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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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Núñez-García LÁ, Feliciano-Guzmán JM, Mireles-Davalos CD, López-Sántiz JR, Ovando-Fonseca JE, Becerril-Vargas E, Jiménez-Martínez ME, Rodríguez-Medina N, Garza-Ramos U, Córdova-Fletes C, Garza-González E. Genomic and phenotypic characterization of Pseudomonas aeruginosa isolates from two Mexican cystic fibrosis attention centers. Microbiol Spectr 2024; 12:e0110024. [PMID: 39440985 PMCID: PMC11619361 DOI: 10.1128/spectrum.01100-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2024] [Accepted: 10/03/2024] [Indexed: 10/25/2024] Open
Abstract
Thirty-nine clinical isolates of Pseudomonas aeruginosa collected from 11 cystic fibrosis (CF) patients at two CF attention centers over 10 years were subjected to whole genome sequencing (WGS). Phenotypic tests (i.e., elastase, motility, biofilm, growth rate, and antibiotic susceptibility) were performed to correlate results. A single strain of P. aeruginosa was found to persist over time in longitudinal isolates. No transmission between patients or centers was observed. A tendency to lack genes related to pyoverdine, flagellum, pili, and O-antigen was observed, whereas those related to biofilm, phenazine, and pyochelin were conserved among isolates. In a patient with a 10-year follow-up, a single strain of P. aeruginosa persisted and showed a gradual decrease in elastase activity and growth rate, demonstrating an adaptive phenotype.IMPORTANCEThis study investigates the genomic and phenotypic characteristics of Pseudomonas aeruginosa isolates from Mexican cystic fibrosis (CF) patients, an underrepresented group in CF research. To our knowledge, it is the first to use whole genome sequencing (WGS) to study longitudinally collected P. aeruginosa isolates from this population, evaluating both genomic features and clonal relationships. Remarkably, the study includes samples from one patient over 10 years, offering an extended observation time compared to existing literature. Unlike similar studies, which often lack phenotypic testing, this research incorporates various virulence-related phenotypic assays, enhancing our understanding of gene-to-phenotype correlations. Two potential mechanisms for the loss of elastolytic activity were identified. Furthermore, we conduct an in-depth mobilome analysis, an area that remains largely unexplored in CF contexts. Whole genome sequencing data are publicly available through the NCBI SRA database, facilitating further re-analysis for studies on P. aeruginosa in CF, as well as epidemiological and population structure research.
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Affiliation(s)
- Luis Ángel Núñez-García
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | | | | | | | | | - Eduardo Becerril-Vargas
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de Mexico, Mexico
| | | | - Nadia Rodríguez-Medina
- Instituto Nacional de Salud Pública, Laboratorio de Resistencia Bacteriana, Cuernavaca, Morelos, Mexico
| | - Ulises Garza-Ramos
- Instituto Nacional de Salud Pública, Laboratorio de Resistencia Bacteriana, Cuernavaca, Morelos, Mexico
| | - Carlos Córdova-Fletes
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Elvira Garza-González
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
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Zhang P, Hu J, Wu W, Shi W, Jiang Y, Yu Y, Zheng X, Qu T. Evolutionary adaptation of KPC-2-producing Pseudomonas aeruginosa high-risk sequence type 463 in a lung transplant patient. Int J Antimicrob Agents 2024; 64:107279. [PMID: 39069228 DOI: 10.1016/j.ijantimicag.2024.107279] [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: 05/07/2024] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024]
Abstract
OBJECTIVES KPC-2-producing Pseudomonas aeruginosa high-risk sequence type (ST) 463 is increasingly prevalent in China and poses severe threats to public health. In this study, we aimed to investigate within-host adaptive evolution of this clone during therapy. METHODS Using nine serial respiratory isolates from a post-lung transplantation patient undergoing multiple antibiotic treatments, we conducted genomic, transcriptomic and phenotypic analyses to uncover the adaptive mechanisms of a KPC-2-producing ST463 P. aeruginosa strain. RESULTS The early-course isolates exhibited low-level resistance to ceftazidime/avibactam (CZA), facilitated by the blaKPC-2 gene's presence on both chromosome and plasmid, and its overexpression. Comparative genomic analysis revealed that chromosomal integration of blaKPC-2 resulted from intracellular replicative transposition of the plasmid-derived IS26-blaKPC-2-IS26 composite transposon. As the infection progressed, selective pressures, predominantly from antibiotic interventions and host immune response, led to significant genomic and phenotypic changes. The late-course isolates developed a Δ242-GT-243 deletion in plasmid-encoded blaKPC-2 (blaKPC-14) after sustained CZA exposure, conferring high-level CZA resistance. Increased expression of pili and extracellular polysaccharides boosted biofilm formation. A D143N mutation in the global regulator vfr rendered the strain aflagellate by abrogating the ability of fleQ to positively regulate flagellar gene expression. The enhancement of antibiotic resistance and immune evasion collaboratively facilitated the prolonged survival of ST463 P. aeruginosa within the host. CONCLUSIONS Our findings highlight the remarkable capacity of ST463 P. aeruginosa in adapting to the dynamic host pressures, supporting its persistence and dissemination in healthcare.
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Affiliation(s)
- Piaopiao Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Juan Hu
- Department of Intensive Care Unit, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wenhao Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Weixiao Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yunsong Yu
- Department of Infectious Diseases, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Xia Zheng
- Department of Intensive Care Unit, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tingting Qu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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4
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Nickerson R, Thornton CS, Johnston B, Lee AHY, Cheng Z. Pseudomonas aeruginosa in chronic lung disease: untangling the dysregulated host immune response. Front Immunol 2024; 15:1405376. [PMID: 39015565 PMCID: PMC11250099 DOI: 10.3389/fimmu.2024.1405376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/14/2024] [Indexed: 07/18/2024] Open
Abstract
Pseudomonas aeruginosa is a highly adaptable opportunistic pathogen capable of exploiting barriers and immune defects to cause chronic lung infections in conditions such as cystic fibrosis. In these contexts, host immune responses are ineffective at clearing persistent bacterial infection, instead driving a cycle of inflammatory lung damage. This review outlines key components of the host immune response to chronic P. aeruginosa infection within the lung, beginning with initial pathogen recognition, followed by a robust yet maladaptive innate immune response, and an ineffective adaptive immune response that propagates lung damage while permitting bacterial persistence. Untangling the interplay between host immunity and chronic P. aeruginosa infection will allow for the development and refinement of strategies to modulate immune-associated lung damage and potentiate the immune system to combat chronic infection more effectively.
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Affiliation(s)
- Rhea Nickerson
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Christina S. Thornton
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Brent Johnston
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Amy H. Y. Lee
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Zhenyu Cheng
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
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5
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Vanderpool EJ, Rumbaugh KP. Host-microbe interactions in chronic rhinosinusitis biofilms and models for investigation. Biofilm 2023; 6:100160. [PMID: 37928619 PMCID: PMC10622848 DOI: 10.1016/j.bioflm.2023.100160] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 11/07/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is a debilitating condition characterized by long-lasting inflammation of the paranasal sinuses. It affects a significant portion of the population, causing a considerable burden on individuals and healthcare systems. The pathogenesis of CRS is multifactorial, with bacterial infections playing a crucial role in CRS development and persistence. In recent years, the presence of biofilms has emerged as a key contributor to the chronicity of sinusitis, further complicating treatment and exacerbating symptoms. This review aims to explore the role of biofilms in CRS, focusing on the involvement of the bacterial species Staphylococcus aureus and Pseudomonas aeruginosa, their interactions in chronic infections, and model systems for studying biofilms in CRS. These species serve as an example of how microbial interplay can influence disease progression and exemplify the need for continued investigation and innovation in CRS research.
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Affiliation(s)
- Emily J. Vanderpool
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Burn Center of Research Excellence, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Kendra P. Rumbaugh
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Burn Center of Research Excellence, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
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6
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Grandy S, Scur M, Dolan K, Nickerson R, Cheng Z. Using model systems to unravel host-Pseudomonas aeruginosa interactions. Environ Microbiol 2023; 25:1765-1784. [PMID: 37290773 DOI: 10.1111/1462-2920.16440] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/29/2023] [Indexed: 06/10/2023]
Abstract
Using model systems in infection biology has led to the discoveries of many pathogen-encoded virulence factors and critical host immune factors to fight pathogenic infections. Studies of the remarkable Pseudomonas aeruginosa bacterium that infects and causes disease in hosts as divergent as humans and plants afford unique opportunities to shed new light on virulence strategies and host defence mechanisms. One of the rationales for using model systems as a discovery tool to characterise bacterial factors driving human infection outcomes is that many P. aeruginosa virulence factors are required for pathogenesis in diverse different hosts. On the other side, many host signalling components, such as the evolutionarily conserved mitogen-activated protein kinases, are involved in immune signalling in a diverse range of hosts. Some model organisms that have less complex immune systems also allow dissection of the direct impacts of innate immunity on host defence without the interference of adaptive immunity. In this review, we start with discussing the occurrence of P. aeruginosa in the environment and the ability of this bacterium to cause disease in various hosts as a natural opportunistic pathogen. We then summarise the use of some model systems to study host defence and P. aeruginosa virulence.
