Emergence of
mcr-8.1
-bearing MDR-hypervirulent
Klebsiella pneumoniae
ST307
Authors: Sheng Jie , Cave Rory , Ter-Stepanyan Mary M. , Lu Siyu , Wang Yingxiong , Liu Taihang , Mkrtchyan Hermine V. 
Published: December 2024

ABSTRACT

We report for the first time whole-genome sequencing of four multidrug-resistant sequence type (ST) 307
Klebsiella pneumoniae
recovered from patients in two hospitals in Armenia. Comparative genomic analysis revealed that the isolates were closely related, with a maximum of 39 single nucleotide polymorphism (SNP) differences in the core genome. All Armenian isolates carried the integrative and conjugative element ICE
Kp
4, which bears the yersiniabactin locus, and shared a common evolutionary origin, diverging around 2005 (95% CI: 1999 to 2011). Antibiotic susceptibility testing showed resistance to several antibiotics, including ampicillin, amoxicillin-clavulanic acid, cefepime, ceftazidime, norfloxacin, levofloxacin, and chloramphenicol. Specifically, isolates designated as ARM03 and ARM06 were resistant to piperacillin-tazobactam, ARM04 and ARM05 had intermediate resistance to both piperacillin-tazobactam and imipenem, and ARM03 showed intermediate resistance to amikacin. We further identified antimicrobial resistance (AMR) genes in four Armenian isolates, including
bla
OXA-1
,
bla
TEM-1D
,
bla
SHV-28
,
dfrA14
,
tet(A
),
sul2
,
qnrB1
,
aac(6´)-Ib-cr
,
strA
,
strB
and the extended-spectrum β-lactamase gene
bla
CTX-M-15
. Additionally, ARM03 and ARM06 also obtained
dfrA5
,
sul1
,
sul3
,
cmlA1
,
mphA
,
aph3-Ia
and the unique colistin resistance gene
mcr-8.1
, which was absent in all other publicly available ST307 isolates. These two isolates also acquired aerobactin siderophore-encoding gene clusters (
iucABCD-iutA
) and the hypermucoidy locus
rmpADC
(ARM06 had
rmpA
fragment). ARM04 and ARM05, as well as ARM03 and ARM06, had nearly identical AMR and virulence genes, along with similar plasmid replicon profiles, respectively. Our findings suggest that a transmission event occurred between the two hospitals in Armenia, likely facilitated by patients or community members, during which
K. pneumoniae
ST307 isolates acquired plasmids carrying AMR and virulence genes.

IMPORTANCE

Multidrug-resistant (MDR)
Klebsiella pneumoniae
sequence type (ST) 307 has emerged as a high-risk clone associated with hospital- and community-acquired infections, posing a major threat to global public health. We report in-depth comparative genomics analyses of
K. pneumoniae
ST307 isolates recovered from patients in Armenia. The unique colistin resistance gene
mcr-8.1
identified in ARM03 and ARM06 was absent in all other ST307 isolates obtained from the publicly available data sets. ARM03 and ARM06 also acquired aerobactin siderophore-encoding gene clusters (
iucABCD-iutA
) and the hypermucoidy locus
rmpADC
(ARM06 possessed incomplete
rmpA
fragment). Our findings suggest that a transmission event has occurred between two hospitals in Armenia either through patients or community members. In addition, the Armenian isolates obtained plasmids carrying virulence and AMR genes during the transmission event. Our study emphasises the importance of genomic surveillance of this emerging MDR-hypervirulent pathogen to provide early interventions.