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Popova L, Carabetta VJ. The Use of Next-Generation Sequencing in Personalized Medicine. Methods Mol Biol 2025; 2866:287-315. [PMID: 39546209 DOI: 10.1007/978-1-0716-4192-7_16] [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] [Indexed: 11/17/2024]
Abstract
The revolutionary progress in development of next-generation sequencing (NGS) technologies has made it possible to deliver accurate genomic information in a timely manner. Over the past several years, NGS has transformed biomedical and clinical research and found its application in the field of personalized medicine. Here we discuss the rise of personalized medicine and the history of NGS. We discuss current applications and uses of NGS in medicine, including infectious diseases, oncology, genomic medicine, and dermatology. We provide a brief discussion of selected studies where NGS was used to respond to wide variety of questions in biomedical research and clinical medicine. Finally, we discuss the challenges of implementing NGS into routine clinical use.
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Affiliation(s)
- Liya Popova
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, USA
| | - Valerie J Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, USA.
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2
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Leestemaker-Palmer A, Bermudez LE. Mycobacteroides abscessus ability to interact with the host mucosal cells plays an important role in pathogenesis of the infection. Crit Rev Microbiol 2024:1-13. [PMID: 39460453 DOI: 10.1080/1040841x.2024.2418130] [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: 06/20/2024] [Revised: 10/08/2024] [Accepted: 10/13/2024] [Indexed: 10/28/2024]
Abstract
Non-tuberculous mycobacteria (NTM) are opportunistic pathogens ubiquitous in the environment. Mycobacteroides abscessus is a relatively new pathogen associated with underlying lung chronic pathologies, accounting for most of the pulmonary infections linked to the rapidly growing mycobacteria group. This includes chronic obstructive pulmonary disease, bronchiectasis, or cystic fibrosis. Patient outcomes from M. abscessus infections are poor due to complicated treatments and other factors. Intrinsic drug resistance plays an important role. The M. abscessus toolbox of resistance is varied leading to complex strategies for treatment. Mechanisms include waxy cell walls, drug export mechanisms, and acquired resistance. Many studies have also shown the impact of extracellular DNA found in the biofilm matrix during early infection and its possible advantage in pathogenicity. In this review, we discuss the current knowledge of early infection focusing on biofilm formation, an environmental strategy, and which treatments prevent its formation improving current antibiotic treatment outcomes in preliminary studies.
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Affiliation(s)
- Amy Leestemaker-Palmer
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Corvallis, OR, USA
| | - Luiz E Bermudez
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Corvallis, OR, USA
- Department of Microbiology, College of Sciences, Oregon State University, Corvallis, OR, USA
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3
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Popova L, Carabetta VJ. The use of next-generation sequencing in personalized medicine. ARXIV 2024:arXiv:2403.03688v1. [PMID: 38495572 PMCID: PMC10942477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The revolutionary progress in development of next-generation sequencing (NGS) technologies has made it possible to deliver accurate genomic information in a timely manner. Over the past several years, NGS has transformed biomedical and clinical research and found its application in the field of personalized medicine. Here we discuss the rise of personalized medicine and the history of NGS. We discuss current applications and uses of NGS in medicine, including infectious diseases, oncology, genomic medicine, and dermatology. We provide a brief discussion of selected studies where NGS was used to respond to wide variety of questions in biomedical research and clinical medicine. Finally, we discuss the challenges of implementing NGS into routine clinical use.
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Affiliation(s)
- Liya Popova
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden NJ, 08103
| | - Valerie J. Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden NJ, 08103
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4
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Walzl A, Marbach H, Belikova D, Vogl C, Ehling-Schulz M, Heilbronner S, Grunert T. Prevalence of the SigB-Deficient Phenotype among Clinical Staphylococcus aureus Isolates Linked to Bovine Mastitis. Antibiotics (Basel) 2023; 12:699. [PMID: 37107061 PMCID: PMC10135042 DOI: 10.3390/antibiotics12040699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/07/2023] Open
Abstract
Phenotypic adaptation has been associated with persistent, therapy-resistant Staphylococcus aureus infections. Recently, we described within-host evolution towards a Sigma factor B (SigB)-deficient phenotype in a non-human host, a naturally infected dairy cow with chronic, persistent mastitis. However, to our knowledge, the prevalence of SigB deficiency among clinical S. aureus isolates remains unknown. In this study, we screened a collection of bovine mastitis isolates for phenotypic traits typical for SigB deficiency: decreased carotenoid pigmentation, increased proteolysis, secretion of α-hemolysin and exoproteins. Overall, 8 out of 77 (10.4%) isolates of our bovine mastitis collection exhibited the SigB-deficient phenotype. These isolates were assigned to various clonal complexes (CC8, CC9, CC97, CC151, CC3666). We further demonstrated a strong positive correlation between asp23-expression (a marker of SigB activity) and carotenoid pigmentation (r = 0.6359, p = 0.0008), underlining the role of pigmentation as a valuable predictor of the functional status of SigB. Sequencing of the sigB operon (mazEF-rsbUVW-sigB) indicated the phosphatase domain of the RsbU protein as a primary target of mutations leading to SigB deficiency. Indeed, by exchanging single nucleotides in rsbU, we could either induce SigB deficiency or restore the SigB phenotype, demonstrating the pivotal role of RsbU for SigB functionality. The data presented highlight the clinical relevance of SigB deficiency, and future studies are needed to exploit its role in staphylococcal infections.
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Affiliation(s)
- Anna Walzl
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Helene Marbach
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Darya Belikova
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, D-72076 Tübingen, Germany
| | - Claus Vogl
- Molecular Genetics, Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Monika Ehling-Schulz
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, D-72076 Tübingen, Germany
| | - Tom Grunert
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
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5
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Long DR, Penewit K, Lo HY, Almazan J, Holmes EA, Bryan AB, Wolter DJ, Lewis JD, Waalkes A, Salipante SJ. In Vitro Selection Identifies Staphylococcus aureus Genes Influencing Biofilm Formation. Infect Immun 2023; 91:e0053822. [PMID: 36847490 PMCID: PMC10016075 DOI: 10.1128/iai.00538-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
Staphylococcus aureus generates biofilms during many chronic human infections, which contributes to its growth and persistence in the host. Multiple genes and pathways necessary for S. aureus biofilm production have been identified, but knowledge is incomplete, and little is known about spontaneous mutations that increase biofilm formation as infection progresses. Here, we performed in vitro selection of four S. aureus laboratory strains (ATCC 29213, JE2, N315, and Newman) to identify mutations associated with enhanced biofilm production. Biofilm formation increased in passaged isolates from all strains, exhibiting from 1.2- to 5-fold the capacity of parental lines. Whole-genome sequencing identified nonsynonymous mutations affecting 23 candidate genes and a genomic duplication encompassing sigB. Six candidate genes significantly impacted biofilm formation as isogenic transposon knockouts: three were previously reported to impact S. aureus biofilm formation (icaR, spdC, and codY), while the remaining three (manA, narH, and fruB) were newly implicated by this study. Plasmid-mediated genetic complementation of manA, narH, and fruB transposon mutants corrected biofilm deficiencies, with high-level expression of manA and fruB further enhancing biofilm formation over basal levels. This work recognizes genes not previously identified as contributing to biofilm formation in S. aureus and reveals genetic changes able to augment biofilm production by that organism.
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Affiliation(s)
- Dustin R. Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Hsin-Yu Lo
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Jared Almazan
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Elizabeth A. Holmes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Andrew B. Bryan
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Daniel J. Wolter
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Janessa D. Lewis
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
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6
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Wong Fok Lung T, Chan LC, Prince A, Yeaman MR, Archer NK, Aman MJ, Proctor RA. Staphylococcus aureus adaptive evolution: Recent insights on how immune evasion, immunometabolic subversion and host genetics impact vaccine development. Front Cell Infect Microbiol 2022; 12:1060810. [PMID: 36636720 PMCID: PMC9831658 DOI: 10.3389/fcimb.2022.1060810] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/16/2022] [Indexed: 12/28/2022] Open
Abstract
Despite meritorious attempts, a S. aureus vaccine that prevents infection or mitigates severity has not yet achieved efficacy endpoints in prospective, randomized clinical trials. This experience underscores the complexity of host-S. aureus interactions, which appear to be greater than many other bacterial pathogens against which successful vaccines have been developed. It is increasingly evident that S. aureus employs strategic countermeasures to evade or exploit human immune responses. From entering host cells to persist in stealthy intracellular reservoirs, to sensing the environmental milieu and leveraging bacterial or host metabolic products to reprogram host immune responses, S. aureus poses considerable challenges for the development of effective vaccines. The fact that this pathogen causes distinct types of infections and can undergo transient genetic, transcriptional or metabolic adaptations in vivo that do not occur in vitro compounds challenges in vaccine development. Notably, the metabolic versatility of both bacterial and host immune cells as they compete for available substrates within specific tissues inevitably impacts the variable repertoire of gene products that may or may not be vaccine antigens. In this respect, S. aureus has chameleon phenotypes that have alluded vaccine strategies thus far. Nonetheless, a number of recent studies have also revealed important new insights into pathogenesis vulnerabilities of S. aureus. A more detailed understanding of host protective immune defenses versus S. aureus adaptive immune evasion mechanisms may offer breakthroughs in the development of effective vaccines, but at present this goal remains a very high bar. Coupled with the recent advances in human genetics and epigenetics, newer vaccine technologies may enable such a goal. If so, future vaccines that protect against or mitigate the severity of S. aureus infections are likely to emerge at the intersection of precision and personalized medicine. For now, the development of S. aureus vaccines or alternative therapies that reduce mortality and morbidity must continue to be pursued.
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Affiliation(s)
| | - Liana C Chan
- Department of Medicine, David Geffen School of Medicine at University of California Loss Angeles (UCLA), Los Angeles, CA, United States.,Divisions of Molecular Medicine and Infectious Diseases, Harbor-University of California Loss Angeles (UCLA) Medical Center, Torrance, CA, United States.,Lundquist Institute for Biomedical Innovation at Harbor-University of California Loss Angeles (UCLA) Medical Center, Torrance, CA, United States
| | - Alice Prince
- Department of Pediatrics, Columbia University, New York, NY, United States
| | - Michael R Yeaman
- Department of Medicine, David Geffen School of Medicine at University of California Loss Angeles (UCLA), Los Angeles, CA, United States.,Divisions of Molecular Medicine and Infectious Diseases, Harbor-University of California Loss Angeles (UCLA) Medical Center, Torrance, CA, United States.,Lundquist Institute for Biomedical Innovation at Harbor-University of California Loss Angeles (UCLA) Medical Center, Torrance, CA, United States
| | - Nathan K Archer
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - M Javad Aman
- Integrated BioTherapeutics, Rockville, MD, United States
| | - Richard A Proctor
- Department of Medicine and Medical Microbiology/Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
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7
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Morgan SJ, Durfey SL, Ravishankar S, Jorth P, Ni W, Skerrett DT, Aitken ML, McKone EF, Salipante SJ, Radey MC, Singh PK. A population-level strain genotyping method to study pathogen strain dynamics in human infections. JCI Insight 2021; 6:e152472. [PMID: 34935640 PMCID: PMC8783678 DOI: 10.1172/jci.insight.152472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A hallmark of chronic bacterial infections is the long-term persistence of 1 or more pathogen species at the compromised site. Repeated detection of the same bacterial species can suggest that a single strain or lineage is continually present. However, infection with multiple strains of a given species, strain acquisition and loss, and changes in strain relative abundance can occur. Detecting strain-level changes and their effects on disease is challenging because most methods require labor-intensive isolate-by-isolate analyses, and thus, only a few cells from large infecting populations can be examined. Here, we present a population-level method for enumerating and measuring the relative abundance of strains called population multi-locus sequence typing (PopMLST). The method exploits PCR amplification of strain-identifying polymorphic loci, next-generation sequencing to measure allelic variants, and informatic methods to determine whether variants arise from sequencing errors or low-abundance strains. These features enable PopMLST to simultaneously interrogate hundreds of bacterial cells that are cultured en masse from patient samples or are present in DNA directly extracted from clinical specimens without ex vivo culture. This method could be used to detect epidemic or super-infecting strains, facilitate understanding of strain dynamics during chronic infections, and enable studies that link strain changes to clinical outcomes.
