Comparative Genomic Analysis of a Clinical Isolate of Klebsiella quasipneumoniae subsp. similipneumoniae, a KPC-2 and OKP-B-6 Beta-Lactamases Producer Harboring Two Drug-Resistance Plasmids from Southeast Brazil

Achour-Rokbani, 2010, Characterization of the ars gene cluster from extremely arsenic-resistant Microbacterium sp. strain A33, Appl. Environ. Microbiol, 76, 948, 10.1128/AEM.01738-09

Almeida, 2004, A System for Automated Bacterial (genome) Integrated Annotation–SABIA, Bioinformatics, 20, 2832, 10.1093/bioinformatics/bth273

Altschul, 1990, Basic local alignment search tool, J. Mol. Biol, 215, 403, 10.1016/S0022-2836(05)80360-2

Alves, 2006, Identification of clinical isolates of indole-positive and indole-negative Klebsiella spp, J. Clin. Microbiol., 44, 3640, 10.1128/JCM.00940-06

Antoine, 2003, Overrepresentation of a gene family encoding extracytoplasmic solute receptors in Bordetella, J. Bacteriol., 185, 1470, 10.1128/JB.185.4.1470-1474.2003

Arena, 2015, Draft genome sequence of the first hypermucoviscous klebsiella quasipneumoniae subsp. quasipneumoniae Isolate from a bloodstream infection, Genome Announc, 3, e00952, 10.1128/genomeA.00952-15

Bankevich, 2012, SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J. Comput. Biol, 19, 455, 10.1089/cmb.2012.0021

Besemer, 2001, GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions, Nucleic Acids Res, 29, 2607, 10.1093/nar/29.12.2607

Blin, 2017, Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae, Environ. Microbiol, 19, 1881, 10.1111/1462-2920.13689

Bobenchik, 2017, Performance of Vitek 2 for antimicrobial susceptibility testing of Acinetobacter baumannii, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia with Vitek 2 (2009 FDA) and CLSI M100S 26th edition breakpoints, J. Clin. Microbiol., 55, 450, 10.1128/JCM.01859-16

Bobik, 2015, Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways, Mol. Microbiol, 98, 193, 10.1111/mmi.13117

Boetzer, 2012, Toward almost closed genomes with GapFiller, Genome Biol., 13, R56, 10.1186/gb-2012-13-6-r56

Bowers, 2016, KlebSeq, a diagnostic tool for surveillance, detection, and monitoring of Klebsiella pneumoniae, J. Clin. Microbiol., 2582

Brinkkötter, 2002, Two class II D-tagatose-bisphosphate aldolases from enteric bacteria, Arch. Microbiol, 177, 410, 10.1007/s00203-002-0406-6

Brisse, 2014, 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, 10.1099/ijs.0.062737-0

Brisse, 2013, wzi Gene sequencing, a rapid method for determination of capsular type for Klebsiella strains, J. Clin. Microbiol., 51, 4073, 10.1128/JCM.01924-13

Brocker, 2009, Citrate utilization by Corynebacterium glutamicum is controlled by the CitAB two-component system through positive regulation of the citrate transport genes citH and tctCBA, J. Bacteriol, 191, 3869, 10.1128/JB.00113-09

Brown, 1995, Molecular genetics and transport analysis of the copper-resistance determinant (pco) from Escherichia coli plasmid pRJ1004, Mol. Microbiol, 17, 1153, 10.1111/j.1365-2958.1995.mmi_17061153.x

Bruen, 2006, A simple and robust statistical test for detecting the presence of recombination, Genetics, 172, 2665, 10.1534/genetics.105.048975

Carattoli, 2011, Plasmids in Gram negatives: molecular typing of resistance plasmids, Int. J. Med. Microbiol, 301, 654, 10.1016/j.ijmm.2011.09.003

Carattoli, 2014, In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing, Antimicrob. Agents Chemother., 58, 3895, 10.1128/AAC.02412-14

