scholarly journals Hypermutator Pseudomonas aeruginosa exploits multiple genetic pathways to develop multidrug resistance during long-term infections in the airways of cystic fibrosis patients

2019 ◽  
Author(s):  
C.A. Colque ◽  
A.G. Albarracín Orio ◽  
S. Feliziani ◽  
R.L. Marvig ◽  
A.R. Tobares ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Chronic Infection ◽  
Antibiotic Resistance Genes ◽  
Resistance Mechanisms ◽  
Multi Drug Resistance ◽  
Genetic Pathways ◽  
Resistance Evolution

ABSTRACTPseudomonas aeruginosa exploits intrinsic and acquired resistance mechanisms to resist almost every antibiotic used in chemotherapy. Antimicrobial resistance in P. aeruginosa isolated from cystic fibrosis (CF) patients is further enhanced by the occurrence of hypermutator strains, a hallmark of chronic CF infections. However, the within-patient genetic diversity of P. aeruginosa populations related to antibiotic resistance remains unexplored. Here, we show the evolution of the mutational resistome profile of a P. aeruginosa hypermutator lineage by performing longitudinal and transversal analyses of isolates collected from a CF patient throughout 20 years of chronic infection. Our results show the accumulation of thousands of mutations with an overall evolutionary history characterized by purifying selection. However, mutations in antibiotic resistance genes appear to be positively selected, driven by antibiotic treatment. Antibiotic resistance increased as infection progressed towards the establishment of a population constituted by genotypically diversified coexisting sub-lineages, all of which converged to multi-drug resistance. These sub-lineages emerged by parallel evolution through distinct evolutionary pathways, which affected genes of the same functional categories. Interestingly, ampC and fstI, encoding the β-lactamase and penicillin-binding protein 3, respectively, were found among the most frequently mutated genes. In fact, both genes were targeted by multiple independent mutational events, which led to a wide diversity of coexisting alleles underlying β-lactam resistance. Our findings indicate that hypermutators, apart from boosting antibiotic resistance evolution by simultaneously targeting several genes, favor the emergence of adaptive innovative alleles by clustering beneficial/compensatory mutations in the same gene, hence expanding P. aeruginosa strategies for persistence.IMPORTANCEBy increasing mutation rates, hypermutators boost antibiotic resistance evolution by enabling bacterial pathogens to fully exploit their genetic potential and achieve resistance mechanisms for almost every known antimicrobial agent. Here, we show how co-existing clones from a P. aeruginosa hypermutator lineage that evolved during 20 years of chronic infection and antibiotic chemotherapy, converged to multidrug resistance by targeting genes from alternative genetic pathways that are part of the broad P. aeruginosa resistome. Within this complex assembly of combinatorial genetic changes, in some specific cases, multiple mutations are needed in the same gene to reach a fine tuned resistance phenotype. Hypermutability enables this genetic edition towards higher resistance profiles by recurrently targeting these genes, thus promoting new epistatic relationships and the emergence of innovative resistance-conferring alleles. Our findings help to understand this link between hypermutability and antibiotic resistance, a key challenge for the design of new therapeutic strategies.

scholarly journals Hypermutator Pseudomonas aeruginosa Exploits Multiple Genetic Pathways To Develop Multidrug Resistance during Long-Term Infections in the Airways of Cystic Fibrosis Patients

2020 ◽  
Vol 64 (5) ◽  
Author(s):  
C. A. Colque ◽  
A. G. Albarracín Orio ◽  
S. Feliziani ◽  
R. L. Marvig ◽  
A. R. Tobares ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Parallel Evolution ◽  
Acquired Resistance ◽  
Antibiotic Resistance Genes ◽  
Purifying Selection ◽  
Chronic Infections ◽  
Content Type

