Dataset Information

Carriage of distinct bla_KPC-2 and bla_OXA-48 plasmids in a single ST11 hypervirulent Klebsiella pneumoniae isolate in Egypt.

ABSTRACT:

Background

Carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) causes serious infections with significant morbidity and mortality. However, the epidemiology and transmission mechanisms of CR-hvKP and the corresponding carbapenem-resistant plasmids require further investigation. Herein, we have characterized an ST11 K. pneumoniae strain EBSI041 from the blood sample encoding both hypervirulence and carbapenem resistance phenotypes from a patient in Egypt.

Results

K. pneumoniae strain EBSI041 showed multidrug-resistance phenotypes, where it was highly resistant to almost all tested antibiotics including carbapenems. And hypervirulence phenotypes of EBSI041 was confirmed by the model of Galleria mellonella infection. Whole-genome sequencing analysis showed that the hybrid plasmid pEBSI041-1 carried a set of virulence factors rmpA, rmpA2, iucABCD and iutA, and six resistance genes aph(3')-VI, armA, msr(E), mph(E), qnrS, and sul2. Besides, bla_OXA-48 and bla_SHV-12 were harboured in a novel conjugative IncL-type plasmid pEBSI041-2. The bla_KPC-2-carrying plasmid pEBSI041-3, a non-conjugative plasmid lacking the conjugative transfer genes, could be transferred with the help of pEBSI041-2, and the two plasmids could fuse into a new plasmid during co-transfer. Moreover, the emergence of the p16HN-263_KPC-like plasmids is likely due to the integration of pEBSI041-3 and pEBSI041-4 via IS26-mediated rearrangement.

Conclusion

To the best of our knowledge, this is the first report on the complete genome sequence of KPC-2- and OXA-48-coproducing hypervirulent K. pneumoniae from Egypt. These results give new insights into the adaptation and evolution of K. pneumoniae during nosocomial infections.

SUBMITTER: Yang Y

PROVIDER: S-EPMC8742346 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:The emergence and spread of carbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious medical problem worldwide. Acquired OXA-48-like carbapenemases encoded by plasmids are important causes of carbapenem resistance in K. pneumoniae. To explore the links between plasmids and bla OXA-48-like genes in K. pneumoniae, we systematically analyzed the variants of bla OXA-48-like plasmid replicon types, phylogenetic patterns, geographic distribution, conjugative transfer regions, and the genetic environments surrounding bla OXA-48-like of 191 bla OXA-48-like-harboring plasmids, which were identified from 4451 plasmids of K. pneumoniae downloaded from GenBank. Our results showed that seven different variants of bla OXA-48-like genes were identified from the 191 bla OXA-48-like-harboring plasmids in K. pneumoniae, with bla OXA-48, bla OXA-232, and bla OXA-181 being highly prevalent. In K. pneumoniae, bla OXA-48 was mainly carried by the composite transposon Tn1999.2 located on IncL/M-type conjugative plasmids, which were mainly geographically distributed in Switzerland, Germany, and China. In K. pneumoniae, the blaOXA-232 gene was mainly carried by 6.1-kb ColKP3-type mobilizable plasmids, which were mainly isolated in India. In K. pneumoniae, bla OXA-181 was mainly carried by a group of 50-kb ColKP3-IncX3 hybrid conjugative plasmids and a group of small ColKP3-type mobilizable plasmids with lengths of 5.9-9.3 kb, the former was sporadically discovered in China, South Korea, India, and Czech Republic, while the latter was almost all isolated in India. In addition, five bla OXA-245-harboring 65.9-kb IncL plasmids of K. pneumoniae isolated in Spain were found to have the genetic context of bla OXA-245 more complicated than that of bla OXA-48-harboring IncL/M-type plasmids, with two copies of IS1R inserted both upstream and downstream of bla OXA-245-lysR. These findings enhance our understanding of the genetic diversity of bla OXA-48-like-harboring plasmids in K. pneumoniae.

