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Shepherd MJ, Fu T, Harrington NE, Kottara A, Cagney K, Chalmers JD, Paterson S, Fothergill JL, Brockhurst MA. Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance. Nat Rev Microbiol 2024:10.1038/s41579-024-01041-1. [PMID: 38689039 DOI: 10.1038/s41579-024-01041-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 05/02/2024]
Abstract
The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages. Within-patient AMR emergence occurs across a wide range of host niches and bacterial species, but the importance of each mechanism varies between bacterial species and infection sites within the body. We identify potential drivers of such differences and discuss how ecological and evolutionary analysis could be embedded within clinical trials of antimicrobials, which are powerful but underused tools for understanding why these mechanisms vary between pathogens, infections and individuals. Ultimately, improving understanding of how host niche, bacterial species and antibiotic mode of action combine to govern the ecological and evolutionary mechanism of AMR emergence in patients will enable more predictive and personalized diagnosis and antimicrobial therapies.
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Affiliation(s)
- Matthew J Shepherd
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK.
| | - Taoran Fu
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Niamh E Harrington
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Anastasia Kottara
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Kendall Cagney
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Joanne L Fothergill
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Michael A Brockhurst
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK.
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2
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Simão FA, Almeida MM, Rosa HS, Marques EA, Leão RS. Genetic determinants of antimicrobial resistance in polymyxin B resistant Pseudomonas aeruginosa isolated from airways of patients with cystic fibrosis. Braz J Microbiol 2024:10.1007/s42770-024-01311-3. [PMID: 38619733 DOI: 10.1007/s42770-024-01311-3] [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: 12/18/2023] [Accepted: 03/21/2024] [Indexed: 04/16/2024] Open
Abstract
Pseudomonas aeruginosa is the main pathogen associated with pulmonary exacerbation in patients with cystic fibrosis (CF). CF is a multisystemic genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator gene, which mainly affects pulmonary function. P. aeruginosa isolated from individuals with CF in Brazil is not commonly associated with multidrug resistance (MDR), especially when compared to global occurrence, where the presence of epidemic clones, capable of expressing resistance to several drugs, is often reported. Due to the recent observations of MDR isolates of P. aeruginosa in our centers, combined with these characteristics, whole-genome sequencing was employed for analyses related to antimicrobial resistance, plasmid identification, search for phages, and characterization of CF clones. All isolates in this study were polymyxin B resistant, exhibiting diverse mutations and reduced susceptibility to carbapenems. Alterations in mexZ can result in the overexpression of the MexXY efflux pump. Mutations in oprD, pmrB, parS, gyrA and parC may confer reduced susceptibility to antimicrobials by affecting permeability, as observed in phenotypic tests. The phage findings led to the assumption of horizontal genetic transfer, implicating dissemination between P. aeruginosa isolates. New sequence types were described, and none of the isolates showed an association with epidemic CF clones. Analysis of the genetic context of P. aeruginosa resistance to polymyxin B allowed us to understand the different mechanisms of resistance to antimicrobials, in addition to subsidizing the understanding of possible relationships with epidemic strains that circulate among individuals with CF observed in other countries.
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Affiliation(s)
- Felipe A Simão
- Laboratório de Microbiologia da Fibrose Cística, Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mila M Almeida
- Laboratório de Microbiologia da Fibrose Cística, Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heloísa S Rosa
- Laboratório de Microbiologia da Fibrose Cística, Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elizabeth A Marques
- Laboratório de Microbiologia da Fibrose Cística, Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Robson S Leão
- Laboratório de Microbiologia da Fibrose Cística, Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.
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3
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Coenye T. Biofilm antimicrobial susceptibility testing: where are we and where could we be going? Clin Microbiol Rev 2023; 36:e0002423. [PMID: 37812003 PMCID: PMC10732061 DOI: 10.1128/cmr.00024-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/27/2023] [Indexed: 10/10/2023] Open
Abstract
Our knowledge about the fundamental aspects of biofilm biology, including the mechanisms behind the reduced antimicrobial susceptibility of biofilms, has increased drastically over the last decades. However, this knowledge has so far not been translated into major changes in clinical practice. While the biofilm concept is increasingly on the radar of clinical microbiologists, physicians, and healthcare professionals in general, the standardized tools to study biofilms in the clinical microbiology laboratory are still lacking; one area in which this is particularly obvious is that of antimicrobial susceptibility testing (AST). It is generally accepted that the biofilm lifestyle has a tremendous impact on antibiotic susceptibility, yet AST is typically still carried out with planktonic cells. On top of that, the microenvironment at the site of infection is an important driver for microbial physiology and hence susceptibility; but this is poorly reflected in current AST methods. The goal of this review is to provide an overview of the state of the art concerning biofilm AST and highlight the knowledge gaps in this area. Subsequently, potential ways to improve biofilm-based AST will be discussed. Finally, bottlenecks currently preventing the use of biofilm AST in clinical practice, as well as the steps needed to get past these bottlenecks, will be discussed.
