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We identified a chromosomal qnrB19 gene within a transposon in a colistin-resistant Escherichia coli strain isolated from the stool sample of an Ecuadorian resident. This finding suggests a more stable acquisition of quinolone resistance on chromosomes than that on plasmids and the potential for propagation to other DNA structures.
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A Gram-stain-negative strain, designated BR102T, isolated from a soil sample in Brazil was characterized by a polyphasic approach. Comparative 16S rRNA gene sequences indicated that strain BR102T belonged to the genus Citrobacter. The recN- and whole-genome-based phylogeny, and multilocus sequence analysis based on concatenated partial fusA, leuS, pyrG and rpoB sequences strongly supported a clade encompassing strain BR102T and a strain from public database that was distinct from currently recognized species of the genus Citrobacter. Average nucleotide identity and digital DNA-DNA hybridization values between strain BR102T and the closest relative Citrobacter freundii ATCC 8090T were 91.8 and 48.8â%, respectively. The ability to metabolize different compounds further discriminated strain BR102T from other closely related species of the genus Citrobacter. The novel variants bla CMY-179 and qnrB97, which encoded a CMY-2-like ß-lactamase and a QnrB-type protein, respectively, were identified in strain BR102T. BR102T was resistant to ampicillin, amoxicillin/clavulanate and cefoxitin. The DNA G+C content of strain BR102T is 51.3âmol%. Based on these results, strain BR102T represents a novel species of the genus Citrobacter, for which the name Citrobacter meridianamericanus sp. nov. is proposed. The type strain is BR102T (=MUM 22.55T=IMI 507229T).
Assuntos
Citrobacter , Genes Bacterianos , Análise de Sequência de DNA , RNA Ribossômico 16S/genética , Ácidos Graxos/química , DNA Bacteriano/genética , Filogenia , Composição de Bases , Técnicas de Tipagem Bacteriana , SoloRESUMO
The main objective of this study was to characterize using whole-genome sequencing analysis, a new variant of the qnrB gene (qnrB89) carried by a fluoroquinolone-susceptible bacterium isolated from mucus of farmed Salmo salar fingerling in Chile. Citrobacter gillenii FP75 was identified by using biochemical tests and 16S ribosomal gene analysis. Nucleotide and amino acid sequences of the qnrB89 gene exhibited an identity to qnrB of 81.24% and 91.59%, respectively. The genetic environment of qnrB89 was characterized by the upstream location of a sequence encoding for a protein containing a heavy metal-binding domain and a gene encoding for a N-acetylmuramoyl-L-alanine amidase protein, whereas downstream to qnrB89 gene were detected the csp and cspG genes, encoding cold-shock proteins. The qnrB89 gene was located on a large chromosomal contig of the FP75 genome and was not associated with the 10-kb plasmid and class 1 integron harbored by the FP75 strain. This study reports for the first time the carriage of a qnrB gene by the C. gillenii species, and its detection in a bacterial strain isolated from farmed salmon in Chile.
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We investigated the phenotypic and molecular characteristics of Extended-Spectrum-ß-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae clinical isolates from four health-care institutions in Hermosillo, Sonora, Mexico. ESBL-producing isolates were collected from February to August 2016. The prevalence of ESBL-producing E. coli and K. pneumoniae was 11.9 and 8.7%, respectively. High dissemination of resistance to ciprofloxacin (88%), trimethoprim/sulfamethoxazole (72%) and aminoglycosides (59%) were detected, as well as susceptibility to meropenem, amikacin and tigecycline. The ESBL found variants were CTX-M-1 (88%) and CTX-M-9 (5%). The plasmid-mediated quinolone resistance (PMQR) gene aac(6´)-Ib-cr was identified in 62% of a representative sample, whereas the qnrB and qnrS genes were detected in 49% of the isolates. PFGE analyses detected many unrelated clones among the hospital or community isolates. A constant programme of epidemiological surveillance is recommended to understand the dynamics of bacterial resistance to both cephalosporin as well as the fluoroquinolone family of antibiotics.
