Real-time PCR for universal antibiotic susceptibility testing

Mycobacterium avium ssp. paratuberculosis and Crohn's Disease-Diagnostic Microbiological Investigations Can Inform New Therapeutic Approaches

Mycobacterium avium ssp. paratuberculosis (MAP) is the cause of Johne's disease (JD), which is a chronic infectious gastrointestinal disease of ruminants and is often fatal. In humans, MAP has been associated with Crohn's disease (CD) for over a century, without conclusive evidence of pathogenicity. Numerous researchers have contributed to the subject, but there is still a need for evidence of the causation of CD by MAP. An infectious aetiology in CD that is attributable to MAP can only be proven by bacteriological investigations. There is an urgency in resolving this question due to the rising global incidence rates of CD. Recent papers have indicated the "therapeutic ceiling" may be close in the development of new biologics. Clinical trial outcomes have demonstrated mild or inconsistent improvements in therapeutic interventions over the last decades when compared with placebo. The necessity to revisit therapeutic options for CD is becoming more urgent and a renewed focus on causation is essential for progress in identifying new treatment options. This manuscript discusses newer interventions, such as vaccination, FMT, dietary remediation and gut microbiome regulation, that will become more relevant as existing therapeutic options expire. Revisiting the MAP theory as a potential infectious cause of CD, rather than the prevailing concept of an "aberrant immune response" will require expanding the current therapeutic programme to include potential new alternatives, and combinations of existing treatments. To advance research on MAP in humans, it is essential for microbiologists and medical scientists to microscopically detect CWDM and to biologically amplify the growth by directed culture.

Integrating rapid pathogen identification and antimicrobial susceptibility testing through multiplex TaqMan qPCR assay

Timely bacterial identification (ID) and antimicrobial susceptibility testing (AST) are of significance for therapy of bacteria-infected patients. In the present study, we developed a multiplex TaqMan qPCR assay for rapid and accurate ID and AST of three common hospital acquired pneumonia species, namely Acinetobacter baumannii, Klebsiella pneumoniae and Staphylococcus aureus. In this assay, DNA extraction and bacterial co-incubation with antibiotics are accomplished based on a common PCR instrument. ID of three bacteria is based on specific conserved DNA sequence fragment (gltA for A. baumannii, phoE for K. pneumoniae and nuc for S. aureus) detection through multiplex TaqMan qPCR assay within 80 min. AST of three bacteria could be acquired within 200 min based on genomic DNA fold change detection after 2 h of antibiotic exposure. Testing of 23 bronchoalveolar lavage fluid samples spiked by different A. baumannii isolates, 20 bronchoalveolar lavage fluid samples spiked by different K. pneumoniae isolates, and 14 bronchoalveolar lavage fluid samples spiked by different S. aureus isolates showed that the multiplex TaqMan qPCR assay had 100% (95% CI: 85.69-100), 100% (95% CI: 83.89-100) and 100% (95% CI:78.47-100) identification agreement with the initial spiked bacteria. Subsequent AST results compared with the standard broth microdilution method showed an overall agreement of 91.30% (95% CI: 73.20 to 97.58) for A. baumannii, 90% (95% CI: 69.90 to 97.21) for K. pneumoniae and 92.86% (95% CI: 68.53 to 98.73) for S. aureus based on the current multiplex TaqMan assay. Due to the high rapidity, good agreement, simplicity, and high throughput, this multiplex TaqMan assay could be helpful for ID and broad-spectrum AST in A. baumannii, K. pneumoniae and S. aureus, as well as potentially applicable for other clinical bacteria by changing the primers and probes.

Electrochemical Detection of Different Foodborne Bacteria for Point-of-Care Applications

Bacterial infections resulting from foodborne pathogenic bacteria cause millions of infections that greatly threaten human health and are one of the leading causes of mortality around the world. To counter this, the early, rapid, and accurate detection of bacterial infections is very important to address serious health issue concerns. We, therefore, present an electrochemical biosensor based on aptamers that selectively bind with the DNA of specific bacteria for the accurate and rapid detection of various foodborne bacteria for the selective determination of bacterial infection types. Different aptamers were synthesized and immobilized on Au electrodes for selective bindings of different types of bacterial DNA (Escherichia coli, Salmonella enterica, and Staphylococcus aureus) for the accurate detection and quantification of bacterial concentrations from 10¹ to 10⁷ CFU/mL without using any labeling methods. Under optimized conditions, the sensor showed a good response to the various concentrations of bacteria, and a robust calibration curve was obtained. The sensor could detect the bacterial concentration at meager quantities and possessed an LOD of 4.2 × 10¹, 6.1 × 10¹, and 4.4 × 10¹ CFU/mL for S. Typhimurium, E. Coli, and S. aureus, respectively, with a linear range from 10⁰ to 10⁴ CFU/mL for the total bacteria probe and 10⁰ to 10³ CFU/mL for individual probes, respectively. The proposed biosensor is simple and rapid and has shown a good response to bacterial DNA detections and thus can be applied in clinical applications and food safety monitoring.

High-Throughput Antimicrobial Susceptibility Testing of Escherichia coli by Wide-Field Mid-Infrared Photothermal Imaging of Protein Synthesis

Antimicrobial resistance poses great threats to global health and economics. Current gold-standard antimicrobial susceptibility testing (AST) requires extensive culture time (36-72 h) to determine susceptibility. There is an urgent need for rapid AST methods to slow down antimicrobial resistance. Here, we present a rapid AST method based on wide-field mid-infrared photothermal imaging of protein synthesis from ¹³C-glucose in Escherichia coli. Our wide-field approach achieved metabolic imaging for hundreds of bacteria at the single-cell resolution within seconds. The perturbed microbial protein synthesis can be probed within 1 h after antibiotic treatment in E. coli cells. The susceptibility of antibiotics with various mechanisms of action has been probed through monitoring protein synthesis, which promises great potential of the proposed platform toward clinical translation.

Rapid identification of methicillin-resistant Staphylococcus aureus by MALDI-TOF MS: A meta-analysis

Invasive infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are associated with high mortality and morbidity. The sooner the pathogen is determined, the better it is beneficial to patient. However, routine laboratory inspections are time-consuming and laborious. A thorough research was conducted in PubMed and Web of Science (until June 2021) to identify studies evaluating the accuracy of MRSA identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). STATA 15.0 software was used to analyze the pooled results of sensitivity, specificity, and 95% confidence intervals (CI). The summary receiver operating characteristic curves (SROC) and area under the curve (AUC) were utilized to show the overall performance of MALDI-TOF MS. Fifteen studies involving 2471 isolates were included in this study after the final selection in this meta-analysis. Using the random effects model forest plot to summarize the overall statistics, the sensitivity of MALDI-TOF MS for identifying MRSA was 92% (95% CI: 81%-97%), and the specificity was 97% (95% CI: 89%-99%). In the SROC curve, the AUC reached 0.99 (95% CI: 97%-99%). Deeks' test showed no significant publication bias in this meta-analysis. Compared with clinical reference methods, MALDI-TOF MS identification of MRSA shows a higher degree of sensitivity and specificity.

