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An Emerging Lineage of Uropathogenic Extended Spectrum β-Lactamase Escherichia coli ST127. Microbiol Spectr 2022; 10:e0251122. [PMID: 36416548 PMCID: PMC9769692 DOI: 10.1128/spectrum.02511-22] [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] [Indexed: 11/24/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is one of the most common causes of urinary tract infections. Here, we report for the first time the whole-genome sequencing (WGS) and analysis of four extended-spectrum β-lactamase (ESBL), UPEC sequence type (ST) 127 isolates that were recovered from patients in five hospitals in Armenia from January to August of 2019. A phylogenetic comparison revealed that our isolates were closely related to each other by their core and accessory genomes, despite having been isolated from different regions and hospitals in Armenia. We identified unique genes in our isolates and in a closely related isolate recovered in France. The unique genes (hemolysin E virulence gene, lactate utilization operon lutABC, and endonuclease restriction modification operon hsdMSR) were identified in three separate genomic regions that were adjacent to prophage genes, including one region containing the TonB-dependent iron siderophore receptor gene ireA, which was only found in 5 other ST127 isolates from the European Nucleotide Archive (ENA). We further identified that these isolates possessed unique virulence and metabolic genes and harbored antibiotic resistance genes, including the ESBL genes blaCTX-M-3 (n = 3), blaCTX-M-236 (n = 1), and blaTEM-1 (n = 1), in addition to a quinolone resistance protein gene qnrD1 (n = 1), which was absent in the ST127 isolates obtained from the ENA. Moreover, a plasmid replicon gene IncI2 (n = 1) was unique to ARM88 of the Armenian isolates. Our findings demonstrate that at the time of this study, E. coli ST127 was a cause of urinary tract infections in patients in different regions of Armenia, with a possibility of cross-country transmission between Armenia and France. IMPORTANCE Whole-genome sequencing studies of pathogens causing infectious diseases are seriously lacking in Armenia, hampering global efforts to track, trace and contain infectious disease outbreaks. In this study, we report for the first-time the whole-genome sequencing and analysis of ESBL UPEC ST127 isolates recovered from hospitalized patients in Armenia and compare them with other E. coli ST127 retrieved from the ENA. We found close genetic similarities of the Armenian isolates, indicating that E. coli ST127 was potentially a dominant lineage causing urinary tract infections in Armenia. Furthermore, we identified unique genes that were horizontally acquired in the clusters of Armenian and French isolates that were absent in other ST127 isolates obtained from the ENA. Our findings highlight a possible cross-country transmission between Armenia and France and the idea that the implementation of WGS surveillance could contribute to global efforts in tackling antibiotic resistance, as bacteria carrying antimicrobial resistance (AMR) genes do not recognize borders.
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Plasmid-mediated quinolone resistance (PMQR) among Enterobacteriales in Latin America: a systematic review. Mol Biol Rep 2019; 47:1471-1483. [DOI: 10.1007/s11033-019-05220-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/30/2019] [Indexed: 01/22/2023]
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Martino F, Tijet N, Melano R, Petroni A, Heinz E, De Belder D, Faccone D, Rapoport M, Biondi E, Rodrigo V, Vazquez M, Pasteran F, Thomson NR, Corso A, Gomez SA. Isolation of five Enterobacteriaceae species harbouring blaNDM-1 and mcr-1 plasmids from a single paediatric patient. PLoS One 2019; 14:e0221960. [PMID: 31498841 PMCID: PMC6733481 DOI: 10.1371/journal.pone.0221960] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/19/2019] [Indexed: 11/18/2022] Open
Abstract
In Argentina, NDM metallo-β-lactamase was first reported in 2013. By now, it has disseminated throughout the country in diverse Gram negative bacteria. Here, we report the case of a paediatric patient that underwent a 1-year hospitalisation due to erythrodermic psoriasis in 2014 and received multiple antimicrobial treatments. During his stay, five isolates were obtained from rectal swabs (rs) or blood culture (bc) suspicious of carbapenemase production: a K. quasipneumoniae subsp. quasipneumoniae (rs), Citrobacter freundii (rs), Escherichia coli (bc), Enterobacter cloacae (rs), and a Serratia marcescens (bc). The isolates were studied with broth microdilution, biparental conjugation and plasmid and whole genome sequencing (Illumina). All isolates harboured an 138,998-bp type 1 IncC plasmid that carried blaNDM-1, bleMBL, blaCMY-6, rmtC, aac(6’)-Ib, and sul1 resistance genes. Additionally, the blaNDM-plasmids contained ISKpn8 an insertion sequence previously described as associated only to blaKPC. One isolate, a colistin-resistant E. coli, also carried a mcr-1-containing an IncI2 plasmid, which did not harbour additional resistance. The whole genome of K. quasipneumoniae subsp. quasipneumoniae isolate was fully sequenced. This isolate harboured, additionally to blaNDM, three plasmid-mediated quinolone resistance genes: qnrB4, qnrB52 and aac(6’)-Ib-cr1. The E. cloacae isolate also harboured qnrA1. These findings alert to the underestimated horizontal dissemination of multidrug-resistant plasmids limiting treatment options with last resort antimicrobials.
