1
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Volling C, Mataseje L, Graña-Miraglia L, Hu X, Anceva-Sami S, Coleman BL, Downing M, Hota S, Jamal AJ, Johnstone J, Katz K, Leis JA, Li A, Mahesh V, Melano R, Muller M, Nayani S, Patel S, Paterson A, Pejkovska M, Ricciuto D, Sultana A, Vikulova T, Zhong Z, McGeer A, Guttman DS, Mulvey MR. Epidemiology of healthcare-associated Pseudomonas aeruginosa in intensive care units: are sink drains to blame? J Hosp Infect 2024; 148:77-86. [PMID: 38554807 DOI: 10.1016/j.jhin.2024.03.009] [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: 11/16/2023] [Revised: 02/23/2024] [Accepted: 03/04/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Pseudomonas aeruginosa (PA) is a common cause of healthcare-associated infection (PA-HAI) in the intensive care unit (ICU). AIM To describe the epidemiology of PA-HAI in ICUs in Ontario, Canada, and to identify episodes of sink-to-patient PA transmission. METHODS This was a prospective cohort study of patients in six ICUs from 2018 to 2019, with retrieval of PA clinical isolates, and PA-screening of antimicrobial-resistant organism surveillance rectal swabs, and of sink drain, air, and faucet samples. All PA isolates underwent whole-genome sequencing. PA-HAI was defined using US National Healthcare Safety Network criteria. ICU-acquired PA was defined as PA isolated from specimens obtained ≥48 h after ICU admission in those with prior negative rectal swabs. Sink-to-patient PA transmission was defined as ICU-acquired PA with close genomic relationship to isolate(s) previously recovered from sinks in a room/bedspace occupied 3-14 days prior to collection date of the relevant patient specimen. FINDINGS Over ten months, 72 PA-HAIs occurred among 60/4263 admissions. The rate of PA-HAI was 2.40 per 1000 patient-ICU-days; higher in patients who were PA-colonized on admission. PA-HAI was associated with longer stay (median: 26 vs 3 days uninfected; P < 0.001) and contributed to death in 22/60 cases (36.7%). Fifty-eight admissions with ICU-acquired PA were identified, contributing 35/72 (48.6%) PA-HAIs. Four patients with five PA-HAIs (6.9%) had closely related isolates previously recovered from their room/bedspace sinks. CONCLUSION Nearly half of PA causing HAI appeared to be acquired in ICUs, and 7% of PA-HAIs were associated with sink-to-patient transmission. Sinks may be an under-recognized reservoir for HAIs.
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Affiliation(s)
- C Volling
- Department of Microbiology, Sinai Health, Toronto, Canada.
| | - L Mataseje
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - L Graña-Miraglia
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - X Hu
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - S Anceva-Sami
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - B L Coleman
- Department of Microbiology, Sinai Health, Toronto, Canada
| | | | - S Hota
- Department of Medicine, University Health Network, Toronto, Canada
| | - A J Jamal
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - J Johnstone
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - K Katz
- Department of Medicine, North York General Hospital, Toronto, Canada
| | - J A Leis
- Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - A Li
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - V Mahesh
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - R Melano
- Pan American Health Organization, Washington, USA
| | - M Muller
- Department of Medicine, Unity Health Toronto, Toronto, Canada
| | - S Nayani
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - S Patel
- Public Health Ontario Laboratory, Toronto, Canada
| | - A Paterson
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - M Pejkovska
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - D Ricciuto
- Department of Medicine, Lakeridge Health, Oshawa, Canada
| | - A Sultana
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - T Vikulova
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - Z Zhong
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - A McGeer
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - D S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada; Centre for the Analysis of Genome Evolution and Function, Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - M R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
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2
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Bloomfield SJ, Palau R, Holden ER, Webber MA, Mather AE. Genomic characterization of Pseudomonas spp. on food: implications for spoilage, antimicrobial resistance and human infection. BMC Microbiol 2024; 24:20. [PMID: 38212698 PMCID: PMC10782663 DOI: 10.1186/s12866-023-03153-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 12/11/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Pseudomonas species are common on food, but their contribution to the antimicrobial resistance gene (ARG) burden within food or as a source of clinical infection is unknown. Pseudomonas aeruginosa is an opportunistic pathogen responsible for a wide range of infections and is often hard to treat due to intrinsic and acquired ARGs commonly carried by this species. This study aimed to understand the potential role of Pseudomonas on food as a reservoir of ARGs and to assess the presence of potentially