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Zhao X, Qin J, Chen G, Yang C, Wei J, Li W, Jia W. Whole-genome sequencing, multilocus sequence typing, and resistance mechanism of the carbapenem-resistant Pseudomonas aeruginosa in China. Microb Pathog 2024; 192:106720. [PMID: 38815778 DOI: 10.1016/j.micpath.2024.106720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/14/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024]
Abstract
Pseudomonas aeruginosa is a significant pathogen responsible for severe multisite infections with high morbidity and mortality rates. This study analyzed carbapenem-resistant Pseudomonas aeruginosa (CRPA) at a tertiary hospital in Shandong, China, using whole-genome sequencing (WGS). The objective was to explore the mechanisms and molecular characteristics of carbapenem resistance. A retrospective analysis of 91 isolates from January 2022 to March 2023 was performed, which included strain identification and antimicrobial susceptibility testing. WGS was utilized to determine the genome sequences of these CRPA strains, and the species were precisely identified using average nucleotide identification (ANI), with further analysis on multilocus sequence typing and strain relatedness. Some strains were found to carry the ampD and oprD genes, while only a few harbored carbapenemase genes or related genes. Notably, all strains possessed the mexA, mexE, and mexX genes. The major lineage identified was ST244, followed by ST235. The study revealed a diverse array of carbapenem resistance mechanisms among hospital isolates, differing from previous studies in mainland China. It highlighted that carbapenem resistance is not due to a single mechanism but rather a combination of enzyme-mediated resistance, AmpC overexpression, OprD dysfunction, and efflux pump overexpression. This research provides valuable insights into the evolutionary mechanisms and molecular features of CRPA resistance in this region, aiding in the national prevention and control of CRPA, and offering references for targeting and developing new drugs.
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Affiliation(s)
- Xue Zhao
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China
| | - Jiangnan Qin
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China
| | - Guang Chen
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China
| | - Chao Yang
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jie Wei
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China
| | - Wanxiang Li
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China
| | - Wei Jia
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China.
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Morales-Espinosa R, Delgado G, Espinosa-Camacho F, Flores-Alanis A, Rodriguez C, Mendez JL, Gonzalez-Pedraza A, Cravioto A. Pseudomonas aeruginosa strains isolated from animal with high virulence genes content and highly sensitive to antimicrobials. J Glob Antimicrob Resist 2024; 37:75-80. [PMID: 38452900 DOI: 10.1016/j.jgar.2024.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024] Open
Abstract
OBJECTIVES P. aeruginosa is one of the most metabolically versatile bacteria having the ability to survive in multiple environments through its accessory genome. An important hallmark of P. aeruginosa is the high level of antibiotic resistance, which often makes eradication difficult and sometimes impossible. Evolutionary forces have led to this bacterium to develop high antimicrobial resistance with a variety of elements contributing to both intrinsic and acquired resistance. The objectives were to genetically and phenotypically characterizer P. aeruginosa strains isolated from companion animals of different species. METHODS We characterized a collection of 39 P. aeruginosa strains isolated from infected animals. The genetic characterization was in relation to chromosomal profile by PFGE; content of virulence gene; presence of genomic islands (GIs); genes of the cytotoxins exported by T3SS: exoU, exoS, exoT and exoY; and type IV pili allele. The phenotypic characterization was based on patterns of susceptibility to different antimicrobials. RESULTS Each strain had a PFGE profile, a high virulence genes content, and a large accessory genome. However, most of the strains presented high sensitivity to almost all antimicrobials tested, showing no acquired resistance (no β-lactamases). The exception to this lack of resistance was seen with penicillin. CONCLUSIONS P. aeruginosa could be a naturally sensitive bacterium to standard antimicrobials but could rapidly develop intrinsic and acquired resistance when the bacterium is exposed to pressure exerted by antibiotics, as observed in hospital settings.
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Affiliation(s)
- Rosario Morales-Espinosa
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México.
| | - Gabriela Delgado
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Fernando Espinosa-Camacho
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Alejandro Flores-Alanis
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Cristina Rodriguez
- Bacteriology Laboratory, Faculty of Veterinary, Universidad Nacional Autónoma de México., Coyoacán, Ciudad de México, México
| | - Jose L Mendez
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Alberto Gonzalez-Pedraza
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Alejandro Cravioto
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
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Aroca Molina KJ, Gutiérrez SJ, Benítez-Campo N, Correa A. Genomic Differences Associated with Resistance and Virulence in Pseudomonas aeruginosa Isolates from Clinical and Environmental Sites. Microorganisms 2024; 12:1116. [PMID: 38930498 PMCID: PMC11205572 DOI: 10.3390/microorganisms12061116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/05/2024] [Accepted: 04/13/2024] [Indexed: 06/28/2024] Open
Abstract
Pseudomonas aeruginosa is a pathogen that causes healthcare-associated infections (HAIs) worldwide. It is unclear whether P. aeruginosa isolated from the natural environment has the same pathogenicity and antimicrobial resistance potential as clinical strains. In this study, virulence- and resistance-associated genes were compared in 14 genomic sequences of clinical and environmental isolates of P. aeruginosa using the VFDB, PATRIC, and CARD databases. All isolates were found to share 62% of virulence genes related to adhesion, motility, secretion systems, and quorum sensing and 72.9% of resistance genes related to efflux pumps and membrane permeability. Our results indicate that both types of isolates possess conserved genetic information associated with virulence and resistance mechanisms regardless of the source. However, none of the environmental isolates were associated with high-risk clones (HRCs). These clones (ST235 and ST111) were found only in clinical isolates, which have an impact on human medical epidemiology due to their ability to spread and persist, indicating a correlation between the clinical environment and increased virulence. The genomic variation and antibiotic susceptibility of environmental isolates of P. aeruginosa suggest potential biotechnological applications if obtained from sources that are under surveillance and investigation to limit the emergence and spread of antibiotic resistant strains.
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Affiliation(s)
- Kelly J. Aroca Molina
- Department of Biology, Faculty of Natural and Exact Sciences, Universidad del Valle, Cali 760042, Colombia; (K.J.A.M.); (S.J.G.)
| | - Sonia Jakeline Gutiérrez
- Department of Biology, Faculty of Natural and Exact Sciences, Universidad del Valle, Cali 760042, Colombia; (K.J.A.M.); (S.J.G.)
| | - Neyla Benítez-Campo
- Department of Biology, Faculty of Natural and Exact Sciences, Universidad del Valle, Cali 760042, Colombia; (K.J.A.M.); (S.J.G.)
| | - Adriana Correa
- Department of Basic Sciences, Universidad Santiago de Cali, Cali 760035, Colombia;
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Rojo-Bezares B, Casado C, Ceniceros T, López M, Chichón G, Lozano C, Ruiz-Roldán L, Sáenz Y. Pseudomonas aeruginosa from river water: antimicrobial resistance, virulence and molecular typing. FEMS Microbiol Ecol 2024; 100:fiae028. [PMID: 38444209 PMCID: PMC11004943 DOI: 10.1093/femsec/fiae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/04/2023] [Accepted: 03/04/2024] [Indexed: 03/07/2024] Open
Abstract
Pseudomonas aeruginosa isolates were recovered from surface river water samples in La Rioja region (Spain) to characterise their antibiotic resistance, molecular typing and virulence mechanisms. Fifty-two P. aeruginosa isolates were isolated from 15 different water samples (45.4%) and belonged to 23 different pulsed-field electrophoresis (PFGE) patterns. All isolates were susceptible to all antibiotics tested, except one carbapenem-resistant P. aeruginosa that showed a premature stop codon in OprD porin. Twenty-two sequence types (STs) (six new ones) were detected among 29 selected P. aeruginosa (one strain with a different PFGE pattern per sample), with ST274 (14%) being the most frequent one. O:6 and O:3 were the predominant serotypes (31%). Seven virulotypes were detected, being 59% exoS-exoY-exoT-exoA-lasA-lasB-lasI-lasR-rhlAB-rhlI-rhlR-aprA-positive P. aeruginosa. It is noteworthy that the exlA gene was identified in three strains (10.3%), and the exoU gene in seven (24.1%), exoS in 18 (62.1%), and both exoS and exoU genes in one strain. High motility ranges were found in these strains. Twenty-seven per cent of strains produced more biofilm biomass, 90% more pyorubin, 83% more pyocyanin and 65.5% more than twice the elastase activity compared with the PAO1 strain. These results highlight the importance of rivers as temporary reservoirs and sources of P. aeruginosa transmission, and show the importance of their epidemiological surveillance in the environment.
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Affiliation(s)
- Beatriz Rojo-Bezares
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Cristina Casado
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Tania Ceniceros
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - María López
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Gabriela Chichón
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Carmen Lozano
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Lidia Ruiz-Roldán
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Yolanda Sáenz
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
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Englisch CN, Wadood NA, Pätzold L, Gallagher A, Krasteva-Christ G, Becker SL, Bischoff M. Establishing an Experimental Pseudomonas aeruginosa Keratitis Model in Mice - Challenges and Solutions. Ann Anat 2023; 249:152099. [PMID: 37105406 DOI: 10.1016/j.aanat.2023.152099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023]
Abstract
BACKGROUND With the ongoing increase in antimicrobial resistances seen in bacterial isolates causing a keratitis in humans, animal models have become an important tool to study new antimicrobial therapies. Nevertheless, the establishment of experimental keratitis is difficult. Here, we discuss the impact of different arrangements, including animal age, bacterial strain and dose as well as epithelium removal on the outcome of experimental keratitis. We therefore present the methods and results of our establishing experiments. METHODS Bacterial load determination and flow cytometry were performed using eye homogenate gained from a 72hours lasting murine Pseudomonas aeruginosa keratitis model. Additionally, the intensity of the infection was scored from 0 to 5, the mice weighed, and blood immune cells counted. RESULTS We found that older C57BL/6N mice (8-11 months) are more susceptible to develop a keratitis than younger mice (5-6 weeks). Epithelium removal has no major impact on infectivity and disease progression in aged mice. P. aeruginosa exoU+ strains, such as PA54, should preferentially be used and highly concentrated (∼ 5×107 CFU). Establishing an infection with the exoU- PAO1 derivative DSM 19880 was not possible. CONCLUSIONS We present a replicable method to achieve a successful experimental P. aeruginosa keratitis in C57BL/6N mice that is sustained or aggravated over the observation period of 3 days in 80% of all animals tested. Our work is of particular interest to all researchers planning the establishment of such experimental models. We show some key aspects that can simplify and quicken the procedure, ultimately saving costs and animal life.
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Affiliation(s)
- Colya N Englisch
- Institute for Medical Microbiology and Hygienics, Saarland University, 66421, Homburg/Saar, Germany.
| | - Noran Abdel Wadood
- Institute for Medical Microbiology and Hygienics, Saarland University, 66421, Homburg/Saar, Germany; Institute of Anatomy and Cell Biology, Saarland University, 66421, Homburg/Saar, Germany.
| | - Linda Pätzold
- Institute for Medical Microbiology and Hygienics, Saarland University, 66421, Homburg/Saar, Germany.
| | | | | | - Sören L Becker
- Institute for Medical Microbiology and Hygienics, Saarland University, 66421, Homburg/Saar, Germany.
| | - Markus Bischoff
- Institute for Medical Microbiology and Hygienics, Saarland University, 66421, Homburg/Saar, Germany.
