To demonstrate the detailed genetic characteristics of a blaNDM–1-carrying multidrug-resistant Aeromonas caviae strain, the complete genome of the A. caviae strain K433 was sequenced by Illumina HiSeq and Oxford nanopore platforms, and mobile genetic elements associated with antibiotic resistance genes were analyzed by a series of bioinformatics methods. A. caviae K433 which was determined to produce class B carbapenemase, was resistant to most antibiotics tested except amikacin. The genome of K433 consisted of a chromosome cK433 (6,482-kb length) and two plasmids: pK433-qnrS (7.212-kb length) and pK433-NDM (200.855-kb length), the last being the first investigated blaNDM-carrying plasmid from Aeromonas spp. By comparison of the backbone and MDR regions from the plasmids studied, they involved a highly homologous sequence structure. This study provides in-depth genetic insights into the plasmids integrated with blaNDM-carrying genetic elements from Aeromonas spp.
Impact statement
We have developed a manually curated online reference database, DANMEL (http://124.239.252.254/danmel/), that addresses the lack of accurate dissection and annotation of the genetic structures of mobile genetic elements (MGEs) with genes for drug resistance. DANMEL contains accurately annotated and genetically dissected reference MGEs covering 5 categories and 135 subcategories/subfamilies of MGEs. Further, DANMEL provides a detailed guide on how to precisely annotate MGEs. DANMEL also provides SEARCH/BLAST functions to facilitate finding reference MGEs. Overall, DANMEL will aid researchers to conduct in‐depth genetic analysis of sequenced bacterial MGEs with drug‐resistance genes and further facilitate a better understanding of bacterial MGEs associated with drug resistance at a genomic level.
This is the first report of extensively drug-resistant
C. portucalensis
harboring both
bla
KPC-2
and
bla
NDM-1
. This study will not only extend the understanding of the structural dissection of plasmids and chromosomes carried in
C. portucalensis
, but also expand knowledge of the genetic environment of the
bla
KPC-2
and
bla
NDM-1
genes.
bla
KPC-2
and
bla
NDM-1
genes have been suggested to facilitate the propagation and persistence of their host bacteria under different antimicrobial selection pressures.
Purpose
This study aimed to explore the genomic characterization of multidrug-resistant IncHI5-carrying
Klebsiella michiganensis
strains and detailed genomic dissection of the IncHI5 plasmids.
Materials and Methods
Through whole-genome sequencing, the IncHI5 plasmid pK92-qnrS was obtained from a single clinical
K. michiganensis
isolate K92. All complete genomes of
K. michiganensis
strains from the Genome database of NCBI were collected and used to construct a maximum likelihood (ML) phylogenetic tree. The epidemiology and geographic distribution of all the
K. michiganensis
strains were conducted. An extensive comparison of the seven IncHI5 plasmids of
K. michiganensis
(one from this study, six from GenBank) was applied.
Results
This study revealed that all
K. michiganensis
strains carrying IncHI5 plasmids from different clonal groups were located in the southeast coastal area of China. The backbone regions of IncHI5 plasmids were composed of replicon (
repHI5B
and
repFIB
), partition (
parABC
), and conjugal transfer (
tra1
/
tra2
). The main accessory resistant regions of IncHI5 could be divided into two categories, Tn
1696
-related region and Tn
6535
-related region. These seven IncHI5 plasmids carried multiple drug-resistance genes which were all mediated by the mobile genetic elements (MGEs).
Conclusion
Data presented here help to provide an overall in-depth understanding of epidemiology and geographic distribution of IncHI5-carrying
K. michiganensis
and the structure and evolutionary history of IncHI5 plasmids.
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