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Swain J, Askenasy I, Rudland Nazeer R, Ho PM, Labrini E, Mancini L, Xu Q, Hollendung F, Sheldon I, Dickson C, Welch A, Agbamu A, Godlee C, Welch M. Pathogenicity and virulence of Pseudomonas aeruginosa: Recent advances and under-investigated topics. Virulence 2025; 16:2503430. [PMID: 40353451 PMCID: PMC12087490 DOI: 10.1080/21505594.2025.2503430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2025] [Revised: 04/23/2025] [Accepted: 05/03/2025] [Indexed: 05/14/2025] Open
Abstract
Pseudomonas aeruginosa is a model for the study of quorum sensing, protein secretion, and biofilm formation. Consequently, it has become one of the most intensely reviewed pathogens, with many excellent articles in the current literature focusing on these aspects of the organism's biology. Here, though, we aim to take a slightly different approach and consider some less well appreciated (but nonetheless important) factors that affect P. aeruginosa virulence. We start by reminding the reader of the global importance of P. aeruginosa infection and that the "virulome" is very niche-specific. Overlooked but obvious questions such as "what prevents secreted protein products from being digested by co-secreted proteases?" are discussed, and we suggest how the nutritional preference(s) of the organism might dictate its environmental reservoirs. Recent studies identifying host genes associated with genetic predisposition towards P. aeruginosa infection (and even infection by specific P. aeruginosa strains) and the role(s) of intracellular P. aeruginosa are introduced. We also discuss the fact that virulence is a high-risk strategy and touch on how expression of the two main classes of virulence factors is regulated. A particular focus is on recent findings highlighting how nutritional status and metabolism are as important as quorum sensing in terms of their impact on virulence, and how co-habiting microbial species at the infection site impact on P. aeruginosa virulence (and vice versa). It is our view that investigation of these issues is likely to dominate many aspects of research into this WHO-designated priority pathogen over the next decade.
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Affiliation(s)
- Jemima Swain
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | - Isabel Askenasy
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | | | - Pok-Man Ho
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | - Edoardo Labrini
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | | | - Qingqing Xu
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | | | | | - Camilla Dickson
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | - Amelie Welch
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | - Adam Agbamu
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | - Camilla Godlee
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, Cambridge University, Cambridge, UK
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2
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Padhy I, Dwibedy SK, Mohapatra SS. Fitness trade-off and the discovery of a novel missense mutation in the PmrB sensor kinase of a colistin-resistant Pseudomonas aeruginosa strain developed by adaptive laboratory evolution. Microb Pathog 2025; 203:107473. [PMID: 40081679 DOI: 10.1016/j.micpath.2025.107473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 02/26/2025] [Accepted: 03/11/2025] [Indexed: 03/16/2025]
Abstract
Pseudomonas aeruginosa is a prominent bacterial pathogen that causes several nosocomial infections and is notorious for its environmental resilience and rapid development of resistance to frontline antibiotics. A major cause of mortality and morbidity among cystic fibrosis patients, multidrug-resistant P. aeruginosa is often targeted with the antibiotic colistin as a last option. However, increasing reports of colistin resistance among P. aeruginosa is a significant concern. Though the molecular mechanisms responsible for the development of colistin resistance are well known, the evolutionary trajectory to colistin resistance is an important area of investigation. In this work, using the adaptive laboratory evolution (ALE) approach we have evolved a colistin-sensitive P. aeruginosa ancestral strain to a resistant one. During the process of laboratory evolution in 106 generations, colistin MIC was increased 32-fold. The evolved strain had lower fitness than the ancestral strain, as evidenced by a lower growth rate. Moreover, the evolved strain produced more biofilm and less pyocyanin pigment. Interestingly, the evolved strain showed collateral sensitivity to several antibiotics, including ampicillin, tetracycline, streptomycin, gentamycin, nalidixic acid, trimethoprim, rifampicin, and chloramphenicol. On analysing various TCS modules involved in the development of colistin resistance, a novel missense mutation (V136G) was detected in the PmrB sensor kinase. In silico analysis indicated that the V136G substitution would destabilize the PmrB kinase structure, making the mutation deleterious. However, the functionality of the PmrB mutant remains to be validated experimentally.
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Affiliation(s)
- Indira Padhy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur, 760007, Odisha, India
| | - Sambit K Dwibedy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur, 760007, Odisha, India; Department of Zoology, SBRG Women's College, Berhampur, 760001, Odisha, India
| | - Saswat S Mohapatra
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur, 760007, Odisha, India.
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Choudhury ST, Piper KR, Montoya-Giraldo M, Ikhimiukor OO, Dettman JR, Kassen R, Andam CP. Heterogeneity in recombination rates and accessory gene co-occurrence distinguish Pseudomonas aeruginosa phylogroups. mSystems 2025; 10:e0030125. [PMID: 40304385 PMCID: PMC12090758 DOI: 10.1128/msystems.00301-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2025] [Accepted: 04/07/2025] [Indexed: 05/02/2025] Open
Abstract
Pseudomonas aeruginosa (class Gammaproteobacteria) is a ubiquitous, ecologically widespread, and metabolically versatile species. It is also an opportunistic pathogen that causes a variety of chronic and acute infections in humans. Its ability to thrive in diverse environments and exhibit a wide range of phenotypes lies in part on its large gene pool, but the processes that govern inter-strain genomic variation remain unclear. Here, we aim to characterize the recombination features and accessory genome structure of P. aeruginosa using 840 globally distributed genome sequences. The species can be subdivided into five phylogenetic sequence clusters (corresponding to known phylogroups), two of which are most prominent. Notable epidemic clones are found in the two phylogroups: ST17, ST111, ST146, ST274, and ST395 in phylogroup 1, and ST235 and ST253 in phylogroup 2. The two phylogroups differ in the frequency and characteristics of homologous recombination in their core genomes, including the specific genes that most frequently recombine and the impact of recombination on sequence diversity. Each phylogroup's accessory genome is characterized by a unique gene pool, co-occurrence networks of shared genes, and anti-phage defense systems. Different pools of antimicrobial resistance and virulence genes exist in the two phylogroups and display dissimilar patterns of co-occurrence. Altogether, our results indicate that each phylogroup displays distinct histories and patterns of acquiring exogenous DNA, which may contribute in part to their predominance in the global population. Our study has important implications for understanding the genome dynamics, within-species heterogeneity, and clinically relevant traits of P. aeruginosa. IMPORTANCE The consummate opportunist Pseudomonas aeruginosa inhabits many nosocomial and non-clinical environments, posing a major health burden worldwide. Our study reveals phylogroup-specific differences in recombination features and co-occurrence networks of accessory genes within the species. This genomic variation partly explains its remarkable ability to exhibit diverse ecological and phenotypic traits, and thus contribute to circumventing clinical and public health intervention strategies to contain it. Our results may help inform efforts to control and prevent P. aeruginosa diseases, including managing transmission, therapeutic efforts, and pathogen circulation in non-clinical environmental reservoirs.
