Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307

Long, S. Wesley; Olsen, Randall J.; Eagar, Todd N.; Beres, Stephen B.; Zhao, Picheng; Davis, James J.; Brettin, Thomas; Xia, Fangfang; Musser, James M.

doi:10.1128/mbio.00489-17

Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307

Journal Article · Tue May 16 00:00:00 EDT 2017 · mBio (Online)

DOI:https://doi.org/10.1128/mbio.00489-17· OSTI ID:1626108

Long, S. Wesley ^[1]; Olsen, Randall J. ^[2]; Eagar, Todd N. ^[3]; Beres, Stephen B. ^[3]; Zhao, Picheng ^[3]; Davis, James J. ^[4]; Brettin, Thomas ^[4]; Xia, Fangfang ^[4]; Musser, James M. ^[2]

Houston Methodist Research Inst. and Houston Methodist Hospital, Houston, TX (United States). Dept. of Pathology and Genomic Medicine. Center for Molecular and Translational Human Infectious Diseases Research; Cornell Univ., Ithaca, NY (United States). Weill Medical College. Dept. of Pathology and Lab. Medicine; DOE/OSTI
Houston Methodist Research Inst. and Houston Methodist Hospital, Houston, TX (United States). Dept. of Pathology and Genomic Medicine. Center for Molecular and Translational Human Infectious Diseases Research; Cornell Univ., Ithaca, NY (United States). Weill Medical College. Dept. of Pathology and Lab. Medicine
Houston Methodist Research Inst. and Houston Methodist Hospital, Houston, TX (United States). Dept. of Pathology and Genomic Medicine. Center for Molecular and Translational Human Infectious Diseases Research
Argonne National Lab. (ANL), Argonne, IL (United States). Computing, Environment and Life Sciences; Univ. of Chicago, IL (United States). Computational Inst.

Klebsiella pneumoniae is a major human pathogen responsible for high morbidity and mortality rates. The emergence and spread of strains resistant to multiple antimicrobial agents and documented large nosocomial outbreaks are especially concerning. To develop new therapeutic strategies for K. pneumoniae, it is imperative to understand the population genomic structure of strains causing human infections. To address this knowledge gap, we sequenced the genomes of 1,777 extended-spectrum beta-lactamase-producing K. pneumoniae strains cultured from patients in the 2,000-bed Houston Methodist Hospital system between September 2011 and May 2015, representing a comprehensive, population-based strain sample. Strains of largely uncharacterized clonal group 307 (CG307) caused more infections than those of well-studied epidemic CG258. Strains varied markedly in gene content and had an extensive array of small and very large plasmids, often containing antimicrobial resistance genes. Some patients with multiple strains cultured over time were infected with genetically distinct clones. We identified 15 strains expressing the New Delhi metallo-beta-lactamase 1 (NDM-1) enzyme that confers broad resistance to nearly all beta-lactam antibiotics. Transcriptome sequencing analysis of 10 phylogenetically diverse strains showed that the global transcriptome of each strain was unique and highly variable. Experimental mouse infection provided new information about immunological parameters of host-pathogen interaction. We exploited the large data set to develop whole-genome sequence-based classifiers that accurately predict clinical antimicrobial resistance for 12 of the 16 antibiotics tested. We conclude that analysis of large, comprehensive, population-based strain samples can assist understanding of the molecular diversity of these organisms and contribute to enhanced translational research.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1626108

Journal Information:: mBio (Online), Journal Name: mBio (Online) Journal Issue: 3 Vol. 8; ISSN 2150-7511

Publisher:: American Society for Microbiology (ASM)Copyright Statement

Country of Publication:: United States

Language:: English

References (82)

