The host response as a tool for infectious disease diagnosis and management

References

• Cox FE. History of human parasitology. Clin Microbiol Rev. 2002 Oct;15(4):595–612. PubMed PMID: 12364371; PubMed Central PMCID: PMC126866.
   PubMed Web of Science ®Google Scholar
• Bryan CP. The Papyrus Ebers. New York, NY: Appleton; 1931.
   Google Scholar
• Waugh TR. The blood sedimentation test; its history, technique, nature and clinical application. Can Med Assoc J. 1923 Aug;13(8):604–608. PubMed PMID: 20314752; PubMed Central PMCID: PMC1707147.
   PubMedGoogle Scholar
• Tillett WS, Francis T. Serological reactions in pneumonia with a non-protein somatic fraction of pneumococcus. J Exp Med. 1930 Sep 30;52(4):561–571. PubMed PMID: 19869788; PubMed Central PMCID: PMC2131884.
   PubMedGoogle Scholar
• Landry ML. Immunoglobulin M for acute infection: true or false?. Clin Vaccine Immunol. 2016 Jul;23(7):540–545. . PubMed PMID: 27193039; PubMed Central PMCID: PMCPMC4933779. eng.
   PubMed Web of Science ®Google Scholar
• Trzeciak S, Dellinger RP, Chansky ME, et al. Serum lactate as a predictor of mortality in patients with infection. Intensive Care Med. 2007 Jun;33(6):970–977. PubMed PMID: 17431582.
   PubMed Web of Science ®Google Scholar
• Mikkelsen ME, Miltiades AN, Gaieski DF, et al. Serum lactate is associated with mortality in severe sepsis independent of organ failure and shock. Crit Care Med. 2009 May;37(5):1670–1677. PubMed PMID: 19325467.
   PubMed Web of Science ®Google Scholar
• Cairns CB. Rude unhinging of the machinery of life: metabolic approaches to hemorrhagic shock. Curr Opin Crit Care. 2001 Dec;7(6):437–443. PubMed PMID: 11805547.
   PubMedGoogle Scholar
• Boulos M, Astiz ME, Barua RS, et al. Impaired mitochondrial function induced by serum from septic shock patients is attenuated by inhibition of nitric oxide synthase and poly(ADP-ribose) synthase. Crit Care Med. 2003 Feb;31(2):353–358. PubMed PMID: 12576936.
   PubMed Web of Science ®Google Scholar
• Trzeciak S, Dellinger RP, Parrillo JE, et al. Early microcirculatory perfusion derangements in patients with severe sepsis and septic shock: relationship to hemodynamics, oxygen transport, and survival. Ann Emerg Med. 2007 Jan;49(1):88–98 e1–2. PubMed PMID: 17095120.
   PubMed Web of Science ®Google Scholar
• Shapiro NI, Trzeciak S, Hollander JE, et al. A prospective, multicenter derivation of a biomarker panel to assess risk of organ dysfunction, shock, and death in emergency department patients with suspected sepsis. Crit Care Med. 2009 Jan;37(1):96–104. PubMed PMID: 19050610.
   PubMed Web of Science ®Google Scholar
• Nguyen HB, Rivers EP, Knoblich BP, et al. Early lactate clearance is associated with improved outcome in severe sepsis and septic shock. Crit Care Med. 2004 Aug;32(8):1637–1642. PubMed PMID: 15286537.
   PubMed Web of Science ®Google Scholar
• Arnold RC, Shapiro NI, Jones AE, et al. Multicenter study of early lactate clearance as a determinant of survival in patients with presumed sepsis. Shock. 2009 Jul;32(1):35–39. PubMed PMID: 19533847.
   PubMed Web of Science ®Google Scholar
• Rhodes A, Evans LE, Alhazzani W, et al. Surviving sepsis campaign: international guidelines for management of sepsis and septic shock: 2016. Intensive Care Med. 2017 Mar;43(3):304–377. PubMed PMID: 28101605.
   PubMed Web of Science ®Google Scholar
• Schierenbeck F, Nijsten MWN, Franco-Cereceda A, et al. Introducing intravascular microdialysis for continuous lactate monitoring in patients undergoing cardiac surgery: a prospective observational study. Crit Care. 2014;18(2):R56. PubMed PMID: 24684807; PubMed Central PMCID: PMCPMC4057446. eng.
   PubMed Web of Science ®Google Scholar
• De Tymowski C, Soussi S, Depret F, et al. On-line plasma lactate concentration monitoring in critically ill patients. Crit Care. 2017;21. PubMed PMID: 28623939; PubMed Central PMCID: PMCPMC5474016. eng. DOI:10.1186/s13054-017-1738-6
   Google Scholar
• Ching TS, Connolly P. Simultaneous transdermal extraction of glucose and lactate from human subjects by reverse iontophoresis. Int J Nanomedicine. 2008 Jun;3(2):211–223. PubMed PMID: 18686780; PubMed Central PMCID: PMCPMC2527667. eng.
   PubMed Web of Science ®Google Scholar
• Sharma S, Saeed A, Johnson C, et al. Rapid, low cost prototyping of transdermal devices for personal healthcare monitoring. Sens and Bio-Sensing Res. 2017;13:104–108. doi: 10.1016/j.sbsr.2016.10.004. PubMed PMID: 28424755; PubMed Central PMCID: PMCPMC5384990. eng.
   Google Scholar
• Assicot M, Gendrel D, Carsin H, et al. High serum procalcitonin concentrations in patients with sepsis and infection. Lancet. 1993 Feb 27;341(8844):515–518. PubMed PMID: 8094770; eng.