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Affiliation(s)
- Samara T. Choudhury
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Kathryn R. Piper
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Manuela Montoya-Giraldo
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Odion O. Ikhimiukor
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Jeremy R. Dettman
- Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada
| | - Rees Kassen
- Department of Biology, McGill University, Montreal, Québec, Canada
| | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
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Hong X, Li Z, Xia W, Tan Z, Hu Y, Zhang L, Liu G. Pseudomonas aeruginosa in wound infections: Genomic characterization and emergence of hypervirulent ST1965/ST3418 strains co-harbouring exoU and exoS. J Glob Antimicrob Resist 2025; 43:220-228. [PMID: 40349843 DOI: 10.1016/j.jgar.2025.05.007] [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: 01/02/2025] [Revised: 05/05/2025] [Accepted: 05/06/2025] [Indexed: 05/14/2025] Open
Abstract
OBJECTIVE To investigate the phenotype and genotype characteristics of Pseudomonas aeruginosa isolates from wound infections. METHODS Seventy-six P. aeruginosa strains isolated from wound infections in a university hospital were analysed. Antimicrobial susceptibility testing, biofilm formation assays, and whole-genome sequencing were performed on all strains. The virulence of potential hypervirulent strains was assessed using a Galleria mellonella infection model. RESULTS Among the 76 tested strains, 49 (64.5%) were susceptible to all tested antibiotics. The β-lactamase-encoding gene positivity rate was 57.9%, while the OprD gene mutation rate was 1.3%. All isolates were classified into 56 distinct multilocus sequence types. Serotype distribution revealed O11 (22.37%, 17/76), O16 (19.74%, 15/76), and O1 (18.42%, 14/76) as the most prevalent. The exoU gene was predominantly associated with serotype O11. Over 80% of strains harboured biofilm-related virulence genes, and all exhibited strong biofilm-forming capacity. Six exoU+/exoS+ strains (serotype O4) were identified, with ST1965 and ST3418 demonstrating potential hypervirulence in the infection model. CONCLUSIONS P. aeruginosa isolates from wound infections displayed sporadic genomic profiles, high antibiotic susceptibility, and robust biofilm formation. The emergence of exoU+/exoS+ hypervirulent clones (ST1965 and ST3418), characterized by enhanced virulence and biofilm production, highlights their potential to cause treatment-refractory infections and severe clinical outcomes. Continuous surveillance and tailored therapeutic approaches are imperative for managing infections caused by these clones.
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Affiliation(s)
- Xin Hong
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China; National Key Clinical Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Zexuan Li
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China; National Key Clinical Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Wenying Xia
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China; National Key Clinical Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Zhongming Tan
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yulin Hu
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China; National Key Clinical Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Litao Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China; National Key Clinical Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Genyan Liu
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China; National Key Clinical Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China.
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Tümmler B, Pallenberg ST, Dittrich AM, Graeber SY, Naehrlich L, Sommerburg O, Mall MA. Progress of personalized medicine of cystic fibrosis in the times of efficient CFTR modulators. Mol Cell Pediatr 2025; 12:6. [PMID: 40320452 PMCID: PMC12050259 DOI: 10.1186/s40348-025-00194-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Accepted: 04/03/2025] [Indexed: 05/08/2025] Open
Abstract
BACKGROUND Cystic fibrosis (CF) is a systemic disorder of exocrine glands that is caused by mutations in the CFTR gene. MAIN BODY The basic defect in people with CF (pwCF) leads to impaired epithelial transport of chloride and bicarbonate that can be assessed by CFTR biomarkers, i.e. the β-adrenergic sweat rate and sweat chloride concentration (SCC), chloride conductance of the nasal respiratory epithelium (NPD), urine secretion of bicarbonate, intestinal current measurements (ICM) of chloride secretory responses in rectal biopsies and in bioassays of chloride transport in organoids or cell cultures. CFTR modulators are a novel class of drugs that improve defective posttranslational processing, trafficking and function of mutant CFTR. By April 2025, triple combination therapy with the CFTR potentiator ivacaftor (IVA) and the CFTR correctors elexacaftor (ELX) and tezacaftor (TEZ) has been approved in Europe for the treatment of all pwCF who do not carry two minimal function CFTR mutations. Previous phase 3 and post-approval phase 4 studies in pwCF who harbour one or two alleles of the major mutation F508del consistently reported significant improvements of lung function and anthropometry upon initiation of ELX/TEZ/IVA compared to baseline. Normalization of SCC, NPD and ICM correlated with clinical outcomes on the population level, but the restoration of CFTR function was diverse and not predictive for clinical outcome in the individual patient. Theratyping of non-F508del CF genotypes in patient-derived organoids and cell cultures revealed for most cases clinically meaningful increases of CFTR activity upon exposure to ELX/TEZ/IVA. Likewise, every second CF patient with non-F508del genotypes improved in SCC and clinical outcome upon exposure to ELX/TEZ/IVA indicating that triple CFTR modulator therapy is potentially beneficial for all pwCF who do not carry two minimal function CFTR mutations. This group who is not eligible for CFTR modulators may opt for gene addition therapy in the future, as the first-in-human trial with a recombinant lentiviral vector is underway. FUTURE DIRECTIONS The upcoming generation of pwCF will probably experience a rather normal life in childhood and adolescence. To classify the upcoming personal signatures of CF disease in the times of efficient modulators, we need more sensitive CFTR biomarkers that address the long-term course of airway and gut microbiome, host defense, epithelial homeostasis and multiorgan metabolism.
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Affiliation(s)
- Burkhard Tümmler
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, 30625, Germany.
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany.