Rapid Detection of MCR-Mediated Colistin Resistance in Escherichia coli

Colistin is one of the last-resort antibiotics for infections caused by multidrug-resistant Gram-negative bacteria. However, the wide spread of novel plasmid-carrying colistin resistance genes mcr-1 and its variants substantially compromise colistin's therapeutic effectiveness and pose a severe danger to public health. To detect colistin-resistant microorganisms induced by mcr genes, rapid and reliable antibiotic susceptibility testing (AST) is imminently needed. In this study, we identified an RNA-based AST (RBAST) to discriminate between colistin-susceptible and mcr-1-mediated colistin-resistant bacteria. After short-time colistin treatment, RBAST can detect differentially expressed RNA biomarkers in bacteria. Those candidate mRNA biomarkers were successfully verified within colistin exposure temporal shifts, concentration shifts, and other mcr-1 variants. Furthermore, a group of clinical strains were effectively distinguished by using the RBAST approach during the 3-h test duration with over 93% accuracy. Taken together, our findings imply that certain mRNA transcripts produced in response to colistin treatment might be useful indicators for the development of fast AST for mcr-positive bacteria.

IMPORTANCE The emergence and prevalence of mcr-1 and its variants in humans, animals, and the environment pose a global public health threat. There is a pressing urgency to develop rapid and accurate methods to identify MCR-positive colistin-resistant bacteria in the clinical samples, providing a basis for subsequent effective antibiotic treatment. Using the specific mRNA signatures, we develop an RNA-based antibiotic susceptibility testing (RBAST) for effectively distinguishing colistin-susceptible and mcr-1-mediated colistin-resistant strains. Meanwhile, the detection efficiency of these RNA biomarkers was evidenced in other mcr variants-carrying strains. By comparing with the traditional AST method, the RBAST method was verified to successfully characterize a set of clinical isolates during 3 h assay time with over 93% accuracy. Our study provides a feasible method for the rapid detection of colistin-resistant strains in clinical practice.

Emerging Diabetic Foot Ulcer Microbiome Analysis Using Cutting Edge Technologies

One of the most prevalent complications of diabetes mellitus are diabetic foot ulcers (DFU). Diabetic foot ulcers represent a complex condition placing individuals at-risk for major lower extremity amputations and are an independent predictor of patient mortality. DFU heal poorly when standard of care therapy is applied. In fact, wound healing occurs only approximately 30% within 12 weeks and only 45% regardless of time when standard of care is utilized. Similarly, diabetic foot infections occur in half of all DFU and conventional microbiologic cultures can take several days to process before a result is known. DFU represent a significant challenge in this regard because DFU often demonstrate polymicrobial growth, become resistant to preferred antibiotic therapy, and do not inform providers about long-term prognosis. In addition, conventional culture yields may be affected by the timing of antibiotic administration and collection of tissue for analysis. This may lead to suboptimal antibiotic administration or debilitating amputations. The microbiome of DFU is a new frontier to better understand the interactions between host organisms and pathogenic ones. Newer molecular techniques are readily available to assist in analyzing the constituency of the microbiome of DFU. These emerging techniques have already been used to study the microbiome of DFU and have clinical implications that may alter standard of care practice in the near future. Here emerging molecular techniques that can provide clinicians with rapid DFU-related-information and help prognosticate outcomes in this vulnerable patient population are presented.

Diagnostic armamentarium of infectious keratitis: A comprehensive review

Infectious keratitis (IK) represents the leading cause of corneal blindness worldwide, particularly in developing countries. A good outcome of IK is contingent upon timely and accurate diagnosis followed by appropriate interventions. Currently, IK is primarily diagnosed on clinical grounds supplemented by microbiological investigations such as microscopic examination with stains, and culture and sensitivity testing. Although this is the most widely accepted practice adopted in most regions, such an approach is challenged by several factors, including indistinguishable clinical features shared among different causative organisms, polymicrobial infection, long diagnostic turnaround time, and variably low culture positivity rate. In this review, we aim to provide a comprehensive overview of the current diagnostic armamentarium of IK, encompassing conventional microbiological investigations, molecular diagnostics (including polymerase chain reaction and mass spectrometry), and imaging modalities (including anterior segment optical coherence tomography and in vivo confocal microscopy). We also highlight the potential roles of emerging technologies such as next-generation sequencing, artificial intelligence-assisted platforms. and tele-medicine in shaping the future diagnostic landscape of IK.

Determination of Klebsiella pneumoniae Susceptibility to Antibiotics Using Infrared Microscopy

Klebsiella pneumoniae (K. pneumoniae) is one of the most aggressive multidrug-resistant bacteria associated with human infections, resulting in high mortality and morbidity. We obtained 1190 K. pneumoniae isolates from different patients with urinary tract infections. The isolates were measured to determine their susceptibility regarding nine specific antibiotics. This study's primary goal is to evaluate the potential of infrared spectroscopy in tandem with machine learning to assess the susceptibility of K. pneumoniae within approximately 20 min following the first culture. Our results confirm that it was possible to classify the isolates into sensitive and resistant with a success rate higher than 80% for the tested antibiotics. These results prove the promising potential of infrared spectroscopy as a powerful method for a K. pneumoniae susceptibility test.

A large-scale investigation and identification of methicillin-resistant Staphylococcus aureus based on peaks binning of matrix-assisted laser desorption ionization-time of flight MS spectra

Recent studies have demonstrated that the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) could be used to detect superbugs, such as methicillin-resistant Staphylococcus aureus (MRSA). Due to an increasingly clinical need to classify between MRSA and methicillin-sensitive Staphylococcus aureus (MSSA) efficiently and effectively, we were motivated to develop a systematic pipeline based on a large-scale dataset of MS spectra. However, the shifting problem of peaks in MS spectra induced a low effectiveness in the classification between MRSA and MSSA isolates. Unlike previous works emphasizing on specific peaks, this study employs a binning method to cluster MS shifting ions into several representative peaks. A variety of bin sizes were evaluated to coalesce drifted or shifted MS peaks to a well-defined structured data. Then, various machine learning methods were performed to carry out the classification between MRSA and MSSA samples. Totally 4858 MS spectra of unique S. aureus isolates, including 2500 MRSA and 2358 MSSA instances, were collected by Chang Gung Memorial Hospitals, at Linkou and Kaohsiung branches, Taiwan. Based on the evaluation of Pearson correlation coefficients and the strategy of forward feature selection, a total of 200 peaks (with the bin size of 10 Da) were identified as the marker attributes for the construction of predictive models. These selected peaks, such as bins 2410-2419, 2450-2459 and 6590-6599 Da, have indicated remarkable differences between MRSA and MSSA, which were effective in the prediction of MRSA. The independent testing has revealed that the random forest model can provide a promising prediction with the area under the receiver operating characteristic curve (AUC) at 0.8450. When comparing to previous works conducted with hundreds of MS spectra, the proposed scheme demonstrates that incorporating machine learning method with a large-scale dataset of clinical MS spectra may be a feasible means for clinical physicians on the administration of correct antibiotics in shorter turn-around-time, which could reduce mortality, avoid drug resistance and shorten length of stay in hospital in the future.

