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Penadés JR, Seed KD, Chen J, Bikard D, Rocha EPC. Genetics, ecology and evolution of phage satellites. Nat Rev Microbiol 2025:10.1038/s41579-025-01156-z. [PMID: 40148600 DOI: 10.1038/s41579-025-01156-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2025] [Indexed: 03/29/2025]
Abstract
Phage satellites are defined as viruses that have a life cycle dependent on a helper virus. Thus, they are often considered as parasites of parasites, although recent work suggests it may be more accurate to consider them as symbionts that evolved along a parasitism-mutualism continuum. Over the past years, multiple studies have examined the fascinating life cycle of these elements, focusing on the characterization of the molecular mechanisms they use to hijack the helper phage machinery for their own packaging and transfer. As some phage satellites encode toxins and other virulence and resistance genes, the impact of these elements on bacterial virulence has also been extensively analysed. Recent studies suggest that satellites have unprecedented roles in the ecology and evolution of bacteria and their mobile genetic elements. In this Review, we explore the genetics and the life cycle of these elements, with special emphasis on the new mechanisms involved in their spread in nature. We discuss the unexpected impact of these elements on the evolution of other mobile genetic elements and their host bacteria, and examine their potential origins.
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Affiliation(s)
- José R Penadés
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK.
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
- School of Health Sciences, Universidad CEU Cardenal Herrera, CEU Universities, Alfara del Patriarca, Spain.
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - John Chen
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - David Bikard
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Synthetic Biology, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
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Ortiz-Cartagena C, Fernández-Grela P, Armán L, Blasco L, Pablo-Marcos D, Bleriot I, Fernández-García L, Ibarguren-Quiles C, Fernández-Cuenca F, Barrio-Pujante A, Aracil B, Calvo-Montes J, Tomás M. The LAMP-CRISPR-Cas13a technique for detecting the CBASS mechanism of phage resistance in bacteria. Front Microbiol 2025; 16:1550534. [PMID: 40196034 PMCID: PMC11973324 DOI: 10.3389/fmicb.2025.1550534] [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: 12/23/2024] [Accepted: 03/03/2025] [Indexed: 04/09/2025] Open
Abstract
Introduction Antimicrobial resistance (AMR) is a major public health threat, driving the need for alternative treatments such as phage therapy. However, bacterial defense mechanisms, often regulated by the quorum sensing (QS) network and encoded in genomic islands (GIs), can generate phage-resistant mutants. Understanding these resistance mechanisms is essential for optimizing phage therapy. Methods This study analyzed 48 Klebsiella pneumoniae strains to identify pathogenicity islands (PAIs) containing anti-phage defense (APD) proteins. We constructed a knockout strain lacking the cyclase gene from the type II CBASS defense systems present in PAIs to investigate QS regulation and its role in cell viability. The LAMP-CRISPR-Cas13a technique was used to confirm gene knockout and to detect the main cyclase in type I CBASS systems, i.e., APECO1. Results A total of 309 pathogenicity islands (PAIs), containing 22.1% of anti-phage defense (APD) proteins, were identified. Type I and II CBASS APD systems were also detected in the genome of the 48, K. pneumoniae strains, and only two type II CBASS systems were located in PAIs. Alluding to these defense mechanisms, the QS revealed to be involved in the regulation of the type II CBASS systems contained in PAIs. Finally, the LAMP-CRISPR-Cas13a technology successfully detected the main cyclases habored in type I and II CBASS systems, respectively. Discussion The study findings highlight the regulatory role of the QS network in APD systems. Notably, this is the first study to develop an innovative biotechnological application for the LAMP-CRISPR-Cas13a rapid-technique (<2 h), thereby helping to optimize phage therapy by detecting bacterial resistance mechanisms and predicting the potential inefficacy of therapeutic phages and thus improving patient prognosis.
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Affiliation(s)
- Concha Ortiz-Cartagena
- Departamento de Microbiología-Hospital A Coruña (HUAC), Grupo de Microbiología Traslacional y Multidisciplinar (Micro-TM), A Coruña, Spain
- Grupo de Estudio de Mecanismos de Acción y Resistencia a los Antimicrobianos (GEMARA) en nombre de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - Patricia Fernández-Grela
- Departamento de Microbiología-Hospital A Coruña (HUAC), Grupo de Microbiología Traslacional y Multidisciplinar (Micro-TM), A Coruña, Spain
- Grupo de Estudio de Mecanismos de Acción y Resistencia a los Antimicrobianos (GEMARA) en nombre de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - Lucia Armán
- Departamento de Microbiología-Hospital A Coruña (HUAC), Grupo de Microbiología Traslacional y Multidisciplinar (Micro-TM), A Coruña, Spain
- Grupo de Estudio de Mecanismos de Acción y Resistencia a los Antimicrobianos (GEMARA) en nombre de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - Lucía Blasco
- Departamento de Microbiología-Hospital A Coruña (HUAC), Grupo de Microbiología Traslacional y Multidisciplinar (Micro-TM), A Coruña, Spain
- Grupo de Estudio de Mecanismos de Acción y Resistencia a los Antimicrobianos (GEMARA) en nombre de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - Daniel Pablo-Marcos
- Grupo de Estudio de Mecanismos de Acción y Resistencia a los Antimicrobianos (GEMARA) en nombre de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
- Microbiology Service, University Hospital Marqués de Valdecilla—IDIVAL, Santander, Spain
| | - Inés Bleriot
- Departamento de Microbiología-Hospital A Coruña (HUAC), Grupo de Microbiología Traslacional y Multidisciplinar (Micro-TM), A Coruña, Spain
- Grupo de Estudio de Mecanismos de Acción y Resistencia a los Antimicrobianos (GEMARA) en nombre de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - Laura Fernández-García
- Departamento de Microbiología-Hospital A Coruña (HUAC), Grupo de Microbiología Traslacional y Multidisciplinar (Micro-TM), A Coruña, Spain
- Grupo de Estudio de Mecanismos de Acción y Resistencia a los Antimicrobianos (GEMARA) en nombre de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - Clara Ibarguren-Quiles
- Departamento de Microbiología-Hospital A Coruña (HUAC), Grupo de Microbiología Traslacional y Multidisciplinar (Micro-TM), A Coruña, Spain
- Grupo de Estudio de Mecanismos de Acción y Resistencia a los Antimicrobianos (GEMARA) en nombre de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - Felipe Fernández-Cuenca
- Grupo de Estudio de Mecanismos de Acción y Resistencia a los Antimicrobianos (GEMARA) en nombre de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
- Microbiology Service, University Hospital Virgen Macarena-IBIS, Seville, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Antonio Barrio-Pujante
- Departamento de Microbiología-Hospital A Coruña (HUAC), Grupo de Microbiología Traslacional y Multidisciplinar (Micro-TM), A Coruña, Spain
- Grupo de Estudio de Mecanismos de Acción y Resistencia a los Antimicrobianos (GEMARA) en nombre de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - Belén Aracil
- Grupo de Estudio de Mecanismos de Acción y Resistencia a los Antimicrobianos (GEMARA) en nombre de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Laboratorio de Referencia e Investigación de Resistencias Antibióticas e Infecciones Sanitarias, Centro Nacional de Microbiología, ISCIII, Majadahonda, Spain
| | - Jorge Calvo-Montes
- Grupo de Estudio de Mecanismos de Acción y Resistencia a los Antimicrobianos (GEMARA) en nombre de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
- Microbiology Service, University Hospital Marqués de Valdecilla—IDIVAL, Santander, Spain
| | - María Tomás
- Departamento de Microbiología-Hospital A Coruña (HUAC), Grupo de Microbiología Traslacional y Multidisciplinar (Micro-TM), A Coruña, Spain
- Grupo de Estudio de Mecanismos de Acción y Resistencia a los Antimicrobianos (GEMARA) en nombre de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
- MEPRAM, Proyecto de Medicina de Precisión contra las resistencias Antimicrobianas, ISCIII, Majadahonda, Spain
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Wang B, Farhan MHR, Yuan L, Sui Y, Chu J, Yang X, Li Y, Huang L, Cheng G. Transfer dynamics of antimicrobial resistance among gram-negative bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176347. [PMID: 39306135 DOI: 10.1016/j.scitotenv.2024.176347] [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: 04/28/2024] [Revised: 09/09/2024] [Accepted: 09/15/2024] [Indexed: 09/26/2024]
Abstract
Antimicrobial resistance (AMR) in gram-negative bacteria (GNBs) is a significant global health concern, exacerbated by mobile genetic elements (MGEs). This review examines the transfer of antibiotic resistance genes (ARGs) within and between different species of GNB facilitated by MGEs, focusing on the roles of plasmids and phages. The impact of non-antibiotic chemicals, environmental factors affecting ARG transfer frequency, and underlying molecular mechanisms of bacterial resistance evolution are also discussed. Additionally, the study critically assesses the impact of fitness costs and compensatory evolution driven by MGEs in host organisms, shedding light on the transfer frequency of ARGs and host evolution within ecosystems. Overall, this comprehensive review highlights the factors and mechanisms influencing ARG movement among diverse GNB species and underscores the importance of implementing holistic One-Health strategies to effectively address the escalating public health challenges associated with AMR.
