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Nii T, Maeda Y, Motooka D, Naito M, Matsumoto Y, Ogawa T, Oguro-Igashira E, Kishikawa T, Yamashita M, Koizumi S, Kurakawa T, Okumura R, Kayama H, Murakami M, Sakaguchi T, Das B, Nakamura S, Okada Y, Kumanogoh A, Takeda K. Genomic repertoires linked with pathogenic potency of arthritogenic Prevotella copri isolated from the gut of patients with rheumatoid arthritis. Ann Rheum Dis 2023; 82:621-629. [PMID: 36627170 PMCID: PMC10176341 DOI: 10.1136/ard-2022-222881] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 12/30/2022] [Indexed: 01/12/2023]
Abstract
OBJECTIVES Prevotella copri is considered to be a contributing factor in rheumatoid arthritis (RA). However, in some non-Westernised countries, healthy individuals also harbour an abundance of P. copri in the intestine. This study investigated the pathogenicity of RA patient-derived P. copri (P. copri RA) compared with healthy control-derived P. copri (P. copri HC). METHODS We obtained 13 P. copri strains from the faeces of patients with RA and healthy controls. Following whole genome sequencing, the sequences of P. copri RA and P. copri HC were compared. To analyse the arthritis-inducing ability of P. copri, we examined two arthritis models (1) a collagen-induced arthritis model harbouring P. copri under specific-pathogen-free conditions and (2) an SKG mouse arthritis model under P. copri-monocolonised conditions. Finally, to evaluate the ability of P. copri to activate innate immune cells, we performed in vitro stimulation of bone marrow-derived dendritic cells (BMDCs) by P. copri RA and P. copri HC. RESULTS Comparative genomic analysis revealed no apparent differences in the core gene contents between P. copri RA and P. copri HC, but pangenome analysis revealed the high genome plasticity of P. copri. We identified a P. copri RA-specific genomic region as a conjugative transposon. In both arthritis models, P. copri RA-induced more severe arthritis than P. copri HC. In vitro BMDC stimulation experiments revealed the upregulation of IL-17 and Th17-related cytokines (IL-6, IL-23) by P. copri RA. CONCLUSION Our findings reveal the genetic diversity of P. copri, and the genomic signatures associated with strong arthritis-inducing ability of P. copri RA. Our study contributes towards elucidation of the complex pathogenesis of RA.
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Affiliation(s)
- Takuro Nii
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Respiratory Medicine, Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- National Hospital Organization Osaka Toneyama Medical Center, Osaka, Japan
| | - Yuichi Maeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Respiratory Medicine, Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Daisuke Motooka
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Mariko Naito
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takao Ogawa
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Respiratory Medicine, Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Eri Oguro-Igashira
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Respiratory Medicine, Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Toshihiro Kishikawa
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Aichi, Japan
| | - Makoto Yamashita
- Research & Innovation Center, Kyowa Hakko Bio Co., Ltd, Ibaraki, Japan
| | - Satoshi Koizumi
- Research & Innovation Center, Kyowa Hakko Bio Co., Ltd, Ibaraki, Japan
| | - Takashi Kurakawa
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Ryu Okumura
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Hisako Kayama
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Institute for Advanced Co-Creation Studies, Osaka University, Osaka, Japan
| | - Mari Murakami
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Taiki Sakaguchi
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Bhabatosh Das
- Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Shota Nakamura
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
| | - Yukinori Okada
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
- Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine, Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
| | - Kiyoshi Takeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
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Govindarajan DK, Kandaswamy K. Virulence factors of uropathogens and their role in host pathogen interactions. Cell Surf 2022; 8:100075. [PMID: 35198842 PMCID: PMC8841375 DOI: 10.1016/j.tcsw.2022.100075] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/01/2022] [Accepted: 02/06/2022] [Indexed: 12/26/2022] Open
Abstract
Gram-positive and Gram-negative bacterial pathogens are commonly found in Urinary Tract Infection (UTI), particularly infected in females like pregnant women, elder people, sexually active, or individuals prone to other risk factors for UTI. In this article, we review the expression of virulence surface proteins and their interaction with host cells for the most frequently isolated uropathogens: Escherichia coli, Enterococcus faecalis, Proteus mirabilis, Klebsiella pneumoniae, and Staphylococcus saprophyticus. In addition to the host cell interaction, surface protein regulation was also discussed in this article. The surface protein regulation serves as a key tool in differentiating the pathogen isotypes. Furthermore, it might provide insights on novel diagnostic methods to detect uropathogen that are otherwise easily overlooked due to limited culture-based assays. In essence, this review shall provide an in-depth understanding on secretion of virulence factors of various uropathogens and their role in host-pathogen interaction, this knowledge might be useful in the development of therapeutics against uropathogens.
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Affiliation(s)
| | - Kumaravel Kandaswamy
- Corresponding author at: Department of Biotechnology, Kumaraguru College of Technology (KCT), Chinnavedampatti, Coimbatore 641049, Tamil Nadu, India.
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Downing T, Lee MJ, Archbold C, McDonnell A, Rahm A. Informing plasmid compatibility with bacterial hosts using protein-protein interaction data. Genomics 2022; 114:110509. [PMID: 36273742 DOI: 10.1016/j.ygeno.2022.110509] [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: 08/19/2022] [Revised: 09/23/2022] [Accepted: 10/19/2022] [Indexed: 01/15/2023]
Abstract
The compatibility of plasmids with new host cells is significant given their role in spreading antimicrobial resistance (AMR) and virulence factor genes. Evaluating this using in vitro screening is laborious and can be informed by computational analyses of plasmid-host compatibility through rates of protein-protein interactions (PPIs) between plasmid and host cell proteins. We identified large excesses of such PPIs in eight important plasmids, including pOXA-48, using most known bacteria (n = 4363). 23 species had high rates of interactions with four blaOXA-48-positive plasmids. We also identified 48 species with high interaction rates with plasmids common in Escherichia coli. We found a strong association between one plasmid and the fimbrial adhesin operon pil, which could enhance host cell adhesion in aqueous environments. An excess rate of PPIs could be a sign of host-plasmid compatibility, which is important for AMR control given that plasmids like pOXA-48 move between species with ease.
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Affiliation(s)
- Tim Downing
- School of Biotechnology, Dublin City University, Dublin, Ireland; The Pirbright Institute, UK.
| | - Min Jie Lee
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Conor Archbold
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Adam McDonnell
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Alexander Rahm
- GAATI Lab, University of French Polynesia, Tahiti, French Polynesia
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Shahri FN, Izanloo A, Goharrizi MASB, Jamali A, Bagheri H, Hjimohammadi A, Ardebili A. Antimicrobial resistance, virulence factors, and genotypes of Pseudomonas aeruginosa clinical isolates from Gorgan, northern Iran. Int Microbiol 2022; 25:709-721. [PMID: 35697891 DOI: 10.1007/s10123-022-00256-7] [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: 02/25/2022] [Revised: 05/23/2022] [Accepted: 05/31/2022] [Indexed: 11/24/2022]
Abstract
Pseudomonas aeruginosa is an important nosocomial pathogen with a capacity of resistance to multiple antibiotics and production of various extracellular and cell-associated virulence factors that clearly contribute to its pathogenicity. The objective of this study was to investigate the antibiotic susceptibility, virulence factors, and clonal relationship among clinical isolates of P. aeruginosa. Different clinical specimens from hospitalized patients were investigated for P. aeruginosa. Susceptibility of the isolates was evaluated by disc diffusion and broth microdilution methods, as described by the Clinical and Laboratory Standards Institute (CLSI) guideline. A total of 97 P. aeruginosa isolates were recovered from clinical specimens. The percentage of isolates resistant to antimicrobials was imipenem 25.77%, meropenem 15.46%, gentamicin 16.49%, tobramycin 15.46%, amikacin 16.49%, ciprofloxacin 20.61%, levofloxacin 24.74, ceftazidime 20.61%, piperacillin 15.46%, piperacillin/tazobactam 12.37%, colistin 9.27%, and polymyxin B 11.34%. Of isolates, 87.62% possessed β-hemolytic activity, 78.35% lecithinase, 59.8% elastase, 37.11% DNase, and 28.86% twitching motility. The frequency of virulence genes in isolates was lasB 82.47%, plcH 82.47%, exoA 58.76%, exoS 56.7%, and pilA 10.3%. ERIC-PCR typing clustered P. aeruginosa isolates to 19 common types (CT1-CT19) containing isolates from different hospitals and 43 single types (ST1-ST43). Colistin and polymyxin B were the most effective agents against the majority of P. aeruginosa isolates, emphasizing the effort to maintain their antibacterial activity as last-line therapy. The frequency of some virulence factors and genes was noticeably high, which is alarming. In addition, more effective strategies and surveillance are necessary to confine and prevent the inter-hospital and/or intra-hospital dissemination of P. aeruginosa between therapeutic centers.
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Affiliation(s)
- Fatemeh Nemati Shahri
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran.,Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, P.O. Box: 4934174515, Gorgan, Iran
| | - Ahdieh Izanloo
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan, Iran
| | | | - Ailar Jamali
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran.,Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, P.O. Box: 4934174515, Gorgan, Iran
| | - Hanieh Bagheri
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Afsaneh Hjimohammadi
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Abdollah Ardebili
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran. .,Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, P.O. Box: 4934174515, Gorgan, Iran.
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Prevalence of algD, pslD, pelF, Ppgl, and PAPI-1 Genes Involved in Biofilm Formation in Clinical Pseudomonas aeruginosa Strains. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1716087. [PMID: 35655484 PMCID: PMC9155974 DOI: 10.1155/2022/1716087] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/26/2022] [Accepted: 05/10/2022] [Indexed: 11/23/2022]
Abstract
Introduction Biofilm formation is one of the main virulence factors in Pseudomonas aeruginosa infections. This study is aimed at investigating the presence of genes involved in biofilm formation in clinical P. aeruginosa isolates. Material and Methods. A cross-sectional study was conducted on 112 P. aeruginosa isolates. The biofilm formation assay was performed on all isolates. Antimicrobial resistance was determined by the disk diffusion method, and the presence of genes was detected by polymerase chain reaction. Isolates were typed with Rep-PCR. Results The results of biofilm formation demonstrated that 85 strains (75.9%) were biofilm producers, and 27 strains (24.1%) were nonproducer isolates. Antibiotic susceptibility pattern in biofilm-positive and biofilm-negative isolates obtained from hospitalized patients showed a high rate of antibiotic resistance to amoxicillin with 95.7% and 92.3%, respectively. Based on PCR amplification results, the frequency of genes involved in biofilm formation among all isolates was as follows: algD (78.6%), pelF (70.5%), pslD (36.6%), Ppgl (0%), and PAPI-1 (77.6%). Rep-PCR typing demonstrated that 112 P. aeruginosa isolates were classified into 57 types according to 70% cut-off. The predominant type was A which contained 15 isolates. Moreover, 7 isolates were clustered in genotype B, followed by C type (6), D (4), E (4), F (4), G (4), H (3), I (3), J (3 isolates), and 12 genotypes, each containing two isolates. Also, 35 isolates were distributed in scattered patterns and showed single types. Conclusion Study results showed significant association between biofilm formation and resistance to antibiotics such as ceftazidime and meropenem. Analysis of Rep-PCR patterns indicated that the evaluated isolates were heterogeneous, relatively.
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Allard N, Neil K, Grenier F, Rodrigue S. The Type IV Pilus of Plasmid TP114 Displays Adhesins Conferring Conjugation Specificity and Is Important for DNA Transfer in the Mouse Gut Microbiota. Microbiol Spectr 2022; 10:e0230321. [PMID: 35293798 PMCID: PMC9045228 DOI: 10.1128/spectrum.02303-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/16/2022] [Indexed: 12/02/2022] Open
Abstract
Type IV pili (T4P) are common bacterial surface appendages involved in different biological processes such as adherence, motility, competence, pathogenesis, and conjugation. In this work, we describe the T4P of TP114, an IncI2 enterobacterial conjugative plasmid recently shown to disseminate at high rates in the mouse intestinal tract. This pilus is composed of the major PilS and minor PilV pilins that are both important for conjugation in broth and in the gut microbiota but not on a solid support. The PilV-coding sequence is part of a shufflon and can bear different C-terminal domains. The shufflon is a multiple DNA inversion system containing many DNA cassettes flanked by recombination sites that are recognized by a shufflon-specific tyrosine recombinase (shufflase) promoting the recombination between DNA segments. The different PilV variants act as adhesins that can modify the affinity for different recipient bacteria. Eight PilV variants were identified in TP114, including one that has not been described in other shufflons. All PilV variants allowed conjugative transfer with different recipient Escherichia coli strains. We conclude that the T4P carried by TP114 plays a major role in mating pair stabilization in broth as well as in the gut microbiota and that the shufflon acts as a biological switch modifying the conjugative host range specificity. IMPORTANCE Conjugative plasmids are involved in horizontal gene transfer in the gut microbiota, which constitutes an important antibiotic resistance gene reservoir. However, the molecular mechanisms used by conjugative plasmids to select recipient bacteria and transfer at high rates in the mouse gut microbiota remain poorly characterized. We studied the type IV pilus carried by TP114 and demonstrated that the minor pilin PilV acts as an adhesin that can efficiently select target cells for conjugative transfer. Moreover, the pilV gene can be rapidly modified by a shufflon, hence modulating the nature of the recipient bacteria during conjugation. Our study highlights the role of mating pair stabilization for conjugation in broth as well as in the gut microbiome and explains how the host spectrum of a plasmid can be expanded simply by remodeling the PilV adhesin.