clinically significant Pseudomonas aeruginosa strains on food. To achieve this, we assessed the genetic relatedness (using whole genome sequencing) and virulence of food-derived isolates to those collected from humans. RESULTS A non-specific culturing approach for Pseudomonas recovered the bacterial genus from 28 of 32 (87.5%) retail food samples, although no P. aeruginosa was identified. The Pseudomonas species recovered were not clinically relevant, contained no ARGs and are likely associated with food spoilage. A specific culture method for P. aeruginosa resulted in the recovery of P. aeruginosa from 14 of 128 (11%) retail food samples; isolates contained between four and seven ARGs each and belonged to 16 sequence types (STs), four of which have been isolated from human infections. Food P. aeruginosa isolates from these STs demonstrated high similarity to human-derived isolates, differing by 41-312 single nucleotide polymorphisms (SNPs). There were diverse P. aeruginosa collected from the same food sample with distinct STs present on some samples and isolates belonging to the same ST differing by 19-67 SNPs. The Galleria mellonella infection model showed that 15 of 16 STs isolated from food displayed virulence between a low-virulence (PAO1) and a high virulence (PA14) control. CONCLUSION The most frequent Pseudomonas recovered from food examined in this study carried no ARGs and are more likely to play a role in food spoilage rather than infection. P. aeruginosa isolates likely to be able to cause human infections and with multidrug resistant genotypes are present on a relatively small but still substantial proportions of retail foods examined. Given the frequency of exposure, the potential contribution of food to the burden of P. aeruginosa infections in humans should be evaluated more closely.
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Affiliation(s)
| | - Raphaёlle Palau
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Emma R Holden
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- University of East Anglia, Norwich, UK.
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3
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Chandler CE, Hofstaedter CE, Hazen TH, Rasko DA, Ernst RK. Genomic and Functional Characterization of Longitudinal Pseudomonas aeruginosa Isolates from Young Patients with Cystic Fibrosis. Microbiol Spectr 2023; 11:e0155623. [PMID: 37358436 PMCID: PMC10433850 DOI: 10.1128/spectrum.01556-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/05/2023] [Indexed: 06/27/2023] Open
Abstract
Individuals with cystic fibrosis (CF) suffer from frequent and recurring microbial airway infections. The Gram-negative bacterium Pseudomonas aeruginosa is one of the most common organisms isolated from CF patient airways. P. aeruginosa establishes chronic infections that persist throughout a patient's lifetime and is a major cause of morbidity and mortality. Throughout the course of infection, P. aeruginosa must evolve and adapt from an initial state of early, transient colonization to chronic colonization of the airways. Here, we examined isolates of P. aeruginosa from children under the age of 3 years old with CF to determine genetic adaptations the bacterium undergoes during this early stage of colonization and infection. These isolates were collected when early aggressive antimicrobial therapy was not the standard of care and therefore highlight strain evolution under limited antibiotic pressure. Examination of specific phenotypic adaptations, such as lipid A palmitoylation, antibiotic resistance, and loss of quorum sensing, did not reveal a clear genetic basis for such changes. Additionally, we demonstrate that the geography of patient origin, within the United States or among other countries, does not appear to significantly influence genetic adaptation. In summary, our results support the long-standing model that patients acquire individual isolates of P. aeruginosa that subsequently become hyperadapted to the patient-specific airway environment. This study provides a multipatient genomic analysis of isolates from young CF patients in the United States and contributes data regarding early colonization and adaptation to the growing body of research about P. aeruginosa evolution in the context of CF airway disease. IMPORTANCE Chronic lung infection with Pseudomonas aeruginosa is of major concern for patients with cystic fibrosis (CF). During infection, P. aeruginosa undergoes genomic and functional adaptation to the hyperinflammatory CF airway, resulting in worsening lung function and pulmonary decline. All studies that describe these adaptations use P. aeruginosa obtained from older children or adults during late chronic lung infection; however, children with CF can be infected with P. aeruginosa as early as 3 months of age. Therefore, it is unclear when these genomic and functional adaptations occur over the course of CF lung infection, as access to P. aeruginosa isolates in children during early infection is limited. Here, we present a unique cohort of CF patients who were identified as being infected with P. aeruginosa at an early age prior to aggressive antibiotic therapy. Furthermore, we performed genomic and functional characterization of these isolates to address whether chronic CF P. aeruginosa phenotypes are present during early infection.
