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Fernandes Santos F, Barcelos Valiatti T, Valêncio A, Cardoso da Silva Ribeiro Á, Streling AP, Tardelli Gomes TA, Cayô R, Gales AC. Unveiling novel threats: Urban river isolation of Aeromonas veronii with unusual VEB-28 extended-spectrum β-lactamase and distinct mcr variants. CHEMOSPHERE 2024; 357:141918. [PMID: 38614394 DOI: 10.1016/j.chemosphere.2024.141918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/15/2024]
Abstract
Aeromonas spp. are frequently encountered in aquatic environments, with Aeromonas veronii emerging as an opportunistic pathogen causing a range of diseases in both humans and animals. Recent reports have raised public health concerns due to the emergence of multidrug-resistant Aeromonas spp. This is particularly noteworthy as these species have demonstrated the ability to acquire and transmit antimicrobial resistance genes (ARGs). In this study, we report the genomic and phenotypic characteristics of the A. veronii TR112 strain, which harbors a novel variant of the Vietnamese Extended-spectrum β-lactamase-encoding gene, blaVEB-28, and two mcr variants recovered from an urban river located in the Metropolitan Region of São Paulo, Brazil. A. veronii TR112 strain exhibited high minimum inhibitory concentrations (MICs) for ceftazidime (64 μg/mL), polymyxin (8 μg/mL), and ciprofloxacin (64 μg/mL). Furthermore, the TR112 strain demonstrated adherence to HeLa and Caco-2 cells within 3 h, cytotoxicity to HeLa cells after 24 h of interaction, and high mortality rates to the Galleria mellonella model. Genomic analysis showed that the TR112 strain belongs to ST257 and presented a range of ARGs conferring resistance to β-lactams (blaVEB-28, blaCphA3, blaOXA-912) and polymyxins (mcr-3 and mcr-3.6). Additionally, we identified a diversity of virulence factor-encoding genes, including those encoding mannose-sensitive hemagglutinin (Msh) pilus, polar flagella, type IV pili, type II secretion system (T2SS), aerolysin (AerA), cytotoxic enterotoxin (Act), hemolysin (HlyA), hemolysin III (HlyIII), thermostable hemolysin (TH), and capsular polysaccharide (CPS). In conclusion, our findings suggest that A. veronii may serve as an environmental reservoir for ARGs and virulence factors, highlighting its importance as a potential pathogen in public health.
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Affiliation(s)
- Fernanda Fernandes Santos
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine. Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil.
| | - Tiago Barcelos Valiatti
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine. Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
| | - André Valêncio
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine. Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
| | - Ághata Cardoso da Silva Ribeiro
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine. Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
| | - Ana Paula Streling
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine. Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil; Houston Methodist Research Institute, Infectious Disease Fellowship Program, Houston, TX, United States
| | - Tânia A Tardelli Gomes
- Universidade Federal de São Paulo (UNIFESP), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
| | - Rodrigo Cayô
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine. Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil; Universidade Federal de São Paulo (UNIFESP), Laboratório de Imunologia e Bacteriologia (LIB), Setor de Biologia Molecular, Microbiologia e Imunologia, Departamento de Ciências Biológicas (DCB), Instituto de Ciências Ambientais, Químicas e Farmacêuticas (ICAQF), Diadema, SP, Brazil
| | - Ana Cristina Gales
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine. Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
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Umair M, Walsh TR, Mohsin M. A systematic review and meta-analysis of carbapenem resistance and its possible treatment options with focus on clinical Enterobacteriaceae: Thirty years of development in Pakistan. Heliyon 2024; 10:e28052. [PMID: 38596009 PMCID: PMC11001782 DOI: 10.1016/j.heliyon.2024.e28052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
Background Carbapenem resistance is epidemic worldwide, these last resort antimicrobials are listed in the WHO 'watch group' with higher resistance potential. During the years 2017-18 Pakistan Antimicrobial Resistance Surveillance System reported an increase in carbapenem resistance. However, a comprehensive information on prevalence and molecular epidemiology of carbapenem resistance in Pakistan is not available. This systematic review and meta-analysis is aimed to report the current carbapenem resistance situation in Pakistan and its treatment options. Methods In this systematic review and meta-analysis, we investigated the pooled prevalence (PPr) of carbapenem resistance in Enterobacteriaceae and non-Enterobacteriaceae by organizing available data, from Web of Science and PubMed by April 2, 2020, in various groups and subgroups including species, years, provinces, extended spectrum β-lactamase production, clinical presentation, carbapenemase and metallo-β-lactamase production, and New Delhi metallo-β-lactamase (NDM) prevalence. Literature review was updated for the studies publisehd by December 07, 2023. Moreover, we descriptively reviewed the molecular epidemiology of carbapenem resistance in Enterobacteriaceae and non-Enterobacteriaceae in Pakistan. Lastly, we statistically explored different treatment options available for carbapenem resistant infections. We used R package 'metafor' for performing meta-analysis and influence diagnostics and determining treatment options. Results From two academic databases Web of Science and PubMed we identified 343 studies. Eighty-eight studies were selected for the systematic review and meta-analysis. Seventy-four studies were selected for phenotypic analysis, 36 for genotypic analysis, and 31 for available treatment options. PPr-ID of 12% [0.12 (0.07, 0.16)] was observed for phenotypic carbapenem resistance in Enterobacteriaceae with more prevalence recorded in Klebsiella pneumoniae 24% [0.24 (0.05, 0.44)] followed by 9% [0.09 (-0.03, 0.20)] in Escherichia coli. During the last two decades we observed a striking increase in carbapenem resistance PPr i.e., from 0% [0.00 (-0.02, 0.03)] to 36% [0.36 (0.17, 0.56)]. blaNDM with PPr 15% [0.15 (0.06, 0.23)] in naive isolates was found to be the fundamental genetic determinant for carbapenem resistance in Enterobacteriaceae in Pakistan. Polymyxin B, colistin, tigecycline, and fosfomycin were identified as the suggested treatment options available for multidrug resistant infections not responding to carbapenems. Various studies reported carbapenem resistance from human, animal, and environment sources. Conclusion In conclusion, we found that NDM-1 producing carbapenem resistant Enterobacteriaceae are increasing in Pakistan. Meta-analysis showed that metallo-β-lactamases producing E. coli ST405 and K. pneumoniae sequence type11 are the major resistant clones. Number of reported studies in various subgroups and inconsistency in following CLSI guidelines are the potential limitations of this meta-analysis. A National antimicrobial resistance (AMR) surveillance strategy based on One Health is urgently needed to check any future AMR crisis in Pakistan.