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Affiliation(s)
- Nancy Allard
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Kevin Neil
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Frédéric Grenier
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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7
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Johnson CM, Harden MM, Grossman AD. Interactions between mobile genetic elements: An anti-phage gene in an integrative and conjugative element protects host cells from predation by a temperate bacteriophage. PLoS Genet 2022; 18:e1010065. [PMID: 35157704 PMCID: PMC8880864 DOI: 10.1371/journal.pgen.1010065] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/25/2022] [Accepted: 02/01/2022] [Indexed: 01/21/2023] Open
Abstract
Most bacterial genomes contain horizontally acquired and transmissible mobile genetic elements, including temperate bacteriophages and integrative and conjugative elements. Little is known about how these elements interact and co-evolved as parts of their host genomes. In many cases, it is not known what advantages, if any, these elements provide to their bacterial hosts. Most strains of Bacillus subtilis contain the temperate phage SPß and the integrative and conjugative element ICEBs1. Here we show that the presence of ICEBs1 in cells protects populations of B. subtilis from predation by SPß, likely providing selective pressure for the maintenance of ICEBs1 in B. subtilis. A single gene in ICEBs1 (yddK, now called spbK for SPß killing) was both necessary and sufficient for this protection. spbK inhibited production of SPß, during both activation of a lysogen and following de novo infection. We found that expression spbK, together with the SPß gene yonE constitutes an abortive infection system that leads to cell death. spbK encodes a TIR (Toll-interleukin-1 receptor)-domain protein with similarity to some plant antiviral proteins and animal innate immune signaling proteins. We postulate that many uncharacterized cargo genes in ICEs may confer selective advantage to cells by protecting against other mobile elements. Chromosomes from virtually all organisms contain genes that were horizontally acquired. In bacteria, many of the horizontally acquired genes are located in mobile genetic elements, elements that promote their own transfer from one cell to another. These elements include viruses and conjugative elements that are parts of the host genome and they can contain genes involved in metabolism, pathogenesis, symbiosis, and antibiotic resistances. Interactions between these elements are poorly understood. Furthermore, the majority of these elements confer no obvious benefit to host cells. We found that the presence of an integrative and conjugative element (ICE) in a bacterial genome protects host cells from predation by a bacteriophage (virus). There is a single gene in the integrative and conjugative element that confers this protection, and one gene in the bacteriophage that likely works together with the ICE gene. When expressed at the same time, these two genes cause cell death, before functional viruses can be made and released to kill other cells. We postulate that other ICEs may confer selective advantage to their host cells by protecting against other mobile elements.
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Affiliation(s)
- Christopher M. Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - M. Michael Harden
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Alan D. Grossman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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Andreopoulos WB, Geller AM, Lucke M, Balewski J, Clum A, Ivanova NN, Levy A. Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes. Nucleic Acids Res 2021; 50:e17. [PMID: 34871418 PMCID: PMC8860608 DOI: 10.1093/nar/gkab1115] [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: 04/20/2021] [Revised: 10/11/2021] [Accepted: 10/23/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many microbial genomes have been sequenced by short read sequencers and have resulted in a mix of contigs that derive from plasmids or chromosomes. New tools that accurately identify plasmids are needed to elucidate new plasmid-borne genes of high biological importance. We have developed Deeplasmid, a deep learning tool for distinguishing plasmids from bacterial chromosomes based on the DNA sequence and its encoded biological data. It requires as input only assembled sequences generated by any sequencing platform and assembly algorithm and its runtime scales linearly with the number of assembled sequences. Deeplasmid achieves an AUC–ROC of over 89%, and it was more accurate than five other plasmid classification methods. Finally, as a proof of concept, we used Deeplasmid to predict new plasmids in the fish pathogen Yersinia ruckeri ATCC 29473 that has no annotated plasmids. Deeplasmid predicted with high reliability that a long assembled contig is part of a plasmid. Using long read sequencing we indeed validated the existence of a 102 kb long plasmid, demonstrating Deeplasmid's ability to detect novel plasmids.
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Affiliation(s)
- William B Andreopoulos
- Joint Genome Institute, US Department of Energy, LBNL Berkeley, CA, USA.,Department of Computer Science, San Jose State University, CA, USA
| | - Alexander M Geller
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Miriam Lucke
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jan Balewski
- National Energy Research Scientific Computing Center (NERSC), Berkeley, CA, USA
| | - Alicia Clum
- Joint Genome Institute, US Department of Energy, LBNL Berkeley, CA, USA
| | - Natalia N Ivanova
- Joint Genome Institute, US Department of Energy, LBNL Berkeley, CA, USA
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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Dangla-Pélissier G, Roux N, Schmidt V, Chambonnier G, Ba M, Sebban-Kreuzer C, de Bentzmann S, Giraud C, Bordi C. The horizontal transfer of Pseudomonas aeruginosa PA14 ICE PAPI-1 is controlled by a transcriptional triad between TprA, NdpA2 and MvaT. Nucleic Acids Res 2021; 49:10956-10974. [PMID: 34643711 PMCID: PMC8565334 DOI: 10.1093/nar/gkab827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/24/2021] [Accepted: 10/06/2021] [Indexed: 01/16/2023] Open
Abstract
Pseudomonas aeruginosa is a major cause of nosocomial infections, particularly in immunocompromised patients or in individuals with cystic fibrosis. Genome sequences reveal that most P. aeruginosa strains contain a significant number of accessory genes gathered in genomic islands. Those genes are essential for P. aeruginosa to invade new ecological niches with high levels of antibiotic usage, like hospitals, or to survive during host infection by providing pathogenicity determinants. P. aeruginosa pathogenicity island 1 (PAPI-1), one of the largest genomic islands, encodes several putative virulence factors, including toxins, biofilm genes and antibiotic-resistance traits. The integrative and conjugative element (ICE) PAPI-1 is horizontally transferable by conjugation via a specialized GI-T4SS, but the mechanism regulating this transfer is currently unknown. Here, we show that this GI-T4SS conjugative machinery is directly induced by TprA, a regulator encoded within PAPI-1. Our data indicate that the nucleotide associated protein NdpA2 acts in synergy with TprA, removing a repressive mechanism exerted by MvaT. In addition, using a transcriptomic approach, we unravelled the regulon controlled by Ndpa2/TprA and showed that they act as major regulators on the genes belonging to PAPI-1. Moreover, TprA and NdpA2 trigger an atypical biofilm structure and enhance ICE PAPI-1 transfer.
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Affiliation(s)
| | - Nicolas Roux
- LISM, IMM, Aix-Marseille University, Marseille 13402, France
| | | | | | - Moly Ba
- LISM, IMM, Aix-Marseille University, Marseille 13402, France
| | | | | | - Caroline Giraud
- U2RM Stress/Virulence, Normandy University, UNICAEN, 14000 Caen, France
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10
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Hao M, Ma W, Dong X, Li X, Cheng F, Wang Y. Comparative genome analysis of multidrug-resistant Pseudomonas aeruginosa JNQH-PA57, a clinically isolated mucoid strain with comprehensive carbapenem resistance mechanisms. BMC Microbiol 2021; 21:133. [PMID: 33932986 PMCID: PMC8088628 DOI: 10.1186/s12866-021-02203-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/19/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The prevalence of clinical multidrug-resistant (MDR) Pseudomonas aeruginosa has been increasing rapidly worldwide over the years and responsible for a wide range of acute and chronic infections with high mortalities. Although hundreds of complete genomes of clinical P. aeruginosa isolates have been sequenced, only a few complete genomes of mucoid strains are available, limiting a comprehensive understanding of this important group of opportunistic pathogens. Herein, the complete genome of a clinically isolated mucoid strain P. aeruginosa JNQH-PA57 was sequenced and assembled using Illumina and Oxford nanopore sequencing technologies. Genomic features, phylogenetic relationships, and comparative genomics of this pathogen were comprehensively analyzed using various bioinformatics tools. A series of phenotypic and molecular-genetic tests were conducted to investigate the mechanisms of carbapenem resistance in this strain. RESULTS Several genomic features of MDR P. aeruginosa JNQH-PA57 were identified based on the whole-genome sequencing. We found that the accessory genome of JNQH-PA57 including several prophages, genomic islands, as well as a PAPI-1 family integrative and conjugative element (ICE), mainly contributed to the larger genome of this strain (6,747,067 bp) compared to other popular P. aeruginosa strains (with an average genome size of 6,445,223 bp) listed in Pseudomonas Genome Database. Colony morphology analysis and biofilm crystal staining assay respectively demonstrated an enhanced alginate production and a thicker biofilm formation capability of JNQH-PA57. A deleted mutation at nt 424 presented in mucA gene, resulted in the upregulated expression of a sigma-factor AlgU and a GDP mannose dehydrogenase AlgD, which might explain the mucoid phenotype of this strain. As for the carbapenem resistance mechanisms, our results revealed that the interplay between impaired OprD porin, chromosomal β-lactamase OXA-488 expression, MexAB-OprM and MexXY-OprM efflux pumps overexpression, synergistically with the alginates-overproducing protective biofilm, conferred the high carbapenem resistance to P. aeruginosa JNQH-PA57. CONCLUSION Based on the genome analysis, we could demonstrate that the upregulated expression of algU and algD, which due to the truncation variant of MucA, might account for the mucoid phenotype of JNQH-PA57. Moreover, the resistance to carbapenem in P. aeruginosa JNQH-PA57 is multifactorial. The dataset presented in this study provided an essential genetic basis for the comprehensive cognition of the physiology, pathogenicity, and carbapenem resistance mechanisms of this clinical mucoid strain.
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Affiliation(s)
- Mingju Hao
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China
| | - Wanshan Ma
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China
| | - Xiutao Dong
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China
| | - Xiaofeng Li
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China
| | - Fang Cheng
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China
| | - Yujiao Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China.
- Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China.
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11
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Elucidating Essential Genes in Plant-Associated Pseudomonas protegens Pf-5 Using Transposon Insertion Sequencing. J Bacteriol 2021; 203:JB.00432-20. [PMID: 33257523 DOI: 10.1128/jb.00432-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/18/2020] [Indexed: 12/30/2022] Open
Abstract
Gene essentiality studies have been performed on numerous bacterial pathogens, but essential gene sets have been determined for only a few plant-associated bacteria. Pseudomonas protegens Pf-5 is a plant-commensal, biocontrol bacterium that can control disease-causing pathogens on a wide range of crops. Work on Pf-5 has mostly focused on secondary metabolism and biocontrol genes, but genome-wide approaches such as high-throughput transposon mutagenesis have not yet been used for this species. In this study, we generated a dense P. protegens Pf-5 transposon mutant library and used transposon-directed insertion site sequencing (TraDIS) to identify 446 genes essential for growth on rich media. Genes required for fundamental cellular machinery were enriched in the essential gene set, while genes related to nutrient biosynthesis, stress responses, and transport were underrepresented. The majority of Pf-5 essential genes were part of the P. protegens core genome. Comparison of the essential gene set of Pf-5 with those of two plant-associated pseudomonads, P. simiae and P. syringae, and the well-studied opportunistic human pathogen P. aeruginosa PA14 showed that the four species share a large number of essential genes, but each species also had uniquely essential genes. Comparison of the Pf-5 in silico-predicted and in vitro-determined essential gene sets highlighted the essential cellular functions that are over- and underestimated by each method. Expanding essentiality studies into bacteria with a range of lifestyles may improve our understanding of the biological processes important for bacterial survival and growth.IMPORTANCE Essential genes are those crucial for survival or normal growth rates in an organism. Essential gene sets have been identified in numerous bacterial pathogens but only a few plant-associated bacteria. Employing genome-wide approaches, such as transposon insertion sequencing, allows for the concurrent analyses of all genes of a bacterial species and rapid determination of essential gene sets. We have used transposon insertion sequencing to systematically analyze thousands of Pseudomonas protegens Pf-5 genes and gain insights into gene functions and interactions that are not readily available using traditional methods. Comparing Pf-5 essential genes with those of three other pseudomonads highlights how gene essentiality varies between closely related species.