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Escherichia coli/efeitos dos fármacos , Klebsiella pneumoniae/efeitos dos fármacos , beta-Lactamases/biossíntese , Farmacorresistência Bacteriana Múltipla/genética , Farmacorresistência Bacteriana Múltipla/fisiologia , Escherichia coli/isolamento & purificação , Humanos , Klebsiella pneumoniae/isolamento & purificação , México , Testes de Sensibilidade Microbiana , FenótipoRESUMO
The aim of this work was to detect Escherichia coli isolates displaying resistance to oxyimino-cephalosporins, quinolones, and colistin in feces from livestock in Uruguay. During 2016-2019, fecal samples from 132 broiler and layer chicken flocks, 100 calves, and 50 pigs, were studied in Uruguay. Samples were cultured on MacConkey Agar plates supplemented with ciprofloxacin, ceftriaxone, or colistin. E. coli isolates were identified by mass spectrometry and antibiotic susceptibility testing was performed by disk diffusion agar method and colistin agar test. Antibiotic resistance genes were detected by polymerase chain reaction and sequencing. The most frequently detected resistance gene was qnrB19, recovered from 87 animals. Regarding plasmid-mediated quinolone resistance genes, qnrS1 was the second in prevalence (23 animals) followed by qnrE1, found in 6 chickens and two calves. Regarding resistance to oxyimino-cephalosporins, 8 different ß-lactamase genes were detected: bla CTX-M-8 and bla CMY-2 were found in 23 and 19 animals, respectively; next, bla CTX-M-2 and bla SHV-12 in 7 animals each, followed by bla CTX-M-14 in 5, bla CTX-M-15 and bla SHV2a in 2, and bla CTX-M-55 in a single animal. Finally, the mcr-1 gene was detected only in 8 pigs from a single farm, and in a chicken. Isolates carrying bla CMY-2 and bla SHV-12 were also found in these animals, including two isolates featuring the bla CMY-2/mcr-1 genotype. To the best of our knowledge, this is the first work in which the search for transferable resistance to highest priority critically important antibiotics for human health is carried out in chickens and pigs chains of production animals in Uruguay.
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Salmonella enterica serovar Paratyphi B variant Java sequence type 28 is prevalent in poultry and poultry meat. We investigated the evolutionary relatedness between sequence type 28 strains from Europe and Latin America using time-resolved phylogeny and principal component analysis. We sequenced isolates from Colombia, Guatemala, Costa Rica, and the Netherlands and complemented them with publicly available genomes from Europe, Africa, and the Middle East. Phylogenetic time trees and effective population sizes (Ne) showed separate clustering of strains from Latin America and Europe. The separation is estimated to have occurred during the 1980s. Ne of strains increased sharply in Europe around 1995 and in Latin America around 2005. Principal component analysis on noncore genes showed a clear distinction between strains from Europe and Latin America, whereas the plasmid gene content was similar. Regardless of the evolutionary separation, similar features of resistance to ß-lactams and quinolones/fluoroquinolones indicated parallel evolution of antimicrobial resistance in both regions.
Assuntos
Salmonella enterica , Salmonella paratyphi B , África , Animais , Antibacterianos/farmacologia , Colômbia , Costa Rica , Farmacorresistência Bacteriana , Farmacorresistência Bacteriana Múltipla , Europa (Continente)/epidemiologia , Guatemala , Indonésia , América Latina/epidemiologia , Oriente Médio , Países Baixos , Filogenia , Aves Domésticas , Salmonella enterica/genética , Salmonella paratyphi B/genéticaRESUMO
[This corrects the article DOI: 10.3389/fmicb.2019.02503.].
