Genome sequencing and annotation of a Campylobacter coli strain isolated from milk with multidrug resistance

Abstract

As the most prevalent bacterial cause of human gastroenteritis, food-borne Campylobacter infections pose a serious threat to public health. Whole Genome Sequencing (WGS) is a tool providing quick and inexpensive approaches for analysis of food-borne pathogen epidemics. Here we report the WGS and annotation of a Campylobacter coli strain, FNW20G12, which was isolated from milk in the United States in 1997 and carries multidrug resistance. The draft genome of FNW20G12 (DDBJ/ENA/GenBank accession number LWIH00000000) contains 1, 855,435 bp (GC content 31.4%) with 1902 annotated coding regions, 48 RNAs and resistance to aminoglycoside, beta-lactams, tetracycline, as well as fluoroquinolones. There are very few genome reports of C. coli from dairy products with multidrug resistance. Here the draft genome of FNW20G12, a C. coli strain isolated from raw milk, is presented to aid in the epidemiology study of C. coli antimicrobial resistance and role in foodborne outbreak.

The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain

“…C. jejuni and C. coli are the main species responsible for the majority of cases of campylobacteriosis [ 84 ]. Recent studies have indicated that Campylobacter isolates are frequently resistant to commonly used antimicrobials such as gentamicin and other aminoglycosides [ 85 , 86 ], tetracyclines, beta-lactams and fluoroquinolones [ 87 ]. Campylobacter isolates have frequently been isolated from raw meat, especially poultry, but also from raw milk, or even water [ 87 ].…”

“…Recent studies have indicated that Campylobacter isolates are frequently resistant to commonly used antimicrobials such as gentamicin and other aminoglycosides [ 85 , 86 ], tetracyclines, beta-lactams and fluoroquinolones [ 87 ]. Campylobacter isolates have frequently been isolated from raw meat, especially poultry, but also from raw milk, or even water [ 87 ]. As reported, in the European Union alone, the number of confirmed cases of campylobacteriosis has steadily increased in the last five years, with 246,307 confirmed human cases in 2016 [ 72 ].…”

Whole Genome Sequencing and Multiplex qPCR Methods to Identify Campylobacter jejuni Encoding cst-II or cst-III Sialyltransferase

“…Whole genome sequencing was performed as described in Liu et al (2016) , using genomic DNA isolated from the three assay controls. Briefly, libraries were prepared using the Nextera XT kit (Illumina) and sequenced using a MiSeq instrument (Illumina) with 251 reading cycles.…”

Análise fenotípica e sequenciamento do genoma completo de linhagens de >i<Campylobacter coli>/i< isoladas de diversas fontes durante 16 anos no Brasil

“…Atualmente, a análise do sequenciamento do genoma completo vem sendo utilizada com êxito em linhagens de Campylobacter, especialmente em linhagens de C. jejuni, tanto em estudos epidemiológicos quando filogenéticos (BIGGS et al, 2011;REVEZ et al, 2014;CLARK et al, 2016;CODY et al, 2017;JOENSEN et al, 2018). Entretanto, estudos genômicos da espécie C. coli são mais escassos e torna-se imprescindível salientar que não existem, até o momento, trabalhos publicados que compararam linhagens de C. coli circulantes no Brasil através de metodologias de sequenciamento de nova geração (LIU et al, 2016;CODY et al, 2017;GHATAK et al, 2017;CANTERO et al, 2018).…”