   PubMed Web of Science ®Google Scholar
• Muller B, White JC, Nylen ES, et al. Ubiquitous expression of the calcitonin-i gene in multiple tissues in response to sepsis. J Clin Endocrinol Metab. 2001 Jan;86(1):396–404. PubMed PMID: 11232031.
   PubMed Web of Science ®Google Scholar
• Moyer MW. New biomarkers sought for improving sepsis management and care. Nat Med. 2012 Jul;18(7):999. . PubMed PMID: 22772541.
   PubMed Web of Science ®Google Scholar
• Wacker C, Prkno A, Brunkhorst FM, et al. Procalcitonin as a diagnostic marker for sepsis: a systematic review and meta-analysis. Lancet Infect Dis. 2013 May;13(5):426–435. PubMed PMID: 23375419.
   PubMed Web of Science ®Google Scholar
• Huang HB, Peng JM, Weng L, et al. Procalcitonin-guided antibiotic therapy in intensive care unit patients: a systematic review and meta-analysis. Ann Intensive Care. 2017 Nov 22;7(1):114. PubMed PMID: 29168046; PubMed Central PMCID: PMCPMC5700008. eng.
   PubMedGoogle Scholar
• Schuetz P, Wirz Y, Sager R, et al. Procalcitonin to initiate or discontinue antibiotics in acute respiratory tract infections. Cochrane Database Syst Rev. 2017;(10). CD007498.pub3. PubMed PMID: CD007498. doi:10.1002/14651858
   PubMed Web of Science ®Google Scholar
• Mimoz O, Benoist JF, Edouard AR, et al. Procalcitonin and C-reactive protein during the early posttraumatic systemic inflammatory response syndrome. Intensive Care Med. 1998 Feb;24(2):185–188. PubMed PMID: 9539079.
   PubMed Web of Science ®Google Scholar
• Loebe M, Locziewski S, Brunkhorst FM, et al. Procalcitonin in patients undergoing cardiopulmonary bypass in open heart surgery-first results of the Procalcitonin in Heart Surgery study (ProHearts). Intensive Care Med. 2000 Mar;26(Suppl 2):S193–8. PubMed PMID: 18470719.
   PubMedGoogle Scholar
• Attar BM, Moore CM, George M, et al. Procalcitonin, and cytokines document a dynamic inflammatory state in non-infected cirrhotic patients with ascites. World J Gastroenterol. 2014 Mar 7;20(9):2374–2382. PubMed PMID: 24605035; PubMed Central PMCID: PMC3942841.
   PubMed Web of Science ®Google Scholar
• Grace E, Turner RM. Use of procalcitonin in patients with various degrees of chronic kidney disease including renal replacement therapy. Clin Infect Dis. 2014September;16:2014.
   Google Scholar
• Nagata J, Kobayashi M, Nishikimi N, et al. Serum procalcitonin (PCT) as a negative screening test for colonic ischemia after open abdominal aortic surgery. E J Vas endovaS Surg: the Official J E Society for Vascular SurG. 2008 Jun;35(6):694–697. PubMed PMID: 18295515.
   PubMed Web of Science ®Google Scholar
• Scire CA, Cavagna L, Perotti C, et al. Diagnostic value of procalcitonin measurement in febrile patients with systemic autoimmune diseases. Clin Exp Rheumatol. 2006 Mar-Apr;24(2):123–128. PubMed PMID: 16762145.
   PubMed Web of Science ®Google Scholar
• Nylen ES, Al Arifi A, Becker KL, et al. Effect of classic heatstroke on serum procalcitonin. Crit Care Med. 1997 Aug;25(8):1362–1365. PubMed PMID: 9267950.
   PubMed Web of Science ®Google Scholar
• Carsin H, Assicot M, Feger F, et al. Evolution and significance of circulating procalcitonin levels compared with IL-6, TNF alpha and endotoxin levels early after thermal injury. Burns. 1997 May;23(3):218–224. PubMed PMID: 9232281.
   PubMed Web of Science ®Google Scholar
• Davis BH, Olsen SH, Ahmad E, et al. Neutrophil CD64 is an improved indicator of infection or sepsis in emergency department patients. Arch Pathol Lab Med. 2006 May;130(5):654–661. PubMed PMID: 16683883.
   PubMed Web of Science ®Google Scholar
• Livaditi O, Kotanidou A, Psarra A, et al. Neutrophil CD64 expression and serum IL-8: sensitive early markers of severity and outcome in sepsis. Cytokine. 2006 Dec;36(5–6):283–290. PubMed PMID: 17368039.
   PubMed Web of Science ®Google Scholar
• Adly AA, Ismail EA, Andrawes NG, et al. Circulating soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) as diagnostic and prognostic marker in neonatal sepsis. Cytokine. 2014 Feb;65(2):184–191. PubMed PMID: 24290866.
   PubMed Web of Science ®Google Scholar
• Ravetti CG, Moura AD, Vieira EL, et al. sTREM-1 predicts intensive care unit and 28-day mortality in cancer patients with severe sepsis and septic shock. J Crit Care. 2015 Apr;30(2):440 e7–440 e13. PubMed PMID: 25541104.
   Web of Science ®Google Scholar
• Huttunen R, Syrjanen J, Vuento R, et al. Plasma level of soluble urokinase-type plasminogen activator receptor as a predictor of disease severity and case fatality in patients with bacteraemia: a prospective cohort study. J Intern Med. 2011 Jul;270(1):32–40. PubMed PMID: 21332843.
   PubMed Web of Science ®Google Scholar
• Sandquist M, Wong HR. Biomarkers of sepsis and their potential value in diagnosis, prognosis and treatment. Expert Rev Clin Immunol. 2014 Oct;10(10):1349–1356. . PubMed PMID: 25142036.
