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Shariati A, Arshadi M, Khosrojerdi MA, Abedinzadeh M, Ganjalishahi M, Maleki A, Heidary M, Khoshnood S. The resistance mechanisms of bacteria against ciprofloxacin and new approaches for enhancing the efficacy of this antibiotic. Front Public Health 2022; 10:1025633. [PMID: 36620240 PMCID: PMC9815622 DOI: 10.3389/fpubh.2022.1025633] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
For around three decades, the fluoroquinolone (FQ) antibiotic ciprofloxacin has been used to treat a range of diseases, including chronic otorrhea, endocarditis, lower respiratory tract, gastrointestinal, skin and soft tissue, and urinary tract infections. Ciprofloxacin's main mode of action is to stop DNA replication by blocking the A subunit of DNA gyrase and having an extra impact on the substances in cell walls. Available in intravenous and oral formulations, ciprofloxacin reaches therapeutic concentrations in the majority of tissues and bodily fluids with a low possibility for side effects. Despite the outstanding qualities of this antibiotic, Salmonella typhi, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa have all shown an increase in ciprofloxacin resistance over time. The rise of infections that are resistant to ciprofloxacin shows that new pharmacological synergisms and derivatives are required. To this end, ciprofloxacin may be more effective against the biofilm community of microorganisms and multi-drug resistant isolates when combined with a variety of antibacterial agents, such as antibiotics from various classes, nanoparticles, natural products, bacteriophages, and photodynamic therapy. This review focuses on the resistance mechanisms of bacteria against ciprofloxacin and new approaches for enhancing its efficacy.
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Affiliation(s)
- Aref Shariati
- Molecular and Medicine Research Center, Khomein University of Medical Sciences, Khomein, Iran
| | - Maniya Arshadi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Mostafa Abedinzadeh
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Mahsa Ganjalishahi
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Abbas Maleki
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Mohsen Heidary
- Department of Laboratory Sciences, School of Paramedical Sciences, Sabzevar University of Medical Sciences, Sabzevar, Iran,Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran,*Correspondence: Mohsen Heidary
| | - Saeed Khoshnood
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran,Student Research Committee, Ilam University of Medical Sciences, Ilam, Iran,Saeed Khoshnood
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Jones F, Hu Y, Coates A. The Efficacy of Using Combination Therapy against Multi-Drug and Extensively Drug-Resistant Pseudomonas aeruginosa in Clinical Settings. Antibiotics (Basel) 2022; 11:323. [PMID: 35326786 PMCID: PMC8944682 DOI: 10.3390/antibiotics11030323] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium which is capable of developing a high level of antibiotic resistance. It has been placed on the WHO's critical priority pathogen list and it is commonly found in ventilator-associated pneumonia infections, blood stream infections and other largely hospital-acquired illnesses. These infections are difficult to effectively treat due to their increasing antibiotic resistance and as such patients are often treated with antibiotic combination regimens. METHODS We conducted a systematic search with screening criteria using the Ovid search engine and the Embase, Ovid Medline, and APA PsycInfo databases. RESULTS It was found that in many cases the combination therapies were able to match or outperform the monotherapies and none performed noticeably worse than the monotherapies. However, the clinical studies were mostly small, only a few were prospective randomized clinical trials and statistical significance was lacking. CONCLUSIONS It was concluded that combination therapies have a place in the treatment of these highly resistant bacteria and, in some cases, there is some evidence to suggest that they provide a more effective treatment than monotherapies.
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Affiliation(s)
| | | | - Anthony Coates
- Institute for Infection and Immunity, St George’s University of London, London SW17 0RE, UK; (F.J.); (Y.H.)
