-
1
-
-
0032911760
-
Inadequate antimicrobial treatment of infections: A risk factor for hospital mortality among critically ill patients
-
Kollef MH, Sherman G, Ward S, Fraser VJ. Inadequate antimicrobial treatment of infections: a risk factor for hospital mortality among critically ill patients. Chest 115(2), 462-474 (1999).
-
(1999)
Chest
, vol.115
, Issue.2
, pp. 462-474
-
-
Kollef, M.H.1
Sherman, G.2
Ward, S.3
Fraser, V.J.4
-
2
-
-
84867677455
-
Inadequate treatment of ventilator-associated and hospital-acquired pneumonia: Risk factors and impact on outcomes
-
Piskin N, Aydemir H, Oztoprak N et al. Inadequate treatment of ventilator-associated and hospital-acquired pneumonia: risk factors and impact on outcomes. BMC Infect. Dis. 12, 268 (2012).
-
(2012)
BMC Infect. Dis
, vol.12
, Issue.268
-
-
Piskin, N.1
Aydemir, H.2
Oztoprak, N.3
-
3
-
-
0030901413
-
Impact of BAL data on the therapy and outcome of ventilator-associated pneumonia
-
Luna CM, Vujacich P, Niederman MS et al. Impact of BAL data on the therapy and outcome of ventilator-associated pneumonia. Chest 111(3), 676-685 (1997).
-
(1997)
Chest
, vol.111
, Issue.3
, pp. 676-685
-
-
Luna, C.M.1
Vujacich, P.2
Niederman, M.S.3
-
4
-
-
84872383048
-
Analytical validation of a novel high multiplexing real-time PCR array for the identification of key pathogens causative of bacterial ventilator-associated pneumonia and their associated resistance genes
-
Bogaerts P, Hamels S, de Mendonca R et al. Analytical validation of a novel high multiplexing real-time PCR array for the identification of key pathogens causative of bacterial ventilator-associated pneumonia and their associated resistance genes. J. Antimicrob. Chemother. 68(2), 340-347 (2013).
-
(2013)
J. Antimicrob. Chemother
, vol.68
, Issue.2
, pp. 340-347
-
-
Bogaerts, P.1
Hamels, S.2
De Mendonca, R.3
-
5
-
-
84930531576
-
Performance and impact of a rapid method combining mass spectrometry and direct antimicrobial susceptibility testing on treatment adequacy of patients with ventilator-associated pneumonia
-
e1-e6
-
Le Dorze M, Gault N, Foucrier A et al. Performance and impact of a rapid method combining mass spectrometry and direct antimicrobial susceptibility testing on treatment adequacy of patients with ventilator-associated pneumonia. Clin. Microbiol. Infect. 21(5), 468, e1-e6 (2014).
-
(2014)
Clin. Microbiol. Infect
, vol.21
, Issue.5
, pp. 468
-
-
Le Dorze, M.1
Gault, N.2
Foucrier, A.3
-
6
-
-
84899504756
-
Gram-stain plus MALDI-TOF MS (matrix-assisted laser desorption ionizationtime of flight mass spectrometry) for a rapid diagnosis of urinary tract infection
-
Burillo A, Rodríguez-Sánchez B, Ramiro A, Cercenado E, Rodríguez-Créixems M, Bouza E. Gram-stain plus MALDI-TOF MS (matrix-assisted laser desorption ionizationtime of flight mass spectrometry) for a rapid diagnosis of urinary tract infection. PLoS ONE 9(1), e86915 (2014).
-
(2014)
PLoS ONE
, vol.9
, Issue.1
-
-
Burillo, A.1
Rodríguez-Sánchez, B.2
Ramiro, A.3
Cercenado, E.4
Rodríguez-Créixems, M.5
Bouza, E.6
-
7
-
-
84857382388
-
Matrix-assisted laser desorption ionization-time of flight mass spectrometrybased functional assay for rapid detection of resistance against β-lactam antibiotics
-
Sparbier K, Schubert S, Weller U, Boogen C, Kostrzewa M. Matrix-assisted laser desorption ionization-time of flight mass spectrometrybased functional assay for rapid detection of resistance against β-lactam antibiotics. J. Clin. Microbiol. 50(3), 927-937 (2012).
