A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiology

Clinical Infectious Diseases

Volumn 67, Issue 6, 2018, Pages e1-e94

  Miller, J Michael ^a   Binnicker, Matthew J ^b   Campbell, Sheldon ^c   Carroll, Karen C ^d   Chapin, Kimberle C ^e   Gilligan, Peter H ^f   Gonzalez, Mark D ^g   Jerris, Robert C ^g   Kehl, Sue C ^h   Patel, Robin ^b   Pritt, Bobbi S ^b   Richter, Sandra S ⁱ   Robinson Dunn, Barbara ^j   Schwartzman, Joseph D ^k   Snyder, James W ^l   Telford, Sam ^m   Theel, Elitza S ^b   Thomson, Richard B ⁿ   Weinstein, Melvin P ^o   Yao, Joseph D ^b  

^a Microbiology Technical Services LLC   (United States)

^b MAYO CLINIC   (United States)

^c YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d DEPARTMENT OF PATHOLOGY   (United States)

^e RHODE ISLAND HOSPITAL   (United States)

^f UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^g CHILDREN'S HEALTHCARE OF ATLANTA   (United States)

^h MEDICAL COLLEGE OF WISCONSIN   (United States)

ⁱ LERNER RESEARCH INSTITUTE   (United States)

^j Beaumont Health ^*  (United States)

^k DARTMOUTH HITCHCOCK MEDICAL CENTER   (United States)

^l University of Louisville School of Medicine   (United States)

^m TUFTS UNIVERSITY   (United States)

ⁿ NORTHSHORE UNIVERSITY HEALTHSYSTEM   (United States)

^o ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

more..

Author keywords

clinical correlation; clinical relevance; microbiology specimens.; specimen collection; specimen management

Indexed keywords

EID: 85053726304     PISSN: 10584838     EISSN: 15376591     Source Type: Journal    
DOI: 10.1093/cid/ciy381     Document Type: Article

References (295)

