Better tests, better care: improved diagnostics for infectious diseases

Paper-based fluorogenic RNA aptamer sensors for label-free detection of small molecules

Sensors based on fluorogenic RNA aptamers have emerged in recent years. These sensors have been used for in vitro and intracellular detection of a broad range of biological and medical targets. However, the potential application of fluorogenic RNA-based sensors for point-of-care testing is still little studied. Here, we report a paper substrate-based portable fluorogenic RNA sensor system. Target detection can be simply performed by rehydration of RNA sensor-embedded filter papers. This affordable sensor system can be used for the selective, sensitive, and rapid detection of different target analytes, such as antibiotics and cellular signaling molecules. We believe that these paper-based fluorogenic RNA sensors show great potential for point-of-care testing of a wide range of targets from small molecules, nucleic acids, proteins, to various pathogens.

Improved diagnostic policy for respiratory tract infections essential for patient management in the emergency department

Aim:

Establishing an optimal diagnostic policy for patients with respiratory tract infections, at the emergency department (ED) of a university hospital in The Netherlands.

Methods:

Adult patients were sampled at admission, during the respiratory season (2014–2015). The FilmArray-RP was implemented at the clinical virology laboratory. Diagnostics were provided from 8 am to 10 pm, weekends included.

Results:

436/492 (89%) results were available while patients were still at the ED. Median TAT from admission to test result was 165 min (IQR: 138–214). No antibiotics were prescribed in 94/207 (45%) patients who tested positive for a virus. 185/330 (56%) hospitalized patients did not need admission with isolation measures. The value-based measure, expressed in euro–hour (€h), increased to tenfold compared with previous policy.

Conclusion:

An optimal policy is essential for patient management, by providing timely, reliable diagnostics.

Comparison of diagnostic accuracies of rapid serological tests and ELISA to molecular diagnostics in patients with suspected coronavirus disease 2019 presenting to the hospital

Objectives

To assess the diagnostic performance of rapid lateral flow immunochromatographic assays (LFAs) compared with an ELISA and nucleic acid amplification tests (NATs) in individuals with suspected coronavirus disease 2019 (COVID-19).

Methods

Patients presenting to a Dutch teaching hospital were eligible between 17 March and 10 April 2020, when they had respiratory symptoms that were suspected for COVID-19. The performances of six different LFAs were evaluated in plasma samples obtained on corresponding respiratory sample dates of NATs testing. Subsequently, the best performing LFA was evaluated in 228 patients and in 50 sera of a historical patient control group.

Results

In the pilot analysis, sensitivity characteristics of LFA were heterogeneous, ranging from 2/20 (10%; 95% CI 0%–23%) to 11/20 (55%; 95% CI 33%–77%). In the total cohort, Orient Gene Biotech COVID-19 IgG/IgM Rapid Test LFA had a sensitivity of 43/99 (43%; 95% CI 34%–53%) and specificity of 126/129 (98%; 95% CI 95%–100%). Sensitivity increased to 31/52 (60%; 95% CI 46%–73%) in patients with at least 7 days of symptoms, and to 21/33 (64%; 95% CI 47%–80%) in patients with C-reactive protein (CRP) ≥100 mg/L. Sensitivity and specificity of Wantai SARS-CoV-2 Ab ELISA was 59/95 (62%; 95% CI 52%–72%) and 125/128 (98%; 95% CI 95%–100%) in all patients, respectively, but sensitivity increased to 38/48 (79%; 95% CI 68%–91%) in patients with at least 7 days of symptoms.

Conclusions

There is large variability in diagnostic test performance between rapid LFAs, but overall limited sensitivity and high specificity in acutely admitted patients. Sensitivity improved in patients with longer existing symptoms or high CRP. LFAs should only be considered as additional triage tools when these may lead to the improvement of hospital logistics.

Enzymatic and Chemical-Based Methods to Inactivate Endogenous Blood Ribonucleases for Nucleic Acid Diagnostics

There are ongoing research efforts into simple and low-cost point-of-care nucleic acid amplification tests (NATs) addressing widespread diagnostic needs in resource-limited clinical settings. Nucleic acid testing for RNA targets in blood specimens typically requires sample preparation that inactivates robust blood ribonucleases (RNases) that can rapidly degrade exogenous RNA. Most NATs rely on decades-old methods that lyse pathogens and inactivate RNases with high concentrations of guanidinium salts. Herein, we investigate alternatives to standard guanidinium-based methods for RNase inactivation using an activity assay with an RNA substrate that fluoresces when cleaved. The effects of proteinase K, nonionic surfactants, SDS, dithiothreitol, and other additives on RNase activity in human serum are reported. Although proteinase K has been widely used in protocols for nuclease inactivation, it was found that high concentrations of proteinase K are unable to eliminate RNase activity in serum, unless used in concert with denaturing concentrations of SDS. It was observed that SDS must be combined with proteinase K, dithiothreitol, or both for irreversible and complete RNase inactivation in serum. This work provides an alternative chemistry for inactivating endogenous RNases for use in simple, low-cost point-of-care NATs for blood-borne pathogens.

[Access to complementary tests for the diagnosis of infectious diseases in primary care paediatric clinics]

INTRODUCTION

The performing of complementary tests in infectious processes can increase the diagnostic precision, the adequacy of treatments, as well as determining the epidemiology and pattern of bacterial resistance of the community. The Infectious Pathology Group of the Spanish Association of Primary Care Paediatrics (GPI-AEPap) has designed this study in order to determine the availability of complementary tests (CT) for paediatricians working in Primary Care of the public health system as well as their results.

MATERIAL AND METHODS

Observational cross-sectional descriptive national study was carried out using a voluntary self-report questionnaire distributed online to all AEPap members and to the subscribers of the PEDIAP distribution list between the months of April and May 2017.

RESULTS

A total of 517 responses were obtained. An analysis was made of the data from the professional environment, as well as those related to the request for basic supplementary tests (blood count, biochemistry, and routine urine analysis), the use of Rapid Antigen Detection Test for group A Streptococcus, bacterial cultures, serology, diagnostic tests for pertussis and tuberculosis (Mantoux), as well as imaging tests.

CONCLUSIONS

There is variability between Autonomous Communities and healthcare areas. Areas for improvement were found in the accessibility to different CT, collection time and sending of samples, delay in receiving results, as well as waiting times for non-urgent imaging tests. These affect the intervention and resolution capacity of the primary care paediatrician.