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Affiliation(s)
- Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
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Jarzynka S, Makarewicz O, Weiss D, Minkiewicz-Zochniak A, Iwańska A, Skorupa W, Padzik M, Augustynowicz-Kopeć E, Olędzka G. The Impact of Pseudomonas aeruginosa Infection in Adult Cystic Fibrosis Patients-A Single Polish Centre Study. Pathogens 2023; 12:1440. [PMID: 38133323 PMCID: PMC10748198 DOI: 10.3390/pathogens12121440] [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: 11/15/2023] [Revised: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Pseudomonas aeruginosa (PA) is one of the most predominant pathogens of lung infections, often causing exacerbations in adult patients with cystic fibrosis (CF). MATERIALS AND METHODS Microbiological characterization of 74 PA isolates and to evaluate the correlations between the bacterial features and 44 adult Polish CF cohort clinical parameters. RESULTS The most common variant in the CF transmembrane conductance regulator (CFTR) gene was F508del (76.3%), followed by 3849+10kbC>T (26.3%). A total of 39.4% of the PA isolates showed multiple resistances. In patients with parameters pointing to a decline in lung function, there was a statistically significant moderate correlation with β-lactam resistance and a weak correlation between hospital frequency and colistin resistance. The mucoidity did not correlate with the biofilm formation ability, which showed 41.9% of the isolates. Proteolytic activity, observed in 60.8% of the clinical isolates, was weakly associated with motility detected in 78.4% of the strains. The genetic profiles of the PA were highly heterogeneous, and a weak positive correlation was established between cluster group and biofilm formation. CONCLUSION The findings suggest that there is a high variety in P. aeruginosa populations in adult CF patients. There is a need to monitor PA strains in groups of patients with cystic fibrosis, in particular, in terms of the occurrence of antibiotic resistance related to a decline in lung function.
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Affiliation(s)
- Sylwia Jarzynka
- Department of Medical Biology, Medical University of Warsaw, Litewska 14/16, 00-575 Warsaw, Poland; (A.M.-Z.); (M.P.); (G.O.)
| | - Oliwia Makarewicz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, 07747 Jena, Germany; (O.M.); (D.W.)
| | - Daniel Weiss
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, 07747 Jena, Germany; (O.M.); (D.W.)
| | - Anna Minkiewicz-Zochniak
- Department of Medical Biology, Medical University of Warsaw, Litewska 14/16, 00-575 Warsaw, Poland; (A.M.-Z.); (M.P.); (G.O.)
| | - Agnieszka Iwańska
- Department of Microbiology, National Institute of Tuberculosis and Lung Diseases, Plocka 26, 01-138 Warsaw, Poland; (A.I.); (E.A.-K.)
| | - Wojciech Skorupa
- First Department of Lung Diseases, National Institute of Tuberculosis and Lung Diseases, Plocka 26, 01-138 Warsaw, Poland;
| | - Marcin Padzik
- Department of Medical Biology, Medical University of Warsaw, Litewska 14/16, 00-575 Warsaw, Poland; (A.M.-Z.); (M.P.); (G.O.)
| | - Ewa Augustynowicz-Kopeć
- Department of Microbiology, National Institute of Tuberculosis and Lung Diseases, Plocka 26, 01-138 Warsaw, Poland; (A.I.); (E.A.-K.)
| | - Gabriela Olędzka
- Department of Medical Biology, Medical University of Warsaw, Litewska 14/16, 00-575 Warsaw, Poland; (A.M.-Z.); (M.P.); (G.O.)
