Corrected Genome Annotations Reveal Gene Loss and Antibiotic Resistance as Drivers in the Fitness Evolution of Salmonella enterica Serovar Typhimurium.

摘要: ABSTRACT Horizontal acquisition of novel chromosomal genes is considered to be a key process in the evolution bacterial pathogens. However, identification gene presence or absence could hindered by inconsistencies genome annotations. Here, we performed cross-annotation omnipresent core and mosaic accessory chromosome Salmonella enterica serovar Typhimurium across total 20 fully assembled genomes deposited into GenBank. Cross-annotation resulted 32% increase number 3-fold decrease identified as (i.e., present some strains only) original annotation. Of remaining noncore genes, vast majority were prophage 255 nonphage actually origin but lost upon emergence S. serovar, suggesting that portion acquired very limited other than prophages. Only horizontally related fitness virulence found four recently sequenced isolates, all located on three different genomic islands harbor multidrug resistance determinants. Thus, extensive use antimicrobials main selection force behind new pathotypes. IMPORTANCE Significant discrepancies annotations mislead conclusions about evolutionary demonstrate here via cross-annotation-based analysis from We conclude despite being able infect broad range vertebrate hosts, diversity almost exclusively loss transfer DNA. after are linked harboring factors. Since factors lead increased virulence, this poses an important research question: overuse misuse act forces for more pathogenic Salmonella?