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Affiliation(s)
- Muhammad Umair
- Institute of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan
- INEOS Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Timothy R. Walsh
- INEOS Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan
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3
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Khan A, Saraf VS, Siddiqui F, Batool T, Noreen Z, Javed S, Ahmad A, Alonazi WB, Ibrahim M, Pucciarelli S, Bokhari H. Multidrug resistance among uropathogenic clonal group A E. Coli isolates from Pakistani women with uncomplicated urinary tract infections. BMC Microbiol 2024; 24:74. [PMID: 38454332 PMCID: PMC10919050 DOI: 10.1186/s12866-024-03221-8] [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: 07/07/2023] [Accepted: 02/09/2024] [Indexed: 03/09/2024] Open
Abstract
OBJECTIVE Multi-drug resistance (MDR) has notably increased in community acquired uropathogens causing urinary tract infections (UTIs), predominantly Escherichia coli. Uropathogenic E. coli causes 80% of uncomplicated community acquired UTIs, particularly in pre-menopausal women. Considering this high prevalence and the potential to spread antimicrobial resistant genes, the current study was conducted to investigate the presence of clinically important strains of E. coli in Pakistani women having uncomplicated cystitis and pyelonephritis. Women belonging to low-income groups were exclusively included in the study. Seventy-four isolates from urine samples were processed, phylotyped, and screened for the presence of two Single Nucleotide Polymorphisms (SNPs) particularly associated with a clinically important clonal group A of E. coli (CgA) followed by antibiotic susceptibility testing and genome sequence analysis. RESULTS Phylogroup B2 was most prevalent in patients and 44% of isolates were positive for the presence of CgA specific SNPs in Fumarate hydratase and DNA gyrase subunit B genes. Antibiotic susceptibility testing showed widespread resistance to trimethoprim-sulfamethoxazole and extended-spectrum beta-lactamase production. The infection analysis revealed the phylogroup B2 to be more pathogenic as compared to the other groups. The genome sequence of E. coli strain U17 revealed genes encoding virulence, multidrug resistance, and host colonization mechanisms. CONCLUSIONS Our research findings not only validate the significant occurrence of multidrug-resistant clonal group A E. coli (CgA) in premenopausal Pakistani women suffering from cystitis and pyelonephritis but also reveal the presence of genes associated withvirulence, and drug efflux pumps. The detection of highly pathogenic, antimicrobial-resistant phylogroup B2 and CgA E. coli strains is likely to help in understanding the epidemiology of the pathogen and may ultimately help to reduce the impact of these strains on human health. Furthermore, the findings of this study will particularly help to reduce the prevalence of uncomplicated UTIs and the cost associated with their treatment in women belonging to low-income groups.
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Affiliation(s)
- Ayesha Khan
- Microbiology and Public Health Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
- Health Services Academy, Opposite NIH, Islamabad, Pakistan
| | - Viqar Sayeed Saraf
- Microbiology and Public Health Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Fariha Siddiqui
- Department of Biosciences, Shifa Tameer e Millat University, Islamabad, Pakistan
| | - Tahira Batool
- Microbiology and Public Health Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Zobia Noreen
- Microbiology and Public Health Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Sundus Javed
- Microbiology and Public Health Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Aftab Ahmad
- Department of Microbiology, Kohsar University Murree, Rawalpindi, Punjab, Pakistan
| | - Wadi B Alonazi
- Health Administration Department, College of Business Administration, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Ibrahim
- Department of Microbiology, Kohsar University Murree, Rawalpindi, Punjab, Pakistan.
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan.
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, via Gentile III da Varano, Camerino, 62032, Italy
| | - Habib Bokhari
- Department of Microbiology, Kohsar University Murree, Rawalpindi, Punjab, Pakistan.
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Conte D, Palmeiro J, Bavaroski A, Rodrigues L, Cardozo D, Tomaz A, Camargo J, Dalla‐Costa L. Antimicrobial resistance in
Aeromonas
species isolated from aquatic environments in Brazil. J Appl Microbiol 2021; 131:169-181. [DOI: https:/doi.org/10.1111/jam.14965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Affiliation(s)
- D. Conte
- Faculdades Pequeno Príncipe (FPP) Curitiba, Paraná Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP) Curitiba, Paraná Brazil
| | - J.K. Palmeiro
- Faculdades Pequeno Príncipe (FPP) Curitiba, Paraná Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP) Curitiba, Paraná Brazil
- Departamento de Análises Clínicas Universidade Federal de Santa Catarina (ACL‐UFSC) Florianópolis, Santa Catarina Brazil
| | - A.A. Bavaroski
- Faculdades Pequeno Príncipe (FPP) Curitiba, Paraná Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP) Curitiba, Paraná Brazil
| | - L.S. Rodrigues
- Faculdades Pequeno Príncipe (FPP) Curitiba, Paraná Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP) Curitiba, Paraná Brazil
| | - D. Cardozo
- Liga Paranaese de Combate ao Câncer ‐ Hospital Erasto Gaertner (HEG) Curitiba, Paraná Brazil
| | - A.P. Tomaz
- Faculdades Pequeno Príncipe (FPP) Curitiba, Paraná Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP) Curitiba, Paraná Brazil
- Complexo Hospital de ClínicasUniversidade Federal do Paraná (CHC‐UFPR) Curitiba, Paraná Brazil
| | - J.O. Camargo
- Departamento de Bioquímica e Biologia Molecular Universidade Federal do Paraná (UFPR) Curitiba, Paraná Brazil
- Setor de Educação Profissional e Tecnológica (SEPT) Programa de Graduação em Bioinformática Universidade Federal do Paraná (UFPR) Curitiba, Paraná Brazil
| | - L.M. Dalla‐Costa
- Faculdades Pequeno Príncipe (FPP) Curitiba, Paraná Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP) Curitiba, Paraná Brazil
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Praski Alzrigat L, Huseby DL, Brandis G, Hughes D. Resistance/fitness trade-off is a barrier to the evolution of MarR inactivation mutants in Escherichia coli. J Antimicrob Chemother 2021; 76:77-83. [PMID: 33089314 PMCID: PMC7729382 DOI: 10.1093/jac/dkaa417] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/09/2020] [Indexed: 12/23/2022] Open
Abstract
Background Mutations that inactivate MarR reduce susceptibility to ciprofloxacin and competitive growth fitness in Escherichia coli. Both phenotypes are caused by overexpression of the MarA regulon, which includes the AcrAB-TolC drug efflux pump. Objectives We asked whether compensatory evolution could reduce the fitness cost of MarR-inactivating mutations without affecting resistance to ciprofloxacin. Methods The cost of overexpressing the AcrAB-TolC efflux pump was measured independently of MarA overexpression. Experimental evolution of MarR-inactive strains was used to select mutants with increased fitness. The acquired mutations were identified and their effects on drug susceptibility were measured. Results Overexpression of the AcrAB-TolC efflux pump was found not to contribute to the fitness cost of MarA regulon overexpression. Fitness-compensatory mutations were selected in marA and lon. The mutations reduced the level of MarA protein thus reducing expression of the MarA regulon. They restored growth fitness but also reduced resistance to ciprofloxacin. Conclusions The fitness cost caused by overexpression of the MarA regulon has multiple contributing factors. Experimental evolution did not identify any single pump-independent cost factor. Instead, efficient fitness compensation occurred only by mechanisms that reduce MarA concentration, which simultaneously reduce the drug resistance phenotype. This resistance/fitness trade-off is a barrier to the successful spread of MarR inactivation mutations in clinical isolates where growth fitness is essential.
