Rapid microbial detection and enumeration using gel microdroplets and colorimetric or fluorescence indicator systems

Encapsulating bacteria in agarose microparticles using microfluidics for high-throughput cell analysis and isolation

The high-throughput analysis and isolation of bacterial cells encapsulated in agarose microparticles using fluorescence-activated cell sorting (FACS) is described. Flow-focusing microfluidic systems were used to create monodisperse microparticles that were ∼30 μm in diameter. The dimensions of these particles made them compatible with flow cytometry and FACS, and the sensitivity of these techniques reduced the incubation time for cell replication before analyses were carried out. The small volume of the microparticles (∼1-50 pL) minimized the quantity of reagents needed for bacterial studies. This platform made it possible to screen and isolate bacteria and apply a combination of techniques to rapidly determine the target of biologically active small molecules. As a pilot study, Escherichia coli cells were encapsulated in agarose microparticles, incubated in the presence of varying concentrations of rifampicin, and analyzed using FACS. The minimum inhibitory concentration of rifampicin was determined, and spontaneous mutants that had developed resistance to the antibiotic were isolated via FACS and characterized by DNA sequencing. The β-subunit of RNA polymerase, RpoB, was confirmed as the target of rifampicin, and Q513L was the mutation most frequently observed. Using this approach, the time and quantity of antibiotics required for the isolation of mutants was reduced by 8- and 150-fold, respectively, compared to conventional microbiological techniques using nutrient agar plates. We envision that this technique will have an important impact on research in chemical biology, natural products chemistry, and the discovery and characterization of biologically active secondary metabolites.

Selection methods for high-producing mammalian cell lines

The selection of high-producing mammalian cell lines represents a bottleneck in process development for the production of biopharmaceuticals. Traditional methods are time consuming (development times often exceed six months) and significantly limited by the number of clones that can be feasibly screened. The market for therapeutic proteins is set to double by 2010, so there is an increasing need to develop methods for the selection of mammalian cell lines stably expressing recombinant products at high levels in an efficient, cost-effective and high-throughput manner. Alternatives include higher throughput methods based on flow-cytometric screening and recently developed automated systems for the selection of high-producing cell lines.

Rapid mycobacteria drug susceptibility testing using Gel Microdrop (GMD) Growth Assay and flow cytometry

Control of multi-drug-resistant tuberculosis has been hampered by the lack of simple, rapid and sensitive methods for assessing bacterial growth and antimicrobial susceptibility. Due to the increasing incidence and high frequency of mutations, it is unlikely that culture methods will disappear in the foreseeable future. Therefore, the need to modernize methods for rapid detection of viable clinical isolates, at a minimum as a gold standard, will persist. Previously, we confirmed the feasibility of using the Gel Microdrop (GMD) Growth Assay for identifying sub-populations of resistant Mycobacteria by testing different laboratory strains. Briefly, this assay format relies on encapsulating single bacterium in agarose microspheres and identifying clonogenic growth using flow cytometry and fluorescent staining. In this study, we modified the GMD Growth Assay to make it suitable for clinical applications. We demonstrated the effectiveness and safety of this novel approach for detecting drug susceptibility in clinically relevant laboratory strains as well as clinical isolates of Mycobacterium tuberculosis. Correlation between results using the GMD Growth Assay format and results using two well characterized methods (Broth Microdilution MIC and BACTEC 460TB) was 87.5% and 90%, respectively. However, due to the inherent sensitivity of flow cytometry and the ability to detect small (<1%) sub-populations of resistant mycobacteria, the GMD Growth Assay identified more cases of drug resistance. Using 4 clinically relevant mycobacterial strains, we assessed susceptibility to primary anti-tuberculosis drugs using both the Broth Microdilution MIC method and the GMD Growth Assay. We performed 24 tests on isoniazid-resistant BCG, Mycobacterium tuberculosis H37Ra and Mycobacterium avium strains. The Broth Microdilution MIC method identified 7 cases (29.1%) of resistance to INH and EMB compared to the GMD Growth Assay which identified resistance in 10 cases (41.6%); in 3 cases (12.5%), resistance to INH and EMB was detected only with the GMD Growth Assay. In addition, using 20 Mycobacterium tuberculosis clinical isolates, we compared results using BACTEC 460TB method performed by collaborators and the GMD Growth Assay. Eight of 20 (40%) clinical isolates, which were not identified as drug-resistant using the conventional BACTEC 460TB method, were resistant to 1, 2, or 3 different concentrations of drugs using the GMD Growth Assay (13 cases of 140 experiments). In one case (isolate 1879), resistance to 10.0 microg/ml of STR detected using BACTEC 460TB method was not confirmed by the GMD Growth Assay. Thus, the overall agreement between these methods was 90% (14 discrepant results of 140 experiments). These data demonstrate that the GMD Growth Assay is an accurate and sensitive method for rapid susceptibility testing of Mycobacterium tuberculosis for use in clinical reference laboratory settings.

