High-throughput analysis of Yersinia pseudotuberculosis gene essentiality in optimised in vitro conditions, and implications for the speciation of Yersinia pestis

Abstract

BackgroundYersinia pseudotuberculosis is a zoonotic pathogen, causing mild gastrointestinal infection in humans. From this comparatively benign pathogenic species emerged the highly virulent plague bacillus, Yersinia pestis, which has experienced significant genetic divergence in a relatively short time span. Much of our knowledge of Yersinia spp. evolution stems from genomic comparison and gene expression studies. Here we apply transposon-directed insertion site sequencing (TraDIS) to describe the essential gene set of Y. pseudotuberculosis IP32953 in optimised in vitro growth conditions, and contrast these with the published essential genes of Y. pestis.ResultsThe essential genes of an organism are the core genetic elements required for basic survival processes in a given growth condition, and are therefore attractive targets for antimicrobials. One such gene we identified is yptb3665, which encodes a peptide deformylase, and here we report for the first time, the sensitivity of Y. pseudotuberculosis to actinonin, a deformylase inhibitor. Comparison of the essential genes of Y. pseudotuberculosis with those of Y. pestis revealed the genes whose importance are shared by both species, as well as genes that were differentially required for growth. In particular, we find that the two species uniquely rely upon different iron acquisition and respiratory metabolic pathways under similar in vitro conditions.ConclusionsThe discovery of uniquely essential genes between the closely related Yersinia spp. represent some of the fundamental, species-defining points of divergence that arose during the evolution of Y. pestis from its ancestor. Furthermore, the shared essential genes represent ideal candidates for the development of novel antimicrobials against both species.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1189-5) contains supplementary material, which is available to authorized users.

Genome-wide assessment of antimicrobial tolerance in Yersinia pseudotuberculosis under ciprofloxacin stress

“…This confirmed that the genes are not essential for survival of Y. pseudotuberculosis under in vitro growth conditions, as suggested by our previously published TraDIS data [18].…”

“…pseudotuberculosis strain IP32953 was previously used to generate a transposon library of approximately 40 000 unique insertion mutants using the Ez-Tn 5 Kan2 transposome complex (Epicentre) as described and validated by Willcocks et al . [18].…”

“…Library preparation for Illumina MiSeq sequencing was performed as described by Willcocks et al . [18] and reads were mapped against the reference genome (European Molecular Biology Laboratory accession number: BX936398).…”

“…We recently constructed and validated a TraDIS library in Y. pseudotuberculosis to identify the genes required for growth in optimized in vitro conditions [18]. In the present work, we utilize this resource to establish, for the first time, the genes involved in resistance to ciprofloxacin stress in enterobacteria.…”

Higher genome variability within metabolism genes associates with recurrent Clostridium difficile infection

“…For instance, in pathogenic Streptococcus agalactiae , the core genome constitutes about 80% of the whole genome, in Helicobacter pylori 77 and 46% in Streptococcus pneumoniae [ 35 ]. On the other hand, the size of the core and essential genome was estimated to be composed of 404 genes [ 36 ], a number comparable to other bacterial species, such as Pseudomonas aeruginosa (321 genes [ 37 ]) and Yersinia pestis (about 500 genes [ 38 ]).…”