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Affiliation(s)
- Bangjuan Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Muhammad Haris Raza Farhan
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Linlin Yuan
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuxin Sui
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinhua Chu
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaohan Yang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuxin Li
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lingli Huang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Guyue Cheng
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.
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Wang Q, Wang M, Yang Q, Feng L, Zhang H, Wang R, Wang R. The role of bacteriophages in facilitating the horizontal transfer of antibiotic resistance genes in municipal wastewater treatment plants. WATER RESEARCH 2024; 268:122776. [PMID: 39541852 DOI: 10.1016/j.watres.2024.122776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 10/23/2024] [Accepted: 11/08/2024] [Indexed: 11/16/2024]
Abstract
Bacteriophages play integral roles in the ecosystem; however, their precise involvement in horizontal gene transfer and the spread of antibiotic resistance genes (ARGs) are not fully understood. In this study, a coculture system involving consortia of bacteriophages and multidrug-resistant bacteria from an aerobic tank in a municipal wastewater treatment plant (WWTP) was established to investigate the functions of bacteriophages in ARG transfer and spread. The results of the cocultivation of the MRB and bacteriophage consortia indicated that the bacterial community remained stable throughout the whole process, but the addition of bacteriophages significantly increased ARG abundance, especially in bacteriophage DNA. Nine out of the 11 identified ARGs significantly increased, indicating that more bacteriophage particles carried ARGs in the system after cocultivation. In addition, 686 plasmids were detected during cocultivation, of which only 3.36 % were identified as conjugative plasmids, which is significantly lower than the proportion found among previously published plasmids (25.2 %, totaling 14,029 plasmids). Our findings revealed that bacteriophages may play important roles in the horizontal transfer of ARGs through both bacteriophage-mediated conduction and an increase in extracellular ARGs; however, conjugative transfer may not be the main mechanism by which multidrug-resistant bacteria acquire and spread ARGs. Unlike in most previous reports, a coculture system of diverse bacteria and bacteriophages was established in this study to assess bacteriophage functions in ARG transfer and dissemination in the environment, overcoming the limitations associated with the isolation of bacteria and bacteriophages, as well as the specificity of bacteriophage hosts.
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Affiliation(s)
- Qiang Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology (Henan Provincial Department of Science and Technology), Henan Normal University, Xinxiang 453007, China
| | - Min Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Qingxiang Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology (Henan Provincial Department of Science and Technology), Henan Normal University, Xinxiang 453007, China.
| | - Lingran Feng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology (Henan Provincial Department of Science and Technology), Henan Normal University, Xinxiang 453007, China
| | - Hao Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology (Henan Provincial Department of Science and Technology), Henan Normal University, Xinxiang 453007, China
| | - Ruifei Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology (Henan Provincial Department of Science and Technology), Henan Normal University, Xinxiang 453007, China
| | - Ruimin Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology (Henan Provincial Department of Science and Technology), Henan Normal University, Xinxiang 453007, China
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Androsiuk L, Maane S, Tal S. CRISPR spacers acquired from plasmids primarily target backbone genes, making them valuable for predicting potential hosts and host range. Microbiol Spectr 2024; 12:e0010424. [PMID: 39508585 PMCID: PMC11619364 DOI: 10.1128/spectrum.00104-24] [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: 01/15/2024] [Accepted: 09/16/2024] [Indexed: 11/15/2024] Open
Abstract
In recent years, there has been a surge in metagenomic studies focused on identifying plasmids in environmental samples. Although these studies have unearthed numerous novel plasmids, enriching our understanding of their environmental roles, a significant gap remains: the scarcity of information regarding the bacterial hosts of these newly discovered plasmids. Furthermore, even when plasmids are identified within bacterial isolates, the reported host is typically limited to the original isolate, with no insights into alternative hosts or the plasmid's potential host range. Given that plasmids depend on hosts for their existence, investigating plasmids without the knowledge of potential hosts offers only a partial perspective. This study introduces a method for identifying potential hosts and host ranges for plasmids through alignment with CRISPR spacers. To validate the method, we compared the PLSDB plasmids database with the CRISPR spacers database, yielding host predictions for 46% of the plasmids. When compared with reported hosts, our predictions achieved 84% concordance at the family level and 99% concordance at the phylum level. Moreover, the method frequently identified multiple potential hosts for a plasmid, thereby enabling predictions of alternative hosts and the host range. Notably, we found that CRISPR spacers predominantly target plasmid backbone genes while sparing functional genes, such as those linked to antibiotic resistance, aligning with our hypothesis that CRISPR spacers are acquired from plasmid-specific regions rather than insertion elements from diverse sources. Finally, we illustrate the network of connections among different bacterial taxa through plasmids, revealing potential pathways for horizontal gene transfer.IMPORTANCEPlasmids are notorious for their role in distributing antibiotic resistance genes, but they may also carry and distribute other environmentally important genes. Since plasmids are not free-living entities and rely on host bacteria for survival and propagation, predicting their hosts is essential. This study presents a method for predicting potential hosts for plasmids and offers insights into the potential paths for spreading functional genes between different bacteria. Understanding plasmid-host relationships is crucial for comprehending the ecological and clinical impact of plasmids and implications for various biological processes.
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Affiliation(s)
- Lucy Androsiuk
- Marine Biology and Biotechnology Program, Department of Life Sciences, Ben-Gurion University of the Negev Eilat Campus, Eilat, Israel
- Israel Oceanographic & Limnological Research Ltd., National Center for Mariculture, Eilat, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Sivan Maane
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shay Tal
- Israel Oceanographic & Limnological Research Ltd., National Center for Mariculture, Eilat, Israel
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Vos M, Buckling A, Kuijper B, Eyre-Walker A, Bontemps C, Leblond P, Dimitriu T. Why do mobile genetic elements transfer DNA of their hosts? Trends Genet 2024; 40:927-938. [PMID: 39304387 DOI: 10.1016/j.tig.2024.07.008] [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: 06/04/2024] [Revised: 07/23/2024] [Accepted: 07/23/2024] [Indexed: 09/22/2024]
Abstract
The prokaryote world is replete with mobile genetic elements (MGEs) - self-replicating entities that can move within and between their hosts. Many MGEs not only transfer their own DNA to new hosts but also transfer host DNA located elsewhere on the chromosome in the process. This could potentially lead to indirect benefits to the host when the resulting increase in chromosomal variation results in more efficient natural selection. We review the diverse ways in which MGEs promote the transfer of host DNA and explore the benefits and costs to MGEs and hosts. In many cases, MGE-mediated transfer of host DNA might not be selected for because of a sex function, but evidence of MGE domestication suggests that there may be host benefits of MGE-mediated sex.
