microbiological techniques


Summary: Techniques used in microbiology.

Top Publications

  1. Lagrange P, Thangaraj S, Dayal R, Despande A, Ganguly N, Girardi E, et al. A toolbox for tuberculosis diagnosis: an Indian multicentric study (2006-2008): microbiological results. PLoS ONE. 2012;7:e43739 pubmed publisher
    ..The aim of this multicentric prospective study in India was to assess the value of several microbiological tools that contribute to the diagnosis of tuberculosis (TB) according to HIV status...
  2. Lagacé Wiens P, Adam H, Karlowsky J, Nichol K, Pang P, Guenther J, et al. Identification of blood culture isolates directly from positive blood cultures by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry and a commercial extraction system: analysis of performance, cost, and turnaround ti. J Clin Microbiol. 2012;50:3324-8 pubmed publisher
    ..However, the use of MALDI-TOF for direct identification is accurate and should result in reduced turnaround time to identification...
  3. Fazili Z, Pfeiffer C, Zhang M, Jain R, Koontz D. Influence of 5,10-methylenetetrahydrofolate reductase polymorphism on whole-blood folate concentrations measured by LC-MS/MS, microbiologic assay, and bio-rad radioassay. Clin Chem. 2008;54:197-201 pubmed
    ..Because BR results are genotype dependent, different regression equations should be used. ..
  4. Rath P, Saner F, Paul A, Lehmann N, Steinmann E, Buer J, et al. Multiplex PCR for rapid and improved diagnosis of bloodstream infections in liver transplant recipients. J Clin Microbiol. 2012;50:2069-71 pubmed publisher
    ..SF yielded a significantly higher positivity rate in the LTX group (52.3%) than in the non-LTX group (30.5%; P = 0.0009). SF may be a powerful tool for the early diagnosis of bloodstream infections in LTX patients. ..
  5. Wallet F, Nseir S, Baumann L, Herwegh S, Sendid B, Boulo M, et al. Preliminary clinical study using a multiplex real-time PCR test for the detection of bacterial and fungal DNA directly in blood. Clin Microbiol Infect. 2010;16:774-9 pubmed publisher
    ..Our results suggest that the LC-SF test may be a valuable complementary tool in the management of patients with clinically suspected sepsis...
  6. Shane B. Folate status assessment history: implications for measurement of biomarkers in NHANES. Am J Clin Nutr. 2011;94:337S-342S pubmed publisher
    ..Past experience with microbiological and competitive protein binding assays indicates some of the technical problems that research will need to address before this promise becomes reality. ..
  7. Lozupone C, Knight R. Species divergence and the measurement of microbial diversity. FEMS Microbiol Rev. 2008;32:557-78 pubmed publisher
    ..Consequently, divergence-based methods are providing new insights into microbial community structure and function. ..
  8. van Belkum A, Welker M, Erhard M, Chatellier S. Biomedical mass spectrometry in today's and tomorrow's clinical microbiology laboratories. J Clin Microbiol. 2012;50:1513-7 pubmed publisher
    ..Herein, we review the current state of the art with respect to this exciting new technology and discuss potential future applications. ..
  9. Kalmbach R, Paul L, Selhub J. Determination of unmetabolized folic acid in human plasma using affinity HPLC. Am J Clin Nutr. 2011;94:343S-347S pubmed publisher
    ..This updated method allows efficient analysis of folate forms in human plasma and tissues without the loss of sensitivity or precision. ..

More Information


  1. Lucignano B, Ranno S, Liesenfeld O, Pizzorno B, Putignani L, Bernaschi P, et al. Multiplex PCR allows rapid and accurate diagnosis of bloodstream infections in newborns and children with suspected sepsis. J Clin Microbiol. 2011;49:2252-8 pubmed publisher
    ..8%] versus n = 26 [1.6%]), respectively; P < 0.0001). SeptiFast served as a highly valuable adjunct to conventional blood culture in children, adding diagnostic value and shortening the time to result (TTR) to 6 h. ..