A Decision-Theoretic Generalization of On-Line Learning and an Application to Boosting Freund, Yoav; Schapire, Robert E. Journal of Computer and System Sciences, Vol. 55, Issue 1 https://doi.org/10.1006/jcss.1997.1504	journal	August 1997
Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads Nurk, Sergey; Bankevich, Anton; Antipov, Dmitry Lecture Notes in Computer Science https://doi.org/10.1007/978-3-642-37195-0_13	book	January 2013
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 São Paulo, Brazil Dropa, Milena; Lincopan, Nilton; Balsalobre, Livia C. Environmental Science and Pollution Research, Vol. 23, Issue 5 https://doi.org/10.1007/s11356-016-6079-5	journal	January 2016
Notch 1 Signaling Regulates Peripheral T Cell Activation Eagar, Todd N.; Tang, Qizhi; Wolfe, Michael Immunity, Vol. 20, Issue 4 https://doi.org/10.1016/S1074-7613(04)00081-0	journal	April 2004
Extended-spectrum β-lactamase-producing Enterobacteriaceae: an emerging public-health concern Pitout, Johann DD; Laupland, Kevin B. The Lancet Infectious Diseases, Vol. 8, Issue 3 https://doi.org/10.1016/S1473-3099(08)70041-0	journal	March 2008
The real threat of Klebsiella pneumoniae carbapenemase-producing bacteria Nordmann, Patrice; Cuzon, Gaelle; Naas, Thierry The Lancet Infectious Diseases, Vol. 9, Issue 4 https://doi.org/10.1016/S1473-3099(09)70054-4	journal	April 2009
Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases Munoz-Price, L. Silvia; Poirel, Laurent; Bonomo, Robert A. The Lancet Infectious Diseases, Vol. 13, Issue 9 https://doi.org/10.1016/S1473-3099(13)70190-7	journal	September 2013
The impact of multidrug resistance on outcomes in ventilator-associated pneumonia Tedja, Rudy; Nowacki, Amy; Fraser, Thomas American Journal of Infection Control, Vol. 42, Issue 5 https://doi.org/10.1016/j.ajic.2013.12.009	journal	May 2014
IL-17 Receptor Signaling in the Lung Epithelium Is Required for Mucosal Chemokine Gradients and Pulmonary Host Defense against K. pneumoniae Chen, Kong; Eddens, Taylor; Trevejo-Nunez, Giraldina Cell Host & Microbe, Vol. 20, Issue 5 https://doi.org/10.1016/j.chom.2016.10.003	journal	November 2016
Is the monoclonal spread of the ST258, KPC-3-producing clone being replaced in southern Italy by the dissemination of multiple clones of carbapenem-nonsusceptible, KPC-3-producing Klebsiella pneumoniae? Geraci, D. M.; Bonura, C.; Giuffrè, M. Clinical Microbiology and Infection, Vol. 21, Issue 3 https://doi.org/10.1016/j.cmi.2014.08.022	journal	March 2015
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 Metcalf, B. J.; Chochua, S.; Gertz, R. E. Clinical Microbiology and Infection, Vol. 22, Issue 12 https://doi.org/10.1016/j.cmi.2016.08.001	journal	December 2016
The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee Ellington, M. J.; Ekelund, O.; Aarestrup, F. M. Clinical Microbiology and Infection, Vol. 23, Issue 1 https://doi.org/10.1016/j.cmi.2016.11.012	journal	January 2017
Emergence of KPC-producing Klebsiella pneumoniae in Texas Hirsch, Elizabeth B.; Chang, Kai-Tai; Lasco, Todd M. Diagnostic Microbiology and Infectious Disease, Vol. 69, Issue 2 https://doi.org/10.1016/j.diagmicrobio.2010.09.003	journal	February 2011
Whole genome mapping of the first reported case of KPC-2–positive Klebsiella pneumoniae ST258 in Nebraska Fowler, Randal C.; Scharn, Caitlyn R.; Ali, Mir A. Diagnostic Microbiology and Infectious Disease, Vol. 79, Issue 3 https://doi.org/10.1016/j.diagmicrobio.2014.03.023	journal	July 2014
Dissemination of multidrug-resistant blaCTX-M-15/IncFIIk plasmids in Klebsiella pneumoniae isolates from hospital- and community-acquired human infections in Tunisia Mansour, Wejdene; Grami, Raoudha; Ben Haj Khalifa, Anis Diagnostic Microbiology and Infectious Disease, Vol. 83, Issue 3 https://doi.org/10.1016/j.diagmicrobio.2015.07.023	journal	November 2015
Outbreak of KPC-2-producing Enterobacteriaceae caused by clonal dissemination of Klebsiella pneumoniae ST307 carrying an IncX3-type plasmid harboring a truncated Tn4401a Kim, Jung Ok; Song, Sae Am; Yoon, Eun-Jeong Diagnostic Microbiology and Infectious Disease, Vol. 87, Issue 4 https://doi.org/10.1016/j.diagmicrobio.2016.12.012	journal	April 2017
