Comparative genome analysis of 15 clinical Shigella flexneri strains regarding virulence and antibiotic resistance


Shigellosis is the major cause of dysentery globally. It is mainly attributed to two Shigella species, Shigella sonnei and Shigella flexneri, which leads to approximately 165 million infections and 1.1 million deaths each year. Rapid increase and widening of spectrum in antibiotics resistance make Shigella hard to be adequately controlled through existing prevention and treatment measures. It has also been observed that enhanced virulence and advent of antibiotic resistance (AR) could arise almost simultaneously. However, genetic linkages between the two factors are missing or largely ignored, which hinders experimental verification of the relationship. In this study, we sequenced 15 clinically isolated S. flexneri strains. Genome assembly, annotation and comparison were performed through routine pipelines. Differential resistant profiles of all 15 S. flexneri strains to nine antibiotics were experimentally verified. Virulence factors (VFs) belonging to 4 categories and 31 functional groups from the Virulence Factor Database (VFDB) were used to screen all Shigella translated CDSs. Distribution patterns of virulence factors were analysed by correlating with the profiles of bacterial antibiotics resistance. In addition, multi-resistant S. flexneri strains were compared with antibiotic-sensitive strains by focusing on the abundance or scarcity of specific groups of VFs. By doing these, a clear view of the relationships between virulence factors and antibiotics resistance in Shigella could be achieved, which not only provides a set of genetic evidence to support the interactions between VFs and AR but could also be used as a guidance for further verification of the relationships through manipulating specific groups of virulence factors.


15 newly sequenced S. flexneri genomes isolated from clinical samples were assembled, annotated and compared by following several standardized genome analysis pipelines [16],[19],[20]. We then identified strain-specific differences in the gain and loss of putative virulence factors in this preliminary study. In addition, abundance of certain functional groups of virulence factors is positively correlated with the extent of antibiotic resistance based on the comparison of the highly resistant and susceptible strains. Several groups of virulence factors were highlighted due to their tight relationships with strong resistant phenotypes, such as chaperone usher and T3SS, etc. Although virulence and resistance develop on different timescales and share no much common mechanisms, they may share some common characteristics [29]. Thus, antibiotic resistance and virulence are likely to have synergistic effects toward efficiently exploiting host cells in order to reproduce and transmit extensively. However, association between virulence and resistance is an increasing problem and the answer to this question is becoming more beneficial for pathogenic bacteria [29]. This study provides a starting point to address the question of how virulence and antibiotic resistance may interplay in Shigella flexneri by looking into the subtle classification of virulence factors into 31 functional groups. Although the result would be much more convincing if we can incorporate other Shigella flexneri genomes from the public database (1121 sub-strains in PATRIC database version 3.5.39) into the study, antibiotic resistance and susceptibility phenotype data for these strains are largely missing, which greatly hinders the understanding of the interactions between the two factors. Thus, in further studies, more antibiotic resistance phenotypes should be deposited into database, together with virulence phenotypes and genomic data. In addition, fitness costs should also be incorporated to tackle the intriguing relationship among virulence, stress resistance, and antibiotic resistance from the bioinformatics point of view.

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