Development and Evaluation of a Loop-Mediated Isothermal Amplification Assay for Rapid and Specific Identification of Carbapenem-Resistant Acinetobacter baumannii Strains Harboring blaOXA-23, and the Epidemiological Survey of Clinical Isolates

Acinetobacter baumannii is an important nosocomial pathogen in hospital-acquired infections, and carbapenem resistance has been increasingly observed worldwide. Oxacillinase production by bla_OXA-23 is a predominant and prevalent carbapenem resistance mechanism of A. baumannii, especially in China. Rapid and specific detection of bla_OXA-23 may offer valuable insight for administration of directed antimicrobial therapy. In this study, we aimed to develop a loop-mediated isothermal amplification (LAMP)-based method for identifying carbapenem-resistant A. baumannii (CRAB) harboring the bla_OXA-23 gene. High-specificity primers for screening bla_OXA-23 were designed and synthesized, and the LAMP reactions were performed. Clinical A. baumannii strains isolated from the Former 307th Hospital of People's Liberation Army were used to determine the sensitivity and specificity of this method compared with those of phenotypic antimicrobial susceptibility testing and the traditional PCR method. Multilocus sequence typing (MLST) was performed to investigate the epidemiology of the A. baumannii bacterial population. Compared with antimicrobial susceptibility testing, the sensitivity and specificity of LAMP in detecting bla_OXA-23 were 88.4% and 97.7%, respectively. However, the LAMP method is much simpler and less time-consuming (within 60 minutes) than conventional PCR and phenotypic susceptibility testing. The 113 isolates could be clustered into 30 sequence types, and most strains (83/113) belonged to clonal complex (CC) 92, which is also the dominant CC in China. The LAMP-based method detected bla_OXA-23 in a simpler manner and could provide rapid results for identifying CRAB. Consequently, bla_OXA-23 may serve as a surrogate marker for the presence of CRAB in patients with serious infections in clinical practice.

Laboratory Tests for COVID-19: A Review of Peer-Reviewed Publications and Implications for Clinical Use

Diagnostic tests for the coronavirus infection 2019 (COVID-19) are critical for prompt diagnosis, treatment and isolation to break the cycle of transmission. A positive real-time reverse-transcriptase polymerase chain reaction (RT-PCR), in conjunction with clinical and epidemiologic data, is the current standard for diagnosis, but several challenges still exist. Serological assays help to understand epidemiology better and to evaluate vaccine responses but they are unreliable for diagnosis in the acute phase of illness or assuming protective immunity. Serology is gaining attention, mainly because of convalescent plasma gaining importance as treatment for clinically worsening COVID-19 patients. We provide a narrative review of peer-reviewed research studies on RT-PCR, serology and antigen immune-assays for COVID-19, briefly describe their lab methods and discuss their limitations for clinical practice.

Computational design of probes to detect bacterial genomes by multivalent binding

Rapid methods for diagnosis of bacterial infections are urgently needed to reduce inappropriate use of antibiotics, which contributes to antimicrobial resistance. In many rapid diagnostic methods, DNA oligonucleotide probes, attached to a surface, bind to specific nucleotide sequences in the DNA of a target pathogen. Typically, each probe binds to a single target sequence; i.e., target-probe binding is monovalent. Here we show using computer simulations that the detection sensitivity and specificity can be improved by designing probes that bind multivalently to the entire length of the pathogen genomic DNA, such that a given probe binds to multiple sites along the target DNA. Our results suggest that multivalent targeting of long pieces of genomic DNA can allow highly sensitive and selective binding of the target DNA, even if competing DNA in the sample also contains binding sites for the same probe sequences. Our results are robust to mild fragmentation of the bacterial genome. Our conclusions may also be relevant for DNA detection in other fields, such as disease diagnostics more broadly, environmental management, and food safety.

Rapid identification of bloodstream bacterial and fungal pathogens and their antibiotic resistance determinants from positively flagged blood cultures using the BioFire FilmArray blood culture identification panel

BACKGROUND/PURPOSE

Rapid and accurate identification of pathogens and their antibiotic resistance directly from flagged blood cultures can aid clinicians in optimizing early antibiotic treatment and improve the clinical outcomes, especially in settings associated with high rates of bloodstream infection caused by vancomycin-resistant Enterococci (VRE) and carbapenem-resistant Enterobacteriaceae (CRE). We compared the results of the BioFire FilmArray Blood Culture Identification (BCID) panel with those of conventional methods for identifying the pathogens and their antibiotic susceptibility status.

METHODS

In total, 100 randomly selected positive blood cultures (BACTEC Plus Aerobic/F bottles or BACTEC Anaerobic Lytic/10 bottles) were analyzed. The pathogen detection efficiency of FilmArray BCID panel was compared with that of conventional method using MALDI-TOF MS system (Bruker MALDI Biotyper) and susceptibility testing by the Vitek 2 system. The sequencing analysis of antibiotic resistance genes was performed for discrepant results obtained from MALDI Biotyper and Vitek 2.

RESULTS

Among the 100 positively flagged blood cultures, 94% of FilmArray BCID panel results were consistent with the MALDI Biotyper results. All five VRE isolates positive for vanA/vanB genes, 10 of 12 Staphylococcus species positive for mecA gene, and only one Klebsiella pneumoniae isolate positive for K. pneumoniae carbapenemase gene (bla_KPC) detected in the FilmArray BCID panel were also concordant with results by the results by conventional susceptibility testing/molecular confirmation.

CONCLUSIONS

The FilmArray BCID panel results not only demonstrated good correlation with conventional blood culture identification and susceptibility results but also provided results rapidly, especially for the early detection of MRSA, VRE and bla_KPC-mediated CRE.

Incorporation of rapid diagnostic tests to improve time to antimicrobial therapy for gram-positive bacteremia and candidemia

Purpose

Even with rapid diagnostic technology to swiftly identify infectious organisms, prompt response is needed to translate results into appropriate actions. The purpose of this study was to determine if the introduction of real-time pharmacist response to positive rapid diagnostic test results would decrease time to antimicrobial therapy for gram-positive bacteremia and candidemia in a community hospital setting.

Methods

A quasi-experimental study was conducted in 2 community hospitals. The study comprised 2 cohorts of adult patients who tested positive for gram-positive bacteremia involving Staphylococcus aureus, Enterococcus faecalis, Enterococcus faecium, or Candida species. The preintervention cohort consisted of patients admitted from November 2017 through May 2018. The intervention cohort consisted of patients admitted from July 2018 through January 2019, after the intervention went live. The primary outcomes were time to optimal antimicrobial therapy and time to effective antimicrobial therapy.

Results

A total of 140 patients were included in the preintervention group, with 124 patients included in the intervention group. The mean (SD) time to effective therapy decreased from 13.9 (21.6) hours in the preintervention group to 8.6 (12.5) hours in the intervention group (hazard ratio [HR], 1.15; 95% confidence interval [CI], 0.89-1.48; P = 0.29). The mean (SD) time to optimal therapy significantly decreased from 53.7 (57.7) hours in the preintervention group to 38.4 (31.5) hours in the intervention group (HR, 1.73; 95% CI, 1.33-2.26; P < 0.001).

Conclusion

The introduction of real-time pharmacist response to positive rapid diagnostic test results led to a significant decrease in time to optimal antimicrobial therapy but did not significantly affect time to effective therapy. The results showed that the allocation of limited resources of a community hospital to such a stewardship program is justifiable.

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.

Translating in vitro diagnostics from centralized laboratories to point-of-care locations using commercially-available handheld meters

There is a growing demand for high-performance point-of-care (POC) diagnostic technologies where in vitro diagnostics (IVD) is fundamental for prevention, identification, and treatment of many diseases. Over the past decade, a shift of IVDs from the centralized laboratories to POC settings is emerging. In this review, we summarize recent progress in translating IVDs from centralized labs to POC settings using commercially available handheld meters. After introducing typical workflows for IVDs and highlight innovative technologies in this area, we discuss advantages of using commercially available handheld meters for translating IVDs from centralized labs to POC settings. We then provide comprehensive coverage of different signal transduction strategies to repurpose the commercially-available handheld meters, including personal glucose meter, pH meter, thermometer and pressure meter, for detecting a wide range of targets by integrating biochemical assays with the meters for POC testing. Finally, we identify remaining challenges and offer future outlook in this area.

