Molecular diversity and plasmid analysis of KPC-producing Escherichia coli

Antimicrobial Agents and Chemotherapy

Volumn 60, Issue 7, 2016, Pages 4073-4081

  Chavda, Kalyan D ^a   Chen, Liang ^a   Jacobs, Michael R ^b   Bonomo, Robert A ^c,d   Kreiswirth, Barry N ^a  

^a RUTGERS UNIVERSITY   (United States)

^b UNIVERSITY HOSPITALS OF CLEVELAND   (United States)

^c LOUIS STOKES CLEVELAND VA MEDICAL CENTER   (United States)

^d CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; CARBAPENEMASE; KLEBSIELLA PNEUMONIAE CARBAPENEMASE; UNCLASSIFIED DRUG; ANTIINFECTIVE AGENT; BACTERIAL PROTEIN; BETA LACTAMASE; CARBAPENEM DERIVATIVE;

ARTICLE; BACTERIAL GENE; BACTERIUM ISOLATION; BLOOD; CARBAPENEM RESISTANT ENTEROBACTERIACEAE; CHIMERA; ESCHERICHIA COLI; GENE DELETION; GENE INSERTION; GENE REPLICATION; GENOTYPE; GEOGRAPHIC DISTRIBUTION; HOSPITAL; MICROBIAL DIVERSITY; MOLECULAR EVOLUTION; MOLECULAR SIZE; NONHUMAN; PLASMID; PLASTICITY; PRIORITY JOURNAL; RECTUM; REPLICON; RESPIRATORY SYSTEM; RETROSPECTIVE STUDY; UNITED STATES; URINALYSIS; DRUG EFFECTS; GENETICS; KLEBSIELLA PNEUMONIAE; METABOLISM; MICROBIAL SENSITIVITY TEST;

ANTI-BACTERIAL AGENTS; BACTERIAL PROTEINS; BETA-LACTAMASES; CARBAPENEMS; ESCHERICHIA COLI; KLEBSIELLA PNEUMONIAE; MICROBIAL SENSITIVITY TESTS; PLASMIDS; UNITED STATES;

EID: 84976873291     PISSN: 00664804     EISSN: 10986596     Source Type: Journal    
DOI: 10.1128/AAC.00452-16     Document Type: Article

References (44)