Castresana, 2000, Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis, Mol. Biol. Evol., 17, 540, 10.1093/oxfordjournals.molbev.a026334

Chen, 2005, VFDB: a reference database for bacterial virulence factors, Nucleic Acids Res., 33, D325, 10.1093/nar/gki008

Chou, 2004, Isolation of a chromosomal region of Klebsiella pneumoniae associated with allantoin metabolism and liver infection, Infect. Immun., 72, 3783, 10.1128/IAI.72.7.3783-3792.2004

Chung, 2002, Overexpression of the Escherichia coli sugE gene confers resistance to a narrow range of quaternary ammonium compounds, J. Bacteriol, 184, 2543, 10.1128/JB.184.9.2543-2545.2002

Coimbra, 2010, MST (molecular serotyping tool): a program for computer-assisted molecular identification of Escherichia coli and Shigella O antigens, J. Clin. Microbiol, 48, 1921, 10.1128/JCM.00357-10

Coimbra, 1999, Identification of Shigella serotypes by restriction of amplified O-antigen gene cluster, Res. Microbiol., 150, 543, 10.1016/S0923-2508(99)00103-5

Conlan, 2016, Plasmid Dynamics in KPC-Positive Klebsiella pneumoniae during long-term patient colonization, MBio, 7, e00742, 10.1128/mBio.00742-16

Darriba, 2012, jModelTest 2: more models, new heuristics and parallel computing, Nat. Methods, 9, 772, 10.1038/nmeth.2109

Delcher, 1999, Improved microbial gene identification with GLIMMER, Nucleic Acids Res., 27, 4636, 10.1093/nar/27.23.4636

Federhen, 2016, Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015), Stand. Genomics Sci, 11, 15, 10.1186/s40793-016-0134-1

Felsenstein, 1989, PHYLIP - phylogeny inference package (Version 3.2), Cladistics, 5, 164

Finn, 2017, InterPro in 2017-beyond protein family and domain annotations, Nucleic Acids Res, 45, D190, 10.1093/nar/gkw1107

Flannery, 2011, Self-transmissibility of the integrative and conjugative element ICEPm1 between clinical isolates requires a functional integrase, relaxase, and type IV secretion system, J. Bacteriol., 193, 4104, 10.1128/JB.05119-11

Flannery, 2009, Identification of a modular pathogenicity island that is widespread among urease-producing uropathogens and shares features with a diverse group of mobile elements, Infect. Immun., 77, 4887, 10.1128/IAI.00705-09

Fonseca, 2017, A one-step multiplex PCR to identify Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae in the clinical routine, Diagn. Microbiol. Infect. Dis., 87, 315, 10.1016/j.diagmicrobio.2017.01.005

Garza-Ramos, 2015, Development of a multiplex-PCR probe system for the proper identification of Klebsiella variicola, BMC Microbiol., 15, 64, 10.1186/s12866-015-0396-6

Goris, 2007, DNA-DNA hybridization values and their relationship to whole-genome sequence similarities, Int. J. Syst. Evol. Microbiol, 57, 81, 10.1099/ijs.0.64483-0

Guindon, 2009, Estimating maximum likelihood phylogenies with PhyML, Methods Mol. Biol., 537, 113, 10.1007/978-1-59745-251-9_6

Haeggman, 2004, Diversity and evolution of the class A chromosomal beta-lactamase gene in Klebsiella pneumoniae, Antimicrob. Agents Chemother, 48, 2400, 10.1128/AAC.48.7.2400-2408.2004

Haines-Menges, 2015, Host sialic acids: a delicacy for the pathogen with discerning taste, Microbiol. Spectr., 10.1128/microbiolspec.MBP-0005-2014

Hochhut, 2000, Mobilization of plasmids and chromosomal DNA mediated by the SXT element, a constin found in Vibrio cholerae O139, J. Bacteriol., 182, 2043, 10.1128/JB.182.7.2043-2047.2000

Holt, 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, 10.1073/pnas.1501049112

