Molecular characterization of blaKHM-1 encoding plasmid in an Enterobacter hormaechei subsp. hoffmannii isolate from blood culture
Autoři:
Kaoru Umeda aff001; Hiromi Nakamura aff001; Akira Fukuda aff001; Takahiro Yamaguchi aff001; Yuki Matsumoto aff002; Daisuke Motooka aff002; Shota Nakamura aff002; Ryuji Kawahara aff001
Působiště autorů:
Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
aff001; Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
aff002
Vyšlo v časopise:
PLoS ONE 15(1)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0227605
Souhrn
KHM-1 was first reported in 1997 in Japan as a novel metallo-β-lactamase mediated by Citrobacter freundii carrying pKHM-1 plasmid. There have been few reports in the clinical field since then. A blaKHM-1–positive Enterobacter hormaechei subsp. hoffmannii in E. cloacae complex, isolate OIPH-N069 was isolated from an inpatient blood culture in 2016. The isolate was characterized by whole-genome sequencing, comparative analysis of the blaKHM-1 encoding plasmid, antimicrobial susceptibility tests, and bacterial conjugation. OIPH-N069 was classified into ST78 of E. cloacae complex, and was multidrug resistant because of the presence of antimicrobial resistance genes in addition to blaKHM-1 on its chromosome and plasmids. blaKHM-1 was located on 136,816 bp of the IncA/C2 plasmid pN069-1, which could be transferred to different bacterial species. The backbone structure, genetic arrangement of the class 1 integron cassette, and the blaKHM-1 gene located downstream of the IncA/C2 antibiotic resistance island, ARI-A, in pN069-1 and pKHM-1 were identical. Horizontal gene transfer of the blaCTX-M-2–ISEcp1 resistance gene module only occurred with pN069-1. The study findings indicate not only the structural conservation of blaKHM-1 encoding plasmids over time and across species, but also the risk of the spread of blaKHM-1 encoding plasmids to other bacterial species and the accumulation of additional resistance genes.
Klíčová slova:
Antimicrobial resistance – Antimicrobials – Comparative genomics – Enterobacteriaceae – Genome analysis – Japan – Plasmids – Sequence databases
Zdroje
1. Logan LK, Weinstein RA. The epidemiology of carbapenem-resistant Enterobacteriaceae: the impact and evolution of a global menace. J Infect Dis. 2017; 215:S28–S36. doi: 10.1093/infdis/jiw282 28375512
2. van Duin D, Doi Y. The global epidemiology of carbapenemase-producing Enterobacteriaceae. Virulence. 2017; 8:460–469. doi: 10.1080/21505594.2016.1222343 27593176
3. Sheu C, Chang Y, Lin S, Chen Y, Hsueh P. Infections caused by carbapenem-resistant Enterobacteriaceae: an update on therapeutic options. Front Microbiol. 2019; 10:80. doi: 10.3389/fmicb.2019.00080 30761114
4. Sekiguchi J, Morita K, Kitao T, Watanabe N, Okazaki M, Miyoshi-Akiyama T, et al. KHM-1, a novel plasmid-mediated metallo-β-lactamase from a Citrobacter freundii clinical isolate. Atimicrob Agents Chemother. 2008; 52:4194–4197.
5. Sutton G, Brinkac L, Clarke T, Fouts D. Enterobacter hormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes. F1000Res. 2018; 7:521. doi: 10.12688/f1000research.14566.2 30430006
6. Clinical and Laboratory Standard Institute. Performance standards for antimicrobial susceptibility testing: Twenty-fifth informational supplement, CLSI document M100-S25. Wayne, PA. Clinical Laboratory Standards Institute. 2015.
7. Dortret L, Poirel L, Nordmann P. Rapid identification of Carbapenemase types in Enterobacteriaceae and Pseudomonas spp. by using a biochemical test. Antimicrob Agents Chemother. 2012; 56:6437–6440. doi: 10.1128/AAC.01395-12 23070158
8. National Institute of Infectious Diseases. Pathogen detection manual, drug resistant bacteria (in Japanese). 2016. Available from:https://www.niid.go.jp/niid/images/lab-manual/ResistantBacteria201612V1.1.pdf.