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12
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Camus L, Vandenesch F, Moreau K. From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment. Microb Genom 2021; 7:mgen000513. [PMID: 33529147 PMCID: PMC8190622 DOI: 10.1099/mgen.0.000513] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa is one of the main microbial species colonizing the lungs of cystic fibrosis patients and is responsible for the decline in respiratory function. Despite the hostile pulmonary environment, P. aeruginosa is able to establish chronic infections thanks to its strong adaptive capacity. Various longitudinal studies have attempted to compare the strains of early infection with the adapted strains of chronic infection. Thanks to new '-omics' techniques, convergent genetic mutations, as well as transcriptomic and proteomic dysregulations have been identified. As a consequence of this evolution, the adapted strains of P. aeruginosa have particular phenotypes that promote persistent infection.
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Affiliation(s)
- Laura Camus
- CIRI – Centre International de Recherche en Infectiologie, Université de Lyon/Inserm U1111/Université Claude Bernard Lyon 1/CNRS UMR5308/ENS de Lyon, Lyon, France
| | - François Vandenesch
- CIRI – Centre International de Recherche en Infectiologie, Université de Lyon/Inserm U1111/Université Claude Bernard Lyon 1/CNRS UMR5308/ENS de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Karen Moreau
- CIRI – Centre International de Recherche en Infectiologie, Université de Lyon/Inserm U1111/Université Claude Bernard Lyon 1/CNRS UMR5308/ENS de Lyon, Lyon, France
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13
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León LM, Park AE, Borges AL, Zhang JY, Bondy-Denomy J. Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa. Nucleic Acids Res 2021; 49:2114-2125. [PMID: 33544853 PMCID: PMC7913775 DOI: 10.1093/nar/gkab006] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/04/2020] [Accepted: 01/05/2021] [Indexed: 12/27/2022] Open
Abstract
Bacteria deploy multiple defenses to prevent mobile genetic element (MGEs) invasion. CRISPR-Cas immune systems use RNA-guided nucleases to target MGEs, which counter with anti-CRISPR (Acr) proteins. Our understanding of the biology and co-evolutionary dynamics of the common Type I-C CRISPR-Cas subtype has lagged because it lacks an in vivo phage-host model system. Here, we show the anti-phage function of a Pseudomonas aeruginosa Type I-C CRISPR-Cas system encoded on a conjugative pKLC102 island, and its Acr-mediated inhibition by distinct MGEs. Seven genes with anti-Type I-C function (acrIC genes) were identified, many with highly acidic amino acid content, including previously described DNA mimic AcrIF2. Four of the acr genes were broad spectrum, also inhibiting I-E or I-F P. aeruginosa CRISPR-Cas subtypes. Dual inhibition comes at a cost, however, as simultaneous expression of Type I-C and I-F systems renders phages expressing the dual inhibitor AcrIF2 more sensitive to targeting. Mutagenesis of numerous acidic residues in AcrIF2 did not impair anti-I-C or anti-I-F function per se but did exacerbate inhibition defects during competition, suggesting that excess negative charge may buffer DNA mimics against competition. Like AcrIF2, five of the Acr proteins block Cascade from binding DNA, while two function downstream, likely preventing Cas3 recruitment or activity. One such inhibitor, AcrIC3, is found in an 'anti-Cas3' cluster within conjugative elements, encoded alongside bona fide Cas3 inhibitors AcrIF3 and AcrIE1. Our findings demonstrate an active battle between an MGE-encoded CRISPR-Cas system and its diverse MGE targets.
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Affiliation(s)
- Lina M León
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Allyson E Park
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adair L Borges
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jenny Y Zhang
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Innovative Genomics Institute, Berkeley, CA 94720, USA
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14
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Tn 6603, a Carrier of Tn 5053 Family Transposons, Occurs in the Chromosome and in a Genomic Island of Pseudomonas aeruginosa Clinical Strains. Microorganisms 2020; 8:microorganisms8121997. [PMID: 33333808 PMCID: PMC7765201 DOI: 10.3390/microorganisms8121997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022] Open
Abstract
Transposons of the Pseudomonasaeruginosa accessory gene pool contribute to phenotype and to genome plasticity. We studied local P. aeruginosa strains to ascertain the encroachment of mer-type res site hunter transposons into clinical settings and their associations with other functional modules. Five different Tn5053 family transposons were detected, all chromosomal. Some were solitary elements; one was in res of Tn1013#, a relative of a reported carrier of int-type res site hunters (class 1 integrons), but most were in res of Tn6603, a new Tn501-related transposon of unknown phenotype. Most of the Tn6603::Tn elements, and some Tn6603 and Tn6603::Tn elements found in GenBank sequences, were at identical sites in an hypothetical gene of P. aeruginosa genomic island PAGI-5v. The island in clonally differing strains was at either of two tRNALys loci, suggesting lateral transfer to these sites. This observation is consistent with the membership of the prototype PAGI-5 island to the ICE family of mobile genetic elements. Additionally, the res site hunters in the nested transposons occupied different positions in the Tn6603 carrier. This suggested independent insertion events on five occasions at least. Tn5053 family members that were mer-/tni-defective were found in Tn6603- and Tn501-like carriers in GenBank sequences of non-clinical Pseudomonas spp. The transposition events in these cases presumably utilized tni functions in trans, as can occur with class 1 integrons. We suggest that in the clinical context, P. aeruginosa strains that carry Tn6603 alone or in PAGI-5v can serve to disseminate functional res site hunters; these in turn can provide the requisite trans-acting tni functions to assist in the dissemination of class 1 integrons, and hence of their associated antibiotic resistance determinants.
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15
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Perez MF, Kurth D, Farías ME, Soria MN, Castillo Villamizar GA, Poehlein A, Daniel R, Dib JR. First Report on the Plasmidome From a High-Altitude Lake of the Andean Puna. Front Microbiol 2020; 11:1343. [PMID: 32655530 PMCID: PMC7324554 DOI: 10.3389/fmicb.2020.01343] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022] Open
Abstract
Mobile genetic elements, including plasmids, drive the evolution of prokaryotic genomes through the horizontal transfer of genes allowing genetic exchange between bacteria. Moreover, plasmids carry accessory genes, which encode functions that may offer an advantage to the host. Thus, it is expected that in a certain ecological niche, plasmids are enriched in accessory functions, which are important for their hosts to proliferate in that niche. Puquio de Campo Naranja is a high-altitude lake from the Andean Puna exposed to multiple extreme conditions, including high UV radiation, alkalinity, high concentrations of arsenic, heavy metals, dissolved salts, high thermal amplitude and low O2 pressure. Microorganisms living in this lake need to develop efficient mechanisms and strategies to cope under these conditions. The aim of this study was to characterize the plasmidome of microbialites from Puquio de Campo Naranja, and identify potential hosts and encoded functions using a deep-sequencing approach. The potential ecological impact of the plasmidome, including plasmids from cultivable and non-cultivable microorganisms, is described for the first time in a lake representing an extreme environment of the Puna. This study showed that the recovered genetic information for the plasmidome was novel in comparison to the metagenome derived from the same environment. The study of the total plasmid population allowed the identification of genetic features typically encoded by plasmids, such as resistance and virulence factors. The resistance genes comprised resistances to heavy metals, antibiotics and stress factors. These results highlight the key role of plasmids for their hosts and impact of extrachromosomal elements to thrive in a certain ecological niche.
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Affiliation(s)
- María Florencia Perez
- Planta Piloto de Procesos Industriales Microbiológicos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Argentina
| | - Daniel Kurth
- Planta Piloto de Procesos Industriales Microbiológicos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Argentina
| | - María Eugenia Farías
- Planta Piloto de Procesos Industriales Microbiológicos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Argentina
| | - Mariana Noelia Soria
- Planta Piloto de Procesos Industriales Microbiológicos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Argentina
| | - Genis Andrés Castillo Villamizar
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany.,Línea Tecnológica Biocorrosión, Corporación para la Investigación de la Corrosión C.I.C., Piedecuesta, Colombia
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Julián Rafael Dib
- Planta Piloto de Procesos Industriales Microbiológicos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Argentina.,Facultad de Bioquímica, Química y Farmacia, Instituto de Microbiología, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
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16
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van Wolferen M, Shajahan A, Heinrich K, Brenzinger S, Black IM, Wagner A, Briegel A, Azadi P, Albers SV. Species-Specific Recognition of Sulfolobales Mediated by UV-Inducible Pili and S-Layer Glycosylation Patterns. mBio 2020; 11:e03014-19. [PMID: 32156822 PMCID: PMC7064770 DOI: 10.1128/mbio.03014-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/21/2020] [Indexed: 01/07/2023] Open
Abstract
The UV-inducible pili system of Sulfolobales (Ups) mediates the formation of species-specific cellular aggregates. Within these aggregates, cells exchange DNA to repair DNA double-strand breaks via homologous recombination. Substitution of the Sulfolobus acidocaldarius pilin subunits UpsA and UpsB with their homologs from Sulfolobus tokodaii showed that these subunits facilitate species-specific aggregation. A region of low conservation within the UpsA homologs is primarily important for this specificity. Aggregation assays in the presence of different sugars showed the importance of N-glycosylation in the recognition process. In addition, the N-glycan decorating the S-layer of S. tokodaii is different from the one of S. acidocaldarius Therefore, each Sulfolobus species seems to have developed a unique UpsA binding pocket and unique N-glycan composition to ensure aggregation and, consequently, also DNA exchange with cells from only the same species, which is essential for DNA repair by homologous recombination.IMPORTANCE Type IV pili can be found on the cell surface of many archaea and bacteria where they play important roles in different processes. The UV-inducible pili system of Sulfolobales (Ups) pili from the crenarchaeal Sulfolobales species are essential in establishing species-specific mating partners, thereby assisting in genome stability. With this work, we show that different Sulfolobus species have specific regions in their Ups pili subunits, which allow them to interact only with cells from the same species. Additionally, different Sulfolobus species have unique surface-layer N-glycosylation patterns. We propose that the unique features of each species allow the recognition of specific mating partners. This knowledge for the first time gives insights into the molecular basis of archaeal self-recognition.
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Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology II-Microbiology, University of Freiburg, Freiburg, Germany
| | - Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia, USA
| | - Kristina Heinrich
- Molecular Biology of Archaea, Institute of Biology II-Microbiology, University of Freiburg, Freiburg, Germany
| | | | - Ian M Black
- Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia, USA
| | - Alexander Wagner
- Molecular Biology of Archaea, Institute of Biology II-Microbiology, University of Freiburg, Freiburg, Germany
| | - Ariane Briegel
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia, USA
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II-Microbiology, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
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17
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ICEKp2: description of an integrative and conjugative element in Klebsiella pneumoniae, co-occurring and interacting with ICEKp1. Sci Rep 2019; 9:13892. [PMID: 31554924 PMCID: PMC6761156 DOI: 10.1038/s41598-019-50456-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/11/2019] [Indexed: 12/28/2022] Open
Abstract
Klebsiella pneumoniae is a human pathogen, prominent in antimicrobial-resistant and nosocomial infection. The integrative and conjugative element ICEKp1 is present in a third of clinical isolates and more prevalent in invasive disease; it provides genetic diversity and enables the spread of virulence-associated genes. We report a second integrative conjugative element that can co-occur with ICEKp1 in K. pneumoniae. This element, ICEKp2, is similar to the Pseudomonas aeruginosa pathogenicity island PAPI. We identified ICEKp2 in K. pneumoniae sequence types ST11, ST258 and ST512, which are associated with carbapenem-resistant outbreaks in China and the US, including isolates with and without ICEKp1. ICEKp2 was competent for excision, but self-mobilisation to recipient Escherichia coli was not detected. In an isolate with both elements, ICEKp2 positively influenced the efficiency of plasmid mobilisation driven by ICEKp1. We propose a putative mechanism, in which a Mob2 ATPase of ICEKp2 may contribute to the ICEKp1 conjugation machinery. Supporting this mechanism, mob2, but not a variant with mutations in the ATPase motif, restored transfer efficiency to an ICEKp2 knockout. This is the first demonstration of the interaction between integrative and conjugative genetic elements in a single Gram-negative bacterium with implications for understanding evolution by horizontal gene transfer.
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18
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Salmonella Genomic Island 3 Is an Integrative and Conjugative Element and Contributes to Copper and Arsenic Tolerance of Salmonella enterica. Antimicrob Agents Chemother 2019; 63:AAC.00429-19. [PMID: 31209002 DOI: 10.1128/aac.00429-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/07/2019] [Indexed: 01/26/2023] Open
Abstract
Salmonella genomic island 3 (SGI3) was first described as a chromosomal island in Salmonella 4,[5],12:i:-, a monophasic variant of Salmonella enterica subsp. enterica serovar Typhimurium. The SGI3 DNA sequence detected from Salmonella 4,[5],12:i:- isolated in Japan was identical to that of a previously reported one across entire length of 81 kb. SGI3 consists of 86 open reading frames, including a copper homeostasis and silver resistance island (CHASRI) and an arsenic tolerance operon, in addition to genes related to conjugative transfer and DNA replication or partitioning, suggesting that the island is a mobile genetic element. We successfully selected transconjugants that acquired SGI3 after filter-mating experiments using the S. enterica serovars Typhimurium, Heidelberg, Hadar, Newport, Cerro, and Thompson as recipients. Southern blot analysis using I-CeuI-digested genomic DNA demonstrated that SGI3 was integrated into a chromosomal fragment of the transconjugants. PCR and sequencing analysis demonstrated that SGI3 was inserted into the 3' end of the tRNA genes pheV or pheR The length of the target site was 52 or 55 bp, and a 55-bp attI sequence indicating generation of the circular form of SGI3 was also detected. The transconjugants had a higher MIC against CuSO4 compared to the recipient strains under anaerobic conditions. Tolerance was defined by the cus gene cluster in the CHASRI. The transconjugants also had distinctly higher MICs against Na2HAsO4 compared to recipient strains under aerobic conditions. These findings clearly demonstrate that SGI3 is an integrative and conjugative element and contributes to the copper and arsenic tolerance of S. enterica.
