Low variation found in Haemophilus influenzae genomes

Genomic variation focusing on antibiotic resistance of Haemophilus influenzae has been categorised on a global scale.

H. influenzae is a common bacterium that causes ear infections. An international team of scientists collaborated to sequence the whole genome of H. influenzae to gain insights into the global variations of the bacteria. Their findings, published in Nature Microbiology, detailed little genetic variation among global populations of H. influenzae.

'Ear infections are one of the most common reasons that antibiotics are prescribed in children, and H. influenzae is one of the most important bacteria that causes these. The extensive antibiotic resistance within these bacterial strains is seen both in our genomic analysis and in practice in healthcare settings, with only one type of effective antibiotic left in some regions of the world,' said Professor Paul Turner, of the Centre for Tropical Medicine and Global Health at the University of Oxford and co-senior author of the study.

There are several strains of H. influenzae found globally, including H. influenzae type B (HiB) and non-typeable H. influenzae (NTHi). The NTHi strain was commonly isolated from samples that were collected from 2007-2008 in the Maela Camp for displaced persons in Thailand, which were included within the study to represent a population with high rates of H. influenzae. These samples contained very few genetic variations, with over half of the isolates containing no single-nucleotide changes in their genomes.

In addition to the Maela Camp samples, researchers analysed data from across the globe, and the total dataset comprised 9849 isolates. There were genomic clusters based on location, however most locations had NTHi as the dominate strain. Multi-drug resistance to antibiotics was most common in the NTHi strains. There were no singularly evolved lineages in any of the location clusters.

'By studying nearly ten thousand samples of H. influenzae, we have started to build a foundation of knowledge about the genetic diversity of the entire species relative to the strain we have a vaccine for. Although H. influenzae is highly recombining, there are evolutionary processes in place that preserve the majority of the genome,' said Dr Neil MacAlasdair, co-first author previously at the Wellcome Sanger Institute and the University of Oslo, Norway, and now at EMBL's European Bioinformatics Institute (EMBL-EBI).

The H. influenzae vaccine protects against H. influenzae type B (Hib) and does not protect against non-typeable H. influenzae (NTHi). The authors are optimistic their findings could provide a baseline for future vaccine developments against NTHi by creating a global vaccine targeting an area of low genetic variation.

'Our study shows that, unlike other bacteria that are major causes of respiratory infections, there are no isolated populations of Haemophilus influenzae in different regions. This is good news, since if there had been many different local variants, it would have been much more challenging to develop a vaccine,' said Dr Anna Pöntinen, of the University of Oslo, and co-first author of the study. 'Our findings endorse our original hypothesis: that it is possible to develop a universal vaccine to protect against all types of infections caused by Haemophilus.'