Deeks JJ, Altman DG. Diagnostic tests 4: likelihood ratios. BMJ. 2004;329:168–169.
ProbID References
Primary literature, guideline documents, and meta-analyses informing likelihood ratio estimates within ProbID.This list will expand as additional syndromes are curated.
General Methods
Pauker SG, Kassirer JP. Therapeutic Decision Making: A Cost-Benefit Analysis. N Engl J Med. 1975;293(5):229-234.
Endocarditis
Delgado V, Ajmone Marsan N, de Waha S, et al. 2023 ESC Guidelines for the management of endocarditis. Eur Heart J. 2023;44(39):3948-4042.
Fowler VG, Durack DT, Selton-Suty C, et al. The 2023 Duke-International Society for Cardiovascular Infectious Diseases Criteria for Infective Endocarditis: Updating the Modified Duke Criteria. Clin Infect Dis. 2023;77(4):518-526.
Bai AD, Steinberg M, Showler A, et al. Diagnostic Accuracy of Transthoracic Echocardiography for Infective Endocarditis Findings Using Transesophageal Echocardiography as the Reference Standard: A Meta-Analysis. J Am Soc Echocardiogr. 2017;30(7):639-646.e8.
San S, Ravis E, Tessonier L, et al. Diagnostic performance of 18F-FDG PET/CT in infective endocarditis: A meta-analysis. Open Heart. 2022;9:e001856.
Tubiana S, Duval X, Alla F, et al. The PREDICT score to guide echocardiography in Staphylococcus aureus bacteremia. Clin Infect Dis. 2015;61(1):18-28.
Tubiana S, Duval X, et al. The VIRSTA score, a prediction score to estimate risk of infective endocarditis and determine priority for echocardiography in patients with Staphylococcus aureus bacteremia. J Infect. 2016;72(5):544-553.
Peinado-Acevedo JS, Chiaramonte R, et al. Validation of VIRSTA and PREDICT Scores in Staphylococcus aureus Bacteremia for Ruling Out Endocarditis. Clin Infect Dis. 2021.
Peinado-Acevedo JS, et al. Prediction Rules for Ruling Out Endocarditis in Patients With Staphylococcus aureus Bacteremia. Clin Infect Dis. 2022;74(8):1442-1450.
Berge A, Krantz A, Östlund H, Nauclér P, Rasmussen M. The DENOVA score efficiently identifies patients with monomicrobial Enterococcus faecalis bacteremia where echocardiography is not necessary. Infection. 2019;47(1):45-50.
Sunnerhagen T, Törnell A, Vikbrant M, et al. HANDOC: A Handy Score to Determine the Need for Echocardiography in Non-beta-hemolytic Streptococcal Bacteremia. Clin Infect Dis. 2018;66(5):693-698.
CAP
Metlay JP, Waterer GW, Long AC, et al. Diagnosis and Treatment of Adults with Community-acquired Pneumonia. Am J Respir Crit Care Med. 2019;200:e45–e67.
Metlay JP, Kapoor WN, Fine MJ. Does this patient have community-acquired pneumonia? Diagnosing pneumonia by history and physical examination. JAMA. 1997;278(17):1440-1445.
Ebell MH, Bentivegna M, Cai X, Hulme C, Kearney M. Accuracy of Biomarkers for the Diagnosis of Adult Community-acquired Pneumonia: A Meta-analysis. Acad Emerg Med. 2020;27(3):195-206.
Klompas M, Calandra T, Singer M. Antibiotics for respiratory tract infections in adults in intensive care units and general wards after implementation of molecular diagnostics: a multicenter cohort study. Infect Control Hosp Epidemiol. 2021;42(2):131-138.
Metlay JP, et al. Adult Outpatients With Suspected Community-Acquired Pneumonia: What Is the Role of Viral Respiratory Diagnostics? An Official American Thoracic Society Clinical Practice Guideline. Am J Respir Crit Care Med. 2024.
Nahum J, et al. IDSA Position Statement on Use of Influenza and SARS-CoV-2 Molecular Assays to Inform Antibacterial Prescribing in Adults with Suspected Community-Acquired Pneumonia. Clin Infect Dis. 2025.
CDI
McDonald LC, Gerding DN, Johnson S, et al. Clinical Practice Guidelines for Clostridioides difficile Infection in Adults and Children. Clin Infect Dis. 2018;66:e1–e48.