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Antimicrobial resistance is an increasing problem worldwide, and Salmonella spp. resistance to quinolone was classified by WHO in the high priority list. Recent studies in Europe and in the US reported the presence of small plasmids carrying quinolone resistance in Enterobacteriaceae isolated from poultry and poultry products. The aims of this study were to identify and characterize plasmid-mediated quinolone resistance in Salmonella spp. and to investigate transduction as a possible mechanism associated to its dissemination. First, we assessed resistance to nalidixic acid and/or ciprofloxacin in 64 Salmonella spp. and detected resistance in eight of them. Genomic analyses determined that six isolates of different serotypes and sources carried an identical 2.7-kb plasmid containing the gene qnrB19 which confers quinolone resistance. The plasmid detected also has high identity with plasmids reported in the US, Europe, and South America. The presence of similar plasmids was later surveyed by PCR in a local Salmonella collection (n = 113) obtained from diverse sources: food (eggs), wild and domestic animals (pigs, horse, chicken), and human clinical cases. qnrB19-carrying plasmids were found in 8/113 Salmonella tested strains. A bioinformatics analysis including Chilean and previously described plasmids revealed over 95.0% of nucleotide identity among all the sequences obtained in this study. Furthermore, we found that a qnrB19-carrying plasmid can be transferred between Salmonella of different serotypes through a P22-mediated transduction. Altogether our results demonstrate that plasmid-mediated quinolone resistance (PMQR) is widespread in Salmonella enterica of different serotypes isolated from human clinical samples, wild and domestic animals, and food in Chile and suggest that transduction could be a plausible mechanism for its dissemination. The occurrence of these antimicrobial resistance elements in Salmonella in a widespread area is of public health and food safety concern, and it indicates the need for increased surveillance for the presence of these plasmids in Salmonella strains and to assess their actual impact in the rise and spread of quinolone resistance.
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The use of antimicrobial growth promoters (AGPs) in sub-therapeutic doses for long periods promotes the selection of resistant microorganisms and the subsequent risk of spreading this resistance to the human population and the environment. Global concern about antimicrobial resistance development and transference of resistance genes from animal to human has been rising. The goal of our research was to evaluate the susceptibility pattern to different classes of antimicrobials of colistin-resistant Escherichia coli from poultry production systems that use AGPs, and characterize the resistance determinants associated to transferable platforms. E. coli strains (n = 41) were obtained from fecal samples collected from typical Argentine commercial broiler farms and susceptibility for 23 antimicrobials, relevant for human or veterinary medicine, was determined. Isolates were tested by PCR for the presence of mcr-1, extended spectrum ß-lactamase encoding genes and plasmid-mediated quinolone resistance (PMQR) coding genes. Conjugation and susceptibility patterns of the transconjugant studies were performed. ERIC-PCR and REP-PCR analysis showed a high diversity of the isolates. Resistance to several antimicrobials was determined and all colistin-resistant isolates harbored the mcr-1 gene. CTX-M-2 cefotaximase was the main mechanism responsible for third generation cephalosporins resistance, and PMQR determinants were also identified. In addition, co-transference of the qnrB determinant on the mcr-1-positive transconjugants was corroborated, which suggests that these resistance genes are likely to be located in the same plasmid. In this work a wide range of antimicrobial resistance mechanisms were identified in E. coli strains isolated from the environment of healthy chickens highlighting the risk of antimicrobial abuse/misuse in animals under intensive production systems and its consequences for public health.
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We describe the first detection of a KPC-2- and QnrB-producing Enterobacter cloacae from a patient with cystic fibrosis. The blaKPC-2 and qnrB-1 genes were located in a 79.8-kb plasmid. The presence of blaKPC-2 and qnrB-1 genes was determined by PCR and sequencing. Mobilization of plasmid containing blaKPC2 gene was assayed by conjugation.
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A molecular survey was conducted in Cochabamba, Bolivia, to characterize the mechanism involved in the resistance to clinically relevant antibiotics. Extended Spectrum β-lactamase encoding genes and plasmid-mediated quinolone resistance (PMQR) markers were investigated in a total of 101 oxyimino-cephalosporin-resistant enterobacteria recovered from different health centers during four months (2012-2013). CTX-M enzymes were detected in all isolates, being the CTX-M-1 group the most prevalent (88.1%). The presence of blaOXA-1 was detected in 76.4% of these isolates. A high quinolone resistance rate was observed among the included isolates. The aac(6′)-Ib-cr gene was the most frequent PMQR identified (83.0%). Furthermore, 6 isolates harbored the qnrB gene. Interestingly, qepA1 (6) and oqxAB (1), were detected in 7 Escherichia coli, being the latter the first to be reported in Bolivia. This study constitutes the first molecular survey on resistance markers in clinical enterobacterial isolates in Cochabamba, Bolivia, contributing to the regional knowledge of the epidemiological situation. The molecular epidemiology observed herein resembles the scene reported in South America.
