Kishida
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, Texas 77030
- Current address: Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aobaku, Sendai, 980-8577, Japan
| | - Natsumi Ogawa-Kishida
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, Texas 77030
- Current address: Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aobaku, Sendai, 980-8577, Japan
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, Texas 77030
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10
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Cooke MB, Herman C. Conjugation's Toolkit: the Roles of Nonstructural Proteins in Bacterial Sex. J Bacteriol 2023; 205:e0043822. [PMID: 36847532 PMCID: PMC10029717 DOI: 10.1128/jb.00438-22] [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] [Indexed: 03/01/2023] Open
Abstract
Bacterial conjugation, a form of horizontal gene transfer, relies on a type 4 secretion system (T4SS) and a set of nonstructural genes that are closely linked. These nonstructural genes aid in the mobile lifestyle of conjugative elements but are not part of the T4SS apparatus for conjugative transfer, such as the membrane pore and relaxosome, or the plasmid maintenance and replication machineries. While these nonstructural genes are not essential for conjugation, they assist in core conjugative functions and mitigate the cellular burden on the host. This review compiles and categorizes known functions of nonstructural genes by the stage of conjugation they modulate: dormancy, transfer, and new host establishment. Themes include establishing a commensalistic relationship with the host, manipulating the host for efficient T4SS assembly and function and assisting in conjugative evasion of recipient cell immune functions. These genes, taken in a broad ecological context, play important roles in ensuring proper propagation of the conjugation system in a natural environment.
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Affiliation(s)
- Matthew B. Cooke
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
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11
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Shen M, Goldlust K, Daniel S, Lesterlin C, Yamaichi Y. Recipient UvrD helicase is involved in single- to double-stranded DNA conversion during conjugative plasmid transfer. Nucleic Acids Res 2023; 51:2790-2799. [PMID: 36772829 PMCID: PMC10085688 DOI: 10.1093/nar/gkad075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/22/2023] [Accepted: 01/24/2023] [Indexed: 02/12/2023] Open
Abstract
Dissemination of antibiotic resistance, a current societal challenge, is often driven by horizontal gene transfer through bacterial conjugation. During conjugative plasmid transfer, single-stranded (ss) DNA is transferred from the donor to the recipient cell. Subsequently, a complete double-stranded (ds) plasmid molecule is generated and plasmid-encoded genes are expressed, allowing successful establishment of the transconjugant cell. Such dynamics of transmission can be modulated by host- or plasmid-encoded factors, either in the donor or in the recipient cell. We applied transposon insertion sequencing to identify host-encoded factors that affect conjugative transfer frequency in Escherichia coli. Disruption of the recipient uvrD gene decreased the acquisition frequency of conjugative plasmids belonging to different incompatibility groups. Results from various UvrD mutants suggested that dsDNA binding activity and interaction with RNA polymerase are dispensable, but ATPase activity is required for successful plasmid establishment of transconjugant cells. Live-cell microscopic imaging showed that the newly transferred ssDNA within a uvrD- recipient often failed to be converted to dsDNA. Our work suggested that in addition to its role in maintaining genome integrity, UvrD is also key for the establishment of horizontally acquired plasmid DNA that drives genome diversity and evolution.
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Affiliation(s)
- Minjia Shen
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.,Graduate School of Structure and Dynamics of Living Systems, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Kelly Goldlust
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Sandra Daniel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Christian Lesterlin
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Yoshiharu Yamaichi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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12
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Couturier A, Virolle C, Goldlust K, Berne-Dedieu A, Reuter A, Nolivos S, Yamaichi Y, Bigot S, Lesterlin C. Real-time visualisation of the intracellular dynamics of conjugative plasmid transfer. Nat Commun 2023; 14:294. [PMID: 36653393 PMCID: PMC9849209 DOI: 10.1038/s41467-023-35978-3] [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: 10/05/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Conjugation is a contact-dependent mechanism for the transfer of plasmid DNA between bacterial cells, which contributes to the dissemination of antibiotic resistance. Here, we use live-cell microscopy to visualise the intracellular dynamics of conjugative transfer of F-plasmid in E. coli, in real time. We show that the transfer of plasmid in single-stranded form (ssDNA) and its subsequent conversion into double-stranded DNA (dsDNA) are fast and efficient processes that occur with specific timing and subcellular localisation. Notably, the ssDNA-to-dsDNA conversion determines the timing of plasmid-encoded protein production. The leading region that first enters the recipient cell carries single-stranded promoters that allow the early and transient synthesis of leading proteins immediately upon entry of the ssDNA plasmid. The subsequent conversion into dsDNA turns off leading gene expression, and activates the expression of other plasmid genes under the control of conventional double-stranded promoters. This molecular strategy allows for the timely production of factors sequentially involved in establishing, maintaining and disseminating the plasmid.
