Abstract
Salmonella is a major foodborne pathogen worldwide, including in Thailand. The rising
antimicrobial resistance (AMR) Salmonella isolates seriously threaten the healthcare system.
However, the bacterial genomic data of non-typhoidal Salmonella (NTS) clinically isolated from
human cases in Chiang Mai and nearby provinces are still under-investigated. Here, we used the
next-generation sequencing (NGS) technology to perform whole genome sequencing (WGS) by the
short-read Illumina Novaseq 6000. Fifty-five isolates of NTS were randomly selected from the
collection of the clinically isolated NTS from patient's stool culture admitted at Maharaj Nakorn
Chiang Mai Hospital (MNCMH) during 2016 – 2021. We also tested each isolate for its to antimicrobial
susceptibility by a disk assay. The WGS (FASTQ) data from a short-read sequencing on fifty isolates
was used for (1) phenotype prediction, (2) genotype assignment, and (3) phylogenomic clustering.
Our data show that sequence types (STs) 34, 11 and 469 are the most predominant ST. The most
prevalence serovars are Enteritidis, Rissen, and Typhimurium, respectively. Most NTS isolates are
resistant to aminoglycoside, fluoroquinolone and microcin. Most NTS isolates harbored common
Salmonella pathogenicity islands (SPIs). Moreover, we used the long-read sequencing by Oxford
Nanopore MinION Mk1C system to analyze the genes on chromosome and plasmids of multidrug
resistance five NTS isolates. Our long-read data exhibited the complete genome sequence on both
chromosome and plasmids. In conclusion, we can develop a pipeline of genomic analysis for
Salmonella here at Faculty of Medicine, Chiang Mai University including a human resource (Dr.
Songphon B.) in this pilot study. However, the interpretation of the Salmonella genomics data
needs further development.