9. Kudo H, Usui M, Nagafuji W, Oka K, Takahashi M, Yamaguchi H, et al. Inhibition effect of flavophospholipol on conjugative transfer of the extended-spectrum β-lactamase and vanA genes. J Antibiot. 2019; 72:79–85. doi: 10.1038/s41429-018-0113-4 30361635
10. Usui M, Hiki M, Murakami K, Ozawa M, Nagai H, Asai T. Evaluation of transferability of R-plasmid in bacteriocin-producing donors to bacteriocin-resistant recipients. Jpn J Infect Dis. 2012; 65:252–255. doi: 10.7883/yoken.65.252 22627309
11. Jin Y, Song X, Liu Y, Wang Y, Zhang B, Fan H, et al. Characteristics of carbapenemase-producing Klebsiella pneumoniae as a cause of neonatal infection in Shandong, China. Exp Ther Med. 2017; 13:1117–1126. doi: 10.3892/etm.2017.4070 28450951
12. Wick R, Judd M, Gorrie C, Holt K. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017; 13:e1005595. doi: 10.1371/journal.pcbi.1005595 28594827
13. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics. 2018; 34:1037–1039. doi: 10.1093/bioinformatics/btx713 29106469
14. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012; 67:2640–2644. doi: 10.1093/jac/dks261 22782487
15. Carattoli A, Zankari E, Garcia-Fernandez A, Voldby Larsen M, Lund O, Villa L, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014; 58:3895–3903. doi: 10.1128/AAC.02412-14 24777092
16. Larsen M, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig R, et al. Multilocus sequence typing of total genome sequenced bacteria. J Clin Microbiol. 2012; 50:1355–1361. doi: 10.1128/JCM.06094-11 22238442
17. Goris J, Konstantinidis K, Klappenbach J, Coenye T, Vandamme P, Tiedje J. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol. 2007; 57:81–91. doi: 10.1099/ijs.0.64483-0 17220447
18. Chavda K, Chen L, Fouts D, Sutton G, Brinkac L, Jenkins S, et al. Comprehensive genome analysis of carbapenemase-producing Enterobacter spp.: New insights into phylogeny, population structure, and resistance mechanisms. MBio. 2016; 7:e02093–e02016. doi: 10.1128/mBio.02093-16 27965456
19. Kim M, Oh H, Park S, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014; 64:346–351. doi: 10.1099/ijs.0.059774-0 24505072
20. Moura A, Soares M, Pereira C, Leitão N, Henriques I, Correia A. INTEGRALL: a database and search engine for integrons, integrases, and gene cassettes. Bioinformatics. 2009; 25:1096–1098. doi: 10.1093/bioinformatics/btp105 19228805
21. Alikhan N, Petty N, Ben Zakour N, Beatson S. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. 2011; 12:402. doi: 10.1186/1471-2164-12-402 21824423
22. Sullivan M, Petty N, Beatson S. Easyfig: a genome comparison visualizer. Bioinformatics. 2011; 27:1009–1010. doi: 10.1093/bioinformatics/btr039 21278367
23. Stoesser N, Sheppard A, Peirano G, Sebra R, Lynch T, Anson L, et al. First report of blaIMP-14 on a plasmid harboring multiple drug resistance genes in Escherichia coli sequence type 131. Antimicrob Agents Chemother. 2016; 60:5068–5071. doi: 10.1128/AAC.00840-16 27246777
24. Sunagawa Y, Akeda Y, Sakamoto N, Takeuchi D, Motooka D, Nakamura S, et al. Genetic characterization of blaNDM-harboring plasmids in carbapenem-resistant Escherichia coli from Myanmer. PLoS ONE. 2017; 12:e0184720. doi: 10.1371/journal.pone.0184720 28910381
25. Annavajhala M, Gomez-Simmonds A, Uhlemann A. Multidrug-resistant Enterobacter cloacae complex emerging as a grobal, dibersifying threat. Front Microbiol. 2019; 10:44. doi: 10.3389/fmicb.2019.00044 30766518
26. Aoki K, Harada S, Yahara K, Ishii Y, Motooka D, Nakamura S,et al. Molecular characterization of IMP-1-producing Enterobacter cloacae complex isolates in Tokyo. J Antimicrob Chemother. 2018; 62:e02091–17.
27. Suzuki Y, Ida M, Kubota H, Ariyoshi T, Murakami K, Kobayashi M, et al. Multiple β-lactam resistance gene-carrying plasmid harbored by Klebsiella quasipneumoniae isolated from urban sewage in Japan. mSphere. 2019; 4:e00391–19. doi: 10.1128/mSphere.00391-19 31554719
28. Magiorakos A, Srinivasan A, Carey R, Carmeli Y, Falagas M, Giske C, et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect. 2011; 18:268–281. doi: 10.1111/j.1469-0691.2011.03570.x 21793988
29. Harmer C, Hall R. The A to Z of A/C plasmids. Plasmid. 2015; 80:63–82. doi: 10.1016/j.plasmid.2015.04.003 25910948
30. Papagiannitsis C, Dolegjska M, Izdebski R, Giakkoupi P, Skalova A, Chudějová K, et al. Characterization of IncA/C2 plasmids carrying an In416-like integron with the blaVIM-19 gene from Klebsiella pneumoniae ST383 of Greek origin. Int J Antimicrob Agents. 2016; 47:158–162. doi: 10.1016/j.ijantimicag.2015.12.001 26795022
31. Kayama S, Shigemoto N, Kuwahara R, Oshima K, Hirakawa H, Hisatsune J, et al. Complete nucleotide sequence of the IncN plasmid encoding IMP-6 and CTX-M-2 from emerging carbapenem-resistant Enterobacteriaceae in Japan. Antimicrob Agents Chemother. 2015; 59:1356–1359. doi: 10.1128/AAC.04759-14 25487806
Článek vyšel v časopise
PLOS One
2020 Číslo 1
- Vyhodnocuje AI zdravotní stav pacientů přesněji než lékaři?
- Další krok vpřed v managementu péče o pacienty s RS – skeny mozku vyhodnotí AI
- Budou elektronické močové svěrače na dálkové ovládání?
- Přírodní neznamená vždy lepší aneb jak se vypořádat s naturalistickým klamem
- Souboj lékaře a TikToku o důvěru pacienta. Kdo vyhrává?
Nejčtenější v tomto čísle
- Severity of misophonia symptoms is associated with worse cognitive control when exposed to misophonia trigger sounds
- Chemical analysis of snus products from the United States and northern Europe
- Calcium dobesilate reduces VEGF signaling by interfering with heparan sulfate binding site and protects from vascular complications in diabetic mice
- Effect of Lactobacillus acidophilus D2/CSL (CECT 4529) supplementation in drinking water on chicken crop and caeca microbiome
Zvyšte si kvalifikaci online z pohodlí domova
Všechny kurzy