Phân tích bộ gen về đa dạng, cấu trúc quần thể, độc lực và kháng kháng sinh trong Klebsiella pneumoniae, một mối đe dọa cấp bách đối với y tế công cộng

Proceedings of the National Academy of Sciences of the United States of America - Tập 112 Số 27 - 2015
Kathryn E. Holt1,2, Heiman Wertheim3,4, Ruth N. Zadoks5,6, Stephen Baker7, Chris A. Whitehouse8, David A. B. Dance9,3, Adam Jenney10,11, Thomas R. Connor12,13, Li Yang Hsu14, Juliëtte A. Severin15, Sylvain Brisse16, Hanwei Cao17,18, Jonathan J. Wilksch2,18, Claire L. Gorrie1,2,18, Mark B. Schultz1, David J. Edwards19, Kinh Van Nguyen20, Trung Vu Nguyen21, Trinh Tuyet Dao21, Martijn Mensink22, Vien Le Minh23,7, Nguyen Thi Khanh Nhu24,7, Constance Schultsz25,26, Kuntaman Kuntaman27, Paul N. Newton9,28, Catrin E. Moore9,28, Richard A. Strugnell2,18, Nicholas R. Thomson29,30
1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
2Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
3Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, OX3 7BN Oxford, United Kingdom;
4Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, National Hospital for Tropical Diseases, Hanoi, Vietnam;
5Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ Glasgow, United Kingdom;
6Quality Milk Production Services, Cornell University, Ithaca, NY 14853; Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ Glasgow, United Kingdom;
7The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research Unit, Ho Chi Minh City, Vietnam
8United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702;
9Lao-Oxford-Mahosot Hospital Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People’s Democratic Republic;
10Departmemt Infectious Diseases and Microbiology Unit, The Alfred Hospital, Melbourne, VIC 3004, Australia;
11Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC 3010, Australia; Departmemt Infectious Diseases and Microbiology Unit, The Alfred Hospital, Melbourne, VIC 3004, Australia;
12Cardiff University School of Biosciences, Cardiff University, Cardiff, Wales, CF10 3AX, United Kingdom;
13Pathogen Genomics, Wellcome Trust Sanger Centre, CB10 1SA Cambridge, United Kingdom; Cardiff University School of Biosciences, Cardiff University, Cardiff, Wales, CF10 3AX, United Kingdom;
14Department of Medicine, National University Health System, Singapore 119228;
15Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, 3015 CE Rotterdam, The Netherlands;
16Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
17Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC 3010, Australia; Peter Doherty Institute, The University of Melbourne, Parkville, VIC 3010, Australia;
18Peter Doherty Institute, The University of Melbourne, Parkville, VIC 3010, Australia;
19aDepartment of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia;
20National Hospital for Tropical Diseases, Hanoi, Vietnam
21qNational Hospital for Tropical Diseases, Hanoi, Vietnam;
22Quality Milk Production Services, Cornell University, Ithaca, NY 14853
23Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, CA 94118-6215;
24School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
25Academic Medical Center, University of Amsterdam, 1012 WX Amsterdam, The Netherlands;
26The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Academic Medical Center, University of Amsterdam, 1012 WX Amsterdam, The Netherlands;
27Department of Clinical Microbiology, Dr. Soetomo Academic Hospital - School of Medicine, Airlangga University, Surabaya, Jawa Timur, Indonesia;
28dNuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, OX3 7BN Oxford, United Kingdom;
29kPathogen Genomics, Wellcome Trust Sanger Centre, CB10 1SA Cambridge, United Kingdom;
30vDepartment of Pathogen Molecular Biology, The London School of Hygiene and Tropical Medicine, WC1E 7HT London, United Kingdom

Tóm tắt

Tầm quan trọng

Klebsiella pneumoniae đang nhanh chóng trở nên không thể điều trị bằng cách sử dụng các loại kháng sinh hàng đầu. Điều này đặc biệt gây phiền toái trong các bệnh viện, nơi nó gây ra một loạt các nhiễm khuẩn cấp tính. Để tiếp cận việc kiểm soát vi khuẩn này, đầu tiên chúng ta cần xác định đó là gì và nó biến đổi di truyền như thế nào. Trong nghiên cứu này, chúng tôi đã xác định các chuỗi DNA của các mẫu K. pneumoniae trên toàn thế giới và trình bày một phân tích chi tiết về các dữ liệu này. Chúng tôi cho thấy có một phổ rộng về sự đa dạng, bao gồm sự biến đổi trong các chuỗi được chia sẻ và sự thu được và mất đi của toàn bộ gen. Sử dụng bản thiết kế chi tiết này, chúng tôi cho thấy có sự kết hợp chưa được công nhận giữa sự sở hữu các hồ sơ gen cụ thể liên quan đến độc lực và kháng thuốc kháng sinh và các kết cục bệnh khác nhau được thấy ở K. pneumoniae.