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3
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Sherrard LJ, Wee BA, Duplancic C, Ramsay KA, Dave KA, Ballard E, Wainwright CE, Grimwood K, Sidjabat HE, Whiley DM, Beatson SA, Kidd TJ, Bell SC. Emergence and impact of oprD mutations in Pseudomonas aeruginosa strains in cystic fibrosis. J Cyst Fibros 2021; 21:e35-e43. [PMID: 33775602 DOI: 10.1016/j.jcf.2021.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Antimicrobial resistance in cystic fibrosis (CF) Pseudomonas aeruginosa airway infection is complex and often attributed to chromosomal mutations. How these mutations emerge in specific strains or whether particular gene mutations are clinically informative is unclear. This study focused on oprD, which encodes an outer membrane porin associated with carbapenem resistance when it is downregulated or inactivated. AIM Determine how mutations in oprD emerge in two prevalent Australian shared CF strains of P. aeruginosa and their clinical relevance. METHODS The two most common shared CF strains in Queensland were investigated using whole genome sequencing and their oprD sequences and antimicrobial resistance phenotypes were established. P. aeruginosa mutants with the most common oprD variants were constructed and characterised. Clinical variables were compared between people with or without evidence of infection with strains harbouring these variants. RESULTS Frequently found nonsense mutations arising from a 1-base pair substitution in oprD evolved independently in three sub-lineages, and are likely major contributors to the reduced carbapenem susceptibility observed in the clinical isolates. Lower baseline FEV1 %predicted was identified as a risk factor for infection with a sub-lineage (odds ratio=0.97; 95% confidence interval 0.96-0.99; p<0.001). However, acquiring these sub-lineage strains did not confer an accelerated decline in FEV1 nor increase the risk of death/lung transplantation. CONCLUSIONS Sub-lineages harbouring specific mutations in oprD have emerged and persisted in the shared strain populations. Infection with the sub-lineages was more likely in people with lower lung function, but this was not predictive of a worse clinical trajectory.
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Affiliation(s)
| | - Bryan A Wee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | | | - Kay A Ramsay
- QIMR Berghofer Medical Research Institute, Brisbane, Australia; Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Keyur A Dave
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Emma Ballard
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Claire E Wainwright
- Faculty of Medicine, The University of Queensland, Brisbane, Australia; Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, Brisbane, Australia
| | - Keith Grimwood
- School of Medicine and Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia; Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Gold Coast, Australia
| | - Hanna E Sidjabat
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia
| | - David M Whiley
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia; Pathology Queensland Central Laboratory, Brisbane, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia; Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
| | - Timothy J Kidd
- QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
| | - Scott C Bell
- QIMR Berghofer Medical Research Institute, Brisbane, Australia; Faculty of Medicine, The University of Queensland, Brisbane, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia; Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia.
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4
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Vaitekenas A, Tai AS, Ramsay JP, Stick SM, Kicic A. Pseudomonas aeruginosa Resistance to Bacteriophages and Its Prevention by Strategic Therapeutic Cocktail Formulation. Antibiotics (Basel) 2021; 10:145. [PMID: 33540528 PMCID: PMC7912912 DOI: 10.3390/antibiotics10020145] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance poses a significant threat to modern healthcare as it limits treatment options for bacterial infections, particularly impacting those with chronic conditions such as cystic fibrosis (CF). Viscous mucus accumulation in the lungs of individuals genetically predisposed to CF leads to recurrent bacterial infections, necessitating prolonged antimicrobial chemotherapy. Pseudomonas aeruginosa infections are the predominant driver of CF lung disease, and airway isolates are frequently resistant to multiple antimicrobials. Bacteriophages, or phages, are viruses that specifically infect bacteria and are a promising alternative to antimicrobials for CF P. aeruginosa infections. However, the narrow host range of P. aeruginosa-targeting phages and the rapid evolution of phage resistance could limit the clinical efficacy of phage therapy. A promising approach to overcome these issues is the strategic development of mixtures of phages (cocktails). The aim is to combine phages with broad host ranges and target multiple distinct bacterial receptors to prevent the evolution of phage resistance. However, further research is required to identify and characterize phage resistance mechanisms in CF-derived P. aeruginosa, which differ from their non-CF counterparts. In this review, we consider the mechanisms of P. aeruginosa phage resistance and how these could be overcome by an effective future phage therapy formulation.