Recent Development of Rapid Antimicrobial Susceptibility Testing Methods through Metabolic Profiling of Bacteria

Due to the inappropriate use and overuse of antibiotics, the emergence and spread of antibiotic-resistant bacteria are increasing and have become a major threat to human health. A key factor in the treatment of bacterial infections and slowing down the emergence of antibiotic resistance is to perform antimicrobial susceptibility testing (AST) of infecting bacteria rapidly to prescribe appropriate drugs and reduce the use of broad-spectrum antibiotics. Current phenotypic AST methods based on the detection of bacterial growth are generally reliable but are too slow. There is an urgent need for new methods that can perform AST rapidly. Bacterial metabolism is a fast process, as bacterial cells double about every 20 to 30 min for fast-growing species. Moreover, bacterial metabolism has shown to be related to drug resistance, so a comparison of differences in microbial metabolic processes in the presence or absence of antimicrobials provides an alternative approach to traditional culture for faster AST. In this review, we summarize recent developments in rapid AST methods through metabolic profiling of bacteria under antibiotic treatment.

Microfluidic Technology for Antibacterial Resistance Study and Antibiotic Susceptibility Testing: Review and Perspective

A review on microfluidic technology for antibacterial resistance study and antibiotic susceptibility testing (AST) is presented here. Antibiotic resistance has become a global health crisis in recent decades, severely threatening public health, patient care, economic growth, and even national security. It is extremely urgent that antibiotic resistance be well looked into and aggressively combated in order for us to survive this crisis. AST has been routinely utilized in determining bacterial susceptibility to antibiotics and identifying potential resistance. Yet conventional methods for AST are increasingly incompetent due to unsatisfactory test speed, high cost, and deficient reliability. Microfluidics has emerged as a powerful and very promising platform technology that has proven capable of addressing the limitation of conventional methods and advancing AST to a new level. Besides, potential technical challenges that are likely to hinder the development of microfluidic technology aimed at AST are observed and discussed. To conclude, it is noted that (1) the translation of microfluidic innovations from laboratories to be ready AST platforms remains a lengthy journey and (2) ensuring all relevant parties engaged in a collaborative and unified mode is foundational to the successful incubation of commercial microfluidic platforms for AST.

Microfluidic Systems for Antimicrobial Susceptibility Testing

Human health is threatened by the spread of antimicrobial resistance and resulting infections. One reason for the resistance spread is the treatment with inappropriate and ineffective antibiotics because standard antimicrobial susceptibility testing methods are time-consuming and laborious. To reduce the antimicrobial susceptibility detection time, minimize treatments with empirical broad-spectrum antibiotics, and thereby combat the further spread of antimicrobial resistance, faster and point-of-care methods are needed. This requires many different research approaches. Microfluidic systems for antimicrobial susceptibility testing offer the possibility to reduce the detection time, as small sample and reagent volumes can be used and the detection of single cells is possible. In some cases, the aim is to use human samples without pretreatment or pre-cultivation. This chapter first provides an overview of conventional detection methods. It then presents the potential of and various current approaches in microfluidics. The focus is on microfluidic methods for phenotypic antimicrobial susceptibility testing.

Antimicrobial properties of diethylamine NONOate, a nitric oxide donor, against Escherichia coli: a pilot study

The emergence of SARS-CoV-2, the causative agent of COVID-19, highlights the increasing need for new and effective antiviral and antimicrobial agents. The FDA has recently banned several active ingredients used in hand sanitizers, including triclosan and benzethonium chloride. Nitric oxide (NO) is involved in the innate immune response and is a major component of macrophage-mediated attack on foreign viruses and bacteria. The specific aim of this study was to assess the antibacterial effects of 2-(N,N-diethylamino)-diazenolate-2-oxide (DEA-NONOate) against Escherichia coli (E. coli). A bacterial growth assay was compared to an adenosine triphosphate (ATP) activity assay at various time points to assess effects of DEA-NONOate on E. coli growth. A UV/Vis spectrophotometer was used to determine concentration of E. coli by measuring optical density (OD) at 630 nm. A luminescent assay was used to measure ATP activity correlating to viable cells. DEA-NONOate at a concentration of 65 mM was able to inhibit the growth of E. coli with the same efficacy as 1 μg ml^-1 concentration of ciprofloxacin. Both the OD and ATP assays demonstrated a 99.9% reduction in E. coli. Both a 1 μg ml^-1 concentration of ciprofloxacin and a 65 mM concentration of DEA-NONOate achieved 99.9% inhibition of E. coli, verified using both optical density measurement of bacterial cultures in 96 well plates and a luminescent ATP activity assay. The bactericidal effects of DEA-NONOate against E. coli is proof-of-concept to pursue evaluation of nitric oxide-based formulations as antimicrobial and antiviral agents as hand sanitizers.

Resistance and Virulence Features of Bacteroides spp. Isolated from Abdominal Infections in Romanian Patients

Anaerobic bacteria are predominant residents of the normal microbiota of the skin and mucous membranes but are also known to be associated with a number of human infections including peritonitis, appendicitis, abscesses, ulcers and wound infections. Herein, we investigate the antibiotic resistance profiles as well as the genetic support of antibiotic resistance and virulence determinants of anaerobic bacteria isolated from intra-abdominal infections. The study was performed on 198 Romanian patients from which different clinical samples were taken intra-operatory and sent for microbiological analyses. From the total number of isolated strains, a subset of 75 Bacteroides spp. were selected and further investigated for antibiotic resistance and virulence features, at phenotypic and genetic level. Our results obtained through the analysis of a significant number of Bacteroides strains could shed light on the virulence potential and mechanisms by which anaerobic bacteria can cause endogenous infections.

Bacterial Isolation Microwell-Plug (μWELLplug) for Rapid Antibiotic Susceptibility Testing Using Morphology Analysis

The rapid and accurate diagnosis of infectious diseases with high morbidity rates is crucial because it can minimize the misuse and overuse of antibiotics and increase survival rates in dreadful conditions. The conventional antibiotic susceptibility test (AST) systems used to choose appropriate antibiotics require long wait times to obtain results and cannot prevent the misuse or overuse of antibiotics by clinicians who need to quickly treat patients and cannot wait to identify the underlying cause of their symptoms. Therefore, several rapid AST (rAST) methods have been developed to provide quick test results, but they are complicated to operate, require additional equipment or materials, and give less accurate results than the conventional AST methods. In this study, we propose an rAST method that can obtain precise outcomes from a simple process with a short running time using a bacterial isolation microwell-plug (μWELLplug) in a conventional 96-well plate. The specifically designed hydrogel component of the μWELLplug provides a simple process for cell isolation and the observation of bacterial growth and morphological changes induced by a variety of antibiotic concentrations. The μWELLplug is placed over each well of the 96-well plate, and then bacterial or eukaryotic cells are isolated in the microwells and treated with different antibiotic concentrations to observe their effects. Saccharomyces cerevisiae (yeast, eukaryote), Streptomyces atratus (actinomycetes, prokaryote), Escherichia coli, Staphylococcus aureus, and methicillin-resistant S. aureus were cultivated and tested using the μWELLplug. The minimum inhibitory concentration values from this system were obtained in 3-4 h and correlated well with those from the conventional AST methods whose running time is 18-24 h.