   PubMed Web of Science ®Google Scholar
• Debiane L, Hachem RY, Al Wohoush I, et al. The utility of proadrenomedullin and procalcitonin in comparison to C-reactive protein as predictors of sepsis and bloodstream infections in critically ill patients with cancer*. Crit Care Med. 2014 Dec;42(12):2500–2507. PubMed PMID: 25083975.
   PubMed Web of Science ®Google Scholar
• Suberviola B, Castellanos-Ortega A, Llorca J, et al. Prognostic value of proadrenomedullin in severe sepsis and septic shock patients with community-acquired pneumonia. Swiss Med Wkly. 2012;142:w13542. PubMed PMID: 22430899.
   PubMed Web of Science ®Google Scholar
• Serrano-Gomez S, Burgos-Angulo G, Nino-Vargas DC, et al. Predictive value of matrix metalloproteinases and their inhibitors for mortality in septic patients: a cohort study. J Intensive Care Med. 2017 Jan 1:885066617732284. PubMed PMID: 28931365; eng. doi: 10.1177/0885066617732284
   PubMedGoogle Scholar
• Ulla M, Pizzolato E, Lucchiari M, et al. Diagnostic and prognostic value of presepsin in the management of sepsis in the emergency department: a multicenter prospective study. Crit Care. 2013;17(4):R168. PubMed PMID: 23899120; PubMed Central PMCID: PMC4056762.
   PubMed Web of Science ®Google Scholar
• Masson S, Caironi P, Spanuth E, et al. Presepsin (soluble CD14 subtype) and procalcitonin levels for mortality prediction in sepsis: data from the Albumin Italian Outcome Sepsis trial. Crit Care. 2014;18(1):R6. PubMed PMID: 24393424; PubMed Central PMCID: PMC4056046.
   PubMed Web of Science ®Google Scholar
• Van Engelen TSR, Wiersinga WJ, Scicluna BP, et al. Biomarkers in Sepsis. Crit Care Clin. 2018 Jan;34(1):139–152. PubMed PMID: 29149935; eng.
   PubMed Web of Science ®Google Scholar
• Brodska H, Valenta J, Pelinkova K, et al. Diagnostic and prognostic value of presepsin vs. established biomarkers in critically ill patients with sepsis or systemic inflammatory response syndrome. Clin Chem Lab Med. 2017 Nov 25 PubMed PMID: 29176018; eng. doi:10.1515/cclm-2017-0839.
   Web of Science ®Google Scholar
• Jedynak M, Siemiatkowski A, Mroczko B, et al. Soluble TREM-1 serum level can early predict mortality of patients with sepsis, severe sepsis and septic shock. Arch Immunol Ther Exp (Warsz). 2017 Dec 27 PubMed PMID: 29282483; eng. doi:10.1007/s00005-017-0499-x.
   PubMed Web of Science ®Google Scholar
• Sargentini V, Collepardo D, Alessandro D, et al. Role of biomarkers in adult sepsis and their application for a good laboratory practice: a pilot study. J Biol Regul Homeost Agents. 2017 Oct-Dec;31(4):1147–1154. doi: M DA PubMed PMID: 29254328; eng.
   PubMed Web of Science ®Google Scholar
• Haran JP, Buglione-Corbett R, Lu S. Cytokine markers as predictors of type of respiratory infection in patients during the influenza season. Am J Emerg Med. 2013 May;31(5):816–821. . PubMed PMID: 23481156.
   PubMed Web of Science ®Google Scholar
• Hanna WJ, Berrens Z, Langner T, et al. Interleukin-27: a novel biomarker in predicting bacterial infection among the critically ill. Crit Care. 2015 Oct 30;19:378. PubMed PMID: 26514771; PubMed Central PMCID: PMCPMC4627377. eng.
   PubMed Web of Science ®Google Scholar
• Goncalves SM, Lagrou K, Rodrigues CS, et al. Evaluation of bronchoalveolar lavage fluid cytokines as biomarkers for invasive pulmonary aspergillosis in at-risk patients. Front Microbiol. 2017;8:2362. PubMed PMID: 29238334; PubMed Central PMCID: PMCPMC5712575. eng.
   PubMed Web of Science ®Google Scholar
• Dano ID, Sadou H, Issaka B, et al. Measurement of Interleukin-6 in cerebrospinal fluid for the diagnosis of bacterial meningitis. Pak J Biol Sci. 2016;19(4):185–190. PubMed PMID: 29022995; eng.
   PubMedGoogle Scholar
• Waage A, Brandtzaeg P, Halstensen A, et al. The complex pattern of cytokines in serum from patients with meningococcal septic shock. Association between interleukin 6, interleukin 1, and fatal outcome. J Exp Med. 1989 Jan 1;169(1):333–338. PubMed PMID: 2783334; PubMed Central PMCID: PMCPMC2189201. eng.
   PubMed Web of Science ®Google Scholar
• Gardlund B, Sjolin J, Nilsson A, et al. Plasma levels of cytokines in primary septic shock in humans: correlation with disease severity. J Infect Dis. 1995 Jul;172(1):296–301. PubMed PMID: 7797935; eng.
   PubMed Web of Science ®Google Scholar
• Freund Y, Delerme S, Goulet H, et al. Serum lactate and procalcitonin measurements in emergency room for the diagnosis and risk-stratification of patients with suspected infection. Biomarkers: Biochemical Indicators of Exp, Resp, and Susceptibility to Chem. 2012 Nov;17(7):590–596. PubMed PMID: 22817478.