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Van den Bossche S, Abatih E, Grassi L, De Broe E, Rigole P, Boelens J, Van Caenegem J, Verhasselt B, Janssens I, Van Braeckel E, Versmessen N, Cools P, Coenye T, Crabbé A. Pooling isolates to address the diversity in antimicrobial susceptibility of Pseudomonas aeruginosa in cystic fibrosis. Microbiol Spectr 2023; 11:e0044923. [PMID: 37982625 PMCID: PMC10714813 DOI: 10.1128/spectrum.00449-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/17/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE People with cystic fibrosis (pwCF) often suffer from chronic lung infections with Pseudomonas aeruginosa. While antibiotics are still commonly used to treat P. aeruginosa infections, there is a high discordance between in vitro and in vivo antibiotic efficacy, which contributes to suboptimal antibiotic therapy. In the present study, we found that isolates from the same sputum sample had highly diverse antibiotic resistance profiles [based on the minimal inhibitory concentration (MIC)], which may explain the reported discrepancy between in vitro and in vivo antibiotic efficacy. Through systematic analysis, we report that pooling nine isolates per sputum sample significantly decreased intrasample diversity in MIC and influenced clinical interpretation of antibiotic susceptibility tests compared to single isolate testing. Hence, pooling of isolates may offer a solution to obtain a consistent MIC test result and could lead to optimizing antibiotic therapy in pwCF and other infectious diseases where diversity in antibiotic resistance is observed.
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Affiliation(s)
| | - Emmanuel Abatih
- Data Analysis and Statistical Science (DASS), Ghent University, Ghent, Belgium
| | - Lucia Grassi
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Emma De Broe
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Petra Rigole
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Jerina Boelens
- Laboratory of Medical Microbiology, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Joris Van Caenegem
- Laboratory of Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | - Bruno Verhasselt
- Laboratory of Medical Microbiology, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Iris Janssens
- Department of Respiratory Medicine, Cystic Fibrosis Reference Centre, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Center for Inflammation Research, Flemish Institute for Biotechnology, Ghent, Belgium
| | - Eva Van Braeckel
- Department of Respiratory Medicine, Cystic Fibrosis Reference Centre, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Nick Versmessen
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Piet Cools
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
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Booth SC, Smith WPJ, Foster KR. The evolution of short- and long-range weapons for bacterial competition. Nat Ecol Evol 2023; 7:2080-2091. [PMID: 38036633 PMCID: PMC10697841 DOI: 10.1038/s41559-023-02234-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 09/22/2023] [Indexed: 12/02/2023]
Abstract
Bacteria possess a diverse range of mechanisms for inhibiting competitors, including bacteriocins, tailocins, type VI secretion systems and contact-dependent inhibition (CDI). Why bacteria have evolved such a wide array of weapon systems remains a mystery. Here we develop an agent-based model to compare short-range weapons that require cell-cell contact, with long-range weapons that rely on diffusion. Our model predicts that contact weapons are useful when an attacking strain is outnumbered, facilitating invasion and establishment. By contrast, ranged weapons tend to be effective only when attackers are abundant. We test our predictions with the opportunistic pathogen Pseudomonas aeruginosa, which naturally carries multiple weapons, including CDI and diffusing tailocins. As predicted, short-range CDI can function at low and high frequencies, while long-range tailocins require high frequency and cell density to function effectively. Head-to-head competition experiments with the two weapon types further support our predictions: a tailocin attacker defeats CDI only when it is numerically dominant, but then we find it can be devastating. Finally, we show that the two weapons work well together when one strain employs both. We conclude that short- and long-range weapons serve different functions and allow bacteria to fight both as individuals and as a group.
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Affiliation(s)
- Sean C Booth
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - William P J Smith
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- Division of Evolution, Infection and Genomics, University of Manchester, Manchester, UK
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
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7
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Spottiswoode N, Hao S, Sanchez-Guerrero E, Detweiler AM, Mekonen H, Neff N, Macmillan H, Schwartz BS, Engel J, DeRisi JL, Miller SA, Langelier CR. In host evolution of beta lactam resistance during active treatment for Pseudomonas aeruginosa bacteremia. Front Cell Infect Microbiol 2023; 13:1241608. [PMID: 37712060 PMCID: PMC10499174 DOI: 10.3389/fcimb.2023.1241608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023] Open
Abstract
Multidrug-resistant (MDR) Pseudomonas aeruginosa has been declared a serious threat by the United States Centers for Disease Control and Prevention. Here, we used whole genome sequencing (WGS) to investigate recurrent P. aeruginosa bloodstream infections in a severely immunocompromised patient. The infections demonstrated unusual, progressive increases in resistance to beta lactam antibiotics in the setting of active treatment with appropriate, guideline-directed agents. WGS followed by comparative genomic analysis of isolates collected over 44 days demonstrated in host evolution of a single P. aeruginosa isolate characterized by stepwise acquisition of two de-novo genetic resistance mechanisms over the course of treatment. We found a novel deletion affecting the ampC repressor ampD and neighboring gene ampE, which associated with initial cefepime treatment failure. This was followed by acquisition of a porin nonsense mutation, OprD, associated with resistance to carbapenems. This study highlights the potential for in-host evolution of P. aeruginosa during bloodstream infections in severely immunocompromised patients despite appropriate antimicrobial therapy. In addition, it demonstrates the utility of WGS for understanding unusual resistance patterns in the clinical context.