1. Baron EJ, Weinstein MP, Dunne WMJ, Yagupsky P, Welch DF, Wilson DM, eds. Cumitech 1C, Blood cultures IV. Washington, DC: ASM Press, 2005.
2. Clinical and Laboratory Standards Institute. Principles and procedures for blood cultures; approved guideline. CLSI document M47-A. Wayne, PA: CLSI, 2007.
3. Baron EJ, Scott JD, Tompkins LS. Prolonged incubation and extensive subculturing do not increase recovery of clinically significant microorganisms from standard automated blood cultures. Clin Infect Dis 2005; 41:1677-80.
4. Petti CA, Bhally HS, Weinstein MP, et al. Utility of extended blood culture incubation for isolation of Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, and Kingella organisms: a retrospective multicenter evaluation. J Clin Microbiol 2006; 44:257-9.
5. Cockerill FR 3rd, Wilson JW, Vetter EA, et al. Optimal testing parameters for blood cultures. Clin Infect Dis 2004; 38:1724-30.
6. Reller ME, Mirrett S, McKnight CM, Reller LB. Role of volume of blood cultured in detection of disseminated infection with Mycobacterium avium complex [abstract 368]. In: 45th Annual Meeting of the Infectious Diseases Society of America, San Diego, CA, 2007.
7. Lee A, Mirrett S, Reller LB, Weinstein MP. Detection of bloodstream infections in adults: how many blood cultures are needed J Clin Microbiol 2007; 45:3546-8.
8. Washer LL, Chenoweth C, Kim HW, et al. Blood culture contamination: a randomized trial evaluating the comparative effectiveness of 3 skin antiseptic interventions. Infect Control Hosp Epidemiol 2013; 34:15-21.
9. Story-Roller E, Weinstein MP. Chlorhexidine versus tincture of iodine for reduction of blood culture contamination rates: a prospective randomized crossover study. J Clin Microbiol 2016; 54:3007-9.
10. Mermel LA, Farr BM, Sherertz RJ, et al; Infectious Diseases Society of America; American College of Critical Care Medicine; Society for Healthcare Epidemiology of America. Guidelines for the management of intravascular catheter-related infections. Clin Infect Dis 2001; 32:1249-72.
11. Pfaller MA. Laboratory diagnosis of catheter-related bacteremia. Infect Dis Clin Prac 1995; 4:206-10.
12. Maki DG, Weise CE, Sarafin HW. A semiquantitative culture method for identifying intravenous-catheter-related infection. N Engl J Med 1977; 296:1305-9.
13. Peterson LR, Smith BA. Nonutility of catheter tip cultures for the diagnosis of central line-associated bloodstream infection. Clin Infect Dis 2015; 60:492-3.
14. Raad I, Hanna HA, Alakech B, Chatzinikolaou I, Johnson MM, Tarrand J. Differential time to positivity: a useful method for diagnosing catheter-related bloodstream infections. Ann Intern Med 2004; 140:18-25.
15. Safdar N, Fine JP, Maki DG. Meta-analysis: methods for diagnosing intravascular device-related bloodstream infection. Ann Intern Med 2005; 142:451-66.
16. Mylonakis E, Clancy CJ, Ostrosky-Zeichner L, et al. T2 magnetic resonance assay for the rapid diagnosis of candidemia in whole blood: a clinical trial. Clin Infect Dis 2015; 60:892-9.
17. Leber AL, Everhart K, Balada-Llasat JM, et al. Multicenter evaluation of Biofire Filmarray meningitis/encephalitis panel for detection of bacteria, viruses, and yeast in cerebrospinal fluid specimens. J Clin Microbiol 2016; 54:2251-61.
18. Hanson KE. The First fully automated molecular diagnostic panel for meningitis and encephalitis: how well does it perform, and when should it be used J Clin Microbiol 2016; 54:2222-4.
19. Wilson MR, Naccache SN, Samayoa E, et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med 2014; 370:2408-17.
20. Christie LJ, Loeffler AM, Honarmand S, et al. Diagnostic challenges of central nervous system tuberculosis. Emerg Infect Dis 2008; 14:1473-5.
21. Greenlee JE. Approach to diagnosis of meningitis. Cerebrospinal fluid evaluation. Infect Dis Clin North Am 1990; 4:583-98.
22. Tunkel AR, Hartman BJ, Kaplan SL, et al. Practice guidelines for the management of bacterial meningitis. Clin Infect Dis 2004; 39:1267-84.
23. Dinnes J, Deeks J, Kunst H, et al. A systematic review of rapid diagnostic tests for the detection of tuberculosis infection. Health Technol Assess 2007; 11:1-196.
24. Garg RK. Tuberculosis of the central nervous system. Postgrad Med J 1999; 75:133-40.
25. Glaser CA, Honarmand S, Anderson LJ, et al. Beyond viruses: clinical profiles and etiologies associated with encephalitis. Clin Infect Dis 2006; 43:1565-77.
26. Tunkel AR, Glaser CA, Bloch KC, et al; Infectious Diseases Society of America. The management of encephalitis: clinical practice guidelines by the Infectious Diseases Society of America. Clin Infect Dis 2008; 47:303-27.
27. Debiasi RL, Tyler KL. Molecular methods for diagnosis of viral encephalitis. Clin Microbiol Rev 2004; 17:903-25, table of contents.
28. Weil AA, Glaser CA, Amad Z, Forghani B. Patients with suspected herpes simplex encephalitis: rethinking an initial negative polymerase chain reaction result. Clin Infect Dis 2002; 34:1154-7.
29. Venkatesan A, Tunkel AR, Bloch KC, et al; International Encephalitis Consortium. Case definitions, diagnostic algorithms, and priorities in encephalitis: consensus statement of the International Encephalitis Consortium. Clin Infect Dis 2013; 57:1114-28.
30. Petersen LR, Marfin AA. West Nile virus: a primer for the clinician. Ann Intern Med 2002; 137:173-9.
31. Schuster FL, Honarmand S, Visvesvara GS, Glaser CA. Detection of antibodies against free-living amoebae Balamuthia mandrillaris and Acanthamoeba species in a population of patients with encephalitis. Clin Infect Dis 2006; 42:1260-5.
32. Murray WJ, Kazacos KR. Raccoon roundworm encephalitis. Clin Infect Dis 2004; 39:1484-92.
33. Walker M, Zunt JR. Parasitic central nervous system infections in immunocompromised hosts. Clin Infect Dis 2005; 40:1005-15.
34. Belay ED, Holman RC, Schonberger LB. Creutzfeldt-Jakob disease surveillance and diagnosis. Clin Infect Dis 2005; 41:834-6.
35. Tunkel AR, Hasbun R, Bhimraj A, et al; 2017 Infectious Diseases Society of America's clinical practice guidelines for healthcare-associated ventriculitis and meningitis. Clin Infect Dis 2017; 64:e34-65.
36. Gray LD, Gilligan PH, Fowler WC, eds. Cumitech 13B. Laboratory diagnosis of ocular infections. Washington, DC: ASM Press, 2010.
37. Kaye S, Sueke H, Romano V, et al. Impression membrane for the diagnosis of microbial keratitis. Br J Ophthalmol 2016; 100:607-10.
38. Givner LB. Periorbital versus orbital cellulitis. Pediatr Infect Dis J 2002; 21:1157-8.
39. Durland M. Periocular infection. 6th ed. Philadelphia: Elsevier Churchill Livingstone, 2005.
40. Everitt HA, Little PS, Smith PW. A randomised controlled trial of management strategies for acute infective conjunctivitis in general practice. BMJ 2006; 333:321.
41. Gigliotti F, Williams WT, Hayden FG, et al. Etiology of acute conjunctivitis in children. J Pediatr 1981; 98:531-6.
42. Leibowitz HM. The red eye. N Engl J Med 2000; 343:345-51.
43. McAnena L, Knowles SJ, Curry A, Cassidy L. Prevalence of gonococcal conjunctivitis in adults and neonates. Eye (Lond) 2015; 29:875-80.
44. Taylor HR, Burton MJ, Haddad D, West S, Wright H. Trachoma. Lancet 2014; 384:2142-52.
45. Thomas PA, Geraldine P. Infectious keratitis. Curr Opin Infect Dis 2007; 20:129-41.
46. Lynn WA, Lightman S. The eye in systemic infection. Lancet 2004; 364:1439-50.
