Multidrug- and Extensively Drug-Resistant Uropathogenic Escherichia coli Clinical Strains: Phylogenetic Groups Widely Associated with Integrons Maintain High Genetic Diversity

Abstract

In recent years, an increase of uropathogenic Escherichia coli (UPEC) strains with Multidrug-resistant (MDR) and Extensively Drug-resistant (XDR) profiles that complicate therapy for urinary tract infections (UTIs) has been observed and has directly impacted costs and extended hospital stays. The aim of this study was to determine MDR- and XDR-UPEC clinical strains, their virulence genes, their phylogenetic groups and to ascertain their relationship with integrons and genetic diversity. From a collection of 500 UPEC strains, 103 were selected with MDR and XDR characteristics. MDR-UPEC strains were mainly associated with phylogenetic groups D (54.87%) and B2 (39.02%) with a high percentage (≥70%) of several fimbrial genes (ecpA, fimH, csgA, and papGII), an iron uptake gene (chuA), and a toxin gene (hlyA). In addition, a moderate frequency (40–70%) of other genes (iutD, tosA, and bcsA) was observed. XDR-UPEC strains were predominantly associated with phylogenetic groups B2 (47.61%) and D (42.85%), which grouped with ≥80 virulence genes, including ecpA, fimH, csgA, papGII, iutD, and chuA. A moderate frequency (40–70%) of the tosA and hlyA genes was observed. The class 1 and 2 integrons that were identified in the MDR- and XDR-UPEC strains were associated with phylogenetic groups D, B2, and A, while the XDR-UPEC strains that were associated with phylogenetic groups B2, D, and A showed an extended-spectrum beta-lactamase (ESBL) phenotype. The modifying enzymes (aadA1, aadB, aacC, ant1, dfrA1, dfrA17, and aadA4) that were identified in the variable region of class 1 and 2 integrons from the MDR strains showed resistance to gentamycin (56.25 and 66.66%, respectively) and trimethoprim-sulfamethoxazole (84.61 and 66.66%, respectively). The MDR- and XDR-UPEC strains were distributed into seven clusters and were closely related to phylogenic groups B2 and D. The diversity analysis by PFGE showed 42.68% of clones of MDR-UPEC and no clonal association in the XDR-UPEC strains. In conclusion, phylogenetic groups including virulence genes are widely associated with two integron classes (1 and 2) in MDR- and XDR-UPEC strains.

Molecular Epidemiology, Antibiotic Resistance, and Virulence Traits of Stenotrophomonas maltophilia Strains Associated With an Outbreak in a Mexican Tertiary Care Hospital

“…Extended-Spectrum β-Lactamase (ESBL) Phenotypic Detection in the S. maltophilia Strains Tests of the antimicrobial susceptibility of the S. maltophilia strains were performed according to the Clinical and Laboratory The extended-spectrum β-lactamase (ESBL) phenotypes were detected via double-disk synergy testing to evaluate the synergistic effects between clavulanic acid and β-lactam antibiotics as previously described by our research group (Ochoa et al, 2016;CLSI, 2018).…”

“…The obtained genomic DNA was used for identification of the resistance genes (sul1, sul2, and qnr) through end-point PCR and the integron classes (1, 2, and 3) by multiplex PCR (Table S1) (Ozkaya et al, 2014). The DNA products were resolved by electrophoresis and stained with 0.5 µg/mL ethidium bromide (Sigma-Aldrich, St. Louis, MO, USA; Ochoa et al, 2016).…”

“…The primers used for the identification of 20 virulence genes (virB,rmlA,fliC,stmPr1,pilU,hlyIII,gspD,papD,afaD,hgbB,entA,tpsB,picN1,motA,zot,fhaB,frpC,fimH,lktD,and hcp) by multiplex PCR were designed based on the following sequences: S. maltophilia K279a, S. maltophilia R551_3, S. maltophilia SJTH1, S. maltophilia NCTC10257, S. maltophilia FDAARGOS_92, 13637, S. maltophilia WZN_1, S. maltophilia JV3, S. maltophilia CSM2, and S. maltophilia ISMMS2 ( Table S2). The PCR products were resolved by electrophoresis on agarose gels and stained with 0.5 µg/mL ethidium bromide for visualization as previously described (Ochoa et al, 2016).…”

“…S. maltophilia strains were analyzed by PFGE according to methods modified by our research group (Ochoa et al, 2016). Briefly, purified DNA was digested with 2 U of Xbal (Invitrogen, Life Technologies, Waltham, MA, USA) at 37 • C for 4 h. The DNA samples were electrophoresed on a CHEF Mapper system from Bio-Rad Life Science Research (Hercules, CA, USA) for 23 h at 200 V (6 V/cm).…”

Effect and Analysis of Bacterial Lysates for the Treatment of Recurrent Urinary Tract Infections in Adults

“…The most common bacteria causing UTIs are Gram-negative bacteria, mainly strains belonging to uropathogenic E. coli (UPEC) pathotype [1][2][3]. Antibiotics are the most commonly prescribed therapy to treat UTIs; however, multidrug-resistant (MDR) UPEC strains have recently emerged, thus hampering the treatment and control of these infections [4,5]. Accordingly, the WHO has included E. coli in a list of pathogens for special consideration due to their MDR profile and the difficulty this poses for the treatment and control of the illnesses these bacteria give rise to.…”