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Affiliation(s)
- Andrew Vaitekenas
- Occupation and the Environment, School of Public Health, Curtin University, Perth, WA 6102, Australia
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, The University of Western Australia, Crawley, WA 6009, Australia; (A.V.); (S.M.S.)
| | - Anna S. Tai
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, WA 6009, Australia;
- Institute for Respiratory Health, Perth, WA 6009, Australia
- Faculty of Health and Medical Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Joshua P. Ramsay
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia;
| | - Stephen M. Stick
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, The University of Western Australia, Crawley, WA 6009, Australia; (A.V.); (S.M.S.)
- Division of Paediatrics, School of Medicine, The University of Western Australia, Perth, WA 6009, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Perth, WA 6009, Australia
- Center for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Anthony Kicic
- Occupation and the Environment, School of Public Health, Curtin University, Perth, WA 6102, Australia
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, The University of Western Australia, Crawley, WA 6009, Australia; (A.V.); (S.M.S.)
- Division of Paediatrics, School of Medicine, The University of Western Australia, Perth, WA 6009, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Perth, WA 6009, Australia
- Center for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
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5
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Azimi S, Roberts AEL, Peng S, Weitz JS, McNally A, Brown SP, Diggle SP. Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations. ISME JOURNAL 2020; 14:1929-1942. [PMID: 32341475 DOI: 10.1038/s41396-020-0652-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/23/2020] [Accepted: 03/31/2020] [Indexed: 12/31/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that chronically infects the lungs of individuals with cystic fibrosis (CF) by forming antibiotic-resistant biofilms. Emergence of phenotypically diverse isolates within CF P. aeruginosa populations has previously been reported; however, the impact of heterogeneity on social behaviors and community function is poorly understood. Here we describe how this heterogeneity impacts on behavioral traits by evolving the strain PAO1 in biofilms grown in a synthetic sputum medium for 50 days. We measured social trait production and antibiotic tolerance, and used a metagenomic approach to analyze and assess genomic changes over the duration of the evolution experiment. We found that (i) evolutionary trajectories were reproducible in independently evolving populations; (ii) over 60% of genomic diversity occurred within the first 10 days of selection. We then focused on quorum sensing (QS), a well-studied P. aeruginosa trait that is commonly mutated in strains isolated from CF lungs. We found that at the population level, (i) evolution in sputum medium selected for decreased the production of QS and QS-dependent traits; (ii) there was a significant correlation between lasR mutant frequency, the loss of protease, and the 3O-C12-HSL signal, and an increase in resistance to clinically relevant β-lactam antibiotics, despite no previous antibiotic exposure. Overall, our findings provide insights into the effect of allelic polymorphism on community functions in diverse P. aeruginosa populations. Further, we demonstrate that P. aeruginosa population and evolutionary dynamics can impact on traits important for virulence and can lead to increased tolerance to β-lactam antibiotics.