1. Yigit H, Queenan AM, Anderson GJ, Domenech-Sanchez A, Biddle JW, Steward CD, Alberti S, Bush K, Tenover FC. 2001. Novel carbapenem-hydrolyzing beta-lactamase, KPC-1, from a carbapenem-resistant strain of Klebsiella pneumoniae. Antimicrob Agents Chemother 45:1151-1161. http://dx.doi.org/10.1128/AAC.45.4.1151-1161.2001.
2. Chavda KD, Chen L, Jacobs MR, Rojtman AD, Bonomo RA, Kreiswirth BN. 2015. Complete sequence of a bla(KPC)-harboring cointegrate plasmid isolated from Escherichia coli. Antimicrob Agents Chemother 59: 2956-2959. http://dx.doi.org/10.1128/AAC.00041-15.
3. KPC-5-harboring IncN and IncX plasmids from Klebsiella pneumoniae strains isolated in New Jersey. Antimicrob Agents Chemother 57:269-276. http://dx.doi.org/10.1128/AAC.01648-12.
4. KPC-harboring IncFIA plasmids in New Jersey and New York hospitals. Antimicrob Agents Chemother 58:2289-2294. http://dx.doi.org/10.1128/AAC.02749-13.
5. Chen L, Chavda KD, Melano RG, Jacobs MR, Koll B, Hong T, Rojtman AD, Levi MH, Bonomo RA, Kreiswirth BN. 2014. Comparative genomic analysis of KPC-encoding pKpQIL-like plasmids and their distribution in New Jersey and New York Hospitals. Antimicrob Agents Chemother 58: 2871-2877. http://dx.doi.org/10.1128/AAC.00120-14.
6. Chen L, Hu H, Chavda KD, Zhao S, Liu R, Liang H, Zhang W, Wang X, Jacobs MR, Bonomo RA, Kreiswirth BN. 2014. Complete sequence of a KPC-producing IncN multidrug-resistant plasmid from an epidemic Escherichia coli sequence type 131 strain in China. Antimicrob Agents Chemother 58:2422-2425. http://dx.doi.org/10.1128/AAC.02587-13.
7. Mathers AJ, Peirano G, Pitout JD. 2015. The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae. Clin Microbiol Rev 28:565-591. http://dx.doi.org/10.1128/CMR.00116-14.
8. Chen L, Mathema B, Chavda KD, DeLeo FR, Bonomo RA, Kreiswirth BN. 2014. Carbapenemase-producing Klebsiella pneumoniae: molecular and genetic decoding. Trends Microbiol 22:686-696. http://dx.doi.org/10.1016/j.tim.2014.09.003.
9. Pitout JD, Nordmann P, Poirel L. 2015. Carbapenemase-producing Klebsiella pneumoniae, a key pathogen set for global nosocomial dominance. Antimicrob Agents Chemother 59:5873-5884. http://dx.doi.org/10.1128/AAC.01019-15.
10. KPC-harboring IncI2 plasmid and its dissemination in New Jersey and New York hospitals. Antimicrob Agents Chemother 57:5019-5025. http://dx.doi.org/10.1128/AAC.01397-13.
11. Bratu S, Brooks S, Burney S, Kochar S, Gupta J, Landman D, Quale J. 2007. Detection and spread of Escherichia coli possessing the plasmid-borne carbapenemase KPC-2 in Brooklyn, New York. Clin Infect Dis 44: 972-975. http://dx.doi.org/10.1086/512370.
12. Nordmann P, Poirel L. 2014. The difficult-to-control spread of carbapenemase producers among Enterobacteriaceae worldwide. Clin Microbiol Infect 20:821-830. http://dx.doi.org/10.1111/1469-0691.12719.
13. Xu G, Jiang Y, An W, Wang H, Zhang X. 2015. Emergence of KPC-2-producing Escherichia coli isolates in an urban river in Harbin, China. World J Microbiol Biotechnol 31:1443-1450. http://dx.doi.org/10.1007/s11274-015-1897-z.
14. Chen L, Mediavilla JR, Endimiani A, Rosenthal ME, Zhao Y, Bonomo RA, Kreiswirth BN. 2011. Multiplex real-time PCR assay for detection and classification of Klebsiella pneumoniae carbapenemase gene (bla KPC) variants. J Clin Microbiol 49:579-585. http://dx.doi.org/10.1128/JCM.01588-10.
15. Wirth T, Falush D, Lan R, Colles F, Mensa P, Wieler LH, Karch H, Reeves PR, Maiden MC, Ochman H, Achtman M. 2006. Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol 60: 1136-1151. http://dx.doi.org/10.1111/j.1365-2958.2006.05172.x.
16. Zhang Y, Wang ZQ, Liu B, Zhang XJ, Jiang F, Xiang JH. 2007. The study of optimal conditions of electroporation in Escherichia coli DH10B strain. Sheng Wu Gong Cheng Xue Bao 23:347-351. (In Chinese.)
17. Barton BM, Harding GP, Zuccarelli AJ. 1995. A general method for detecting and sizing large plasmids. Anal Biochem 226:235-240. http://dx.doi.org/10.1006/abio.1995.1220.
18. Carattoli A, Bertini A, Villa L, Falbo V, Hopkins KL, Threlfall EJ. 2005. Identification of plasmids by PCR-based replicon typing. J Microbiol Methods 63:219-228. http://dx.doi.org/10.1016/j.mimet.2005.03.018.
19. Chen L, Chavda KD, Melano RG, Jacobs MR, Levi MH, Bonomo RA, Kreiswirth BN. 2013. Complete sequence of a bla(KPC-2)-harboring IncFII(K1) plasmid from a Klebsiella pneumoniae sequence type 258 strain. Antimicrob Agents Chemother 57:1542-1545. http://dx.doi.org/10.1128/AAC.02332-12.
20. Sullivan MJ, Petty NK, Beatson SA. 2011. Easyfig: a genome comparison visualizer. Bioinformatics 27:1009-1010. http://dx.doi.org/10.1093/bioinformatics/btr039.
21. Darling AE, Mau B, Perna NT. 2010. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147. http://dx.doi.org/10.1371/journal.pone.0011147.
22. CLSI. 2012. Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically. Approved standard, 9th ed (M07-A9). CLSI, Wayne, PA.
23. CLSI. 2014. Performance standards for antimicrobial susceptibility testing; 24th informational supplement (M100-S24). CLSI, Wayne, PA.
