Population genomic analysis of 1,777 extended-spectrum beta-lactamase-producing Klebsiella pneumoniae isolates, Houston, Texas: Unexpected abundance of clonal group 307

mBio

Volumn 8, Issue 3, 2017, Pages

  Long, S Wesley ^a,b   Olsen, Randall J ^a,b   Eagar, Todd N ^a   Beres, Stephen B ^a   Zhao, Picheng ^a   Davis, James J ^c,d   Brettin, Thomas ^c,d   Xia, Fangfang ^c,d   Musser, James M ^a,b  

^a HOUSTON METHODIST HOSPITAL   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

^c ARGONNE NATIONAL LABORATORY   (United States)

^d UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIINFECTIVE AGENT; BETA LACTAM ANTIBIOTIC; METALLO BETA LACTAMASE; TRANSCRIPTOME; BACTERIAL DNA; BETA LACTAMASE; BETA-LACTAMASE NDM-1;

ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CONTROLLED STUDY; EXTENDED SPECTRUM BETA LACTAMASE PRODUCING KLEBSIELLA PNEUMONIAE; GENE SEQUENCE; HOST PATHOGEN INTERACTION; MOLECULAR CLONING; MOUSE; NONHUMAN; PHYLOGENY; PLASMID; POPULATION GENETIC STRUCTURE; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA SEQUENCE; WHOLE GENOME SEQUENCING; ANIMAL; BACTERIUM IDENTIFICATION; BIOSYNTHESIS; CLASSIFICATION; DRUG EFFECTS; ENZYMOLOGY; EPIDEMIC; ESCHERICHIA COLI INFECTION; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; KLEBSIELLA INFECTION; KLEBSIELLA PNEUMONIAE; METAGENOMICS; MICROBIAL SENSITIVITY TEST; MICROBIOLOGY; MOLECULAR TYPING; MULTIDRUG RESISTANCE; PULSED FIELD GEL ELECTROPHORESIS; TEXAS;

ANIMALS; ANTI-BACTERIAL AGENTS; BACTERIAL TYPING TECHNIQUES; BETA-LACTAMASES; DISEASE OUTBREAKS; DNA, BACTERIAL; DRUG RESISTANCE, MULTIPLE, BACTERIAL; ELECTROPHORESIS, GEL, PULSED-FIELD; ESCHERICHIA COLI INFECTIONS; GENE EXPRESSION PROFILING; GENOME, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HOST-PATHOGEN INTERACTIONS; HUMANS; KLEBSIELLA INFECTIONS; KLEBSIELLA PNEUMONIAE; METAGENOMICS; MICE; MICROBIAL SENSITIVITY TESTS; MOLECULAR TYPING; PLASMIDS; TEXAS;

EID: 85020468434     PISSN: 21612129     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00489-17     Document Type: Article

References (77)

1. Munoz-Price LS, Poirel L, Bonomo RA, Schwaber MJ, Daikos GL, Cormican M, Cornaglia G, Garau J, Gniadkowski M, Hayden MK, Kumarasamy K, Livermore DM, Maya JJ, Nordmann P, Patel JB, Paterson DL, Pitout J, Villegas MV, Wang H, Woodford N, Quinn JP. 2013. Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases. Lancet Infect Dis 13:785-796. https://doi.org/10.1016/S1473-3099(13)70190-7.
2. Endimiani A, Choudhary Y, Bonomo RA. 2009. In vitro activity of NXL104 in combination with beta-lactams against Klebsiella pneumoniae isolates producing KPC carbapenemases. Antimicrob Agents Chemother 53: 3599-3601. https://doi.org/10.1128/AAC.00641-09.
3. Snitkin ES, Zelazny AM, Thomas PJ, Stock F, NISC Comparative Sequencing Program Group, Henderson DK, Palmore TN, Segre JA. 2012. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med 4:148ra116. https://doi.org/10.1126/scitranslmed.3004129.
4. Centers for Disease Control and Prevention (CDC). 2013. Notes from the field: hospital outbreak of carbapenem-resistant Klebsiella pneumoniae producing New Delhi metallo-beta-lactamase—Denver, Colorado, 2012. MMWR Morb Mortal Wkly Rep 62:108. https://www.cdc.gov/mmwr/preview/mmwrhtml/mm6206a5.htm.