   Google Scholar
• Liu B, Chen YX, Yin Q, et al. Diagnostic value and prognostic evaluation of Presepsin for sepsis in an emergency department. Crit Care. 2013;17(5):R244. PubMed PMID: 24138799; PubMed Central PMCID: PMC4056322.
   PubMed Web of Science ®Google Scholar
• Wong HR, Salisbury S, Xiao Q, et al. The pediatric sepsis biomarker risk model. Crit Care. 2012 Oct 1;16(5):R174. PubMed PMID: 23025259; PubMed Central PMCID: PMC3682273.
   PubMed Web of Science ®Google Scholar
• Wong HR, Cvijanovich NZ, Anas N, et al. Pediatric sepsis biomarker risk model-ii: redefining the pediatric sepsis biomarker risk model with septic shock phenotype. Crit Care Med. 2016 Nov;44(11):2010–2017. PubMed PMID: 27513537; PubMed Central PMCID: PMCPMC5201138. eng.
   PubMed Web of Science ®Google Scholar
• Self W, Rosen J, Sharp S, et al. Diagnostic accuracy of febridx: a rapid test to detect immune responses to viral and bacterial upper respiratory infections. J Clin Med. 2017;6(10):94. PubMed PMID.
   Web of Science ®Google Scholar
• Illumina Introduces the NovaSeq Series—a New Architecture Designed to Usher in the $100 Genome [Internet]. bussinesswire.com: Business Wire; 2017 [cited 2018 Apr 30].
   Google Scholar
• Covolo L, Rubinelli S, Ceretti E, et al. Internet-based direct-to-consumer genetic testing: a systematic review. J Med Internet Res. 2015 Dec;17(12). PubMed PMID: 26677835; PubMed Central PMCID: PMCPMC4704942. eng. DOI:10.2196/jmir.4378.
   PubMed Web of Science ®Google Scholar
• Delgado-Morales R, Esteller M. Opening up the DNA methylome of dementia. Mol Psychiatry. 2017 Apr;22(4):485–496. . PubMed PMID: 28044062; PubMed Central PMCID: PMCPMC5378809. eng.
   PubMed Web of Science ®Google Scholar
• Aberg KA, McClay JL, Nerella S, et al. Methylome-wide association study of schizophrenia: identifying blood biomarker signatures of environmental insults. JAMA Psychiatry. 2014 Mar;71(3):255–264. PubMed PMID: 24402055; PubMed Central PMCID: PMCPMC4331014. eng.
   PubMed Web of Science ®Google Scholar
• Levenson VV. DNA methylation as a universal biomarker. Expert Rev Mol Diagn. 2010 May;10(4):481–488. . PubMed PMID: 20465502; PubMed Central PMCID: PMCPMC2933138. eng.
   PubMed Web of Science ®Google Scholar
• Silmon De Monerri NC, Kim K. Pathogens hijack the epigenome: a new twist on host-pathogen interactions. Am J Pathol. 2014 Apr;184(4):897–911. . PubMed PMID: 24525150; PubMed Central PMCID: PMCPMC3970002. eng.
   PubMed Web of Science ®Google Scholar
• Lv J, Liu H, Su J, et al. DiseaseMeth: a human disease methylation database. Nucleic Acids Res. 2012 Jan;40(Database issue):D1030–5. PubMed PMID: 22135302; PubMed Central PMCID: PMCPMC3245164. eng.
   PubMedGoogle Scholar
• Xiong Y, Wei Y, Gu Y, et al. DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database. Nucleic Acids Res. 2017 Jan 4;45(Database issue):D888–95. PubMed PMID: 27899673; PubMed Central PMCID: PMCPMC5210584. eng.
   PubMedGoogle Scholar
• Baginsky S, Hennig L, Zimmermann P, et al. Gene expression analysis, proteomics, and network discovery. Plant Physiol. 2010 Feb;152(2):402–410. PubMed PMID: 20018595; PubMed Central PMCID: PMC2815903.
   PubMed Web of Science ®Google Scholar
• Lowe R, Shirley N, Bleackley M, et al. Transcriptomics technologies. PLoS Comput Biol. 2017 May;13(5):e1005457. PubMed PMID: 28545146; PubMed Central PMCID: PMCPMC5436640. eng.
   PubMed Web of Science ®Google Scholar
• Wang J, Chen J, Sen S. MicroRNA as biomarkers and diagnostics. J Cell Physiol. 2016 Jan;231(1):25–30. . PubMed PMID: 26031493; eng.
   PubMed Web of Science ®Google Scholar
• Garalde DR, Snell EA, Jachimowicz D, et al. Highly parallel direct RNA sequencing on an array of nanopores. Nat Methods. 2018 Jan;15. PubMed PMID: 29334379; eng. DOI:10.1038/nmeth.4577.
   PubMed Web of Science ®Google Scholar
• Cao C, Long YT. Biological nanopores: confined spaces for electrochemical single-molecule analysis. Acc Chem Res. 2018 Jan 24. PubMed PMID: 29364650; eng. doi:10.1021/acs.accounts.7b00143
   Web of Science ®Google Scholar
• Marinov GK. On the design and prospects of direct RNA sequencing. Brief Funct Genomics. 2017 Nov 1;16(6):326–335. . PubMed PMID: 28334071; eng.
   PubMed Web of Science ®Google Scholar
• Gygi SP, Rochon Y, Franza BR, et al. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol. 1999 Mar;19(3):1720–1730. PubMed PMID: 10022859; PubMed Central PMCID: PMCPMC83965. eng.
   PubMed Web of Science ®Google Scholar
• Tian Q, Stepaniants SB, Mao M, et al. Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Molecular & Cellular Proteomics: MCP. 2004 Oct;3(10):960–969. PubMed PMID: 15238602; eng.