Electrical antimicrobial susceptibility testing based on aptamer-functionalized capacitance sensor array for clinical isolates

To prescribe effective antibiotics to patients with bacterial infections in a timely manner and to avoid the misuse of antibiotics, a rapid antimicrobial susceptibility test (AST) is essential. However, conventional AST methods require more than 16 h to provide results; thus, we developed an electrical AST (e-AST) system, which provides results within 6 h. The proposed e-AST is based on an array of 60 aptamer-functionalized capacitance sensors that are comparable to currently available AST panels and a pattern-matching algorithm. The performance of the e-AST was evaluated in comparison with that of broth microdilution as the reference test for clinical strains isolated from septic patients. A total of 4,554 tests using e-AST showed a categorical agreement of 97% with a minor error of 2.2%, major error of 0.38%, and very major error of 0.38%. We expect that the proposed e-AST could potentially aid antimicrobial stewardship efforts and lead to improved patient outcomes.

In vitro evaluation of various antimicrobials against field mycoplasma gallisepticum and mycoplasma synoviae isolates in Egypt

Among many avian mycoplasmas, Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS) are recognized as the main etiological agents of respiratory diseases and infectious synovitis in chickens and turkeys causing tremendous economic losses worldwide. Therefore, proper treatment is promoted for the control of these diseases. This study was the first in Egypt to evaluate the in vitro efficacy of various antimicrobials against field MG and MS isolates recovered from chicken and turkey flocks using both conventional broth microdilution and quantitative real-time polymerase chain reaction assays. Totally, 47 mycoplasma isolates were recovered from 160 collected tracheal samples (29.4%). Of these, 44 MG (27.5%) and 3 MS (1.9%) were identified using conventional and molecular assays. The in vitro susceptibilities of 4 representative mycoplasma field isolates (3 MG and one MS) to 8 antibiotics and 4 essential oils were investigated. The tested isolates showed various susceptibilities to tested antimicrobials. Toldin CRD, followed by clove, cumin, and cinnamon oils were effective against both MG and MS clinical isolates with minimum inhibitory concentration (MIC) values ranging from 0.49 to 15.63 µg/mL. Similarly, tylvalosin was the most active antibiotic against MG and MS isolates with the lowest MIC values (0.015 to 0.03 µg/mL). DNA loads of both MG mgc2 and MS vlhA genes were markedly decreased upon treatment with majority of the tested antimicrobials confirming their effectiveness as was also evaluated by conventional MIC results. In conclusion, Toldin CRD and tylvalosin were found to be the most effective antimicrobials in this study. This finding highlights the importance of using these antimicrobials in controlling mycoplasma infections in chickens and turkeys.

Differential DNA accessibility to polymerase enables 30-minute phenotypic β-lactam antibiotic susceptibility testing of carbapenem-resistant Enterobacteriaceae

The rise in carbapenem-resistant Enterobacteriaceae (CRE) infections has created a global health emergency, underlining the critical need to develop faster diagnostics to treat swiftly and correctly. Although rapid pathogen-identification (ID) tests are being developed, gold-standard antibiotic susceptibility testing (AST) remains unacceptably slow (1-2 d), and innovative approaches for rapid phenotypic ASTs for CREs are urgently needed. Motivated by this need, in this manuscript we tested the hypothesis that upon treatment with β-lactam antibiotics, susceptible Enterobacteriaceae isolates would become sufficiently permeabilized, making some of their DNA accessible to added polymerase and primers. Further, we hypothesized that this accessible DNA would be detectable directly by isothermal amplification methods that do not fully lyse bacterial cells. We build on these results to develop the polymerase-accessibility AST (pol-aAST), a new phenotypic approach for β-lactams, the major antibiotic class for gram-negative infections. We test isolates of the 3 causative pathogens of CRE infections using ceftriaxone (CRO), ertapenem (ETP), and meropenem (MEM) and demonstrate agreement with gold-standard AST. Importantly, pol-aAST correctly categorized resistant isolates that are undetectable by current genotypic methods (negative for β-lactamase genes or lacking predictive genotypes). We also test contrived and clinical urine samples. We show that the pol-aAST can be performed in 30 min sample-to-answer using contrived urine samples and has the potential to be performed directly on clinical urine specimens.

Nanoarray Digital Polymerase Chain Reaction with High-Resolution Melt for Enabling Broad Bacteria Identification and Pheno-Molecular Antimicrobial Susceptibility Test

Toward combating infectious diseases caused by pathogenic bacteria, there remains an unmet need for diagnostic tools that can broadly identify the causative bacteria and determine their antimicrobial susceptibilities from complex and even polymicrobial samples in a timely manner. To address this need, a microfluidic and machine-learning-based platform that performs broad bacteria identification (ID) and rapid yet reliable antimicrobial susceptibility testing (AST) is developed. Specifically, this platform builds on "pheno-molecular AST", a strategy that transforms nucleic acid amplification tests (NAATs) into phenotypic AST through quantitative detection of bacterial genomic replication, and utilizes digital polymerase chain reaction (PCR) and digital high-resolution melt (HRM) to quantify and identify bacterial DNA molecules. Bacterial species are identified using integrated experiment-machine learning algorithm via HRM profiles. Digital DNA quantification allows for rapid growth measurement that reflects susceptibility profiles of each bacterial species within only 30 min of antibiotic exposure. As a demonstration, multiple bacterial species and their susceptibility profiles in a spiked-in polymicrobial urine specimen were correctly identified with a total turnaround time of ∼4 h. With further development and clinical validation, this platform holds the potential for improving clinical diagnostics and enabling targeted antibiotic treatments.

Whole Slide Imaging for High-Throughput Sensing Antibiotic Resistance at Single-Bacterium Level and Its Application to Rapid Antibiotic Susceptibility Testing

Since conventional culture-based antibiotic susceptibility testing (AST) methods are too time-consuming (typically 24–72 h), rapid AST is urgently needed for preventing the increasing emergence and spread of antibiotic resistant infections. Although several phenotypic antibiotic resistance sensing modalities are able to reduce the AST time to a few hours or less, concerning the biological heterogeneity, their accuracy or limit of detection are limited by low throughput. Here, we present a rapid AST method based on whole slide imaging (WSI)-enabled high-throughput sensing antibiotic resistance at single-bacterium level. The time for determining the minimum inhibitory concentration (MIC) was theoretically shortest, which ensures that the growth of each individual cell present in a large population is inhibited. As a demonstration, our technique was able to sense the growth of at least several thousand bacteria at single-cell level. Reliable MIC of Enterobacter cloacae against gentamicin was obtained within 1 h, while the gold standard broth dilution method required at least 16 h for the same result. In addition, the application of our method prevails over other imaging-based AST approaches in allowing rapid and accurate determination of antibiotic susceptibility for phenotypically heterogeneous samples, in which the number of antibiotic resistant cells was negligible compared to that of the susceptible cells. Hence, our method shows great promise for both rapid AST determination and point-of-care testing of complex clinical bacteria isolates.

