Urinary microbiome in renal transplant patients with BK polyomavirus reactivation

Introduction. BK polyomavirus (BKPyV) reactivation is a significant health risk among renal transplant recipients that can lead to nephropathy and allograft loss.Hypothesis/Gap statement. While the microbiota is increasingly recognized as an important determinant of viral infection and pathogenesis, as well as itself undergoing compositional changes in response to infection, the urinary microbiome has yet to be investigated in the context of BK polyomavirus reactivation.Aim. This study aimed to investigate associations between the urinary microbiome and BKPyV-DNAemia in renal transplant patients.Methodology. Shotgun metagenomics of the urinary microbiome was conducted for 22 renal transplant recipients, 11 of whom had BKPyV-DNAemia. Sequence data were analysed using two complementary approaches to identify common microbiome associations with BKPyV-DNAemia: (1) Kaiju - a DNA-to-Protein method that captures bacteria, archaea, fungi, microeukaryotes and DNA viruses and (2) MetaPhlAn4 - a DNA-to-Marker method using a reference database of specific marker genes of prokaryotes.Results. We found increased observed diversity of bacterial taxa in control patients compared to those with BKPyV-DNAemia for data analysed with MetaPhlAn4 (P=0.037) but not Kaiju (P>0.05), which followed a similar trend. Significant differences in microbial beta diversity between the control and BKPyV-DNAemia patient group were identified for the Kaiju dataset (P=0.027) but not for MetaPhlAn4 (P>0.05), with viral reads likely driving these differences in the Kaiju dataset. Both Kaiju and MetaPhlAn4 identified Proteobacteria, Firmicutes and Actinobacteria as bacterial phyla with greatest relative abundance across samples. Screening bacterial species data generated from Kaiju and MetaPhlAn4 against a database of 243 human pathogens identified 8 pathogenic species recovered from both datasets that were present in the urinary microbiome of renal transplant patients.Conclusion. The observed evidence for differences in microbiome diversity and composition associated with BKPyV-DNAemia may play an important role in its pathology and guide the development of diagnostic biomarkers. Our findings warrant further investigation across larger patient cohorts that are more evenly balanced for gender.