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Affiliation(s)
- Courtney E. Chandler
- Department of Microbial Pathogenesis, University of Maryland—Baltimore, Baltimore, Maryland, USA
| | - Casey E. Hofstaedter
- Department of Microbial Pathogenesis, University of Maryland—Baltimore, Baltimore, Maryland, USA
- Medical Scientist Training Program, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Tracy H. Hazen
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland—Baltimore, Baltimore, Maryland, USA
| | - David A. Rasko
- Department of Microbial Pathogenesis, University of Maryland—Baltimore, Baltimore, Maryland, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland—Baltimore, Baltimore, Maryland, USA
- Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Robert K. Ernst
- Department of Microbial Pathogenesis, University of Maryland—Baltimore, Baltimore, Maryland, USA
- Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, Maryland, USA
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4
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Cramer N, Klockgether J, Tümmler B. Microevolution of Pseudomonas aeruginosa in the airways of people with cystic fibrosis. Curr Opin Immunol 2023; 83:102328. [PMID: 37116385 DOI: 10.1016/j.coi.2023.102328] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/30/2023]
Abstract
The chronic infections of cystic fibrosis (CF) airways with Pseudomonas aeruginosa are a paradigm of how environmental bacteria can conquer, adapt, and persist in an atypical habitat and successfully evade defense mechanisms and chemotherapy in a susceptible host. The within-host evolution of intraclonal diversity has been examined by whole-genome sequencing, phenotyping, and competitive fitness experiments of serial P. aeruginosa isolates collected from CF airways since onset of colonization for a period of up to 40 years. The spectrum of de novo mutations and the adaptation of phenotype and fitness of the bacterial progeny were more influenced by the living conditions in the CF lung than by the clone type of their ancestor and its genetic repertoire.
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Affiliation(s)
- Nina Cramer
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, D-30625 Hannover, Germany
| | - Jens Klockgether
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, D-30625 Hannover, Germany
| | - Burkhard Tümmler
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, D-30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany.