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Affiliation(s)
- Sheyda Azimi
- Center for Microbial Dynamics & Infection, Georgia Institute of Technology, Atlanta, GA, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Aled E L Roberts
- Microbiology & Infectious Diseases Group, Institute of Life Science, Swansea University Medical School, Swansea, UK
| | - Shengyun Peng
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Joshua S Weitz
- Center for Microbial Dynamics & Infection, Georgia Institute of Technology, Atlanta, GA, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Samuel P Brown
- Center for Microbial Dynamics & Infection, Georgia Institute of Technology, Atlanta, GA, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Stephen P Diggle
- Center for Microbial Dynamics & Infection, Georgia Institute of Technology, Atlanta, GA, USA. .,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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6
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Epidemiology of Clonal Pseudomonas aeruginosa Infection in a Canadian Cystic Fibrosis Population. Ann Am Thorac Soc 2019; 15:827-836. [PMID: 29911888 DOI: 10.1513/annalsats.201801-007oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
RATIONALE The extent of the genetic relatedness among Pseudomonas aeruginosa isolates and its impact on clinical outcomes in the cystic fibrosis (CF) population is poorly understood. OBJECTIVES The objectives of this study were to determine the prevalence of clonal P. aeruginosa infection in Canada and to associate P. aeruginosa genotypes with clinical outcomes. METHODS This was an observational study of adult and pediatric patients with CF across Canada. Isolates were typed using multilocus sequence typing. A clone was defined as sharing at least six of seven alleles. Genotyping results were associated with clinical outcomes, including forced expiratory volume in 1 second, body mass index, rate of pulmonary exacerbation, and death/transplant. RESULTS A total of 1,537 P. aeruginosa isolates were genotyped to 403 unique sequence types (STs) in 402 individuals with CF. Although 39% of STs were shared, most were shared only among a small number of subjects, and the majority (79%) of the genetic diversity in P. aeruginosa isolates was observed between patients. There were no significant differences in clinical outcomes according to genotype. However, patients with a dynamic, changing ST infection pattern had both a steeper decline in forced expiratory volume in 1 second (-2.9% predicted change/yr, 95% confidence interval [CI] = -3.8 to -1.9 compared with 0.4, 95% CI = -0.3 to 1.0; P < 0.001) and body mass index (-1.0 percentile change/yr, 95% CI = -1.6 to -0.3 compared with -0.1, 95% CI = -0.7 to 0.5; P = 0.047) than those with a stable infection with the same ST. CONCLUSIONS There was no widespread sharing of dominant clones in our CF population, and the majority of the genetic diversity in P. aeruginosa was observed between patients. Changing genotypes over time within an individual was associated with worse clinical outcomes.
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7
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Kidd TJ, Grimwood K, Bell SC. Abolition of Pseudomonas aeruginosa AUST-01 from an Australian CF center: Do other strains remain? Pediatr Pulmonol 2019; 54:515-516. [PMID: 30741479 DOI: 10.1002/ppul.24258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/03/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,The University of Queensland, Child Health Research Centre, Brisbane, Australia
| | - Keith Grimwood
- School of Medicine and Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia.,Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Gold Coast, Australia
| | - Scott C Bell
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, Australia
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8
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Rehman A, Patrick WM, Lamont IL. Mechanisms of ciprofloxacin resistance in Pseudomonas aeruginosa: new approaches to an old problem. J Med Microbiol 2019; 68:1-10. [DOI: 10.1099/jmm.0.000873] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Attika Rehman
- 1Department of Biochemistry, University of Otago, New Zealand
| | - Wayne M. Patrick
- 1Department of Biochemistry, University of Otago, New Zealand
- 2School of Biological Sciences, Victoria University of Wellington, New Zealand
| | - Iain L. Lamont
- 1Department of Biochemistry, University of Otago, New Zealand
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9
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Wee BA, Tai AS, Sherrard LJ, Ben Zakour NL, Hanks KR, Kidd TJ, Ramsay KA, Lamont I, Whiley DM, Bell SC, Beatson SA. Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre. BMC Genomics 2018; 19:644. [PMID: 30165811 PMCID: PMC6117919 DOI: 10.1186/s12864-018-5018-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/14/2018] [Indexed: 11/18/2022] Open
Abstract
