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Decoding the genetic structure of conjugative plasmids in international clones of Klebsiella pneumoniae: A deep dive into blaKPC, blaNDM, blaOXA-48, and blaGES genes
Carbapanem-resistant Klebsiella pneumoniae is a globally healthcare crisis. The distribution of plasmids carrying carbapenemase genes among K . pneumoniae poses a serious threat in clinical settings. Here, we characterized the genetic structure of plasmids harboring major carbapenemases (e.g. bla KP...
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Published in: | PloS one 2023-11, Vol.18 (11), p.e0292288-e0292288 |
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Main Authors: | , , , , |
Format: | Article |
Language: | English |
Subjects: | |
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Online Access: | Get full text |
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Summary: | Carbapanem-resistant
Klebsiella pneumoniae
is a globally healthcare crisis. The distribution of plasmids carrying carbapenemase genes among
K
.
pneumoniae
poses a serious threat in clinical settings. Here, we characterized the genetic structure of plasmids harboring major carbapenemases (e.g.
bla
KPC
,
bla
NDM
,
bla
OXA-48
-like
,
and
bla
GES
) from
K
.
pneumoniae
using bioinformatics tools. The plasmids carrying at least one major carbapenemase gene were retrieved from the GenBank database. The DNA length, Inc type, and conjugal apparatus of these plasmids were detected. Additionally, allele types, co-existence, co-occurrence of carbapenemase genes, gene repetition, and sequence types of isolates, were characterized. There were 2254 plasmids harboring carbapenemase genes in the database. This study revealed that
bla
KPC-2
,
bla
NDM-1
,
bla
OXA-48
, and
bla
GES-5
were the most prevalent allele types. Out of 1140 (50%) plasmids were potentially conjugative. IncFII, IncR, IncX3, and IncL replicon types were predominant. The co-existence analysis revealed that the most prevalent of other resistance genes were
bla
TEM-1
(related to
bla
KPC
),
bla
OXA-232
(related to
bla
OXA-48
),
ble
MBL
(related to
bla
NDM
), and
aac (6′)-Ib4
(related to
bla
GES
). The co-occurrence of carbapenemases was detected in 42 plasmids while 15 plasmids contained carbapenemase gene repetitions. Sequence alignments highlighted that plasmids carrying
bla
KPC
and
bla
OXA-48
-like were more homogeneous whereas the plasmids carrying
bla
NDM
were divergent. It seems that
K
.
pneumoniae
utilizes diversity of genetic flexibility and recombination for resistance against carbapenems. The genetic structure of the plasmids showed that class I and III, Tn3 family, Tn5403 family derivatives, and Tn7-like elements were strongly associated with carbapenemases. The mobilizable plasmids carrying carbapenemases play an important role in the spread of these genes. In addition, gene repetition maybe is related to carbapenem heteroresistance. According to MST (minimum spanning tree) results, the majority of plasmids belonged to sequence type (ST) 11, ST14, and ST12. These international clones have a high capacity to acquire the carbapenemase-containing plasmids. |
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ISSN: | 1932-6203 1932-6203 |
DOI: | 10.1371/journal.pone.0292288 |