The Point-of-Care Laboratory in Clinical Microbiology

Abbott realtime MTB assay for detecting Mycobacterium tuberculosis complex in respiratory specimens: a cost-benefit analysis

PURPOSE

Molecular screening for Mycobacterium tuberculosis (MTB) can lead to rapid empirical treatment inception and reduce hospitalization time and complementary diagnostic tests. However, in low-prevalence settings, the cost-benefit balance remains controversial due to the high cost.

METHODS

We used a Markov model to perform an economic analysis to evaluate the profit after implementing molecular MTB screening (Period B) compared with conventional culture testing (Period A) in respiratory samples from 7,452 consecutive subjects with presumed tuberculosis (TB).

RESULTS

The proportion of positivity was comparable between both periods (P > 0.05), with a total of 2.16 and 1.78 samples/patient requested in periods A and B, respectively (P < 0.001). The mean length of hospital stay was 8.66 days (95%CI: 7.63-9.70) in Period B and 11.51 days (95%CI: 10.15-12.87) in Period A (P = 0.001). The healthcare costs associated with diagnosing patients with presumed TB were reduced by €717.95 per patient with PCR screening. The probability of remaining hospitalized and the need for a greater number of outpatient specialty care visits were the variables with the most weight in the model.

CONCLUSION

Employing PCR as an MTB screening method in a low-prevalence setting may increase the profits to the system.

An online monitoring device for measuring the concentration of four types of in-situ microorganisms by using the near-infrared band

Using optical density at 600 nm (OD600) to measure the microbial concentration is a popular approach due to its advantages like quick response and non-destructive. However, the OD600 measurement might be affected by the metabolic pigment, and it would become invalid when the solution dilution is insufficient. To overcome these issues, we proposed to adopt a more robust wavelength at 890 nm to quantify the attenuation of transmission light. After selecting this light source, we designed the light path and the circuit of the online monitoring device. Meanwhile, the random forest algorithm was introduced for temperature compensation and improving the stability of the device. This device was verified by monitoring the microbial concentration of four strains (Yeast, Bacillus, Arthrobacter, and Escherichia coli). The experimental result suggested that the mean absolute percentage error reached 4.11 %, 4.28 %, 4.49 %, and 4.53 % respectively, which is helpful to improve the accuracy of microbial concentration measurement.

Tackling Infectious Diseases with Rapid Molecular Diagnosis and Innovative Prevention

Infectious diseases (IDs) are a leading cause of death. The diversity and adaptability of microbes represent a continuing risk to health. Combining vision with passion, our transdisciplinary medical research team has been focussing its work on the better management of infectious diseases for saving human lives over the past five decades through medical discoveries and innovations that helped change the practice of medicine. The team used a multiple-faceted and integrated approach to control infectious diseases through fundamental discoveries and by developing innovative prevention tools and rapid molecular diagnostic tests to fulfill the various unmet needs of patients and health professionals in the field of ID. In this article, as objectives, we put in context two main research areas of ID management: innovative infection prevention that is woman-controlled, and the rapid molecular diagnosis of infection and resistance. We also explain how our transdisciplinary approach encompassing specialists from diverse fields ranging from biology to engineering was instrumental in achieving success. Furthermore, we discuss our vision of the future for translational research to better tackle IDs.

Precise determination of reaction conditions for accurate quantification in digital PCR by real-time fluorescence monitoring within microwells

Real-time digital polymerase chain reaction (qdPCR) provides enhanced precision in the field of molecular diagnostics by integrating absolute quantification with process information. However, the optimal reaction conditions are traditionally determined through multiple iterative of experiments. Therefore, we proposed a novel approach to precisely determine the optimal reaction conditions for qdPCR using a standard process, employing real-time fluorescence monitoring within microwells. The temperature-sensitive fluorophore intensity presented the real temperature of each microwell. This enabled us to determine the optimal denaturation and annealing time for qdPCR based on the corresponding critical temperatures derived from the melting curves and amplification efficiency, respectively. To confirm this method, we developed an ultrathin laminated chip (UTL chip) and chose a target that need to be absolutely quantitative. The UTL chip was designed using a fluid‒solid‒thermal coupling simulation model and exhibited a faster thermal response than a commercial dPCR chip. By leveraging our precise determination of reaction conditions and utilizing the UTL chip, 40 cycles of amplification were achieved within 18 min. This was accomplished by precisely controlling the denaturation temperature at 2 s and the annealing temperature at 10 s. Furthermore, the absolutely quantitative of DNA showed good correlation (R2 > 0.999) with the concentration gradient detection using the optimal reaction conditions with the UTL chip for qdPCR. Our proposed method can significantly improve the accuracy and efficiency of determining qdPCR conditions, which holds great promise for application in molecular diagnostics.

Rapid Minimum Inhibitory Concentration (MIC) Analysis Using Lyophilized Reagent Beads in a Novel Multiphase, Single-Vessel Assay

Antimicrobial resistance (AMR) is a global threat fueled by incorrect (and overuse) of antibiotic drugs, giving rise to the evolution of multi- and extreme drug-resistant bacterial strains. The longer time to antibiotic administration (TTA) associated with the gold standard bacterial culture method has been responsible for the empirical usage of antibiotics and is a key factor in the rise of AMR. While polymerase chain reaction (PCR) and other nucleic acid amplification methods are rapidly replacing traditional culture methods, their scope has been restricted mainly to detect genotypic determinants of resistance and provide little to no information on phenotypic susceptibility to antibiotics. The work presented here aims to provide phenotypic antimicrobial susceptibility testing (AST) information by pairing short growth periods (~3-4 h) with downstream PCR assays to ultimately predict minimum inhibitory concentration (MIC) values of antibiotic treatment. To further simplify the dual workflows of the AST and PCR assays, these reactions are carried out in a single-vessel format (PCR tube) using novel lyophilized reagent beads (LRBs), which store dried PCR reagents along with primers and enzymes, and antibiotic drugs separately. The two reactions are separated in space and time using a melting paraffin wax seal, thus eliminating the need to transfer reagents across different consumables and minimizing user interactions. Finally, these two-step single-vessel reactions are multiplexed by using a microfluidic manifold that allows simultaneous testing of an unknown bacterial sample against different antibiotics at varying concentrations. The LRBs used in the microfluidic system showed no interference with the bacterial growth and PCR assays and provided an innovative platform for rapid point-of-care diagnostics (POC-Dx).

Role of Point-of-Care Diagnostics in Lower- and Middle-Income Countries and Austere Environments

INTRODUCTION

Austere environments include the wilderness and many lower- and middle-income countries, with many of these countries facing unrest and war. The access to advanced diagnostic equipment is often unaffordable, even if available, and the equipment is often liable to break down.

METHODS

A short review paper examining the options available to medical professionals to undertake clinical and point-of-care diagnostic testing in resource-constrained environments that also illustrates the development of mobile advanced diagnostic equipment. The aim is to provide an overview of the spectrum and functionality of these devices beyond clinical acumen.

RESULTS

Details and examples of products covering all aspects of diagnostic testing are provided. Where relevant, reliability and cost implications are discussed.

CONCLUSIONS

The review highlights the need for more cost-effective accessible and utilitarian products and devices that will bring cost-effective health care to many in lower- and middle-income or austere environments.