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Affiliation(s)
- Sarah J. Morgan
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Samantha L. Durfey
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Sumedha Ravishankar
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Peter Jorth
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Wendy Ni
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Duncan T. Skerrett
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Moira L. Aitken
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Matthew C. Radey
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Pradeep K. Singh
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
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8
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Lavigne JP, Hosny M, Dunyach-Remy C, Boutet-Dubois A, Schuldiner S, Cellier N, Yahiaoui-Martinez A, Molle V, La Scola B, Marchandin H, Sotto A. Long-Term Intrahost Evolution of Staphylococcus aureus Among Diabetic Patients With Foot Infections. Front Microbiol 2021; 12:741406. [PMID: 34552578 PMCID: PMC8452158 DOI: 10.3389/fmicb.2021.741406] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/11/2021] [Indexed: 01/22/2023] Open
Abstract
Staphylococcus aureus is one of the main pathogens isolated from diabetic foot infections (DFI). The purpose of this study was to evaluate the importance of the persistence of S. aureus in this environment and the possible modifications of the bacterial genome content over time. Molecular typing of S. aureus isolates cultured from patients with the same DFI over a 7-year study revealed a 25% rate of persistence of this species in 48 patients, with a short median persistence time of 12weeks (range: 4-52weeks). Non-specific clonal complexes were linked to this persistence. During the follow-up, bla genes were acquired in three cases, whereas some virulence markers were lost in all cases after a long period of colonization (21.5weeks). Only one patient (2%) had a long-term persistence of 48weeks. The genome sequencing of a clonal pair of early/late strains isolated in this patient showed mutations in genes encoding bacterial defence and two-component signal transduction systems. Although, this study suggests that the long-term persistence of S. aureus in DFI is a rare event, genomic evolution is observed, highlighting the low adaptive ability of S. aureus to the specific environment and stressful conditions of diabetic foot ulcers. These results provide the basis for better understanding of S. aureus dynamics during persistent colonization in chronic wounds.
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Affiliation(s)
- Jean-Philippe Lavigne
- VBIC, INSERM U1047, Service de Microbiologie et Hygiène Hospitalière, Université de Montpellier, CHU Nîmes, Nîmes, France
| | - Michel Hosny
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Catherine Dunyach-Remy
- VBIC, INSERM U1047, Service de Microbiologie et Hygiène Hospitalière, Université de Montpellier, CHU Nîmes, Nîmes, France
| | - Adeline Boutet-Dubois
- VBIC, INSERM U1047, Service de Microbiologie et Hygiène Hospitalière, Université de Montpellier, CHU Nîmes, Nîmes, France
| | - Sophie Schuldiner
- VBIC, INSERM U1047, Service des Maladies Métaboliques et Endocriniennes, Université de Montpellier, CHU Nîmes, Nîmes, France
| | | | - Alex Yahiaoui-Martinez
- VBIC, INSERM U1047, Service de Microbiologie et Hygiène Hospitalière, Université de Montpellier, CHU Nîmes, Nîmes, France
| | - Virginie Molle
- Laboratory of Pathogen Host Interactions, UMR 5235, CNRS, Université de Montpellier, Montpellier, France
| | - Bernard La Scola
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Hélène Marchandin
- HydroSciences Montpellier, CNRS, IRD, Service de Microbiologie et Hygiène Hospitalière, Université de Montpellier, CHU Nîmes, Nîmes, France
| | - Albert Sotto
- VBIC, INSERM U1047, Service des Maladies Infectieuses et Tropicales, Université de Montpellier, CHU Nîmes, Nîmes, France
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9
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Rumpf C, Lange J, Schwartbeck B, Kahl BC. Staphylococcus aureus and Cystic Fibrosis-A Close Relationship. What Can We Learn from Sequencing Studies? Pathogens 2021; 10:1177. [PMID: 34578208 PMCID: PMC8466686 DOI: 10.3390/pathogens10091177] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 01/13/2023] Open
Abstract
Staphylococcus aureus is next to Pseudomonas aeruginosa the most isolated pathogen from the airways of cystic fibrosis (CF) patients, who are often infected by a dominant S. aureus clone for extended periods. To be able to persist, the pathogen has to adapt to the hostile niche of the airways to counteract host defence, antibiotic therapy and the competition with coinfecting pathogens. S. aureus is equipped with many virulence factors including adhesins, toxins that are localized on the chromosome, on plasmids or are phage-related. S. aureus is especially versatile and adaptation and evolution of the pathogen occurs by the acquisition of new genes by horizontal gene transfer (HGT), changes in nucleotides (single nucleotide variations, SNVs) that can cause a selective advantage for the bacteria and become fixed in subpopulations. Methicillin-resistant S. aureus are a special threat to CF patients due to the more severe lung disease occurring in infected patients. Today, with decreasing costs for sequencing, more and more studies using S. aureus isolates cultured from CF patients are being published, which use whole genome sequencing (WGS), multilocus sequence typing (MLST) or spa-sequence typing (spa-typing) to follow the population dynamics of S. aureus, elucidate the underlying mechanisms of phenotypic variants, newly acquired resistance or adaptation to the host response in this particular niche. In the first part of this review, an introduction to the genetic make-up and the pathogenesis of S. aureus with respect to CF is provided. The second part presents an overview of recent studies and their findings using genotypic methods such as single or multilocus sequencing and whole genome sequencing, which identify factors contributing to the adaptation of S. aureus and its evolution in the airways of individuals with CF.
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Affiliation(s)
| | | | | | - Barbara C. Kahl
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (C.R.); (J.L.); (B.S.)
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10
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Within-Host Adaptation of Staphylococcus aureus in a Bovine Mastitis Infection Is Associated with Increased Cytotoxicity. Int J Mol Sci 2021; 22:ijms22168840. [PMID: 34445550 PMCID: PMC8396210 DOI: 10.3390/ijms22168840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/04/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022] Open
Abstract
Within-host adaptation is a typical feature of chronic, persistent Staphylococcus aureus infections. Research projects addressing adaptive changes due to bacterial in-host evolution increase our understanding of the pathogen’s strategies to survive and persist for a long time in various hosts such as human and bovine. In this study, we investigated the adaptive processes of S. aureus during chronic, persistent bovine mastitis using a previously isolated isogenic strain pair from a dairy cow with chronic, subclinical mastitis, in which the last variant (host-adapted, Sigma factor SigB-deficient) quickly replaced the initial, dominant variant. The strain pair was cultivated under specific in vitro infection-relevant growth-limiting conditions (iron-depleted RPMI under oxygen limitation). We used a combinatory approach of surfaceomics, molecular spectroscopic fingerprinting and in vitro phenotypic assays. Cellular cytotoxicity assays using red blood cells and bovine mammary epithelial cells (MAC-T) revealed changes towards a more cytotoxic phenotype in the host-adapted isolate with an increased alpha-hemolysin (α-toxin) secretion, suggesting an improved capacity to penetrate and disseminate the udder tissue. Our results foster the hypothesis that within-host evolved SigB-deficiency favours extracellular persistence in S. aureus infections. Here, we provide new insights into one possible adaptive strategy employed by S. aureus during chronic, bovine mastitis, and we emphasise the need to analyse genotype–phenotype associations under different infection-relevant growth conditions.
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11
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Long DR, Wolter DJ, Lee M, Precit M, McLean K, Holmes E, Penewit K, Waalkes A, Hoffman LR, Salipante SJ. Polyclonality, Shared Strains, and Convergent Evolution in Chronic Cystic Fibrosis Staphylococcus aureus Airway Infection. Am J Respir Crit Care Med 2021; 203:1127-1137. [PMID: 33296290 DOI: 10.1164/rccm.202003-0735oc] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Rationale: Staphylococcus aureus is the most common respiratory pathogen isolated from patients with cystic fibrosis (CF) in the United States. Although modes of acquisition and genetic adaptation have been described for Pseudomonas aeruginosa, resulting in improved diagnosis and treatment, these features remain more poorly defined for S. aureus.Objectives: To characterize the molecular epidemiology and genetic adaptation of S. aureus during chronic CF airway infection and in response to antibiotic therapy.Methods: We performed whole-genome sequencing of 1,382 S. aureus isolates collected longitudinally over a mean 2.2 years from 246 children with CF at five U.S. centers between 2008 and 2017. Results were integrated with clinical and demographic data to characterize bacterial population dynamics and identify common genetic targets of in vivo adaptation.Measurements and Main Results: Results showed that 45.5% of patients carried multiple, coexisting S. aureus lineages, often having different antibiotic susceptibility profiles. Adaptation during the course of infection commonly occurred in a set of genes related to persistence and antimicrobial resistance. Individual sequence types demonstrated wide geographic distribution, and we identified limited strain-sharing among children linked by common household or clinical exposures. Unlike P. aeruginosa, S. aureus genetic diversity was unconstrained, with an ongoing flow of new genetic elements into the population of isolates from children with CF.Conclusions: CF airways are frequently coinfected by multiple, genetically distinct S. aureus lineages, indicating that current clinical procedures for sampling isolates and selecting antibiotics are likely inadequate. Strains can be shared by patients in close domestic or clinical contact and can undergo convergent evolution in key persistence and antimicrobial-resistance genes, suggesting novel diagnostic and therapeutic approaches for future study.
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Affiliation(s)
- Dustin R Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine
| | - Daniel J Wolter
- Department of Pediatrics.,Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, Washington
| | | | | | - Kathryn McLean
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington; and
| | - Elizabeth Holmes
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington; and
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington; and
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington; and
| | - Lucas R Hoffman
- Department of Pediatrics.,Department of Microbiology, and.,Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, Washington
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington; and
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12
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Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus. Commun Biol 2021; 4:793. [PMID: 34172889 PMCID: PMC8233327 DOI: 10.1038/s42003-021-02339-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
While microbiological resistance to vancomycin in Staphylococcus aureus is rare, clinical vancomycin treatment failures are common, and methicillin-resistant S. aureus (MRSA) strains isolated from patients after prolonged vancomycin treatment failure remain susceptible. Adaptive laboratory evolution was utilized to uncover mutational mechanisms associated with MRSA vancomycin resistance in a physiological medium as well as a bacteriological medium used in clinical susceptibility testing. Sequencing of resistant clones revealed shared and media-specific mutational outcomes, with an overlap in cell wall regulons (walKRyycHI, vraSRT). Evolved strains displayed similar properties to resistant clinical isolates in their genetic and phenotypic traits. Importantly, resistant phenotypes that developed in physiological media did not translate into resistance in bacteriological media. Further, a bacteriological media-specific mechanism for vancomycin resistance associated with a mutated mprF was confirmed. This study bridges the gap between the understanding of clinical and microbiological vancomycin resistance in S. aureus and expands the number of allelic variants (18 ± 4 mutations for the top 5 mutated genes) that result in vancomycin resistance phenotypes.
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13
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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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14
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Haim MS, Zaheer R, Bharat A, Di Gregorio S, Di Conza J, Galanternik L, Lubovich S, Golding GR, Graham MR, Van Domselaar G, Cardona ST, Mollerach M. Comparative genomics of ST5 and ST30 methicillin-resistant Staphylococcus aureus sequential isolates recovered from paediatric patients with cystic fibrosis. Microb Genom 2021; 7:mgen000510. [PMID: 33599606 PMCID: PMC8190608 DOI: 10.1099/mgen.0.000510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/21/2020] [Indexed: 12/28/2022] Open
Abstract
Staphylococcus aureus chronic airway infection in patients with cystic fibrosis (CF) allows this pathogen to adapt over time in response to different selection pressures. We have previously shown that the main sequence types related to community-acquired methicillin-resistant S. aureus (MRSA) infections in Argentina - ST5 and ST30 - are also frequently isolated from the sputum of patients with CF, but in these patients they usually display multi-drug antimicrobial resistance. In this study, we sequenced the genomes of MRSA from four paediatric CF patients with the goal of identifying mutations among sequential isolates, especially those possibly related to antimicrobial resistance and virulence, which might contribute to the adaptation of the pathogen in the airways of patients with CF. Our results revealed genetic differences in sequential MRSA strains isolated from patients with CF in both their core and accessory genomes. Although the genetic adaptation of S. aureus was distinct in different hosts, we detected independent mutations in thyA, htrA, rpsJ and gyrA - which are known to have crucial roles in S. aureus virulence and antimicrobial resistance - in isolates recovered from multiple patients. Moreover, we identified allelic variants that were detected in all of the isolates recovered after a certain time point; these non-synonymous mutations were in genes associated with antimicrobial resistance, virulence, iron scavenging and oxidative stress resistance. In conclusion, our results provide evidence of genetic variability among sequential MRSA isolates that could be implicated in the adaptation of these strains during chronic CF airway infection.