| | - Sophia Theres Pallenberg
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, 30625, Germany
| | - Anna-Maria Dittrich
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, 30625, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany
| | - Simon Y Graeber
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, and Cystic Fibrosis Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany
| | - Lutz Naehrlich
- Department of Pediatrics, Justus Liebig University Giessen, Giessen, Germany
- Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Giessen, Germany
| | - Olaf Sommerburg
- Division of Pediatric Pneumology and Allergy, and Cystic Fibrosis Center, Department of Pediatrics, University of Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL),, University of Heidelberg, Heidelberg, Germany
| | - Marcus A Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, and Cystic Fibrosis Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany
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Li J, Shao Z, Cheng K, Yang Q, Ju H, Tang X, Zhang S, Li J. Coral-associated Symbiodiniaceae exhibit host specificity but lack phylosymbiosis, with Cladocopium and Durusdinium showing different cophylogenetic patterns. THE NEW PHYTOLOGIST 2025. [PMID: 40317738 DOI: 10.1111/nph.70184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2025] [Accepted: 04/09/2025] [Indexed: 05/07/2025]
Abstract
Altering the composition of the Symbiodiniaceae community to adapt to anomalous sea water warming represents a potential survival mechanism for scleractinian corals. However, the processes of Symbiodiniaceae assembly and long-standing evolution of coral-Symbiodiniaceae interactions remain unclear. Here, we utilized ITS2 (internal transcribed spacer 2) amplicon sequencing and the SymPortal framework to investigate the diversity and specificity of Symbiodiniaceae across 39 scleractinian coral species. Furthermore, we tested phylosymbiosis and cophylogeny between coral hosts and their Symbiodiniaceae. In our study, environmental samples exhibited the highest Symbiodiniaceae diversity. Cladocopium and Durusdinium dominated the Symbiodiniaceae communities, with significant β-diversity differences among coral species. Additionally, host specificity was widespread in Symbiodiniaceae, especially Durusdinium spp., yet lacked a phylosymbiotic pattern. Moreover, Cladocopium spp. showed cophylogenetic congruence with their hosts, while there was no evidence for Durusdinium spp. Furthermore, host switching was the predominant evolutionary event, implying its contribution to Cladocopium diversification. These findings suggest that Symbiodiniaceae assembly does not recapitulate host phylogeny, and host specificity alone does not drive phylosymbiosis or cophylogeny. As environmental reservoirs, free-living Symbiodiniaceae may influence symbiotic communities. Additionally, Durusdinium-coral associations lack cophylogenetic signals, indicating more flexible partnerships than Cladocopium. Overall, our results enhance understanding of Symbiodiniaceae assembly and coral-Symbiodiniaceae evolutionary interactions.
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Affiliation(s)
- Jiaxin Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Zhuang Shao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Keke Cheng
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Huimin Ju
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Xiaoyu Tang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Sanya National Marine Ecosystem Research Station, Chinese Academy of Sciences, Sanya, 572000, China
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Sanya National Marine Ecosystem Research Station, Chinese Academy of Sciences, Sanya, 572000, China
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Büchler AC, Klaassen CHW, de Goeij I, Vos MC, Voor In 't Holt AF, Severin JA. Outbreak investigations of contact patients and the hospital environment after detection of carbapenemase-producing Pseudomonas aeruginosa on general hospital wards. J Hosp Infect 2025; 159:11-19. [PMID: 39986654 DOI: 10.1016/j.jhin.2025.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 02/09/2025] [Accepted: 02/10/2025] [Indexed: 02/24/2025]
Abstract
BACKGROUND Carbapenemase-producing Pseudomonas aeruginosa (CPPA) is known to cause outbreaks in healthcare settings. Outbreak investigations, including screening of contact patients and the environment, are key in infection prevention and control (IPC) management to contain them. AIM The aim of this study was to determine the yield of outbreak investigations performed after unexpected detections of CPPA in clinical or screening cultures of patients hospitalized on a general ward. METHODS In this retrospective cohort study, we included all adult patients newly detected with CPPA ('index patients') while hospitalized on a general ward from June 2011 to December 2021. We evaluated the outbreak investigations performed, i.e., screening of epidemiologically linked patients ('contact patients') and the environment. Isolates were analysed by whole-genome sequencing (WGS). FINDINGS Outbreak investigations of 34 of 38 (89.5%) index patients were evaluated, with screening of contact patients performed in 34 (100%) and the environment in 18 (52.9%). CPPA was detected in eight (44.4%) of the environmental screenings, and WGS confirmed relatedness to the index in four (22.2%). A total of 1707 of 1982 (86.1%) identified contact patients were screened, of which eight carried CPPA (0.5%). WGS confirmed transmission from index patient to contact patient in five of these (0.3%). CONCLUSION Environmental screening should be part of outbreak investigations for CPPA, as it identifies sources which enables timely installation of targeted IPC measures. Identification of index-to-contact patient transmission was rare in our setting, thus implying reconsideration of the definition of contact patients at high risk is needed.
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Affiliation(s)
- A C Büchler
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - C H W Klaassen
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - I de Goeij
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - M C Vos
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - A F Voor In 't Holt
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - J A Severin
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands.
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Pei Y, Hamar P, Pei DS. Deciphering Multidrug-Resistant Pseudomonas aeruginosa: Mechanistic Insights and Environmental Risks. TOXICS 2025; 13:303. [PMID: 40278619 PMCID: PMC12030990 DOI: 10.3390/toxics13040303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2025] [Revised: 04/01/2025] [Accepted: 04/11/2025] [Indexed: 04/26/2025]
Abstract
The rise of multidrug-resistant (MDR) Pseudomonas aeruginosa (P. aeruginosa) presents a significant challenge to clinical treatment and environmental risks. This review delves into the complex mechanisms underlying MDR development in P. aeruginosa, such as genetic mutations, horizontal gene transfer (HGT), and the interaction between virulence factors and resistance genes. It evaluates current detection methods, from traditional bacteriology to advanced molecular techniques, emphasizing the need for rapid and accurate diagnostics. This review also examines therapeutic strategies, including broad-spectrum antibiotics, novel drug candidates, combination therapies, and innovative approaches like RNA interference, CRISPR-Cas9 gene editing, and bridge RNA-guided gene editing. Importantly, this review highlights the distribution, migration, and environmental risks of MDR P. aeruginosa, underscoring its adaptability to diverse environments. It concludes by stressing the necessity for continued research and development in antimicrobial resistance, advocating for an integrated approach that combines genomics, clinical practice, and environmental considerations to devise innovative solutions and preserve antibiotic efficacy.
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Affiliation(s)
- Yang Pei
- School of Public Health, Chongqing Medical University, Chongqing 400016, China
- Chongqing No.11 Middle School, Chongqing 400061, China
- Chongqing Miankai Biotechnology Research Institute Co., Ltd., Chongqing 400025, China
| | - Péter Hamar
- Institute of Translational Medicine, Semmelweis University, Tűzoltó Utca 37-47, 1094 Budapest, Hungary
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing 400016, China
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Wang Y, Xiao Q, Yang Q, Long Y, Jiang Z, Zhang T, Hu Y, Gao B, Chen X, Wang T, Xiao L. Impact of Pseudomonas aeruginosa biofilm formation by different sequence types on treating lower limb vascular infections. CURRENT RESEARCH IN MICROBIAL SCIENCES 2025; 8:100379. [PMID: 40395473 PMCID: PMC12090236 DOI: 10.1016/j.crmicr.2025.100379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2025] Open
Abstract
Pseudomonas aeruginosa is a major contributor to persistent chronic infections in clinical practice, owing to its robust biofilm formation capacity and frequent antimicrobial resistance acquisition. However, most current studies focus on single strains and thus overlook phenotypic differences among coexisting strains within the same host. With that in mind, we proposed a hypothesis that P. aeruginosa strains from the same patient, yet with distinct genetic backgrounds, might exhibit differing resistance profiles and virulence genes. To test this hypothesis, we selected three strains with different sequence types (STs), all isolated from the chronic wounds of a patient with long-term bilateral lower limb infections. By employing multilocus sequence typing, antimicrobial susceptibility testing, biofilm gene quantification, growth kinetics assays, Galleria mellonella virulence experiments, and phylogenetic reconstruction, we systematically evaluated the relationships between these strains'biofilm formation and virulence. The results revealed significant genetic diversity and evolutionary origin variations among the three strains. Notably, ST2584 (WYDPA-23-3) exhibited multidrug resistance (resistant to 7 of the 12 tested antibiotics) and the highest growth rate, whereas ST270 (WYDPA-23-2)-despite the downregulation of pelA, a gene linked to extracellular matrix biogenesis-demonstrated a 2.3-fold increase in biofilm formation and the highest larval lethality. By comparing multiple strains coexisting in the same host, this study further elucidates the role of P. aeruginosa biofilm in sustaining chronic infections and offers valuable guidance for optimizing clinical treatment strategies and antibiotic selection. In light of these findings, developing rapid and precise biofilm detection methods and designing innovative drugs targeting high biofilm-producing strains should be prioritized.