-
(2012)
J. Clin. Microbiol
, vol.50
, Issue.3
, pp. 927-937
-
-
Sparbier, K.1
Schubert, S.2
Weller, U.3
Boogen, C.4
Kostrzewa, M.5
-
8
-
-
84865231395
-
Transforming clinical microbiology with bacterial genome sequencing
-
Didelot X, Bowden R, Wilson DJ, Peto TEA, Crook DW. Transforming clinical microbiology with bacterial genome sequencing. Nat. Rev. Genet. 13(9), 601-612 (2012).
-
(2012)
Nat. Rev. Genet
, vol.13
, Issue.9
, pp. 601-612
-
-
Didelot, X.1
Bowden, R.2
Wilson, D.J.3
Peto, T.E.A.4
Crook, D.W.5
-
9
-
-
84891529869
-
Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples
-
Hasman H, Saputra D, Sicheritz-Ponten T et al. Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J. Clin. Microbiol. 52(1), 139-146 (2014).
-
(2014)
J. Clin. Microbiol
, vol.52
, Issue.1
, pp. 139-146
-
-
Hasman, H.1
Saputra, D.2
Sicheritz-Ponten, T.3
-
11
-
-
84894586819
-
Rapid resistome fingerprinting and clonal lineage profiling of carbapenem-resistant Klebsiella pneumoniae isolates by targeted nextgeneration sequencing
-
Arena F, Rolfe PA, Doran G et al. Rapid resistome fingerprinting and clonal lineage profiling of carbapenem-resistant Klebsiella pneumoniae isolates by targeted nextgeneration sequencing. J. Clin. Microbiol. 52(3), 987-990 (2014).
-
(2014)
J. Clin. Microbiol
, vol.52
, Issue.3
, pp. 987-990
-
-
Arena, F.1
Rolfe, P.A.2
Doran, G.3
-
12
-
-
84893041172
-
Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis
-
Lim YW, Evangelista JS, Schmieder R et al. Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis. J. Clin. Microbiol. 52(2), 425-437 (2014).
-
(2014)
J. Clin. Microbiol
, vol.52
, Issue.2
, pp. 425-437
-
-
Lim, Y.W.1
Evangelista, J.S.2
Schmieder, R.3
-
13
-
-
84888796738
-
Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data
-
Stoesser N, Batty EM, Eyre DW et al. Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J. Antimicrob. Chemother. 68(10), 2234-2244 (2013).
-
(2013)
J. Antimicrob. Chemother
, vol.68
, Issue.10
, pp. 2234-2244
-
-
Stoesser, N.1
Batty, E.M.2
Eyre, D.W.3
-
14
-
-
84880432120
-
Whole-genome sequencing for rapid susceptibility testing of M. Tuberculosis
-
Köser CU, Bryant JM, Becq J et al. Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis. N. Engl. J. Med. 369(3), 290-292 (2013).
-
(2013)
N. Engl. J. Med
, vol.369
, Issue.3
, pp. 290-292
-
-
Köser, C.U.1
Bryant, J.M.2
Becq, J.3
-
15
-
-
84943793968
-
WGS accurately predicts antimicrobial resistance in Escherichia coli
-
Tyson GH, McDermott PF, Li C et al. WGS accurately predicts antimicrobial resistance in Escherichia coli. J. Antimicrob. Chemother. 70(10), 2763-2769 (2015).
-
(2015)
J. Antimicrob. Chemother
, vol.70
, Issue.10
, pp. 2763-2769
-
-
Tyson, G.H.1
McDermott, P.F.2
Li, C.3
-
16
-
-
84882269831
-
Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology
-
Reuter S, Ellington MJ, Cartwright EJP et al. Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology. JAMA Intern. Med. 173(15), 1397-1404 (2013).
