Clonal Structure, Virulence Factor-encoding Genes and Antibiotic Resistance of Escherichia coli, Causing Urinary Tract Infections and Other Extraintestinal Infections in Humans in Spain and France during 2016

Abstract

Escherichia coli is the main pathogen responsible for extraintestinal infections. A total of 196 clinical E. coli consecutively isolated during 2016 in Spain (100 from Lucus Augusti hospital in Lugo) and France (96 from Beaujon hospital in Clichy) were characterized. Phylogroups, clonotypes, sequence types (STs), O:H serotypes, virulence factor (VF)-encoding genes and antibiotic resistance were determined. Approximately 10% of the infections were caused by ST131 isolates in both hospitals and approximately 60% of these infections were caused by isolates belonging to only 10 STs (ST10, ST12, ST58, ST69, ST73, ST88, ST95, ST127, ST131, ST141). ST88 isolates were frequent, especially in Spain, while ST141 isolates significantly predominated in France. The 23 ST131 isolates displayed four clonotypes: CH40-30, CH40-41, CH40-22 and CH40-298. Only 13 (6.6%) isolates were carriers of extended-spectrum beta-lactamase (ESBL) enzymes. However, 37.2% of the isolates were multidrug-resistant (MDR). Approximately 40% of the MDR isolates belonged to only four of the dominant clones (B2-CH40-30-ST131, B2-CH40-41-ST131, C-CH4-39-ST88 and D-CH35-27-ST69). Among the remaining MDR isolates, two isolates belonged to B2-CH14-64-ST1193, i.e., the new global emergent MDR clone. Moreover, a hybrid extraintestinal pathogenic E.coli (ExPEC)/enteroaggregative isolate belonging to the A-CH11-54-ST10 clone was identified.

High Prevalence and Diversity of Cephalosporin-Resistant Enterobacteriaceae Including Extraintestinal Pathogenic E. coli CC648 Lineage in Rural and Urban Dogs in Northwest Spain

“…Poultry products can act as a reservoir for human extraintestinal Enterobacteriaceae pathogens [ 34 , 35 , 36 ], so we also hypothesize that such products could be playing a role in their transmission between animals, particularly in rural environments. Importantly, MDR E. coli of human clinical origin and characterized as A-ST93 (CH11-neg), B1-ST453 (CH6-31), and F-ST1485 (CH231-58) were also recently reported in the same health area (Galicia) [ 37 , 38 ]. This reinforces the importance of “One-Health” actions against dissemination of antimicrobial resistance.…”

Clinical Relevance of Antibiotic Susceptibility Profiles for Screening Gram-negative Microorganisms Resistant to Beta-Lactam Antibiotics

“…Reports on the in vitro effect of FEP against Enterobacterales are highly varied, and numerous E. coli isolates have been found to be susceptible to this antimicrobial [ 17 ]. FEP can be clinically active in some cases, although it is not recommended for infections caused by ESBL-producing bacteria because of the high failure rate [ 18 , 19 , 20 ].…”

High diversity and variability of pipolins among a wide range of pathogenic Escherichia coli strains

“…The source of 3- 373-03_S1_C2 A 5,293 -iutA, iucD, gad, iha IncFII, IncB/O/ K/Z, Col(BS512) --9/3 (I-E) LREC237 D* 524 aEPEC chuA, ompT, fimH, eae astA, cif, eae, ehxA, espA, espB, espF, espJ, etpD P , gad, katP, nleA, nleB, tccP, tir IncFIB/IncX1, ColRNAI, NT 4P, 1 M, 1S, 2U CALIN P 9/1 (I-E Diversity of pipolin-harboring E. coli strains. Although some of the strains in the LREC collection have been described in detail throughout the last years [13][14][15][16][17] , the pipolin-positive strains remained uncharacterized. We performed now a detailed molecular characterization, both by conventional methods and wholegenome sequence (WGS) analysis ( Table 2 and Table S1).…”