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Affiliation(s)
- F. Martino
- Servicio Antimicrobianos (National Reference Laboratory on Antimicrobial Resistance), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - N. Tijet
- Public Health Ontario Laboratories, Toronto, Ontario, Canada
| | - R. Melano
- Public Health Ontario Laboratories, Toronto, Ontario, Canada
| | - A. Petroni
- Servicio Antimicrobianos (National Reference Laboratory on Antimicrobial Resistance), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - E. Heinz
- The Welcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - D. De Belder
- Servicio Antimicrobianos (National Reference Laboratory on Antimicrobial Resistance), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - D. Faccone
- Servicio Antimicrobianos (National Reference Laboratory on Antimicrobial Resistance), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - M. Rapoport
- Servicio Antimicrobianos (National Reference Laboratory on Antimicrobial Resistance), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - E. Biondi
- Hospital de Niños “Dr. Ricardo Gutiérrez”, Ciudad Autónoma de Buenos Aires, Argentina
| | - V. Rodrigo
- Hospital de Niños “Dr. Ricardo Gutiérrez”, Ciudad Autónoma de Buenos Aires, Argentina
| | - M. Vazquez
- Hospital de Niños “Dr. Ricardo Gutiérrez”, Ciudad Autónoma de Buenos Aires, Argentina
| | - F. Pasteran
- Servicio Antimicrobianos (National Reference Laboratory on Antimicrobial Resistance), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - N. R. Thomson
- The Welcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - A. Corso
- Servicio Antimicrobianos (National Reference Laboratory on Antimicrobial Resistance), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - S. A. Gomez
- Servicio Antimicrobianos (National Reference Laboratory on Antimicrobial Resistance), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail:
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Li P, Liu D, Zhang X, Tuo H, Lei C, Xie X, Gu J, Zhang A. Characterization of Plasmid-Mediated Quinolone Resistance in Gram-Negative Bacterial Strains from Animals and Humans in China. Microb Drug Resist 2019; 25:1050-1056. [DOI: 10.1089/mdr.2018.0405] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Ping Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Dan Liu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Xiuzhong Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Hongmei Tuo
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Xianjun Xie
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Ju Gu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Anyun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, P.R. China
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Abstract
While the description of resistance to quinolones is almost as old as these antimicrobial agents themselves, transferable mechanisms of quinolone resistance (TMQR) remained absent from the scenario for more than 36 years, appearing first as sporadic events and afterward as epidemics. In 1998, the first TMQR was soundly described, that is, QnrA. The presence of QnrA was almost anecdotal for years, but in the middle of the first decade of the 21st century, there was an explosion of TMQR descriptions, which definitively changed the epidemiology of quinolone resistance. Currently, 3 different clinically relevant mechanisms of quinolone resistance are encoded within mobile elements: (i) target protection, which is mediated by 7 different families of Qnr (QnrA, QnrB, QnrC, QnrD, QnrE, QnrS, and QnrVC), which overall account for more than 100 recognized alleles; (ii) antibiotic efflux, which is mediated by 2 main transferable efflux pumps (QepA and OqxAB), which together account for more than 30 alleles, and a series of other efflux pumps (e.g., QacBIII), which at present have been sporadically described; and (iii) antibiotic modification, which is mediated by the enzymes AAC(6')Ib-cr, from which different alleles have been claimed, as well as CrpP, a newly described phosphorylase.
