Full characterization of an IncR plasmid harboring qnrSI recovered from a VIM-11-producing Pseudomonas aeruginosa

Abstract Metallo-p-lactamases (MBL) producing Pseudomonas aeruginosa isolates have been well characterized. Quinolones are commonly used in the treatment of carbapenem-resistant P. aeruginosa infections; however, data about PMQR in this species are scarce. The objective of this study was to report the simultaneous presence of qnrS and blaV-M-n in P. aeruginosa, and to characterize the qnrS-harboring plasmid. Thirty-eight carbapenem-resistant P. aeruginosa isolates were recovered from a hospital in Buenos Aires during 2012. Screening forMBL was assessed by the double disk synergy test using EDTA and carbapenem discs. Plasmid DNA extraction was performed by a method using phenol-chloroform. PCR followed by sequencing was carried out to determine each MBL and PMQR allele. PCR-BseGI-RFLP was performed to detect aac-(6')-Ib-cr. The gyrA-QRDR was sequenced in those PMQR-harboring isolates. Plasmid incompatibility groups and addiction systems were characterized by PCR. The PMQR-carrying plasmid was sequenced using Illumina technology, annotated using RAST and manually curated. Eleven/38 isolates were VIM producers (blaVIM-2 and blaVIM-11) while 1/38 harbored blaIMP-13. One isolate harbored blaVIM-11 and the PMQR qnrSI; however, both markers were located in different plasmids. The qnrSí-harboring plasmid (pP6qnrS1) was 117 945 bp in size, presented 154 CDS and corresponded to the IncR group. In addition to qnrSI, it harbored several aminoglycoside resis-tance markers. Although pP6qnrS1 was non-conjugative, it presented an oriT which made it possible for this plasmid to be transferable. This is the first report on P. aeruginosa carrying both blaVIM-11 and qnrSI, plus the first detection of an IncR plasmid in Argentina.

Resumen Las quinolonas son comúnmente utilizadas en el tratamiento de las infecciones producidas por Pseudomonas aeruginosa resistentes a carbapenems (PARC); aun así, la información sobre la resistencia a quinolonas mediada por plásmidos (PMQR) en esta especie es escasa. El objetivo de este trabajo fue reportar la presencia simultánea de los genes qnrS y blaVIM-11 en PARC y caracterizar el plásmido portador de qnrS. Durante 2012 se recuperaron 38 PARC en un hospital de Buenos Aires. El tamizaje para detectar producción de metalo-beta-lactamasas (MBL) se llevó a cabo mediante sinergia de doble disco utilizando EDTA y carbapenems. El ADN plasmídico fue extraído utilizando fenolcloroformo. Para determinar los alelos de los genes implicados en la síntesis de MBL y de PMQR, se llevó a cabo PCR-secuenciación. Para la detección de aac-(6')-Ib-cr se realizó PCR-BseGI-RFLP. En aquellos aislamientos portadores de PMQR se secuenció el gen gyrA. Los grupos de incompatibilidad y sistemas de adicción fueron caracterizados por PCR. El plásmido portador de PMQR fue secuenciado completamente y curado manualmente. De 38 aislamientos, 11 fueron productores de VIM (blaVIM-2 y blaVIM-11), mientras que uno contenía blaIMP-13. Si bien un aislamiento fue portador de blaVIM-11 y de qnrSI, dichos marcadores se encontraban en distintos plásmidos. El plásmido portador de qnrSI (pP6qnrS1) presentó un tamaño de 117.945 pby 154 secuencias codificantes (CDS); este correspondió al grupo de incompatibilidad IncR. Además de qnrSI, el plásmido portaba diversos marcadores de resistencia a aminoglucósidos. Aun cuando pP6qnrS1 no resultó conjugativo, presentó un oriT, de modo que posiblemente sea transferible. Este es el primer informe acerca de PARC portadora de blaVIM-11 y de qnrSI en simultáneo, además, es la primera descripción de un plásmido IncR en Argentina.

