Pathogenic entero- and salivatypes harbour changes in microbiome virulence and antimicrobial resistance genes with increasing chronic liver disease severity

ABSTRACT Background & Aims Life-threatening complications of cirrhosis are triggered by bacterial infections, with the ever-increasing threat of antimicrobial resistance (AMR). Alterations in the gut microbiome in decompensated cirrhosis (DC) and acute-on-chronic liver failure (ACLF) are recognised to influence clinical outcomes, whilst the role of the oral microbiome is still being explored. Our aims were to simultaneously interrogate the gut and oral micro- and mycobiome in cirrhotic patients, and assess microbial community structure overlap in relation to clinical outcomes, as well as alterations in virulence factors and AMR genes. Methods 18 healthy controls (HC), 20 stable cirrhotics (SC), 50 DC, 18 ACLF and 15 with non-liver sepsis (NLS) i.e. severe infection but without cirrhosis, were recruited at a tertiary liver centre. Shotgun metagenomic sequencing was undertaken from saliva (S) and faecal (F) samples (paired where possible). ‘Salivatypes’ and ‘enterotypes’ based on clustering of genera were calculated and compared in relation to cirrhosis severity and in relation to specific clinical parameters. Virulence and antimicrobial resistance genes (ARGs) were evaluated in both oral and gut niches, and distinct resistotypes identified. Results Specific saliva- and enterotypes revealed a greater proportion of pathobionts with concomitant reduction in autochthonous genera with increasing cirrhosis severity, and in those with hyperammonemia. Overlap between oral and gut microbiome communities was observed and was significantly higher in DC and ACLF vs SC and HCs, independent of antimicrobial, beta-blocker and acid suppressant use. Two distinct gut microbiome clusters [ENT2/ENT3] harboured genes encoding for the phosphoenolpyruvate:sugar phosphotransferase system (PTS) system and other virulence factors in patients with DC and ACLF. Substantial numbers of ARGs (oral: 1,218 and gut: 672) were detected with 575 ARGs common to both sites. The cirrhosis resistome was significantly different to HCs, with three and four resistotypes identified for the oral and gut microbiome, respectively. Discussion Oral and gut microbiome profiles differ significantly with increasing severity of cirrhosis, with progressive dominance of pathobionts and loss of commensals. DC and ACLF have significantly worse microbial diversity than NLS, despite similar antimicrobial exposure, supporting the additive patho-biological effect of cirrhosis. The degree of microbial community overlap between sites, frequency of virulence factors and presence of ARGs, all increment significantly with hepatic decompensation. These alterations may predispose to higher infection risk, poorer response to antimicrobial therapy and worsening outcomes, and provide the rationale for developing non-antibiotic-dependent microbiome-modulating therapies.