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1.  Single cell antimicrobial susceptibility testing by confined microchannels and electrokinetic loading 
Analytical chemistry  2013;85(8):3971-3976.
Multidrug-resistant pathogens are an emerging global health problem. In addition to the need of developing new antibiotics in the pipeline, the ability to rapidly determine the antibiotic resistance profiles of bacteria represents one of the most crucial steps toward the management of infectious diseases and the prevention of multidrug-resistant pathogens. Here, we report a single cell antimicrobial susceptibility testing (AST) approach for rapid determination of the antibiotic resistance of bacterial pathogens. By confining individual bacteria in gas permeable microchannels with dimensions comparable to a single bacterium, the antibiotic resistance of the bacteria can be monitored in real-time at the single cell level. To facilitate the dynamic loading of the bacteria into the confined microchannels for observation, AC electrokinetics is demonstrated for capturing bacteria to defined locations in high-conductivity AST buffer. The electrokinetic technique achieves a loading efficiency of about 75% with a negligible effect on the bacterial growth rate. To optimize the protocol for single cell AST, the bacterial growth rate of individual bacteria under different antibiotic conditions has been determined systematically. The applicability of single cell AST is demonstrated by the rapid determination of the antimicrobial resistant profiles of uropathogenic clinical isolates in Mueller-Hinton media and in urine. The antibiotic resistance profiles of bacteria can be determined in less than one hour compared to days in standard culture-based AST techniques.
PMCID: PMC4102406  PMID: 23445209
2.  A Gravity-Driven Microfluidic Particle Sorting Device with Hydrodynamic Separation Amplification 
Analytical chemistry  2007;79(4):1369-1376.
This paper describes a simple microfluidic sorting system that can perform size-profiling and continuous mass-dependent separation of particles through combined use of gravity (1g) and hydrodynamic flows capable of rapidly amplifying sedimentation-based separation between particles. Operation of the device relies on two microfluidic transport processes: i) initial hydrodynamic focusing of particles in a microchannel oriented parallel to gravity, ii) subsequent sample separation where positional difference between particles with different mass generated by sedimentation is further amplified by hydrodynamic flows whose streamlines gradually widen out due to the geometry of a widening microchannel oriented perpendicular to gravity. The microfluidic sorting device was fabricated in poly(dimethylsiloxane) (PDMS), and hydrodynamic flows in microchannels were driven by gravity without using external pumps. We conducted theoretical and experimental studies on fluid dynamic characteristics of laminar flows in widening microchannels and hydrodynamic amplification of particle separation. Direct trajectory monitoring, collection, and post-analysis of separated particles were performed using polystyrene microbeads with different sizes to demonstrate rapid (< 1 min) and high-purity (> 99.9 %) separation. Finally, we demonstrated biomedical applications of our system by isolating small-sized (diameter < 6 μm) perfluorocarbon liquid droplets from polydisperse droplet emulsions, which is crucial in preparing contrast agents for safe, reliable ultrasound medical imaging, tracers for magnetic resonance imaging, or transpulmonary droplets used in ultrasound-based occlusion therapy for cancer treatment. Our method enables straightforward, rapid real-time size-monitoring and continuous separation of particles in simple stand-alone microfabricated devices without the need for bulky and complex external power sources. We believe that this system will provide a useful tool o separate colloids and particles for various analytical and preparative applications, and may hold 3 potential for separation of cells or development of diagnostic tools requiring point-of-care sample preparation or testing.
PMCID: PMC2527745  PMID: 17297936
3.  Rapid Antimicrobial Susceptibility Determination of Uropathogens in Clinical Urine Specimens by Use of ATP Bioluminescence▿  
Journal of Clinical Microbiology  2008;46(4):1213-1219.
We describe the first direct testing of the antimicrobial susceptibilities of bacterial pathogens in human clinical fluid samples by the use of ATP bioluminescence. We developed an ATP bioluminescence assay that eliminates somatic sources of ATP to selectively quantify the bacterial load in clinical urine specimens with a sensitivity of <1,000 CFU per milliliter. There was a log-log relationship between light emission and the numbers of CFU in clinical urine specimens. A clinical study was performed to evaluate the accuracy of the ATP bioluminescence assay for determination of the antimicrobial susceptibilities of uropathogens in clinical urine specimens tested in a blinded manner. ATP bioluminescent bacterial density quantitation was used to determine the inoculation volume in growth medium with and without antibiotics. After incubation at 37°C for 120 min, the ATP bioluminescence assay was repeated to evaluate the uropathogen response to antibiotics. The ability of the ATP bioluminescence assay to discriminate between antimicrobial susceptibility and resistance was determined by comparison of the results obtained by the ATP bioluminescence assay with the results obtained by standard clinical microbiology methods. Receiver operator characteristic curves were used to determine the optimal threshold for discriminating between susceptibility and resistance. Susceptibility and resistance were correctly predicted in 87% and 95% of cases, respectively, for an overall unweighted accuracy of 91%, when the results were stratified by antibiotic. For samples in which the pathogen was susceptible, the accuracy improved to 95% when the results for samples with less than a 25-fold increase in the amount of bacterial ATP in the medium without antibiotics were excluded. These data indicate that a rapid bioluminescent antimicrobial susceptibility assay may be useful for the management of urinary tract infections.
PMCID: PMC2292911  PMID: 18272708
4.  Controlled viable release of selectively captured label-free cells in microchannels† 
Lab on a chip  2011;11(23):10.1039/c1lc20487d.