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Affiliation(s)
- Shannen Grandy
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Michal Scur
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Kathleen Dolan
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Rhea Nickerson
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Zhenyu Cheng
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
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7
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Cafaro V, Bosso A, Di Nardo I, D’Amato A, Izzo I, De Riccardis F, Siepi M, Culurciello R, D’Urzo N, Chiarot E, Torre A, Pizzo E, Merola M, Notomista E. The Antimicrobial, Antibiofilm and Anti-Inflammatory Activities of P13#1, a Cathelicidin-like Achiral Peptoid. Pharmaceuticals (Basel) 2023; 16:1386. [PMID: 37895857 PMCID: PMC10610514 DOI: 10.3390/ph16101386] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Cationic antimicrobial peptides (CAMPs) are powerful molecules with antimicrobial, antibiofilm and endotoxin-scavenging activities. These properties make CAMPs very attractive drugs in the face of the rapid increase in multidrug-resistant (MDR) pathogens, but they are limited by their susceptibility to proteolytic degradation. An intriguing solution to this issue could be the development of functional mimics of CAMPs with structures that enable the evasion of proteases. Peptoids (N-substituted glycine oligomers) are an important class of peptidomimetics with interesting benefits: easy synthetic access, intrinsic proteolytic stability and promising bioactivities. Here, we report the characterization of P13#1, a 13-residue peptoid specifically designed to mimic cathelicidins, the best-known and most widespread family of CAMPs. P13#1 showed all the biological activities typically associated with cathelicidins: bactericidal activity over a wide spectrum of strains, including several ESKAPE pathogens; the ability to act in combination with different classes of conventional antibiotics; antibiofilm activity against preformed biofilms of Pseudomonas aeruginosa, comparable to that of human cathelicidin LL-37; limited toxicity; and an ability to inhibit LPS-induced proinflammatory effects which is comparable to that of "the last resource" antibiotic colistin. We further studied the interaction of P13#1 with SDS, LPSs and bacterial cells by using a fluorescent version of P13#1. Finally, in a subcutaneous infection mouse model, it showed antimicrobial and anti-inflammatory activities comparable to ampicillin and gentamicin without apparent toxicity. The collected data indicate that P13#1 is an excellent candidate for the formulation of new antimicrobial therapies.
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Affiliation(s)
- Valeria Cafaro
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (V.C.); (A.B.); (I.D.N.); (M.S.); (R.C.); (N.D.); (E.P.)
| | - Andrea Bosso
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (V.C.); (A.B.); (I.D.N.); (M.S.); (R.C.); (N.D.); (E.P.)
| | - Ilaria Di Nardo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (V.C.); (A.B.); (I.D.N.); (M.S.); (R.C.); (N.D.); (E.P.)
| | - Assunta D’Amato
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, 84084 Fisciano, Italy; (A.D.); (I.I.); (F.D.R.)
| | - Irene Izzo
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, 84084 Fisciano, Italy; (A.D.); (I.I.); (F.D.R.)
| | - Francesco De Riccardis
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, 84084 Fisciano, Italy; (A.D.); (I.I.); (F.D.R.)
| | - Marialuisa Siepi
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (V.C.); (A.B.); (I.D.N.); (M.S.); (R.C.); (N.D.); (E.P.)
| | - Rosanna Culurciello
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (V.C.); (A.B.); (I.D.N.); (M.S.); (R.C.); (N.D.); (E.P.)
| | - Nunzia D’Urzo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (V.C.); (A.B.); (I.D.N.); (M.S.); (R.C.); (N.D.); (E.P.)
| | | | | | - Elio Pizzo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (V.C.); (A.B.); (I.D.N.); (M.S.); (R.C.); (N.D.); (E.P.)
| | - Marcello Merola
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (V.C.); (A.B.); (I.D.N.); (M.S.); (R.C.); (N.D.); (E.P.)
| | - Eugenio Notomista
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (V.C.); (A.B.); (I.D.N.); (M.S.); (R.C.); (N.D.); (E.P.)
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8
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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: 0.5] [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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9
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Gómez-Martínez J, Rocha-Gracia RDC, Bello-López E, Cevallos MA, Castañeda-Lucio M, Sáenz Y, Jiménez-Flores G, Cortés-Cortés G, López-García A, Lozano-Zarain P. Comparative Genomics of Pseudomonas aeruginosa Strains Isolated from Different Ecological Niches. Antibiotics (Basel) 2023; 12:antibiotics12050866. [PMID: 37237769 DOI: 10.3390/antibiotics12050866] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
The Pseudomonas aeruginosa genome can change to adapt to different ecological niches. We compared four genomes from a Mexican hospital and 59 genomes from GenBank from different niches, such as urine, sputum, and environmental. The ST analysis showed that high-risk STs (ST235, ST773, and ST27) were present in the genomes of the three niches from GenBank, and the STs of Mexican genomes (ST167, ST2731, and ST549) differed from the GenBank genomes. Phylogenetic analysis showed that the genomes were clustering according to their ST and not their niche. When analyzing the genomic content, we observed that environmental genomes had genes involved in adapting to the environment not found in the clinics and that their mechanisms of resistance were mutations in antibiotic resistance-related genes. In contrast, clinical genomes from GenBank had resistance genes, in mobile/mobilizable genetic elements in the chromosome, except for the Mexican genomes that carried them mostly in plasmids. This was related to the presence of CRISPR-Cas and anti-CRISPR; however, Mexican strains only had plasmids and CRISPR-Cas. blaOXA-488 (a variant of blaOXA50) with higher activity against carbapenems was more prevalent in sputum genomes. The virulome analysis showed that exoS was most prevalent in the genomes of urinary samples and exoU and pldA in sputum samples. This study provides evidence regarding the genetic variability among P. aeruginosa isolated from different niches.
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Affiliation(s)
- Jessica Gómez-Martínez
- Posgrado en Microbiología, Centro de Investigaciones de Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - Rosa Del Carmen Rocha-Gracia
- Posgrado en Microbiología, Centro de Investigaciones de Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - Elena Bello-López
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Miguel Angel Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Miguel Castañeda-Lucio
- Posgrado en Microbiología, Centro de Investigaciones de Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - Yolanda Sáenz
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Guadalupe Jiménez-Flores
- Laboratorio Clínico, Área de Microbiología, Hospital Regional Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Puebla 72570, Mexico
| | - Gerardo Cortés-Cortés
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alma López-García
- Posgrado en Microbiología, Centro de Investigaciones de Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - Patricia Lozano-Zarain
- Posgrado en Microbiología, Centro de Investigaciones de Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
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Mutual Effects of Single and Combined CFTR Modulators and Bacterial Infection in Cystic Fibrosis. Microbiol Spectr 2023; 11:e0408322. [PMID: 36625583 PMCID: PMC9927584 DOI: 10.1128/spectrum.04083-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) modulators improve clinical outcomes with varied efficacies in patients with CF. However, the mutual effects of CFTR modulators and bacterial adaptation, together with antibiotic regimens, can influence clinical outcomes. We evaluated the effects of ivacaftor (IVA), lumacaftor (LUM), tezacaftor, elexacaftor, and a three-modulator combination of elexacaftor, tezacaftor, and ivacaftor (ETI), alone or combined with antibiotics, on sequential CF isolates. IVA and ETI showed direct antimicrobial activities against Staphylococcus aureus but not against Pseudomonas aeruginosa. Additive effects or synergies were observed between the CFTR modulators and antibiotics against both species, independently of adaptation to the CF lung. IVA and LUM were the most effective in potentiating antibiotic activity against S. aureus, while IVA and ETI enhanced mainly polymyxin activity against P. aeruginosa. Next, we evaluated the effect of P. aeruginosa pneumonia on the pharmacokinetics of IVA in mice. IVA and its metabolites in plasma, lung, and epithelial lining fluid were increased by P. aeruginosa infection. Thus, CFTR modulators can have direct antimicrobial properties and/or enhance antibiotic activity against initial and adapted S. aureus and P. aeruginosa isolates. Furthermore, bacterial infection impacts airway exposure to IVA, potentially affecting its efficacy. Our findings suggest optimizing host- and pathogen-directed therapies to improve efficacy for personalized treatment. IMPORTANCE CFTR modulators have been developed to correct and/or enhance CFTR activity in patients with specific cystic fibrosis (CF) genotypes. However, it is of great importance to identify potential off-targets of these novel therapies to understand how they affect lung physiology in CF. Since bacterial infections are one of the hallmarks of CF lung disease, the effects (if any) of CFTR modulators on bacteria could impact their efficacy. This work highlights a mutual interaction between CFTR modulators and opportunistic bacterial infections; in particular, it shows that (i) CFTR modulators have an antibacterial activity per se and influence antibiotic efficacy, and (ii) bacterial airway infections affect levels of CFTR modulators in the airways. These findings may help optimize host- and pathogen-directed drug regimens to improve the efficacy of personalized treatment.
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11
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Hamed MM, Abdelsamie AS, Rox K, Schütz C, Kany AM, Röhrig T, Schmelz S, Blankenfeldt W, Arce‐Rodriguez A, Borrero‐de Acuña JM, Jahn D, Rademacher J, Ringshausen FC, Cramer N, Tümmler B, Hirsch AKH, Hartmann RW, Empting M. Towards Translation of PqsR Inverse Agonists: From In Vitro Efficacy Optimization to In Vivo Proof-of-Principle. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204443. [PMID: 36596691 PMCID: PMC9929129 DOI: 10.1002/advs.202204443] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Pseudomonas aeruginosa (PA) is an opportunistic human pathogen, which is involved in a wide range of dangerous infections. It develops alarming resistances toward antibiotic treatment. Therefore, alternative strategies, which suppress pathogenicity or synergize with antibiotic treatments are in great need to combat these infections more effectively. One promising approach is to disarm the bacteria by interfering with their quorum sensing (QS) system, which regulates the release of various virulence factors as well as biofilm formation. Herein, this work reports the rational design, optimization, and in-depth profiling of a new class of Pseudomonas quinolone signaling receptor (PqsR) inverse agonists. The resulting frontrunner compound features a pyrimidine-based scaffold, high in vitro and in vivo efficacy, favorable pharmacokinetics as well as clean safety pharmacology characteristics, which provide the basis for potential pulmonary as well as systemic routes of administration. An X-ray crystal structure in complex with PqsR facilitated further structure-guided lead optimization. The compound demonstrates potent pyocyanin suppression, synergizes with aminoglycoside antibiotic tobramycin against PA biofilms, and is active against a panel of clinical isolates from bronchiectasis patients. Importantly, this in vitro effect translated into in vivo efficacy in a neutropenic thigh infection model in mice providing a proof-of-principle for adjunctive treatment scenarios.