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Affiliation(s)
- María Sol Haim
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Rahat Zaheer
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Amrita Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Sabrina Di Gregorio
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - José Di Conza
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | - Silvina Lubovich
- Hospital de Niños 'Dr Ricardo Gutiérrez', Buenos Aires, Argentina
| | - George R. Golding
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - Morag R. Graham
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - Silvia T. Cardona
- Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Marta Mollerach
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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15
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Temporal Changes in Patient-Matched Staphylococcus epidermidis Isolates from Infections: towards Defining a 'True' Persistent Infection. Microorganisms 2020; 8:microorganisms8101508. [PMID: 33007861 PMCID: PMC7601538 DOI: 10.3390/microorganisms8101508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus epidermidis is found naturally on the skin but is a common cause of persistent orthopaedic device-related infections (ODRIs). This study used a pan-genome and gene-by-gene approach to analyse the clonality of whole genome sequences (WGS) of 115 S. epidermidis isolates from 55 patients with persistent ODRIs. Analysis of the 522 gene core genome revealed that the isolates clustered into three clades, and MLST analysis showed that 83% of the isolates belonged to clonal complex 2 (CC2). Analysis also found 13 isolate pairs had different MLST types and less than 70% similarity within the genes; hence, these were defined as re-infection by a different S. epidermidis strain. Comparison of allelic diversity in the remaining 102 isolates (49 patients) revealed that 6 patients had microevolved infections (>7 allele differences), and only 37 patients (77 isolates) had a ‘true’ persistent infection. Analysis of the core genomes of isolate pairs from 37 patients found 110/841 genes had variations; mainly in metabolism associated genes. The accessory genome consisted of 2936 genes; with an average size of 1515 genes. To conclude, this study demonstrates the advantage of using WGS for identifying the accuracy of a persistent infection diagnosis. Hence, persistent infections can be defined as ‘true’ persistent infections if the core genome of paired isolates has ≤7 allele differences; microevolved persistent infection if the paired isolates have >7 allele differences but same MLST type; and polyclonal if they are the same species but a different MLST type.
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16
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Mrochen DM, Fernandes de Oliveira LM, Raafat D, Holtfreter S. Staphylococcus aureus Host Tropism and Its Implications for Murine Infection Models. Int J Mol Sci 2020; 21:E7061. [PMID: 32992784 PMCID: PMC7582387 DOI: 10.3390/ijms21197061] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/11/2022] Open
Abstract
Staphylococcus aureus (S. aureus) is a pathobiont of humans as well as a multitude of animal species. The high prevalence of multi-resistant and more virulent strains of S. aureus necessitates the development of new prevention and treatment strategies for S. aureus infection. Major advances towards understanding the pathogenesis of S. aureus diseases have been made using conventional mouse models, i.e., by infecting naïve laboratory mice with human-adapted S.aureus strains. However, the failure to transfer certain results obtained in these murine systems to humans highlights the limitations of such models. Indeed, numerous S. aureus vaccine candidates showed promising results in conventional mouse models but failed to offer protection in human clinical trials. These limitations arise not only from the widely discussed physiological differences between mice and humans, but also from the lack of attention that is paid to the specific interactions of S. aureus with its respective host. For instance, animal-derived S. aureus lineages show a high degree of host tropism and carry a repertoire of host-specific virulence and immune evasion factors. Mouse-adapted S.aureus strains, humanized mice, and microbiome-optimized mice are promising approaches to overcome these limitations and could improve transferability of animal experiments to human trials in the future.
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Affiliation(s)
- Daniel M. Mrochen
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Strasse DZ 7, 17475 Greifswald, Germany; (L.M.F.d.O.); (D.R.); (S.H.)
| | - Liliane M. Fernandes de Oliveira
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Strasse DZ 7, 17475 Greifswald, Germany; (L.M.F.d.O.); (D.R.); (S.H.)
| | - Dina Raafat
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Strasse DZ 7, 17475 Greifswald, Germany; (L.M.F.d.O.); (D.R.); (S.H.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, 21521 Alexandria, Egypt
| | - Silva Holtfreter
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Strasse DZ 7, 17475 Greifswald, Germany; (L.M.F.d.O.); (D.R.); (S.H.)
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17
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Tan X, Coureuil M, Ramond E, Euphrasie D, Dupuis M, Tros F, Meyer J, Nemazanyy I, Chhuon C, Guerrera IC, Ferroni A, Sermet-Gaudelus I, Nassif X, Charbit A, Jamet A. Chronic Staphylococcus aureus Lung Infection Correlates With Proteogenomic and Metabolic Adaptations Leading to an Increased Intracellular Persistence. Clin Infect Dis 2020; 69:1937-1945. [PMID: 30753350 DOI: 10.1093/cid/ciz106] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/31/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Chronic lung infection in cystic fibrosis (CF) patients by Staphylococcus aureus is a well-established epidemiological fact. Indeed, S. aureus is the most commonly identified pathogen in the lungs of CF patients. Improving our understanding of the mechanisms associated with the persistence of S. aureus is therefore an important issue. METHODS We selected pairs of sequential S. aureus isolates from 3 patients with CF and from 1 patient with non-CF chronic lung disease. We used a combination of genomic, proteomic, and metabolomic approaches with functional assays for in-depth characterization of S. aureus long-term persistence. RESULTS In this study, we show that late S. aureus isolates from CF patients have an increased ability for intracellular survival in CF bronchial epithelial-F508del cells compared to ancestral early isolates. Importantly, the increased ability to persist intracellularly was confirmed for S. aureus isolates within the own-patient F508del epithelial cells. An increased ability to form biofilm was also demonstrated. Furthermore, we identified the underlying genetic modifications that induce altered protein expression profiles and notable metabolic changes. These modifications affect several metabolic pathways and virulence regulators that could constitute therapeutic targets. CONCLUSIONS Our results strongly suggest that the intracellular environment might constitute an important niche of persistence and relapse necessitating adapted antibiotic treatments.
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Affiliation(s)
- Xin Tan
- Université Paris Descartes, INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades. Team: Pathogenesis of Systemic Infections, Paris, France
| | - Mathieu Coureuil
- Université Paris Descartes, INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades. Team: Pathogenesis of Systemic Infections, Paris, France
| | - Elodie Ramond
- Université Paris Descartes, INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades. Team: Pathogenesis of Systemic Infections, Paris, France
| | - Daniel Euphrasie
- Université Paris Descartes, INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades. Team: Pathogenesis of Systemic Infections, Paris, France
| | - Marion Dupuis
- Université Paris Descartes, INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades. Team: Pathogenesis of Systemic Infections, Paris, France
| | - Fabiola Tros
- Université Paris Descartes, INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades. Team: Pathogenesis of Systemic Infections, Paris, France
| | - Julie Meyer
- Université Paris Descartes, INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades. Team: Pathogenesis of Systemic Infections, Paris, France
| | - Ivan Nemazanyy
- Plateforme d'étude du métabolisme, Structure Fédérative de Recherche INSERM US24/CNRS UMS3633, Paris, France
| | - Cerina Chhuon
- Plateforme Protéome Institut Necker-Enfants Malades, PPN, Structure Fédérative de Recherche SFR Necker, University Paris Descartes, Paris, France
| | - Ida Chiara Guerrera
- Proteomics platform 3P5-Necker, Université Paris Descartes - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Agnes Ferroni
- Laboratoire de Microbiologie de l'hopital Necker, University Paris Descartes, Paris, France
| | - Isabelle Sermet-Gaudelus
- Université Paris Descartes, INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades. Team: Canalopathies épithéliales: la mucoviscidose et autres maladies, Paris, France
| | - Xavier Nassif
- Université Paris Descartes, INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades. Team: Pathogenesis of Systemic Infections, Paris, France
| | - Alain Charbit
- Université Paris Descartes, INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades. Team: Pathogenesis of Systemic Infections, Paris, France
| | - Anne Jamet
- Université Paris Descartes, INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades. Team: Pathogenesis of Systemic Infections, Paris, France
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18
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Bernardy EE, Petit RA, Raghuram V, Alexander AM, Read TD, Goldberg JB. Genotypic and Phenotypic Diversity of Staphylococcus aureus Isolates from Cystic Fibrosis Patient Lung Infections and Their Interactions with Pseudomonas aeruginosa. mBio 2020; 11. [PMID: 32576671 DOI: 10.31234/osf.io/9whp4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023] Open
Abstract
Staphylococcus aureus has recently overtaken Pseudomonas aeruginosa as the most commonly recognized bacterial pathogen that infects the respiratory tracts of individuals with the genetic disease cystic fibrosis (CF) in the United States. Most studies of S. aureus in CF patient lung infections have focused on a few isolates, often exclusively laboratory-adapted strains, and how they are killed by P. aeruginosa Less is known about the diversity of S. aureus CF patient lung isolates in terms of both their virulence and their interaction with P. aeruginosa To begin to address this gap, we recently sequenced 64 clinical S. aureus isolates and a reference isolate, JE2. Here, we analyzed the antibiotic resistance genotypes, sequence types, clonal complexes, spa types, agr types, and presence/absence of other known virulence factor genes of these isolates. We hypothesized that virulence phenotypes of S. aureus, namely, toxin production and the mucoid phenotype, would be lost in these isolates due to adaptation in the CF patient lung. In contrast to these expectations, we found that most isolates can lyse both rabbit and sheep blood (67.7%) and produce polysaccharide (69.2%), suggesting that these phenotypes were not lost during adaptation to the CF lung. We also identified three distinct phenotypic groups of S. aureus based on their survival in the presence of nonmucoid P. aeruginosa laboratory strain PAO1 and its mucoid derivative. Altogether, our work provides greater insight into the diversity of S. aureus isolates from CF patients, specifically the distribution of important virulence factors and their interaction with P. aeruginosa, all of which have implications in patient health.IMPORTANCEStaphylococcus aureus is now the most frequently detected recognized pathogen in the lungs of individuals who have cystic fibrosis (CF) in the United States, followed closely by Pseudomonas aeruginosa When these pathogens are found to coinfect the CF lung, patients have a significantly worse prognosis. While P. aeruginosa has been rigorously studied in the context of bacterial pathogenesis in CF, less is known about S. aureus Here, we present an in-depth study of 64 S. aureus clinical isolates from CF patients, for which we investigated genetic diversity utilizing whole-genome sequencing, virulence phenotypes, and interactions with P. aeruginosa We found that S. aureus isolated from CF lungs are phylogenetically diverse; most retain known virulence factors and vary in their interactions with P. aeruginosa (i.e., they range from being highly sensitive to P. aeruginosa to completely tolerant to it). Deepening our understanding of how S. aureus responds to its environment and other microbes in the CF lung will enable future development of effective treatments and preventative measures against these formidable infections.
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Affiliation(s)
- Eryn E Bernardy
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis, and Sleep, Emory University, Atlanta, Georgia, USA
- Emory-Children's Center for Cystic Fibrosis Research, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Robert A Petit
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
| | - Vishnu Raghuram
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis, and Sleep, Emory University, Atlanta, Georgia, USA
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Ashley M Alexander
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis, and Sleep, Emory University, Atlanta, Georgia, USA
- Population Biology, Ecology, and Evolution Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Timothy D Read
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
- Population Biology, Ecology, and Evolution Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Joanna B Goldberg
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis, and Sleep, Emory University, Atlanta, Georgia, USA
- Emory-Children's Center for Cystic Fibrosis Research, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
- Population Biology, Ecology, and Evolution Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
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19
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Bernardy EE, Petit RA, Raghuram V, Alexander AM, Read TD, Goldberg JB. Genotypic and Phenotypic Diversity of Staphylococcus aureus Isolates from Cystic Fibrosis Patient Lung Infections and Their Interactions with Pseudomonas aeruginosa. mBio 2020; 11:mBio.00735-20. [PMID: 32576671 PMCID: PMC7315118 DOI: 10.1128/mbio.00735-20] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Staphylococcus aureus has recently overtaken Pseudomonas aeruginosa as the most commonly recognized bacterial pathogen that infects the respiratory tracts of individuals with the genetic disease cystic fibrosis (CF) in the United States. Most studies of S. aureus in CF patient lung infections have focused on a few isolates, often exclusively laboratory-adapted strains, and how they are killed by P. aeruginosa Less is known about the diversity of S. aureus CF patient lung isolates in terms of both their virulence and their interaction with P. aeruginosa To begin to address this gap, we recently sequenced 64 clinical S. aureus isolates and a reference isolate, JE2. Here, we analyzed the antibiotic resistance genotypes, sequence types, clonal complexes, spa types, agr types, and presence/absence of other known virulence factor genes of these isolates. We hypothesized that virulence phenotypes of S. aureus, namely, toxin production and the mucoid phenotype, would be lost in these isolates due to adaptation in the CF patient lung. In contrast to these expectations, we found that most isolates can lyse both rabbit and sheep blood (67.7%) and produce polysaccharide (69.2%), suggesting that these phenotypes were not lost during adaptation to the CF lung. We also identified three distinct phenotypic groups of S. aureus based on their survival in the presence of nonmucoid P. aeruginosa laboratory strain PAO1 and its mucoid derivative. Altogether, our work provides greater insight into the diversity of S. aureus isolates from CF patients, specifically the distribution of important virulence factors and their interaction with P. aeruginosa, all of which have implications in patient health.IMPORTANCEStaphylococcus aureus is now the most frequently detected recognized pathogen in the lungs of individuals who have cystic fibrosis (CF) in the United States, followed closely by Pseudomonas aeruginosa When these pathogens are found to coinfect the CF lung, patients have a significantly worse prognosis. While P. aeruginosa has been rigorously studied in the context of bacterial pathogenesis in CF, less is known about S. aureus Here, we present an in-depth study of 64 S. aureus clinical isolates from CF patients, for which we investigated genetic diversity utilizing whole-genome sequencing, virulence phenotypes, and interactions with P. aeruginosa We found that S. aureus isolated from CF lungs are phylogenetically diverse; most retain known virulence factors and vary in their interactions with P. aeruginosa (i.e., they range from being highly sensitive to P. aeruginosa to completely tolerant to it). Deepening our understanding of how S. aureus responds to its environment and other microbes in the CF lung will enable future development of effective treatments and preventative measures against these formidable infections.