Từ khóa

#Klebsiella pneumoniae #đa dạng bộ gen #cấu trúc quần thể #độc lực #kháng thuốc kháng sinh #y tế công cộng #bệnh viện #nhiễm khuẩn cấp tính #gen di truyền #phân tích bộ gen #hồ sơ gen #kết cục bệnh.

Tài liệu tham khảo

RN Jones, Microbial etiologies of hospital-acquired bacterial pneumonia and ventilator-associated bacterial pneumonia. Clin Infect Dis 51, S81–S87 (2010).

AG Falade, AI Ayede, Epidemiology, aetiology and management of childhood acute community-acquired pneumonia in developing countries—a review. Afr J Med Med Sci 40, 293–308 (2011).

WR Jarvis, VP Munn, AK Highsmith, DH Culver, JM Hughes, The epidemiology of nosocomial infections caused by Klebsiella pneumoniae. Infect Control 6, 68–74 (1985).

R Podschun, U Ullmann, Klebsiella spp. as nosocomial pathogens: Epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin Microbiol Rev 11, 589–603 (1998).

S Brisse F Grimont P Grimont The genus Klebsiella. The Prokaryotes A Handbook on the Biology of Bacteria 3rd edition eds Dworkin M Falkow S Rosenberg E Schleifer K-H Stackebrandt E (Springer New York) 3rd Ed. Vol 6: Proteobacteria: Gamma Subclass. (2006).

AS Shon, RP Bajwa, TA Russo, Hypervirulent (hypermucoviscous) Klebsiella pneumoniae: A new and dangerous breed. Virulence 4, 107–118 (2013).

CA Broberg, M Palacios, VL Miller, Klebsiella: A long way to go towards understanding this enigmatic jet-setter. F1000Prime Rep 6, 64–76 (2014).

S Jang, , Pleuritis and suppurative pneumonia associated with a hypermucoviscosity phenotype of Klebsiella pneumoniae in California sea lions (Zalophus californianus). Vet Microbiol 141, 174–177 (2010).

NA Twenhafel, , Multisystemic abscesses in African green monkeys (Chlorocebus aethiops) with invasive Klebsiella pneumoniae—identification of the hypermucoviscosity phenotype. Vet Pathol 45, 226–231 (2008).

Y Schukken, , The “other” gram-negative bacteria in mastitis: Klebsiella, serratia, and more. Vet Clin North Am Food Anim Pract 28, 239–256 (2012).

ST Bagley, Habitat association of Klebsiella species. Infect Control 6, 52–58 (1985).

S Bialek-Davenet, , Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups. Emerg Infect Dis 20, 1812–1820 (2014).

S Brisse, , Virulent clones of Klebsiella pneumoniae: Identification and evolutionary scenario based on genomic and phenotypic characterization. PLoS ONE 4, e4982 (2009).

C Struve, KA Krogfelt, Pathogenic potential of environmental Klebsiella pneumoniae isolates. Environ Microbiol 6, 584–590 (2004).

S Brisse, J Verhoef, Phylogenetic diversity of Klebsiella pneumoniae and Klebsiella oxytoca clinical isolates revealed by randomly amplified polymorphic DNA, gyrA and parC genes sequencing and automated ribotyping. Int J Syst Evol Microbiol 51, 915–924 (2001).

C Fevre, V Passet, FX Weill, PA Grimont, S Brisse, Variants of the Klebsiella pneumoniae OKP chromosomal beta-lactamase are divided into two main groups, OKP-A and OKP-B. Antimicrob Agents Chemother 49, 5149–5152 (2005).

S Brisse, V Passet, PA Grimont, Description of Klebsiella quasipneumoniae sp. nov., isolated from human infections, with two subspecies, Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and Klebsiella quasipneumoniae subsp. similipneumoniae subsp. nov., and demonstration that Klebsiella singaporensis is a junior heterotypic synonym of Klebsiella variicola. Int J Syst Evol Microbiol 64, 3146–3152 (2014).

M Rosenblueth, L Martínez, J Silva, E Martínez-Romero, Klebsiella variicola, a novel species with clinical and plant-associated isolates. Syst Appl Microbiol 27, 27–35 (2004).

