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

• Published in: Molecular biology reports 2021-04, Vol.48 (4), p.3265-3276
• Main Authors: Varghese, Rosemol, Neeravi, Ayyanraj, Jacob, Jobin John, Vasudevan, Karthick, Kumar, Jones Lionel, Subramanian, Nithya, Veeraraghavan, Balaji
• Format: Article
• Language: English
• Subjects: Amino acid sequence; Animal Anatomy; Animal Biochemistry; Antibiotics; Antigenic variants; Biomedical and Life Sciences; Cloning; Drug resistance; Genomes; Genomics; Histology; Life Sciences; Morphology; Multilocus sequence typing; Nucleotide sequence; Original Article; Penicillin; Streptococcus infections; Streptococcus pneumoniae; Vaccines; Whole genome sequencing
• ISSN: 0301-4851; 1573-4978
• DOI: 10.1007/s11033-021-06353-6

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 Taiwan 19F -14. The WGSs of CC320 study isolates showed high genomic similarity to the Taiwan 19F -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 Taiwan 19F -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.