Extensive inter-strain diversity among clinical isolates of Shigella flexneri with reference to its serotype, virulence traits and plasmid incompatibility types, a study from south India over a 6-year period

BACKGROUND: Shigella has evolved as a result of acquiring extragenetic material through horizontal gene exchange. These aid in the rapid emergence of bacterial inter-strain diversity in virulence factors and serotype variants through O-antigenic switching. Plasmid incompatibility typing of isolates is insightful in understanding local expansion of virulence plasmids, as whether virulence dissemination involves diverse plasmids or one dominant ‘epidemic’ type. The broad question underlying this study was that of how inter-strain genetic, serotype and plasmid incompatibility type variations can help understand the emergence of Shigella as a highly virulent pathogen. RESULTS: A total of 101 confirmed isolates of S. flexneri were included in this study. The distribution of the subtypes were variable, type 2a (48/101, 47.5%), type 6 (15/101, 14.9%), type 1b (8/101, 7.9%), type 1 variant (7/101, 6.9%), type 3b (12/101, 11.9% 0, type 4 (6/101, 6.0%), variant Y (2/101, 1.9%) and variant X (1/101, 1%). All had the ipaH gene (101/101, 100%) followed by ompA (92/101, 91.1%), ial (84/101, 83.4%), sen (82/101, 81.2%), virF (84/101, 83.2%), set1A and set1B (59/101, 58.4%). Out of the total of 49 isolates that showed all the virulence related genes studied here the IncIγ plasmid was detected in all isolates studied followed by FII (33/49, 67.3%), FIIS (20/49, 40.8%). Inc K was positive in two isolates (2/49, 4%) studied. The inc groups IncI1-α, Inc T were detected in 1 isolate each and Inc L and Inc P formed part of the multireplicon in the same isolate. CONCLUSIONS: In order to estimate the burden of the disease caused by the new serotypes, it is important to have knowledge of the locally prevalent serotype. This will prove helpful in developing strategies for prevention of same especially since, the immunity in such diseases is serotype specific. Thus, the emergence of non-typable atypical serotypes of S. flexneri from natural infections needs to be investigated further. This study highlights the emergence of genetic variants exhibiting resistance to many antibiotics which needs to be studied for understanding the ever-changing landscape of this pathogen. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13099-019-0314-9) contains supplementary material, which is available to authorized users.