Se llevó a cabo un relevamiento molecular de la resistencia a antibióticos de importancia clínica en aislamientos recuperados en Cochabamba, Bolivia. Se estudiaron los genes codificantes de β-lactamasas de espectro extendido y de resistencia a quinolonas de localización plasmídica (PMQR) en un total de 101 aislamientos de enterobacterias resistentes a oximinocefalosporinas recuperados en distintos centros de salud, durante 4 meses (2012-2013). En todos ellos se detectó la presencia de cefotaximasas, las CTX-M grupo 1 fueron las más prevalentes (88,1%). La presencia de blaOXA-1 se detectó en el 76,4% de estos aislamientos. Se observó una elevada proporción de aislamientos resistentes a quinolonas. El gen aac(6′)-Ib-cr fue el determinante PMQR más frecuentemente identificado (83%). Además, 6 aislamientos resultaron ser portadores de qnrB. Por otro lado, cabe remarcar que 7 Escherichia coli presentaron qepA1 (6) y oqxAB (1); se documenta así por primera vez la presencia de oqxAB en Bolivia. Este estudio constituye el primer relevamiento de marcadores de resistencia en aislamientos clínicos de enterobacterias en Cochabamba, Bolivia; de este modo se contribuye al conocimiento regional de la situación epidemiológica, la cual presenta un escenario similar al observado en el resto de Latinoamérica.
Assuntos
Plasmídeos/efeitos dos fármacos , beta-Lactamases/efeitos dos fármacos , Resistência Microbiana a Medicamentos , Quinolonas/farmacologia , Enterobacteriaceae/isolamento & purificação , Bolívia/epidemiologia , Enterobacteriaceae/efeitos dos fármacosRESUMO
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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Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Farmacorresistência Bacteriana/genética , Klebsiella pneumoniae/genética , Quinolonas/farmacologia , Idoso , Sequência de Aminoácidos , DNA Girase/genética , Farmacorresistência Bacteriana Múltipla/genética , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Feminino , Transferência Genética Horizontal/genética , Humanos , Klebsiella pneumoniae/efeitos dos fármacos , Testes de Sensibilidade Microbiana , Plasmídeos/genéticaRESUMO
A molecular survey was conducted in Cochabamba, Bolivia, to characterize the mechanism involved in the resistance to clinically relevant antibiotics. Extended Spectrum ß-lactamase encoding genes and plasmid-mediated quinolone resistance (PMQR) markers were investigated in a total of 101 oxyimino-cephalosporin-resistant enterobacteria recovered from different health centers during four months (2012-2013). CTX-M enzymes were detected in all isolates, being the CTX-M-1 group the most prevalent (88.1%). The presence of blaOXA-1 was detected in 76.4% of these isolates. A high quinolone resistance rate was observed among the included isolates. The aac(6')-Ib-cr gene was the most frequent PMQR identified (83.0%). Furthermore, 6 isolates harbored the qnrB gene. Interestingly, qepA1 (6) and oqxAB (1), were detected in 7 Escherichia coli, being the latter the first to be reported in Bolivia. This study constitutes the first molecular survey on resistance markers in clinical enterobacterial isolates in Cochabamba, Bolivia, contributing to the regional knowledge of the epidemiological situation. The molecular epidemiology observed herein resembles the scene reported in South America.
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Farmacorresistência Bacteriana , Farmacorresistência Bacteriana Múltipla , Enterobacteriaceae , Antibacterianos/farmacologia , Bolívia , Enterobacteriaceae/efeitos dos fármacos , Enterobacteriaceae/genética , Testes de Sensibilidade Microbiana , Inquéritos e Questionários , beta-LactamasesRESUMO
Fluoroquinolone resistance can be conferred through chromosomal mutations or by the acquisition of plasmids carrying genes such as the quinolone resistance gene (qnr). In this study, 3,309 strains of commensal Escherichia coli were isolated in Ecuador from: (i) humans and chickens in a rural northern coastal area (n = 2368, 71.5%) and (ii) chickens from an industrial poultry operation (n = 827, 25%). In addition, 114 fluoroquinolone-resistant strains from patients with urinary tract infections who were treated at three urban hospitals in Quito, Ecuador were analyzed. All of the isolates were subjected to antibiotic susceptibility screening. Fluoroquinolone-resistant isolates (FRIs) were then screened for the presence of qnrB genes. A significantly higher phenotypic resistance to fluoroquinolones was determined in E. coli strains from chickens in both the rural area (22%) and the industrial operation (10%) than in strains isolated from humans in the rural communities (3%). However, the rates of qnrB genes in E. coli isolates from healthy humans in the rural communities (11 of 35 isolates, 31%) was higher than in chickens from either the industrial operations (3 of 81 isolates, 6%) or the rural communities (7 of 251 isolates, 2.8%). The occurrence of qnrB genes in human FRIs obtained from urban hospitals was low (1 of 114 isolates, 0.9%). These results suggested that the qnrB gene is more widely distributed in rural settings, where antibiotic usage is low, than in urban hospitals and industrial poultry operations. The role of qnrB in clinical resistance to fluoroquinolones is thus far unknown.