ABSTRACT Pseudomonas aeruginosa exploits intrinsic and acquired resistance mechanisms to resist almost every antibiotic used in chemotherapy. Antimicrobial resistance in P. aeruginosa isolates recovered from cystic fibrosis (CF) patients is further enhanced by the occurrence of hypermutator strains, a hallmark of chronic infections in CF patients. However, the within-patient genetic diversity of P. aeruginosa populations related to antibiotic resistance remains unexplored. Here, we show the evolution of the mutational resistome profile of a P. aeruginosa hypermutator lineage by performing longitudinal and transversal analyses of isolates collected from a CF patient throughout 20 years of chronic infection. Our results show the accumulation of thousands of mutations, with an overall evolutionary history characterized by purifying selection. However, mutations in antibiotic resistance genes appear to have been positively selected, driven by antibiotic treatment. Antibiotic resistance increased as infection progressed toward the establishment of a population constituted by genotypically diversified coexisting sublineages, all of which converged to multidrug resistance. These sublineages emerged by parallel evolution through distinct evolutionary pathways, which affected genes of the same functional categories. Interestingly, ampC and ftsI, encoding the β-lactamase and penicillin-binding protein 3, respectively, were found to be among the most frequently mutated genes. In fact, both genes were targeted by multiple independent mutational events, which led to a wide diversity of coexisting alleles underlying β-lactam resistance. Our findings indicate that hypermutators, apart from boosting antibiotic resistance evolution by simultaneously targeting several genes, favor the emergence of adaptive innovative alleles by clustering beneficial/compensatory mutations in the same gene, hence expanding P. aeruginosa strategies for persistence.

scholarly journals Draft Genome Sequences of Five Pseudomonas aeruginosa Clinical Strains Isolated from Sputum Samples from Cystic Fibrosis Patients: TABLE 1

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
M. B. Couger ◽  
Anna Wright ◽  
Erika I. Lutter ◽  
Noha Youssef
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Virulence Factors ◽  
Resistance Genes ◽  
Draft Genome ◽  
Antibiotic Resistance Genes ◽  
Genome Sequences ◽  
Clinical Strains ◽  
Chronic Colonization

We report here the draft genome sequences of five Pseudomonas aeruginosa isolates obtained from sputum samples from two cystic fibrosis patients with chronic colonization. These closely related strains harbor 225 to 493 genes absent from the P. aeruginosa POA1 genome and contain 178 to 179 virulence factors and 29 to 31 antibiotic resistance genes.

scholarly journals Mechanisms of Antimicrobial Resistance in Pseudomonas aeruginosa and a Multi-Pronged Approach to Combat its Infection in Veterinary Science and Public Health: A Review

2021 ◽  
Vol 26 (01) ◽  
pp. 1-8
Author(s):  
Bahar-e- Mustafa
Keyword(s):  
Public Health ◽  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Molecular Mechanisms ◽  
Resistance Mechanisms ◽  
Modern Technology ◽  
Multi Drug Resistance ◽  
Resistance Development ◽  
Over Expression ◽  
Permeability Modification

Pseudomonas aeruginosa is one of the most important nosocomial pathogens associated with a variety of medical and veterinary infections and therefore, it presents a major public health threat. Different classes of antibiotics are being used to treat its infections which are increasing selective pressure to multi-drug resistance development. Resistance to antibiotics in P. aeruginosa is due to many of the common and unique mechanisms which include: reducing membrane permeability, modification or inactivation of antibiotics, alteration of enzymes, modification of target sites and over-expression of efflux systems. Over or under expression of the genes of porin channels and components of efflux systems play a major role in the resistance mechanisms of P. aeruginosa. To overcome the problem of the emergence of antibiotic resistance, many new strategies are being employed to control infections caused by P. aeruginosa. These include the use of herbs/medicinal plants and phage therapy. With the advent of modern technology, the molecular mechanisms of these alternative therapies are being elucidated and may be used in future to treat P. aeruginosa infections in humans and veterinary clinics. This review thus highlights the mechanisms of antibiotic resistance of P. aeruginosa against the commonly used antimicrobials and also some alternative strategies to control P. aeruginosa infection. © 2021 Friends Science Publishers

scholarly journals Antimicrobial Susceptibility Profiles among Pseudomonas aeruginosa Isolated from Professional SCUBA Divers with Otitis Externa, Swimming Pools and the Ocean at a Diving Operation in South Africa