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19
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Flores-Ríos R, Quatrini R, Loyola A. Endogenous and Foreign Nucleoid-Associated Proteins of Bacteria: Occurrence, Interactions and Effects on Mobile Genetic Elements and Host's Biology. Comput Struct Biotechnol J 2019; 17:746-756. [PMID: 31303979 PMCID: PMC6606824 DOI: 10.1016/j.csbj.2019.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 02/08/2023] Open
Abstract
Mobile Genetic Elements (MGEs) are mosaics of functional gene modules of diverse evolutionary origin and are generally divergent from the hosts´ genetic background. Existing biases in base composition and codon usage of these elements` genes impose transcription and translation limitations that may affect the physical and regulatory integration of MGEs in new hosts. Stable appropriation of the foreign DNA depends on a number of host factors among which are the Nucleoid-Associated Proteins (NAPs). These small, basic, highly abundant proteins bind and bend DNA, altering its topology and folding, thereby affecting all known essential DNA metabolism related processes. Both chromosomally- (endogenous) and MGE- (foreign) encoded NAPs have been shown to exist in bacteria. While the role of host-encoded NAPs in xenogeneic silencing of both episomal (plasmids) and integrative MGEs (pathogenicity islands and prophages) is well acknowledged, less is known about the role of MGE-encoded NAPs in the foreign elements biology or their influence on the host's chromosome expression dynamics. Here we review existing literature on the topic, present examples on the positive and negative effects that endogenous and foreign NAPs exert on global transcriptional gene expression, MGE integrative and excisive recombination dynamics, persistence and transfer to suitable hosts and discuss the nature and relevance of synergistic and antagonizing higher order interactions between diverse types of NAPs.
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Affiliation(s)
| | - Raquel Quatrini
- Fundación Ciencia y Vida, Avenida Zañartu 1482, Ñuñoa, Santiago, Chile.,Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - Alejandra Loyola
- Fundación Ciencia y Vida, Avenida Zañartu 1482, Ñuñoa, Santiago, Chile
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20
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Wu H, Wang D, Tang M, Ma LZ. The advance of assembly of exopolysaccharide Psl biosynthesis machinery in Pseudomonas aeruginosa. Microbiologyopen 2019; 8:e857. [PMID: 31070012 PMCID: PMC6813494 DOI: 10.1002/mbo3.857] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 01/25/2023] Open
Abstract
Biofilms are microbial communities embedded in extracellular matrix. Exopolysaccharide Psl (ePsl) is a key biofilm matrix component that initiates attachment, maintains biofilms architecture, and protects bacteria within biofilms of Pseudomonas aeruginosa, an opportunistic pathogen. There are at least 12 Psl proteins involved in the biosynthesis of this exopolysaccharide. However, it remains unclear about the function of each Psl protein and how these proteins work together during the biosynthesis of ePsl. PslG has been characterized as a degrader of ePsl in extracellular or periplasm and PslD is predicted to be a transporter. In this study, we found that PslG and its glycoside hydrolytic activity were also involved in the biosynthesis of ePsl. PslG localized mainly in the inner membrane and some in the periplasm. The inner membrane association of PslG was critical for the biosynthesis of ePsl. The expression of PslA, PslD, and PslE helped PslG remain in the inner membrane. The bacterial two‐hybrid results suggested that PslE could interacted with either PslA, PslD, or PslG. The strongest interaction was found between PslE and PslD. Consistently, PslD was disabled to localize on the outer membrane in the ΔpslE strain, suggesting that the PslE‐PslD interaction affected the localization of PslD. Our results shed light on the assembly of ePsl biosynthesis machinery and suggested that the membrane‐associated PslG was a part of ePsl biosynthesis proteins complex.
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Affiliation(s)
- Huijun Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Di Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Maomao Tang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Luyan Z Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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Flores-Ríos R, Moya-Beltrán A, Pareja-Barrueto C, Arenas-Salinas M, Valenzuela S, Orellana O, Quatrini R. The Type IV Secretion System of ICE Afe1: Formation of a Conjugative Pilus in Acidithiobacillus ferrooxidans. Front Microbiol 2019; 10:30. [PMID: 30804894 PMCID: PMC6370655 DOI: 10.3389/fmicb.2019.00030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/09/2019] [Indexed: 01/10/2023] Open
Abstract
The dispersal of mobile genetic elements and their gene cargo relies on type IV secretion systems (T4SS). In this work the ICEAfe1 Tra-type T4SS nanomachine, encoded in the publicly available genome of Acidithiobacillus ferrooxidans ATCC 23270TY, was characterized in terms of its organization, conservation, expression and mating bridge formation. Twenty-one conjugative genes grouped in four genetic clusters encode the ICEAfe1 T4SS, containing all the indispensable functions for the formation and stabilization of the pili and for DNA processing. The clusters' organization resembles that of other mobile genetic elements (such as plasmids and integrative and conjugative elements-ICEs). Sequence conservation, genetic organization and distribution of the tra system in the genomes of other sequenced Acidithiobacillus spp. suggests that the ICEAfe1 T4SS could mediate the lateral gene transfer between related bacteria. All ICEAfe1 T4SS genes are transcriptionally active and expressed from four independent operons. The transcriptional levels of selected marker genes increase in response to Mitomycin C treatment, a DNA damage elicitor that has acknowledged stimulatory effects on excision rates and gene expression of other ICEs, including ICEAfe1. Using a tailor-made pilin-antiserum against ICEAfe1 T4SS TraA pilin and epifluorescence microscopy, the presence of the conjugative pili on the cell surface of A. ferrooxidans could be demonstrated. Additionally, immunodetection assays, by immunogold, allowed the identification of pili-like extracellular structures. Together, the results obtained in this work demonstrate that the ICEAfe1 T4SS is phylogenetically conserved within the taxon, is expressed at mRNA and protein levels in vivo in the A. ferrooxidans type strain, and produces a pili-like structure of extracellular and intercellular localization in this model acidophile, supporting its functionality. Additional efforts will be required to prove conjugation of the ICEAfe1 or parts of this element through the cognate T4SS.
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Affiliation(s)
- Rodrigo Flores-Ríos
- Fundación Ciencia y Vida, Santiago, Chile.,Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Ana Moya-Beltrán
- Fundación Ciencia y Vida, Santiago, Chile.,Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | | | - Mauricio Arenas-Salinas
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | | | - Omar Orellana
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Raquel Quatrini
- Fundación Ciencia y Vida, Santiago, Chile.,Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
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Bahramian A, Khoshnood S, Shariati A, Doustdar F, Chirani AS, Heidary M. Molecular characterization of the pilS2 gene and its association with the frequency of Pseudomonas aeruginosa plasmid pKLC102 and PAPI-1 pathogenicity island. Infect Drug Resist 2019; 12:221-227. [PMID: 30666137 PMCID: PMC6333160 DOI: 10.2147/idr.s188527] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION Pseudomonas aeruginosa is the most common opportunistic pathogen associated with a broad range of infections, including cystic fibrosis, ocular, otitis media, and burn infections. The aim of this study was to show the frequency of the pilS2 gene, and its association with P. aeruginosa plasmid pKLC102 and PAPI-1 pathogenicity island among P. aeruginosa strains. METHODS The samples were collected from patients with cystic fibrosis, ocular, otitis media, and burn infections between January 2016 and November 2017. DNA was extracted using the DNA extraction kit and was used for PCR assay. PCR with 4 primer-pairs including 976 F/PAPI-1R, 4542 F/intF, SojR/4541 F, and intF/sojR was performed to identify PAPI-1. pKLC102 was detected using three other primer-pairs including cp10F/cp10R, cp44F/cp44R, and cp97F/cp97R. RESULTS A total of 112 P. aeruginosa isolates were collected from patients with cystic fibrosis (36), burn (20), otitis media (26), and ocular (30) infections. The results of PCR showed that pilS2 gene was identified in 96 (85%) strains. PAPI-1-attB integration was detected among 38 (33.9%) isolates and the circular form of PAPI-1 detected among 17 (14%) isolates. In addition, 79 (70.5%) strains were found to be positive for pKLC102. CONCLUSION We found that the majority of the isolates may be susceptible to transfer this significant island and the related element pKLC102 into recipient isolates lacking the island owing to high association of the PilS2 pilus with the islands in the studied strains. It is anticipated that strains isolated from burn and eye with the highest rate of PilS2, PAPI-1, and pKLC102 association have a high level of antibiotic resistance.
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Affiliation(s)
- Aghil Bahramian
- Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeed Khoshnood
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Aref Shariati
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farahnoosh Doustdar
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Salimi Chirani
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Heidary
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Student Research Committee, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
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23
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Wrobel A, Ottoni C, Leo JC, Linke D. pYR4 From a Norwegian Isolate of Yersinia ruckeri Is a Putative Virulence Plasmid Encoding Both a Type IV Pilus and a Type IV Secretion System. Front Cell Infect Microbiol 2018; 8:373. [PMID: 30460204 PMCID: PMC6232867 DOI: 10.3389/fcimb.2018.00373] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/04/2018] [Indexed: 01/14/2023] Open
Abstract
Enteric redmouth disease caused by the pathogen Yersinia ruckeri is a significant problem for fish farming around the world. Despite its importance, only a few virulence factors of Y. ruckeri have been identified and studied in detail. Here, we report and analyze the complete DNA sequence of pYR4, a plasmid from a highly pathogenic Norwegian Y. ruckeri isolate, sequenced using PacBio SMRT technology. Like the well-known pYV plasmid of human pathogenic Yersiniae, pYR4 is a member of the IncFII family. Thirty-one percent of the pYR4 sequence is unique compared to other Y. ruckeri plasmids. The unique regions contain, among others genes, a large number of mobile genetic elements and two partitioning systems. The G+C content of pYR4 is higher than that of the Y. ruckeri NVH_3758 genome, indicating its relatively recent horizontal acquisition. pYR4, as well as the related plasmid pYR3, comprises operons that encode for type IV pili and for a conjugation system (tra). In contrast to other Yersinia plasmids, pYR4 cannot be cured at elevated temperatures. Our study highlights the power of PacBio sequencing technology for identifying mis-assembled segments of genomic sequences. Comparative analysis of pYR4 and other Y. ruckeri plasmids and genomes, which were sequenced by second and the third generation sequencing technologies, showed errors in second generation sequencing assemblies. Specifically, in the Y. ruckeri 150 and Y. ruckeri ATCC29473 genome assemblies, we mapped the entire pYR3 plasmid sequence. Placing plasmid sequences on the chromosome can result in erroneous biological conclusions. Thus, PacBio sequencing or similar long-read methods should always be preferred for de novo genome sequencing. As the tra operons of pYR3, although misplaced on the chromosome during the genome assembly process, were demonstrated to have an effect on virulence, and type IV pili are virulence factors in many bacteria, we suggest that pYR4 directly contributes to Y. ruckeri virulence.