-
(2013)
JAMA Intern. Med
, vol.173
, Issue.15
, pp. 1397-1404
-
-
Reuter, S.1
Ellington, M.J.2
Cartwright, E.J.P.3
-
17
-
-
84873467253
-
A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak
-
Reuter S, Harrison TG, Köser CU et al. A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak. BMJ Open 3(1), e002175 (2013).
-
(2013)
BMJ Open
, vol.3
, Issue.1
-
-
Reuter, S.1
Harrison, T.G.2
Köser, C.U.3
-
18
-
-
84873034794
-
Rapid whole-genome sequencing for investigation of a suspected tuberculosis outbreak
-
Török ME, Reuter S, Bryant J et al. Rapid whole-genome sequencing for investigation of a suspected tuberculosis outbreak. J. Clin. Microbiol. 51(2), 611-614 (2013).
-
(2013)
J. Clin. Microbiol
, vol.51
, Issue.2
, pp. 611-614
-
-
Török, M.E.1
Reuter, S.2
Bryant, J.3
-
19
-
-
84862199752
-
Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak
-
Köser CU, Holden MTG, Ellington MJ et al. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N. Engl. J. Med. 366(24), 2267-2275 (2012).
-
(2012)
N. Engl. J. Med
, vol.366
, Issue.24
, pp. 2267-2275
-
-
Köser, C.U.1
Holden, M.T.G.2
Ellington, M.J.3
-
20
-
-
84926462931
-
Dynamics of MDR Enterobacter cloacae outbreaks in a neonatal unit in Nepal: Insights using wider sampling frames and next-generation sequencing
-
Stoesser N, Sheppard AE, Shakya M et al. Dynamics of MDR Enterobacter cloacae outbreaks in a neonatal unit in Nepal: insights using wider sampling frames and next-generation sequencing. J. Antimicrob. Chemother. 70(4), 1008-1015 (2015).
-
(2015)
J. Antimicrob. Chemother
, vol.70
, Issue.4
, pp. 1008-1015
-
-
Stoesser, N.1
Sheppard, A.E.2
Shakya, M.3
-
21
-
-
84912084358
-
Genome sequencing of an extended series of NDMproducing 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 EM et al. Genome sequencing of an extended series of NDMproducing 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(12), 7347-7357 (2014).
-
(2014)
Antimicrob. Agents Chemother
, vol.58
, Issue.12
, pp. 7347-7357
-
-
Stoesser, N.1
Giess, A.2
Batty, E.M.3
-
22
-
-
13644269309
-
Infectious Diseases Society of America. Guidelines for the management of adults with hospitalacquired, ventilator-associated, and healthcare-associated pneumonia
-
American Thoracic Society, Infectious Diseases Society of America. Guidelines for the management of adults with hospitalacquired, ventilator-associated, and healthcare-associated pneumonia. Am. J. Respir. Crit. Care Med. 171(4), 388-416 (2005).
-
(2005)
Am. J. Respir. Crit. Care Med
, vol.171
, Issue.4
, pp. 388-416
-
-
Thoracic Society, A.1
-
23
-
-
84884249133
-
Causes, consequences, and perspectives in the variations of intestinal density of colonization of multidrug-resistant enterobacteria
-
Ruppé E, Andremont A. Causes, consequences, and perspectives in the variations of intestinal density of colonization of multidrug-resistant enterobacteria. Front. Microbiol. 4, 129 (2013).
-
(2013)
Front. Microbiol
, vol.4
, Issue.129
-
-
Ruppé, E.1
Andremont, A.2
-
24
-
-
84874051309
-
Emergence of imipenem-resistant Gram-negative bacilli in intestinal flora of intensive care patients
-
Armand-Lefèvre L, Angebault C, Barbier F et al. Emergence of imipenem-resistant Gram-negative bacilli in intestinal flora of intensive care patients. Antimicrob. Agents Chemother. 57(3), 1488-1495 (2013).
