Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages.

Autor: Jacob JJ; Christian Medical College, Vellore, India., Pragasam AK; Christian Medical College, Vellore, India., Vasudevan K; Christian Medical College, Vellore, India.; REVA University, Bangalore, India., Velmurugan A; Christian Medical College, Vellore, India., Priya Teekaraman M; Christian Medical College, Vellore, India., Priya Thirumoorthy T; Christian Medical College, Vellore, India., Ray P; Post Graduate Institute of Medical & Educational Research, Chandigarh, India., Gupta M; Post Graduate Institute of Medical & Educational Research, Chandigarh, India., Kapil A; All India Institute of Medical Sciences, New Delhi, India., Bai SP; Kanchi Kamakoti Childs Trust Hospital, Chennai, India., Nagaraj S; St. John's Medical College, Bengaluru, India., Saigal K; Chacha Nehru Bal Chikitsalaya, Delhi, India., Chandola TR; Centre for Health Research & Development-Society for Applied Studies, New Delhi, India., Thomas M; Christian Medical College, Ludhiana, India., Bavdekar A; KEM Hospital & Research Centre, Pune, India., Ebenezer SE; The Duncan Hospital, Raxaul, India., Shastri J; Topiwala National Medical College & BYL Nair Charitable Hospital, Mumbai, India., De A; Topiwala National Medical College & BYL Nair Charitable Hospital, Mumbai, India., Dutta S; ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India., Alexander AP; Lady Willingdon Hospital, Manali, India., Koshy RM; Makunda Christian Leprosy & General Hospital, Karimjang, India., Jinka DR; Rural Development Trust Hospital, Bathalapalli, Andhra Pradesh, India., Singh A; Chinchpada Christian Hospital, Nandurbar, India., Srivastava SK; Department of Microbiology, SSN College, University of Delhi, Delhi, India., Anandan S; Christian Medical College, Vellore, India., Dougan G; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom., John J; Christian Medical College, Vellore, India., Kang G; Christian Medical College, Vellore, India., Veeraraghavan B; Christian Medical College, Vellore, India., Mutreja A; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom.
Jazyk: angličtina
Zdroj: PLoS pathogens [PLoS Pathog] 2023 Apr 28; Vol. 19 (4), pp. e1010650. Date of Electronic Publication: 2023 Apr 28 (Print Publication: 2023).
DOI: 10.1371/journal.ppat.1010650
Abstrakt: Paratyphoid fever caused by S. Paratyphi A is endemic in parts of South Asia and Southeast Asia. The proportion of enteric fever cases caused by S. Paratyphi A has substantially increased, yet only limited data is available on the population structure and genetic diversity of this serovar. We examined the phylogenetic distribution and evolutionary trajectory of S. Paratyphi A isolates collected as part of the Indian enteric fever surveillance study "Surveillance of Enteric Fever in India (SEFI)." In the study period (2017-2020), S. Paratyphi A comprised 17.6% (441/2503) of total enteric fever cases in India, with the isolates highly susceptible to all the major antibiotics used for treatment except fluoroquinolones. Phylogenetic analysis clustered the global S. Paratyphi A collection into seven lineages (A-G), and the present study isolates were distributed in lineages A, C and F. Our analysis highlights that the genome degradation events and gene acquisitions or losses are key molecular events in the evolution of new S. Paratyphi A lineages/sub-lineages. A total of 10 hypothetically disrupted coding sequences (HDCS) or pseudogenes-forming mutations possibly associated with the emergence of lineages were identified. The pan-genome analysis identified the insertion of P2/PSP3 phage and acquisition of IncX1 plasmid during the selection in 2.3.2/2.3.3 and 1.2.2 genotypes, respectively. We have identified six characteristic missense mutations associated with lipopolysaccharide (LPS) biosynthesis genes of S. Paratyphi A, however, these mutations confer only a low structural impact and possibly have minimal impact on vaccine effectiveness. Since S. Paratyphi A is human-restricted, high levels of genetic drift are not expected unless these bacteria transmit to naive hosts. However, public-health investigation and monitoring by means of genomic surveillance would be constantly needed to avoid S. Paratyphi A serovar becoming a public health threat similar to the S. Typhi of today.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2023 Jacob et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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