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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
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Disease relevance of Microbiology

  • We retrospectively surveyed microbiology records from all 10 hospitals in Pima County, Arizona, to identify patients who had Streptococcus pyogenes isolated from blood, sterile body fluid, or tissue biopsy specimens between April 1985 and March 1990 [1].
  • Isolates were obtained from the Clinical Microbiology Laboratory. RESULTS: Four hundred thirty-two isolates of ceftazidime-resistant Klebsiella pneumoniae were recovered during a 19-month study period [2].
  • Does yogurt enriched with Bifidobacterium longum affect colonic microbiology and fecal metabolites in health subjects [3]?
  • Clinical presentation and assessment of CF lung disease including diagnostic microbiology and other measures of pulmonary health are reviewed [4].
  • To determine the importance of lower airway bacterial infection in COPD we studied 40 outpatients with stable COPD (Group A: age 61.1 +/- 9.9 yr; [mean +/- SD]; FEV1/FVC 51.7 +/- 12.5) and 29 outpatients with exacerbated COPD (Group B: age 63.4, SD 9.0 yr; FEV1/FVC 52.0, SD 9.6), using the protected specimen brush (PSB) for microbiology sampling [5].

High impact information on Microbiology

  • We studied the effect of this policy on the pattern of erythromycin resistance throughout Finland. METHODS: From 1991 through 1996, a total of 39,247 group A streptococcal isolates from throat swabs (82 percent of the isolates) and pus samples (18 percent) and 290 isolates from blood cultures were studied in regional microbiology laboratories [6].
  • Perspectives: microbiology. Mice are not furry petri dishes [7].
  • Microbiology. Action at a distance--bacterial flagellar assembly [8].
  • In the past few years, an important question in microbiology has arisen from reports indicating that several pathogenic bacteria have evolved virulence factors directed towards a Ras subfamily of GTPases, namely the Rho GTPases [9].
  • Making optimum use of the microbiology laboratory. II. Urine, respiratory, wound, and cervicovaginal exudate [10].

Chemical compound and disease context of Microbiology


Biological context of Microbiology

  • This phase 1 study examined the safety, microbiology, immunology, and virology of TNF blockade using etanercept (soluble TNF receptor, Enbrel) during the initial treatment of HIV-associated tuberculosis [16].
  • In this issue of Molecular Microbiology, Sandin and colleagues have comprehensively analysed the regions of M5 protein that contribute to phagocytosis resistance and opsonization [17].
  • METHODS: One hundred and ninety eight subjects were studied: 42 patients with extrapulmonary tuberculosis confirmed by microbiology and/or histology, 24 subjects with healed pulmonary or extrapulmonary tuberculosis, 44 patients with a defined non-tuberculous disease, and 88 healthy volunteers (44 PPD negative and 44 PPD positive) [18].
  • STUDY DESIGN: The microbiology and epidemiology of three resistant strains were characterized and 12,761 other strains were evaluated for fluoroquinolone susceptibility as part of the Gonococcal Isolate Surveillance Project of the Centers for Disease Control and Prevention. RESULTS: Fluoroquinolone-resistant strains may appear sporadically [19].
  • Automation will continue to be an important part of the clinical microbiology laboratory and in the future will include more molecular biology technologies, such as the polymerase chain reaction [20].

Anatomical context of Microbiology

  • Infection by the obligate human pathogens Neisseria meningitidis (MC) and Neisseria gonorrhoeae (GC) reduces the expression of host epithelial cell transferrin receptor 1 (TfR-1) (Bonnah et al., 2000, Cellular Microbiology 2: 207-218) [21].
  • beta-Lactamase expression was examined in 1000 consecutive Gram-negative bacilli isolated from urine, wound swab, sputum or blood specimens received at the Microbiology Laboratory of the Royal London Hospital. This survey, performed between January and April, 1991, followed a similar study undertaken in early 1982 [22].
  • Soluble NAD(P)(+)-linked formaldehyde oxidation was the major activity in cells cultured in low-copper medium and expressing the soluble methane monooxygenase (Tate and Dalton, Microbiology 145:159-167, 1999; Vorholt et al., J. Bacteriol. 180:5351-5356, 1998) [23].
  • As an adaptation process to the growth retardation provoked by the presence of nonlethal concentrations of ergosterol biosynthesis inhibitors, Ustilago maydis alters the ratio of linoleic to oleic acid bound to plasma membrane complex lipids [Hernández, A., Cooke, D.T., Lewis, M. & Clarkson, D.T. (1997) Microbiology 143, 3165-3174] [24].
  • The three methods of detection were cytological examination of the oral mucosa, and direct culture methods from mucosal smears using Sabouraud's dextrose agar (Becton Dickinson Microbiology Systems, Cockeysville, MD) and Oricult-N (Orion Diagnostica, Espoo, Finland) [25].