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Affiliation(s)
- Eryn E Bernardy
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis, and Sleep, Emory University, Atlanta, Georgia, USA
- Emory-Children's Center for Cystic Fibrosis Research, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Robert A Petit
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
| | - Vishnu Raghuram
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis, and Sleep, Emory University, Atlanta, Georgia, USA
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Ashley M Alexander
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis, and Sleep, Emory University, Atlanta, Georgia, USA
- Population Biology, Ecology, and Evolution Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Timothy D Read
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
- Population Biology, Ecology, and Evolution Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Joanna B Goldberg
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis, and Sleep, Emory University, Atlanta, Georgia, USA
- Emory-Children's Center for Cystic Fibrosis Research, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
- Population Biology, Ecology, and Evolution Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
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20
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Within-host evolution of bovine Staphylococcus aureus selects for a SigB-deficient pathotype characterized by reduced virulence but enhanced proteolytic activity and biofilm formation. Sci Rep 2019; 9:13479. [PMID: 31530887 PMCID: PMC6748969 DOI: 10.1038/s41598-019-49981-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/02/2019] [Indexed: 12/21/2022] Open
Abstract
Staphylococcus aureus is a major cause of bovine mastitis, commonly leading to long-lasting, persistent and recurrent infections. Thereby, S. aureus constantly refines and permanently adapts to the bovine udder environment. In this work, we followed S. aureus within-host adaptation over the course of three months in a naturally infected dairy cattle with chronic, subclinical mastitis. Whole genome sequence analysis revealed a complete replacement of the initial predominant variant by another isogenic variant. We report for the first time within-host evolution towards a sigma factor SigB-deficient pathotype in S. aureus bovine mastitis, associated with a single nucleotide polymorphism in rsbU (G368A → G122D), a contributor to SigB-functionality. The emerged SigB-deficient pathotype exhibits a substantial shift to new phenotypic traits comprising strong proteolytic activity and poly-N-acetylglucosamine (PNAG)-based biofilm production. This possibly unlocks new nutritional resources and promotes immune evasion, presumably facilitating extracellular persistence within the host. Moreover, we observed an adaptation towards attenuated virulence using a mouse infection model. This study extends the role of sigma factor SigB in S. aureus pathogenesis, so far described to be required for intracellular persistence during chronic infections. Our findings suggest that S. aureus SigB-deficiency is an alternative mechanism for persistence and underpin the clinical relevance of staphylococcal SigB-deficient variants which are consistently isolated during human chronic infections.
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21
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Treffon J, Block D, Moche M, Reiss S, Fuchs S, Engelmann S, Becher D, Langhanki L, Mellmann A, Peters G, Kahl BC. Adaptation of Staphylococcus aureus to Airway Environments in Patients With Cystic Fibrosis by Upregulation of Superoxide Dismutase M and Iron-Scavenging Proteins. J Infect Dis 2019; 217:1453-1461. [PMID: 29325044 DOI: 10.1093/infdis/jiy012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 01/05/2018] [Indexed: 01/24/2023] Open
Abstract
Adaptation of S. aureus to the hostile environment of CF airways resulted in changed abundance of proteins involved in energy metabolism, cellular processes, transport and binding, but most importantly in an iron-scavenging phenotype and increased activity of superoxide dismutase M.
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Affiliation(s)
| | | | - Martin Moche
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Greifswald
| | - Swantje Reiss
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Greifswald
| | - Stephan Fuchs
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Greifswald.,Department of Infectious Diseases, Robert Koch Institute, Wernigerode
| | - Susanne Engelmann
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Greifswald.,Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany.,Microbial Proteomics, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Greifswald
| | - Lars Langhanki
- Institute of Hygiene, University Hospital Münster, Münster
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22
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Azarian T, Ridgway JP, Yin Z, David MZ. Long-Term Intrahost Evolution of Methicillin Resistant Staphylococcus aureus Among Cystic Fibrosis Patients With Respiratory Carriage. Front Genet 2019; 10:546. [PMID: 31244886 PMCID: PMC6581716 DOI: 10.3389/fgene.2019.00546] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/22/2019] [Indexed: 12/29/2022] Open
Abstract
Staphylococcus aureus is the most commonly identified airway colonizer of cystic fibrosis (CF) patients, and infections with methicillin-resistant S. aureus (MRSA) are associated with poor outcomes. Yet, little is known about the intrahost evolution of S. aureus among CF patients. We investigated convergent evolution and adaptation of MRSA among four CF patients with long-term respiratory carriage. For each patient, we performed whole-genome sequencing on an average of 21 isolates (range: 19–23) carried for a mean of 1,403 days (range: 903–1,679), including 25 pairs of isolates collected on the same day. We assessed intrahost diversity, population structure, evolutionary history, evidence of switched intergenic regions (IGRs), and signatures of adaptation in the context of patient age, antibiotic treatment, and co-colonizing microbes. Phylogenetic analysis delineated distinct multilocus sequence type ST5 (n = 3) and ST72 (n = 1) clonal populations in addition to sporadic, non-clonal isolates, and uncovered a putative transmission event. Variation in antibiotic resistance was observed within clonal populations, even among isolates collected on the same day. Rates of molecular evolution ranged from 2.21 to 8.64 nucleotide polymorphisms per year, and lineage ages were consistent with acquisition of colonization in early childhood followed by subsequent persistence of multiple sub-populations. Selection analysis of 1,622 core genes present in all four clonal populations (n = 79) found 11 genes variable in three subjects – most notably, ATP-dependent protease clpX, 2-oxoglutarate dehydrogenase odhA, fmtC, and transcription-repair coupling factor mfd. Only one gene, staphylococcal protein A (spa), was found to have evidence of gene-wide diversifying selection. We identified three instances of intrahost IGR switching events, two of which flanked genes related to quorum sensing. The complex microbial ecology of the CF airway poses challenges for management. We illustrate appreciable intrahost diversity as well as persistence of a dominant lineage. We also show that intrahost adaptation is a continual process, despite purifying selective pressure, and provide targets that should be investigated further for their function in CF adaptation.
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Affiliation(s)
- Taj Azarian
- College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Jessica P Ridgway
- Department of Medicine, University of Chicago, Chicago, IL, United States
| | - Zachary Yin
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Michael Z David
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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23
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Artificial Selection for Pathogenicity Mutations in Staphylococcus aureus Identifies Novel Factors Relevant to Chronic Infection. Infect Immun 2019; 87:IAI.00884-18. [PMID: 30642903 DOI: 10.1128/iai.00884-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 01/10/2019] [Indexed: 02/06/2023] Open
Abstract
Adaptation of Staphylococcus aureus to host microenvironments during chronic infection involves spontaneous mutations, yet changes underlying adaptive phenotypes remain incompletely explored. Here, we employed artificial selection and whole-genome sequencing to better characterize spontaneous chromosomal mutations that alter two pathogenicity phenotypes relevant to chronic infection in S. aureus: intracellular invasiveness and intracellular cytotoxicity. We identified 23 genes whose alteration coincided with enhanced virulence, 11 that were previously known and 12 (52%) that had no previously described role in S. aureus pathogenicity. Using precision genome editing, transposon mutants, and gene complementation, we empirically assessed the contributions of individual genes to the two virulence phenotypes. We functionally validated 14 of 21 genes tested as measurably influencing invasion and/or cytotoxicity, including 8 newly implicated by this study. We identified inactivating mutations (murA, ndhC, and a hypothetical membrane protein) and gain-of-function mutations (aroE Thr182Ile, yhcF Thr74Ile, and Asp486Glu in a hypothetical peptidase) in previously unrecognized S. aureus virulence genes that enhance pathogenesis when introduced into a clean genetic background, as well as a novel activating mutation in the known virulence regulator gene saeS (Ala106Thr). Investigation of potentially epistatic interactions identified a tufA mutation (Ala271Val) that enhances virulence only in the context of purine operon repressor gene (purR) inactivation. This project reveals a functionally diverse range of genes affected by gain- or loss-of-function mutations that contribute to S. aureus adaptive virulence phenotypes. More generally, the work establishes artificial selection as a means to determine the genetic mechanisms underlying complex bacterial phenotypes relevant to adaptation during infection.
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24
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Dengler Haunreiter V, Boumasmoud M, Häffner N, Wipfli D, Leimer N, Rachmühl C, Kühnert D, Achermann Y, Zbinden R, Benussi S, Vulin C, Zinkernagel AS. In-host evolution of Staphylococcus epidermidis in a pacemaker-associated endocarditis resulting in increased antibiotic tolerance. Nat Commun 2019; 10:1149. [PMID: 30850614 PMCID: PMC6408453 DOI: 10.1038/s41467-019-09053-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/13/2019] [Indexed: 02/05/2023] Open
Abstract
Treatment failure in biofilm-associated bacterial infections is an important healthcare issue. In vitro studies and mouse models suggest that bacteria enter a slow-growing/non-growing state that results in transient tolerance to antibiotics in the absence of a specific resistance mechanism. However, little clinical confirmation of antibiotic tolerant bacteria in patients exists. In this study we investigate a Staphylococcus epidermidis pacemaker-associated endocarditis, in a patient who developed a break-through bacteremia despite taking antibiotics to which the S. epidermidis isolate is fully susceptible in vitro. Characterization of the clinical S. epidermidis isolates reveals in-host evolution over the 16-week infection period, resulting in increased antibiotic tolerance of the entire population due to a prolonged lag time until growth resumption and a reduced growth rate. Furthermore, we observe adaptation towards an increased biofilm formation capacity and genetic diversification of the S. epidermidis isolates within the patient.
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Affiliation(s)
- Vanina Dengler Haunreiter
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Mathilde Boumasmoud
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Nicola Häffner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Dennis Wipfli
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Nadja Leimer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 02115, Boston, MA, USA
| | - Carole Rachmühl
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland
| | - Denise Kühnert
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Yvonne Achermann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Reinhard Zbinden
- Institute of Medical Microbiology, University of Zurich, 8006, Zurich, Switzerland
| | - Stefano Benussi
- Department of Cardiac Surgery, University Heart Center, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Clement Vulin
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag, 8600, Dübendorf, Switzerland
| | - Annelies S Zinkernagel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland.
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25
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Perez-Lopez MI, Mendez-Reina R, Trier S, Herrfurth C, Feussner I, Bernal A, Forero-Shelton M, Leidy C. Variations in carotenoid content and acyl chain composition in exponential, stationary and biofilm states of Staphylococcus aureus, and their influence on membrane biophysical properties. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:978-987. [PMID: 30771288 DOI: 10.1016/j.bbamem.2019.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 02/01/2019] [Accepted: 02/04/2019] [Indexed: 01/01/2023]
Abstract
Bacteria are often found in close association with surfaces, resulting in the formation of biofilms. In Staphylococcus aureus (S. aureus), biofilms are implicated in the resilience of chronic infections, presenting a serious clinical problem world-wide. Here, S. aureus biofilms are grown under flow within clinical catheters at 37 °C. The lipid composition and biophysical properties of lipid extracts from these biofilms are compared with those from exponential growth and stationary phase cells. Biofilms show a reduction in iso and anteiso branching compensated by an increase in saturated fatty acids compared to stationary phase. A drastic reduction in carotenoid levels is also observed during biofilm formation. Thermotropic measurements of Laurdan GP and DPH polarization, show a reduction of lipid packing at 37 °C for biofilms compared to stationary phase. We studied the effects of carotenoid content on DMPG and DPPG model membranes showing trends in thermotropic behavior consistent with those observed in bacterial isolates, indicating that carotenoids participate in modulating lipid packing. Additionally, bending elastic constant (kc) measurements using vesicle fluctuation analysis (VFA) show that the presence of carotenoids can increase membrane bending rigidity. The antimicrobial peptide Magainin H2 was less activity on liposomes composed of stationary phase compared to biofilms or exponential growth isolates. This study contributes to an understanding of how Staphylococcus aureus modulates the composition of its membrane lipids, and how those changes affect the biophysical properties of membranes, which in turn may play a role in its virulence and its resistance to different membrane-active antimicrobial agents.