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Affiliation(s)
- Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, Penryn TR10 9FE, UK; Environment and Sustainability Institute, University of Exeter, Penryn TR10 9FE, UK.
| | - Angus Buckling
- Environment and Sustainability Institute, University of Exeter, Penryn TR10 9FE, UK
| | - Bram Kuijper
- Centre for Ecology and Conservation, University of Exeter, Penryn TR10 9FE, UK
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Cyril Bontemps
- Université de Lorraine, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), DynAMic, F-54000 Nancy, France
| | - Pierre Leblond
- Université de Lorraine, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), DynAMic, F-54000 Nancy, France
| | - Tatiana Dimitriu
- Environment and Sustainability Institute, University of Exeter, Penryn TR10 9FE, UK; Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
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Ma Z, Qian C, Yao Z, Tang M, Chen K, Zhao D, Hu P, Zhou T, Cao J. Coexistence of plasmid-mediated tmexCD2-toprJ2, blaIMP-4, and blaNDM-1 in Klebsiella quasipneumoniae. Microbiol Spectr 2024; 12:e0387423. [PMID: 39162556 PMCID: PMC11448383 DOI: 10.1128/spectrum.03874-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 07/07/2024] [Indexed: 08/21/2024] Open
Abstract
Klebsiella quasipneumoniae is a potential pathogen that has not been studied comprehensively. The emergence of multidrug-resistant (MDR) K. quasipneumoniae, specifically strains resistant to tigecycline and carbapenem, presents a significant challenge to clinical treatment. This investigation aimed to characterize MDR K. quasipneumoniae strain FK8966, co-carrying tmexCD2-toprJ2, blaIMP-4, and blaNDM-1 by plasmids. It was observed that FK8966's MDR was primarily because of the IncHI1B-like plasmid co-carrying tmexCD2-toprJ2 and blaIMP-4, and an IncFIB(K)/IncFII(K) plasmid harboring blaNDM-1. Furthermore, the phylogenetic analysis revealed that IncHI1B-like plasmids carrying tmexCD2-toprJ2 were disseminated among different bacteria, specifically in China. Additionally, according to the comparative genomic analysis, the MDR regions indicated that the tmexCD2-toprJ2 gene cluster was inserted into the umuC gene, while blaIMP-4 was present in transposon TnAs3 linked to the class 1 integron (IntI1). It was also observed that an ΔTn3000 insertion with blaNDM-1 made a novel blaNDM-1 harboring IncFIB(K)/IncFII(K) plasmid. The antimicrobial resistance prevalence and phylogenetic analyses of K. quasipneumoniae strains indicated that FK8966 is a distinct MDR branch of K. quasipneumoniae. Furthermore, CRISPR-Cas system analysis showed that many K. quasipneumoniae CRISPR-Cas systems lacked spacers matching the two aforementioned novel resistance plasmids, suggesting that these resistance plasmids have the potential to disseminate within K. quasipneumoniae. Therefore, the spread of MDR K. quasipneumoniae and plasmids warrants further attention.IMPORTANCEThe emergence of multidrug-resistant K. quasipneumoniae poses a great threat to clinical care, and the situation is exacerbated by the dissemination of tigecycline- and carbapenem-resistant genes. Therefore, monitoring these pathogens and their resistance plasmids is urgent and crucial. This study identified tigecycline- and carbapenem-resistant K. quasipneumoniae strain, FK8966. Furthermore, it is the first study to report the coexistence of tmexCD2-toprJ2, blaIMP-4, and blaNDM-1 in K. quasipneumoniae. Moreover, the CRISPR-Cas system of many K. quasipneumoniae lacks spacers that match the plasmids carried by FK8966, which are crucial for mediating resistance against tigecycline and carbapenems, indicating their potential to disseminate within K. quasipneumoniae.
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Affiliation(s)
- Zhexiao Ma
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Changrui Qian
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Zhuocheng Yao
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Miran Tang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Kaixin Chen
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Deyi Zhao
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Panjie Hu
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Tieli Zhou
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jianming Cao
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
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Trosvik P, Noordzij HT, de Muinck EJ. Antibiotic resistance gene dynamics in the commensal infant gut microbiome over the first year of life. Sci Rep 2024; 14:18701. [PMID: 39134593 PMCID: PMC11319485 DOI: 10.1038/s41598-024-69275-w] [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: 04/24/2024] [Accepted: 08/02/2024] [Indexed: 08/15/2024] Open
Abstract
Colonization of the infant gut is an important developmental process characterized by high carriage of antimicrobial resistance genes (ARGs) and high abundances of pathobionts. The horizontal transfer of ARGs to pathogenic bacteria represents a major public health concern. However, there is still a paucity of longitudinal studies surveilling ARGs in healthy infant guts at high temporal resolution. Furthermore, we do not yet have a clear view of how temporal variation in ARG carriage relates to the dynamics of specific bacterial populations, as well as community virulence potential. Here, we performed deep shotgun metagenomic sequencing of monthly fecal samples from a cohort of 12 infants, covering the first year of life to interrogate the infant gut microbiome for ARG content. We further relate ARG dynamics to the dynamics of taxa, virulence potential, as well as the potential for ARG mobilization. We identify a core resistome dominated by efflux systems typically associated with Enterobacteriaceae. Overall ARG carriage declined over the first year of life and showed strong contemporaneous correlation with the population dynamics of Proteobacteria. Furthermore, the majority of ARGs could be further mapped to metagenome-assembled genomes (MAGs) classified to this phylum. We were able to assign a large number of ARGs to E. coli by correlating the temporal dynamics of individual genes with species dynamics, and we show that the temporal dynamics of ARGs and virulence factors are highly correlated, suggesting close taxonomic associations between these two gene classes. Finally, we identify ARGs linked with various categories of mobile genetic elements, demonstrating preferential linkage among mobility categories and resistance to different drug classes. While individual variation in ARG carriage is substantial during infancy there is a clear reduction over the first year of life. With few exceptions, ARG abundances closely track the dynamics of pathobionts and community virulence potential. These findings emphasize the potential for development of resistant pathogens in the developing infant gut, and the importance of effective surveillance in order to detect such events.
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Affiliation(s)
- Pål Trosvik
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Hanna Theodora Noordzij
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Eric Jacques de Muinck
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Pharmacy, University of Oslo, Oslo, Norway
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9
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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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10
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Cyriaque V, Ibarra-Chávez R, Kuchina A, Seelig G, Nesme J, Madsen JS. Single-cell RNA sequencing reveals plasmid constrains bacterial population heterogeneity and identifies a non-conjugating subpopulation. Nat Commun 2024; 15:5853. [PMID: 38997267 PMCID: PMC11245611 DOI: 10.1038/s41467-024-49793-x] [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: 03/13/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024] Open
Abstract
Transcriptional heterogeneity in isogenic bacterial populations can play various roles in bacterial evolution, but its detection remains technically challenging. Here, we use microbial split-pool ligation transcriptomics to study the relationship between bacterial subpopulation formation and plasmid-host interactions at the single-cell level. We find that single-cell transcript abundances are influenced by bacterial growth state and plasmid carriage. Moreover, plasmid carriage constrains the formation of bacterial subpopulations. Plasmid genes, including those with core functions such as replication and maintenance, exhibit transcriptional heterogeneity associated with cell activity. Notably, we identify a cell subpopulation that does not transcribe conjugal plasmid transfer genes, which may help reduce plasmid burden on a subset of cells. Our study advances the understanding of plasmid-mediated subpopulation dynamics and provides insights into the plasmid-bacteria interplay.
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Affiliation(s)
- Valentine Cyriaque
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark.
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, Mons, Belgium.
| | | | - Anna Kuchina
- Institute for Systems Biology, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
| | - Georg Seelig
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
- Paul G. Allen School for Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Joseph Nesme
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
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11
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Beamud B, Benz F, Bikard D. Going viral: The role of mobile genetic elements in bacterial immunity. Cell Host Microbe 2024; 32:804-819. [PMID: 38870898 DOI: 10.1016/j.chom.2024.05.017] [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: 03/25/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024]
Abstract
Bacteriophages and other mobile genetic elements (MGEs) pose a significant threat to bacteria, subjecting them to constant attacks. In response, bacteria have evolved a sophisticated immune system that employs diverse defensive strategies and mechanisms. Remarkably, a growing body of evidence suggests that most of these defenses are encoded by MGEs themselves. This realization challenges our traditional understanding of bacterial immunity and raises intriguing questions about the evolutionary forces at play. Our review provides a comprehensive overview of the latest findings on the main families of MGEs and the defense systems they encode. We also highlight how a vast diversity of defense systems remains to be discovered and their mechanism of mobility understood. Altogether, the composition and distribution of defense systems in bacterial genomes only makes sense in the light of the ecological and evolutionary interactions of a complex network of MGEs.