Selective capture of cells from bodily fluids in microchannels has broadly transformed medicine enabling circulating tumor cell isolation, rapid CD4+ cell counting for HIV monitoring, and diagnosis of infectious diseases. Although cell capture methods have been demonstrated in microfluidic systems, the release of captured cells remains a significant challenge. Viable retrieval of captured label-free cells in microchannels will enable a new era in biological sciences by allowing cultivation and post-processing. The significant challenge in release comes from the fact that the cells adhere strongly to the microchannel surface, especially when immuno-based immobilization methods are used. Even though fluid shear and enzymes have been used to detach captured cells in microchannels, these methods are known to harm cells and affect cellular characteristics. This paper describes a new technology to release the selectively captured label-free cells in microchannels without the use of fluid shear or enzymes. We have successfully released the captured CD4+ cells (3.6% of the mononuclear blood cells) from blood in microfluidic channels with high specificity (89% ± 8%), viability (94% ± 4%), and release efficiency (59% ± 4%). We have further validated our system by specifically capturing and controllably releasing the CD34+ stem cells from whole blood, which were quantified to be 19 cells per million blood cells in the blood samples used in this study. Our results also indicated that both CD4+ and CD34+ cells released from the microchannels were healthy and amenable for in vitro culture. Manual flow based microfluidic method utilizes inexpensive, easy to fabricate microchannels allowing selective label-free cell capture and release in less than 10 minutes, which can also be used at the point-of-care. The presented technology can be used to isolate and purify a broad spectrum of cells from mixed populations offering widespread applications in applied biological sciences, such as tissue engineering, regenerative medicine, rare cell and stem cell isolation, proteomic/genomic research, and clonal/population analyses.
PMCID: PMC3814023  PMID: 22002065
5.  Direct antimicrobial susceptibility testing for acute urinary tract infections in women. 
Journal of Clinical Microbiology  1995;33(9):2316-2323.
Despite its theoretical advantages, direct antimicrobial susceptibility testing (DST) of urine specimens remains controversial largely because of concerns regarding its accuracy, particularly with mixed cultures. To evaluate the performance of DST in the setting of acute urinary tract infection (UTI), we performed DST using 25 traditional and contemporary antimicrobial agents on urine specimens from 162 women with suspected acute uncomplicated UTI, and compared these results with the results of standardized disk diffusion susceptibility tests done on the same specimens. Direct tests were interpretable for 129 specimens, i.e., 80% of all specimens and 85% of the 152 specimens that met the culture criteria for UTI. Of the 2,983 individual comparisons between the direct and standard tests, 0.8% represented very major errors, 0.6% represented major errors, 3.1% represented minor errors, and 95.5% were in agreement. Errors were more common in association with older antimicrobial agents and agents with a high prevalence of antimicrobial resistance, non-Escherichia coli strains, low urine bacterial concentrations, sparse or mixed growth in the direct test, and the presence of multiple significant organisms in urine. The urine leukocyte concentration was > or = 15/mm3 in all subjects and did not differentiate between specimens that gave an interpretable direct test and those that did not. Calculation of the sensitivity of DST in identifying antimicrobial resistance supplemented conventional error rate analysis. We conclude that when used selectively and interpreted carefully, DST of urine specimens offers an efficient, rapid, and accurate method for antimicrobial susceptibility determination for acute UTI, particularly when the urine bacterial concentration is > 10(5) CFU/ml.
PMCID: PMC228402  PMID: 7494020
6.  A Real-Time PCR Antibiogram for Drug-Resistant Sepsis 
PLoS ONE  2011;6(12):e28528.
Current molecular diagnostic techniques for susceptibility testing of septicemia rely on genotyping for the presence of known resistance cassettes. This technique is intrinsically vulnerable due to the inability to detect newly emergent resistance genes. Traditional phenotypic susceptibility testing has always been a superior method to assay for resistance; however, relying on the multi-day growth period to determine which antimicrobial to administer jeopardizes patient survival. These factors have resulted in the widespread and deleterious use of broad-spectrum antimicrobials. The real-time PCR antibiogram, described herein, combines universal phenotypic susceptibility testing with the rapid diagnostic capabilities of PCR. We have developed a procedure that determines susceptibility by monitoring pathogenic load with the highly conserved 16S rRNA gene in blood samples exposed to different antimicrobial drugs. The optimized protocol removes heme and human background DNA from blood, which allows standard real-time PCR detection systems to be employed with high sensitivity (<100 CFU/mL). Three strains of E. coli, two of which were antimicrobial resistant, were spiked into whole blood and exposed to three different antibiotics. After real-time PCR-based determination of pathogenic load, a ΔCt<3.0 between untreated and treated samples was found to indicate antimicrobial resistance (P<0.01). Minimum inhibitory concentration was determined for susceptible bacteria and pan-bacterial detection was demonstrated with 3 Gram-negative and 2 Gram-positive bacteria. Species identification was performed via analysis of the hypervariable amplicons. In summary, we have developed a universal diagnostic phenotyping technique that assays for the susceptibility of drug-resistant septicemia with the speed of PCR. The real-time PCR antibiogram achieves detection, susceptibility testing, minimum inhibitory concentration determination, and identification in less than 24 hours.
PMCID: PMC3229610  PMID: 22164303
7.  The Microfluidic Probe: Operation and Use for Localized Surface Processing 
Microfluidic devices allow assays to be performed using minute amounts of sample and have recently been used to control the microenvironment of cells. Microfluidics is commonly associated with closed microchannels which limit their use to samples that can be introduced, and cultured in the case of cells, within a confined volume. On the other hand, micropipetting system have been used to locally perfuse cells and surfaces, notably using push-pull setups where one pipette acts as source and the other one as sink, but the confinement of the flow is difficult in three dimensions. Furthermore, pipettes are fragile and difficult to position and hence are used in static configuration only.