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Affiliation(s)
| | - Claudio Ottoni
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Jack C Leo
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Dirk Linke
- Department of Biosciences, University of Oslo, Oslo, Norway
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24
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Campos Calero G, Caballero Gómez N, Benomar N, Pérez Montoro B, Knapp CW, Gálvez A, Abriouel H. Deciphering Resistome and Virulome Diversity in a Porcine Slaughterhouse and Pork Products Through Its Production Chain. Front Microbiol 2018; 9:2099. [PMID: 30258416 PMCID: PMC6144875 DOI: 10.3389/fmicb.2018.02099] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/16/2018] [Indexed: 12/11/2022] Open
Abstract
We aimed to better understand resistome and virulome patterns on animal and process-area surfaces through a pig slaughterhouse to track possible contamination within the food production chain. Culture-dependent methods revealed high levels of microbial contamination, corresponding to mesophilic and pathogenic bacteria on both the animal and process-area surfaces mainly in the anesthesia (AA and AS) zone followed by “scorching and whip” (FA and FS) zone and also in the end products. To evaluate the potential risk of antibiotic resistance and virulence determinants, shotgun metagenomic DNA-sequencing of isolates from selected areas/products uncovered a high diversity and richness of antibiotic resistance genes (ARGs): 55–62 genes in the anesthesia area (AA and AS) and 35–40 in “animal-arrival zone” (MA and MS). The “scorching and whip” (FA and FS) area, however, exhibited lowered abundance of ARGs (1–6), indicating that the scalding and depilating process (an intermediate zone between “anesthesia” and “scorching and whip”) significantly decreased bacterial load by 1–3 log10 but also diminished the resistome. The high prevalence of antibiotic-inactivating enzyme genes in the “animal-arrival zone” (60–65%) and “anesthesia” area (56%) were mainly represented by those for aminoglycoside (46–51%) and lincosamide (14–19%) resistance, which did not reflect selective pressures by antibiotics most commonly used in pig therapy—tetracyclines and beta-lactams. Contrary to ARGs, greater number of virulence resistance genes were detected after evisceration in some products such as kidney, which reflected the poor hygienic practices. More than 19 general virulence features—mainly adherence, secretion system, chemotaxis and motility, invasion and motility were detected in some products. However, immune evasion determinants were detected in almost all samples analyzed from the beginning of the process, with highest amounts found from the anesthesia area. We conclude that there are two main sources of contamination in a pig slaughterhouse: the microorganisms carried on the animals’ hide, and those from the evisceration step. As such, focussing control measures, e.g., enhanced disinfection procedures, on these contamination-source areas may reduce risks to food safety and consumer health, since the antibiotic and virulence determinants may spread to end products and the environment; further, ARG and virulence traits can exacerbate pathogen treatments.
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Affiliation(s)
- Guillermo Campos Calero
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Natacha Caballero Gómez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Nabil Benomar
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Beatriz Pérez Montoro
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Charles W Knapp
- Centre for Water, Environment, Sustainability & Public Health, Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, United Kingdom
| | - Antonio Gálvez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Hikmate Abriouel
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
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25
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Barton IS, Fuqua C, Platt TG. Ecological and evolutionary dynamics of a model facultative pathogen: Agrobacterium and crown gall disease of plants. Environ Microbiol 2018; 20:16-29. [PMID: 29105274 PMCID: PMC5764771 DOI: 10.1111/1462-2920.13976] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 10/20/2017] [Accepted: 10/25/2017] [Indexed: 01/09/2023]
Abstract
Many important pathogens maintain significant populations in highly disparate disease and non-disease environments. The consequences of this environmental heterogeneity in shaping the ecological and evolutionary dynamics of these facultative pathogens are incompletely understood. Agrobacterium tumefaciens, the causative agent for crown gall disease of plants has proven a productive model for many aspects of interactions between pathogens and their hosts and with other microbes. In this review, we highlight how this past work provides valuable context for the use of this system to examine how heterogeneity and transitions between disease and non-disease environments influence the ecology and evolution of facultative pathogens. We focus on several features common among facultative pathogens, such as the physiological remodelling required to colonize hosts from environmental reservoirs and the consequences of competition with host and non-host associated microbiota. In addition, we discuss how the life history of facultative pathogens likely often results in ecological tradeoffs associated with performance in disease and non-disease environments. These pathogens may therefore have different competitive dynamics in disease and non-disease environments and are subject to shifting selective pressures that can result in pathoadaptation or the within-host spread of avirulent phenotypes.
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Affiliation(s)
- Ian S. Barton
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Thomas G. Platt
- Division of Biology, Kansas State University, Manhattan, KS, USA
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26
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Bañuelos-Vazquez LA, Torres Tejerizo G, Brom S. Regulation of conjugative transfer of plasmids and integrative conjugative elements. Plasmid 2017; 91:82-89. [DOI: 10.1016/j.plasmid.2017.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 10/25/2022]
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27
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Morales-Espinosa R, Delgado G, Espinosa LF, Isselo D, Méndez JL, Rodriguez C, Miranda G, Cravioto A. Fingerprint Analysis and Identification of Strains ST309 as a Potential High Risk Clone in a Pseudomonas aeruginosa Population Isolated from Children with Bacteremia in Mexico City. Front Microbiol 2017; 8:313. [PMID: 28298909 PMCID: PMC5331068 DOI: 10.3389/fmicb.2017.00313] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/15/2017] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen and is associated with nosocomial infections. Its ability to thrive in a broad range of environments is due to a large and diverse genome of which its accessory genome is part. The objective of this study was to characterize P. aeruginosa strains isolated from children who developed bacteremia, using pulse-field gel electrophoresis, and in terms of its genomic islands, virulence genes, multilocus sequence type, and antimicrobial susceptibility. Our results showed that P. aeruginosa strains presented the seven virulence genes: toxA, lasB, lecA, algR, plcH, phzA1, and toxR, a type IV pilin alleles (TFP) group I or II. Additionally, we detected a novel pilin and accessory gene, expanding the number of TFP alleles to group VI. All strains presented the PAPI-2 Island and the majority were exoU+ and exoS+ genotype. Ten percent of the strains were multi-drug resistant phenotype, 18% extensively drug-resistant, 68% moderately resistant and only 3% were susceptible to all the antimicrobial tested. The most prevalent acquired β-Lactamase was KPC. We identified a group of ST309 strains, as a potential high risk clone. Our finding also showed that the strains isolated from patients with bacteremia have important virulence factors involved in colonization and dissemination as: a TFP group I or II; the presence of the exoU gene within the PAPI-2 island and the presence of the exoS gene.
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Affiliation(s)
- Rosario Morales-Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México Mexico City, Mexico
| | - Gabriela Delgado
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México Mexico City, Mexico
| | - Luis F Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México Mexico City, Mexico
| | - Dassaev Isselo
- Servicio de Pediatría, Hospital Regional 36 San Alejandro, IMSS Puebla, Mexico
| | - José L Méndez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México Mexico City, Mexico
| | - Cristina Rodriguez
- Laboratorio de Bacteriología, Facultad de Veterinaria y Zootecnia, Universidad Nacional Autónoma de México Mexico City, Mexico
| | - Guadalupe Miranda
- Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Unidad de Investigación en Epidemiología Hospitalaria Mexico City, Mexico
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28
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Hong TP, Carter MQ, Struffi P, Casonato S, Hao Y, Lam JS, Lory S, Jousson O. Conjugative type IVb pilus recognizes lipopolysaccharide of recipient cells to initiate PAPI-1 pathogenicity island transfer in Pseudomonas aeruginosa. BMC Microbiol 2017; 17:31. [PMID: 28173753 PMCID: PMC5297154 DOI: 10.1186/s12866-017-0943-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 02/03/2017] [Indexed: 12/31/2022] Open
Abstract
Background Pseudomonas aeruginosa pathogenicity island 1 (PAPI-1) is one of the largest genomic islands of this important opportunistic human pathogen. Previous studies have shown that PAPI-1 encodes several putative virulence factors, including a major regulator of biofilm formation and antibiotic-resistance traits. PAPI-1 is horizontally transferable into recipient strains lacking this island via conjugation mediated by the specialized type IV pilus. The PAPI-1 encodes a cluster of ten genes associated with the synthesis and assembly of the type IV pilus. The PAPI-1 acquisition mechanism is currently not well understood. Results In this study, we performed a series of conjugation experiments and identified determinants of PAPI-1 acquisition by analyzing transfer efficiency between the donor and a series of mutant recipient strains. Our data show that common polysaccharide antigen (CPA) lipopolysaccharide (LPS), a homopolymer of D-rhamnose, is required for initiating PAPI-1 transfer, suggesting that this structure acts as a receptor for conjugative type IV pilus in recipient strains. These results were substantiated by experimental evidence from PAPI-1 transfer assay experiments, in which outer membrane or LPS preparations from well-defined LPS mutants were added to the transfer mix to assess the role of P. aeruginosa LPS in PAPI-1 transfer and in vitro binding experiments between pilin fusion protein GST-pilV2’ and immobilized LPS molecules were performed. Our data also showed that P. aeruginosa strains that had already acquired a copy of PAPI-1 were unable to import additional copies of the island, and that such strains produced proportionally lower amounts of CPA LPS compared to the strains lacking PAPI-1. Conclusions These results suggest that a PAPI-1 exclusion mechanism exists in P. aeruginosa that might serve to regulate the avoidance of uncontrolled expansions of the bacterial genome. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0943-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Toan Phuoc Hong
- Centre for Integrative Biology, University of Trento, 38123, Trento, Italy
| | - Michelle Q Carter
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Paolo Struffi
- Centre for Integrative Biology, University of Trento, 38123, Trento, Italy
| | - Stefano Casonato
- Centre for Integrative Biology, University of Trento, 38123, Trento, Italy
| | - Youai Hao
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Joseph S Lam
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Stephen Lory
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Olivier Jousson
- Centre for Integrative Biology, University of Trento, 38123, Trento, Italy.
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N M, J M, V U, H N M. Unraveling genomic and phenotypic nature of multidrug-resistant (MDR) Pseudomonas aeruginosa VRFPA04 isolated from keratitis patient. Microbiol Res 2016; 193:140-149. [PMID: 27825482 DOI: 10.1016/j.micres.2016.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 09/29/2016] [Accepted: 10/08/2016] [Indexed: 02/07/2023]
Abstract
Multidrug-resistant (MDR) Pseudomonas aeruginosa VRFPA04, obtained from a keratitis patient was found to exhibit resistance to betalactam (Penicillins, cephalosporins, including carbapenems, except aztreonam), aminoglycosides, quinolone group of drugs and susceptible to colistin. The complete genome sequencing of the ocular isolate to measure and ascertain the degree of multidrug resistance in VRFPA04 strain resulted in 6,818,030bp (6.8Mb) genome sizes, which happen to be the third largest genome available in the Genbank to date. Two chromosomally integrated class I integrons carrying blaVIM-2 carbapenemase gene, multiple secretory systems consisting of types I-VI and VIII proteins and ocular virulence factors exo-T, Y, U and exotoxin A, a gene that inhibits protein synthesis which could have caused corneal cell death and Phytohormone auxin biosynthetic protein were detected in the genome of VRFPA04 Genome. In addition, 58 Regions of Genomic Plasticity (RGPs) regions, multiple phage genomes, genomic islands, CRISPR genes and RND family efflux pumps, such as MexCD-OprJ and MexEF-OprN and its regulators, MexT and MexR, were unraveled in VRFPA04. Thus, the current study reveals the virulence factors and resistome nature of an ocular isolate P aeruginosa VRFPA04 genome.
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Affiliation(s)
- Murugan N
- Dept of Microbiology, L & T Microbiology Research Centre, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, 6000 06, India; School of Chemical & Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, 613401, India
| | - Malathi J
- Dept of Microbiology, L & T Microbiology Research Centre, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, 6000 06, India.
| | - Umashankar V
- Centre for Bioinformatics, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, 6000 06, India
| | - Madhavan H N
- Dept of Microbiology, L & T Microbiology Research Centre, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, 6000 06, India
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30
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Kang Y, Gu X, Hao Y, Hu J. Autoclave treatment of pig manure does not reduce the risk of transmission and transfer of tetracycline resistance genes in soil: successive determinations with soil column experiments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:4551-4560. [PMID: 26517996 DOI: 10.1007/s11356-015-5671-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 10/21/2015] [Indexed: 06/05/2023]
Abstract
The increasing use of antibiotics, especially tetracycline, in livestock feed adversely affects animal health and ecological integrity. Therefore, approaches to decrease this risk are urgently needed. High temperatures facilitate antibiotic degradation; whether this reduces transmission risk and transfer of tetracycline-resistant bacteria (TRBs) and tetracycline resistance genes (TRGs) in soil remains unknown. Successive experiments with soil columns evaluated the effects of autoclaving pig manure (APM) on soil TRB populations and TRGs over time at different soil depths. The data showed sharp increases in TRB populations and TRGs in each subsoil layer of PM (non-APM) and APM treatments within 30 days, indicating that TRBs and TRGs transferred rapidly. The level of TRBs in the upper soil layers was approximately 15-fold higher than in subsoils. TRBs were not dependent on PM and APM levels, especially in the late phase. Nevertheless, higher levels of APM led to rapid expansion of TRBs as compared to PM. Moreover, temporal changes in TRB frequencies in total culturable bacteria (TCBs) were similar to TRBs, indicating that the impact of PM or APM on TRBs was more obvious than for TCBs. TRBs were hypothesized to depend on the numbers of TRGs and indigenous recipient bacteria. In the plough layer, five TRGs (tetB, tetG, tetM, tetW, and tetB/P) existed in each treatment within 150 days. Selective pressure of TC may not be a necessary condition for the transfer and persistence of TRGs in soil. High temperatures might reduce TRBs in PM, which had minimal impact on the transmission and transfer of TRGs in soil. Identifying alternatives to decrease TRG transmission remains a major challenge.
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Affiliation(s)
- Yijun Kang
- College of Marine and Bio-engineering, Yancheng Teachers University, Yancheng, Jiangsu, Peoples Republic of China
| | - Xian Gu
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, Peoples Republic of China
| | - Yangyang Hao
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, Peoples Republic of China
| | - Jian Hu
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, Peoples Republic of China.