47. Pepose JS, Margolis TP, LaRussa P, Pavan-Langston D. Ocular complications of smallpox vaccination. Am J Ophthalmol 2003; 136:343-52.
48. Goldschmidt P, Rostane H, Saint-Jean C, et al. Effects of topical anaesthetics and fluorescein on the real-time PCR used for the diagnosis of herpesviruses and Acanthamoeba keratitis. Br J Ophthalmol 2006; 90:1354-6.
49. Seitzman GD, Cevallos V, Margolis TP. Rose bengal and lissamine green inhibit detection of herpes simplex virus by PCR. Am J Ophthalmol 2006; 141:756-8.
50. McLaughlin-Borlace L, Stapleton F, Matheson M, Dart JK. Bacterial biofilm on contact lenses and lens storage cases in wearers with microbial keratitis. J Appl Microbiol 1998; 84:827-38.
51. Yung MS, Boost M, Cho P, Yap M. Microbial contamination of contact lenses and lens care accessories of soft contact lens wearers (university students) in Hong Kong. Ophthalmic Physiol Opt 2007; 27:11-21.
52. Centers for Disease Control and Prevention. Acanthamoeba keratitis multiple states, 2005-2007. MMWR Morb Mortal Wkly Rep 2007; 56:532-4.
53. Chang DC, Grant GB, O'Donnell K, et al; Fusarium Keratitis Investigation Team. Multistate outbreak of Fusarium keratitis associated with use of a contact lens solution. JAMA 2006; 296:953-63.
54. Ross J, Roy SL, Mathers WD, et al. Clinical characteristics of Acanthamoeba keratitis infections in 28 states, 2008 to 2011. Cornea 2014; 33:161-8.
55. Edelstein SL, DeMatteo J, Stoeger CG, Macsai MS, Wang CH. Report of the Eye Bank Association of America medical review subcommittee on adverse reactions reported from 2007 to 2014. Cornea 2016; 35:917-26.
56. Younger JR, Johnson RD, Holland GN, et al; UCLA Cornea Service. Microbiologic and histopathologic assessment of corneal biopsies in the evaluation of microbial keratitis. Am J Ophthalmol 2012; 154:512-9. e512.
57. Davis JL, Miller DM, Ruiz P. Diagnostic testing of vitrectomy specimens. Am J Ophthalmol 2005; 140:822-9.
58. Durand ML. Bacterial and fungal endophthalmitis. Clin Microbiol Rev 2017; 30:597-613.
59. Hanscom TA. Postoperative endophthalmitis. Clin Infect Dis 2004; 38:542-6.
60. Lemley CA, Han DP. Endophthalmitis: a review of current evaluation and management. Retina 2007; 27:662-80.
61. Essex RW, Yi Q, Charles PG, Allen PJ. Post-traumatic endophthalmitis. Ophthalmology 2004; 111:2015-22.
62. Jackson TL, Eykyn SJ, Graham EM, Stanford MR. Endogenous bacterial endophthalmitis: a 17-year prospective series and review of 267 reported cases. Surv Ophthalmol 2003; 48:403-23.
63. Ness T, Pelz K, Hansen LL. Endogenous endophthalmitis: microorganisms, disposition and prognosis. Acta Ophthalmol Scand 2007; 85:852-6.
64. Bosch-Driessen LE, Berendschot TT, Ongkosuwito JV, Rothova A. Ocular toxoplasmosis: clinical features and prognosis of 154 patients. Ophthalmology 2002; 109:869-78.
65. Jeroudi A, Yeh S. Diagnostic vitrectomy for infectious uveitis. Int Ophthalmol Clin 2014; 54:173-97.
66. Anwar Z, Galor A, Albini TA, Miller D, Perez V, Davis JL. The diagnostic utility of anterior chamber paracentesis with polymerase chain reaction in anterior uveitis. Am J Ophthalmol 2013; 155:781-6.
67. Woolston S, Cohen SE, Fanfair RN, Lewis SC, Marra CM, Golden MR. A Cluster of ocular syphilis cases-Seattle, Washington, and San Francisco, California, 2014-2015. MMWR Morb Mortal Wkly Rep 2015; 64:1150-1.
68. Santos FF, Nascimento H, Muccioli C, et al. Detection of Toxoplasma gondii DNA in peripheral blood and aqueous humor of patients with toxoplasmic active focal necrotizing retinochoroiditis using real-time PCR. Arq Bras Oftalmol 2015; 78:356-8.
69. Chronopoulos A, Roquelaure D, Souteyrand G, Seebach JD, Schutz JS, Thumann G. Aqueous humor polymerase chain reaction in uveitis-utility and safety. BMC Ophthalmol 2016; 16:189.
70. Villard O, Filisetti D, Roch-Deries F, Garweg J, Flament J, Candolfi E. Comparison of enzyme-linked immunosorbent assay, immunoblotting, and PCR for diagnosis of toxoplasmic chorioretinitis. J Clin Microbiol 2003; 41:3537-41.
71. Bou G, Figueroa MS, Marti-Belda P, Navas E, Guerrero A. Value of PCR for detection of Toxoplasma gondii in aqueous humor and blood samples from immunocompetent patients with ocular toxoplasmosis. J Clin Microbiol 1999; 37:3465-8.
72. Westeneng AC, Rothova A, de Boer JH, de Groot-Mijnes JD. Infectious uveitis in immunocompromised patients and the diagnostic value of polymerase chain reaction and Goldmann-Witmer coefficient in aqueous analysis. Am J Ophthalmol 2007; 144:781-5.
73. Butler NJ, Thorne JE. Current status of HIV infection and ocular disease. Curr Opin Ophthalmol 2012; 23:517-22.
74. Jabs DA, Martin BK, Forman MS, Ricks MO; Cytomegalovirus Retinitis and Viral Resistance Research Group. Cytomegalovirus (CMV) blood DNA load, CMV retinitis progression, and occurrence of resistant CMV in patients with CMV retinitis. J Infect Dis 2005; 192:640-9.
75. Kotton CN, Kumar D, Caliendo AM, et al; Transplantation Society International CMV Consensus Group. International consensus guidelines on the management of cytomegalovirus in solid organ transplantation. Transplantation 2010; 89:779-95.
76. Doan T, Wilson MR, Crawford ED, et al. Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens. Genome Med 2016; 8:90.
77. Thomson RB, Jr. Bacterial infections of the upper respiratory tract. In: Borriello SP, Murray PR, Funke G, eds. Topley and Wilson's microbiology and microbial infections. 10th ed. Vol 1. London: Hodder Arnold Ltd, 2006:606-21.
78. Brook I. Microbiology and management of peritonsillar, retropharyngeal, and parapharyngeal abscesses. J Oral Maxillofacial Surg 2004; 62:1545-50.
79. Reynolds SC, Chow AW. Life-threatening infections of the peripharyngeal and deep fascial spaces of the head and neck. Infect Dis Clin N Am 2007; 21:557-76, viii.
80. Rautemaa R, Lauhio A, Cullinan MP, Seymour GJ. Oral infections and systemic disease-an emerging problem in medicine. Clinical Microbiol Infect 2007; 13:1041-7.
81. Riordan T. Human infection with Fusobacterium necrophorum (necrobacillosis), with a focus on Lemierre's syndrome. Clin Microbiol Reviews 2007; 20:622-59.
82. Phillips I, Taylor E, Eykyn S. The rapid laboratory diagnosis of anaerobic infection. Infection 1980; 8(Suppl 2):S155-8.
83. Belmont MJ, Behar PM, Wax MK. Atypical presentations of actinomycosis. Head Neck 1999; 21:264-8.
84. Lee ES, Chae SW, Lim HH, Hwang SJ, Suh HK. Clinical experiences with acute mastoiditis-1988 through 1998. Ear Nose Throat J 2000; 79:884-8, 890-2.
85. Rubin Grandis J, Branstetter BF 4th, Yu VL. The changing face of malignant (necrotising) external otitis: clinical, radiological, and anatomic correlations. Lancet Infect Dis 2004; 4:34-9.
86. Grijalva CG, Nuorti JP, Griffin MR. Antibiotic prescription rates for acute respiratory tract infections in US ambulatory settings. JAMA 2009; 302:758-66.
87. Lieberthal AS, Carroll AE, Chonmaitree T, et al. Clinical practice guideline: the diagnosis and management of acute otitis media. Pediatrics 2013; 131:e964-9.
88. Klein JO, Bluestone CD. Otitis media. In: Cherry JD, Harrison GJ, Kaplan SL, Steinback WJ, Hotez PJ, eds. Feigin and Cherry's textbook of pediatric infectious diseases, 7th ed. Philadelphia: Saunders Elsevier, 2014:209-32.
