Emerging and resistant infections

Annals of the American Thoracic Society

Volumn 11, Issue , 2014, Pages S193-S200

  Clancy, Cornelius J ^a,b   Kalil, Andre C ^c   Fowler, Vance G ^d   Ghedin, Elodie ^a   Kolls, Jay K ^a   Nguyen, M Hong ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^b VETERANS AFFAIRS MEDICAL CENTER   (United States)

^c UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

^d DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Influenza; Pneumonia; Staphylococcus aureus; Ventilator associated pneumonia

Indexed keywords

ANTIBIOTIC AGENT; ANTIINFECTIVE AGENT; OSELTAMIVIR; PROCALCITONIN;

ANTIBIOTIC RESISTANCE; ANTIBIOTIC THERAPY; BACILLI; CONFERENCE PAPER; DISEASE TRANSMISSION; DRUG USE; ENVIRONMENTAL FACTOR; GENE SEQUENCE; GENETIC TRAIT; GENETIC VARIABILITY; GENETICS; GENOME; HEALTH CARE ASSOCIATED PNEUMONIA; HEREDITY; HUMAN; IMMUNE RESPONSE; INFECTION SENSITIVITY; MOLECULAR EPIDEMIOLOGY; MOLECULAR EVOLUTION; MORTALITY; NONHUMAN; PSEUDOMONAS AERUGINOSA; STAPHYLOCOCCUS AUREUS; STAPHYLOCOCCUS INFECTION; TREATMENT DURATION; TREATMENT OUTCOME; VENTILATOR ASSOCIATED PNEUMONIA; RESPIRATORY TRACT INFECTIONS;

ANTI-BACTERIAL AGENTS; DRUG RESISTANCE, MICROBIAL; HUMANS; RESPIRATORY TRACT INFECTIONS;

EID: 84911484587     PISSN: 23296933     EISSN: 23256621     Source Type: Journal    
DOI: 10.1513/AnnalsATS.201402-069PL     Document Type: Conference Paper

References (56)

