AUTHOR=Ewers Christa , de Jong Anno , Prenger-Berninghoff Ellen , El Garch Farid , Leidner Ursula , Tiwari Sumeet K. , Semmler Torsten 

TITLE=Genomic Diversity and Virulence Potential of ESBL- and AmpC-β-Lactamase-Producing Escherichia coli Strains From Healthy Food Animals Across Europe

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.626774

DOI=10.3389/fmicb.2021.626774

ISSN=1664-302X

ABSTRACT=<p>The role of livestock animals as a putative source of ESBL/pAmpC <italic>E. coli</italic> for humans is a central issue of research. In a large-scale pan-European surveillance, 2,993 commensal <italic>Escherichia</italic> spp. isolates were recovered from randomly collected fecal samples of healthy cattle, pigs and chickens in various abattoirs. One-hundred <italic>Escherichia</italic> spp. isolates (0.5% from cattle, 1.3% pigs, 8.0% chickens) fulfilled the criteria for cefotaxime and ceftazidime non-wildtype (EUCAST). <italic>In silico</italic> screening of WGS data of 99 isolates (98 <italic>E. coli</italic> and 1 <italic>E. fergusonii</italic>) revealed <italic>bla</italic><sub>SHV</sub><sub>–</sub><sub>12</sub> (32.3%), <italic>bla</italic><sub>CTX</sub><sub>–</sub><sub>M</sub><sub>–</sub><sub>1</sub> (24.2%), and <italic>bla</italic><sub>CMY</sub><sub>–</sub><sub>2</sub> (22.2%) as predominant ESBL/pAmpC types. Other types were <italic>bla</italic><sub>SHV</sub><sub>–</sub><sub>2</sub> (1.0%), <italic>bla</italic><sub>CTX</sub><sub>–</sub><sub>M</sub><sub>–</sub><sub>2</sub><sub>/</sub><sub>–</sub><sub>14</sub><sub>/</sub><sub>–</sub><sub>15</sub> (1.0/6.1/1.0%), and <italic>bla</italic><sub>TEM</sub><sub>–</sub><sub>52</sub> (5.1%). Six isolates revealed AmpC-promoter mutations (position −42 (C &gt; T) and one carried <italic>mcr-1</italic>. The majority (91.3%) of ESBL/pAmpC genes were located on plasmids. SHV-12 was mainly (50%) encoded on IncI1α plasmids (pST-3/-26/-95), followed by IncX3 (12.5%) and IncK2 (3.1%). The <italic>bla</italic><sub>TEM</sub><sub>–</sub><sub>52</sub> genes were located on IncI1α-pST-36 (60%) and IncX1 plasmids (20%). The dominant plasmid lineage among CTX-M-1 isolates was IncI1α (pST-3/-295/-317) (87.5%), followed by IncN-pST-1 (8.3%). CMY-2 was mostly identified on IncI1α (pST-12/-2) (54.5%) and IncK2 (31.8%) plasmids. Several plasmids revealed high similarity to published plasmids from human and animal Enterobacteriaceae. The isolates were assigned to phylogroups A/C (34.7/7.1%), B1 (27.6%), B2 (3.1%), D/F (9.2/10.2%), E (5.1%), and to <italic>E</italic>. clades (3.0%). With 51 known and 2 novel MLST types, a wide variety of STs was found, including STs previously observed in human isolates (ST10/38/117/131/648). ESBL/AmpC types or STs were rarely correlated with the geographic origin of the isolates or animal species. Virulence gene typing identified extraintestinal pathogenic <italic>E. coli</italic> (ExPEC; 2.0%), avian pathogenic <italic>E. coli</italic> (APEC; 51.5%), and atypical enteropathogenic <italic>E. coli</italic> (EPEC; 6.1%). In conclusion, the high diversity of STs and phylogenetic groups provides hardly any hint for clonal spread of single lineages but hints toward the dissemination of cephalosporin resistance genes in livestock via distinct, globally successful plasmid lineages. Even though a number of isolates could not be assigned to a distinct pathotype, our finding of combined multidrug-resistance and virulence in this facultative pathogen should be considered an additional threat to public health.</p>