Pickles, Pectin, and Penicillin

My professional life has been devoted to the study of microbial products and their biosynthesis, regulation, and overproduction. These have included primary metabolites (glutamic acid, tryptophan, inosinic acid, guanylic acid, vitamin B(12), riboflavin, pantothenic acid, ethanol, and lactic acid) and secondary metabolites (penicillin, cephalosporins, streptomycin, fosfomycin, gramicidin S, rapamycin, indolmycin, microcin B17, fumagillin, mycotoxins, Monascus pigments, and tetramethylpyrazine). Other areas included microbial nutrition, strain improvement, bioconversions of statins and beta-lactams, sporulation and germination, plasmid stability, gel microdroplets, and the production of double-stranded RNA, the polymer xanthan, and enzymes (polygalacturonase, protease, cellulase). Most of the studies were carried out with me by devoted and hardworking industrial scientists for 15 years at Merck & Co. and by similarly characterized students, postdoctorals, and visiting scientists during my 32 years at the Massachusetts Institute of Technology. I owe much of my success to my mentors from academia and industry. My recent research activities with undergraduate students at the Charles A. Dana Research Institute for Scientists Emeriti (R.I.S.E.) at Drew University have been very rewarding and are allowing me to continue my career.

Rapid evaluation of biocidal activity using a transposon-encoded catechol 2,3-dioxygenase from Pseudomonas putida

Pseudomonas putida (UWC1), containing a genetically-engineered plasmid (pQM899), that encodes for the production of catechol 2,3-dioxygenase (C230), was used as a potential means of rapidly estimating bactericidal activity of chlorhexidine diacetate (CHA), phenol, cetylpyridinium chloride (CPC) and phenylmercuric nitrate (PMN). Enzyme C230 converts catechol to 2-hydroxymuconic semialdehyde (2-HMS), which is yellow in colour, via a meta cleavage pathway. Ideal conditions for production and measurement spectrophotometrically of 2-HMS were determined. However, the correlation between this method and viable plate counts was not sufficiently accurate to enable 2-HMS production to provide a sufficiently sensitive determination of biocidal activity. An alternative method, synchronous scanning fluorimetry, in which the decrease in catechol concentration was measured under standardized conditions, provided a good dose-response histogram for all the biocides tested. Although, in comparison with plate counts, there was an underestimation of the bactericidal effects of phenol an PMN, the results of this study suggest that this method has potential in determining the bactericidal efficacy of agents such as CHA and CPC.

Gel microdrop technology for rapid isolation of rare and high producer cells

Secreted proteins are a therapeutic cornerstone of the biotechnology industry, and numerous recombinant products, including human growth hormone, human erythropoietin and granulocyte-colony stimulating factor, are now widely prescribed. In addition to bioprocessing applications, GMD technology should benefit the emerging fields of cellular and gene therapy. The ability to assess rapidly and precisely the productivity of cells for ex vivo cell screening and expansion is a unique approach with numerous research and therapeutic uses.

