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Comparative genomics of invasive Streptococcus pneumoniae CC320/271 serotype 19F/19A before the introduction of pneumococcal vaccine in India

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Abstract

The emergence of multi drug resistant clone CC320 serotype19F/19A and their capsular (cps) antigenic variants due to selective pressures such as vaccine had been reported worldwide. Hence, it is important to identify the prevalent clones, sequence types and cps variants of serotype 19F/19A in India, where PCV13 has been recently introduced. Multi-locus sequence typing (MLST) was performed for all (n = 21) invasive S. pneumoniae isolates of serotype 19A (n = 5) and 19F (n = 16) collected between the years 2012 and 2018 from children less than 5 years. The genome characterization by whole genome sequencing for the Sequence types (STs) 320 and 271(n = 7) were performed and compared with another six Indian WGSs of similar STs available from the GPS platform. The predominant STs in the serotype 19F/19A study isolates were of CC320: ST 320, 236 and 271, associated with PMEN clone Taiwan19F-14. The WGSs of CC320 study isolates showed high genomic similarity to the Taiwan19F-14 clone, and the penicillin binding protein (PBP) amino acid sequence similarity was 100% for PBP1A, 93% for PBP 2B and 2X. Whilst PBP comparison with other global MDR ST320 strains revealed that the ST320 clones in India are of low-level penicillin resistance. The presence of a few ST320/19A/19F invasive isolates with high similarity to the Taiwan clone suggests slow and gradual expansion of Taiwan19F-14 associated CC320 clones in India. Since serotype 19F/19A is covered by PCV13 vaccine, the expansion of 19F/19A cones with non-PCV13 vaccine serotype in India should be monitored.

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Acknowledgements

The authors thank Department of clinical Microbiology, Christian Medical College (CMC), Vellore for providing all necessary facilities and Ms. Catherine Trueman (Clinical Pharmacist) for helping in language editing.

Genome sequence accession numbers

The accession numbers of the WGS of the seven study isolates are NIFF00000000, NIFG00000000, VBQV0000000, VUOM0000000, VUOO00000000, VUON00000000 and VUOP00000000.

Funding

The study has been partly supported by the Christian Medical College institutional review board (IRB Min.No: 8200).

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Authors and Affiliations

  1. Department of Clinical Microbiology, Christian Medical College, Vellore, India

    Rosemol Varghese, Ayyanraj Neeravi, Jobin John Jacob, Karthick Vasudevan, Jones Lionel Kumar & Balaji Veeraraghavan

  2. Department of Child Health, Christian Medical College, Vellore, India

    Nithya Subramanian

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  1. Rosemol Varghese
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Correspondence to Balaji Veeraraghavan.

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The study has been approved by Christian Medical College institutional review board (IRB Min.No:8200).

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Varghese, R., Neeravi, A., Jacob, J.J. et al. Comparative genomics of invasive Streptococcus pneumoniae CC320/271 serotype 19F/19A before the introduction of pneumococcal vaccine in India. Mol Biol Rep 48, 3265–3276 (2021). https://doi.org/10.1007/s11033-021-06353-6

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