TY - JOUR AU - Foxman, B. PY - 2010 DA - 2010// TI - The epidemiology of urinary tract infection JO - Nat Rev Urol. VL - 7 ID - Foxman2010 ER - TY - JOUR AU - Dason, S. AU - Dason, J. T. AU - Kapoor, A. PY - 2011 DA - 2011// TI - Guidelines for the diagnosis and management of recurrent urinary tract infection in women JO - J Can Urol Assoc. VL - 5 ID - Dason2011 ER - TY - JOUR AU - Bouchillon, S. K. AU - Badal, R. E. AU - Hoban, D. J. AU - Hawser, S. P. PY - 2013 DA - 2013// TI - Antimicrobial susceptibility of inpatient urinary tract isolates of gram-negative bacilli in the United States: results from the Study for Monitoring Antimicrobial Resistance Trends (SMART) Program: 2009–2011 JO - Clin Ther VL - 35 ID - Bouchillon2013 ER - TY - JOUR AU - Brubaker, L. AU - Wolfe, A. J. PY - 2015 DA - 2015// TI - The new world of the urinary microbiome in women linda JO - Am J Obstet Gynecol VL - 213 ID - Brubaker2015 ER - TY - JOUR AU - Koves, B. AU - Wullt, B. PY - 2016 DA - 2016// TI - The roles of the host and the pathogens in urinary tract infections JO - Eur Urol Suppl. VL - 15 ID - Koves2016 ER - TY - JOUR AU - Schmiemann, G. AU - Kniehl, E. AU - Gebhardt, K. AU - Matejczyk, M. M. AU - Hummers-Pradier, E. PY - 2010 DA - 2010// TI - The diagnosis of urinary tract infection: a systematic review JO - Dtsch Ärzteblatt Int. VL - 107 ID - Schmiemann2010 ER - TY - JOUR AU - Hilt, E. E. AU - McKinley, K. AU - Pearce, M. M. AU - Rosenfeld, A. B. AU - Zilliox, M. J. AU - Mueller, E. R. PY - 2014 DA - 2014// TI - Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder JO - J Clin Microbiol VL - 52 ID - Hilt2014 ER - TY - JOUR AU - Wolfe, A. J. AU - Brubaker, L. PY - 2015 DA - 2015// TI - “Sterile Urine” and the presence of bacteria JO - Eur Urol VL - 68 ID - Wolfe2015 ER - TY - JOUR AU - Ferreira, L. AU - Sánchez-Juanes, F. AU - Muñoz-Bellido, J. L. AU - González-Buitrago, J. M. PY - 2011 DA - 2011// TI - Rapid method for direct identification of bacteria in urine and blood culture samples by matrix-assisted laser desorption ionization time-of-flight mass spectrometry: intact cell vs extraction method JO - Clin Microbiol Infect. VL - 17 ID - Ferreira2011 ER - TY - JOUR AU - Burd, E. M. AU - Kehl, K. S. PY - 2011 DA - 2011// TI - A critical appraisal of the role of the clinical microbiology laboratory in the diagnosis of urinary tract infections JO - J Clin Microbiol VL - 49 ID - Burd2011 ER - TY - JOUR AU - Cavagnolo, R. PY - 1995 DA - 1995// TI - Evaluation of incubation times for urine cultures JO - J Clin Microbiol VL - 33 ID - Cavagnolo1995 ER - TY - JOUR AU - Brilha, S. AU - Proença, H. AU - Cristino, J. M. AU - Hänscheid, T. PY - 2010 DA - 2010// TI - Use of flow cytometry (Sysmex UF-100) to screen for positive urine cultures: in search for the ideal cut-off JO - Clin Chem Lab Med VL - 48 ID - Brilha2010 ER - TY - JOUR AU - Delanghe, J. AU - Speeckaert, M. PY - 2014 DA - 2014// TI - Preanalytical requirements of urinalysis JO - Biochem Medica. VL - 24 ID - Delanghe2014 ER - TY - JOUR AU - Davenport, M. AU - Mach, K. E. AU - Shortliffe, L. M. D. AU - Banaei, N. AU - Wang, H. AU - Liao, J. C. PY - 2017 DA - 2017// TI - New and developing diagnostic technologies for urinary tract infections JO - Nat Rev Urol. VL - 14 ID - Davenport2017 ER - TY - JOUR AU - Franco-Duarte, R. AU - Černáková, L. AU - Kadam, S. AU - Kaushik, K. S. AU - Salehi, B. AU - Bevilacqua, A. PY - 2019 DA - 2019// TI - Advances in chemical and biological methods to identify microorganisms—from past to present JO - Microorganisms. VL - 7 ID - Franco-Duarte2019 ER - TY - JOUR AU - Singhal, N. AU - Kumar, M. AU - Kanaujia, P. K. AU - Virdi, J. S. PY - 2015 DA - 2015// TI - MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis JO - Front Microbiol. VL - 6 ID - Singhal2015 ER - TY - JOUR AU - Zboromyrska, Y. AU - Rubio, E. AU - Alejo, I. AU - Vergara, A. AU - Mons, A. AU - Campo, I. PY - 2016 DA - 2016// TI - Development of a new protocol for rapid bacterial identification and susceptibility testing directly from urine samples JO - Clin Microbiol Infect VL - 22 ID - Zboromyrska2016 ER - TY - JOUR AU - Rosa, R. AU - Grosso, S. AU - Lorenzi, G. AU - Bruschetta, G. AU - Camporese, A. PY - 2018 DA - 2018// TI - Evaluation of the new Sysmex UF-5000 fluorescence flow cytometry analyser for ruling out bacterial urinary tract infection and for prediction of Gram negative bacteria in urine cultures JO - Clin Chim Acta VL - 484 ID - Rosa2018 ER - TY - JOUR AU - Zee, A. AU - Roorda, L. AU - Bosman, G. AU - Ossewaarde, J. M. PY - 2016 DA - 2016// TI - Molecular diagnosis of urinary tract infections by semi-quantitative detection of uropathogens in a routine clinical hospital setting JO - PLoS ONE. VL - 11 ID - Zee2016 ER - TY - JOUR AU - Mignard, S. AU - Flandrois, J. P. PY - 2006 DA - 2006// TI - 16S rRNA sequencing in routine bacterial identification: a 30-month experiment JO - J Microbiol Methods VL - 67 ID - Mignard2006 ER - TY - JOUR AU - Sabat, A. J. AU - Zanten, E. AU - Akkerboom, V. AU - Wisselink, G. AU - Slochteren, K. AU - Boer, R. F. PY - 2017 DA - 2017// TI - Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification-increased discrimination of closely related species JO - Sci Rep. VL - 7 ID - Sabat2017 ER - TY - JOUR AU - Mann, M. AU - Hendrickson, R. C. AU - Pandey, A. PY - 2001 DA - 2001// TI - Analysis of proteins and proteomes by mass spectrometry JO - Annu Rev Biochem VL - 70 ID - Mann2001 ER - TY - JOUR AU - Cheng, K. AU - Chui, H. AU - Domish, L. AU - Hernandez, D. AU - Wang, G. PY - 2016 DA - 2016// TI - Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria JO - Proteomics Clin Appl. VL - 10 ID - Cheng2016 ER - TY - JOUR AU - Lévesque, S. AU - Dufresne, P. J. AU - Soualhine, H. AU - Domingo, M. C. AU - Bekal, S. AU - Lefebvre, B. PY - 2015 DA - 2015// TI - A side by side comparison of Bruker Biotyper and VITEK MS: utility of MALDI-TOF MS technology for microorganism identification in a public health reference laboratory JO - PLoS ONE VL - 10 ID - Lévesque2015 ER - TY - JOUR AU - Jang, K. S. AU - Kim, Y. H. PY - 2018 DA - 2018// TI - Rapid and robust MALDI-TOF MS techniques for microbial identification: a brief overview of their diverse applications JO - J Microbiol. VL - 56 ID - Jang2018 ER - TY - JOUR AU - Li, Y. AU - Shan, M. AU - Zhu, Z. AU - Mao, X. AU - Yan, M. AU - Chen, Y. PY - 2019 DA - 2019// TI - Application of MALDI-TOF MS to rapid identification of anaerobic bacteria JO - BMC Infect Dis. VL - 19 ID - Li2019 ER - TY - JOUR AU - Lathrop, J. T. AU - Jeffery, D. A. AU - Shea, Y. R. AU - Scholl, P. F. AU - Chan, M. M. PY - 2016 DA - 2016// TI - US food and drug administration perspectives on clinical mass spectrometry JO - Clin Chem VL - 62 ID - Lathrop2016 ER - TY - JOUR AU - Patel, R. PY - 2015 DA - 2015// TI - MALDI-TOF MS for the diagnosis of infectious diseases JO - Clin Chem VL - 61 ID - Patel2015 ER - TY - JOUR AU - Henzel, W. J. AU - Watanabe, C. AU - Stults, J. T. PY - 2003 DA - 2003// TI - Protein identification: the origins of peptide mass fingerprinting JO - J Am Soc Mass Spectrom VL - 14 ID - Henzel2003 ER - TY - JOUR AU - Karlsson, R. AU - Gonzales-siles, L. AU - Boulund, F. AU - Svensson-stadler, L. AU - Skovbjerg, S. AU - Karlsson, A. PY - 2015 DA - 2015// TI - Proteotyping: proteomic characterization, classification and identification of microorganisms—a prospectus JO - Syst Appl Microbiol VL - 38 ID - Karlsson2015 ER - TY - JOUR AU - Veron, L. AU - Mailler, S. AU - Girard, V. AU - Muller, B. H. AU - L’Hostis, G. AU - Ducruix, C. PY - 2015 DA - 2015// TI - Rapid urine preparation prior to identification of uropathogens by MALDI-TOF MS JO - Eur J Clin Microbiol Infect Dis VL - 34 ID - Veron2015 ER - TY - JOUR AU - Kitagawa, K. AU - Shigemura, K. AU - Onuma, K. I. AU - Nishida, M. AU - Fujiwara, M. AU - Kobayashi, S. PY - 2018 DA - 2018// TI - Improved bacterial identification directly from urine samples with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry JO - J Clin Lab Anal. VL - 32 ID - Kitagawa2018 ER - TY - JOUR AU - Yu, Y. AU - Sikorski, P. AU - Bowman-Gholston, C. AU - Cacciabeve, N. AU - Nelson, K. E. AU - Pieper, R. PY - 2015 DA - 2015// TI - Diagnosing inflammation and infection in the urinary system via proteomics JO - J Transl Med. VL - 13 ID - Yu2015 ER - TY - JOUR AU - Íñigo, M. AU - Coello, A. AU - Fernández-Rivas, G. AU - Rivaya, B. AU - Hidalgo, J. AU - Quesada, M. D. PY - 2016 DA - 2016// TI - Direct identification of urinary tract pathogens from urine samples, combining urine screening methods and matrix-assisted laser desorption ionization—time of flight mass spectrometry JO - J Clin Microbiol VL - 54 ID - Íñigo2016 ER - TY - JOUR AU - Shao, W. AU - Zhang, M. AU - Lam, H. AU - Lau, S. C. K. PY - 2015 DA - 2015// TI - A peptide identification-free, genome sequence-independent shotgun proteomics workflow for strain-level bacterial differentiation JO - Sci Rep. VL - 5 ID - Shao2015 ER - TY - JOUR AU - Boulund, F. AU - Karlsson, R. AU - Gonzales-Siles, L. AU - Johnning, A. AU - Karami, N. AU - AL-Bayati, O. PY - 2017 DA - 2017// TI - Typing and characterization of bacteria using bottom-up tandem mass spectrometry proteomics JO - Mol Cell Proteomics. VL - 16 ID - Boulund2017 ER - TY - STD TI - Boulund F, Karlsson R, Gonzales-Siles L, Johnning A, Karami N, AL-Bayati O, et al. Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics. Mol Cell Proteomics. 2017;16(6):1052–63. http://www.mcponline.org/lookup/doi/10.1074/mcp.M116.061721. UR - http://www.mcponline.org/lookup/doi/10.1074/mcp.M116.061721 ID - ref37 ER - TY - JOUR AU - Alves, G. AU - Wang, G. AU - Ogurtsov, A. Y. AU - Drake, S. K. AU - Gucek, M. AU - Sacks, D. B. PY - 2018 DA - 2018// TI - Rapid classification and identification of multiple high-resolution tandem mass spectrometry JO - J Am Soc Mass Spectrom VL - 29 ID - Alves2018 ER - TY - JOUR AU - Karlsson, R. AU - Davidson, M. AU - Svensson-Stadler, L. AU - Karlsson, A. AU - Olesen, K. AU - Carlsohn, E. PY - 2012 DA - 2012// TI - Strain-level typing and identification of bacteria using mass spectrometry-based proteomics JO - J Proteome Res. VL - 11 ID - Karlsson2012 ER - TY - JOUR AU - Yu, Y. AU - Sikorski, P. AU - Smith, M. AU - Bowman-Gholston, C. AU - Cacciabeve, N. AU - Nelson, K. E. PY - 2017 DA - 2017// TI - Comprehensive metaproteomic analyses of urine in the presence and absence of neutrophil-associated inflammation in the urinary tract JO - Theranostics. VL - 7 ID - Yu2017 ER - TY - JOUR AU - Lifshitz, E. AU - Kramer, L. PY - 2000 DA - 2000// TI - Outpatient urine culture: does collection technique matter? JO - Arch Intern Med VL - 160 ID - Lifshitz2000 ER - TY - JOUR AU - Price, T. K. AU - Dune, T. AU - Hilt, E. E. AU - Thomas-White, K. J. AU - Kliethermes, S. AU - Brincat, C. PY - 2016 DA - 2016// TI - The clinical urine culture: enhanced techniques improve detection of clinically relevant microorganisms JO - J Clin Microbiol VL - 54 ID - Price2016 ER - TY - JOUR AU - Bolyen, E. AU - Rideout, J. R. AU - Dillon, M. R. AU - Bokulich, N. A. AU - Abnet, C. C. AU - Al-Ghalith, G. A. PY - 2019 DA - 2019// TI - Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 JO - Nat Biotechnol VL - 37 ID - Bolyen2019 ER - TY - JOUR AU - Callahan, B. J. AU - McMurdie, P. J. AU - Rosen, M. J. AU - Han, A. W. AU - Johnson, A. J. A. AU - Holmes, S. P. PY - 2016 DA - 2016// TI - DADA2: high-resolution sample inference from Illumina amplicon data JO - Nat Methods VL - 13 ID - Callahan2016 ER - TY - JOUR AU - Bokulich, N. A. AU - Kaehler, B. D. AU - Rideout, J. R. AU - Dillon, M. AU - Bolyen, E. AU - Knight, R. PY - 2018 DA - 2018// TI - Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2′s q2-feature-classifier plugin JO - Microbiome. VL - 6 ID - Bokulich2018 ER - TY - JOUR AU - McDonald, D. AU - Price, M. N. AU - Goodrich, J. AU - Nawrocki, E. P. AU - Desantis, T. Z. AU - Probst, A. PY - 2012 DA - 2012// TI - An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea JO - ISME J VL - 6 ID - McDonald2012 ER - TY - JOUR AU - Kotaskova, I. AU - Obrucova, H. AU - Malisova, B. AU - Videnska, P. AU - Zwinsova, B. AU - Peroutkova, T. PY - 2019 DA - 2019// TI - Molecular techniques complement culture-based assessment of bacteria composition in mixed biofilms of urinary tract catheter-related samples JO - Front Microbiol. VL - 10 ID - Kotaskova2019 ER - TY - JOUR AU - Naum, M. AU - Brown, E. W. AU - Mason-Gamer, R. J. PY - 2008 DA - 2008// TI - Is 16S rDNA a reliable phylogenetic marker to characterize relationships below the family level in the enterobacteriaceae? JO - J Mol Evol VL - 66 ID - Naum2008 ER - TY - JOUR AU - Lough, M. E. AU - Shradar, E. AU - Hsieh, C. AU - Hedlin, H. PY - 2019 DA - 2019// TI - Contamination in adult midstream clean-catch urine cultures in the emergency department: a randomized controlled trial JO - J Emerg Nurs. VL - 45 ID - Lough2019 ER - TY - JOUR AU - Huang, B. AU - Zhang, L. AU - Zhang, W. AU - Liao, K. AU - Zhang, S. AU - Zhang, Z. PY - 2017 DA - 2017// TI - Direct detection and identification of bacterial pathogens from urine with optimized specimen processing and enhanced testing algorithm JO - J Clin Microbiol VL - 55 ID - Huang2017 ER - TY - JOUR AU - Sigdel, T. K. AU - Nicora, C. D. AU - Hsieh, S. C. AU - Dai, H. AU - Qian, W. J. AU - Camp, D. G. PY - 2014 DA - 2014// TI - Optimization for peptide sample preparation for urine peptidomics JO - Clin Proteomics VL - 11 ID - Sigdel2014 ER - TY - JOUR AU - Cottrell, J. S. PY - 2011 DA - 2011// TI - Protein identification using MS/MS data JO - J Proteomics. VL - 74 ID - Cottrell2011 ER - TY - JOUR AU - Perkins, D. N. AU - Pappin, D. J. AU - Creasy, D. M. AU - Cottrell, J. S. PY - 1999 DA - 1999// TI - Probability-based protein identification by searching sequence databases using mass spectrometry data JO - Electrophoresis. VL - 20 ID - Perkins1999 ER - TY - JOUR AU - Zhang, X. AU - Li, L. AU - Mayne, J. AU - Ning, Z. AU - Stintzi, A. AU - Figeys, D. PY - 2018 DA - 2018// TI - Assessing the impact of protein extraction methods for human gut metaproteomics JO - J Proteomics. VL - 180 UR - https://doi.org/10.1016/j.jprot.2017.07.001 DO - 10.1016/j.jprot.2017.07.001 ID - Zhang2018 ER - TY - JOUR AU - Harpole, M. AU - Davis, J. AU - Espina, V. PY - 2016 DA - 2016// TI - Current state of the art for enhancing urine biomarker discovery JO - Expert Rev Proteomics. VL - 13 ID - Harpole2016 ER - TY - JOUR AU - Koenig, T. AU - Menze, B. H. AU - Kirchner, M. AU - Monigatti, F. AU - Parker, K. C. AU - Patterson, T. PY - 2008 DA - 2008// TI - Robust prediction of the MASCOT score for an improved quality assessment in mass spectrometric proteomics JO - J Proteome Res VL - 7 ID - Koenig2008 ER - TY - JOUR AU - Adachi, J. AU - Kumar, C. AU - Zhang, Y. AU - Olsen, J. V. AU - Mann, M. PY - 2006 DA - 2006// TI - The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins JO - Genome Biol. VL - 7 ID - Adachi2006 ER - TY - JOUR AU - Lin, L. AU - Yu, Q. AU - Zheng, J. AU - Cai, Z. AU - Tian, R. PY - 2018 DA - 2018// TI - Fast quantitative urinary proteomic profiling workflow for biomarker discovery in kidney cancer JO - Clin Proteomics. VL - 15 ID - Lin2018 ER -