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van Belkum A, Soriaga LB, LaFave MC, Akella S, Veyrieras JB, Barbu EM, Shortridge D, Blanc B, Hannum G, Zambardi G, Miller K, Enright MC, Mugnier N, Brami D, Schicklin S, Felderman M, Schwartz AS, Richardson TH, Peterson TC, Hubby B, Cady KC. Phylogenetic Distribution of CRISPR-Cas Systems in Antibiotic-Resistant Pseudomonas aeruginosa. mBio 2015; 6:e01796-15. [PMID: 26604259 PMCID: PMC4669384 DOI: 10.1128/mbio.01796-15] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 10/26/2015] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED Pseudomonas aeruginosa is an antibiotic-refractory pathogen with a large genome and extensive genotypic diversity. Historically, P. aeruginosa has been a major model system for understanding the molecular mechanisms underlying type I clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein (CRISPR-Cas)-based bacterial immune system function. However, little information on the phylogenetic distribution and potential role of these CRISPR-Cas systems in molding the P. aeruginosa accessory genome and antibiotic resistance elements is known. Computational approaches were used to identify and characterize CRISPR-Cas systems within 672 genomes, and in the process, we identified a previously unreported and putatively mobile type I-C P. aeruginosa CRISPR-Cas system. Furthermore, genomes harboring noninhibited type I-F and I-E CRISPR-Cas systems were on average ~300 kb smaller than those without a CRISPR-Cas system. In silico analysis demonstrated that the accessory genome (n = 22,036 genes) harbored the majority of identified CRISPR-Cas targets. We also assembled a global spacer library that aided the identification of difficult-to-characterize mobile genetic elements within next-generation sequencing (NGS) data and allowed CRISPR typing of a majority of P. aeruginosa strains. In summary, our analysis demonstrated that CRISPR-Cas systems play an important role in shaping the accessory genomes of globally distributed P. aeruginosa isolates. IMPORTANCE P. aeruginosa is both an antibiotic-refractory pathogen and an important model system for type I CRISPR-Cas bacterial immune systems. By combining the genome sequences of 672 newly and previously sequenced genomes, we were able to provide a global view of the phylogenetic distribution, conservation, and potential targets of these systems. This analysis identified a new and putatively mobile P. aeruginosa CRISPR-Cas subtype, characterized the diverse distribution of known CRISPR-inhibiting genes, and provided a potential new use for CRISPR spacer libraries in accessory genome analysis. Our data demonstrated the importance of CRISPR-Cas systems in modulating the accessory genomes of globally distributed strains while also providing substantial data for subsequent genomic and experimental studies in multiple fields. Understanding why certain genotypes of P. aeruginosa are clinically prevalent and adept at horizontally acquiring virulence and antibiotic resistance elements is of major clinical and economic importance.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Mark C Enright
- Manchester Metropolitan University, Manchester, United Kingdom
| | | | - Daniel Brami
- Synthetic Genomics, Inc., La Jolla, California, USA
| | | | | | | | | | | | - Bolyn Hubby
- Synthetic Genomics, Inc., La Jolla, California, USA
| | - Kyle C Cady
- Synthetic Genomics, Inc., La Jolla, California, USA
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32
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Varga JJ, Barbier M, Mulet X, Bielecki P, Bartell JA, Owings JP, Martinez-Ramos I, Hittle LE, Davis MR, Damron FH, Liechti GW, Puchałka J, dos Santos VAPM, Ernst RK, Papin JA, Albertí S, Oliver A, Goldberg JB. Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains. BMC Genomics 2015; 16:883. [PMID: 26519161 PMCID: PMC4628258 DOI: 10.1186/s12864-015-2069-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/03/2015] [Indexed: 01/24/2023] Open
Abstract
Background Pseudomonas aeruginosa is an environmentally ubiquitous Gram-negative bacterium and important opportunistic human pathogen, causing severe chronic respiratory infections in patients with underlying conditions such as cystic fibrosis (CF) or bronchiectasis. In order to identify mechanisms responsible for adaptation during bronchiectasis infections, a bronchiectasis isolate, PAHM4, was phenotypically and genotypically characterized. Results This strain displays phenotypes that have been associated with chronic respiratory infections in CF including alginate over-production, rough lipopolysaccharide, quorum-sensing deficiency, loss of motility, decreased protease secretion, and hypermutation. Hypermutation is a key adaptation of this bacterium during the course of chronic respiratory infections and analysis indicates that PAHM4 encodes a mutated mutS gene responsible for a ~1,000-fold increase in mutation rate compared to wild-type laboratory strain P. aeruginosa PAO1. Antibiotic resistance profiles and sequence data indicate that this strain acquired numerous mutations associated with increased resistance levels to β-lactams, aminoglycosides, and fluoroquinolones when compared to PAO1. Sequencing of PAHM4 revealed a 6.38 Mbp genome, 5.9 % of which were unrecognized in previously reported P. aeruginosa genome sequences. Transcriptome analysis suggests a general down-regulation of virulence factors, while metabolism of amino acids and lipids is up-regulated when compared to PAO1 and metabolic modeling identified further potential differences between PAO1 and PAHM4. Conclusions This work provides insights into the potential differential adaptation of this bacterium to the lung of patients with bronchiectasis compared to other clinical settings such as cystic fibrosis, findings that should aid the development of disease-appropriate treatment strategies for P. aeruginosa infections. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2069-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John J Varga
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Emory + Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA. .,Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA.
| | - Xavier Mulet
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma, de Mallorca, Spain.
| | - Piotr Bielecki
- Synthetic and Systems Biology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany. .,Present address: Immunobiology Department, Yale University, School of Medicine, New Haven, CT, 06511, USA.
| | - Jennifer A Bartell
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
| | - Joshua P Owings
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Emory + Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| | | | - Lauren E Hittle
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, University of Maryland, Baltimore, MD, USA.
| | - Michael R Davis
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| | - F Heath Damron
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA. .,Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA.
| | - George W Liechti
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| | - Jacek Puchałka
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma, de Mallorca, Spain. .,Present address: Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany.
| | - Vitor A P Martins dos Santos
- Systems and Synthetic Biology, Wageningen University, Wageningen, Netherlands. .,Present address: Chair of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands. .,Present address: LifeGlimmer GmbH, Berlin, Germany.
| | - Robert K Ernst
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, University of Maryland, Baltimore, MD, USA.
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
| | - Sebastian Albertí
- IUNICS, University of the Balearic Islands, Palma, de Mallorca, Spain.
| | - Antonio Oliver
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma, de Mallorca, Spain.
| | - Joanna B Goldberg
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Emory + Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
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Abstract
Horizontal gene transfer plays a major role in microbial evolution, allowing microbes to acquire new genes and phenotypes. Integrative and conjugative elements (ICEs, a.k.a. conjugative transposons) are modular mobile genetic elements integrated into a host genome and are passively propagated during chromosomal replication and cell division. Induction of ICE gene expression leads to excision, production of the conserved conjugation machinery (a type IV secretion system), and the potential to transfer DNA to appropriate recipients. ICEs typically contain cargo genes that are not usually related to the ICE life cycle and that confer phenotypes to host cells. We summarize the life cycle and discovery of ICEs, some of the regulatory mechanisms, and how the types of cargo have influenced our view of ICEs. We discuss how ICEs can acquire new cargo genes and describe challenges to the field and various perspectives on ICE biology.
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Affiliation(s)
- Christopher M Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; ,
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34
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Vanga BR, Ramakrishnan P, Butler RC, Toth IK, Ronson CW, Jacobs JME, Pitman AR. Mobilization of horizontally acquired island 2 is induced in planta in the phytopathogen Pectobacterium atrosepticum SCRI1043 and involves the putative relaxase ECA0613 and quorum sensing. Environ Microbiol 2015; 17:4730-44. [PMID: 26271942 DOI: 10.1111/1462-2920.13024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 01/30/2023]
Abstract
Integrative and conjugative elements (ICEs) contribute to the rapid evolution of bacterial pathogens via horizontal gene transfer of virulence determinants. ICEs have common mechanisms for transmission, yet the cues triggering this process under natural environmental or physiological conditions are largely unknown. In this study, mobilization of the putative ICE horizontally acquired island 2 (HAI2), present in the chromosome of the phytopathogen Pectobacterium atrosepticum SCRI1043, was examined during infection of the host plant potato. Under these conditions, mobilization of HAI2 increased markedly compared with in vitro cultures. In planta-induced mobilization of HAI2 was regulated by quorum sensing and involved the putative ICE-encoded relaxase ECA0613. Disruption of ECA0613 also reduced transcription of genes involved in production of coronafacic acid (Cfa), the major virulence factor harboured on HAI2, whereas their expression was unaffected in the quorum-sensing (expI) mutant. Thus, suppression of cfa gene expression was not regulated by the mobilization of the ICE per se, but was due directly to inactivation of the relaxase. The identification of genetic factors associated solely with in planta mobilization of an ICE demonstrates that this process is highly adapted to the natural environment of the bacterial host and can influence the expression of virulence determinants.
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Affiliation(s)
- Bhanupratap R Vanga
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch, 8140, New Zealand.,Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Pavithra Ramakrishnan
- Bioprotection Research Centre, Lincoln University, PO Box 84, Canterbury, 7647, New Zealand
| | - Ruth C Butler
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Ian K Toth
- James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Jeanne M E Jacobs
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch, 8140, New Zealand.,Bioprotection Research Centre, Lincoln University, PO Box 84, Canterbury, 7647, New Zealand
| | - Andrew R Pitman
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch, 8140, New Zealand.,Bioprotection Research Centre, Lincoln University, PO Box 84, Canterbury, 7647, New Zealand
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35
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Beier R, Foley S, Davidson M, White D, McDermott P, Bodeis-Jones S, Zhao S, Andrews K, Crippen T, Sheffield C, Poole T, Anderson R, Nisbet D. Characterization of antibiotic and disinfectant susceptibility profiles among Pseudomonas aeruginosa
veterinary isolates recovered during 1994-2003. J Appl Microbiol 2014; 118:326-42. [DOI: 10.1111/jam.12707] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/06/2014] [Accepted: 11/14/2014] [Indexed: 11/28/2022]
Affiliation(s)
- R.C. Beier
- Southern Plains Agricultural Research Center; Agricultural Research Service; U.S. Department of Agriculture; College Station TX USA
| | - S.L. Foley
- Division of Microbiology, National Center for Toxicological Research; U.S. Food and Drug Administration; Jefferson AR USA
| | - M.K. Davidson
- Office of Research; Center for Veterinary Medicine; U.S. Food and Drug Administration; Laurel MD USA
| | - D.G. White
- Office of Research; Center for Veterinary Medicine; U.S. Food and Drug Administration; Laurel MD USA
| | - P.F. McDermott
- Office of Research; Center for Veterinary Medicine; U.S. Food and Drug Administration; Laurel MD USA
| | - S. Bodeis-Jones
- Office of Research; Center for Veterinary Medicine; U.S. Food and Drug Administration; Laurel MD USA
| | - S. Zhao
- Office of Research; Center for Veterinary Medicine; U.S. Food and Drug Administration; Laurel MD USA
| | - K. Andrews
- Southern Plains Agricultural Research Center; Agricultural Research Service; U.S. Department of Agriculture; College Station TX USA
| | - T.L. Crippen
- Southern Plains Agricultural Research Center; Agricultural Research Service; U.S. Department of Agriculture; College Station TX USA
| | - C.L. Sheffield
- Southern Plains Agricultural Research Center; Agricultural Research Service; U.S. Department of Agriculture; College Station TX USA
| | - T.L. Poole
- Southern Plains Agricultural Research Center; Agricultural Research Service; U.S. Department of Agriculture; College Station TX USA
| | - R.C. Anderson
- Southern Plains Agricultural Research Center; Agricultural Research Service; U.S. Department of Agriculture; College Station TX USA
| | - D.J. Nisbet
- Southern Plains Agricultural Research Center; Agricultural Research Service; U.S. Department of Agriculture; College Station TX USA
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36
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Dettman JR, Rodrigue N, Kassen R. Genome-wide patterns of recombination in the opportunistic human pathogen Pseudomonas aeruginosa. Genome Biol Evol 2014; 7:18-34. [PMID: 25480685 PMCID: PMC4316616 DOI: 10.1093/gbe/evu260] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The bacterium Pseudomonas aeruginosa is a significant cause of acute nosocomial infections as well as chronic respiratory infections in patients with cystic fibrosis (CF). Recent reports of the intercontinental spread of a CF-specific epidemic strain, combined with high intrinsic levels of antibiotic resistance, have made this opportunistic pathogen an important public health concern. Strain-specific differences correlate with variation in clinical outcomes of infected CF patients, increasing the urgency to understand the evolutionary origin of genetic factors conferring important phenotypes that enable infection, virulence, or resistance. Here, we describe the genome-wide patterns of homologous and nonhomologous recombination in P. aeruginosa, and the extent to which the genomes are affected by these diversity-generating processes. Based on whole-genome sequence data from 32 clinical isolates of P. aeruginosa, we examined the rate and distribution of recombination along the genome, and its effect on the reconstruction of phylogenetic relationships. Multiple lines of evidence suggested that recombination was common and usually involves short stretches of DNA (200-300 bp). Although mutation was the main source of nucleotide diversity, the import of polymorphisms by homologous recombination contributed nearly as much. We also identified the genomic regions with frequent recombination, and the specific sequences of recombinant origin within epidemic strains. The functional characteristics of the genes contained therein were examined for potential associations with a pathogenic lifestyle or adaptation to the CF lung environment. A common link between many of the high-recombination genes was their functional affiliation with the cell wall, suggesting that the products of recombination may be maintained by selection for variation in cell-surface molecules that allows for evasion of the host immune system.