89. Ngo CC, Massa HM, Thornton RB, Cripps AW. Predominant bacteria detected from the middle ear fluid of children experiencing otitis media: a systematic review. PLoS One 2016; 11:e0150949.
90. Sillanpaa S, Kramma L, Oikarinen S, et al. Next-generation sequencing combined with specific PCR assays to determine the bacterial 16s rRNA gene profiles of middle ear fluid collected from children with acute otitis media. mSphere 2017; 2:e00006-17.
91. Mittal R, Lisi CV, Gerring R, et al. Current concepts in the pathogenesis and treatment of chronic suppurative otitis media. J Med Microbiol 2015; 64:1103-16.
92. Baron EJ. Specimen collection, transport, and processing: bacteriology. In: Jorgensen JH, Pfaller MA, Carroll KC, et al, eds. Manual of clinical microbiology. 11th ed. Washington, DC: ASM Press, 2015:270-315.
93. Orlandi RR, Kingdom TT, Hwang PH, et al. International consensus statement on allergy and rhinology: rhinosinusitis. Int Forum Allergy Rhinol 2016; 6(Suppl 1):S22-209.
94. Brook I. Microbiology of chronic rhinosinusitis. Eur J Clin Microbiol Infect Dis 2016; 35:1059-68.
95. DeMuri GP, Wald ER. Sinusitis. In: Bennett JE, Dolin R, Blaser MJ, eds. Mandell, Douglas, and Bennett's principles and practices of infectious diseases. 8th ed. Philadelphia: Elsevier Churchill Livingstone, 2015:774-83.
96. Cherry JD, Mundi J, Shapiro NL. Rhinosinusitis. In: Cherry JD, Harrison GJ, Kaplan SL, Steinback WJ, Hotez PJ, eds. Feigin and Cherry's textbook of pediatric infectious diseases, 7th ed. Philadelphia: Saunders Elsevier, 2014:193-203.
97. Chow AW, Benninger MS, Brook I, et al. IDSA clinical practice guideline for acute bacterial rhinosinusitis in children and adults. Clin Infect Dis 2012; 54:e72-112.
98. Orlandi RR. Biopsy and specimen collection in chronic rhinosinusitis. Annals Otol Rhinol Laryngol 2004; 193(Suppl):24-6.
99. Wessels MR. Streptococcal pharyngitis. N Engl J Med 2011; 364:648-55.
100. Flores AR, Caserta MT. Pharyngitis. In: Bennett JE, Dolin R, Blaser MJ, eds. Mandell, Douglas, and Bennett's principles and practices of infectious diseases. 8th ed. Philadelphia: Elsevier Churchill Livingstone, 2015:753-9.
101. Bourbeau PP. Role of the microbiology laboratory in diagnosis and management of pharyngitis. J Clin Microbiol 2003; 41:3467-72.
102. Neuner JM, Hamel MB, Phillips RS, Bona K, Aronson MD. Diagnosis and management of adults with pharyngitis. A cost-effectiveness analysis. Ann Intern Med 2003; 139:113-22.
103. Shulman ST, Bisno AL, Clegg HW, et al. Clinical practice guideline for the diagnosis and management of group A streptococcal pharyngitis: 2012 update by the Infectious Diseases Society of America. Clin Infect Dis 2012; 55:e86-102.
104. Cohen DM, Russo ME, Jaggi P, Kline J, Gluckman W, Parekh A. Multicenter clinical evaluation of the novel Alere i Strep A isothermal nucleic acid amplification test. J Clin Microbiol 2015; 53:2258-61.
105. Wang F, Tian Y, Chen L, et al. Accurate detection of Streptococcus pyogenes at the point of care using the Cobas Liat Strep A Nucleic Acid Test. Clin Pediatr (Phila) 2017; 56:1128-34.
106. Klug TE, Rusan M, Fuursted K, Ovesen T, Jorgensen AW. A systematic review of Fusobacterium necrophorum-positive acute tonsillitis: prevalence, methods of detection, patient characteristics, and the usefulness of the Centor score. Eur J Clin Microbiol Infect Dis 2016; 35:1903-12.
107. Bank S, Christensen K, Kristensen LH, Prag J. A cost-effectiveness analysis of identifying Fusobacterium necrophorum in throat swabs followed by antibiotic treatment to reduce the incidence of Lemierre's syndrome and peritonsillar abscesses. Eur J Clin Microbiol Infect Dis 2013; 32:71-8.
108. Amess JA, O'Neill W, Giollariabhaigh CN, Dytrych JK. A six-month audit of the isolation of Fusobacterium necrophorum from patients with sore throat in a district general hospital. Br J Biomed Sci 2007; 64:63-5.
109. Ralston SL, Lieger AS, Meissner HC, et al. Clinical practice guideline: the diagnosis, management, and prevention of bronchiolitis. Pediatrics 2014; 134:e1474-1502.
110. Hasegawa K, Mansbach JM, Camargo CA Jr. Infectious pathogens and bronchiolitis outcomes. Expert Rev Anti Infect Ther 2014; 12:817-28.
111. Mansbach JM, Piedra PA, Teach SJ, et al; MARC-30 Investigators. Prospective multicenter study of viral etiology and hospital length of stay in children with severe bronchiolitis. Arch Pediatr Adolesc Med 2012; 166:700-6.
112. Musher DM, Thorner A. Community-acquired pneumonia. N Engl J Med 2014; 371:1619-27.
113. Mandell LA, Wunderink RG, Anzueto A, et al. Infectious Diseases Society of America/American Thoracic Society consensus guidelines on the management of community-acquired pneumonia in adults. Clin Infect Dis 2007; 44(Suppl 2):S27-72.
114. Bradley JS, Byington CL, Shah SS, et al. The management of community acquired pneumonia in infants and children older than 3 months of age: clinical practice guidelines by the Pediatric Infectious Diseases Society and the Infectious Diseases Society of America. Clin Infect Dis 2011; 53:e25-76.
115. Parrish SC, Myers J, Lazarus A. Nontuberculous mycobacterial pulmonary infections in non-HIV patients. Postgrad Med 2008; 120:78-86.
116. Kalil AC, Metersky ML, Klompas M, et al. Management of adults with hospital-acquired and ventilator-associated pneumonia: 2016 clinical practice guidelines by the Infectious Diseases Society of America and the American Thoracic Society. Clin Infect Dis 2016; 63:e61-111.
117. Corcoran JP, Wrightson JM, Belcher E, Decamp MM, Feller-Kopman D, Rahman NM. Pleural infection: past, present, and future directions. Lancet Respir Med 2015; 563-77.
118. Maskell NA, Daview CWH, Nunn AJ, et al; First Multicenter Intrapleural Sepsis Trial (MIST1). U. K. controlled trial of intrapleural streptokinase for pleural infection. N Engl J Med 2005; 865-74.
119. Menzies SM, Rahman NM, Wrightson JM, et al. Blood culture bottle culture of pleural fluid in pleural infection. Thorax 2011; 66:658-62.
120. Wilcox ME, Chong CA, Stanbrook MB, Tricco AC, Wong C, Straus SE. Does this patient have an exudative pleural effusion The Rational Clinical Examination systematic review. JAMA 2014; 311:2422-31.
121. Lewinsohn DM, Leonard MK, LoBue PA, et al. Official American Thoracic Society/Infectious Diseases Society of America/Centers for Disease Control and Prevention clinical practice guidelines: diagnosis of tuberculosis in adults and children. Clin Infect Dis 2017; 64:e1-33.
122. Gopi A, Madhavan SM, Sharma SK, Sahn SA. Diagnosis and treatment of tuberculous pleural effusion in 2006. Chest 2007; 131:880-9.
123. Parkins MD, Floto RA. Emerging bacterial pathogens and changing concepts of bacterial pathogenesis in cystic fibrosis. J Cyst Fibros 2015; 14:293-304.
124. Lipuma JJ. The changing microbial epidemiology in cystic fibrosis. Clin Microbiol Rev 2010; 23:299-323.
125. Hickey PW, Sutton DA, Fothergill AW, et al. Trichosporon mycotoxinivorans, a novel respiratory pathogen in patients with cystic fibrosis. J Clin Microbiol 2009; 47:3091-7.
126. Gilligan PH, Kiska DL, Appleman MD, eds. Cumitech 43: cystic fibrosis microbiology. Washington, DC: ASM Press, 2006.
127. Pihet M, Carrere J, Cimon B, et al. Occurrence and relevance of filamentous fungi in respiratory secretions of patients with cystic fibrosis-a review. Med Mycol 2009; 47:387-97.