Background Chronic lung infections caused by Pseudomonas aeruginosa are a significant cause of morbidity and mortality in people with cystic fibrosis (CF). Shared P. aeruginosa strains, that can be transmitted between patients, are of concern and in Australia the AUST-02 shared strain is predominant in individuals attending CF centres in Queensland and Western Australia. M3L7 is a multidrug resistant sub-type of AUST-02 that was recently identified in a Queensland CF centre and was shown to be associated with poorer clinical outcomes. The main aim of this study was to resolve the relationship of the emergent M3L7 sub-type within the AUST-02 group of strains using whole genome sequencing. Results A whole genome core phylogeny of 63 isolates indicated that M3L7 is a monophyletic sub-lineage within the context of the broader AUST-02 group. Relatively short branch lengths connected all of the M3L7 isolates. A phylogeny based on nucleotide polymorphisms present across the genome showed that the chronological estimation of the most recent common ancestor was around 2001 (± 3 years). SNP differences between sequential non-hypermutator M3L7 isolates collected 3–4 years apart from five patients suggested both continuous infection of the same strain and cross-infection of some M3L7 variants between patients. The majority of polymorphisms that were characteristic of M3L7 (i.e. acquired after divergence from all other AUST-02 isolates sequenced) were found to produce non-synonymous mutations in virulence and antibiotic resistance genes. Conclusions M3L7 has recently diverged from a common ancestor, indicating descent from a single carrier at a CF treatment centre in Australia. Both adaptation to the lung and transmission of M3L7 between adults attending this centre may have contributed to its rapid dissemination. Further genomic investigations are required on multiple intra-sample isolates of this sub-type to decipher potential mechanisms which facilitates its epidemiological success. Electronic supplementary material The online version of this article (10.1186/s12864-018-5018-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bryan A Wee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.,Present Address: Usher Institute of Population Health Sciences & Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Anna S Tai
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia.,Department of Respiratory Medicine, Western Australia Adult Cystic Fibrosis Centre, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Laura J Sherrard
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Present Address: School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom
| | - Nouri L Ben Zakour
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Kirt R Hanks
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.,Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK.,Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Kay A Ramsay
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Present Address: Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Iain Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - David M Whiley
- Faculty of Medicine, UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia.,Microbiology Department, Pathology Queensland Central Laboratory, Brisbane, QLD, Australia
| | - Scott C Bell
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia. .,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.
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10
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Epidemiology, Biology, and Impact of Clonal Pseudomonas aeruginosa Infections in Cystic Fibrosis. Clin Microbiol Rev 2018; 31:31/4/e00019-18. [PMID: 30158299 DOI: 10.1128/cmr.00019-18] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chronic lower airway infection with Pseudomonas aeruginosa is a major contributor to morbidity and mortality in individuals suffering from the genetic disease cystic fibrosis (CF). Whereas it was long presumed that each patient independently acquired unique strains of P. aeruginosa present in their living environment, multiple studies have since demonstrated that shared strains of P. aeruginosa exist among individuals with CF. Many of these shared strains, often referred to as clonal or epidemic strains, can be transmitted from one CF individual to another, potentially reaching epidemic status. Numerous epidemic P. aeruginosa strains have been described from different parts of the world and are often associated with an antibiotic-resistant phenotype. Importantly, infection with these strains often portends a worse prognosis than for infection with nonclonal strains, including an increased pulmonary exacerbation rate, exaggerated lung function decline, and progression to end-stage lung disease. This review describes the global epidemiology of clonal P. aeruginosa strains in CF and summarizes the current literature regarding the underlying biology and clinical impact of globally important CF clones. Mechanisms associated with patient-to-patient transmission are discussed, and best-evidence practices to prevent infections are highlighted. Preventing new infections with epidemic P. aeruginosa strains is of paramount importance in mitigating CF disease progression.
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11
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Abstract
PURPOSE OF REVIEW Anaerobic bacteria are not only normal commensals, but are also considered opportunistic pathogens and have been identified as persistent members of the lower airway community in people with cystic fibrosis of all ages and stages of disease. Currently, the role of anaerobic bacteria in cystic fibrosis lower airway disease is not well understood. Therefore, this review describes the recent studies relating to the potential pathophysiological role(s) of anaerobes within the cystic fibrosis lungs. RECENT FINDINGS The most frequently identified anaerobic bacteria in the lower airways are common to both cystic fibrosis and healthy lungs. Studies have shown that in cystic fibrosis, the relative abundance of anaerobes fluctuates in the lower airways with reduced lung function and increased inflammation associated with a decreased anaerobic load. However, anaerobes found within the lower airways also produce virulence factors, may cause a host inflammatory response and interact synergistically with recognized pathogens. SUMMARY Anaerobic bacteria are potentially members of the airway microbiota in health but could also contribute to the pathogenesis of lower airway disease in cystic fibrosis via both direct and indirect mechanisms. A personalized treatment strategy that maintains a normal microbial community may be possible in the future.