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Affiliation(s)
- Jeremy R Dettman
- Department of Biology and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, Canada
| | - Nicolas Rodrigue
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Rees Kassen
- Department of Biology and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, Canada
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37
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Gómez-Lozano M, Marvig RL, Tulstrup MVL, Molin S. Expression of antisense small RNAs in response to stress in Pseudomonas aeruginosa. BMC Genomics 2014; 15:783. [PMID: 25213728 PMCID: PMC4180829 DOI: 10.1186/1471-2164-15-783] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 09/03/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND RNA sequencing technologies reveal that bacteria express RNA molecules other than mRNA, rRNA or tRNA. During the last years genome-wide bacterial transcriptomes have been shown to comprise intergenic RNA, antisense RNA, and untranslated regions, all capable of performing diverse regulatory functions. RESULTS In this study we used RNA-seq to identify 232 antisense RNAs (asRNAs) in the opportunistic pathogen Pseudomonas aeruginosa grown under 13 different conditions. The conditions studied include exponential and stationary growth as well as osmotic, oxidative and antibiotic stress. We found a significant overrepresentation of asRNAs that are transcribed opposite to genes involved in cell division and in cell wall, lipopolysaccharide (LPS), and capsule biosynthesis, most likely reflecting the conditions used in this study. A substantial number of asRNAs significantly changed their expression under osmotic, oxidative and antibiotic stress, suggesting that asRNAs may play regulatory roles during these conditions. We also made a comparison between the asRNAs detected in this study in P. aeruginosa PAO1 with the asRNAs detected in two previous studies in P. aeruginosa PA14, and found that the extent of overlap between the studies is very limited. CONCLUSIONS RNA-seq experiments are revealing hundreds of novel transcripts in all bacterial genomes investigated. The comparison between independent studies that used RNA-seq to detect novel asRNAs in P. aeruginosa shows that the overlap between the results reported is very narrow. It is necessary to address how reproducibility of these kind of studies should be reported in order to avoid misleading conclusions when comparing data generated by non-identical methods.
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Affiliation(s)
- María Gómez-Lozano
- />Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- />Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Rasmus L Marvig
- />Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Monica VL Tulstrup
- />Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Søren Molin
- />Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- />Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
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38
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Juhas M. Type IV secretion systems and genomic islands-mediated horizontal gene transfer in Pseudomonas and Haemophilus. Microbiol Res 2014; 170:10-7. [PMID: 25183653 DOI: 10.1016/j.micres.2014.06.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 06/28/2014] [Accepted: 06/30/2014] [Indexed: 11/16/2022]
Abstract
Bacterial secretion systems, such as type IV secretion systems (T4SSs) are multi-subunit machines transferring macromolecules across membranes. Besides proteins, T4SSs also transfer nucleoprotein complexes, thus having a significant impact on the evolution of bacterial species. By T4SS-mediated horizontal gene transfer bacteria can acquire a broad spectrum of fitness genes allowing them to thrive in the wide variety of environments. Furthermore, acquisition of antibiotic-resistance and virulence genes can lead to the emergence of novel 'superbugs'. This review provides an update on the investigation of T4SSs. It highlights the role T4SSs play in the horizontal gene transfer, particularly in the evolution of catabolic pathways, antibiotic-resistance and virulence in Haemophilus and Pseudomonas.
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Affiliation(s)
- Mario Juhas
- Department of Pathology, University of Cambridge, Tennis Court Road, CB2 1QP Cambridge, UK.
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39
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Rearrangement of a large novel Pseudomonas aeruginosa gene island in strains isolated from a patient developing ventilator-associated pneumonia. J Clin Microbiol 2014; 52:2430-8. [PMID: 24789195 DOI: 10.1128/jcm.01626-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Bacterial gene islands add to the genetic repertoire of opportunistic pathogens. Here, we perform comparative analyses of three Pseudomonas aeruginosa strains isolated sequentially over a 3-week period from a patient with ventilator-associated pneumonia (VAP) who received clindamycin and piperacillin-tazobactam as part of their treatment regime. While all three strains appeared to be clonal by standard pulsed-field gel electrophoresis, whole-genome sequencing revealed subtle alterations in the chromosomal organization of the last two strains; specifically, an inversion event within a novel 124-kb gene island (PAGI 12) composed of 137 open reading frames [ORFs]. Predicted ORFs in the island included metabolism and virulence genes. Overexpression of a gene island-borne putative β-lactamase gene was observed following piperacillin-tazobactam exposure and only in those strains that had undergone the inversion event, indicating altered gene regulation following genomic remodeling. Examination of a separate cohort of 76 patients with VAP for integration at this tRNA(lys) recombination site demonstrated that patients exhibiting evidence of integration at this site had significantly higher 28-day mortality. These findings provide evidence that P. aeruginosa can integrate, rapidly remodel, and express exogenous genes, which likely contributes to its fitness in a clinical setting.
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40
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Redefining the PF06864 Pfam family based on Burkholderia pseudomallei PilO2(Bp) S-SAD crystal structure. PLoS One 2014; 9:e94981. [PMID: 24728008 PMCID: PMC3984277 DOI: 10.1371/journal.pone.0094981] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 03/21/2014] [Indexed: 01/07/2023] Open
Abstract
Type IV pili are surface-exposed filaments and bacterial virulence factors, represented by the Tfpa and Tfpb types, which assemble via specific machineries. The Tfpb group is further divided into seven variants, linked to heterogeneity in the assembly machineries. Here we focus on PilO2(Bp), a protein component of the Tfpb R64 thin pilus variant assembly machinery from the pathogen Burkholderia pseudomallei. PilO2(Bp) belongs to the PF06864 Pfam family, for which an improved definition is presented based on newly derived Hidden Markov Model (HMM) profiles. The 3D structure of the N-terminal domain of PilO2(Bp) (N-PilO2(Bp)), here reported, is the first structural representative of the PF06864 family. N-PilO2(Bp) presents an actin-like ATPase fold that is shown to be present in BfpC, a different variant assembly protein; the new HMM profiles classify BfpC as a PF06864 member. Our results provide structural insight into the PF06864 family and on the Type IV pili assembly machinery.
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41
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Tu Q, Yu H, He Z, Deng Y, Wu L, Van Nostrand JD, Zhou A, Voordeckers J, Lee YJ, Qin Y, Hemme CL, Shi Z, Xue K, Yuan T, Wang A, Zhou J. GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis. Mol Ecol Resour 2014; 14:914-28. [PMID: 24520909 DOI: 10.1111/1755-0998.12239] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 02/02/2014] [Accepted: 02/05/2014] [Indexed: 01/21/2023]
Abstract
Micro-organisms play critical roles in many important biogeochemical processes in the Earth's biosphere. However, understanding and characterizing the functional capacity of microbial communities are still difficult due to the extremely diverse and often uncultivable nature of most micro-organisms. In this study, we developed a new functional gene array, GeoChip 4, for analysing the functional diversity, composition, structure, metabolic potential/activity and dynamics of microbial communities. GeoChip 4 contained approximately 82 000 probes covering 141 995 coding sequences from 410 functional gene families related to microbial carbon (C), nitrogen (N), sulphur (S), and phosphorus (P) cycling, energy metabolism, antibiotic resistance, metal resistance/reduction, organic remediation, stress responses, bacteriophage and virulence. A total of 173 archaeal, 4138 bacterial, 404 eukaryotic and 252 viral strains were targeted, providing the ability to analyse targeted functional gene families of micro-organisms included in all four domains. Experimental assessment using different amounts of DNA suggested that as little as 500 ng environmental DNA was required for good hybridization, and the signal intensities detected were well correlated with the DNA amount used. GeoChip 4 was then applied to study the effect of long-term warming on soil microbial communities at a Central Oklahoma site, with results indicating that microbial communities respond to long-term warming by enriching carbon degradation, nutrient cycling (nitrogen and phosphorous) and stress response gene families. To the best of our knowledge, GeoChip 4 is the most comprehensive functional gene array for microbial community analysis.
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Affiliation(s)
- Qichao Tu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, 73019, USA
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42
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Wee BA, Woolfit M, Beatson SA, Petty NK. A distinct and divergent lineage of genomic island-associated Type IV Secretion Systems in Legionella. PLoS One 2013; 8:e82221. [PMID: 24358157 PMCID: PMC3864950 DOI: 10.1371/journal.pone.0082221] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 10/25/2013] [Indexed: 12/21/2022] Open
Abstract
Legionella encodes multiple classes of Type IV Secretion Systems (T4SSs), including the Dot/Icm protein secretion system that is essential for intracellular multiplication in amoebal and human hosts. Other T4SSs not essential for virulence are thought to facilitate the acquisition of niche-specific adaptation genes including the numerous effector genes that are a hallmark of this genus. Previously, we identified two novel gene clusters in the draft genome of Legionella pneumophila strain 130b that encode homologues of a subtype of T4SS, the genomic island-associated T4SS (GI-T4SS), usually associated with integrative and conjugative elements (ICE). In this study, we performed genomic analyses of 14 homologous GI-T4SS clusters found in eight publicly available Legionella genomes and show that this cluster is unusually well conserved in a region of high plasticity. Phylogenetic analyses show that Legionella GI-T4SSs are substantially divergent from other members of this subtype of T4SS and represent a novel clade of GI-T4SSs only found in this genus. The GI-T4SS was found to be under purifying selection, suggesting it is functional and may play an important role in the evolution and adaptation of Legionella. Like other GI-T4SSs, the Legionella clusters are also associated with ICEs, but lack the typical integration and replication modules of related ICEs. The absence of complete replication and DNA pre-processing modules, together with the presence of Legionella-specific regulatory elements, suggest the Legionella GI-T4SS-associated ICE is unique and may employ novel mechanisms of regulation, maintenance and excision. The Legionella GI-T4SS cluster was found to be associated with several cargo genes, including numerous antibiotic resistance and virulence factors, which may confer a fitness benefit to the organism. The in-silico characterisation of this new T4SS furthers our understanding of the diversity of secretion systems involved in the frequent horizontal gene transfers that allow Legionella to adapt to and exploit diverse environmental niches.
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Affiliation(s)
- Bryan A. Wee
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Megan Woolfit
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Scott A. Beatson
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- * E-mail: (NKP); (SAB)
| | - Nicola K. Petty
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales, Australia
- * E-mail: (NKP); (SAB)
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Abstract
Type IV pili (T4P) are multifunctional protein fibers produced on the surfaces of a wide variety of bacteria and archaea. The major subunit of T4P is the type IV pilin, and structurally related proteins are found as components of the type II secretion (T2S) system, where they are called pseudopilins; of DNA uptake/competence systems in both Gram-negative and Gram-positive species; and of flagella, pili, and sugar-binding systems in the archaea. This broad distribution of a single protein family implies both a common evolutionary origin and a highly adaptable functional plan. The type IV pilin is a remarkably versatile architectural module that has been adopted widely for a variety of functions, including motility, attachment to chemically diverse surfaces, electrical conductance, acquisition of DNA, and secretion of a broad range of structurally distinct protein substrates. In this review, we consider recent advances in this research area, from structural revelations to insights into diversity, posttranslational modifications, regulation, and function.
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van Wolferen M, Ajon M, Driessen AJM, Albers SV. Molecular analysis of the UV-inducible pili operon from Sulfolobus acidocaldarius. Microbiologyopen 2013; 2:928-37. [PMID: 24106028 PMCID: PMC3892339 DOI: 10.1002/mbo3.128] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 07/21/2013] [Accepted: 07/29/2013] [Indexed: 11/09/2022] Open
Abstract
Upon ultraviolet (UV) stress, hyperthermophilic Sulfolobus species show a highly induced transcription of a gene cluster responsible for pili biogenesis: the UV-inducible pili operon (ups operon). This operon is involved in UV-induced pili assembly, cellular aggregation, and subsequent DNA exchange between cells. As the system increases the fitness of Sulfolobus cells after UV light exposure, we assume that transfer of DNA takes place in order to repair UV-induced DNA damages via homologous recombination. Here, we studied all genes present in the ups cluster via gene deletion analysis with a focus on UpsX, a protein that shows no identifiable functional domains. UspX does not seem to be structurally essential for UV-induced pili formation and cellular aggregation, but appears to be important for efficient DNA transfer. In addition, we could show that pilin subunits UpsA and UpsB probably both function as major pilin subunits in the ups pili.
