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

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.

Salmonella Contamination in Ready-to-Eat Tilapia Sashimi Processing Plants.

In this study, we investigated contamination rates and possible contamination routes of Salmonella in two typical tilapia sashimi processing plants in Taiwan. We found that the overall isolation rate was 5.0% ( n = 61), from a total of 1,218 samples collected in a year from different processing sections (freezing, scaling and bleeding, visceral removal, washing and disinfection, and packaging) and from different operating times (before processing and 3 and 6 h after processing began). In plant A, which is a relatively well-operated plant compared with plant B, Salmonella was only found in the freezing, scaling and bleeding, and visceral removal sections, with isolation rates ranging from 0 to 9.3%. No Salmonella was identified in the final ready-to-eat products at plant A. In plant B, Salmonella was found in all sections and in the final products, with isolation rates ranging from 4.6 to 36.1%. Regarding the processing times, the contamination rates increased significantly ( P < 0.05) 3 h after processing began in plant B. Among the isolates, 10 serotypes were detected, some of which are commonly observed in human salmonellosis cases in Taiwan, indicating a risk of zoonoses. However, only four isolates showed antimicrobial resistance in the current study. With molecular subtyping, we observed accumulated and persistent Salmonellae contamination patterns in plant B. These results suggest that inadequate sanitation impairs the foodborne pathogen control program in tilapia sashimi plants.