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Affiliation(s)
- Mostafa M. Hamed
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
| | - Ahmed S. Abdelsamie
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
- Department of Chemistry of Natural and Microbial ProductsInstitute of Pharmaceutical and Drug Industries ResearchNational Research CentreEl‐Buhouth St.DokkiCairo12622Egypt
| | - Katharina Rox
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
- Department of Chemical Biology (CBIO)Helmholtz Centre for Infection Research (HZI)Inhoffenstr. 7 Braunschweig38124SaarbrückenGermany
| | - Christian Schütz
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
| | - Andreas M. Kany
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
| | - Teresa Röhrig
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
| | - Stefan Schmelz
- Department of Structure and Function of Proteins (SFPR)Helmholtz Centre for Infection Research (HZI)Inhoffenstr. 7 Braunschweig38124SaarbrückenGermany
| | - Wulf Blankenfeldt
- Department of Structure and Function of Proteins (SFPR)Helmholtz Centre for Infection Research (HZI)Inhoffenstr. 7 Braunschweig38124SaarbrückenGermany
- Institute for BiochemistryBiotechnology and BioinformaticsTechnische Universität BraunschweigBraunschweigGermany
| | | | - José Manuel Borrero‐de Acuña
- Institute of MicrobiologyTechnische Universität Braunschweig38106BraunschweigGermany
- Braunschweig Integrated Centre of Systems Biology (BRICS)Technische Universität Braunschweig38106BraunschweigGermany
- Departamento de MicrobiologíaFacultad de BiologíaUniversidad de SevillaAv. de la Reina Mercedesno. 6SevillaCP 41012Spain
| | - Dieter Jahn
- Institute of MicrobiologyTechnische Universität Braunschweig38106BraunschweigGermany
- Braunschweig Integrated Centre of Systems Biology (BRICS)Technische Universität Braunschweig38106BraunschweigGermany
| | - Jessica Rademacher
- Department for Respiratory MedicineMedizinische Hochschule HannoverCarl‐Neuberg‐Str. 130625HannoverGermany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH)German Center for Lung Research (DZL)30625HannoverGermany
| | - Felix C. Ringshausen
- Department for Respiratory MedicineMedizinische Hochschule HannoverCarl‐Neuberg‐Str. 130625HannoverGermany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH)German Center for Lung Research (DZL)30625HannoverGermany
- European Reference Network on Rare and Complex Respiratory Diseases (ERN‐ LUNG)FrankfurtGermany
| | - Nina Cramer
- Department for Pediatric PneumologyAllergology and NeonatologyMedizinische Hochschule HannoverCarl‐Neuberg‐Str. 130625HannoverGermany
| | - Burkhard Tümmler
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH)German Center for Lung Research (DZL)30625HannoverGermany
- Department for Pediatric PneumologyAllergology and NeonatologyMedizinische Hochschule HannoverCarl‐Neuberg‐Str. 130625HannoverGermany
| | - Anna K. H. Hirsch
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
- Department of PharmacySaarland University Campus E8.166123SaarbrückenGermany
| | - Rolf W. Hartmann
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
- Department of PharmacySaarland University Campus E8.166123SaarbrückenGermany
| | - Martin Empting
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
- Department of PharmacySaarland University Campus E8.166123SaarbrückenGermany
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12
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Di Bonaventura G, Lupetti V, Verginelli F, Giancristofaro S, Barbieri R, Gherardi G, Pompilio A. Repurposing the Veterinary Antibiotic Apramycin for Antibacterial and Antibiofilm Activity Against Pseudomonas aeruginosa From Cystic Fibrosis Patients. Front Microbiol 2022; 12:801152. [PMID: 35185826 PMCID: PMC8851335 DOI: 10.3389/fmicb.2021.801152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/10/2021] [Indexed: 11/13/2022] Open
Abstract
Objectives: To evaluate the in vitro antibacterial, antibiofilm, and antivirulence activities of apramycin, comparatively to tobramycin, against a set of P. aeruginosa from chronically infected cystic fibrosis (CF) patients. Methods The activity of antibiotics against planktonic cells was assessed by performing MIC, MBC, and time-kill assays. The activity against mature biofilms was evaluated, in a microtiter plate, both in terms of dispersion (crystal violet assay) and residual viability (viable cell count). The effect of drug exposure on selected P. aeruginosa virulence genes expression was assessed by real-time Reverse Transcription quantitative PCR (RT-qPCR). Results Apramycin MIC90 and MBC90 values were found at least fourfold lower than those for tobramycin. A comparable trend was observed for mucoid strains. Only 4 out of 24 strains (16.6%) showed an apramycin MIC higher than the epidemiological cut-off value of 64 mg/L, whereas a higher resistance rate was observed for tobramycin (62.5%; p < 0.01 vs. apramycin). In time-kill analyses, both aminoglycosides were found bactericidal, although apramycin showed a more rapid effect and did not allow for regrowth. Apramycin generally stimulated biofilm biomass formation, whereas tobramycin showed opposite trends depending on the strain tested. Both drugs caused a highly significant, dose-dependent reduction of biofilm viability, regardless of strain and concentration tested. The exposure to apramycin and tobramycin caused increased expression of mexA and mexC (multidrug efflux pumps), whereas tobramycin specifically increased the expression of aprA (alkaline protease) and toxA (exotoxin A). Neither apramycin nor tobramycin showed cytotoxic potential toward IB3-1 bronchial epithelial CF cells. Conclusion Our results warrant future pharmacokinetic and pharmacodynamic studies for supporting the rationale to repurpose apramycin, a veterinary aminoglycoside, for CF lung infections.
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Affiliation(s)
- Giovanni Di Bonaventura
- Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
- Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
- *Correspondence: Giovanni Di Bonaventura,
| | - Veronica Lupetti
- Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
- Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Fabio Verginelli
- Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
- Department of Pharmacy, “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
- Fabio Verginelli,
| | - Sara Giancristofaro
- Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
- Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
- Department of Infectious Disease, Istituto Superiore di Sanità, Rome, Italy
| | - Rosemary Barbieri
- Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
- Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
| | | | - Arianna Pompilio
- Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
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13
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Mixed Populations and Co-Infection: Pseudomonas aeruginosa and Staphylococcus aureus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:397-424. [DOI: 10.1007/978-3-031-08491-1_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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14
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Ferrara S, Carrubba R, Santoro S, Bertoni G. The Small RNA ErsA Impacts the Anaerobic Metabolism of Pseudomonas aeruginosa Through Post-Transcriptional Modulation of the Master Regulator Anr. Front Microbiol 2021; 12:691608. [PMID: 34759894 PMCID: PMC8575079 DOI: 10.3389/fmicb.2021.691608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/27/2021] [Indexed: 01/05/2023] Open
Abstract
Pseudomonas aeruginosa is one of the most critical opportunistic pathogens in humans, able to cause both lethal acute and chronic lung infections. In previous work, we indicated that the small RNA ErsA plays a role in the regulatory network of P. aeruginosa pathogenicity in airways infection. To give further insight into the lifestyle functions that could be either directly or indirectly regulated by ErsA during infection, we reanalyzed the categories of genes whose transcription appeared dysregulated in an ersA knock-out mutant of the P. aeruginosa PAO1 reference strain. This preliminary analysis indicated ErsA as a candidate co-modulator of denitrification and in general, the anaerobiosis response, a characteristic physiologic state of P. aeruginosa during chronic infection of the lung of cystic fibrosis (CF) patients. To explain the pattern of dysregulation of the anaerobic-lifestyle genes in the lack of ErsA, we postulated that ErsA regulation could target the expression of Anr, a well-known transcription factor that modulates a broad regulon of anoxia-responsive genes, and also Dnr, required for the transcription activation of the denitrification machinery. Our results show that ErsA positively regulates Anr expression at the post-transcriptional level while no direct ErsA-mediated regulatory effect on Dnr was observed. However, Dnr is transcriptionally downregulated in the absence of ErsA and this is consistent with the well-characterized regulatory link between Anr and Dnr. Anr regulatory function is critical for P. aeruginosa anaerobic growth, both through denitrification and fermentation of arginine. Interestingly, we found that, differently from the laboratory strain PAO1, ErsA deletion strongly impairs the anaerobic growth by both denitrification and arginine fermentation of the RP73 clinical isolate, a multi-drug resistant P. aeruginosa CF-adapted strain. This suggests that P. aeruginosa adaptation to CF lung might result in a higher dependence on ErsA for the transduction of the multiple signals to the regulatory network of key functions for survivance in such a complex environment. Together, our results suggest that ErsA takes an upper place in the regulatory network of airways infection, transducing host inputs to biofilm-related factors, as underlined in our previous reports, and to functions that allow P. aeruginosa to thrive in low-oxygen conditions.