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5
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Hall KM, Pursell ZF, Morici LA. The role of the Pseudomonas aeruginosa hypermutator phenotype on the shift from acute to chronic virulence during respiratory infection. Front Cell Infect Microbiol 2022; 12:943346. [PMID: 35937684 PMCID: PMC9355025 DOI: 10.3389/fcimb.2022.943346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic respiratory infection (CRI) with Pseudomonas aeruginosa (Pa) presents many unique challenges that complicate treatment. One notable challenge is the hypermutator phenotype which is present in up to 60% of sampled CRI patient isolates. Hypermutation can be caused by deactivating mutations in DNA mismatch repair (MMR) genes including mutS, mutL, and uvrD. In vitro and in vivo studies have demonstrated hypermutator strains to be less virulent than wild-type Pa. However, patients colonized with hypermutators display poorer lung function and a higher incidence of treatment failure. Hypermutation and MMR-deficiency create increased genetic diversity and population heterogeneity due to elevated mutation rates. MMR-deficient strains demonstrate higher rates of mucoidy, a hallmark virulence determinant of Pa during CRI in cystic fibrosis patients. The mucoid phenotype results from simple sequence repeat mutations in the mucA gene made in the absence of functional MMR. Mutations in Pa are further increased in the absence of MMR, leading to microcolony biofilm formation, further lineage diversification, and population heterogeneity which enhance bacterial persistence and host immune evasion. Hypermutation facilitates the adaptation to the lung microenvironment, enabling survival among nutritional complexity and microaerobic or anaerobic conditions. Mutations in key acute-to-chronic virulence “switch” genes, such as retS, bfmS, and ampR, are also catalyzed by hypermutation. Consequently, strong positive selection for many loss-of-function pathoadaptive mutations is seen in hypermutators and enriched in genes such as lasR. This results in the characteristic loss of Pa acute infection virulence factors, including quorum sensing, flagellar motility, and type III secretion. Further study of the role of hypermutation on Pa chronic infection is needed to better inform treatment regimens against CRI with hypermutator strains.
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Affiliation(s)
- Kalen M. Hall
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, United States
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Zachary F. Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Lisa A. Morici
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, United States
- *Correspondence: Lisa A. Morici,
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6
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Sherrard LJ, Wee BA, Duplancic C, Ramsay KA, Dave KA, Ballard E, Wainwright CE, Grimwood K, Sidjabat HE, Whiley DM, Beatson SA, Kidd TJ, Bell SC. Emergence and impact of oprD mutations in Pseudomonas aeruginosa strains in cystic fibrosis. J Cyst Fibros 2021; 21:e35-e43. [PMID: 33775602 DOI: 10.1016/j.jcf.2021.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Antimicrobial resistance in cystic fibrosis (CF) Pseudomonas aeruginosa airway infection is complex and often attributed to chromosomal mutations. How these mutations emerge in specific strains or whether particular gene mutations are clinically informative is unclear. This study focused on oprD, which encodes an outer membrane porin associated with carbapenem resistance when it is downregulated or inactivated. AIM Determine how mutations in oprD emerge in two prevalent Australian shared CF strains of P. aeruginosa and their clinical relevance. METHODS The two most common shared CF strains in Queensland were investigated using whole genome sequencing and their oprD sequences and antimicrobial resistance phenotypes were established. P. aeruginosa mutants with the most common oprD variants were constructed and characterised. Clinical variables were compared between people with or without evidence of infection with strains harbouring these variants. RESULTS Frequently found nonsense mutations arising from a 1-base pair substitution in oprD evolved independently in three sub-lineages, and are likely major contributors to the reduced carbapenem susceptibility observed in the clinical isolates. Lower baseline FEV1 %predicted was identified as a risk factor for infection with a sub-lineage (odds ratio=0.97; 95% confidence interval 0.96-0.99; p<0.001). However, acquiring these sub-lineage strains did not confer an accelerated decline in FEV1 nor increase the risk of death/lung transplantation. CONCLUSIONS Sub-lineages harbouring specific mutations in oprD have emerged and persisted in the shared strain populations. Infection with the sub-lineages was more likely in people with lower lung function, but this was not predictive of a worse clinical trajectory.
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Affiliation(s)
| | - Bryan A Wee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | | | - Kay A Ramsay
- QIMR Berghofer Medical Research Institute, Brisbane, Australia; Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Keyur A Dave
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Emma Ballard
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Claire E Wainwright
- Faculty of Medicine, The University of Queensland, Brisbane, Australia; Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, Brisbane, Australia
| | - Keith Grimwood
- School of Medicine and Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia; Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Gold Coast, Australia
| | - Hanna E Sidjabat
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia
| | - David M Whiley
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia; Pathology Queensland Central Laboratory, Brisbane, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia; Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
| | - Timothy J Kidd
- QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
| | - Scott C Bell
- QIMR Berghofer Medical Research Institute, Brisbane, Australia; Faculty of Medicine, The University of Queensland, Brisbane, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia; Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia.