128. Carroll KC, Adams LL. Etiology, epidemiology and diagnosis of lower respiratory tract infections in immunocompromised patients. Microbiol Spec 2016; 4:DMIH2-0029.
129. Sangoi AR, Rogers WM, Longacre TA, Montoya JG, Baron EJ, Banaei N. Challenges and pitfalls of morphologic identification of fungal infections in histologic and cytologic specimens: a ten-year retrospective review at a single institution. Am J Clin Pathol 2009; 131:364-75.
130. Chartrand C, Leeflang MM, Minion J, Brewer T, Pai M. Accuracy of rapid influenza diagnostic tests: a meta-analysis. Ann Intern Med 2012; 156:500-11.
131. Sinclair A, Xie X, Teltscher M, Dendukuri N. Systematic review and meta-analysis of a urine-based pneumococcal antigen test for diagnosis of community-acquired pneumonia caused by Streptococcus pneumoniae. J Clin Microbiol 2013; 51:2303-10.
132. Bordetella cultures 3. 11. 6. In: Clinical microbiology procedures handbook, 4th ed. Leber AL, ed. Washington, DC: ASM Press, 2016.
133. Zou M, Tang L, Zhao S, et al. Systematic review and meta-analysis of detecting galactomannan in bronchoalveolar lavage fluid for diagnosing invasive aspergillosis. PLoS One 2012; 7:1-12.
134. Onishi A, Sugiyama D, Kogata Y, et al. Diagnostic accuracy of serum 1, 3-?-D-glucan for Pneumocystis jiroveci pneumonia, invasive candidiasis, and invasive aspergillosis: systematic review and meta-analysis. J Clin Microbiol 2012; 50:7-15.
135. Cincinnati Children's Hospital Medical Center. Evidence-based clinical care guideline for acute gastroenteritis (AGE) in children aged 2 months through 5 years. Cincinnati, OH: Cincinnati Children's Hospital Medical Center, 2006.
136. Chey WD, Leontiadis GI, Howden CW, Moss SF. ACG clinical guideline: treatment of Helicobacter pylori infection. Am J Gastroenterol 2017; 112:212-39.
137. Megraud F, Lehours P. Helicobacter pylori detection and antimicrobial susceptibility testing. Clin Microbiol Rev 2007; 20:280-322.
138. Binnicker MJ. Multiplex molecular panels for diagnosis of gastrointestinal infection: performance, result interpretation, and cost-effectiveness. J Clin Microbiol 2015; 53:3723-8.
139. Rohner P, Pittet D, Pepey B, Nije-Kinge T, Auckenthaler R. Etiological agents of infectious diarrhea: implications for requests for microbial culture. J Clin Microbiol 1997; 35:1427-32.
140. Church DL, Cadrain G, Kabani A, Jadavji T, Trevenen C. Practice guidelines for ordering stool cultures in a pediatric population. Alberta Children's Hospital, Calgary, Alberta, Canada. Am J Clin Pathol 1995; 103:149-53.
141. Kotton CN, Lankowski AJ, Hohmann EL. Comparison of rectal swabs with fecal cultures for detection of Salmonella Typhimurium in adult volunteers. Diag Microbiol Infect Dis 2006; 56:123-6.
142. Rishmawi N, Ghneim R, Kattan R, et al. Survival of fastidious and nonfastidious aerobic bacteria in three bacterial transport swab systems. J Clin Microbiol 2007; 45:1278-83.
143. [No authors listed]. Importance of culture confirmation of Shiga toxin-producing Escherichia coli infection as illustrated by outbreaks of gastroenteritis-New York and North Carolina, 2005. MMWR Morb Mortal Wkly Rep 2006; 55:1042-598.
144. Riddle MS, DuPont HL, Connor BA. ACG clinical guideline: diagnosis, treatment, and prevention of acute diarrheal infections in adults. Am J Gastroenterol 2016; 111:602-22.
145. Lindstrom M, Korkeala H. Laboratory diagnostics of botulism. Clin Microbiol Rev 2006; 19:298-314.
146. Reller ME, Lema CA, Perl TM, et al. Yield of stool culture with isolate toxin testing versus a two-step algorithm including stool toxin testing for detection of toxigenic Clostridium difficile. J Clin Microbiol 2007; 45:3601-5.
147. Burnham CA, Caroll KC. Clostriduim difficile infection: an ongoing conundrum for clinicians and clinical laboratories. Clin Microbiol Rev 2013; 26:604-32.
148. Surawicz CM, Brandt LJ, Binion DG, et al. Guidelines for diagnosis, treatment, and prevention of Clostridium difficile infections. Am J Gastroenterol 2013; 108:478-98.
149. Luo RF, Banaei N. Is repeat PCR needed for diagnosis of Clostridium difficile infection J Clin Microbiol 2010; 48:3738-41.
150. McDonald CL, Gerding DN, Johnson S, et al. Clinical practice guidelines for Clostridium difficile in adults and children: 2017 update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA). Clin Infect Dis 2018; 66:e1-48.
151. Sammons JS, Toltzis P. Pitfalls in diagnosis of pediatric Clostridium difficile infection. Infect Dis Clin N Am 2015; 29:465-76.
152. McDonald LC, Killgore GE, Thompson A, et al. An epidemic, toxin gene-variant strain of Clostridium difficile. N Engl J Med 2005; 353:2433-41.
153. Warny M, Pepin J, Fang A, et al. Toxin production by an emerging strain of Clostridium difficile associated with outbreaks of severe disease in North America and Europe. Lancet 2005; 366:1079-84.
154. Cartwright CP. Utility of multiple-stool-specimen ova and parasite examinations in a high-prevalence setting. J Clin Microbiol 1999; 37:2408-11.
155. Rosenblatt JE. Clinical importance of adequately performed stool ova and parasite examinations. Clin Infect Dis 2006; 42:979-80.
156. Tanyuksel M, Petri WA, Jr. Laboratory diagnosis of amebiasis. Clin Microbiol Rev 2003; 16:713-29.
157. Kioumis IP, Kuti JL, Nicolau DP. Intra-abdominal infections: considerations for the use of the carbapenems. Expert Opin Pharmacother 2007; 8:167-82.
158. Levison ME, Bush LM. Peritonitis and Intraperitoneal abscesses. In: Mandell GL, Bennett JE, Dolin R, eds. Mandell, Douglas, and Bennett's principles and practice of infectious diseases. 6th ed. Philadelphia, PA: Elsevier Churchill Livingstone, 2005:927-51.
159. Strauss E, Caly WR. Spontaneous bacterial peritonitis: a therapeutic update. Expert Rev Anti Infect Ther 2006; 4:249-60.
160. Montravers P, Guglielminotti J, Zappella N, et al. Clinical features and outcome of postoperative peritonitis following bariatric surgery. Obes Surg 2013; 23:1536-44.
161. Montravers P, Augustin P, Zappella N, et al. Diagnosis and management of the postoperative surgical and medical complications of bariatric surgery. Anaesth Crit Care Pain Med 2015; 34:45-52.
162. Solomkin JS, Mazuski JE, Baron EJ, et al. Guidelines for the selection of anti-infective agents for complicated intra-abdominal infections. Clin Infect Dis 2003; 37:997-1005.
163. Troidle L, Finkelstein F. Treatment and outcome of CPD-associated peritonitis. Ann Clin Microbiol Antimicrob 2006; 5:6.
164. von Graevenitz A, Amsterdam D. Microbiological aspects of peritonitis associated with continuous ambulatory peritoneal dialysis. Clin Microbiol Rev 1992; 5:36-48.
165. Bourbeau P, Riley J, Heiter BJ, Master R, Young C, Pierson C. Use of the BacT/ Alert blood culture system for culture of sterile body fluids other than blood. J Clin Microbiol 1998; 36:3273-7.
166. Johannsen EC, Madoff LC. Infections of the liver and biliary system. In: Mandell GL, Bennett JE, Dolin R, eds. Mandell, Douglas, and Bennett's principles and practice of infectious diseases. 6th ed. Philadelphia, PA: Elsevier Churchill Livingstone, 2005:951-59.
167. Mohsen AH, Green ST, Read RC, McKendrick MW. Liver abscess in adults: ten years experience in a UK centre. QJM 2002; 95:797-802.
