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Garoff L, Huseby DL, Praski Alzrigat L, Hughes D. Effect of aminoacyl-tRNA synthetase mutations on susceptibility to ciprofloxacin in Escherichia coli. J Antimicrob Chemother 2019; 73:3285-3292. [PMID: 30239743 DOI: 10.1093/jac/dky356] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/09/2018] [Indexed: 11/13/2022] Open
Abstract
Background Chromosomal mutations that reduce ciprofloxacin susceptibility in Escherichia coli characteristically map to drug target genes (gyrAB and parCE), and genes encoding regulators of the AcrAB-TolC efflux pump. Mutations in RNA polymerase can also reduce susceptibility, by up-regulating the MdtK efflux pump. Objectives We asked whether mutations in additional chromosomal gene classes could reduce susceptibility to ciprofloxacin. Methods Experimental evolution, complemented by WGS analysis, was used to select and identify mutations that reduce susceptibility to ciprofloxacin. Transcriptome analysis, genetic reconstructions, susceptibility measurements and competition assays were used to identify significant genes and explore the mechanism of resistance. Results Mutations in three different aminoacyl-tRNA synthetase genes (leuS, aspS and thrS) were shown to reduce susceptibility to ciprofloxacin. For two of the genes (leuS and aspS) the mechanism was partially dependent on RelA activity. Two independently selected mutations in leuS (Asp162Asn and Ser496Pro) were studied in most detail, revealing that they induce transcriptome changes similar to a stringent response, including up-regulation of three efflux-associated loci (mdtK, acrZ and ydhIJK). Genetic analysis showed that reduced susceptibility depended on the activity of these loci. Broader antimicrobial susceptibility testing showed that the leuS mutations also reduce susceptibility to additional classes of antibiotics (chloramphenicol, rifampicin, mecillinam, ampicillin and trimethoprim). Conclusions The identification of mutations in multiple tRNA synthetase genes that reduce susceptibility to ciprofloxacin and other antibiotics reveals the existence of a large mutational target that could contribute to resistance development by up-regulation of an array of efflux pumps.
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Affiliation(s)
- Linnéa Garoff
- Uppsala University, Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala, Sweden
| | - Douglas L Huseby
- Uppsala University, Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala, Sweden
| | - Lisa Praski Alzrigat
- Uppsala University, Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala, Sweden
| | - Diarmaid Hughes
- Uppsala University, Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala, Sweden
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Abstract
Many antibiotics available in the clinic today directly inhibit bacterial translation. Despite the past success of such drugs, their efficacy is diminishing with the spread of antibiotic resistance. Through the use of ribosomal modifications, ribosomal protection proteins, translation elongation factors and mistranslation, many pathogens are able to establish resistance to common therapeutics. However, current efforts in drug discovery are focused on overcoming these obstacles through the modification or discovery of new treatment options. Here, we provide an overview for common mechanisms of resistance to translation-targeting drugs and summarize several important breakthroughs in recent drug development.
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Affiliation(s)
- Anne Witzky
- 1 Department of Molecular Genetics, Ohio State University , Columbus, OH 43210 , USA.,2 Center for RNA Biology, Ohio State University , Columbus, OH 43210 , USA
| | - Rodney Tollerson
- 2 Center for RNA Biology, Ohio State University , Columbus, OH 43210 , USA.,3 Department of Microbiology, Ohio State University , Columbus, OH 43210 , USA
| | - Michael Ibba
- 2 Center for RNA Biology, Ohio State University , Columbus, OH 43210 , USA.,3 Department of Microbiology, Ohio State University , Columbus, OH 43210 , USA