The microfluidic probe (MFP) circumvents the constraints imposed by the construction of closed microfluidic channels and instead of enclosing the sample into the microfluidic system, the microfluidic flow can be directly delivered onto the sample, and scanned across the sample, using the MFP. . The injection and aspiration openings are located within a few tens of micrometers of one another so that a microjet injected into the gap is confined by the hydrodynamic forces of the surrounding liquid and entirely aspirated back into the other opening. The microjet can be flushed across the substrate surface and provides a precise tool for localized deposition/delivery of reagents which can be used over large areas by scanning the probe across the surface. In this video we present the microfluidic probe1 (MFP). We explain in detail how to assemble the MFP, mount it atop an inverted microscope, and align it relative to the substrate surface, and finally show how to use it to process a substrate surface immersed in a buffer.
PMCID: PMC2794887  PMID: 19578328
8.  A Biosensor Platform for Rapid Antimicrobial Susceptibility Testing Directly From Clinical Samples 
The Journal of urology  2010;185(1):148-153.
A significant barrier to efficient antibiotic management of infection is that the standard diagnostic methodologies do not provide results at the point of care. The delays between sample collection and bacterial culture and antibiotic susceptibility reporting have led to empirical use of antibiotics, contributing to the emergence of drug resistant pathogens. As a key step toward the development of a point of care device for determining the antibiotic susceptibility of urinary tract pathogens, we report on a biosensor based antimicrobial susceptibility test.
Materials and Methods
For assay development bacteria were cultured with or without antibiotics, and growth was quantitated by determining viable counts and electrochemical biosensor measurement of bacterial 16S rRNA. To determine antibiotic susceptibility directly from patient samples, urine was cultured on antibiotic plates for 2.5 hours and growth was determined by electrochemical measurement of bacterial 16S rRNA. For assay validation 252 urine samples were collected from patients at the Spinal Cord Injury Service at Veterans Affairs Palo Alto Health Care System. The biosensor based antimicrobial susceptibility test was completed for samples containing gram-negative organisms. Pathogen identification and antibiotic susceptibility results were compared between our assay and standard microbiological analysis.
A direct biosensor quantitation of bacterial 16S rRNA can be used to monitor bacterial growth for a biosensor based antimicrobial susceptibility test. Clinical validation of a biosensor based antimicrobial susceptibility test with patient urine samples demonstrated that this test was 94% accurate in 368 pathogen-antibiotic tests compared to standard microbiological analysis.
This biosensor based antimicrobial susceptibility test, in concert with our previously described pathogen identification assay, can provide culture and susceptibility information directly from a urine sample within 3.5 hours.
PMCID: PMC4051414  PMID: 21074208
urinary tract infections; biosensing techniques; microbial sensitivity tests; point-of-care systems
9.  Development of a digital microfluidic platform for point of care testing 
Lab on a chip  2008;8(12):2091-2104.
Point of care testing is playing an increasingly important role in improving the clinical outcome in health care management. The salient features of a point of care device are quick results, integrated sample preparation and processing, small sample volumes, portability, multifunctionality and low cost. In this paper, we demonstrate some of these salient features utilizing an electrowetting-based Digital Microfluidic platform. We demonstrate the performance of magnetic bead-based immunoassays (cardiac troponin I) on a digital microfluidic cartridge in less than 8 minutes using whole blood samples. Using the same microfluidic cartridge, a 40-cycle real-time polymerase chain reaction was performed within 12 minutes by shuttling a droplet between two thermal zones. We further demonstrate, on the same cartridge, the capability to perform sample preparation for bacterial and fungal infectious disease pathogens (methicillin-resistance Staphylococcus aureus and Candida albicans) and for human genomic DNA using magnetic beads. In addition to rapid results and integrated sample preparation, electrowetting-based digital microfluidic instruments are highly portable because fluid pumping is performed electronically. All the digital microfluidic chips presented here were fabricated on printed circuit boards utilizing mass production techniques that keep the cost of the chip low. Due to the modularity and scalability afforded by digital microfluidics, multifunctional testing capability, such as combinations within and between immunoassays, DNA amplification, and enzymatic assays, can be brought to the point of care at a relatively low cost because a single chip can be configured in software for different assays required along the path of care.
PMCID: PMC2726010  PMID: 19023472
10.  Biological implications of polydimethylsiloxane-based microfluidic cell culture† 
Lab on a chip  2009;9(15):2132-2139.
Polydimethylsiloxane (PDMS) has become a staple of the microfluidics community by virtue of its simple fabrication process and material attributes, such as gas permeability, optical transparency, and flexibility. As microfluidic systems are put toward biological problems and increasingly utilized as cell culture platforms, the material properties of PDMS must be considered in a biological context. Two properties of PDMS were addressed in this study: the leaching of uncured oligomers from the polymer network into microchannel media, and the absorption of small, hydrophobic molecules (i.e. estrogen) from serum-containing media into the polymer bulk. Uncured PDMS oligomers were detectable via MALDI-MS in microchannel media both before and after Soxhlet extraction of PDMS devices in ethanol. Additionally, PDMS oligomers were identified in the plasma membranes of NMuMG cells cultured in PDMS microchannels for 24 hours. Cells cultured in extracted microchannels also contained a detectable amount of uncured PDMS. It was shown that MCF-7 cells seeded directly on PDMS inserts were responsive to hydrophilic prolactin but not hydrophobic estrogen, reflecting its specificity for absorbing small, hydrophobic molecules; and the presence of PDMS floating in wells significantly reduced cellular response to estrogen in a serum-dependent manner. Quantification of estrogen via ELISA revealed that microchannel estrogen partitioned rapidly into the surrounding PDMS to a ratio of approximately 9:1. Pretreatments such as blocking with serum or pre-absorbing estrogen for 24 hours did not affect estrogen loss from PDMS-based microchannels. These findings highlight the importance of careful consideration of culture system properties when determining an appropriate environment for biological experiments.
