Controlled-diffusion centrifugal microfluidic for rapid antibiotic susceptibility testing

The abuse of antibiotics has become a global public safety issue, leading to the development of antimicrobial resistance (AMR). The development of antimicrobial susceptibility testing (AST) is crucial in reducing the growth of AMR. However, traditional AST methods are time-consuming (e.g., 24-72 h), labor-intensive, and costly. Here, we propose a controlled-diffusion centrifugal microfluidic platform (CCM) for rapid AST to obtain highly precise minimum inhibitory concentration (MIC) values. Antibiotic concentration gradients are generated by controlled moving and diffusing of antibiotic and buffer solution along the main microchannel within 3 min. The solution and bacterial suspension are then injected into the outermost reaction chamber by simple centrifugation. The CCM successfully determined the MIC for three commonly used antibiotics in clinical settings within 4-9 h. To further enhance practicality, reduce costs, and meet point-of-care testing demands, we have developed an integrated mobile detection platform for automated MIC value acquisition. The proposed CCM is a simple, low-cost, and portable method for rapid AST with broad clinical and in vitro applications.

Microbial Etiologies of Otitis Media with Resistance Pattern in a Tertiary Care Hospital in North India

Aim

The study aimed to evaluate the bacterial and fungal profiles in Otitis Media (OM), Acute Otitis Media (AOM), and Chronic Otitis Media (COM) and the sensitivity patterns to antibiotics available in our hospital settings.

Materials and Methods

A total of 150 clinically diagnosed cases of OM (AOM or COM) with ear discharge were enrolled. Swabs were cultured for microbial flora. Drug susceptibility testing was conducted using the Kirby-Bauer disc diffusion method.

Results

The most common bacteria isolated in AOM was Streptococcus spp., and in COM it was Staphylococcus aureus. Among fungal isolates, Candida albicans dominate. The antimicrobial profile of the organisms revealed maximum sensitivity to Fluoroquinolones.

Conclusions

Correct diagnosis and precise antibiotic prescription reduce the load of antibiotic resistance.

First large-scale study of antimicrobial susceptibility data, and genetic resistance determinants, in Fusobacterium necrophorum highlighting the importance of continuing focused susceptibility trend surveillance

OBJECTIVES

The objective of the study was to explore antimicrobial resistance gene determinant, and phenotypic antibiotic susceptibility, data for Fusobacterium necrophorum from a collection of UK strains. Antimicrobial resistance genes detected in publicly available assembled whole genome sequences were investigated for comparison.

METHODS

Three hundred and eighty five F. necrophorum strains (1982-2019) were revived from cryovials (Prolab). Subsequent to sequencing (Illumina) and quality checking, 374 whole genomes were available for analysis. Genomes were interrogated, using BioNumerics (bioMérieux; v 8.1), for the presence of known antimicrobial resistance genes (ARGs). Agar dilution susceptibility results for 313 F. necrophorum isolates (2016-2021) were also examined.

RESULTS

The phenotypic data for the 313 contemporary strains demonstrated potential resistance to penicillin in three isolates, using EUCAST v 11.0 breakpoints, and 73 (23%) strains using v 13.0 analysis. All strains were susceptible to multiple agents using v 11.0 guidance other than clindamycin (n = 2). Employing v 13.0 breakpoints, metronidazole (n = 3) and meropenem (n = 13) resistance were also detected. The tet(O), tet(M), tet(40), aph(3')-III, ant(6)-la and bla_OXA-85 ARGs were present in publicly available genomes. tet(M), tet(32), erm(A) and erm(B) were found within the UK strains, with correspondingly raised clindamycin and tetracycline minimum inhibitory concentrations.

CONCLUSIONS

Susceptibility to antibiotics recommended for the treatment of F. necrophorum infections should not be assumed. With evidence of potential ARG transmission from oral bacteria, and the detection of a transposon-mediated beta-lactamase resistance determinant in F. necrophorum, surveillance of both phenotypic and genotypic antimicrobial susceptibility trends must continue, and increase.

Advances in the screening of antimicrobial compounds using electrochemical biosensors: is there room for nanomaterials?

The abusive use of antimicrobial compounds and the associated appearance of antimicrobial resistant strains are a major threat to human health. An improved antimicrobial administration involves a faster diagnosis and detection of resistances. Antimicrobial susceptibility testing (AST) are the reference techniques for this purpose, relying mainly in the use of culture techniques. The long time required for analysis and the lack of reproducibility of these techniques have fostered the development of high-throughput AST methods, including electrochemical biosensors. In this review, recent electrochemical methods used in AST have been revised, with particular attention on those used for the evaluation of new drug candidates. The role of nanomaterials in these biosensing platforms has also been questioned, inferring that it is of minor importance compared to other applications.