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Affiliation(s)
- Silvia Ferrara
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Riccardo Carrubba
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Silvia Santoro
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Giovanni Bertoni
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
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15
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Effect of iron chelation on anti-pseudomonal activity of doxycycline. Int J Antimicrob Agents 2021; 58:106438. [PMID: 34547423 PMCID: PMC8617590 DOI: 10.1016/j.ijantimicag.2021.106438] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/09/2021] [Accepted: 09/12/2021] [Indexed: 11/20/2022]
Abstract
High affinity iron chelation enhances the antibacterial activity of tetracyclines. High affinity iron chelation synergises with doxycycline against P. aeruginosa. Doxycycline chelates iron and loses antibacterial activity. Iron chelation re-establishes the susceptibility of iron bound doxycycline. Iron chelation enhances doxycycline activity in a biofilm setting.
Background Increasing resistance of microorganisms to antimicrobial agents is a growing concern and there is a lack of novel agents. This has stimulated the exploration of novel strategies for treatment of infection. Objective To investigate synergistic interactions between five tetracyclines and tobramycin with an iron chelator (CP762) against two reference strains and nine clinical isolates of Pseudomonas aeruginosa from cystic fibrosis patients. Method Microdilution assays for minimal inhibitory concentration determination and checkerboard assays were used to assess synergy between antibiotics and CP762. Given the iron-binding capacity of tetracyclines, the binding of iron with doxycycline was investigated using Job's plot methodology. Synergy between the iron-bound form of doxycycline and CP762 was compared with that of unbound doxycycline and CP762. Enhancement of doxycycline anti-biofilm activity was also assessed. Results There was synergy between CP762 and all tetracyclines, except minocycline, against the reference strains but that against clinical isolates was variable. Synergy was not demonstrated for tobramycin against any of the strains tested. This led to the hypothesis that iron chelation preserves the binding of tetracyclines to the bacterial ribosome. Susceptibility to iron-bound doxycycline was decreased by two- to four-fold and synergistic interactions with the iron chelator were consistently more intense with iron-bound doxycycline than with doxycycline alone. The doxycycline–iron chelator combination also significantly reduced cell viability in established biofilms. Conclusion The data in this study provide evidence that iron chelation enhances the anti-pseudomonal activity of tetracyclines, specifically doxycycline.
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16
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Jurado-Martín I, Sainz-Mejías M, McClean S. Pseudomonas aeruginosa: An Audacious Pathogen with an Adaptable Arsenal of Virulence Factors. Int J Mol Sci 2021; 22:3128. [PMID: 33803907 PMCID: PMC8003266 DOI: 10.3390/ijms22063128] [Citation(s) in RCA: 328] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa is a dominant pathogen in people with cystic fibrosis (CF) contributing to morbidity and mortality. Its tremendous ability to adapt greatly facilitates its capacity to cause chronic infections. The adaptability and flexibility of the pathogen are afforded by the extensive number of virulence factors it has at its disposal, providing P. aeruginosa with the facility to tailor its response against the different stressors in the environment. A deep understanding of these virulence mechanisms is crucial for the design of therapeutic strategies and vaccines against this multi-resistant pathogen. Therefore, this review describes the main virulence factors of P. aeruginosa and the adaptations it undergoes to persist in hostile environments such as the CF respiratory tract. The very large P. aeruginosa genome (5 to 7 MB) contributes considerably to its adaptive capacity; consequently, genomic studies have provided significant insights into elucidating P. aeruginosa evolution and its interactions with the host throughout the course of infection.
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Affiliation(s)
| | | | - Siobhán McClean
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin 4 D04 V1W8, Ireland; (I.J.-M.); (M.S.-M.)
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17
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Abstract
Within-host adaptation is a hallmark of chronic bacterial infections, involving substantial genomic changes. Recent large-scale genomic data from prolonged infections allow the examination of adaptive strategies employed by different pathogens and open the door to investigate whether they converge toward similar strategies. Here, we compiled extensive data of whole-genome sequences of bacterial isolates belonging to miscellaneous species sampled at sequential time points during clinical infections. Analysis of these data revealed that different species share some common adaptive strategies, achieved by mutating various genes. Although the same genes were often mutated in several strains within a species, different genes related to the same pathway, structure, or function were changed in other species utilizing the same adaptive strategy (e.g., mutating flagellar genes). Strategies exploited by various bacterial species were often predicted to be driven by the host immune system, a powerful selective pressure that is not species specific. Remarkably, we find adaptive strategies identified previously within single species to be ubiquitous. Two striking examples are shifts from siderophore-based to heme-based iron scavenging (previously shown for Pseudomonas aeruginosa) and changes in glycerol-phosphate metabolism (previously shown to decrease sensitivity to antibiotics in Mycobacterium tuberculosis). Virulence factors were often adaptively affected in different species, indicating shifts from acute to chronic virulence and virulence attenuation during infection. Our study presents a global view on common within-host adaptive strategies employed by different bacterial species and provides a rich resource for further studying these processes.
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Affiliation(s)
- Yair E Gatt
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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18
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Camus L, Briaud P, Vandenesch F, Moreau K. How Bacterial Adaptation to Cystic Fibrosis Environment Shapes Interactions Between Pseudomonas aeruginosa and Staphylococcus aureus. Front Microbiol 2021; 12:617784. [PMID: 33746915 PMCID: PMC7966511 DOI: 10.3389/fmicb.2021.617784] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/10/2021] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa and Staphylococcus aureus are the two most prevalent bacteria species in the lungs of cystic fibrosis (CF) patients and are associated with poor clinical outcomes. Co-infection by the two species is a frequent situation that promotes their interaction. The ability of P. aeruginosa to outperform S. aureus has been widely described, and this competitive interaction was, for a long time, the only one considered. More recently, several studies have described that the two species are able to coexist. This change in relationship is linked to the evolution of bacterial strains in the lungs. This review attempts to decipher how bacterial adaptation to the CF environment can induce a change in the type of interaction and promote coexisting interaction between P. aeruginosa and S. aureus. The impact of coexistence on the establishment and maintenance of a chronic infection will also be presented, by considering the latest research on the subject.
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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 UMR 5308/ENS de Lyon, Lyon, France
| | - Paul Briaud
- CIRI-Centre International de Recherche en Infectiologie, Université de Lyon/Inserm U1111/Université Claude Bernard Lyon 1/CNRS UMR 5308/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 UMR 5308/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 UMR 5308/ENS de Lyon, Lyon, France
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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: 30] [Impact Index Per Article: 7.5] [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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Cigana C, Castandet J, Sprynski N, Melessike M, Beyria L, Ranucci S, Alcalá-Franco B, Rossi A, Bragonzi A, Zalacain M, Everett M. Pseudomonas aeruginosa Elastase Contributes to the Establishment of Chronic Lung Colonization and Modulates the Immune Response in a Murine Model. Front Microbiol 2021; 11:620819. [PMID: 33510733 PMCID: PMC7836092 DOI: 10.3389/fmicb.2020.620819] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
Chronic infection by Pseudomonas aeruginosa in cystic fibrosis (CF) patients is a major contributor to progressive lung damage and is poorly treated by available antibiotic therapy. An alternative approach to the development of additional antibiotic treatments is to identify complementary therapies which target bacterial virulence factors necessary for the establishment and/or maintenance of the chronic infection. The P. aeruginosa elastase (LasB) has been suggested as an attractive anti-virulence target due to its extracellular location, its harmful degradative effects on host tissues and the immune system, and the potential to inhibit its activity using small molecule inhibitors. However, while the relevance of LasB in acute P. aeruginosa infection has been demonstrated, it is still unclear whether this elastase might also play a role in the early phase of chronic lung colonization. By analyzing clinical P. aeruginosa clonal isolates from a CF patient, we found that the isolate RP45, collected in the early phase of persistence, produces large amounts of active LasB, while its clonal variant RP73, collected after years of colonization, does not produce it. When a mouse model of persistent pneumonia was used, deletion of the lasB gene in RP45 resulted in a significant reduction in mean bacterial numbers and incidence of chronic lung colonization at Day 7 post-challenge compared to those mice infected with wild-type (wt) RP45. Furthermore, deletion of lasB in strain RP45 also resulted in an increase in immunomodulators associated with innate and adaptive immune responses in infected animals. In contrast, deletion of the lasB gene in RP73 did not affect the establishment of chronic infection. Overall, these results indicate that LasB contributes to the adaptation of P. aeruginosa to a persistent lifestyle. In addition, these findings support pharmacological inhibition of LasB as a potentially useful therapeutic intervention for P. aeruginosa-infected CF patients prior to the establishment of a chronic infection.
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Affiliation(s)
- Cristina Cigana
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | | | - Medede Melessike
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Serena Ranucci
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Nurix Therapeutics, San Francisco, CA, United States
| | - Beatriz Alcalá-Franco
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alice Rossi
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandra Bragonzi
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
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21
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Sainz-Mejías M, Jurado-Martín I, McClean S. Understanding Pseudomonas aeruginosa-Host Interactions: The Ongoing Quest for an Efficacious Vaccine. Cells 2020; 9:cells9122617. [PMID: 33291484 PMCID: PMC7762141 DOI: 10.3390/cells9122617] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/18/2022] Open
Abstract
Pseudomonas aeruginosa is a leading cause of chronic respiratory infections in people with cystic fibrosis (CF), bronchiectasis or chronic obstructive pulmonary disease (COPD), and acute infections in immunocompromised individuals. The adaptability of this opportunistic pathogen has hampered the development of antimicrobial therapies, and consequently, it remains a major threat to public health. Due to its antimicrobial resistance, vaccines represent an alternative strategy to tackle the pathogen, yet despite over 50 years of research on anti-Pseudomonas vaccines, no vaccine has been licensed. Nevertheless, there have been many advances in this field, including a better understanding of the host immune response and the biology of P. aeruginosa. Multiple antigens and adjuvants have been investigated with varying results. Although the most effective protective response remains to be established, it is clear that a polarised Th2 response is sub-optimal, and a mixed Th1/Th2 or Th1/Th17 response appears beneficial. This comprehensive review collates the current understanding of the complexities of P. aeruginosa-host interactions and its implication in vaccine design, with a view to understanding the current state of Pseudomonal vaccine development and the direction of future efforts. It highlights the importance of the incorporation of appropriate adjuvants to the protective antigen to yield optimal protection.