Johnson S, Lavergne V, Skinner AM, et al. Clinical Practice Guideline by the IDSA and SHEA: 2021 Focused Update Guidelines on Management of Clostridioides difficile Infection in Adults. Clin Infect Dis. 2021;73(5):e1029-e1044.
Kraft CS, Parrott JS, Cornish NE, et al. A Laboratory Medicine Best Practices Systematic Review and Meta-analysis of Nucleic Acid Amplification Tests (NAATs) and Algorithms Including NAATs for the Diagnosis of Clostridioides difficile in Adults. Clin Microbiol Rev. 2019;32(3):e00032-18.
UTI
Gupta K, Hooton TM, Naber KG, et al. International Clinical Practice Guidelines for the Treatment of Acute Uncomplicated Cystitis and Pyelonephritis in Women: A 2010 Update by IDSA and ESCMID. Clin Infect Dis. 2011;52(5):e103-e120.
Bent S, Nallamothu BK, Simel DL, Fihn SD, Saint S. Does this woman have an acute uncomplicated urinary tract infection? JAMA. 2002;287(20):2701-2710.
Deville WL, Yzermans JC, van Duijn NP, et al. The urine dipstick test useful to rule out infections. A meta-analysis of the accuracy. BMC Urol. 2004;4:4.
PJP
Brown A, Miah A, et al. Accuracy of Pneumocystis jirovecii PCR assays in respiratory samples for diagnosis of Pneumocystis pneumonia: a systematic review and meta-analysis. Clin Infect Dis. 2024.
Del Corpo O, Butler-Laporte G, Sheppard DC, et al. Diagnostic accuracy of serum (1-3)-beta-D-glucan for Pneumocystis jirovecii pneumonia: a systematic review and meta-analysis. Clin Microbiol Infect. 2020;26(9):1137-1143.
Veintimilla C, Kuncio D, Mays JA, et al. Accuracy of Microscopy and PCR for the Diagnosis of Pneumocystis jirovecii from Bronchoalveolar Lavage in a Real-World Clinical Setting. J Fungi (Basel). 2023;9(4):414.
Mappin-Kasirer B, et al. A diagnostic model for Pneumocystis jirovecii pneumonia in patients requiring bronchoscopy and bronchoalveolar lavage. BMC Infect Dis. 2024;24:1311.
Wills M, et al. Utility of Chest X-ray Features in Presumed HIV-Associated Pneumocystis jirovecii Pneumonia: A Systematic Review and Meta-Analysis. Open Forum Infect Dis. 2024;11(5):ofae146.
Shin HJ, et al. Risk factors for Pneumocystis jirovecii pneumonia in patients with autoimmune diseases receiving non-high-dose steroids. Sci Rep. 2019;9:1911.
Invasive Candidiasis
Pappas PG, Kauffman CA, Andes DR, et al. Clinical Practice Guideline for the Management of Candidiasis: 2016 Update by the IDSA. Clin Infect Dis. 2016;62(4):e1-e50.
Clancy CJ, Nguyen MH. Finding the "missing 50%" of invasive candidiasis: how nonculture diagnostics will improve understanding of disease spectrum and transform patient care. Clin Infect Dis. 2013;56(9):1284-1292.
Bassetti M, Giacobbe DR, Vena A, et al. Incidence and outcome of invasive candidiasis in intensive care units (EUCANDICU): a multinational prospective observational study. Crit Care. 2019;23:219.
León C, Ruiz-Santana S, Saavedra P, et al. A bedside scoring system (Candida score) for early antifungal treatment in nonneutropenic critically ill patients with Candida colonization. Crit Care Med. 2006;34(3):730-737.
Karageorgopoulos DE, Vouloumanou EK, Ntziora F, et al. beta-D-glucan assay for the diagnosis of invasive fungal infections: a meta-analysis. Clin Infect Dis. 2011;52(6):750-770.
Mikulska M, Calandra T, Sanguinetti M, Poulain D, Viscoli C. The use of mannan antigen and anti-mannan antibodies in the diagnosis of invasive candidiasis: recommendations from the 3rd European Conference on Infections in Leukemia. Crit Care. 2010;14(6):R222.
Tang HJ, et al. The diagnostic accuracy of T2Candida to detect candidemia: a systematic review and meta-analysis. BMC Infect Dis. 2019;19:271.