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Unravelling complex transposable elements surrounding bla GES-16 in a Pseudomonas aeruginosa ExoU strain. J Glob Antimicrob Resist 2022; 30:143-147. [PMID: 35447384 DOI: 10.1016/j.jgar.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 03/16/2022] [Accepted: 04/11/2022] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES We characterised the complex surrounding regions of blaGES-16 in a Pseudomonas aeruginosa exoU+ strain (P-10.226) in Brazil. METHODS Species identification was performed by MALDI-TOF MS, and the antimicrobial susceptibility profile was determined by broth microdilution based on European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. The whole genome sequencing (WGS) of P-10.226 strain was performed using both short-read paired-end sequencing on the Illumina MiSeq platform as well as the long-read Oxford Nanopore MinION. RESULTS WGS analysis showed that P-10.226 carried blaGES-16, which was found as a gene cassette inserted into a novel class I integron, In1992 (aadB-blaOXA-56-blaGES-16-aadB-aadA6c), whose 3'-CS was truncated by a nested transposable element, IS5564::ISPa157. The structure was even more complex since IS6100-ΔIS6100 structure and a TnAs2-like harbouring the operon merRTPADE was found downstream In1992. Fragments of TnAs3 harbouring 25-bp imperfect inverted repeats were identified bordering the intl1 of In1992 and also flanking IS6100-ΔIS6100, which might be genetic marks of its previous presence in the genome. Interestingly, In1992 also shows a distinct cassette array from In581 (blaGES-16-dfrA22-aacA27-aadA1), which was previously reported in Serratia marcescens strains recovered in Brazil. Finally, exoU gene, which encodes a potent cytotoxin of type III secretion systems (T3SS) effector proteins from P. aeruginosa and is associated to severe infections, was also detected. CONCLUSION We described the novel In1992 carrying blaGES-16 surrounded by complex transposition events in a XDR P. aeruginosa strain. The identification of many sets of direct repeats adjacent to TnAs3 fragments indicates a major past of transposition events that shaped the current genetic environment of In1992.
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Hardy KS, Tessmer MH, Frank DW, Audia JP. Perspectives on the Pseudomonas aeruginosa Type III Secretion System Effector ExoU and Its Subversion of the Host Innate Immune Response to Infection. Toxins (Basel) 2021; 13:880. [PMID: 34941717 PMCID: PMC8708460 DOI: 10.3390/toxins13120880] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/19/2021] [Accepted: 12/04/2021] [Indexed: 12/02/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic, Gram-negative pathogen and an important cause of hospital acquired infections, especially in immunocompromised patients. Highly virulent P. aeruginosa strains use a type III secretion system (T3SS) to inject exoenzyme effectors directly into the cytoplasm of a target host cell. P. aeruginosa strains that express the T3SS effector, ExoU, associate with adverse outcomes in critically ill patients with pneumonia, owing to the ability of ExoU to rapidly damage host cell membranes and subvert the innate immune response to infection. Herein, we review the structure, function, regulation, and virulence characteristics of the T3SS effector ExoU, a highly cytotoxic phospholipase A2 enzyme.
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Affiliation(s)
- Kierra S. Hardy
- Department of Microbiology and Immunology, University of South Alabama College of Medicine, Mobile, AL 36608, USA;
- Center for Lung Biology, University of South Alabama College of Medicine, Mobile, AL 36608, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Maxx H. Tessmer
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA;
| | - Dara W. Frank
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jonathon P. Audia
- Department of Microbiology and Immunology, University of South Alabama College of Medicine, Mobile, AL 36608, USA;
- Center for Lung Biology, University of South Alabama College of Medicine, Mobile, AL 36608, USA
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Laborda P, Sanz-García F, Hernando-Amado S, Martínez JL. Pseudomonas aeruginosa: an antibiotic resilient pathogen with environmental origin. Curr Opin Microbiol 2021; 64:125-132. [PMID: 34710741 DOI: 10.1016/j.mib.2021.09.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/31/2021] [Accepted: 09/23/2021] [Indexed: 12/24/2022]
Abstract
Pseudomonas aeruginosa, a bacterium characterized for its low antibiotics' susceptibility, is one of the most relevant opportunistic pathogens, causing infections at hospitals and in cystic fibrosis patients. Besides its relevance for human health, P. aeruginosa colonizes environmental ecosystems; therefore the elements driving its infectivity and antibiotic resistance must be analyzed from a One-Health perspective. Although some epidemic clones have been described, there are not specific lineages linked to infections, suggesting that P. aeruginosa virulence and antibiotic resistance determinants evolved in nature to play functions other than infecting the human host and avoiding antimicrobial treatment. Herein, we review current information on the population structure of P. aeruginosa and on the functional role that its resistance and virulence determinants have in non-clinical ecosystems.
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Affiliation(s)
- Pablo Laborda
- Centro Nacional de Biotecnología, CSIC, 28049, Madrid, Spain
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Espinosa-Camacho LF, Delgado G, Cravioto A, Morales-Espinosa R. Diversity in the composition of the accessory genome of Mexican Pseudomonas aeruginosa strains. Genes Genomics 2021; 44:53-77. [PMID: 34410625 DOI: 10.1007/s13258-021-01155-3] [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: 03/05/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Pseudomonas aeruginosa is an important opportunistic pathogen especially in nosocomial infections due to its easy adaptation to different environments; this characteristic is due to the great genetic diversity that presents its genome. In addition, it is considered a pathogen of critical priority due to the high antimicrobial resistance. OBJECTIVES The aim of this study was to characterize the mobile genetic elements present in the chromosome of six Mexican P. aeruginosa strains isolated from adults with pneumonia and children with bacteremia. METHODS The genomic DNA of six P. aeruginosa strains were isolated and sequenced using PacBio RS-II platform. They were annotated using Prokaryotic Genome Annotation Pipeline and manually curated and analyzed for the presence of mobile genetic elements, antibiotic resistances genes, efflux pumps and virulence factors using several bioinformatics programs and databases. RESULTS The global analysis of the strains chromosomes showed a novel chromosomal rearrangement in two strains, possibly mediated by subsequent recombination and inversion events. They have a high content of mobile genetic elements: 21 genomic islands, four new islets, four different integrative conjugative elements, 28 different prophages, one CRISPR-Cas arrangements, and one class 1 integron. The acquisition of antimicrobials resistance genes into these elements are in concordance with their phenotype of multi-drug resistance. CONCLUSION The accessory genome increased the ability of the strains to adapt or survive to the hospital environment, promote genomic plasticity and chromosomal rearrangements, which may affect the expression or functionality of the gene and might influence the clinical outcome, having an impact on the treatment.
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Affiliation(s)
- Luis F Espinosa-Camacho
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, C.P. 04510, Mexico City, Mexico
| | - Gabriela Delgado
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, C.P. 04510, Mexico City, Mexico
| | - Alejandro Cravioto
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, C.P. 04510, Mexico City, Mexico
| | - Rosario Morales-Espinosa
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, C.P. 04510, Mexico City, Mexico.
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10
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Lee C, Klockgether J, Fischer S, Trcek J, Tümmler B, Römling U. Why? - Successful Pseudomonas aeruginosa clones with a focus on clone C. FEMS Microbiol Rev 2021; 44:740-762. [PMID: 32990729 PMCID: PMC7685784 DOI: 10.1093/femsre/fuaa029] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/12/2020] [Indexed: 12/20/2022] Open
Abstract
The environmental species Pseudomonas aeruginosa thrives in a variety of habitats. Within the epidemic population structure of P. aeruginosa, occassionally highly successful clones that are equally capable to succeed in the environment and the human host arise. Framed by a highly conserved core genome, individual members of successful clones are characterized by a high variability in their accessory genome. The abundance of successful clones might be funded in specific features of the core genome or, although not mutually exclusive, in the variability of the accessory genome. In clone C, one of the most predominant clones, the plasmid pKLC102 and the PACGI-1 genomic island are two ubiquitous accessory genetic elements. The conserved transmissible locus of protein quality control (TLPQC) at the border of PACGI-1 is a unique horizontally transferred compository element, which codes predominantly for stress-related cargo gene products such as involved in protein homeostasis. As a hallmark, most TLPQC xenologues possess a core genome equivalent. With elevated temperature tolerance as a characteristic of clone C strains, the unique P. aeruginosa and clone C specific disaggregase ClpG is a major contributor to tolerance. As other successful clones, such as PA14, do not encode the TLPQC locus, ubiquitous denominators of success, if existing, need to be identified.
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Affiliation(s)
- Changhan Lee
- Department of Microbiology, Tumor and Cell Biology, Biomedicum C8, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Jens Klockgether
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Sebastian Fischer
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Janja Trcek
- Faculty of Natural Sciences and Mathematics, Department of Biology, University of Maribor, Maribor, 2000, Slovenia
| | - Burkhard Tümmler
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Biomedicum C8, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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Horna G, Ruiz J. Type 3 secretion system of Pseudomonas aeruginosa. Microbiol Res 2021; 246:126719. [PMID: 33582609 DOI: 10.1016/j.micres.2021.126719] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 12/27/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen, mainly affecting severe patients, such as those in intensive care units (ICUs). High levels of antibiotic resistance and a long battery of virulence factors characterise this pathogen. Among virulence factors, the T3SS (Type 3 Secretion Systems) are especially relevant, being one of the most important virulence factors in P. aeruginosa. T3SS are a complex "molecular syringe" able to inject different effectors in host cells, subverting cell machinery influencing immune responses, and increasing bacterial survival rates. While T3SS have been largely studied and the molecular structure and main effector functions have been established, a series of questions and further points remain to be clarified or established. The key role of T3SS in P. aeruginosa virulence has resulted in the search for T3SS-targeting molecules able to impair their functions and subsequently improve patient outcomes. This review aims to summarise the most relevant features of the P. aeruginosa T3SS.
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Affiliation(s)
- Gertrudis Horna
- Universidad Catolica Los Angeles de Chimbote, Instituto de Investigación, Chimbote, Peru.
| | - Joaquim Ruiz
- Laboratorio de Microbiología Molecular y Genómica Bacteriana, Universidad Científica del Sur, Panamericana Sur, Km 19, Lima, Peru.