Project description:IntroductionCeftazidime/avibactam (CZA) is an effective alternative for the treatment of infections caused by KPC-producing carbapenem-resistant Klebsiella pneumoniae (CRKP). However, KPC variants with CZA resistance have been observed in clinical isolates, further limiting the treatment options of clinical use.MethodsIn this study, we isolated three KPC-14-producing CRKP from two patients in intensive care units without CZA therapy. The antimicrobial susceptibility was determined using the broth microdilution method. Three CRKP were subjected to whole-genome sequencing to analyze the phylogenetic relatedness and the carriage of antimicrobial resistance genes and virulence factors. Long-read sequencing was also performed to obtain the complete sequences of the plasmids. The horizontal transfer of the blaKPC-14 gene was evaluated by conjugation experiments.ResultsThree CRKP displayed resistance or reduced susceptibility to ceftazidime/avibactam, colistin, and tigecycline. Single-nucleotide polymorphism (SNP) analysis demonstrated the close phylogenetic distance between these strains. A highly similar IncFII/IncR plasmid encoding blaKPC-14 was shared by three CRKP, with blaKPC-14 located in an NTEKPC-Ib element with the core region of ISKpn27- blaKPC-14-ISKpn6. This structure containing blaKPC-14 was also observed in another tet(A)-carrying plasmid that belonged to an unknown Inc-type in two out of three isolates. The horizontal transferability of these integrated plasmids to Escherichia coli EC600 was confirmed by the cotransmission of tet(A) and blaKPC-14 genes, but the single transfer of blaKPC-14 on the IncFII/IncR plasmid failed. Three CRKP expressed yersiniabactin and carried a hypervirulence plasmid encoding rmpA2 and aerobactin-related genes, and were thus classified as carbapenem-resistant hypervirulent K. pneumoniae (hvKP).DiscussionIn this study, we reported the evolution of a mosaic plasmid encoding the blaKPC-14 gene via mobile elements in extensively drug-resistant hvKP. The blaKPC-14 gene is prone to integrate into other conjugative plasmids via the NTEKPC-Ib element, further facilitating the spread of ceftazidime/avibactam resistance.

Project description:The emergence of carbapenemase-producing Enterobacterales (CPE) infections is a major global public health threat. Rapid and accurate detection of pathogenic bacteria is essential to optimize treatment and timely avoid further transmission of these bacteria. Here, we aimed to develop a rapid on site visualization detection method for CPE using improved recombinase polymerase amplification (RPA) combined with lateral flow strip (LFS) method, based on four most popular carbapenemase genes: bla KPC, bla NDM, bla OXA-48-like, and bla IMP. All available allelic variants of the above carbapenemases were downloaded from the β-lactamase database, and the conserved regions were used as targets for RPA assay. Five primer sets were designed targeting to each carbapenemase gene and the RPA amplification products were analyzed by agarose gel electrophoresis. FITC-labeled specific probes were selected, combined with the best performance primer set (Biotin-labeled on the reverse primer), and detected by RPA-LFS. Mismatches were made to exclude the false positive signals interference. This assay was evaluated in 207 clinically validated carbapenem-resistant Enterobacterales (CRE) isolates and made a comparison with conventional PCR. Results showed that the established RPA-LFS assay for CPE could be realized within 30 min at a constant temperature of 37°C and visually detected amplification products without the need for special equipment. This assay could specifically differentiate the four classes of carbapenemases without cross-reactivity and shared a minimum detection limit of 100 fg/reaction (for bla KPC, bla NDM, and bla OXA-48-like) or 1000 fg/reaction (for bla IMP), which is ten times more sensitive than PCR. Furthermore, the detection of 207 pre-validated clinically CRE strains using the RPA-LFS method resulted in 134 bla KPC, 69 bla NDM, 3 bla OXA-48-like, and 1 bla IMP. The results of the RPA-LFS assay were in consistent with PCR, indicating that this method shared high sensitivity and specificity. Therefore, the RPA-LFS method for CPE may be a simple, specific, and sensitive method for the rapid diagnosis of carbapenemase Enterobacterales.

Dataset Information

Carriage of distinct bla_KPC-2 and bla_OXA-48 plasmids in a single ST11 hypervirulent Klebsiella pneumoniae isolate in Egypt.

Background

Results

Conclusion

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Dataset Information

Carriage of distinct blaKPC-2 and blaOXA-48 plasmids in a single ST11 hypervirulent Klebsiella pneumoniae isolate in Egypt.

Background

Results

Conclusion

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Carriage of distinct bla_KPC-2 and bla_OXA-48 plasmids in a single ST11 hypervirulent Klebsiella pneumoniae isolate in Egypt.