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Genomic characterization of Haemophilus influenzae: a focus on the capsule locus
Caelin C Potts1, Nadav Topaz2, Lorraine D Rodriguez-Rivera3
1Bacterial Meningitis Laboratory, Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Mailstop H17-2, Atlanta, GA, 30329, USA.
Insights
Whole genome sequencing (WGS) reveals greater genetic diversity in non-typeable Haemophilus influenzae (NTHi) than typeable strains. A new WGS serotyping method accurately identifies H. influenzae capsule types.
Area of Science:
- Microbiology
- Genomics
- Infectious Diseases
Background:
- Haemophilus influenzae (Hi) causes invasive diseases like meningitis and pneumonia.
- Typeable Hi has six serotypes (a-f) with a capsule, a key virulence factor.
- Non-typeable H. influenzae (NTHi) lacks a capsule and is linked to various infections.
Purpose of the Study:
- To analyze the genetic diversity of typeable and non-typeable H. influenzae.
- To develop and validate a whole genome sequencing (WGS) based method for H. influenzae serotyping.
Main Methods:
- Whole genome sequencing (WGS) of 395 typeable and 293 NTHi isolates.
- Phylogenetic analysis and multilocus sequence typing for genetic diversity assessment.
- Development and validation of a WGS serotyping method against slide agglutination (SAST) and real-time PCR (rt-PCR).
Main Results:
- Typeable H. influenzae isolates clustered by serotype and sequence type (ST).
- NTHi isolates exhibited significant genetic diversity with 7 subclades and 125 STs.
- The WGS serotyping method showed high concordance (99.9%-100%) with existing methods.
Conclusions:
- Genomic analysis highlights greater genetic diversity in NTHi compared to typeable H. influenzae.
- WGS serotyping is an accurate and reliable alternative for H. influenzae serotyping.
Background:
Haemophilus influenzae (Hi) can cause invasive diseases such as meningitis, pneumonia, or sepsis. Typeable Hi includes six serotypes (a through f), each expressing a unique capsular polysaccharide. The capsule, encoded by the genes within the capsule locus, is a major virulence factor of typeable Hi. Non-typeable (NTHi) does not express capsule and is associated with invasive and non-invasive diseases.
Methods:
A total of 395 typeable and 293 NTHi isolates were characterized by whole genome sequencing (WGS). Phylogenetic analysis and multilocus sequence typing were used to characterize the overall genetic diversity. Pair-wise comparisons were used to evaluate the capsule loci. A WGS serotyping method was developed to predict the Hi serotype. WGS serotyping results were compared to slide agglutination (SAST) or real-time PCR (rt-PCR) serotyping.
Results:
Isolates of each Hi serotype clustered into one or two subclades, with each subclade being associated with a distinct sequence type (ST). NTHi isolates were genetically diverse, with seven subclades and 125 STs being detected. Regions I and III of the capsule locus were conserved among the six serotypes (≥82% nucleotide identity). In contrast, genes in Region II were less conserved, with only six gene pairs from all serotypes showing ≥56% nucleotide identity. The WGS serotyping method was 99.9% concordant with SAST and 100% concordant with rt-PCR in determining the Hi serotype.
Conclusions:
Genomic analysis revealed a higher degree of genetic diversity among NTHi compared to typeable Hi. The WGS serotyping method accurately predicted the Hi capsule type and can serve as an alternative method for Hi serotyping.
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