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Phenotypic and Genomic Comparison of the Two Most Common ExoU-Positive Pseudomonas aeruginosa Clones, PA14 and ST235. mSystems 2020; 5:5/6/e01007-20. [PMID: 33293405 PMCID: PMC7743143 DOI: 10.1128/msystems.01007-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genotyping of 2,882 Pseudomonas aeruginosa isolates that had been collected during the last 40 years identified the ExoU-positive lineages PA14 (ST253) and ST235 as the second and third most frequent clones in the P. aeruginosa population. Both clones were approximately 2-fold more frequently detected in animate habitats than in soil or aquatic habitats. While ST253 clone isolates were causing mainly acute and chronic infections in humans, ST235 isolates had been preferentially collected from hospitalized patients with severe acute infections, particularly, keratitis, urinary tract infections, burn wounds, and ventilator-associated pneumonia. The two major exoU clones differed substantially in the composition and flexibility of the accessory genome and by more than 8,000 amino acid sequences. Pronounced sequence variation between orthologs was noted in genes encoding elements of secretion systems and secreted effector molecules, including the type III secretion system, indicating the modes of action of the different clones. When comparing representatives of the two clones in batch culture, the PA14 strain orchestrated the quorum sensing circuitry for the expression of pathogenic traits and stopped growing in batch culture when it entered the stationary phase, but the quorum sensing-deficient ST235 strain expressed high type III secretion activity and continued to grow and to divide. In summary, unrestricted growth, high constitutive type III secretion activity, and facilitated uptake of foreign DNA could be major features that have made ST235 a global high-risk clone associated with poor outcomes of acute nosocomial infections.IMPORTANCE The ubiquitous and metabolically versatile environmental bacterium Pseudomonas aeruginosa can cause infections in a wide variety of hosts, including insects, plants, animals, and humans. P. aeruginosa is one of the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens that are the major cause of nosocomial infections in the United States and are a threat all over the world because of their capacity to become increasingly resistant to all available antibiotics. Most experimental work on P. aeruginosa has been performed with reference strains PAO1 and PA14, providing deep insight into key metabolic and regulatory pathways thought to be applicable to all P. aeruginosa strains. However, this comparative study on the two most common exoU-positive clones taught us that there are major lineages in the population such as the global high-risk clone ST235 that exhibit uncommon traits of lifestyle, genome mobility, and pathogenicity distinct from those in our knowledge gained from the studies with the reference strains.
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Cepas V, Soto SM. Relationship between Virulence and Resistance among Gram-Negative Bacteria. Antibiotics (Basel) 2020; 9:antibiotics9100719. [PMID: 33092201 PMCID: PMC7589547 DOI: 10.3390/antibiotics9100719] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 01/04/2023] Open
Abstract
Bacteria present in the human body are innocuous, providing beneficial functions, some of which are necessary for correct body function. However, other bacteria are able to colonize, invade, and cause damage to different tissues, and these are categorised as pathogens. These pathogenic bacteria possess several factors that enable them to be more virulent and cause infection. Bacteria have a great capacity to adapt to different niches and environmental conditions (presence of antibiotics, iron depletion, etc.). Antibiotic pressure has favoured the emergence and spread of antibiotic-resistant bacteria worldwide. Several studies have reported the presence of a relationship (both positive and negative, and both direct and indirect) between antimicrobial resistance and virulence among bacterial pathogens. This review studies the relationship among the most important Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa) taking into account two points of view: (i) the effect the acquisition of resistance has on virulence, and (ii) co-selection of resistance and virulence. The relationship between resistance and virulence among bacteria depends on the bacterial species, the specific mechanisms of resistance and virulence, the ecological niche, and the host.
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Khan M, Stapleton F, Summers S, Rice SA, Willcox MDP. Antibiotic Resistance Characteristics of Pseudomonas aeruginosa Isolated from Keratitis in Australia and India. Antibiotics (Basel) 2020; 9:antibiotics9090600. [PMID: 32937932 PMCID: PMC7559795 DOI: 10.3390/antibiotics9090600] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 02/07/2023] Open
Abstract
This study investigated genomic differences in Australian and Indian Pseudomonas aeruginosa isolates from keratitis (infection of the cornea). Overall, the Indian isolates were resistant to more antibiotics, with some of those isolates being multi-drug resistant. Acquired genes were related to resistance to fluoroquinolones, aminoglycosides, beta-lactams, macrolides, sulphonamides, and tetracycline and were more frequent in Indian (96%) than in Australian (35%) isolates (p = 0.02). Indian isolates had large numbers of gene variations (median 50,006, IQR = 26,967-50,600) compared to Australian isolates (median 26,317, IQR = 25,681-33,780). There were a larger number of mutations in the mutL and uvrD genes associated with the mismatch repair (MMR) system in Indian isolates, which may result in strains losing their efficacy for DNA repair. The number of gene variations were greater in isolates carrying MMR system genes or exoU. In the phylogenetic division, the number of core genes were similar in both groups, but Indian isolates had larger numbers of pan genes (median 6518, IQR = 6040-6935). Clones related to three different sequence types-ST308, ST316, and ST491-were found among Indian isolates. Only one clone, ST233, containing two strains was present in Australian isolates. The most striking differences between Australian and Indian isolates were carriage of exoU (that encodes a cytolytic phospholipase) in Indian isolates and exoS (that encodes for GTPase activator activity) in Australian isolates, large number of acquired resistance genes, greater changes to MMR genes, and a larger pan genome as well as increased overall genetic variation in the Indian isolates.
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Affiliation(s)
- Mahjabeen Khan
- School of Optometry and Vision Science, UNSW, Sydney, NSW 2052, Australia; (M.K.); (F.S.)
| | - Fiona Stapleton
- School of Optometry and Vision Science, UNSW, Sydney, NSW 2052, Australia; (M.K.); (F.S.)
| | - Stephen Summers
- The Singapore Centre for Environment Life Sciences Engineering (SCELSE), The School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore; (S.S.); (S.A.R.)
| | - Scott A. Rice
- The Singapore Centre for Environment Life Sciences Engineering (SCELSE), The School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore; (S.S.); (S.A.R.)
- The ithree Institute, The University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Mark D. P. Willcox
- School of Optometry and Vision Science, UNSW, Sydney, NSW 2052, Australia; (M.K.); (F.S.)
- Correspondence: ; Tel.: +61-2-9385-4164
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Secondary in-hospital epidemiological investigation after an outbreak of Pseudomonas aeruginosa ST357. J Infect Chemother 2020; 26:257-265. [DOI: 10.1016/j.jiac.2019.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/04/2019] [Accepted: 09/24/2019] [Indexed: 12/27/2022]
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Sawa T, Momiyama K, Mihara T, Kainuma A, Kinoshita M, Moriyama K. Molecular epidemiology of clinically high-risk Pseudomonas aeruginosa strains: Practical overview. Microbiol Immunol 2020; 64:331-344. [PMID: 31965613 DOI: 10.1111/1348-0421.12776] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/07/2020] [Accepted: 01/20/2020] [Indexed: 12/13/2022]
Abstract
In recent years, numerous outbreaks of multidrug-resistant Pseudomonas aeruginosa have been reported across the world. Once an outbreak occurs, besides routinely testing isolates for susceptibility to antimicrobials, it is required to check their virulence genotypes and clonality profiles. Replacing pulsed-field gel electrophoresis DNA fingerprinting are faster, easier-to-use, and less expensive polymerase chain reaction (PCR)-based methods for characterizing hospital isolates. P. aeruginosa possesses a mosaic genome structure and a highly conserved core genome displaying low sequence diversity and a highly variable accessory genome that communicates with other Pseudomonas species via horizontal gene transfer. Multiple-locus variable-number tandem-repeat analysis and multilocus sequence typing methods allow for phylogenetic analysis of isolates by PCR amplification of target genes with the support of Internet-based services. The target genes located in the core genome regions usually contain low-frequency mutations, allowing the resulting phylogenetic trees to infer evolutionary processes. The multiplex PCR-based open reading frame typing (POT) method, integron PCR, and exoenzyme genotyping can determine a genotype by PCR amplifying a specific insertion gene in the accessory genome region using a single or a multiple primer set. Thus, analyzing P. aeruginosa isolates for their clonality, virulence factors, and resistance characteristics is achievable by combining the clonality evaluation of the core genome based on multiple-locus targeting methods with other methods that can identify specific virulence and antimicrobial genes. Software packages such as eBURST, R, and Dendroscope, which are powerful tools for phylogenetic analyses, enable researchers and clinicians to visualize clonality associations in clinical isolates.
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Affiliation(s)
- Teiji Sawa
- Department of Anesthesiology, School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kyoko Momiyama
- School of Pharmacy, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Toshihito Mihara
- Department of Anesthesiology, School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Atsushi Kainuma
- Department of Anesthesiology, School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Mao Kinoshita
- Department of Anesthesiology, School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kiyoshi Moriyama
- Department of Anesthesiology, School of Medicine, Kyorin University, Tokyo, Japan
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Ozer EA, Nnah E, Didelot X, Whitaker RJ, Hauser AR. The Population Structure of Pseudomonas aeruginosa Is Characterized by Genetic Isolation of exoU+ and exoS+ Lineages. Genome Biol Evol 2019; 11:1780-1796. [PMID: 31173069 PMCID: PMC6690169 DOI: 10.1093/gbe/evz119] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2019] [Indexed: 02/06/2023] Open
Abstract
The diversification of microbial populations may be driven by many factors including adaptation to distinct ecological niches and barriers to recombination. We examined the population structure of the bacterial pathogen Pseudomonas aeruginosa by analyzing whole-genome sequences of 739 isolates from diverse sources. We confirmed that the population structure of P. aeruginosa consists of two major groups (referred to as Groups A and B) and at least two minor groups (Groups C1 and C2). Evidence for frequent intragroup but limited intergroup recombination in the core genome was observed, consistent with sexual isolation of the groups. Likewise, accessory genome analysis demonstrated more gene flow within Groups A and B than between these groups, and a few accessory genomic elements were nearly specific to one or the other group. In particular, the exoS gene was highly overrepresented in Group A compared with Group B isolates (99.4% vs. 1.1%) and the exoU gene was highly overrepresented in Group B compared with Group A isolates (95.2% vs. 1.8%). The exoS and exoU genes encode effector proteins secreted by the P. aeruginosa type III secretion system. Together these results suggest that the major P. aeruginosa groups defined in part by the exoS and exoU genes are divergent from each other, and that these groups are genetically isolated and may be ecologically distinct. Although both groups were globally distributed and caused human infections, certain groups predominated in some clinical contexts.
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Affiliation(s)
- Egon A Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine
| | - Ekpeno Nnah
- Lurie Children's Hospital, Chicago, Illinois
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Rachel J Whitaker
- Department of Microbiology and the Carl R. Woese Institute of Genomic Biology, University of Illinois, Urbana-Champaign
| | - Alan R Hauser
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine.,Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine
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High frequency of the exoU+/exoS+ genotype associated with multidrug-resistant "high-risk clones" of Pseudomonas aeruginosa clinical isolates from Peruvian hospitals. Sci Rep 2019; 9:10874. [PMID: 31350412 PMCID: PMC6659710 DOI: 10.1038/s41598-019-47303-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 07/15/2019] [Indexed: 01/09/2023] Open
Abstract
The type III secretion system of Pseudomonas aeruginosa is an important virulence factor contributing to the cytotoxicity and the invasion process of this microorganism. The current study aimed to determine the presence of the exoU+/exoS+ genotype in P. aeruginosa clinical isolates. The presence of exoS, exoT, exoU and exoY was determined in 189 P. aeruginosa by PCR, and the presence/absence of exoU was analysed according to source infection, clonal relationships, biofilm formation, motility and antimicrobial susceptibility. The gyrA, parC, oprD, efflux pump regulators and β-lactamases genes were also analysed by PCR/sequencing. The exoS, exoT and exoY genes were found in 100% of the isolates. Meanwhile, exoU was present in 43/189 (22.8%) of the isolates, being significantly associated with multidrug resistance, extensively drug resistance as well as with higher level quinolone resistance. However, the presence of β-lactamases, mutations in gyrA and parC, and relevant modifications in efflux pumps and OprD were not significantly associated with exoU+ isolates. MLST analysis of a subset of 25 isolates showed 8 different STs displaying the exoU+/exoS+ genotype. The MDR basis of the exoU+ isolates remain to be elucidated. Furthermore, the clinical implications and spread of exoU+/exoS+ P. aeruginosa isolates need to be established.