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7
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Nain Z, Karim MM. Whole-genome sequence, functional annotation, and comparative genomics of the high biofilm-producing multidrug-resistant Pseudomonas aeruginosa MZ4A isolated from clinical waste. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2020.100999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Camus L, Vandenesch F, Moreau K. From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment. Microb Genom 2021; 7:mgen000513. [PMID: 33529147 PMCID: PMC8190622 DOI: 10.1099/mgen.0.000513] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa is one of the main microbial species colonizing the lungs of cystic fibrosis patients and is responsible for the decline in respiratory function. Despite the hostile pulmonary environment, P. aeruginosa is able to establish chronic infections thanks to its strong adaptive capacity. Various longitudinal studies have attempted to compare the strains of early infection with the adapted strains of chronic infection. Thanks to new '-omics' techniques, convergent genetic mutations, as well as transcriptomic and proteomic dysregulations have been identified. As a consequence of this evolution, the adapted strains of P. aeruginosa have particular phenotypes that promote persistent infection.
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Affiliation(s)
- Laura Camus
- CIRI – Centre International de Recherche en Infectiologie, Université de Lyon/Inserm U1111/Université Claude Bernard Lyon 1/CNRS UMR5308/ENS de Lyon, Lyon, France
| | - François Vandenesch
- CIRI – Centre International de Recherche en Infectiologie, Université de Lyon/Inserm U1111/Université Claude Bernard Lyon 1/CNRS UMR5308/ENS de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Karen Moreau
- CIRI – Centre International de Recherche en Infectiologie, Université de Lyon/Inserm U1111/Université Claude Bernard Lyon 1/CNRS UMR5308/ENS de Lyon, Lyon, France
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9
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Pseudomonas aeruginosa Resistance to Bacteriophages and Its Prevention by Strategic Therapeutic Cocktail Formulation. Antibiotics (Basel) 2021; 10:antibiotics10020145. [PMID: 33540528 PMCID: PMC7912912 DOI: 10.3390/antibiotics10020145] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance poses a significant threat to modern healthcare as it limits treatment options for bacterial infections, particularly impacting those with chronic conditions such as cystic fibrosis (CF). Viscous mucus accumulation in the lungs of individuals genetically predisposed to CF leads to recurrent bacterial infections, necessitating prolonged antimicrobial chemotherapy. Pseudomonas aeruginosa infections are the predominant driver of CF lung disease, and airway isolates are frequently resistant to multiple antimicrobials. Bacteriophages, or phages, are viruses that specifically infect bacteria and are a promising alternative to antimicrobials for CF P. aeruginosa infections. However, the narrow host range of P. aeruginosa-targeting phages and the rapid evolution of phage resistance could limit the clinical efficacy of phage therapy. A promising approach to overcome these issues is the strategic development of mixtures of phages (cocktails). The aim is to combine phages with broad host ranges and target multiple distinct bacterial receptors to prevent the evolution of phage resistance. However, further research is required to identify and characterize phage resistance mechanisms in CF-derived P. aeruginosa, which differ from their non-CF counterparts. In this review, we consider the mechanisms of P. aeruginosa phage resistance and how these could be overcome by an effective future phage therapy formulation.