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12
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Tai AS, Sherrard LJ, Kidd TJ, Ramsay KA, Buckley C, Syrmis M, Grimwood K, Bell SC, Whiley DM. Antibiotic perturbation of mixed-strain Pseudomonas aeruginosa infection in patients with cystic fibrosis. BMC Pulm Med 2017; 17:138. [PMID: 29096618 PMCID: PMC5667482 DOI: 10.1186/s12890-017-0482-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/25/2017] [Indexed: 12/20/2022] Open
Abstract
Background Pulmonary exacerbations in cystic fibrosis (CF) remain poorly understood and treatment is usually targeted at Pseudomonas aeruginosa. Within Australia a predominant shared P. aeruginosa strain (AUST-02) is associated with greater treatment needs. This single centre study assessed temporal shared strain population dynamics during and after antibiotic treatment of exacerbations. Methods Sputum was collected from 12 adult patients with a history of chronic AUST-02 infection at four time-points during and after treatment of an exacerbation. Forty-eight P. aeruginosa isolates within each sample underwent AUST-02 allele-specific PCR and SNP-based strain genotyping. Results Various commonly shared Australian strains (AUST-01, 0.1%; AUST-02, 54.3%; AUST-06, 36.6%; AUST-07, 4.6%; AUST-11, 4.3%) and two unique strains (0.1%) were identified from 45 sputum samples (2160 isolates). Based on within-patient relative abundance of strains, a “single-strain infection” (n = 7) or “mixed-strain infection” (n = 5) was assigned to each patient. A significant temporal variation in the P. aeruginosa population composition was found for those with mixed-strain infection (P < 0.001). Patients with mixed-strain infections had more long-term treatment requirements than those with single-strain infection. Moreover, despite both groups having similar lung function at study entry, patients with single-strain infection had greater improvement in FEV1% predicted following their exacerbation treatment (P = 0.02). Conclusion Pulmonary exacerbations may reveal multiple, unrelated P. aeruginosa strains whose relative abundance with one another may change rapidly, in a sustained and unpredictable manner. Electronic supplementary material The online version of this article (10.1186/s12890-017-0482-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna S Tai
- School of Medicine, The University of Queensland, Brisbane, QLD, Australia. .,Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia. .,Western Australia Adult Cystic Fibrosis Centre, Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Hospital Avenue, Perth, WA, 6009, Australia.