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Affiliation(s)
- Natasha Spottiswoode
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Samantha Hao
- Johns Hopkins School of Medicine, Baltimore, Maryland, MD, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | | | | | - Honey Mekonen
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Henriette Macmillan
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Brian S. Schwartz
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Joanne Engel
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Steven A. Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, United States
- Delve Bio Inc., San Francisco, CA, United States
| | - Charles R. Langelier
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
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8
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Rymer TL, Pillay N. The effects of antibiotics and illness on gut microbial composition in the fawn-footed mosaic-tailed rat (Melomys cervinipes). PLoS One 2023; 18:e0281533. [PMID: 36827295 PMCID: PMC9956021 DOI: 10.1371/journal.pone.0281533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/25/2023] [Indexed: 02/25/2023] Open
Abstract
The gut microbiota are critical for maintaining the health and physiological function of individuals. However, illness and treatment with antibiotics can disrupt bacterial community composition, the consequences of which are largely unknown in wild animals. In this study, we described and quantified the changes in bacterial community composition in response to illness and treatment with antibiotics in a native Australian rodent, the fawn-footed mosaic-tailed rat (Melomys cervinipes). We collected faecal samples during an undiagnosed illness outbreak in a captive colony of animals, and again at least one year later, and quantified the microbiome at each time point using 16s ribosomal rRNA gene sequencing. Gut bacterial composition was quantified at different taxonomic levels, up to family. Gut bacterial composition changed between time periods, indicating that illness, treatment with antibiotics, or a combination affects bacterial communities. While some bacterial groups increased in abundance, others decreased, suggesting differential effects and possible co-adapted and synergistic interactions. Our findings provide a greater understanding of the dynamic nature of the gut microbiome of a native Australian rodent species and provides insights into the management and ethical well-being of animals kept under captive conditions.
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Affiliation(s)
- Tasmin L. Rymer
- College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
- Centre for Tropical Environmental and Sustainability Sciences, James Cook University, Queensland, Australia
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - Neville Pillay
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Sader HS, Mendes RE, Arends SJR, Carvalhaes CG, Shortridge D, Castanheira M. Comparative activity of newer β-lactam/β-lactamase inhibitor combinations against Pseudomonas aeruginosa isolates from US medical centres (2020-2021). Int J Antimicrob Agents 2023; 61:106744. [PMID: 36738849 DOI: 10.1016/j.ijantimicag.2023.106744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 01/25/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
OBJECTIVES To evaluate the in-vitro activity of ceftazidime-avibactam, ceftolozane-tazobactam, meropenem-vaborbactam, imipenem-relebactam and comparator agents against contemporary Pseudomonas aeruginosa isolates from US hospitals. METHODS In total, 3184 isolates were collected consecutively from 71 US medical centres in 2020-2021, and susceptibility tested by reference broth microdilution. Clinical Laboratory Standard Institute breakpoints were applied. RESULTS Ceftazidime-avibactam [97.0% susceptible (S)], ceftolozane-tazobactam (98.0%S), imipenem-relebactam (97.3%S) and tobramycin (96.4%S) were the most active agents against the aggregate P. aeruginosa isolate collection, and retained good activity against piperacillin-tazobactam-non-susceptible, meropenem-non-susceptible and multi-drug-resistant (MDR) isolates. All other antimicrobials tested showed limited activity against piperacillin-tazobactam-non-susceptible, meropenem-non-susceptible and MDR isolates. The most common infections were pneumonia (45.9%), skin and skin structure infections (19.0%), urinary tract infections (17.0%) and bloodstream infections (11.7%); ceftazidime-avibactam, ceftolozane-tazobactam and imipenem-relebactam showed consistent activity against isolates from these infection types. Susceptibility to piperacillin-tazobactam and meropenem was lower among isolates from pneumonia compared with other infection types. CONCLUSIONS Ceftazidime-avibactam, ceftolozane-tazobactam and imipenem-relebactam were highly active, and exhibited similar coverage against a large contemporary collection of P. aeruginosa isolates from US hospitals. Cross-resistance among the newer β-lactams/β-lactam inhibitors (BL/BLIs) varied markedly; ≥72.1% of isolates resistant to one of the three newer BL/BLIs approved for P. aeruginosa treatment remained susceptible to at least one of the other two BL/BLIs, indicating that all three should be tested in the clinical laboratory. These three BL/BLIs represent valuable therapeutic options for P. aeruginosa infection.