5. Mathers AJ, Stoesser N, Sheppard AE, Pankhurst L, Giess A, Yeh AJ, Didelot X, Turner SD, Sebra R, Kasarskis A, Peto T, Crook D, Sifri CD. 2015. Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing. Antimicrob Agents Chemother 59:1656-1663. https://doi.org/10.1128/AAC.04292-14.
6. 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.
7. Wright MS, Perez F, Brinkac L, Jacobs MR, Kaye K, Cober E, van Duin D, Marshall SH, Hujer AM, Rudin SD, Hujer KM, Bonomo RA, Adams MD. 2014. Population structure of KPC-producing Klebsiella pneumoniae isolates from midwestern U.S. hospitals. Antimicrob Agents Chemother 58:4961-4965. https://doi.org/10.1128/AAC.00125-14.
8. Chung The H, Karkey A, Pham Thanh D, Boinett CJ, Cain AK, Ellington M, Baker KS, Dongol S, Thompson C, Harris SR, Jombart T, Le Thi Phuong T, Tran Do Hoang N, Ha Thanh T, Shretha S, Joshi S, Basnyat B, Thwaites G, Thomson NR, Rabaa MA, Baker S. 2015. A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae. EMBO Mol Med 7:227-239. https://doi.org/10.15252/emmm.201404767.
9. Bogdanovich T, Adams-Haduch JM, Tian G-B, Nguyen MH, Kwak EJ, Muto CA, Doi Y. 2011. Colistin-resistant, Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae belonging to the international epidemic clone ST258. Clin Infect Dis 53:373-376. https://doi.org/10.1093/cid/cir401.
10. Castanheira M, Farrell SE, Wanger A, Rolston KV, Jones RN, Mendes RE. 2013. Rapid expansion of KPC-2-producing Klebsiella pneumoniae isolates in two Texas hospitals due to clonal spread of ST258 and ST307 lineages. Microb Drug Resist 19:295-297. https://doi.org/10.1089/mdr.2012.0238.
11. Chen L, Chavda KD, Mediavilla JR, Zhao Y, Fraimow HS, Jenkins SG, Levi MH, Hong T, Rojtman AD, Ginocchio CC, Bonomo RA, Kreiswirth BN. 2012. Multiplex real-time PCR for detection of an epidemic KPC-producing Klebsiella pneumoniae ST258 clone. Antimicrob Agents Chemother 56: 3444-3447. https://doi.org/10.1128/AAC.00316-12.
12. Fowler RC, Scharn CR, Ali MA, Cavalieri SJ, Goering RV, Hanson ND. 2014. Whole genome mapping of the first reported case of KPC-2-positive Klebsiella pneumoniae ST258 in Nebraska. Diagn Microbiol Infect Dis 79:384-386. https://doi.org/10.1016/j.diagmicrobio.2014.03.023.
13. Kitchel B, Rasheed JK, Patel JB, Srinivasan A, Navon-Venezia S, Carmeli Y, Brolund A, Giske CG. 2009. Molecular epidemiology of KPC-producing Klebsiella pneumoniae isolates in the United States: clonal expansion of multilocus sequence type 258. Antimicrob Agents Chemother 53: 3365-3370. https://doi.org/10.1128/AAC.00126-09.
14. Bowers JR, Kitchel B, Driebe EM, MacCannell DR, Roe C, Lemmer D, de Man T, Rasheed JK, Engelthaler DM, Keim P, Limbago BM. 2015. Genomic analysis of the emergence and rapid global dissemination of the clonal group 258 Klebsiella pneumoniae pandemic. PLoS One 10:e0133727. https://doi.org/10.1371/journal.pone.0133727.
15. Yigit H, Queenan AM, Anderson GJ, Domenech-Sanchez A, Biddle JW, Steward CD, Alberti S, Bush K, Tenover FC. 2001. Novel carbapenemhydrolyzing beta-lactamase, KPC-1, from a carbapenem-resistant strain of Klebsiella pneumoniae. Antimicrob Agents Chemother 45:1151-1161. https://doi.org/10.1128/AAC.45.4.1151-1161.2001.
16. Nordmann P, Cuzon G, Naas T. 2009. The real threat of Klebsiella pneumoniae carbapenemase-producing bacteria. Lancet Infect Dis 9:228-236. https://doi.org/10.1016/S1473-3099(09)70054-4.