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Affiliation(s)
- Lisa Praski Alzrigat
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Sweden
| | - Douglas L Huseby
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Sweden
| | - Gerrit Brandis
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Sweden
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6
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Brandis G, Gockel J, Garoff L, Guy L, Hughes D. Expression of the qepA1 gene is induced under antibiotic exposure. J Antimicrob Chemother 2021; 76:1433-1440. [PMID: 33608713 PMCID: PMC8120332 DOI: 10.1093/jac/dkab045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/28/2021] [Indexed: 11/13/2022] Open
Abstract
Background The qepA1 gene encodes an efflux pump that reduces susceptibility to ciprofloxacin. Little is known about the regulation of qepA1 expression. Objectives To assess the potential role of ciprofloxacin and other antibiotics in the regulation of qepA1 gene expression. To identify the promoter that drives qepA1 expression and other factors involved in expression regulation. To assess whether the identified features are universal among qepA alleles. Methods A translational qepA1-yfp fusion under the control of the qepA1 upstream region was cloned into the Escherichia coli chromosome. Expression of the fusion protein was measured in the presence of various antibiotics. Deletions within the upstream region were introduced to identify regions involved in gene expression and regulation. The qepA1 coding sequence and upstream region were compared with all available qepA sequences. Results Cellular stress caused by the presence of various antibiotics can induce qepA1 expression. The qepA1 gene is fused to a class I integron and gene expression is driven by the Pc promoter within the integrase gene. A segment within the integron belonging to a truncated dfrB4 gene is essential for the regulation of qepA1 expression. This genetic context is universal among all sequenced qepA alleles. Conclusions The fusion of the qepA1 gene to a class I integron has created a novel regulatory unit that enables qepA1 expression to be under the control of antibiotic exposure. This setup mitigates potential negative effects of QepA1 production on bacterial fitness by restricting high-level expression to environmental conditions in which QepA1 is beneficial.
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Affiliation(s)
- Gerrit Brandis
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Box 582, Uppsala, Sweden
| | - Jonas Gockel
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Box 582, Uppsala, Sweden
| | - Linnéa Garoff
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Box 582, Uppsala, Sweden
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Box 582, Uppsala, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Box 582, Uppsala, Sweden
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7
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Antibiotic resistance in Pakistan: a systematic review of past decade. BMC Infect Dis 2021; 21:244. [PMID: 33676421 PMCID: PMC7937258 DOI: 10.1186/s12879-021-05906-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Background During the last six decades, extensive use of antibiotics has selected resistant strains, increasing the rate of fatal infectious diseases, and exerting an economic burden on society. This situation is widely accepted as a global problem, yet its degree is not well elucidated in many regions of the world. Up till now, no systemic analysis of Antimicrobial resistance (AMR) in Pakistan has been published. The current study aims to describe the antibiotic-resistance scenario of Pakistan from human samples of the last 10 y, to find the gaps in surveillances and methodology and recommendations for researchers and prescribers founded on these outcomes. Methods Original research articles analyzed the pattern of Antibiotic resistance of any World Health Organization (WHO) enlisted priority pathogens in Pakistan (published onward 2009 till March 2020), were collected from PubMed, Google scholar, and PakMedi Net search engines. These articles were selected based on predefined inclusion and exclusion criteria. Data about the study characteristics and antibiotic-resistance for a given bacterium were excluded from literature. Antibiotic resistance to a particular bacterium was calculated as a median resistance with 95% Confidence Interval (CI). Results Studies published in the last 10 y showed that Urinary Tract Infection (UTI) is the most reported clinical diagnosis (16.1%) in Pakistan. E. coli were reported in 28 (30.11%) studies showing high resistance to antibiotics’ first line. Methicillin-resistant Staphylococcus aureus (MRSA) was found in 49% of S. aureus’ total reported cases. Phenotypic resistance pattern has mostly been evaluated by Disk Diffusion Method (DDM) (82.8%), taken Clinical Laboratory Standards Institute (CLSI) as a breakpoint reference guideline (in 79.6% studies). Only 28 (30.11%) studies have made molecular identification of the resistance gene. blaTEM (78.94% in Shigella spp) and blaNDM-1 (32.75% in Klebsiella spp) are the prominent reported resistant genes followed by VanA (45.53% in Enterococcus spp), mcr-1 (1.61% in Acinetobacter spp), and blaKPC-2 (31.67% in E. coli). Most of the studies were from Sindh (40.86%), followed by Punjab (35.48%), while Baluchistan’s AMR data was not available. Conclusion Outcomes of our study emphasize that most of the pathogens show high resistance to commonly used antibiotics; also, we find gaps in surveillances and breaches in methodological data. Based on these findings, we recommend the regularization of surveillance practice and precise actions to combat the region’s AMR.
