Characterization of a blaNDM-1-Bearing IncHI5-Like Plasmid From Klebsiella pneumoniae of Infant Origin

Abstract

The spread of plasmid-mediated carbapenem-resistant clinical isolates is a serious threat to global health. In this study, an emerging NDM-encoding IncHI5-like plasmid from Klebsiella pneumoniae of infant patient origin was characterized, and the plasmid was compared to the available IncHI5-like plasmids to better understand the genetic composition and evolution of this emerging plasmid. Clinical isolate C39 was identified as K. pneumoniae and belonged to the ST37 and KL15 serotype. Whole genome sequencing (WGS) and analysis revealed that it harbored two plasmids, one of which was a large IncHI5-like plasmid pC39-334kb encoding a wide variety of antimicrobial resistance genes clustered in a single multidrug resistance (MDR) region. The blaNDM-1 gene was located on a ΔISAba125-blaNDM-1-bleMBL-trpF-dsbC structure. Comparative genomic analysis showed that it shared a similar backbone with four IncHI5-like plasmids and the IncHI5 plasmid pNDM-1-EC12, and these six plasmids differed from typical IncHI5 plasmids. The replication genes of IncHI5-like plasmids shared 97.06% (repHI5B) and 97.99% (repFIB-like) nucleotide identity with those of IncHI5 plasmids. Given that pNDM-1-EC12 and all IncHI5-like plasmids are closely related genetically, the occurrence of IncHI5-like plasmid is likely associated with the mutation of the replication genes of pNDM-1-EC12-like IncHI5 plasmids. All available IncHI5-like plasmids harbored 262 core genes encoding replication and maintenance functions and carried distinct MDR regions. Furthermore, 80% of them (4/5) were found in K. pneumoniae from Chinese nosocomial settings. To conclude, this study expands our knowledge of the evolution history of IncHI5-like plasmids, and more attention should be paid to track the evolution pathway of them among clinical, animal, and environmental settings.

Genomic Epidemiology Insights on NDM-Producing Pathogens Revealed the Pivotal Role of Plasmids on bla NDM Transmission

“…The pKP-13-14-NDM-9 plasmid that was isolated from K. pneumoniae was 358,655 bp in size. Although IncHI5-like plasmids were reported to carry bla NDM-1 in previous studies ( 12 , 13 ), pKP-13-14-NDM-9 was the first IncHI5-like plasmid positive for bla NDM-9 . The core genetic environment of bla NDM-9 is IS 26 -ΔIS Aba125 - bla NDM-9 - ble MBL - trpF - mocA - cutA -IS CR1 , and a similar genetic environment (IS 26 -ΔIS Aba125 - bla NDM-1 - ble MBL - trpF - mocA - cutA -IS CR1 ) was found in pKP-14-2-131-NDM-1.…”

Deciphering the Epidemiological Characteristics and Molecular Features of blaKPC–2- or blaNDM–1-Positive Klebsiella pneumoniae Isolates in a Newly Established Hospital

“…The emergence of novel bla NDM−1bearing MDR plasmid in ST304 K. pneumoniae C20 implied that the novel plasmid mediated the transmission of bla NDM−1 and expanded the host ranges of bla NDM−1 . Furthermore, the detailed analysis of IncHI5-like bla NDM−1 -bearing plasmid in C39 has been reported in another study; the plasmid was 334,893 bp in length and possessed a large MDR region, which contained abundant AMR genes and mobile elements (Liu et al, 2021). A total of six classes of virulence factor analysis were conducted among these isolates.…”

Epidemiology of Klebsiella michiganensis Carrying Multidrug-Resistant IncHI5 Plasmids in the Southeast Coastal Area of China

“… 2–4 , 6–8 IncHI5 plasmids, a subgroup of IncHI, usually carry a variety of MGEs and drug resistance genes according to previous reports. 9 , 12 , 40 , 41 The K. michiganensis carrying IncHI5 plasmids were identified frequently in the last two years. 16 , 17 The similarities and differences of the genome structure of IncHI5 plasmids and the population and geographic distribution within the K. michiganensis species have urgently needed to be studied.…”