   PubMed Web of Science ®Google Scholar
• Maier T, Guell M, Serrano L. Correlation of mRNA and protein in complex biological samples. FEBS Lett. 2009 Dec 17;583(24):3966–3973. . PubMed PMID: 19850042; eng.
   PubMed Web of Science ®Google Scholar
• Li H, Han J, Pan J, et al. Current trends in quantitative proteomics - an update. J Mass Spectrom. 2017 May;52(5):319–341. PubMed PMID: 28418607; eng.
   PubMed Web of Science ®Google Scholar
• Park JM, Park JH, Mun DG, et al. Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks. Sci Rep. 2015;5. PubMed PMID: 26657352; PubMed Central PMCID: PMCPMC4676070. eng. DOI:10.1038/srep18189
   Web of Science ®Google Scholar
• Giudice G, Petsalaki E. Proteomics and phosphoproteomics in precision medicine: applications and challenges. Brief Bioinform. 2017 Oct 25. PubMed PMID: 29077858; eng. doi:10.1093/bib/bbx141
   PubMedGoogle Scholar
• Gowda GAN, Djukovic D. Overview of mass spectrometry-based metabolomics: opportunities and challenges. Methods Mol Bio (Clifton, NJ). 2014;1198:3–12. PubMed PMID: 25270919; PubMed Central PMCID: PMCPMC4336784. eng.
   PubMedGoogle Scholar
• Martin NJ, Bunch J, Cooper HJ. Dried blood spot proteomics: surface extraction of endogenous proteins coupled with automated sample preparation and mass spectrometry analysis. J Am Soc Mass Spectrom. 2013 Aug;24(8):1242–1249. . PubMed PMID: 23728546; PubMed Central PMCID: PMCPMC3713260. eng.
   PubMed Web of Science ®Google Scholar
• Harris LN, Ismaila N, McShane LM, et al. Use of biomarkers to guide decisions on adjuvant systemic therapy for women with early-stage invasive breast cancer: american society of clinical oncology clinical practice guideline. J Clin Oncol. 2016 Apr 1;34(10):1134–1150. PubMed PMID: 26858339; PubMed Central PMCID: PMCPMC4933134. eng.
   PubMed Web of Science ®Google Scholar
• Manjili MH, Najarian K, Wang XY. Signatures of tumor–immune interactions as biomarkers for breast cancer prognosis. Future Oncol. 2012 Jun;8(6):703–711. . PubMed PMID: 22764768; PubMed Central PMCID: PMCPMC4634870. eng.
   PubMed Web of Science ®Google Scholar
• Raman G, Avendano EE, Chen M AHRQ technology assessments. update on emerging genetic tests currently available for clinical use in common cancers. Rockville (MD): Agency for Healthcare Research and Quality (US); 2013.
   Google Scholar
• Hsueh EC, DeBloom JR, Lee J, et al. Interim analysis of survival in a prospective, multi-center registry cohort of cutaneous melanoma tested with a prognostic 31-gene expression profile test. J Hematol Oncol. 2017;10. PubMed PMID: 28851416; PubMed Central PMCID: PMCPMC5576286. eng. DOI:10.1186/s13045-017-0520-1
   Web of Science ®Google Scholar
• Van Laar R, Flinchum R, Brown N, et al. Translating a gene expression signature for multiple myeloma prognosis into a robust high-throughput assay for clinical use. BMC Med Genomics. 2014;7:25. PubMed PMID: 24885236; PubMed Central PMCID: PMCPMC4032347. eng.
   PubMed Web of Science ®Google Scholar
• Saini S. PSA and beyond: alternative prostate cancer biomarkers. Cell Oncol (Dordr). 2016 Apr;39(2):97–106. PubMed PMID: 26790878; PubMed Central PMCID: PMCPMC4821699. eng.
   PubMed Web of Science ®Google Scholar
• Kloos RT. Molecular profiling of thyroid nodules: current role for the afirma gene expression classifier on clinical decision making. Mol Imaging Radionucl Ther. 2017 Feb;26(Suppl 1):36–49. PubMed PMID: 28117288; PubMed Central PMCID: PMCPMC5283710. eng.
   PubMedGoogle Scholar
• Vargas J, Lima JA, Kraus WE, et al. Use of the Corus(R) CAD gene expression test for assessment of obstructive coronary artery disease likelihood in symptomatic non-diabetic patients. PLoS Curr. 2013;5. PubMed PMID: 24043473; PubMed Central PMCID: PMC3770834. doi:10.1371/currents.eogt.0f04f6081905998fa92b99593478aeab
   PubMedGoogle Scholar
• Crespo-Leiro MG, Stypmann J, Schulz U, et al. Clinical usefulness of gene-expression profile to rule out acute rejection after heart transplantation: CARGO II. Eur Heart J. 2016 Sep 1;37(33):2591–2601. PubMed PMID: 26746629; PubMed Central PMCID: PMCPMC5015661. eng.
   PubMed Web of Science ®Google Scholar
• Lytkin NI, McVoy L, Weitkamp JH, et al. Expanding the understanding of biases in development of clinical-grade molecular signatures: a case study in acute respiratory viral infections [Research Support, N.I.H., Extramural]. PLoS One . 2011;6(6):e20662. PubMed PMID: 21673802; PubMed Central PMCID: PMC3105991. eng. .
   PubMed Web of Science ®Google Scholar
• Carvalho CM, Chang J, Lucas JE, et al. High-dimensional sparse factor modeling: applications in gene expression genomics. J Am Stat Assoc. 2008 Dec 1;103(484):1438–1456. PubMed PMID: 21218139; PubMed Central PMCID: PMC3017385.
