Molecular Epidemiology, Microbial Virulence, and Resistance of Carbapenem-Resistant <i>Enterobacterales</i> Isolates in a Teaching Hospital in Guangzhou, China

Abstract

Infection caused by carbapenem-resistant Enterobacterales (CRE) is a global public health problem. We performed whole-genome sequencing to investigate the molecular epidemiological characteristics of local CRE infections and understand the prevalence of hypervirulent carbapenem-resistant Klebsiella pneumoniae (CRKP). Analysis of multiLocus sequence typing (MLST), antibiotic resistance genes, plasmid replicons, virulence genes, and the genetic environment was also performed. Klebsiella pneumoniae (89, 60.95%) was the most common CRE species, primarily prevalent in the intensive care unit (36, 40.45%). Most CRE strains showed a high resistance rate to multiple antibiotics, especially cephalosporins and carbapenems. However, most of these isolates were susceptible to tigecycline (81.7%). Notably, the predominant sequence type (ST) of CRKP isolates was ST11 (80.90%, 72/89), with 93.05% as Klebsiella pneumoniae carbapenemase (KPC)-ST11. In Escherichia coli isolates, ST410 (21.43%, 6/28) was the predominant type, with approximately half carrying bla NDM-5 , and importantly, the ST167 carbapenem-resistant Escherichia coli (CRECO) harbors both New Delhi metallo-β-lactamase (NDM)-5 and KPC-2. In Enterobacter cloacae isolates, three cases of ST88 were carrying the bla NDM-1 gene, and the ST594 carbapenem-resistant Enterobacter cloacae (CRECC) carrying NDM-1 and KPC-2 has also been identified. In addition, we found three novel STs, ST5386–ST5388. The IncFII (pHN7A8) (98.41%, 62/63) was the most common plasmid replicon type in KPC-2-producing CRKP strains, and the predominant plasmid ST of IncF was [f33:A-:B-] ( n = 73). Two CRKP isolates were found to carry 4 virulence genes ( iut A, iro B, rmp A, and rmp A2). As concluded, among CRKP strains, ST11 was the predominant ST with bla KPC-2 , and a large proportion of CRKP strains co-harbor bla KPC-2 , bla SHV , bla CTX-M , bla TEB-1B , and fos A. The predominant carbapenemase genes carried by CRECO and CRECC were bla NDM-1 and bla CTX-M , respectively.