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Antibiotic resistance in Pseudomonas aeruginosa - Mechanisms, epidemiology and evolution. Drug Resist Updat 2019; 44:100640. [PMID: 31492517 DOI: 10.1016/j.drup.2019.07.002] [Citation(s) in RCA: 233] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022]
Abstract
Antibiotics are powerful drugs used in the treatment of bacterial infections. The inappropriate use of these medicines has driven the dissemination of antibiotic resistance (AR) in most bacteria. Pseudomonas aeruginosa is an opportunistic pathogen commonly involved in environmental- and difficult-to-treat hospital-acquired infections. This species is frequently resistant to several antibiotics, being in the "critical" category of the WHO's priority pathogens list for research and development of new antibiotics. In addition to a remarkable intrinsic resistance to several antibiotics, P. aeruginosa can acquire resistance through chromosomal mutations and acquisition of AR genes. P. aeruginosa has one of the largest bacterial genomes and possesses a significant assortment of genes acquired by horizontal gene transfer (HGT), which are frequently localized within integrons and mobile genetic elements (MGEs), such as transposons, insertion sequences, genomic islands, phages, plasmids and integrative and conjugative elements (ICEs). This genomic diversity results in a non-clonal population structure, punctuated by specific clones that are associated with significant morbidity and mortality worldwide, the so-called high-risk clones. Acquisition of MGEs produces a fitness cost in the host, that can be eased over time by compensatory mutations during MGE-host coevolution. Even though plasmids and ICEs are important drivers of AR, the underlying evolutionary traits that promote this dissemination are poorly understood. In this review, we provide a comprehensive description of the main strategies involved in AR in P. aeruginosa and the leading drivers of HGT in this species. The most recently developed genomic tools that allowed a better understanding of the features contributing for the success of P. aeruginosa are discussed.
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Botelho J, Grosso F, Peixe L. WITHDRAWN: Antibiotic resistance in Pseudomonas aeruginosa – mechanisms, epidemiology and evolution. Drug Resist Updat 2019. [DOI: 10.1016/j.drup.2019.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Impact of FiuA Outer Membrane Receptor Polymorphism on the Resistance of Pseudomonas aeruginosa toward Peptidoglycan Lipid II-Targeting PaeM Pyocins. J Bacteriol 2019; 201:JB.00164-19. [PMID: 30988031 DOI: 10.1128/jb.00164-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 04/04/2019] [Indexed: 12/29/2022] Open
Abstract
Certain Pseudomonas aeruginosa strains produce a homolog of colicin M, namely, PaeM, that specifically inhibits peptidoglycan biosynthesis of susceptible P. aeruginosa strains by hydrolyzing the lipid II intermediate precursor. Two variants of this pyocin were identified whose sequences mainly differed in the N-terminal protein moiety, i.e., the region involved in the binding to the FiuA outer membrane receptor and translocation into the periplasm. The antibacterial activity of these two variants, PaeM1 and PaeM2, was tested against various P. aeruginosa strains comprising reference strains PAO1 and PA14, PaeM-producing strains, and 60 clinical isolates. Seven of these strains, including PAO1, were susceptible to only one variant (2 to PaeM1 and 5 to PaeM2), and 11 were affected by both. The remaining strains, including PA14 and four PaeM1 producers, were resistant to both variants. The differences in the antibacterial spectra of the two PaeM homologs prompted us to investigate the molecular determinants allowing their internalization into P. aeruginosa cells, taking the PAO1 strain that is susceptible to PaeM2 but resistant to PaeM1 as the indicator strain. Heterologous expression of fiuA gene orthologs from different strains into PAO1, site-directed mutagenesis experiments, and construction of PaeM chimeric proteins provided evidence that the cell susceptibility and discrimination differences between the PaeM variants resulted from a polymorphism of both the pyocin and the outer membrane receptor FiuA. Moreover, we found that a third component, TonB1, a protein involved in iron transport in P. aeruginosa, working together with FiuA and the ExbB/ExbD complex, was directly implicated in this discrimination.IMPORTANCE Bacterial antibiotic resistance constitutes a threat to human health, imposing the need for identification of new targets and development of new strategies to fight multiresistant pathogens. Bacteriocins and other weapons that bacteria have themselves developed to kill competitors are therefore of great interest and a valuable source of inspiration for us. Attention was paid here to two variants of a colicin M homolog (PaeM) produced by certain strains of P. aeruginosa that inhibit the growth of their congeners by blocking cell wall peptidoglycan synthesis. Molecular determinants allowing recognition of these pyocins by the outer membrane receptor FiuA were identified, and a receptor polymorphism affecting the susceptibility of P. aeruginosa clinical strains was highlighted, providing new insights into the potential use of these pyocins as an alternative to antibiotics.
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Subedi D, Kohli GS, Vijay AK, Willcox M, Rice SA. Accessory genome of the multi-drug resistant ocular isolate of Pseudomonas aeruginosa PA34. PLoS One 2019; 14:e0215038. [PMID: 30986237 PMCID: PMC6464166 DOI: 10.1371/journal.pone.0215038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 03/25/2019] [Indexed: 02/07/2023] Open
Abstract
Bacteria can acquire an accessory genome through the horizontal transfer of genetic elements from non-parental lineages. This leads to rapid genetic evolution allowing traits such as antibiotic resistance and virulence to spread through bacterial communities. The study of complete genomes of bacterial strains helps to understand the genomic traits associated with virulence and antibiotic resistance. We aimed to investigate the complete accessory genome of an ocular isolate of Pseudomonas aeruginosa strain PA34. We obtained the complete genome of PA34 utilising genome sequence reads from Illumina and Oxford Nanopore Technology followed by PCR to close any identified gaps. In-depth genomic analysis was performed using various bioinformatics tools. The susceptibility to heavy metals and cytotoxicity was determined to confirm expression of certain traits. The complete genome of PA34 includes a chromosome of 6.8 Mbp and two plasmids of 95.4 Kbp (pMKPA34-1) and 26.8 Kbp (pMKPA34-2). PA34 had a large accessory genome of 1,213 genes and had 543 unique genes not present in other strains. These exclusive genes encoded features related to metal and antibiotic resistance, phage integrase and transposons. At least 24 genomic islands (GIs) were predicated in the complete chromosome, of which two were integrated into novel sites. Eleven GIs carried virulence factors or replaced pathogenic genes. A bacteriophage carried the aminoglycoside resistance gene (AAC(3)-IId). The two plasmids carried other six antibiotic resistance genes. The large accessory genome of this ocular isolate plays a large role in shaping its virulence and antibiotic resistance.
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Affiliation(s)
- Dinesh Subedi
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
- * E-mail:
| | - Gurjeet Singh Kohli
- The Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ajay Kumar Vijay
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
| | - Mark Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
| | - Scott A. Rice
- The Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- The ithree Institute, The University of Technology Sydney, Sydney, New South Wales, Australia
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Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites. Sci Rep 2018; 8:15668. [PMID: 30353070 PMCID: PMC6199293 DOI: 10.1038/s41598-018-34020-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022] Open
Abstract
The large and complex genome of Pseudomonas aeruginosa, which consists of significant portions (up to 20%) of transferable genetic elements contributes to the rapid development of antibiotic resistance. The whole genome sequences of 22 strains isolated from eye and cystic fibrosis patients in Australia and India between 1992 and 2007 were used to compare genomic divergence and phylogenetic relationships as well as genes for antibiotic resistance and virulence factors. Analysis of the pangenome indicated a large variation in the size of accessory genome amongst 22 stains and the size of the accessory genome correlated with number of genomic islands, insertion sequences and prophages. The strains were diverse in terms of sequence type and dissimilar to that of global epidemic P. aeruginosa clones. Of the eye isolates, 62% clustered together within a single lineage. Indian eye isolates possessed genes associated with resistance to aminoglycoside, beta-lactams, sulphonamide, quaternary ammonium compounds, tetracycline, trimethoprims and chloramphenicols. These genes were, however, absent in Australian isolates regardless of source. Overall, our results provide valuable information for understanding the genomic diversity of P. aeruginosa isolated from two different infection types and countries.
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Brüggemann H, Migliorini LB, Sales ROD, Koga PCM, Souza AVD, Jensen A, Poehlein A, Brzuszkiewicz E, Doi AM, Pasternak J, Martino MDV, Severino P. Comparative Genomics of Nonoutbreak Pseudomonas aeruginosa Strains Underlines Genome Plasticity and Geographic Relatedness of the Global Clone ST235. Genome Biol Evol 2018; 10:1852-1857. [PMID: 29982603 PMCID: PMC6063271 DOI: 10.1093/gbe/evy139] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2018] [Indexed: 02/07/2023] Open
Abstract
Pseudomonas aeruginosa is an important opportunistic pathogen in hospitals, responsible for various infections that are difficult to treat due to intrinsic and acquired antibiotic resistance. Here, 20 epidemiologically unrelated strains isolated from patients in a general hospital over a time period of two decades were analyzed using whole genome sequencing. The genomes were compared in order to assess the presence of a predominant clone or sequence type (ST). No clonal structure was identified, but core genome-based single nucleotide polymorphism (SNP) analysis distinguished two major, previously identified phylogenetic groups. Interestingly, most of the older strains isolated between 1994 and 1998 harbored exoU, encoding a cytotoxic phospholipase. In contrast, most strains isolated between 2011 and 2016 were exoU-negative and phylogenetically very distinct from the older strains, suggesting a population shift of nosocomial P. aeruginosa over time. Three out of 20 strains were ST235 strains, a global high-risk clonal lineage; these carried several additional resistance determinants including aac(6’)Ib-cr encoding an aminoglycoside N-acetyltransferase that confers resistance to fluoroquinolones. Core genome comparison with ST235 strains from other parts of the world showed that the three strains clustered together with other Brazilian/Argentinean isolates. Despite this regional relatedness, the individuality of each of the three ST235 strains was revealed by core genome-based SNPs and the presence of genomic islands in the accessory genome. Similarly, strain-specific characteristics were detected for the remaining strains, indicative of individual evolutionary histories and elevated genome plasticity.