Pathogens ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 91
Author(s):  
Kevin Maclean ◽  
Fernande Olpa J Pankendem Njamo ◽  
Mahloro Hope Serepa-Dlamini ◽  
Kulsum Kondiah ◽  
Ezekiel Green
Keyword(s):  
South Africa ◽  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Otitis Externa ◽  
Antibiotic Resistance Genes ◽  
Pcr Amplification ◽  
Multi Drug Resistance ◽  
Scuba Divers ◽  
Class 1 ◽  
Synergy Test

SCUBA divers are predisposed to otitis externa caused by Pseudomonas aeruginosa, which is becoming increasingly multi-drug resistant (MDR). The present work assessed the antibiotic resistance profiles of P. aeruginosa obtained from SCUBA divers and their environment in Sodwana Bay, South Africa. Bacterial isolates from a total of 137 random water and ear swab samples were identified using biochemical and molecular methods. P. aeruginosa strains were further evaluated for antibiotic susceptibility using the Kirby–Bauer assay. Double disk synergy test (DDST) to confirm metallo-β-lactamase (MBL) production and PCR amplification of specific antibiotic resistance genes was performed. All (100%) 22 P. aeruginosa isolates recovered were resistant to 6 of the β-lactams tested including imipenem but exhibited susceptibility to trimethoprim–sulfamethoxazole. MBL production was observed in 77% of isolates while the most prevalent extended-spectrum β-lactamase (ESBL) genes present included blaAmpC (86.9%) followed by blaTEM (82.6%). Sulfonamide resistance was largely encoded by sul1 (63.6%) and sul2 (77.3%) genes with a high abundance of class 1 integrons (77.3%) of which 18.2% carried both Intl1 and Intl2. P. aeruginosa found in Sodwana Bay exhibits multi-drug resistance (MDRce) to several pharmaceutically important drugs with the potential to transfer antibiotic resistance to other bacteria if the judicious use of antibiotics for their treatment is not practiced.

scholarly journals Combining Functional Genomics and Whole-Genome Sequencing to Detect Antibiotic Resistance Genes in Bacterial Strains Co-Occurring Simultaneously in a Brazilian Hospital

Antibiotics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 419
Author(s):  
Tiago Cabral Borelli ◽  
Gabriel Lencioni Lovate ◽  
Ana Flavia Tonelli Scaranello ◽  
Lucas Ferreira Ribeiro ◽  
Livia Zaramela ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Functional Genomics ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Resistance Mechanisms ◽  
Multi Drug Resistance ◽  
Resistant Bacteria ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Bacterial Strains

(1) Background: The rise of multi-antibiotic resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in bacteria of several species isolated from an intensive care unit in Brazil. (2) Methods: We used whole-genome analysis to identify antibiotic resistance genes (ARGs) and plasmids in 34 strains of Gram-negative and Gram-positive bacteria, providing the first genomic description of Morganella morganii and Ralstonia mannitolilytica clinical isolates from South America. (3) Results: We identified a high abundance of beta-lactamase genes in resistant organisms, including seven extended-spectrum beta-lactamases (OXA-1, OXA-10, CTX-M-1, KPC, TEM, HYDRO, BLP) shared between organisms from different species. Additionally, we identified several ARG-carrying plasmids indicating the potential for a fast transmission of resistance mechanism between bacterial strains. Furthermore, we uncovered two pairs of (near) identical plasmids exhibiting multi-drug resistance. Finally, since many highly resistant strains carry several different ARGs, we used functional genomics to investigate which of them were indeed functional. In this sense, for three bacterial strains (Escherichia coli, Klebsiella pneumoniae, and M. morganii), we identified six beta-lactamase genes out of 15 predicted in silico as those mainly responsible for the resistance mechanisms observed, corroborating the existence of redundant resistance mechanisms in these organisms. (4) Conclusions: Systematic studies similar to the one presented here should help to prevent outbreaks of novel multidrug-resistant bacteria in healthcare facilities.

scholarly journals Clonal Dissemination, Emergence of Mutator Lineages and Antibiotic Resistance Evolution in Pseudomonas aeruginosa Cystic Fibrosis Chronic Lung Infection

