Antimicrobial resistance, plasmid, virulence, multilocus sequence typing and pulsed-field gel electrophoresis profiles of Salmonella enterica serovar Typhimurium clinical and environmental isolates from India.

Priyanka Jain,Sudhanthiramani Sudhanthirakodi,Shanta Dutta,Ujjwayni Ray,Goutam Chowdhury,Shalini Anandan,Sangeeta Joshi,Asish Mukhopadhyay,Yung-Fu Chang

doi:10.1371/journal.pone.0207954

Abstract

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common serovar associated with non-typhoidal salmonellosis globally. However, there is insufficient data on molecular characterization of S. Typhimurium isolates from India. This study was undertaken to determine the antimicrobial resistance (AMR), plasmid, virulence profiles and molecular subtypes of S. Typhimurium Indian isolates (n = 70) of clinical and environmental origin isolated during 2010–2017. Antimicrobial susceptibility and minimum inhibitory concentrations were determined by disc diffusion and E-test methods respectively. Plasmid extraction was done following standard protocol. AMR genes, virulence genes and plasmid incompatibility types were detected by PCR; Pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) were used for molecular subtyping. Majority (57%) of the study isolates was pan susceptible; five AMR profiles were observed among the resistant (43%) isolates. AMR was significantly (p = 0.004) associated with extra-intestinal isolates than intestinal isolates.The class 1 integron and plasmid-mediated quinolone resistance genes (qnrB1, qnrS1) in the resistant isolates were transferable by conjugation. Plasmids (≥1) ranging from 1.9 to 254kb size and of IncFIIS and/or FIB type were found in most isolates. A total of 39 pulsotypes by PFGE and four sequence types by MLST like ST36 (55.7%), ST19 (32.9%), ST313 (10%) and ST213 (1.4%) were observed. ST36 and ST19 were found circulating in both clinical and environmental host, while ST313 isolates had an exclusive clinical origin. All ST19 isolates (100%) were drug-resistant, while isolates belonging to ST313 (100%), ST213 (100%) and ST36 (82%) were pan susceptible. The virulence plasmid (VP) genes (spvB- spvC) were present in all genotypes except ST36. The VP was significantly (p<0.001) associated with extra-intestinal than intestinal isolates. Some environmental and clinical isolates were clonal indicating their zoonotic transmission. Knowledge on the molecular subtypes and AMR profiles of locally prevalent Salmonella serotypes is important for effective control of spread of resistant organisms. The MLST of S. Typhimurium isolates and its association with AMR, virulence profiles was not reported earlier from India.

Highlights

Non-typhoidal Salmonella (NTS) infections represent a major zoonotic public health problem worldwide
Typhimurium study isolates were pan susceptible to all antimicrobials tested, while thirty (42.9%) isolates showed resistance to at least one antimicrobial
The study provides a brief overview of the antimicrobial resistance (AMR), plasmid, virulence profiles as well as multi-locus sequence typing (MLST) and Pulsed-field gel electrophoresis (PFGE) subtypes of S

Summary

Introduction

Non-typhoidal Salmonella (NTS) infections represent a major zoonotic public health problem worldwide. Enteritidis causing human infections across the globe [1, 2]. Typhimurium infections have been more commonly reported from sub-Saharan African countries, where it is an important cause of morbidity and mortality in children under 5 years of age, second only to pneumococcal pneumonia [3, 4]. It has been implicated in causing several foodborne outbreaks in adults [5, 6] as well as diarrhoeal and/or septicaemic outbreaks in neonates and pediatrics [7, 8]

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