hicap:in silicoserotyping of theHaemophilus influenzaecapsule locus

Abstract

Haemophilus influenzae exclusively colonises the human nasopharynx and can cause a variety of respiratory infections as well as invasive diseases including meningitis and sepsis. A key virulence determinant of H. influenzae is the polysaccharide capsule of which six serotypes are known, each encoded by a distinct variation of the capsule biosynthesis locus (cap-a to cap-f). H. influenzae type b (Hib) was historically responsible for the majority of invasive H. influenzae disease and prevalence has been markedly reduced in countries that have implemented vaccination programs targeting this serotype. In the postvaccine era, non-typeable H. influenzae emerged as the most dominant group causing disease but in recent years a resurgence of encapsulated H. influenzae strains has also been observed, most notably serotype a. Given the increasing incidence of encapsulated strains and the high frequency of Hib in countries without vaccination programs, there is growing interest in genomic epidemiology of H. influenzae. Here we present hicap, a software tool for rapid in silico serotype prediction from H. influenzae genome sequences. hicap is written using Python3 and is freely available at https://github.com/scwatts/hicap under the GPL3 license. To demonstrate the utility of hicap, we used it to investigate the cap locus diversity and distribution in 691 high-quality H. influenzae genomes from GenBank. These analyses identified cap loci in 95 genomes and confirmed the general association of each serotype with a unique clonal lineage and also identified occasional recombination between lineages giving rise to hybrid cap loci (2% of encapsulated strains). 7 non-typeable H. influenzae (NTHi) [2]. 8Biosynthesis of the polysaccharide capsule is controlled by the cap loci (cap-a to cap-f), which 9 each include three contiguous but functionally distinct regions (I, II, and III) ( Figure 1). Regions I 10 and III are common to all six cap loci, and are associated with cellular transport (bex operon, region 11

On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference

“…It enables phylogenetic trees to be quickly reconstructed from a large number of genomes without the burden of multiple sequence alignments (see e.g. 2,29, [44][45][46][47][48][49][50][51][52]. This report confirms this view by showing that proper evolutionary distances can be easily derived from MH p-distance estimates, therefore enabling accurate phylogenetic inferences.…”

Genomic diversity and antimicrobial resistance ofHaemophiluscolonising the airways of young children with cystic fibrosis

“…For each species, maximum-likelihood core-genome SNV phylogenies were inferred from alignments of SNV alleles at sites present in ≥95% of genomes (264,940 variable sites for 901 Hi genomes, 329,046 variable sites for 97 Hpi genomes), using IQ-TREE v2.1.0 (24) and visualised with ggtree v1.14.6 (25) in R v3.5.2 (26). Hi capsular serotype loci were detected from genome assemblies using hicap v1.0.0 (27), and sequence types (STs) were assigned to Hi read sets using SRST2 v.0.2.0 (28) with the Hi multi-locus sequence typing (MLST) database (29).…”