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Affiliation(s)
| | - Leticia Busato Migliorini
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | - Romario Oliveira de Sales
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | | | - Andrea Vieira de Souza
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | - Anders Jensen
- Department of Biomedicine, Aarhus University, Denmark
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Germany
| | - Elzbieta Brzuszkiewicz
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Germany
| | - Andre Mario Doi
- Laboratorio Clinico, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | - Jacyr Pasternak
- Laboratorio Clinico, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | | | - Patricia Severino
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
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Environmental and Clinical Pseudomonas aeruginosa Isolates with Pooled Presence of exo S, exo U, exo T and exo Y genes. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.3.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Subedi D, Vijay AK, Kohli GS, Rice SA, Willcox M. Association between possession of ExoU and antibiotic resistance in Pseudomonas aeruginosa. PLoS One 2018; 13:e0204936. [PMID: 30265709 PMCID: PMC6161911 DOI: 10.1371/journal.pone.0204936] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/17/2018] [Indexed: 12/22/2022] Open
Abstract
Virulent strains of Pseudomonas aeruginosa are often associated with an acquired cytotoxic protein, exoenzyme U (ExoU) that rapidly destroys the cell membranes of host cells by its phospholipase activity. Strains possessing the exoU gene are predominant in eye infections and are more resistant to antibiotics. Thus, it is essential to understand treatment options for these strains. Here, we have investigated the resistance profiles and genes associated with resistance for fluoroquinolone and beta-lactams. A total of 22 strains of P. aeruginosa from anterior eye infections, microbial keratitis (MK), and the lungs of cystic fibrosis (CF) patients were used. Based on whole genome sequencing, the prevalence of the exoU gene was 61.5% in MK isolates whereas none of the CF isolates possessed this gene. Overall, higher antibiotic resistance was observed in the isolates possessing exoU. Of the exoU strains, all except one were resistant to fluoroquinolones, 100% were resistant to beta-lactams. 75% had mutations in quinolone resistance determining regions (T81I gyrA and/or S87L parC) which correlated with fluoroquinolone resistance. In addition, exoU strains had mutations at K76Q, A110T, and V126E in ampC, Q155I and V356I in ampR and E114A, G283E, and M288R in mexR genes that are associated with higher beta-lactamase and efflux pump activities. In contrast, such mutations were not observed in the strains lacking exoU. The expression of the ampC gene increased by up to nine-fold in all eight exoU strains and the ampR was upregulated in seven exoU strains compared to PAO1. The expression of mexR gene was 1.4 to 3.6 fold lower in 75% of exoU strains. This study highlights the association between virulence traits and antibiotic resistance in pathogenic P. aeruginosa.
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Affiliation(s)
- Dinesh Subedi
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
- * E-mail:
| | - Ajay Kumar Vijay
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
| | - Gurjeet Singh Kohli
- The Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Scott A. Rice
- The Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore
- The ithree institute, The University of Technology Sydney, Sydney NSW Australia
| | - Mark Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
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Botelho J, Grosso F, Peixe L. Unravelling the genome of a Pseudomonas aeruginosa isolate belonging to the high-risk clone ST235 reveals an integrative conjugative element housing a blaGES-6 carbapenemase. J Antimicrob Chemother 2018; 73:77-83. [PMID: 29029083 DOI: 10.1093/jac/dkx337] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/19/2017] [Indexed: 12/12/2022] Open
Abstract
Objectives In Pseudomonas aeruginosa, the blaGES-6 carbapenemase gene was previously associated with an In1076 class I integron. Here, we conducted a genome-based analysis and explored the genetic platform associated with the mobility of this gene. Methods WGS of a blaGES-6-harbouring P. aeruginosa isolate (FFUP_PS_690) was performed with Illumina HiSeq, de novo assembly was performed using SPAdes and subsequent bioinformatic analysis was performed concerning antibiotic resistance genes, virulence features and mobile genetic elements. Results The FFUP_PS_690 isolate belongs to the ST235 high-risk clone and houses a novel integrative conjugative element (ICE), hereby named ICEPae690. This clc-like ICE comprises the blaGES-6-harbouring In1076 integron and specific modules. An ExoU island A variant was also identified. Conclusions The presence of a 'hitch-hiking' blaGES-6-harbouring In1076 integron in an ICE and an exoU-carrying genomic island highlight the potential spread of these elements through conjugation and/or clonal expansion of the ST235 lineage.
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Affiliation(s)
- João Botelho
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Filipa Grosso
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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28
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Miyoshi-Akiyama T, Tada T, Ohmagari N, Viet Hung N, Tharavichitkul P, Pokhrel BM, Gniadkowski M, Shimojima M, Kirikae T. Emergence and Spread of Epidemic Multidrug-Resistant Pseudomonas aeruginosa. Genome Biol Evol 2018; 9:3238-3245. [PMID: 29202180 PMCID: PMC5726472 DOI: 10.1093/gbe/evx243] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2017] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is one of the most common nosocomial pathogens worldwide. Although the emergence of multidrug-resistant (MDR) P. aeruginosa is a critical problem in medical practice, the key features involved in the emergence and spread of MDR P. aeruginosa remain unknown. This study utilized whole genome sequence (WGS) analyses to define the population structure of 185 P. aeruginosa clinical isolates from several countries. Of these 185 isolates, 136 were categorized into sequence type (ST) 235, one of the most common types worldwide. Phylogenetic analysis showed that these isolates fell within seven subclades. Each subclade harbors characteristic drug resistance genes and a characteristic genetic background confined to a geographic location, suggesting that clonal expansion following antibiotic exposure is the driving force in generating the population structure of MDR P. aeruginosa. WGS analyses also showed that the substitution rate was markedly higher in ST235 MDR P. aeruginosa than in other strains. Notably, almost all ST235 isolates harbor the specific type IV secretion system and very few or none harbor the CRISPR/CAS system. These findings may help explain the mechanism underlying the emergence and spread of ST235 P. aeruginosa as the predominant MDR lineage.
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Affiliation(s)
- Tohru Miyoshi-Akiyama
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Tatsuya Tada
- Department of Infectious Diseases, National Center for Global Health and Medicine, Tokyo, Japan
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | | | | | - Bharat Mani Pokhrel
- Department of Microbiology, Tribuvan University Teaching Hospital, Kathmandu, Nepal
| | | | | | - Teruo Kirikae
- Department of Infectious Diseases, National Center for Global Health and Medicine, Tokyo, Japan
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29
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Ozer EA. ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements. BMC Bioinformatics 2018; 19:150. [PMID: 29678129 PMCID: PMC5910555 DOI: 10.1186/s12859-018-2154-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 04/11/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The non-conserved accessory genome of bacteria can be associated with important adaptive characteristics that can contribute to niche specificity or pathogenicity of strains. High degrees of structural and compositional diversity in genomic islands and other elements of the accessory genome can complicate characterization of accessory genome contents among populations of strains. Methods for easily and effectively defining the distributions of discrete elements of the accessory genome among bacterial strains in a population are needed to explore the relationships between the flexible genome and bacterial adaptive traits. RESULTS We have developed the open-source software package ClustAGE. This program, written in Perl, uses BLAST to cluster nucleotide accessory genomic elements from the genomes of multiple bacterial strains and to identify their distribution within the study population. The program output can be used in combination with strain phenotype data or other characteristics to detect associations. Optional graphical output is available for visualizing accessory genome gene content and distribution patterns. The capabilities of the software are demonstrated on a collection of 14 Pseudomonas aeruginosa genome sequences. CONCLUSIONS The ClustAGE software and utilities are effective for identifying characteristics and distributions of accessory genomic elements among groups of bacterial genomes. The ability to easily and effectively characterize the accessory genome of a sequence collection may provide a better understanding of the accessory genome's contribution to a species' adaptation and pathogenesis. The ClustAGE source code can be downloaded from https://clustage.sourceforge.io and a limited web-based implementation is available at http://vfsmspineagent.fsm.northwestern.edu/cgi-bin/clustage.cgi .
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Affiliation(s)
- Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
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Abdouchakour F, Aujoulat F, Licznar-Fajardo P, Marchandin H, Toubiana M, Parer S, Lotthé A, Jumas-Bilak E. Intraclonal variations of resistance and phenotype in Pseudomonas aeruginosa epidemic high-risk clone ST308: A key to success within a hospital? Int J Med Microbiol 2017; 308:279-289. [PMID: 29276044 DOI: 10.1016/j.ijmm.2017.11.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 10/28/2017] [Accepted: 11/19/2017] [Indexed: 10/18/2022] Open
Abstract
Most multidrug-resistant (MDR) and extensively drug-resistant (XDR) P. aeruginosa strains belonged to epidemic high-risk (EHR) clones that succeeded worldwide in the context of hospital outbreaks. In order to study the intraclonal diversity in EHR P. aeruginosa, we selected clinical and environmental strains of the EHR clone ST308 that caused outbreak clusters over five years in a hospital and then persisted in the hospital environment during four additional years, causing sporadic infections. Unexpectedly, resistance phenotype was very diverse within the population, independently of the origin (environmental or human) and the period of isolation (during or after outbreaks). Most MDR/XDR strains belonged to clusters in pulsed-field gel electrophoresis (PFGE) while singleton strains instead displayed susceptible or moderately resistant phenotypes. High diversity was observed for motility and biofilm formation without correlation with the origin and the period. Resistance to biocides was not linked to epidemic success or to environmental persistence. Finally, the EHR clone ST308 did not display common adaptive traits, nor traits related to an origin or a period of isolation in the hospital. The major character of this EHR clone ST308 is its intraclonal diversity that probably warrants its adaptation and persistence in hospital whatever the conditions and therefore its epidemic behaviour. This diversity could result from adaptive radiation with the evolution of multiple lineages that fill available niches within a complex ecosystem such as a hospital.
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Affiliation(s)
- F Abdouchakour
- Université de Montpellier, UMR 5569 HydroSciences, équipe Pathogènes Hydriques Santé Environnements, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France
| | - F Aujoulat
- Université de Montpellier, UMR 5569 HydroSciences, équipe Pathogènes Hydriques Santé Environnements, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France
| | - P Licznar-Fajardo
- Université de Montpellier, UMR 5569 HydroSciences, équipe Pathogènes Hydriques Santé Environnements, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France; Département d'Hygiène Hospitalière, CHRU Montpellier, Hôpital St Eloi, 80 Avenue Augustin Fliche, 34090 Montpellier, France
| | - H Marchandin
- Université de Montpellier, UMR 5569 HydroSciences, équipe Pathogènes Hydriques Santé Environnements, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France; Department of Microbiology, Nîmes University Hospital, Place du Professeur Robert Debré, 30029 Nîmes, France
| | - M Toubiana
- Université de Montpellier, UMR 5569 HydroSciences, équipe Pathogènes Hydriques Santé Environnements, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France
| | - S Parer
- Université de Montpellier, UMR 5569 HydroSciences, équipe Pathogènes Hydriques Santé Environnements, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France; Département d'Hygiène Hospitalière, CHRU Montpellier, Hôpital St Eloi, 80 Avenue Augustin Fliche, 34090 Montpellier, France
| | - A Lotthé
- Université de Montpellier, UMR 5569 HydroSciences, équipe Pathogènes Hydriques Santé Environnements, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France; Département d'Hygiène Hospitalière, CHRU Montpellier, Hôpital St Eloi, 80 Avenue Augustin Fliche, 34090 Montpellier, France
| | - E Jumas-Bilak
- Université de Montpellier, UMR 5569 HydroSciences, équipe Pathogènes Hydriques Santé Environnements, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France; Département d'Hygiène Hospitalière, CHRU Montpellier, Hôpital St Eloi, 80 Avenue Augustin Fliche, 34090 Montpellier, France.