17. Deleo FR, Chen L, Porcella SF, Martens CA, Kobayashi SD, Porter AR, Chavda KD, Jacobs MR, Mathema B, Olsen RJ, Bonomo RA, Musser JM, Kreiswirth BN. 2014. Molecular dissection of the evolution of carbapenem-resistant multilocus sequence type 258 Klebsiella pneumoniae. Proc Natl Acad Sci U S A 111:4988-4993. https://doi.org/10.1073/pnas.1321364111.
18. Rodrigues C, Machado E, Ramos H, Peixe L, Novais Â. 2014. Expansion of ESBL-producing Klebsiella pneumoniae in hospitalized patients: a successful story of international clones (ST15, ST147, ST336) and epidemic plasmids (IncR, IncFIIK). Int J Med Microbiol 304:1100-1108. https://doi.org/10.1016/j.ijmm.2014.08.003.
19. Munoz-Price LS, Quinn JP. 2009. The spread of Klebsiella pneumonia carbapenemases: a tale of strains, plasmids, and transposons. Clin Infect Dis 49:1739-1741. https://doi.org/10.1086/648078.
20. Richter SN, Frasson I, Franchin E, Bergo C, Lavezzo E, Barzon L, Cavallaro A, Palù G. 2012. KPC-mediated resistance in Klebsiella pneumoniae in two hospitals in Padua, Italy, June 2009-December 2011: massive spreading of a KPC-3-encoding plasmid and involvement of non-intensive care units. Gut Pathog 4:7. https://doi.org/10.1186/1757-4749-4-7.
21. Pitout JD, Laupland KB. 2008. Extended-spectrum beta-lactamaseproducing Enterobacteriaceae: an emerging public-health concern. Lancet Infect Dis 8:159-166. https://doi.org/10.1016/S1473-3099(08)70041-0.
22. President’s Council of Advisors on Science and Technology. 2014. Report to the president on combating antibiotic resistance. Centers for Disease Control and Prevention, Atlanta, GA. https://www.cdc.gov/drugresistance/pdf/report-to-the-president-on-combating-antibiotic-resistance.pdf.
23. Emerson MO, Bratter J, Howell J, Jeanty PW, Cline M. 2012. Houston region grows more racially/ethnically diverse, with small declines in segregation. A joint report analyzing census data from 1990, 2000, and 2010. Rice University, Houston, TX. http://kinder.rice.edu/uploadedFiles/Urban_Research_Center/Media/Houston%20Region%20Grows%20More %20Ethnically%20Diverse%202-13.pdf.
24. Gomez SA, Pasteran FG, Faccone D, Tijet N, Rapoport M, Lucero C, Lastovetska O, Albornoz E, Galas M, Melano RG, Corso A, Petroni A. 2011. Clonal dissemination of Klebsiella pneumoniae ST258 harbouring KPC-2 in Argentina. Clin Microbiol Infect 17:1520-1524. https://doi.org/10.1111/j.1469-0691.2011.03600.x.
25. Di Carlo P, Gulotta G, Casuccio A, Pantuso G, Raineri M, Farulla CA, Bonventre S, Guadagnino G, Ingrassia D, Cocorullo G, Mammina C, Giarratano A. 2013. KPC-3 Klebsiella pneumoniae ST258 clone infection in postoperative abdominal surgery patients in an intensive care setting: analysis of a case series of 30 patients. BMC Anesthesiol 13. https://doi.org/10.1186/1471-2253-13-13.
26. Valentín-Martín A, Valverde-De Francisco A, Bosque-Vall M, Cantón-Moreno R. 2013. First report of colistin-resistant KPC-2 producing ST258-Klebsiella pneumoniae in Spain. Enferm Infecc Microbiol Clin 31:489-491. https://doi.org/10.1016/j.eimc.2012.12.002.
27. Rodríguez-Zulueta P, Silva-Sanchez J, Barrios H, Reyes-Mar J, Velez-Perez F, Arroyo-Escalante S, Ochoa-Carrera L, Delgado-Sapien G, Morales-Espinoza MdR, Tamayo-Legorreta E, Hernandez-Castro R, Garza-Ramos U. 2013. First outbreak of KPC-3-producing Klebsiella pneumoniae (ST258) clinical isolates in a Mexican medical center. Antimicrob Agents Chemother 57:4086-4088. https://doi.org/10.1128/AAC.02530-12.