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Affiliation(s)
- Maria Isabel Perez-Lopez
- Department of Physics, Universidad de los Andes, Bogotá, Colombia; Biological Sciences Department, Universidad de los Andes, Bogotá, Colombia
| | | | - Steve Trier
- Department of Physics, Universidad de los Andes, Bogotá, Colombia
| | - Cornelia Herrfurth
- Department of Plant Biochemistry, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Goettingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Goettingen, Germany; Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
| | - Adriana Bernal
- Biological Sciences Department, Universidad de los Andes, Bogotá, Colombia
| | | | - Chad Leidy
- Department of Physics, Universidad de los Andes, Bogotá, Colombia.
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26
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Levade I, Terrat Y, Leducq JB, Weil AA, Mayo-Smith LM, Chowdhury F, Khan AI, Boncy J, Buteau J, Ivers LC, Ryan ET, Charles RC, Calderwood SB, Qadri F, Harris JB, LaRocque RC, Shapiro BJ. Vibrio cholerae genomic diversity within and between patients. Microb Genom 2019; 3. [PMID: 29306353 PMCID: PMC5761273 DOI: 10.1099/mgen.0.000142] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Cholera is a severe, water-borne diarrhoeal disease caused by toxin-producing strains of the bacterium Vibrio cholerae. Comparative genomics has revealed 'waves' of cholera transmission and evolution, in which clones are successively replaced over decades and centuries. However, the extent of V. cholerae genetic diversity within an epidemic or even within an individual patient is poorly understood. Here, we characterized V. cholerae genomic diversity at a micro-epidemiological level within and between individual patients from Bangladesh and Haiti. To capture within-patient diversity, we isolated multiple (8 to 20) V. cholerae colonies from each of eight patients, sequenced their genomes and identified point mutations and gene gain/loss events. We found limited but detectable diversity at the level of point mutations within hosts (zero to three single nucleotide variants within each patient), and comparatively higher gene content variation within hosts (at least one gain/loss event per patient, and up to 103 events in one patient). Much of the gene content variation appeared to be due to gain and loss of phage and plasmids within the V. cholerae population, with occasional exchanges between V. cholerae and other members of the gut microbiota. We also show that certain intra-host variants have phenotypic consequences. For example, the acquisition of a Bacteroides plasmid and non-synonymous mutations in a sensor histidine kinase gene both reduced biofilm formation, an important trait for environmental survival. Together, our results show that V. cholerae is measurably evolving within patients, with possible implications for disease outcomes and transmission dynamics.
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Affiliation(s)
- Inès Levade
- 1Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada
| | - Yves Terrat
- 1Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada
| | - Jean-Baptiste Leducq
- 1Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada
| | - Ana A Weil
- 2Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,3Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Leslie M Mayo-Smith
- 2Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Fahima Chowdhury
- 4Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Ashraful I Khan
- 4Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Jacques Boncy
- 5National Public Health Laboratory, Ministry of Public Health and Population, Port-au-Prince, Haiti
| | - Josiane Buteau
- 5National Public Health Laboratory, Ministry of Public Health and Population, Port-au-Prince, Haiti
| | - Louise C Ivers
- 3Department of Medicine, Harvard Medical School, Boston, MA, USA.,6Division of Global Health Equity, Brigham and Women's Hospital, Boston, MA, USA.,7Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Edward T Ryan
- 2Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,3Department of Medicine, Harvard Medical School, Boston, MA, USA.,8Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Richelle C Charles
- 2Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,3Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Stephen B Calderwood
- 2Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,3Department of Medicine, Harvard Medical School, Boston, MA, USA.,9Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Firdausi Qadri
- 4Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Jason B Harris
- 2Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,10Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Regina C LaRocque
- 2Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,3Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - B Jesse Shapiro
- 1Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada
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27
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Bernardy EE, Petit RA, Moller AG, Blumenthal JA, McAdam AJ, Priebe GP, Chande AT, Rishishwar L, Jordan IK, Read TD, Goldberg JB. Whole-Genome Sequences of Staphylococcus aureus Isolates from Cystic Fibrosis Lung Infections. Microbiol Resour Announc 2019; 8:e01564-18. [PMID: 30687841 PMCID: PMC6346173 DOI: 10.1128/mra.01564-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 12/12/2018] [Indexed: 02/05/2023] Open
Abstract
Staphylococcus aureus is an early colonizer in the lungs of individuals with cystic fibrosis (CF), but surprisingly, only a limited number of genomes from CF-associated S. aureus isolates have been sequenced. Here, we present the whole-genome sequences of 65 S. aureus isolates obtained from 50 individuals with CF.
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Affiliation(s)
- Eryn E. Bernardy
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Emory University, Atlanta, Georgia, USA
- Emory-Children’s Center for Cystic Fibrosis Research, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Robert A. Petit
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
| | - Abraham G. Moller
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
| | - Jennifer A. Blumenthal
- Division of Critical Care Medicine, Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts, USA
- Departments of Anaesthesia and Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Alexander J. McAdam
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Gregory P. Priebe
- Division of Critical Care Medicine, Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts, USA
- Departments of Anaesthesia and Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Aroon T. Chande
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Lavanya Rishishwar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - I. King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Timothy D. Read
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
| | - Joanna B. Goldberg
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Emory University, Atlanta, Georgia, USA
- Emory-Children’s Center for Cystic Fibrosis Research, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
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28
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Manara S, Pasolli E, Dolce D, Ravenni N, Campana S, Armanini F, Asnicar F, Mengoni A, Galli L, Montagnani C, Venturini E, Rota-Stabelli O, Grandi G, Taccetti G, Segata N. Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital. Genome Med 2018; 10:82. [PMID: 30424799 PMCID: PMC6234625 DOI: 10.1186/s13073-018-0593-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/29/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Staphylococcus aureus is an opportunistic pathogen and a leading cause of nosocomial infections. It can acquire resistance to all the antibiotics that entered the clinics to date, and the World Health Organization defined it as a high-priority pathogen for research and development of new antibiotics. A deeper understanding of the genetic variability of S. aureus in clinical settings would lead to a better comprehension of its pathogenic potential and improved strategies to contrast its virulence and resistance. However, the number of comprehensive studies addressing clinical cohorts of S. aureus infections by simultaneously looking at the epidemiology, phylogenetic reconstruction, genomic characterisation, and transmission pathways of infective clones is currently low, thus limiting global surveillance and epidemiological monitoring. METHODS We applied whole-genome shotgun sequencing (WGS) to 184 S. aureus isolates from 135 patients treated in different operative units of an Italian paediatric hospital over a timespan of 3 years, including both methicillin-resistant S. aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) from different infection types. We typed known and unknown clones from their genomes by multilocus sequence typing (MLST), Staphylococcal Cassette Chromosome mec (SCCmec), Staphylococcal protein A gene (spa), and Panton-Valentine Leukocidin (PVL), and we inferred their whole-genome phylogeny. We explored the prevalence of virulence and antibiotic resistance genes in our cohort, and the conservation of genes encoding vaccine candidates. We also performed a timed phylogenetic investigation for a potential outbreak of a newly emerging nosocomial clone. RESULTS The phylogeny of the 135 single-patient S. aureus isolates showed a high level of diversity, including 80 different lineages, and co-presence of local, global, livestock-associated, and hypervirulent clones. Five of these clones do not have representative genomes in public databases. Variability in the epidemiology is mirrored by variability in the SCCmec cassettes, with some novel variants of the type IV cassette carrying extra antibiotic resistances. Virulence and resistance genes were unevenly distributed across different clones and infection types, with highly resistant and lowly virulent clones showing strong association with chronic diseases, and highly virulent strains only reported in acute infections. Antigens included in vaccine formulations undergoing clinical trials were conserved at different levels in our cohort, with only a few highly prevalent genes fully conserved, potentially explaining the difficulty of developing a vaccine against S. aureus. We also found a recently diverged ST1-SCCmecIV-t127 PVL- clone suspected to be hospital-specific, but time-resolved integrative phylogenetic analysis refuted this hypothesis and suggested that this quickly emerging lineage was acquired independently by patients. CONCLUSIONS Whole genome sequencing allowed us to study the epidemiology and genomic repertoire of S. aureus in a clinical setting and provided evidence of its often underestimated complexity. Some virulence factors and clones are specific of disease types, but the variability and dispensability of many antigens considered for vaccine development together with the quickly changing epidemiology of S. aureus makes it very challenging to develop full-coverage therapies and vaccines. Expanding WGS-based surveillance of S. aureus to many more hospitals would allow the identification of specific strains representing the main burden of infection and therefore reassessing the efforts for the discovery of new treatments and clinical practices.
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Affiliation(s)
- Serena Manara
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Edoardo Pasolli
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Daniela Dolce
- Cystic Fibrosis Center, Interdisciplinary Specialist Department, Anna Meyer Children's University Hospital, Florence, Italy
| | - Novella Ravenni
- Cystic Fibrosis Center, Interdisciplinary Specialist Department, Anna Meyer Children's University Hospital, Florence, Italy
| | - Silvia Campana
- Cystic Fibrosis Center, Interdisciplinary Specialist Department, Anna Meyer Children's University Hospital, Florence, Italy
| | | | | | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
| | - Luisa Galli
- Department of Health Sciences, University of Florence, Florence, Italy
- Infectious Diseases Unit, Anna Meyer Children's University Hospital, Florence, Italy
| | - Carlotta Montagnani
- Infectious Diseases Unit, Anna Meyer Children's University Hospital, Florence, Italy
| | - Elisabetta Venturini
- Infectious Diseases Unit, Anna Meyer Children's University Hospital, Florence, Italy
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Guido Grandi
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Giovanni Taccetti
- Cystic Fibrosis Center, Interdisciplinary Specialist Department, Anna Meyer Children's University Hospital, Florence, Italy
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, Trento, Italy.
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29
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Antagonistic Pleiotropy in the Bifunctional Surface Protein FadL (OmpP1) during Adaptation of Haemophilus influenzae to Chronic Lung Infection Associated with Chronic Obstructive Pulmonary Disease. mBio 2018; 9:mBio.01176-18. [PMID: 30254117 PMCID: PMC6156194 DOI: 10.1128/mbio.01176-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Tracking bacterial evolution during chronic infection provides insights into how host selection pressures shape bacterial genomes. The human-restricted opportunistic pathogen nontypeable Haemophilus influenzae (NTHi) infects the lower airways of patients suffering chronic obstructive pulmonary disease (COPD) and contributes to disease progression. To identify bacterial genetic variation associated with bacterial adaptation to the COPD lung, we sequenced the genomes of 92 isolates collected from the sputum of 13 COPD patients over 1 to 9 years. Individuals were colonized by distinct clonal types (CTs) over time, but the same CT was often reisolated at a later time or found in different patients. Although genomes from the same CT were nearly identical, intra-CT variation due to mutation and recombination occurred. Recurrent mutations in several genes were likely involved in COPD lung adaptation. Notably, nearly a third of CTs were polymorphic for null alleles of ompP1 (also called fadL), which encodes a bifunctional membrane protein that both binds the human carcinoembryonic antigen-related cell adhesion molecule 1 (hCEACAM1) receptor and imports long-chain fatty acids (LCFAs). Our computational studies provide plausible three-dimensional models for FadL's interaction with hCEACAM1 and LCFA binding. We show that recurrent fadL mutations are likely a case of antagonistic pleiotropy, since loss of FadL reduces NTHi's ability to infect epithelia but also increases its resistance to bactericidal LCFAs enriched within the COPD lung. Supporting this interpretation, truncated fadL alleles are common in publicly available NTHi genomes isolated from the lower airway tract but rare in others. These results shed light on molecular mechanisms of bacterial pathoadaptation and guide future research toward developing novel COPD therapeutics.IMPORTANCE Nontypeable Haemophilus influenzae is an important pathogen in patients with chronic obstructive pulmonary disease (COPD). To elucidate the bacterial pathways undergoing in vivo evolutionary adaptation, we compared bacterial genomes collected over time from 13 COPD patients and identified recurrent genetic changes arising in independent bacterial lineages colonizing different patients. Besides finding changes in phase-variable genes, we found recurrent loss-of-function mutations in the ompP1 (fadL) gene. We show that loss of OmpP1/FadL function reduces this bacterium's ability to infect cells via the hCEACAM1 epithelial receptor but also increases its resistance to bactericidal fatty acids enriched within the COPD lung, suggesting a case of antagonistic pleiotropy that restricts ΔfadL strains' niche. These results show how H. influenzae adapts to host-generated inflammatory mediators in the COPD airways.