Respiratory pathogens among ill pilgrims and the potential benefit of using point-of-care rapid molecular diagnostic tools during the Hajj

We investigated respiratory pathogens among ill Hajj pilgrims from Marseille. We also discuss the potential role of point-of-care (POC) rapid molecular diagnostic tools for this purpose. Clinical data were collected using a standardised questionnaire. Influenza A and B viruses, human rhinovirus and human coronaviruses, Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae and Klebsiella pneumoniae were investigated using real-time PCR in respiratory samples obtained during travel, at the onset of symptoms. 207 participants were included. A cough, expectoration, rhinitis and a sore throat were the most frequent respiratory symptoms, followed by loss of voice and dyspnoea. 38.7% and 25.1% of pilgrims reported a fever and influenza-like symptoms, respectively. 59.4% pilgrims received antibiotics. Rhinovirus (40.6%) was the most frequent pathogen, followed by S. aureus (35.8%) and H. influenzae (30.4%). Virus and bacteria co-infections were identified in 28.5% of participants. 25.1% pilgrims who were positive for respiratory bacteria did not receive antibiotic treatment. In the context of the Hajj pilgrimage, it is important to detect infections that can be easily managed with appropriate treatment, and those that can affect prognosis, requiring hospitalisation. POC rapid molecular diagnostic tools could be used for patient management at small Hajj medical missions and to rationalise antibiotic consumption among Hajj pilgrims.

Forty Years of Molecular Diagnostics for Infectious Diseases

Nearly 40 years have elapsed since the invention of the PCR, with its extremely sensitive and specific ability to detect nucleic acids via in vitro enzyme-mediated amplification. In turn, more than 2 years have passed since the onset of the coronavirus disease 2019 (COVID-19) pandemic, during which time molecular diagnostics for infectious diseases have assumed a larger global role than ever before. In this context, we review broadly the progression of molecular techniques in clinical microbiology, to their current prominence. Notably, these methods now entail both the detection and quantification of microbial nucleic acids, along with their sequence-based characterization. Overall, we seek to provide a combined perspective on the techniques themselves, as well as how they have come to shape health care at the intersection of technologic innovation, pathophysiologic knowledge, clinical/laboratory logistics, and even financial/regulatory factors.

An Innovative Test for the Rapid Detection of Specific IgG Antibodies in Human Whole-Blood for the Diagnosis of Opisthorchis viverrini Infection

Chronic human liver fluke infections caused by Opisthorchis viverrini and Clonorchis sinensis can last for decades and cause liver and biliary diseases, including life-threatening pathology prior to cholangiocarcinoma (CCA). CCA generally has a poor prognosis. Serological diagnosis can support parasitological examination in diagnosing disease and screening for the risk of CCA. Here, we present an improved and innovative lateral flow immunochromatographic test (ICT) kit that uses whole-blood samples (WBS) rather than serum to diagnose human opisthorchiasis, which also successfully diagnosed human clonorchiasis. This ICT includes a soluble worm extract of O. viverrini adults and colloidal-gold-labeled conjugates of the IgG antibody to evaluate the diagnostic values with simulated WBS (n = 347). Simulated WBS were obtained by the spiking infection sera with red blood cells. The diagnostic sensitivity, specificity, positive and negative predictive values, and accuracy for detecting opisthorchiasis were 95.5%, 87.0%, 80.5%, 97.2%, and 90.1%, respectively. For clonorchiasis, these findings were 85.7%, 87.0%, 53.6%, 97.2%, and 86.8%, respectively. Combined for both diseases, they were 93.2%, 87.0%, 84.0%, 94.6%, and 89.6%, respectively. The ICT kit can possibly replace the ICT platforms for antibody detection in serum samples in field surveys in remote areas where sophisticated equipment is not available.

Real-time metagenomics-based diagnosis of community-acquired meningitis: A prospective series, southern France

BACKGROUND

Point-Of-Care (POC) diagnosis of life-threatening community-acquired meningitis currently relies on multiplexed RT-PCR assays, that lack genotyping and antibiotic susceptibility profiling. We assessed the usefulness of real-time metagenomics (RTM) directly applied to the cerebrospinal fluid (CSF) for the identification, typing and susceptibility profiling of pathogens responsible for community-acquired meningitis.

METHODS

A series of 52 CSF samples from patients suspected of having community-acquired meningitis, were investigated at POC by direct RTM in parallel to routine real-time multiplex PCR (RT-PCR) and bacterial culture, for the detection of pathogens. RTM-generated sequences were blasted in real-time against an in-house database incorporating the panel of 12 most prevalent pathogens and against NCBI using EPI2ME online software, for pathogen identification. In-silico antibiogram and genotype prediction were determined using the ResFinder bio-tool and MLST online software.

FINDINGS

Over eight months, routine multiplex RT-PCR yielded 49/52 positive CSFs, including 21 Streptococcus pneumoniae, nine Neisseria meningitidis, eight Haemophilus influenzae, three Streptococcus agalactiae, three Herpesvirus-1, two Listeria monocytogenes, and one each of Escherichia coli, Staphylococcus aureus and Varicella-Zoster Virus. Parallel RTM agreed with the results of 47/52 CSFs and revealed two discordant multiplex RT-PCR false positives, one H. influenzae and one S. pneumoniae. Both multiplex RT-PCR and RTM agreed on the negativity of three CSFs. While multiplex RT-PCR routinely took 90 min, RTM took 120 min, although the pipeline analysis detected the pathogen genome after 20 min of sequencing in 33 CSF samples; and after two hours in 14 additional CSFs; yielding > 50% genome coverage in 19 CSFs. RTM identified 14 pathogen genotypes, including a majority of H. influenzae b, N. meningitidis B and S. pneumoniae 11A and 3A. In all 16 susceptible cultured bacteria, the in-silico antibiogram agreed with the in-vitro antibiogram in 10 cases, available within 48 h in routine bacteriology.

INTERPRETATION

In addition to pathogen detection, RTM applied to CSF samples offered supplementary information on bacterial profiling and genotyping. These data provide the proof-of-concept that RTM could be implemented in a POC laboratory for one-shot diagnostic and genomic surveillance of pathogens responsible for life-threatening meningitis.

FUNDING

This work was supported by the French Government under the Investments in the Future programme managed by the National Agency for Research reference: Méditerranée Infection 10-IAHU-03.

Clinical Microbiology in Detection and Identification of Emerging Microbial Pathogens: Past, Present and Future

Clinical microbiology has possessed a marvellous past, an important present and a bright future. Western medicine modernization started with the discovery of bacterial pathogens, and from then, clinical bacteriology became a cornerstone of diagnostics. Today, clinical microbiology uses standard techniques including Gram stain morphology, in vitro culture, antigen and antibody assays, and molecular biology both to establish a diagnosis and monitor the progression of microbial infections. Clinical microbiology has played a critical role in pathogen detection and characterization for emerging infectious diseases as evidenced by the ongoing COVID-19 pandemic. Revolutionary changes are on the way in clinical microbiology with the application of “-omic” techniques, including transcriptomics and metabolomics, and optimization of clinical practice configurations to improve outcomes of patients with infectious diseases.

Point-of-care diagnostic tests for tuberculosis disease

Rapid diagnosis is one key pillar to end tuberculosis (TB). Point-of-care tests (POCTs) facilitate early detection, immediate treatment, and reduced transmission of TB disease. This Review evaluates current diagnostic assays endorsed by the World Health Organization and identifies the gaps between existing conventional tests and the ideal POCT. We discuss the commercial development of new rapid tests and research studies on nonsputum-based diagnostic biomarkers from both pathogen and host. Last, we highlight advances in integrated microfluidics technology that may aid the development of new POCTs.

