Genomic Serotyping, Clinical Manifestations, and Antimicrobial Resistance of Nontyphoidal Salmonella Gastroenteritis in Hospitalized Children in Ho Chi Minh City, Vietnam

Abstract

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.

The Gut Microbiome of Healthy Vietnamese Adults and Children Is a Major Reservoir for Resistance Genes Against Critical Antimicrobials

“…Additionally, cephalosporins are a commonly used antimicrobial class in Vietnam [ 6 ] and we detected bla CMY , bla SHV, and bla TEM in the fecal samples. More specifically, we identified bla CTX-M , a group of ESBL genes that have been commonly found in a range of enteric pathogens, including Shigella and Salmonella [ 12 , 34 ], in several samples from young children. The diversity of AMR genes identified corroborates with a previous study conducted in untreated sewage from countries with different economic backgrounds, which concluded that the global distribution of AMR genes is not only dependent on the socioeconomic status of each country, but also that Vietnam is one of the countries with the most divergent distribution of AMR genes [ 35 ].…”

Genomic Characterization of Multidrug-Resistant Salmonella Serovars Derby and Rissen From the Pig Value Chain in Vietnam

“…Furthermore, MDR Salmonella species are also widely disseminated in Vietnamese pigs (5,8), poultry (13), seafood (5), and humans (41). In our study, 69% of the strains were MDR, and S. Derby carried more ARGs than S. Rissen.…”

“…FosA was included recently in the Resfinder database, which determines the importance of keeping track of the updates of public databases (43). No ESBL-and AmpC-producing isolates were detected in our study, whereas in other published studies in Vietnam, such strains were also detected in pigs (5) and in humans (41). One isolate carried mcr-1 (Table 3), which was also detected in Vietnamese pigs (8) and poultry samples (14).…”

“…Genes tetA and/or tetM were identified in all isolates (Table 3), such as in pigs, sampled in 2019 in the same country (13). The bla TEM.1 and/or bla LAP, genes were detected in 65.21% (Table 3) of the isolates, which were also identified in Vietnamese Salmonella strains identified in pigs (13) and humans (41). Almost all ARGs detected in those studies were previously observed in Vietnamese strains (13,41).…”

“…The bla TEM.1 and/or bla LAP, genes were detected in 65.21% (Table 3) of the isolates, which were also identified in Vietnamese Salmonella strains identified in pigs (13) and humans (41). Almost all ARGs detected in those studies were previously observed in Vietnamese strains (13,41). The exception was the detection of fosA7.3; this gene was found in 56.5% of the samples.…”