Prevalence of plasmid-mediated quinolone resistance genes in Klebsiella pneumoniae strains in pediatrics in China / 中华微生物学和免疫学杂志

Objective To investigate the prevalence of plasmid-mediated quinolone resistance (PMQR) genes among clinical isolates of Klebsiella pneumoniae (K.pneumoniae) in pediatrics.MethodsA total of 131 non-duplicate clinical isolates of K.pneumoniae were collected in the Affiliated Children′s Hospital of Capital Institute of Pediatrics from 2010 to 2012.PMQR genes [qnrA, qnrB, qnrS, aac(6′)-Ⅰb-cr and qepA], mutations in the quinolone resistance-determining region (QRDR) and extended spectrum β-lactamases (ESBLs) genes in those strains were analyzed by PCR.Minimum inhibitory concentrations (MIC) of different antibiotics against those K.pneumoniae strains were determined by broth microdilution method and E-test according to the guidelines issued by the Clinical and Laboratory Standards Institute (CLSI).Transferability of the PMQR genes was examined by conjugation test with the sodiumazide-resistant Escherichia coli J53.Results Among the 131 isolates, 9.92% were resistant to quinolone and 30.5% were positive for PMQR genes, including 6.87% harboring qnrB gene, 22.9% harboring qnrS gene and 4.58% harboring aac(6′)-Ⅰb-cr gene.Neither qnrA-positive nor qepA-positive strain was detected.Among these PMQR genes-positive isolates, 90% were ESBLs-producing strains and two presented mutations in gyrA and parC genes.Conjugation test showed that these PMQR genes could be transferred horizontally and the ciprofloxacin resistance increased 2 to 32 folds in transconjugants.Conclusion This study indicates that the PMQR gene-carrying rate is high in K.pneumoniae strains isolated in paediatrics in China.Most of the PMQR gene-positive strains are also ESBLs-producing strains.The PMQR genes could be transferred horizontally in bacteria.

Pesquisa de genes de resistência a quinolonas em bacilos Gram negativos de origem clínica e ambiental / Research for genes of quinolone resistance in Gram negative bacilli from clinical and environmental origin

Introdução. Quinolonas são antimicrobianos sintéticos que inibem as enzimas DNA-girase e topoisomerase IV resultando na morte bacteriana. São altamente eficazes no tratamento de infecções bacterianas, especialmente causadas por bactérias Gram negativas, e portanto amplamente utilizados na medicina humana e veterinária, na qual também são empregados como profiláticos. Porém, o uso indiscriminado e inadequado levou ao aumento de bactérias resistentes a estes compostos. Esta resistência pode ocorrer devido a mutações nas enzimas DNA-girase e topoisomerase IV, e também por genes contidos em plasmídeos. Estes últimos são os principais responsáveis pela disseminação e circulação da resistência entre o meio ambiente e o ambiente hospitalar. Objetivos. Pesquisar genes de resistência a antimicrobianos do grupo das quinolonas em bactérias Gram negativas de origem clínica e ambiental que apresentam resistência fenotípica a este grupo. Material e Métodos. 73 cepas de Enterobacteriaceae e Aeromonas sp. de origem clínica e ambiental foram selecionadas para o estudo, e avaliadas quanto à sensibilidade aos antimicrobianos do grupo das quinolonas e à pesquisa de genes de resistência a este mesmo grupo e mutações no gene que codifica a enzima DNA-girase por meio de PCR e sequenciamento. Resultados. Das 73 cepas previamente selecionadas para compor o estudo, 65 foram utilizadas, devido à exclusão de perfis clonais similares. Nestas, foram observados os genes, qnrS1 (1,5 por cento ), qnrS2 (26,2 por cento ), qnrB1 (3,1 por cento ), qnrB19 (12,3 por cento ), qnrD1 (1,5 por cento ), aac(6)-Ib-cr (10,8 por cento ), oqxA (43,1 por cento ) e oqxB (41,5 por cento ), e duas variantes determinadas qnrB-like (3,1 por cento ) e qnrB69-like (1,5 por cento ). Os genes qnrA, qnrC e qepA não foram identificados. Mutações na enzima DNA-girase foram observadas em 97,9 por cento das cepas positivas para algum dos genes pesquisados...