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31
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Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
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Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
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32
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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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Kaiser SJ, Mutters NT, DeRosa A, Ewers C, Frank U, Günther F. Determinants for persistence of Pseudomonas aeruginosa in hospitals: interplay between resistance, virulence and biofilm formation. Eur J Clin Microbiol Infect Dis 2016; 36:243-253. [PMID: 27734161 DOI: 10.1007/s10096-016-2792-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/14/2016] [Indexed: 12/27/2022]
Abstract
Pseudomonas aeruginosa (Pa) is one of the major bacterial pathogens causing nosocomial infections. During the past few decades, multidrug-resistant (MDR) and extensively drug-resistant (XDR) lineages of Pa have emerged in hospital settings with increasing numbers. However, it remains unclear which determinants of Pa facilitated this spread. A total of 211 clinical XDR and 38 susceptible clinical Pa isolates (nonXDR), as well as 47 environmental isolates (EI), were collected at the Heidelberg University Hospital. We used RAPD PCR to identify genetic clusters. Carriage of carbapenamases (CPM) and virulence genes were analyzed by PCR, biofilm formation capacity was assessed, in vitro fitness was evaluated using competitive growth assays, and interaction with the host's immune system was analyzed using serum killing and neutrophil killing assays. XDR isolates showed significantly elevated biofilm formation (p < 0.05) and higher competitive fitness compared to nonXDR and EI isolates. Thirty percent (62/205) of the XDR isolates carried a CPM. Similarities in distribution of virulence factors, as well as biofilm formation properties, between CPM+ Pa isolates and EI and between CPM- and nonXDR isolates were detected. Molecular typing revealed two distinct genetic clusters within the XDR population, which were characterized by even higher biofilm formation. In contrast, XDR isolates were more susceptible to the immune response than nonXDR isolates. Our study provides evidence that the ability to form biofilms is an outstanding determinant for persistence and endemic spread of Pa in the hospital setting.
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Affiliation(s)
- S J Kaiser
- Department of Infectious Diseases, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - N T Mutters
- Department of Infectious Diseases, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - A DeRosa
- Department of Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - C Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - U Frank
- Department of Infectious Diseases, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - F Günther
- Department of Infectious Diseases, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany.
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34
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Agnello M, Finkel SE, Wong-Beringer A. Fitness Cost of Fluoroquinolone Resistance in Clinical Isolates of Pseudomonas aeruginosa Differs by Type III Secretion Genotype. Front Microbiol 2016; 7:1591. [PMID: 27757111 PMCID: PMC5047889 DOI: 10.3389/fmicb.2016.01591] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/22/2016] [Indexed: 12/23/2022] Open
Abstract
Fluoroquinolone (FQ) resistance is highly prevalent among clinical strains of Pseudomonas aeruginosa, limiting treatment options. We have reported previously that highly virulent strains containing the exoU gene of the type III secretion system are more likely to be FQ-resistant than strains containing the exoS gene, as well as more likely to acquire resistance-conferring mutations in gyrA/B and parC/E. We hypothesize that FQ-resistance imposes a lower fitness cost on exoU compared to exoS strains, thus allowing for better adaptation to the FQ-rich clinical environment. We created isogenic mutants containing a common FQ-resistance conferring point mutation in parC from three exoU to three exoS clinical isolates and tested fitness in vitro using head-to-head competition assays. The mutation differentially affected fitness in the exoU and exoS strains tested. While the addition of the parC mutation dramatically increased fitness in one of the exoU strains leaving the other two unaffected, all three exoS strains displayed a general decrease in fitness. In addition, we found that exoU strains may be able to compensate for the fitness costs associated with the mutation through better regulation of supercoiling compared to the exoS strains. These results may provide a biological explanation for the observed predominance of the virulent exoU genotype in FQ-resistant clinical subpopulations and represent the first investigation into potential differences in fitness costs of FQ-resistance that are linked to the virulence genotype of P. aeruginosa. Understanding the fitness costs of antibiotic resistance and possibilities of compensation for these costs is essential for the rational development of strategies to combat the problem of antibiotic resistance.
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Affiliation(s)
- Melissa Agnello
- School of Pharmacy, University of Southern California Los Angeles, CA, USA
| | - Steven E Finkel
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California Los Angeles, CA, USA
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35
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Abstract
Bacterial sphingomyelinases and phospholipases are a heterogeneous group of esterases which are usually surface associated or secreted by a wide variety of Gram-positive and Gram-negative bacteria. These enzymes hydrolyze sphingomyelin and glycerophospholipids, respectively, generating products identical to the ones produced by eukaryotic enzymes which play crucial roles in distinct physiological processes, including membrane dynamics, cellular signaling, migration, growth, and death. Several bacterial sphingomyelinases and phospholipases are essential for virulence of extracellular, facultative, or obligate intracellular pathogens, as these enzymes contribute to phagosomal escape or phagosomal maturation avoidance, favoring tissue colonization, infection establishment and progression, or immune response evasion. This work presents a classification proposal for bacterial sphingomyelinases and phospholipases that considers not only their enzymatic activities but also their structural aspects. An overview of the main physiopathological activities is provided for each enzyme type, as are examples in which inactivation of a sphingomyelinase- or a phospholipase-encoding gene impairs the virulence of a pathogen. The identification of sphingomyelinases and phospholipases important for bacterial pathogenesis and the development of inhibitors for these enzymes could generate candidate vaccines and therapeutic agents, which will diminish the impacts of the associated human and animal diseases.
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Lund-Palau H, Turnbull AR, Bush A, Bardin E, Cameron L, Soren O, Wierre-Gore N, Alton EWFW, Bundy JG, Connett G, Faust SN, Filloux A, Freemont P, Jones A, Khoo V, Morales S, Murphy R, Pabary R, Simbo A, Schelenz S, Takats Z, Webb J, Williams HD, Davies JC. Pseudomonas aeruginosa infection in cystic fibrosis: pathophysiological mechanisms and therapeutic approaches. Expert Rev Respir Med 2016; 10:685-97. [PMID: 27175979 DOI: 10.1080/17476348.2016.1177460] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pseudomonas aeruginosa is a remarkably versatile environmental bacterium with an extraordinary capacity to infect the cystic fibrosis (CF) lung. Infection with P. aeruginosa occurs early, and although eradication can be achieved following early detection, chronic infection occurs in over 60% of adults with CF. Chronic infection is associated with accelerated disease progression and increased mortality. Extensive research has revealed complex mechanisms by which P. aeruginosa adapts to and persists within the CF airway. Yet knowledge gaps remain, and prevention and treatment strategies are limited by the lack of sensitive detection methods and by a narrow armoury of antibiotics. Further developments in this field are urgently needed in order to improve morbidity and mortality in people with CF. Here, we summarize current knowledge of pathophysiological mechanisms underlying P. aeruginosa infection in CF. Established treatments are discussed, and an overview is offered of novel detection methods and therapeutic strategies in development.
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Affiliation(s)
- Helena Lund-Palau
- a Department of Gene Therapy, National Heart and Lung Institute , Imperial College , London , UK
| | - Andrew R Turnbull
- a Department of Gene Therapy, National Heart and Lung Institute , Imperial College , London , UK.,b Department of Respiratory Paediatrics , Royal Brompton and Harefield NHS Foundation Trust , London , UK
| | - Andrew Bush
- b Department of Respiratory Paediatrics , Royal Brompton and Harefield NHS Foundation Trust , London , UK.,c National Heart and Lung Institute, Imperial College , London , UK
| | - Emmanuelle Bardin
- d Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine , Imperial College , London , UK
| | - Loren Cameron
- e Department of Medicine , Imperial College , London , UK
| | - Odel Soren
- f Biological Sciences, Institute for Life Sciences , University of Southampton , Southampton , UK
| | | | - Eric W F W Alton
- a Department of Gene Therapy, National Heart and Lung Institute , Imperial College , London , UK
| | - Jacob G Bundy
- c National Heart and Lung Institute, Imperial College , London , UK
| | - Gary Connett
- g NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust , University of Southampton , Southampton , UK
| | - Saul N Faust
- g NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust , University of Southampton , Southampton , UK
| | - Alain Filloux
- h Department of Life Sciences , Imperial College , London , UK
| | - Paul Freemont
- e Department of Medicine , Imperial College , London , UK
| | - Andy Jones
- i Department of Respiratory Medicine , Royal Brompton Hospital , London , UK
| | - Valerie Khoo
- c National Heart and Lung Institute, Imperial College , London , UK
| | | | - Ronan Murphy
- a Department of Gene Therapy, National Heart and Lung Institute , Imperial College , London , UK
| | - Rishi Pabary
- a Department of Gene Therapy, National Heart and Lung Institute , Imperial College , London , UK
| | - Ameze Simbo
- a Department of Gene Therapy, National Heart and Lung Institute , Imperial College , London , UK
| | - Silke Schelenz
- k Department of Microbiology , Royal Brompton Hospital , London UK
| | - Zoltan Takats
- d Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine , Imperial College , London , UK
| | - Jeremy Webb
- k Department of Microbiology , Royal Brompton Hospital , London UK
| | - Huw D Williams
- g NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust , University of Southampton , Southampton , UK
| | - Jane C Davies
- a Department of Gene Therapy, National Heart and Lung Institute , Imperial College , London , UK.,b Department of Respiratory Paediatrics , Royal Brompton and Harefield NHS Foundation Trust , London , UK
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James GA, Ge Zhao A, Usui M, Underwood RA, Nguyen H, Beyenal H, deLancey Pulcini E, Agostinho Hunt A, Bernstein HC, Fleckman P, Olerud J, Williamson KS, Franklin MJ, Stewart PS. Microsensor and transcriptomic signatures of oxygen depletion in biofilms associated with chronic wounds. Wound Repair Regen 2016; 24:373-83. [PMID: 26748963 PMCID: PMC6208129 DOI: 10.1111/wrr.12401] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 12/29/2015] [Indexed: 12/25/2022]
Abstract
Biofilms have been implicated in delayed wound healing, although the mechanisms by which biofilms impair wound healing are poorly understood. Many species of bacteria produce exotoxins and exoenzymes that may inhibit healing. In addition, oxygen consumption by biofilms and by the responding leukocytes, may impede wound healing by depleting the oxygen that is required for healing. In this study, oxygen microsensors to measure oxygen transects through in vitro cultured biofilms, biofilms formed in vivo within scabs from a diabetic (db/db) mouse wound model, and ex vivo human chronic wound specimens was used. The results showed that oxygen levels within mouse scabs had steep gradients that reached minima ranging from 17 to 72 mmHg on live mice and from 6.4 to 1.1 mmHg on euthanized mice. The oxygen gradients in the mouse scabs were similar to those observed for clinical isolates cultured in vitro and for human ex vivo specimens. To characterize the metabolic activities of the bacteria in the mouse scabs, transcriptomics analyses of Pseudomonas aeruginosa biofilms associated with the db/db mice wounds was performed. The results demonstrated that the bacteria expressed genes for metabolic activities associated with cell growth. Interestingly, the transcriptome results also indicated that the bacteria within the wounds experienced oxygen-limitation stress. Among the bacterial genes that were expressed in vivo were genes associated with the Anr-mediated hypoxia-stress response. Other bacterial stress response genes highly expressed in vivo were genes associated with stationary-phase growth, osmotic stress, and RpoH-mediated heat shock stress. Overall, the results supported the hypothesis that bacterial biofilms in chronic wounds promote chronicity by contributing to the maintenance of localized low oxygen tensions, through their metabolic activities and through their recruitment of cells that consume oxygen for host defensive processes.