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8
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Conte D, Palmeiro JK, Bavaroski AA, Rodrigues LS, Cardozo D, Tomaz AP, Camargo JO, Dalla-Costa LM. Antimicrobial resistance in Aeromonas species isolated from aquatic environments in Brazil. J Appl Microbiol 2020; 131:169-181. [PMID: 33306232 DOI: 10.1111/jam.14965] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/16/2020] [Accepted: 12/07/2020] [Indexed: 11/28/2022]
Abstract
AIM The current study was conducted to determine the antimicrobial resistance profile and genetic relatedness of Aeromonas sp. isolated from healthcare and urban effluents, wastewater treatment plant (WWTP) and river water. METHODS AND RESULTS We detected the presence of genes conferring resistance to β-lactam, quinolone and aminoglycoside. Multilocus sequence typing was carried out to differentiate the strains, and multilocus phylogenetic analysis was used to identify the species. A total of 28 cefotaxime-resistant Aeromonas sp. strains were identified, harbouring uncommon Guiana-extended-spectrum (GES)-type β-lactamases (GES-1, GES-5, GES-7 and GES-16). Multidrug-resistant Aeromonas sp. were found in hospital wastewater, WWTP and sanitary effluent, and A. caviae was identified as the most prevalent species (85·7%). CONCLUSION The release of untreated healthcare effluents, presence of antimicrobials in the environment, in addition to multidrug-resistant Aeromonas sp., are all potential factors for the spread of resistance. SIGNIFICANCE AND IMPACT OF THE STUDY We identified a vast repertoire of antimicrobial resistance genes (ARG) in Aeromonas sp. from diverse aquatic ecosystems, including those that encode enzymes degrading broad-spectrum antimicrobials widely used to treat healthcare-associated infections. Hospital and sanitary effluents serve as potential sources of bacteria harbouring ARG and are a threat to public health.
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Affiliation(s)
- D Conte
- Faculdades Pequeno Príncipe (FPP), Curitiba, Paraná, Brazil.,Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Curitiba, Paraná, Brazil
| | - J K Palmeiro
- Faculdades Pequeno Príncipe (FPP), Curitiba, Paraná, Brazil.,Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Curitiba, Paraná, Brazil.,Departamento de Análises Clínicas, Universidade Federal de Santa Catarina (ACL-UFSC), Florianópolis, Santa Catarina, Brazil
| | - A A Bavaroski
- Faculdades Pequeno Príncipe (FPP), Curitiba, Paraná, Brazil.,Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Curitiba, Paraná, Brazil
| | - L S Rodrigues
- Faculdades Pequeno Príncipe (FPP), Curitiba, Paraná, Brazil.,Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Curitiba, Paraná, Brazil
| | - D Cardozo
- Liga Paranaese de Combate ao Câncer - Hospital Erasto Gaertner (HEG), Curitiba, Paraná, Brazil
| | - A P Tomaz
- Faculdades Pequeno Príncipe (FPP), Curitiba, Paraná, Brazil.,Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Curitiba, Paraná, Brazil.,Complexo Hospital de Clínicas, Universidade Federal do Paraná (CHC-UFPR), Curitiba, Paraná, Brazil
| | - J O Camargo
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil.,Setor de Educação Profissional e Tecnológica (SEPT), Programa de Graduação em Bioinformática, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| | - L M Dalla-Costa
- Faculdades Pequeno Príncipe (FPP), Curitiba, Paraná, Brazil.,Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Curitiba, Paraná, Brazil
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9
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Garoff L, Pietsch F, Huseby DL, Lilja T, Brandis G, Hughes D. Population Bottlenecks Strongly Influence the Evolutionary Trajectory to Fluoroquinolone Resistance in Escherichia coli. Mol Biol Evol 2020; 37:1637-1646. [PMID: 32031639 PMCID: PMC7253196 DOI: 10.1093/molbev/msaa032] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Experimental evolution is a powerful tool to study genetic trajectories to antibiotic resistance under selection. A confounding factor is that outcomes may be heavily influenced by the choice of experimental parameters. For practical purposes (minimizing culture volumes), most experimental evolution studies with bacteria use transmission bottleneck sizes of 5 × 106 cfu. We currently have a poor understanding of how the choice of transmission bottleneck size affects the accumulation of deleterious versus high-fitness mutations when resistance requires multiple mutations, and how this relates outcome to clinical resistance. We addressed this using experimental evolution of resistance to ciprofloxacin in Escherichia coli. Populations were passaged with three different transmission bottlenecks, including single cell (to maximize genetic drift) and bottlenecks spanning the reciprocal of the frequency of drug target mutations (108 and 1010). The 1010 bottlenecks selected overwhelmingly mutations in drug target genes, and the resulting genotypes corresponded closely to those found in resistant clinical isolates. In contrast, both the 108 and single-cell bottlenecks selected mutations in three different gene classes: 1) drug targets, 2) efflux pump repressors, and 3) transcription-translation genes, including many mutations with low fitness. Accordingly, bottlenecks smaller than the average nucleotide substitution rate significantly altered the experimental outcome away from genotypes observed in resistant clinical isolates. These data could be applied in designing experimental evolution studies to increase their predictive power and to explore the interplay between different environmental conditions, where transmission bottlenecks might vary, and resulting evolutionary trajectories.
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Affiliation(s)
- Linnéa Garoff
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Franziska Pietsch
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Douglas L Huseby
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Tua Lilja
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Gerrit Brandis
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
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10
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MacFadden DR, Coburn B, Břinda K, Corbeil A, Daneman N, Fisman D, Lee RS, Lipsitch M, McGeer A, Melano RG, Mubareka S, Hanage WP. Using Genetic Distance from Archived Samples for the Prediction of Antibiotic Resistance in Escherichia coli. Antimicrob Agents Chemother 2020; 64:e02417-19. [PMID: 32152083 PMCID: PMC7179619 DOI: 10.1128/aac.02417-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/02/2020] [Indexed: 11/20/2022] Open
Abstract
The rising rates of antibiotic resistance increasingly compromise empirical treatment. Knowing the antibiotic susceptibility of a pathogen's close genetic relative(s) may improve empirical antibiotic selection. Using genomic and phenotypic data for Escherichia coli isolates from three separate clinically derived databases, we evaluated multiple genomic methods and statistical models for predicting antibiotic susceptibility, focusing on potentially rapidly available information, such as lineage or genetic distance from archived isolates. We applied these methods to derive and validate the prediction of antibiotic susceptibility to common antibiotics. We evaluated 968 separate episodes of suspected and confirmed infection with Escherichia coli from three geographically and temporally separated databases in Ontario, Canada, from 2010 to 2018. Across all approaches, model performance (area under the curve [AUC]) ranges for predicting antibiotic susceptibility were the greatest for ciprofloxacin (AUC, 0.76 to 0.97) and the lowest for trimethoprim-sulfamethoxazole (AUC, 0.51 to 0.80). When a model predicted that an isolate was susceptible, the resulting (posttest) probabilities of susceptibility were sufficient to warrant empirical therapy for most antibiotics (mean, 92%). An approach combining multiple models could permit the use of narrower-spectrum oral agents in 2 out of every 3 patients while maintaining high treatment adequacy (∼90%). Methods based on genetic relatedness to archived samples of E. coli could be used to predict antibiotic resistance and improve antibiotic selection.