  2. Ferroni A, Suarez S, Beretti J, Dauphin B, Bille E, Meyer J, et al. Real-time identification of bacteria and Candida species in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol. 2010;48:1542-8 pubmed publisher
    ..MALDI-TOF-MS is currently the fastest technique to accurately identify microorganisms grown in positive blood culture broths. ..
  3. Andersson A, Lindberg M, Jakobsson H, Backhed F, Nyrén P, Engstrand L. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE. 2008;3:e2836 pubmed publisher
    ..Here we applied the technique to analyze microbial communities in throat, stomach and fecal samples. Our results demonstrate the applicability of barcoded pyrosequencing as a high-throughput method for comparative microbial ecology. ..
  4. Tsukatani T, Suenaga H, Higuchi T, Akao T, Ishiyama M, Ezoe K, et al. Colorimetric cell proliferation assay for microorganisms in microtiter plate using water-soluble tetrazolium salts. J Microbiol Methods. 2008;75:109-16 pubmed publisher
    ..Linear relationships between the absorbance and viable microbial cell density were obtained in all microorganisms, suggesting that the absorbance change reflected the microbial cell proliferation. ..
  5. Ecker D, Sampath R, Massire C, Blyn L, Hall T, Eshoo M, et al. Ibis T5000: a universal biosensor approach for microbiology. Nat Rev Microbiol. 2008;6:553-8 pubmed publisher
  6. Lamoth F, Jaton K, Prod hom G, Senn L, Bille J, Calandra T, et al. Multiplex blood PCR in combination with blood cultures for improvement of microbiological documentation of infection in febrile neutropenia. J Clin Microbiol. 2010;48:3510-6 pubmed publisher
    ..Technical adjustments may enhance the efficiency of this new molecular tool in this specific setting...
  7. Kaleta E, Clark A, Johnson D, Gamage D, Wysocki V, Cherkaoui A, et al. Use of PCR coupled with electrospray ionization mass spectrometry for rapid identification of bacterial and yeast bloodstream pathogens from blood culture bottles. J Clin Microbiol. 2011;49:345-53 pubmed publisher
  8. Sekirov I, Russell S, Antunes L, Finlay B. Gut microbiota in health and disease. Physiol Rev. 2010;90:859-904 pubmed publisher
    ..The advances in modeling and analysis of gut microbiota will further our knowledge of their role in health and disease, allowing customization of existing and future therapeutic and prophylactic modalities. ..
  9. Kaleta E, Clark A, Cherkaoui A, Wysocki V, Ingram E, Schrenzel J, et al. Comparative analysis of PCR-electrospray ionization/mass spectrometry (MS) and MALDI-TOF/MS for the identification of bacteria and yeast from positive blood culture bottles. Clin Chem. 2011;57:1057-67 pubmed publisher
  10. Maubon D, Hamidfar Roy R, Courby S, Vesin A, Maurin M, Pavese P, et al. Therapeutic impact and diagnostic performance of multiplex PCR in patients with malignancies and suspected sepsis. J Infect. 2010;61:335-42 pubmed publisher
    ..In cancer patients with suspected sepsis, LC-SF detected 11/55 (20%) true pathogens not recovered from BCs and would have improved the initial management in 11/110 (10%) patients. ..
  11. Tsalik E, Jones D, Nicholson B, Waring L, Liesenfeld O, Park L, et al. Multiplex PCR to diagnose bloodstream infections in patients admitted from the emergency department with sepsis. J Clin Microbiol. 2010;48:26-33 pubmed publisher
    ..Current microbiological techniques are limited in their diagnostic capacities and timeliness...
  12. Orszag P, Disqué C, Keim S, Lorenz M, Wiesner O, Hadem J, et al. Monitoring of patients supported by extracorporeal membrane oxygenation for systemic infections by broad-range rRNA gene PCR amplification and sequence analysis. J Clin Microbiol. 2014;52:307-11 pubmed publisher
    ..With 45% of positive samples, SepsiTest was 13 to 75 h faster than BC. SepsiTest indicated bacteremias in 25% of patients who were BC negative. ..
