Antimicrobial resistance of Escherichia coli, isolated from children's intestinal microbiota.

Recent studies have shown that bacterial resistance existed long before antimicrobials were used in medicine, and not only pathogens are resistant to antibiotics. 511 strains of E. coli isolated from the intestinal microbiota of children aged 1 month to 17 years living in St. Petersburg were studied: the susceptibility to 15 antibiotics was determined by the disk diffusion method, as well as the susceptibility to 6 commercial bacteriophages produced by «Microgen¼ (Russia). The b-lactamase genes of molecular families TEM, SHV, OXA, and CTX-M were detected by multiplex PCR. 39,3% E. coli isolates were resistant to one or more antimicrobial classes. The proportion of multidrug resistant isolates (resistant to 3 or more classes) was 16,6%. Multidrug resistance to clinically significant antimicrobial classes (extended-spectrum cephalosporins (ESC) + fluoroquinolones + aminoglycosides) was detected in 0,8% isolates. Resistance to aminopenicillins was detected in 29,5%, ESC - 11,2%, fluoroquinolones - 13,3%, tetracycline - 20,0%, chloramphenicol - 9,8%, aminoglycosides - 2,5% isolates. b-lactam resistance was due to the beta-lactamase production: to ampicillin - the molecular family TEM (81,9%), ESC - the CTX-M molecular family (87,7%) CTX-M1 - (66%) and CTX-M9 groups (34%). 43,5% multidrug resistant E. coli isolates were susceptible to at least one of the six commercial bacteriophages produced by «Microgen¼. The study showed that the intestinal microbiota of children is an important reservoir of E. coli resistant (including multidrug resistance) to various classes of antibiotics, and bacteriophage therapy is an alternative method for eradication of antibiotic-resistant E. coli.

[Phylogenetic groups and virulence genes of Escherichia coli strains isolated from the children gut microbiota.]

Escherichia coli is characterized by a wide intraspecific diversity. The species includes both commensals and pathogens that cause diarrhea and extra-intestinal diseases. Pathogenic strains differ from non-pathogenic ones by the presence of virulence factors and their genes. The phylogenetic structure of the species is represented by four main groups (A, B1, B2, D), which differ in their prevalence among residents of different geographical regions. Pathogenic members of the species have been studied in detail, while non-pathogenic strains have not received such attention. This report presents the results of a study of 511 E. coli strains isolated from the gut microbiota of children without diarrhea and urinary tract infections, aged from 1 month to 17 years, living in St. Petersburg. The main phylogenetic groups were determined by PCR, and E. coli virulence genes associated with diarrhea and extra-intestinal diseases were identified. Results: population structure of E. coli is represented by the following groups: A-33.3%, B1-6.7%, B2-34.0%, D-26%. In the studied population 2.5% of strains belonded to EPEC and 4.5% to EAggEC. EPEC virulence genes were more often detected in strains of phylogroup B1, and EAggEC virulence genes in isolates of phylogroup D. The prevalence of extra - intestinal virulence genes was as follows: pap - 29.5%; sfa - 19.8%; afa - 3.3%; hly - 20.9%; cnf - 17.4%; aer-20.0%. The pap, sfa, hly, and cnf genes were detected mostly in the B2 phylogenetic group. Obtained data shows the similarity of E. coli phylogenetic groups structure in St. Petersburg with E. coli populations isolated from residents of Paris and Sydney. Analysis of the virulence genes prevalence showed the dependence of their presence on the genetic background bacteria.

[Antimicrobial resistance and clinical significant resistance mechanisms of Salmonella isolated in 2014-2018 in St.Petersburg, Russia.]

The article presents the results of antimicrobial resistance monitoring of Salmonella isolated from children and adults with diarrhea in St. Petersburg in 2014-2018. In 746 isolates of 42 serovars more than 90,0% belonged to three: S. enteritidis (79,6%), S. typhimurium (6,8%) and S. infantis (3,8%). The antimicrobial susceptibility testing (according the EUCAST) to 7 classes of antimicrobials revealed the resistance in 78,6% of Salmonella. Low-level quinolone resistance (MIC of ciprofloxacin 0,12-0,5 mg/l) was detected in 63,3% isolates (S. enteritidis -71,0%, S. typhimurium - 15,7%, S. infantis - 89,3%) and was due to five kinds of single nucleotide substitutions in gyrA: Asp87Tyr - 36,1% of studied isolates (only S. infantis); Ser83Phe - 22,2% (only S. enteritidis); Asp87Asn - 19,4% (S. enteritidis, S. typhimurium, S. hadar, S. newport); Ser83Tyr -11,1% (S. enteritidis and S. infantis) and Asp87Gly - 8,3% (only S. enteritidis). Only in one S. kentucky isolate with high-level fluoroquinolone resistance (MIC of ciprofloxacin > 8,0 mg/l) two substitutions (Ser83Phe and Asp87Asn) were detected. Two Salmonella isolates (S. typhimurium and S. corvallis) had plasmid-mediated quinolone resistance (qnrS). Extended-spectrum cephalosporin resistance was found in 6 Salmonella serovars (1,6%). The bla-genes were detected: of genetic group CTX-M1 - in 10 isolates (serovars S. typhimurium, S. enteritidis, S. abony, S. coeln and S. virchow), CTX-M2 - in 2 S. typhimurium isolates, CTX-M9 - in three S. enteritidis isolates. In one S. typhimurium CTX-M1 and CTX-M2 were detected. The gene of CMY-2 (molecular class C cephalosporinase) was revealed in two isolates (S. newport and S. enteritidis). Our study showed that Salmonella (the main bacterial pathogen of acute diarrhea in children and adults) isolated in Saint-Petersburg had antimicrobial resistance to drugs of choice for salmonellosis treatment.