28. Marsh JW, Krauland MG, Nelson JS, Schlackman JL, Brooks AM, Pasculle AW, Shutt KA, Doi Y, Querry AM, Muto CA, Harrison LH. 2015. Genomic epidemiology of an endoscope-associated outbreak of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae. PLoS One 10: e0144310. https://doi.org/10.1371/journal.pone.0144310.
29. Tedja R, Nowacki A, Fraser T, Fatica C, Griffiths L, Gordon S, Isada C, van Duin D. 2014. The impact of multidrug resistance on outcomes in ventilator-associated pneumonia. Am J Infect Control 42:542-545. https://doi.org/10.1016/j.ajic.2013.12.009.
30. 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. https://doi.org/10.1016/j.tim.2014.09.003.
31. Lee CR, Lee JH, Park KS, Kim YB, Jeong BC, Lee SH. 2016. Global dissemination of carbapenemase-producing Klebsiella pneumoniae: epidemiology, genetic context, treatment options, and detection methods. Front Microbiol 7:895. https://doi.org/10.3389/fmicb.2016.00895.
32. Pitout JDD, Nordmann P, Poirel L. 2015. Carbapenemase-producing Klebsiella pneumoniae, a key pathogen set for global nosocomial dominance. Antimicrob Agents Chemother 59:5873-5884. https://doi.org/10.1128/AAC.01019-15.
33. Bonura C, Giuffrè M, Aleo A, Fasciana T, Di Bernardo F, Stampone T, Giammanco A, Palma DM, Mammina C. 2015. An update of the evolving epidemic of blaKPC carrying Klebsiella pneumoniae in Sicily, Italy, 2014: emergence of multiple non-ST258 clones. PLoS One 10:e0132936. https://doi.org/10.1371/journal.pone.0132936.
34. Park DJ, Yu JK, Park KG, Park YJ. 2015. Genotypes of ciprofloxacinresistant Klebsiella pneumoniae in Korea and their characteristics according to the genetic lineages. Microb Drug Resist 21:622-630. https://doi.org/10.1089/mdr.2015.0001.
35. Ocampo AM, Chen L, Cienfuegos AV, Roncancio G, Chavda KD, Kreiswirth BN, Jiménez JN. 2015. A two-year surveillance in five Colombian tertiary care hospitals reveals high frequency of non-CG258 clones of carbapenem-resistant Klebsiella pneumoniae with distinct clinical characteristics. Antimicrob Agents Chemother 60:332-342. https://doi.org/10.1128/AAC.01775-15.
36. Ahn C, Yoon SS, Yong TS, Jeong SH, Lee K. 2016. The resistance mechanism and clonal distribution of tigecycline-nonsusceptible Klebsiella pneumoniae isolates in Korea. Yonsei Med J 57:641-646. https://doi.org/10.3349/ymj.2016.57.3.641.
37. Ruiz-Garbajosa P, Hernández-García M, Beatobe L, Tato M, Méndez MI, Grandal M, Aranzábal L, Alonso S, Lópaz MÁ, Astray J, Cantón R. 2016. A single-day point-prevalence study of faecal carriers in long-term care hospitals in Madrid (Spain) depicts a complex clonal and polyclonal dissemination of carbapenemase-producing Enterobacteriaceae. J Antimicrob Chemother 71:348-352. https://doi.org/10.1093/jac/dkv355.
38. Mansour W, Grami R, Ben Haj Khalifa A, Dahmen S, Châtre P, Haenni M, Aouni M, Madec JY. 2015. Dissemination of multidrug-resistant blaCTXM-15/IncFIIk plasmids in Klebsiella pneumoniae isolates from hospitaland community-acquired human infections in Tunisia. Diagn Microbiol Infect Dis 83:298-304. https://doi.org/10.1016/j.diagmicrobio.2015.07.023.
39. Gona F, Barbera F, Pasquariello AC, Grossi P, Gridelli B, Mezzatesta ML, Caio C, Stefani S, Conaldi PG. 2014. In vivo multiclonal transfer of blaKPC-3 from Klebsiella pneumoniae to Escherichia coli in surgery patients. Clin Microbiol Infect 20:O633-O635. https://doi.org/10.1111/1469-0691.12577.
40. Habeeb MA, Haque A, Nematzadeh S, Iversen A, Giske CG. 2013. High prevalence of 16S rRNA methylase RmtB among CTX-M extendedspectrum beta-lactamase-producing Klebsiella pneumoniae from Islamabad, Pakistan. Int J Antimicrob Agents 41:524-526. https://doi.org/10.1016/j.ijantimicag.2013.02.017.