First report of colistin-resistant KPC-2 producing ST258-Klebsiella pneumoniae in Spain Valentín-Martín, Amparo; Valverde-De Francisco, Aránzazu; Bosque-Vall, Montserrat Enfermedades Infecciosas y Microbiología Clínica, Vol. 31, Issue 7 https://doi.org/10.1016/j.eimc.2012.12.002	journal	August 2013
High prevalence of 16S rRNA methylase RmtB among CTX-M extended-spectrum β-lactamase-producing Klebsiella pneumoniae from Islamabad, Pakistan Habeeb, Muhammad Asif; Haque, Abdul; Nematzadeh, Shoeib International Journal of Antimicrobial Agents, Vol. 41, Issue 6 https://doi.org/10.1016/j.ijantimicag.2013.02.017	journal	June 2013
Emergence of New Delhi metallo-β-lactamase type 1-producing Enterobacteriaceae and non-Enterobacteriaceae: global case detection and bacterial surveillance Bushnell, Greta; Mitrani-Gold, Fanny; Mundy, Linda M. International Journal of Infectious Diseases, Vol. 17, Issue 5 https://doi.org/10.1016/j.ijid.2012.11.025	journal	May 2013
Expansion of ESBL-producing Klebsiella pneumoniae in hospitalized patients: A successful story of international clones (ST15, ST147, ST336) and epidemic plasmids (IncR, IncFIIK) Rodrigues, Carla; Machado, Elisabete; Ramos, Helena International Journal of Medical Microbiology, Vol. 304, Issue 8 https://doi.org/10.1016/j.ijmm.2014.08.003	journal	November 2014
Carbapenemase-producing Klebsiella pneumoniae: molecular and genetic decoding Chen, Liang; Mathema, Barun; Chavda, Kalyan D. Trends in Microbiology, Vol. 22, Issue 12 https://doi.org/10.1016/j.tim.2014.09.003	journal	December 2014
An SHR–SCR module specifies legume cortical cell fate to enable nodulation Dong, Wentao; Zhu, Yayun; Chang, Huizhong Nature, Vol. 589, Issue 7843 https://doi.org/10.1038/s41586-020-3016-z	journal	December 2020
Using eye movements to detect visual field loss: a pragmatic assessment using simulated scotoma Asfaw, Daniel S.; Jones, Pete R.; Edwards, Laura A. Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-66196-2	journal	June 2020
Circuit Depth Reduction for Gate-Model Quantum Computers Gyongyosi, Laszlo; Imre, Sandor Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-67014-5	journal	July 2020
Antimicrobial Resistance Prediction in PATRIC and RAST Davis, James J.; Boisvert, Sébastien; Brettin, Thomas Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep27930	journal	June 2016
Molecular dissection of the evolution of carbapenem-resistant multilocus sequence type 258 Klebsiella pneumoniae DeLeo, Frank R.; Chen, Liang; Porcella, Stephen F. Proceedings of the National Academy of Sciences, Vol. 111, Issue 13 https://doi.org/10.1073/pnas.1321364111	journal	March 2014
Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae , an urgent threat to public health Holt, Kathryn E.; Wertheim, Heiman; Zadoks, Ruth N. Proceedings of the National Academy of Sciences, Vol. 112, Issue 27 https://doi.org/10.1073/pnas.1501049112	journal	June 2015
The Spread of Klebsiella pneumoniae Carbapenemases: A Tale of Strains, Plasmids, and Transposons Munoz‐Price, L. Silvia; Quinn, John P. Clinical Infectious Diseases, Vol. 49, Issue 11 https://doi.org/10.1086/648078	journal	December 2009
Rapid Expansion of KPC-2-Producing Klebsiella pneumoniae Isolates in Two Texas Hospitals due to Clonal Spread of ST258 and ST307 Lineages Castanheira, Mariana; Farrell, Sarah E.; Wanger, Audrey Microbial Drug Resistance, Vol. 19, Issue 4 https://doi.org/10.1089/mdr.2012.0238	journal	August 2013
Genotypes of Ciprofloxacin-Resistant Klebsiella pneumoniae in Korea and Their Characteristics According to the Genetic Lineages Park, Dong Jin; Yu, Jin Kyung; Park, Kang Gyun Microbial Drug Resistance, Vol. 21, Issue 6 https://doi.org/10.1089/mdr.2015.0001	journal	December 2015
MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis Kumar, S.; Stecher, G.; Peterson, D. Bioinformatics, Vol. 28, Issue 20 https://doi.org/10.1093/bioinformatics/bts507	journal	August 2012
Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data Liu, Yongchao; Schröder, Jan; Schmidt, Bertil Bioinformatics, Vol. 29, Issue 3 https://doi.org/10.1093/bioinformatics/bts690	journal	November 2012
Trimmomatic: a flexible trimmer for Illumina sequence data Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern Bioinformatics, Vol. 30, Issue 15 https://doi.org/10.1093/bioinformatics/btu170	journal	April 2014
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 Gupta, Kalpana; Hooton, Thomas M.; Naber, Kurt G. Clinical Infectious Diseases, Vol. 52, Issue 5 https://doi.org/10.1093/cid/ciq257	journal	March 2011
Colistin-Resistant, Klebsiella pneumoniae Carbapenemase (KPC)-Producing Klebsiella pneumoniae Belonging to the International Epidemic Clone ST258 Bogdanovich, T.; Adams-Haduch, J. M.; Tian, G. -B. Clinical Infectious Diseases, Vol. 53, Issue 4 https://doi.org/10.1093/cid/cir401	journal	August 2011
Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258 Wyres, Kelly L.; Gorrie, Claire; Edwards, David J. Genome Biology and Evolution, Vol. 7, Issue 5 https://doi.org/10.1093/gbe/evv062	journal	April 2015
Carbapenem-Resistant Klebsiella pneumoniae Exhibit Variability in Capsular Polysaccharide and Capsule Associated Virulence Traits Diago-Navarro, Elizabeth; Chen, Liang; Passet, Virginie The Journal of Infectious Diseases, Vol. 210, Issue 5 https://doi.org/10.1093/infdis/jiu157	journal	March 2014
Complete sequencing of an IncH plasmid carrying the blaNDM-1, blaCTX-M-15 and qnrB1 genes Villa, Laura; Poirel, Laurent; Nordmann, Patrice Journal of Antimicrobial Chemotherapy, Vol. 67, Issue 7 https://doi.org/10.1093/jac/dks114	journal	April 2012
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 Paltansing, S.; Kraakman, M. E. M.; Ras, J. M. C. Journal of Antimicrobial Chemotherapy, Vol. 68, Issue 1 https://doi.org/10.1093/jac/dks365	journal	September 2012
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 Ruiz-Garbajosa, Patricia; Hernández-García, Marta; Beatobe, Lorena Journal of Antimicrobial Chemotherapy, Vol. 71, Issue 2 https://doi.org/10.1093/jac/dkv355	journal	October 2015
Prediction of antibiotic resistance from antibiotic resistance genes detected in antibiotic-resistant commensal Escherichia coli using PCR or WGS Moran, Robert A.; Anantham, Sashindran; Holt, Kathryn E. Journal of Antimicrobial Chemotherapy https://doi.org/10.1093/jac/dkw511	journal	December 2016
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro Molecular Biology and Evolution, Vol. 33, Issue 7 https://doi.org/10.1093/molbev/msw054	journal	March 2016
PATRIC, the bacterial bioinformatics database and analysis resource Wattam, Alice R.; Abraham, David; Dalay, Oral Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1099	journal	November 2013
Identification of Klebsiella capsule synthesis loci from whole genome data Wyres, Kelly L.; Wick, Ryan R.; Gorrie, Claire Microbial Genomics, Vol. 2, Issue 12 https://doi.org/10.1099/mgen.0.000102	journal	December 2016
Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations Lam, Margaret M. C.; Wick, Ryan R.; Wyres, Kelly L. Microbial Genomics, Vol. 4, Issue 9 https://doi.org/10.1099/mgen.0.000196	journal	September 2018
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs Inouye, Michael; Dashnow, Harriet; Raven, Lesley https://doi.org/10.1101/006627	posted_content	July 2014
Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations Lam, Margaret M. C.; Wick, Ryan R.; Wyres, Kelly L. https://doi.org/10.1101/098178	posted_content	March 2018
In vivo multiclonal transfer of blaKPC-3 from Klebsiella pneumoniae to Escherichia coli in surgery patients Gona, F.; Barbera, F.; Pasquariello, A. C. Clinical Microbiology and Infection, Vol. 20, Issue 10 https://doi.org/10.1111/1469-0691.12577	journal	October 2014
Clonal dissemination of Klebsiella pneumoniae ST258 harbouring KPC-2 in Argentina Gomez, S. A.; Pasteran, F. G.; Faccone, D. Clinical Microbiology and Infection, Vol. 17, Issue 10 https://doi.org/10.1111/j.1469-0691.2011.03600.x	journal	October 2011
Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing Snitkin, E. S.; Zelazny, A. M.; Thomas, P. J. Science Translational Medicine, Vol. 4, Issue 148 https://doi.org/10.1126/scitranslmed.3004129	journal	August 2012