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Affiliation(s)
- Beatriz Beamud
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France.
| | - Fabienne Benz
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | - David Bikard
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France.
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12
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Notarbartolo V, Badiane BA, Insinga V, Giuffrè M. Antimicrobial Stewardship: A Correct Management to Reduce Sepsis in NICU Settings. Antibiotics (Basel) 2024; 13:520. [PMID: 38927186 PMCID: PMC11200753 DOI: 10.3390/antibiotics13060520] [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: 04/25/2024] [Revised: 05/25/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
The discovery of antimicrobial drugs has led to a significant increase in survival from infections; however, they are very often prescribed and administered, even when their use is not necessary and appropriate. Newborns are particularly exposed to infections due to the poor effectiveness and the immaturity of their immune systems. For this reason, in Neonatal Intensive Care Units (NICUs), the use of antimicrobial drugs is often decisive and life-saving, and it must be started promptly to ensure its effectiveness in consideration of the possible rapid evolution of the infection towards sepsis. Nevertheless, the misuse of antibiotics in the neonatal period leads not only to an increase in the development and wide spreading of antimicrobial resistance (AMR) but it is also associated with various short-term (e.g., alterations of the microbiota) and long-term (e.g., increased risk of allergic disease and obesity) effects. It appears fundamental to use antibiotics only when strictly necessary; specific decision-making algorithms and electronic calculators can help limit the use of unnecessary antibiotic drugs. The aim of this narrative review is to summarize the right balance between the risks and benefits of antimicrobial therapy in NICUs; for this purpose, specific Antimicrobial Stewardship Programs (ASPs) in neonatal care and the creation of a specific antimicrobial stewardship team are requested.
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Affiliation(s)
- Veronica Notarbartolo
- Neonatology and Neonatal Intensive Care Unit, University Hospital “Paolo Giaccone”, 90127 Palermo, Italy;
| | - Bintu Ayla Badiane
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, 90127 Palermo, Italy; (B.A.B.); (M.G.)
| | - Vincenzo Insinga
- Neonatology and Neonatal Intensive Care Unit, University Hospital “Paolo Giaccone”, 90127 Palermo, Italy;
| | - Mario Giuffrè
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, 90127 Palermo, Italy; (B.A.B.); (M.G.)
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13
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Turchi B, Campobasso C, Nardinocchi A, Wagemans J, Torracca B, Lood C, Di Giuseppe G, Nieri P, Bertelloni F, Turini L, Ruffo V, Lavigne R, Di Luca M. Isolation and characterization of novel Staphylococcus aureus bacteriophage Hesat from dairy origin. Appl Microbiol Biotechnol 2024; 108:299. [PMID: 38619619 PMCID: PMC11018700 DOI: 10.1007/s00253-024-13129-y] [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: 09/05/2023] [Revised: 03/05/2024] [Accepted: 03/27/2024] [Indexed: 04/16/2024]
Abstract
A novel temperate phage, named Hesat, was isolated by the incubation of a dairy strain of Staphylococcus aureus belonging to spa-type t127 with either bovine or ovine milk. Hesat represents a new species of temperate phage within the Phietavirus genus of the Azeredovirinae subfamily. Its genome has a length of 43,129 bp and a GC content of 35.11% and contains 75 predicted ORFs, some of which linked to virulence. This includes (i) a pathogenicity island (SaPln2), homologous to the type II toxin-antitoxin system PemK/MazF family toxin; (ii) a DUF3113 protein (gp30) that is putatively involved in the derepression of the global repressor Stl; and (iii) a cluster coding for a PVL. Genomic analysis of the host strain indicates Hesat is a resident prophage. Interestingly, its induction was obtained by exposing the bacterium to milk, while the conventional mitomycin C-based approach failed. The host range of phage Hesat appears to be broad, as it was able to lyse 24 out of 30 tested S. aureus isolates. Furthermore, when tested at high titer (108 PFU/ml), Hesat phage was also able to lyse a Staphylococcus muscae isolate, a coagulase-negative staphylococcal strain. KEY POINTS: • A new phage species was isolated from a Staphylococcus aureus bovine strain. • Pathogenicity island and PVL genes are encoded within phage genome. • The phage is active against most of S. aureus strains from both animal and human origins.
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Affiliation(s)
- Barbara Turchi
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Claudia Campobasso
- Department of Biology, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
| | - Arianna Nardinocchi
- Department of Biology, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
| | - Jeroen Wagemans
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
| | - Beatrice Torracca
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Cédric Lood
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
- Department of Microbial and Molecular Systems, Centre for Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Box 2460, 3001, Leuven, Belgium
| | | | - Paola Nieri
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano 6, 56126, Pisa, Italy
| | - Fabrizio Bertelloni
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Luca Turini
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Valeria Ruffo
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
| | - Mariagrazia Di Luca
- Department of Biology, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy.
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14
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Zorea A, Pellow D, Levin L, Pilosof S, Friedman J, Shamir R, Mizrahi I. Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases. Nat Commun 2024; 15:3147. [PMID: 38605009 PMCID: PMC11009399 DOI: 10.1038/s41467-024-47272-x] [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: 08/17/2023] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
Plasmids are pivotal in driving bacterial evolution through horizontal gene transfer. Here, we investigated 3467 human gut microbiome samples across continents and disease states, analyzing 11,086 plasmids. Our analyses reveal that plasmid dispersal is predominantly stochastic, indicating neutral processes as the primary driver of their wide distribution. We find that only 20-25% of plasmid DNA is being selected in various disease states, constraining its distribution across hosts. Selective pressures shape specific plasmid segments with distinct ecological functions, influenced by plasmid mobilization lifestyle, antibiotic usage, and inflammatory gut diseases. Notably, these elements are more commonly shared within groups of individuals with similar health conditions, such as Inflammatory Bowel Disease (IBD), regardless of geographic location across continents. These segments contain essential genes such as iron transport mechanisms- a distinctive gut signature of IBD that impacts the severity of inflammation. Our findings shed light on mechanisms driving plasmid dispersal and selection in the human gut, highlighting their role as carriers of vital gene pools impacting bacterial hosts and ecosystem dynamics.
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Affiliation(s)
- Alvah Zorea
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
| | - David Pellow
- Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Liron Levin
- Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
| | - Shai Pilosof
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
| | - Jonathan Friedman
- Institute of Environmental Sciences, Hebrew University, Rehovot, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel.
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel.
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel.
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15
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Dewan I, Uecker H. Is the distribution of plasmid lengths bimodal? Plasmid 2024; 129-130:102721. [PMID: 38320634 DOI: 10.1016/j.plasmid.2024.102721] [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: 09/10/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/08/2024]
Abstract
The length of a plasmid is a key property which is linked to many aspects of plasmid biology. When distributions of plasmid lengths are shown in the literature, they are usually plotted with length on a logarithmic scale. However, a quantity and its logarithm have distinct distributions which may differ considerably in shape. Mistaking the distribution of log-lengths for the distribution of lengths can therefore lead to distorted conclusions about the distribution; in particular, the distribution of log-lengths may be bimodal when the distribution of lengths is only unimodal. This particular confusion has arisen in the literature where the length distribution is often claimed to be bimodal based on examination of what is in fact the log-length distribution. While the length distribution is indeed bimodal within many bacterial families, it is not across the ensemble of all plasmids. We suggest that authors should be careful to show the plasmid length distribution, or to distinguish the two distributions, to avoid misleading inferences.