1. Boucher HW, Talbot GH, Bradley JS, Edwards JE, Gilbert D, Rice LB, Scheld M, Spellberg B, Bartlett J. Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America. Clin Infect Dis 2009;48:1-12.
2. National Nosocomial Infections Surveillance System. National Nosocomial Infections Surveillance (NNIS) System Report, data summary from January 1992 through June 2004, issued October 2004. Am J Infect Control 2004;32:470-485.
3. Rello J, Ollendorf DA, Oster G, Vera-Llonch M, Bellm L, Redman R, Kollef MH; VAP Outcomes Scientific Advisory Group. Epidemiology and outcomes of ventilator-associated pneumonia in a large US database. Chest 2002;122:2115-2121.
4. Chastre J, Wolff M, Fagon JY, Chevret S, Thomas F, Wermert D, Clementi E, Gonzalez J, Jusserand D, Asfar P, et al.; PneumA Trial Group. Comparison of 8 vs 15 days of antibiotic therapy for ventilator-associated pneumonia in adults: a randomized trial. JAMA 2003;290:2588-2598.
5. Singh N, Rogers P, Atwood CW, Wagener MM, Yu VL. Short-course empiric antibiotic therapy for patients with pulmonary infiltrates in the intensive care unit: a proposed solution for indiscriminate antibiotic prescription. Am J Respir Crit Care Med 2000;162:505-511.
6. Costelloe C, Metcalfe C, Lovering A, Mant D, Hay AD. Effect of antibiotic prescribing in primary care on antimicrobial resistance in individual patients: systematic review and meta-analysis. BMJ 2010;340:c2096.
7. Micek ST, Ward S, Fraser VJ, Kollef MH. A randomized controlled trial of an antibiotic discontinuation policy for clinically suspected ventilator-associated pneumonia. Chest 2004;125:1791-1799.
8. Berton DC, Kalil AC, Teixeira PJ. Quantitative versus qualitative cultures of respiratory secretions for clinical outcomes in patients with ventilator-associated pneumonia. Cochrane Database Syst Rev 2012;(1):CD006482.
9. Fekih Hassen M, Ayed S, Ben Sik Ali H, Gharbi R, Marghli S, Elatrous S. [Duration of antibiotic therapy for ventilator-associated pneumonia: comparison of 7 and 10 days: a pilot study] [Article in French]. Ann Fr Anesth Reanim 2009;28:16-23.
10. Pugh R, Grant C, Cooke RP, Dempsey G. Short-course versus prolonged-course antibiotic therapy for hospital-acquired pneumonia in critically ill adults. Cochrane Database Syst Rev 2011;(10):CD007577.
11. Müller B, Becker KL, Schächinger H, Rickenbacher PR, Huber PR, Zimmerli W, Ritz R. Calcitonin precursors are reliable markers of sepsis in a medical intensive care unit. Crit Care Med 2000;28:977-983.
12. Stolz D, Smyrnios N, Eggimann P, Pargger H, Thakkar N, Siegemund M, Marsch S, Azzola A, Rakic J, Mueller B, et al. Procalcitonin for reduced antibiotic exposure in ventilator-associated pneumonia: a randomised study. Eur Respir J 2009;34:1364-1375.
13. Bouadma L, Luyt CE, Tubach F, Cracco C, Alvarez A, Schwebel C, Schortgen F, Lasocki S, Veber B, Dehoux M, et al.; PRORATA trial group. Use of procalcitonin to reduce patients' exposure to antibiotics in intensive care units (PRORATA trial): a multicentre randomised controlled trial. Lancet 2010;375:463-474.
14. Schuetz P, Müller B, Christ-Crain M, Stolz D, Tamm M, Bouadma L, Luyt CE, Wolff M, Chastre J, Tubach F, et al. Procalcitonin to initiate or discontinue antibiotics in acute respiratory tract infections. Cochrane Database Syst Rev 2012;(9):CD007498.
15. Schuetz P, Briel M, Christ-Crain M, Stolz D, Bouadma L, Wolff M, Luyt CE, Chastre J, Tubach F, Kristoffersen KB, et al. Procalcitonin to guide initiation and duration of antibiotic treatment in acute respiratory infections: an individual patient data meta-analysis. Clin Infect Dis 2012;55:651-662.
16. Heyland DK, Johnson AP, Reynolds SC, Muscedere J. Procalcitonin for reduced antibiotic exposure in the critical care setting: a systematic review and an economic evaluation. Crit Care Med 2011;39:1792-1799.
17. Kopterides P, Siempos II, Tsangaris I, Tsantes A, Armaganidis A. Procalcitonin-guided algorithms of antibiotic therapy in the intensive care unit: a systematic review and meta-analysis of randomized controlled trials. Crit Care Med 2010;38:2229-2241.
18. Fowler VG Jr, Olsen MK, Corey GR, Woods CW, Cabell CH, Reller LB, Cheng AC, Dudley T, Oddone EZ. Clinical identifiers of complicated Staphylococcus aureus bacteremia. Arch Intern Med 2003;163:2066-2072.