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Affiliation(s)
- Agathe Couturier
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Chloé Virolle
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Kelly Goldlust
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Annick Berne-Dedieu
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Audrey Reuter
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Sophie Nolivos
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Yoshiharu Yamaichi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sarah Bigot
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France.
| | - Christian Lesterlin
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France.
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13
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Xiao X, Liu Z, Chen X, Peng K, Li R, Liu Y, Wang Z. Persistence of plasmid and tet(X4) in an Escherichia coli isolate coharboring blaNDM-5 and mcr-1 after acquiring an IncFII tet(X4)-positive plasmid. Front Microbiol 2022; 13:1010387. [PMID: 36338060 PMCID: PMC9626518 DOI: 10.3389/fmicb.2022.1010387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/26/2022] [Indexed: 11/19/2022] Open
Abstract
The prevalence of plasmid-mediated tigecycline resistance gene tet(X4) is presenting an increasing trend. Once tet(X4)-bearing plasmids are captured by multidrug-resistant bacteria, such as blaNDM and mcr-coharboring bacteria, it will promote bacteria to develop an ultra-broad resistance spectrum, limiting clinical treatment options. However, little is known about the destiny of such bacteria or how they will evolve in the future. Herein, we constructed a multidrug-resistant bacteria coharboring tet(X4), blaNDM-5, and mcr-1 by introducing a tet(X4)-bearing plasmid into a blaNDM-5 and mcr-1 positive E. coli strain. Subsequently, the stability of tet(X4) and the plasmid was measured after being evolved under tigecycline or antibiotic-free circumstance. Interestingly, we observed both tet(X4)-bearing plasmids in tigecycline treated strains and non-tigecycline treated strains were stable, which might be jointly affected by the increased conjugation frequency and the structural alterations of the tet(X4)-positive plasmid. However, the stability of tet(X4) gene showed different scenarios in the two types of evolved strains. The tet(X4) gene in non-tigecycline treated strains was stable whereas the tet(X4) gene was discarded rapidly in tigecycline treated strains. Accordingly, we found the expression levels of tet(X4) gene in tigecycline-treated strains were several times higher than in non-tigecycline treated strains and ancestral strains, which might in turn impose a stronger burden on the host bacteria. SNPs analysis revealed that a myriad of mutations occurred in genes involving in conjugation transfer, and the missense mutation of marR gene in chromosome of tigecycline treated strains might account for the completely different stability of tet(X4)-bearing plasmid and tet(X4) gene. Collectively, these findings shed a light on the possibility of the emergence of multidrug resistant bacteria due to the transmission of tet(X4)-bearing plasmid, and highlighted that the antibiotic residues may be critical to the development of such bacteria.
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Affiliation(s)
- Xia Xiao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
| | - Ziyi Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
| | - Xiaojun Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
| | - Kai Peng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- *Correspondence: Zhiqiang Wang,
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14
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Lima-Noronha MA, Fonseca DLH, Oliveira RS, Freitas RR, Park JH, Galhardo RS. Sending out an SOS - the bacterial DNA damage response. Genet Mol Biol 2022; 45:e20220107. [PMID: 36288458 PMCID: PMC9578287 DOI: 10.1590/1678-4685-gmb-2022-0107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/15/2022] [Indexed: 11/04/2022] Open
Abstract
The term “SOS response” was first coined by Radman in 1974, in an intellectual effort to put together the data suggestive of a concerted gene expression program in cells undergoing DNA damage. A large amount of information about this cellular response has been collected over the following decades. In this review, we will focus on a few of the relevant aspects about the SOS response: its mechanism of control and the stressors which activate it, the diversity of regulated genes in different species, its role in mutagenesis and evolution including the development of antimicrobial resistance, and its relationship with mobile genetic elements.