Rapid detection of bacterial infection and viability assessment with high specificity and sensitivity using Raman microspectroscopy

Infectious diseases caused by bacteria still pose major diagnostic challenges in spite of the availability of various molecular approaches. Irrespective of the type of infection, rapid identification of the causative pathogen with a high degree of sensitivity and specificity is essential for initiating appropriate treatment. While existing methods like PCR possess high sensitivity, they are incapable of identifying the viability status of the pathogen and those which can, like culturing, are inherently slow. To overcome these limitations, we developed a diagnostic platform based on Raman microspectroscopy, capable of detecting biochemical signatures from a single bacterium for identification as well as viability assessment. The study also establishes a decontamination protocol for handling live pathogenic bacteria which does not affect identification and viability testing, showing applicability in the analysis of sputum samples containing pathogenic mycobacterial strains. The minimal sample processing along with multivariate analysis of spectroscopic signatures provides an interface for automatic classification, allowing the prediction of unknown samples by mapping signatures onto available datasets. Also, the novelty of the current work is the demonstration of simultaneous identification and viability assessment at a single bacterial level for pathogenic bacteria. Graphical abstract.

A good career start can open doors: the plusses and minuses of an international graduate student program-a student's perspective

There are many Ph.D. programs from various funding agencies that provide excellent starts to a scientific career. Multinational Ph.D. positions attract students because they provide students with much-required exposure to the international scientific community at an early stage of the career. For this reason, multinational Ph.D. positions can be considered as a better career opportunity over Ph.D. positions confined to a single country. In addition, these multidisciplinary research programs connect different organizations to deal with the problems of global interest. One of these multi-disciplinary research programs is the viral and bacterial adhesion network training-innovative training network (ViBrANT). ViBrANT is a multifaceted platform that develops the required skillsets in young researchers and thereby also contributes to building a multidisciplinary research community. Is this the only parameter to be considered or are there other factors that can also stimulate one’s career development? In this perspective article, I will discuss the key reasons why I chose a multinational Ph.D. program along with the merits of being part of ViBrANT. I also discuss the challenges I faced while moving from India to the United Kingdom.

Companion and complementary diagnostics for infectious diseases

INTRODUCTION

Companion diagnostics (CDx) are important in oncology therapeutic decision-making, but specific regulatory-approved CDx for infectious disease treatment are officially lacking. While not approved as CDx, several ID diagnostics are used as CDx. The diagnostics community, manufacturers, and regulatory agencies have made major efforts to ensure that diagnostics for new antimicrobials are available at or near release of new agents.

AREAS COVERED

This review highlights the status of Complementary and companion diagnostic (c/CDx) in the infectious disease literature, with a focus on genotypic antimicrobial resistance testing against pathogens as a class of diagnostic tests.

EXPERT OPINION

CRISPR, sepsis markers, and narrow spectrum antimicrobials, in addition to current and emerging technologies, present opportunities for infectious disease c/CDx. Challenges include slow guideline revision, high costs for regulatory approval, lengthy buy in by agencies, discordant pharmaceutical/diagnostic partnerships, and higher treatment costs. The number of patients and available medications used to treat different infectious diseases is well suited to support competing diagnostic tests. However, newer approaches to treatment (for example, narrow spectrum antibiotics), may be well suited for a small number of patients, i.e. a niche market in support of a CDx. The current emphasis is rapid and point-of-care (POC) diagnostic platforms as well as changes in treatment.

Current and Future Perspectives on Isothermal Nucleic Acid Amplification Technologies for Diagnosing Infections

Nucleic acid amplification technology (NAAT) has assumed a critical position in disease diagnosis in recent times and contributed significantly to healthcare. Application of these methods has resulted in a more sensitive, accurate and rapid diagnosis of infectious diseases than older traditional methods like culture-based identification. NAAT such as the polymerase chain reaction (PCR) is widely applied but seldom available to resource-limited settings. Isothermal amplification (IA) methods provide a rapid, sensitive, specific, simpler and less expensive procedure for detecting nucleic acid from samples. However, not all of these IA techniques find regular applications in infectious diseases diagnosis. Disease diagnosis and treatment could be improved, and the rapidly increasing problem of antimicrobial resistance reduced, with improvement, adaptation, and application of isothermal amplification methods in clinical settings, especially in developing countries. This review centres on some isothermal techniques that have found documented applications in infectious diseases diagnosis, highlighting their principles, development, strengths, setbacks and imminent potentials for use at points of care.

Glycoengineering bioconjugate vaccines, therapeutics, and diagnostics in E. coli

The first, general glycosylation pathway in bacteria, the N-linked glycosylation system of Campylobacter jejuni, was discovered two decades ago. Since then, many diverse prokaryotic glycosylation systems have been characterized, including O-linked glycosylation systems that have no homologous counterparts in eukaryotic organisms. Shortly after these discoveries, glycosylation pathways were recombinantly introduced into E. coli creating the field of bacterial glycoengineering. Bacterial glycoengineering is an emerging biotechnological tool that harnesses prokaryotic glycosylation systems for the generation of recombinantly glycosylated proteins using E. coli as a host. Over the last decade, as our understanding of prokaryotic glycosylation systems has advanced, so too has the glycoengineering toolbox. Currently, glycoengineering utilizes two broad approaches to recombinantly glycosylate proteins, both of which can generate N- or O-linkages: oligosaccharyltransferase (OTase)-dependent and OTase-independent. This review discusses the applications of these bacterial glycoengineering techniques as they relate to the development of glycoconjugate vaccines, therapeutic proteins, and diagnostics.

A Simple and Fast Assay Based on Carboxyfluorescein-Loaded Liposome for Quantitative DNA Detection

The development of an innovative and easy way to run assays for the quantitative detection of DNA present in biological fluids (i.e., blood, urine, and saliva) is of great interest for early diagnosis (e.g., tumors) and personalized medicine. Herein, a new quantitative assay based on the use of highly sensitive carboxyfluorescein-loaded liposomes as signal amplification systems is reported. The method has been tested for the detection of low amounts of DNA sequences. The reported proof of concept exploits a target DNA molecule as a linker between two complementary oligonucleotides. One oligonucleotide is biotinylated at its 3' end and binds to streptavidin-coupled magnetic beads, whereas the other one is conjugated to a cholesterol molecule incorporated in the phospholipidic bilayer of the fluorescent liposomes. In the presence of the target fragment, the correct formation of a construct takes place as witnessed by a strong fluorescence signal, amplified by dissolving lipidic nanoparticles with Triton X-100. The system is able to detect specific nucleotide sequences with a very low detection threshold of target DNA (tens of picomolar). The assay allows the detection of both single- and double-stranded DNA. Studies performed in human blood serum show the correct assembling of the probe but with a reduction of limit of detection (up to ∼1 nM). This liposome signal amplification strategy could be used not only for the detection of DNA but also for other nucleic acids (mRNA; microRNA) that are difficult to be quantified by currently available protocols.

Canadian Burden of Skin Disease From 1990 to 2017: Results From the Global Burden of Disease 2017 Study [Formula: see text]

Background

Skin diseases can have high morbidity that can be costly to society and individuals. To date, there has been no comprehensive assessment of the burden of skin disease in Canada.

