Abstract
Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), is a global health concern and its treatment is problematic due to the rise in antimicrobial resistance (AMR). Rapid detection of patients infected with AMR positive S. Typhi is, therefore, crucial to prevent further spreading. Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated genes (CRISPR-Cas), is an adaptive immune system that initially was used for typing purposes. Later, it was discovered to play a role in defense against phages and plasmids, including ones that carry AMR genes, and, at present, it is being explored for its usage in diagnostics. Despite the availability of whole-genome sequences (WGS), very few studied the CRISPR-Cas system of S. Typhi, let alone in typing purposes or relation to AMR. In the present study, we analyzed the CRISPR-Cas system of S. Typhi using WGS data of 1059 isolates obtained from Bangladesh, India, Nepal, and Pakistan in combination with demographic data and AMR status. Our results reveal that the S. Typhi CRISPR loci can be classified into two groups: A (evidence level >2) and B (evidence level ≤2), in which we identified a total of 47 unique spacers and 15 unique direct repeats. Further analysis of the identified spacers and repeats demonstrated specific patterns that harbored significant associations with genotype, demographic characteristics, and AMR status, thus raising the possibility of their usage as biomarkers. Potential spacer targets were identified and, interestingly, the phage-targeting spacers belonged to the group-A and plasmid-targeting spacers to the group-B CRISPR loci. Further analyses of the spacer targets led to the identification of an S. Typhi protospacer adjacent motif (PAM) sequence, TTTCA/T. New cas-genes known as DinG, DEDDh, and WYL were also discovered in the S. Typhi genome. However, a specific variant of the WYL gene was only identified in the extensively drug-resistant (XDR) lineage from Pakistan and ciprofloxacin-resistant lineage from Bangladesh. From this work, we conclude that there are strong correlations between variations identified in the S. Typhi CRISPR-Cas system and endemic AMR positive S. Typhi isolates.
Highlights
IntroductionTyphoid fever is a systemic enteric infection, caused by Salmonella enterica serovar Typhi
Typhoid fever is a systemic enteric infection, caused by Salmonella enterica serovar Typhi (S.Typhi), a human-restricted bacterial pathogen [1,2]
We further identified unique spacer targets in bacteriophages and plasmids that led to the identification of a specific protospacer adjacent motif (PAM) sequence for S
Summary
Typhoid fever is a systemic enteric infection, caused by Salmonella enterica serovar Typhi Typhi), a human-restricted bacterial pathogen [1,2]. It is estimated to lead to 117 thousand deaths and 11 million episodes of illnesses every year and remains a major global public health concern [3]. Typhi makes typhoid fever highly endemic in areas with poor water and sanitation systems, especially the South Asian countries such as Bangladesh, India, Nepal, and Pakistan [3,4]. Treating typhoid fever has become harder, because of the increasing antimicrobial resistance (AMR) [5]. A highly clonal and extensively drug-resistant (XDR)
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