Identification of Genes to Differentiate Closely Related Salmonella Lineages

Abstract

Background Salmonella are important human and animal pathogens. Though highly related, the Salmonella lineages may be strictly adapted to different hosts or cause different diseases, from mild local illness like gastroenteritis to fatal systemic infections like typhoid. Therefore, rapid and accurate identification of Salmonella is essential for timely and correct diagnosis of Salmonella infections. The current identification methods such as 16S rRNA sequencing and multilocus sequence typing are expensive and time consuming. Additionally, these methods often do not have sufficient distinguishing resolution among the Salmonella lineages.Methodologies/Principal FindingsWe compared 27 completely sequenced Salmonella genomes to identify possible genomic features that could be used for differentiation of individual lineages. We concatenated 2372 core genes in each of the 27 genomes and constructed a neighbor-joining tree. On the tree, strains of each serotype were clustered tightly together and different serotypes were unambiguously separated with clear genetic distances, demonstrating systematic genomic divergence among the Salmonella lineages. We made detailed comparisons among the 27 genomes and identified distinct sets of genomic differences, including nucleotide variations and genomic islands (GIs), among the Salmonella lineages. Two core genes STM4261 and entF together could unambiguously distinguish all Salmonella lineages compared in this study. Additionally, strains of a lineage have a common set of GIs and closely related lineages have similar sets of GIs.Conclusions Salmonella lineages have accumulated distinct sets of mutations and laterally acquired DNA (e.g., GIs) in evolution. Two genes entF and STM4261 have diverged sufficiently among the Salmonella lineages to be used for their differentiation. Further investigation of the distinct sets of mutations and GIs will lead to novel insights into genomic evolution of Salmonella and greatly facilitate the elucidation of pathogeneses of Salmonella infections.

Comparative Genome Analysis of Hungarian and Global Strains of Salmonella Infantis

“…Accordingly, S. Infantis strains of humans and poultry have been studied worldwide (Shahada et al, 2006(Shahada et al, , 2010Cloeckaert et al, 2007;Nógrády et al, 2007Nógrády et al, , 2008Nógrády et al, , 2012Gal-Mor et al, 2010;Dionisi et al, 2011;Tate et al, 2017) and a growing portion of strains proved to be MDR. So far, only few genomic analyses have been reported on different Salmonella serovars (Zou et al, 2013) and S. Infantis strains (Yokoyama et al, 2014), with special regard to MDR S. Infantis of the respective countries (Franco et al, 2015;Hindermann et al, 2017;Szmolka et al, 2018;Acar et al, 2019). Here we provide a comprehensive analysis about the possible relations between S. Infantis strains from different countries and between S. Infantis and other non-Infantis serovars.…”

“…Analyzing "non-Infantis" and "Infantis only" genomes separately confirmed that the distinguishing resolution was generally better in the Infantis only system as compared to the combined analysis on "non-Infantis" plus "Infantis." As the S. Infantis genomes were missing from the analyses of Zou et al (2013), we also wanted to get some idea about possible differentiation of S. Infantis from the main Salmonella serovars. Here we did not only confirm the results of Zou et al (2013) about genetic distances between the tested Salmonella serovars and S. Infantis, but also confirmed our findings on genomic distances between certain lineages of S. Infantis.…”

“…In addition to S. Infantis, genome sequences of 26 Salmonella strains representing 13 most common Salmonella serovars in animals and humans based on the paper of Zou et al (2013) were also included into the analyzes. Each of these serovars was represented by two strains, except Paratyphi, where three strains were included for the biovars A, B, and C ( Supplementary Table S1).…”

In silico Identification of Serovar-Specific Genes for Salmonella Serotyping

“…Recently, with the development of whole-genome sequencing technology, the relevant genomic regions of the rfb gene cluster for O antigen, gene fliC and gene fljB for H antigens, and genes targeted by MLST can be extracted and used for serovar identification. Several studies have identified serovar-specific genes or DNA fragments for serotyping through whole-genome sequencing based genomic comparison (Zou et al, 2013, 2016; Laing et al, 2017). However, these serovar-specific genes or DNA fragments only distinguished a small number of serovars.…”

Quantifying the Survival of Multiple Salmonella enterica Serovars In Vivo via Massively Parallel Whole-Genome Sequencing To Predict Zoonotic Risk

“…Serovars of S. enterica can be identified by various serological and molecular methods, such as serotyping ( 20 ), multiplex PCRs ( 21 – 23 ), and multilocus sequence typing (MLST) ( 24 – 26 ). They can be also distinguished at the genetic level by single nucleotide polymorphisms (SNPs) in conserved genes, such as rpoB ( 27 ), or hypervariable regions within them ( 28 – 30 ), and the discriminatory powers of other genes continue to be explored ( 31 , 32 ). With whole-genome sequencing becoming routine for the surveillance of S. enterica ( 33 – 35 ), there is an ever-increasing database of sequenced strains.…”