Phase variation in pneumococcal populations during carriage in the human nasopharynx

Abstract

Streptococcus pneumoniae is one of the world's leading bacterial pathogens, responsible for pneumonia, septicaemia and meningitis. Asymptomatic colonisation of the nasopharynx is considered to be a prerequisite for these severe infections, however little is understood about the biological changes that permit the pneumococcus to switch from asymptomatic coloniser to invasive pathogen. A phase variable type I restriction-modification (R-M) system (SpnIII) has been linked to a change in capsule expression and to the ability to successfully colonise the murine nasopharynx. Using our laboratory data, we have developed a Markov change model that allows prediction of the expected level of phase variation within a population, and as a result measures when populations deviate from those expected at random. Using this model, we have analysed samples from the experimental Human pneumococcal Carriage (EHPC) project. Here we show, through mathematical modelling, that the patterns of dominant SpnIII alleles expressed in the human nasopharynx are significantly different than those predicted by stochastic switching alone. Our inter-disciplinary work demonstrates that the expression of alternative methylation patterns should be an important consideration in studies of pneumococcal colonisation.

Site-Specific Recombination – How Simple DNA Inversions Produce Complex Phenotypic Heterogeneity in Bacterial Populations

“…The mechanism of recombination of the cod locus is not yet fully understood, and may involve redundancy among recombinases or other factors that contribute to shuffling between hsdS alleles. Recent work examining S. pneumoniae strains recovered from the human nasopharynx showed over-representation of one variant state (SpnIIID), suggesting that bacteria with this methylation pattern and phasevarion have greater fitness in this environment [77].…”

Pathogenic Differences of Type 1 Restriction-Modification Allele Variants in Experimental Listeria monocytogenes Meningitis

“…Lees et al (2017) were unable to detect observable selective advantages of hsdS variants in clinical blood and CSF samples, however analysis of these samples was complicated by the lack of known infecting strain. In contrast, a model infection as presented here, and in De Ste Croix et al (2020b), with a starting inoculum of defined bacterial composition, allows for results to be analyzed in comparison to the inoculating dose and can therefore account for differences in the input population.…”

“…PV DNA methylation systems have been proposed as one mechanism which could allow global gene expression changes through alternate methylation of the genome (Srikhanta et al, 2005;Manso et al, 2014). PV type I restriction modification systems (RMS) have been implicated in species such as S. pneumoniae (Manso et al, 2014;Li et al, 2016;Kwun et al, 2018;De Ste Croix et al, 2019, 2020b, Streptococcus suis (Atack et al, 2018), Mycoplasma pulmonis (Sitaraman et al, 2002) and L. monocytogenes (Fagerlund et al, 2016) as potential epigenetic regulators of bacterial virulence. In L. monocytogenes, as in many other bacterial species, RMS tend to be specific to the accessory genome of single phylogenetic units such as sequence type or clonal complex (Chen et al, 2017;De Ste Croix et al, 2017;Lee et al, 2019;Zamudio et al, 2020).…”

Multi-Valent Protein Hybrid Pneumococcal Vaccines: A Strategy for the Next Generation of Vaccines

“…Like many other successful bacterial pathogens, Spn undergoes phase variation during which surface components, such as capsule, shift stochastically from high to low levels of expression. The frequency of specific phase-variants in distinct anatomical sites in turn being the result of anatomical-site specific selective pressures in the host environment [ 39 ]. Bacteria on the mucosal surface have been shown to be less encapsulated than blood-isolated counterparts, thereby exposing surface adhesins, and thus antibodies directed at capsule are at a disadvantage in promoting opsonophagocytosis at the mucosal level.…”