Advances in the Rapid Diagnostic of Viral Respiratory Tract Infections

Viral infections are a significant public health problem, primarily due to their high transmission rate, various pathological manifestations, ranging from mild to severe symptoms and subclinical onset. Laboratory diagnostic tests for infectious diseases, with a short enough turnaround time, are promising tools to improve patient care, antiviral therapeutic decisions, and infection prevention. Numerous microbiological molecular and serological diagnostic testing devices have been developed and authorised as benchtop systems, and only a few as rapid miniaturised, fully automated, portable digital platforms. Their successful implementation in virology relies on their performance and impact on patient management. This review describes the current progress and perspectives in developing micro- and nanotechnology-based solutions for rapidly detecting human viral respiratory infectious diseases. It provides a nonexhaustive overview of currently commercially available and under-study diagnostic testing methods and discusses the sampling and viral genetic trends as preanalytical components influencing the results. We describe the clinical performance of tests, focusing on alternatives such as microfluidics-, biosensors-, Internet-of-Things (IoT)-based devices for rapid and accurate viral loads and immunological responses detection. The conclusions highlight the potential impact of the newly developed devices on laboratory diagnostic and clinical outcomes.

Evaluation of ligand modified poly (N-Isopropyl acrylamide) hydrogel for etiological diagnosis of corneal infection

Corneal ulcers, a leading cause of blindness in the developing world are treated inappropriately without prior microbiology assessment because of issues related to availability or cost of accessing these services.

In this work we aimed to develop a device for identifying the presence of Gram-positive or Gram-negative bacteria or fungi that can be used by someone without the need for a microbiology laboratory. Working with branched poly (N-isopropyl acrylamide) (PNIPAM) tagged with Vancomycin, Polymyxin B, or Amphotericin B to bind Gram-positive bacteria, Gram-negative bacteria and fungi respectively, grafted onto a single hydrogel we demonstrated specific binding of the organisms. The limit of detection of the microbes by these polymers was between 10 and 4 organisms per high power field (100X) for bacteria and fungi binding polymers respectively. Using ex vivo and animal cornea infection models infected with bacteria, fungi or both we than demonstrated that the triple functionalised hydrogel could pick up all 3 organisms after being in place for 30 min. To confirm the presence of bacteria and fungi we used conventional microbiology techniques and fluorescently labelled ligands or dyes.

While we need to develop an easy-to-use either a colorimetric or an imaging system to detect the fluorescent signals, this study presents for the first time a simple to use hydrogel system, which can be applied to infected eyes and specifically binds different classes of infecting agents within a short space of time. Ultimately this diagnostic system will not require trained microbiologists for its use and will be used at the point-of-care.

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Functionalised branched Poly N-isopropyl acrylamide binds corneal ulcer causing microorganisms.

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The functionalised polymers demonstrated specific binding to gram positive, gram negative and fungi.

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Grafting three different polymers on a single hydrogel retained this specific binding for microorganisms.

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Triple functionalised hydrogels were effective in picking up microorganisms in ex-vivo and animal cornea infection models.

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Application for a duration of 30 min was sufficient to pick up enough organisms for subsequent identification.

Optimizing antimicrobial use: challenges, advances and opportunities

An optimal antimicrobial dose provides enough drug to achieve a clinical response while minimizing toxicity and development of drug resistance. There can be considerable variability in pharmacokinetics, for example, owing to comorbidities or other medications, which affects antimicrobial pharmacodynamics and, thus, treatment success. Although current approaches to antimicrobial dose optimization address fixed variability, better methods to monitor and rapidly adjust antimicrobial dosing are required to understand and react to residual variability that occurs within and between individuals. We review current challenges to the wider implementation of antimicrobial dose optimization and highlight novel solutions, including biosensor-based, real-time therapeutic drug monitoring and computer-controlled, closed-loop control systems. Precision antimicrobial dosing promises to improve patient outcome and is important for antimicrobial stewardship and the prevention of antimicrobial resistance.

Blood culture diagnostics: a Nordic multicentre survey comparison of practices in clinical microbiology laboratories

OBJECTIVES

Accurate and rapid microbiological diagnostics are crucial to tailor treatment and improve outcomes in patients with severe infections. This study aimed to assess blood culture diagnostics in the Nordic countries and to compare them with those of a previous survey conducted in Sweden in 2013.

METHODS

An online questionnaire was designed and distributed to the Nordic clinical microbiology laboratories (CMLs) (n = 76) in January 2018.

RESULTS

The response rate was 64% (49/76). Around-the-clock incubation of blood cultures (BCs) was supported in 82% of the CMLs (40/49), although in six of these access to the incubators around the clock was not given to all of the cabinets in the catchment area, and 41% of the sites (20/49) did not assist with satellite incubators. Almost half (49%, 24/49) of the CMLs offered opening hours for ≥10 h during weekdays, more commonly in CMLs with an annual output ≥30 000 BCs. Still, positive BCs were left unprocessed for 60-70% of the day due to restrictive opening hours. Treatment advice was given by 23% of CMLs (11/48) in ≥75% of the phone contacts. Rapid analyses (species identification and susceptibility testing with short incubation), performed on aliquots from positive cultures, were implemented in 18% of CMLs (9/49). Compared to 2013, species identification from subcultured colonies (<6 h) had become more common.

CONCLUSIONS

CMLs have taken action to improve aspects of BC diagnostics, implementing satellite incubators, rapid species identification and susceptibility testing. However, the limited opening hours and availability of clinical microbiologists are confining the advantages of these changes.

Point-of-Care Testing in Microbiology

Point-of-care (POC) or near patient testing for infectious diseases is a rapidly expanding space that is part of an ongoing effort to bring care closer to the patient. Traditional POC tests were known for their limited utility, but advances in technology have seen significant improvements in performance of these assays. The increasing promise of these tests is also coupled with their increasing complexity, which requires the oversight of qualified laboratory-trained personnel.

Detection of SARS-CoV-2 at the point of care

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of COVID-19. Testing for SARS-CoV-2 infection is a critical element of the public health response to COVID-19. Point-of-care (POC) tests can drive patient management decisions for infectious diseases, including COVID-19. POC tests are available for the diagnosis of SARS-CoV-2 infections and include those that detect SARS-CoV-2 antigens as well as amplified RNA sequences. We provide a review of SARS-CoV-2 POC tests including their performance, settings for which they might be used, their impact and future directions. Further optimization and validation, new technologies as well as studies to determine clinical and epidemiological impact of SARS-CoV-2 POC tests are needed.