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30
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Isolation and characterization of two lytic bacteriophages against Staphylococcus aureus from India: newer therapeutic agents against Bovine mastitis. Vet Res Commun 2018; 42:289-295. [PMID: 30219981 DOI: 10.1007/s11259-018-9736-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/30/2018] [Indexed: 01/19/2023]
Abstract
Bovine mastitis causes severe economic losses to dairy farmers. Staphylococcus aureus, is one of the most important pathogen implicated in etiology of clinical and subclinical mastitis in bovines. In view of increasing antimicrobial resistance alternatives to antibiotic therapy are much needed. The present decade has witnessed a renewed interest in phage based therapeutics and diagnostics. The present study, describes isolation and characterization of two lytic phages SAJK-IND and MSP against Staphylococcus aureus having a potential to be used in therapy against mastitis. SAJK-IND and MSP phages belonged to Myoviridae and Podoviridae families, respectively. TEM imaging of the two phages revealed an iscosahedral head. MSP phage has a short non contractile tail. SAJK-IND and MSP have a burst size of 44 ± 3 and 25 ± 5 PFU/ infected cell, respectively. SAJK-IND and MSP phages revealed ̴ 12 and ̴16 proteins, respectively on SDS-PAGE analysis. The lytic activity of the phages was specific for Staphylococcus aureus. SAJK-IND revealed 100% lytic activity against several strains of Staphylococcus aureus isolated from mastitis milk samples whereas, MSP had only 40% lytic activity. SAJK-IND phage genome was sequenced, assembled and deposited in Genbank under accession no MG010123.
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31
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Pena Amaya P, Haim MS, Fernández S, Di Gregorio S, Teper A, Vázquez M, Lubovich S, Galanternik L, Mollerach M. Molecular Epidemiology of Methicillin-Resistant Staphylococcus aureus in Cystic Fibrosis Patients from Argentina. Microb Drug Resist 2018; 24:613-620. [DOI: 10.1089/mdr.2017.0162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Paula Pena Amaya
- Hospital de Niños “Dr. Ricardo Gutiérrez,” Buenos Aires, Argentina
| | - Maria S. Haim
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Microbiología, Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
| | - Silvina Fernández
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Microbiología, Buenos Aires, Argentina
| | - Sabrina Di Gregorio
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Microbiología, Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
| | - Alejandro Teper
- Hospital de Niños “Dr. Ricardo Gutiérrez,” Buenos Aires, Argentina
| | - Miryam Vázquez
- Hospital de Niños “Dr. Ricardo Gutiérrez,” Buenos Aires, Argentina
| | - Silvina Lubovich
- Hospital de Niños “Dr. Ricardo Gutiérrez,” Buenos Aires, Argentina
| | | | - Marta Mollerach
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Microbiología, Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
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32
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Efficient and Scalable Precision Genome Editing in Staphylococcus aureus through Conditional Recombineering and CRISPR/Cas9-Mediated Counterselection. mBio 2018; 9:mBio.00067-18. [PMID: 29463653 PMCID: PMC5821094 DOI: 10.1128/mbio.00067-18] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Staphylococcus aureus is an important human pathogen, but studies of the organism have suffered from the lack of a robust tool set for its genetic and genomic manipulation. Here we report the development of a system for the facile and high-throughput genomic engineering of S. aureus using single-stranded DNA (ssDNA) oligonucleotide recombineering coupled with clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-mediated counterselection. We identify recombinase EF2132, derived from Enterococcus faecalis, as being capable of integrating single-stranded DNA oligonucleotides into the S. aureus genome. We found that EF2132 can readily mediate recombineering across multiple characterized strains (3 of 3 tested) and primary clinical isolates (6 of 6 tested), typically yielding thousands of recombinants per transformation. Surprisingly, we also found that some S. aureus strains are naturally recombinogenic at measurable frequencies when oligonucleotides are introduced by electroporation, even without exogenous recombinase expression. We construct a temperature-sensitive, two-vector system which enables conditional recombineering and CRISPR/Cas9-mediated counterselection in S. aureus without permanently introducing exogenous genetic material or unintended genetic lesions. We demonstrate the ability of this system to efficiently and precisely engineer point mutations and large single-gene deletions in the S. aureus genome and to yield highly enriched populations of engineered recombinants even in the absence of an externally selectable phenotype. By virtue of utilizing inexpensive, commercially synthesized synthetic DNA oligonucleotides as substrates for recombineering and counterselection, this system provides a scalable, versatile, precise, inexpensive, and generally useful tool for producing isogenic strains in S. aureus which will enable the high-throughput functional assessment of genome variation and gene function across multiple strain backgrounds. Engineering genetic changes in bacteria is critical to understanding the function of particular genes or mutations but is currently a laborious and technically challenging process to perform for the important human pathogen Staphylococcus aureus. In an effort to develop methods which are rapid, easy, scalable, versatile, and inexpensive, here we describe a system for incorporating synthetic, mutagenic DNA molecules into the S. aureus genome and for eliminating cells that lack the engineered mutation. This method allows efficient, precise, and high-throughput genetic engineering of S. aureus strains and will facilitate studies seeking to address a variety of issues about the function of particular genes and specific mutations.
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Caretti A, Vasso M, Bonezzi FT, Gallina A, Trinchera M, Rossi A, Adami R, Casas J, Falleni M, Tosi D, Bragonzi A, Ghidoni R, Gelfi C, Signorelli P. Myriocin treatment of CF lung infection and inflammation: complex analyses for enigmatic lipids. Naunyn Schmiedebergs Arch Pharmacol 2017; 390:775-790. [PMID: 28439630 DOI: 10.1007/s00210-017-1373-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/04/2017] [Indexed: 12/30/2022]
Abstract
Our aim was to use quantitative and qualitative analyses to gain further insight into the role of ceramide in cystic fibrosis (CF). Sphingolipid ceramide is a known inflammatory mediator, and its accumulation in inflamed lung has been reported in different types of emphysema, chronic obstructive pulmonary disease and CF. CF is caused by a mutation of the chloride channel and associated with hyperinflammation of the respiratory airways and high susceptibility to ongoing infections. We have previously demonstrated that de novo ceramide synthesis is enhanced in lung inflammation and sustains Pseudomonas aeruginosa pulmonary infection in a CF murine model. We used liquid chromatography and matrix-assisted laser desorption/ionization (MALDI) imaging coupled with mass spectrometry, confocal laser scan microscopy and histology analyses to reveal otherwise undecipherable information. We demonstrated that (i) upregulated ceramide synthesis in the alveoli is strictly related to alveolar infection and inflammation, (ii) alveolar ceramide (C16) can be specifically targeted by nanocarrier delivery of the ceramide synthesis inhibitor myriocin (Myr) and (iii) Myr is able to downmodulate pro-inflammatory lyso-PC, favouring an increase in anti-inflammatory PCs. We concluded that Myr modulates alveolar lipids milieu, reducing hyperinflammation and favouring anti-microbial effective response in CF mouse model.
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Affiliation(s)
- Anna Caretti
- Biochemistry and Molecular Biology Laboratory, Department of Health Sciences, University of Milan, Via A.di Rudinì 8, 20142, Milan, Italy
| | - Michele Vasso
- Lita Institute, Segrate, University of Milan, Milan, Italy
| | - Fabiola Tecla Bonezzi
- Biochemistry and Molecular Biology Laboratory, Department of Health Sciences, University of Milan, Via A.di Rudinì 8, 20142, Milan, Italy
| | - Andrea Gallina
- Biochemistry and Molecular Biology Laboratory, Department of Health Sciences, University of Milan, Via A.di Rudinì 8, 20142, Milan, Italy
| | - Marco Trinchera
- Department of Medicine Clinical and Experimental, University of Insubria Medical School, Varese, Italy
| | - Alice Rossi
- Infections and Cystic Fibrosis Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Raffaella Adami
- Biochemistry and Molecular Biology Laboratory, Department of Health Sciences, University of Milan, Via A.di Rudinì 8, 20142, Milan, Italy
| | - Josefina Casas
- Research Unit on Bioactive Molecules, Department of Biomedicinal Chemistry, Catalan Institute of Advanced Chemistry (IQAC/CSIC), Barcelona, Spain
| | - Monica Falleni
- Biochemistry and Molecular Biology Laboratory, Department of Health Sciences, University of Milan, Via A.di Rudinì 8, 20142, Milan, Italy
| | - Delfina Tosi
- Biochemistry and Molecular Biology Laboratory, Department of Health Sciences, University of Milan, Via A.di Rudinì 8, 20142, Milan, Italy
| | - Alessandra Bragonzi
- Infections and Cystic Fibrosis Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Riccardo Ghidoni
- Biochemistry and Molecular Biology Laboratory, Department of Health Sciences, University of Milan, Via A.di Rudinì 8, 20142, Milan, Italy
| | - Cecilia Gelfi
- Lita Institute, Segrate, University of Milan, Milan, Italy
| | - Paola Signorelli
- Biochemistry and Molecular Biology Laboratory, Department of Health Sciences, University of Milan, Via A.di Rudinì 8, 20142, Milan, Italy.
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Lymperopoulou DS, Coil DA, Schichnes D, Lindow SE, Jospin G, Eisen JA, Adams RI. Draft genome sequences of eight bacteria isolated from the indoor environment: Staphylococcus capitis strain H36, S. capitis strain H65, S. cohnii strain H62, S. hominis strain H69, Microbacterium sp. strain H83, Mycobacterium iranicum strain H39, Plantibacter sp. strain H53, and Pseudomonas oryzihabitans strain H72. Stand Genomic Sci 2017; 12:17. [PMID: 28163826 PMCID: PMC5282799 DOI: 10.1186/s40793-017-0223-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/08/2016] [Indexed: 11/10/2022] Open
Abstract
We report here the draft genome sequences of eight bacterial strains of the genera Staphylococcus, Microbacterium, Mycobacterium, Plantibacter, and Pseudomonas. These isolates were obtained from aerosol sampling of bathrooms of five residences in the San Francisco Bay area. Taxonomic classifications as well as the genome sequence and gene annotation of the isolates are described. As part of the "Built Environment Reference Genome" project, these isolates and associated genome data provide valuable resources for studying the microbiology of the built environment.
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Affiliation(s)
| | - David A. Coil
- Genome Center, University of California Davis, Davis, USA
| | - Denise Schichnes
- CNR Biological Imaging Facility, University of California Berkeley, Berkeley, USA
| | - Steven E. Lindow
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA USA
| | | | - Jonathan A. Eisen
- Genome Center, University of California Davis, Davis, USA
- Department of Evolution and Ecology, University of California Davis, Davis, USA
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA USA
| | - Rachel I. Adams
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA USA
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35
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Transcriptome Profiling of Antimicrobial Resistance in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2016; 60:4722-33. [PMID: 27216077 DOI: 10.1128/aac.00075-16] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/19/2016] [Indexed: 11/20/2022] Open
Abstract
Emerging resistance to antimicrobials and the lack of new antibiotic drug candidates underscore the need for optimization of current diagnostics and therapies to diminish the evolution and spread of multidrug resistance. As the antibiotic resistance status of a bacterial pathogen is defined by its genome, resistance profiling by applying next-generation sequencing (NGS) technologies may in the future accomplish pathogen identification, prompt initiation of targeted individualized treatment, and the implementation of optimized infection control measures. In this study, qualitative RNA sequencing was used to identify key genetic determinants of antibiotic resistance in 135 clinical Pseudomonas aeruginosa isolates from diverse geographic and infection site origins. By applying transcriptome-wide association studies, adaptive variations associated with resistance to the antibiotic classes fluoroquinolones, aminoglycosides, and β-lactams were identified. Besides potential novel biomarkers with a direct correlation to resistance, global patterns of phenotype-associated gene expression and sequence variations were identified by predictive machine learning approaches. Our research serves to establish genotype-based molecular diagnostic tools for the identification of the current resistance profiles of bacterial pathogens and paves the way for faster diagnostics for more efficient, targeted treatment strategies to also mitigate the future potential for resistance evolution.
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36
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Evolution of Ceftaroline-Resistant Mrsa in a Child with Cystic Fibrosis Following Repeated Antibiotic Exposure. Pediatr Infect Dis J 2016; 35:813-5. [PMID: 27093165 DOI: 10.1097/inf.0000000000001171] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Ceftaroline is the first β-lactam antibiotic with activity against methicillin-resistant Staphylococcus aureus (MRSA). We describe a ceftaroline-resistant MRSA strain, isolated from a girl with cystic fibrosis after 22 ceftaroline treatment courses. MRSA genome sequencing documented a Tyr446Asn alteration in penicillin binding protein 2 that appeared responsible for resistance. Noncompartmental ceftaroline pharmacokinetic evaluation in our patient documented increased clearance and volume of distribution compared with adults.