19. Fowler VG Jr, Miro JM, Hoen B, Cabell CH, Abrutyn E, Rubinstein E, Corey GR, Spelman D, Bradley SF, Barsic B, et al.; ICE Investigators. Staphylococcus aureus endocarditis: a consequence of medical progress. JAMA 2005;293:3012-3021.
20. van Rijen MM, Bonten M, Wenzel RP, Kluytmans JA. Intranasal mupirocin for reduction of Staphylococcus aureus infections in surgical patients with nasal carriage: a systematic review. J Antimicrob Chemother 2008;61:254-261.
21. Bode LG, Kluytmans JA, Wertheim HF, Bogaers D, Vandenbroucke-Grauls CM, Roosendaal R, Troelstra A, Box AT, Voss A, van der Tweel I, et al. Preventing surgical-site infections in nasal carriers of Staphylococcus aureus. N Engl J Med 2010;362:9-17.
22. Huang SS, Septimus E, Kleinman K, Moody J, Hickok J, Avery TR, Lankiewicz J, Gombosev A, Terpstra L, Hartford F, et al.; CDC Prevention Epicenters Program; AHRQ DECIDE Network and Healthcare-Associated Infections Program. Targeted versus universal decolonization to prevent ICU infection. N Engl J Med 2013;368:2255-2265.
23. Lowy FD. Staphylococcus aureus infections. N Engl J Med 1998;339:520-532.
24. Fowler VG Jr, Nelson CL, McIntyre LM, Kreiswirth BN, Monk A, Archer GL, Federspiel J, Naidich S, Remortel B, Rude T, et al. Potential associations between hematogenous complications and bacterial genotype in Staphylococcus aureus infection. J Infect Dis 2007;196:738-747.
25. Nienaber JJ, Sharma Kuinkel BK, Clarke-Pearson M, Lamlertthon S, Park L, Rude TH, Barriere S, Woods CW, Chu VH, Marín M, et al.; International Collaboration on Endocarditis-Microbiology Investigators. Methicillin-susceptible Staphylococcus aureus endocarditis isolates are associated with clonal complex 30 genotype and a distinct repertoire of enterotoxins and adhesins. J Infect Dis 2011;204:704-713.
26. Lower SK, Lamlertthon S, Casillas-Ituarte NN, Lins RD, Yongsunthon R, Taylor ES, DiBartola AC, Edmonson C, McIntyre LM, Reller LB, et al. Polymorphisms in fibronectin binding protein A of Staphylococcus aureus are associated with infection of cardiovascular devices. Proc Natl Acad Sci USA 2011;108:18372-18377.
27. Proctor RA, Mosher DF, Olbrantz PJ. Fibronectin binding to Staphylococcus aureus. J Biol Chem 1982;257:14788-14794.
28. Hill PC, Wong CG, Voss LM, Taylor SL, Pottumarthy S, Drinkovic D, Morris AJ. Prospective study of 125 cases of Staphylococcus aureus bacteremia in children in New Zealand. Pediatr Infect Dis J 2001;20:868-873.
29. Embil J, Ramotar K, Romance L, Alfa M, Conly J, Cronk S, Taylor G, Sutherland B, Louie T, Henderson E, et al. Methicillin-resistant Staphylococcus aureus in tertiary care institutions on the Canadian prairies 1990-1992. Infect Control Hosp Epidemiol 1994;15:646-651.
30. Maguire GP, Arthur AD, Boustead PJ, Dwyer B, Currie BJ. Clinical experience and outcomes of community-acquired and nosocomial methicillin-resistant Staphylococcus aureus in a northern Australian hospital. J Hosp Infect 1998;38:273-281.
31. Klevens RM, Morrison MA, Nadle J, Petit S, Gershman K, Ray S, Harrison LH, Lynfield R, Dumyati G, Townes JM, et al.; Active Bacterial Core surveillance (ABCs) MRSA Investigators. Invasive methicillin-resistant Staphylococcus aureus infections in the United States. JAMA 2007;298:1763-1771.
32. Miller LS, Cho JS. Immunity against Staphylococcus aureus cutaneous infections. Nat Rev Immunol 2011;11:505-518.
33. Netea MG, van der Meer JW. Immunodeficiency and genetic defects of pattern-recognition receptors. N Engl J Med 2011;364:60-70.
34. von Köckritz-Blickwede M, Rohde M, Oehmcke S, Miller LS, Cheung AL, Herwald H, Foster S, Medina E. Immunological mechanisms underlying the genetic predisposition to severe Staphylococcus aureus infection in the mouse model. Am J Pathol 2008;173:1657-1668.
35. Ahn SH, Deshmukh H, Johnson N, Cowell LG, Rude TH, Scott WK, Nelson CL, Zaas AK, Marchuk DA, Keum S, et al. Two genes on A/J chromosome 18 are associated with susceptibility to Staphylococcus aureus infection by combined microarray and QTL analyses. PLoS Pathog 2010;6:e1001088.
36. Seok J, Warren HS, Cuenca AG, Mindrinos MN, Baker HV, Xu W, Richards DR, McDonald-Smith GP, Gao H, Hennessy L, et al.; Inflammation and Host Response to Injury, Large Scale Collaborative Research Program. Genomic responses in mouse models poorly mimic human in flammatory diseases. Proc Natl Acad Sci USA 2013;110:3507-3512.