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Affiliation(s)
- Ian Dewan
- Research group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
| | - Hildegard Uecker
- Research group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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16
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Moraïs S, Mazor M, Tovar-Herrera O, Zehavi T, Zorea A, Ifrach M, Bogumil D, Brandis A, Walter J, Elia N, Gur E, Mizrahi I. Plasmid-encoded toxin defence mediates mutualistic microbial interactions. Nat Microbiol 2024; 9:108-119. [PMID: 38151647 PMCID: PMC10769881 DOI: 10.1038/s41564-023-01521-9] [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: 07/18/2022] [Accepted: 10/11/2023] [Indexed: 12/29/2023]
Abstract
Gut environments harbour dense microbial ecosystems in which plasmids are widely distributed. Plasmids facilitate the exchange of genetic material among microorganisms while enabling the transfer of a diverse array of accessory functions. However, their precise impact on microbial community composition and function remains largely unexplored. Here we identify a prevalent bacterial toxin and a plasmid-encoded resistance mechanism that mediates the interaction between Lactobacilli and Enterococci. This plasmid is widespread across ecosystems, including the rumen and human gut microbiota. Biochemical characterization of the plasmid revealed a defence mechanism against reuterin, a toxin produced by various gut microbes, such as Limosilactobacillus reuteri. Using a targeted metabolomic approach, we find reuterin to be prevalent across rumen ecosystems with impacts on microbial community structure. Enterococcus strains carrying the protective plasmid were isolated and their interactions with L. reuteri, the toxin producer, were studied in vitro. Interestingly, we found that by conferring resistance against reuterin, the plasmid mediates metabolic exchange between the defending and the attacking microbial species, resulting in a beneficial relationship or mutualism. Hence, we reveal here an ecological role for a plasmid-coded defence system in mediating a beneficial interaction.
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Affiliation(s)
- Sarah Moraïs
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Michael Mazor
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Omar Tovar-Herrera
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Tamar Zehavi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Alvah Zorea
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Morya Ifrach
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - David Bogumil
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Jens Walter
- Department of Medicine, University College Cork, Cork, Ireland
| | - Natalie Elia
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Eyal Gur
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
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17
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Nies F, Wein T, Hanke DM, Springstein BL, Alcorta J, Taubenheim C, Dagan T. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:656-668. [PMID: 37794696 PMCID: PMC10667661 DOI: 10.1111/1758-2229.13203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023]
Abstract
Small cryptic plasmids have no clear effect on the host fitness and their functional repertoire remains obscure. The naturally competent cyanobacterium Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their evolution with this species is supported by horizontal transfer remains understudied. Here, we show that the small cryptic plasmid DNA is transferred in the population exclusively by natural transformation, where the transfer frequency of plasmid-encoded genes is similar to that of chromosome-encoded genes. Establishing a system to follow gene transfer, we compared the transfer frequency of genes encoded in cryptic plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations of two Synechocystis sp. PCC 6803 labtypes (termed Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake in the Sevilla labtype ranged among the lowest detected transfer rates in our experiments. Our study indicates that horizontal DNA transfer via natural transformation is frequent in the evolution of small cryptic plasmids that reside in naturally competent organisms. Furthermore, we suggest that the contribution of natural transformation to cryptic plasmid persistence in Synechocystis is limited.
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Affiliation(s)
- Fabian Nies
- Institute of General MicrobiologyKiel UniversityKielGermany
| | - Tanita Wein
- Institute of General MicrobiologyKiel UniversityKielGermany
- Present address:
Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | | | - Benjamin L. Springstein
- Institute of General MicrobiologyKiel UniversityKielGermany
- Present address:
Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Jaime Alcorta
- Department of Molecular Genetics and Microbiology, Biological Sciences FacultyPontifical Catholic University of ChileSantiagoChile
| | - Claudia Taubenheim
- Institute of General MicrobiologyKiel UniversityKielGermany
- Present address:
Department of Internal Medicine IIUniversity Medical Center Schleswig‐HolsteinKielGermany
| | - Tal Dagan
- Institute of General MicrobiologyKiel UniversityKielGermany
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18
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Ibarra‐Chávez R, Reboud J, Penadés JR, Cooper JM. Phage-Inducible Chromosomal Islands as a Diagnostic Platform to Capture and Detect Bacterial Pathogens. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301643. [PMID: 37358000 PMCID: PMC10460865 DOI: 10.1002/advs.202301643] [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: 03/13/2023] [Revised: 06/06/2023] [Indexed: 06/27/2023]
Abstract
Phage-inducible chromosomal islands (PICIs) are a family of phage satellites that hijack phage components to facilitate their mobility and spread. Recently, these genetic constructs are repurposed as antibacterial drones, enabling a new toolbox for unorthodox applications in biotechnology. To illustrate a new suite of functions, the authors have developed a user-friendly diagnostic system, based upon PICI transduction to selectively enrich bacteria, allowing the detection and sequential recovery of Escherichia coli and Staphylococcus aureus. The system enables high transfer rates and sensitivities in comparison with phages, with detection down to ≈50 CFU mL-1 . In contrast to conventional detection strategies, which often rely on nucleic acid molecular assays, and cannot differentiate between dead and live organisms, this approach enables visual sensing of viable pathogens only, through the expression of a reporter gene encoded in the PICI. The approach extends diagnostic sensing mechanisms beyond cell-free synthetic biology strategies, enabling new synthetic biology/biosensing toolkits.
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Affiliation(s)
- Rodrigo Ibarra‐Chávez
- Department of BiologySection of MicrobiologyUniversity of CopenhagenUniversitetsparken 15, bldg. 1CopenhagenDK2100Denmark
- Institute of InfectionImmunity and InflammationCollege of MedicalVeterinary and Life SciencesUniversity of GlasgowGlasgowG12 8TAUK
- Division of Biomedical EngineeringJames Watt School of EngineeringUniversity of GlasgowGlasgowG12 8QQUK
| | - Julien Reboud
- Division of Biomedical EngineeringJames Watt School of EngineeringUniversity of GlasgowGlasgowG12 8QQUK
| | - José R. Penadés
- Institute of InfectionImmunity and InflammationCollege of MedicalVeterinary and Life SciencesUniversity of GlasgowGlasgowG12 8TAUK
- Departamento de Ciencias BiomédicasUniversidad CEU Cardenal HerreraMoncada46113Spain
- Centre for Bacterial Resistance BiologyImperial College LondonSouth KensingtonSW7 2AZUK
| | - Jonathan M. Cooper
- Division of Biomedical EngineeringJames Watt School of EngineeringUniversity of GlasgowGlasgowG12 8QQUK
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19
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Petrovic Fabijan A, Iredell J, Danis-Wlodarczyk K, Kebriaei R, Abedon ST. Translating phage therapy into the clinic: Recent accomplishments but continuing challenges. PLoS Biol 2023; 21:e3002119. [PMID: 37220114 PMCID: PMC10204993 DOI: 10.1371/journal.pbio.3002119] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Phage therapy is a medical form of biological control of bacterial infections, one that uses naturally occurring viruses, called bacteriophages or phages, as antibacterial agents. Pioneered over 100 years ago, phage therapy nonetheless is currently experiencing a resurgence in interest, with growing numbers of clinical case studies being published. This renewed enthusiasm is due in large part to phage therapy holding promise for providing safe and effective cures for bacterial infections that traditional antibiotics acting alone have been unable to clear. This Essay introduces basic phage biology, provides an outline of the long history of phage therapy, highlights some advantages of using phages as antibacterial agents, and provides an overview of recent phage therapy clinical successes. Although phage therapy has clear clinical potential, it faces biological, regulatory, and economic challenges to its further implementation and more mainstream acceptance.