Introduction. Quinolones are synthetic antimicrobial agents that inhibit DNA gyrase and topoisomerase IV enzymes resulting in bacterial death. They are highly effective in the treatment of bacterial infections, especially the ones caused by Gram negative bacteria, as well as for prophylaxy. Therefore they are widely used in human and veterinary medicine. However, indiscriminate and improper use led to an increase of bacteria resistance to these compounds. This resistance can be due to mutations in DNA gyrase and topoisomerase IV enzymes and also by genes contained in plasmids, which are mainly responsible for the spread and transmission of resistance between the environment and the hospital set. Objectives. To search for genes of resistance to quinolone antimicrobial agents in Gram-negative bacteria from clinical and environmental strains that present phenotypic resistance to this group. Material and Methods. 73 strains of Enterobacteriaceae and Aeromonas spp., from clinical and environmental origin, were selected for this study, and evaluated for antimicrobial susceptibility of quinolone and search of resistance genes in this same group and also for mutations in the gene encoding the enzyme DNA gyrase by PCR and sequencing. Results. Of the 73 strains previously selected to compose this study, 65 were used, due to the exclusion of similar clonal profiles. In these, genes qnrS1 (1.5 per cent ), qnrS2 (26.2 per cent ) qnrB1 (3.1 per cent ), qnrB19 (12.3 per cent ) qnrD1 (1.5 per cent ) aac(6')-Ib-cr (10.8 per cent ) oqxA (43.1 per cent ) and oqxB (41.5 per cent ) were observed, and two variants were named as qnrB-like (3.1 per cent ) and qnrB69-like (1.5 per cent ). The qnrA, qnrC and qepA genes were not identified. Mutations in DNA gyrase enzyme were observed in 97.9 per cent of the positive strains for at least one of the genes studied. It was possible to establish the association of aac(6')-Ib-cr with class 1 integron gene in four strains...

Screening of quinolone resistance determinants in ciprofloxacin-resistant Acinetobact-er baumannii isolates / 军事医学

Objective To investigate the quinolone resistance determinants in ciprofloxacin-resistant Acinetobacter bau-mannii (ABA)clinical isolates.Methods One hundred and fourteen ciprofloxacin-resistant ABA strains were collected from six Chinese hospitals .The quinolone resistance determining region ( QRDR) of 4 target genes ( gyrA, gyrB, parC and parE) was amplified , sequenced and compared with the reference genome of ATCC 17978 to identify possible resistance-related mutations.Nine plasmid-mediated quinolone resistance (PMQR) genes (qnrA, qnrB, qnrC, qnrD, qnrS, qepA, aac(6′)-Ⅰb-cr, oqxA and oqxB) were also amplified, and the amplicons were then sequenced to determine their character-istics.Results Almost all isolates (113/114, 99.1%) harbored a substitution in codon 83 of gyrA gene, leading to a Ser83Leu mutation.Meanwhile,58.8%(67/114) of the isolates possessed dual mutations of GyrA-Ser83Leu and GyrA-Ser80Leu, which were known determinants for ciprofloxacin resistance .There were also multiple non-synonymous substitu-tions in gyrB, leading to Arg393Ser, Arg393Cys, Thr401Ala, Pro406Ser, Val430Phe, Cys440Ser and Gly480Arg muta-tions with prevalence rates of 95.6%, 0.9%, 96.5%, 96.5%, 100%, 96.5%and 96.5%,respectively.For parE, all the seven mutations were synonymous and found in more than 96%of the tested isolates.For PMQR genes, although 83.3%(95/114) of the isolates were positive for aac(6′)-Ⅰb, nocrmutations were identified.None of the other eight PMDR genes were found in our strain collection .Conclusion Although multiple mutations are identified in gyrB and parE, these mutations might be the characteristic SNP markers for specific clones , unlikely linked to quinolone resistance .No PMQR is found in the tested isolates.Mutations in chromosomal QRDR (GyrA-Ser83Leu and ParC-Ser80Leu) are the main determi-nants of ciprofloxacin resistance in our ABA collection .

