Detection of international high-risk clones of food-borne pathogens Salmonella and Escherichia coli in the Russian Federation

Abstract

The use of whole genome sequencing, standard analyze methods and international databases allows to detect international high-risk clones of food-borne pathogens, to assess their evolution and geographical distribution due to international trade of animal food products and farm animals. In Saint-Petersburg, Russian Federation, Salmonella Newport, Salmonella Kentucky and Escherichia coli O26:H11 of well-known international high-risk clones were first identified from patients with diarrhea. Two S. Kentucky strains isolated in 2015 and 2019 were identical to the international clone ST198 widely distributed in European countries: had multidrug resistance, high-level fluoroquinolone resistance (MIC of ciprofloxacin 32,0 mg/l) due to three single-nucleotide substitutions in the gyrA (Ser83Phe and Asp87Asn) and parC (Ser80Ile). In 2008, a multidrug resistant S. Newport strain resistant to extended-spectrum cephalosporins due to AmpC-cephalosporinase CMY-2 was isolated, belonging to the international clone of S. Newport MDR-AmpC/CMY-2 which caused sporadic cases and outbreaks in the USA and Europe in the 2000s. The plasmid containing the blaCMY-2 had a PstI-restriction profile, one of the most prevalent in the international clone. E. coli O26:H11 strains, isolated in Saint-Petersburg, produced the shiga-like toxin STX1 (stx1a), had additional virulence genes: ehxA (enterohemolysin), katP (catalase peroxidase), espP (serine protease), as well as cba (colicin B), gad (glutamate decarboxylase), cif (type III secreted effector), iss (increased serum survival), belonged to the phylogenetic group B1 and the international high-risk clone E. coli O26:H11 ST21 widely distributed in Europe and the USA. 25% of the strains had multidrug resistance and produced CTX-M extended spectrum beta-lactamases. In the Russian Federation E. coli O26 is consider as the pathogen of diarrheal diseases and registered as Enteropathogenic E. coli in routine bacteriological laboratories without detecting of H-antigen and shiga-like toxins.