Avni T, Leibovici L, Paul M. PCR diagnosis of invasive candidiasis: systematic review and meta-analysis. J Clin Microbiol. 2011;49(2):665-670.
Clancy CJ, Nguyen MH. Diagnosing Invasive Candidiasis. J Fungi (Basel). 2018;4(1):27.
Invasive Mold Infection
Patterson TF, Thompson GR 3rd, Denning DW, et al. Practice Guidelines for the Diagnosis and Management of Aspergillosis: 2016 Update by the IDSA. Clin Infect Dis. 2016;63(4):e1-e60.
Donnelly JP, Chen SC, Kauffman CA, et al. Revision and Update of the Consensus Definitions of Invasive Fungal Disease from the EORTC/MSGERC. Clin Infect Dis. 2020;71(6):1367-1376.
Cruciani M, Mengoli C, Loeffler J, et al. Polymerase chain reaction blood tests for the diagnosis of invasive aspergillosis in immunocompromised people. Cochrane Database Syst Rev. 2019;9:CD009551.
Feys S, Almyroudi MP, Braspenning R, et al. A visual and comprehensive review on COVID-19-associated pulmonary aspergillosis (CAPA). Lancet Infect Dis. 2022;22(11):1621-1632.
Leeflang MMG, Debets-Ossenkopp YJ, Wang J, et al. Galactomannan detection for invasive aspergillosis in immunocompromised patients. Cochrane Database Syst Rev. 2015;12:CD007394.
Heng SC, Morrissey O, Chen SCA, et al. Clinical utility of bronchoalveolar lavage fluid galactomannan in diagnosis of invasive pulmonary aspergillosis: a meta-analysis. Crit Rev Microbiol. 2015;41(1):124-134.
Huang BG, Zhang YT, Zeng WT. Diagnostic value of beta-D-glucan in invasive aspergillosis: a systematic review and meta-analysis. Clin Respir J. 2024;18(2):e13760.
Zhang J, Yu Y, Yang C, et al. The role of aspergillus lateral flow assays in diagnosing invasive pulmonary aspergillosis: a systematic review and meta-analysis. Heliyon. 2024;10(17):e34569.
Avni T, Levy I, Sprecher H, et al. Diagnostic accuracy of PCR alone compared to galactomannan in bronchoalveolar lavage fluid for diagnosis of invasive pulmonary aspergillosis: a systematic review. J Clin Microbiol. 2012;50(11):3652-3658.
Brown AC, Hennequin C, Alvarez-Moreno C, et al. Mucorales PCR in blood and bronchoalveolar lavage for diagnosis of mucormycosis: a systematic review and meta-analysis. Int J Infect Dis. 2025;153:107941.
Agarwal R, et al. The diagnostic performance of halo and reversed halo signs for invasive mold infections in compromised hosts: A systematic review and meta-analysis. Eur J Radiol. 2020;122:108843.
PJI
Parvizi J, Tan TL, Goswami K, et al. The 2018 Definition of Periprosthetic Hip and Knee Infection: An Evidence-Based and Validated Criteria. J Arthroplasty. 2018;33(5):1309-1314.e2.
Cortes-Penfield NW, Kulkarni PA, Theel ES. Prosthetic Joint Infection: Diagnostic Challenges and New Developments. Clin Infect Dis. 2023;76(1):e181-e188.
Tarabichi M, Shohat N, Goswami K, et al. C-Reactive Protein and Erythrocyte Sedimentation Rate Have Variable Sensitivity and Specificity for the Diagnosis of Periprosthetic Joint Infection in Total Knee Arthroplasty: A Clinical Study. J Arthroplasty. 2024.
Paul S, et al. Utility of alpha-defensin in diagnosing periprosthetic joint infection: a systematic review and meta-analysis. J Bone Jt Infect. 2025;10:525-538.
Poursalehian M, et al. Diagnostic value of synovial fluid leucocyte esterase strip test in periprosthetic joint infection: a systematic review and meta-analysis. Arthroplasty. 2025;7:34.
Watanabe M, et al. Preoperative Synovial Fluid Culture, Intraoperative Tissue Culture, and Sonication Fluid Culture in Diagnosing Periprosthetic Joint Infection: A Diagnostic Accuracy Study and Meta-analysis. J Arthroplasty. 2024.
Jun Y, Jiang Y, Xu Y, et al. Diagnostic Value of Synovial Fluid Polymerase Chain Reaction for Periprosthetic Joint Infection: A Meta-analysis. Surg Infect (Larchmt). 2018;19(7):683-691.