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Affiliation(s)
- Derek R MacFadden
- Division of Infectious Diseases, University of Toronto, Toronto, Canada
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Ottawa Hospital Research Institute, Ottawa, Canada
| | - Bryan Coburn
- Division of Infectious Diseases, University of Toronto, Toronto, Canada
- University Health Network, Toronto, Canada
| | - Karel Břinda
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Antoine Corbeil
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Nick Daneman
- Division of Infectious Diseases, University of Toronto, Toronto, Canada
| | - David Fisman
- Division of Infectious Diseases, University of Toronto, Toronto, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Robyn S Lee
- Harvard Medical School, Boston, Massachusetts, USA
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Marc Lipsitch
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Allison McGeer
- Division of Infectious Diseases, University of Toronto, Toronto, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Roberto G Melano
- Public Health Ontario Laboratory, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Samira Mubareka
- Division of Infectious Diseases, University of Toronto, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - William P Hanage
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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11
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Garoff L, Yadav K, Hughes D. Increased expression of Qnr is sufficient to confer clinical resistance to ciprofloxacin in Escherichia coli. J Antimicrob Chemother 2019; 73:348-352. [PMID: 29106520 PMCID: PMC5890660 DOI: 10.1093/jac/dkx375] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/15/2017] [Indexed: 02/05/2023] Open
Abstract
Background Ciprofloxacin, a fluoroquinolone, targets two essential bacterial enzymes, DNA gyrase and topoisomerase IV. Plasmid-borne qnr genes, encoding proteins that protect DNA gyrase and topoisomerase IV from inhibition by fluoroquinolones, contribute to resistance development. However, the presence of a plasmid-borne qnr gene alone is insufficient to confer clinical resistance. Objectives We asked whether the level of expression of qnr was a limiting factor in its ability to confer clinical resistance and whether expression could be increased without reducing fitness or viability. Methods qnrB and qnrS were recombineered onto the chromosome of Escherichia coli under the control of constitutive promoters of various strengths. Expression was measured by qPCR, MIC and relative fitness as a function of expression level were determined. Results For both qnr genes there was a positive relationship between the level of qnr mRNA and the MIC of ciprofloxacin. The highest MICs achieved with qnrB or qnrS as the sole resistance determinant were 0.375 and 1 mg/L, respectively, and were reached at expression levels that did not affect growth rate or viability. The qnrS-mediated MIC is above the EUCAST clinical breakpoint for resistance to ciprofloxacin. In the absence of Lon protease activity, overexpression of qnr genes was associated with high fitness cost, possibly explaining observations of toxicity in other genetic backgrounds. Conclusions The ability to generate a high MIC without incurring a fitness cost shows that, in an appropriate genetic context, qnrS has the potential to generate clinical resistance to ciprofloxacin in one step.
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Affiliation(s)
- Linnéa Garoff
- Department of Medical Biochemistry and Microbiology, Biomedical Centre (Box 582), Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Kavita Yadav
- Department of Medical Biochemistry and Microbiology, Biomedical Centre (Box 582), Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Biomedical Centre (Box 582), Uppsala University, Husargatan 3, Uppsala 75123, Sweden
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12
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Zaman TU, Alrodayyan M, Albladi M, Aldrees M, Siddique MI, Aljohani S, Balkhy HH. Clonal diversity and genetic profiling of antibiotic resistance among multidrug/carbapenem-resistant Klebsiella pneumoniae isolates from a tertiary care hospital in Saudi Arabia. BMC Infect Dis 2018; 18:205. [PMID: 29724185 PMCID: PMC5934806 DOI: 10.1186/s12879-018-3114-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/25/2018] [Indexed: 11/10/2022] Open
Abstract
Background The nexus between resistance determinants, plasmid type, and clonality appears to play a crucial role in the dissemination and survival of carbapenem-resistant Klebsiella pneumoniae (CRKP). The incidence of infections involving CRKP in Saudi Arabia is increasing and there is a need for detailed molecular profiling of this pathogen for CRKP surveillance and control. Methods The resistance determinants of 71 non-redundant CRKP isolates were investigated by polymerase chain reaction (PCR) and sequencing. Plasmid typing was performed using PCR-based replicon typing and the clonality of isolates was determined by multilocus sequence typing. Capsular polysaccharide synthesis genes and other virulence factors were examined using multiplex PCR. Diversity was calculated using DIVEIN, clonal relationship was determined using eBURST, and phylogenetic analysis was performed using SplitsTree4. Results A polyclonal OXA-48 gene alone was the most common carbapenemase detected in 48/71 (67.6%) isolates followed by NDM-1 alone in 9/71 (12.7%) isolates. Coproduction of OXA-48 and NDM-1 was observed in 6/71 (8.5%) isolates. Both carbapenemase genes could be transferred into an Escherichia coli recipient. CTX-M-15 was the most abundant extended-spectrum β-lactamase gene detected in 47/71 (66.2%) isolates, whereas clone-specific CTX-M-14 (ST-199 and -709) was found in 15/71 (21%) isolates. Sixty-seven of 71 isolates were positive for one or more plasmid replicons. The replicons detected were: IncFII; IncFIIK; IncFIA; IncFIB; L/M; IncI1; and IncN. FIIK and L/M were predominant, with 69 and 67% positivity, respectively. All isolates were negative for the magA (K1), rmpA, and K2 genes and presented a non-hypermucoviscous phenotype. Conclusion A polyclonal CRKP reservoir of sequence types (STs)-37, − 199, and − 152 was observed and ST-152 appeared to be a “frequent carrier” of the NDM-1 gene. ST-199, a singleton not previously reported, showed a sequence diversity suggestive of positive selection. A significant association was evident between resistance determinants and the clonal types of K. pneumoniae: all ST-152 isolates were positive for NDM-1 but negative for OXA-48; ST-199 isolates were positive for OXA-48 but negative for NDM-1; and ST-709 and -199 isolates were positive for CTX-M-14. The incidence of certain clonal types in large numbers predicts an outbreak-like situation and warrants stringent surveillance and infection control. Electronic supplementary material The online version of this article (10.1186/s12879-018-3114-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Taher Uz Zaman
- Infectious Diseases Section, King Abdullah International Medical Research Center National Guard Health Affairs, P.O. Box 22490, Mail Code 1515, Riyadh, 11426, Kingdom of Saudi Arabia. .,King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia.