  13. Stamm R, Harper M, Houghton L. Quantitation of whole-blood total folate within defined MTHFR C677T genotype groups by isotope dilution-liquid chromatography-tandem mass spectrometry differs from microbiologic assay. J Nutr. 2012;142:2154-60 pubmed publisher
    ..ID-LC-MS/MS procedures have the potential to offer a high degree of accuracy; however, further work is needed to determine the origin of the pyrazino-s-triazine derivative. ..
  14. Pfaller M, Wolk D, Lowery T. T2MR and T2Candida: novel technology for the rapid diagnosis of candidemia and invasive candidiasis. Future Microbiol. 2016;11:103-17 pubmed publisher
    ..This test enables detection of Candida directly from the patient sample, a significant advance for the rapid and accurate diagnosis of invasive candidiasis. ..
  15. Decker J, Slawson R. An evaluation of behavioral health compliance and microbial risk factors on student populations within a high-density campus. J Am Coll Health. 2012;60:584-95 pubmed publisher
    ..A consideration of physical space along with behavioral factors is required in order to properly assess risk pathways in the establishment of an evidence-based infection control plan for universities and their contiguous communities. ..
  16. Kumari V, Banerjee T, Kumar P, Pandey S, Tilak R. Emergence of non-albicans Candida among candidal vulvovaginitis cases and study of their potential virulence factors, from a tertiary care center, North India. Indian J Pathol Microbiol. 2013;56:144-7 pubmed publisher
    ..Therefore, we recommend that microbiological investigation upto species level should be mandatory to determine the emergence of non-albicans Candida as a major cause of VVC. ..
  17. Döğen A, Ilkit M, de Hoog G. Black yeast habitat choices and species spectrum on high altitude creosote-treated railway ties. Fungal Biol. 2013;117:692-6 pubmed publisher
    ..These results suggest that hydrocarbons, particularly creosote-treated oak woods, support the growth of black yeasts, some of which are opportunists in humans. ..
  18. Kok J, Chen S, Dwyer D, Iredell J. Current status of matrix-assisted laser desorption ionisation-time of flight mass spectrometry in the clinical microbiology laboratory. Pathology. 2013;45:4-17 pubmed publisher
    ..Novel applications include strain typing and the detection of antimicrobial resistance, but these are not widely used. This review discusses the technical aspects, current applications, and limitations of MALDI-TOF MS...
  19. Dalpke A, Hofko M, Zimmermann S. Development and evaluation of a real-time PCR assay for detection of Pneumocystis jirovecii on the fully automated BD MAX platform. J Clin Microbiol. 2013;51:2337-43 pubmed publisher
    ..The BD MAX assay required liquefaction of highly viscous samples with dithiothreitol as the only manual step, thus offering advantages for timely availability of molecular-based detection assays...
  20. Berovic M, Habijanic J, Boh B, Wraber B, Petravic Tominac V. Production of Lingzhi or Reishi medicinal mushroom, Ganoderma lucidum (W.Curt. :Fr.) P. Karst. (higher Basidiomycetes), biomass and polysaccharides by solid state cultivation. Int J Med Mushrooms. 2012;14:513-20 pubmed
    ..Final concentration of biomass was 0.68 mg/g of solid substrate, while proportions of extracellular and intracellular polysaccharides were 4.5 mg/g and 1.05 mg/g, respectively. ..
  21. Fontana C, Favaro M, Bossa M, Minelli S, Altieri A, Pelliccioni M, et al. Improved diagnosis of central venous catheter-related bloodstream infections using the HB&L UROQUATTRO™ system. Eur J Clin Microbiol Infect Dis. 2012;31:3139-44 pubmed publisher
    ..Moreover, the use of the HB&L UROQUATTRO™ system allowed us to significantly reduce diagnosis time; a negative CRBSI diagnosis could be made within 6 h and a positive diagnosis could be made within 22-28 h. ..
  22. Goyer M, Lucchi G, Ducoroy P, Vagner O, Bonnin A, Dalle F. Optimization of the preanalytical steps of matrix-assisted laser desorption ionization-time of flight mass spectrometry identification provides a flexible and efficient tool for identification of clinical yeast isolates in medical laboratories. J Clin Microbiol. 2012;50:3066-8 pubmed publisher
    ..1 and 96.2% of the 183 clinical yeast isolates prospectively tested were correctly identified after 48 and 72 h of preincubation, respectively. ..
