Genomic and phylogenetic analysis ofSalmonellaTyphimurium and its monophasic variants responsible for invasive endemic infections in Colombia

Abstract

Salmonellosis is an endemic human infection, associated with both sporadic cases and outbreaks throughout Colombia. Typhimurium is the most common Colombian serovar of Salmonella enterica, responsible for 32.5% of the Salmonella infections. Whole genome sequencing (WGS) is being used increasingly in Europe and the USA to study the epidemiology of Salmonella, but there has not yet been a WGS-based analysis of Salmonella associated with bloodstream infection in Colombia. Here, we analysed 209 genome sequences of Colombian S. Typhimurium and monophasic S. 4,[5],12:i:-isolates from Colombia from 1999 to 2017. We used a core genome-based maximum likelihood tree to define seven distinct clusters which were predominantly Sequence Type (ST) 19isolates. We also identified the first ST313 and monophasic ST34 isolates to be reported in Colombia. The history of each cluster was reconstructed with a Bayesian tree to reveal a timeline of evolution. Cluster 7 was closely related to European multidrug-resistant (MDR) DT104. Cluster 4 became the dominant variant of Salmonella in 2016, and resistance to nalidixic acid was associated with a plasmid-encoded qnrB19 gene. Our findings suggest multiple transfers of S. Typhimurium between Europe and Colombia.

Class 1 integrons in clinical and swine industry isolates of Salmonella Typhimurium from Colombia, dating 1997 to 2017

“…Regarding the integrons located in SGI-1 variants, the result are agree with that in Colombia circulated the pandemic S. Typhimurium MDR DT104 (Li et al, 2019), but with variations during the time. Surveillance of isolates associated with the S. Typhimurium MDR DT104 pandemic showed the same MDR signature of this phage type, which were also identified within the global time line in which it appeared and spread throughout the world (Leekitcharoenphon et al, 2016).…”

“…Regarding clonality, the 30 S. Typhimurium isolates belong to worldwide spread ST19 that circulates in Colombia (Li et al, 2019) and the SNP phylogenetic analysis suggests that the different mobile elements identified in this study affect the subpopulations lineages. We observed that the 11 S. Typhimurium isolates bearing IntI1-Col1 belong to a subclonal lineage (Figure 5A), whereas the isolates with SGI-1 grouped in another branch (Figure 5B).…”

“…The isolates were resistant from 1 to 5 antimicrobial families with a total of 51 antimicrobial-resistant profiles, most of them were multidrug-resistant profiles (see Table S1 and the data published by Li et. al., 2019 (S1 Table-metadata of the samples (Li et al ., 2019)).…”

Genotypic Characterization of Antimicrobial Resistant Salmonella spp. Strains from Three Poultry Processing Plants in Colombia

“…Furthermore, S. Paratyphi B was the second most frequently isolated serotype among all Salmonella isolates, and were distributed throughout the different processing sites. Previously published work reported that S. Paratyphi B dT+ and S. Heidelberg were the most prevalent serotypes isolated from farms and retail meat samples in Colombia during 2008 and 2009 [28]. There were also three S. Typhimurium ST19 strains isolated from plant B with a high abundance of AMR genes.…”

“…isolates recovered from retailed chicken carcasses in Bogota. Another study conducted by the same group [28] reported the AMR profiles of 378 Salmonella spp. isolates from chicken carcasses available in wet markets, supermarkets, and independent markets, collected in six different Departments.…”