Plasmid-mediated quinolone resistance (PMQR) and mutations in the topoisomerase genes of Salmonella enterica strains from Brazil

The objective of this study was to identify mutations in the Quinolone Resistance Determining sources Regions (QRDR) of the gyrA, gyrB, parC, and parE genes and to determine if any of the qnr variants or the aac(6')-Ib-cr variant were present in strains of Salmonella spp. isolated in Brazil. A total of 126 Salmonella spp. strains from epidemic (n = 114) and poultry (n = 12) origin were evaluated. One hundred and twelve strains (88.8%) were resistant to nalidixic acid (NAL) and 29 (23.01%) showed a reduced susceptibility to ciprofloxacin (Cip). The mutations identified were substitutions limited to the QRDR of the gyrA gene in the codons for Serine 83, Aspartate 87 and Alanine 131. The sensitivity to NAL seems to be a good phenotypic indication of distinguishing mutated and nonmutated strains in the QRDR, however the double mutation in gyrA did not cause resistance to ciprofloxacin. The qnrA1 and qnrB19 genes were detected, respectively, in one epidemic strain of S. Enteritidis and one strain of S. Corvallis of poultry origin. Despite previous detection of qnr genes in Brazil, this is the first report of qnr gene detection in Salmonella, and also the first detection of qnrB19 gene in this country. The results alert for the continuous monitoring of quinolone resistance determinants in order to minimize the emergence and selection of Salmonella spp. strains showing reduced susceptibility or resistance to quinolones.

Mutations in gyrA and parC Genes and Plasmid-Mediated Quinolone Resistance in Non-typhoid Salmonella Isolated from Pediatric Patients with Diarrhea in Seoul

A total of 91 non-typhoid Salmonella isolated from pediatric patients with diarrhea in Seoul from 2003 to 2009 was tested for antimicrobial susceptibility of nalidixic acid (NA). Forty strains of NA resistance or intermediate susceptible non-typhoid Salmonella were identified and their minimum inhibitory concentrations (MICs) of NA, ciprofloxacin (CIP), and norfloxacin (NOR) were determined. Of the 40 isolates, 26 were resistant to NA (MIC >256 microg/ml). Only one isolate was high-level resistant to CIP (12 microg/ml) and NOR (48 microg/ml). Mutations in gyrA and parC genes were studied by PCR and sequencing. All NA-resistant isolates carried point mutations in the gyrA quinolone resistance determining regions (QRDR) at codon 83 or 87 (MICs of NA, >256 microg/ml; MICs of CIP, 0.047~0.25 microg/ml; MICs of NOR, 0.38~1.5 microg/ml). A double change in GyrA was found in one Salmonella Enteritidis (MIC of CIP, 12 microg/ml; MIC of NOR, 48 microg/ml). In respect of the ParC protein, a single change at Thr57-->Ser was found in 3 isolates (MICs of NA, >256 microg/ml; MICs of CIP, 0.19~0.25 microg/ml; MICs of NOR, 1 microg/ml). At the same time, these strains changed from Ser83 to Tyr in the gyrA. The result of the investigation for the prevalence of plasmid-mediated quinolone resistance (PMQR) genes, 14 isolates harbored qnr gene among 40 isolates. All of 14 isolates showed decreased susceptibility at NA (MICs 4~16 microg/ml) and except one strain, all of qnr genes were identified as qnrB. Mutations in the gyrA gene and production of PMQR determinants were critical for quinolone resistance and decreased susceptibility to fluoroquinolone in these isolates.