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Affiliation(s)
- Yudi Wang
- Southern Medical University, Guangdong, 510515, China
- Shanghai Fengxian District Central Hospital, Shanghai, 201499, China
| | - Qian Xiao
- Shanghai Fengxian District Central Hospital, Shanghai, 201499, China
| | - Qiong Yang
- Shanghai Fengxian District Central Hospital, Shanghai, 201499, China
- Jinzhou Medical University, Liaoning, 121001, China
| | - Yulin Long
- Southern Medical University, Guangdong, 510515, China
- Shanghai Fengxian District Central Hospital, Shanghai, 201499, China
| | - Zhibiao Jiang
- Shanghai Fengxian District Central Hospital, Shanghai, 201499, China
| | - Tantao Zhang
- Shanghai Fengxian District Central Hospital, Shanghai, 201499, China
| | - Ying Hu
- Shanghai Fengxian District Central Hospital, Shanghai, 201499, China
| | - Bingru Gao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Xuanyu Chen
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Ting Wang
- Shanghai Urban Construction Vocational College, Shanghai, 201415, China
| | - Linlin Xiao
- Southern Medical University, Guangdong, 510515, China
- Shanghai Fengxian District Central Hospital, Shanghai, 201499, China
- Jinzhou Medical University, Liaoning, 121001, China
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10
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Yao J, Hu Y, Wang X, Sheng J, Zhang Y, Zhao X, Wang J, Xu X, Li X. Carbapenem-resistant Morganella morganii carrying blaKPC-2 or blaNDM-1 in the clinic: one-decade genomic epidemiology analysis. Microbiol Spectr 2025; 13:e0247624. [PMID: 40029330 PMCID: PMC11960177 DOI: 10.1128/spectrum.02476-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2024] [Accepted: 01/22/2025] [Indexed: 03/05/2025] Open
Abstract
Carbapenem-resistant Morganella morganii (CRMM) isolates, particularly those producing Klebsiella pneumoniae carbapenemase-2 (KPC-2) or New Delhi metallo-β-lactamase-1 (NDM-1), are increasingly being recognized as causative agents of nosocomial infections. However, systematic phylogeography and genetic characterization of these isolates worldwide are still lacking. Here, through seven years of surveillance of CRMM in a tertiary hospital, we analyzed the genomic characteristics of blaKPC-2- or blaNDM-1-positive CRMM isolates. Furthermore, we conducted a global genomic epidemiological study of Morganella spp. harboring blaKPC or blaNDM using the NCBI database over the past decade. By combining the timeline of isolate collection with the structural analysis of the plasmids, we traced the evolution of the IncL/M plasmid, which acquired the blaKPC-2 gene. Our findings indicate that horizontal transfer of Tn6296 based on IS26 is crucial for the transmission of blaKPC in CRMM isolates. Additionally, the Tn125 transposon appears to have played an important role in early plasmid-mediated dissemination of blaNDM; however, it has been surpassed in recent years by other elements, including IS26 and ISCR. In summary, through phylogeographic analysis of Morganella spp. globally, we elucidated their spatial-temporal distribution and revealed the evolutionary characteristics of KPC- or NDM-producing CRMM isolates as the predominant "epidemic" clone. IMPORTANCE Currently, infections attributable to carbapenem-resistant Morganella morganii (CRMM) isolates harboring blaKPC or blaNDM are on the rise, highlighting the increasing severity of acquired antimicrobial resistance. However, systematic phylogeographic and genetic characterization of these isolates worldwide is still lacking. In this study, we elucidated the spatial-temporal distribution and evolutionary trajectory of blaKPC and blaNDM genes within their core genetic environments. We emphasize the necessity of strengthening surveillance and controlling these organisms in clinical settings to prevent the generation of so-called "superbug" isolates.
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Affiliation(s)
- Jiayao Yao
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Yueyue Hu
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Xinru Wang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Jie Sheng
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Ying Zhang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Xiaofei Zhao
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Jiaqing Wang
- Shaoxing Central Hospital, The Central Affiliated Hospital, Shaoxing University, Shaoxing, China
| | - Xiufang Xu
- School of Medical Imaging, Hangzhou Medical College, Hangzhou, China
| | - Xi Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
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11
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Zhou H, Negrón O, Abbondante S, Marshall M, Jones B, Ong E, Chumbler N, Tunkey C, Dixon G, Lin H, Plante O, Pearlman E, Gadjeva M. Spatial transcriptomics identifies novel Pseudomonas aeruginosa virulence factors. CELL GENOMICS 2025; 5:100805. [PMID: 40081336 PMCID: PMC11960532 DOI: 10.1016/j.xgen.2025.100805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 11/22/2024] [Accepted: 02/10/2025] [Indexed: 03/16/2025]
Abstract
To examine host-pathogen interactions, we leveraged a dual spatial transcriptomics approach that simultaneously captures the expression of Pseudomonas aeruginosa genes alongside the entire host transcriptome using a murine model of ocular infection. This method revealed differential pathogen- and host-specific gene expression patterns in infected corneas, which generated a unified transcriptional map of infection. By integrating these data, we developed a predictive ridge regression model trained on images from infected tissues. The model achieved an R2 score of 0.923 in predicting bacterial burden distributions and identifying novel biomarkers associated with disease severity. Among iron acquisition pathogen-specific gene transcripts that showed significant enrichment at the host-pathogen interface, we discovered the novel virulence mediator PA2590, which was required for bacterial virulence. This study therefore highlights the power of combining bacterial and host spatial transcriptomics to uncover complex host-pathogen interactions and identify potentially druggable targets.