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Dominguez JE, Faccone D, Tijet N, Gomez S, Corso A, Fernández-Miyakawa ME, Melano RG. Characterization of Escherichia coli Carrying mcr- 1-Plasmids Recovered From Food Animals From Argentina. Front Cell Infect Microbiol 2019; 9:41. [PMID: 30895173 PMCID: PMC6414435 DOI: 10.3389/fcimb.2019.00041] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 02/08/2019] [Indexed: 11/16/2022] Open
Abstract
In this study, we found mcr-1.1 and mcr-1.5 genes carried by IncI2 plasmids in a subset of Escherichia coli isolates recovered from commercial broiler farms in Argentina. The comparative analysis of the sequences of these plasmids with those described in human clinical isolates suggests that this replicon-type is one of the main mcr-disseminator sources in Argentina.
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Affiliation(s)
- Johana E Dominguez
- Laboratorio de Bacteriología General, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto de Patobiología, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Diego Faccone
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Servicio de Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) "Dr. C. Malbrán", Buenos Aires, Argentina
| | | | - Sonia Gomez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Servicio de Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) "Dr. C. Malbrán", Buenos Aires, Argentina
| | - Alejandra Corso
- Servicio de Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) "Dr. C. Malbrán", Buenos Aires, Argentina
| | - Mariano E Fernández-Miyakawa
- Laboratorio de Bacteriología General, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto de Patobiología, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Roberto G Melano
- Public Health Ontario Laboratory, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Sinai Health System, Mount Sinai Hospital, Toronto, ON, Canada
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Hamed SM, Elkhatib WF, El-Mahallawy HA, Helmy MM, Ashour MS, Aboshanab KMA. Multiple mechanisms contributing to ciprofloxacin resistance among Gram negative bacteria causing infections to cancer patients. Sci Rep 2018; 8:12268. [PMID: 30115947 PMCID: PMC6095922 DOI: 10.1038/s41598-018-30756-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/01/2018] [Indexed: 11/22/2022] Open
Abstract
Fluoroquinolones have been used for prophylaxis against infections in cancer patients but their impact on the resistance mechanisms still require further investigation. To elucidate mechanisms underlying ciprofloxacin (CIP) resistance in Gram-negative pathogens causing infections to cancer patients, 169 isolates were investigated. Broth microdilution assays showed high-level CIP resistance in 89.3% of the isolates. Target site mutations were analyzed using PCR and DNA sequencing in 15 selected isolates. Of them, all had gyrA mutations (codons 83 and 87) with parC mutations (codons 80 and 84) in 93.3%. All isolates were screened for plasmid-mediated quinolone resistance (PMQR) genes and 56.8% of them were positive in this respect. Among PMQR genes, aac(6′)-Ib-cr predominated (42.6%) while qnr genes were harbored by 32.5%. This comprised qnrS in 26.6% and qnrB in 6.5%. Clonality of the qnr-positive isolates using ERIC-PCR revealed that most of them were not clonal. CIP MIC reduction by CCCP, an efflux pump inhibitor, was studied and the results revealed that contribution of efflux activity was observed in 18.3% of the isolates. Furthermore, most fluoroquinolone resistance mechanisms were detected among Gram-negative isolates recovered from cancer patients. Target site mutations had the highest impact on CIP resistance as compared to PMQRs and efflux activity.
