Genomic analysis of a pan-resistant isolate of Klebsiella pneumoniae, United States 2016

mBio

Volumn 9, Issue 2, 2018, Pages

  de Man, Tom J B ^a   Lutgring, Joseph D ^a,b   Lonsway, David R ^a   Anderson, Karen F ^a   Kiehlbauch, Julia A ^c,d   Chen, Lei ^e   Walters, Maroya Spalding ^a   Sjölund Karlsson, Maria ^a   Rasheed, J Kamile ^a   Kallen, Alexander ^a   Halpin, Alison Laufer ^a  

^a NATIONAL CENTER FOR EMERGING AND ZOONOTIC INFECTIOUS DISEASES   (United States)

^b EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c Nevada State Health Laboratory   (United States)

^d UNIVERSITY OF NEVADA   (United States)

^e Air Quality Management Division   (United States)

Author keywords

Carbapenems; Colistin; Klebsiella pneumoniae; Plasmid mediated resistance; Whole genome sequencing

Indexed keywords

AMIKACIN; AMPICILLIN; AVIBACTAM; AZTREONAM; BETA LACTAM; BETA LACTAMASE; CEFAZOLIN; CEFEPIME; CEFOTAXIME; CEFOXITIN; CEFTAZIDIME; CEFTRIAXONE; CHLORAMPHENICOL; CIPROFLOXACIN; CLAVULANIC ACID; COLISTIN; COTRIMOXAZOLE; DORIPENEM; FOSFOMYCIN; GENTAMICIN; IMIPENEM; LEVOFLOXACIN; MACROLIDE; MEROPENEM; PIPERACILLIN PLUS TAZOBACTAM; POLYMYXIN B; TETRACYCLINE; TIGECYCLINE; TOBRAMYCIN; UNINDEXED DRUG; ANTIINFECTIVE AGENT;

ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENETICS; BACTERIUM ISOLATE; BACTERIUM ISOLATION; BETA LACTAMASE GENE; BLACMY 6 GENE; BLACTX M 15 GENE; BLANDM 1 GENE; BLASHV 28 GENE; CHINA; CONTROLLED STUDY; GENE SEQUENCE; GENETIC ANALYSIS; GRAM NEGATIVE BACTERIUM; INDIA; KENYA; KLEBSIELLA PNEUMONIAE; NEPAL; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PRIORITY JOURNAL; SEQUENCE ANALYSIS; UNITED STATES; AGED; BACTERIAL GENOME; CASE REPORT; DNA SEQUENCE; DRUG EFFECT; FEMALE; GENETICS; HUMAN; ISOLATION AND PURIFICATION; KLEBSIELLA INFECTION; MICROBIAL SENSITIVITY TEST; MICROBIOLOGY; MULTIDRUG RESISTANCE;

AGED; ANTI-BACTERIAL AGENTS; CHINA; DRUG RESISTANCE, MULTIPLE, BACTERIAL; FEMALE; GENES, BACTERIAL; GENOME, BACTERIAL; HUMANS; KLEBSIELLA INFECTIONS; KLEBSIELLA PNEUMONIAE; MICROBIAL SENSITIVITY TESTS; PLASMIDS; SEQUENCE ANALYSIS, DNA; UNITED STATES;

EID: 85046168204     PISSN: 21612129     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00440-18     Document Type: Article

References (25)