-
(2013)
Antimicrob. Agents Chemother
, vol.57
, Issue.3
, pp. 1488-1495
-
-
Armand-Lefèvre, L.1
Angebault, C.2
Barbier, F.3
-
25
-
-
0034727835
-
Effect of antibiotic therapy on the density of vancomycin-resistant enterococci in the stool of colonized patients
-
Donskey CJ, Chowdhry TK, Hecker MT et al. Effect of antibiotic therapy on the density of vancomycin-resistant enterococci in the stool of colonized patients. N. Engl. J. Med. 343(26), 1925-1932 (2000).
-
(2000)
N. Engl. J. Med
, vol.343
, Issue.26
, pp. 1925-1932
-
-
Donskey, C.J.1
Chowdhry, T.K.2
Hecker, M.T.3
-
26
-
-
84930824439
-
Elaboration of a consensual definition of de-escalation allowing a ranking of β-lactams
-
e1-e10
-
Weiss E, Zahar J-R, Lesprit P et al. Elaboration of a consensual definition of de-escalation allowing a ranking of β-lactams. Clin. Microbiol. Infect. 21(7), 649, e1-e10 (2015).
-
(2015)
Clin. Microbiol. Infect
, vol.21
, Issue.7
, pp. 649
-
-
Weiss, E.1
Zahar, J.-R.2
Lesprit, P.3
-
27
-
-
77955694435
-
Microbial etiologies of hospitalacquired bacterial pneumonia and ventilatorassociated bacterial pneumonia
-
Jones RN. Microbial etiologies of hospitalacquired bacterial pneumonia and ventilatorassociated bacterial pneumonia. Clin. Infect. Dis. Off. Publ. Infect. Dis. Soc. Am. 51(Suppl. 1), S81-S87 (2010).
-
(2010)
Clin. Infect. Dis. Off. Publ. Infect. Dis. Soc. Am
, vol.51
, pp. S81-S87
-
-
Jones, R.N.1
-
28
-
-
84888269806
-
A comparison of microbiology and demographics among patients with healthcare-associated, hospital-acquired, and ventilator-associated pneumonia: A retrospective analysis of 1184 patients from a large, international study
-
Quartin AA, Scerpella EG, Puttagunta S, Kett DH. A comparison of microbiology and demographics among patients with healthcare-associated, hospital-acquired, and ventilator-associated pneumonia: a retrospective analysis of 1184 patients from a large, international study. BMC Infect. Dis. 13, 561 (2013).
-
(2013)
BMC Infect. Dis
, vol.13
, Issue.561
-
-
Quartin, A.A.1
Scerpella, E.G.2
Puttagunta, S.3
Kett, D.H.4
-
29
-
-
30344451643
-
Epidemiology and outcomes of health-care-associated pneumonia: Results from a large US database of culture-positive pneumonia
-
Kollef MH, Shorr A, Tabak YP, Gupta V, Liu LZ, Johannes RS. Epidemiology and outcomes of health-care-associated pneumonia: results from a large US database of culture-positive pneumonia. Chest 128(6), 3854-3862 (2005).
-
(2005)
Chest
, vol.128
, Issue.6
, pp. 3854-3862
-
-
Kollef, M.H.1
Shorr, A.2
Tabak, Y.P.3
Gupta, V.4
Liu, L.Z.5
Johannes, R.S.6
-
30
-
-
84155171838
-
High prevalence of multidrug-resistant nonfermenters in hospital-acquired pneumonia in Asia
-
Chung DR, Song J-H, Kim SH et al. High prevalence of multidrug-resistant nonfermenters in hospital-acquired pneumonia in Asia. Am. J. Respir. Crit. Care Med. 184(12), 1409-1417 (2011).