M Maatallah, , Klebsiella variicola is a frequent cause of bloodstream infection in the stockholm area, and associated with higher mortality compared to K. pneumoniae. PLoS ONE 9, e113539 (2014).

; Centers for Disease Control and Prevention Antibiotic Resistance Threats in the United States 2013 (Centers Dis Control Atlanta). (2013).

; Department of Health and Department for Environment Food & Rural Affairs UK Five Year Antimicrobial Resistance Strategy 2013 to 2018. (Department of Health London). (2013).

J Chaves, , SHV-1 beta-lactamase is mainly a chromosomally encoded species-specific enzyme in Klebsiella pneumoniae. Antimicrob Agents Chemother 45, 2856–2861 (2001).

J Sirot, , Klebsiella pneumoniae and other Enterobacteriaceae producing novel plasmid-mediated beta-lactamases markedly active against third-generation cephalosporins: Epidemiologic studies. Rev Infect Dis 10, 850–859 (1988).

P Nordmann, G Cuzon, T Naas, The real threat of Klebsiella pneumoniae carbapenemase-producing bacteria. Lancet Infect Dis 9, 228–236 (2009).

P Nordmann, L Poirel, TR Walsh, DM Livermore, The emerging NDM carbapenemases. Trends Microbiol 19, 588–595 (2011).

L Chen, , Carbapenemase-producing Klebsiella pneumoniae: Molecular and genetic decoding. Trends Microbiol 22, 686–696 (2014).

ES Snitkin Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med 4(148):148ra116. (2012).

MS Wright, , Population structure of KPC-producing Klebsiella pneumoniae isolates from midwestern U.S. hospitals. Antimicrob Agents Chemother 58, 4961–4965 (2014).

L Chen, B Mathema, JD Pitout, FR DeLeo, BN Kreiswirth, Epidemic Klebsiella pneumoniae ST258 is a hybrid strain. MBio 5, e01355-14 (2014).

FR Deleo Molecular dissection of the evolution of carbapenem-resistant multilocus sequence type 258 Klebsiella pneumoniae. Proc Natl Acad Sci USA 111(13):4988–4993. (2014).

AJ Mathers, , Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: Insights into endemicity from whole-genome sequencing. Antimicrob Agents Chemother 59, 1656–1663 (2015).

M Richter, R Rosselló-Móra, Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106, 19126–19131 (2009).

SK Sheppard, ND McCarthy, D Falush, MC Maiden, Convergence of Campylobacter species: Implications for bacterial evolution. Science 320, 237–239 (2008).

ME de Melo, AB Cabral, MA Maciel, VM da Silveira, AC de Souza Lopes, Phylogenetic groups among Klebsiella pneumoniae isolates from Brazil: Relationship with antimicrobial resistance and origin. Curr Microbiol 62, 1596–1601 (2011).

S Brisse, T van Himbergen, K Kusters, J Verhoef, Development of a rapid identification method for Klebsiella pneumoniae phylogenetic groups and analysis of 420 clinical isolates. Clin Microbiol Infect 10, 942–945 (2004).

DE Fouts, , Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice. PLoS Genet 4, e1000141 (2008).

AA Pinto-Tomás, , Symbiotic nitrogen fixation in the fungus gardens of leaf-cutter ants. Science 326, 1120–1123 (2009).

T Pommier, B Canbäck, P Lundberg, A Hagström, A Tunlid, RAMI: A tool for identification and characterization of phylogenetic clusters in microbial communities. Bioinformatics 25, 736–742 (2009).

DJ Lawson, G Hellenthal, S Myers, D Falush, Inference of population structure using dense haplotype data. PLoS Genet 8, e1002453 (2012).

E Carniel The Yersinia high-pathogenicity island: An iron-uptake island. Microbes Infect 3(7):561–569. (2001).

X Nassif, PJ Sansonetti, Correlation of the virulence of Klebsiella pneumoniae K1 and K2 with the presence of a plasmid encoding aerobactin. Infect Immun 54, 603–608 (1986).

J Putze, , Genetic structure and distribution of the colibactin genomic island among members of the family Enterobacteriaceae. Infect Immun 77, 4696–4703 (2009).

YT Chen, , Sequencing and analysis of the large virulence plasmid pLVPK of Klebsiella pneumoniae CG43. Gene 337, 189–198 (2004).

R Lagos, , Structure, organization and characterization of the gene cluster involved in the production of microcin E492, a channel-forming bacteriocin. Mol Microbiol 42, 229–243 (2001).

