Comparison of Conventional Molecular and Whole-Genome Sequencing Methods for Differentiating Salmonella enterica Serovar Schwarzengrund Isolates Obtained from Food and Animal Sources

Abstract

Over the last decade, Salmonella enterica serovar Schwarzengrund has become more prevalent in Asia, Europe, and the US with the simultaneous emergence of multidrug-resistant isolates. As these pathogens are responsible for many sporadic illnesses and chronic complications, as well as outbreaks over many countries, improved surveillance is urgently needed. For 20 years, pulsed-field gel electrophoresis (PFGE) has been the gold standard for determining bacterial relatedness by targeting genome-wide restriction enzyme polymorphisms. Despite its utility, recent studies have reported that PFGE results correlate poorly with that of closely related outbreak strains and clonally dominant endemic strains. Due to these concerns, alternative amplification-based molecular methods for bacterial strain typing have been developed, including clustered regular interspaced short palindromic repeats (CRISPR) and multilocus sequence typing (MLST). Furthermore, as the cost of sequencing continues to decrease, whole genome sequencing (WGS) is poised to replace other molecular strain typing methods. In this study, we assessed the discriminatory power of PFGE, CRISPR, MLST, and WGS methods to differentiate between 23 epidemiologically unrelated S. enterica serovar Schwarzengrund isolates collected over an 18-year period from distinct locations in Taiwan. The discriminatory index (DI) of each method for different isolates was calculated, resulting in values between 0 (not discriminatory) and 1 (highly discriminatory). Our results showed that WGS has the greatest resolution (DI = 0.982) compared to PFGE (DI = 0.938), CRISPR (DI = 0.906), and MLST (DI = 0.463) methods. In conclusion, the WGS typing approach was shown to be the most sensitive for S. enterica serovar Schwarzengrund fingerprinting.

Comparison of Reference-Based Assembly and De Novo Assembly for Bacterial Plasmid Reconstruction and AMR Gene Localization in Salmonella enterica Serovar Schwarzengrund Isolates

“…Hence, in the current study, a strategy to reconstruct bacterial plasmids and fully characterize the presence of AMR genes and their genomic location in S. enterica serovar Schwarzengrund isolates was developed. Moreover, as a follow-up study, three multidrug-resistant S. enterica serovar Schwarzengrund isolates with multiple plasmids of different size ranges were chosen for in-depth characterization [17,18].…”

“…Three multidrug-resistant Salmonella enterica serovar Schwarzengrund strains (SS09, SS12, and SS15) with multiple plasmids isolated from animal sources were prepared according to our previous studies [17,18] (Table S1). In brief, these strains were revived in tryptic soy broth and grown overnight at 37 °C.…”

Antimicrobial Drug-Resistant Salmonella in Urban Cats: Is There an Actual Risk to Public Health?

“…In humans, infections caused by Salmonella spp. are associated with severe food-borne illnesses, especially in the case of acute gastroenteritis, which is caused by consuming contaminated water and food products [8,9].…”