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Affiliation(s)
- Samira M Hamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts, 6th of October, Giza, Egypt
| | - Walid F Elkhatib
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, African Union Organization St. Abbassia, Cairo, 11566, Egypt.
| | - Hadir A El-Mahallawy
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mai M Helmy
- Department of Microbiology and Immunology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Mohamed S Ashour
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Khaled M A Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, African Union Organization St. Abbassia, Cairo, 11566, Egypt
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Omidvar Panah M, Najafi M, Peymani A. Plasmid-mediated quinolones resistance in clinically important bacteria. THE JOURNAL OF QAZVIN UNIVERSITY OF MEDICAL SCIENCES 2018. [DOI: 10.29252/qums.22.2.90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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Ares-Arroyo M, Bernabe-Balas C, Santos-Lopez A, Baquero MR, Prasad KN, Cid D, Martin-Espada C, San Millan A, Gonzalez-Zorn B. PCR-Based Analysis of ColE1 Plasmids in Clinical Isolates and Metagenomic Samples Reveals Their Importance as Gene Capture Platforms. Front Microbiol 2018; 9:469. [PMID: 29615998 PMCID: PMC5864857 DOI: 10.3389/fmicb.2018.00469] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/28/2018] [Indexed: 02/04/2023] Open
Abstract
ColE1 plasmids are important vehicles for the spread of antibiotic resistance in the Enterobacteriaceae and Pasteurellaceae families of bacteria. Their monitoring is essential, as they harbor important resistant determinants in humans, animals and the environment. In this work, we have analyzed ColE1 replicons using bioinformatic and experimental approaches. First, we carried out a computational study examining the structure of different ColE1 plasmids deposited in databases. Bioinformatic analysis of these ColE1 replicons revealed a mosaic genetic structure consisting of a host-adapted conserved region responsible for the housekeeping functions of the plasmid, and a variable region encoding a wide variety of genes, including multiple antibiotic resistance determinants. From this exhaustive computational analysis we developed a new PCR-based technique, targeting a specific sequence in the conserved region, for the screening, capture and sequencing of these small plasmids, either specific for Enterobacteriaceae or specific for Pasteurellaceae. To validate this PCR-based system, we tested various collections of isolates from both bacterial families, finding that ColE1 replicons were not only highly prevalent in antibiotic-resistant isolates, but also present in susceptible bacteria. In Pasteurellaceae, ColE1 plasmids carried almost exclusively antibiotic resistance genes. In Enterobacteriaceae, these plasmids encoded a large range of traits, including not only antibiotic resistance determinants, but also a wide variety of genes, showing the huge genetic plasticity of these small replicons. Finally, we also used a metagenomic approach in order to validate this technique, performing this PCR system using total DNA extractions from fecal samples from poultry, turkeys, pigs and humans. Using Illumina sequencing of the PCR products we identified a great diversity of genes encoded by ColE1 replicons, including different antibiotic resistance determinants, supporting the previous results achieved with the collections of bacterial isolates. In addition, we detected cryptic ColE1 plasmids in both families with no known genes in their variable region, which we have named sentinel plasmids. In conclusion, in this work we present a useful genetic tool for the detection and analysis of ColE1 plasmids, and confirm their important role in the dissemination of antibiotic resistance, especially in the Pasteurellaceae family of bacteria.
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Affiliation(s)
- Manuel Ares-Arroyo
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Cristina Bernabe-Balas
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Alfonso Santos-Lopez
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Maria R Baquero
- Departamento de Microbiología, Facultad de Veterinaria, Universidad Alfonso X el Sabio, Madrid, Spain
| | - Kashi N Prasad
- Department of Microbiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Dolores Cid
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Carmen Martin-Espada
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Alvaro San Millan
- Servicio de Microbiología Hospital Universitario Ramón y Cajal, Instituto de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Bruno Gonzalez-Zorn
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
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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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qnrE1, a Member of a New Family of Plasmid-Located Quinolone Resistance Genes, Originated from the Chromosome of Enterobacter Species. Antimicrob Agents Chemother 2017; 61:AAC.02555-16. [PMID: 28193666 DOI: 10.1128/aac.02555-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/06/2017] [Indexed: 12/14/2022] Open
Abstract
qnrE1, found in a clinical Klebsiella pneumoniae isolate, was undetectable by PCR assays used for the six qnr families. qnrE1 was located on a conjugative plasmid (ca. 185 kb) and differed from qnrB alleles by 25%. Phylogenetic reconstructions of qnr genes and proteins and analysis of the qnrE1 surroundings showed that this gene belongs to a new qnr family and was likely mobilized by ISEcp1 from the chromosome of Enterobacter spp. to plasmids of K. pneumoniae.
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