Emerging Analytical Techniques for Rapid Pathogen Identification and Susceptibility Testing

In the face of looming threats from multi-drug resistant microorganisms, there is a growing need for technologies that will enable rapid identification and drug susceptibility profiling of these pathogens in health care settings. In particular, recent progress in microfluidics and nucleic acid amplification is pushing the boundaries of timescale for diagnosing bacterial infections. With a diverse range of techniques and parallel developments in the field of analytical chemistry, an integrative perspective is needed to understand the significance of these developments. This review examines the scope of new developments in assay technologies grouped by key enabling domains of research. First, we examine recent development in nucleic acid amplification assays for rapid identification and drug susceptibility testing in bacterial infections. Next, we examine advances in microfluidics that facilitate acceleration of diagnostic assays via integration and scale. Lastly, recentdevelopments in biosensor technologies are reviewed. We conclude this review with perspectives on the use of emerging concepts to develop paradigm-changing assays.

How to accelerate antimicrobial susceptibility testing

BACKGROUND

Antimicrobial susceptibility testing (AST) results are crucial for timely administration of effective antimicrobial treatment, and, thus, should be made available to clinicians as fast as possible. In particular, increasing rates of multidrug-resistant organisms emphasize the need for rapid AST (rAST).

OBJECTIVES

This article aims to provide microbiologists and clinicians with a critical overview of the current state of possibilities to accelerate AST. We also intend to discuss technical and strategic aspects of rAST, which may be helpful to academic researchers and assay developers in the industry.

SOURCES

We have reviewed literature on rAST methods and their implementation in routine diagnostics.

CONTENT

Phenotypic rAST is universal, mechanism-independent and allows exact categorization, but it demands time for the microorganisms to start the growth and to express the response to antibiotics. Detection of selected resistance mechanisms is more rapid, but the interpretation of its clinical impact is limited. Technical challenges of phenotypic rAST include inoculum effect, delayed expression of resistance, lag phase and initial biomass increase in susceptible isolates. Criteria for a successful rAST assay are ease of use, random access, capacity for simultaneous testing of multiple specimens, affordability and financial attractiveness for industry. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based AST seems to be particularly promising, as it can optimally be combined with MALDI-TOF MS identification. Direct testing from clinical specimens provides particularly early findings, with positive blood cultures being the most suitable specimen type. Polymicrobial samples and inoculum effect are serious obstacles for direct AST from other clinical specimens. Next to the technology improvement, optimization of pre-analytics and laboratory organization is essential.

IMPLICATIONS

It appears feasible to generate an AST report within the same working shift; however, only affordable and easy-to-use rAST technologies have a chance to enter broad diagnostic routine. Efforts should be made by industry, authorities and academia to enable wide dissemination of rAST in clinical diagnostics.

A Guide to Bacterial Culture Identification And Results Interpretation

PURPOSE

To provide a guide to interpreting bacterial culture results.

METHODS

Studies were identified via a PubMed literature search (from 1966 to January 2018). Search terms included microbial sensitivity tests, microbial drug resistance, and anti-infective agents/pharmacology. Articles were included if they were published in English. References within identified articles were also reviewed.

RESULTS

This paper reviewed core concepts of interpreting bacterial culture results, including timing of cultures, common culture sites, potential for contamination, interpreting the Gram stain, role of rapid diagnostic tests, conventional antibiotic susceptibility testing, and automated testing.

CONCLUSION

This guide can assist pharmacists in their role as integral members of the antimicrobial stewardship team in an effort to improve patient care.

A rapid and simple detection method for phenotypic antimicrobial resistance in Escherichia coli by loop-mediated isothermal amplification

PURPOSE

In infectious disease therapy, administration of adequate antimicrobial agents is essential for preventing the emergence and spread of resistant bacteria. However, conventional antimicrobial susceptibility testing (AST), based on bacterial growth, is time consuming; therefore, a rapid, simple assay is needed for the timely selection of appropriate antibiotics in clinical laboratories. Here, we established a simple, cost-effective, time-saving and highly sensitive AST assay based on loop-mediated isothermal amplification (LAMP).

METHODOLOGY

The targeted bacteria were cultivated for a short period with or without antibiotic before the LAMP reaction. The time to detect a positive reaction with LAMP was used to generate a threshold time (Tt) value, and subtraction of the Tt value for an antibiotic-free sample from the Tt value in an antibiotic-exposed sample generated the ΔTt value, which was used as a marker of antimicrobial susceptibility. The ΔTt value generated using the LAMP-based assay simply and quickly detected antimicrobial resistance in clinical Escherichia coli isolates.

RESULTS

Detection of susceptibility to levofloxacin using the ΔTt value perfectly matched with the results of the conventional assay. In addition, the sensitivity and specificity for the detection of ampicillin, trimethoprim-sulfamethoxazole and fosfomycin resistance were 100 %, 93.8 %, 100 % and 80.0 %, 93.3 %, 97.6 %, respectively.

CONCLUSION

These results showed that this LAMP-based AST has high sensitivity and specificity for detecting resistant strains and a significant time advantage compared with the conventional method.

Rapid antibiotic susceptibility testing from blood culture bottles with species agnostic real-time polymerase chain reaction

Development and implementation of rapid antimicrobial susceptibility testing is critical for guiding patient care and improving clinical outcomes, especially in cases of sepsis. One approach to reduce the time-to-answer for antimicrobial susceptibility is monitoring the inhibition of DNA production, as differences in DNA concentrations are more quickly impacted compared to optical density changes in traditional antimicrobial susceptibility testing. Here, we use real-time PCR to rapidly determine antimicrobial susceptibility after short incubations with antibiotic. Application of this assay to a collection of 144 isolates in mock blood culture, covering medically relevant pathogens displaying high rates of resistance, provided susceptibility data in under 4 hours. This assay provided categorical agreement with a reference method in 96.3% of cases across all species. Sequencing of a subset of PCR amplicons showed accurate genus level identification. Overall, implementation of this method could provide accurate susceptibility results with a reduced time-to-answer for a number of medically relevant bacteria commonly isolated from blood culture.