Huson, 2006, Application of phylogenetic networks in evolutionary studies, Mol. Biol. Evol, 23, 254, 10.1093/molbev/msj030

Hussein, 1981, Citrate-dependent iron transport system in Escherichia coli K-12, Eur. J. Biochem., 117, 431, 10.1111/j.1432-1033.1981.tb06357.x

Jia, 2017, CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database, Nucleic Acids Res, 45, D566, 10.1093/nar/gkw1004

Jiang, 1995, Molecular cloning, mapping, and regulation of Pho regulon genes for phosphonate breakdown by the phosphonatase pathway of Salmonella typhimurium LT2, J. Bacteriol., 177, 6411, 10.1128/jb.177.22.6411-6421.1995

Kaplan, 2015, Genomic and functional characterization of qnr-encoding plasmids from municipal wastewater biosolid Klebsiella pneumoniae isolates, Front. Microbiol., 6, 1354, 10.3389/fmicb.2015.01354

Katoh, 2013, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol, 30, 772, 10.1093/molbev/mst010

Lagesen, 2007, RNAmmer: consistent and rapid annotation of ribosomal RNA genes, Nucleic Acids Res., 35, 3100, 10.1093/nar/gkm160

Lähteenmäki, 2001, Bacterial plasminogen activators and receptors, FEMS Microbiol. Rev, 25, 531, 10.1111/j.1574-6976.2001.tb00590.x

Lechner, 2011, Proteinortho: detection of (co-) orthologs in large-scale analysis, BMC Bioinformatics, 12, 124, 10.1186/1471-2105-12-124

Letunic, 2016, Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees, Nucleic Acids Res, 44, W242, 10.1093/nar/gkw290

Lewis, 2004, The Tricarballylate utilization (tcuRABC) genes of Salmonella enterica serovar Typhimurium LT2, J. Bacteriol, 186, 1629, 10.1128/JB.186.6.1629-1637.2004

Lin, 2012, Complete genome sequence of Klebsiella pneumoniae 1084, a hypermucoviscosity-negative K1 clinical strain, J. Bacteriol, 194, 6316, 10.1128/JB.01548-12

Lin, 2011, Assessment of hypermucoviscosity as a virulence factor for experimental Klebsiella pneumoniae infections: comparative virulence analysis with hypermucoviscosity-negative strain, BMC Microbiol., 11, 50, 10.1186/1471-2180-11-50

Liu, 2009, ARDB–Antibiotic Resistance Genes Database, Nucleic Acids Res., 37, D443, 10.1093/nar/gkn656

Liu, 2015, Production of novel NaN3-resistant creatine amidinohydrolase in recombinant Escherichia coli, Bioengineered, 6, 248, 10.1080/21655979.2015.1052919

Liu, 1986, Klebsiella pneumoniae liver abscess associated with septic endophthalmitis, Arch. Intern. Med., 146, 1913, 10.1001/archinte.1986.00360220057011

Long, 2017, Whole-genome sequencing of human clinical Klebsiella pneumoniae isolates reveals misidentification and misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae, mSphere, 2, e00290, 10.1128/mSphereDirect.00290-17

Lowe, 1997, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res, 25, 955, 10.1093/nar/25.5.0955

McGrath, 2013, Organophosphonates revealed: new insights into the microbial metabolism of ancient molecules, Nat. Rev. Microbiol, 11, 412, 10.1038/nrmicro3011

Meyer, 2009, Replication and conjugative mobilization of broad host-range IncQ plasmids, Plasmid, 62, 57, 10.1016/j.plasmid.2009.05.001

Mollenkopf, 2017, Carbapenemase-producing enterobacteriaceae recovered from the environment of a swine farrow-to-finish operation in the United States, Antimicrob. Agents Chemother, 61, e02348, 10.1128/AAC.01298-16

Nicoletti, 2015, Characterization of BKC-1 class A carbapenemase from Klebsiella pneumoniae clinical isolates in Brazil, Antimicrob. Agents Chemother., 59, 5159, 10.1128/AAC.00158-15

