Title : Antibiotic resistance burden and gut microbiome alterations in patients with non-alcoholic fatty liver disease: A pilot study from a tertiary care centre in North India
Abstract:
Background: Non-alcoholic fatty liver disease (NAFLD) is a rapidly increasing hepatic disorder, affecting nearly 25–30% of the global population. Emerging evidence suggests that alterations in gut microbiota composition, often mediated by antibiotic exposure, may contribute to NAFLD progression and severity. Conversely, patients with advanced NAFLD or NASH often require prolonged or recurrent antibiotic treatments for associated complications, which may drive antibiotic resistance (ABR). However, the relationship between NAFLD, its clinical spectrum, and ABR in human subjects remains underexplored, especially in Indian cohorts.
Objective: To identify the prevalence and spectrum of antibiotic resistance among NAFLD patients, and to explore its correlation with disease stage, metabolic parameters, and prior antibiotic exposure.
Methods: A prospective, observational study was conducted at the Department of Gastroenterology and Department of Microbiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow, from January 2024 to June 2025. Adult patients (18–70 years) with ultrasonography-confirmed non-alcoholic fatty liver disease (NAFLD) or metabolic dysfunction–associated steatotic liver disease (MASLD) were enrolled after obtaining informed consent. Exclusion criteria included chronic viral hepatitis, autoimmune liver disease, and recent (<3 months) antibiotic therapy. Clinical data, anthropometry, liver function tests, fasting lipid profile, HbA1c, and inflammatory markers (CRP, IL-6) were recorded.Stool samples were collected for microbiome analysis using 16S rRNA gene sequencing and culture-based sensitivity testing against a panel of antibiotics (β-lactams, fluoroquinolones, aminoglycosides, and carbapenems). Minimum inhibitory concentrations (MICs) were determined by broth microdilution following CLSI guidelines. NAFLD severity was assessed by transient elastography (FibroScan) and serum fibrosis scores (FIB-4, NFS). Associations between fatty liver severity, gut microbiota composition, and antibiotic resistance profiles were evaluated using multivariate logistic regression and Spearman correlation.
Results: Among the 120 NAFLD patients included, the mean age was 47.2 ± 10.5 years, with a male-to-female ratio of 1.4:1. The prevalence of multi-drug resistant (MDR) organisms increased progressively with disease severity: NAFL – 18%, NASH without fibrosis – 35%, and NASH with fibrosis – 56% (p for trend < 0.01). The most frequently isolated resistant pathogens were Escherichia coli (ESBL-producers, 42%), Klebsiella pneumoniae (carbapenem-resistant, 18%), and Enterococcus faecium (vancomycin-resistant, 12%). Patients with ≥3 antibiotic exposures in the previous year demonstrated significantly higher MDR rates (OR: 2.1; 95% CI: 1.3–3.4; p < 0.05). In subgroup analysis, MDR prevalence was highest in those with advanced fibrosis (≥F3), accompanied by higher liver stiffness measurements and serum ALT levels.
Conclusion: This pilot dataset from SGPGIMS suggests a graded association between NAFLD severity and the prevalence of MDR organisms in gut and blood isolates. The findings point to a potential bidirectional relationship, wherein NAFLD progression may foster antibiotic resistance through microbiome alterations, while recurrent antibiotic exposure may exacerbate liver disease via dysbiosis and metabolic inflammation. These results underscore the necessity for integrated management strategies combining antimicrobial stewardship with metabolic and hepatology care pathways. Large-scale, prospective, multi-center studies incorporating resistome and metagenomic profiling are warranted to validate these findings and guide precision interventions.