41. Doi Y, Hazen TH, Boitano M, Tsai Y-C, Clark TA, Korlach J, Rasko DA. 2014. Whole-genome assembly of Klebsiella pneumoniae coproducing NDM-1 and OXA-232 carbapenemases using single-molecule, real-time sequencing. Antimicrob Agents Chemother 58:5947-5953. https://doi.org/10.1128/AAC.03180-14.
42. Villa L, Poirel L, Nordmann P, Carta C, Carattoli A. 2012. Complete sequencing of an IncH plasmid carrying the blaNDM-1, blaCTX-M-15 and qnrB1 genes. J Antimicrob Chemother 67:1645-1650. https://doi.org/10.1093/jac/dks114.
43. Hirsch EB, Chang KT, Lasco TM, Caeiro JP, Tam VH. 2011. Emergence of KPC-producing Klebsiella pneumoniae in Texas. Diagn Microbiol Infect Dis 69:234-235. https://doi.org/10.1016/j.diagmicrobio.2010.09.003.
44. Paltansing S, Kraakman MEM, Ras JMC, Wessels E, Bernards AT. 2013. Characterization of fluoroquinolone and cephalosporin resistance mechanisms in Enterobacteriaceae isolated in a Dutch teaching hospital reveals the presence of an Escherichia coli ST131 clone with a specific mutation in parE. J Antimicrob Chemother 68:40-45. https://doi.org/10.1093/jac/dks365.
45. Gomez-Simmonds A, Greenman M, Sullivan SB, Tanner JP, Sowash MG, Whittier S, Uhlemann A-C. 2015. Population structure of Klebsiella pneumoniae causing bloodstream infections at a New York City tertiary care hospital: diversification of multidrug-resistant isolates. J Clin Microbiol 53:2060-2067. https://doi.org/10.1128/JCM.03455-14.
46. Dropa M, Lincopan N, Balsalobre LC, Oliveira DE, Moura RA, Fernandes MR, da Silva QM, Matté GR, Sato MIZ, Matté MH. 2016. Genetic background of novel sequence types of CTX-M-8-and CTX-M-15-producing Escherichia coli and Klebsiella pneumoniae from public wastewater treatment plants in Sao Paulo, Brazil. Environ Sci Pollut Res Int 23:4953-4958. https://doi.org/10.1007/s11356-016-6079-5.
47. Geraci DM, Bonura C, Giuffrè M, Saporito L, Graziano G, Aleo A, Fasciana T, Di Bernardo F, Stampone T, Palma DM, Mammina C. 2015. Is the monoclonal spread of the ST258, KPC-3-producing clone being replaced in southern Italy by the dissemination of multiple clones of carbapenemnonsusceptible, KPC-3-producing Klebsiella pneumoniae? Clin Microbiol Infect 21:e15-e17. https://doi.org/10.1016/j.cmi.2014.08.022.
48. Kim JO, Song SA, Yoon EJ, Shin JH, Lee H, Jeong SH, Lee K. 2017. Outbreak of KPC-2-producing Enterobacteriaceae caused by clonal dissemination of Klebsiella pneumoniae ST307 carrying an IncX3-type plasmid harboring a truncated Tn4401a. Diagn Microbiol Infect Dis 87: 343-348. https://doi.org/10.1016/j.diagmicrobio.2016.12.012.
49. Wyres KL, Gorrie C, Edwards DJ, Wertheim HFL, Hsu LY, Van Kinh N, Zadoks R, Baker S, Holt KE. 2015. Extensive capsule locus variation and large-scale genomic recombination within the Klebsiella pneumoniae clonal group 258. Genome Biol Evol 7:1267-1279. https://doi.org/10.1093/gbe/evv062.
50. Wyres KL, Wick RR, Gorrie C, Jenney A, Follador R, Thomson NR, Holt KE. 2016. Identification of Klebsiella capsule synthesis loci from whole genome data. Microb Genom 2:e000102. https://doi.org/10.1099/mgen.0.000102.
51. Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, Jenney A, Connor TR, Hsu LY, Severin J, Brisse S, Cao H, Wilksch J, Gorrie C, Schultz MB, Edwards DJ, Nguyen KV, Nguyen TV, Dao TT, Mensink M, Minh VL, Nhu NTK, Schultsz C, Kuntaman K, Newton PN, Moore CE, Strugnell RA, Thomson NR. 2015. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci U S A 112:E3574-E3581. https://doi.org/10.1073/pnas.1501049112.