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37
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Azarian T, Daum RS, Petty LA, Steinbeck JL, Yin Z, Nolan D, Boyle-Vavra S, Hanage WP, Salemi M, David MZ. Intrahost Evolution of Methicillin-Resistant Staphylococcus aureus USA300 Among Individuals With Reoccurring Skin and Soft-Tissue Infections. J Infect Dis 2016; 214:895-905. [PMID: 27288537 DOI: 10.1093/infdis/jiw242] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/31/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) USA300 is the leading cause of MRSA infections in the United States and has caused an epidemic of skin and soft-tissue infections. Recurrent infections with USA300 MRSA are common, yet intrahost evolution during persistence on an individual has not been studied. This gap hinders the ability to clinically manage recurrent infections and reconstruct transmission networks. METHODS To characterize bacterial intrahost evolution, we examined the clinical courses of 4 subjects with 3-6 recurrent USA300 MRSA infections, using patient clinical data, including antibiotic exposure history, and whole-genome sequencing and phylogenetic analysis of all available MRSA isolates (n = 29). RESULTS Among sequential isolates, we found variability in diversity, accumulation of mutations, and mobile genetic elements. Selection for antimicrobial-resistant populations was observed through both an increase in the number of plasmids conferring multidrug resistance and strain replacement by a resistant population. Two of 4 subjects had strain replacement with a genetically distinct USA300 MRSA population. DISCUSSIONS During a 5-year period in 4 subjects, we identified development of antimicrobial resistance, intrahost evolution, and strain replacement among isolates from patients with recurrent MRSA infections. This calls into question the efficacy of decolonization to prevent recurrent infections and highlights the adaptive potential of USA300 and the need for effective sampling.
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Affiliation(s)
- Taj Azarian
- Center for Communicable Disease Dynamics, Department of Epidemiology, T. H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | | | | | | | | | - David Nolan
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine Emerging Pathogens Institute, University of Florida, Gainesville
| | | | - W P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, T. H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine Emerging Pathogens Institute, University of Florida, Gainesville
| | - Michael Z David
- Department of Pediatrics Department of Medicine, University of Chicago, Illinois
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38
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Trouillet-Assant S, Lelièvre L, Martins-Simões P, Gonzaga L, Tasse J, Valour F, Rasigade JP, Vandenesch F, Muniz Guedes RL, Ribeiro de Vasconcelos AT, Caillon J, Lustig S, Ferry T, Jacqueline C, Loss de Morais G, Laurent F. Adaptive processes of Staphylococcus aureus isolates during the progression from acute to chronic bone and joint infections in patients. Cell Microbiol 2016; 18:1405-14. [PMID: 26918656 DOI: 10.1111/cmi.12582] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 02/20/2016] [Indexed: 11/28/2022]
Abstract
Staphylococcus aureus bone and joint infection (BJI) is associated with significant rates of chronicity and relapse. In this study, we investigated how S. aureus is able to adapt to the human environment by comparing isolates from single patients with persisting or relapsing BJIs that were recovered during the initial and recurrent BJI episodes. In vitro and in vivo assays and whole-genome sequencing analyses revealed that the recurrent isolates induced a reduced inflammatory response, formed more biofilms, persisted longer in the intracellular compartments of host bone cells, were less cytotoxic and induced less mortality in a mouse infection model compared with the initial isolates despite the lack of significant changes at the genomic level. These findings suggest that S. aureus BJI chronicization is associated with an in vivo bacterial phenotypical adaptation that leads to decreased virulence and host immune escape, which is linked to increased intraosteoblastic persistence and biofilm formation.
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Affiliation(s)
- Sophie Trouillet-Assant
- Centre International de Recherche en Infectiologie, INSERM U1111, Pathogenesis of staphylococcal infections, University of Lyon 1, Lyon, France. .,Department of Clinical Microbiology, Northern Hospital Group, Hospices Civils de Lyon, Lyon, France.
| | - Lucie Lelièvre
- Centre International de Recherche en Infectiologie, INSERM U1111, Pathogenesis of staphylococcal infections, University of Lyon 1, Lyon, France
| | - Patrícia Martins-Simões
- Centre International de Recherche en Infectiologie, INSERM U1111, Pathogenesis of staphylococcal infections, University of Lyon 1, Lyon, France.,Department of Clinical Microbiology, Northern Hospital Group, Hospices Civils de Lyon, Lyon, France
| | - Luiz Gonzaga
- Bioinformatics Laboratory - LABINFO, National Laboratory of Scientific Computation - LNCC/MCTI, Petrópolis, Brazil
| | - Jason Tasse
- Centre International de Recherche en Infectiologie, INSERM U1111, Pathogenesis of staphylococcal infections, University of Lyon 1, Lyon, France.,Department of Clinical Microbiology, Northern Hospital Group, Hospices Civils de Lyon, Lyon, France
| | - Florent Valour
- Centre International de Recherche en Infectiologie, INSERM U1111, Pathogenesis of staphylococcal infections, University of Lyon 1, Lyon, France.,Infectious Diseases Department, Northern Hospital Group, Hospices Civils de Lyon, Lyon, France
| | - Jean-Philippe Rasigade
- Centre International de Recherche en Infectiologie, INSERM U1111, Pathogenesis of staphylococcal infections, University of Lyon 1, Lyon, France.,Department of Clinical Microbiology, Northern Hospital Group, Hospices Civils de Lyon, Lyon, France.,National Reference Center for Staphylococci, Hospices Civils de Lyon, Lyon, France
| | - François Vandenesch
- Centre International de Recherche en Infectiologie, INSERM U1111, Pathogenesis of staphylococcal infections, University of Lyon 1, Lyon, France.,Department of Clinical Microbiology, Northern Hospital Group, Hospices Civils de Lyon, Lyon, France.,National Reference Center for Staphylococci, Hospices Civils de Lyon, Lyon, France
| | - Rafael Lucas Muniz Guedes
- Bioinformatics Laboratory - LABINFO, National Laboratory of Scientific Computation - LNCC/MCTI, Petrópolis, Brazil
| | | | - Jocelyne Caillon
- University of Nantes, Medical School, UPRES EA, 3826, Nantes, France
| | - Sebastien Lustig
- Orthopedic Surgery Department, Northern Hospital Group, Hospices Civils de Lyon, Lyon, France
| | - Tristan Ferry
- Centre International de Recherche en Infectiologie, INSERM U1111, Pathogenesis of staphylococcal infections, University of Lyon 1, Lyon, France.,Infectious Diseases Department, Northern Hospital Group, Hospices Civils de Lyon, Lyon, France
| | - Cédric Jacqueline
- University of Nantes, Medical School, UPRES EA, 3826, Nantes, France
| | - Guilherme Loss de Morais
- Bioinformatics Laboratory - LABINFO, National Laboratory of Scientific Computation - LNCC/MCTI, Petrópolis, Brazil
| | - Frédéric Laurent
- Centre International de Recherche en Infectiologie, INSERM U1111, Pathogenesis of staphylococcal infections, University of Lyon 1, Lyon, France.,Department of Clinical Microbiology, Northern Hospital Group, Hospices Civils de Lyon, Lyon, France.,National Reference Center for Staphylococci, Hospices Civils de Lyon, Lyon, France
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39
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O’Neill MB, Mortimer TD, Pepperell CS. Diversity of Mycobacterium tuberculosis across Evolutionary Scales. PLoS Pathog 2015; 11:e1005257. [PMID: 26562841 PMCID: PMC4642946 DOI: 10.1371/journal.ppat.1005257] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 10/12/2015] [Indexed: 11/28/2022] Open
Abstract
Tuberculosis (TB) is a global public health emergency. Increasingly drug resistant strains of Mycobacterium tuberculosis (M.tb) continue to emerge and spread, highlighting adaptability of this pathogen. Most studies of M.tb evolution have relied on ‘between-host’ samples, in which each person with TB is represented by a single M.tb isolate. However, individuals with TB commonly harbor populations of M.tb numbering in the billions. Here, we use analyses of M.tb genomic data from within and between hosts to gain insight into influences shaping genetic diversity of this pathogen. We find that the amount of M.tb genetic diversity harbored by individuals with TB can vary dramatically, likely as a function of disease severity. Surprisingly, we did not find an appreciable impact of TB treatment on M.tb diversity. In examining genomic data from M.tb samples within and between hosts with TB, we find that genes involved in the regulation, synthesis, and transportation of immunomodulatory cell envelope lipids appear repeatedly in the extremes of various statistical measures of diversity. Many of these genes have been identified as possible targets of selection in other studies employing different methods and data sets. Taken together, these observations suggest that M.tb cell envelope lipids are targets of selection within hosts. Many of these lipids are specific to pathogenic mycobacteria and, in some cases, human-pathogenic mycobacteria. We speculate that rapid adaptation of cell envelope lipids is facilitated by functional redundancy, flexibility in their metabolism, and their roles mediating interactions with the host. Tuberculosis (TB) is a grave threat to global public health and is the second leading cause of death due to infectious disease. The causative agent, Mycobacterium tuberculosis (M.tb), has emerged in increasingly drug resistant forms that hamper our efforts to control TB. We need a better understanding of M.tb adaptation to guide development of more effective TB treatment and control strategies. The goal of this study was to gain insight into M.tb evolution within individual patients with TB. We found that TB patients harbor a diverse population of M.tb. We further found evidence to suggest that the bacterial population evolves measurably in response to selection pressures imposed by the environment within hosts. Changes were particularly notable in M.tb genes involved in the regulation, synthesis, and transportation of lipids and glycolipids of the bacterial cell envelope. These findings have important implications for drug and vaccine development, and provide insight into TB host pathogen interactions.
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Affiliation(s)
- Mary B. O’Neill
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Tatum D. Mortimer
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Caitlin S. Pepperell
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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40
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Genetic Adaptation of Achromobacter sp. during Persistence in the Lungs of Cystic Fibrosis Patients. PLoS One 2015; 10:e0136790. [PMID: 26313451 PMCID: PMC4552427 DOI: 10.1371/journal.pone.0136790] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 08/07/2015] [Indexed: 12/26/2022] Open
Abstract
Achromobacter species are increasingly isolated from the respiratory tract of cystic fibrosis patients and often a chronic infection is established. How Achromobacter sp. adapts to the human host remains uncharacterised. By comparing longitudinally collected isolates of Achromobacter sp. isolated from five CF patients, we have investigated the within-host evolution of clonal lineages. The majority of identified mutations were isolate-specific suggesting co-evolution of several subpopulations from the original infecting isolate. The largest proportion of mutated genes were involved in the general metabolism of the bacterium, but genes involved in virulence and antimicrobial resistance were also affected. A number of virulence genes required for initiation of acute infection were selected against, e.g. genes of the type I and type III secretion systems and genes related to pilus and flagellum formation or function. Six antimicrobial resistance genes or their regulatory genes were mutated, including large deletions affecting the repressor genes of an RND-family efflux pump and a beta-lactamase. Convergent evolution was observed for five genes that were all implicated in bacterial virulence. Characterisation of genes involved in adaptation of Achromobacter to the human host is required for understanding the pathogen-host interaction and facilitate design of future therapeutic interventions.
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41
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Gao W, Monk IR, Tobias NJ, Gladman SL, Seemann T, Stinear TP, Howden BP. Large tandem chromosome expansions facilitate niche adaptation during persistent infection with drug-resistant Staphylococcus aureus. Microb Genom 2015; 1:e000026. [PMID: 28348811 PMCID: PMC5320569 DOI: 10.1099/mgen.0.000026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 06/15/2015] [Indexed: 01/25/2023] Open
Abstract
We used genomics to study the evolution of meticillin-resistant Staphylococcus aureus (MRSA) during a complex, protracted clinical infection. Preparing closed MRSA genomes from days 0 and 115 allowed us to precisely reconstruct all genetic changes that occurred. Twenty-three MRSA blood cultures were also obtained during treatment, yielding 44 colony morphotypes that varied in size, haemolysis and antibiotic susceptibility. A subset of 15 isolates was sequenced and shown to harbour a total of 37 sequence polymorphisms. Eighty per cent of all mutations occurred from day 45 onwards, which coincided with the appearance of discrete chromosome expansions, and concluded in the day 115 isolate with a 98 kb tandem DNA duplication. In all heterogeneous vancomycin-intermediate Staphylococcus aureus isolates, the chromosomal amplification spanned at least a 20 kb region that notably included mprF, a gene involved in resistance to antimicrobial peptides, and parC, an essential DNA replication gene with an unusual V463 codon insertion. Restoration of the chromosome after serial passage under non-selective growth was accompanied by increased susceptibility to antimicrobial peptide killing and reduced vancomycin resistance, two signature phenotypes that help explain the clinical persistence of this strain. Elevated expression of the V463 parC was deleterious to the cell and reduced colony size, but did not alter ciprofloxacin susceptibility. In this study, we identified large DNA expansions as a clinically relevant mechanism of S. aureus resistance and persistence, demonstrating the extent to which bacterial chromosomes remodel in the face of antibiotic and host immune pressures.