Associations of Microbiology with chemical compounds

  • This paper will discuss the magnitude and microbiology of H2/CO2 acetogenesis in animal guts, its impact on host animal nutrition, competition for H2 between anaerobic microbes, and the global significance of intestinal H2/CO2 acetogenesis [26].
  • Currently, countercurrent immunoelectrophoresis, latex particle agglutination, and coagglutination are the techniques most used in microbiology laboratories [27].
  • Several isolates were reported by the clinical microbiology laboratories as being susceptible to imipenem [28].
  • In this issue, XopD is shown to remove SUMO groups from host cell proteins, while in previous issues of Molecular Microbiology, HopPtoD2 was shown to function as a tyrosine phosphatase and AvrRpt2 as probably a cysteine protease that targets the host RIN4 protein [29].
  • Clinical microbiology of azithromycin [30].

Gene context of Microbiology

  • RFLP analysis for katG and direct DNA sequencing of rpoB and rpsL may be practical methods for routine use in clinical microbiology laboratories or molecular pathology laboratories with good molecular capabilities and autosequencers [31].
  • We aimed to investigate the distribution of polymorphisms in the IL-1 gene family among periodontitis patients and controls, taking into account smoking and microbiology as additional variables [32].
  • Patient pulmonary diagnosis (based on cytology and microbiology) was compared with patient blood and BAL-soluble and cell-bound CD4 and CD8 to determine the relationship of these markers to disease states in this population [33].
  • Measurements of values of qualitative and quantitative microbiology, neutrophil infiltration (myeloperoxidase), oxygen free radicals (superoxide anion, superoxide dismutase, catalase, and gluthatione peroxidase), and cytokines (tumor necrosis factor-alpha and interleukin-1beta) were taken at different times after Zymosan administration [34].
  • Our approach was: (a) immediate notification of all MRSA isolates by the microbiology laboratory; (b) strict isolation; (c) cohorting; (d) bathing patients with an iodophor; (e) surveillance cultures of patients and staff; (f) treatment of all colonized persons; and (g) strict isolation on readmission [35].