Objectives

To evaluate the burden of 18 skin and subcutaneous diseases from 1990 to 2017 in Canada using the Global Burden of Disease (GBD) data.

Methods

The 2017 GBD study measures health loss from 359 diseases and injuries in 195 countries; we evaluated trends in population health in Canada from 1990 to 2017 using incidence, prevalence, mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life years (DALYs). Data are presented as rates (per 100 000), counts, or percent change with the uncertainty interval in brackets.

Results

From 1990 to 2017 for all skin diseases, DALY rates increased by 8% to 971 per 100 000 (674-1319), YLD rates increased by 8% to 897 per 100 000 (616-1235), YLL rates increased by 4% to 74 per 100 000 (53-89), and death rates increased by 18% to 5 per 100 000 (3-6). DALY rates for melanoma increased by 2% to 54 per 100 000 (39-68), for keratinocyte carcinoma by 14% to 17 per 100 000 (16-19), and for skin and subcutaneous disease by 8% to 900 per 100 000 (619-1233). The observed over expected ratios were higher for skin and subcutaneous disease (1.37) and keratinocyte carcinoma (1.17) and were lower for melanoma (0.73).

Conclusions

The burden of skin disease has increased in Canada since 1990. These results can be used to guide health policy regarding skin disease in Canada.

Structure-Function Studies on IMD-0354 Identifies Highly Active Colistin Adjuvants

Infections caused by multidrug-resistant (MDR) bacteria, particularly Gram-negative bacteria, are an escalating global health threat. Often clinicians are forced to administer the last-resort antibiotic colistin; however, colistin resistance is becoming increasingly prevalent, giving rise to the potential for a situation in which there are no treatment options for MDR Gram-negative infections. The development of adjuvants that circumvent bacterial resistance mechanisms is a promising orthogonal approach to the development of new antibiotics. We recently disclosed that the known IKK-β inhibitor IMD-0354 potently suppresses colistin resistance in several Gram-negative strains. In this study, we explore the structure-activity relationship (SAR) between the IMD-0354 scaffold and colistin resistance suppression, and identify several compounds with more potent activity than the parent against highly colistin-resistant strains of Acinetobacter baumannii and Klebsiella pneumoniae.

Diagnostic Microbiology from the Beginning to the Future: Regional Antibiograms as Public Health Tools to Slow Down Antibiotic Resistance

Infectious diseases is the only area of medicine where we can isolate the cause and study it in the laboratory under conditions similar to human body. Once isolated, we are able to determine the most optimal drug to treat it. Unfortunately, it is also the only specialty where after making truly wondrous strides we find ourselves at the crossroads of a public health crisis in the form of ongoing antibiotic resistance. Among the factors responsible for the current status, is the suboptimal utilization of the diagnostic microbiology laboratory. In this review authors provide a short historical perspective of diagnostic microbiology. The focus of discussion is the generation and utilization of cumulative antibiograms at the institutional and regional levels and discuss the pitfalls in large national databases with respect to the day-to-day patient care. This public health tool to slow down antibiotic resistance happens to be low-tech and inexpensive.

Biotechnological innovations in farm and pet animal disease diagnosis

The application of innovative diagnostic technologies for the detection of animal pathogens at an early stage is essential in restricting the economic loss incurred due to emerging infectious animal diseases. The desirable characteristics of such diagnostic methods are easy to use, cost-effective, highly sensitive, and specific, coupled with the high-throughput detection capabilities. The enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) are still the most common assays used for the detection of animal pathogens across the globe. However, utilizing the principles of ELISA and PCR, several serological and molecular technologies have been developed to achieve higher sensitivity, rapid, and point-of-care (POC) detection such as lateral flow assays, biosensors, loop-mediated isothermal amplification, recombinase polymerase amplification, and molecular platforms for field-level detection of animal pathogens. Furthermore, animal disease diagnostics need to be updated regularly to capture new, emerging and divergent infectious pathogens, and biotechnological innovations are helpful in fulfilling the rising demand for such diagnostics for the welfare of the society. Therefore, this chapter primarily describes and discusses in detail the serological, molecular, novel high-throughput, and POC assays to detect pathogens affecting farm and companion animals.

A nanoparticle pseudo pathogen for rapid detection and diagnosis of virus infection

We herein report a new rapid blood test for virus infection detection and diagnosis. A citrate gold nanoparticle is first coated with a virus lysate to form a gold nanoparticle pseudo pathogen. The gold nanoparticle pseudo virus is then mixed with a blood plasma or serum samples. If the blood sample is from a positive patient, the activated immune molecules in the blood such as antibodies, complement proteins and others will react with the nanoparticle pseudo virus, leading to nanoparticle aggregate formation. The nanoparticle aggregate formation is detected and measured using a particle sizing technique called dynamic light scattering. In this study, we applied this test for Zika virus infection detection. We tested blood plasma samples from 85 Zika positive patients, 40 Dengue positive patients, 10 Chikungunya positive patients, and 78 non-patient control samples collected from both endemic and non-endemic locations. The study shows that the new test has a higher sensitivity compared to some existing commercial tests in the market, while maintaining a similar specificity. Within 7 days from the symptom onset, the new test can detect 43% of the infected patients while a commercial anti-Zika IgM test detects only 26% of the infected patients. Within 14 days from the symptom onset, our new test detects 73% of the infected patients while the same commercial anti-Zika IgM test detects 53% of the infected patients. The test is extremely simple, easy to develop, with test results obtained within minutes. This new test platform may be potentially adapted for the detection and diagnosis of a wide range of viral infectious diseases, for example, the currently ongoing COVID-19.

•

A rapid blood test for point-of-care virus infectious disease detection and diagnosis.

•

The test uses a gold nanoparticle pseudo virus particle to detect active immune response from patient’s blood.

•

The test is a single-step process with results obtained within 20 min.

•

The test shows significantly better sensitivity than a commercially available serology test.

•

The test platform may be adapted to develop diagnostic tests for different virus infections.

Diagnosis of Tuberculosis: Nanodiagnostics Approaches

Tuberculosis (TB) remains one of the most devastating infectious diseases worldwide. The burden of TB is alarmingly high in developing countries, where diagnosis latent TB infection (LTBI), Extra-pulmonary tuberculosis (EPTB), drug-resistant tuberculosis (DR-TB), HIV-associated TB, and paediatric TB is still a challenge. This is mainly due to delayed or misdiagnosis of TB, which continues to fuel its worldwide epidemic. The ideal diagnostic test is still unavailable, and conventional methods remain a necessity for TB diagnosis, though with poor diagnostic ability. The nanoparticles have shown potential for the improvement of drug delivery, reducing treatment frequency and diagnosis of various diseases. The engineering of antigens/antibody nanocarriers represents an exciting front in the field of diagnostics, potentially flagging the way toward development of better diagnostics for TB. This chapter discusses the presently available tests for TB diagnostics and also highlights the recent advancement in the nanotechnology-based detection tests for M. tuberculosis.

Detection of cardiovascular disease associated miR-29a using paper-based microfluidics and surface enhanced Raman scattering

A paper-based microfluidics self-testing device capable of colorimetric and SERS-based sensing of cardiovascular disease associated miR-29a has been developed for improving patient care and triage.