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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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Khong WX, Marimuthu K, Teo J, Ding Y, Xia E, Lee JJ, Ong RTH, Venkatachalam I, Cherng B, Pada SK, Choong WL, Smitasin N, Ooi ST, Deepak RN, Kurup A, Fong R, Van La M, Tan TY, Koh TH, Lin RTP, Tan EL, Krishnan PU, Singh S, Pitout JD, Teo YY, Yang L, Ng OT. Tracking inter-institutional spread of NDM and identification of a novel NDM-positive plasmid, pSg1-NDM, using next-generation sequencing approaches. J Antimicrob Chemother 2016; 71:3081-3089. [PMID: 27494913 DOI: 10.1093/jac/dkw277] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 05/23/2016] [Accepted: 06/09/2016] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Owing to gene transposition and plasmid conjugation, New Delhi metallo-β-lactamase (NDM) is typically identified among varied Enterobacteriaceae species and STs. We used WGS to characterize the chromosomal and plasmid molecular epidemiology of NDM transmission involving four institutions in Singapore. METHODS Thirty-three Enterobacteriaceae isolates (collection years 2010-14) were sequenced using short-read sequencing-by-synthesis and analysed. Long-read single molecule, real-time sequencing (SMRTS) was used to characterize genetically a novel plasmid pSg1-NDM carried on Klebsiella pneumoniae ST147. RESULTS In 20 (61%) isolates, blaNDM was located on the pNDM-ECS01 plasmid in the background of multiple bacterial STs, including eight K. pneumoniae STs and five Escherichia coli STs. In six (18%) isolates, a novel blaNDM-positive plasmid, pSg1-NDM, was found only in K. pneumoniae ST147. The pSg1-NDM-K. pneumoniae ST147 clone (Sg1-NDM) was fully sequenced using SMRTS. pSg1-NDM, a 90 103 bp IncR plasmid, carried genes responsible for resistance to six classes of antimicrobials. A large portion of pSg1-NDM had no significant homology to any known plasmids in GenBank. pSg1-NDM had no conjugative transfer region. Combined chromosomal-plasmid phylogenetic analysis revealed five clusters of clonal bacterial NDM-positive plasmid transmission, of which two were inter-institution clusters. The largest inter-institution cluster involved six K. pneumoniae ST147-pSg1-NDM isolates. Fifteen patients were involved in transmission clusters, of which four had ward contact, six had hospital contact and five had an unknown transmission link. CONCLUSIONS A combined sequencing-by-synthesis and SMRTS approach can determine effectively the transmission clusters of blaNDM and genetically characterize novel plasmids. Plasmid molecular epidemiology is important to understanding NDM spread as blaNDM-positive plasmids can conjugate extensively across species and STs.
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Affiliation(s)
- Wei Xin Khong
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, 11 Jalan Tan Tock Seng, 308433, Singapore
| | - Kalisvar Marimuthu
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, 11 Jalan Tan Tock Seng, 308433, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Rd 119228, NUHS Tower Block, Level 11, 117597, Singapore
| | - Jeanette Teo
- National University Hospital, 5 Lower Kent Ridge Rd, 119074, Singapore
| | - Yichen Ding
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Eryu Xia
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Centre for Life Sciences (CeLS), #05-01Medical Drive, 117456, Singapore
| | - Jia Jun Lee
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, 11 Jalan Tan Tock Seng, 308433, Singapore
| | - Rick Twee-Hee Ong
- Centre for Infectious Disease Epidemiology and Research, Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, #10-01, 117549, Singapore
| | | | | | - Surinder Kaur Pada
- Ng Teng Fong General Hospital, 1 Jurong East Street 21, 609606, Singapore
| | - Weng Lam Choong
- Ng Teng Fong General Hospital, 1 Jurong East Street 21, 609606, Singapore
| | - Nares Smitasin
- National University Hospital, 5 Lower Kent Ridge Rd, 119074, Singapore
| | - Say Tat Ooi
- Khoo Teck Puat Hospital, 90 Yishun Central, 768828, Singapore
| | | | - Asok Kurup
- Mount Elizabeth Hospital, 3 Mount Elizabeth, 228510, Singapore
| | - Raymond Fong
- Changi General Hospital, 2 Simei Street 3, 529889, Singapore
| | - My Van La
- National Public Health Laboratory, College of Medicine Building, 16 College Road, 169854, Singapore
| | - Thean Yen Tan
- Changi General Hospital, 2 Simei Street 3, 529889, Singapore
| | - Tse Hsien Koh
- Singapore General Hospital, Outram Road, 169608, Singapore
| | - Raymond Tzer Pin Lin
- National University Hospital, 5 Lower Kent Ridge Rd, 119074, Singapore.,National Public Health Laboratory, College of Medicine Building, 16 College Road, 169854, Singapore
| | - Eng Lee Tan
- Singapore Polytechnic, 500 Dover Road, 139651, Singapore
| | | | | | - Johann D Pitout
- Division of Microbiology, 1829 Ranchlands Blvd NW, Calgary, AB T3G 2A7, Canada.,Departments of Pathology and Laboratory Medicine, Microbiology Immunology and Infectious Diseases, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada.,Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Yik-Ying Teo
