Genomic Analysis of a Pan-Resistant Isolate of Klebsiella pneumoniae, United States 2016

Abstract

Antimicrobial resistance is a threat to public health globally and leads to an estimated 23,000 deaths annually in the United States alone. Here, we report the genomic characterization of an unusual Klebsiella pneumoniae, nonsusceptible to all 26 antibiotics tested, that was isolated from a U.S.

Patient: The isolate harbored four known beta-lactamase genes, including plasmid-mediated bla_NDM-1 and bla_CMY-6, as well as chromosomal bla_CTX-M-15 and bla_SHV-28, which accounted for resistance to all beta-lactams tested. In addition, sequence analysis identified mechanisms that could explain all other reported nonsusceptibility results, including nonsusceptibility to colistin, tigecycline, and chloramphenicol. Two plasmids, IncA/C2 and IncFIB, were closely related to mobile elements described previously and isolated from Gram-negative bacteria from China, Nepal, India, the United States, and Kenya, suggesting possible origins of the isolate and plasmids. This is one of the first K. pneumoniae isolates in the United States to have been reported to the Centers for Disease Control and Prevention (CDC) as nonsusceptible to all drugs tested, including all beta-lactams, colistin, and tigecycline.IMPORTANCE Antimicrobial resistance is a major public health threat worldwide. Bacteria that are nonsusceptible or resistant to all antimicrobials available are of major concern to patients and the public because of lack of treatment options and potential for spread. A Klebsiella pneumoniae strain that was nonsusceptible to all tested antibiotics was isolated from a U.S.

Patient: Mechanisms that could explain all observed phenotypic antimicrobial resistance phenotypes, including resistance to colistin and beta-lactams, were identified through whole-genome sequencing. The large variety of resistance determinants identified demonstrates the usefulness of whole-genome sequencing for detecting these genes in an outbreak response. Sequencing of isolates with rare and unusual phenotypes can provide information on how these extremely resistant isolates develop, including whether resistance is acquired on mobile elements or accumulated through chromosomal mutations. Moreover, this provides further insight into not only detecting these highly resistant organisms but also preventing their spread.

Keywords: Klebsiella pneumoniae; carbapenems; colistin; plasmid-mediated resistance; whole-genome sequencing.

FIG 1

(A) Chromosomal integration of bla_CTX-M-15 by an ISEc9 insertion sequence. The bla_CTX-M-15 gene is highlighted in red, mobile elements are peach, and all other genes are blue. Numbers indicate chromosomal locations. (B) The nonconjugative IncFIB(pKPHS1) p1605752FIB_2 plasmid carried by our isolate (I) was highly similar to a plasmid previously isolated in Nepal from K. pneumoniae strain ST15 (II). Gray areas indicate regions of similarity; white areas represent nonhomologous regions. No known antimicrobial resistance genes were present on either plasmid. (C) Conjugative IncA/C2 p1605752AC2 plasmid of our isolate (II) compared to the two most closely related IncA/C2 plasmids, pNDM-KN (I) and pNDM-US (III). Gray areas indicate regions of similarity; white areas represent nonhomologous regions. Known antimicrobial resistance genes are indicated with colored arrows.

FIG 2

Our isolate, DHQP1605752_NV, clustered with 140 publicly available Klebsiella pneumoniae genome sequences. Presence or absence of known carbapenamase genes is listed for all isolates.