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10
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Cao Q, Yang N, Wang Y, Xu C, Zhang X, Fan K, Chen F, Liang H, Zhang Y, Deng X, Feng Y, Yang CG, Wu M, Bae T, Lan L. Mutation-induced remodeling of the BfmRS two-component system in Pseudomonas aeruginosa clinical isolates. Sci Signal 2020; 13:13/656/eaaz1529. [PMID: 33144518 DOI: 10.1126/scisignal.aaz1529] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Genetic mutations are a primary driving force behind the adaptive evolution of bacterial pathogens. Multiple clinical isolates of Pseudomonas aeruginosa, an important human pathogen, have naturally evolved one or more missense mutations in bfmS, which encodes the sensor histidine kinase of the BfmRS two-component system (TCS). A mutant BfmS protein containing both the L181P and E376Q substitutions increased the phosphorylation and thus the transcriptional regulatory activity of its cognate downstream response regulator, BfmR. This reduced acute virulence and enhanced biofilm formation, both of which are phenotypic changes associated with a chronic infection state. The increased phosphorylation of BfmR was due, at least in part, to the cross-phosphorylation of BfmR by GtrS, a noncognate sensor kinase. Other spontaneous missense mutations in bfmS, such as A42E/G347D, T242R, and R393H, also caused a similar remodeling of the BfmRS TCS in P. aeruginosa This study highlights the plasticity of TCSs mediated by spontaneous mutations and suggests that mutation-induced activation of BfmRS may contribute to host adaptation by P. aeruginosa during chronic infections.
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Affiliation(s)
- Qiao Cao
- College of Life Science, Northwest University, Xi'an 710127, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Nana Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yanhui Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chenchen Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xue Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ke Fan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Feifei Chen
- College of Life Science, Northwest University, Xi'an 710127, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Haihua Liang
- College of Life Science, Northwest University, Xi'an 710127, China
| | - Yingchao Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong 999077, China
| | - Xin Deng
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong 999077, China
| | - Youjun Feng
- School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Min Wu
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, ND 58203-9037, USA
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN 46408, USA
| | - Lefu Lan
- College of Life Science, Northwest University, Xi'an 710127, China. .,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.,NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
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11
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Gene Loss and Acquisition in Lineages of Pseudomonas aeruginosa Evolving in Cystic Fibrosis Patient Airways. mBio 2020; 11:mBio.02359-20. [PMID: 33109761 PMCID: PMC7593970 DOI: 10.1128/mbio.02359-20] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bacterial airway infections, predominantly caused by P. aeruginosa, are a major cause of mortality and morbidity of CF patients. While short insertions and deletions as well as point mutations occurring during infection are well studied, there is a lack of understanding of how gene loss and acquisition play roles in bacterial adaptation to the human airways. Here, we investigated P. aeruginosa within-host evolution with regard to gene loss and acquisition. We show that during long-term infection P. aeruginosa genomes tend to lose genes, in particular, genes related to virulence. This adaptive strategy allows reduction of the genome size and evasion of the host’s immune response. This knowledge is crucial to understand the basic mutational steps that, on the timescale of years, diversify lineages and adds to the identification of bacterial genetic determinants that have implications for CF disease. Genome analyses have documented that there are differences in gene repertoire between evolutionary distant lineages of the same bacterial species; however, less is known about microevolutionary dynamics of gene loss and acquisition within bacterial lineages as they evolve over years. Here, we analyzed the genomes of 45 Pseudomonas aeruginosa lineages evolving in the lungs of cystic fibrosis (CF) patients to identify genes that are lost or acquired during the first years of infection. On average, lineage genome content changed by 88 genes (range, 0 to 473). Genes were more often lost than acquired, and prophage genes were more variable than bacterial genes. We identified convergent loss or acquisition of the same genes across lineages, suggesting selection for loss and acquisition of certain genes in the host environment. We found that a notable proportion of such genes are associated with virulence; a trait previously shown to be important for adaptation. Furthermore, we also compared the genomes across lineages to show that the within-lineage variable genes (i.e., genes that had been lost or acquired during the infection) often belonged to genomic content not shared across all lineages. In sum, our analysis adds to the knowledge on the pace and drivers of gene loss and acquisition in bacteria evolving over years in a human host environment and provides a basis to further understand how gene loss and acquisition play roles in lineage differentiation and host adaptation.
