Whole Genome Sequencing of 39 Invasive Streptococcus pneumoniae Sequence Type 199 Isolates Revealed Switches from Serotype 19A to 15B

Abstract

Streptococcus pneumoniae is a major pathogen that causes different invasive pneumococcal diseases (IPD). The pneumococcal polysaccharide capsule is a main virulence factor. More than 94 capsule types have been described, but only a limited number of capsule types accounted for the majority of IPD cases before the introduction of pneumococcal vaccines. After the introduction of the conjugated pneumococcal vaccine PCV7, which covered the seven most frequent serotypes in IPD in the USA, an increase in IPD caused by non-vaccine serotypes was observed, and serotype 19A, which belongs to sequence type (ST) 199, was among the most prevalent STs. After the introduction of the extended vaccine PCV13, which includes serotype 19A, serogroup 15B/C increased in IPD. Therefore, whole genome sequences of 39 isolates of ST199 from Germany (collected between 1998 and 2011) with serotype 19A (n = 24) and serogroup 15B/C (n = 15) were obtained using an Illumina platform and were analysed to identify capsular switches within ST199. Two 19A to 15B/C serotype switch events were identified. Both events occurred before the introduction of PCV7, which indicates that a capsular switch from 19A to 15B among ST199 isolates is not unusual and is not directly linked to the vaccination. The observed serotype replacement appears to be the result of a vacant niche due to the displacement of vaccine serotypes that is now successfully occupied by ST199 clones.

The Pneumococcal Serotype 15C Capsule Is Partially O-Acetylated and Allows for Limited Evasion of 23-Valent Pneumococcal Polysaccharide Vaccine-Elicited Anti-Serotype 15B Antibodies

“…1). Both clinical isolates belong to sequence type 199 (a genotype commonly associated with serotypes 15B and 15C [35][36][37][38][39]) and contain mixed populations of transparent and opaque colonies (see Table S1 in the supplemental material). BLS141 and BLS142 were produced by inserting rpsL (Sm r ), a gene conferring streptomycin (Sm) resistance, into the background of strains 0556-97 and 3031-06, respectively.…”

Longitudinal characterization of nasopharyngeal colonization with Streptococcus pneumoniae in a South African birth cohort post 13-valent pneumococcal conjugate vaccine implementation

“…Animal models suggest that 15B/15C is equally capable of causing middle ear infections as 19A 41 . An increase in 15B/15C IPD cases have been noted from the UK and USA 42 , 43 . A higher valency PCV vaccine, PCV15, is currently under development, and includes all PCV13 serotypes plus 22F and 33F 44 .…”

Puzzling Over the Pneumococcal Pangenome

“…Pneumococcus researchers have the privilege of studying a species with an abundance of genomic data ( Jolley and Maiden, 2010 ; Riley et al, 2012 ). There are multiple genome-wide studies, including detailed annotations of single genomes and comparative analyses of lineages, serotypes, and populations ( Dopazo et al, 2001 ; Hoskins et al, 2001 ; Tettelin et al, 2001 ; Hiller et al, 2007 ; Lanie et al, 2007 ; Croucher et al, 2009 , 2011 , 2013a , 2014b ; Ding et al, 2009 ; Donati et al, 2010 ; Everett et al, 2012 ; Wyres et al, 2012 ; Chewapreecha et al, 2014 ; Chaguza et al, 2016b , 2017 ; Lees et al, 2017 ; Makarewicz et al, 2017 ; Aprianto et al, 2018 ; Azarian et al, 2018 ). The selective pressure imposed by multivalent pneumococcal conjugate vaccines, provides a unique opportunity to observe population dynamics and investigate the pangenome under an instance of dramatic selection.…”