Whole genome sequencing to study the phylogenetic structure of serotype a Haemophilus influenzae recovered from patients in Canada

Abstract

This study examined the phylogenetic structure of serotype a Haemophilus influenzae (Hia) isolates recovered from patients in Canada. Hia isolates from 490 separate patients and an American Type Culture Collection (ATCC) strain were analyzed by multilocus sequence typing (MLST), with 18 different sequence types (STs) identified. Most (85.7%) Hia patient isolates were typed as ST-23 and another 12.7% belonged to 14 different STs with 6, 5, or 4 MLST gene loci related to ST-23 (ST-23 complex). Core genome single-nucleotide variation phylogeny (SNVPhyl) on whole genome sequence (WGS) data of 121 Hia patient isolates representing all identified STs and the ATCC strain revealed 2 phylogenetic populations, with all the ST-23 complex isolates within 1 population. The other phylogenetic population contained only the ATCC strain and 3 patient isolates. Concatenated hitABC sequences retrieved from WGS data and analyzed by MEGA (Molecular Evolutionary Genetic Analysis) alignment confirmed the phylogeny obtained by SNVPhyl. The sodC gene was found only in isolates in the minor phylogenetic population. The 2 phylogenetic populations of the Canadian Hia isolates are similar to the 2 clonal divisions described for serotype b H. influenzae. Combining MLST, core SNVPhyl, and hitABC gene sequence alignment showed that most (99.4%) Canadian Hia patient isolates belonged to 1 major phylogenetic population.

Learning from –omics strategies applied to uncover Haemophilus influenzae host-pathogen interactions: Current status and perspectives

“…Notably, in the frame of transition to whole genome sequencing (WGS)-based surveillance, bioinformatics tools for in silico rapid determination of H. influenzae serotypes from WGS data have been developed [13] , [17] . Moreover, capsulated strains genomic closeness has been illustrated for invasive H. influenzae type f (Hif) and type a (Hia) isolates [22] , [23] . Thus, Hif may present a pattern of unique or missing genes maybe increasing the virulence, with the presence of the sap2 operon, aef3 fimbriae, and genes for kanamycin nucleotidyltransferase, iron-utilization and putative YadA-like trimeric autotransporters, and the absence of an operon for de novo histidine biosynthesis, a hmg locus for lipooligosaccharide (LOS) biosynthesis and biofilm formation, and a molybdate transport system [22] .…”

“… Type of study Purpose-outcome of the study References A. H. influenzae bacterial whole genome sequencing A1. Population structure of capsulated and non-capsulated (non-typeable) clinical isolates [13] , [14] , [15] , [16] , [17] , [18] , [20] , [21] , [22] , [23] , [24] A2. Within-host pathoadaptive traits on longitudinally collected strain sets from chronic respiratory samples – genome evolution in natural settings [32] , [33] , [34] , [36] A3.…”

A Narrative Review of the Molecular Epidemiology and Laboratory Surveillance of Vaccine Preventable Bacterial Meningitis Agents: Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae and Streptococcus agalactiae

“…Genetic analysis of Hia has revealed a population biology very similar to Hib, i.e., (a) with two phylogenetic populations similar to the clonal divisions I and II descried for Hib; and (b) with most invasive Hia isolates clustered together in a phylogenetic population (named clonal division I as for the majority of invasive Hib strains), represented by isolates typed by MLST as ST-23 and many STs related to ST-23 as single, double, or triple locus variants [100,101]. Another clone within this larger genetic population of clonal division I and identified by MLST as ST-4 has been reported in Brazil to be associated with more severe disease and higher case fatality rate [102].…”

“…Another clone within this larger genetic population of clonal division I and identified by MLST as ST-4 has been reported in Brazil to be associated with more severe disease and higher case fatality rate [102]. In contrast to clonal division I Hia, clonal division II Hia is rarely isolated from invasive disease cases in Canada [101] and has not been found associated with invasive disease in Alaska [100]. However, clonal division II Hia identified by MLST as ST-62 has been found in 75% (21/28) of the Hia invasive disease case isolates from children < 18 years old in Utah, United States [103].…”

“…Similar development for H. influenzae appears to be lacking for now. Traditional analysis of the population biology of encapsulated H. influenzae divided them into two clonal divisions [128], and WGS analysis of the recently emerged serotype a H. influenzae also revealed two populations [101] like the two clonal divisions described using multilocus enzyme electrophoresis of Hib [128]. However, the definition of lineages of non-typeable H. influenzae may need further study and discussion because their genetic background appear to be much more diverse than the encapsulated or serotypeable strains of H. influenzae [129].…”