Whole genome sequence analysis of Avian Pathogenic E. coli to assess their potential as reservoirs of antimicrobial resistance and as potential zoonotic pathogens
- Publication Type:
- Thesis
- Issue Date:
- 2020
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Antimicrobial resistance (AMR) is a complex, global health challenge requiring a One Health framework, acknowledging the interconnectedness of human, animal and environmental microbiospheres, in order to understand its reservoirs, transfer mechanisms and evolution. ๐๐ด๐ค๐ฉ๐ฆ๐ณ๐ช๐ค๐ฉ๐ช๐ข ๐ค๐ฐ๐ญ๐ช is a model โOne Health organismโ as it is a gastrointestinal commensal of diverse vertebrate species, a common contaminant of foodstuffs and natural environments, increasingly multidrug resistant (MDR) and a major human pathogen.
Within humans, extraintestinal pathogenic ๐. ๐ค๐ฐ๐ญ๐ช (ExPEC) cause severe disease, including urinary tract infections (UTIs) and blood sepsis. Similarly, avian pathogenic ๐. ๐ค๐ฐ๐ญ๐ช (APEC), a subset of ExPEC, cause significant economic losses in the poultry sector. Despite known phylogenetic and genotypic similarities between the two, it is still not possible to define them with genomic data alone and their transit between poultry and humans is poorly characterised. Genomic data on Australian APEC in particular is lacking, hampering efforts to assess and mitigate their threat to human and animal health.
Accordingly, we characterised the genomes of 95 Australian MDR APEC sourced from four Australian states. ST117 and clonal-complex 350 were abundant, however pandemic human ExPEC lineages also featured, including ST95, ST73 and ST131. Almost all strains carried large ColV-like virulence plasmids, however no strains carried genes conferring resistance to critically important antimicrobials (CIAs), such as carbapenems, extended-spectrum ฮฒโlactams, fluoroquinolones and colistin, except one exhibiting a fluoroquinolone-resistance associated mutation. This attests to the value of strict antimicrobial use regulations in food animals in Australia.
One strain carried a novel variant of ๐๐ข๐ญ๐ฎ๐ฐ๐ฏ๐ฆ๐ญ๐ญ๐ข genomic island 1 (SGI1) named SGI1-B-Ec1. SGI1 is an integrative mobilisable element that confers resistance to five different classes of antimicrobials and may confer pathogenicity traits. It was originally characterised in outbreak strains of ๐๐ข๐ญ๐ฎ๐ฐ๐ฏ๐ฆ๐ญ๐ญ๐ข ๐ฆ๐ฏ๐ต๐ฆ๐ณ๐ช๐ค๐ข serovar Typhimurium, however SGI1-related elements (SGI1-REs) have been reported in diverse genera, some carrying CIA-resistance genes. The first identification of an SGI1-RE in ๐. ๐ค๐ฐ๐ญ๐ช is alarming as it indicates other more clinically significant SGI1-REs may exist within Australian food-animals. Subsequently, high-throughput analysis of 455,632 bacterial genomes revealed previously undescribed SGI1-REs in ๐. ๐ค๐ฐ๐ญ๐ช, ๐๐ญ๐ฆ๐ฃ๐ด๐ช๐ฆ๐ญ๐ญ๐ข ๐ฑ๐ฏ๐ฆ๐ถ๐ฎ๐ฐ๐ฏ๐ช๐ข๐ฆ, ๐๐ช๐ฃ๐ณ๐ช๐ฐ ๐ค๐ฉ๐ฐ๐ญ๐ฆ๐ณ๐ข๐ฆ and ๐๐ณ๐ฐ๐ฏ๐ฐ๐ฃ๐ข๐ค๐ต๐ฆ๐ณ ๐ด๐ข๐ป๐ข๐ฌ๐ช๐ช.
This data provides valuable insight into the current AMR status of Australian MDR APEC, as well as the spread and evolution of SGI1 and SGI1-REs within Gammaproteobacteriaceae. Large-scale, One Health-oriented genomic epidemiological studies are urgently required into APEC and bacterial populations more broadly to identify and mitigate their threat to human and animal health.
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