  23. Boase S, Foreman A, Cleland E, Tan L, Melton Kreft R, Pant H, et al. The microbiome of chronic rhinosinusitis: culture, molecular diagnostics and biofilm detection. BMC Infect Dis. 2013;13:210 pubmed publisher
    ..Comparison with molecular analysis suggests that the detection threshold of FISH and culture is related to organism abundance and, furthermore, culture tends to select for rapidly growing organisms. ..
  24. Montesinos I, Argudín M, Hites M, Ahajjam F, Dodémont M, Dagyaran C, et al. Culture-Based Methods and Molecular Tools for Azole-Resistant Aspergillus fumigatus Detection in a Belgian University Hospital. J Clin Microbiol. 2017;55:2391-2399 pubmed publisher
    ..Hence, a rapid method for resistance detection may be useful to improve patient management. Centers that care for immunocompromised patients should perform routine surveillance to determine their local epidemiology. ..
  25. Lee Y, Van Nostrand J, Tu Q, Lu Z, Cheng L, Yuan T, et al. The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. ISME J. 2013;7:1974-84 pubmed publisher
  26. Cai J, Chen M, Wang Y, Pan J, Li A, Zhang D. Culture and motion analysis of diatom Bacillaria paradoxa on a microfluidic platform. Curr Microbiol. 2013;67:652-8 pubmed publisher
    ..The successful culture of diatoms on a microfluidic platform may be used for biosensing chips and the creation of gasoline-producing diatom solar panels. ..
  27. Stobbe A, Daniels J, Espindola A, Verma R, Melcher U, Ochoa Corona F, et al. E-probe Diagnostic Nucleic acid Analysis (EDNA): a theoretical approach for handling of next generation sequencing data for diagnostics. J Microbiol Methods. 2013;94:356-66 pubmed publisher
    ..The E-probe Diagnostic Nucleic acid Analysis (EDNA) process provides the framework for a new sequence-based detection system that eliminates the need for assembly of NGS data. ..
  28. Walsh J, Hyman J, Borzhemskaya L, Bowen A, McKellar C, Ullery M, et al. Rapid intrinsic fluorescence method for direct identification of pathogens in blood cultures. MBio. 2013;4:e00865-13 pubmed publisher
  29. Bunyaratavej S, Pattanaprichakul P, Leeyaphan C, Rujitharanawong C, Muanprasart C, Matthapan L, et al. The Use of Adhesive Tapes to Transfer Skin-scrapings for Sequential Laboratory Diagnosis of Dermatophytosis. Med Mycol J. 2016;57:E9-13 pubmed publisher
    ..On the other hand, the sensitivity of fungal cultures gradually declines as storage time is extended. ..
  30. Jensen R, Hagen F, Astvad K, Tyron A, Meis J, Arendrup M. Azole-resistant Aspergillus fumigatus in Denmark: a laboratory-based study on resistance mechanisms and genotypes. Clin Microbiol Infect. 2016;22:570.e1-9 pubmed publisher
    ..Furthermore, although complex, genotyping supported the hypotheses regarding clonal expansion and the potential of a single origin for the TR34/L98H clone. ..
  31. Lu Y, Slater F, Bello Mendoza R, Batstone D. Shearing of biofilms enables selective layer based microbial sampling and analysis. Biotechnol Bioeng. 2013;110:2600-5 pubmed publisher
    ..The strength of the shear-bulk molecular method over FISH was that a deeper phylogenetic profile could be obtained, even with TRFLP, and that prior knowledge of the community is not required. ..
  32. Couturier M, Barney T, Alger G, Hymas W, Stevenson J, Hillyard D, et al. Evaluation of the FilmArray® Respiratory Panel for clinical use in a large children's hospital. J Clin Lab Anal. 2013;27:148-54 pubmed publisher
    ..FARP overall performed better than DFA with the exception of Adenovirus, making the FARP an attractive alternative to laboratories looking to replace DFA with a rapid, user-friendly, multiplex molecular assay. ..