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Centre for Life Sciences (CeLS), #05-01Medical Drive, 117456, Singapore.,Centre for Infectious Disease Epidemiology and Research, Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, #10-01, 117549, Singapore.,Department of Statistics & Applied Probability, Block S16, Level 7, 6 Science Drive 2, Faculty of Science, National University of Singapore, 117546, Singapore.,Life Sciences Institute, National University of Singapore, Centre for Life 42 Sciences, #05-02, 28 Medical Drive, 117456, Singapore.,Genome Institute of Singapore, 60 Biopolis St, #02-01, 138672, Singapore
| | - Liang Yang
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Oon Tek Ng
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, 11 Jalan Tan Tock Seng, 308433, Singapore
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Khong WX, Xia E, Marimuthu K, Xu W, Teo YY, Tan EL, Neo S, Krishnan PU, Ang BSP, Lye DCB, Chow ALP, Ong RTH, Ng OT. Local transmission and global dissemination of New Delhi Metallo-Beta-Lactamase (NDM): a whole genome analysis. BMC Genomics 2016; 17:452. [PMID: 27297071 PMCID: PMC4906610 DOI: 10.1186/s12864-016-2740-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 05/14/2016] [Indexed: 12/13/2022] Open
Abstract
Background New Delhi metallo-β-lactamase (blaNDM), a plasmid-borne carbapenemase gene associated with significant mortality and severely limited treatment options, is of global public health concern as it is found in extremely diverse Gram-negative bacterial strains. This study thus aims to genetically characterize local and global spread of blaNDM. Methods To investigate local transmission patterns in the context of a single hospital, whole genome sequencing data of the first 11 blaNDM-positive bacteria isolated in a local hospital were analyzed to: (1) identify and compare blaNDM-positive plasmids; and (2) study the phylogenetic relationship of the bacteria chromosomes. The global analysis was conducted by analyzing 2749 complete plasmid sequences (including 39 blaNDM-positive plasmids) in the NCBI database, where: (1) the plasmids were clustered based on their gene composition similarity; (2) phylogenetic study was conducted for each blaNDM-positive plasmid cluster to infer the phylogenetic relationship within each cluster; (3) gene transposition events introducing blaNDM into different plasmid backbones were identified; and (4) clustering pattern was correlated with the plasmids’ incompatibility group and geographical distribution. Results Analysis of the first 11 blaNDM-positive isolates from a single hospital revealed very low blaNDM-positive plasmid diversity. Local transmission was characterized by clonal spread of a predominant plasmid with 2 sporadic instances of plasmid introduction. In contrast to the low diversity locally, global blaNDM spread involved marked plasmid diversity with no predominant bacterial clone. Thirty-nine (1.4 %) out of the 2749 complete plasmid sequences were blaNDM-positive, and could be resolved into 7 clusters, which were associated with plasmid incompatibility group and geographical distribution. The blaNDM gene module was witnessed to mobilize between different plasmid backbones on at least 6 independent occasions. Conclusions Our analysis revealed the complex genetic pathways of blaNDM spread, with global dissemination characterized mainly by transposition of the blaNDM gene cassette into varied plasmids. Early local transmission following plasmid introduction is characterized by plasmid conjugation and bacterial spread. Our findings emphasize the importance of plasmid molecular epidemiology in understanding blaNDM spread. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2740-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Xin Khong
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
| | - Eryu Xia
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
| | - Kalisvar Marimuthu
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wenting Xu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Yik-Ying Teo
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Eng Lee Tan
- Centre for Biomedical and Life Sciences, Singapore Polytechnic, Singapore, Singapore.,Department of Pediatrics, University Children's Medical Institute, National University of Singapore, Singapore, Singapore
| | - Shiyong Neo
- Centre for Biomedical and Life Sciences, Singapore Polytechnic, Singapore, Singapore
| | | | - Brenda S P Ang
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
| | - David C B Lye
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Angela L P Chow
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Oon Tek Ng
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore. .,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore. .,Communicable Disease Centre, Tan Tock Seng Hospital, 11, Jalan Tan Tock Seng, Singapore, 308433, Singapore.
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