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22
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Comparative genomics of the sequential Pseudomonas aeruginosa isolates obtained from the continuous imipenem stress evolution. Appl Microbiol Biotechnol 2020; 104:10655-10667. [PMID: 33151366 DOI: 10.1007/s00253-020-10994-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/29/2020] [Accepted: 10/31/2020] [Indexed: 12/24/2022]
Abstract
Pseudomonas aeruginosa is a major opportunistic human pathogen that causes nosocomial infections, and the proportion of carbapenem resistance has recently dramatically increased in P. aeruginosa due to the overuse of them. In this study, strains G10 and G20, with minimum inhibitory concentration (MIC) of imipenem of 16 μg/ml and more than 32 μg/ml, were isolated during continuous subculture of cells exposed to stepwise increasing concentrations of imipenem, respectively. The genomes of G10 and G20 were sequenced and compared with parental strain (P. aeruginosa ATCC 27853, G0). There were 59, 59, and 58 genes involved in antibiotic resistance which were predicted in G0, G10, and G20, respectively, while 374, 366, and 363 genes involved in virulence factors were identified among these three strains. Due to the significantly different MICs of imipenem and highly similar profiles of antibiotic resistance and virulence factors related genes among three strains, the specific genetic variations that occurred were identified and compared, including single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), and structural variations (SVs). The increase in the MIC of imipenem was proposed to be linked to mutations involved in polyamine biosynthesis, biofilm formation, OprD, and efflux pump functions. This study aims to clarify the underlying mechanism of imipenem resistance and provide alternative strategies for reducing resistance in P. aeruginosa. KEY POINTS: • Strains with different imipenem MIC were obtained via laboratory selection evolution. • Whole genomes of two strains with different MIC of imipenem were sequenced. • Underlying mechanism of imipenem resistance was clarified via comparative genomics.
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23
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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: 22] [Impact Index Per Article: 4.4] [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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24
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The Small RNA ErsA Plays a Role in the Regulatory Network of Pseudomonas aeruginosa Pathogenicity in Airway Infections. mSphere 2020; 5:5/5/e00909-20. [PMID: 33055260 PMCID: PMC7565897 DOI: 10.1128/msphere.00909-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial small RNAs play a remarkable role in the regulation of functions involved in host-pathogen interaction. ErsA is a small RNA of Pseudomonas aeruginosa that contributes to the regulation of bacterial virulence traits such as biofilm formation and motility. Shown to take part in a regulatory circuit under the control of the envelope stress response sigma factor σ22, ErsA targets posttranscriptionally the key virulence-associated gene algC Moreover, ErsA contributes to biofilm development and motility through the posttranscriptional modulation of the transcription factor AmrZ. Intending to evaluate the regulatory relevance of ErsA in the pathogenesis of respiratory infections, we analyzed the impact of ErsA-mediated regulation on the virulence potential of P. aeruginosa and the stimulation of the inflammatory response during the infection of bronchial epithelial cells and a murine model. Furthermore, we assessed ErsA expression in a collection of P. aeruginosa clinical pulmonary isolates and investigated the link of ErsA with acquired antibiotic resistance by generating an ersA gene deletion mutant in a multidrug-resistant P. aeruginosa strain which has long been adapted in the airways of a cystic fibrosis (CF) patient. Our results show that the ErsA-mediated regulation is relevant for the P. aeruginosa pathogenicity during acute infection and contributes to the stimulation of the host inflammatory response. Besides, ErsA was able to be subjected to selective pressure for P. aeruginosa pathoadaptation and acquirement of resistance to antibiotics commonly used in clinical practice during chronic CF infections. Our findings establish the role of ErsA as an important regulatory element in the host-pathogen interaction.IMPORTANCE Pseudomonas aeruginosa is one of the most critical multidrug-resistant opportunistic pathogens in humans, able to cause both lethal acute and chronic lung infections. Thorough knowledge of the regulatory mechanisms involved in the establishment and persistence of the airways infections by P. aeruginosa remains elusive. Emerging candidates as molecular regulators of pathogenesis in P. aeruginosa are small RNAs, which act posttranscriptionally as signal transducers of host cues. Known for being involved in the regulation of biofilm formation and responsive to envelope stress response, we show that the small RNA ErsA can play regulatory roles in acute infection, stimulation of host inflammatory response, and mechanisms of acquirement of antibiotic resistance and adaptation during the chronic lung infections of cystic fibrosis patients. Elucidating the complexity of the networks regulating host-pathogen interactions is crucial to identify novel targets for future therapeutic applications.
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25
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Fodor A, Abate BA, Deák P, Fodor L, Gyenge E, Klein MG, Koncz Z, Muvevi J, Ötvös L, Székely G, Vozik D, Makrai L. Multidrug Resistance (MDR) and Collateral Sensitivity in Bacteria, with Special Attention to Genetic and Evolutionary Aspects and to the Perspectives of Antimicrobial Peptides-A Review. Pathogens 2020; 9:pathogens9070522. [PMID: 32610480 PMCID: PMC7399985 DOI: 10.3390/pathogens9070522] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/18/2022] Open
Abstract
Antibiotic poly-resistance (multidrug-, extreme-, and pan-drug resistance) is controlled by adaptive evolution. Darwinian and Lamarckian interpretations of resistance evolution are discussed. Arguments for, and against, pessimistic forecasts on a fatal “post-antibiotic era” are evaluated. In commensal niches, the appearance of a new antibiotic resistance often reduces fitness, but compensatory mutations may counteract this tendency. The appearance of new antibiotic resistance is frequently accompanied by a collateral sensitivity to other resistances. Organisms with an expanding open pan-genome, such as Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, can withstand an increased number of resistances by exploiting their evolutionary plasticity and disseminating clonally or poly-clonally. Multidrug-resistant pathogen clones can become predominant under antibiotic stress conditions but, under the influence of negative frequency-dependent selection, are prevented from rising to dominance in a population in a commensal niche. Antimicrobial peptides have a great potential to combat multidrug resistance, since antibiotic-resistant bacteria have shown a high frequency of collateral sensitivity to antimicrobial peptides. In addition, the mobility patterns of antibiotic resistance, and antimicrobial peptide resistance, genes are completely different. The integron trade in commensal niches is fortunately limited by the species-specificity of resistance genes. Hence, we theorize that the suggested post-antibiotic era has not yet come, and indeed might never come.
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Affiliation(s)
- András Fodor
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary;
- Correspondence: or (A.F.); (L.M.); Tel.: +36-(30)-490-9294 (A.F.); +36-(30)-271-2513 (L.M.)
| | - Birhan Addisie Abate
- Ethiopian Biotechnology Institute, Agricultural Biotechnology Directorate, Addis Ababa 5954, Ethiopia;
| | - Péter Deák
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary;
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary
| | - László Fodor
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, P.O. Box 22, H-1581 Budapest, Hungary;
| | - Ervin Gyenge
- Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania; (E.G.); (G.S.)
- Institute for Research-Development-Innovation in Applied Natural Sciences, Babeș-Bolyai University, 30 Fântânele St., 400294 Cluj-Napoca, Romania
| | - Michael G. Klein
- Department of Entomology, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691, USA;
| | - Zsuzsanna Koncz
- Max-Planck Institut für Pflanzenzüchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Köln, Germany;
| | | | - László Ötvös
- OLPE, LLC, Audubon, PA 19403-1965, USA;
- Institute of Medical Microbiology, Semmelweis University, H-1085 Budapest, Hungary
- Arrevus, Inc., Raleigh, NC 27612, USA
| | - Gyöngyi Székely
- Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania; (E.G.); (G.S.)
- Institute for Research-Development-Innovation in Applied Natural Sciences, Babeș-Bolyai University, 30 Fântânele St., 400294 Cluj-Napoca, Romania
- Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania
| | - Dávid Vozik
- Research Institute on Bioengineering, Membrane Technology and Energetics, Faculty of Engineering, University of Veszprem, H-8200 Veszprém, Hungary; or or
| | - László Makrai
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, P.O. Box 22, H-1581 Budapest, Hungary;
- Correspondence: or (A.F.); (L.M.); Tel.: +36-(30)-490-9294 (A.F.); +36-(30)-271-2513 (L.M.)