In situ hybridization to chromosomes stabilized in gel microdrops

Conventional chromosome in situ hybridization procedures rely on fixation to glass slides followed by microscopic evaluation. This report describes the development of a microdrop in situ hybridization to chromosomes in suspension. Chromosomes encapsulated in gel microdrops (GMDs) composed of an agarose matrix withstood stringent hybridization and denaturation conditions. Because of the increased stability, hybridization to encapsulated chromosomes was detected by flow cytometry as well as conventional microscopy. Thus, the MISH method offers a means for chromosome hybridization without slides and may enable identification and isolation of chromosome using hybridization rather than nucleic acid binding dyes.

Rapid assay for mycobacterial growth and antibiotic susceptibility using gel microdrop encapsulation

Effective control of tuberculosis transmission in vulnerable population groups is dependent on rapid identification of the infectious agent and its drug susceptibility. However, the slow growth rate of mycobacteria has undermined the ability to quickly identify antimicrobial resistance. These studies describe a mycobacterial growth assay based on microencapsulation technology used in conjunction with flow cytometric analysis. Mycobacteria were encapsulated in agarose gel microdrops approximately 25 microns in diameter, and colony growth was monitored by using flow cytometry to evaluate the intensity of auramine staining after culture for various times at 37 degrees C. By this method, colony growth of Mycobacterium bovis and M. smegmatis could be quantified within 1 to 3 days after encapsulation. Inhibition of growth by rifampin and isoniazid was also evaluated in this time period, and the presence of an isoniazid-resistant subpopulation representing 3% of the total microorganisms could be detected. This use of encapsulation and flow cytometry has the potential to facilitate rapid and automated evaluation of inhibition of growth by antimicrobial agents and shorten the time frame for analysis of clinical specimens.

Treponema pallidum in gel microdroplets: a novel strategy for investigation of treponemal molecular architecture

Controversy exists regarding the constituents and antigenic properties of the Treponema pallidum outer membrane; a major point of contention concerns the cellular location(s) of the spirochaete's lipoprotein immunogens. To address these issues and circumvent problems associated with prior efforts to localize treponemal surface antigens, we developed a novel strategy for investigating T. pallidum molecular architecture. Virulent treponemes were encapsulated in porous agarose beads (gel microdroplets) and then probed in the presence or absence of Triton X-100. Intact, encapsulated treponemes were not labelled by monospecific antisera directed against four major T. pallidum lipoproteins or a candidate T. pallidum outer membrane protein (TpN50) with C-terminal sequence homology to Escherichia coli OmpA or by human or rabbit syphilitic serum. Each of these immunologic reagents, however, labelled encapsulated treponemes co-incubated with detergent. In contrast, antibodies generated against isolated T. pallidum outer membranes labelled intact organisms and the pattern of fluorescence was consistent with the distribution of rare outer membrane proteins visualized by freeze-fracture electron microscopy. In addition to providing strong evidence that the protein portions of treponemal lipoproteins are located within the periplasmic space, these studies have extended our understanding of the topographical relationships among T. pallidum cell envelope constituents. They also demonstrate the feasibility of generating antibodies against rare outer membrane proteins and detecting them on the surfaces of virulent treponemes.

Rapid Clonal Growth Measurements at the Single-Cell Level: Gel Microdroplets and Flow Cytometry

We describe a new, general method for rapidly measuring clonal growth of large numbers of individual members of a cell population. This method is based on microculture of individual colony-forming units in gel microdrops (GMDs; here agarose; 20 to 90 mu in diameter), which are sufficiently robust to be handled much like cells, and diffusionally transparent for molecules of interest. Flow cytometry provides rapid measurements of GMD-entrapped microcolonies, and permits subpopulation analysis. Here the method is demonstrated with mammalian, fungal and bacterial species. Additional results illustrate rapid determination of a drug-resistant subpopulation in a mixed species sample, and nutrient sensitivity for a murine hybridoma.

Sampling: a critical problem in biosensing

Biosensing is widely recognised to be of potentially major importance to medicine and related fields, but in spite of a large number of impressive and important advances, widespread practical application has lagged. We examine the thesis that 'sampling' is a process which involves all of the phenomena which are associated with the transport of analyte molecules to the active sensor site, and that problems associated with this process are now the limiting factor in further use of many existing biosensors. We conclude that an integrated process of sampling and sensing should be emphasised in developing new biosensing systems, and propose several new approaches.