Host-Pathogen Adhesion as the Basis of Innovative Diagnostics for Emerging Pathogens

Infectious diseases are an existential health threat, potentiated by emerging and re-emerging viruses and increasing bacterial antibiotic resistance. Targeted treatment of infectious diseases requires precision diagnostics, especially in cases where broad-range therapeutics such as antibiotics fail. There is thus an increasing need for new approaches to develop sensitive and specific in vitro diagnostic (IVD) tests. Basic science and translational research are needed to identify key microbial molecules as diagnostic targets, to identify relevant host counterparts, and to use this knowledge in developing or improving IVD. In this regard, an overlooked feature is the capacity of pathogens to adhere specifically to host cells and tissues. The molecular entities relevant for pathogen–surface interaction are the so-called adhesins. Adhesins vary from protein compounds to (poly-)saccharides or lipid structures that interact with eukaryotic host cell matrix molecules and receptors. Such interactions co-define the specificity and sensitivity of a diagnostic test. Currently, adhesin-receptor binding is typically used in the pre-analytical phase of IVD tests, focusing on pathogen enrichment. Further exploration of adhesin–ligand interaction, supported by present high-throughput “omics” technologies, might stimulate a new generation of broadly applicable pathogen detection and characterization tools. This review describes recent results of novel structure-defining technologies allowing for detailed molecular analysis of adhesins, their receptors and complexes. Since the host ligands evolve slowly, the corresponding adhesin interaction is under selective pressure to maintain a constant receptor binding domain. IVD should exploit such conserved binding sites and, in particular, use the human ligand to enrich the pathogen. We provide an inventory of methods based on adhesion factors and pathogen attachment mechanisms, which can also be of relevance to currently emerging pathogens, including SARS-CoV-2, the causative agent of COVID-19.

Comparative assessment of immunochromatographic test kits using somatic antigens from adult Opisthorchis viverrini and IgG and IgG4 conjugates for serodiagnosis of human opisthorchiasis

Chronic infections of humans with Opisthorchis viverrini and Clonorchis sinensis spanning decades may lead to life-threatening pathology prior to cholangiocarcinoma (CCA), which usually has a poor prognosis. Serological tools can support the parasitological examination in clinical diagnosis and support screening for risk of CCA. We developed novel immunochromatographic test kits using a soluble, somatic tissue extract of adult O. viverrini worms as an antigen and colloidal gold-labeled conjugates of IgG and IgG4 antibodies, and evaluated the diagnostic values of both the OvSO-IgG and OvSO-IgG4 kits. For diagnosis of human opisthorchiasis individually, the diagnostic sensitivity, specificity, and positive and negative predictive values with 95% confidence intervals in the OvSO-IgG kit were 86.6% (78.9-92.3), 89.5% (84.2-93.5), 82.9% (74.8-89.2), and 91.9% (87.0-95.4), respectively, while the 75% (65.9-82.7), 98.4% (95.5-99.7), 96.6% (90.3-99.3), and 87% (81.7-91.2), respectively, for the OvSO-IgG4 kit at the prevalence of infection of 37.1%. Twenty-three (76.7%) and 14 (46.7%) of 30 clonorchiasis sera showed positive reactivity with the OvSO-IgG and OvSO-IgG4 kits, respectively. There was 84.1% (κ-value = 0.649) concordance between the two kits, which was statistically significant (p < 0.001). Both ICT kits can be employed as quick and easy point-of-care diagnostic tools, and hence, the OvSO-IgG and OvSO-IgG4 kits can support expanded capacity for clinical diagnosis of human opisthorchiasis and clonorchiasis. These kits may find utility in large-scale surveys in endemic areas where there are limited sophisticated medical facilities or capacity.

Biosensors Designed for Clinical Applications

Emerging and validated biomarkers promise to revolutionize clinical practice, shifting the emphasis away from the management of chronic disease towards prevention, early diagnosis and early intervention. The challenge of detecting these low abundance protein and nucleic acid biomarkers within the clinical context demands the development of highly sensitive, even single molecule, assays that are also capable of selectively measuring a small number of defined analytes in complex samples such as whole blood, interstitial fluid, saliva or urine. Success relies on significant innovations in nanomaterials, bioreceptor engineering, transduction strategies and microfluidics. Primarily using examples from our work, this article discusses some recent advance in the selective and sensitive detection of disease biomarkers, highlights key innovations in sensor materials and identifies issues and challenges that need to be carefully considered especially for researchers entering the field.

Contagion Management at the Méditerranée Infection University Hospital Institute

The Méditerranée Infection University Hospital Institute (IHU) is located in a recent building, which includes experts on a wide range of infectious disease. The IHU strategy is to develop innovative tools, including epidemiological monitoring, point-of-care laboratories, and the ability to mass screen the population. In this study, we review the strategy and guidelines proposed by the IHU and its application to the COVID-19 pandemic and summarise the various challenges it raises. Early diagnosis enables contagious patients to be isolated and treatment to be initiated at an early stage to reduce the microbial load and contagiousness. In the context of the COVID-19 pandemic, we had to deal with a shortage of personal protective equipment and reagents and a massive influx of patients. Between 27 January 2020 and 5 January 2021, 434,925 nasopharyngeal samples were tested for the presence of SARS-CoV-2. Of them, 12,055 patients with COVID-19 were followed up in our out-patient clinic, and 1888 patients were hospitalised in the Institute. By constantly adapting our strategy to the ongoing situation, the IHU has succeeded in expanding and upgrading its equipment and improving circuits and flows to better manage infected patients.

Understanding the role of the gut in undernutrition: what can technology tell us?

Gut function remains largely underinvestigated in undernutrition, despite its critical role in essential nutrient digestion, absorption and assimilation. In areas of high enteropathogen burden, alterations in gut barrier function and subsequent inflammatory effects are observable but remain poorly characterised. Environmental enteropathy (EE)-a condition that affects both gut morphology and function and is characterised by blunted villi, inflammation and increased permeability-is thought to play a role in impaired linear growth (stunting) and severe acute malnutrition. However, the lack of tools to quantitatively characterise gut functional capacity has hampered both our understanding of gut pathogenesis in undernutrition and evaluation of gut-targeted therapies to accelerate nutritional recovery. Here we survey the technology landscape for potential solutions to improve assessment of gut function, focussing on devices that could be deployed at point-of-care in low-income and middle-income countries (LMICs). We assess the potential for technological innovation to assess gut morphology, function, barrier integrity and immune response in undernutrition, and highlight the approaches that are currently most suitable for deployment and development. This article focuses on EE and undernutrition in LMICs, but many of these technologies may also become useful in monitoring of other gut pathologies.

Detection of targeted bacteria species on filtration membranes

The detection of pathogens in aquatic environments issues a time-consuming challenge, but it is an essential task to prevent the spread of diseases. We have developed a new point-of-care (POC) method for the fast and efficient detection of Legionella pneumophila in water. The method consists first of the generation of immunocomplexes of bacteria species with its corresponding targeted fluorescence-labelled serogroup-specific antibodies, and second a concentration step of pathogens with a membrane filter. Third, on the filtration membrane, our method can detect the fluorescence intensity corresponding to the pathogen concentration. Thus selective and efficient evidence for the presence of bacteria can be evaluated. We tested our system on fluorescent Escherichia coli bacteria and were able to reach an accurate determination of 1000 cells. The technique was furthermore tested on Legionella pneumophila cells, which were labelled with fluorescence-labelled antibodies as a proof of principle. Furthermore, we were able to verify this method in the presence of other bacteria species. We were able to detect bacteria cells within half an hour, a substantial advancement compared to the prevailling state of the art detection method based on the cultivation of Legionella pneumophila. Hence, this system represents the basis for future developments in analysis of pathogens.