Population Structure of KPC-Producing Klebsiella pneumoniae Isolates from Midwestern U.S. Hospitals Wright, Meredith S.; Perez, Federico; Brinkac, Lauren Antimicrobial Agents and Chemotherapy, Vol. 58, Issue 8 https://doi.org/10.1128/AAC.00125-14	journal	June 2014
Molecular Epidemiology of KPC-Producing Klebsiella pneumoniae Isolates in the United States: Clonal Expansion of Multilocus Sequence Type 258 Kitchel, B.; Rasheed, J. K.; Patel, J. B. Antimicrobial Agents and Chemotherapy, Vol. 53, Issue 8 https://doi.org/10.1128/AAC.00126-09	journal	June 2009
Multiplex Real-Time PCR for Detection of an Epidemic KPC-Producing Klebsiella pneumoniae ST258 Clone Chen, Liang; Chavda, Kalyan D.; Mediavilla, José R. Antimicrobial Agents and Chemotherapy, Vol. 56, Issue 6 https://doi.org/10.1128/AAC.00316-12	journal	March 2012
In Vitro Activity of NXL104 in Combination with β-Lactams against Klebsiella pneumoniae Isolates Producing KPC Carbapenemases Endimiani, Andrea; Choudhary, Yuvraj; Bonomo, Robert A. Antimicrobial Agents and Chemotherapy, Vol. 53, Issue 8 https://doi.org/10.1128/AAC.00641-09	journal	June 2009
Carbapenemase-Producing Klebsiella pneumoniae, a Key Pathogen Set for Global Nosocomial Dominance Pitout, Johann D. D.; Nordmann, Patrice; Poirel, Laurent Antimicrobial Agents and Chemotherapy, Vol. 59, Issue 10 https://doi.org/10.1128/AAC.01019-15	journal	July 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 Ocampo, Ana M.; Chen, Liang; Cienfuegos, Astrid V. Antimicrobial Agents and Chemotherapy, Vol. 60, Issue 1 https://doi.org/10.1128/AAC.01775-15	journal	October 2015
First Outbreak of KPC-3-Producing Klebsiella pneumoniae (ST258) Clinical Isolates in a Mexican Medical Center Rodríguez-Zulueta, Patricia; Silva-Sánchez, Jesús; Barrios, Humberto Antimicrobial Agents and Chemotherapy, Vol. 57, Issue 8 https://doi.org/10.1128/AAC.02530-12	journal	June 2013
Whole-Genome Assembly of Klebsiella pneumoniae Coproducing NDM-1 and OXA-232 Carbapenemases Using Single-Molecule, Real-Time Sequencing Doi, Yohei; Hazen, Tracy H.; Boitano, Matthew Antimicrobial Agents and Chemotherapy, Vol. 58, Issue 10 https://doi.org/10.1128/AAC.03180-14	journal	July 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 Stoesser, N.; Giess, A.; Batty, E. M. Antimicrobial Agents and Chemotherapy, Vol. 58, Issue 12 https://doi.org/10.1128/AAC.03900-14	journal	September 2014
Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae at a Single Institution: Insights into Endemicity from Whole-Genome Sequencing Mathers, Amy J.; Stoesser, Nicole; Sheppard, Anna E. Antimicrobial Agents and Chemotherapy, Vol. 59, Issue 3 https://doi.org/10.1128/AAC.04292-14	journal	January 2015
Novel Carbapenem-Hydrolyzing β-Lactamase, KPC-1, from a Carbapenem-Resistant Strain of Klebsiella pneumoniae Yigit, Hesna; Queenan, Anne Marie; Anderson, Gregory J. Antimicrobial Agents and Chemotherapy, Vol. 45, Issue 4 https://doi.org/10.1128/AAC.45.4.1151-1161.2001	journal	April 2001
Klebsiella pneumoniae Yersiniabactin Promotes Respiratory Tract Infection through Evasion of Lipocalin 2 Bachman, Michael A.; Oyler, Jennifer E.; Burns, Samuel H. Infection and Immunity, Vol. 79, Issue 8 https://doi.org/10.1128/IAI.05114-11	journal	May 2011
Clinical Laboratory Response to a Mock Outbreak of Invasive Bacterial Infections: a Preparedness Study Olsen, R. J.; Fittipaldi, N.; Kachroo, P. Journal of Clinical Microbiology, Vol. 52, Issue 12 https://doi.org/10.1128/JCM.02164-14	journal	September 2014
Population Structure of Klebsiella pneumoniae Causing Bloodstream Infections at a New York City Tertiary Care Hospital: Diversification of Multidrug-Resistant Isolates Gomez-Simmonds, Angela; Greenman, Michelle; Sullivan, Sean B. Journal of Clinical Microbiology, Vol. 53, Issue 7 https://doi.org/10.1128/JCM.03455-14	journal	April 2015