PMCID: PMC2792742  PMID: 19606288
11.  Implementation of Microfluidic Sandwich ELISA for Superior Detection of Plant Pathogens 
PLoS ONE  2013;8(12):e83231.
Rapid and economical screening of plant pathogens is a high-priority need in the seed industry. Crop quality control and disease surveillance demand early and accurate detection in addition to robustness, scalability, and cost efficiency typically required for selective breeding and certification programs. Compared to conventional bench-top detection techniques routinely employed, a microfluidic-based approach offers unique benefits to address these needs simultaneously. To our knowledge, this work reports the first attempt to perform microfluidic sandwich ELISA for Acidovorax citrulli (Ac), watermelon silver mottle virus (WSMoV), and melon yellow spot virus (MYSV) screening. The immunoassay occurs on the surface of a reaction chamber represented by a microfluidic channel. The capillary force within the microchannel draws a reagent into the reaction chamber as well as facilitates assay incubation. Because the underlying pad automatically absorbs excess fluid, the only operation required is sequential loading of buffers/reagents. Buffer selection, antibody concentrations, and sample loading scheme were optimized for each pathogen. Assay optimization reveals that the 20-folds lower sample volume demanded by the microchannel structure outweighs the 2- to 4-folds higher antibody concentrations required, resulting in overall 5–10 folds of reagent savings. In addition to cutting the assay time by more than 50%, the new platform offers 65% cost savings from less reagent consumption and labor cost. Our study also shows 12.5-, 2-, and 4-fold improvement in assay sensitivity for Ac, WSMoV, and MYSV, respectively. Practical feasibility is demonstrated using 19 real plant samples. Given a standard 96-well plate format, the developed assay is compatible with commercial fluorescent plate readers and readily amendable to robotic liquid handling systems for completely hand-free assay automation.
PMCID: PMC3871650  PMID: 24376668
12.  Highly Efficient Circulating Tumor Cell Isolation from Whole Blood and Label-Free Enumeration Using Polymer-Based Microfluidics with an Integrated Conductivity Sensor 
A novel microfluidic device that can selectively and specifically isolate exceedingly small numbers of circulating tumor cells (CTCs) through a monoclonal antibody (mAB) mediated process by sampling large input volumes (≥1 mL) of whole blood directly in short time periods (<37 min) was demonstrated. The CTCs were concentrated into small volumes (190 nL), and the number of cells captured was read without labeling using an integrated conductivity sensor following release from the capture surface. The microfluidic device contained a series (51) of high-aspect ratio microchannels (35 μm width × 150 μm depth) that were replicated in poly(methyl methacrylate), PMMA, from a metal mold master. The microchannel walls were covalently decorated with mABs directed against breast cancer cells overexpressing the epithelial cell adhesion molecule (EpCAM). This microfluidic device could accept inputs of whole blood, and its CTC capture efficiency was made highly quantitative (>97%) by designing capture channels with the appropriate widths and heights. The isolated CTCs were readily released from the mAB capturing surface using trypsin. The released CTCs were then enumerated on-device using a novel, label-free solution conductivity route capable of detecting single tumor cells traveling through the detection electrodes. The conductivity readout provided near 100% detection efficiency and exquisite specificity for CTCs due to scaling factors and the nonoptimal electrical properties of potential interferences (erythrocytes or leukocytes). The simplicity in manufacturing the device and its ease of operation make it attractive for clinical applications requiring one-time use operation.
PMCID: PMC2526315  PMID: 18557614
13.  Prevalence of extended spectrum beta lactamase producing Escherichia coli and Klebsiella pneumoniae urinary isolates in a tertiary care hospital in Kathmandu, Nepal 
BMC Research Notes  2013;6:487.
Escherichia coli and Klebsiella pneumoniae are the major bacterial pathogens being isolated and reported from mid stream urine (MSU) specimens, globally. These uropathogens are mostly implicated as the major extended spectrum beta-lactamase (ESBL) producers, severely limiting the therapeutic management in cases of urinary tract infections. Limited studies had been reported from Nepal investigating the ESBL producers among uropathogens. This study was designed to assess the prevalence of ESBL producing E.coli and K. pneumoniae in urinary isolates at a centrally located major tertiary care hospital in Kathmandu valley, Nepal.
Between September 2011 and May 2012, during the nine months period, 6308 MSU specimens were collected aseptically from the same number of clinically suspected patients of urinary tract infections. The samples were cultured on MacConkey agar and blood agar. The isolates with significant bacteriuria (105 CFU / ml) were identified based on standard laboratory procedures. Antimicrobial susceptibility tests were carried out using various antimicrobial discs alongwith ceftriaxone on E.coli and K. pneumoniae isolates by Kirby Bauer disc diffusion method as per the recommendations of CLSI. On initial screening with ceftriaxone (30 μg) disc showing resistance was then confirmed for ESBL production by phenotypic confirmatory disc diffusion test (PCDDT) using ceftazidime (30 ug) and ceftazidime + clavulanic acid (30 μg + 10ug) disc as per guidelines of CLSI (2011).
Out of a total of 6308 MSU specimens investigated for significant bacteriuria, E.coli isolates were 444 (7.04%) and K.pneuminiae were 145 (2.3%) making a total of 589 (9.34%). Initial screening with ceftriaxone disc revealed 155 isolates of E.coli and 70 isolates of K.pneumoniae to be resistant. Further testing by PCDDT method showed 60/444 (=13.51%) of E. coli and 24/145 (=16.55%) of K. pneumoniae isolates to be confirmed ESBL producers. These ESBL – producer uropathogens showed high degree of resistance to ceftriaxone (100.0%), amoxycillin, fluoroquinolones and co-trimoxazole.