Affordable mobile microfluidic diagnostics: minimum requirements for smartphones and digital imaging for colorimetric and fluorometric anti-dengue and anti-SARS-CoV-2 antibody detection

Background: Miniaturised bioassays permit diagnostic testing near the patient, and the results can be recorded digitally using inexpensive cameras including smartphone and mobile phone cameras. Although digital cameras are now inexpensive and portable, the minimum performance required for microfluidic diagnostic bioassays has not been defined. We present a systematic comparison of a wide range of different digital cameras for capturing and measuring results of microfluidic bioassays and describe a framework to specify performance requirements to quantify immunoassays. Methods: A set of 200 µm diameter microchannels was filled with a range of concentrations of dyes used in colorimetric and fluorometric enzyme immunoassays. These were imaged in parallel using cameras of varying cost and performance ranging from <£30 to >£500. Results: Higher resolution imaging allowed larger numbers of microdevices to be resolved and analysed in a single image. In contrast, low quality cameras were still able to quantify results but for fewer samples. In some cases, an additional macro lens was added to focus closely. If image resolution was sufficient to identify individual microfluidic channels as separate lines, all cameras were able to quantify a similar range of concentrations of both colorimetric and fluorometric dyes. However, the mid-range cameras performed better, with the lowest cost cameras only allowing one or two samples to be quantified per image. Consistent with these findings, we demonstrate that quantitation (to determine endpoint titre) of antibodies against dengue and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viruses is possible using a wide range of digital imaging devices including the mid-range smartphone iPhone 6S and a budget Android smartphone costing <£50. Conclusions: In conclusion, while more expensive and higher quality cameras allow larger numbers of devices to be simultaneously imaged, even the lowest resolution and cheapest cameras were sufficient to record and quantify immunoassay results.

A pocket-sized device automates multiplexed point-of-care RNA testing for rapid screening of infectious pathogens

Rapid screening of infectious pathogens at the point-of-care (POC) is ideally low-cost, portable, easy to use, and capable of multiplex detection with high sensitivity. However, satisfying all these features in a single device without compromise remains a challenging task. Here, we introduce an ultraportable, automated RNA amplification testing device that allows rapid screening of infectious pathogens from clinical samples. In this device, 3D-printed structural parts incorporated with off-the-shelf mechanic/electronic components are utilized to create an inexpensive and automated droplet manipulation platform. On this platform, a simple configuration that couples a linear displacement of the chip with a tunable magnet array allows parallel and versatile droplet operations, including mixing, splitting, transporting, and merging. By exploiting a multi-channel droplet array chip to preload necessary reagents in "water-in-oil" format, bacteria lysis, RNA extraction and amplification are seamlessly integrated and implemented by the combination of droplet operations. Furthermore, visual readout and geometrically-multiplexed quantitative detection are provided by an integrated wireless video camera-enabled wide-field fluorescence imaging. We demonstrated that this droplet-based device could have a shorter RNA extraction time (12 min) and lower detection limits for pathogenic RNA (approaching to 10² copies per reaction). We also verified its clinical applicability for the rapid screening of four sexually transmitted pathogens from urine specimens. Results show that the sample-to-answer assay could be completed in approximately 42 min, with 100% concordance with the laboratory-based molecular testing. The exhibiting features may render this microdevice an easily accessible POC molecular diagnostic platform for infectious disease, especially in resource-limited settings.

Current and Future Trends in the Laboratory Diagnosis of Sexually Transmitted Infections

Sexually transmitted infections (STIs) continue to exert a considerable public health and social burden globally, particularly for developing countries. Due to the high prevalence of asymptomatic infections and the limitations of symptom-based (syndromic) diagnosis, confirmation of infection using laboratory tools is essential to choose the most appropriate course of treatment and to screen at-risk groups. Numerous laboratory tests and platforms have been developed for gonorrhea, chlamydia, syphilis, trichomoniasis, genital mycoplasmas, herpesviruses, and human papillomavirus. Point-of-care testing is now a possibility, and microfluidic and high-throughput omics technologies promise to revolutionize the diagnosis of STIs. The scope of this paper is to provide an updated overview of the current laboratory diagnostic tools for these infections, highlighting their advantages, limitations, and point-of-care adaptability. The diagnostic applicability of the latest molecular and biochemical approaches is also discussed.

Colorimetric loop-mediated isothermal amplification (LAMP) for cost-effective and quantitative detection of SARS-CoV-2: the change in color in LAMP-based assays quantitatively correlates with viral copy number

We demonstrate a loop-mediated isothermal amplification (LAMP) method to detect and amplify SARS-CoV-2 genetic sequences using a set of in-house designed initiators that target regions encoding the N protein. We were able to detect and amplify SARS-CoV-2 nucleic acids in the range of 62 to 2 × 105 DNA copies by this straightforward method. Using synthetic SARS-CoV-2 samples and RNA extracts from patients, we demonstrate that colorimetric LAMP is a quantitative method comparable in diagnostic performance to RT-qPCR (i.e., sensitivity of 92.85% and specificity of 81.25% in a set of 44 RNA extracts from patients analyzed in a hospital setting).

Emerging Options for the Diagnosis of Bacterial Infections and the Characterization of Antimicrobial Resistance

Precise and rapid identification and characterization of pathogens and antimicrobial resistance patterns are critical for the adequate treatment of infections, which represent an increasing problem in intensive care medicine. The current situation remains far from satisfactory in terms of turnaround times and overall efficacy. Application of an ineffective antimicrobial agent or the unnecessary use of broad-spectrum antibiotics worsens the patient prognosis and further accelerates the generation of resistant mutants. Here, we provide an overview that includes an evaluation and comparison of existing tools used to diagnose bacterial infections, together with a consideration of the underlying molecular principles and technologies. Special emphasis is placed on emerging developments that may lead to significant improvements in point of care detection and diagnosis of multi-resistant pathogens, and new directions that may be used to guide antibiotic therapy.

Preventing contamination of PCR-based multiplex assays including the use of a dedicated biosafety cabinet

We retrospectively investigated cases of false-positive diagnoses using the BIOFIRE® FilmArray® meningitis/encephalitis (ME) panel to measure the impact of using a dedicated biosafety cabinet combined with preventive measures to reduce the prevalence of false-positive diagnoses due to pre-analytical in-laboratory contamination. False-positive results were identified by reviewing clinical data, biological parameters and cytology results of cerebrospinal fluid (CSF) samples showing discrepant results between the FilmArray ME panel and routine PCR assays. A total of 327 CSF were analysed over 16 weeks in point-of-care (POC) A and B, over two 8-week periods, periods 1 and 2. The analysis yielded 30 (9·17%) detection of at least one pathogen including 21/30 (70%) viruses and 9/30 (30%) bacteria. During period 1, POC-A and POC-B manipulated CSF under a non-dedicated hood featuring laminar flow, whereas during period 2, CSFs were manipulated under a dedicated biosafety cabinet without any airflow in POC-A. During period 1, false positives were detected in 3/114 CSF (2·63%) in POC-A and 1/36 (2·77%) in POC-B (P = 0·97); during period 2, false positives were detected in 0/139 CSF (0%) in POC-A and 1/38 (2·63%) in POC-B (P = 0·23). All false positives were bacterial. The use of a dedicated cabinet without ventilation along with preventive measures during period 2 in POC-A significantly reduced the number of false-positive results (P = 0·05). Preventive measures described in this study can mitigate false positives when using PCR-based multiplex assays such as the BIOFIRE FilmArray ME Panel for the diagnosis of meningitis and other infectious diseases.

