RESUMO
The Pseudomonas aeruginosa genome can change to adapt to different ecological niches. We compared four genomes from a Mexican hospital and 59 genomes from GenBank from different niches, such as urine, sputum, and environmental. The ST analysis showed that high-risk STs (ST235, ST773, and ST27) were present in the genomes of the three niches from GenBank, and the STs of Mexican genomes (ST167, ST2731, and ST549) differed from the GenBank genomes. Phylogenetic analysis showed that the genomes were clustering according to their ST and not their niche. When analyzing the genomic content, we observed that environmental genomes had genes involved in adapting to the environment not found in the clinics and that their mechanisms of resistance were mutations in antibiotic resistance-related genes. In contrast, clinical genomes from GenBank had resistance genes, in mobile/mobilizable genetic elements in the chromosome, except for the Mexican genomes that carried them mostly in plasmids. This was related to the presence of CRISPR-Cas and anti-CRISPR; however, Mexican strains only had plasmids and CRISPR-Cas. blaOXA-488 (a variant of blaOXA50) with higher activity against carbapenems was more prevalent in sputum genomes. The virulome analysis showed that exoS was most prevalent in the genomes of urinary samples and exoU and pldA in sputum samples. This study provides evidence regarding the genetic variability among P. aeruginosa isolated from different niches.
RESUMO
blaIMP and blaVIM are the most detected plasmid-encoded carbapenemase genes in Pseudomonas aeruginosa. Previous studies have reported plasmid sequences carrying blaIMP variants, except blaIMP-56. In this study, we aimed to characterize a plasmid carrying blaIMP-56 in a P. aeruginosa strain isolated from a Mexican hospital. The whole genome of P. aeruginosa strain PE52 was sequenced using Illumina Miseq 2 × 150 bp, with 5 million paired-end reads. We characterized a 27 kb plasmid (pPE52IMP) that carried blaIMP-56. The phylogenetic analysis of RepA in pPE52IMP and 33 P. aeruginosa plasmids carrying resistance genes reported in the GenBank revealed that pPE52IMP and four plasmids (pMATVIM-7, unnamed (FDAARGOS_570), pD5170990, and pMRVIM0713) were in the same clade. These closely related plasmids belonged to the MOBP11 subfamily and had similar backbones. Another plasmid (p4130-KPC) had a similar backbone to pPE52IMP; however, its RepA was truncated. In these plasmids, the resistance genes blaKPC-2, blaVIM variants, aac(6')-Ib4, blaOXA variants, and blaIMP-56 were inserted between phd and resolvase genes. This study describes a new family of plasmids carrying resistance genes, with a similar backbone, the same RepA, and belonging to the MOBP11 subfamily in P. aeruginosa. In addition, our characterized plasmid harboring blaIMP-56 (pPE52IMP) belongs to this family.
RESUMO
Resumen La vaginosis bacteriana (VB) es una alteración frecuente de la microbiota vaginal en mujeres en edad reproductiva. El diagnóstico puede ser efectuado aplicando criterios clínicos o por la evaluación de los morfotipos bacterianos presentes en la tinción de Gram realizada a la secreción vaginal o mediante procedimientos microbiológicos, los cuales se desarrollaron como una alternativa al diagnóstico clínico, reemplazándolo paulatinamente. El objetivo del presente trabajo fue determinar la efectividad de los métodos de Amsel e Ison-Hay, para el diagnóstico de vaginosis bacteriana, empleando el método de Nugent como estándar. En este estudio se analizaron 305 muestras de secreción vaginal de pacientes del Hospital Regional ISSSTE Puebla. Las muestras se procesaron y analizaron para el diagnóstico de VB, siguiendo las recomendaciones de los métodos de Amsel, Nugent e Ison-Hay. El análisis de los resultados indicó un 12.8 % por Nugent, 31.1 % de VB por el método de Amsel y 36.7 % por Ison-Hay; sugiriendo que ambas técnicas muestran una alta tasa de falsos positivos. La sensibilidad para el método de Amsel e Ison-Hay fue de 97.44 %, la especificidad fue de 78.57 % y 72.18 % para Amsel e Ison-Hay, respectivamente. En conclusión, dado a los resultados obtenidos y a las mínimas diferencias entre los métodos analizados, se recomienda realizar los criterios de Amsel, seguidos de la observación de la tinción de Gram del flujo vaginal para la valoración de la microbiota por el método de Ison-Hay, para tener un mejor diagnóstico de VB, cuando no se emplea el método de Nugent.