Recent Advances in the Race to Design a Rapid Diagnostic Test for Antimicrobial Resistance

Even with advances in antibiotic therapies, bacterial infections persistently plague society and have amounted to one of the most prevalent issues in healthcare today. Moreover, the improper and excessive administration of antibiotics has led to resistance of many pathogens to prescribed therapies, rendering such antibiotics ineffective against infections. While the identification and detection of bacteria in a patient's sample is critical for point-of-care diagnostics and in a clinical setting, the consequent determination of the correct antibiotic for a patient-tailored therapy is equally crucial. As a result, many recent research efforts have been focused on the development of sensors and systems that correctly guide a physician to the best antibiotic to prescribe for an infection, which can in turn, significantly reduce the instances of antibiotic resistance and the evolution of bacteria "superbugs." This review details the advantages and shortcomings of the recent advances (focusing from 2016 and onward) made in the developments of antimicrobial susceptibility testing (AST) measurements. Detection of antibiotic resistance by genomic AST techniques relies on the prediction of antibiotic resistance via extracted bacterial DNA content, while phenotypic determinations typically track physiological changes in cells and/or populations exposed to antibiotics. Regardless of the method used for AST, factors such as cost, scalability, and assay time need to be weighed into their design. With all of the expansive innovation in the field, which technology and sensing systems demonstrate the potential to detect antimicrobial resistance in a clinical setting?

A "Culture" Shift: Broad Bacterial Detection, Identification, and Antimicrobial Susceptibility Testing Directly from Whole Blood

BACKGROUND

The time required for bloodstream pathogen detection, identification (ID), and antimicrobial susceptibility testing (AST) does not satisfy the acute needs of disease management. Conventional methods take up to 3 days for ID and AST. Molecular diagnostics have reduced times for ID, but their promise to supplant culture is unmet because AST times remain slow. We developed a combined quantitative PCR (qPCR)-based ID+AST assay with sequential detection, ID, and AST of leading nosocomial bacterial pathogens.

METHODS

ID+AST was performed on whole blood samples by (a) removing blood cells, (b) brief bacterial enrichment, (c) bacterial detection and ID, and (d) species-specific antimicrobial treatment. Broad-spectrum qPCR of the internal transcribed spacer between the 16S and 23S was amplified for detection. High-resolution melting identified the species with a curve classifier. AST was enabled by Ct differences between treated and untreated samples.

RESULTS

A detection limit of 1 CFU/mL was achieved for Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus. All species were accurately identified by unique melting curves. Antimicrobial minimum inhibitory concentrations were identified with Ct differences of ≥1 cycle. Using an RNA target allowed reduction of AST incubation time from 60 min to 5 min. Rapid-cycle amplification reduced qPCR times by 83% to 30 min.

CONCLUSIONS

Combined, sequential ID+AST protocols allow rapid and reliable detection, ID, and AST for the diagnosis of bloodstream infections, enabling conversion of empiric to targeted therapy by the second dose of antimicrobials.

RNA markers enable phenotypic test of antibiotic susceptibility in Neisseria gonorrhoeae after 10 minutes of ciprofloxacin exposure

Antimicrobial-resistant Neisseria gonorrhoeae is an urgent public-health threat, with continued worldwide incidents of infection and rising resistance to antimicrobials. Traditional culture-based methods for antibiotic susceptibility testing are unacceptably slow (1-2 days), resulting in the use of broad-spectrum antibiotics and the further development and spread of resistance. Critically needed is a rapid antibiotic susceptibility test (AST) that can guide treatment at the point-of-care. Rapid phenotypic approaches using quantification of DNA have been demonstrated for fast-growing organisms (e.g. E. coli) but are challenging for slower-growing pathogens such as N. gonorrhoeae. Here, we investigate the potential of RNA signatures to provide phenotypic responses to antibiotics in N. gonorrhoeae that are faster and greater in magnitude compared with DNA. Using RNA sequencing, we identified antibiotic-responsive transcripts. Significant shifts (>4-fold change) in transcript levels occurred within 5 min of antibiotic exposure. We designed assays for responsive transcripts with the highest abundances and fold changes, and validated gene expression using digital PCR. Using the top two markers (porB and rpmB) we correctly determined the antibiotic susceptibility and resistance of 49 clinical isolates after 10 min exposure to ciprofloxacin. RNA signatures are therefore promising as an approach on which to build rapid AST devices for N. gonorrhoeae at the point-of-care, which is critical for disease management, surveillance, and antibiotic stewardship efforts.

Rapid pathogen-specific phenotypic antibiotic susceptibility testing using digital LAMP quantification in clinical samples

Rapid antimicrobial susceptibility testing (AST) is urgently needed for informing treatment decisions and preventing the spread of antimicrobial resistance resulting from the misuse and overuse of antibiotics. To date, no phenotypic AST exists that can be performed within a single patient visit (30 min) directly from clinical samples. We show that AST results can be obtained by using digital nucleic acid quantification to measure the phenotypic response of Escherichia coli present within clinical urine samples exposed to an antibiotic for 15 min. We performed this rapid AST using our ultrafast (~7 min) digital real-time loop-mediated isothermal amplification (dLAMP) assay [area under the curve (AUC), 0.96] and compared the results to a commercial (~2 hours) digital polymerase chain reaction assay (AUC, 0.98). The rapid dLAMP assay can be used with SlipChip microfluidic devices to determine the phenotypic antibiotic susceptibility of E. coli directly from clinical urine samples in less than 30 min. With further development for additional pathogens, antibiotics, and sample types, rapid digital AST (dAST) could enable rapid clinical decision-making, improve management of infectious diseases, and facilitate antimicrobial stewardship.

New Laboratory Tools for Emerging Bacterial Challenges

Since its creation, the Méditerranée-Infection foundation has aimed at optimizing the management of infectious diseases and surveying the local and global epidemiology. This pivotal role was permitted by the development of rational sampling, point-of-care tests, and extended automation as well as new technologies, including mass spectrometry for colony identification, real-time genomics for isolate characterization, and the development of versatile and permissive culture systems. By identifying and characterizing emerging microbial pathogens, these developments provided significant breakthroughs in infectious diseases.

Parallel susceptibility testing of bacteria through culture-quantitative PCR in 96-well plates

OBJECTIVE

The methods combining culture and quantitative PCR(qPCR) offer new solutions for rapid antibiotic susceptibility testing(AST). However, the multiple steps of DNA extraction and cold storage of PCR reagents needed make them unsuitable for rapid high throughput AST. In this study, a parallel culture-qPCR method was developed to overcome above problems.

METHOD

In this method, bacteria culture and DNA extraction automatically and simultaneously completed through using a common PCR instrument as a controllable heating device. A lyophilized 16S rDNA targeted qPCR reagent was also developed, which was stable and could be kept at 4°C for long time and at 37°C for about two months.

RESULT

Testing of 36 P. aeruginosa isolates and 28 S. aureus isolates showed that the method had good agreements with the standard broth microdilution method, with an overall agreement of 97.22% (95% CI, 85.83-99.51) for P. aeruginosa and 96.43% (95% CI, 79.76-99.81) for S. aureus. This method could test 12 samples against a panel of up to 7 antibiotics simultaneously in two 96-well PCR plates within 4h, which greatly improves the testing efficiency of the culture-qPCR method.

CONCLUSION

With rapidness to obtain results and the capabilities for automation and multiple-sample testing, the parallel culture-qPCR method would have great potentials in clinical labs.