HY Cheng, , RmpA regulation of capsular polysaccharide biosynthesis in Klebsiella pneumoniae CG43. J Bacteriol 192, 3144–3158 (2010).

YC Lai, HL Peng, HY Chang, RmpA2, an activator of capsule biosynthesis in Klebsiella pneumoniae CG43, regulates K2 cps gene expression at the transcriptional level. J Bacteriol 185, 788–800 (2003).

HC Chou, , Isolation of a chromosomal region of Klebsiella pneumoniae associated with allantoin metabolism and liver infection. Infect Immun 72, 3783–3792 (2004).

LC Ma, CT Fang, CZ Lee, CT Shun, JT Wang, Genomic heterogeneity in Klebsiella pneumoniae strains is associated with primary pyogenic liver abscess and metastatic infection. J Infect Dis 192, 117–128 (2005).

YC Lai, GT Lin, SL Yang, HY Chang, HL Peng, Identification and characterization of KvgAS, a two-component system in Klebsiella pneumoniae CG43. FEMS Microbiol Lett 218, 121–126 (2003).

KM Wu, , Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis. J Bacteriol 191, 4492–4501 (2009).

VI Holden MA Bachman Diverging roles of bacterial siderophores during infection. Metallomics 10.1039/c4mt00333k. (2015).

NJ Croucher, , Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat Genet 45, 656–663 (2013).

AB Ibarz-Pavón, , Changes in serogroup and genotype prevalence among carried meningococci in the United Kingdom during vaccine implementation. J Infect Dis 204, 1046–1053 (2011).

JF Turton, , Genetically similar isolates of Klebsiella pneumoniae serotype K1 causing liver abscesses in three continents. J Med Microbiol 56, 593–597 (2007).

CH Liao, YT Huang, CY Chang, HS Hsu, PR Hsueh, Capsular serotypes and multilocus sequence types of bacteremic Klebsiella pneumoniae isolates associated with different types of infections. Eur J Clin Microbiol Infect Dis 33, 365–369 (2014).

LK Siu, , Molecular typing and virulence analysis of serotype K1 Klebsiella pneumoniae strains isolated from liver abscess patients and stool samples from noninfectious subjects in Hong Kong, Singapore, and Taiwan. J Clin Microbiol 49, 3761–3765 (2011).

WL Yu, , Comparison of prevalence of virulence factors for Klebsiella pneumoniae liver abscesses between isolates with capsular K1/K2 and non-K1/K2 serotypes. Diagn Microbiol Infect Dis 62, 1–6 (2008).

VP Richards, , Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae. Infect Genet Evol 11, 1263–1275 (2011).

A Carattoli, , In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58, 3895–3903 (2014).

MA Bachman, S Lenio, L Schmidt, JE Oyler, JN Weiser, Interaction of lipocalin 2, transferrin, and siderophores determines the replicative niche of Klebsiella pneumoniae during pneumonia. MBio 3, e00224-11 (2012).

J Shin, K Soo Ko, Single origin of three plasmids bearing blaCTX-M-15 from different Klebsiella pneumoniae clones. J Antimicrob Chemother 69, 969–972 (2014).

YM Liu, , Clinical and molecular characteristics of emerging hypervirulent Klebsiella pneumoniae bloodstream infections in mainland China. Antimicrob Agents Chemother 58, 5379–5385 (2014).

D Cejas, , First isolate of KPC-2-producing Klebsiella pneumonaie sequence type 23 from the Americas. J Clin Microbiol 52, 3483–3485 (2014).

S Conlan Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Sci Transl Med 6(254):254ra126. (2014).

S Gaiarsa, , Genomic epidemiology of Klebsiella pneumoniae: The Italian scenario, and novel insights into the origin and global evolution of resistance to carbapenem antibiotics. Antimicrob Agents Chemother 59, 389–396 (2014).

CU Köser, MJ Ellington, SJ Peacock, Whole-genome sequencing to control antimicrobial resistance. Trends Genet 30, 401–407 (2014).

N Stoesser, , 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 (2014).

M Inouye SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med 6(11):90–106. (2014).

F Meyer, , The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9, 386–396 (2008).

SK Gupta, , ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother 58, 212–220 (2014).

S Brisse, , wzi Gene sequencing, a rapid method for determination of capsular type for Klebsiella strains. J Clin Microbiol 51, 4073–4078 (2013).

Thông tin
Thông tin xuất bản

Proceedings of the National Academy of Sciences of the United States of America

Tập 112 Số 27

Thông tin tác giả