PLoS ONE ◽  
2013 ◽  
Vol 8 (8) ◽  
pp. e71001 ◽  
Author(s):  
Carla López-Causapé ◽  
Estrella Rojo-Molinero ◽  
Xavier Mulet ◽  
Gabriel Cabot ◽  
Bartolomé Moyà ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Lung Infection ◽  
Resistance Evolution ◽  
Chronic Lung Infection

scholarly journals Competition in Biofilms between Cystic Fibrosis Isolates ofPseudomonas aeruginosaIs Shaped by R-Pyocins

mBio ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. e01828-18 ◽  
Author(s):  
Olubukola Oluyombo ◽  
Christopher N. Penfold ◽  
Stephen P. Diggle
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Clinical Problem ◽  
Opportunistic Pathogen ◽  
Resistance Mechanisms ◽  
Content Type ◽  
Global Concern ◽  
Antibiofilm Agents ◽  
Major Clinical Problem

ABSTRACTPseudomonas aeruginosais an opportunistic pathogen and the leading cause of morbidity and mortality in cystic fibrosis (CF) patients.P. aeruginosainfections are difficult to treat due to a number of antibiotic resistance mechanisms and the organism’s propensity to form multicellular biofilms. Epidemic strains ofP. aeruginosaoften dominate within the lungs of individual CF patients, but how they achieve this is poorly understood. One way that strains ofP. aeruginosacan compete is by producing chromosomally encoded bacteriocins, called pyocins. Three major classes of pyocin have been identified inP. aeruginosa: soluble pyocins (S types) and tailocins (R and F types). In this study, we investigated the distribution of S- and R-type pyocins in 24 clinical strains isolated from individual CF patients and then focused on understanding their roles in interstrain competition. We found that (i) each strain produced only one R-pyocin type, but the number of S-pyocins varied between strains, (ii) R-pyocins were generally important for strain dominance during competition assays in planktonic cultures and biofilm communities in strains with both disparate R- and S-pyocin subtypes, and (iii) purified R-pyocins demonstrated significant antimicrobial activity against established biofilms. Our work provides support for a role played by R-pyocins in the competition betweenP. aeruginosastrains and helps explain why certain strains and lineages ofP. aeruginosadominate and displace others during CF infection. Furthermore, we demonstrate the potential of exploiting R-pyocins for therapeutic gains in an era when antibiotic resistance is a global concern.IMPORTANCEA major clinical problem caused byPseudomonas aeruginosa, is chronic biofilm infection of the lungs in individuals with cystic fibrosis (CF). EpidemicP. aeruginosastrains dominate and displace others during CF infection, but these intraspecies interactions remain poorly understood. Here we demonstrate that R-pyocins (bacteriocins) are important factors in driving competitive interactions in biofilms betweenP. aeruginosastrains isolated from different CF patients. In addition, we found that these phage-like pyocins are inhibitory against mature biofilms of susceptible strains. This highlights the potential of R-pyocins as antimicrobial and antibiofilm agents at a time when new antimicrobial therapies are desperately needed.

scholarly journals Competition in biofilms between cystic fibrosis isolates ofPseudomonas aeruginosais shaped by R-pyocins

2018 ◽  
Author(s):  
Olubukola Oluyombo ◽  
Christopher N. Penfold ◽  
Stephen P. Diggle
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Species Interactions ◽  
Clinical Problem ◽  
Opportunistic Pathogen ◽  
Resistance Mechanisms ◽  
Global Concern ◽  
Human Infections ◽  
Antibiofilm Agents