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26
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Cigana C, Ranucci S, Rossi A, De Fino I, Melessike M, Bragonzi A. Antibiotic efficacy varies based on the infection model and treatment regimen for Pseudomonas aeruginosa. Eur Respir J 2020; 55:13993003.02456-2018. [PMID: 31624114 PMCID: PMC7057181 DOI: 10.1183/13993003.02456-2018] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 10/10/2019] [Indexed: 12/14/2022]
Abstract
Antibiotic discovery and preclinical testing are needed to combat the Pseudomonas aeruginosa health threat. Most frequently, antibiotic efficacy is tested in models of acute respiratory infection, with chronic pneumonia remaining largely unexplored. This approach generates serious concerns about the evaluation of treatment for chronically infected patients, and highlights the need for animal models that mimic the course of human disease. In this study, the efficacy of the marketed antibacterial drugs tobramycin (TOB) and colistin (COL) was tested in murine models of acute and chronic P. aeruginosa pulmonary infection. Different administration routes (intranasal, aerosol or subcutaneous) and treatment schedules (soon or 7 days post-infection) were tested. In the acute infection model, aerosol and subcutaneous administration of TOB reduced the bacterial burden and inflammatory response, while intranasal treatment showed modest efficacy. COL reduced the bacterial burden less effectively but dampened inflammation. Mice treated soon after chronic infection for 7 days with daily aerosol or subcutaneous administration of TOB showed higher and more rapid body weight recovery and reduced bacterial burden and inflammation than vehicle-treated mice. COL-treated mice showed no improvement in body weight or change in inflammation. Modest bacterial burden reduction was recorded only with aerosol COL administration. When treatment for chronic infection was commenced 7 days after infection, both TOB and COL failed to reduce P. aeruginosa burden and inflammation, or aid in recovery of body weight. Our findings suggest that the animal model and treatment regimen should be carefully chosen based on the type of infection to assess antibiotic efficacy. Disease-specific animal models and treatment regimens are essential in order to optimise anti-Pseudomonas drug testinghttp://bit.ly/2ISfBiB
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Affiliation(s)
- Cristina Cigana
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milano, Italy.,Both authors contributed equally and share senior authorship
| | - Serena Ranucci
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Alice Rossi
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Ida De Fino
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Medede Melessike
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Alessandra Bragonzi
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milano, Italy .,Both authors contributed equally and share senior authorship
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27
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Skariyachan S, Gopal D, Kadam SP, Muddebihalkar AG, Uttarkar A, Niranjan V. Carbon fullerene acts as potential lead molecule against prospective molecular targets of biofilm-producing multidrug-resistant Acinetobacter baumanni and Pseudomonas aerugenosa: computational modeling and MD simulation studies. J Biomol Struct Dyn 2020; 39:1121-1137. [PMID: 32036742 DOI: 10.1080/07391102.2020.1726821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
This study aimed to screen putative drug targets associated with biofilm formation of multidrug-resistant Acinetobacter baumannii and Pseudomonas areugenosa and prioritize carbon nano-fullerene as potential lead molecule by structure-based virtual screening. Based on the functional role, 36 and 83 genes that are involved in biofilm formation of A. baumannii and P. areugenosa respectively were selected and metabolic network was computationally constructed. The genes that lack three-dimensional structures were predicted and validated. Carbon nano-fullerene selected as lead molecule and their drug-likeliness and pharmacokinetics properties were computationally predicted. The binding potential of carbon nano-fullerene toward selected drug targets was modeled and compared with the binding of conventional drugs, doripenem, and polymyxin-B with their usual targets. The stabilities of four best-docked complexes were confirmed by molecular dynamic (MD) simulation. This study suggested that selected genes demonstrated relevant interactions in the constructed metabolic pathways. Carbon fullerene exhibited significant binding abilities to most of the prioritized targets in comparison with the binding of last-resort antibiotics and their usual target. The four best ligand-receptor interactions predicted by molecular docking revealed that stability throughout MD simulation. Notably, carbon fullerene exhibited profound binding with outer membrane protein (OmpA) and ribonuclease-HII (rnhB) of A. baumannii and 2-heptyl-4(1H)-quinolone synthase (pqsBC) and chemotaxis protein (wspA) of P. aeruginosa. Thus, the current study suggested that carbon fullerene was probably used as potential lead molecules toward selected targets of A. baumannii and P. aeruginosa and the applied aspects probably scaled up to design promising lead molecules toward these pathogens. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sinosh Skariyachan
- Department of Microbiology, St. Pius X College, Rajapuram, Kasaragod, India
| | - Dharshini Gopal
- Department of Biotechnology, Dayananda Sagar College of Engineering, Bengaluru, India
| | - Sanjana Pratab Kadam
- Department of Biotechnology, Dayananda Sagar College of Engineering, Bengaluru, India
| | - Aditi G Muddebihalkar
- Department of Biotechnology, Dayananda Sagar College of Engineering, Bengaluru, India.,Department of Biotechnology, RV College of Engineering, Bengaluru, India
| | - Akshay Uttarkar
- Department of Biotechnology, RV College of Engineering, Bengaluru, India
| | - Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, Bengaluru, India
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28
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Amison RT, Faure ME, O'Shaughnessy BG, Bruce KD, Hu Y, Coates A, Page CP. The small quinolone derived compound HT61 enhances the effect of tobramycin against Pseudomonas aeruginosa in vitro and in vivo. Pulm Pharmacol Ther 2019; 61:101884. [PMID: 31887372 DOI: 10.1016/j.pupt.2019.101884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 12/25/2019] [Indexed: 11/26/2022]
Abstract
HT61 is a small quinolone-derived compound previously demonstrated to exhibit bactericidal activity against gram-positive bacteria including methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA). When combined with the classical antibiotics and antiseptics neomycin, gentamicin, mupirocin and chlorhexidine, HT61 demonstrated synergistic bactericidal activity against both MSSA and MRSA infections in vitro. In this study, we investigated the individual antimicrobial activity of HT61 alongside its capability to potentiate the efficacy of tobramycin against both a tobramycin sensitive laboratory reference strain (PAO1) and tobramycin resistant clinical isolates (RP73, NN2) of the gram-negative bacteria Pseudomonas aeruginosa (P. aeruginosa). Using broth microdilution methods, the MICs of HT61 were assessed against all strains, as well as the effect of HT61 in combination with tobramycin using both the chequerboard method and bacterial time-kill assays. A murine model of pulmonary infection was also used to evaluate the combination therapy of tobramycin and HT61 in vivo. In these studies, we demonstrated significant synergism between HT61 and tobramycin against the tobramycin resistant P. aeruginosa strains RP73 and NN2, whilst an additive/intermediate effect was observed for P. aeruginosa strain PA01 which was further confirmed using bacterial time kill analysis. In addition, the enhancement of tobramycin by HT61 was also evident in in vitro assays of biofilm eradication. Finally, in vivo studies revealed analogous effects to those observed in vitro with HT61 significantly reducing bacterial load when administered in combination with tobramycin against each of the three P. aeruginosa strains at the highest tested dose (10 mg/kg).
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Affiliation(s)
- R T Amison
- Sackler Institute of Pulmonary Pharmacology, School of Cancer and Pharmaceutical Sciences, King's College London, London, SE1 9NH, UK.
| | - M-E Faure
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE1 9NH, UK
| | - B G O'Shaughnessy
- Sackler Institute of Pulmonary Pharmacology, School of Cancer and Pharmaceutical Sciences, King's College London, London, SE1 9NH, UK
| | - K D Bruce
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE1 9NH, UK
| | - Y Hu
- Institute of Infection and Immunity, St George's, University of London, Cranmer Terrace, London, SW17 ORE, UK
| | - A Coates
- Institute of Infection and Immunity, St George's, University of London, Cranmer Terrace, London, SW17 ORE, UK
| | - C P Page
- Sackler Institute of Pulmonary Pharmacology, School of Cancer and Pharmaceutical Sciences, King's College London, London, SE1 9NH, UK
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29
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Maisetta G, Grassi L, Esin S, Kaya E, Morelli A, Puppi D, Piras M, Chiellini F, Pifferi M, Batoni G. Targeting Pseudomonas aeruginosa in the Sputum of Primary Ciliary Dyskinesia Patients with a Combinatorial Strategy Having Antibacterial and Anti-Virulence Potential. Int J Mol Sci 2019; 21:ijms21010069. [PMID: 31861859 PMCID: PMC6981532 DOI: 10.3390/ijms21010069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 12/16/2022] Open
Abstract
In primary ciliary dyskinesia (PCD) patients, Pseudomonas aeruginosa is a major opportunistic pathogen, frequently involved in chronic infections of the lower airways. Infections by this bacterial species correlates with a worsening clinical prognosis and recalcitrance to currently available therapeutics. The antimicrobial peptide, lin-SB056-1, in combination with the cation chelator ethylenediaminetetraacetic acid (EDTA), was previously demonstrated to be bactericidal against P. aeruginosa in an artificial sputum medium. The purpose of this study was to validate the anti-P. aeruginosa activity of such a combination in PCD sputum and to evaluate the in vitro anti-virulence effects of EDTA. In combination with EDTA, lin-SB056-1 was able to significantly reduce the load of endogenous P. aeruginosa ex vivo in the sputum of PCD patients. In addition, EDTA markedly reduced the production of relevant bacterial virulence factors (e.g., pyocyanin, proteases, LasA) in vitro by two representative mucoid strains of P. aeruginosa isolated from the sputum of PCD patients. These results indicate that the lin-SB056-1/EDTA combination may exert a dual antimicrobial and anti-virulence action against P. aeruginosa, suggesting a therapeutic potential against chronic airway infections sustained by this bacterium.
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Affiliation(s)
- Giuseppantonio Maisetta
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56123 Pisa, Italy; (L.G.); (S.E.); (E.K.); (G.B.)