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Affiliation(s)
- Hao Zhou
- Department of Biological Sciences, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates; Moderna, Inc., 325 Binney St., Cambridge, MA 02142, UK
| | - Oscar Negrón
- Moderna, Inc., 325 Binney St., Cambridge, MA 02142, UK
| | - Serena Abbondante
- Department of Ophthalmology, School of Medicine, University of California, Irvine, 843 Health Sciences Rd., Irvine, CA 92697, USA
| | - Michaela Marshall
- Department of Ophthalmology, School of Medicine, University of California, Irvine, 843 Health Sciences Rd., Irvine, CA 92697, USA
| | - Brandon Jones
- Moderna, Inc., 325 Binney St., Cambridge, MA 02142, UK
| | - Edison Ong
- Moderna, Inc., 325 Binney St., Cambridge, MA 02142, UK
| | | | | | - Groves Dixon
- Moderna, Inc., 325 Binney St., Cambridge, MA 02142, UK
| | - Haining Lin
- Moderna, Inc., 325 Binney St., Cambridge, MA 02142, UK
| | | | - Eric Pearlman
- Department of Ophthalmology, School of Medicine, University of California, Irvine, 843 Health Sciences Rd., Irvine, CA 92697, USA.
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12
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Schator D, Kumar NG, Chong SJU, Jung TK, Jedel E, Smith BE, Evans DJ, Fleiszig SMJ. Cross-membrane cooperation among bacteria can facilitate intracellular pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.09.637186. [PMID: 39975129 PMCID: PMC11839010 DOI: 10.1101/2025.02.09.637186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen able to cause life- and sight-threating infections. Once considered an extracellular pathogen, numerous studies have shown it can survive intracellularly. Previously, we showed that P. aeruginosa inside cells can diversify into distinct subpopulations in vacuoles and the cytoplasm. Here, we report that the transition from vacuoles to cytoplasm requires collaboration with the extracellular subpopulation, through Ca2+ influx enabled by their type III secretion system (T3SS) translocon pore proteins. Moreover, we show that collaboration among P. aeruginosa subpopulations can contribute to disseminating intracellular bacteria in vivo in a mouse infection model. This study provides the basis for future studies to investigate how cooperation of extracellular and intracellular bacteria within the host may contribute to disease progression and persistence.
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Affiliation(s)
- Daniel Schator
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA, USA
| | - Naren G Kumar
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA, USA
| | - Samuel Joseph U Chong
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA, USA
| | - Timothy K Jung
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA, USA
| | - Eric Jedel
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA, USA
- Graduate Program in Infectious Diseases & Immunity, University of California, Berkeley, CA, USA
| | - Benjamin E Smith
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA, USA
- Graduate Group in Vision Science, University of California, Berkeley, CA, USA
| | - David J Evans
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA, USA
- College of Pharmacy, Touro University California, Vallejo, CA, USA
| | - Suzanne M J Fleiszig
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA, USA
- Graduate Group in Vision Science, University of California, Berkeley, CA, USA
- Graduate Groups in Microbiology and Infectious Diseases & Immunity, University of California, Berkeley, CA, USA
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13
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Pont S, Nilly F, Berry L, Bonhoure A, Alford MA, Louis M, Nogaret P, Bains M, Lesouhaitier O, Hancock REW, Plésiat P, Blanc-Potard AB. Intracellular Pseudomonas aeruginosa persist and evade antibiotic treatment in a wound infection model. PLoS Pathog 2025; 21:e1012922. [PMID: 39946497 PMCID: PMC11825101 DOI: 10.1371/journal.ppat.1012922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 01/22/2025] [Indexed: 02/17/2025] Open
Abstract
Persistent bacterial infections evade host immunity and resist antibiotic treatments through various mechanisms that are difficult to evaluate in a living host. Pseudomonas aeruginosa is a main cause of chronic infections in patients with cystic fibrosis (CF) and wounds. Here, by immersing wounded zebrafish embryos in a suspension of P. aeruginosa isolates from CF patients, we established a model of persistent infection that mimics a murine chronic skin infection model. Live and electron microscopy revealed persisting aggregated P. aeruginosa inside zebrafish cells, including macrophages, at unprecedented resolution. Persistent P. aeruginosa exhibited adaptive resistance to several antibiotics, host cell permeable drugs being the most efficient. Moreover, persistent bacteria could be partly re-sensitized to antibiotics upon addition of anti-biofilm molecules that dispersed the bacterial aggregates in vivo. Collectively, this study demonstrates that an intracellular location protects persistent P. aeruginosa in vivo in wounded zebrafish embryos from host innate immunity and antibiotics, and provides new insights into efficient treatments against chronic infections.
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Affiliation(s)
- Stéphane Pont
- Laboratory of Pathogens and Host Immunity (LPHI), Université de Montpellier, CNRS, Inserm, 34095, Montpellier, France
| | - Flore Nilly
- Laboratory of Pathogens and Host Immunity (LPHI), Université de Montpellier, CNRS, Inserm, 34095, Montpellier, France
| | - Laurence Berry
- Laboratory of Pathogens and Host Immunity (LPHI), Université de Montpellier, CNRS, Inserm, 34095, Montpellier, France
| | - Anne Bonhoure
- Laboratory of Pathogens and Host Immunity (LPHI), Université de Montpellier, CNRS, Inserm, 34095, Montpellier, France
| | - Morgan A. Alford
- Center for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, Canada
| | - Mélissande Louis
- CBSA UR4312, Laboratoire de microbiologie Communication Bactérienne et Stratégies Anti-Infectieuses, Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
| | - Pauline Nogaret
- Laboratory of Pathogens and Host Immunity (LPHI), Université de Montpellier, CNRS, Inserm, 34095, Montpellier, France
| | - Manjeet Bains
- Center for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, Canada
| | - Olivier Lesouhaitier
- CBSA UR4312, Laboratoire de microbiologie Communication Bactérienne et Stratégies Anti-Infectieuses, Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
| | - Robert E. W. Hancock
- Center for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, Canada
| | - Patrick Plésiat
- UMR6249 CNRS Chrono-environnement, Université de Franche-Comté, Besançon, France
| | - Anne-Béatrice Blanc-Potard
- Laboratory of Pathogens and Host Immunity (LPHI), Université de Montpellier, CNRS, Inserm, 34095, Montpellier, France
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14
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Laing RA, Foster MJ, Hassani MA, Kotzen B, Huang W, Shea T, Schaffner SF, Cerar T, Freimark L, Ruzic-Sabljic E, Liveris D, Reed KD, Branda JA, Steere AC, Wormser GP, Strle F, Sabeti PC, Earl A, Schwartz I, Strle K, Lemieux JE. Complex exchanges among plasmids and clonal expansion of lineages shape the population structure and virulence of Borrelia burgdorferi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.29.635312. [PMID: 39974970 PMCID: PMC11838331 DOI: 10.1101/2025.01.29.635312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Background In the United States, Borrelia burgdorferi (Bb) is the principal etiologic agent of Lyme disease. The complex structure of Bb genomes has posed challenges for genomic studies because homology among the bacterium's many plasmids, which account for ~40% of the genome by length, has made them difficult to sequence and assemble. Results We used long-read sequencing to generate near-complete assemblies of 62 isolates of human-derived Bb and collected public genomes with plasmid sequences. We characterized genetic diversity and population structure in the resulting set of 82 plasmid-complete Borrelia burgdorferi sensu stricto genomes. The Bb core genome is encoded by a chromosome and the conserved plasmids cp26, lp54, and lp17; the accessory genome is encoded by all other plasmids and the distal arm of the chromosome. Near-complete genomes reveal that the most granular Bb genotypes are clonal expansions of complex rearrangements among accessory genome elements. Ribosomal spacer types (RST) represent multiple collections of such genotypes, whereas OspC types are usually clonal. Structural rearrangements are non-randomly distributed throughout the genome, with cp32 plasmids undergoing dense exchanges and most linear plasmids, except lp54, sharing blocks among themselves and with the distal arm of the chromosome. OspC type A strains, known to possess greater virulence in humans, are distinguished by the presence of lp28-1 and lp56. Rearrangements among plasmids tended to preserve gene content, suggesting functional constraints among gene networks. Using k-partite graph decompositions, we identified gene sets with correlation patterns suggestive of conserved functional modules. Conclusions Long-read assemblies reveal that Bb population genetic structure results from clonal expansion of lineages that have undergone complex rearrangements among plasmid-encoded accessory genome elements. Genetic structure is preserved among genes even when plasmid rearrangements occur, suggesting that selection among epistatic loci maintains functional genetic networks. The analysis of near-complete genomes assembled using long-read sequencing methods advances our understanding of Bb biology and Lyme disease pathogenesis by providing the first detailed view of population variation in previously inaccessible areas of the Bb genome.
