Abstract
ObjectiveSalmonella Typhimurium is the most dominant Salmonella serovar around the world. It is associated with foodborne gastroenteritis outbreaks but has recently been associated with invasive illness and deaths. Characterization of S. Typhimurium is therefore very crucial for epidemiological surveillance. Phage typing has been used for decades for subtyping of S. Typhimurium to determine the epidemiological relation among isolates. Recent studies however have suggested that high throughput clustered regular interspaced short palindromic repeats (CRISPR) typing has the potential to replace phage typing. This study aimed to determine the efficacy of high-throughput CRISPR typing over conventional phage typing in epidemiological surveillance and outbreak investigation of S. Typhimurium.ResultsIn silico analysis of whole genome sequences (WGS) of well-documented phage types of S. Typhimurium reveals the presence of different CRISPR type among strains belong to the same phage type. Furthermore, different phage types of S. Typhimurium share identical CRISPR type. Interestingly, identical spacers were detected among outbreak and non-outbreak associated DT8 strains of S. Typhimurium. Therefore, CRISPR typing is not useful for the epidemiological surveillance and outbreak investigation of S. Typhimurium and phage typing, until it is replaced by WGS, is still the gold standard method for epidemiological surveillance of S. Typhimurium.
Highlights
Salmonellosis is one of the most common causes of foodborne disease worldwide
Typhimurium and phage typing, until it is replaced by whole genome sequences (WGS), is still the gold standard method for epidemiological surveillance of S
Typhimurium in order to determine the efficacy of high-throughput clustered regular interspaced short palindromic repeats (CRISPR) and CRISPOL typing over conventional phage typing in epidemiological surveillance of S
Summary
In silico analysis of genome sequences of control and well documented phage types of S. Typhimurium that belong to phage type DT1 including strains DT1, TM 68-619 and TM 65-111 have different spacers and subsequently show different CRISPR/CRISPOL type; 8579/430, 2536/54 and 7387/90 respectively. Typhimurium belong to different phage types such as DT99, DT56, U319 and DT40 (S05-2864) have identical spacer sequences and identical CRISPR/ CRISPOL type (7433/14). Typhimurium belong to phage type DT120 have different spacers and subsequently different CRISPR/CRISPOL type including S02-3776 (9921/1759), 07_2198 (9911/1753), M16-2000 (9510/1428), and S/20160374 (322/1). Some strains belong to phage types DT120 (S/20160374 and S/20160407), DT20a (MS150110), DT193 (MS150007) and untypable strain (MS150097) have identical spacers and share the same CRISPR/ CRISPOL type (322/1). Other strains belong to phage type DT135 show different spacers and subsequently different CRISPR/CRISPOL type; 5753/396 in DT135 and 3247/66 in MS150100 (Table 2). Different phage types including DT7, DT193, U311, DT41 showed identical CRISPOL type as ‘1’ (Table 3)
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