An emerging and moderately high prevalence of ESBL-producing E. coli and K. pneumoniae was observed and confirmed in the urinary isolates investigated. It is essential to have a regular and routine monitoring of ESBL producing clinical isolates in laboratory practice.
PMCID: PMC4222089  PMID: 24274894
Antimicrobial resistance; Extended spectrum beta lactamase (ESBL); Escherichia coli; Klebsiella pneumoniae; Mid stream urine (MSU); Prevalence; Urinary isolates
14.  Uropathogenic Escherichia coli Modulates Immune Responses and Its Curli Fimbriae Interact with the Antimicrobial Peptide LL-37 
PLoS Pathogens  2010;6(7):e1001010.
Bacterial growth in multicellular communities, or biofilms, offers many potential advantages over single-cell growth, including resistance to antimicrobial factors. Here we describe the interaction between the biofilm-promoting components curli fimbriae and cellulose of uropathogenic E. coli and the endogenous antimicrobial defense in the urinary tract. We also demonstrate the impact of this interplay on the pathogenesis of urinary tract infections. Our results suggest that curli and cellulose exhibit differential and complementary functions. Both of these biofilm components were expressed by a high proportion of clinical E. coli isolates. Curli promoted adherence to epithelial cells and resistance against the human antimicrobial peptide LL-37, but also increased the induction of the proinflammatory cytokine IL-8. Cellulose production, on the other hand, reduced immune induction and hence delayed bacterial elimination from the kidneys. Interestingly, LL-37 inhibited curli formation by preventing the polymerization of the major curli subunit, CsgA. Thus, even relatively low concentrations of LL-37 inhibited curli-mediated biofilm formation in vitro. Taken together, our data demonstrate that biofilm components are involved in the pathogenesis of urinary tract infections by E. coli and can be a target of local immune defense mechanisms.
Author Summary
Most infections of the urinary tract are caused by uropathogenic E. coli. On abiotic surfaces, these bacteria are able to form biofilms, which protect them from various adverse environmental conditions. In this study, we sought to investigate whether two E. coli biofilm components, curli fimbriae and cellulose, provide a similar protection against innate immune defense mechanisms of the urinary tract. We put special emphasis on the interaction with the human antimicrobial peptide LL-37, which plays a crucial role in the protection against uropathogenic E. coli. We demonstrate that curli expression specifically reduces bacterial sensitivity to LL-37 by binding the peptide before reaching the bacterial cell membrane and exhibiting its bactericidal activity. A more general protection is mediated by cellulose, possibly by hiding immunogenic surface structures of the bacterium. In addition to providing protection, curli are also targeted by the immune system. The formation of new curli fibers is inhibited in the presence of LL-37. Moreover, curliated bacteria show higher immunogenicity than their non-curliated counterparts. Cellulose expression, on the other hand, appears to impair initial host colonization. In conclusion, our findings demonstrate an example of the tight interplay between bacterial virulence factors and the host immune defense.
PMCID: PMC2908543  PMID: 20661475
15.  A Peptide Derived from Phage Display Library Exhibits Antibacterial Activity against E. coli and Pseudomonas aeruginosa 
PLoS ONE  2013;8(2):e56081.
Emergence of drug resistant strains to currently available antibiotics has resulted in the quest for novel antimicrobial agents. Antimicrobial peptides (AMPs) are receiving attention as alternatives to antibiotics. In this study, we used phage-display random peptide library to identify peptides binding to the cell surface of E. coli. The peptide with sequence RLLFRKIRRLKR (EC5) bound to the cell surface of E. coli and exhibited certain features common to AMPs and was rich in Arginine and Lysine residues. Antimicrobial activity of the peptide was tested in vitro by growth inhibition assays and the bacterial membrane permeabilization assay. The peptide was highly active against Gram-negative organisms and showed significant bactericidal activity against E. coli and P. aeruginosa resulting in a reduction of 5 log10 CFU/ml. In homologous plasma and platelets, incubation of EC5 with the bacteria resulted in significant reduction of E. coli and P. aeruginosa, compared to the peptide-free controls. The peptide was non-hemolytic and non-cytotoxic when tested on eukaryotic cells in culture. EC5 was able to permeabilize the outer membrane of E. coli and P. aeruginosa causing rapid depolarization of cytoplasmic membrane resulting in killing of the cells at 5 minutes of exposure. The secondary structure of the peptide showed a α-helical conformation in the presence of aqueous environment. The bacterial lipid interaction with the peptide was also investigated using Molecular Dynamic Simulations. Thus this study demonstrates that peptides identified to bind to bacterial cell surface through phage-display screening may additionally aid in identifying and developing novel antimicrobial peptides.
PMCID: PMC3569419  PMID: 23409125
16.  Oxygen Gradients for Open Well Cellular Cultures via Microfluidic Substrates 
Lab on a chip  2010;10(18):2394-2401.
Controlling oxygen concentration at a microscale level can benefit experimental investigations involving oxidative stress, ischemia, and reactive oxygen species (ROS) mediated cellular pathways. Here, we report the application of microfluidic gradient generation in an open-well culture model, in which a gradient of gas is delivered via diffusion through a gas permeable substrate that separates cells from the gas microchannels below. By using diffusion to localize oxygen delivery, microgradients of oxygen concentrations can be rapidly and controllably applied without exposing cells to mechanical stresses or reducing culture volumes inside microfluidic culture chambers. Furthermore, we demonstrate the modulation of intracellular ROS levels in Madin-Darby canine kidney (MDCK) cells by applying these oxygen microgradients. Increases in ROS levels consistent with both oxidative stress and hypoxic exposures were observed in MDCK cells. The measured ROS increases were comparable to 100 μM hydrogen peroxide exposure in a control comparison, which is within the range of standard ROS induction methods. Incubation with 200 μM vitamin C was able to demodulate the ROS response at both hypoxic and hyperoxic exposures. By providing microfluidic controlled gradients, constant ROS exposure, and a shear-free open well design, the devices introduced here greatly improve upon standard oxygen-based culturing methods.