ABSTRACTPseudomonas aeruginosais an opportunistic pathogen responsible for a number of different human infections and is the leading cause of morbidity and mortality in cystic fibrosis (CF) patients.P. aeruginosainfections are difficult to treat due to a number of antibiotic resistance mechanisms and the organisms propensity to form multicellular biofilms. Epidemic strains ofP. aeruginosaoften dominate within the lungs of individual CF patients, but how they achieve this is poorly understood. One of the ways strains ofP. aeruginosacan compete, is by producing chromosomally encoded bacteriocins, called pyocins. Three major classes of pyocin have been identified inP. aeruginosa:soluble pyocins (S-types) and tailocins (R- and F-types). In this study, we investigated the distribution of S- and R-type pyocins in 24 clinical strains isolated from individual CF patients and then focused on understanding their roles on inter-strain competition. We found that (i) each strain produced only one R-pyocin type, but the number of S-pyocins varied between strains; (ii) R-pyocins were generally important for strain dominance during competition assays in planktonic cultures and biofilm communities in strains with both disparate R and S pyocin sub-types. (iii) purified R-pyocins demonstrated significant antimicrobial activity against established biofilms. Our work provides support for a key role played by R-pyocins in the competition betweenP. aeruginosastrains, and may help explain why certain strains and lineages ofP. aeruginosadominate and displace others during CF lung infection. Furthermore, we demonstrate the potential of exploiting R-pyocins for therapeutic gains in an era when antibiotic resistance is a global concern.IMPORTANCEA major clinical problem caused byPseudomonas aeruginosa, is chronic biofilm infection of the lungs in individuals with cystic fibrosis (CF). EpidemicP. aeruginosastrains dominate and displace others during CF infection, but these intra-species interactions remain poorly understood. Here we demonstrate that R-pyocins (bacterocins) are important factors in driving competitive interactions in biofilms betweenP. aeruginosastrains isolated from different CF patients. In addition, we found that these phage-like pyocins are inhibitory against mature biofilms of susceptible strains. This highlights the potential of R-pyocins as antimicrobial and antibiofilm agents, at a time when new antimicrobial therapies are desperately needed.

scholarly journals Combining functional and structural genomics to track antibiotic resistance genes in mobile elements in clinical bacterial strains

2020 ◽  
Author(s):  
Tiago Cabral Borelli ◽  
Gabriel Lencioni Lovate ◽  
Ana Flavia Tonelli Scaranello ◽  
Lucas Ferreira Ribeiro ◽  
Livia Zaramela ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
South America ◽  
Functional Genomics ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Resistance Mechanisms ◽  
Multi Drug Resistance ◽  
Resistant Bacteria ◽  
Beta Lactamase ◽  
Bacterial Strains

AbstractThe rise of multi-antibiotics resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in bacteria of several species isolated from an intensive care unit in Brazil. We used whole-genome analysis to identify antibiotic resistance genes (ARGs) and plasmids in 35 strains of Gram-negative and Gram-positive bacteria, including the first genomic description of Morganella morganii and Ralstonia mannitolilytica clinical isolates from South America. We identify a high abundance of beta-lactamase genes in highly resistant organisms, including seven extended-spectrum β-lactamases shared between organisms from different species. Additionally, we identify several ARGs-carrying plasmids indicating the potential for fast transmission of resistance mechanism between bacterial strains, comprising a novel IncFII plasmid recently introduced in Brazil from Asia. Through comparative genomic analysis, we demonstrate that some pathogens identified here are very distantly related to other bacteria isolated worldwide, demonstrating the potential existence of endemic bacterial pathogens in Brazil. Also, we uncovered at least two couples of (near)-identical plasmids exhibiting multi-drug resistance, suggesting that plasmids were transmitted between bacteria of the same or different species in the hospital studied. Finally, since many highly resistant strains carry several different ARGs, we used functional genomics to investigate which of them were indeed functional. In this sense, for three bacterial strains (Escherichia coli, Klebsiella pneumoniae, and M. morganii), we identify six beta-lactamase genes out of 15 predicted in silico as the main responsible for the resistance mechanisms observed, corroborating the existence of redundant resistance mechanisms in these organisms.ImportanceBig data and large-scale sequencing projects have revolutionized the field, achieving a greater understanding of ARGs identification and spreading at global level. However, given that microbiota and associated ARGs may fluctuate across geographic zones, hospital-associated infections within clinical units still remain underexplored in Brazil – the largest country in South America; 210 million inhabitants – and neighboring countries. This work highlighted the identification of several ARGs shared between species co-occurring simultaneously into a Brazilian hospital, some of them associated with large plasmids, mostly endowed with transposable elements. Also, genomic features of clinically underrepresented pathogens such M. morganii and B. cepacia were revealed. Taken together, our results demonstrate how structural and functional genomics can help to identify emerging mechanisms of shared antibiotic resistance in bacteria from clinical environments. Systematic studies as the one presented here should help to prevent outbreaks of novel multidrug resistance bacteria in healthcare facilities.

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