Multi-reagents dispensing centrifugal microfluidics for point-of-care testing

Point-of-care testing (POCT) has shown great advantages for public health monitoring in resource-limited settings. However, developing of POCT tools with automated and accurate quantitative dispensing of multiple reagents and samples is challenging. Here, we demonstrate a novel multi-reagents dispensing centrifugal microfluidics (MDCM) that allows rapid and automated dispensing of multiple reagents and samples with high throughput and accuracy. The MDCM was designed with multiple aliquoting units with the hydrophobic valve at different radial positions. All reagents and samples were loaded simultaneously, dispensed in parallel by centrifugation at low speed, and then introduced into the reaction chamber sequentially by centrifugation at high speed. Two MDCM chips are demonstrated, including a uniform concentration generator and a gradient concentration generator. The concentration coefficient of variation (CV) among the independent reaction chambers was lower than 0.56%, and the theoretical quantitative concentration gradient was strongly correlated with the actual concentration gradient (R² = 0.9938). We have successfully applied the MDCM to loop-mediated isothermal amplification (LAMP)-based nucleic acid detection for multiple infectious pathogens and antimicrobial susceptibility testing (AST) for kanamycin sulfate against E. coli. To further extend the applications, the MDCM has also been applied to bicinchoninic acid (BCA) protein assays with online calibration, reducing the detection time from 2 h to 10 min with a twenty-fold reduction in reagent consumption. These results indicated that the MDCM is a high potential platform for POCT.

A microfluidic microwell device operated by the automated microfluidic control system for surface-enhanced Raman scattering-based antimicrobial susceptibility testing

Bloodstream infection (BSI) is a serious public health issue worldwide. Timely and effective antibiotics for controlling infection are crucial towards patient outcomes. However, the current culture-based methods of identifying bacteria and antimicrobial susceptibility testing (AST) remain labor-intensive and time-consuming, and are unable to provide early support to physicians in critical hours. To improve the effectiveness of early antibiotic therapy, Surface-enhanced Raman scattering (SERS) technology, has been used in bacterial detection and AST based on its high specificity and label-free features. To simplify sample preparation steps in SERS-AST, we proposed an automated microfluidic control system to integrate all required procedures into a single device. Our preliminary results demonstrated the system can achieve on-chip reagent replacement, bacteria trapping, and buffer exchange. Finally, in-situ SERS-AST was performed within 3.5 h by loading isolates of ampicilin susceptible and resistant E. coli and clear discrimination of two strains under antibiotic treatment was demonstrated. Overall, our system can standardize and simplify the SERS-AST protocol and implicate parallel bacterial detection. This prototypical integration demonstrates timely microbiological support to optimize early antibiotic therapy for fighting bacteremia.

A New Method for Determination of Minimum Biofilm Eradication Concentration for Accurate Antimicrobial Therapy

Antimicrobial susceptibility testing (AST) is an important technique to find the susceptibility pattern of clinical isolates in order to administer the appropriate drug. One such technique is minimum inhibitory concentration (MIC), which not only identifies the right drug but also suggests the appropriate concentration necessary to neutralize the organisms in planktonic form. MIC can vary in case of adherent organisms since they form biofilms and activate survival mechanisms like quorum sensing. Here we have strategized a new method which used an inoculator plate, a resazurin dye, and a standard plate to identify minimum biofilm eradication concentration (MBEC) of adherent organisms.

Correcting a Fundamental Flaw in the Paradigm for Antimicrobial Susceptibility Testing

The emergence and prevalence of antibiotic-resistant bacteria are an increasing cause of death worldwide, resulting in a global ‘call to action’ to avoid receding into an era lacking effective antibiotics. Despite the urgency, the healthcare industry still relies on a single in vitro bioassay to determine antibiotic efficacy. This assay fails to incorporate environmental factors normally present during host-pathogen interactions in vivo that significantly impact antibiotic efficacy. Here we report that standard antimicrobial susceptibility testing (AST) failed to detect antibiotics that are in fact effective in vivo; and frequently identified antibiotics that were instead ineffective as further confirmed in mouse models of infection and sepsis. Notably, AST performed in media mimicking host environments succeeded in identifying specific antibiotics that were effective in bacterial clearance and host survival, even though these same antibiotics failed in results using standard test media. Similarly, our revised media further identified antibiotics that were ineffective in vivo despite passing the AST standard for clinical use. Supplementation of AST medium with sodium bicarbonate, an abundant in vivo molecule that stimulates global changes in bacterial structure and gene expression, was found to be an important factor improving the predictive value of AST in the assignment of appropriate therapy. These findings have the potential to improve the means by which antibiotics are developed, tested, and prescribed.