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Affiliation(s)
- Aleksandra Petrovic Fabijan
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Jonathan Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Westmead Hospital, Western Sydney Local Health District, Westmead, New South Wales, Australia
| | - Katarzyna Danis-Wlodarczyk
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, United States of America
| | - Razieh Kebriaei
- P3 Research Laboratory, College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
| | - Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Mansfield, Ohio, United States of America
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20
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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: 34] [Impact Index Per Article: 17.0] [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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21
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Al-Trad EI, Chew CH, Che Hamzah AM, Suhaili Z, Rahman NIA, Ismail S, Puah SM, Chua KH, Kwong SM, Yeo CC. The Plasmidomic Landscape of Clinical Methicillin-Resistant Staphylococcus aureus Isolates from Malaysia. Antibiotics (Basel) 2023; 12:antibiotics12040733. [PMID: 37107095 PMCID: PMC10135026 DOI: 10.3390/antibiotics12040733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a priority nosocomial pathogen with plasmids playing a crucial role in its genetic adaptability, particularly in the acquisition and spread of antimicrobial resistance. In this study, the genome sequences of 79 MSRA clinical isolates from Terengganu, Malaysia, (obtained between 2016 and 2020) along with an additional 15 Malaysian MRSA genomes from GenBank were analyzed for their plasmid content. The majority (90%, 85/94) of the Malaysian MRSA isolates harbored 1-4 plasmids each. In total, 189 plasmid sequences were identified ranging in size from 2.3 kb to ca. 58 kb, spanning all seven distinctive plasmid replication initiator (replicase) types. Resistance genes (either to antimicrobials, heavy metals, and/or biocides) were found in 74% (140/189) of these plasmids. Small plasmids (<5 kb) were predominant (63.5%, 120/189) with a RepL replicase plasmid harboring the ermC gene that confers resistance to macrolides, lincosamides, and streptogramin B (MLSB) identified in 63 MRSA isolates. A low carriage of conjugative plasmids was observed (n = 2), but the majority (64.5%, 122/189) of the non-conjugative plasmids have mobilizable potential. The results obtained enabled us to gain a rare view of the plasmidomic landscape of Malaysian MRSA isolates and reinforces their importance in the evolution of this pathogen.
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Affiliation(s)
- Esra'a I Al-Trad
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu 20400, Malaysia
| | - Ching Hoong Chew
- Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Kuala Nerus 21300, Malaysia
| | | | - Zarizal Suhaili
- Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut 22200, Malaysia
| | - Nor Iza A Rahman
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu 20400, Malaysia
| | - Salwani Ismail
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu 20400, Malaysia
| | - Suat Moi Puah
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Stephen M Kwong
- Infectious Diseases & Microbiology, School of Medicine, Western Sydney University, Campbelltown 2560, Australia
| | - Chew Chieng Yeo
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu 20400, Malaysia
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22
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Jiang L, Zhu H, Wei J, Jiang L, Li Y, Li R, Wang Z, Wang M. Enterobacteriaceae genome-wide analysis reveals roles for P1-like phage-plasmids in transmission of mcr-1, tetX4 and other antibiotic resistance genes. Genomics 2023; 115:110572. [PMID: 36746220 DOI: 10.1016/j.ygeno.2023.110572] [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: 09/16/2022] [Revised: 12/23/2022] [Accepted: 02/02/2023] [Indexed: 02/07/2023]
Abstract
P1 -like phage-plasmids (PPs) are important gene vehicles in isolated pathogens. In this study, we conducted genome-wide and cross-species analysis of antimicrobial resistance genes (ARGs) from 35 ARG-positive P1-like PPs. LS-BSR analysis reveal that P1-like PPs had in common 7 highly variable regions and carried 48 different ARG subtypes. The most prevalent gene groups were the colistin resistance gene mcr-1 and a class 1 integron. Analysis of the flanking sequences of mcr-1 indicated an "IS30-mcr-1-ORF-IS30" as the core cluster. In particular, we found an mcr-1- and blaCTX-M-55-coharboring large fusion P1-like PP. Also, tet(X4) was detected and flanking sequences indicated tet(X4)-bearing cluster can formed a larger size fusion plasmid mediated a wider spread via IS26 hotspots. Overall, this study demonstrated that P1-like PPs can not only mobilize a large number of ARGs in variable regions but also form larger hybrid P1-like PPs that would increase their ability to spread antimicrobial resistance.
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Affiliation(s)
- Li Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Heng Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Jingyi Wei
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Lei Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Yan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China; International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou, Jiangsu 225009, China.
| | - Mianzhi Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China.
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23
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Horne T, Orr VT, Hall JP. How do interactions between mobile genetic elements affect horizontal gene transfer? Curr Opin Microbiol 2023; 73:102282. [PMID: 36863168 DOI: 10.1016/j.mib.2023.102282] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 03/03/2023]
Abstract
Horizontal gene transfer is central to bacterial adaptation and is facilitated by mobile genetic elements (MGEs). Increasingly, MGEs are being studied as agents with their own interests and adaptations, and the interactions MGEs have with one another are recognised as having a powerful effect on the flow of traits between microbes. Collaborations and conflicts between MGEs are nuanced and can both promote and inhibit the acquisition of new genetic material, shaping the maintenance of newly acquired genes and the dissemination of important adaptive traits through microbiomes. We review recent studies that shed light on this dynamic and oftentimes interlaced interplay, highlighting the importance of genome defence systems in mediating MGE-MGE conflicts, and outlining the consequences for evolutionary change, that resonate from the molecular to microbiome and ecosystem levels.
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Affiliation(s)
- Tanya Horne
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Victoria T Orr
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - James Pj Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.
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24
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Sanz-Frasquet C, Ciges-Tomas JR, Alite C, Penadés JR, Marina A. The Bacteriophage-Phage-Inducible Chromosomal Island Arms Race Designs an Interkingdom Inhibitor of dUTPases. Microbiol Spectr 2023; 11:e0323222. [PMID: 36622213 PMCID: PMC9927489 DOI: 10.1128/spectrum.03232-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/18/2022] [Indexed: 01/10/2023] Open
Abstract
Stl, the master repressor of the Staphylococcus aureus pathogenicity islands (SaPIs), targets phage-encoded proteins to derepress and synchronize the SaPI and the helper phage life cycles. To activate their cycle, some SaPI Stls target both phage dimeric and phage trimeric dUTPases (Duts) as antirepressors, which are structurally unrelated proteins that perform identical functions for the phage. This intimate link between the SaPI's repressor and the phage inducer has imposed an evolutionary optimization of Stl that allows the interaction with Duts from unrelated organisms. In this work, we structurally characterize this sophisticated mechanism of specialization by solving the structure of the prototypical SaPIbov1 Stl in complex with a prokaryotic and a eukaryotic trimeric Dut. The heterocomplexes with Mycobacterium tuberculosis and Homo sapiens Duts show the molecular strategy of Stl to target trimeric Duts from different kingdoms. Our structural results confirm the participation of the five catalytic motifs of trimeric Duts in Stl binding, including the C-terminal flexible motif V that increases the affinity by embracing Stl. In silico and in vitro analyses with a monomeric Dut support the capacity of Stl to recognize this third family of Duts, confirming this protein as a universal Dut inhibitor in the different kingdoms of life. IMPORTANCE Stl, the Staphylococcus aureus pathogenicity island (SaPI) master repressor, targets phage-encoded proteins to derepress and synchronize the SaPI and the helper phage life cycles. This fascinating phage-SaPI arms race is exemplified by the Stl from SaPIbov1 which targets phage dimeric and trimeric dUTPases (Duts), structurally unrelated proteins with identical functions in the phages. By solving the structure of the Stl in complex with a prokaryotic (M. tuberculosis) and a eukaryotic (human) trimeric Dut, we showed that Stl has developed a sophisticated substrate mimicry strategy to target trimeric Duts. Since all these Duts present identical catalytic mechanisms, Stl is able to interact with Duts from different kingdoms. In addition, in silico modeling with monomeric Dut supports the capacity of Stl to recognize this third family of Duts, confirming this protein as a universal Dut inhibitor.