-
(2011)
Am. J. Respir. Crit. Care Med
, vol.184
, Issue.12
, pp. 1409-1417
-
-
Chung, D.R.1
Song, J.-H.2
Kim, S.H.3
-
31
-
-
84962431437
-
Surveillance des infections nosocomiales en réanimation adulte
-
Réseau REA-RAISIN. Surveillance des infections nosocomiales en réanimation adulte. Réseau REA-Raisin, France (2014).
-
(2014)
Réseau REA-Raisin, France
-
-
Rea-Raisin, R.1
-
32
-
-
84859930602
-
Ventilator-associated pneumonia and ICU mortality in severe ARDS patients ventilated according to a lung-protective strategy
-
Forel J-M, Voillet F, Pulina D et al. Ventilator-associated pneumonia and ICU mortality in severe ARDS patients ventilated according to a lung-protective strategy. Crit. Care Lond. Engl. 16(2), R65 (2012).
-
(2012)
Crit. Care Lond. Engl
, vol.16
, Issue.2
, pp. R65
-
-
Forel, J.-M.1
Voillet, F.2
Pulina, D.3
-
33
-
-
77749343661
-
Validation of the American Thoracic Society - Infectious Diseases Society of America guidelines for hospital-acquired pneumonia in the intensive care unit
-
Ferrer M, Liapikou A, Valencia M et al. Validation of the American Thoracic Society - Infectious Diseases Society of America guidelines for hospital-acquired pneumonia in the intensive care unit. Clin. Infect. Dis. Off. Publ. Infect. Dis. Soc. Am. 50(7), 945-952 (2010).
-
(2010)
Clin. Infect. Dis. Off. Publ. Infect. Dis. Soc. Am
, vol.50
, Issue.7
, pp. 945-952
-
-
Ferrer, M.1
Liapikou, A.2
Valencia, M.3
-
34
-
-
34249071381
-
When to include polymyxins in the empirical antibiotic regimen in critically ill patients with fever? A decision analysis approach
-
Falagas ME, Rafailidis PI. When to include polymyxins in the empirical antibiotic regimen in critically ill patients with fever? A decision analysis approach. Shock Augusta Ga. 27(6), 605-609 (2007).
-
(2007)
Shock Augusta Ga
, vol.27
, Issue.6
, pp. 605-609
-
-
Falagas, M.E.1
Rafailidis, P.I.2
-
35
-
-
84923081620
-
What is a resistance gene? Ranking risk in resistomes
-
Martínez JL, Coque TM, Baquero F. What is a resistance gene? Ranking risk in resistomes. Nat. Rev. Microbiol. 13(2), 116-123 (2015).
-
(2015)
Nat. Rev. Microbiol
, vol.13
, Issue.2
, pp. 116-123
-
-
Martínez, J.L.1
Coque, T.M.2
Baquero, F.3
-
36
-
-
77954783864
-
The antibiotic resistome
-
Wright GD. The antibiotic resistome. Expert Opin. Drug Discov. 5(8), 779-788 (2010).
-
(2010)
Expert Opin. Drug Discov
, vol.5
, Issue.8
, pp. 779-788
-
-
Wright, G.D.1
-
37
-
-
69549086653
-
Functional characterization of the antibiotic resistance reservoir in the human microflora
-
Sommer MOA, Dantas G, Church GM. Functional characterization of the antibiotic resistance reservoir in the human microflora. Science 325(5944), 1128-1131 (2009).
-
(2009)
Science
, vol.325
, Issue.5944
, pp. 1128-1131
-
-
Sommer, M.O.A.1
Dantas, G.2
Church, G.M.3
-
38
-
-
84880050412
-
Country-specific antibiotic use practices impact the human gut resistome
-
Forslund K, Sunagawa S, Kultima JR et al. Country-specific antibiotic use practices impact the human gut resistome. Genome Res. 23(7), 1163-1169 (2013).