52. Lam MMC, Wick RR, Wyres KL, Gorrie C, Judd LM, Brisse S, Jenney A, Holt KE. 2017. Frequent emergence of pathogenic lineages of Klebsiella pneumoniae via mobilisation of yersiniabactin and colibactin. bioRxiv https://doi.org/10.1101/098178.
53. Diago-Navarro E, Chen L, Passet V, Burack S, Ulacia-Hernando A, Kodiyanplakkal RP, Levi MH, Brisse S, Kreiswirth BN, Fries BC. 2014. Carbapenem-resistant Klebsiella pneumoniae exhibit variability in capsular polysaccharide and capsule associated virulence traits. J Infect Dis 210:803-813. https://doi.org/10.1093/infdis/jiu157.
54. Mehta SC, Rice K, Palzkill T. 2015. Natural variants of the KPC-2 carbapenemase have evolved increased catalytic efficiency for ceftazidime hydrolysis at the cost of enzyme stability. PLoS Pathog 11:e1004949. https://doi.org/10.1371/journal.ppat.1004949.
55. Bushnell G, Mitrani-Gold F, Mundy LM. 2013. Emergence of New Delhi metallo-beta-lactamase type 1-producing enterobacteriaceae and nonenterobacteriaceae: global case detection and bacterial surveillance. Int J Infect Dis 17:e325-e333. https://doi.org/10.1016/j.ijid.2012.11.025.
56. Gupta K, Hooton TM, Naber KG, Wullt B, Colgan R, Miller LG, Moran GJ, Nicolle LE, Raz R, Schaeffer AJ, Soper DE. 2011. International clinical practice guidelines for the treatment of acute uncomplicated cystitis and pyelonephritis in women: a 2010 update by the Infectious Diseases Society of America and the European Society for Microbiology and Infectious Diseases. Clin Infect Dis 52:e103-e120. https://doi.org/10.1093/cid/ciq257.
57. Freund Y, Schapire RE. 1997. A decision-theoretic generalization of on-line learning and an application to boosting. J Comput Syst Sci 55:119-139. https://doi.org/10.1006/jcss.1997.1504.
58. Hastie T, Rosset S, Zhu J, Zou H. 2009. Multi-class AdaBoost. Stat Interface 2:349-360. https://doi.org/10.4310/SII.2009.v2.n3.a8.
59. Ellington MJ, Ekelund O, Aarestrup FM, Canton R, Doumith M, Giske C, Grundman H, Hasman H, Holden MTG, Hopkins KL, Iredell J, Kahlmeter G, Köser CU, MacGowan A, Mevius D, Mulvey M, Naas T, Peto T, Rolain J-M, Samuelsen Ø, Woodford N. 2017. The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST subcommittee. Clin Microbiol Infect 23:2-22. https://doi.org/10.1016/j.cmi.2016.11.012.
60. Metcalf BJ, Chochua S, Gertz RE, Jr., Li Z, Walker H, Tran T, Hawkins PA, Glennen A, Lynfield R, Li Y, McGee L, Beall B, Active Bacterial Core Surveillance Team. 2016. Using whole genome sequencing to identify resistance determinants and predict antimicrobial resistance phenotypes for year 2015 invasive pneumococcal disease isolates recovered in the United States. Clin Microbiol Infect 22:1002.e1-1002.e8. https://doi.org/10.1016/j.cmi.2016.08.001.
61. Moran RA, Anantham S, Holt KE, Hall RM. 2017. Prediction of antibiotic resistance from antibiotic resistance genes detected in antibioticresistant commensal Escherichia coli using PCR or WGS. J Antimicrob Chemother 72:700-704. https://doi.org/10.1093/jac/dkw511.
62. Davis JJ, Boisvert S, Brettin T, Kenyon RW, Mao C, Olson R, Overbeek R, Santerre J, Shukla M, Wattam AR, Will R, Xia F, Stevens R. 2016. Antimicrobial resistance prediction in PATRIC and RAST. Sci Rep 6:27930. https://doi.org/10.1038/srep27930.