  33. Bansal V, Bharde A, Ramanathan R, Bhargava S. Inorganic materials using 'unusual' microorganisms. Adv Colloid Interface Sci. 2012;179-182:150-68 pubmed publisher
  34. Dharmik P, Gomashe A, Wadher B. Surveillance of antibiotic susceptibility pattern among shigella flexneri strain isolated in Nagpur district during three years period, January 2009-January 2012. Indian J Med Sci. 2010;64:493-500 pubmed publisher
    ..According to current findings, Quinolones and Cephalosporins are the drug of choice for the diarrheic patients. In conclusion, systematic monitoring is needed to identify changes in the antimicrobial resistance. ..
  35. Lemloh M, Hoos S, Görtz H, Brümmer F. Isolation of alveolar plates from Coleps hirtus. Eur J Protistol. 2013;49:62-6 pubmed publisher
    ..Since there are indications of a mineral phase within the alveolar plates, the presented results will allow to study C. hirtus alveolar plates also in the context of biomineralisation. ..
  36. Burl S, Holder B, Lo B, Kampmann B. Optimisation of a functional mycobacterial growth-inhibition assay to improve its suitability for infant TB vaccine studies. J Immunol Methods. 2013;394:121-4 pubmed publisher
    ..These results confirm the suitability of the BCG-lux assay for functional studies of vaccine immunogenicity and immunopathogenesis in young children and could play a role in late-phase TB vaccine trials of novel candidates. ..
  37. Huang L, Zhang Y, Sun L. Time to positivity of blood culture can predict different Candida species instead of pathogen concentration in candidemia. Eur J Clin Microbiol Infect Dis. 2013;32:917-22 pubmed publisher
    ..tropicalis from other Candida species in candidemia, and it is not associated with antifungal agent susceptibility and patients' clinical characteristics. TTP cannot predict pathogen concentration in the blood of candidemic patients. ..
  38. Tu Q, Li J, Shi Z, Chen Y, Lin L, Li J, et al. HuMiChip2 for strain level identification and functional profiling of human microbiomes. Appl Microbiol Biotechnol. 2017;101:423-435 pubmed publisher
    ..These results suggest that the developed HuMiChip2 is a useful microbial ecological microarray for both strain-level identification and functional profiling of human microbiomes. ..
  39. Pahlow S, Kloß S, Blättel V, Kirsch K, Hübner U, Cialla D, et al. Isolation and enrichment of pathogens with a surface-modified aluminium chip for Raman spectroscopic applications. Chemphyschem. 2013;14:3600-5 pubmed publisher
    ..Subsequent identification is done by recording Raman spectra of the bacteria. Further, it is shown that classification with chemometric methods is possible. ..
  40. Fothergill A, Kasinathan V, Hyman J, Walsh J, Drake T, Wang Y. Rapid identification of bacteria and yeasts from positive-blood-culture bottles by using a lysis-filtration method and matrix-assisted laser desorption ionization-time of flight mass spectrum analysis with the SARAMIS database. J Clin Microbiol. 2013;51:805-9 pubmed publisher
    ..This study demonstrates the effectiveness of the new lysis-filtration method for identifying microorganisms directly from positive-blood-culture bottles in a clinical setting. ..
  41. Brzozowski A, Silk B, Berkelman R, Loveys D, Caliendo A. Use, location, and timeliness of clinical microbiology testing in Georgia for select infectious diseases. J Public Health Manag Pract. 2012;18:E4-E10 pubmed publisher
    ..These unsettling findings have adverse implications for both patient care and public health surveillance; they indicate an immediate need to study nationally the use and timeliness of clinical microbiologic testing. ..
  42. Chandrakar S, Dias M, Shetty P, Tiewsoh J, Guarro J. Isolation and Characterization of an Unknown Chrysosporium sp. Producing Subcutaneous Mycosis in an Immunocompromised Patient. Mycopathologia. 2016;181:115-8 pubmed publisher
    ..8S-ITS2 rDNA revealed belonging to the order Onygenales and most closely related to Chrysosporium spp. isolated from a fowl. Of the 65 species within the genus Chrysosporium, very few have been reported as pathogenic. ..
