Characterisation of Ornithobacterium hominis colonisation dynamics and interaction with the nasopharyngeal microbiome in a South African birth cohort

  1. Celine C De Allende
  2. Susannah J Salter
  3. Siobhan E Brigg
  4. Shantelle Claassen-Weitz
  5. Kilaza S Mwaikono
  6. Lesley Workman
  7. Heather J Zar
  8. Mark P Nicol
  9. Julian Parkhill
  10. Felix S Dube
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Abstract

Ornithobacterium hominis is a recently described Gram-negative bacterium that colonises the human nasopharynx and may be associated with poor upper respiratory tract health. Here, we describe the isolation of O. hominis from samples collected from a South African birth cohort, creating the first archive of cultured strains of the species from Africa. Sequenced genomes from this archive reveal that South African O. hominis is more similar to Australian strains than those from Southeast Asia, and that it may share genes with other members of the microbiome that are relevant for virulence, colonisation, and antibiotic resistance. Leveraging existing microbiome data from the cohort, O. hominis was found to be closely associated with bacterial co-colonisers that are rare in non-carrier individuals, including Suttonella , Helcococcus , Moraxella spp., and Gracilibacteria. Their collective acquisition has a significant impact on the diversity of nasopharyngeal communities that contain O. hominis . Individuals who have not yet acquired O. hominis have a higher abundance of Moraxella (particularly M. lincolnii ) than individuals who never acquire O. hominis , suggesting that this could be a precursor state for successful colonisation. Finally, a novel co-coloniser species, Helcococcus ekapensis , was successfully isolated and sequenced.

Data Summary

Ornithobacterium hominis data have been deposited under project accession ERP149886. This comprises genome sequences for isolates SA-OH-C1 (ERR13967269), SA-OH-C2 (ERR13967270), SA-OH-C3 (ERR13967271), SA-OH-C4 (ERR13967272, ERR13967275), SA-OH-C5 (ERR13967273), SA-OH-C6 (ERR13967274, ERR13967276). Previously published 16S rRNA gene data are deposited under project accessions PRJNA790843 and PRJNA548658. Helcococcus ekapensis genome data are deposited under project accession PRJEB85661.

Software used

  • AMRFinderPlus v3.12.8: https://github.com/ncbi/amr

  • AssembleBAC-ONT v1.1.1: https://github.com/avantonder/assembleBAC-ONT

  • BAKTA v1.8.1: https://bakta.computational.bio/

  • BLAST v2.16.0: https://blast.ncbi.nlm.nih.gov/Blast.cgi

  • Comprehensive Antibiotic Resistance Database (CARD) Resistance Gene Identifier (RGI) tool v1.2.1: https://card.mcmaster.ca/analyze/rgi

  • Decontam v1.12 (R package): https://github.com/benjjneb/decontam

  • Eggnog-mapper v2.0.1: http://eggnog-mapper.embl.de/

  • FastANI v1.1.0: https://github.com/ParBLiSS/FastANI

  • Flye v2.9.2: https://github.com/fenderglass/Flye

  • Guppy v6.5.7: https://community.nanoporetech.com/downloads/guppy/release_notes

  • ISEScan v1.7.2.3: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1

  • Medaka v1.9.1: https://github.com/nanoporetech/medaka

  • MEGA11: https://www.megasoftware.net/

  • MMseqs2 v17: https://github.com/soedinglab/MMseqs2

  • Mothur v1.44.3: https://github.com/mothur/mothur

  • NetCoMi v1.2.0 (R package): https://github.com/stefpeschel/NetCoMi

  • Panaroo v1.4.3: https://github.com/gtonkinhill/panaroo

  • PHASTEST: https://phastest.ca/submissions/new

  • Prowler (commit ID c3041ba): https://github.com/ProwlerForNanopore/ProwlerTrimmer

  • R v4.4.3: https://www.r-project.org/

Databases used

  • Comprehensive Antibiotic Resistance Database (CARD): https://card.mcmaster.ca/

  • European Nucleotide Archive: https://www.ebi.ac.uk/ena/

  • Genome Taxonomy Database (GTDB) release 09-RS220: https://gtdb.ecogenomic.org/

  • RefSeq release 228: https://www.ncbi.nlm.nih.gov/refseq/about/prokaryotes/

  • SILVA v132: https://www.arb-silva.de/

Impact statement

First described in 2019, Ornithobacterium hominis is an understudied bacterium that may be associated with poor respiratory health in children. The study builds upon existing knowledge of O. hominis by describing the first African isolates of the species, its potential as a reservoir of virulence and antibiotic resistance genes in the upper respiratory tract, and the unique microbiome profile of O. hominis carriers.

Article activity feed

  1. Version published to 10.1101/2025.05.24.655922v1 on bioRxiv