- Correspondence: ; Tel.: +39-050-2213692; Fax: +39-050-2213711
| | - Lucia Grassi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56123 Pisa, Italy; (L.G.); (S.E.); (E.K.); (G.B.)
| | - Semih Esin
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56123 Pisa, Italy; (L.G.); (S.E.); (E.K.); (G.B.)
| | - Esingül Kaya
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56123 Pisa, Italy; (L.G.); (S.E.); (E.K.); (G.B.)
| | - Andrea Morelli
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy; (A.M.); (D.P.); (F.C.)
| | - Dario Puppi
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy; (A.M.); (D.P.); (F.C.)
| | - Martina Piras
- Section of Pneumology and Allergology, Unit of Pediatrics, Pisa University Hospital, 56126 Pisa, Italy; (M.P.); (M.P.)
| | - Federica Chiellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy; (A.M.); (D.P.); (F.C.)
| | - Massimo Pifferi
- Section of Pneumology and Allergology, Unit of Pediatrics, Pisa University Hospital, 56126 Pisa, Italy; (M.P.); (M.P.)
| | - Giovanna Batoni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56123 Pisa, Italy; (L.G.); (S.E.); (E.K.); (G.B.)
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30
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Cutone A, Lepanto MS, Rosa L, Scotti MJ, Rossi A, Ranucci S, De Fino I, Bragonzi A, Valenti P, Musci G, Berlutti F. Aerosolized Bovine Lactoferrin Counteracts Infection, Inflammation and Iron Dysbalance in A Cystic Fibrosis Mouse Model of Pseudomonas aeruginosa Chronic Lung Infection. Int J Mol Sci 2019; 20:ijms20092128. [PMID: 31052156 PMCID: PMC6540064 DOI: 10.3390/ijms20092128] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 02/07/2023] Open
Abstract
Cystic fibrosis (CF) is a genetic disorder affecting several organs including airways. Bacterial infection, inflammation and iron dysbalance play a major role in the chronicity and severity of the lung pathology. The aim of this study was to investigate the effect of lactoferrin (Lf), a multifunctional iron-chelating glycoprotein of innate immunity, in a CF murine model of Pseudomonas aeruginosa chronic lung infection. To induce chronic lung infection, C57BL/6 mice, either cystic fibrosis transmembrane conductance regulator (CFTR)-deficient (Cftrtm1UNCTgN(FABPCFTR)#Jaw) or wild-type (WT), were intra-tracheally inoculated with multidrug-resistant MDR-RP73 P. aeruginosa embedded in agar beads. Treatments with aerosolized bovine Lf (bLf) or saline were started five minutes after infection and repeated daily for six days. Our results demonstrated that aerosolized bLf was effective in significantly reducing both pulmonary bacterial load and infiltrated leukocytes in infected CF mice. Furthermore, for the first time, we showed that bLf reduced pulmonary iron overload, in both WT and CF mice. In particular, at molecular level, a significant decrease of both the iron exporter ferroportin and iron storage ferritin, as well as luminal iron content was observed. Overall, bLf acts as a potent multi-targeting agent able to break the vicious cycle induced by P. aeruginosa, inflammation and iron dysbalance, thus mitigating the severity of CF-related pathology and sequelae.
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Affiliation(s)
- Antimo Cutone
- Department of Biosciences and Territory, University of Molise, 86090 Pesche, Italy.
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy.
| | - Maria Stefania Lepanto
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy.
| | - Luigi Rosa
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy.
| | - Mellani Jinnett Scotti
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy.
| | - Alice Rossi
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milano, Italy.
| | - Serena Ranucci
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milano, Italy.
| | - Ida De Fino
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milano, Italy.
| | - Alessandra Bragonzi
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milano, Italy.
| | - Piera Valenti
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy.
| | - Giovanni Musci
- Department of Biosciences and Territory, University of Molise, 86090 Pesche, Italy.
| | - Francesca Berlutti
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy.
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31
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Bianconi I, D'Arcangelo S, Esposito A, Benedet M, Piffer E, Dinnella G, Gualdi P, Schinella M, Baldo E, Donati C, Jousson O. Persistence and Microevolution of Pseudomonas aeruginosa in the Cystic Fibrosis Lung: A Single-Patient Longitudinal Genomic Study. Front Microbiol 2019; 9:3242. [PMID: 30692969 PMCID: PMC6340092 DOI: 10.3389/fmicb.2018.03242] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/13/2018] [Indexed: 11/13/2022] Open
Abstract
Background: During its persistence in cystic fibrosis (CF) airways, P. aeruginosa develops a series of phenotypic changes by the accumulation of pathoadaptive mutations. A better understanding of the role of these mutations in the adaptive process, with particular reference to the development of multidrug resistance (MDR), is essential for future development of novel therapeutic approaches, including the identification of new drug targets and the implementation of more efficient antibiotic therapy. Although several whole-genome sequencing studies on P. aeruginosa CF lineages have been published, the evolutionary trajectories in relation to the development of antimicrobial resistance remain mostly unexplored to date. In this study, we monitored the adaptive changes of P. aeruginosa during its microevolution in the CF airways to provide an innovative, genome-wide picture of mutations and persistent phenotypes and to point out potential novel mechanisms allowing survival in CF patients under antibiotic therapy. Results: We obtained whole genome sequences of 40 P. aeruginosa clinical CF strains isolated at Trentino Regional Support CF Centre (Rovereto, Italy) from a single CF patient over an 8-year period (2007-2014). Genotypic analysis of the P. aeruginosa isolates revealed a clonal population dominated by the Sequence Type 390 and three closely related variants, indicating that all members of the population likely belong to the same clonal lineage and evolved from a common ancestor. While the majority of early isolates were susceptible to most antibiotics tested, over time resistant phenotypes increased in the persistent population. Genomic analyses of the population indicated a correlation between the evolution of antibiotic resistance profiles and phylogenetic relationships, and a number of putative pathoadaptive variations were identified. Conclusion: This study provides valuable insights into the within-host adaptation and microevolution of P. aeruginosa in the CF lung and revealed the emergence of an MDR phenotype over time, which could not be comprehensively explained by the variations found in known resistance genes. Further investigations on uncharacterized variations disclosed in this study should help to increase our understanding of the development of MDR phenotype and the poor outcome of antibiotic therapies in many CF patients.
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Affiliation(s)
- Irene Bianconi
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | | | - Alfonso Esposito
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Mattia Benedet
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Elena Piffer
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Grazia Dinnella
- Trentino Cystic Fibrosis Support Centre, Rovereto Hospital, Rovereto, Italy
| | - Paola Gualdi
- Operative Unit of Clinical Pathology, Rovereto Hospital, Rovereto, Italy
| | - Michele Schinella
- Operative Unit of Clinical Pathology, Rovereto Hospital, Rovereto, Italy
| | - Ermanno Baldo
- Trentino Cystic Fibrosis Support Centre, Rovereto Hospital, Rovereto, Italy
| | - Claudio Donati
- Centro Ricerca e Innovazione, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Olivier Jousson
- Centre for Integrative Biology, University of Trento, Trento, Italy
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32
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Orfanos S, Gomez C, Baron S, Akkisetty R, Dufeu N, Coltey B, Thomas PA, Rolain JM, Reynaud-Gaubert M. Impact of gram negative bacteria airway recolonization on the occurrence of chronic lung allograft dysfunction after lung transplantation in a population of cystic fibrosis patients. BMC Microbiol 2018; 18:88. [PMID: 30126365 PMCID: PMC6102836 DOI: 10.1186/s12866-018-1231-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 08/10/2018] [Indexed: 12/15/2022] Open
Abstract
Background Chronic Lung Allograft Dysfunction (CLAD) is the main cause of morbidity and mortality after the first year following lung transplantation (LTx). Risk factors of CLAD have been extensively studied, but the association between gram-negative bacteria (GNB) bronchial colonization and the development of CLAD is controversial. The purpose of our study was to investigate the association between post-transplant recolonization with the same species or de-novo colonization with a new GNB species and CLAD. The same analysis was performed on a sub-group of patients at the strain level using Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry technique. Results Forty adult cystic fibrosis (CF) patients who underwent a first bilateral LTx in the University Hospital of Marseille, between January 2010 and December 2014, were included in the study. Patients with GNB de-novo colonization had a higher risk of developing CLAD (OR = 6.72, p = 0.04) and a lower rate of CLAD-free survival (p = 0.005) compared to patients with GNB recolonization. No conclusion could be drawn from the subgroup MALDI-TOF MS analysis at the strain level. Conclusion Post-LTx GNB airway recolonization seems to be a protective factor against CLAD, whereas de-novo colonization with a new species of GNB seems to be a risk factor for CLAD. Electronic supplementary material The online version of this article (10.1186/s12866-018-1231-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah Orfanos
- Aix-Marseille University, Faculté de médecine, Marseille, France.