   PubMed Web of Science ®Google Scholar
• Chen M, Carlson D, Zaas A, et al. Detection of viruses via statistical gene expression analysis. IEEE Trans Biomed Eng. 2011 Mar;58(3):468–479. PubMed PMID: 20643599; eng.
   PubMed Web of Science ®Google Scholar
• Wu Y, Liu Y. Functional robust support vector machines for sparse and irregular longitudinal data. J Compl Grap Stat: Joint Pub Ameri Stat Ass, Inst Mathl Sta, Inter Found NA. 2013 Apr 1;22(2):379–395. . PubMed PMID: 23734071; PubMed Central PMCID: PMC3668975.
   Google Scholar
• Pankla R, Buddhisa S, Berry M, et al. Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis. Genome Biol. 2009;10(11):R127. PubMed PMID: 19903332; PubMed Central PMCID: PMC3091321.
   PubMed Web of Science ®Google Scholar
• Langley RJ, Tsalik EL, Velkinburgh JCV et al.An Integrated clinico-metabolomic model improves prediction of death in sepsis. Sci Transl Med2013Jul 245195195ra95
   PubMed Web of Science ®Google Scholar
• Montgomery JLNJ, Deneris M, Jones J, et al. Rapid discrimination of viral and bacterial infections by host transcriptomic analysis using the filmarray® system. oral presentation, Abstract 3472 presented at: ASM-Microbe; 2017; New Orleans2017.
   Google Scholar
• Khine AASA, Parmar V, Yuan R, et al. Rapid discrimination of viral and bacterial infections by host transcriptomic analysis using the filmarray® system. oral presentation, Abstract 3472 presented at: ASM-Microbe; New Orleans2017.
   Google Scholar
• Khatri K, Klein JA, Haserick JR, et al. Microfluidic capillary electrophoresis-mass spectrometry for analysis of monosaccharides, oligosaccharides, and glycopeptides. Anal Chem. 2017 Jun 20;89(12):6645–6655. PubMed PMID: 28530388; PubMed Central PMCID: PMCPMC5554952. eng.
   PubMed Web of Science ®Google Scholar
• Finfer S, Bellomo R, Lipman J, et al. Adult-population incidence of severe sepsis in Australian and New Zealand intensive care units. Intensive Care Med. 2004 Apr;30(4):589–596. PubMed PMID: 14963646.
   PubMed Web of Science ®Google Scholar
• Martin GS, Mannino DM, Eaton S, et al. The epidemiology of sepsis in the United States from 1979 through 2000. N Engl J Med. 2003 Apr 17;348(16):1546–1554. PubMed PMID: 12700374.
   PubMed Web of Science ®Google Scholar
• Sundararajan V, Macisaac CM, Presneill JJ, et al. Epidemiology of sepsis in Victoria, Australia. Crit Care Med. 2005 Jan;33(1):71–80. PubMed PMID: 15644651.
   PubMed Web of Science ®Google Scholar
• McHugh L, Seldon TA, Brandon RA, et al. A molecular host response assay to discriminate between sepsis and infection-negative systemic inflammation in critically ill patients: discovery and validation in independent cohorts. PLoS Med. 2015;12(12):e1001916. .
   PubMed Web of Science ®Google Scholar
• Zimmerman JJ, Sullivan E, Yager TD, et al. Diagnostic accuracy of a host gene expression signature that discriminates clinical severe sepsis syndrome and infection-negative systemic inflammation among critically Ill children. Crit Care Med. 2017 Apr;45(4):e418–e425. PubMed PMID: 27655322.
   PubMed Web of Science ®Google Scholar
• SeptiCYTE FDA. 510(k) Premarket Notification. FDA, White Oak, MD: Health TCfDaReditor, 2017
   Google Scholar
• Koster-Brouwer ME, Verboom DM, Scicluna BP, et al. Validation of a novel molecular host response assay to diagnose infection in hospitalized patients admitted to the ICU with acute respiratory failure. Crit Care Med. 2018 Mar;46(3):368–374. PubMed PMID: 29474322; eng.
   PubMed Web of Science ®Google Scholar
• Scicluna BP, Klein Klouwenberg PMC, Van Vught LA, et al. A molecular biomarker to diagnose community-acquired pneumonia on intensive care unit admission. Am J Respir Crit Care Med. 2015. 10.1164/rccm.201502-0355OC.
   Google Scholar
• Sweeney TE, Khatri P. Benchmarking sepsis gene expression diagnostics using public data*. PubMed PMID: 00003246–201701000–00001 Crit Care Med. 2017;451:1–10.
   PubMed Web of Science ®Google Scholar
• Dix A, Hünniger K, Weber M, et al. Biomarker-based classification of bacterial and fungal whole-blood infections in a genome-wide expression study [Original Research]. Front Microbiol. 2015 2015 Mar 11;6. doi: 10.3389/fmicb.2015.00171. English.
   PubMed Web of Science ®Google Scholar
• Davenport EE, Burnham KL, Radhakrishnan J, et al. Genomic landscape of the individual host response and outcomes in sepsis: a prospective cohort study. Lancet Respir Med. 2016 Feb 22 PubMed PMID: 26917434. doi:10.1016/S2213-2600(16)00046-1.
   PubMed Web of Science ®Google Scholar
• Sweeney TE, Azad TD, Donato M, et al. Unsupervised analysis of transcriptomics in bacterial sepsis across multiple datasets reveals three robust clusters. Crit Care Med. 2018 Jun;46(6):915–925. doi:10.1097/CCM.0000000000003084.
   PubMed Web of Science ®Google Scholar
• Wong HR, Cvijanovich N, Lin R, et al. Identification of pediatric septic shock subclasses based on genome-wide expression profiling. BMC Med. 2009 Jul 22;7:34. PubMed PMID: 19624809; PubMed Central PMCID: PMCPMC2720987. eng.