63. Craddock RC, Bellec P, Margules DS, Nichols BN, Pfannmöller JP, Badhwar A, Kennedy D, Poline J, Toro R, Cipollini B, Rokem A, Clark D, Gorgolewski KJ, Craddock RC, Craddock RC, Clark DJ, Das S, Madjar C, Sengupta A, Mohades Z, Dery S, Deng W, Earl E, Demeter DV, Mills K, Mihai G, Ruzic L, Ketz N, Reineberg A, Reddan MC, Goddings A, Gonzalez-Castillo J, Gorgolewski KJ, Froehlich C, Dekel G, Margulies DS, Craddock RC, Fulcher BD, Glatard T, Das S, Madjar C, Sengupta A, Mohades Z, Dery S, Deng W, Earl E, Demeter DV, Mills K, Mihai G, Ruzik L, et al. 2016. 2015 Brainhack proceedings. Gigascience 5(Suppl 1):46. https://doi.org/10.1186/s13742-016-0147-0.
64. Chen K, Eddens T, Trevejo-Nunez G, Way EE, Elsegeiny W, Ricks DM, Garg AV, Erb CJ, Bo M, Wang T, Chen W, Lee JS, Gaffen SL, Kolls JK. 2016. IL-17 receptor signaling in the lung epithelium is required for mucosal chemokine gradients and pulmonary host defense against K. pneumoniae. Cell Host Microbe 20:596-605. https://doi.org/10.1016/j.chom.2016.10.003.
65. Bachman MA, Miller VL, Weiser JN. 2009. Mucosal lipocalin 2 has proinflammatory and iron-sequestering effects in response to bacterial enterobactin. PLoS Pathog 5:e1000622. https://doi.org/10.1371/journal.ppat.1000622.
66. Bachman MA, Oyler JE, Burns SH, Caza M, Lepine F, Dozois CM, Weiser JN. 2011. Klebsiella pneumoniae yersiniabactin promotes respiratory tract infection through evasion of lipocalin 2. Infect Immun 79:3309-3316. https://doi.org/10.1128/IAI.05114-11.
67. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114-2120. https://doi.org/10.1093/bioinformatics/btu170.
68. Liu Y, Schroder J, Schmidt B. 2013. Musket: a multistage k-mer spectrumbased error corrector for Illumina sequence data. Bioinformatics 29: 308-315. https://doi.org/10.1093/bioinformatics/bts690.
69. Garrison E, Marth G. 2012. Haplotype-based variant detection from short-read sequencing. arXiv arXiv:1207.3907v2 [q-bio.GN]. http://arXiv.org/abs/1207.3907v2.
70. Price MN, Dehal PS, Arkin AP. 2010. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS One 5:e9490. https://doi.org/10.1371/journal.pone.0009490.
71. Inouye M, Dashnow H, Raven LA, Schultz MB, Pope BJ, Tomita T, Zobel J, Holt KE. 2014. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med 6:90. https://doi.org/10.1186/s13073-014-0090-6.
72. Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A, Lapidus A, Prjibelsky A, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, McLean J, Lasken R, Clingenpeel SR, Woyke T, Tesler G, Alekseyev MA, Pevzner PA. 2013. Assembling genomes and mini-metagenomes from highly chimeric reads, p 158-170. In Deng M, Jiang R, Sun F, Zhang X (ed), Research in computational molecular biology: 17th Annual International Conference, RECOMB 2013, Beijing, China, April 7-10, 2013. Springer, Berlin, Germany. http://link.springer.com/chapter/10.1007/ 978-3-642-37195-0_13.
73. Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33:1870-1874. https://doi.org/10.1093/molbev/msw054.
74. Kumar S, Stecher G, Peterson D, Tamura K. 2012. MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis. Bioinformatics 28:2685-2686. https://doi.org/10.1093/bioinformatics/bts507.
75. Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, Machi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJC, Yoo HS, Zhang C, Zhang Y, Sobral BW. 2014. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 42:D581-D591. https://doi.org/10.1093/nar/gkt1099.
76. Olsen RJ, Fittipaldi N, Kachroo P, Sanson MA, Long SW, Como-Sabetti KJ, Valson C, Cantu C, Lynfield R, Van Beneden C, Beres SB, Musser JM. 2014. Clinical laboratory response to a mock outbreak of invasive bacterial infections: a preparedness study. J Clin Microbiol 52:4210-4216. https://doi.org/10.1128/JCM.02164-14.
77. Eagar TN, Tang Q, Wolfe M, He Y, Pear WS, Bluestone JA. 2004. Notch 1 signaling regulates peripheral T cell activation. Immunity 20:407-415. https://doi.org/10.1016/S1074-7613(04)00081-0.