168. Wong WM, Wong BC, Hui CK, et al. Pyogenic liver abscess: retrospective analysis of 80 cases over a 10-year period. J Gastroenterol Hepatol 2002; 17:1001-7.
169. Haque R, Huston CD, Hughes M, Houpt E, Petri WA, Jr. Amebiasis. N Engl J Med 2003; 348:1565-73.
170. Ooi LL, Leong SS. Splenic abscesses from 1987 to 1995. Am J Surg 1997; 174:87-93.
171. Madoff LC. Splenic abscess. In: Mandell GL, Bennett JE, Dolin R, ed. Mandell, Douglas, and Bennett's principles and practice of infectious diseases. 6th ed. Philadelphia, PA: Elsevier Churchill Livingstone, 2005:967-68.
172. Baron MJ, Madoff LC. Pancreatic infections. In: Mandell GL, Bennett JE, Dolin R, eds. Mandell, Douglas, and Bennett's principles and practice of infectious diseases. 6th ed. Philadelphia, PA: Elsevier Churchill Livingstone, 2005:959-66.
173. Forsmark CE, Baillie J. AGA Institute technical review on acute pancreatitis. Gastroenterology 2007; 132:2022-44.
174. Yagupsky P. Kingella kingae: carriage, transmission, and disease. Clin Microbiol Rev 2015; 28:54-79.
175. Lipsky BA, Berendt AR, Cornia PB, et al. 2012 Infectious Diseases Society of America clinical practice guideline for the diagnosis and treatment of diabetic foot infections. Clin Infect Dis 2012; 54:e132-73.
176. Berbari EF, Kanj SS, Kowalski TJ, et al. 2015 Infectious Diseases Society of America (IDSA) clinical practice guidelines for the diagnosis and treatment of native vertebral osteomyelitis in adults. Clin Infect Dis 2015; 61:e26-46.
177. Tande AJ, Patel R. Prosthetic joint infection. Clin Microbiol Rev 2014; 27:302-45.
178. Osmon DR, Berbari EF, Berendt AR, et al. Diagnosis and management of prosthetic joint infection: clinical practice guidelines by the Infectious Diseases Society of America. Clin Infect Dis 2013; 56:e1-25.
179. Peel TN, Spelman T, Dylla BL, et al. Optimal periprosthetic tissue specimen number for diagnosis of prosthetic joint infection. J Clin Microbiol 2017; 55:234-43.
180. Roux AL, Sivadon-Tardy V, Bauer T, et al. Diagnosis of prosthetic joint infection by beadmill processing of a periprosthetic specimen. Clin Microbiol Infect 2011; 17:447-50.
181. Trampuz A, Piper KE, Jacobson MJ, et al. Sonication of removed hip and knee prostheses for diagnosis of infection. N Engl J Med 2007; 357:654-63.
182. 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 the Infectious Diseases Society of America and the European Society for Microbiology and Infectious Diseases. Clin Infect Dis 2011; 52:e103-120.
183. Nicolle LE, Bradley S, Colgan R, et al. Infectious Diseases Society of America guidelines for the diagnosis and treatment of asymptomatic bacteriuria in adults. Clin Infect Dis 2005; 40:643-54. Erratum appears in Clin Infect Dis 2005; 40:1556.
184. McCarter YS, Burd EM, Hall GS, Zervos M, eds. Cumitech 2C: laboratory diagnosis of urinary tract infections. Washington, DC: ASM Press, 2009.
185. Bennett JE, Dolin R, Blaser MJ. Mandell, Douglas, and Bennett's principles and practice of infectious diseases. New York: Elsevier Health Sciences, 2014.
186. Pfaller M, Ringenberg B, Rames L, Hegeman J, Koontz F. The usefulness of screening tests for pyuria in combination with culture in the diagnosis of urinary tract infection. Diagn Microbiol Infect Dis 1987; 6:207-15.
187. Clarridge JE, Johnson JR, Pezzlo MT. Cumitech 2B, Laboratory diagnosis of urinary tract infections. Washington, DC: American Society of Microbiology, 1998.
188. Subcommittee on Urinary Tract Infection, Steering Committee on Quality Improvement and Management. Urinary tract infection: clinical practice guideline for the diagnosis and management of the initial UTI in febrile infants and children 2 to 24 months. Pediatrics 2011; 128:595-610.
189. Doern CD, Richardson SE. Diagnosis of urinary tract infections in children. J Clin Microbiol 2016 54:2233-42.
190. Krieger JN. Prostatitis revisited: new definitions, new approaches. Infect Dis Clinics N Am 2003; 17:395-409.
191. Meares EM Jr. Acute and chronic prostatitis: diagnosis and treatment. Infect Dis Clin North Am 1987; 1:855-73.
192. Schaeffer AJ. Clinical practice. Chronic prostatitis and the chronic pelvic pain syndrome. N Engl J Med 2006; 355:1690-8.
193. Konkle KS, Clemens JQ. New paradigms in understanding chronic pelvic pain syndrome. Curr Urol Rep 2011; 12:278-83.
194. Hagley M. Epididymo-orchitis and epididymitis: a review of causes and management of unusual forms. Int J STD AIDS 2003; 14:372-7; quiz 378.
195. Centers for Disease Control and Prevention. Sexually transmitted disease treatment guidelines. MMWR Morb Mortal Wkly Rep 2015; 64:1-135.
196. Centers for Disease Control and Prevention. Sexually transmitted diseases treatment guidelines, 2010. MMWR Morb Mortal Wkly Rep 2010; 59:58-61.
197. Augenbraun MH. Genital skin and mucous membrane lesions. In: Bennett JE, Dolin R, Blaser MJ, eds. Mandell, Douglas, and Bennett's principles and practice of infectious diseases. 8th ed. Vol 1. Philadelphia, PA: Elsevier, 2014.
198. Hobbs MM, Lapple DM, Lawing LF, et al. Methods for detection of Trichomonas vaginalis in the male partners of infected women: implications for control of trichomoniasis. J Clin Microbiol 2006; 44:3994-99.
199. Massad LS, Einstein MH, Huh WK. 2012 Updated consensus guidelines for the management of abnormal cervical cancer screening tests and cancer precursors. J Lower Gen Tract Dis 2013; 17:S1YS27.
200. Wright TC, Massad LS, Dunton CJ, et al. 2006 consensus guidelines for the management of women with abnormal cervical cancer screening tests. Am J Obstet Gynecol 2007; 197:346-55.
201. Wright TC, Stoler MH, Behrens CM, et al. Primary cervical cancer screening with human papillomavirus: end of study results from the ATHENA study using HPV as the first-line screening test. Gynecol Oncol 2015; 136:189-97.
202. Huh WK, Ault KA, Chelmow D, et al. Use of primary high-risk human papillomavirus testing for cervical cancer screening: interim clinical guidance. J Low Genit Tract Dis 2015; 19:91-6.
203. Stoler MH, Austin RM, Zhao C. Point counter-point: cervical cancer screening should be done by primary papilloma virus testing with genotyping and reflex cytology for women over the age of 25. J Clin Microbiol 2015; 53:2798-804.
204. Centers for Disease Control and Prevention. Syphilis testing algorithms using treponemal tests for initial screening-four laboratories, New York City, 2005-2006. MMWR Morb Mortal Wkly Rep 2008; 57:872-5.
205. deVoux A, Kent JB, Macomber K, et al, Notes from the field: cluster of lympongranuloma venereum cases among men who have sex with men-Michigan. MMWR Morb Mortal Wkly Rep 2016; 65:920-1.
206. McCormack W, Augenbraun MH. Vulvovaginitis and cervicitis. In: Bennett JE Dolin R, Blaser MJ, eds. Mandell, Douglas, and Bennett's principles and practice of infectious diseases. 8th ed. Vol 1. Philadelphia, PA: Elsevier, 2014.
207. Muzny CA, Blackburn RJ, Sinsky RJ, et al. Added benefit of nucleic acid amplification testing for the diagnosis of Trichomonas vaginalis among men and women attending a sexually transmitted diseases clinic. Clin Infect Dis 2014; 59:834-41.
208. Ginnocchio CC, Chapin KC, Smith JS, et al. Prevalence of Trichomonas vaginalis and coinfection with Chlamydia trachomatis and Neisseria gonorrhoeae in the United States as determined by the APTIMA Trichomonas vaginalis nucleic acid amplification assay. J Clin Microbiol 2012. doi:10. 1128/ JCM. 00748-12JCM. 00748-12.