   PubMed Web of Science ®Google Scholar
• Wong HR, Cvijanovich NZ, Anas N, et al. Endotype transitions during the acute phase of pediatric septic shock reflect changing risk and treatment response. Crit Care Med. 2018 Mar;46(3):e242–e249. PubMed PMID: 29252929; PubMed Central PMCID: PMCPMC5825261. eng.
   PubMed Web of Science ®Google Scholar
• Liu V, Escobar GJ, Greene JD, et al. HOspital deaths in patients with sepsis from 2 independent cohorts. JAMA. 2014 Jul 2;312(1):90–92.
   PubMed Web of Science ®Google Scholar
• Tsalik EL, Langley RJ, Dinwiddie DL, et al. An integrated transcriptome and expressed variant analysis of sepsis survival and death. Genome Med. 2014;6(11):111. PubMed PMID: 25538794; PubMed Central PMCID: PMC4274761.
   PubMedGoogle Scholar
• Sweeney TE, Perumal TM, Henao R, et al.
   Google Scholar
• Wong HR, Lindsell CJ, Pettila V, et al. A multibiomarker-based outcome risk stratification model for adult septic shock*. Crit Care Med. 2014 Apr;42(4):781–789. PubMed PMID: 24335447.
   PubMed Web of Science ®Google Scholar
• Fleming-Dutra KE, Hersh AL, Shapiro DJ, et al. Prevalence of inappropriate antibiotic prescriptions among us ambulatory care visits, 2010–2011. JAMA. 2016 May 3;315(17):1864–1873. PubMed PMID: 27139059.
   PubMed Web of Science ®Google Scholar
• Donnelly JP, Baddley JW, Wang HE. Antibiotic utilization for acute respiratory tract infections in U.S. emergency departments. PubMed PMID: 24342652; PubMed Central PMCID: PMCPMC3957838. eng Antimicrob Agents Chemother. 2014;583:1451–1457.
   PubMed Web of Science ®Google Scholar
• Chen L, Todd R, Kiehlbauch J, et al. Notes from the field: pan-resistant new delhi metallo-beta-lactamase-producing Klebsiella pneumoniae - Washoe County, Nevada, 2016. MMWR Morb Mortal Wkly Rep. 2017 Jan 13;66(1):33. PubMed PMID: 28081065.
   PubMed Web of Science ®Google Scholar
• Shehab N, Lovegrove MC, Geller AI, et al. US emergency department visits for outpatient adverse drug events, 2013–2014. JAMA. 2016;316(20):2115–2125.
   PubMed Web of Science ®Google Scholar
• Herberg JA, Kaforou M, Wright VJ, et al. DIagnostic test accuracy of a 2-transcript host rna signature for discriminating bacterial vs viral infection in febrile children. JAMA. 2016;316(8):835–845.
   PubMed Web of Science ®Google Scholar
• Suarez NM, Bunsow E, Falsey AR, et al. Transcriptional profiling is superior to procalcitonin to discriminate bacterial vs viral lower respiratory tract infections in hospitalized adults. J Infect Dis. 2015January;29:2015.
   Google Scholar
• Bhattacharya S, Rosenberg AF, Peterson DR, et al. Transcriptomic biomarkers to discriminate bacterial from nonbacterial infection in adults hospitalized with respiratory illness. Sci Rep. 2017 Jul 26;7(1):6548. PubMed PMID: 28747714; PubMed Central PMCID: PMCPMC5529430. eng.
   PubMedGoogle Scholar
• Mahajan P, Kuppermann N, Mejias A, et al. ASsociation of rna biosignatures with bacterial infections in febrile infants aged 60 days or younger. JAMA. 2016;316(8):846–857.
   PubMed Web of Science ®Google Scholar
• Tsalik EL, Henao R, Nichols M, et al. Host gene expression classifiers diagnose acute respiratory illness etiology. Sci Transl Med. 2016 Jan 20;8(322):322ra11. PubMed PMID: 26791949; PubMed Central PMCID: PMCPMC4905578.
   PubMed Web of Science ®Google Scholar
• Oved K, Cohen A, Boico O, et al. A novel host-proteome signature for distinguishing between acute bacterial and viral infections. PloS One . 2015;10(3):e0120012. PubMed PMID: 25785720; PubMed Central PMCID: PMC4364938. .
   PubMed Web of Science ®Google Scholar
• Van Houten CB, De Groot JAH, Klein A, et al. A host-protein based assay to differentiate between bacterial and viral infections in preschool children (OPPORTUNITY): a double-blind, multicentre, validation study. Lancet Infect Dis. 2017;17(4):431–440.
   PubMed Web of Science ®Google Scholar
• Eden E, Srugo I, Gottlieb T, et al. Diagnostic accuracy of a TRAIL, IP-10 and CRP combination for discriminating bacterial and viral etiologies at the emergency department. J Infect. 2016 Aug;73(2):177–180. PubMed PMID: 27255416.
   PubMed Web of Science ®Google Scholar
• Almasan A, Ashkenazi A. Apo2L/TRAIL: apoptosis signaling, biology, and potential for cancer therapy. Cytokine Growth Factor Rev. 2003 Jun-Aug;14(3–4):337–348. PubMed PMID: 12787570.
   PubMed Web of Science ®Google Scholar
• Liu M, Guo S, Stiles JK. The emerging role of CXCL10 in cancer (Review). Oncol Lett. 2011 Jul;2(4):583–589. . PubMed PMID: 22848232; PubMed Central PMCID: PMC3406435.