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Affiliation(s)
- Marco A. Lima-Noronha
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Douglas L. H. Fonseca
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Renatta S. Oliveira
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Rúbia R. Freitas
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Jung H. Park
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Rodrigo S. Galhardo
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
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15
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Al Mamun AAM, Kissoon K, Kishida K, Shropshire WC, Hanson B, Christie PJ. IncFV plasmid pED208: Sequence analysis and evidence for translocation of maintenance/leading region proteins through diverse type IV secretion systems. Plasmid 2022; 123-124:102652. [PMID: 36228885 PMCID: PMC10018792 DOI: 10.1016/j.plasmid.2022.102652] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/02/2022] [Accepted: 10/04/2022] [Indexed: 12/04/2022]
Abstract
Two phylogenetically distantly-related IncF plasmids, F and pED208, serve as important models for mechanistic and structural studies of F-like type IV secretion systems (T4SSFs) and F pili. Here, we present the pED208 sequence and compare it to F and pUMNF18, the closest match to pED208 in the NCBI database. As expected, gene content of the three cargo regions varies extensively, although the maintenance/leading regions (MLRs) and transfer (Tra) regions also carry novel genes or motifs with predicted modulatory effects on plasmid stability, dissemination and host range. By use of a Cre recombinase assay for translocation (CRAfT), we recently reported that pED208-carrying donors translocate several products of the MLR (ParA, ParB1, ParB2, SSB, PsiB, PsiA) intercellularly through the T4SSF. Here, we extend these findings by reporting that pED208-carrying donors translocate 10 additional MLR proteins during conjugation. In contrast, two F plasmid-encoded toxin components of toxin-antitoxin (TA) modules, CcdB and SrnB, were not translocated at detectable levels through the T4SSF. Remarkably, most or all of the pED208-encoded MLR proteins and CcdB and SrnB were translocated through heterologous T4SSs encoded by IncN and IncP plasmids pKM101 and RP4, respectively. Together, our sequence analyses underscore the genomic diversity of the F plasmid superfamily, and our experimental data demonstrate the promiscuous nature of conjugation machines for protein translocation. Our findings raise intriguing questions about the nature of T4SS translocation signals and of the biological and evolutionary consequences of conjugative protein transfer.
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Affiliation(s)
- Abu Amar M Al Mamun
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, TX 77030, United States of America.
| | - Kimberly Kissoon
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, TX 77030, United States of America
| | - Kouhei Kishida
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, TX 77030, United States of America
| | - William C Shropshire
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA; Center for Infectious Diseases, University of Texas Health Science Center, School of Public Health, Houston, TX, USA
| | - Blake Hanson
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA; Center for Infectious Diseases, University of Texas Health Science Center, School of Public Health, Houston, TX, USA
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, TX 77030, United States of America.
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16
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Kürekci C, Lu X, Celil BG, Disli HB, Mohsin M, Wang Z, Li R. Emergence and Characterization of Tigecycline Resistance Gene tet(X4) in ST609 Escherichia coli Isolates from Wastewater in Turkey. Microbiol Spectr 2022; 10:e0073222. [PMID: 35863037 PMCID: PMC9431179 DOI: 10.1128/spectrum.00732-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/27/2022] [Indexed: 12/31/2022] Open
Abstract
Emergence of pathogens harboring tigecycline resistance genes incurs great concerns. Wastewater is recognized as the important reservoir of antimicrobial resistance genes. Here we characterized the phenotypes and genotypes of bacteria carrying tet(X4) from wastewater in Turkey for the first time. Four tet(X4)-positive Escherichia coli isolates were identified and characterized by PCR, Sanger sequencing, antimicrobial susceptibility testing, conjugation assays, Illumina sequencing, nanopore sequencing and bioinformatic analysis. Four tet(X4)-harboring isolates were multidrug-resistant (MDR) bacteria and the tet(X4) gene was nontransferable in four isolates. Genetic analysis revealed that tet(X4) genes in four isolates were located on plasmids co-harboring two replicons IncFIA(HI1) and IncFIB(K). However, none of the four plasmids carried genes associated with horizontal transfer of plasmids. The coexistence of blaSHV-12-bearing IncX3-type plasmid and tet(X4)-harboring plasmid was also found in one isolate. These findings indicate that continuous surveillance of the tet(X4)-bearing isolates in different environments worldwide should be strengthened. IMPORTANCE The emergence of tigecycline resistance genes in humans and animals in China seriously threatens the clinical utility of tigecycline, but the molecular epidemiology of tigecycline-resistant bacteria in other countries remained largely unknown. Therefore, it is necessary to learn the prevalence and molecular characteristics of bacteria carrying tigecycline resistance genes, particularly the mobilizable tet(X4), in other countries. In the study, we first described the presence and molecular characteristics of the tet(X4)-positive E. coli isolates from wastewater in Turkey. Four tet(X4)-bearing isolates belonged to ST609, an E. coli clone commonly found from humans, animals and the environment. These findings highlight the importance of monitoring the tet(X4) gene in different settings globally.