-
(2013)
Genome Res
, vol.23
, Issue.7
, pp. 1163-1169
-
-
Forslund, K.1
Sunagawa, S.2
Kultima, J.R.3
-
39
-
-
84896696110
-
-
Ghosh TS, Gupta SS, Nair GB, Mande SS. In silico analysis of antibiotic resistance genes in the gut microflora of individuals from diverse geographies and age-groups. PLoS ONE 8(12), e83823 (2013).
-
(2013)
In Silico Analysis of Antibiotic Resistance Genes in the Gut Microflora of Individuals from Diverse Geographies and Age-groups. PLoS ONE
, vol.8
, Issue.12
-
-
Ghosh, T.S.1
Gupta, S.S.2
Nair, G.B.3
Mande, S.S.4
-
40
-
-
84891906623
-
Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes
-
Moore AM, Patel S, Forsberg KJ et al. Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes. PLoS ONE 8(11), e78822 (2013).
-
(2013)
PLoS ONE
, vol.8
, Issue.11
-
-
Moore, A.M.1
Patel, S.2
Forsberg, K.J.3
-
41
-
-
84880831180
-
Metagenomewide analysis of antibiotic resistance genes in a large cohort of human gut microbiota
-
Hu Y, Yang X, Qin J et al. Metagenomewide analysis of antibiotic resistance genes in a large cohort of human gut microbiota. Nat. Commun. 4, 2151 (2013).
-
(2013)
Nat. Commun
, vol.4
, Issue.2151
-
-
Hu, Y.1
Yang, X.2
Qin, J.3
-
43
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18(5), 821-829 (2008).
-
(2008)
Genome Res
, vol.18
, Issue.5
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
44
-
-
84942887758
-
SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
-
Luo R, Liu B, Xie Y et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1(1), 18 (2012).
-
(2012)
GigaScience
, vol.1
, Issue.1
, pp. 18
-
-
Luo, R.1
Liu, B.2
Xie, Y.3
-
45
-
-
84867397631
-
MetaVelvet: An extension of Velvet assembler to de novo metagenome assembly from short sequence reads
-
Namiki T, Hachiya T, Tanaka H, Sakakibara Y. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res. 40(20), e155 (2012).
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.20
, pp. e155
-
-
Namiki, T.1
Hachiya, T.2
Tanaka, H.3
Sakakibara, Y.4
-
46
-
-
84861728077
-
A de novo metagenomic assembly program for shotgun DNA reads
-
Lai B, Ding R, Li Y, Duan L, Zhu H. A de novo metagenomic assembly program for shotgun DNA reads. Bioinforma. Oxf. Engl. 28(11), 1455-1462 (2012).
-
(2012)
Bioinforma. Oxf. Engl
, vol.28
, Issue.11
, pp. 1455-1462
-
-
Lai, B.1
Ding, R.2
Li, Y.3
Duan, L.4
Zhu, H.5
-
47
-
-
84926472171
-
Improved data analysis for the MinION nanopore sequencer
-
Jain M, Fiddes IT, Miga KH, Olsen HE, Paten B, Akeson M. Improved data analysis for the MinION nanopore sequencer. Nat. Methods. 12(4), 351-356 (2015).
-
(2015)
Nat. Methods
, vol.12
, Issue.4
, pp. 351-356
-
-
Jain, M.1
Fiddes, I.T.2
Miga, K.H.3
Olsen, H.E.4
Paten, B.5
Akeson, M.6
-
48
-
-
58149234737
-
Real-time DNA sequencing from single polymerase molecules
-
Eid J, Fehr A, Gray J et al. Real-time DNA sequencing from single polymerase molecules. Science 323(5910), 133-138 (2009).
-
(2009)
Science
, vol.323
, Issue.5910
, pp. 133-138
-
-
Eid, J.1
Fehr, A.2
Gray, J.3
-
49
-
-
84904255806
-
A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
-
Naccache SN, Federman S, Veeraraghavan N et al. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res. 24(7), 1180-1192 (2014).
