Escherichia Coli that Produces ExtendedSpectrum Beta-Lactamases Showed a Great Diversity of Clones and Plasmids in Spanish Chicken Meat, According to Comparative Phylogenomics

Abstract

From farm to fork, there is a greater chance of coming into contact with bacteria resistant to antibiotics
because animal food items are significant sources of zoonotic agents. Therefore, using a One Health
approach, our goal was to identify and thoroughly characterize E. coli from the poultry industry that
produces Extended-Spectrum Beta-Lactamase (ESBL). 48 samples of chicken meat were gathered from
16 locations in La Rioja (Northern Spain) between December 2021 and March 2022. The disk-diffusion
method was used to evaluate antibiotic susceptibility testing. When plated on MacConkey-agar, 40 E.
coli isolates were found in 33 out of 48 chicken meat samples examined (68.8%). Furthermore, six
ESBL-E. coli (6/48, 12.5%) were isolated by Whole-Genome Sequencing on MacConkey-agar
supplemented with cefotaxime. Clones and ESBL genes were found to be highly diverse, including
ST1140-E/blaCTX-M-32 (n=1), ST752-A/blaTEM-52 (n=1), ST117-B2/blaCTX-M-1/blaSHV-12 (n=2), ST10-
A/blaSHV-12 (n=1), and ST223-B1/blaSHV-12 (n=1). The blaSHV-12/blaCTX-M-1/blaCTX-M-32 genes were
detected on three IncI1-plasmids (pST3-CC3) in two genetic environments: i) IS26-smc-glpR-blaSHV-12-
IS26; and ii) wbuC-blaCTX-M-32/blaCTX-M-1-ISEcp1. An IS4-mediated composite transposon flanked a
P1-like phage-plasmid that carried the blaTEM-52 gene. An IncHI2 plasmid contained additional genes
that conferred resistance to aminoglycosides, chloramphenicol, and sulphonamides, in addition to a
blaSHV-12 gene flanked by an IS26-mediated composite transposon. Our six genomes were mapped
with publicly available genomes (n=2588) related to the STs found in order to analyze the cross-sectoral
relatedness of our ESBL-E. coli isolates. This showed that one of our genomes (X3078-ST117) showed
strong similarities (34–40 allelic differences) with a small number of genomes belonging to ST117 from
the poultry sector in Germany and the USA. This investigation showed that chicken meat in Spain still
contains a significant percentage of ESBL-E. coli. Furthermore, the IncI1-blaCTX-M-1-32/blaSHV-12
plasmids and the ST117 clone may be examples of effective clones and plasmids that have been
modified for the chicken host.