Illustration Content List Entry with Summary Sentence
The devices presented here can generate complex oxygen gradients over rapid timescales, permitting investigation of a number of difficult-to-model physiological systems.
PMCID: PMC3188960  PMID: 20559583
17.  A microfluidic platform for rapid, stress-induced antibiotic susceptibility testing of Staphylococcus aureus 
Lab on a chip  2012;12(21):4523-4532.
The emergence and spread of bacterial resistance to ever increasing classes of antibiotics intensifies the need for fast phenotype-based clinical tests for determining antibiotic susceptibility. Standard susceptibility testing relies on the passive observation of bacterial growth inhibition in the presence of antibiotics. In this paper, we present a novel microfluidic platform for antibiotic susceptibility testing basedon stress-activation of biosynthetic pathways that are the primary targets of antibiotics. We chose Staphylococcus aureus as a model system due to its clinical importance, and we selected bacterial cell wall biosynthesis as the primary target of both stress and antibiotic. Enzymatic and mechanical stresses were used to damage the bacterial cell wall, and a β-lactam antibiotic interfered with the repair process, resulting in rapid cell death of strains that harbor no resistance mechanism. In contrast, resistant bacteria remained viable under the assay conditions. Bacteria, covalently-bound to the bottom of the microfluidic channel, were subjected to mechanical shear stress created by flowing culture media through the microfluidic channel and to enzymatic stress with sub-inhibitory concentrations of the bactericidal agent lysostaphin. Bacterial cell death was monitored via fluorescence using the Sytox Green dead cell stain, and rates of killing were measured for the bacterial samples in the presence and absence of oxacillin. Using model susceptible (Sanger 476) and resistant (MW2) S. aureus strains, a metric was established to separate susceptible and resistant staphylococci based on normalized fluorescence values after 60 minutes of exposure to stress and antibiotic. Because this groundbreaking approach is not based on standard methodology, it circumvents the need for minimum inhibitory concentration (MIC) measurements and long wait times. We demonstrate the successful development of a rapid microfluidic-based and stress-activated antibiotic susceptibility test by correctly designating the phenotypes of 16 additional clinically relevant S. aureus strains in a blinded study. In addition to future clinical utility, this method has great potential for studying the effects of various stresses on bacteria and their antibiotic susceptibility.
PMCID: PMC3489182  PMID: 22968495
18.  Integrated Microfluidic Reactors 
Nano today  2009;4(6):470-481.
Microfluidic reactors exhibit intrinsic advantages of reduced chemical consumption, safety, high surface-area-to-volume ratios, and improved control over mass and heat transfer superior to the macroscopic reaction setting. In contract to a continuous-flow microfluidic system composed of only a microchannel network, an integrated microfluidic system represents a scalable integration of a microchannel network with functional microfluidic modules, thus enabling the execution and automation of complicated chemical reactions in a single device. In this review, we summarize recent progresses on the development of integrated microfluidics-based chemical reactors for (i) parallel screening of in situ click chemistry libraries, (ii) multistep synthesis of radiolabeled imaging probes for positron emission tomography (PET), (iii) sequential preparation of individually addressable conducting polymer nanowire (CPNW), and (iv) solid-phase synthesis of DNA oligonucleotides. These proof-of-principle demonstrations validate the feasibility and set a solid foundation for exploring a broad application of the integrated microfluidic system.
PMCID: PMC2832182  PMID: 20209065
Integrated microfluidics; Chemical screening, In situ click chemistry; Sequential synthesis, Positron emission tomography probes; Oligonucleotide synthesis; Conducting polymer nanowires
19.  Real-Time Optical Antimicrobial Susceptibility Testing 
Journal of Clinical Microbiology  2013;51(7):2047-2053.
Rapid antibiotic susceptibility testing is in high demand in health care fields as antimicrobial-resistant bacterial strains emerge and spread. Here, we describe an optical screening system (oCelloScope) which, based on time-lapse imaging of 96 bacteria-antibiotic combinations at a time, introduces real-time detection of bacterial growth and antimicrobial susceptibility with imaging material to support the automatically generated graphs. Automated antibiotic susceptibility tests of a monoculture showed statistically significant antibiotic effects within 6 min and within 30 min in complex samples from pigs suffering from catheter-associated urinary tract infections. The oCelloScope system provides a fast high-throughput screening method for detecting bacterial susceptibility that might entail an earlier diagnosis and introduction of appropriate targeted therapy and thus combat the threat from multidrug-resistant pathogenic bacteria. The oCelloScope system can be employed for a broad range of applications within bacteriology and might present new vistas as a point-of-care instrument in clinical and veterinary settings.
PMCID: PMC3697729  PMID: 23596243
20.  Comparative Prevalence of Antimicrobial Resistance in Community-Acquired Urinary Tract Infection Cases from Representative States of Northern and Southern India 
Context: Urinary tract infections (UTIs) are amongst the most common infections described in outpatient settings. Increased antimicrobial resistance (AMR) of urinary tract pathogens is a matter of global public health concern. Treatment of UTI depends on both prevalence and antimicrobial resistance (AMR) of causative bacteria at any specific geographical location.
Aim: This study was undertaken to compare the prevalence of uropathogens and their AMR profile in two different geographical parts of India.