Yersinia pestis: the Natural History of Plague

The Gram-negative bacterium Yersinia pestis is responsible for deadly plague, a zoonotic disease established in stable foci in the Americas, Africa, and Eurasia. Its persistence in the environment relies on the subtle balance between Y. pestis-contaminated soils, burrowing and nonburrowing mammals exhibiting variable degrees of plague susceptibility, and their associated fleas. Transmission from one host to another relies mainly on infected flea bites, inducing typical painful, enlarged lymph nodes referred to as buboes, followed by septicemic dissemination of the pathogen. In contrast, droplet inhalation after close contact with infected mammals induces primary pneumonic plague. Finally, the rarely reported consumption of contaminated raw meat causes pharyngeal and gastrointestinal plague. Point-of-care diagnosis, early antibiotic treatment, and confinement measures contribute to outbreak control despite residual mortality. Mandatory primary prevention relies on the active surveillance of established plague foci and ectoparasite control. Plague is acknowledged to have infected human populations for at least 5,000 years in Eurasia. Y. pestis genomes recovered from affected archaeological sites have suggested clonal evolution from a common ancestor shared with the closely related enteric pathogen Yersinia pseudotuberculosis and have indicated that ymt gene acquisition during the Bronze Age conferred Y. pestis with ectoparasite transmissibility while maintaining its enteric transmissibility. Three historic pandemics, starting in 541 AD and continuing until today, have been described. At present, the third pandemic has become largely quiescent, with hundreds of human cases being reported mainly in a few impoverished African countries, where zoonotic plague is mostly transmitted to people by rodent-associated flea bites.

Exploratory Use of Fluorescent SmartProbes for the Rapid Detection of Microbial Isolates Causing Corneal Ulcer

PURPOSE

To explore the use of optical SmartProbes for the rapid evaluation of corneal scrapes from patients with suspected microbial keratitis, as a clinical alternative to Gram stain.

DESIGN

Experimental study with evaluation of a diagnostic technology.

METHODS

Corneal scrapes were collected from 267 patients presenting with microbial keratitis at a referral cornea clinic in South India. Corneal scrapes were flooded with SmartProbes (BAC One or BAC Two) and evaluated by fluorescence microscopy (without the need for sample washing or further processing). The SmartProbe-labeled samples were scored as bacteria/fungi/none (BAC One) or gram-negative bacteria/none (BAC Two) and compared to Gram stain results.

RESULTS

Compared to Gram stain, BAC One demonstrated sensitivity and specificity of 80.0% and 87.5%, respectively, positive and negative predictive values (PPV, NPV) of 93.8% and 65.1%, and an accuracy of 82.2. BAC Two demonstrated sensitivity and specificity of 93.3% and 84.8%, respectively, an NPV of 99.2%, and an accuracy of 85.6%. When the corresponding culture results were compared to the Gram stain result, the sensitivity and specificity were 73.4% and 70.7%, the PPV and NPVs were 86.5% and 51.0%, and overall accuracy was 72.6.

CONCLUSIONS

Fluorescent SmartProbes offer a comparative method to Gram stain for delineating gram-positive or gram-negative bacteria or fungi within corneal scrapes. We demonstrate equivalent or higher sensitivity, specificity, PPV and NPVs, and accuracy than culture to Gram stain. Our approach has scope for point-of-care clinical application to aid in the diagnosis of microbial keratitis.

Evaluation of the Diagnostic Efficacy of Xpert CT/NG for Chlamydia trachomatis and Neisseria gonorrhoeae

BACKGROUND

Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are widely spread across the world. Asymptomatic or inconspicuous CT/NG infections are difficult to diagnose and treat. Traditional methods have the disadvantages of low detection rate, inaccurate results, and long detection time. However, Xpert CT/NG makes up for the aforementioned shortcomings and has research value and popularization significance.

METHODS

PubMed, Embase, Cochrane Library, and Web of Science were systematically searched, and studies were screened using Xpert CT/NG for diagnosing CT/NG. QUADAS-2 was used to evaluate the quality of the eligible studies. Then, two groups of researchers independently extracted data from these studies. Meta-analyses of sensitivity (SEN), specificity (SPE), positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and the area under the curve (AUC) of the summary receiver operating characteristic (SROC) curve were conducted using Meta-DiSc 1.4. Finally, Deek's funnel plots were made using Stata 12.0 to evaluate publication bias.

RESULTS

14 studies were identified, and 46 fourfold tables were extracted in this meta-analysis. The pooled SEN, SPE, PLR, NLR, DOR, and AUC in diagnosing CT were 0.94 (95% confidence interval (CI): 0.93-0.95), 0.99 (95% CI: 0.99-1.00), 97.17 (95% CI: 56.76-166.32), 0.07 (95% CI: 0.04-0.12), 1857.25 (95% CI: 943.78-3654.86), and 0.9960, respectively. The pooled SEN, SPE, PLR, NLR, DOR, and AUC in diagnosing NG were 0.95 (95% CI: 0.93-0.96), 1.00 (95% CI: 1.00-1.00), 278.15 (95% CI: 152.41-507.63), 0.08 (95% CI: 0.06-0.12), 4290.70 (95% CI: 2161.78-8516.16), and 0.9980, respectively.

CONCLUSIONS

Xpert CT/NG had high diagnostic sensitivity and specificity for CT and NG. However, more evidence is required to confirm that Xpert CT/NG might serve as the primary method for detecting CT and NG and even the gold standard for diagnosis in the future.

An outbreak of relapsing fever unmasked by microbial paleoserology, 16th century, France

OBJECTIVES

Depicting past epidemics currently relies on DNA-based detection of pathogens, an approach limited to pathogens with well-preserved DNA sequences. We used paleoserology as a complementary approach detecting specific antibodies under a mini line-blot format including positive and negative control antigens.

METHODS

Mini line blot assay incorporated skim milk as negative control, Staphylococcus aureus as positive control, and antigens prepared from lice-borne pathogens Rickettsia prowazekii, Borrelia recurrentis, Bartonella quintana, and Yersinia pestis. Paleoserums were extracted from rehydrated dental pulp recovered from buried individuals. Mini line blots observed with the naked eye, were quantified using a scanner and appropriate software. Paleoserology was applied to the indirect detection of lice-borne pathogens in seven skeletons exhumed from a 16th-17th century suspected military burial site (Auxi-le-Château); and 14 civils exhumed from a 5th-13th century burial site (Saint-Mont). Direct detection of pathogens was performed using quantitative real-time PCR.

RESULTS

In Auxi-le-Château, paleoserology yielded 7/7 interpretable paleoserums including 7/7 positives for B. recurrentis including one also positive for B. quintana. In Saint-Mont, paleoserology yielded 8/14 interpretable paleoserums and none reacted against any of the four pathogens. Antibodies against R. prowazekii and Y. pestis were not detected. The seroprevalence was significantly higher in the military burial site of Auxi-le-Château than in the civil burial site of Saint-Mont. Real-time PCR detection of B. quintana yielded 5/21 positive (3 at Saint-Mont and 2 at Auxi-le-Château) whereas B. recurrentis was not detected.

CONCLUSIONS

Paleoserology unmasked an outbreak of relapsing B. recurrentis fever in one 16th - 17th century military garrison, missed by real-time PCR. Paleoserology offers a new tool for investigating past epidemics, in complement to DNA sequence-based approaches.

