Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major threat to global health. Here, we report the draft genome sequence of a Klebsiella pneumoniae clinical strain carrying mcr-8.1 and blaNDM-5.
ABSTRACT
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major threat to global health. Here, we report the draft genome sequence of a Klebsiella pneumoniae clinical strain carrying mcr-8.1 and blaNDM-5.
ANNOUNCEMENT
Infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) have been increasing in recent years in hospitals and communities, which has attracted concern worldwide (1). Polymyxin is used as the last-resort antimicrobial drug for treating CRKP (2) infections. The mcr gene encodes the production of an enzyme which can alter the cell membrane of CRKP, enabling the bacteria to be resistant to polymyxin. However, a variety of mcr gene subtypes have been found since the first report of the plasmid-mediated colistin resistance gene mcr-1 in 2015 (3–9). Studies show that the use of colistin has probably accelerated the dissemination of the mcr gene in animals and humans. K. pneumoniae strain 163109936 was recovered from the sputum sample of a 37-year-old male patient in the bone marrow transplantation department at a tertiary hospital in Hunan Province, China, in August 2016. The sputum was then plated and screened using sheep blood agar overnight. The MIC of colistin was determined using the broth microdilution method. The study was approved by the Human Ethics Committee of Xiangya Hospital of Central South University in Changsha, China (number 201806861). Strain 163109936 is resistant to ertapenem (MIC, ≥8 μg/ml), imipenem (MIC, ≥16 μg/ml), meropenem (MIC, 6 μg/ml), and polymyxin B (MIC, 8 μg/ml). The extensive drug resistance caught our attention. Therefore, this isolate was subjected to whole-genome sequencing.
The isolate was grown on LB broth at 37°C and harvested by centrifugation at 10,000 rpm for 1 min. Genomic DNA from strain 163109936 was extracted from the sample using a TIANamp bacterial DNA kit (Tiangen Biotech Co. Ltd., Beijing, China). The library was generated using the MGIEasy universal DNA library prep set (item number 1000006985). Sequencing was performed on a BGISEQ-500 sequencing platform (MGI, Shenzhen, China) with the paired-end 150-bp strategy. A total of 0.811 Gb was generated, and raw reads were filtered using fastp v 0.18.0 (10) and SOAPnuke (11) v 2.1.2 with default settings. The clean reads were assembled using SPAdes v 3.10.1 (12) with default settings. A total of 163 contigs (N50, 346,937 bp; N90, 34,594 bp; total length, 5,813,626 bp) were generated with 56.64% G+C content. The genome with a size of 5.8 Mb was annotated using Prokka v 1.14 (13) with default settings. Multilocus sequence typing (MLST) of K. pneumoniae was performed according to the protocol described on the Pasteur Institute MLST website (http://bigsdb.pasteur.fr/klebsiella/). The strain belongs to sequence type 685 (ST685), which has been found in China, Italy, and Turkey (14, 15).
The K. pneumoniae strain 163109936 genome contains 5,426 coding sequences and 88 tRNA genes. Antimicrobial resistance genes were identified using Resistance Gene Identifier v 4.0.3 (16) with default settings. According to our results, the strain was positive for several antimicrobial resistance genes, including blaNDM-5 (carbapenemase gene), blaTEM-1, and blaCTX-M-65. Most importantly, the colistin resistance gene mcr-8.1 was also found. The presence of these genes could confer polymixin resistance, though this would need to be further validated. Plasmid replicons were also predicted with the presence of 10 replicons, IncFIB, IncFII, ColRNAI, IncR, Col, IncFIA, IncX3, TrfA, IncHI2A, and IncHI2.
In conclusion, a polymyxin-resistant Klebsiella pneumoniae clinical strain carrying mcr-8.1 and blaNDM-5 was characterized. This reminds us that continuous monitoring of polymyxin resistance is urgent in clinical practice.
Data availability.
This draft genome sequence has been deposited at GenBank under the accession number JACJVA000000000. The version described in this paper is version JACJVA010000000. The raw reads have been submitted to the Sequence Read Archive (SRA) database under the accession number SRR12995617.
ACKNOWLEDGMENTS
This work was supported by the Science, Technology, and Innovation Commission of Shenzhen Municipality under grant number JCYJ20170412153155228 and the National Natural Science Foundation of China (grant number 81672066). We are also grateful for the support by China National GeneBank (CNGB).
