The healthy human gut as a covert reservoir for mobile antimicrobial resistance: nationwide genomic surveillance of Enterobacter cloacae complex in China.

BACKGROUND

Enterobacter cloacae complex (ECC) is a formidable opportunistic pathogen, yet its ecological niche and role as a silent reservoir for antimicrobial resistance (AMR) in the healthy human gut remain underappreciated. Herein, we aim to characterize the prevalence, genomic epidemiology, and mobile resistome of ECC in a widespread healthy demographic.

METHODS

In a nationwide, cross-sectional genomic surveillance study conducted across China (2024-2025), we analyzed 10,300 fecal samples from healthy individuals across 31 provinces. High-resolution whole-genome sequencing (WGS), comparative genomics, and conjugation assays were employed to resolve species identity, delineate phylogenetic relationships, and trace the mobility of high-priority resistance determinants.

RESULTS

We recovered 148 non-duplicate ECC isolates, establishing a community carriage prevalence of 1.44%. Among them, Enterobacter hormaechei emerged as the predominant species (49.3%). WGS revealed a highly diverse population structure harboring critical resistance determinants, including mcr genes (4.1%), tet(X4) (3.4%), and carbapenemases (9.5%, predominantly blaNDM). Notably, this study provides, to our knowledge, the first evidence of tet(X4)-positive ECC in the gut carriage of healthy individuals in China. While mcr and tet(X4) were dispersed across diverse sequence types (STs), blaNDM carriage was strongly concentrated in specific lineages, notably ST143 and ST171. Genomic and conjugation analyses showed that tet(X4), blaNDM, and mcr were associated with conserved mobile genetic contexts (e.g., an IS1 family transposase-hydrolase-tet(X4)-IS91-like element ISVsa3 structure for tigecycline resistance), and successful transfer was confirmed for selected representative blaNDM-positive isolates.

CONCLUSIONS

The healthy human gastrointestinal tract can harbor ECC isolates carrying clinically important AMR determinants, including resistance genes located within mobile genetic contexts. These findings support the integration of community-based genomic surveillance into AMR monitoring strategies to better understand asymptomatic carriage of resistant ECC.