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Pseudomonas aeruginosa Isolates From a Cohort of Mexican Children With Cystic Fibrosis Show Adaptation to a Chronic Phenotype. Pediatr Infect Dis J 2020; 39:899-906. [PMID: 32453200 DOI: 10.1097/inf.0000000000002714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Long-term persistence of Pseudomonas aeruginosa in the lung of individuals with cystic fibrosis (CF) is associated with progressive selection of diverse genotypes and phenotypes. This bacterial adaptation leads to chronic infection and increased morbidity and mortality. The aim of this study was to establish the prevalence, clonal relatedness, antimicrobial susceptibility and virulence-associated phenotypes of P. aeruginosa isolates in a cohort of 50 Mexican children with CF-associated chronic lung infection. METHODS Clonal relatedness of P. aeruginosa isolates was verified by pulsed-field gel electrophoresis. The antimicrobial susceptibility was determined by an automated system that performs bacterial identificación and antibiotic susceptibility testing (VITEK 2) and/or broth microdilution method. Biofilm formation was quantified with the crystal violet method; swarming motility was measured on soft agar, and susceptibility to normal human serum determined by reduction of colony formed units (CFUs). RESULTS High prevalence of P. aeruginosa colonization among Mexican children with CF was confirmed; 20% (10/49) of clones identified showed a multidrug-resistant phenotype and 8.2% (4/49) an extensive drug resistance phenotype; 26.5% (13/49) of the isolates were resistant to colistin, 42.9% (21/49) presented a phenotype of adaptation associated with chronic infection and 79.6% (39/49) showed increased ability to survive in normal human serum. CONCLUSIONS This cohort of children with CF reveals that colonizing P. aeruginosa strains predominantly display resistance to several first-line antibiotics, although most isolates were susceptible to meropenem and tobramycin; 42.9% of isolates showed a phenotype consistent with adaptation to chronic lung infection.
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Azimi S, Roberts AEL, Peng S, Weitz JS, McNally A, Brown SP, Diggle SP. Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations. ISME JOURNAL 2020; 14:1929-1942. [PMID: 32341475 DOI: 10.1038/s41396-020-0652-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/23/2020] [Accepted: 03/31/2020] [Indexed: 12/31/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that chronically infects the lungs of individuals with cystic fibrosis (CF) by forming antibiotic-resistant biofilms. Emergence of phenotypically diverse isolates within CF P. aeruginosa populations has previously been reported; however, the impact of heterogeneity on social behaviors and community function is poorly understood. Here we describe how this heterogeneity impacts on behavioral traits by evolving the strain PAO1 in biofilms grown in a synthetic sputum medium for 50 days. We measured social trait production and antibiotic tolerance, and used a metagenomic approach to analyze and assess genomic changes over the duration of the evolution experiment. We found that (i) evolutionary trajectories were reproducible in independently evolving populations; (ii) over 60% of genomic diversity occurred within the first 10 days of selection. We then focused on quorum sensing (QS), a well-studied P. aeruginosa trait that is commonly mutated in strains isolated from CF lungs. We found that at the population level, (i) evolution in sputum medium selected for decreased the production of QS and QS-dependent traits; (ii) there was a significant correlation between lasR mutant frequency, the loss of protease, and the 3O-C12-HSL signal, and an increase in resistance to clinically relevant β-lactam antibiotics, despite no previous antibiotic exposure. Overall, our findings provide insights into the effect of allelic polymorphism on community functions in diverse P. aeruginosa populations. Further, we demonstrate that P. aeruginosa population and evolutionary dynamics can impact on traits important for virulence and can lead to increased tolerance to β-lactam antibiotics.