REFERENCES
- 1.Mendes AC, Novais A, Campos J, Rodrigues C, Santos C, Antunes P, Ramos H, Peixe L. 2018. mcr-1 in carbapenemase-producing Klebsiella pneumoniae with hospitalized patients, Portugal, 2016–2017. Emerg Infect Dis 24:762–766. doi: 10.3201/eid2404.171787. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Petrosillo N, Taglietti F, Granata G. 2019. Treatment options for colistin resistant Klebsiella pneumoniae: present and future. J Clin Med 8:934. doi: 10.3390/jcm8070934. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Dhaouadi S, Soufi L, Hamza A, Fedida D, Zied C, Awadhi E, Mtibaa M, Hassen B, Cherif A, Torres C, Abbassi MS, Landolsi RB. 2020. Co-occurrence of mcr-1 mediated colistin resistance and β-lactamase-encoding genes in multidrug-resistant Escherichia coli from broiler chickens with colibacillosis in Tunisia. J Glob Antimicrob Resist 22:538–545. doi: 10.1016/j.jgar.2020.03.017. [DOI] [PubMed] [Google Scholar]
- 4.Wang X, Wang Y, Zhou Y, Li J, Yin W, Wang S, Zhang S, Shen J, Shen Z, Wang Y. 2019. Emergence of a novel mobile colistin resistance gene, mcr-8, in NDM-producing Klebsiella pneumoniae. Emerg Microbe Infect 7:122. doi: 10.1038/s41426-018-0124-z. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Yuan Y, Li Y, Wang G, Li C, Xiang L, She J, Yang Y, Zhong F, Zhang L. 2019. Coproduction Of MCR-9 and NDM-1 by colistin-resistant Enterobacter hormaechei isolated from bloodstream infection. Infect Drug Resist 12:2979–2985. doi: 10.2147/IDR.S217168. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Wang C, Feng Y, Liu L, Wei L, Kang M, Zong Z. 2020. Identification of novel mobile colistin resistance gene mcr-10. Emerg Microbes Infect 9:508–516. doi: 10.1080/22221751.2020.1732231. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Fernandes MR, Cerdeira L, Silva MM, Sellera FP, Muñoz M, Junior FG, Azevedo SS, Power P, Gutkind G, Lincopan N. 2018. Novel mcr-5.3 variant in a CTX-M-8-producing Escherichia coli ST711 isolated from an infected horse. J Antimicrob Chemother 73:3520–3522. doi: 10.1093/jac/dky341. [DOI] [PubMed] [Google Scholar]
- 8.Yang YQ, Li YX, Lei CW, Zhang AY, Wang HN. 2018. Novel plasmid-mediated colistin resistance gene mcr-7.1 in Klebsiella pneumoniae. J Antimicrob Chemother 73:1791–1795. doi: 10.1093/jac/dky111. [DOI] [PubMed] [Google Scholar]
- 9.Liu Y-Y, Wang Y, Walsh TR, Yi L-X, Zhang R, Spencer J, Doi Y, Tian G, Dong B, Huang X, Yu L-F, Gu D, Ren H, Chen X, Lv L, He D, Zhou H, Liang Z, Liu J-H, Shen J. 2016. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect Dis 16:161–168. doi: 10.1016/S1473-3099(15)00424-7. [DOI] [PubMed] [Google Scholar]
- 10.Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890. doi: 10.1093/bioinformatics/bty560. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Chen Y, Chen Y, Shi C, Huang Z, Zhang Y, Li S, Li Y, Ye J, Yu C, Li Z, Zhang X, Wang J, Yang H, Fang L, Chen Q. 2018. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience 7:1–6. doi: 10.1093/gigascience/gix120. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A, Lapidus A, Prjibelsky A, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R. 2013. Assembling genomes and mini-metagenomes from highly chimeric reads, p 158–170. In Deng M, Jiang R, Sun F, Zhang X (eds), Research in computational molecular biology. RECOMB 2013. Lecture notes in computer science, vol 7821. Springer, Berlin, Germany. [Google Scholar]
- 13.Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi: 10.1093/bioinformatics/btu153. [DOI] [PubMed] [Google Scholar]
- 14.Bianchi A, Pregliasco FE, Consonni M, Tesauro M. 2016. Genotypic diversity of Legionella pneumophila in environmental and clinical strains assessed by sequence-based typing, in association with retrospective clinical surveillance in northern Italy. Ann Agric Environ Med 23:248–253. doi: 10.5604/12321966.1203885. [DOI] [PubMed] [Google Scholar]
- 15.Çavuşoğlu C, Yılmaz FF. 2017. Molecular epidemiology of human Mycobacterium bovis infection in Aegean Region, Turkey. Mikrobiyol Bul 51:165–170. (In Turkish.) doi: 10.5578/mb.53963. [DOI] [PubMed] [Google Scholar]
- 16.Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen A-LV, Cheng AA, Liu S, Min SY, Miroshnichenko A, Tran H-K, Werfalli RE, Nasir JA, Oloni M, Speicher DJ, Florescu A, Singh B, Faltyn M, Hernandez-Koutoucheva A, Sharma AN, Bordeleau E, Pawlowski AC, Zubyk HL, Dooley D, Griffiths E, Maguire F, Winsor GL, Beiko RG, Brinkman FSL, Hsiao WWL, Domselaar GV, McArthur AG. 2020. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 48:D517–D525. doi: 10.1093/nar/gkz935. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
This draft genome sequence has been deposited at GenBank under the accession number JACJVA000000000. The version described in this paper is version JACJVA010000000. The raw reads have been submitted to the Sequence Read Archive (SRA) database under the accession number SRR12995617.