Diagnostic tools for bacterial infections in travellers: Current and future options

International travel has increased dramatically over the past 50 years, and travel destinations have diversified. Although physicians are more familiar with the panel of aetiological agents responsible for illnesses of returning travellers, thanks to regular epidemiological studies, the spectrum of pathogens potentially encountered in various travel destinations is nevertheless increasing. In addition, the wide array of approaches currently available and addressed in this paper could render the procedures for microbiological analyses increasingly complex. As the time to result is crucial to adequately manage patients, modern approaches have been developed to shorten diagnosis delays. The syndromic approach, which consists of simultaneously testing a wide panel of microorganisms, substantially increases the diagnostic yield with significant time savings, particularly when coupled with point-of-care laboratories. The tools commonly used for this purpose are immunochromatographic tests, mainly targeting bacterial antigens, and multiplex real-time PCR. The emergence of next-generation sequencing technologies, which enable random amplification of genetic material of any microbe present in a clinical specimen, provides further exciting perspectives in the diagnosis of infectious diseases.

Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection

The coronavirus disease 2019 (COVID-19) pandemic has crudely demonstrated the need for massive and rapid diagnostics. By the first week of July, more than 10,000,000 positive cases of COVID-19 have been reported worldwide, although this number could be greatly underestimated. In the case of an epidemic emergency, the first line of response should be based on commercially available and validated resources. Here, we demonstrate the use of the miniPCR, a commercial compact and portable PCR device recently available on the market, in combination with a commercial well-plate reader as a diagnostic system for detecting genetic material of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19. We used the miniPCR to detect and amplify SARS-CoV-2 DNA sequences using the sets of initiators recommended by the World Health Organization (WHO) for targeting three different regions that encode for the N protein. Prior to amplification, samples were combined with a DNA intercalating reagent (i.e., EvaGreen Dye). Sample fluorescence after amplification was then read using a commercial 96-well plate reader. This straightforward method allows the detection and amplification of SARS-CoV-2 nucleic acids in the range of ~625 to 2×105 DNA copies. The accuracy and simplicity of this diagnostics strategy may provide a cost-efficient and reliable alternative for COVID-19 pandemic testing, particularly in underdeveloped regions where RT-QPCR instrument availability may be limited. The portability, ease of use, and reproducibility of the miniPCR makes it a reliable alternative for deployment in point-of-care SARS-CoV-2 detection efforts during pandemics.

Point-of-Care Testing in Microbiology: A Mechanism for Improving Patient Outcomes

BACKGROUND

Increasingly, demands for improved health and quality of life conflict with the realities of delivering healthcare in an environment of higher expenditures, adherence to test utilization, and patient-centered experience. Patient-centered care is commonly identified as a goal of healthcare delivery, and yet healthcare systems struggle with delivery of care to patients, often failing to identify the seriously ill and capitalize on the predictive qualities of diagnostic testing. Point-of-care (POC) testing provides access to rapid diagnosis and predictive value key to realizing patient outcomes. An evaluation of cost-effective models and the clinical impact of POC testing for clinical microbiology is needed.

CONTENT

Accurate and rapid diagnostics have the potential to affect healthcare decisions to a degree well out of proportion to their cost. Contemporary healthcare models increasingly view POC testing as a mechanism for efficient deployment of healthcare. POC testing can deliver rapid diagnosis in environments where testing results can be used to direct management during patient visits and in areas where centralized laboratory testing may limit access to care. Nucleic acid assays, designed for POC testing, can match, or exceed, the sensitivity of conventional laboratory-based testing, eliminating the need for confirmation testing. Here, the goals of POC testing for microbiology, applications, and technologies, as well as outcomes and value propositions, are discussed.

SUMMARY

The combination of rapid reporting, an increasing array of organisms capable of causing disease, actionable resulting, and improved patient outcomes is key in the evolution of POC testing in clinical microbiology.

Distributed Microbiology Testing: Bringing Infectious Disease Diagnostics to Point of Care

We discuss the current practice of point-of-care diagnostics in infectious diseases as methods transition from antigen-based to molecular, and beyond simple molecular to the next generations of point-of-care testing methods. We evaluate the role of point-of-care at different sites of care and describe and evaluate trends likely to be driven by advances in molecular methodology, emerging biomarkers, and informatics. We describe strengths, weaknesses, opportunities, and threats to the development of point-of-care diagnostics in the near (1-10 years) and more distant (10-20 years) future.

Current and Future Point-of-Care Tests for Emerging and New Respiratory Viruses and Future Perspectives

The availability of pathogen-specific treatment options for respiratory tract infections (RTIs) increased the need for rapid diagnostic tests. Besides, retrospective studies, improved lab-based detection methods and the intensified search for new viruses since the beginning of the twenty-first century led to the discovery of several novel respiratory viruses. Among them are human bocavirus (HBoV), human coronaviruses (HCoV-HKU1, -NL63), human metapneumovirus (HMPV), rhinovirus type C (RV-C), and human polyomaviruses (KIPyV, WUPyV). Additionally, new viruses like SARS coronavirus (SARS-CoV), MERS coronavirus (MERS-CoV), novel strains of influenza virus A and B, and (most recently) SARS coronavirus 2 (SARS-CoV-2) have emerged. Although clinical presentation may be similar among different viruses, associated symptoms may range from a mild cold to a severe respiratory illness, and thus require a fast and reliable diagnosis. The increasing number of commercially available rapid point-of-care tests (POCTs) for respiratory viruses illustrates both the need for this kind of tests but also the problem, i.e., that the majority of such assays has significant limitations. In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings. While prototypes for some methods already exist, other ideas are still experimental, but all of them give an outlook of what can be expected as the next generation of POCTs.

Fluorescent Hybridization of Mycobacterium leprae in Skin Samples Collected in Burkina Faso

Leprosy is caused by Mycobacterium leprae, and it remains underdiagnosed in Burkina Faso. We investigated the use of fluorescent in situ hybridization (FISH) for detecting M. leprae in 27 skin samples (skin biopsy samples, slit skin samples, and skin lesion swabs) collected from 21 patients from Burkina Faso and three from Côte d'Ivoire who were suspected of having cutaneous leprosy. In all seven Ziehl-Neelsen-positive skin samples (four skin biopsy samples and three skin swabs collected from the same patient), FISH specifically identified M. leprae, including one FISH-positive skin biopsy sample that remained negative after testing with PCR targeting the rpoB gene and with the GenoType LepraeDR assay. Twenty other skin samples and three negative controls all remained negative for Ziehl-Neelsen staining, FISH, and rpoB PCR. These data indicate the usefulness of a microscopic examination of skin samples after FISH for first-line diagnosis of cutaneous leprosy. Accordingly, FISH represents a potentially useful point-of-care test for the diagnosis of cutaneous leprosy.

Point of care and oral fluid hepatitis B testing in remote Indigenous communities of northern Australia

Many Indigenous Australians in northern Australia living with chronic hepatitis B are unaware of their diagnosis due to low screening rates. A venous blood point of care test (POCT) or oral fluid laboratory test could improve testing uptake in this region. The purpose of this study was to assess the field performance of venous blood POCT and laboratory performance of an oral fluid hepatitis B surface antigen (HBsAg) test in Indigenous individuals living in remote northern Australian communities. The study was conducted with four very remote communities in the tropical north of Australia's Northern Territory. Community research workers collected venous blood and oral fluid samples. We performed the venous blood POCT for HBsAg in the field. We assessed the venous blood and oral fluid specimens for the presence of HBsAg using standard laboratory assays. We calculated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the POCT and oral fluid test, using serum laboratory detection of HBsAg as the gold standard. From 215 enrolled participants, 155 POCT and 197 oral fluid tests had corresponding serum HBsAg results. The POCT had a sensitivity of 91.7% and specificity of 100%. Based on a population prevalence of 6%, the PPV was 100% and NPV was 99.5%. The oral fluid test had a sensitivity of 56.8%, specificity of 98.1%, PPV of 97.3% and NPV of 65.9%. The venous blood POCT has excellent test characteristics and could be used to identify individuals with chronic HBV infection in high prevalence communities with limited access to health care. Oral fluid performance was suboptimal.