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Standard antimicrobial susceptibility testing (AST) is fundamentally flawed because it is based largely on in vitro efficacy.

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AST performed under conditions that mimic natural infections improves the assignment of appropriate antibiotic therapy.

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In vivo altered susceptibility (IVAS) provides a new paradigm for drug discovery and therapeutic intervention.

Drug testing often excludes potent antibiotics for the treatment of bacterial infections, while frequently identifying antibiotics that are ineffective. However, drug testing under conditions that mimic natural infections succeeded in identifying effective antibiotics, even though these same antibiotics failed standard tests. This work suggests that standard drug-testing may be hindering patient treatment and slowing the process of discovery of new, effective, and safe antibiotics because it disqualifies effective compounds. These findings call for an overhaul of standardized drug testing which hasn't changed in > 50 years.

Comparison of Clinical Laboratory Standards Institute and European Committee on Antimicrobial Susceptibility Testing guidelines for the interpretation of antibiotic susceptibility at a University teaching hospital in Nairobi, Kenya: a cross-sectional study

Background

The Clinical Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines are the most popular breakpoint guidelines used in antimicrobial susceptibility testing worldwide. The EUCAST guidelines are freely available to users while CLSI is available for non-members as a package of three documents for US $500 annually. This is prohibitive for clinical microbiology laboratories in resource poor settings. We set out to compare antibiotic susceptibility determined by the two guidelines to determine whether adoption of EUCAST guidelines would significantly affect our susceptibility patterns.

Methods

We reviewed minimum inhibitory concentrations (MIC) of various antibiotics routinely reported for Escherichia coli (E. coli), Staphylococcus aureus (S. aureus) and Pseudomonas aeruginosa (P. aeruginosa) isolates from an automated microbiology identification system (VITEK-2) at the Aga Khan University Hospital Nairobi’s Pathology department. These MICs were then analyzed using both CLSI 2015 and EUCAST 2015 guidelines and classified as resistant, intermediate or susceptible. We compared the susceptibility and agreement between the CLSI and EUCAST categorizations.

Results

Susceptibility data from a total of 5165 E. coli, 1103 S. aureus and 532 P. aeruginosa isolates were included. The concordance rates of the two guidelines for E. coli, S. aureus and P. aeruginosa ranged from 78.2 to 100 %, 94.6 to 100 % and 89.1 to 95.5 % respectively. The kappa statistics for E. coli MICs revealed perfect agreement between CLSI and EUCAST for cefotaxime, ceftriaxone and trimethoprim–sulfamethoxazole, almost perfect agreement for ampicillin, ciprofloxacin, cefuroxime, gentamicin and ceftazidime, substantial agreement for meropenem, moderate agreement for cefepime and amoxicillin-clavulanate, fair agreement for nitrofurantoin and poor agreement for amikacin. For S. aureus the kappa statistics revealed perfect agreement for penicillin, trimethoprim–sulfamethoxazole, levofloxacin, oxacillin, linezolid and vancomycin, almost perfect agreement for clindamycin, erythromycin and tetracycline and moderate agreement for gentamicin. For P. aeruginosa the kappa analysis revealed moderate to almost perfect agreement for all the anti-pseudomonal antibiotics.

Conclusion

The results show comparable antibiotic susceptibility patterns between CLSI and EUCAST breakpoints. Given that EUCAST guidelines are freely available, it makes it easier for laboratories in resource poor settings to have an updated and readily available reference for interpreting antibiotic susceptibilities.

Rapid clinical bacteriology and its future impact

Clinical microbiology has always been a slowly evolving and conservative science. The sub-field of bacteriology has been and still is dominated for over a century by culture-based technologies. The integration of serological and molecular methodologies during the seventies and eighties of the previous century took place relatively slowly and in a cumbersome fashion. When nucleic acid amplification technologies became available in the early nineties, the predicted "revolution" was again slow but in the end a real paradigm shift did take place. Several of the culture-based technologies were successfully replaced by tests aimed at nucleic acid detection. More recently a second revolution occurred. Mass spectrometry was introduced and broadly accepted as a new diagnostic gold standard for microbial species identification. Apparently, the diagnostic landscape is changing, albeit slowly, and the combination of newly identified infectious etiologies and the availability of innovative technologies has now opened new avenues for modernizing clinical microbiology. However, the improvement of microbial antibiotic susceptibility testing is still lagging behind. In this review we aim to sketch the most recent developments in laboratory-based clinical bacteriology and to provide an overview of emerging novel diagnostic approaches.