Materials and Methods: Clean-catch mid-stream urine samples were collected from adult patients, bacterial flora isolated from human urine was evaluated for antimicrobial susceptibility profile using Kirby Bauer’s disc diffusion method among patients from Hyderabad (Southern India), Rajasthan and Punjab (Northern India). The data were analysed using Chi-square (χ2) test, confidence interval (CI), odds ratio (OR) analysis and p-value using SPSS 16 software.
Results: Escherichia coli (55.1%) were the most prevalent isolates followed by Enterococcus faecalis (15.8%). Amikacin was the most active antimicrobial agents which showed low resistance rate of 14%. The present study revealed the geographical difference in prevalence of uropathogens with Klebsiella pneumoniae being the second most common uropathogen followed by E. faecalis in the states from northern India while no K. pneumoniae was seen in samples from southern India but E. faecalis was the second most prevalent organism.
Conclusion: Therefore, development of regional surveillance programs is highly recommended for implementation of national CA-UTI guidelines in Indian settings.
PMCID: PMC4225884  PMID: 25386432
Antimicrobial resistance; Bacteriuria and antibiotics; Community-acquired urinary yract infections; Uropathogens
21.  Microfluidic Chip-Based Detection and Intraspecies Strain Discrimination of Salmonella Serovars Derived from Whole Blood of Septic Mice 
Salmonella is a zoonotic pathogen that poses a considerable public health and economic burden in the United States and worldwide. Resultant human diseases range from enterocolitis to bacteremia to sepsis and are acutely dependent on the particular serovar of Salmonella enterica subsp. enterica, which comprises over 99% of human-pathogenic S. enterica isolates. Point-of-care methods for detection and strain discrimination of Salmonella serovars would thus have considerable benefit to medical, veterinary, and field applications that safeguard public health and reduce industry-associated losses. Here we describe a single, disposable microfluidic chip that supports isothermal amplification and sequence-specific detection and discrimination of Salmonella serovars derived from whole blood of septic mice. The integrated microfluidic electrochemical DNA (IMED) chip consists of an amplification chamber that supports loop-mediated isothermal amplification (LAMP), a rapid, single-temperature amplification method as an alternative to PCR that offers advantages in terms of sensitivity, reaction speed, and amplicon yield. The amplification chamber is connected via a microchannel to a detection chamber containing a reagentless, multiplexed (here biplex) sensing array for sequence-specific electrochemical DNA (E-DNA) detection of the LAMP products. Validation of the IMED device was assessed by the detection and discrimination of S. enterica subsp. enterica serovars Typhimurium and Choleraesuis, the causative agents of enterocolitis and sepsis in humans, respectively. IMED chips conferred rapid (under 2 h) detection and discrimination of these strains at clinically relevant levels (<1,000 CFU/ml) from whole, unprocessed blood collected from septic animals. The IMED-based chip assay shows considerable promise as a rapid, inexpensive, and portable point-of-care diagnostic platform for the detection and strain-specific discrimination of microbial pathogens.
PMCID: PMC3623251  PMID: 23354710
22.  Millisecond Kinetics on a Microfluidic Chip Using Nanoliters of Reagents 
Journal of the American Chemical Society  2003;125(47):14613-14619.
This paper describes a microfluidic chip for performing kinetic measurements with better than millisecond resolution. Rapid kinetic measurements in microfluidic systems are complicated by two problems: mixing is slow and dispersion is large. These problems also complicate biochemical assays performed in microfluidic chips. We have recently shown (Song, H.; Tice, J. D.; Ismagilov, R. F. Angew. Chem., Int. Ed. 2003, 42, 768–772) how multiphase fluid flow in microchannels can be used to address both problems by transporting the reagents inside aqueous droplets (plugs) surrounded by an immiscible fluid. Here, this droplet-based microfluidic system was used to extract kinetic parameters of an enzymatic reaction. Rapid single-turnover kinetics of ribonuclease A (RNase A) was measured with better than millisecond resolution using sub-microliter volumes of solutions. To obtain the single-turnover rate constant (k = 1100 ± 250 s−1), four new features for this microfluidics platform were demonstrated: (i) rapid on-chip dilution, (ii) multiple time range access, (iii) biocompatibility with RNase A, and (iv) explicit treatment of mixing for improving time resolution of the system. These features are discussed using kinetics of RNase A. From fluorescent images integrated for 2–4 s, each kinetic profile can be obtained using less than 150 nL of solutions of reagents because this system relies on chaotic advection inside moving droplets rather than on turbulence to achieve rapid mixing. Fabrication of these devices in PDMS is straightforward and no specialized equipment, except for a standard microscope with a CCD camera, is needed to run the experiments. This microfluidic platform could serve as an inexpensive and economical complement to stopped-flow methods for a broad range of time-resolved experiments and assays in chemistry and biochemistry.
PMCID: PMC1769313  PMID: 14624612
23.  A microfluidic platform for generating large-scale nearly identical human microphysiological system arrays 
Lab on a chip  2013;13(15):2990-2998.
This paper reports a polydimethylsiloxane microfluidic model system that can develop an array of nearly identical human microtissues with interconnected vascular networks. The microfluidic system design is based on an analogy with an electric circuit, applying resistive circuit concepts to design pressure dividers in serially-connected microtissue chambers. A long microchannel (550, 620 and 775 mm) creates a resistive circuit with a large hydraulic resistance. Two media reservoirs with a large cross-sectional area and of different heights are connected to the entrance and exit of the long microchannel to serve as a pressure source, and create a near constant pressure drop along the long microchannel. Microtissue chambers (0.12 μl) serve as a two-terminal resistive component with an input impedance > 50-fold larger than the long microchannel. Connecting each microtissue chamber to two different positions along the long microchannel creates a series of pressure dividers. Each microtissue chamber enables a controlled pressure drop of a segment of the microchannel without altering the hydrodynamic behaviour of the microchannel. The result is a controlled and predictable microphysiological environment within the microchamber. Interstitial flow, a mechanical cue for stimulating vasculogenesis, was verified by finite element simulation and experiments. The simplicity of this design enabled the development of multiple microtissue arrays (5, 12, and 30 microtissues) by co-culturing endothelial cells, stromal cells, and fibrin within the microchambers over two and three week periods. This methodology enables the culturing of a large array of microtissues with interconnected vascular networks for biological studies and applications such as drug development.