Abstract Bacterial vaginosis (BV) is a frequent alteration of the vaginal microbiota in women of reproductive age. The diagnosis can be made by applying clinical criteria or by the evaluation of bacterial morphotypes present in Gram stain performed to vaginal secretion or by microbiological procedures, which were developed as an alternative to clinical diagnosis, gradually replacing it. The objective of this work was to determine the effectiveness of the Amsel and Ison-Hay methods, used for the diagnosis of bacterial vaginosis using the Nugent method as a standard. In this study, 305 samples of vaginal discharge from patients of the ISSSTE Puebla Regional Hospital were analyzed. The samples were processed and analyzed for the diagnosis of BV following the recommendations of the Amsel, Nugent and Ison-Hay methods. The analysis of the results indicated 12.8 % by Nugent, 31.1 % of BV by the Amsel method and 36.7 % by Ison-Hay; suggesting that both techniques show a high rate of false positives. The sensitivity for the Amsel and Ison-Hay method was 97.44 %, the specificity was 78.57 % and 72.18 % for Amsel and Ison-Hay, respectively. In conclusion, given the results obtained and the minimal differences between the analyzed methods, it is recommended to perform the Amsel criteria, followed by the observation of Gram staining of the vaginal flow for the assessment of the microbiota by the Ison-Hay method, to have a better diagnosis of BV, when the Nugent method is not used.
RESUMO
PURPOSE: Pseudomonas aeruginosa infections in hospitals constitute an important problem due to the increasing multidrug resistance (MDR) and carbapenems resistance. The knowledge of resistance mechanisms in Pseudomonas strains is an important issue for an adequate antimicrobial treatment. Therefore, the objective was to investigate other antimicrobial resistance mechanisms in MDR P. aeruginosa strains carrying bla IMP, make a partial plasmids characterization, and determine if modifications in oprD gene affect the expression of the OprD protein. METHODOLOGY: Susceptibility testing was performed by Kirby Baüer and by Minimum Inhibitory Concentration (presence/absence of efflux pump inhibitor); molecular typing by Pulsed-field gel electrophoresis (PFGE), resistance genotyping and integrons by PCR and sequencing; OprD expression by Western blot; plasmid characterization by MOB Typing Technique, molecular size by PFGE-S1; and bla IMP location by Southern blot. RESULTS: Among the 59 studied P. aeruginosa isolates, 41 multidrug resistance and carbapenems resistance isolates were detected and classified in 38 different PFGE patterns. Thirteen strains carried bla IMP; 16 bla GES and four carried both genes. This study centered on the 17 strains har-boring bla IMP. New variants of ß-lactamases were identified (bla GES-32, bla IMP-56, bla IMP-62) inside of new arrangements of class 1 integrons. The presence of bla IMP gene was detected in two plasmids in the same strain. The participation of the OprD protein and efflux pumps in the resistance to carbapenems and quinolones is shown. No expression of the porin OprD due to stop codon or IS in the gene was found. CONCLUSIONS: This study shows the participation of different resistance mechanisms, which are reflected in the levels of MIC to carbapenems. This is the first report of the presence of three new variants of ß-lactamases inside of new arrangements of class 1 integrons, as well as the presence of two plasmids carrying bla IMP in the same P. aeruginosa strain isolated in a Mexican hospital.
