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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety and Quality » Research » Publications at this Location » Publication #363990

Research Project: Genomic and Metagenomic Differences in Foodborne Pathogens and Determination of Ecological Niches and Reservoirs

Location: Meat Safety and Quality

Title: Characterisation of early positive mcr-1 resistance gene and plasmidome in Escherichia coli pathogenic strains associated with variable phylogroups under colistin selection

item MACORI, GUERRINO - University College Dublin
item NGUYEN, SCOTT - University College Dublin
item NAITHANI, ANKITA - University College Dublin
item HURLEY, DANIEL - University College Dublin
item BAI, LI - University College Dublin
item EL GARACH, FARID - Vetoquinol Sa
item WOEHRLÉ, FRÉDÉRIQUE - Vetoquinol Sa
item MIOSSEC, CHRISTINE - Vetoquinol Sa
item ROQUES, BENJAMIN - University College Dublin
item O'GAORA, PEADAR - University College Dublin
item Bono, James - Jim
item FANNING, SEAMUS - University College Dublin

Submitted to: Antibiotics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/23/2021
Publication Date: 8/25/2021
Citation: Macori, G., Nguyen, S.V., Naithani, A., Hurley, D., Bai, L., El Garach, F., Woehrlé, F., Miossec, C., Roques, B., O'Gaora, P., Bono, J.L., Fanning, S. 2021. Characterisation of early positive mcr-1 resistance gene and plasmidome in Escherichia coli pathogenic strains associated with variable phylogroups under colistin selection. Antibiotics. 10. Article 1041.

Interpretive Summary: Escherichia coli (E. coli) is a bacterium of importance to the agri-food industry, particularly the beef and dairy sectors, as it causes two common bovine diseases: diarrhea and mastitis. These infectious agents not only exert an impact on animal welfare, but also on productivity of bovine-derived foodstuffs. Therefore, it is important to characterize E. coli strains responsible for these infections. The E. coli strains were genetically diverse and contained an assortment of complex genetic elements that encoded antibiotic resistant and virulence genes. The genetic elements also contained a mechanism to transfer themselves to other bacteria. Use of this genomic information may prevent economic losses and increase animal wellness as well as improving food safety and reducing public health risks.

Technical Abstract: An antibiotic susceptibility monitoring programme was conducted from 2004 to 2010, resulting in a collection of 143 Escherichia coli cultured from bovine faecal samples (diarrhoea) and milk-aliquots (mastitis). The isolates were subjected to whole-genome sequencing and were distributed in phylogroups A, B1, B2, C, D, E, and G with no correlation for particular genotypes with athotypes. In fact, the population structure showed that the strains belonging to the different phylogroups matched broadly to ST complexes; however, the isolates are randomly associated with the diseases, highlighting the necessity to investigate the virulence factors more accurately in order to identify the mechanisms by which they cause disease. The antimicrobial resistance was assessed phenotypically, confirming the genomic prediction on three isolates that were resistant to colistin, although one isolate was positive for the presence of the gene mcr-1 but susceptible to colistin. To further characterise the genomic context, the four strains were sequenced by using a single-molecule long read approach. Genetic analyses indicated that these four isolates harboured complex and diverse plasmids encoding not only antibiotic resistant genes (including mcr-1 and bla) but also virulence genes (siderophore, ColV, T4SS). A detailed description of the plasmids of these four E. coli strains, which are linked to bovine mastitis and diarrhoea, is presented for the first time along with the characterisation of the predicted antibiotic resistance genes. The study highlighted the diversity of incompatibility types encoding complex antibiotic resistance elements such as Tn6330, ISEcp1 Tn6029, and IS5075. The mcr-1 resistance determinant was identified in IncHI2 plasmids pCFS3273- 1 and pCFS3292-1, thus providing some of the earliest examples of mcr-1 reported in Europe, and these sequences may be a representative of the early mcr-1 plasmidome characterisation in the EU/EEA.