Genotypic-Phenotypic Discrepancies between Antibiotic Resistance Characteristics of Escherichia coli Isolates from Calves in Management Settings with High and Low Antibiotic Use

Abstract

We hypothesized that bacterial populations growing in the absence of antibiotics will accumulate more resistance gene mutations than bacterial populations growing in the presence of antibiotics. If this is so, the prevalence of dysfunctional resistance genes (resistance pseudogenes) could provide a measure of the level of antibiotic exposure present in a given environment. As a proof-of-concept test, we assayed field strains of Escherichia coli for their resistance genotypes using a resistance gene microarray and further characterized isolates that had resistance phenotype-genotype discrepancies. We found a small but significant association between the prevalence of isolates with resistance pseudogenes and the lower antibiotic use environment of a beef cow-calf operation versus a higher antibiotic use dairy calf ranch (Fisher's exact test, P ‫؍‬ 0.044). Other significant findings include a very strong association between the dairy calf ranch isolates and phenotypes unexplained by well-known resistance genes (Fisher's exact test, P < 0.0001). Two novel resistance genes were discovered in E. coli isolates from the dairy calf ranch, one associated with resistance to aminoglycosides and one associated with resistance to trimethoprim. In addition, isolates resistant to expanded-spectrum cephalosporins but negative for bla CMY-2 had mutations in the promoter regions of the chromosomal E. coli ampC gene consistent with reported overexpression of native AmpC beta-lactamase. Similar mutations in hospital E. coli isolates have been reported worldwide. Prevalence or rates of E. coli ampC promoter mutations may be used as a marker for high expanded-spectrum cephalosporin use environments.

Whole-Genome Sequencing of Drug-Resistant Salmonella enterica Isolates from Dairy Cattle and Humans in New York and Washington States Reveals Source and Geographic Associations

“…Here, more than 50% of these discrepancies were attributed to S. Dublin isolates from the Washington State clade, which carry an allele on a truncated strA that appeared to not confer STR resistance, while still being identified computationally as an STR resistance determinant. Similar discrepancies have been observed in a previous study (35) of Escherichia coli isolates from dairy calves; in this study, point mutations in strA were hypothesized to affect its ability to confer STR resistance. Additionally, a previous study that assessed phenotypic and genotypic resistance in nontyphoidal Salmonella isolated from retail meat and human clinical samples also found STR (P Ϫ :G ϩ ) discrepancies to be the most common (27).…”

Molecular identification of aminoglycoside-modifying enzymes in clinical isolates of Escherichia coli resistant to amoxicillin/clavulanic acid isolated in Spain

“…It is possible that these differences are related to some extend to the fact that adequate breakpoints are still to be defined for some compounds and that EUCAST epidemiological breakpoints for some compounds are very different from the CLSI clinical breakpoints. In E. coli, Davis et al [28] observed genotypic-phenotypic discrepancies to aminoglycosides in 24.7% of strains and characterised mutations or deletions in inactive AME genes in isolates where the gene was present but the expected corresponding phenotype resistance was absent.…”

Commentary on genetic mechanisms of antimicrobial resistance in bacteria from U.S. food animals: ESBLs are here

“…Since then, CTX-M-type ESBLs have been found in E. coli collected from healthy dairy calves in the western U.S. (Davis et al, 2011) and from 5 of 20 dairy farms in Ohio (Mollenkopf et al, 2012); in clinical Salmonella enterica isolates from swine in Minnesota and from turkeys in 4 states (Wittum et al, 2012); in E. coli from swine finishing barns in Michigan and Ohio and in Klebsiella pneumoniae from swine in Illinois (Mollenkopf et al, 2013). …”

“…Given the situation in other livestock species and in other countries, we expect the lack of detection of CTX-M-type ESBLs in U.S. chicken isolates is more the result of lack of appropriate studies than a real absence of these on chicken farms. In addition to CTX-M-type ESBLs, the study of dairy calves in the western U.S. also found E. coli expressing OXA-type ESBLs (Davis et al, 2011). …”