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10
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Hoque MN, Jahan MI, Hossain MA, Sultana M. Genomic diversity and molecular epidemiology of a multidrug-resistant Pseudomonas aeruginosa DMC30b isolated from a hospitalized burn patient in Bangladesh. J Glob Antimicrob Resist 2022; 31:110-118. [PMID: 36058512 DOI: 10.1016/j.jgar.2022.08.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/02/2022] [Accepted: 08/29/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES Pseudomonas aeruginosa is a key opportunistic pathogen causing a wide range of community- and hospital-acquired infections in immunocompromised or catheterized patients. Here, we report the complete genome sequence of a multidrug-resistant (MDR) P. aeruginosa DMC30b to elucidate the genetic diversity, molecular epidemiology, and underlying mechanisms for antimicrobial resistance and virulence. METHODS P. aeruginosa DMC30b was isolated from septic wound swab of a severe burn patient. Whole-genome sequencing was performed under Ion Torrent platform. The genome was assembled using the SPAdes v. 3.12.01 in an integrated Genome Analysis Platform for Ion Torrent sequence data. The genome was annotated using the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline. In-silico predictions of antimicrobial resistance genes, virulence factor genes, and metabolic functional potentials were performed using different curated bioinformatics tools. RESULTS P. aeruginosa DMC30b was found as a MDR strain and belonged to sequence type 244 (ST244). The complete genome size is 6 994 756 bp with a coverage of 76.76x, guanine-cytosine content of 65.7% and a Benchmarking Universal Single-Copy Orthologs score of 100. The genome of P. aeruginosa DMC30b harboured two predicted plasmid replicons (e,g. IncP-6; 78 007 bp and ColRNAI; 9359 bp), 35 resistomes (antimicrobial resistance genes) conferring resistance to 18 different antibiotics (including four beta-lactam classes), and 214 virulence factor genes. It was identified as the 167th ST244 strain among ∼ 5800 whole-genome sequences of P. aeruginosa available in the NCBI database. CONCLUSION The MDR P. aeruginosa DMC30b was identified as the 167th ST244 complete genome to be submitted to the NCBI, and the first ST244 isolate sequenced from Bangladesh. The complete genome data with high genetic diversity and underlying mechanisms for antimicrobial resistance and virulence of P. aeruginosa DMC30b will aid in understanding the evolution and phylogeny of such high-risk clones and provide a solid basis for further research on MDR or extensively drug resistant strains.
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Affiliation(s)
- M Nazmul Hoque
- Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - M Ishrat Jahan
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.
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11
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Glasgow AMA, Greene CM. Epithelial damage in the cystic fibrosis lung: the role of host and microbial factors. Expert Rev Respir Med 2022; 16:737-748. [PMID: 35833354 DOI: 10.1080/17476348.2022.2100350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The airway epithelium is a key system within the lung. It acts as a physical barrier to inhaled factors, and can actively remove unwanted microbes and particles from the lung via the mucociliary escalator. On a physiological level, it senses the presence of pathogens and initiates innate immune responses to combat their effects. Hydration of the airways is also controlled by the epithelium. Within the cystic fibrosis (CF) lung, these properties are suboptimal and contribute to the pulmonary manifestations of CF. AREAS COVERED In this review, we discuss how various host and microbial factors can contribute to airway epithelium dysfunction in the CF lung focusing on mechanisms relating to the mucociliary escalator and protease expression and function. We also explore how alterations in microRNA expression can impact the behavior of the airway epithelium. EXPERT OPINION Notwithstanding the unprecedented benefits that CFTR modulator drugs now provide to the health of CF sufferers, it will be important to delve more deeply into additional mechanisms underpinning CF lung disease such as those illustrated here in an attempt to counteract these aberrant processes and further enhance quality of life for people with CF.
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Affiliation(s)
- Arlene M A Glasgow
- Lung Biology Group, Department of Clinical Microbiology, Royal College of Surgeons in Ireland (RCSI), Education and Research Centre, Beaumont Hospital, Dublin, Ireland
| | - Catherine M Greene
- Lung Biology Group, Department of Clinical Microbiology, Royal College of Surgeons in Ireland (RCSI), Education and Research Centre, Beaumont Hospital, Dublin, Ireland
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