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Affiliation(s)
- Rachel A. Laing
- Massachusetts General Hospital, Harvard Medical School
- Broad Institute of MIT and Harvard
| | - Michael J. Foster
- Massachusetts General Hospital, Harvard Medical School
- Broad Institute of MIT and Harvard
| | - M. Amine Hassani
- Massachusetts General Hospital, Harvard Medical School
- Broad Institute of MIT and Harvard
| | - Benjamin Kotzen
- Massachusetts General Hospital, Harvard Medical School
- Broad Institute of MIT and Harvard
| | - Weihua Huang
- New York Medical College
- East Carolina University
| | | | | | | | | | | | | | | | | | | | | | | | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard
- Harvard University
- Harvard T.H.Chan School of Public Health
| | | | | | | | - Jacob E. Lemieux
- Massachusetts General Hospital, Harvard Medical School
- Broad Institute of MIT and Harvard
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15
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Figueroa W, Cazares A, Ashworth EA, Weimann A, Kadioglu A, Floto RA, Welch M. Mutations in mexT bypass the stringent response dependency of virulence in Pseudomonas aeruginosa. Cell Rep 2025; 44:115079. [PMID: 39708318 DOI: 10.1016/j.celrep.2024.115079] [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: 03/19/2024] [Revised: 10/14/2024] [Accepted: 11/26/2024] [Indexed: 12/23/2024] Open
Abstract
Pseudomonas aeruginosa produces a wealth of virulence factors whose production is controlled via an intricate regulatory systems network. Here, we uncover a major player in the evolution and regulation of virulence that enhances host colonization and antibiotic resistance. By characterizing a collection of mutants lacking the stringent response (SR), a system key for virulence, we show that the loss of the central regulator MexT bypasses absence of the SR, restoring full activation of virulence pathways. Notably, mexT mutations were associated with resistance to aminoglycosides and the last-resort antibiotic, colistin. Analysis of thousands of P. aeruginosa genomes revealed that mexT mutations are widespread in isolates linked to aggressive antibiotic treatment. Furthermore, in vivo experiments in a murine pulmonary model revealed that mexT mutants display a hypervirulent phenotype associated with bacteremia. Altogether, these findings uncover a key regulator that acts as a genetic switch in the regulation of virulence and antimicrobial resistance.
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Affiliation(s)
- Wendy Figueroa
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK; Victor Phillip Dahdaleh Heart & Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Adrian Cazares
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Eleri A Ashworth
- Department of Clinical Infection, Microbiology & Immunology, University of Liverpool, Liverpool L69 7BE, UK
| | - Aaron Weimann
- Victor Phillip Dahdaleh Heart & Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, UK; Molecular Immunity Unit, University of Cambridge, Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology & Immunology, University of Liverpool, Liverpool L69 7BE, UK
| | - R Andres Floto
- Victor Phillip Dahdaleh Heart & Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, UK; Molecular Immunity Unit, University of Cambridge, Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK; Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.
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16
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Wimalasekara RL, White D, Kumar A. Targeting Acinetobacter baumannii resistance-nodulation-division efflux pump transcriptional regulators to combat antimicrobial resistance. NPJ ANTIMICROBIALS AND RESISTANCE 2025; 3:4. [PMID: 39863717 PMCID: PMC11762787 DOI: 10.1038/s44259-024-00074-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2024] [Accepted: 12/17/2024] [Indexed: 01/27/2025]
Abstract
Regulatory elements controlling gene expression fine-tune bacterial responses to environmental cues, including antimicrobials, to optimize survival. Acinetobacter baumannii, a pathogen notorious for antimicrobial resistance, relies on efficient efflux systems. Though the role of efflux systems in antibiotic expulsion are well recognized, the regulatory mechanisms controlling their expression remain understudied. This review explores the current understanding of these regulators, aiming to inspire strategies to combat bacterial resistance and improve therapeutic outcomes.
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Affiliation(s)
| | - Dawn White
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada.
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17
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Habich A, Chaves Vargas V, Robinson LA, Allsopp LP, Unterweger D. Distribution of the four type VI secretion systems in Pseudomonas aeruginosa and classification of their core and accessory effectors. Nat Commun 2025; 16:888. [PMID: 39837841 PMCID: PMC11751169 DOI: 10.1038/s41467-024-54649-5] [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: 12/18/2023] [Accepted: 11/14/2024] [Indexed: 01/23/2025] Open
Abstract
Bacterial type VI secretion systems (T6SSs) are puncturing molecular machines that transport effector proteins to kill microbes, manipulate eukaryotic cells, or facilitate nutrient uptake. How and why T6SS machines and effectors differ within a species is not fully understood. Here, we applied molecular population genetics to the T6SSs in a global population of the opportunistic pathogen Pseudomonas aeruginosa. We reveal varying occurrence of up to four distinct T6SS machines. Moreover, we define conserved core T6SS effectors, likely critical for the biology of P. aeruginosa, and accessory effectors that can exhibit mutual exclusivity between strains. By ancestral reconstruction, we observed dynamic changes in the gain and loss of effector genes in the species' evolutionary history. Our work highlights the potential importance of T6SS intraspecific diversity in bacterial ecology and evolution.