Analytical, diagnostic and therapeutic context of Microbiology


  1. The changing epidemiology of invasive group A streptococcal infections and the emergence of streptococcal toxic shock-like syndrome. A retrospective population-based study. Hoge, C.W., Schwartz, B., Talkington, D.F., Breiman, R.F., MacNeill, E.M., Englender, S.J. JAMA (1993) [Pubmed]
  2. Nosocomial outbreak of Klebsiella infection resistant to late-generation cephalosporins. Meyer, K.S., Urban, C., Eagan, J.A., Berger, B.J., Rahal, J.J. Ann. Intern. Med. (1993) [Pubmed]
  3. Does yogurt enriched with Bifidobacterium longum affect colonic microbiology and fecal metabolites in health subjects? Bartram, H.P., Scheppach, W., Gerlach, S., Ruckdeschel, G., Kelber, E., Kasper, H. Am. J. Clin. Nutr. (1994) [Pubmed]
  4. Pathophysiology and management of pulmonary infections in cystic fibrosis. Gibson, R.L., Burns, J.L., Ramsey, B.W. Am. J. Respir. Crit. Care Med. (2003) [Pubmed]
  5. Bacterial infection in chronic obstructive pulmonary disease. A study of stable and exacerbated outpatients using the protected specimen brush. Monsó, E., Ruiz, J., Rosell, A., Manterola, J., Fiz, J., Morera, J., Ausina, V. Am. J. Respir. Crit. Care Med. (1995) [Pubmed]
  6. The effect of changes in the consumption of macrolide antibiotics on erythromycin resistance in group A streptococci in Finland. Finnish Study Group for Antimicrobial Resistance. Seppälä, H., Klaukka, T., Vuopio-Varkila, J., Muotiala, A., Helenius, H., Lager, K., Huovinen, P. N. Engl. J. Med. (1997) [Pubmed]
  7. Perspectives: microbiology. Mice are not furry petri dishes. Bull, J., Levin, B. Science (2000) [Pubmed]
  8. Microbiology. Action at a distance--bacterial flagellar assembly. Macnab, R.M. Science (2000) [Pubmed]
  9. Bacterial virulence factors targeting Rho GTPases: parasitism or symbiosis? Boquet, P., Lemichez, E. Trends Cell Biol. (2003) [Pubmed]
  10. Making optimum use of the microbiology laboratory. II. Urine, respiratory, wound, and cervicovaginal exudate. Bartlett, R.C. JAMA (1982) [Pubmed]
  11. Comparison of tests for detection of methicillin-resistant Staphylococcus aureus in a clinical microbiology laboratory. Unal, S., Werner, K., DeGirolami, P., Barsanti, F., Eliopoulos, G. Antimicrob. Agents Chemother. (1994) [Pubmed]
  12. Electron microscopy of the gonococcal capsule. Hendley, J.O., Powell, K.R., Salomonsky, N.L., Rodewald, R.R. J. Infect. Dis. (1981) [Pubmed]
  13. Aminoglycoside resistance among Pseudomonas aeruginosa isolates with an unusual disk diffusion antibiogram. Clark, R.B., Sanders, C.C., Pakiz, C.B., Hostetter, M.K. Antimicrob. Agents Chemother. (1988) [Pubmed]
  14. Failure of the disk diffusion test to detect tobramycin resistance in kanamycin-resistant Escherichia coli strains. Santanam, P. J. Clin. Microbiol. (1984) [Pubmed]
  15. Evaluation of BBL crystal MRSA ID system. Knapp, C.C., Ludwig, M.D., Washington, J.A. J. Clin. Microbiol. (1994) [Pubmed]
  16. A study of the safety, immunology, virology, and microbiology of adjunctive etanercept in HIV-1-associated tuberculosis. Wallis, R.S., Kyambadde, P., Johnson, J.L., Horter, L., Kittle, R., Pohle, M., Ducar, C., Millard, M., Mayanja-Kizza, H., Whalen, C., Okwera, A. AIDS (2004) [Pubmed]
  17. Domains of group A streptococcal M protein that confer resistance to phagocytosis, opsonization and protection: implications for vaccine development. McArthur, J.D., Walker, M.J. Mol. Microbiol. (2006) [Pubmed]
  18. Detection of IgG and IgA against the mycobacterial antigen A60 in patients with extrapulmonary tuberculosis. Alifano, M., De Pascalis, R., Sofia, M., Faraone, S., Del Pezzo, M., Covelli, I. Thorax (1998) [Pubmed]
  19. Quinolone-resistant Neisseria gonorrhoeae: the beginning of the end? Report of quinolone-resistant isolates and surveillance in the southwestern United States, 1989 to 1997. Ehret, J.M., Judson, F.N. Sexually transmitted diseases. (1998) [Pubmed]
  20. Automation in clinical microbiology. Woods, G.L. Am. J. Clin. Pathol. (1992) [Pubmed]
  21. Expression of epithelial cell iron-related genes upon infection by Neisseria meningitidis. Bonnah, R.A., Muckenthaler, M.U., Carlson, H., Minana, B., Enns, C.A., Hentze, M.W., So, M. Cell. Microbiol. (2004) [Pubmed]