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Antibacterianos/farmacologia , Farmacorresistência Bacteriana , Infecções por Escherichia coli/microbiologia , Infecções por Escherichia coli/veterinária , Proteínas de Escherichia coli/genética , Escherichia coli/efeitos dos fármacos , Escherichia coli/isolamento & purificação , Fluoroquinolonas/farmacologia , Doenças das Aves Domésticas/microbiologia , Animais , Galinhas , Equador , Escherichia coli/classificação , Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Humanos , Testes de Sensibilidade Microbiana , Dados de Sequência Molecular , FilogeniaRESUMO
The emergence of extended-spectrum ß-lactamases and plasmid-mediated resistance to quinolones has been previously found to be associated with the dissemination of complex class 1 integrons in Argentina. In this study, we analyzed their distribution through time and evaluated the functionality of the Orf513 protein, which is the putative recombinase of the ISCR1 mobile element. We investigated the presence of the orf513, blaCTX-M-2, dfrA3b, qnrB10 and blaDHA-1 genes by PCR and DNA sequencing as well as their linkage to class 1 integrons in 451 non-epidemiologically related nosocomial strains resistant to at least one expanded-spectrum cephalosporin and to one aminoglycoside, isolated between 1989 and 2010 from 7 hospitals from Buenos Aires City. The epidemiology of complex class 1 integrons was found to be notably different among fermenting (94/171) and non-fermenting clinical bacilli isolates (1/280). The ISCR1::qnrB10 positive isolates were found since 1993, confirming its presence in clinical isolates more than a decade before its first description. As expected, In35::ISCR1::blaCTX-M-2 was the most common complex class 1 integron among Enterobacteriaceae isolates, particularly in Proteus mirabilis. Experimental analysis corroborated the activity of the Orf513 protein, which was found to bind specific DNA sequences containing the previously suggested oriIS region. These findings showed the high dispersion and maintenance of complex class 1 integrons across time in our nosocomial isolates. The contribution of the ISCR1 mobile element to multidrug resistant phenotypes is significant due to its sustained association to class 1 integrons.
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Infecções por Enterobacteriaceae/microbiologia , Enterobacteriaceae/genética , Genes Bacterianos/genética , Integrons/genética , Argentina , Sequência de Bases , Infecção Hospitalar/microbiologia , Enterobacteriaceae/enzimologia , Enterobacteriaceae/isolamento & purificação , Humanos , Dados de Sequência Molecular , Fases de Leitura Aberta , beta-Lactamases/genéticaRESUMO
In this study, we investigated the presence of plasmid-mediated quinolone resistance (PMQR) genes among 101 ciprofloxacin-resistant urinary Escherichia coli isolates and searched for mutations in the quinolone-resistance-determining regions (QRDRs) of the DNA gyrase and topoisomerase IV genes in PMQR-carrying isolates. Eight isolates harboured the qnr and aac(6')-Ib-cr genes (3 qnrS1, 1 qnrB19 and 4 aac(6')-Ib-cr). A mutational analysis of the QRDRs in qnr and aac(6')-Ib-cr-positive isolates revealed mutations in gyrA, parC and parE that might be associated with high levels of resistance to quinolones. No mutation was detected in gyrB. Rare gyrA, parC and parE mutations were detected outside of the QRDRs. This is the first report of qnrB19, qnrS1 and aac(6')-Ib-cr -carrying E. coli isolates in Brazil.