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

Chung-Wen Hu,I-Chen Li,Chung-Hsi Chou,Keh-Ming Wu,Rayean Wu,Zeng-Weng Chen

doi:10.3390/microorganisms9102046

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.

Highlights

IntroductionSalmonellosis is a public health concern in both industrialized and developing countries
By using the restriction enzyme XbaI, pulsedfield gel electrophoresis (PFGE) profiling generated from the 24 S. enterica serovar Schwarzengrund isolates identified 14 unique patterns (A through N) (Figure 1), and yielded a discriminatory index (DI) value of 0.938 (Table 2)
Among the 24 isolates examined by multilocus sequence typing (MLST), 16 isolates were assigned to ST96, while eight isolates were clustered together into ST322, resulting in a DI value of 0.463 (Table 2)

Summary

Introduction

Salmonellosis is a public health concern in both industrialized and developing countries. Nontyphoidal Salmonella serovars cause high morbidity and mortality, as well as considerable global economic loss each year [1]. Salmonellosis is characterized by self-limiting gastroenteritis, and usually results from consuming contaminated animal products, such as poultry, meat, eggs, or dairy [2]. As Salmonella can infect human hosts by different sources, accurately identifying and discriminating between isolates is important for global public health authorities to detect outbreaks and track the originating sources [3]. For over 50 years, surveillance data from the Centers for Disease Control and Prevention (CDC) for Salmonella serotype designation have been collected through

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