| | - Laura J Sherrard
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.,Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK.,Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Kay A Ramsay
- School of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Cameron Buckley
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Melanie Syrmis
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia.,Pathology Queensland, Microbiology Department, Brisbane, QLD, Australia
| | - Keith Grimwood
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia.,Menzies Health Institute Queensland, Griffith University and Gold Coast Health, Gold Coast, QLD, Australia
| | - Scott C Bell
- Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - David M Whiley
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia.,Pathology Queensland, Microbiology Department, Brisbane, QLD, Australia
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Sherrard LJ, Tai AS, Wee BA, Ramsay KA, Kidd TJ, Ben Zakour NL, Whiley DM, Beatson SA, Bell SC. Within-host whole genome analysis of an antibiotic resistant Pseudomonas aeruginosa strain sub-type in cystic fibrosis. PLoS One 2017; 12:e0172179. [PMID: 28273168 PMCID: PMC5342179 DOI: 10.1371/journal.pone.0172179] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/31/2017] [Indexed: 02/07/2023] Open
Abstract
A Pseudomonas aeruginosa AUST-02 strain sub-type (M3L7) has been identified in Australia, infects the lungs of some people with cystic fibrosis and is associated with antibiotic resistance. Multiple clonal lineages may emerge during treatment with mutations in chromosomally encoded antibiotic resistance genes commonly observed. Here we describe the within-host diversity and antibiotic resistance of M3L7 during and after antibiotic treatment of an acute pulmonary exacerbation using whole genome sequencing and show both variation and shared mutations in important genes. Eleven isolates from an M3L7 population (n = 134) isolated over 3 months from an individual with cystic fibrosis underwent whole genome sequencing. A phylogeny based on core genome SNPs identified three distinct phylogenetic groups comprising two groups with higher rates of mutation (hypermutators) and one non-hypermutator group. Genomes were screened for acquired antibiotic resistance genes with the result suggesting that M3L7 resistance is principally driven by chromosomal mutations as no acquired mechanisms were detected. Small genetic variations, shared by all 11 isolates, were found in 49 genes associated with antibiotic resistance including frame-shift mutations (mexA, mexT), premature stop codons (oprD, mexB) and mutations in quinolone-resistance determining regions (gyrA, parE). However, whole genome sequencing also revealed mutations in 21 genes that were acquired following divergence of groups, which may also impact the activity of antibiotics and multi-drug efflux pumps. Comparison of mutations with minimum inhibitory concentrations of anti-pseudomonal antibiotics could not easily explain all resistance profiles observed. These data further demonstrate the complexity of chronic and antibiotic resistant P. aeruginosa infection where a multitude of co-existing genotypically diverse sub-lineages might co-exist during and after intravenous antibiotic treatment.
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Affiliation(s)
- Laura J. Sherrard
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Anna S. Tai
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
- Western Australia Adult Cystic Fibrosis Centre, Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Bryan A. Wee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Kay A. Ramsay
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Timothy J. Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Centre for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Nouri L. Ben Zakour
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - David M. Whiley
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
- Pathology Queensland, Microbiology Department, Brisbane, QLD, Australia
| | - Scott A. Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Scott C. Bell
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
- * E-mail:
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14
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Cystic fibrosis lung environment and Pseudomonas aeruginosa infection. BMC Pulm Med 2016; 16:174. [PMID: 27919253 PMCID: PMC5139081 DOI: 10.1186/s12890-016-0339-5] [Citation(s) in RCA: 229] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/24/2016] [Indexed: 12/20/2022] Open
Abstract
Background The airways of patients with cystic fibrosis (CF) are highly complex, subject to various environmental conditions as well as a distinct microbiota. Pseudomonas aeruginosa is recognized as one of the most important pulmonary pathogens and the predominant cause of morbidity and mortality in CF. A multifarious interplay between the host, pathogens, microbiota, and the environment shapes the course of the disease. There have been several excellent reviews detailing CF pathology, Pseudomonas and the role of environment in CF but only a few reviews connect these entities with regards to influence on the overall course of the disease. A holistic understanding of contributing factors is pertinent to inform new research and therapeutics. Discussion In this article, we discuss the deterministic alterations in lung physiology as a result of CF. We also revisit the impact of those changes on the microbiota, with special emphasis on P. aeruginosa and the influence of other non-genetic factors on CF. Substantial past and current research on various genetic and non-genetic aspects of cystic fibrosis has been reviewed to assess the effect of different factors on CF pulmonary infection. A thorough review of contributing factors in CF and the alterations in lung physiology indicate that CF lung infection is multi-factorial with no isolated cause that should be solely targeted to control disease progression. A combinatorial approach may be required to ensure better disease outcomes. Conclusion CF lung infection is a complex disease and requires a broad multidisciplinary approach to improve CF disease outcomes. A holistic understanding of the underlying mechanisms and non-genetic contributing factors in CF is central to development of new and targeted therapeutic strategies.
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