Growth of Escherichia coli on the GaAs (001) surface

Detection of pathogenic bacteria and monitoring their susceptibility to antibiotics are of great importance in the fields of medicine, pharmaceutical research, as well as water and food industries. In order to develop a photonic biosensor for detection of bacteria by taking advantage of photoluminescence (PL) of GaAs-based devices, we have investigated the capture and growth of Escherichia coli K12 on bare and biofunctionalized surfaces of GaAs (001) - a material of interest for capping different semiconductor microstructures. The results were compared with the capture and growth of Escherichia coli K12 on Au surfaces that have commonly been applied for studying a variety of biological and biochemical reactions. We found that neither GaAs nor Au-coated glass wafers placed in Petri dishes inoculated with bacteria inhibited bacterial growth in nutrient agar, regardless of the wafers being bare or biofunctionalized. However, the capture and growth of bacteria on biofunctionalized surfaces of GaAs and Au wafers kept in a flow cell and exposed to different concentrations of bacteria and growth medium revealed that the initial surface coverage and the subsequent bacterial growth were dependent on the biofunctionalization architecture, with antibody-coated surfaces clearly being most efficient in capturing bacteria and offering better conditions for growth of bacteria. We have observed that, as long as the GaAs wafers were exposed to bacterial suspensions at concentrations of at least 10⁵ CFU/mL, bacteria could grow on the surface of wafers, regardless of the type of biofunctionalization architecture used to capture the bacteria. These results provide important insight towards the successful development of GaAs-based devices designed for photonic monitoring of bacterial reactions to different biochemical environments.

Aptamer-functionalized capacitance sensors for real-time monitoring of bacterial growth and antibiotic susceptibility

To prevent spread of infection and antibiotic resistance, fast and accurate diagnosis of bacterial infection and subsequent administration of antimicrobial agents are important. However, conventional methods for bacterial detection and antibiotic susceptibility testing (AST) require more than two days, leading to delays that have contributed to an increase in antibiotic-resistant bacteria. Here, we report an aptamer-functionalized capacitance sensor array that can monitor bacterial growth and antibiotic susceptibility in real-time. While E. coli and S. aureus were cultured, the capacitance increased over time, and apparent bacterial growth curves were observed even when 10 CFU/mL bacteria was inoculated. Furthermore, because of the selectivity of aptamers, bacteria could be identified within 1h using the capacitance sensor array functionalized with aptamers. In addition to bacterial growth, antibiotic susceptibility could be monitored in real-time. When bacteria were treated with antibiotics above the minimum inhibitory concentration (MIC), the capacitance decreased because the bacterial growth was inhibited. These results demonstrate that the aptamer-functionalized capacitance sensor array might be applied for rapid ASTs.

Rapid Antibiotic Susceptibility Testing of Uropathogenic E. coli by Tracking Submicron Scale Motion of Single Bacterial Cells

To combat antibiotic resistance, a rapid antibiotic susceptibility testing (AST) technology that can identify resistant infections at disease onset is required. Current clinical AST technologies take 1-3 days, which is often too slow for accurate treatment. Here we demonstrate a rapid AST method by tracking sub-μm scale bacterial motion with an optical imaging and tracking technique. We apply the method to clinically relevant bacterial pathogens, Escherichia coli O157: H7 and uropathogenic E. coli (UPEC) loosely tethered to a glass surface. By analyzing dose-dependent sub-μm motion changes in a population of bacterial cells, we obtain the minimum bactericidal concentration within 2 h using human urine samples spiked with UPEC. We validate the AST method using the standard culture-based AST methods. In addition to population studies, the method allows single cell analysis, which can identify subpopulations of resistance strains within a sample.

First Report on a Randomized Investigation of Antimicrobial Resistance in Fecal Indicator Bacteria from Livestock, Poultry, and Humans in Tanzania

This study provides an estimate of antimicrobial resistance in intestinal indicator bacteria from humans (n = 97) and food animals (n = 388) in Tanzania. More than 70% of all fecal samples contained tetracycline (TE), sulfamethoxazole (STX), and ampicillin (AMP)-resistant coliforms, while cefotaxime (CTX)-resistant coliforms were observed in 40% of all samples. The average Log₁₀ colony forming units/g of CTX-resistant coliforms in samples from humans were 2.20. Of 390 Escherichia coli tested, 66.4% were resistant to TE, 54.9% to STX, 54.9% to streptomycin, and 36.4% to CTX. Isolates were commonly (65.1%) multiresistant. All CTX-resistant isolates contained bla_CTX-M gene type. AMP- and vancomycin-resistant enterococci were rare, and the average concentrations in positive samples were low (log₁₀ 0.9 and 0.4, respectively). A low-to-moderate resistance (2.1-15%) was detected in 240 enterococci isolates to the drugs tested, except for rifampicin resistance (75.2% of isolates). The average number of sulII gene copies varied between Log₁₀ 5.37 and 5.68 with no significant difference between sample source, while cattle had significantly higher number of tetW genes than humans. These findings, based on randomly obtained samples, will be instrumental in designing antimicrobial resistance (AMR) intervention strategies for Tanzania.

Current and emerging techniques for antibiotic susceptibility tests

Infectious diseases caused by bacterial pathogens are a worldwide burden. Serious bacterial infection-related complications, such as sepsis, affect over a million people every year with mortality rates ranging from 30% to 50%. Crucial clinical microbiology laboratory responsibilities associated with patient management and treatment include isolating and identifying the causative bacterium and performing antibiotic susceptibility tests (ASTs), which are labor-intensive, complex, imprecise, and slow (taking days, depending on the growth rate of the pathogen). Considering the life-threatening condition of a septic patient and the increasing prevalence of antibiotic-resistant bacteria in hospitals, rapid and automated diagnostic tools are needed. This review summarizes the existing commercial AST methods and discusses some of the promising emerging AST tools that will empower humans to win the evolutionary war between microbial genes and human wits.

Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility after only 15 Minutes of Antibiotic Exposure

Rapid antimicrobial susceptibility testing (AST) would decrease misuse and overuse of antibiotics. The "holy grail" of AST is a phenotype-based test that can be performed within a doctor visit. Such a test requires the ability to determine a pathogen's susceptibility after only a short antibiotic exposure. Herein, digital PCR (dPCR) was employed to test whether measuring DNA replication of the target pathogen through digital single-molecule counting would shorten the required time of antibiotic exposure. Partitioning bacterial chromosomal DNA into many small volumes during dPCR enabled AST results after short exposure times by 1) precise quantification and 2) a measurement of how antibiotics affect the states of macromolecular assembly of bacterial chromosomes. This digital AST (dAST) determined susceptibility of clinical isolates from urinary tract infections (UTIs) after 15 min of exposure for all four antibiotic classes relevant to UTIs. This work lays the foundation to develop a rapid, point-of-care AST and strengthen global antibiotic stewardship.