  43. Cronquist A, Mody R, Atkinson R, Besser J, Tobin D Angelo M, Hurd S, et al. Impacts of culture-independent diagnostic practices on public health surveillance for bacterial enteric pathogens. Clin Infect Dis. 2012;54 Suppl 5:S432-9 pubmed publisher
    ..Public health practitioners must clearly explain the value of surveillance, especially how outbreak detection benefits the public, and collaborate with all stakeholders to develop solutions. ..
  44. Daboit T, Magagnin C, Heidrich D, Castrillón M, Mendes S, Vettorato G, et al. A case of relapsed chromoblastomycosis due to Fonsecaea monophora: antifungal susceptibility and phylogenetic analysis. Mycopathologia. 2013;176:139-44 pubmed publisher
    ..Furthermore, the identification of the agent by molecular techniques is important for epidemiological purposes. To the best of our knowledge, this is the first case of relapsed chromoblastomycosis caused by F. monophora in Brazil. ..
  45. Stavnsbjerg C, Frimodt Møller N, Moser C, Bjarnsholt T. Comparison of two commercial broad-range PCR and sequencing assays for identification of bacteria in culture-negative clinical samples. BMC Infect Dis. 2017;17:233 pubmed publisher
    ..The UMD SelectNA assay was valuable for the identification of pathogens in culture-negative samples; however, due to the sensitive nature of the assay, extreme care is suggested in order to avoid false positives. ..
  46. Martínez M, Massora S, Mandomando I, Ussene E, Jordao D, Lovane L, et al. Infectious cause of death determination using minimally invasive autopsies in developing countries. Diagn Microbiol Infect Dis. 2016;84:80-86 pubmed publisher
    ..The combination of classical cultures, serological tests and molecular assays performed in samples obtained through MIA allows the identification of most infectious agents causing death. ..
  47. Pierce M, Ward J, Dobbs F. False positives in Biolog EcoPlates™ and MT2 MicroPlates™ caused by calcium. J Microbiol Methods. 2014;97:20-4 pubmed publisher
    ..Future studies involving Biolog EcoPlates and MicroPlates should take this effect into account, and the dilution of samples is strongly recommended to diminish the "calcium effect." ..
  48. Rosenvinge F, Dzajic E, Knudsen E, Malig S, Andersen L, Løvig A, et al. Performance of matrix-assisted laser desorption-time of flight mass spectrometry for identification of clinical yeast isolates. Mycoses. 2013;56:229-35 pubmed publisher
    ..Both MALDI-TOF-MS systems are fast, have built-in databases that cover the majority of clinically relevant Candida species, and have an accuracy that outperforms our conventional identification systems. ..
  49. Gaudin V, De Courville A, Hedou C, Rault A, Diomandé S, Creff Froger C, et al. Evaluation and validation of two microbiological tests for screening antibiotic residues in honey according to the European guideline for the validation of screening methods. Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2013;30:234-43 pubmed publisher
    ..The Premi®Test kit could be recommended for reliable use in routine control due to its low detection capabilities (except for aminoglycosides), but the disadvantage is a high false-positive rate of 14%. ..
  50. Portillo M, Leff J, Lauber C, Fierer N. Cell size distributions of soil bacterial and archaeal taxa. Appl Environ Microbiol. 2013;79:7610-7 pubmed publisher
    ..Size fractionation not only provides important insight into the life history strategies of soil microbial taxa but also is a useful tool to enable more focused investigations into those taxa that remain poorly characterized. ..
  51. Chan A, Cartwright E, Reddy S, Kraft C, Wang Y. Pichia anomala (Candida pelliculosa) fungemia in a patient with sickle cell disease. Mycopathologia. 2013;176:273-7 pubmed publisher
    ..The organism was identified as P. anomala by MALDI-TOF VITEK mass spectrometry and VITEK 2 yeast identification card. Pichia anomala should be considered in sickle cell patients with recurrent fungemia. ..
  52. Farrell J, Sampath R, Ecker D, Bonomo R. "Salvage microbiology": detection of bacteria directly from clinical specimens following initiation of antimicrobial treatment. PLoS ONE. 2013;8:e66349 pubmed publisher
  53. Shakya M, Quince C, Campbell J, Yang Z, Schadt C, Podar M. Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environ Microbiol. 2013;15:1882-99 pubmed publisher