Genomic serotyping, clinical manifestations, and antimicrobial resistance of non-typhoidal Salmonella gastroenteritis in hospitalized children in Ho Chi Minh City, Vietnam


Vu Thuy DuongHao Chung TheTran Do Hoang NhuHa Thanh TuyenJames I CampbellPham Van MinhHoang Le PhucTran Thi Hong ChauNguyen Minh NgocLu Lan ViAlison E MatherStephen Baker


Nontyphoidal Salmonella (NTS) are among the most common aetiological agents of diarrhoeal diseases worldwide and have become the most commonly detected bacterial pathogen in children hospitalised with diarrhoea in Vietnam. Aiming to better understand the epidemiology, serovar distribution, antimicrobial resistance (AMR), and clinical manifestation of NTS gastroenteritis in Vietnam, we conducted a clinical genomics investigation of NTS isolated from diarrheal children admitted to one of three tertiary hospitals in Ho Chi Minh City. Between May 2014 and April 2016, 3,166 children hospitalized with dysentery were recruited into the study; 478 (∼15%) children were found to be infected with NTS by stool culture. Molecular serotyping of the 450 generated genomes identified a diverse collection of serogroups (B, C1, C2-C3, D1, E1, G, I, K, N, O, Q); however, S. Typhimurium was the most predominant serovar, accounting for 41.8% (188/450) of NTS isolates. We observed a high prevalence of AMR to first line treatments recommended by WHO and more than half (53.8%, 242/450) of NTS isolates were multi-drug resistant (MDR; resistant to ≥3 antimicrobial classes). AMR gene detection positively correlated with phenotypic AMR testing, and resistance to empirical antimicrobials was associated with a significantly longer hospitalization (0.91 days, p=0.04). Our work shows that genome sequencing is a powerful epidemiological tool to characterize the serovar diversity and AMR profiles in NTS. We propose a revaluation of empirical antimicrobials for dysenteric diarrhoea and endorse the use of whole genome sequencing for sustained surveillance of NTS internationally.

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