| | - Carine Gomez
- Aix-Marseille University, Faculté de médecine, Marseille, France.,Department of Respiratory Diseases, Lung Transplant Team, University Hospital of Marseille, Marseille, France
| | - Sophie Baron
- Aix-Marseille University, Faculté de médecine, Marseille, France.,URMITE CNRS IRD UMR 6236, IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Ritesh Akkisetty
- Department of Biology, Drexel University College of Art and Sciences, Philadelphia, USA
| | - Nadine Dufeu
- Department of Respiratory Diseases, Lung Transplant Team, University Hospital of Marseille, Marseille, France
| | - Bérengère Coltey
- Department of Respiratory Diseases, Lung Transplant Team, University Hospital of Marseille, Marseille, France
| | - Pascal Alexandre Thomas
- Aix-Marseille University, Faculté de médecine, Marseille, France.,Department of Thoracic Surgery, Lung Transplant Team APHM, University Hospital of Marseille, Marseille, France
| | - Jean Marc Rolain
- Aix-Marseille University, Faculté de médecine, Marseille, France.,URMITE CNRS IRD UMR 6236, IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Martine Reynaud-Gaubert
- Aix-Marseille University, Faculté de médecine, Marseille, France.,Department of Respiratory Diseases, Lung Transplant Team, University Hospital of Marseille, Marseille, France
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Esposito A, Pompilio A, Bettua C, Crocetta V, Giacobazzi E, Fiscarelli E, Jousson O, Di Bonaventura G. Evolution of Stenotrophomonas maltophilia in Cystic Fibrosis Lung over Chronic Infection: A Genomic and Phenotypic Population Study. Front Microbiol 2017; 8:1590. [PMID: 28894437 PMCID: PMC5581383 DOI: 10.3389/fmicb.2017.01590] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/04/2017] [Indexed: 12/18/2022] Open
Abstract
Stenotrophomonas maltophilia has been recognized as an emerging multi-drug resistant opportunistic pathogen in cystic fibrosis (CF) patients. We report a comparative genomic and phenotypic analysis of 91 S. maltophilia strains from 10 CF patients over a 12-year period. Draft genome analyses included in silico Multi-Locus Sequence Typing (MLST), Single-Nucleotide Polymorphisms (SNPs), and pangenome characterization. Growth rate, biofilm formation, motility, mutation frequency, in vivo virulence, and in vitro antibiotic susceptibility were determined and compared with population structure over time. The population consisted of 20 different sequence types (STs), 11 of which are new ones. Pangenome and SNPs data showed that this population is composed of three major phylogenetic lineages. All patients were colonized by multiple STs, although most of them were found in a single patient and showed persistence over years. Only few phenotypes showed some correlation with population phylogenetic structure. Our results show that S. maltophilia adaptation to CF lung is associated with consistent genotypic and phenotypic heterogeneity. Stenotrophomonas maltophilia infecting multiple hosts likely experiences different selection pressures depending on the host environment. The poor genotype-phenotype correlation suggests the existence of complex regulatory mechanisms that need to be explored in order to better design therapeutic strategies.
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Affiliation(s)
- Alfonso Esposito
- Centre for Integrative Biology, University of TrentoTrento, Italy
| | - Arianna Pompilio
- Department of Medical, Oral, and Biotechnological Sciences, Center of Excellence on Aging and Translational Medicine (CeSI-MeT), Università degli Studi "G. d'Annunzio" Chieti-PescaraChieti, Italy
| | - Clotilde Bettua
- Centre for Integrative Biology, University of TrentoTrento, Italy
| | - Valentina Crocetta
- Department of Medical, Oral, and Biotechnological Sciences, Center of Excellence on Aging and Translational Medicine (CeSI-MeT), Università degli Studi "G. d'Annunzio" Chieti-PescaraChieti, Italy
| | | | - Ersilia Fiscarelli
- Laboratory of Cystic Fibrosis Microbiology, "Bambino Gesù" HospitalRome, Italy
| | - Olivier Jousson
- Centre for Integrative Biology, University of TrentoTrento, Italy
| | - Giovanni Di Bonaventura
- Department of Medical, Oral, and Biotechnological Sciences, Center of Excellence on Aging and Translational Medicine (CeSI-MeT), Università degli Studi "G. d'Annunzio" Chieti-PescaraChieti, Italy
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34
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Prat C, Lacoma A. Bacteria in the respiratory tract-how to treat? Or do not treat? Int J Infect Dis 2017; 51:113-122. [PMID: 27776777 DOI: 10.1016/j.ijid.2016.09.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/30/2016] [Accepted: 09/04/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Acute and chronic respiratory tract infections are a common cause of inappropriate antimicrobial prescription. Antimicrobial therapy leads to the development of resistance and the emergence of opportunistic pathogens that substitute the indigenous microbiota. METHODS This review explores the major challenges and lines of research to adequately establish the clinical role of bacteria and the indications for antimicrobial treatment, and reviews novel therapeutic approaches. RESULTS In patients with chronic pulmonary diseases and structural disturbances of the bronchial tree or the lung parenchyma, clinical and radiographic signs and symptoms are almost constantly present, including a basal inflammatory response. Bacterial adaptative changes and differential phenotypes are described, depending on the clinical role and niche occupied. The respiratory tract has areas that are potentially inaccessible to antimicrobials. Novel therapeutic approaches include new ways of administering antimicrobials that may allow intracellular delivery or delivery across biofilms, targeting the functions essential for infection, such as regulatory systems, or the virulence factors required to cause host damage and disease. Alternatives to antibiotics and antimicrobial adjuvants are under development. CONCLUSIONS Prudent treatment, novel targets, and improved drug delivery systems will contribute to reduce the emergence of antimicrobial resistance in lower respiratory tract infections.
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Affiliation(s)
- Cristina Prat
- Microbiology Department, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Ctra del Canyet s/n, 08916 Badalona, Barcelona, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
| | - Alicia Lacoma
- Microbiology Department, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Ctra del Canyet s/n, 08916 Badalona, Barcelona, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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35
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Delavat F, Miyazaki R, Carraro N, Pradervand N, van der Meer JR. The hidden life of integrative and conjugative elements. FEMS Microbiol Rev 2017; 41:512-537. [PMID: 28369623 PMCID: PMC5812530 DOI: 10.1093/femsre/fux008] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/20/2017] [Indexed: 01/01/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are widespread mobile DNA that transmit both vertically, in a host-integrated state, and horizontally, through excision and transfer to new recipients. Different families of ICEs have been discovered with more or less restricted host ranges, which operate by similar mechanisms but differ in regulatory networks, evolutionary origin and the types of variable genes they contribute to the host. Based on reviewing recent experimental data, we propose a general model of ICE life style that explains the transition between vertical and horizontal transmission as a result of a bistable decision in the ICE-host partnership. In the large majority of cells, the ICE remains silent and integrated, but hidden at low to very low frequencies in the population specialized host cells appear in which the ICE starts its process of horizontal transmission. This bistable process leads to host cell differentiation, ICE excision and transfer, when suitable recipients are present. The ratio of ICE bistability (i.e. ratio of horizontal to vertical transmission) is the outcome of a balance between fitness costs imposed by the ICE horizontal transmission process on the host cell, and selection for ICE distribution (i.e. ICE 'fitness'). From this emerges a picture of ICEs as elements that have adapted to a mostly confined life style within their host, but with a very effective and dynamic transfer from a subpopulation of dedicated cells.
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Affiliation(s)
- François Delavat
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne Switzerland
| | - Ryo Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki 305-8566, Japan
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne Switzerland
| | - Nicolas Pradervand
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne Switzerland
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Comparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits. mSystems 2017; 2:mSystems00001-17. [PMID: 28293680 PMCID: PMC5347184 DOI: 10.1128/msystems.00001-17] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/30/2017] [Indexed: 01/30/2023] Open
Abstract
Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes. Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species, leading to high mortalities and economic losses in aquaculture. Although putative virulence factors have been identified, the mechanism of pathogenesis of V. anguillarum is not fully understood. Here, we analyzed whole-genome sequences of a collection of V. anguillarum strains and compared them to virulence of the strains as determined in larval challenge assays. Previously identified virulence factors were globally distributed among the strains, with some genetic diversity. However, the pan-genome revealed that six out of nine high-virulence strains possessed a unique accessory genome that was attributed to pathogenic genomic islands, prophage-like elements, virulence factors, and a new set of gene clusters involved in biosynthesis, modification, and transport of polysaccharides. In contrast, V. anguillarum strains that were medium to nonvirulent had a high degree of genomic homogeneity. Finally, we found that a phylogeny based on the core genomes clustered the strains with moderate to no virulence, while six out of nine high-virulence strains represented phylogenetically separate clusters. Hence, we suggest a link between genotype and virulence characteristics of Vibrio anguillarum, which can be used to unravel the molecular evolution of V. anguillarum and can also be important from survey and diagnostic perspectives. IMPORTANCE Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes.
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37
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Valenti P, Frioni A, Rossi A, Ranucci S, De Fino I, Cutone A, Rosa L, Bragonzi A, Berlutti F. Aerosolized bovine lactoferrin reduces neutrophils and pro-inflammatory cytokines in mouse models of Pseudomonas aeruginosa lung infections. Biochem Cell Biol 2016; 95:41-47. [PMID: 28129511 DOI: 10.1139/bcb-2016-0050] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Lactoferrin (Lf), an iron-chelating glycoprotein of innate immunity, produced by exocrine glands and neutrophils in infection/inflammation sites, is one of the most abundant defence molecules in airway secretions. Lf, a pleiotropic molecule, exhibits antibacterial and anti-inflammatory functions. These properties may play a relevant role in airway infections characterized by exaggerated inflammatory response, as in Pseudomonas aeruginosa lung infection in cystic fibrosis (CF) subjects. To verify the Lf role in Pseudomonas aeruginosa lung infection, we evaluated the efficacy of aerosolized bovine Lf (bLf) in mouse models of P. aeruginosa acute and chronic lung infections. C57BL/6NCrl mice were challenged with 106 CFUs of P. aeruginosa PAO1 (acute infection) or MDR-RP73 strain (chronic infection) by intra-tracheal administration. In both acute and chronic infections, aerosolized bLf resulted in nonsignificant reduction of bacterial load but significant decrease of the neutrophil recruitment and pro-inflammatory cytokine levels. Moreover, in chronic infection the bLf-treated mice recovered body weight faster and to a higher extent than the control mice. These findings add new insights into the benefits of bLf as a mediator of general health and its potential therapeutic applications.
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Affiliation(s)
- Piera Valenti
- a Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Alessandra Frioni
- a Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Alice Rossi
- b Infection and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Serena Ranucci
- b Infection and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Ida De Fino
- b Infection and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Antimo Cutone
- a Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Luigi Rosa
- a Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Alessandra Bragonzi
- b Infection and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Berlutti
- a Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy
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