24. Naas T, Cuzon G, Gaillot O, Courcol R, Nordmann P. 2011. When carbapenem-hydrolyzing β-lactamase KPC meets Escherichia coli ST131 in France. Antimicrob Agents Chemother 55:4933-4934. http://dx.doi.org/10.1128/AAC.00719-11.
25. Chang J, Yu J, Lee H, Ryu H, Park K, Park YJ. 2014. Prevalence and characteristics of lactose non-fermenting Escherichia coli in urinary isolates. J Infect Chemother 20:738-740. http://dx.doi.org/10.1016/j.jiac.2014.07.005.
26. Carattoli A, Zankari E, Garcia-Fernandez A, Voldby Larsen M, Lund O, Villa L, Moller Aarestrup F, Hasman H. 2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895-3903. http://dx.doi.org/10.1128/AAC.02412-14.
27. Toh H, Weiss BL, Perkin SA, Yamashita A, Oshima K, Hattori M, Aksoy S. 2006. Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host. Genome Res 16:149-156.
28. Yamaguchi Y, Inouye M. 2009. mRNA interferases, sequence-specific endoribonucleases from the toxin-antitoxin systems. Prog Mol Biol Transl Sci 85:467-500. http://dx.doi.org/10.1016/S0079-6603(08)00812-X.
29. SHV-12, and qnrS1 from an Escherichia coli sequence type 648 strain. Antimicrob Agents Chemother 58:6974-6977. http://dx.doi.org/10.1128/AAC.03632-14.
30. Conlan S, Thomas PJ, Deming C, Park M, Lau AF, Dekker JP, Snitkin ES, Clark TA, Luong K, Song Y, Tsai YC, Boitano M, Dayal J, Brooks SY, Schmidt B, Young AC, Thomas JW, Bouffard GG, Blakesley RW, Mullikin JC, Korlach J, Henderson DK, Frank KM, Palmore TN, Segre JA. 2014. Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Sci Transl Med 6:254ra126. http://dx.doi.org/10.1126/scitranslmed.3009845.
31. Langer PJ, Shanabruch WG, Walker GC. 1981. Functional organization of plasmid pKM101. J Bacteriol 145:1310-1316.
32. Villa L, Garcia-Fernandez A, Fortini D, Carattoli A. 2010. Replicon sequence typing of IncF plasmids carrying virulence and resistance determinants. J Antimicrob Chemother 65:2518-2529. http://dx.doi.org/10.1093/jac/dkq347.
33. Leavitt A, Chmelnitsky I, Carmeli Y, Navon-Venezia S. 2010. Complete nucleotide sequence of KPC-3-encoding plasmid pKpQIL in the epidemic Klebsiella pneumoniae sequence type 258. Antimicrob Agents Chemother 54:4493-4496. http://dx.doi.org/10.1128/AAC.00175-10.
34. Liu P, Li P, Jiang X, Bi D, Xie Y, Tai C, Deng Z, Rajakumar K, Ou H-Y. 2012. Complete genome sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a multidrug-resistant strain isolated from human sputum. J Bacteriol 194:1841-1842. http://dx.doi.org/10.1128/JB.00043-12.
35. DHA-1, qnrB4, and armA. Antimicrob Agents Chemother 54:3967-3969. http://dx.doi.org/10.1128/AAC.00137-10.
36. Aibinu I, Odugbemi T, Koenig W, Ghebremedhin B. 2012. Sequence type ST131 and ST10 complex (ST617) predominant among CTX-M-15-producing Escherichia coli isolates from Nigeria. Clin Microbiol Infect 18:E49-E51. http://dx.doi.org/10.1111/j.1469-0691.2011.03730.x.
37. CTX-M-15 and qnrS1 genes. Antimicrob Agents Chemother 56:2763-2766. http://dx.doi.org/10.1128/AAC.06001-11.
38. CTX-M IncFII plasmids and clones of Escherichia coli from pets in France. J Antimicrob Chemother 68:2797-2801. http://dx.doi.org/10.1093/jac/dkt291.
39. Ben Sallem R, Ben Slama K, Estepa V, Cheikhna EO, Mohamed AM, Chairat S, Ruiz-Larrea F, Boudabous A, Torres C. 2015. Detection of CTX-M-15-producing Escherichia coli isolates of lineages ST410-A, ST617-A and ST354-D in faecal samples of hospitalized patients in a Mauritanian hospital. J Chemother 27:114-116. http://dx.doi.org/10.1179/1973947814Y.0000000172.
40. Tamang MD, Nam HM, Jang GC, Kim SR, Chae MH, Jung SC, Byun JW, Park YH, Lim SK. 2012. Molecular characterization of extended-spectrum-beta-lactamase-producing and plasmid-mediated AmpC betalactamase-producing Escherichia coli isolated from stray dogs in South Korea. Antimicrob Agents Chemother 56:2705-2712. http://dx.doi.org/10.1128/AAC.05598-11.
41. Lau SH, Reddy S, Cheesbrough J, Bolton FJ, Willshaw G, Cheasty T, Fox AJ, Upton M. 2008. Major uropathogenic Escherichia coli strain isolated in the northwest of England identified by multilocus sequence typing. J Clin Microbiol 46:1076-1080. http://dx.doi.org/10.1128/JCM.02065-07.
42. Guo S, Wakeham D, Brouwers HJ, Cobbold RN, Abraham S, Mollinger JL, Johnson JR, Chapman TA, Gordon DM, Barrs VR, Trott DJ. 2015. Human-associated fluoroquinolone-resistant Escherichia coli clonal lineages, including ST354, isolated from canine feces and extraintestinal infections in Australia. Microbes Infect 17:266-274. http://dx.doi.org/10.1016/j.micinf.2014.12.016.
43. Peirano G, Bradford PA, Kazmierczak KM, Badal RE, Hackel M, Hoban DJ, Pitout JD. 2014. Global incidence of carbapenemase-producing Escherichia coli ST131. Emerg Infect Dis 20:1928-1931. http://dx.doi.org/10.3201/eid2011.141388.
44. Platell JL, Trott DJ, Johnson JR, Heisig P, Heisig A, Clabots CR, Johnston B, Cobbold RN. 2012. Prominence of an O75 clonal group (clonal complex 14) among non-ST131 fluoroquinolone-resistant Escherichia coli causing extraintestinal infections in humans and dogs in Australia. Antimicrob Agents Chemother 56:3898-3904. http://dx.doi.org/10.1128/AAC.06120-11.