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Affiliation(s)
- Antonia Habich
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Verónica Chaves Vargas
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Luca A Robinson
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Luke P Allsopp
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Daniel Unterweger
- Institute for Experimental Medicine, Kiel University, Kiel, Germany.
- Max Planck Institute for Evolutionary Biology, Plön, Germany.
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18
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Carey CJ, Duggan N, Drabinska J, McClean S. Harnessing hypoxia: bacterial adaptation and chronic infection in cystic fibrosis. FEMS Microbiol Rev 2025; 49:fuaf018. [PMID: 40312783 PMCID: PMC12071387 DOI: 10.1093/femsre/fuaf018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 04/04/2025] [Accepted: 04/29/2025] [Indexed: 05/03/2025] Open
Abstract
The exquisite ability of bacteria to adapt to their environment is essential for their capacity to colonize hostile niches. In the cystic fibrosis (CF) lung, hypoxia is among several environmental stresses that opportunistic pathogens must overcome to persist and chronically colonize. Although the role of hypoxia in the host has been widely reviewed, the impact of hypoxia on bacterial pathogens has not yet been studied extensively. This review considers the bacterial oxygen-sensing mechanisms in three species that effectively colonize the lungs of people with CF, namely Pseudomonas aeruginosa, Burkholderia cepacia complex, and Mycobacterium abscessus and draws parallels between their three proposed oxygen-sensing two-component systems: BfiSR, FixLJ, and DosRS, respectively. Moreover, each species expresses regulons that respond to hypoxia: Anr, Lxa, and DosR, and encode multiple proteins that share similar homologies and function. Many adaptations that these pathogens undergo during chronic infection, including antibiotic resistance, protease expression, or changes in motility, have parallels in the responses of the respective species to hypoxia. It is likely that exposure to hypoxia in their environmental habitats predispose these pathogens to colonization of hypoxic niches, arming them with mechanisms than enable their evasion of the immune system and establish chronic infections. Overcoming hypoxia presents a new target for therapeutic options against chronic lung infections.
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Affiliation(s)
- Ciarán J Carey
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Niamh Duggan
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Joanna Drabinska
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Siobhán McClean
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
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19
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Bae HW, Choi SY, Ki HJ, Cho YH. Pseudomonas aeruginosa as a model bacterium in antiphage defense research. FEMS Microbiol Rev 2025; 49:fuaf014. [PMID: 40240293 PMCID: PMC12035536 DOI: 10.1093/femsre/fuaf014] [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: 12/31/2024] [Revised: 04/09/2025] [Accepted: 04/15/2025] [Indexed: 04/18/2025] Open
Abstract
Bacteriophages, or phages, depend on their bacterial hosts for proliferation, leading to a coevolutionary relationship characterized by on-going arms races, where bacteria evolve diverse antiphage defense systems. The development of in silico methods and high-throughput screening techniques has dramatically expanded our understanding of bacterial antiphage defense systems, enormously increasing the known repertoire of the distinct mechanisms across various bacterial species. These advances have revealed that bacterial antiphage defense systems exhibit a remarkable level of complexity, ranging from highly conserved to specialized mechanisms, underscoring the intricate nature of bacterial antiphage defense systems. In this review, we provide a concise snapshot of antiphage defense research highlighting two preponderantly commandeered approaches and classification of the known antiphage defense systems. A special focus is placed on the model bacterial pathogen, Pseudomonas aeruginosa in antiphage defense research. We explore the complexity and adaptability of these systems, which play crucial roles in genome evolution and adaptation of P. aeruginosa in response to an arsenal of diverse phage strains, emphasizing the importance of this organism as a key emerging model bacterium in recent antiphage defense research.
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Affiliation(s)
- Hee-Won Bae
- Program of Biopharmaceutical Science, Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Korea
| | - Shin-Yae Choi
- Program of Biopharmaceutical Science, Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Korea
| | - Hyeong-Jun Ki
- Program of Biopharmaceutical Science, Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Korea
| | - You-Hee Cho
- Program of Biopharmaceutical Science, Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Korea
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20
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Hafner L, Gadin E, Huang L, Frouin A, Laporte F, Gaultier C, Vieira A, Maudet C, Varet H, Moura A, Bracq-Dieye H, Tessaud-Rita N, Maury M, Dazas M, Legendre R, Gastineau P, Tsai YH, Coppée JY, Charlier C, Patin E, Chikhi R, Rocha EPC, Leclercq A, Disson O, Aschard H, Lecuit M. Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes. Nat Microbiol 2024; 9:3345-3361. [PMID: 39578578 DOI: 10.1038/s41564-024-01859-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 10/14/2024] [Indexed: 11/24/2024]
Abstract
Microbial pathogenesis is mediated by the expression of virulence genes. However, as microbes with identical virulence gene content can differ in their pathogenic potential, other virulence determinants must be involved. Here, by combining comparative genomics and transcriptomics of a large collection of isolates of the model pathogen Listeria monocytogenes, time-lapse microscopy, in vitro evolution and in vivo experiments, we show that the individual stress responsiveness of L. monocytogenes isolates determines their respective levels of virulence in vivo and reflects their degree of host adaptation. The transcriptional signature that accounts for the heterogeneity in the virulence of L. monocytogenes species is mediated by the stress response regulator SigB and driven by differential stress responsiveness. The tuning of SigB pathway responsiveness is polygenic and influenced by multiple, individually rare gene variations. This study reveals an overarching determinant of microbial virulence, challenging the paradigm of accessory virulence gene content as the major determinant of intraspecies virulence heterogeneity.
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Affiliation(s)
- Lukas Hafner
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Enzo Gadin
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Lei Huang
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Arthur Frouin
- Statistical Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS USR375, Paris, France
| | - Fabien Laporte
- Statistical Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS USR375, Paris, France
| | - Charlotte Gaultier
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Afonso Vieira
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Claire Maudet
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Hugo Varet
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
| | - Alexandra Moura
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
- National Reference Center and WHO Collaborating Center Listeria, Institut Pasteur, Paris, France
| | - Hélène Bracq-Dieye
- National Reference Center and WHO Collaborating Center Listeria, Institut Pasteur, Paris, France
| | - Nathalie Tessaud-Rita
- National Reference Center and WHO Collaborating Center Listeria, Institut Pasteur, Paris, France
| | - Mylène Maury
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
- National Reference Center and WHO Collaborating Center Listeria, Institut Pasteur, Paris, France
| | - Melody Dazas
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Rachel Legendre
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
| | - Pauline Gastineau
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Yu-Huan Tsai
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Jean-Yves Coppée
- Transcriptome et Epigenome Platform, Biomics, Center for Technological Resources and Research, Institut Pasteur, Université Paris Cité, Paris, France
| | - Caroline Charlier
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
- National Reference Center and WHO Collaborating Center Listeria, Institut Pasteur, Paris, France
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, Institut Imagine, APHP, Paris, France
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Rayan Chikhi
- Sequence Bioinformatics Group, Institut Pasteur, Université Paris Cité, Paris, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3525, Paris, France
| | - Alexandre Leclercq
- National Reference Center and WHO Collaborating Center Listeria, Institut Pasteur, Paris, France
| | - Olivier Disson
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Hugues Aschard
- Statistical Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS USR375, Paris, France
| | - Marc Lecuit
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France.