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Affiliation(s)
- Carla Sanz-Frasquet
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - J. Rafael Ciges-Tomas
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Christian Alite
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - José R. Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
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25
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Ares-Arroyo M, Coluzzi C, P.C. Rocha E. Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation. Nucleic Acids Res 2022; 51:3001-3016. [PMID: 36442505 PMCID: PMC10123127 DOI: 10.1093/nar/gkac1079] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/17/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022] Open
Abstract
Abstract
Plasmids can be transferred between cells by conjugation, thereby driving bacterial evolution by horizontal gene transfer. Yet, we ignore the molecular mechanisms of transfer for many plasmids because they lack all protein-coding genes required for conjugation. We solved this conundrum by identifying hundreds of plasmids and chromosomes with conjugative origins of transfer in Escherichia coli and Staphylococcus aureus. These plasmids (pOriT) hijack the relaxases of conjugative or mobilizable elements, but not both. The functional dependencies between pOriT and other plasmids explain their co-occurrence: pOriT are abundant in cells with many plasmids, whereas conjugative plasmids are the most common in the others. We systematically characterized plasmid mobility in relation to conjugation and alternative mechanisms of transfer and can now propose a putative mechanism of transfer for ∼90% of them. In most cases, plasmid mobility seems to involve conjugation. Interestingly, the mechanisms of mobility are important determinants of plasmid-encoded accessory traits, since pOriTs have the highest densities of antimicrobial resistance genes, whereas plasmids lacking putative mechanisms of transfer have the lowest. We illuminate the evolutionary relationships between plasmids and suggest that many pOriT may have arisen by gene deletions in other types of plasmids. These results suggest that most plasmids can be transferred by conjugation.
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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
| | - Eduardo P.C. Rocha
- Institut Pasteur, Université de Paris Cité , CNRS UMR3525, Microbial Evolutionary Genomics, Paris , France
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26
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Wang M, Jiang L, Wei J, Zhu H, Zhang J, Liu Z, Zhang W, He X, Liu Y, Li R, Xiao X, Sun Y, Zeng Z, Wang Z. Similarities of P1-Like Phage Plasmids and Their Role in the Dissemination of blaCTX-M-55. Microbiol Spectr 2022; 10:e0141022. [PMID: 36069562 PMCID: PMC9603915 DOI: 10.1128/spectrum.01410-22] [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: 04/18/2022] [Accepted: 08/18/2022] [Indexed: 12/30/2022] Open
Abstract
The P1-like phage plasmid (PP) has been widely used as a molecular biology tool, but its role as an active accessory cargo element is not fully understood. In this study, we provide insights into the structural features and gene content similarities of 77 P1-like PPs in the RefSeq database. We also describe a P1-like PP carrying a blaCTX-M-55 gene, JL22, which was isolated from a clinical strain of Escherichia coli from a duck farm. P1-like PPs were very similar and conserved based on gene content similarities, with only eight highly variable regions. Importantly, two kinds of replicon types, namely, IncY and p0111, were identified and can be used to specifically identify the P1-like phage. JL22 is similar to P1, acquiring an important foreign DNA fragment with two obvious features, namely, the plasmid replication gene repA' (p0111) replacing the gene repA (IncY) and a 4,200-bp fragment mobilized by IS1380 and IS5 and containing a blaCTX-M-55 gene and a trpB gene encoding tryptophan synthase (indole salvaging). The JL22 phage could be induced but had no lytic capacities. However, a lysogenic recipient and intact structure of JL22 virions were observed, showing that the extended-spectrum β-lactamase blaCTX-M-55 gene was successfully transferred. Overall, conserved genes can be a good complement to improve the identification efficiency and accuracy in future screening for P1-like PPs. Moreover, the highly conserved structures may be important for their prevalence and dissemination. IMPORTANCE As a PP, P1 DNA exists as a low-copy-number plasmid and replicates autonomously with a lysogenization style. This unique mode of P1-like elements probably indicates a stable contribution to antibiotic resistance. After analyzing these elements, we show that P1-like PPs are very similar and conserved, with only eight highly variable regions. Moreover, we observed the occurrence of replicon IncY and p0111 only in the P1-like PP community, implying that these conserved regions, coupled with IncY and p0111, can be an important complement in future screening of P1-like PPs. Identification and characterization of JL22 confirmed our findings that major changes were located in variable regions, including the first detection of blaCTX-M-55 in such a mobile genetic element. This suggests that these variable regions may facilitate foreign DNA mobilization. This study features a comprehensive genetic analysis of P1-like PPs, providing new insights into the dissemination mechanisms of antibiotic resistance through P1 PPs.
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Affiliation(s)
- Mianzhi Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Priority Academic Program Development of Jiangsu Higher Education Institutions, Yangzhou, China
| | - Li Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Priority Academic Program Development of Jiangsu Higher Education Institutions, Yangzhou, China
| | - Jingyi Wei
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Priority Academic Program Development of Jiangsu Higher Education Institutions, Yangzhou, China
| | - Heng Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Priority Academic Program Development of Jiangsu Higher Education Institutions, Yangzhou, China
| | - Junxuan Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangzhou, China
| | - Ziyi Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Priority Academic Program Development of Jiangsu Higher Education Institutions, Yangzhou, China
| | - Wenhui Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Priority Academic Program Development of Jiangsu Higher Education Institutions, Yangzhou, China
| | - Xiaolu He
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangzhou, China
| | - Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Priority Academic Program Development of Jiangsu Higher Education Institutions, Yangzhou, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Priority Academic Program Development of Jiangsu Higher Education Institutions, Yangzhou, China
| | - Xia Xiao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Priority Academic Program Development of Jiangsu Higher Education Institutions, Yangzhou, China
| | - Yongxue Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhenling Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Priority Academic Program Development of Jiangsu Higher Education Institutions, Yangzhou, China
- International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou, China
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27
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Haudiquet M, de Sousa JM, Touchon M, Rocha EPC. Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210234. [PMID: 35989606 PMCID: PMC9393566 DOI: 10.1098/rstb.2021.0234] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Horizontal gene transfer (HGT) drives microbial adaptation but is often under the control of mobile genetic elements (MGEs) whose interests are not necessarily aligned with those of their hosts. In general, transfer is costly to the donor cell while potentially beneficial to the recipients. The diversity and plasticity of cell–MGEs interactions, and those among MGEs, result in complex evolutionary processes where the source, or even the existence of selection for maintaining a function in the genome, is often unclear. For example, MGE-driven HGT depends on cell envelope structures and defense systems, but many of these are transferred by MGEs themselves. MGEs can spur periods of intense gene transfer by increasing their own rates of horizontal transmission upon communicating, eavesdropping, or sensing the environment and the host physiology. This may result in high-frequency transfer of host genes unrelated to the MGE. Here, we review how MGEs drive HGT and how their transfer mechanisms, selective pressures and genomic traits affect gene flow, and therefore adaptation, in microbial populations. The encoding of many adaptive niche-defining microbial traits in MGEs means that intragenomic conflicts and alliances between cells and their MGEs are key to microbial functional diversification. This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
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Affiliation(s)
- Matthieu Haudiquet
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| | - Jorge Moura de Sousa
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| | - Marie Touchon
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
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28
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Wang J, Pei J, Liu M, Huang R, Li J, Liao S, Liang J. Identification and Evolutionary Relationship of Corynebacterium striatum Clinical Isolates. Pathogens 2022; 11:pathogens11091012. [PMID: 36145444 PMCID: PMC9501166 DOI: 10.3390/pathogens11091012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 08/27/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Corynebacterium striatum has developed into a new community-acquired and hospital-acquired multi-drug resistance (MDR) bacterium, and is a potential target pathogen for infection control and antibacterial management projects. In this study, non-duplicate samples of inpatients were collected from a local central hospital. Mass spectrometry showed that 54 C. striatum isolates mainly appeared in secretion and sputum from 14 departments. Protein fingerprint cluster analysis showed that the isolates were divided into four groups, most of which appeared in summer. The drug resistance test showed that all strains had multi-drug resistance, with high resistance rates to lincosamides, quinolones and tetracycline detected. Further analysis of the phylogenetic tree of C. striatum was conducted by cloning the 16S rRNA gene. It was found that isolates in the same department had high homology and tended to be located in the same branch or to be crossed in the same main branch. The strains in the same evolutionary branch group had the same drug resistance. Screening of site-specific recombinant elements revealed that 18 strains had integrase genes with the same sequence. This study shows that there may be mobile genetic elements in clinical isolates that drive gene exchange among strains, thus causing the cross-infection, spread and evolution of pathogenic bacteria in the hospital.