KPC - 3 Klebsiella pneumoniaeST258 clone infection in postoperative abdominal surgery patients in an intensive care setting: analysis of a case series of 30 patients Di Carlo, Paola; Gulotta, Gaspare; Casuccio, Alessandra BMC Anesthesiology, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2253-13-13	journal	July 2013
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 Richter, Sara N.; Frasson, Ilaria; Franchin, Elisa Gut Pathogens, Vol. 4, Issue 1 https://doi.org/10.1186/1757-4749-4-7	journal	January 2012
Characterization and functional analysis of phytoene synthase gene family in tobacco Wang, Zhaojun; Zhang, Lin; Dong, Chen BMC Plant Biology, Vol. 21, Issue 1 https://doi.org/10.1186/s12870-020-02816-3	journal	January 2021
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs Inouye, Michael; Dashnow, Harriet; Raven, Lesley-Ann Genome Medicine, Vol. 6, Issue 11 https://doi.org/10.1186/s13073-014-0090-6	journal	November 2014
2015 Brainhack Proceedings Craddock, R. Cameron; Bellec, Pierre; Margules, Daniel S. GigaScience, Vol. 5, Issue S1 https://doi.org/10.1186/s13742-016-0147-0	journal	November 2016
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
An Update of the Evolving Epidemic of blaKPC Carrying Klebsiella pneumoniae in Sicily, Italy, 2014: Emergence of Multiple Non-ST258 Clones Bonura, Celestino; Giuffrè, Mario; Aleo, Aurora PLOS ONE, Vol. 10, Issue 7 https://doi.org/10.1371/journal.pone.0132936	journal	July 2015
Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic Bowers, Jolene R.; Kitchel, Brandon; Driebe, Elizabeth M. PLOS ONE, Vol. 10, Issue 7 https://doi.org/10.1371/journal.pone.0133727	journal	July 2015
Genomic Epidemiology of an Endoscope-Associated Outbreak of Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae Marsh, Jane W.; Krauland, Mary G.; Nelson, Jemma S. PLOS ONE, Vol. 10, Issue 12 https://doi.org/10.1371/journal.pone.0144310	journal	December 2015
Mucosal Lipocalin 2 Has Pro-Inflammatory and Iron-Sequestering Effects in Response to Bacterial Enterobactin Bachman, Michael A.; Miller, Virginia L.; Weiser, Jeffrey N. PLoS Pathogens, Vol. 5, Issue 10 https://doi.org/10.1371/journal.ppat.1000622	journal	October 2009
Natural Variants of the KPC-2 Carbapenemase have Evolved Increased Catalytic Efficiency for Ceftazidime Hydrolysis at the Cost of Enzyme Stability Mehta, Shrenik C.; Rice, Kacie; Palzkill, Timothy PLOS Pathogens, Vol. 11, Issue 6 https://doi.org/10.1371/journal.ppat.1004949	journal	June 2015
A high‐resolution genomic analysis of multidrug‐resistant hospital outbreaks of Klebsiella pneumoniae Chung The, Hao; Karkey, Abhilasha; Pham Thanh, Duy EMBO Molecular Medicine, Vol. 7, Issue 3 https://doi.org/10.15252/emmm.201404767	journal	February 2015
Emergence of New Delhi metallo-β-lactamase type 1-producing Enterobacteriaceae and non-Enterobacteriaceae: global case detection and bacterial surveillance Fanny, Mitrani-Gold,; Linda, Mundy,; Greta, Bushnell, The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/3z25-jh84	text	January 2013
Mucosal Lipocalin 2 Has Pro-Inflammatory and Iron-Sequestering Effects in Response to Bacterial Enterobactin A., Bachman, Michael; N., Weiser, Jeffrey; L., Miller, Virginia The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/90mq-ja16	text	January 2009
Population Structure of KPC-Producing Klebsiella pneumoniae Isolates from Midwestern U.S. Hospitals David, van Duin,; M., Hujer, Andrea; D., Adams, Mark The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/g3wk-gk85	text	January 2014
The Resistance Mechanism and Clonal Distribution of Tigecycline-Nonsusceptible Klebsiella pneumoniae Isolates in Korea Ahn, Chulsoo; Yoon, Sang Sun; Yong, Tae Soon Yonsei Medical Journal, Vol. 57, Issue 3 https://doi.org/10.3349/ymj.2016.57.3.641	journal	January 2016
Global Dissemination of Carbapenemase-Producing Klebsiella pneumoniae: Epidemiology, Genetic Context, Treatment Options, and Detection Methods Lee, Chang-Ro; Lee, Jung Hun; Park, Kwang Seung Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00895	journal	June 2016
Multi-class AdaBoost Hastie, Trevor; Rosset, Saharon; Zhu, Ji Statistics and Its Interface, Vol. 2, Issue 3 https://doi.org/10.4310/SII.2009.v2.n3.a8	journal	January 2009