  22. Survey of the prevalence of beta-lactamases amongst 1000 gram-negative bacilli isolated consecutively at the Royal London Hospital. Liu, P.Y., Gur, D., Hall, L.M., Livermore, D.M. J. Antimicrob. Chemother. (1992) [Pubmed]
  23. Membrane-associated quinoprotein formaldehyde dehydrogenase from Methylococcus capsulatus Bath. Zahn, J.A., Bergmann, D.J., Boyd, J.M., Kunz, R.C., DiSpirito, A.A. J. Bacteriol. (2001) [Pubmed]
  24. In vivo activation of plasma membrane H(+)-ATPase hydrolytic activity by complex lipid-bound unsaturated fatty acids in Ustilago maydis. Hernández, A., Cooke, D.T., Clarkson, D.T. Eur. J. Biochem. (2002) [Pubmed]
  25. The detection of oral Candida in pediatric leukemia patients. Stinnett, E.A., Childers, N.K., Wright, J.T., Rodu, B.K., Bradley, E.L. Pediatric dentistry. (1992) [Pubmed]
  26. Microbial H2/CO2 acetogenesis in animal guts: nature and nutritional significance. Breznak, J.A., Kane, M.D. FEMS Microbiol. Rev. (1990) [Pubmed]
  27. Antigen detection in cerebrospinal fluid--pros and cons. Kaplan, S.L. Am. J. Med. (1983) [Pubmed]
  28. Rapid spread of carbapenem-resistant Klebsiella pneumoniae in New York City: a new threat to our antibiotic armamentarium. Bratu, S., Landman, D., Haag, R., Recco, R., Eramo, A., Alam, M., Quale, J. Arch. Intern. Med. (2005) [Pubmed]
  29. New effects of type III effectors. Innes, R. Mol. Microbiol. (2003) [Pubmed]
  30. Clinical microbiology of azithromycin. Neu, H.C. Am. J. Med. (1991) [Pubmed]
  31. Detection of resistance to isoniazid, rifampin, and streptomycin in clinical isolates of Mycobacterium tuberculosis by molecular methods. Nachamkin, I., Kang, C., Weinstein, M.P. Clin. Infect. Dis. (1997) [Pubmed]
  32. Polymorphisms of the interleukin-1 gene family, oral microbial pathogens, and smoking in adult periodontitis. Laine, M.L., Farré, M.A., González, G., van Dijk, L.J., Ham, A.J., Winkel, E.G., Crusius, J.B., Vandenbroucke, J.P., van Winkelhoff, A.J., Peña, A.S. J. Dent. Res. (2001) [Pubmed]
  33. Soluble versus cell-bound CD4, CD8 from bronchoalveolar lavage: correlation with pulmonary diagnoses in human immunodeficiency virus-infected individuals. Willsie, S.K., Herndon, B.L., Miller, L., Dew, M. J. Leukoc. Biol. (1996) [Pubmed]
  34. P- and E-selectin blockade can control bacterial translocation and modulate systemic inflammatory response. García-Criado, F.J., Lozano, F.S., Barros, M.B., Parreño, F.C., Fresnadillo, M.J., García-Sánchez, J.E., Gomez-Alonso, A. Journal of investigative surgery : the official journal of the Academy of Surgical Research. (2005) [Pubmed]
  35. A seven-year experience with methicillin-resistant Staphylococcus aureus. Cohen, S.H., Morita, M.M., Bradford, M. Am. J. Med. (1991) [Pubmed]
  36. Epidemiological fingerprinting of Enterobacter cloacae by small-fragment restriction endonuclease analysis and pulsed-field gel electrophoresis of genomic restriction fragments. Haertl, R., Bandlow, G. J. Clin. Microbiol. (1993) [Pubmed]
  37. Point prevalence, microbiology and fluconazole susceptibility patterns of yeast isolates colonizing the oral cavities of HIV-infected patients in the era of highly active antiretroviral therapy. Barchiesi, F., Maracci, M., Radi, B., Arzeni, D., Baldassarri, I., Giacometti, A., Scalise, G. J. Antimicrob. Chemother. (2002) [Pubmed]
  38. Specific identification and targeted characterization of Bifidobacterium lactis from different environmental isolates by a combined multiplex-PCR approach. Ventura, M., Reniero, R., Zink, R. Appl. Environ. Microbiol. (2001) [Pubmed]
  39. Reliability of two new test kits for rapid diagnosis of respiratory syncytial virus infection. Rothbarth, P.H., Hermus, M.C., Schrijnemakers, P. J. Clin. Microbiol. (1991) [Pubmed]
  40. Multiplex PCR for simultaneous identification of Staphylococcus aureus and detection of methicillin and mupirocin resistance. Pérez-Roth, E., Claverie-Martín, F., Villar, J., Méndez-Alvarez, S. J. Clin. Microbiol. (2001) [Pubmed]
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