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Affiliation(s)
- Jiao Wang
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang 441053, China
- Correspondence: (J.W.); (J.P.)
| | - Jiao Pei
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang 441021, China
- Correspondence: (J.W.); (J.P.)
| | - Mingming Liu
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang 441053, China
| | - Rui Huang
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang 441053, China
| | - Jiqiang Li
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang 441053, China
| | - Shiying Liao
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang 441053, China
| | - Jian Liang
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang 441021, China
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Martinez J, Ant TH, Murdochy SM, Tong L, da Silva Filipe A, Sinkins SP. Genome sequencing and comparative analysis of Wolbachia strain wAlbA reveals Wolbachia-associated plasmids are common. PLoS Genet 2022; 18:e1010406. [PMID: 36121852 PMCID: PMC9560607 DOI: 10.1371/journal.pgen.1010406] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/13/2022] [Accepted: 09/02/2022] [Indexed: 11/18/2022] Open
Abstract
Wolbachia are widespread maternally-transmitted bacteria of arthropods that often spread by manipulating their host's reproduction through cytoplasmic incompatibility (CI). Their invasive potential is currently being harnessed in field trials aiming to control mosquito-borne diseases. Wolbachia genomes commonly harbour prophage regions encoding the cif genes which confer their ability to induce CI. Recently, a plasmid-like element was discovered in wPip, a Wolbachia strain infecting Culex mosquitoes; however, it is unclear how common such extra-chromosomal elements are in Wolbachia. Here we sequenced the complete genome of wAlbA, a strain of the symbiont found in Aedes albopictus, after eliminating the co-infecting and higher density wAlbB strain that previously made sequencing of wAlbA challenging. We show that wAlbA is associated with two new plasmids and identified additional Wolbachia plasmids and related chromosomal islands in over 20% of publicly available Wolbachia genome datasets. These plasmids encode a variety of accessory genes, including several phage-like DNA packaging genes as well as genes potentially contributing to host-symbiont interactions. In particular, we recovered divergent homologues of the cif genes in both Wolbachia- and Rickettsia-associated plasmids. Our results indicate that plasmids are common in Wolbachia and raise fundamental questions around their role in symbiosis. In addition, our comparative analysis provides useful information for the future development of genetic tools to manipulate and study Wolbachia symbionts.
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Affiliation(s)
- Julien Martinez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Thomas H. Ant
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Shivan M. Murdochy
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Steven P. Sinkins
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors. Cell 2022; 185:3248-3262.e20. [PMID: 35985290 DOI: 10.1016/j.cell.2022.07.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/08/2022] [Accepted: 07/18/2022] [Indexed: 01/26/2023]
Abstract
Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
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31
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Dimitriu T. Evolution of horizontal transmission in antimicrobial resistance plasmids. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35849537 DOI: 10.1099/mic.0.001214] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Mobile genetic elements (MGEs) are one of the main vectors for the spread of antimicrobial resistance (AMR) across bacteria, due to their ability to move horizontally between bacterial lineages. Horizontal transmission of AMR can increase AMR prevalence at multiple scales, from increasing the prevalence of infections by resistant bacteria to pathogen epidemics and worldwide spread of AMR across species. Among MGEs, conjugative plasmids are the main contributors to the spread of AMR. This review discusses the selective pressures acting on MGEs and their hosts to promote or limit the horizontal transmission of MGEs, the mechanisms by which transmission rates can evolve, and their implications for limiting the spread of AMR, with a focus on AMR plasmids.
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32
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Finstrlová A, Mašlaňová I, Blasdel Reuter BG, Doškař J, Götz F, Pantůček R. Global Transcriptomic Analysis of Bacteriophage-Host Interactions between a Kayvirus Therapeutic Phage and Staphylococcus aureus. Microbiol Spectr 2022; 10:e0012322. [PMID: 35435752 PMCID: PMC9241854 DOI: 10.1128/spectrum.00123-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/28/2022] [Indexed: 11/20/2022] Open
Abstract
Kayviruses are polyvalent broad host range staphylococcal phages with a potential to combat staphylococcal infections. However, the implementation of rational phage therapy in medicine requires a thorough understanding of the interactions between bacteriophages and pathogens at omics level. To evaluate the effect of a phage used in therapy on its host bacterium, we performed differential transcriptomic analysis by RNA-Seq from bacteriophage K of genus Kayvirus infecting two Staphylococcus aureus strains, prophage-less strain SH1000 and quadruple lysogenic strain Newman. The temporal transcriptional profile of phage K was comparable in both strains except for a few loci encoding hypothetical proteins. Stranded sequencing revealed transcription of phage noncoding RNAs that may play a role in the regulation of phage and host gene expression. The transcriptional response of S. aureus to phage K infection resembles a general stress response with differential expression of genes involved in a DNA damage response. The host transcriptional changes involved upregulation of nucleotide, amino acid and energy synthesis and transporter genes and downregulation of host transcription factors. The interaction of phage K with variable genetic elements of the host showed slight upregulation of gene expression of prophage integrases and antirepressors. The virulence genes involved in adhesion and immune evasion were only marginally affected, making phage K suitable for therapy. IMPORTANCE Bacterium Staphylococcus aureus is a common human and veterinary pathogen that causes mild to life-threatening infections. As strains of S. aureus are becoming increasingly resistant to multiple antibiotics, the need to search for new therapeutics is urgent. A promising alternative to antibiotic treatment of staphylococcal infections is a phage therapy using lytic phages from the genus Kayvirus. Here, we present a comprehensive view on the phage-bacterium interactions on transcriptomic level that improves the knowledge of molecular mechanisms underlying the Kayvirus lytic action. The results will ensure safer usage of the phage therapeutics and may also serve as a basis for the development of new antibacterial strategies.
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Affiliation(s)
- Adéla Finstrlová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ivana Mašlaňová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Jiří Doškař
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Friedrich Götz
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
| | - Roman Pantůček
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
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Coluzzi C, Garcillán-Barcia MP, de la Cruz F, Rocha EPC. Evolution of plasmid mobility: origin and fate of conjugative and non-conjugative plasmids. Mol Biol Evol 2022; 39:6593704. [PMID: 35639760 PMCID: PMC9185392 DOI: 10.1093/molbev/msac115] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Conjugation drives the horizontal transfer of adaptive traits across prokaryotes. One-fourth of the plasmids encode the functions necessary to conjugate autonomously, the others being eventually mobilizable by conjugation. To understand the evolution of plasmid mobility, we studied plasmid size, gene repertoires, and conjugation-related genes. Plasmid gene repertoires were found to vary rapidly in relation to the evolutionary rate of relaxases, for example, most pairs of plasmids with 95% identical relaxases have fewer than 50% of homologs. Among 249 recent transitions of mobility type, we observed a clear excess of plasmids losing the capacity to conjugate. These transitions are associated with even greater changes in gene repertoires, possibly mediated by transposable elements, including pseudogenization of the conjugation locus, exchange of replicases reducing the problem of incompatibility, and extensive loss of other genes. At the microevolutionary scale of plasmid taxonomy, transitions of mobility type sometimes result in the creation of novel taxonomic units. Interestingly, most transitions from conjugative to mobilizable plasmids seem to be lost in the long term. This suggests a source-sink dynamic, where conjugative plasmids generate nonconjugative plasmids that tend to be poorly adapted and are frequently lost. Still, in some cases, these relaxases seem to have evolved to become efficient at plasmid mobilization in trans, possibly by hijacking multiple conjugative systems. This resulted in specialized relaxases of mobilizable plasmids. In conclusion, the evolution of plasmid mobility is frequent, shapes the patterns of gene flow in bacteria, the dynamics of gene repertoires, and the ecology of plasmids.
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Affiliation(s)
- Charles Coluzzi
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011, Santander, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011, Santander, Spain
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
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Balasubramanian D, López-Pérez M, Grant TA, Ogbunugafor CB, Almagro-Moreno S. Molecular mechanisms and drivers of pathogen emergence. Trends Microbiol 2022; 30:898-911. [DOI: 10.1016/j.tim.2022.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 02/05/2022] [Accepted: 02/10/2022] [Indexed: 12/21/2022]
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