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Affiliation(s)
- Cemil Kürekci
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Hatay Mustafa Kemal University, Hatay, Turkey
| | - Xiaoyu Lu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, P. R. China
| | - Büsra Gülay Celil
- Graduate School of Health Sciences, Hatay Mustafa Kemal University, Hatay, Turkey
| | - Hüseyin Burak Disli
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Hatay Mustafa Kemal University, Hatay, Turkey
| | - Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, P. R. China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, P. R. China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu Province, P. R. China
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17
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Eisenreich W, Rudel T, Heesemann J, Goebel W. Link Between Antibiotic Persistence and Antibiotic Resistance in Bacterial Pathogens. Front Cell Infect Microbiol 2022; 12:900848. [PMID: 35928205 PMCID: PMC9343593 DOI: 10.3389/fcimb.2022.900848] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022] Open
Abstract
Both, antibiotic persistence and antibiotic resistance characterize phenotypes of survival in which a bacterial cell becomes insensitive to one (or even) more antibiotic(s). However, the molecular basis for these two antibiotic-tolerant phenotypes is fundamentally different. Whereas antibiotic resistance is genetically determined and hence represents a rather stable phenotype, antibiotic persistence marks a transient physiological state triggered by various stress-inducing conditions that switches back to the original antibiotic sensitive state once the environmental situation improves. The molecular basics of antibiotic resistance are in principle well understood. This is not the case for antibiotic persistence. Under all culture conditions, there is a stochastically formed, subpopulation of persister cells in bacterial populations, the size of which depends on the culture conditions. The proportion of persisters in a bacterial population increases under different stress conditions, including treatment with bactericidal antibiotics (BCAs). Various models have been proposed to explain the formation of persistence in bacteria. We recently hypothesized that all physiological culture conditions leading to persistence converge in the inability of the bacteria to re-initiate a new round of DNA replication caused by an insufficient level of the initiator complex ATP-DnaA and hence by the lack of formation of a functional orisome. Here, we extend this hypothesis by proposing that in this persistence state the bacteria become more susceptible to mutation-based antibiotic resistance provided they are equipped with error-prone DNA repair functions. This is - in our opinion - in particular the case when such bacterial populations are exposed to BCAs.
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Affiliation(s)
- Wolfgang Eisenreich
- Bavarian NMR Center – Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
- *Correspondence: Wolfgang Eisenreich,
| | - Thomas Rudel
- Chair of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jürgen Heesemann
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
| | - Werner Goebel
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
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18
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Kishida K, Bosserman RE, Harb L, Khara P, Song L, Hu B, Zeng L, Christie PJ. Contributions of F‐specific Subunits to the F
Plasmid‐Encoded
Type
IV
Secretion System and F pilus. Mol Microbiol 2022; 117:1275-1290. [DOI: 10.1111/mmi.14908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/26/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Kouhei Kishida
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
| | - Rachel E. Bosserman
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
- Current address: Department of Medicine, Division of Infectious Diseases Washington School of Medicine St. Louis, MO, 63110
| | - Laith Harb
- Department of Biochemistry and Biophysics, Texas A&M University College Station TX, 77843 USA
- Center for Phage Technology, Texas A&M University College Station TX, 77843 USA
| | - Pratick Khara
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
| | - Liqiang Song
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
| | - Bo Hu
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University College Station TX, 77843 USA
- Center for Phage Technology, Texas A&M University College Station TX, 77843 USA
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
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19
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Shen Z, Tang CM, Liu GY. Towards a better understanding of antimicrobial resistance dissemination: what can be learnt from studying model conjugative plasmids? Mil Med Res 2022; 9:3. [PMID: 35012680 PMCID: PMC8744291 DOI: 10.1186/s40779-021-00362-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/26/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria can evolve rapidly by acquiring new traits such as virulence, metabolic properties, and most importantly, antimicrobial resistance, through horizontal gene transfer (HGT). Multidrug resistance in bacteria, especially in Gram-negative organisms, has become a global public health threat often through the spread of mobile genetic elements. Conjugation represents a major form of HGT and involves the transfer of DNA from a donor bacterium to a recipient by direct contact. Conjugative plasmids, a major vehicle for the dissemination of antimicrobial resistance, are selfish elements capable of mediating their own transmission through conjugation. To spread to and survive in a new bacterial host, conjugative plasmids have evolved mechanisms to circumvent both host defense systems and compete with co-resident plasmids. Such mechanisms have mostly been studied in model plasmids such as the F plasmid, rather than in conjugative plasmids that confer antimicrobial resistance (AMR) in important human pathogens. A better understanding of these mechanisms is crucial for predicting the flow of antimicrobial resistance-conferring conjugative plasmids among bacterial populations and guiding the rational design of strategies to halt the spread of antimicrobial resistance. Here, we review mechanisms employed by conjugative plasmids that promote their transmission and establishment in Gram-negative bacteria, by following the life cycle of conjugative plasmids.
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Affiliation(s)
- Zhen Shen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.,Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Guang-Yu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
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