Paczosa, 2016, Klebsiella pneumoniae: going on the offense with a strong defense, Microbiol. Mol. Biol. Rev, 80, 629, 10.1128/MMBR.00078-15

Petkau, 2010, Interactive microbial genome visualization with GView, Bioinformatics, 26, 3125, 10.1093/bioinformatics/btq588

Poulin-Laprade, 2015, The extended regulatory networks of SXT/R391 integrative and conjugative elements and IncA/C conjugative plasmids, Front. Microbiol., 6, 837, 10.3389/fmicb.2015.00837

Ramos, 2014, Comparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanisms, BMC Genomics, 15, 54, 10.1186/1471-2164-15-54

Randall, 2015, Silver resistance in Gram-negative bacteria: a dissection of endogenous and exogenous mechanisms. J. Antimicrob, Chemother, 70, 1037, 10.1093/jac/dku523

Richter, 2016, JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison, Bioinformatics, 32, 929, 10.1093/bioinformatics/btv681

Scholz, 1989, Complete nucleotide sequence and gene organization of the broad-host-range plasmid RSF1010, Gene, 75, 271, 10.1016/0378-1119(89)90273-4

Shankar, 2017, Draft genome of a hypervirulent Klebsiella quasipneumoniae subsp. similipneumoniae with novel sequence type ST2320 isolated from a chronic liver disease patient, J. Glob. Antimicrob. Resist., 9, 30, 10.1016/j.jgar.2017.01.004

Souza, 2012, AtlasT4SS: a curated database for type IV secretion systems, BMC Microbiol., 12, 172, 10.1186/1471-2180-12-172

Sütterlin, 2017, High frequency of silver resistance genes in invasive isolates of Enterobacter and Klebsiella species, J. Hosp. Infect., 96, 256, 10.1016/j.jhin.2017.04.017

Tamura, 2013, MEGA6: Molecular Evolutionary Genetics Analysis version 6.0, Mol. Biol. Evol, 30, 2725, 10.1093/molbev/mst197

Taylor, 2002, Genomic variability of o islands encoding tellurite resistance in enterohemorrhagic Escherichia coli O157:H7 isolates, J. Bacteriol, 184, 4690, 10.1128/JB.184.17.4690-4698.2002

Ternan, 1998, Phosphate starvation-independent 2-aminoethylphosphonic acid biodegradation in a newly isolated strain of Pseudomonas putida, NG2, Syst. Appl. Microbiol, 21, 346, 10.1016/S0723-2020(98)80043-X

Thiennimitr, 2011, Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota, Proc. Natl. Acad. Sci. U.SA., 108, 17480, 10.1073/pnas.1107857108

Torres, 2009, Defining, treating and preventing hospital acquired pneumonia: European perspective, Intensive Care Med., 35, 9, 10.1007/s00134-008-1336-9

Widenhorn, 1989, Genetic regulation of the tricarboxylate transport operon (tctI) of Salmonella typhimurium, J. Bacteriol, 171, 4436, 10.1128/jb.171.8.4436-4441.1989

Wong, 1994, Randomly amplified polymorphic DNA typing: a useful tool for rapid epidemiological typing of Klebsiella pneumoniae, Epidemiol. Infect, 113, 445, 10.1017/S095026880006845X

Wu, 2009, Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis, J. Bacteriol., 191, 4492, 10.1128/JB.00315-09

Wyres, 2016, Identification of Klebsiella capsule synthesis loci from whole genome data, Microb. Genomics, 2, e000102, 10.1099/mgen.0.000102

Yoon, 2014, Origin in Acinetobacter guillouiae and dissemination of the aminoglycoside-modifying enzyme Aph(3')-VI, MBio, 5, e01972, 10.1128/mBio.01972-14

Zankari, 2012, Identification of acquired antimicrobial resistance genes, J. Antimicrob. Chemother., 67, 2640, 10.1093/jac/dks261