MinION sequencing of Streptococcus suis allows for functional characterization of bacteria by multilocus sequence typing and antimicrobial resistance profiling

In recent years, high-throughput sequencing has revolutionized disease diagnosis by its powerful ability to provide high resolution genomic information. The Oxford Nanopore MinION sequencer has unparalleled potential as a rapid disease diagnostic tool due to its high mobility, accessibility, and short turnaround time. However, there is a lack of rigorous quality assessment and control processes standardizing the testing on the MinION, which is necessary for incorporation into a diagnostic workflow. Thus, our study examined the use of the MinION sequencer for bacterial whole genome generation and characterization. Using Streptococcus suis as a model, we optimized DNA isolation and treatments to be used for MinION sequencing and standardized de novo assembly to quickly generate a full-length consensus sequence achieving a 99.4% average accuracy. The consensus genomes from MinION sequencing were able to accurately predict the multilocus sequence type in 8 out of 10 samples and identified antimicrobial resistance profiles for 100% of the samples, despite the concern of a high error rate. The inability to unequivocally predict sequence types was due to difficulty in differentiating high identity alleles, which was overcome by applying additional error correction methods to increase consensus accuracy. This manuscript provides methods for the use of MinION sequencing for identification of S. suis genome sequence, sequence type, and antibiotic resistance profile that can be used as a framework for identification and classification of other pathogens.

Reliable Serological Diagnostic Tests for Arboviruses: Feasible or Utopia?

Infections with arthropod-borne viruses are increasing globally as a result of climate and demographic changes, global dispersion of insect vectors, and increased air travel. The similar symptomatology of arboviral diseases and the cocirculation of different arboviruses in Africa, Asia, and South America complicate diagnosis. Despite the high sensitivity and specificity of molecular diagnostic tests, their utility is limited to the short viremic phase of arbovirus infections, and therefore the diagnosis of infection is frequently missed in clinical practice. Conversely, the duration of antibody responses provides a wider window of opportunity, making diagnosis more dependent on IgM/IgG detection. This review discusses the issues underlying the low specificity of antibody-detection assays, and addresses the challenges and strategies for discovering more specific biomarkers to enable a more accurate diagnosis.

FebriDx®: A Rapid Diagnostic Test for Differentiating Bacterial and Viral Aetiologies in Acute Respiratory Infections

FebriDx® is a rapid, point-of-care diagnostic test that is designed to aid in the differentiation of bacterial and viral acute respiratory infections (ARIs), thus helping to guide decisions regarding the prescription of antibiotics in the outpatient setting. FebriDx carries a CE mark for use in the EU and is also approved in several other countries, including Canada, Saudi Arabia and Singapore. It is indicated for use in patients > 2 years old with symptoms consistent with a community-acquired ARI. The test involves the use of an immunoassay on a fingerstick blood sample to provide simultaneous, qualitative measurement of elevated levels of C-reactive protein (CRP) and myxovirus resistance protein A (MxA). In two prospective, multicentre studies in patients with acute upper respiratory tract infections, FebriDx was shown to be both sensitive and specific in identifying patients with a clinically significant infection and in differentiating between infections of bacterial and viral aetiology. The test is simple, requires no additional equipment and produces actionable results in ~ 10 min. As was demonstrated in a small, retrospective analysis, FebriDx results can help guide (improve) antibiotic prescribing decisions. Reducing the unnecessary or inappropriate prescription of antibiotics for ARIs of probable viral aetiology is important for antibiotic stewardship and can also reduce the unnecessary exposure of patients to the risk of antibiotic-related adverse events. FebriDx thus represents a useful diagnostic tool in the outpatient setting.

E-cigarette, or vaping, product use associated lung injury (EVALI): case series and diagnostic approach

BACKGROUND

Since June, 2019, more than 1000 new cases of e-cigarette, or vaping, product use associated lung injury (EVALI) have been reported in the USA. Patients presented with dyspnoea, cough, and were found to be hypoxaemic with bilateral airspace opacities on chest imaging. Most patients required management in the intensive care unit and steroid therapy. All patients recovered with cessation of vaping, supportive care, and steroid therapy and remained symptom free at follow up. E-cigarette use continues to rapidly escalate in the USA, particularly among youth.

METHODS

Cases were defined as patients admitted to the University of Rochester Medical Center (Rochester, NY, USA) who had used e-cigarettes or another vaping device in the 30 days before presentation, and who had bilateral airspace opacification on chest imaging (CT or x-ray). Case details were obtained via medical record review and patient interviews over the past 3 months including symptomatology, physical exam data, imaging studies, laboratory data, vaping history, and subsequent outpatient follow-up data. In collaboration with the New York State Department of Health, our hospital developed a novel clinical practice algorithm based on statewide physician feedback along with input from experts in environmental health, medical toxicology, infectious disease, epidemiology, and chronic disease prevention.

FINDINGS

We report 12 cases treated for suspected EVALI at our medical centre between June 6, 2019, and Sept 15, 2019. Ten (83%) patients had dyspnoea, fever, and emesis and nine (75%) had cough. 11 (92%) patients reported the use of e-cigarette cartridges containing tetrahydrocannabinol oil. Although eight (67%) patients required admission to the intensive care unit for hypoxaemic respiratory failure, no deaths occurred. The median hospitalisation duration was 7 days (IQR 7-8). All patients completing follow up (6 [50%]) had resolution of previous chest CT findings and normal spirometry. The clinical algorithm focuses on the key signs and symptoms of EVALI and the importance of ruling out infection and other cardiopulmonary conditions before making a presumptive diagnosis of EVALI.

INTERPRETATION

Patients with suspected EVALI in our cohort had life-threatening hypoxaemia, with 67% requiring management in the intensive care unit. Despite the severity of presentation, similar to previous reports of patients with EVALI, most patients improved within 1-2 weeks of initial presentation after vaping cessation and administration of systemic corticosteroids when needed. Almost all (92%) patients with suspected EVALI reported vaping a THC product, making THC containing e-liquids or oils a key focus on the ongoing nationwide investigations into the cause of EVALI. Additional research is required to understand the potential toxins, underlying pathophysiological mechanisms, and identification of susceptible individuals at higher risk for hospitalisation due to EVALI. To our knowledge we present the first clinical practice algorithm for the evaluation and management of EVALI, which will be useful for both acute management and improved accurate reporting of this life-threatening respiratory illness.

FUNDING

None.

Evaluation of a new Rapid Antimicrobial Susceptibility system for Gram-negative and Gram-positive bloodstream infections: speed and accuracy of Alfred 60AST

BACKGROUND

Blood stream infections (BSIs) are a major cause of morbidity and mortality. The time from taking blood cultures to obtain results of antibiotic sensitivity can be up to five days which impacts patient care. The Alfred 60 AST™ can reduce laboratory time from positive culture bottle to susceptibility results from 16 to 25 h to 5-6 h, transforming patient care. To evaluate the diagnostic accuracy of a rapid antimicrobial susceptibility system, the Alfred 60 AST™, in clinical isolates from patients with BSIs and confirm time to results. 301 Gram-negative and 86 Gram-positive isolates were analysed directly from positive blood culture bottles following Gram staining. Antimicrobial susceptibility results and time-to-results obtained by rapid Alfred 60 AST system and BD Phoenix were compared .