-
(2014)
Genome Res
, vol.24
, Issue.7
, pp. 1180-1192
-
-
Naccache, S.N.1
Federman, S.2
Veeraraghavan, N.3
-
50
-
-
84899090573
-
Kraken: Ultrafast metagenomic sequence classification using exact alignments
-
Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15(3), R46 (2014).
-
(2014)
Genome Biol
, vol.15
, Issue.3
, pp. R46
-
-
Wood, D.E.1
Salzberg, S.L.2
-
51
-
-
84904548768
-
Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps
-
Burton JN, Liachko I, Dunham MJ, Shendure J. Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps. G3 Bethesda Md 4(7), 1339-1346 (2014).
-
(2014)
G3 Bethesda Md
, vol.4
, Issue.7
, pp. 1339-1346
-
-
Burton, J.N.1
Liachko, I.2
Dunham, M.J.3
Shendure, J.4
-
53
-
-
84867587461
-
Identification of acquired antimicrobial resistance genes
-
Zankari E, Hasman H, Cosentino S et al. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67(11), 2640-2644 (2012).
-
(2012)
J. Antimicrob. Chemother
, vol.67
, Issue.11
, pp. 2640-2644
-
-
Zankari, E.1
Hasman, H.2
Cosentino, S.3
-
54
-
-
84891552789
-
ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes
-
Gupta SK, Padmanabhan BR, Diene SM et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob. Agents Chemother. 58(1), 212-220 (2014).
-
(2014)
Antimicrob. Agents Chemother
, vol.58
, Issue.1
, pp. 212-220
-
-
Gupta, S.K.1
Padmanabhan, B.R.2
Diene, S.M.3
-
55
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinforma. Oxf. Engl. 22(13), 1658-1659 (2006).
-
(2006)
Bioinforma. Oxf. Engl
, vol.22
, Issue.13
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
56
-
-
0029073602
-
Extended-spectrum plasmidmediated beta-lactamases
-
Sirot D. Extended-spectrum plasmidmediated beta-lactamases. J. Antimicrob. Chemother. 36(Suppl. A), 19-34 (1995).
-
(1995)
J. Antimicrob. Chemother
, vol.36
, pp. 19-34
-
-
Sirot, D.1
-
57
-
-
20444447520
-
Gene mutations responsible for overexpression of AmpC beta-lactamase in some clinical isolates of Enterobacter cloacae
-
Kaneko K, Okamoto R, Nakano R, Kawakami S, Inoue M. Gene mutations responsible for overexpression of AmpC beta-lactamase in some clinical isolates of Enterobacter cloacae. J. Clin. Microbiol. 43(6), 2955-2958 (2005).
-
(2005)
J. Clin. Microbiol
, vol.43
, Issue.6
, pp. 2955-2958
-
-
Kaneko, K.1
Okamoto, R.2
Nakano, R.3
Kawakami, S.4
Inoue, M.5
-
58
-
-
84897134429
-
Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing
-
Gordon NC, Price JR, Cole K et al. Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing. J. Clin. Microbiol. 52(4), 1182-1191 (2014).
-
(2014)
J. Clin. Microbiol
, vol.52
, Issue.4
, pp. 1182-1191
-
-
Gordon, N.C.1
Price, J.R.2
Cole, K.3
-
59
-
-
84920164355
-
The resistome of Pseudomonas aeruginosa in relationship to phenotypic susceptibility
-
Kos VN, Déraspe M, McLaughlin RE et al. The resistome of Pseudomonas aeruginosa in relationship to phenotypic susceptibility. Antimicrob. Agents Chemother. 59(1), 427-436 (2015).
-
(2015)
Antimicrob. Agents Chemother
, vol.59
, Issue.1
, pp. 427-436
-
-
Kos, V.N.1
Déraspe, M.2
McLaughlin, R.E.3
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