Consolidation of Clinical Microbiology Laboratories and Introduction of Transformative Technologies

Clinical microbiology is experiencing revolutionary advances in the deployment of molecular, genome sequencing-based, and mass spectrometry-driven detection, identification, and characterization assays. Laboratory automation and the linkage of information systems for big(ger) data management, including artificial intelligence (AI) approaches, also are being introduced. The initial optimism associated with these developments has now entered a more reality-driven phase of reflection on the significant challenges, complexities, and health care benefits posed by these innovations. With this in mind, the ongoing process of clinical laboratory consolidation, covering large geographical regions, represents an opportunity for the efficient and cost-effective introduction of new laboratory technologies and improvements in translational research and development. This will further define and generate the mandatory infrastructure used in validation and implementation of newer high-throughput diagnostic approaches. Effective, structured access to large numbers of well-documented biobanked biological materials from networked laboratories will release countless opportunities for clinical and scientific infectious disease research and will generate positive health care impacts. We describe why consolidation of clinical microbiology laboratories will generate quality benefits for many, if not most, aspects of the services separate institutions already provided individually. We also define the important role of innovative and large-scale diagnostic platforms. Such platforms lend themselves particularly well to computational (AI)-driven genomics and bioinformatics applications. These and other diagnostic innovations will allow for better infectious disease detection, surveillance, and prevention with novel translational research and optimized (diagnostic) product and service development opportunities as key results.

Essential role of laboratory physicians in transformation of laboratory practice and management to a value-based patient-centric model

The laboratory is a vital part of the continuum of patient care. In fact, there are few programs in the healthcare system that do not rely on ready access and availability of complex diagnostic laboratory services. The existing transactional model of laboratory "medical practice" will not be able to meet the needs of the healthcare system as it rapidly shifts toward value-based care and precision medicine, which demands that practice be based on total system indicators, clinical effectiveness, and patient outcomes. Laboratory "value" will no longer be focused primarily on internal testing quality and efficiencies but rather on the relative cost of diagnostic testing compared to direct improvement in clinical and system outcomes. The medical laboratory as a "business" focused on operational efficiency and cost-controls must transform to become an essential clinical service that is a tightly integrated equal partner in direct patient care. We would argue that this paradigm shift would not be necessary if laboratory services had remained a "patient-centric" medical practice throughout the last few decades. This review is focused on the essential role of laboratory physicians in transforming laboratory practice and management to a value-based patient-centric model. Value-based practice is necessary not only to meet the challenges of the new precision medicine world order but also to bring about sustainable healthcare service delivery.

Testing the repatriated for SARS-Cov2: Should laboratory-based quarantine replace traditional quarantine?

Background

An ongoing epidemic of respiratory diseases caused by a novel coronavirus (COVID 2019, SARS-CoV2) started in Wuhan, Hubei, in China at the end of December 2019. The French government decided to repatriate the 337 French nationals living in Wuhan and place them in quarantine in their home country. We decided to test them all for SARS-Cov2 twice in order to reduce anxiety among the population and decision-makers.

Methods

We investigated the presence of SARS-CoV-19 in asymptomatic carriers by testing all repatriated patients within the first 24 h of their arrival in France and at day 5. Viral RNA was extracted from pooled nasal and oropharyngeal swab fluids or sputum in the absence of nasal/oropharyngeal swabs. Detection of SARS-CoV-2 RNA was then carried out using several real-time reverse transcription (RT)-PCR assays.

Results

We tested 337 passengers at day 0 and day 5. All the tests for SARS-CoV2 were negative. By optimising the sampling process, sending samples sequentially and reducing the time-scale for biological analysis, we were able to test the samples within 5 h (including sampling, shipment and biological tests).

Conclusion

Optimising our procedures reduces anxiety and reassures the population and decision makers.

Development of point-of-care testing tool using immunochromatography for rapid diagnosis of human paragonimiasis

Paragonimiasis, an important food-borne zoonosis, is caused by lung flukes of the genus Paragonimus. Several million people are actually infected or at risk. Paragonimiasis is a re-emerging disease in developing countries. Diagnosis of pulmonary paragonimiasis is made by finding eggs in sputa and/or fecal samples. Eggs are typically not found in ectopic paragonimiasis cases, so diagnosis depends on supportive information, such as a history of eating fresh water crabs or crayfishes, radiographic findings and immunological tests. Here, a new point-of-care-testing (POCT) tool is presented. It uses immunochromatography for serodiagnosis of human paragonimiasis using excretory-secretory antigen from Paragonimus heterotremus. It proved effective in diagnosing infections due to P. heterotremus, and was also successfully diagnosed with sera from infections with P. westermani and P. miyazakii. The diagnostic sensitivity, specificity, positive and negative predictive values and accuracy were 97.9%, 87.6%, 78%, 98.9%, and 90.8%, respectively. The developed POCT tool is rapid and simple to use not only for clinical diagnosis of paragonimiasis at the bedside or at well-equipped laboratories, but also at local and remote hospitals with limited facilities. Moreover, the POCT tool could be applied for epidemiological surveys of paragonimaisis in Asia where P. heterotremus, P. westermani and P. miyazakii are endemic.

Rapid diagnostic tests for infectious diseases in the emergency department

Background

Rapid diagnostic tests (RDTs) for infectious diseases, with a turnaround time of less than 2 hours, are promising tools that could improve patient care, antimicrobial stewardship and infection prevention in the emergency department (ED) setting. Numerous RDTs have been developed, although not necessarily for the ED environment. Their successful implementation in the ED relies on their performance and impact on patient management.

Objectives

The aim of this narrative review was to provide an overview of currently available RDTs for infectious diseases in the ED.

Sources

PubMed was searched through August 2019 for available studies on RDTs for infectious diseases. Inclusion criteria included: commercial tests approved by the US Food and Drug Administration (FDA) or Conformité Européenne (CE) in vitro diagnostic devices with data on clinical samples, ability to run on fully automated systems and result delivery within 2 hours.

Content

A nonexhaustive list of representative commercially available FDA- or CE-approved assays was categorized by clinical syndrome: pharyngitis and upper respiratory tract infection, lower respiratory tract infection, gastrointestinal infection, meningitis and encephalitis, fever in returning travellers and sexually transmitted infection, including HIV. The performance of tests was described on the basis of clinical validation studies. Further, their impact on clinical outcomes and anti-infective use was discussed with a focus on ED-based studies.

Implications

Clinicians should be familiar with the distinctive features of each RDT and individual performance characteristics for each target. Their integration into ED work flow should be preplanned considering local constraints of given settings. Additional clinical studies are needed to further evaluate their clinical effectiveness and cost-effectiveness.

Detection of Borrelia crocidurae in a vaginal swab after miscarriage, rural Senegal, Western Africa

Tick-borne relapsing fever (TBRF) borreliae are one of the main causes of fever in rural Africa and can cause miscarriages. This article reports Borrelia crocidurae as a probable cause of spontaneous miscarriage, which was detected through vaginal self-sampling. This appears to be the first such report.