Development of a Genoserotyping Method for Salmonella Infantis Detection on the Basis of Pangenome Analysis

Abstract

In recent years, Salmonella Infantis has become a predominant serovariant in clinical and poultry isolates, thereby imposing a substantial economic burden on both public health and the livestock industry. With the aim of coping with the steep increase in serovar Infantis prevalence, a polymerase chain reaction (PCR)-based rapid and accurate diagnostic assay was developed in this study through pangenome profiling of 60 Salmonella serovars. A gene marker, SIN_02055, was identified, which is present in the S. Infantis genome but not in the pangenome of the other serovars. Primers specific to SIN_02055 were used to accurately detect serovar Infantis, and to successfully differentiate Infantis from the other 59 serovars in real-time PCR with a R2 of 0.999 and an efficiency of 95.76%. The developed method was applied to 54 Salmonella strains belonging to eight dominant serovars, and distinguished Infantis from the other seven serovars with an accuracy of 100%. The diagnostic primer set also did not show false positive amplification with 32 strains from eight non-Salmonella bacterial species. This cost-effective and rapid method can be considered an alternative to the classic serotyping using antisera.

Rapid Real-Time Polymerase Chain Reaction for Salmonella Serotyping Based on Novel Unique Gene Markers by Pangenome Analysis

“…Based on the pangenome analysis, serovar-specific primer pairs that can accurately detect Salmonella serovars were developed ( Table 3 ). An Infantis-specific primer pair was developed in the previous study ( Yang et al, 2021 ).…”

“…primer pairs that can accurately detect Salmonella serovars were developed (Table 3). An Infantis-specific primer pair was developed in the previous study (Yang et al, 2021). In this study, our method was applied against 232 Salmonella strains.…”

“…As a result of these limitations, serotyping by antigenic agglutination and biochemical tests has been replaced by molecular serotyping ( Zhang et al, 2019 ). For the rapid diagnosis or tracking of Salmonella serovars, epidemiological investigations have been conducted by molecular serotyping analysis based on pulsed-field gel electrophoresis, plasmid profiles, and polymerase chain reactions (PCRs) ( Ozdemir and Acar, 2014 ; Gad et al, 2018 ; Yang et al, 2021 ). Notably, the PCR-based method is widely used for early diagnosis because it can diagnose a few bacteria in the specimen and can yield rapid results.…”

Rapid Detection of Salmonella Enteritidis, Typhimurium, and Thompson by Specific Peak Analysis Using Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry

“…The serotypes of the isolates used in this study were confirmed using a traditional serotyping method, as described in a previous study [ 1 ], and compared with the results of MALDI–TOF MS. Serology was performed using slide agglutination tests with commercial monovalent or polyvalent somatic O and flagellar H antisera (Difco), according to the manufacturer’s instructions. Serovars of isolates were determined using antigenic formulae based on the White–Kauffmann–Le Minor scheme [ 9 ].…”

“…Salmonella , one of the main causes of foodborne diseases, is a significant public health concern. Salmonella is known to be spread primarily through the consumption of contaminated food or water [ 1 , 2 , 3 ]. Salmonella infection can cause serious illness in humans, especially infants and the elderly, causing diseases such as typhoid fever and gastroenteritis and even leading to death [ 4 ].…”