Emergence and genomic characterization of Klebsiella pneumoniae and Escherichia coli harboring tet(X4) disseminated by Black kites (Milvus migrans)

Abstract

The emergence of plasmid-mediated tigecycline resistance gene tet(X4) among clinically relevant bacteria has raised serious concerns since tigecycline is considered as last-resort drug against serious infections caused by multidrug-resistant bacteria. We herein focused on the isolation and molecular characterization of tet(X4)-positive Klebsiella pneumoniae (K. pneumoniae) and Escherichia coli (E. coli) in wild bird populations with anthropogenic interaction in Faisalabad, Pakistan. A total of 150 birds including black kites (Milvus migrans) and house crows (Corvus splendens) were screened for the presence of tigecycline resistance K. pneumoniaeand E. coli. We found two K. pneumoniae and one E. coliisolate carrying tet(X4) originated from black kites. A combination of short- and long-read sequencing strategy showed that tet(X4) was located on a broad host range IncFII plasmid family inK. pneumoniae isolates whereas on an IncFII-IncFIB hybrid plasmid in E. coli. We also found an integrative and conjugative element ICEKp2 in K. pneumoniae isolate KP8336. The combination of tet(X4) and a known virulence associated ICEKp2 in a wild bird with significant human interaction is particularly worrisome. We demonstrated the first description of tet(X4) gene in the WHO critical-priority pathogen K. pneumoniae among wild birds with known anthropogenic interaction and dispersal potential. The potential risk of global transmission of tet(X4)-positive K. pneumoniae and E. coli warrant comprehensive evaluation.