1. CDC. 2013. Antibiotic resistance threats in the United States, 2013. CDC, Atlanta, GA. http://www.cdc.gov.
2. Patel G, Huprikar S, Factor SH, Jenkins SG, Calfee DP. 2008. Outcomes of carbapenem-resistant Klebsiella pneumoniae infection and the impact of antimicrobial and adjunctive therapies. Infect Control Hosp Epidemiol 29:1099-1106. https://doi.org/10.1086/592412.
3. Gupta N, Limbago BM, Patel JB, Kallen AJ. 2011. Carbapenem-resistant Enterobacteriaceae: epidemiology and prevention. Clin Infect Dis 53:60-67. https://doi.org/10.1093/cid/cir202.
4. Wright H, Bonomo RA, Paterson DL. 2017. New agents for the treatment of infections with Gram-negative bacteria: restoring the miracle or false dawn? Clin Microbiol Infect 23:704-712. https://doi.org/10.1016/j.cmi.2017.09.001.
5. Li J, Nation RL, Turnidge JD, Milne RW, Coulthard K, Rayner CR, Paterson DL. 2006. Colistin: the re-emerging antibiotic for multidrug-resistant Gram-negative bacterial infections. Lancet Infect Dis 6:589-601. https:// doi.org/10.1016/S1473-3099(06)70580-1.
6. 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. https://doi.org/10.1016/S1473-3099(15)00424-7.
7. Chen L, Todd R, Kiehlbauch J, Walters M, Kallen A. 2017. Notes from the field: pan-resistant New Delhi metallo-beta-lactamase-producing Klebsiella pneumoniae-Washoe County, Nevada, 2016. Morb Mortal Wkly Rep 66:33. https://doi.org/10.15585/mmwr.mm6601a7.
8. de Man TJB, Perry KA, Lawsin A, Coulliette AD, Jensen B, Toney NC, Limbago BM, Noble-Wang J. 2016. Draft genome sequence of Mycobacterium wolinskyi, a rapid-growing species of nontuberculous mycobacteria. Genome Announc 4:e00138-16. https://doi.org/10.1128/genomeA.00138-16.
9. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563-569. https://doi.org/10.1038/ nmeth.2474.
10. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963. https://doi.org/10.1371/journal.pone.0112963.
11. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV. 2012. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67:2640-2644. https://doi.org/10.1093/jac/dks261.
12. de Man TJB, Limbago BM. 2016. SSTAR, a stand-alone easy-to-use antimicrobial resistance gene predictor. mSphere 1:e00050-15. https://doi.org/10.1128/mSphere.00050-15.
13. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614-6624. https://doi.org/10.1093/nar/gkw569.
14. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. 2006. ISfinder:the reference centre for bacterial insertion sequences. Nucleic Acids Res 34:D32-D36. https://doi.org/10.1093/nar/gkj014.
15. Lee MY, Ko KS, Kang CI, Chung DR, Peck KR, Song JH. 2011. High prevalence of CTX-M-15-producing Klebsiella pneumoniae isolates in Asian countries: diverse clones and clonal dissemination. Int J Antimicrob Agents 38:160-163. https://doi.org/10.1016/j.ijantimicag.2011.03.020.
16. Caspar Y, Maillet M, Pavese P, Francony G, Brion JP, Mallaret MR, Bonnet R, Robin F, Beyrouthy R, Maurin M. 2017. mcr-1 colistin resistance in ESBL-producing Klebsiella pneumoniae, France. Emerg Infect Dis 23:874-876. https://doi.org/10.3201/eid2305.161942.
17. Harmer CJ, Hall RM. 2015. The A to Z of A/C plasmids. Plasmid 80:63-82. https://doi.org/10.1016/j.plasmid.2015.04.003.
18. Partridge SR. 2011. Analysis of antibiotic resistance regions in Gramnegative bacteria. FEMS Microbiol Rev 35:820-855. https://doi.org/10.1111/j.1574-6976.2011.00277.x.
19. Landman D, Bratu S, Quale J. 2009. Contribution of OmpK36 to carbapenem susceptibility in KPC-producing Klebsiella pneumoniae. J Med Microbiol 58:1303-1308. https://doi.org/10.1099/jmm.0.012575-0.
20. Cannatelli A, Giani T, D’Andrea MM, Di Pilato V, Arena F, Conte V, Tryfinopoulou K, Vatopoulos A, Rossolini GM; COLGRIT Study Group. 2014. MgrB inactivation is a common mechanism of colistin resistance in KPC-producing Klebsiella pneumoniae of clinical origin. Antimicrob Agents Chemother 58:5696-5703. https://doi.org/10.1128/ AAC.03110-14.
21. Deguchi T, Fukuoka A, Yasuda M, Nakano M, Ozeki S, Kanematsu E, Nishino Y, Ishihara S, Ban Y, Kawada Y. 1997. Alterations in the GyrA subunit of DNA gyrase and the ParC subunit of topoisomerase IV in quinolone-resistant clinical isolates of Klebsiella pneumoniae. Antimicrob Agents Chemother 41:699-701.
22. Sheng ZK, Hu F, Wang W, Guo Q, Chen Z, Xu X, Zhu D, Wang M. 2014. Mechanisms of tigecycline resistance among Klebsiella pneumoniae clinical isolates. Antimicrob Agents Chemother 58:6982-6985. https://doi.org/10.1128/AAC.03808-14.
23. Nikaido H. 1996. Multidrug efflux pumps of gram-negative bacteria. J Bacteriol 178:5853-5859. https://doi.org/10.1128/jb.178.20.5853-5859.1996.
24. Lamers RP, Cavallari JF, Burrows LL. 2013. The efflux inhibitor phenylalanine-arginine beta-naphthylamide (PAβN) permeabilizes the outer membrane of gram-negative bacteria. PLoS One 8:e60666. https:// doi.org/10.1371/journal.pone.0060666.
25. Stoesser N, Giess A, Batty EM, Sheppard AE, Walker AS, Wilson DJ, Didelot X, Bashir A, Sebra R, Kasarskis A, Sthapit B, Shakya M, Kelly D, Pollard AJ, Peto TEA, Crook DW, Donnelly P, Thorson S, Amatya P, Joshi S. 2014. Genome sequencing of an extended series of NDM-producing Klebsiella pneumoniae isolates from neonatal infections in a Nepali hospital characterizes the extent of community-versus hospital-associated transmission in an endemic setting. Antimicrob Agents Chemother 58:7347-7357. https://doi.org/10.1128/AAC.03900-14.