RESULTS

A total of 2196 antimicrobial susceptibility test results (AST) were performed: 1863 Gram-negative and 333 Gram-positive. AST categorical agreement (CA) for Alfred 60 AST™ was 95% (1772/1863) for Gram-negative and 89% (295/333) for Gram-positive isolates. Gram-negative CA: ampicillin 96% (290/301); ciprofloxacin 95% (283/297); ceftriaxone 96% (75/78); meropenem 97% (288/297); piperacillin-tazobactam 95% (280/295); gentamicin 94% (279/297) and amikacin 93% (277/298). The median time to susceptibility results from blood culture flagging positive was 6.3 h vs 20 h (p < 0.01) for Alfred system vs BD Phoenix™.

CONCLUSION

Alfred 60 AST system greatly reduced time to antimicrobial susceptibility results in Gram-negative and Gram-positive BSIs with good performance and cost, particularly for Gram-negative bacteraemia.

mNGS in clinical microbiology laboratories: on the road to maturity

Metagenomic next-generation sequencing (mNGS) is increasingly being applied in clinical laboratories for unbiased culture-independent diagnosis. Whether it can be a next routine pathogen identification tool has become a topic of concern. We review the current implementation of this new technology for infectious disease diagnostics and discuss the feasibility of transforming mNGS into a routine diagnostic test. Since 2008, numerous studies from over 20 countries have revealed the practicality of mNGS in the work-up of undiagnosed infectious diseases. mNGS performs well in identifying rare, novel, difficult-to-detect and coinfected pathogens directly from clinical samples and presents great potential in resistance prediction by sequencing the antibiotic resistance genes, providing new diagnostic evidence that can be used to guide treatment options and improve antibiotic stewardship. Many physicians recognized mNGS as a last resort method to address clinical infection problems. Although several hurdles, such as workflow validation, quality control, method standardisation, and data interpretation, remain before mNGS can be implemented routinely in clinical laboratories, they are temporary and can be overcome by rapidly evolving technologies. With more validated workflows, lower cost and turnaround time, and simplified interpretation criteria, mNGS will be widely accepted in clinical practice. Overall, mNGS is transforming the landscape of clinical microbiology laboratories, and to ensure that it is properly utilised in clinical diagnosis, both physicians and microbiologists should have a thorough understanding of the power and limitations of this method.

Simple microfluidic device for detecting the negative dielectrophoresis of DNA labeled microbeads

We propose a new microfluidic device that can be used to determine the change in the negative dielectrophoresis (n-DEP) of dielectric microbeads when a small amount of DNA is attached to them. We previously proposed a DNA detection method based on changes in the DEP of microbeads induced by the attachment of DNA. When target DNA is attached to the microbeads having n-DEP property, the DEP changes from negative to positive. This occurs because electric charges of the DNA increase the surface conductance of the microbeads. Thus, only the DNA-labeled microbeads are attracted to a microelectrode by positive DEP. The trapped DNA-labeled microbeads can be counted by dielectrophoretic impedance measurements. A large amount of DNA (approximately 10⁵ DNA molecules) is required to change the DEP from negative to positive. Even though this method can be combined with DNA amplification, reducing the amount of DNA required can help us to shorten the reaction time. In this study, we aimed to detect DNA less than 10⁵ DNA molecules by determining the change in the n-DEP change. To achieve this, we proposed a simple microfluidic device consisting of a single microchannel and a single pair of microelectrodes. Numerical simulations revealed that the device can identify the slight change in the n-DEP of the microbeads corresponding to the attachment of a small amount of DNA. In practical experiments, the fabricated device distinguished 10-1000 DNA molecules per microbead. This method represents a fast and easy method of DNA detection when combined with DNA amplification techniques.

Rapid Rule Out of Culture-Negative Bloodstream Infections by Use of a Novel Approach to Universal Detection of Bacteria and Fungi

BACKGROUND

Currently it can take up to 5 days to rule out bloodstream infection. With the low yield of blood cultures (approximately 10%), a significant number of patients are potentially exposed to inappropriate therapy that can lead to adverse events. More rapid rule out can accelerate deescalation or cessation of antimicrobial therapy, improving patient outcomes.

METHODS

A method is described, termed enzymatic template generation and amplification (ETGA), that universally and sensitively detects DNA polymerase activity liberated from viable bacteria and fungi isolated from blood culture samples as a measure of bloodstream infection. ETGA was applied in a diagnostic test format to identify negative blood cultures after an overnight incubation. Performance data for a prototype (Cognitor) and automated (Magnitor) version of the test are presented.

RESULTS

The Cognitor manual assay displayed analytical reactivity for a panel of the 20 most prevalent causes of bloodstream infection, with a detection range of 28-9050 CFU/mL. Validation with 1457 clinical blood cultures showed a negative predictive value of 99.0% compared to blood culture incubation for 5 days. Magnitor showed an improved detection range of 1-67 CFU/mL, allowing for detection of bacteria-supplemented blood cultures after 2-8 h incubation, and Candida albicans-supplemented blood cultures at 16-22 h, 5-15 h faster than blood culture. Removing an aliquot from a blood culture bottle and replacing the bottle into the incubator was shown not to result in contaminating organisms being introduced.

CONCLUSIONS

The described method displays excellent breadth and detection for microbial cells and demonstrates the capability of confirming negative blood cultures after an overnight incubation in a blood culture instrument.

ELIMU-MDx: a web-based, open-source platform for storage, management and analysis of diagnostic qPCR data

The Electronic Laboratory Information and Management Utensil for Molecular Diagnostics (ELIMU-MDx) is a user-friendly platform designed and built to accelerate the turnaround time of diagnostic qPCR assays. ELIMU-MDx is compliant with Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines and has extensive data-import capabilities for all major qPCR instruments by using the RDML data standard. This platform was designed as an open-source software tool and can be accessed through the web browser on all major operating systems.

A positive pneumococcal urinary antigen test promotes narrow spectrum antibiotic use in patients with non-invasive pneumococcal pneumonia

BACKGROUND

We compared changes in antibiotics in patients diagnosed with noninvasive pneumococcal pneumonia (NPP) by pneumoccocal urinary antigen tests or respiratory cultures.

METHODS

We compared patients diagnosed by pneumococcal urinary antigen tests or respiratory cultures that grew Streptococcus pneumoniae. We assessed the time from sample receipt to final result and antibiotic regimens, including an Antibiotic Spectrum Index (ASI).

RESULTS

Seventy-two cases of NPP were diagnosed by pneumococcal urinary antigen and 87 by respiratory cultures, with a median time from sample receipt to final result of 0.21 days (interquartile range (IQR) 0.17-1.17) and 3.21 days (IQR 3.17-4.21 days), respectively. Among 123 cases without antibiotic allergies, between days 0 and 2, the ASI decreased in 36% (18/50) of cases diagnosed by urinary antigen compared to 10% (7/73) of cases diagnosed by respiratory culture (P < 0.01).

CONCLUSIONS

Positive pneumococcal urinary antigen tests lead to early deescalation of antibiotics more frequently than respiratory cultures.