Cell-on-hydrogel platform made of agar and alginate for rapid, low-cost, multidimensional test of antimicrobial susceptibility

Antimicrobial resistance (AMR) is a rapidly increasing threat to the effective treatment of infectious diseases worldwide. The two major remedies include: (1) using narrow-spectrum antibiotics based on rapid diagnosis; and (2) developing new antibiotics. A key part of both remedies is the antimicrobial susceptibility test (AST). However, the current standard ASTs that monitor colony formation are costly and time-consuming and the new strategies proposed are not yet practical to be implemented. Herein, we report a strategy to fabricate whole-hydrogel microfluidic chips using alginate-doped agar. This agar-based microfabrication makes it possible to prepare inexpensive hydrogel devices, and allows a seamless link between microfluidics and conventional agar-based cell culture. Different from common microfluidic systems, in our system the cells are cultured on top of the device, similar to normal agar plate culture; on the other hand, the microfluidic channels inside the hydrogel allow precise generation of linear gradient of drugs, thus giving a better performance than the conventional disk diffusion method. Cells in this system are not exposed to any shear flow, which allows the reliable tracking of individual cells and AST results to be obtained within 2-3 hours. Furthermore, our system could test the synergistic effect of drugs through two-dimensional gradient generation. Finally, the platform could be directly implemented to new drug discovery and other applications wherein a fast, cost-efficient method for studying the response of microorganisms upon drug administration is desirable.

A primer on on-demand polymerase chain reaction technology

Efforts to reduce health care-associated infections (HAIs) have grown in both scale and sophistication over the past few decades; however, the increasing threat of antimicrobial resistance and the impact of new legislation regarding HAIs on health care economics make the fight against them all the more urgent. On-demand polymerase chain reaction (PCR) technology has proven to be a highly effective weapon in this fight, offering the ability to accurately and efficiently identify disease-causing pathogens such that targeted and directed therapy can be initiated at the point of care. As a result, on-demand PCR technology has far-reaching influences on HAI rates, health care outcomes, hospital length of stay, isolation days, patient satisfaction, antibiotic stewardship, and health care economics. The basics of on-demand PCR technology and its potential to impact health care have not been widely incorporated into health care education and enrichment programs for many of those involved in infection control and prevention, however. This article serves as a primer on on-demand PCR technology and its ramifications.

Conjugated Polythiophene for Rapid, Simple, and High-Throughput Screening of Antimicrobial Photosensitizers

The cationic conjugated poly[3-(3'-N,N,N-triethylamino-1'-propyloxy)-4-methyl-2,5-thiophene hydrochloride] (PMNT) has been developed for high-throughput screening of photodynamic antimicrobial chemotherapy photosensitizers (PSs). The bacterial number can be detected quantitatively by PMNT via various fluorescence quenching efficiencies. The photosensitized inactivation of bacteria is not efficient with ineffective PSs, and thus the bacteria grow exponentially and can be coated tightly by PMNT through electrostatic and hydrophobic interactions, resulting in aggregates and fluorescence quenching of PMNT, whereas, conversely, effective PSs lead to original and strong fluorescence of PMNT. This new platform of high-throughput screening is promising for discovering new PSs.

Microbiology and treatment of acute apical abscesses

Acute apical abscess is the most common form of dental abscess and is caused by infection of the root canal of the tooth. It is usually localized intraorally, but in some cases the apical abscess may spread and result in severe complications or even mortality. The reasons why dental root canal infections can become symptomatic and evolve to severe spreading and sometimes life-threatening abscesses remain elusive. Studies using culture and advanced molecular microbiology methods for microbial identification in apical abscesses have demonstrated a multispecies community conspicuously dominated by anaerobic bacteria. Species/phylotypes commonly found in these infections belong to the genera Fusobacterium, Parvimonas, Prevotella, Porphyromonas, Dialister, Streptococcus, and Treponema. Advances in DNA sequencing technologies and computational biology have substantially enhanced the knowledge of the microbiota associated with acute apical abscesses and shed some light on the etiopathogeny of this disease. Species richness and abundance and the resulting network of interactions among community members may affect the collective pathogenicity and contribute to the development of acute infections. Disease modifiers, including transient or permanent host-related factors, may also influence the development and severity of acute abscesses. This review focuses on the current evidence about the etiology and treatment of acute apical abscesses and how the process is influenced by host-related factors and proposes future directions in research, diagnosis, and therapeutic approaches to deal with this disease.

Feasibility study demonstrating that enzymatic template generation and amplification can be employed as a novel method for molecular antimicrobial susceptibility testing

Background

Antimicrobial Susceptibility Testing (AST) is a methodology in which the sensitivity of a microorganism is determined via its inability to proliferate in the presence of an antimicrobial agent. Results are reported as minimum inhibitory concentrations (MICs). The present study demonstrates that measurement of DNA polymerase activity via Enzymatic Template Generation and Amplification (ETGA) can be used as a novel means of determining the MIC of a microbe to an antibiotic agent much sooner than the current standardized method.

Methods

Time course analysis of ETGA is presented from bacterial cultures containing antibiotic agents and compared to the end-point results of standard macrobroth method AST.

Results

MIC determinations from ETGA results at 4, 6, and 22 hours are compared to the MICs from the standard method and the results are shown to be in agreement. Additionally, reliable AST analysis using ETGA can be performed on bacteria harvested directly from spiked blood cultures.

Conclusions

AST analysis with ETGA is shown to be equivalent to AST analysis using gene-specific qPCR assays against the measured microbe. Future development of this novel method for performing AST in a clinical setting is discussed.

Establishing drug resistance in microorganisms by mass spectrometry

A rapid method to determine drug resistance in bacteria based on mass spectrometry is presented. In it, a mass spectrum of an intact microorganism grown in drug-containing stable isotope-labeled media is compared with a mass spectrum of the intact microorganism grown in non-labeled media without the drug present. Drug resistance is determined by predicting characteristic mass shifts of one or more microorganism biomarkers using bioinformatics algorithms. Observing such characteristic mass shifts indicates that the microorganism is viable even in the presence of the drug, thus incorporating the isotopic label into characteristic biomarker molecules. The performance of the method is illustrated on the example of intact E. coli, grown in control (unlabeled) and (13)C-labeled media, and analyzed by MALDI TOF MS. Algorithms for data analysis are presented as well.

Molecular detection of CF lung pathogens: current status and future potential

Molecular diagnostic tests, based on the detection and identification of nucleic acids in human biological samples, are increasingly employed in the diagnosis of infectious diseases and may be of future benefit to CF microbiology services. Our growing understanding of the complex polymicrobial nature of CF airway infection has highlighted current and likely future shortcomings in standard diagnostic practices. Failure to detect fastidious or slow growing microbes and misidentification of newly emerging pathogens could potentially be addressed using culture-independent molecular technologies with high target specificity. This review considers existing molecular diagnostic tests in the context of the key requirements for an envisaged CF microbiology focussed assay. The issues of assay speed, throughput, detection of multiple pathogens, data interpretation and antimicrobial susceptibility testing are discussed.