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Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages
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 examin...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10171690/ https://www.ncbi.nlm.nih.gov/pubmed/37115804 http://dx.doi.org/10.1371/journal.ppat.1010650 |
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author | Jacob, Jobin John Pragasam, Agila K Vasudevan, Karthick Velmurugan, Aravind Priya Teekaraman, Monisha Priya Thirumoorthy, Tharani Ray, Pallab Gupta, Madhu Kapil, Arti Bai, Sulochana Putil Nagaraj, Savitha Saigal, Karnika Chandola, Temsunaro Rongsen Thomas, Maria Bavdekar, Ashish Ebenezer, Sheena Evelyn Shastri, Jayanthi De, Anuradha Dutta, Shantha Alexander, Anna P. Koshy, Roshine Mary Jinka, Dasaratha R. Singh, Ashita Srivastava, Sunil Kumar Anandan, Shalini Dougan, Gordon John, Jacob Kang, Gagandeep Veeraraghavan, Balaji Mutreja, Ankur |
author_facet | Jacob, Jobin John Pragasam, Agila K Vasudevan, Karthick Velmurugan, Aravind Priya Teekaraman, Monisha Priya Thirumoorthy, Tharani Ray, Pallab Gupta, Madhu Kapil, Arti Bai, Sulochana Putil Nagaraj, Savitha Saigal, Karnika Chandola, Temsunaro Rongsen Thomas, Maria Bavdekar, Ashish Ebenezer, Sheena Evelyn Shastri, Jayanthi De, Anuradha Dutta, Shantha Alexander, Anna P. Koshy, Roshine Mary Jinka, Dasaratha R. Singh, Ashita Srivastava, Sunil Kumar Anandan, Shalini Dougan, Gordon John, Jacob Kang, Gagandeep Veeraraghavan, Balaji Mutreja, Ankur |
author_sort | Jacob, Jobin John |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-10171690 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-101716902023-05-11 Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages Jacob, Jobin John Pragasam, Agila K Vasudevan, Karthick Velmurugan, Aravind Priya Teekaraman, Monisha Priya Thirumoorthy, Tharani Ray, Pallab Gupta, Madhu Kapil, Arti Bai, Sulochana Putil Nagaraj, Savitha Saigal, Karnika Chandola, Temsunaro Rongsen Thomas, Maria Bavdekar, Ashish Ebenezer, Sheena Evelyn Shastri, Jayanthi De, Anuradha Dutta, Shantha Alexander, Anna P. Koshy, Roshine Mary Jinka, Dasaratha R. Singh, Ashita Srivastava, Sunil Kumar Anandan, Shalini Dougan, Gordon John, Jacob Kang, Gagandeep Veeraraghavan, Balaji Mutreja, Ankur PLoS Pathog Research Article 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. Public Library of Science 2023-04-28 /pmc/articles/PMC10171690/ /pubmed/37115804 http://dx.doi.org/10.1371/journal.ppat.1010650 Text en © 2023 Jacob et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Jacob, Jobin John Pragasam, Agila K Vasudevan, Karthick Velmurugan, Aravind Priya Teekaraman, Monisha Priya Thirumoorthy, Tharani Ray, Pallab Gupta, Madhu Kapil, Arti Bai, Sulochana Putil Nagaraj, Savitha Saigal, Karnika Chandola, Temsunaro Rongsen Thomas, Maria Bavdekar, Ashish Ebenezer, Sheena Evelyn Shastri, Jayanthi De, Anuradha Dutta, Shantha Alexander, Anna P. Koshy, Roshine Mary Jinka, Dasaratha R. Singh, Ashita Srivastava, Sunil Kumar Anandan, Shalini Dougan, Gordon John, Jacob Kang, Gagandeep Veeraraghavan, Balaji Mutreja, Ankur Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages |
title | Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages |
title_full | Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages |
title_fullStr | Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages |
title_full_unstemmed | Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages |
title_short | Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages |
title_sort | genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of s. paratyphi a lineages |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10171690/ https://www.ncbi.nlm.nih.gov/pubmed/37115804 http://dx.doi.org/10.1371/journal.ppat.1010650 |
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