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Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Max Planck Institute for terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043, Marburg, Germany
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Skurnik D, Roux D, Aschard H, Cattoir V, Yoder-Himes D, Lory S, Pier GB. A comprehensive analysis of in vitro and in vivo genetic fitness of Pseudomonas aeruginosa using high-throughput sequencing of transposon libraries. PLoS Pathog 2013; 9:e1003582. [PMID: 24039572 PMCID: PMC3764216 DOI: 10.1371/journal.ppat.1003582] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 07/12/2013] [Indexed: 01/22/2023] Open
Abstract
High-throughput sequencing of transposon (Tn) libraries created within entire genomes identifies and quantifies the contribution of individual genes and operons to the fitness of organisms in different environments. We used insertion-sequencing (INSeq) to analyze the contribution to fitness of all non-essential genes in the chromosome of Pseudomonas aeruginosa strain PA14 based on a library of ∼300,000 individual Tn insertions. In vitro growth in LB provided a baseline for comparison with the survival of the Tn insertion strains following 6 days of colonization of the murine gastrointestinal tract as well as a comparison with Tn-inserts subsequently able to systemically disseminate to the spleen following induction of neutropenia. Sequencing was performed following DNA extraction from the recovered bacteria, digestion with the MmeI restriction enzyme that hydrolyzes DNA 16 bp away from the end of the Tn insert, and fractionation into oligonucleotides of 1,200-1,500 bp that were prepared for high-throughput sequencing. Changes in frequency of Tn inserts into the P. aeruginosa genome were used to quantify in vivo fitness resulting from loss of a gene. 636 genes had <10 sequencing reads in LB, thus defined as unable to grow in this medium. During in vivo infection there were major losses of strains with Tn inserts in almost all known virulence factors, as well as respiration, energy utilization, ion pumps, nutritional genes and prophages. Many new candidates for virulence factors were also identified. There were consistent changes in the recovery of Tn inserts in genes within most operons and Tn insertions into some genes enhanced in vivo fitness. Strikingly, 90% of the non-essential genes were required for in vivo survival following systemic dissemination during neutropenia. These experiments resulted in the identification of the P. aeruginosa strain PA14 genes necessary for optimal survival in the mucosal and systemic environments of a mammalian host.
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Affiliation(s)
- David Skurnik
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Damien Roux
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hugues Aschard
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Vincent Cattoir
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Deborah Yoder-Himes
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stephen Lory
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gerald B. Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
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Stockwell VO, Davis EW, Carey A, Shaffer BT, Mavrodi DV, Hassan KA, Hockett K, Thomashow LS, Paulsen IT, Loper JE. pA506, a conjugative plasmid of the plant epiphyte Pseudomonas fluorescens A506. Appl Environ Microbiol 2013; 79:5272-82. [PMID: 23811504 PMCID: PMC3753976 DOI: 10.1128/aem.01354-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 06/21/2013] [Indexed: 11/20/2022] Open
Abstract
Conjugative plasmids are known to facilitate the acquisition and dispersal of genes contributing to the fitness of Pseudomonas spp. Here, we report the characterization of pA506, the 57-kb conjugative plasmid of Pseudomonas fluorescens A506, a plant epiphyte used in the United States for the biological control of fire blight disease of pear and apple. Twenty-nine of the 67 open reading frames (ORFs) of pA506 have putative functions in conjugation, including a type IV secretion system related to that of MOBP6 family plasmids and a gene cluster for type IV pili. We demonstrate that pA506 is self-transmissible via conjugation between A506 and strains of Pseudomonas spp. or the Enterobacteriaceae. The origin of vegetative replication (oriV) of pA506 is typical of those in pPT23A family plasmids, which are present in many pathovars of Pseudomonas syringae, but pA506 lacks repA, a defining locus for pPT23A plasmids, and has a novel partitioning region. We selected a plasmid-cured derivative of A506 and compared it to the wild type to identify plasmid-encoded phenotypes. pA506 conferred UV resistance, presumably due to the plasmid-borne rulAB genes, but did not influence epiphytic fitness of A506 on pear or apple blossoms in the field. pA506 does not appear to confer resistance to antibiotics or other toxic elements. Based on the conjugative nature of pA506 and the large number of its genes that are shared with plasmids from diverse groups of environmental bacteria, the plasmid is likely to serve as a vehicle for genetic exchange between A506 and its coinhabitants on plant surfaces.
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Affiliation(s)
- Virginia O. Stockwell
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Edward W. Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Agricultural Research Service, U.S. Department of Agriculture, Corvallis, Oregon, USA
| | - Alyssa Carey
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Agricultural Research Service, U.S. Department of Agriculture, Corvallis, Oregon, USA
| | - Brenda T. Shaffer
- Agricultural Research Service, U.S. Department of Agriculture, Corvallis, Oregon, USA
| | - Dmitri V. Mavrodi
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Karl A. Hassan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Kevin Hockett
- Agricultural Research Service, U.S. Department of Agriculture, Corvallis, Oregon, USA
| | - Linda S. Thomashow
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
- Agricultural Research Service, U.S. Department of Agriculture, Pullman, Washington, USA
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Joyce E. Loper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Agricultural Research Service, U.S. Department of Agriculture, Corvallis, Oregon, USA
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47
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The genome of Pseudomonas fluorescens strain R124 demonstrates phenotypic adaptation to the mineral environment. J Bacteriol 2013; 195:4793-803. [PMID: 23995634 DOI: 10.1128/jb.00825-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Microbial adaptation to environmental conditions is a complex process, including acquisition of positive traits through horizontal gene transfer or the modification of existing genes through duplication and/or mutation. In this study, we examined the adaptation of a Pseudomonas fluorescens isolate (R124) from the nutrient-limited mineral environment of a silica cave in comparison with P. fluorescens isolates from surface soil and the rhizosphere. Examination of metal homeostasis gene pathways demonstrated a high degree of conservation, suggesting that such systems remain functionally similar across chemical environments. The examination of genomic islands unique to our strain revealed the presence of genes involved in carbohydrate metabolism, aromatic carbon metabolism, and carbon turnover, confirmed through phenotypic assays, suggesting the acquisition of potentially novel mechanisms for energy metabolism in this strain. We also identified a twitching motility phenotype active at low-nutrient concentrations that may allow alternative exploratory mechanisms for this organism in a geochemical environment. Two sets of candidate twitching motility genes are present within the genome, one on the chromosome and one on a plasmid; however, a plasmid knockout identified the functional gene as being present on the chromosome. This work highlights the plasticity of the Pseudomonas genome, allowing the acquisition of novel nutrient-scavenging pathways across diverse geochemical environments while maintaining a core of functional stress response genes.
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Mikkelsen H, Hui K, Barraud N, Filloux A. The pathogenicity island encoded PvrSR/RcsCB regulatory network controls biofilm formation and dispersal in Pseudomonas aeruginosa PA14. Mol Microbiol 2013; 89:450-63. [PMID: 23750818 PMCID: PMC3842833 DOI: 10.1111/mmi.12287] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2013] [Indexed: 01/14/2023]
Abstract
Pseudomonas aeruginosa biofilm formation is linked to persistent infections in humans. Biofilm formation is facilitated by extracellular appendages, some of which are assembled by the Chaperone Usher Pathway (Cup). The cupD gene cluster is located on the PAPI-1 pathogenicity island of strain PA14 and has probably been acquired together with four genes encoding two-component signal transduction proteins. We have previously showed that the RcsB response regulator activates expression of the cupD genes, which leads to the production of CupD fimbriae and increased attachment. Here we show that RcsB activity is tightly modulated by two sensors, RcsC and PvrS. While PvrS acts as a kinase that enhances RcsB activity, RcsC has a dual function, first as a phosphorelay, and second as a phosphatase. We found that, under certain growth conditions, overexpression of RcsB readily induces biofilm dispersal. Microarray analysis shows that RcsB positively controls expression of pvrR that encodes the phosphodiesterase required for this dispersal process. Finally, in addition to the PAPI-1 encoded cupD genes, RcsB controls several genes on the core genome, some of which encode orphan response regulators. We thus discovered that RcsB is central to a large regulatory network that fine-tunes the switch between biofilm formation and dispersal.
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Affiliation(s)
- Helga Mikkelsen
- Imperial College London, Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, South Kensington Campus, Flowers Building, SW7 2AZ, London, UK
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49
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Lee YJ, van Nostrand JD, Tu Q, Lu Z, Cheng L, Yuan T, Deng Y, Carter MQ, He Z, Wu L, Yang F, Xu J, Zhou J. The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. ISME JOURNAL 2013; 7:1974-84. [PMID: 23765101 DOI: 10.1038/ismej.2013.88] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 04/10/2013] [Accepted: 04/20/2013] [Indexed: 12/21/2022]
Abstract
Pathogens present in the environment pose a serious threat to human, plant and animal health as evidenced by recent outbreaks. As many pathogens can survive and proliferate in the environment, it is important to understand their population dynamics and pathogenic potential in the environment. To assess pathogenic potential in diverse habitats, we developed a functional gene array, the PathoChip, constructed with key virulence genes related to major virulence factors, such as adherence, colonization, motility, invasion, toxin, immune evasion and iron uptake. A total of 3715 best probes were selected from 13 virulence factors, covering 7417 coding sequences from 1397 microbial species (2336 strains). The specificity of the PathoChip was computationally verified, and approximately 98% of the probes provided specificity at or below the species level, proving its excellent capability for the detection of target sequences with high discrimination power. We applied this array to community samples from soil, seawater and human saliva to assess the occurrence of virulence genes in natural environments. Both the abundance and diversity of virulence genes increased in stressed conditions compared with their corresponding controls, indicating a possible increase in abundance of pathogenic bacteria under environmental perturbations such as warming or oil spills. Statistical analyses showed that microbial communities harboring virulence genes were responsive to environmental perturbations, which drove changes in abundance and distribution of virulence genes. The PathoChip provides a useful tool to identify virulence genes in microbial populations, examine the dynamics of virulence genes in response to environmental perturbations and determine the pathogenic potential of microbial communities.
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Affiliation(s)
- Yong-Jin Lee
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
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50
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Vercoe RB, Chang JT, Dy RL, Taylor C, Gristwood T, Clulow JS, Richter C, Przybilski R, Pitman AR, Fineran PC. Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or remodel pathogenicity islands. PLoS Genet 2013; 9:e1003454. [PMID: 23637624 PMCID: PMC3630108 DOI: 10.1371/journal.pgen.1003454] [Citation(s) in RCA: 248] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Accepted: 03/02/2013] [Indexed: 12/26/2022] Open
Abstract
In prokaryotes, clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (Cas) proteins constitute a defence system against bacteriophages and plasmids. CRISPR/Cas systems acquire short spacer sequences from foreign genetic elements and incorporate these into their CRISPR arrays, generating a memory of past invaders. Defence is provided by short non-coding RNAs that guide Cas proteins to cleave complementary nucleic acids. While most spacers are acquired from phages and plasmids, there are examples of spacers that match genes elsewhere in the host bacterial chromosome. In Pectobacterium atrosepticum the type I-F CRISPR/Cas system has acquired a self-complementary spacer that perfectly matches a protospacer target in a horizontally acquired island (HAI2) involved in plant pathogenicity. Given the paucity of experimental data about CRISPR/Cas-mediated chromosomal targeting, we examined this process by developing a tightly controlled system. Chromosomal targeting was highly toxic via targeting of DNA and resulted in growth inhibition and cellular filamentation. The toxic phenotype was avoided by mutations in the cas operon, the CRISPR repeats, the protospacer target, and protospacer-adjacent motif (PAM) beside the target. Indeed, the natural self-targeting spacer was non-toxic due to a single nucleotide mutation adjacent to the target in the PAM sequence. Furthermore, we show that chromosomal targeting can result in large-scale genomic alterations, including the remodelling or deletion of entire pre-existing pathogenicity islands. These features can be engineered for the targeted deletion of large regions of bacterial chromosomes. In conclusion, in DNA-targeting CRISPR/Cas systems, chromosomal interference is deleterious by causing DNA damage and providing a strong selective pressure for genome alterations, which may have consequences for bacterial evolution and pathogenicity.
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Affiliation(s)
- Reuben B. Vercoe
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James T. Chang
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Ron L. Dy
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Corinda Taylor
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Tamzin Gristwood
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James S. Clulow
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Corinna Richter
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Rita Przybilski
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Andrew R. Pitman
- New Zealand Institute for Plant and Food Research, Christchurch, New Zealand
- Bio-Protection Research Centre, Lincoln University, Canterbury, New Zealand
| | - Peter C. Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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