The grey-headed flying fox (Pteropus poliocephalus) is a mammal found on the East coast of Australia, infamously renowned for harbouring human pathogens such as Australian bat lyssavirus and Menangle virus. We have recently shown that these animals harbour bacterial pathogens including Klebsiella pneumoniae and closely related species in the Klebsiella pneumoniae Species Complex (KpSC). KpSC diversity was low within wild flying fox colonies and almost completely uniform within captive colonies, harbouring little antimicrobial resistance and human virulence factors. However, there remains a lack of in-depth knowledge about the genomic diversity of KpSC from these and other bat populations.
We leveraged existing draft genomes for 39 KpSC isolates from grey-headed flying foxes and generated long read data for each of thirteen distinct KpSC sequence types present in the population (defined by 7-gene chromosomal multi-locus sequence typing). This was used to construct high quality completed genomes to facilitate high resolution genomic comparison, track isolates relationships to each other, and identify and track plasmid transmission. Additionally, we generated in silico genome scale metabolic models to predict and compare growth substrate usage to those of 59 KpSC from human and environmental sources; however, no substrates were overrepresented in either group.
Out of 13 sequence types making up the flying fox isolates, five were overrepresented (≥2 each). High resolution comparison indicated three sequence types (ST5033 and ST4938 from wild colonies, ST5035 from captive colony) were clonal (≤ 25 pairwise single nucleotide polymorphisms). In one case, two clonal Klebsiella africana isolates (ST4938) were found at two flying fox colonies located 100 km from each other. Interspecies horizontal plasmid transmission between K. pneumoniae and K. africana was observed for a single plasmid, pFF1003_1, which also crossed multiple sequence types.
Together our data strongly indicate that KpSC are able to transmit within the flying fox population or a common food/water source, and that these isolates can harbour plasmids with similarity to those found in human derived KpSC.