| | - Maha Alrodayyan
- Infectious Diseases Section, King Abdullah International Medical Research Center National Guard Health Affairs, P.O. Box 22490, Mail Code 1515, Riyadh, 11426, Kingdom of Saudi Arabia.,King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Maha Albladi
- Infectious Diseases Section, King Abdullah International Medical Research Center National Guard Health Affairs, P.O. Box 22490, Mail Code 1515, Riyadh, 11426, Kingdom of Saudi Arabia.,King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed Aldrees
- Infectious Diseases Section, King Abdullah International Medical Research Center National Guard Health Affairs, P.O. Box 22490, Mail Code 1515, Riyadh, 11426, Kingdom of Saudi Arabia.,King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | | | - Sameera Aljohani
- King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia.,Microbiology Section- King Abdul-Aziz Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Hanan H Balkhy
- Infectious Diseases Section, King Abdullah International Medical Research Center National Guard Health Affairs, P.O. Box 22490, Mail Code 1515, Riyadh, 11426, Kingdom of Saudi Arabia. .,King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia. .,Infection Prevention and Control Prevention, King Abdul-Aziz Medical City, National Guard Health Affairs, P.O. Box 22490, Riyadh-11426, Riyadh, Kingdom of Saudi Arabia.
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Vinué L, Hooper DC, Jacoby GA. Chromosomal mutations that accompany qnr in clinical isolates of Escherichia coli. Int J Antimicrob Agents 2018; 51:479-483. [PMID: 29360506 DOI: 10.1016/j.ijantimicag.2018.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 10/18/2022]
Abstract
We examined 13 qnr-positive and 14 qnr-negative clinical isolates of Escherichia coli for mutations previously seen in a qnr-containing laboratory strain exposed to supra minimum inhibitory concentrations (MICs) of ciprofloxacin. Among the qnr-positive strains, those with ciprofloxacin MICs of ≥ 2 µg/mL had at least one mutation in gyrA. Mutations in parC were present in strains with a ciprofloxacin MIC of ≥ 128 µg/mL. The 6 most ciprofloxacin-resistant strains contained additional plasmid-mediated quinolone resistance determinants. aac(6')-Ib-cr was found in 5 of the 6 strains. Eleven of the 13 strains had alterations in MarR, 9 in SoxR, and 5 had mutations in AcrR. All had elevated expression of at least one efflux pump gene, predominantly acrA (92% of the strains), followed by mdtE (54%) and ydhE (46%). Nine had functionally silent alterations in rfa, two had mutations in gmhB, and one of these also had a mutation in surA. An E. coli with ciprofloxacin MIC of 1024 µg/mL contained 4 different plasmid-mediated quinolone resistance determinants as well as gyrA, parC, parE and pump overexpression mutations. Nine of the 14 qnr-negative strains had mutations in topoisomerase genes with a ciprofloxacin MIC of 0.25 to 256 µg/mL. The three most resistant strains also had mutations in parE. Twelve had alterations in MarR, 10 in SoxR and 5 in AcrR. Ten of the 14 strains had elevated expression of efflux pumps with acrA (71.4%), followed by ydhE (50%) and mdtE (14.3%). A diversity of resistance mechanisms occurs in clinical isolates with and without qnr genes.
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Affiliation(s)
- Laura Vinué
- Massachusetts General Hospital, Boston, Massachusetts, USA.
| | - David C Hooper
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | - George A Jacoby
- Lahey Hospital and Medical Center, Burlington, Massachusetts, USA
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14
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Praski Alzrigat L, Huseby DL, Brandis G, Hughes D. Fitness cost constrains the spectrum of marR mutations in ciprofloxacin-resistant Escherichia coli. J Antimicrob Chemother 2017; 72:3016-3024. [PMID: 28962020 PMCID: PMC5890708 DOI: 10.1093/jac/dkx270] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 06/12/2017] [Accepted: 07/07/2017] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES To determine whether the spectrum of mutations in marR in ciprofloxacin-resistant clinical isolates of Escherichia coli shows evidence of selection bias, either to reduce fitness costs, or to increase drug resistance. MarR is a repressor protein that regulates, via MarA, expression of the Mar regulon, including the multidrug efflux pump AcrAB-TolC. METHODS Isogenic strains carrying 36 different marR alleles identified in resistant clinical isolates, or selected for resistance in vitro, were constructed. Drug susceptibility and relative fitness in growth competition assays were measured for all strains. The expression level of marA, and of various efflux pump components, as a function of specific mutations in marR, was measured by qPCR. RESULTS The spectrum of genetic alterations in marR in clinical isolates is strongly biased against inactivating mutations. In general, the alleles found in clinical isolates conferred a lower level of resistance and imposed a lower growth fitness cost than mutations selected in vitro. The level of expression of MarA correlated well with the MIC of ciprofloxacin. This supports the functional connection between mutations in marR and reduced susceptibility to ciprofloxacin. CONCLUSIONS Mutations in marR selected in ciprofloxacin-resistant clinical isolates are strongly biased against inactivating mutations. Selection favours mutant alleles that have the lowest fitness costs, even though these cause only modest reductions in drug susceptibility. This suggests that selection for high relative fitness is more important than selection for increased resistance in determining which alleles of marR will be selected in resistant clinical isolates.