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Affiliation(s)
- Wei Gao
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne, Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
- Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Ian R. Monk
- Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Nicholas J. Tobias
- Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Simon L. Gladman
- Victorian Life Sciences Computation Initiative, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Torsten Seemann
- Victorian Life Sciences Computation Initiative, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
- Correspondence: Timothy P. Stinear ()
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne, Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
- Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
- Infectious Diseases Department, Austin Hospital, Heidelberg, Victoria 3084, Australia
- Benjamin P. Howden ()
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42
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Hospital-associated microbiota and implications for nosocomial infections. Trends Mol Med 2015; 21:427-32. [PMID: 25907678 DOI: 10.1016/j.molmed.2015.03.005] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 12/23/2022]
Abstract
The rise of high-throughput sequencing technologies and culture-independent microbial surveys has the potential to revolutionize our understanding of how microbes colonize, move about, and evolve in hospital environments. Genome analysis of individual organisms, characterization of population dynamics, and microbial community ecology are facilitating the identification of novel pathogens, the tracking of disease outbreaks, and the study of the evolution of antibiotic resistance. Here we review the recent applications of these methods to microbial ecology studies in hospitals and discuss their potential to influence hospital management policy and practice and to reduce nosocomial infections and the spread of antibiotic resistance.
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43
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Bacterial Adaptation during Chronic Respiratory Infections. Pathogens 2015; 4:66-89. [PMID: 25738646 PMCID: PMC4384073 DOI: 10.3390/pathogens4010066] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/15/2015] [Accepted: 02/25/2015] [Indexed: 01/22/2023] Open
Abstract
Chronic lung infections are associated with increased morbidity and mortality for individuals with underlying respiratory conditions such as cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD). The process of chronic colonisation allows pathogens to adapt over time to cope with changing selection pressures, co-infecting species and antimicrobial therapies. These adaptations can occur due to environmental pressures in the lung such as inflammatory responses, hypoxia, nutrient deficiency, osmolarity, low pH and antibiotic therapies. Phenotypic adaptations in bacterial pathogens from acute to chronic infection include, but are not limited to, antibiotic resistance, exopolysaccharide production (mucoidy), loss in motility, formation of small colony variants, increased mutation rate, quorum sensing and altered production of virulence factors associated with chronic infection. The evolution of Pseudomonas aeruginosa during chronic lung infection has been widely studied. More recently, the adaptations that other chronically colonising respiratory pathogens, including Staphylococcus aureus, Burkholderia cepacia complex and Haemophilus influenzae undergo during chronic infection have also been investigated. This review aims to examine the adaptations utilised by different bacterial pathogens to aid in their evolution from acute to chronic pathogens of the immunocompromised lung including CF and COPD.
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Long SW, Olsen RJ, Mehta SC, Palzkill T, Cernoch PL, Perez KK, Musick WL, Rosato AE, Musser JM. PBP2a mutations causing high-level Ceftaroline resistance in clinical methicillin-resistant Staphylococcus aureus isolates. Antimicrob Agents Chemother 2014; 58:6668-74. [PMID: 25155594 PMCID: PMC4249384 DOI: 10.1128/aac.03622-14] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/16/2014] [Indexed: 12/25/2022] Open
Abstract
Ceftaroline is the first member of a novel class of cephalosporins approved for use in the United States. Although prior studies have identified eight ceftaroline-resistant methicillin-resistant Staphylococcus aureus (MRSA) isolates in Europe and Asia with MICs ranging from 4 to 8 mg/liter, high-level resistance to ceftaroline (>32 mg/liter) has not been described in MRSA strains isolated in the United States. We isolated a ceftaroline-resistant (MIC > 32 mg/liter) MRSA strain from the blood of a cystic fibrosis patient and five MRSA strains from the respiratory tract of this patient. Whole-genome sequencing identified two amino acid-altering mutations uniquely present in the ceftaroline-binding pocket of the transpeptidase region of penicillin-binding protein 2a (PBP2a) in ceftaroline-resistant isolates. Biochemical analyses and the study of isogenic mutant strains confirmed that these changes caused ceftaroline resistance. Thus, we identified the molecular mechanism of ceftaroline resistance in the first MRSA strain with high-level ceftaroline resistance isolated in the United States.
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Affiliation(s)
- S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - Shrenik C Mehta
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Timothy Palzkill
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Patricia L Cernoch
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - Katherine K Perez
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA Department of Pharmacy, Houston Methodist Hospital, Houston, Texas, USA
| | - William L Musick
- Department of Pharmacy, Houston Methodist Hospital, Houston, Texas, USA
| | - Adriana E Rosato
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
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Transcriptional adaptations during long-term persistence of Staphylococcus aureus in the airways of a cystic fibrosis patient. Int J Med Microbiol 2014; 305:38-46. [PMID: 25439320 DOI: 10.1016/j.ijmm.2014.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 08/22/2014] [Accepted: 10/20/2014] [Indexed: 12/16/2022] Open
Abstract
The lungs of Cystic fibrosis (CF) patients are often colonized and/or infected by Staphylococcus aureus for years, mostly by one predominant clone. For long-term survival in this environment, S. aureus needs to adapt during its interactions with host factors, antibiotics, and other pathogens. Here, we study long-term transcriptional as well as genomic adaptations of an isogenic pair of S. aureus isolates from a single patient using RNA sequencing (RNA-Seq) and whole genome sequencing (WGS). Mimicking in vivo conditions, we cultivated the S. aureus isolates using artificial sputum medium before harvesting RNA for subsequent analysis. We confirmed our RNA-Seq data using quantitative real-time (qRT)-PCR and additionally investigated intermediate isolates from the same patient representing in total 13.2 years of persistence in the CF airways. Comparative RNA-Seq analysis of the first and the last ("late") isolate revealed significant differences in the late isolate after 13.2 years of persistence. Of the 2545 genes expressed in both isolates that were cultivated aerobically, 256 genes were up- and 161 were down-regulated with a minimum 2-fold change (2f). Focusing on 25 highly (≥8f) up- (n=9) or down- (n=16) regulated genes, we identified several genes encoding for virulence factors involved in immune evasion, bacterial spread or secretion (e.g. spa, sak, and esxA). Moreover, these genes displayed similar expression trends under aerobic, microaerophilic and anaerobic conditions. Further qRT-PCR-experiments of highly up- or down-regulated genes within intermediate S. aureus isolates resulted in different gene expression patterns over the years. Using sequencing analysis of the differently expressed genes and their upstream regions in the late S. aureus isolate resulted in only few genomic alterations. Comparative transcriptomic analysis revealed adaptive changes affecting mainly genes involved in host-pathogen interaction. Although the underlying mechanisms were not known, our results suggest adaptive processes beyond genomic mutations triggered by local factors rather than by activation of global regulators.
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Dalhoff A. Pharmacokinetics and pharmacodynamics of aerosolized antibacterial agents in chronically infected cystic fibrosis patients. Clin Microbiol Rev 2014; 27:753-82. [PMID: 25278574 PMCID: PMC4187638 DOI: 10.1128/cmr.00022-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacteria adapt to growth in lungs of patients with cystic fibrosis (CF) by selection of heterogeneously resistant variants that are not detected by conventional susceptibility testing but are selected for rapidly during antibacterial treatment. Therefore, total bacterial counts and antibiotic susceptibilities are misleading indicators of infection and are not helpful as guides for therapy decisions or efficacy endpoints. High drug concentrations delivered by aerosol may maximize efficacy, as decreased drug susceptibilities of the pathogens are compensated for by high target site concentrations. However, reductions of the bacterial load in sputum and improvements in lung function were within the same ranges following aerosolized and conventional therapies. Furthermore, the use of conventional pharmacokinetic/pharmacodynamic (PK/PD) surrogates correlating pharmacokinetics in serum with clinical cure and presumed or proven eradication of the pathogen as a basis for PK/PD investigations in CF patients is irrelevant, as minimization of systemic exposure is one of the main objectives of aerosolized therapy; in addition, bacterial pathogens cannot be eradicated, and chronic infection cannot be cured. Consequently, conventional PK/PD surrogates are not applicable to CF patients. It is nonetheless obvious that systemic exposure of patients, with all its sequelae, is minimized and that the burden of oral treatment for CF patients suffering from chronic infections is reduced.
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Affiliation(s)
- Axel Dalhoff
- University Medical Center Schleswig-Holstein, Institute for Infection Medicine, Kiel, Germany
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Koch G, Yepes A, Förstner KU, Wermser C, Stengel ST, Modamio J, Ohlsen K, Foster KR, Lopez D. Evolution of resistance to a last-resort antibiotic in Staphylococcus aureus via bacterial competition. Cell 2014; 158:1060-1071. [PMID: 25171407 PMCID: PMC4163622 DOI: 10.1016/j.cell.2014.06.046] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 04/28/2014] [Accepted: 06/23/2014] [Indexed: 01/02/2023]
Abstract
Antibiotic resistance is a key medical concern, with antibiotic use likely being an important cause. However, here we describe an alternative route to clinically relevant antibiotic resistance that occurs solely due to competitive interactions among bacterial cells. We consistently observe that isolates of Methicillin-resistant Staphylococcus aureus diversify spontaneously into two distinct, sequentially arising strains. The first evolved strain outgrows the parent strain via secretion of surfactants and a toxic bacteriocin. The second is resistant to the bacteriocin. Importantly, this second strain is also resistant to intermediate levels of vancomycin. This so-called VISA (vancomycin-intermediate S. aureus) phenotype is seen in many hard-to-treat clinical isolates. This strain diversification also occurs during in vivo infection in a mouse model, which is consistent with the fact that both coevolved phenotypes resemble strains commonly found in clinic. Our study shows how competition between coevolving bacterial strains can generate antibiotic resistance and recapitulate key clinical phenotypes.
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Affiliation(s)
- Gudrun Koch
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
| | - Ana Yepes
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
| | - Konrad U Förstner
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Charlotte Wermser
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
| | - Stephanie T Stengel
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
| | - Jennifer Modamio
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
| | - Knut Ohlsen
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Kevin R Foster
- Department of Zoology, University of Oxford, Oxford OX1 3QU, UK; Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3QU, UK
| | - Daniel Lopez
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany.
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48
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The Agr quorum-sensing system regulates fibronectin binding but not hemolysis in the absence of a functional electron transport chain. Infect Immun 2014; 82:4337-47. [PMID: 25092909 DOI: 10.1128/iai.02254-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Staphylococcus aureus is responsible for numerous chronic and recurrent infections, which are frequently associated with the emergence of small-colony variants (SCVs) that lack a functional electron transport chain. SCVs exhibit enhanced expression of fibronectin-binding protein (FnBP) and greatly reduced hemolysin production, although the basis for this is unclear. One hypothesis is that these phenotypes are a consequence of the reduced Agr activity of SCVs, while an alternative is that the lack of a functional electron transport chain and the resulting reduction in ATP production are responsible. Disruption of the electron transport chain of S. aureus genetically (hemB and menD) or chemically, using 2-n-heptyl-4-hydroxyquinoline N-oxide (HQNO), inhibited both growth and Agr activity and conferred an SCV phenotype. Supplementation of the culture medium with synthetic autoinducing peptide (sAIP) significantly increased Agr expression in both hemB mutant strains and S. aureus grown with HQNO and significantly reduced staphylococcal adhesion to fibronectin. However, sAIP did not promote hemolysin expression in hemB mutant strains or S. aureus grown with HQNO. Therefore, while Agr regulates fibronectin binding in SCVs, it cannot promote hemolysin production in the absence of a functional electron transport chain.
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McAdam PR, Richardson EJ, Fitzgerald JR. High-throughput sequencing for the study of bacterial pathogen biology. Curr Opin Microbiol 2014; 19:106-113. [PMID: 25033019 PMCID: PMC4150483 DOI: 10.1016/j.mib.2014.06.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 06/02/2014] [Accepted: 06/07/2014] [Indexed: 12/23/2022]
Abstract
A revolution in sequencing technologies in recent years has led to dramatically increased throughput and reduced cost of bacterial genome sequencing. An increasing number of applications of the new technologies are providing broad insights into bacterial evolution, epidemiology, and pathogenesis. For example, the capacity to sequence large numbers of bacterial isolates is enabling high resolution phylogenetic analyses of bacterial populations leading to greatly enhanced understanding of the emergence, adaptation, and transmission of pathogenic clones. In addition, RNA-seq offers improved quantification and resolution for transcriptomic analysis, and the combination of high-throughput sequencing with transposon mutagenesis is a powerful approach for the identification of bacterial determinants required for survival in vivo. In this concise review we provide selected examples of how high throughput sequencing is being applied to understand the biology of bacterial pathogens, and discuss future technological advances likely to have a profound impact on the field.
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Affiliation(s)
- Paul R McAdam
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, United Kingdom
| | - Emily J Richardson
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, United Kingdom
| | - J Ross Fitzgerald
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, United Kingdom.
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50
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Hartfield M, Murall CL, Alizon S. Clinical applications of pathogen phylogenies. Trends Mol Med 2014; 20:394-404. [DOI: 10.1016/j.molmed.2014.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/02/2014] [Accepted: 04/03/2014] [Indexed: 12/16/2022]
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