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Affiliation(s)
- Garth A James
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana
| | - Alice Ge Zhao
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Marcia Usui
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Robert A Underwood
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Hung Nguyen
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington
| | - Haluk Beyenal
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington
| | | | - Alessandra Agostinho Hunt
- Department of Microbiology and Molecular Genetics, 5180 Biomedical and Physical Sciences, Michigan State University, East Lansing, Michigan
| | - Hans C Bernstein
- Pacific Northwest National Laboratory, Chemical and Biological Signature Science, Richland, Washington
| | - Philip Fleckman
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington
| | - John Olerud
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Kerry S Williamson
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana
| | - Michael J Franklin
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana
| | - Philip S Stewart
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana
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Wagner S, Sommer R, Hinsberger S, Lu C, Hartmann RW, Empting M, Titz A. Novel Strategies for the Treatment of Pseudomonas aeruginosa Infections. J Med Chem 2016; 59:5929-69. [DOI: 10.1021/acs.jmedchem.5b01698] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Stefanie Wagner
- Chemical
Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), 30625 Standort Hannover-Braunschweig, Germany
| | - Roman Sommer
- Chemical
Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), 30625 Standort Hannover-Braunschweig, Germany
| | - Stefan Hinsberger
- Deutsches Zentrum für Infektionsforschung (DZIF), 30625 Standort Hannover-Braunschweig, Germany
- Drug
Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany
| | - Cenbin Lu
- Deutsches Zentrum für Infektionsforschung (DZIF), 30625 Standort Hannover-Braunschweig, Germany
- Drug
Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany
| | - Rolf W. Hartmann
- Deutsches Zentrum für Infektionsforschung (DZIF), 30625 Standort Hannover-Braunschweig, Germany
- Drug
Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany
| | - Martin Empting
- Deutsches Zentrum für Infektionsforschung (DZIF), 30625 Standort Hannover-Braunschweig, Germany
- Drug
Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany
| | - Alexander Titz
- Chemical
Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), 30625 Standort Hannover-Braunschweig, Germany
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Wiehlmann L, Cramer N, Tümmler B. Habitat-associated skew of clone abundance in the Pseudomonas aeruginosa population. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:955-960. [PMID: 26419222 DOI: 10.1111/1758-2229.12340] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 09/24/2015] [Accepted: 09/25/2015] [Indexed: 06/05/2023]
Abstract
The population structure of the cosmopolitan Pseudomonas aeruginosa was investigated by genotyping 2921 isolates from 1448 independent habitats with a custom-made 58 binary marker microarray. Of 323 identified clone types, 109 clones made up 82% of the population. The 20 most frequent clones had an absolute share of 44% indicating that the P. aeruginosa population is dominated by few epidemic clonal complexes. The frequency distribution of common clones was different between inanimate habitats and human niches. The three most abundant clones in the environment were rare among isolates from human infection. Conversely, disease-associated isolates either belonged to ubiquitous clones such as C and PA14 or to clones that were uncommon in the environment. The P. aeruginosa population consists of major clones that are just as versatile in their habitat and geographic origin as the whole species and of minor clones with preference for a peculiar niche.
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Affiliation(s)
- Lutz Wiehlmann
- Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research, Hannover, Germany
| | - Nina Cramer
- Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', Hannover Medical School, Hannover, Germany
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Lee C, Wigren E, Trček J, Peters V, Kim J, Hasni MS, Nimtz M, Lindqvist Y, Park C, Curth U, Lünsdorf H, Römling U. A novel protein quality control mechanism contributes to heat shock resistance of worldwide-distributed Pseudomonas aeruginosa clone C strains. Environ Microbiol 2015; 17:4511-26. [PMID: 26014207 DOI: 10.1111/1462-2920.12915] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 05/19/2015] [Indexed: 11/30/2022]
Abstract
Pseudomonas aeruginosa is a highly successful nosocomial pathogen capable of causing a wide variety of infections with clone C strains most prevalent worldwide. In this study, we initially characterize a molecular mechanism of survival unique to clone C strains. We identified a P. aeruginosa clone C-specific genomic island (PACGI-1) that contains the highly expressed small heat shock protein sHsp20c, the founding member of a novel subclass of class B bacterial small heat shock proteins. sHsp20c and adjacent gene products are involved in resistance against heat shock. Heat stable sHsp20c is unconventionally expressed in stationary phase in a wide temperature range from 20 to 42°C. Purified sHsp20c has characteristic features of small heat shock protein class B as it is monodisperse, forms sphere-like 24-meric oligomers and exhibits significant chaperone activity. As the P. aeruginosa clone C population is significantly more heat shock resistant than genetically unrelated P. aeruginosa strains without sHsp20c, the horizontally acquired shsp20c operon might contribute to the survival of worldwide-distributed clone C strains.
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Affiliation(s)
- Changhan Lee
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Edvard Wigren
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Janja Trček
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Verena Peters
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Jihong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Korea
| | - Muhammad Sharif Hasni
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Manfred Nimtz
- The Helmholtz Center for Infection Research, Braunschweig, 38124, Germany
| | - Ylva Lindqvist
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Chankyu Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Korea
| | - Ute Curth
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, 30625, Germany
| | - Heinrich Lünsdorf
- The Helmholtz Center for Infection Research, Braunschweig, 38124, Germany
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
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Sawa T, Shimizu M, Moriyama K, Wiener-Kronish JP. Association between Pseudomonas aeruginosa type III secretion, antibiotic resistance, and clinical outcome: a review. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2014; 18:668. [PMID: 25672496 PMCID: PMC4331484 DOI: 10.1186/s13054-014-0668-9] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pseudomonas aeruginosa uses a complex type III secretion system to inject the toxins ExoS, ExoT, ExoU, and ExoY into the cytosol of target eukaryotic cells. This system is regulated by the exoenzyme S regulon and includes the transcriptional activator ExsA. Of the four toxins, ExoU is characterized as the major virulence factor responsible for alveolar epithelial injury in patients with P. aeruginosa pneumonia. Virulent strains of P. aeruginosa possess the exoU gene, whereas non-virulent strains lack this particular gene. The mechanism of virulence for the exoU+ genotype relies on the presence of a pathogenic gene cluster (PAPI-2) encoding exoU and its chaperone, spcU. The ExoU toxin has a patatin-like phospholipase domain in its N-terminal, exhibits phospholipase A2 activity, and requires a eukaryotic cell factor for activation. The C-terminal of ExoU has a ubiquitinylation mechanism of activation. This probably induces a structural change in enzymatic active sites required for phospholipase A2 activity. In P. aeruginosa clinical isolates, the exoU+ genotype correlates with a fluoroquinolone resistance phenotype. Additionally, poor clinical outcomes have been observed in patients with pneumonia caused by exoU+-fluoroquinolone-resistant isolates. Therefore, the potential exists to improve clinical outcomes in patients with P. aeruginosa pneumonia by identifying virulent and antimicrobial drug-resistant strains through exoU genotyping or ExoU protein phenotyping or both.
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A type III secretion negative clinical strain of Pseudomonas aeruginosa employs a two-partner secreted exolysin to induce hemorrhagic pneumonia. Cell Host Microbe 2014; 15:164-76. [PMID: 24528863 DOI: 10.1016/j.chom.2014.01.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/05/2013] [Accepted: 01/02/2014] [Indexed: 11/21/2022]
Abstract
Virulence of Pseudomonas aeruginosa is typically attributed to its type III secretion system (T3SS). A taxonomic outlier, the P. aeruginosa PA7 strain, lacks a T3SS locus, and no virulence phenotype is attributed to PA7. We characterized a PA7-related, T3SS-negative P. aeruginosa strain, CLJ1, isolated from a patient with fatal hemorrhagic pneumonia. CLJ1 is highly virulent in mice, leading to lung hemorrhage and septicemia. CLJ1-infected primary endothelial cells display characteristics of membrane damage and permeabilization. Proteomic analysis of CLJ1 culture supernatants identified a hemolysin/hemagglutinin family pore-forming toxin, Exolysin (ExlA), that is exported via ExlB, representing a putative two-partner secretion system. A recombinant P. aeruginosa PAO1ΔpscD::exlBA strain, deficient for T3SS but engineered to express ExlA, gained lytic capacity on endothelial cells and full virulence in mice, demonstrating that ExlA is necessary and sufficient for pathogenicity. This highlights clinically relevant T3SS-independent hypervirulence, isolates, and points to a broader P. aeruginosa pathogenic repertoire.
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Ghequire MGK, De Mot R. Ribosomally encoded antibacterial proteins and peptides from Pseudomonas. FEMS Microbiol Rev 2014; 38:523-68. [PMID: 24923764 DOI: 10.1111/1574-6976.12079] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/05/2014] [Accepted: 05/16/2014] [Indexed: 12/26/2022] Open
Abstract
Members of the Pseudomonas genus produce diverse secondary metabolites affecting other bacteria, fungi or predating nematodes and protozoa but are also equipped with the capacity to secrete different types of ribosomally encoded toxic peptides and proteins, ranging from small microcins to large tailocins. Studies with the human pathogen Pseudomonas aeruginosa have revealed that effector proteins of type VI secretion systems are part of the antibacterial armamentarium deployed by pseudomonads. A novel class of antibacterial proteins with structural similarity to plant lectins was discovered by studying antagonism among plant-associated Pseudomonas strains. A genomic perspective on pseudomonad bacteriocinogeny shows that the modular architecture of S pyocins of P. aeruginosa is retained in a large diversified group of bacteriocins, most of which target DNA or RNA. Similar modularity is present in as yet poorly characterized Rhs (recombination hot spot) proteins and CDI (contact-dependent inhibition) proteins. Well-delimited domains for receptor recognition or cytotoxicity enable the design of chimeric toxins with novel functionalities, which has been applied successfully for S and R pyocins. Little is known regarding how these antibacterials are released and ultimately reach their targets. Other remaining issues concern the identification of environmental triggers activating these systems and assessment of their ecological impact in niches populated by pseudomonads.
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Cho HH, Kwon KC, Kim S, Koo SH. Correlation between virulence genotype and fluoroquinolone resistance in carbapenem-resistant Pseudomonas aeruginosa. Ann Lab Med 2014; 34:286-92. [PMID: 24982833 PMCID: PMC4071185 DOI: 10.3343/alm.2014.34.4.286] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/22/2014] [Accepted: 05/07/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is a clinically important pathogen that causes opportunistic infections and nosocomial outbreaks. Recently, the type III secretion system (TTSS) has been shown to play an important role in the virulence of P. aeruginosa. ExoU, in particular, has the greatest impact on disease severity. We examined the relationship among the TTSS effector genotype (exoS and exoU), fluoroquinolone resistance, and target site mutations in 66 carbapenem-resistant P. aeruginosa strains. METHODS Sixty-six carbapenem-resistant P. aeruginosa strains were collected from patients in a university hospital in Daejeon, Korea, from January 2008 to May 2012. Minimum inhibitory concentrations (MICs) of fluoroquinolones (ciprofloxacin and levofloxacin) were determined by using the agar dilution method. We used PCR and sequencing to determine the TTSS effector genotype and quinolone resistance-determining regions (QRDRs) of the respective target genes gyrA, gyrB, parC, and parE. RESULTS A higher proportion of exoU+ strains were fluoroquinolone-resistant than exoS+ strains (93.2%, 41/44 vs. 45.0%, 9/20; P≤0.0001). Additionally, exoU+ strains were more likely to carry combined mutations than exoS+ strains (97.6%, 40/41 vs. 70%, 7/10; P=0.021), and MIC increased as the number of active mutations increased. CONCLUSIONS The recent overuse of fluoroquinolone has led to both increased resistance and enhanced virulence of carbapenem-resistant P. aeruginosa. These data indicate a specific relationship among exoU genotype, fluoroquinolone resistance, and resistance-conferring mutations.