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Affiliation(s)
- Lisa Praski Alzrigat
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center Box 582, Husargatan 3, S-75123 Uppsala, Sweden
| | - Douglas L Huseby
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center Box 582, Husargatan 3, S-75123 Uppsala, Sweden
| | - Gerrit Brandis
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center Box 582, Husargatan 3, S-75123 Uppsala, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center Box 582, Husargatan 3, S-75123 Uppsala, Sweden
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15
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Huseby DL, Pietsch F, Brandis G, Garoff L, Tegehall A, Hughes D. Mutation Supply and Relative Fitness Shape the Genotypes of Ciprofloxacin-Resistant Escherichia coli. Mol Biol Evol 2017; 34:1029-1039. [PMID: 28087782 PMCID: PMC5400412 DOI: 10.1093/molbev/msx052] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Ciprofloxacin is an important antibacterial drug targeting Type II topoisomerases, highly active against Gram-negatives including Escherichia coli. The evolution of resistance to ciprofloxacin in E. coli always requires multiple genetic changes, usually including mutations affecting two different drug target genes, gyrA and parC. Resistant mutants selected in vitro or in vivo can have many different mutations in target genes and efflux regulator genes that contribute to resistance. Among resistant clinical isolates the genotype, gyrA S83L D87N, parC S80I is significantly overrepresented suggesting that it has a selective advantage. However, the evolutionary or functional significance of this high frequency resistance genotype is not fully understood. By combining experimental data and mathematical modeling, we addressed the reasons for the predominance of this specific genotype. The experimental data were used to model trajectories of mutational resistance evolution under different conditions of drug exposure and population bottlenecks. We identified the order in which specific mutations are selected in the clinical genotype, showed that the high frequency genotype could be selected over a range of drug selective pressures, and was strongly influenced by the relative fitness of alternative mutations and factors affecting mutation supply. Our data map for the first time the fitness landscape that constrains the evolutionary trajectories taken during the development of clinical resistance to ciprofloxacin and explain the predominance of the most frequently selected genotype. This study provides strong support for the use of in vitro competition assays as a tool to trace evolutionary trajectories, not only in the antibiotic resistance field.
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Affiliation(s)
- Douglas L Huseby
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Franziska Pietsch
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Gerrit Brandis
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Linnéa Garoff
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Angelica Tegehall
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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16
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Conte D, Palmeiro JK, da Silva Nogueira K, de Lima TMR, Cardoso MA, Pontarolo R, Degaut Pontes FL, Dalla-Costa LM. Characterization of CTX-M enzymes, quinolone resistance determinants, and antimicrobial residues from hospital sewage, wastewater treatment plant, and river water. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 136:62-69. [PMID: 27816836 DOI: 10.1016/j.ecoenv.2016.10.031] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/21/2016] [Accepted: 10/25/2016] [Indexed: 05/09/2023]
Abstract
Multidrug-resistant (MDR) bacteria are widespread in hospitals and have been increasingly isolated from aquatic environments. The aim of the present study was to characterize extended-spectrum β-lactamase (ESBL) and quinolone-resistant Enterobacteriaceae from a hospital effluent, sanitary effluent, inflow sewage, aeration tank, and outflow sewage within a wastewater treatment plant (WWTP), as well as river water upstream and downstream (URW and DRW, respectively), of the point where the WWTP treated effluent was discharged. β-lactamase (bla) genes, plasmid-mediated quinolone resistance (PMQR), and quinolone resistance-determining regions (QRDRs) were assessed by amplification and sequencing in 55 ESBL-positive and/or quinolone-resistant isolates. Ciprofloxacin residue was evaluated by high performance liquid chromatography. ESBL-producing isolates were identified in both raw (n=29) and treated (n=26) water; they included Escherichia coli (32), Klebsiella pneumoniae (22) and Klebsiella oxytoca (1). Resistance to both cephalosporins and quinolone was observed in 34.4% of E. coli and 27.3% of K. pneumoniae. Resistance to carbapenems was found in 5.4% of K. pneumoniae and in K. oxytoca. Results indicate the presence of blaCTX-M (51/55, 92.7%) and blaSHV (8/55, 14.5%) ESBLs, and blaGES (2/55, 3.6%) carbapenemase-encoding resistance determinants. Genes conferring quinolone resistance were detected at all sites, except in the inflow sewage and aeration tanks. Quinolone resistance was primarily attributed to amino acid substitutions in the QRDR of GyrA (47%) or to the presence of PMQR (aac-(6')-Ib-cr, oqxAB, qnrS, and/or qnrB; 52.9%) determinants. Ciprofloxacin residue was absent only from URW. Our results have shown strains carrying ESBL genes, PMQR determinants, and mutations in the gyrA QRDR genes mainly in hospital effluent, URW, and DRW samples. Antimicrobial use, and the inefficient removal of MDR bacteria and antibiotic residue during sewage treatment, may contribute to the emergence and spreading of resistance in the environment, making this a natural reservoir.
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Affiliation(s)
- Danieli Conte
- Faculdades e Instituto de Pesquisa Pelé Pequeno Príncipe (FPP/IPPPP), Curitiba, Paraná, Brazil.
| | - Jussara Kasuko Palmeiro
- Faculdades e Instituto de Pesquisa Pelé Pequeno Príncipe (FPP/IPPPP), Curitiba, Paraná, Brazil; Hospital de Clínicas, Universidade Federal do Paraná (HC-UFPR), Curitiba, Paraná, Brazil.
| | - Keite da Silva Nogueira
- Departamento de Patologia Básica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil.
| | | | - Marco André Cardoso
- Faculdades e Instituto de Pesquisa Pelé Pequeno Príncipe (FPP/IPPPP), Curitiba, Paraná, Brazil; Pharmacy Department, Health Sciences Sector, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil.
| | - Roberto Pontarolo
- Pharmacy Department, Health Sciences Sector, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil.
| | - Flávia Lada Degaut Pontes
- Pharmacy Department, Health Sciences Sector, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil.
| | - Libera Maria Dalla-Costa
- Faculdades e Instituto de Pesquisa Pelé Pequeno Príncipe (FPP/IPPPP), Curitiba, Paraná, Brazil; Hospital de Clínicas, Universidade Federal do Paraná (HC-UFPR), Curitiba, Paraná, Brazil.