209. Schwebke JR. Trichomonas vaginalis. In: Bennett JE, Dolin R, Blaser MJ, eds. Mandell, Douglas, and Bennett's principles and practice of infectious diseases. 8th ed. Vol 2. Philadelphia, PA: Elsevier, 2014.
210. Cartwright CP, Lembke BD, Ramachandran K, et al. Development and validation of a semiquantitative, multitarget PCR assay for diagnosis of bacterial vaginosis. J Clin Microbiol 2012; 50:2321-9
211. Huppert J, Mortensen J, Reed J, et al. Rapid antigen testing compares favorably with transcription-mediated amplification assay for the detection of Trichomonas vaginalis in young women. Clin Infect Dis 2007; 45:194-8.
212. Kusters JG, Reuland EA, Bouter S, et al. A multiplex real-time PCR assay for routine diagnosis of bacterial vaginosis. Eur J Clin Microbiol Infect Dis 2015; 34:1779-85.
213. Dois JA, Molenaar D, van der Helm JJ, et al. Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity. BMC Infect Dis 2016; 16:1-19.
214. Andrea SB, Chapin KC. Comparison of APTIMA Trichomonas vaginalis transcription-mediated amplification assay and BD Affirm VPIII for detection of Trichomonas vaginalis in symptomatic women: performance parameters and epidemiologic implications. J Clin Microbiol 2011; 49:866-9.
215. Munson E, Bykowski H, Munson KL, et al. Clinical laboratory assessment of Mycoplasma genitalium transcription-mediated amplification using primary female urogenital specimens. J Clin Microbiol 2016; 54:432-8.
216. Tan L. Clinical and diagnostic challenge of antimicrobial resistance in Mycoplasma genitalium. MLO Med Lab Obs 2017; 2017:8-12.
217. Augenbraun MH, McCormack W. Urethritis. In: Bennett JE, Dolin R, Blaser MJ, eds. Mandell, Douglas, and Bennett's principles and practice of infectious diseases. 8th ed. Vol 1. Philadelphia, PA: Elsevier, 2014.
218. Soper D. Infections of the female pelvis. In: Bennett JE, Dolin R, Blaser MJ, eds. Mandell, Douglas, and Bennett's principles and practice of infectious diseases. 8th ed. Vol 1. Philadelphia, PA: Elsevier, 2014.
219. Westhoff C. IUDs and colonization or infection with Actinomyces. Contraception 2007; 75(6 Suppl):S48-50.
220. Chan PA, Robinette A, Montgomery M, et al. Extragenital infections caused by Chlamydia trachomatis and Neisseria gonorrhoeae: a review of the literature. Infect Dis Obstet Gynecol 2016. doi:10. 1155/2016/5758387.
221. Girardet RG, Lahoti S, Howard LA, et al. Epidemiology of sexually transmitted infections in suspected child victims of sexual assault. Pediatrics 2009; 124:79-86.
222. Silk BJ, Date KA, Jackson KA, et al. Invasive listeriosis in the Foodborne Diseases Active Surveillance Network (FoodNet), 2004-2009: further targeted prevention needed for higher-risk groups. Clin Infect Dis 2012; 54(Suppl 5):S396-404.
223. Stevens DL, Bisno AL, Chambers HF, et al. Practice guidelines for the diagnosis and management of skin and soft-tissue infections: 2014 update by the Infectious Disease Society of America. Clin Infect Dis 2014; 59:e10-52.
224. Church D, Elsayed S, Reid O, Winston B, Lindsay R. Burn wound infections. Clin Microbiol Rev 2006; 19:403-34.
225. Thomson RB Jr. Specimen collection, transport, and processing: bacteriology. In: Murray PR Baron EJ, Jorgensen JH, Landry ML, Pfaller MA, ed. Manual of Clinical Microbiology. Washington, DC: ASM Press, 2007:294.
226. Merriam CV, Fernandez HT, Citron DM, Tyrrell KL, Warren YA, Goldstein EJ. Bacteriology of human bite wound infections. Anaerobe 2003; 9:83-6.
227. Brook I. Microbiology and management of human and animal bite wound infections. Prim Care 2003; 30:25-39, v.
228. Revis DR Jr, Spanierman CS. Human bite infections, 2006. Available at: www. emedicine. com/ped/TOPIC246. htm. Accessed 5 June 2018.
229. Conrads G, Citron DM, Mutters R, Jang S, Goldstein EJ. Fusobacterium canifelinum sp. nov., from the oral cavity of cats and dogs. Syst Appl Microbiol 2004; 27:407-13.
230. Dalamaga M, Karmaniolas K, Chavelas C, Liatis S, Matekovits H, Migdalis I. Pseudomonas fluorescens cutaneous abscess and recurrent bacteremia following a dog bite. Int J Dermatol 2005; 44:347-9.
231. Deshmukh PM, Camp CJ, Rose FB, Narayanan S. Capnocytophaga canimorsus sepsis with purpura fulminans and symmetrical gangrene following a dog bite in a shelter employee. Am J Med Sci 2004; 327:369-72.
232. Kaiser RM, Garman RL, Bruce MG, Weyant RS, Ashford DA. Clinical significance and epidemiology of NO-1, an unusual bacterium associated with dog and cat bites. Emerg Infect Dis 2002; 8:171-4.
233. Lawson PA, Malnick H, Collins MD, et al. Description of Kingella potus sp. nov., an organism isolated from a wound caused by an animal bite. J Clin Microbiol 2005; 43:3526-9.
234. Lehtinen VA, Kaukonen T, Ikaheimo I, Mahonen SM, Koskela M, Ylipalosaari P. Mycobacterium fortuitum infection after a brown bear bite. J Clin Microbiol 2005; 43:1009.
235. Ngan N, Morris A, de Chalain T. Mycobacterium fortuitum infection caused by a cat bite. N Z Med J 2005; 118:U1354.
236. Southern PM, Jr. Tenosynovitis caused by Mycobacterium kansasii associated with a dog bite. Am J Med Sci 2004; 327:258-61.
237. Talan DA, Citron DM, Abrahamian FM, Moran GJ, Goldstein EJ. Bacteriologic analysis of infected dog and cat bites. Emergency Medicine Animal Bite Infection Study Group. N Engl J Med 1999; 340:85-92.
238. von Graevenitz A, Bowman J, Del Notaro C, Ritzler M. Human infection with Halomonas venusta following fish bite. J Clin Microbiol 2000; 38:3123-4.
239. Abbott SL, Janda JM. Enterobacter cancerogenus ("Enterobacter taylorae") infections associated with severe trauma or crush injuries. Am J Clin Pathol 1997; 107:359-61.
240. Bisno AL. Cutaneous infections: microbiologic and epidemiologic considerations. Am J Med 1984; 76:172-9.
241. Brazier JS, Duerden BI, Hall V, et al. Isolation and identification of Clostridium spp. from infections associated with the injection of drugs: experiences of a microbiological investigation team. J Med Microbiol 2002; 51:985-9.
242. Eron LJ. Targeting lurking pathogens in acute traumatic and chronic wounds. J Emerg Med 1999; 17:189-95.
243. Barnard BM. Fighting surgical site infections, 2002. Available at: http://www. infectioncontroltoday. com/articles/241
244. Shafii SM, Donate G, Mannari RJ, Payne WG, Robson MC. Diagnostic dilemmas: cutaneous fungal bipolaris infection. Wounds 2006; 18:19-24.
245. Vennewald I, Wollina U. Cutaneous infections due to opportunistic molds: uncommon presentations. Clinics Dermatol 2005; 23:565-71.
246. Wormser GP, Dattwyler RJ, Shapiro ED, et al. The clinical assessment, treatment, and prevention of Lyme disease, human granulocytic anaplasmosis, and babesiosis: clinical practice guidelines by the Infectious Diseases Society of America. Clin Infect Dis 2006; 43:1089-134.
247. Pritt BS, Mead PS, et al. Identification of a novel pathogenic Borrelia species causing Lyme borreliosis with unusually high spirochaeaemia: a descriptive study. Lancet Infect Dis 2016; 16:556-64.
248. Lantos PM, Charini WA, Medoff G, et al. Final report of the Lyme disease review panel of the Infectious Diseases Society of America. Clin Infect Dis 2010; 51:1-5.