Cited By (26)

A crash course in sequencing for a microbiologist Kozińska, Aleksandra; Seweryn, Paulina; Sitkiewicz, Izabela Journal of Applied Genetics, Vol. 60, Issue 1 https://doi.org/10.1007/s13353-019-00482-2	journal	January 2019
CelB is a suitable marker for rapid and specific identification of Klebsiella pneumoniae by the loop-mediated isothermal amplification (LAMP) assay Tian, Yichen; Wang, Lefei; Zhang, Jinyang Brazilian Journal of Microbiology, Vol. 50, Issue 4 https://doi.org/10.1007/s42770-019-00144-9	journal	August 2019
Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis Kachroo, Priyanka; Eraso, Jesus M.; Beres, Stephen B. Nature Genetics, Vol. 51, Issue 3 https://doi.org/10.1038/s41588-018-0343-1	journal	February 2019
Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae Nguyen, Marcus; Brettin, Thomas; Long, S. Wesley Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-017-18972-w	journal	January 2018
No association between resistance mutations, empiric antibiotic, and mortality in ceftriaxone-resistant Escherichia coli and Klebsiella pneumoniae bacteremia Heng, Shi Thong; Chen, Swaine L.; Wong, Joshua G. X. Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-31081-6	journal	August 2018
A core genome approach that enables prospective and dynamic monitoring of infectious outbreaks Aggelen, Helen van; Kolde, Raivo; Chamarthi, Hareesh Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-44189-0	journal	May 2019
PATRIC as a unique resource for studying antimicrobial resistance Antonopoulos, Dionysios A.; Assaf, Rida; Aziz, Ramy Karam Briefings in Bioinformatics, Vol. 20, Issue 4 https://doi.org/10.1093/bib/bbx083	journal	July 2017
Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307 Wyres, Kelly L.; Hawkey, Jane; Hetland, Marit A. K. Journal of Antimicrobial Chemotherapy, Vol. 74, Issue 3 https://doi.org/10.1093/jac/dky492	journal	December 2018
Convergence of virulence and MDR in a single plasmid vector in MDR Klebsiella pneumoniae ST15 Lam, Margaret M. C.; Wyres, Kelly L.; Wick, Ryan R. Journal of Antimicrobial Chemotherapy, Vol. 74, Issue 5 https://doi.org/10.1093/jac/dkz028	journal	February 2019
Evaluation of risk factors for colistin resistance among uropathogenic isolates of Escherichia coli and Klebsiella pneumoniae: a case–control study Kaza, Parinitha; Mahindroo, Jaspreet; Veeraraghavan, Balaji Journal of Medical Microbiology, Vol. 68, Issue 6 https://doi.org/10.1099/jmm.0.000986	journal	June 2019
Caribbean multi-centre study of Klebsiella pneumoniae: whole-genome sequencing, antimicrobial resistance and virulence factors Heinz, Eva; Brindle, Richard; Morgan-McCalla, Andrina Microbial Genomics, Vol. 5, Issue 5 https://doi.org/10.1099/mgen.0.000266	journal	May 2019
Kaptive Web: user-friendly capsule and lipopolysaccharide serotype prediction for Klebsiella genomes Wick, Ryan R.; Heinz, Eva; Holt, Kathryn E. https://doi.org/10.1101/260125	posted_content	February 2018
High-resolution sweep metagenomics using fast probabilistic inference Mäklin, Tommi; Kallonen, Teemu; David, Sophia https://doi.org/10.1101/332544	posted_content	July 2019
Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307 Wyres, Kelly L.; Hawkey, Jane; Hetland, Marit A. K. https://doi.org/10.1101/352740	posted_content	June 2018
On the front line of Klebsiella pneumoniae surface structures understanding: establishment of Fourier Transform Infrared (FT-IR) spectroscopy as a capsule typing method Rodrigues, Carla; Sousa, Clara; Lopes, João Almeida https://doi.org/10.1101/554816	posted_content	February 2019
Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes Wick, Ryan R.; Heinz, Eva; Holt, Kathryn E. Journal of Clinical Microbiology, Vol. 56, Issue 6 https://doi.org/10.1128/jcm.00197-18	journal	April 2018
Genome-Based Prediction of Bacterial Antibiotic Resistance Su, Michelle; Satola, Sarah W.; Read, Timothy D. Journal of Clinical Microbiology, Vol. 57, Issue 3 https://doi.org/10.1128/jcm.01405-18	journal	October 2018
Development and Evaluation of a Novel Protein-Based Assay for Specific Detection of KPC β-Lactamases from Klebsiella pneumoniae Clinical Isolates Lu, Shuo; Soeung, Victoria; Nguyen, Hoang A. T. mSphere, Vol. 5, Issue 1 https://doi.org/10.1128/msphere.00918-19	journal	January 2020
Whole-Genome Sequencing of Human Clinical Klebsiella pneumoniae Isolates Reveals Misidentification and Misunderstandings of Klebsiella pneumoniae , Klebsiella variicola , and Klebsiella quasipneumoniae Long, S. Wesley; Linson, Sarah E.; Ojeda Saavedra, Matthew mSphere, Vol. 2, Issue 4 https://doi.org/10.1128/mspheredirect.00290-17	journal	August 2017
Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center Ellington, Matthew J.; Heinz, Eva; Wailan, Alexander M. Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1785-1	journal	September 2019
High-resolution sweep metagenomics using fast probabilistic inference Mäklin, Tommi; Kallonen, Teemu; David, Sophia Wellcome Open Research, Vol. 5 https://doi.org/10.12688/wellcomeopenres.15639.1	journal	January 2020
High-resolution sweep metagenomics using fast probabilistic inference Mäklin, Tommi; Kallonen, Teemu; David, Sophia Wellcome Open Research, Vol. 5 https://doi.org/10.12688/wellcomeopenres.15639.2	journal	January 2020
Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center Ellington, Matthew J.; Heinz, Eva; Wailan, Alexander M. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.56900	text	January 2019
Klebsiella pneumoniae ST307 with bla _OXA-181, South Africa, 2014–2016 Lowe, Michelle; Kock, Marleen M.; Coetzee, Jennifer Emerging Infectious Diseases, Vol. 25, Issue 4 https://doi.org/10.3201/eid2504.181482	journal	April 2019
Colonization, Infection, and the Accessory Genome of Klebsiella pneumoniae Martin, Rebekah M.; Bachman, Michael A. Frontiers in Cellular and Infection Microbiology, Vol. 8 https://doi.org/10.3389/fcimb.2018.00004	journal	January 2018
Small Klebsiella pneumoniae Plasmids: Neglected Contributors to Antibiotic Resistance Ramirez, Maria S.; Iriarte, Andrés; Reyes-Lamothe, Rodrigo Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02182	journal	September 2019

Similar Records

Whole-Genome Sequencing of Human Clinical Klebsiella pneumoniae Isolates Reveals Misidentification and Misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae

Journal Article · Tue Aug 01 20:00:00 EDT 2017 · mSphere · OSTI ID:1626162

Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae

Journal Article · Wed Jan 10 19:00:00 EST 2018 · Scientific Reports · OSTI ID:1421958

Resistance Determinants and Mobile Genetic Elements of an NDM-1-Encoding Klebsiella pneumoniae Strain

Journal Article · Thu Jun 05 20:00:00 EDT 2014 · PLoS ONE · OSTI ID:1627702

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Bacterial
Genome
Klebsiella Infections
Klebsiella pneumoniae
Microbiology
beta-lactamases

Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307

Citation Formats

References (82)

Cited By (26)

Similar Records

Related Subjects