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17
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Pietsch F, Bergman JM, Brandis G, Marcusson LL, Zorzet A, Huseby DL, Hughes D. Ciprofloxacin selects for RNA polymerase mutations with pleiotropic antibiotic resistance effects. J Antimicrob Chemother 2016; 72:75-84. [PMID: 27621175 DOI: 10.1093/jac/dkw364] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 08/02/2016] [Accepted: 08/02/2016] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Resistance to the fluoroquinolone drug ciprofloxacin is commonly linked to mutations that alter the drug target or increase drug efflux via the major AcrAB-TolC transporter. Very little is known about other mutations that might also reduce susceptibility to ciprofloxacin. We discovered that an Escherichia coli strain experimentally evolved for resistance to ciprofloxacin had acquired a mutation in rpoB, the gene coding for the β-subunit of RNA polymerase. The aim of this work was to determine whether this mutation, and other mutations in rpoB, contribute to ciprofloxacin resistance and, if so, by which mechanism. METHODS Independent lineages of E. coli were evolved in the presence of ciprofloxacin and clones from endpoint cultures were screened for mutations in rpoB. Ciprofloxacin-selected rpoB mutations were identified and characterized in terms of effects on susceptibility and mode of action. RESULTS Mutations in rpoB were selected at a high frequency in 3 out of 10 evolved lineages, in each case arising after the occurrence of mutations affecting topoisomerases and drug efflux. All ciprofloxacin-selected rpoB mutations had a high fitness cost in the absence of drug, but conferred a competitive advantage in the presence of ciprofloxacin. RNA sequencing and quantitative RT-PCR analysis showed that expression of mdtK, encoding a multidrug efflux transporter, was significantly increased by the ciprofloxacin-selected rpoB mutations. The susceptibility phenotype was shown to depend on the presence of an active mdtK and a mutant rpoB allele. CONCLUSIONS These data identify mutations in RNA polymerase as novel contributors to the evolution of resistance to ciprofloxacin and show that the phenotype is mediated by increased MdtK-dependent drug efflux.
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Affiliation(s)
- Franziska Pietsch
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Jessica M Bergman
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Gerrit Brandis
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Linda L Marcusson
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Anna Zorzet
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Douglas L Huseby
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Uppsala, Sweden
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18
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Characterization of Ciprofloxacin-Resistant and Ciprofloxacin-Susceptible Uropathogenic Escherichia coli Obtained from Patients with Gynecological Cancer. Curr Microbiol 2016; 73:624-632. [DOI: 10.1007/s00284-016-1104-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/18/2016] [Indexed: 11/26/2022]
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19
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Hughes D. Selection and evolution of resistance to antimicrobial drugs. IUBMB Life 2014; 66:521-9. [PMID: 24933583 DOI: 10.1002/iub.1278] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 05/21/2014] [Indexed: 01/22/2023]
Abstract
The overuse and misuse of antibiotics over many years has selected a high frequency of resistance among medically important bacterial pathogens. The evolution of resistance is complex, frequently involving multiple genetic alterations that minimize biological fitness costs and/or increase the resistance level. Resistance is selected at very low drug concentrations, such as found widely distributed in the environment, and this selects for resistant mutants with a high fitness. Once resistance with high fitness is established in a community it is very difficult to reduce its frequency. Addressing the problem of resistance is essential if we are to ensure a future where we can continue to enjoy effective medical control of bacterial infections. This will require several actions including the discovery and development of novel antibiotics, the creation of a continuous pipeline of drug discovery, and the implementation of effective global antibiotic stewardship to reduce the misuse of antibiotics and their release into the environment.
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Affiliation(s)
- Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
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20
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Alouache S, Estepa V, Messai Y, Ruiz E, Torres C, Bakour R. Characterization of ESBLs and Associated Quinolone Resistance inEscherichia coliandKlebsiella pneumoniaeIsolates from an Urban Wastewater Treatment Plant in Algeria. Microb Drug Resist 2014; 20:30-8. [DOI: 10.1089/mdr.2012.0264] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Souhila Alouache
- Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene, Algiers, Algeria
- High National School of Marine Sciences and Coastal Management, Campus Universitaire de Dely-Ibrahim, Algiers, Algeria
| | - Vanesa Estepa
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Logrono, Spain
| | - Yamina Messai
- Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene, Algiers, Algeria
| | - Elena Ruiz
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Logrono, Spain
| | - Carmen Torres
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Logrono, Spain
| | - Rabah Bakour
- Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene, Algiers, Algeria
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Predictive diagnostics for Escherichia coli infections based on the clonal association of antimicrobial resistance and clinical outcome. J Clin Microbiol 2013; 51:2991-9. [PMID: 23843485 DOI: 10.1128/jcm.00984-13] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The ability to identify bacterial pathogens at the subspecies level in clinical diagnostics is currently limited. We investigated whether splitting Escherichia coli species into clonal groups (clonotypes) predicts antimicrobial susceptibility or clinical outcome. A total of 1,679 extraintestinal E. coli isolates (collected from 2010 to 2012) were collected from one German and 5 U.S. clinical microbiology laboratories. Clonotype identity was determined by fumC and fimH (CH) sequencing. The associations of clonotype with antimicrobial susceptibility and clinical variables were evaluated. CH typing divided the isolates into >200 CH clonotypes, with 93% of the isolates belonging to clonotypes with ≥ 2 isolates. Antimicrobial susceptibility varied substantially among clonotypes but was consistent across different locations. Clonotype-guided antimicrobial selection significantly reduced "drug-bug" mismatch compared to that which occurs with the use of conventional empirical therapy. With trimethoprim-sulfamethoxazole and fluoroquinolones, the drug-bug mismatch was predicted to decrease 62% and 78%, respectively. Recurrent or persistent urinary tract infection and clinical sepsis were significantly correlated with specific clonotypes, especially with CH40-30 (also known as H30), a recently described clonotype within sequence type 131 (ST131). We were able to clonotype directly from patient urine samples within 1 to 3 h of obtaining the specimen. In E. coli, subspecies-level identification by clonotyping can be used to significantly improve empirical predictions of antimicrobial susceptibility and clinical outcomes in a timely manner.
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Andersson DI, Hughes D. Evolution of antibiotic resistance at non-lethal drug concentrations. Drug Resist Updat 2012; 15:162-72. [PMID: 22516308 DOI: 10.1016/j.drup.2012.03.005] [Citation(s) in RCA: 193] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 03/22/2012] [Accepted: 03/26/2012] [Indexed: 11/30/2022]
Abstract
Human use of antimicrobials in the clinic, community and agricultural systems has driven selection for resistance in bacteria. Resistance can be selected at antibiotic concentrations that are either lethal or non-lethal, and here we argue that selection and enrichment for antibiotic resistant bacteria is often a consequence of weak, non-lethal selective pressures - caused by low levels of antibiotics - that operates on small differences in relative bacterial fitness. Such conditions may occur during antibiotic therapy or in anthropogenically drug-polluted natural environments. Non-lethal selection increases rates of mutant appearance and promotes enrichment of highly fit mutants and stable mutators.
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Affiliation(s)
- Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Box 582, SE-75123 Uppsala, Sweden.
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