Zhu Y, Zhang F, Chen W, et al. Risk factors for periprosthetic joint infection after total joint arthroplasty: a systematic review and meta-analysis. Int Wound J. 2016;13(6):1213-1221.
Active TB
van't Hoog AH, Langendam MW, Mitchell E, et al. Symptom- and chest-radiography screening for active pulmonary tuberculosis in HIV-negative adults and adolescents: a systematic review and meta-analysis. Cochrane Database Syst Rev. 2022;9:CD010890.
Steingart KR, Schiller I, Horne DJ, Pai M, Boehme CC, Dendukuri N. Xpert MTB/RIF assay for pulmonary tuberculosis and rifampicin resistance in adults. Cochrane Database Syst Rev. 2014;CD009593.
Liu C, Cui Y, Li L, et al. The Value of Xpert MTB/RIF in Bronchoalveolar Lavage Fluid in the Diagnosis of Pulmonary Tuberculosis: A Systematic Review and Meta-analysis. J Clin Microbiol. 2021;59(1):e02170-20.
Davis JL, Cattamanchi A, Cuevas LE, Hopewell PC, Steingart KR. Diagnostic accuracy of same-day microscopy versus standard microscopy for pulmonary tuberculosis: a systematic review and meta-analysis. Lancet Infect Dis. 2013;13(2):147-154.
You L, Ma H, Lin S, et al. Performance of metagenomic next-generation sequencing versus conventional tests in pulmonary tuberculosis diagnosis: a systematic review and meta-analysis. Syst Rev. 2024;13:284.
AlAlyani H, Alhaqbani M, Althomali O, et al. Evaluating Interferon-Gamma Release Assays for Diagnosing Active Tuberculosis in Adults: A Systematic Review and Meta-Analysis. Diagnostics (Basel). 2025;15(18):2343.
Jeon CY, Murray MB. Diabetes mellitus increases the risk of active tuberculosis: a systematic review of 13 observational studies. PLoS Med. 2008;5(7):e152.
Fox GJ, Barry SE, Britton WJ, Marks GB. Contact investigation for tuberculosis: a systematic review and meta-analysis. PLoS Med. 2013;10(11):e1001432.
Cords O, Martinez L, Warren JL, et al. Incidence and prevalence of tuberculosis in incarcerated populations: a systematic review and meta-analysis. Lancet Public Health. 2021;6(5):e300-e308.
Beijer U, Wolf A, Fazel S. Prevalence of tuberculosis, hepatitis C virus, and HIV in homeless people: a systematic review and meta-analysis. Lancet Infect Dis. 2012;12(11):859-870.
World Health Organization. Global tuberculosis report 2024. Geneva: WHO; 2024.
World Health Organization. WHO consolidated guidelines on tuberculosis. Module 3: Diagnosis – rapid diagnostics for tuberculosis detection, 2021 update.
VAP
Kalil AC, Metersky ML, Klompas M, et al. Management of Adults With Hospital-acquired and Ventilator-associated Pneumonia: 2016 Clinical Practice Guidelines by the IDSA and ATS. Clin Infect Dis. 2016;63(5):e61-e111.
Fernando SM, Tran A, Cheng W, et al. Diagnosis of ventilator-associated pneumonia in critically ill adult patients-a systematic review and meta-analysis. Intensive Care Med. 2020;46(6):1170-1179.
Cook DJ, Walter SD, Cook RJ, et al. Incidence of and risk factors for ventilator-associated pneumonia in critically ill patients. Ann Intern Med. 1998;129(6):433-440.
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 ICU. Crit Care. 2010;14(1):R35. [Oxygenation criterion performance in suspected VAP cohorts is often poor; see also subsequent prospective analyses.]
Ferrer M, et al. Accuracy of the PaO2/FiO2 Ratio for the Diagnosis of Ventilator-Associated Pneumonia. J Clin Med. 2019;8(8):1217. (Used here for the PaO2/FiO2 <=240 diagnostic-performance caution/derivation in suspected VAP.)
Ochoa-Hein E, et al. Risk factors associated with ventilator-associated pneumonia in critically ill patients: a systematic review and meta-analysis. Ann Clin Microbiol Antimicrob. 2025;24:57. (Used for pooled VAP risk-factor associations that inform the optional pretest modifier layer.)