Overdiagnosis paradigm: not suitable for decreasing the overuse of antibiotics

This paper summarises the discussion during the workshop on 'Overdiagnosis and overtreatment of infectious diseases in general practice. How and where to break the endless loop?' The workshop was organised as part of the overdiagnosis conference carried out in August 2018 in Copenhagen, Denmark. During the workshop, participants from all over the world reflected on the challenges of embracing the overdiagnosis paradigm as a tool to advance understanding and to find solutions to the unnecessary use of antibiotics in primary health care. It was concluded that the narrow view of the overdiagnosis paradigm does not provide theoretical resources to address the problem of the inherent connection between diagnostic error and treatment decision. In contrast to the overdiagnosis paradigm, the too much medicine paradigm is an umbrella term suitable to frame actions that recognise the complexity of the decision-making process during the consultation and its impact on overtreatment.

What the public think about participation in medical research during an influenza pandemic: an international cross-sectional survey

OBJECTIVES

The public and patients are primary contributors and beneficiaries of pandemic-relevant clinical research. However, their views on research participation during a pandemic have not been systematically studied. We aimed to understand public views regarding participation in clinical research during a hypothetical influenza pandemic.

STUDY DESIGN

This is an international cross-sectional survey.

METHODS

We surveyed the views of nationally representative samples of people in Belgium, Poland, Spain, Ireland, the United Kingdom, Canada, Australia and New Zealand, using a scenario-based instrument during the 2017 regional influenza season. Descriptive and regression analyses were conducted.

RESULTS

Of the 6804 respondents, 5572 (81.8%) thought pandemic-relevant research was important, and 5089 (74.8%) thought 'special rules' should be applied to make this research feasible. The respondents indicated willingness to take part in lower risk (4715, 69.3%) and higher risk (3585, 52.7%) primary care and lower risk (4780, 70.3%) and higher risk (4113, 60.4%) intensive care unit (ICU) study scenarios. For primary care studies, most (3972, 58.4%) participants preferred standard enrolment procedures such as prospective written informed consent, but 2327 (34.2%) thought simplified procedures would be acceptable. For ICU studies, 2800 (41.2%) preferred deferred consent, and 2623 (38.6%) preferred prospective third-party consent. Greater knowledge about pandemics, trust in a health professional, trust in the government, therapeutic misconception and having had ICU experience as a patient or carer predicted increased willingness to participate in pandemic-relevant research.

CONCLUSIONS

Our study indicates current public support for pandemic-relevant clinical research. Tailored information and initiatives to advance research literacy and maintain trust are required to support pandemic-relevant research participation and engagement.

Comparative Study of CDST & Multiplex PCR to Detect MBL Producing Gram-Negative Bacilli among VAP Patients Admitted in a Public Medical College Hospital of Bangladesh

Background: Ventilator-associated pneumonia (VAP) is the most common nosocomial infection in intensive care units (ICU), which accounts for 25% of all ICU infection. Documenting carbapenem-resistant gram-negative bacilli is very important as these strains may often cause outbreaks in the ICU setting and are responsible for the increased mortality and morbidity or limiting therapeutic options. The classical phenotypic method cannot provide an efficient means of diagnosis of the metallo-β-lactamases (MBLs) producer. Polymerase chain reaction (PCR) assays have lessened the importance of the phenotypic approach by detecting metallo-β-lactamase resistance genes such as New Delhi metallo-β-lactamase (NDM), Imipenemase (IMP), Verona integron-encoded metallo-β-lactamase (VIM), Sao Paulo metallo-β-lactamase (SPM), Germany Imipenemase (GIM). Objective: To compare the results of the Combined Disc Synergy Test (CDST) with that of the multiplex PCR to detect MBL-producing gram-negative bacilli. Materials and Method: A total of 105 endotracheal aspirates (ETA) samples were collected from the ICU of a public school in Bangladesh. This cross-sectional study was carried out in the Department of Microbiology, Chittagong for quantitative culture, CDST test, and multiplex PCR for bla_IMP, bla_VIM, bla_NDM genes of MBL producers. Results: Among the 105 clinically suspected VAP cases, the quantitative culture was positive in 95 (90%) and among 95 g-negative bacilli isolated from VAP patients, 46 (48.42%) were imipenem resistant, 30 (65.22%) were MBL producers by CDST, 21 (45.65%) were identified as MBL producers by multiplex PCR. Conclusion: PCR was highly sensitive and specific for the detection of MBL producers.

Whole Genome Sequencing for Surveillance of Diphtheria in Low Incidence Settings

Corynebacterium diphtheriae (C. diphtheriae) is a relatively rare pathogen in most Western countries. While toxin producing strains can cause pharyngeal diphtheria with potentially fatal outcomes, the more common presentation is wound infections. The diphtheria toxin is encoded on a prophage and can also be carried by Corynebacterium ulcerans and Corynebacterium pseudotuberculosis. Currently, across Europe, infections are mainly diagnosed in travelers and refugees from regions where diphtheria is more endemic, patients from urban areas with poor hygiene, and intravenous drug users. About half of the cases are non-toxin producing isolates. Rapid identification of the bacterial pathogen and toxin production is a critical element of patient and outbreak management. Beside the immediate clinical management of the patient, public health agencies should be informed of toxigenic C. diphtheriae diagnoses as soon as possible. The collection of case-related epidemiological data from the patient is often challenging due to language barriers and social circumstances. However, information on patient contacts, vaccine status and travel/refugee route, where appropriate, is critical, and should be documented. In addition, isolates should be characterized using high resolution typing, in order to identify transmissions and outbreaks. In recent years, whole genome sequencing (WGS) has become the gold standard of high-resolution typing methods, allowing detailed investigations of pathogen transmissions. De-centralized sequencing strategies with redundancy in sequencing capacities, followed by data exchange may be a valuable future option, especially since WGS becomes more available and portable. In this context, the sharing of sequence data, using public available platforms, is essential. A close interaction between microbiology laboratories, treating physicians, refugee centers, social workers, and public health officials is a key element in successful management of suspected outbreaks. Analyzing bacterial isolates at reference centers may further help to provide more specialized microbiological techniques and to standardize information, but this is also more time consuming during an outbreak. Centralized communication strategies between public health agencies and laboratories helps considerably in establishing and coordinating effective surveillance and infection control. We review the current literature on high-resolution typing of C. diphtheriae and share our own experience with the coordination of a Swiss-German outbreak.

Characterization and engineering of a DNA polymerase reveals a single amino-acid substitution in the fingers subdomain to increase strand-displacement activity of A-family prokaryotic DNA polymerases

Background

The discovery of thermostable DNA polymerases such as Taq DNA polymerase revolutionized amplification of DNA by polymerase chain reaction methods that rely on thermal cycling for strand separation. These methods are widely used in the laboratory for medical research, clinical diagnostics, criminal forensics and general molecular biology research. Today there is a growing demand for on-site molecular diagnostics; so-called ‘Point-of-Care tests’. Isothermal nucleic acid amplification techniques do not require a thermal cycler making these techniques more suitable for performing Point-of-Care tests at ambient temperatures compared to traditional polymerase chain reaction methods. Strand-displacement activity is essential for such isothermal nucleic acid amplification; however, the selection of DNA polymerases with inherent strand-displacement activity that are capable of performing DNA synthesis at ambient temperatures is currently limited.