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Affiliation(s)
- Sheyda Azimi
- Center for Microbial Dynamics & Infection, Georgia Institute of Technology, Atlanta, GA, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Aled E L Roberts
- Microbiology & Infectious Diseases Group, Institute of Life Science, Swansea University Medical School, Swansea, UK
| | - Shengyun Peng
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Joshua S Weitz
- Center for Microbial Dynamics & Infection, Georgia Institute of Technology, Atlanta, GA, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Samuel P Brown
- Center for Microbial Dynamics & Infection, Georgia Institute of Technology, Atlanta, GA, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Stephen P Diggle
- Center for Microbial Dynamics & Infection, Georgia Institute of Technology, Atlanta, GA, USA. .,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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Sener Okur D, Yuruyen C, Gungor O, Aktas Z, Erturan Z, Akcakaya N, Camcioglu Y, Cokugras H, Koksalan K. Genotypic characterization of Pseudomonas aeruginosa isolates from Turkish children with cystic fibrosis. Infect Drug Resist 2019; 12:675-685. [PMID: 31114258 PMCID: PMC6497484 DOI: 10.2147/idr.s183151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/15/2019] [Indexed: 02/03/2023] Open
Abstract
Objective: To identify epidemic and other transmissible Pseudomonas aeruginosa strains, genotypic analyses are required. The aim of this study was to assess the distribution of P. aeruginosa strains within the Turkish pediatric cystic fibrosis (CF) clinic population. Methods: Eighteen patients attending the pediatric CF clinic of Cerrahpasa Medical Faculty were investigated in the study. Throat swab and/or sputum samples were taken from each patient at 3-month intervals. The isolates of patients were analyzed by pulsed-field gel electrophoresis (PFGE). The intra- and interpatient genotypic heterogeneity of isolates was examined to determine the clonal isolates of P. aeruginosa within the cohort. Results: A total of 108 clinical isolates of P. aeruginosa were obtained from 18 patients between May 2013 and May 2014. The pulsotypes of the first patient’s isolates could not be obtained by PFGE. From the remaining 17 patients and 101 isolates, 55 distinct pulsotypes were detected. The number of pulsotypes observed in more than one patient (minor clonal strains, cluster strains) was 8 (14.5%), and one of them colonized three patients. However, none of them was detected in more than three patients. These pulsotypes were composed of 20 isolates. In addition, with the PFGE analysis of 81 isolates, we detected 47 (85.6%) pulsotypes, which belonged to only one patient. Over different periods of this study, only 2 (11.8%) patients were colonized with the same pulsotype. Conclusion: Our study indicates that there was considerable genomic diversity among the P. aeruginosa isolates in our clinic. The presence of shared pulsotypes supports cross-transmission between patients.
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Affiliation(s)
- Dicle Sener Okur
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Infectious Diseases, 34098 Kocamustafapasa, Istanbul, Turkey
| | - Caner Yuruyen
- Istanbul University Istanbul, Faculty of Medicine, Department of Microbiology and Clinical Microbiology, 34390 Capa, Istanbul, Turkey
| | - Ozge Gungor
- Istanbul University Istanbul, Faculty of Medicine, Department of Microbiology and Clinical Microbiology, 34390 Capa, Istanbul, Turkey
| | - Zerrin Aktas
- Istanbul University Istanbul, Faculty of Medicine, Department of Microbiology and Clinical Microbiology, 34390 Capa, Istanbul, Turkey
| | - Zayre Erturan
- Istanbul University Istanbul, Faculty of Medicine, Department of Microbiology and Clinical Microbiology, 34390 Capa, Istanbul, Turkey
| | - Necla Akcakaya
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Infectious Diseases, Clinical Immunology and Allergy, 34098 Kocamustafapasa, Istanbul, Turkey
| | - Yildiz Camcioglu
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Infectious Diseases, Clinical Immunology and Allergy, 34098 Kocamustafapasa, Istanbul, Turkey
| | - Haluk Cokugras
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Infectious Diseases, Clinical Immunology and Allergy, 34098 Kocamustafapasa, Istanbul, Turkey
| | - Kaya Koksalan
- Istanbul University, Institute for Medical Experimental Research (DETAE), 34390 Capa, Istanbul, Turkey
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