PMCID: PMC3734340  PMID: 23723013
24.  Hospital and Community Isolates of Uropathogens and their Antibiotic Sensitivity Pattern from a Tertiary Care Hospital in North West India 
Urinary tract infection remains one of the most common infections, both in the community and in the hospital. The causative pathogen profile varies from region to region, but Escherichia coli (E. coli) remains the most common causative pathogen. The sensitivity of uropathogens to different drugs varies in different areas, and changes with time. This necessitates periodic studies of the causative uropathogens and their antibiotic sensitivity pattern.
To investigate the profile of common uropathogens and assess their antibiotic sensitivity patterns to commonly used antimicrobial agents.
Materials and Methods:
Analysis of all urine specimens submitted for culture and sensitivity was carried out over a 1-year period in a tertiary care hospital in North West India. Urine culture was done by a semi-quantitative method. Antibiotic sensitivity was done on bacterial isolates according to the Clinical and Laboratory Standards Institute CLSI guidelines for disc diffusion susceptibility test. Data was analysed for significance using Chi square test.
Of a total of 6348 urine specimens received over the 1-year study period, 41.8% (2653) of the urine samples were culture positive. The most common bacterial isolate was E. coli (45.7%, 1103/2412), followed by Coagulase-negative Staphylococci (18.6%, 449/2412) and Klebsiella species (8.3%, 199/2412). The Candida species’ isolation rate was 10.3% (277/2689). The uropathogens displayed a very high level of resistance to fluroquinolones 70.3% (1084/1542)[Inpatient Department (IPD) – 70.5%(572/812), Outpatient Department (OPD) – 70.2%(512/730)] and cephalosporins 75.1%(1158/1542)[IPD – 73.8%(599/812), OPD – 76.6%(559/730)], whereas resistance to nitrofurantoin 19.8%(305/1542) [ IPD – 23.9%, OPD – 15.2%(111/730)], amikacin 32.4%(573/1769) [IPD – 36.1%(235/934), OPD – 28.1%(235/835)] and cephoperazone + sulbactam combination 22%(349/1583) [IPD – 26.2%(244/914), OPD – 15.8%(105/669)] was low.
Empiric selection of antimicrobial agents should be based on the antibiotic sensitivity pattern of the uropathogens prevalent in that area, which is derived from epidemiological studies carried out in that environment.
PMCID: PMC3952297  PMID: 24669331
Antibiotic resistance; Urinary tract infections; Uropathogens
25.  Use of Artificial Sputum Medium to Test Antibiotic Efficacy Against Pseudomonas aeruginosa in Conditions More Relevant to the Cystic Fibrosis Lung 
There is growing concern about the relevance of in vitro antimicrobial susceptibility tests when applied to isolates of P. aeruginosa from cystic fibrosis (CF) patients. Existing methods rely on single or a few isolates grown aerobically and planktonically. Predetermined cut-offs are used to define whether the bacteria are sensitive or resistant to any given antibiotic1. However, during chronic lung infections in CF, P. aeruginosa populations exist in biofilms and there is evidence that the environment is largely microaerophilic2. The stark difference in conditions between bacteria in the lung and those during diagnostic testing has called into question the reliability and even relevance of these tests3.
Artificial sputum medium (ASM) is a culture medium containing the components of CF patient sputum, including amino acids, mucin and free DNA. P. aeruginosa growth in ASM mimics growth during CF infections, with the formation of self-aggregating biofilm structures and population divergence4,5,6. The aim of this study was to develop a microtitre-plate assay to study antimicrobial susceptibility of P. aeruginosa based on growth in ASM, which is applicable to both microaerophilic and aerobic conditions.
An ASM assay was developed in a microtitre plate format. P. aeruginosa biofilms were allowed to develop for 3 days prior to incubation with antimicrobial agents at different concentrations for 24 hours. After biofilm disruption, cell viability was measured by staining with resazurin. This assay was used to ascertain the sessile cell minimum inhibitory concentration (SMIC) of tobramycin for 15 different P. aeruginosa isolates under aerobic and microaerophilic conditions and SMIC values were compared to those obtained with standard broth growth. Whilst there was some evidence for increased MIC values for isolates grown in ASM when compared to their planktonic counterparts, the biggest differences were found with bacteria tested in microaerophilic conditions, which showed a much increased resistance up to a >128 fold, towards tobramycin in the ASM system when compared to assays carried out in aerobic conditions.
The lack of association between current susceptibility testing methods and clinical outcome has questioned the validity of current methods3. Several in vitro models have been used previously to study P. aeruginosa biofilms7, 8. However, these methods rely on surface attached biofilms, whereas the ASM biofilms resemble those observed in the CF lung9 . In addition, reduced oxygen concentration in the mucus has been shown to alter the behavior of P. aeruginosa2 and affect antibiotic susceptibility10. Therefore using ASM under microaerophilic conditions may provide a more realistic environment in which to study antimicrobial susceptibility.
PMCID: PMC3471314  PMID: 22711026
Immunology;  Issue 64;  Microbiology;  Pseudomonas aeruginosa;  antimicrobial susceptibility;  artificial sputum media;  lung infection;  cystic fibrosis;  diagnostics;  plankton

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