Results

We have characterized the large fragment of a DNA polymerase I originating from the marine psychrophilic bacterium Psychrobacillus sp. The enzyme showed optimal polymerase activity at pH 8–9 and 25–110 mM NaCl/KCl. The polymerase was capable of performing polymerase as well as robust strand-displacement DNA synthesis at ambient temperatures (25–37 °C). Through molecular evolution and screening of thousand variants we have identified a single amino-acid exchange of Asp to Ala at position 422 which induced a 2.5-fold increase in strand-displacement activity of the enzyme.

Transferring the mutation of the conserved Asp residue to corresponding thermophilic homologues from Ureibacillus thermosphaericus and Geobacillus stearothermophilus also resulted in a significant increase in the strand-displacement activity of the enzymes.

Conclusions

Substituting Asp with Ala at positon 422 resulted in a significant increase in strand-displacement activity of three prokaryotic A-family DNA polymerases adapted to different environmental temperatures i.e. being psychrophilic and thermophilic of origin. This strongly indicates an important role for the 422 position and the O1-helix for strand-displacement activity of DNA polymerase I. The D422A variants generated here may be highly useful for isothermal nucleic acid amplification at a wide temperature scale.

Electronic supplementary material

The online version of this article (10.1186/s12860-019-0216-1) contains supplementary material, which is available to authorized users.

Establishing Clinical Utility for Diagnostic Tests Using a Randomized Controlled, Virtual Patient Trial Design

Demonstrating clinical utility for diagnostic tests and securing coverage and reimbursement requires high quality and, ideally, randomized controlled trial (RCT) data. Traditional RCTs are often too costly, slow, and cumbersome for diagnostic firms. Alternative data options are needed. We evaluated four RCTs using virtual patients to demonstrate clinical utility. Each study used a similar pre-post intervention, two round design to facilitate comparison. Representative samples of physicians were recruited and randomized into control and intervention arms. All physicians were asked to care for their virtual patients during two assessment rounds, separated by a multi-week time interval. Between rounds, intervention physicians reviewed educational materials on the diagnostic test. All physician responses were scored against evidence-based care criteria. RCTs using virtual patients can demonstrate clinical utility for a variety of diagnostic test types, including: (1) an advanced multi-biomarker blood test, (2) a chromosomal microarray, (3) a proteomic assay analysis, and (4) a multiplex immunofluorescence imaging platform. In two studies, utility was demonstrated for all targeted patient populations, while in the other two studies, utility was only demonstrated for a select sub-segment of the intended patient population. Of these four tests, two received positive coverage decisions from Palmetto, one utilized the study results to support commercial payer adjudications, and the fourth company went out of business. RCTs using virtual patients are a cost-effective approach to demonstrate the presence or absence of clinical utility.

PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research

Understanding the relationship between the pathophysiology of infectious disease, the biology of the causative agent and the development of therapeutic and diagnostic approaches is dependent on the synthesis of a wide range of types of information. Provision of a comprehensive and integrated disease phenotype knowledgebase has the potential to provide novel and orthogonal sources of information for the understanding of infectious agent pathogenesis, and support for research on disease mechanisms. We have developed PathoPhenoDB, a database containing pathogen-to-phenotype associations. PathoPhenoDB relies on manual curation of pathogen-disease relations, on ontology-based text mining as well as manual curation to associate host disease phenotypes with infectious agents. Using Semantic Web technologies, PathoPhenoDB also links to knowledge about drug resistance mechanisms and drugs used in the treatment of infectious diseases. PathoPhenoDB is accessible at http://patho.phenomebrowser.net/ , and the data are freely available through a public SPARQL endpoint.

What is the role of rapid molecular testing for seniors and other at-risk adults with respiratory syncytial virus infections?

Lower respiratory tract infections are a leading cause of hospitalization and viruses are important causal pathogens, especially in the elderly, immunocompromised patients and those with respiratory or cardiovascular comorbidities. Respiratory syncytial virus (RSV) is recognized as comprising a substantial burden of morbidity and mortality in older and at-risk adults, and the emergence of rapid point-of-care molecular testing has made it possible to confirm an RSV diagnosis accurately, in a clinically actionable timeframe. RSV patients have significantly higher healthcare resource use (including hospital stays and emergency room/urgent care visits) than non-RSV matched controls, especially if aged ≥65 years, a longer length of hospitalization than those with influenza, and associated costs nearly three times higher. We found no direct clinical outcome data specific to rapid molecular testing for RSV in adults and very little in children. There is very limited evidence that prompt diagnosis may reduce hospital length of stay but this and other outcome parameters need confirmation in larger, prospective clinical trials. Regarding reducing inappropriate antibiotic prescribing, the picture is mixed and testing alone is unlikely to change entrenched habits. There is little incentive for clinicians to order routine RSV tests in adults given the absence of a specific antiviral therapy. However, with numerous vaccine and antiviral candidates in clinical development, we believe it is good practice to plan and start establishing standardized testing protocols - perhaps as part of outcome studies. For especially vulnerable patients, e.g., immunocompromised and transplant patients, prompt accurate RSV diagnosis may prevent disease spread and save lives.

Framework for DNA Quantification and Outlier Detection Using Multidimensional Standard Curves

Real-time PCR is a highly sensitive and powerful technology for the quantification of DNA and has become the method of choice in microbiology, bioengineering, and molecular biology. Currently, the analysis of real-time PCR data is hampered by only considering a single feature of the amplification profile to generate a standard curve. The current “gold standard” is the cycle-threshold (C_t) method which is known to provide poor quantification under inconsistent reaction efficiencies. Multiple single-feature methods have been developed to overcome the limitations of the C_t method; however, there is an unexplored area of combining multiple features in order to benefit from their joint information. Here, we propose a novel framework that combines existing standard curve methods into a multidimensional standard curve. This is achieved by considering multiple features together such that each amplification curve is viewed as a point in a multidimensional space. Contrary to only considering a single-feature, in the multidimensional space, data points do not fall exactly on the standard curve, which enables a similarity measure between amplification curves based on distances between data points. We show that this framework expands the capabilities of standard curves in order to optimize quantification performance, provide a measure of how suitable an amplification curve is for a standard, and thus automatically detect outliers and increase the reliability of quantification. Our aim is to provide an affordable solution to enhance existing diagnostic settings through maximizing the amount of information extracted from conventional instruments.

A review of methods for the detection of pathogenic microorganisms

The testing and rapid detection of pathogenic organisms is a crucial protocol in the prevention and identification of crises related to health, safety and wellbeing. Pathogen detection has become one of the most challenging aspects in the food and water industries, because of the rapid spread of waterborne and foodborne diseases in the community and at significant costs. With the prospect of inevitable population growth, and an influx of tourism to certain water bodies testing will become a requirement to control and prevent possible outbreaks of potentially fatal illnesses. The legislation is already particularly rigorous in the food industry, where failure to detect pathogenic materials represents a catastrophic event, particularly for the elderly, very young or immune-compromised population types. In spite of the need and requirement for rapid analytical testing, conventional and standard bacterial detection assays may take up to seven days to yield a result. Given the advent of new technologies, biosensors, chemical knowledge and miniaturisation of instrumentation this timescale is not acceptable. This review presents an opportunity to fill a knowledge gap for an extremely important research area; discussing the main techniques, biology, chemistry, miniaturisation, sensing and the emerging state-of-the-art research and developments for detection of pathogens in food, water, blood and faecal samples.