249. Kalish RA, McHugh G, Granquist J, Shea B, Ruthazer R, Steere AC. Persistence of immunoglobulin M or immunoglobulin G antibody responses to Borrelia burgdorferi 10-20 years after active Lyme disease. Clin Infect Dis 2001; 33:780-5.
250. Fallon BA, Pavlicova M, Coffino SW, Brewer C. A comparison of Lyme disease serologic test results from 4 laboratories in patients with persistent symptoms after antibiotic treatment. Clin Infect Dis 2014; 59:1705-10.
251. Centers for Disease Control and Prevention. Notice to readers. Caution regarding testing for Lyme disease. MMWR Morb Mortal Wkly Rep 2005; 54:125.
252. Molloy PJ, Weeks KE, Todd B, Wormser GP. Seroreactivity to the C6 peptide in Borrelia miyamotoi occurring in the northeastern United States. Clin Infect Dis 2018; 66:1407-10.
253. Chapman AS, Bakken JS, Folk SM, et al. Diagnosis and management of tickborne rickettsial diseases: Rocky Mountain spotted fever, ehrlichioses, and anaplasmosis- United States: a practical guide for physicians and other health-care and public health professionals. MMWR Recomm Rep 2006; 55:1-27.
254. Dumler JS, Madigan JE, Pusterla N, Bakken JS. Ehrlichioses in humans: epidemiology, clinical presentation, diagnosis, and treatment. Clin Infect Dis 2007; 45(Suppl 1):S45-51.
255. Parola P, Davoust B, Raoult D. Tick-and flea-borne rickettsial emerging zoonoses. Vet Res 2005; 36:469-92.
256. Rebaudet S, Parola P. Epidemiology of relapsing fever borreliosis in Europe. FEMS Immunol Med Microbiol 2006; 48:11-5.
257. Stanek G, Reiter M. The expanding Lyme Borrelia complex-clinical significance of genomic species Clin Microbiol Infect 2011; 17:487-93.
258. Reed KD. Laboratory testing for Lyme disease: possibilities and practicalities. J Clin Microbiol 2002; 40:319-24.
259. Aguero-Rosenfeld ME, Wang G, Schwartz I, Wormser GP. Diagnosis of Lyme borreliosis. Clin Microbiol Rev 2005; 18:484-509.
260. Wilske B. Diagnosis of Lyme borreliosis in Europe. Vector Borne Zoonotic Dis 2003; 3:215-27.
261. Aguero-Rosenfeld ME. Laboratory aspects of tick-borne diseases: Lyme, human granulocytic ehrlichiosis and babesiosis. Mt Sinai J Med 2003; 70:197-206.
262. Pritt BS, Sloan LM, Johnson DK, et al. Emergence of a new pathogenic Ehrlichia species, Wisconsin and Minnesota, 2009. N Engl J Med 2011; 365:422-9.
263. Landry ML. Immunoglobulin M for acute infection: true or false Clin Vaccine Immunol 2016; 23:540-5.
264. Clinical and Laboratory Standards Institute. Criteria for laboratory testing and diagnosis of human immunodeficiency virus infection; approved guideline. CLSI document M53-A. Wayne, PA: CLSI, 2011.
265. Centers for Disease Control and Prevention/Association of Public Health Laboratories. Laboratory testing for the diagnosis of HIV infection: updated recommendations. 2014. Available at http://stacks. cdc. gov/view/cdc/23447. Accessed 5 June 2018.
266. Zetola NM, Pilcher CD. Diagnosis and management of acute HIV infection. Infect Dis Clin N Am 2007; 21:19-48, vii.
267. Read JS. Diagnosis of HIV-1 infection in children younger than 18 months in the United States. Pediatrics 2007; 120:e1547-62.
268. Kimberlin DW. Diagnosis of herpes simplex virus in the era of polymerase chain reaction. Pediatr Infect Dis J 2006; 25:841-2.
269. Expert working group on HHV-6 and 7 laboratory diagnosis and testing. Can Commun Dis Rep 2000; 26(Suppl 4):i-iv, 1-27, i-iv passim.
270. Ramirez MM, Mastrobattista JM. Diagnosis and management of human parvovirus B19 infection. Clin Perinatol 2005; 32:697-704.
271. Anderson MJ, Higgins PG, Davis LR, et al. Experimental parvovirual infection in humans. J Infect Dis 1985; 152:257-65.
272. Heegaard ED, Brown KE. Human parvovirus B19. Clin Microbiol Rev 2002; 15:485-505.
273. Soderlung-Venemo M, Hokynar K, Nieminen J, Rautakorpi H, Hedman K. Persistence of human parvovirus B19 in human tissues. Pathol Biol (Paris) 2002; 50:307-16.
274. van Binnendijk RS, van den Hof S, van den Kerkhof H, et al. Evaluation of serological and virological tests in the diagnosis of clinical and subclinical measles virus infections during an outbreak of measles in the Netherlands. J Infect Dis 2003; 188:898-903.
275. Krause CH, Eastick K, Ogilvie MM. Real-time PCR for mumps diagnosis on clinical specimens-comparison with results of conventional methods of virus detection and nested PCR. J Clin Virol 2006; 37:184-9.
276. Blanckaert K, De Vriese AS. Current recommendations for diagnosis and management of polyoma BK virus nephropathy in renal transplant recipients. Nephrol Dial Transplant 2006; 21:3364-7.
277. Tang KF, Ooi EE. Diagnosis of dengue: an update. Exp Rev Anti Infect Ther 2012; 10:895-907.
278. Teixeira MG, Barreto ML. Diagnosis and management of dengue. BMJ 2009; 339:b4338.
279. Centers for Disease Control and Prevention. Positive test results for acute hepatitis A virus infection among persons with no recent history of acute hepatitis- United States, 2002-2004. MMWR Morb Mortal Wkly Rep 2005; 54:453-6.
280. Kamar N, Dalton HR, Abravanel F, Izopet J. Hepatitis E virus infection. Clin Microbiol Rev 2014; 27:116-38.
281. Gish RG, Locarnini SA. Chronic hepatitis B: current testing strategies. Clin Gastroenterol Hepatol 2006; 4:666-76.
282. Valsamakis A. Molecular testing in the diagnosis and management of chronic hepatitis B. Clin Microbiol Rev 2007; 20:426-39.
283. Centers for Disease Control and Prevention. Recommendations for the identification of chronic hepatitis C virus infection among persons born during 1945-1965. MMWR Recomm Rep 2012; 61(RR-4):1-32.
284. Petersen LR, Marfin AA. West Nile virus: a primer for the clinician. Ann Intern Med 2002; 137:173-9.
285. Mejas A, Ramilo. Parainfluenza viruses. In: Long S, Pickering LK, Prober CG, eds. Principles and practice of pediatric infectious diseases, 4th ed. Philadelphia, PA: Elsevier, 2012:1123-4.
286. Rasmussen SA, Jamieson DJ, Hoein MA, Petersen LR. Zika virus and birth defects. N Engl J Med 2016; 374:1981-7.
287. Oduyebo T, Petersen EE, Rasmussen SA, et al. Update: interim guidelines for health care providers caring for pregnant women and women of reproductive age with possible Zika virus exposure-United States, 2016. MMWR Morb Mortal Wkly Rep 2016; 65:122-7.
288. Guerrant RL, Walker DH, Weller PF. Tropical infectious diseases: principles, pathogens, and practice. 3rd ed. Philadelphia: Saunders, 2011.
289. Centers for Disease Control and Prevention. DPDx-laboratory identification of parasitic diseases of public health concern. Atlanta, GA: CDC, 2017.
290. Garcia LS. Diagnostic medical parasitology. 5th ed. Santa Monica, CA: ASM Press, 2007.
291. Garcia LS, Bullock-Iacullo SL, Fritsche TR, et al. Laboratory diagnosis of bloodborne parasitic disease; approved guidelines, NCCLS document M15-A. Wayne, PA: National Committee for Clinical Laboratory Standards, 2000.
292. World Health Organization. Malaria rapid diagnostics tests. Geneva, Switzerland: WHO, 2017.
293. Pritt BS. Plasmodium and Babesia. In: Jorgensen JH, Pfaller MA, Carroll KC, et al, eds. Manual of clinical microbiology, 11th ed. Washington, DC: ASM Press, 2015:2338-46.
294. Norgan AP, Arguello HE, Sloan LM, Fernholz EC, Pritt BP. A method for reducing the sloughing of thick blood films for malaria diagnosis. Malar J 2013; 12:231.
295. Mathison BA, Pritt BS. Update on malaria diagnostics and test utilization. J Clin Microbiol 2017; 55:2009-17.