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Affiliation(s)
- Hye Hyun Cho
- Department of Biomedical Laboratory Science, Jeonju Kijeon College, Jeonju, Korea
| | - Kye Chul Kwon
- Department of Laboratory Medicine, College of Medicine, Chungnam National University, Daejeon, Korea
| | - Semi Kim
- Department of Laboratory Medicine, College of Medicine, Chungnam National University, Daejeon, Korea
| | - Sun Hoe Koo
- Department of Laboratory Medicine, College of Medicine, Chungnam National University, Daejeon, Korea
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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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An rhs gene linked to the second type VI secretion cluster is a feature of the Pseudomonas aeruginosa strain PA14. J Bacteriol 2013; 196:800-10. [PMID: 24317402 PMCID: PMC3911176 DOI: 10.1128/jb.00863-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The type VI secretion system (T6SS) of Gram-negative bacteria has been involved in various processes, notably bacterial competition and eukaryotic cell subversion. Most Pseudomonas aeruginosa strains possess three T6SS gene clusters, but only the function of the first T6SS (H1-T6SS) has been clearly elucidated. It is involved in the secretion of three toxins (Tse1 to -3) that target bacterial competitors. In the case of the H2- and H3-T6SS, no clear function has been assigned, and only one effector has been associated with these systems. Yet the H2-T6SS was proposed to promote P. aeruginosa internalization in nonphagocytic epithelial cells. Although the H2-T6SS genetic organization is conserved across P. aeruginosa isolates, one feature is the presence of an additional transcriptional unit in the PA14 strain H2-T6SS cluster, which is divergent from the core H2-T6SS genes. A specific set of four genes encodes an Hcp protein (Hcp2), a VgrG protein (VgrG14), an Rhs element (PA14_43100 or RhsP2), and a protein with no homologies with previously characterized proteins (PA14_43090). In this study, we engineered a P. aeruginosa PA14 strain carrying an arabinose-inducible H2-T6SS on the chromosome. We showed that arabinose induction readily promotes assembly of the H2-T6SS, as seen by monitoring Hcp2 secretion. We further studied the secretion fate of VgrG14 and RhsP2, but these were not detectable in the extracellular medium. We finally investigated whether activation of the PA14 H2-T6SS gene cluster could influence phenotypic traits such as internalization in eukaryotic cells, and we reported noteworthy differences compared to strain PAO1, which may be accounted for by the described genetic differences.
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Rahman MS, Gillespie JJ, Kaur SJ, Sears KT, Ceraul SM, Beier-Sexton M, Azad AF. Rickettsia typhi possesses phospholipase A2 enzymes that are involved in infection of host cells. PLoS Pathog 2013; 9:e1003399. [PMID: 23818842 PMCID: PMC3688537 DOI: 10.1371/journal.ppat.1003399] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 04/19/2013] [Indexed: 11/18/2022] Open
Abstract
The long-standing proposal that phospholipase A2 (PLA2) enzymes are involved in rickettsial infection of host cells has been given support by the recent characterization of a patatin phospholipase (Pat2) with PLA2 activity from the pathogens Rickettsia prowazekii and R. typhi. However, pat2 is not encoded in all Rickettsia genomes; yet another uncharacterized patatin (Pat1) is indeed ubiquitous. Here, evolutionary analysis of both patatins across 46 Rickettsia genomes revealed 1) pat1 and pat2 loci are syntenic across all genomes, 2) both Pat1 and Pat2 do not contain predicted Sec-dependent signal sequences, 3) pat2 has been pseudogenized multiple times in rickettsial evolution, and 4) ubiquitous pat1 forms two divergent groups (pat1A and pat1B) with strong evidence for recombination between pat1B and plasmid-encoded homologs. In light of these findings, we extended the characterization of R. typhi Pat1 and Pat2 proteins and determined their role in the infection process. As previously demonstrated for Pat2, we determined that 1) Pat1 is expressed and secreted into the host cytoplasm during R. typhi infection, 2) expression of recombinant Pat1 is cytotoxic to yeast cells, 3) recombinant Pat1 possesses PLA2 activity that requires a host cofactor, and 4) both Pat1 cytotoxicity and PLA2 activity were reduced by PLA2 inhibitors and abolished by site-directed mutagenesis of catalytic Ser/Asp residues. To ascertain the role of Pat1 and Pat2 in R. typhi infection, antibodies to both proteins were used to pretreat rickettsiae. Subsequent invasion and plaque assays both indicated a significant decrease in R. typhi infection compared to that by pre-immune IgG. Furthermore, antibody-pretreatment of R. typhi blocked/delayed phagosomal escapes. Together, these data suggest both enzymes are involved early in the infection process. Collectively, our study suggests that R. typhi utilizes two evolutionary divergent patatin phospholipases to support its intracellular life cycle, a mechanism distinguishing it from other rickettsial species.
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Affiliation(s)
- M Sayeedur Rahman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
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Petit SMC, Lavenir R, Colinon-Dupuich C, Boukerb AM, Cholley P, Bertrand X, Freney J, Doléans-Jordheim A, Nazaret S, Laurent F, Cournoyer B. Lagooning of wastewaters favors dissemination of clinically relevant Pseudomonas aeruginosa. Res Microbiol 2013; 164:856-66. [PMID: 23792168 DOI: 10.1016/j.resmic.2013.06.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 06/02/2013] [Indexed: 12/01/2022]
Abstract
The significance of wastewater treatment lagoons (WWTLs) as point sources of clinically relevant Pseudomonas aeruginosa that can disseminate through rural and peri-urban catchments was investigated. A panel of P. aeruginosa strains collected over three years from WWTLs and community-acquired infections was compared by pulsed field gel electrophoresis (PFGE) DNA fingerprinting and multilocus sequence typing (MLST). Forty-four distantly related PFGE profiles and four clonal complexes were found among the WWTL strains analyzed. Some genotypes were repeatedly detected from different parts of WWTLs, including the influent, suggesting an ability to migrate and persist over time. MLST showed all investigated lineages to match sequence types described in other countries and strains from major clinical clones such as PA14 of ST253 and "C" of ST17 were observed. Some of these genotypes matched isolates from community-acquired infections recorded in the WWTL geographic area. Most WWTL strains harbored the main P. aeruginosa virulence genes; 13% harbored exoU-encoded cytoxins, but on at least six different genomic islands, with some of these showing signs of genomic instability. P. aeruginosa appeared to be highly successful opportunistic colonizers of WWTLs. Lagooning of wastewaters was found to favor dissemination of clinically relevant P. aeruginosa among peri-urban watersheds.
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Affiliation(s)
- Stéphanie M-C Petit
- Université de Lyon, Lyon, France; Research Group on Bacterial Opportunistic Pathogens and Environment, UMR5557 Ecologie Microbienne, Doua Campus, Université Lyon 1, CNRS, VetAgro Sup, 69622 Villeurbanne, France
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Zhou J, Watt S, Wang J, Nakayama S, Sayre DA, Lam YF, Lee VT, Sintim HO. Potent suppression of c-di-GMP synthesis via I-site allosteric inhibition of diguanylate cyclases with 2'-F-c-di-GMP. Bioorg Med Chem 2013; 21:4396-404. [PMID: 23685177 DOI: 10.1016/j.bmc.2013.04.050] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 04/10/2013] [Accepted: 04/19/2013] [Indexed: 11/29/2022]
Abstract
Cyclic-di-GMP (c-di-GMP) is a central regulator of bacterial behavior. Various studies have implicated c-di-GMP in biofilm formation and virulence factor production in multitudes of bacteria. Hence it is expected that the disruption of c-di-GMP signaling could provide an effective means to disrupt biofilm and/or virulence factor formation in several bacteria of clinical relevance. C-di-GMP achieves the regulation of bacterial phenotype via binding to several effector molecules including transcription factors, enzymes and riboswitches. Crystal structure analyses of c-di-GMP effector molecules, in complex with the ligand, reveal that various classes of c-di-GMP receptors recognize this dinucleotide using different sets of recognition elements. Therefore, it is plausible that different analogues of c-di-GMP could be used to selectively modulate a specific class of c-di-GMP binding receptors, and hence modulate the bacterial phenotype. Thus far only a detailed study of the differential binding of c-di-GMP analogues to riboswitches, but not proteins, has been reported. In this report, we prepared various 2'-modified analogues of c-di-GMP and studied both polymorphisms of these analogues using DOSY NMR and the binding to several effector proteins, such as PilZ-containing proteins, diguanylate cyclases (DGC) containing I-sites, and phoshphodiesterases (PDE). 2'-Modification of c-di-GMP did not adversely affect the propensity to form higher aggregates, such as octameric forms, in the presence of potassium salts. Interestingly, we find that the selective binding to different classes of c-di-GMP binding proteins could be achieved with the 2'-modified analogues and that 2'-F analogue of c-di-GMP binds to the I-site of DGCs better (four times) than the native dinucleotide, c-di-GMP, whereas c-di-GMP binds to PDEs better (10 times) than 2'-F-c-di-GMP. 2'-F-c-di-GMP potently inhibits c-di-GMP synthesis by DGCs and hence raises the potential that cell permeable analogues of 2'-F-c-di-GMP could be used to disrupt c-di-GMP signaling in bacteria.
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Affiliation(s)
- Jie Zhou
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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50
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Lee JY, Peck KR, Ko KS. Selective advantages of two major clones of carbapenem-resistant Pseudomonas aeruginosa isolates (CC235 and CC641) from Korea: antimicrobial resistance, virulence and biofilm-forming activity. J Med Microbiol 2013; 62:1015-1024. [PMID: 23558139 DOI: 10.1099/jmm.0.055426-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The characteristics of carbapenem-resistant P. aeruginosa (CRPA) isolates from Korea were investigated. Two major clones, clonal complex (CC) 235 and CC641, were identified. CC235, an important international clone, might have been imported recently in Korea as this clone displayed a homogeneous genotype, oprD mutation and antimicrobial resistance profile. While 13 ST235 isolates harboured the blaIMP-6 gene, which conferred high-level meropenem resistance, CC641 isolates showed high biofilm-forming activity. CC235 and CC641 isolates showed distinct distribution of ferripyoverdine receptor type and virulence markers. While all CC235 isolates were of the fpvAIIb type and exoS(-)/exoU(+), CC641 isolates were exoS(+)/exoU(-), and all but one showed the fpvAIII type. CC235 and CC641 isolates were also characterized by different extracellular protease activity: staphylolysin and elastase activities in CC235 and CC641, respectively. Two major CRPA clones in Korea seem to be predominant, reflecting their selective advantage by virtue of antimicrobial resistance, virulence and biofilm-forming activity.
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Affiliation(s)
- Ji-Young Lee
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Korea
| | - Kwan Soo Ko
- Asia Pacific Foundation for Infectious Diseases, Seoul 135-710, Korea.,Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
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