37. Ahn SH, Tsalik EL, Cyr DD, Zhang Y, van Velkinburgh JC, Langley RJ, Glickman SW, Cairns CB, Zaas AK, Rivers EP, et al. Gene expression-based classifiers identify Staphylococcus aureus infection in mice and humans. PLoS ONE 2013;8:e48979.
38. Nelson CL, Pelak K, Podgoreanu MV, Ahn SH, Scott WK, Allen AS, Cowell LG, Rude TH, Zhang Y, Tong A, et al. A genome-wide association study of variants associated with acquisition of Staphylococcus aureus bacteremia in a healthcare setting. BMC Infect Dis 2014;14:83.
39. Dugan VG, Saira K, Ghedin E. Large-scale sequencing and the natural history of model human RNA viruses. Future Virol 2012;7:563-573.
40. Steinhauer DA, Domingo E, Holland JJ. Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase. Gene 1992;122:281-288.
41. Bragstad K, Nielsen LP, Fomsgaard A. The evolution of human influenza A viruses from 1999 to 2006: a complete genome study. Virol J 2008;5:40.
42. Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, Holmes EC. The genomic and epidemiological dynamics of human influenza A virus. Nature 2008;453:615-619.
43. Bahl J, Nelson MI, Chan KH, Chen R, Vijaykrishna D, Halpin RA, Stockwell TB, Lin X, Wentworth DE, Ghedin E, et al. Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans. Proc Natl Acad Sci USA 2011;108:19359-19364.
44. Nelson MI, Edelman L, Spiro DJ, Boyne AR, Bera J, Halpin R, Sengamalay N, Ghedin E, Miller MA, Simonsen L, et al. Molecular epidemiology of A/H3N2 and A/H1N1 influenza virus during a single epidemic season in the United States. PLoS Pathog 2008;4:e1000133.
45. Nelson MI, Viboud C, Simonsen L, Bennett RT, Griesemer SB, St George K, Taylor J, Spiro DJ, Sengamalay NA, Ghedin E, et al. Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918. PLoS Pathog 2008;4:e1000012.
46. Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, Sessions WM, Xu X, Skepner E, Deyde V, et al. Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 2009;325:197-201.
47. Nelson M, Spiro D, Wentworth D, Beck E, Fan J, Ghedin E, Halpin R, Bera J, Hine E, Proudfoot K, et al. The early diversification of influenza A/H1N1pdm. PLoS Curr 2009;1:RRN1126.
48. Nelson MI, Tan Y, Ghedin E, Wentworth DE, St George K, Edelman L, Beck ET, Fan J, Lam TT, Kumar S, et al. Phylogeography of the spring and fall waves of the H1N1/09 pandemic influenza virus in the United States. J Virol 2011;85:828-834.
49. Holmes EC, Ghedin E, Halpin RA, Stockwell TB, Zhang XQ, Fleming R, Davey R, Benson CA, Mehta S, Taplitz R, et al.; INSIGHT FLU002 Study Group. Extensive geographical mixing of 2009 human H1N1 influenza A virus in a single university community. J Virol 2011;85:6923-6929.
50. Ghedin E, Wentworth DE, Halpin RA, Lin X, Bera J, DePasse J, Fitch A, Griesemer S, Hine E, Katzel DA, et al. Unseasonal transmission of H3N2 influenza A virus during the swine-origin H1N1 pandemic. J Virol 2010;84:5715-5718.
51. Ghedin E, Holmes EC, DePasse JV, Pinilla LT, Fitch A, Hamelin ME, Papenburg J, Boivin G. Presence of oseltamivir-resistant pandemic A/H1N1 minor variants before drug therapy with subsequent selection and transmission. J Infect Dis 2012;206:1504-1511.
52. Baz M, Abed Y, Papenburg J, Bouhy X, Hamelin ME, Boivin G. Emergence of oseltamivir-resistant pandemic H1N1 virus during prophylaxis. N Engl J Med 2009;361:2296-2297.
53. Cordey S, Junier T, Gerlach D, Gobbini F, Farinelli L, Zdobnov EM, Winther B, Tapparel C, Kaiser L. Rhinovirus genome evolution during experimental human infection. PLoS ONE 2010;5:e10588.
54. Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, Salazar MG, Sun C, Grayson T, Wang S, Li H, et al. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci USA 2008;105:7552-7557.
55. Baz M, Abed Y, McDonald J, Boivin G. Characterization of multidrug-resistant infl uenza A/H3N2 viruses shed during 1 year by an immunocompromised child. Clin Infect Dis 2006;43:1555-1561.
56. Poon LL, Chan KH, Chu DK, Fung CC, Cheng CK, Ip DK, Leung GM, Peiris JS, Cowling BJ. Viral genetic sequence variations in pandemic H1N1/2009 and seasonal H3N2 influenza viruses within an individual, a household and a community. J Clin Virol 2011;52:146-150.