   PubMed Web of Science ®Google Scholar
• Ramirez LA, Arango TA, Thompson E, et al. High IP-10 levels decrease T cell function in HIV-1-infected individuals on ART. J Leukoc Biol. 2014 Dec;96(6):1055–1063. PubMed PMID: 25157027; PubMed Central PMCID: PMC4226794.
   PubMed Web of Science ®Google Scholar
• Davenport EE, Antrobus RD, Lillie PJ, et al. Transcriptomic profiling facilitates classification of response to influenza challenge. J Mol Med. 2015 Jan;93(1):105–114. PubMed PMID: 25345603; PubMed Central PMCID: PMC4281383.
   PubMed Web of Science ®Google Scholar
• Woods CW, McClain MT, Chen M, et al. A host transcriptional signature for presymptomatic detection of infection in humans exposed to influenza H1N1 or H3N2. PLoS One. 2013;8(1):e52198. PubMed PMID: 23326326; PubMed Central PMCID: PMCPMC3541408.
   PubMed Web of Science ®Google Scholar
• McClain MT, Nicholson BP, Park LP, et al. A genomic signature of influenza infection shows potential for presymptomatic detection, guiding early therapy, and monitoring clinical responses. Open Forum Infect Dis. 2016;3(1). doi:10.1093/ofid/ofw007. Jan 1.
   PubMed Web of Science ®Google Scholar
• Burke TW, Henao R, Soderblom E, et al. Nasopharyngeal protein biomarkers of acute respiratory virus infection. EBioMedicine. 2017 Mar;17:172–181. PubMed PMID: 28238698; PubMed Central PMCID: PMCPMC5360578. eng.
   PubMed Web of Science ®Google Scholar
• Van Oort P, Povoa P, Schnabel R, et al. The potential role of exhaled breath analysis in the diagnostic process of pneumonia - a systematic review. J Breath Res. 2018 Jan; 2.DOI:10.1088/1752-7163/aaa499 PubMed PMID: 29292698; eng.
   PubMed Web of Science ®Google Scholar
• WHO. Global tuberculosis control: World Health Organization; Geneva: WHO; 2011.
   Google Scholar
• Preez ID, Luies L, Loots DT. Metabolomics biomarkers for tuberculosis diagnostics: current status and future objectives. Biomark Med. 2017 Feb;11(2):179–194. . PubMed PMID: 28097879; eng.
   PubMed Web of Science ®Google Scholar
• De Groote MA, Sterling DG, Hraha T, et al. Discovery and validation of a six-marker serum protein signature for the diagnosis of active pulmonary tuberculosis. J Clin Microbiol. 2017 Oct;55(10):3057–3071. PubMed PMID: 28794177; PubMed Central PMCID: PMCPMC5625392. eng.
   PubMed Web of Science ®Google Scholar
• Zak DE, Penn-Nicholson A, Scriba TJ, et al. A blood RNA signature for tuberculosis disease risk: a prospective cohort study. Lancet (London, England). 2016 Jun 4;387(10035):2312–2322. PubMed PMID: 27017310; PubMed Central PMCID: PMCPMC5392204. eng.
   PubMed Web of Science ®Google Scholar
• Zhou M, Yu G, Yang X, et al. Circulating microRNAs as biomarkers for the early diagnosis of childhood tuberculosis infection. Mol Med Rep. 2016 Jun;13(6):4620–4626. PubMed PMID: 27082104; PubMed Central PMCID: PMCPMC4878571. eng.
   PubMed Web of Science ®Google Scholar
• Steere AC, McHugh G, Damle N, et al. Prospective study of serologic tests for lyme disease. Clin Infect Dis. 2008 Jul 15;47(2):188–195. PubMed PMID: 18532885; PubMed Central PMCID: PMCPMC5538270. eng.
   PubMed Web of Science ®Google Scholar
• Molins CR, Ashton LV, Wormser GP, et al. Development of a metabolic biosignature for detection of early Lyme disease. Clin Infect Dis. 2015 Jun 15;60(12):1767–1775. PubMed PMID: 25761869; PubMed Central PMCID: PMCPMC4810808. eng.
   PubMed Web of Science ®Google Scholar
• Soloski MJ, Crowder LA, Lahey LJ, et al. Serum inflammatory mediators as markers of human Lyme disease activity. PloS One. 2014;9(4):e93243. PubMed PMID: 24740099; PubMed Central PMCID: PMCPMC3989169. eng.
   PubMed Web of Science ®Google Scholar
• Bouquet J, Soloski MJ, Swei A, et al. Longitudinal transcriptome analysis reveals a sustained differential gene expression signature in patients treated for acute lyme disease. mBio. 2016 Feb 12;7(1):e00100–16. PubMed PMID: 26873097; PubMed Central PMCID: PMCPMC4791844. eng.
   PubMed Web of Science ®Google Scholar
• WHO. Ebola virus disease Fact Sheet: World Health Organization; Geneva: WHO; 2018.
   Google Scholar
• Broadhurst MJ, Kelly JD, Miller A, et al. ReEBOV antigen rapid test kit for point-of-care and laboratory-based testing for Ebola virus disease: a field validation study. The Lancet. 2015;386(9996):867–874.
   PubMed Web of Science ®Google Scholar
• Liu X, Speranza E, Muñoz-Fontela C, et al. Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus [journal article]. Genome Biol. 2017;18(1):4.
   PubMedGoogle Scholar
• Eisfeld A, Halfmann P, Wendler PJ, et al. Multi-platform ’Omics analysis of human Ebola virus disease pathogenesis. 22. 2017 Dec 13;22(6):817–829. doi:10.1016/j.chom.2017.10.011.
   Google Scholar