- National Reference Center and WHO Collaborating Center Listeria, Institut Pasteur, Paris, France.
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, Institut Imagine, APHP, Paris, France.
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21
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Harrington NE, Kottara A, Cagney K, Shepherd MJ, Grimsey EM, Fu T, Hull RC, Chong CE, Baker KS, Childs DZ, Fothergill JL, Chalmers JD, Brockhurst MA, Paterson S. Global genomic diversity of Pseudomonas aeruginosa in bronchiectasis. J Infect 2024; 89:106275. [PMID: 39293722 DOI: 10.1016/j.jinf.2024.106275] [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: 07/15/2024] [Revised: 08/30/2024] [Accepted: 09/11/2024] [Indexed: 09/20/2024]
Abstract
OBJECTIVES Pseudomonas aeruginosa is the most common pathogen in the bronchiectasis lung, associated with worsened outcomes. P. aeruginosa genomic studies in this context have been limited to single-country, European studies. We aimed to determine strain diversity, adaptation mechanisms, and AMR features to better inform treatment. METHODS P. aeruginosa from 180 bronchiectasis patients in 15 countries, obtained prior to a phase 3, randomised clinical trial (ORBIT-3), were analysed by whole-genome sequencing. Phylogenetic groups and sequence types were determined, and between versus within patient genetic diversity compared using Analysis of Molecular Variance (AMOVA). The frequency of AMR-associated genes and mutations was also determined. RESULTS A total of 2854 P. aeruginosa isolates were analysed, predominantly belonging to phylogenetic group 1 (83%, n = 2359). Genetic diversity was far greater between than within patients, responsible for >99.9% of total diversity (AMOVA: phylogroup 1: df = 145, P < 0.01). Numerous pathways were under selection, some shared with CF (e.g., motility, iron acquisition), some unique to bronchiectasis (e.g., novel efflux pump PA1874). Multidrug resistance features were also frequent. CONCLUSIONS We present a 10-fold increase in the availability of genomic data for P. aeruginosa in bronchiectasis, highlighting key distinctions with cystic fibrosis and potential targets for future treatments.
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Affiliation(s)
- N E Harrington
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 3BX, UK.
| | - A Kottara
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, M13 9NT, UK
| | - K Cagney
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 3BX, UK
| | - M J Shepherd
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, M13 9NT, UK
| | - E M Grimsey
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, M13 9NT, UK
| | - T Fu
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, M13 9NT, UK
| | - R C Hull
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - C E Chong
- Department of Genetics, University of Cambridge, CB2 3EH Cambridge, UK
| | - K S Baker
- Department of Genetics, University of Cambridge, CB2 3EH Cambridge, UK
| | - D Z Childs
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN Sheffield, UK
| | - J L Fothergill
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 3BX, UK
| | - J D Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - M A Brockhurst
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, M13 9NT, UK
| | - S Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 3BX, UK
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22
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Herrmann C, Lingner M, Herrmann S, Brockhausen I, Tümmler B. Mucin adhesion of serial cystic fibrosis airways Pseudomonas aeruginosa isolates. Front Cell Infect Microbiol 2024; 14:1448104. [PMID: 39239637 PMCID: PMC11374773 DOI: 10.3389/fcimb.2024.1448104] [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: 06/12/2024] [Accepted: 07/30/2024] [Indexed: 09/07/2024] Open
Abstract
The chronic airway infections with Pseudomonas aeruginosa are the major co-morbidity in people with cystic fibrosis (CF). Within CF lungs, P. aeruginosa persists in the conducting airways together with human mucins as the most abundant structural component of its microenvironment. We investigated the adhesion of 41 serial CF airway P. aeruginosa isolates to airway mucin preparations from CF sputa. Mucins and bacteria were retrieved from five modulator-naïve patients with advanced CF lung disease. The P. aeruginosa isolates from CF airways and non-CF reference strains showed a strain-specific signature in their adhesion to ovine, porcine and bovine submaxillary mucins and CF airway mucins ranging from no or low to moderate and strong binding. Serial CF clonal isolates and colony morphotypes from the same sputum sample were as heterogeneous in their affinity to mucin as representatives of other clones thus making 'mucin binding' one of the most variable intraclonal phenotypic traits of P. aeruginosa known to date. Most P. aeruginosa CF airway isolates did not adhere more strongly to CF airway mucins than to plastic surfaces. The strong binders, however, exhibited a strain-specific affinity gradient to O-glycans, CF airway and mammalian submaxillary mucins.
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Affiliation(s)
- Christian Herrmann
- Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Hannover, Germany
- Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Meike Lingner
- Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Hannover, Germany
- Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Susanne Herrmann
- Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Hannover, Germany
- Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Inka Brockhausen
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Burkhard Tümmler
- Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Hannover, Germany
- Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, Hannover, Germany
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23
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Askenasy I, Swain JEV, Ho PM, Nazeer RR, Welch A, Bényei ÉB, Mancini L, Nir S, Liao P, Welch M. 'Wild Type'. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001495. [PMID: 39212644 PMCID: PMC11364142 DOI: 10.1099/mic.0.001495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
In this opinion piece, we consider the meaning of the term 'wild type' in the context of microbiology. This is especially pertinent in the post-genomic era, where we have a greater awareness of species diversity than ever before. Genomic heterogeneity, in vitro evolution/selection pressures, definition of 'the wild', the size and importance of the pan-genome, gene-gene interactions (epistasis), and the nature of the 'wild-type gene' are all discussed. We conclude that wild type is an outdated and even misleading phrase that should be gradually phased out.
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Affiliation(s)
- Isabel Askenasy
- Department of Biochemistry, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, Cambridge, UK
| | - Jemima E. V. Swain
- Department of Biochemistry, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, Cambridge, UK
| | - Pok-Man Ho
- Department of Biochemistry, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, Cambridge, UK
| | - Rahan Rudland Nazeer
- Department of Biochemistry, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, Cambridge, UK
| | - Amelie Welch
- Department of Biochemistry, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, Cambridge, UK
| | - Éva Bernadett Bényei
- Department of Biochemistry, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, Cambridge, UK
| | - Leonardo Mancini
- Department of Biochemistry, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, Cambridge, UK
| | - Sivan Nir
- Department of Biochemistry, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, Cambridge, UK
| | - Pinyu Liao
- Department of Biochemistry, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, Cambridge, UK
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