Technology for automated, rapid, and quantitative PCR or reverse transcription-PCR clinical testing

QBox: An Automated Portable System for Multiplex Quantum Dot Barcode Diagnostics

The COVID-19 pandemic accelerated the development of automated systems for detecting molecular targets for the point-of-care. However, these systems have limited multiplexing capabilities because of the need to alter their hardware to accommodate additional targets and probes. Quantum dot barcodes address this multiplexing obstacle, but their assays have multiple steps that rely on extensive training and laboratory equipment. Here, we built a portable cartridge-and-instrument system that automates the extraction, reverse transcription, amplification, and detection steps of a quantum dot barcode assay. This entire workflow can be completed in 40 minutes. We clinically validated the system with SARS-CoV-2 patient samples (n = 50, 92% sensitivity, 100% specificity). We then demonstrated multiplexing with 4-barcode respiratory and 5-barcode bloodborne pathogen panels. Our portable system opens quantum dot barcodes for broad use in rapid multiplexed detection of infectious pathogens with the potential for detecting cancer and other genetic diseases.

Diagnostic performance of a point-of-care molecular system for the detection of SARS-CoV-2 in Peru

The present study assessed the diagnostic performance of the Xpert®Xpress SARS-CoV-2 test in comparison with the Charité protocol real-time RT PCR for the detection of SARS-CoV-2 in Peruvian patients. This was a diagnostic test study that included 100 nasal and pharyngeal swab samples. We obtained an overall concordance of 98.70% (95%CI: 92.98-99.97), with a kappa coefficient of 0.97 (95%CI: 0.86-1.00) and sensitivity and relative specificity rates of 100% and 96.15%, respectively. Additionally, the percentage of the area under the ROC curve was 98.08% in both cases, and an analytical specificity rate of 100% was obtained for the different respiratory viruses evaluated. In conclusion, the Xpert®Xpress SARS-CoV-2 test, by using nasal and pharyngeal swab samples, was highly sensitive and specific, and the kappa coefficient showed an excellent correlation when compared to the reference test. Motivation for the study. To describe and evaluate a closed molecular platform, easy to use and of importance in Peru for the management of diseases of public health priority, now implemented for the detection of SARS-CoV-2. Main findings. Highly sensitive and specific molecular test, with excellent correlation compared to the reference test for detecting SARS-CoV-2. Implications. Can be used in point-of-care laboratories for rapid molecular detection of different infectious agents, including SARS-CoV-2. Little expertise and minimal infrastructure are required to implement it.

Novel and reported compensatory mutations in rpoABC genes found in drug resistant tuberculosis outbreaks

Background

Rifampicin (RIF) is a key first-line drug used to treat tuberculosis, a primarily pulmonary disease caused by Mycobacterium tuberculosis. RIF resistance is caused by mutations in rpoB, at the cost of slower growth and reduced transcription efficiency. Antibiotic resistance to RIF is prevalent despite this fitness cost. Compensatory mutations in rpoABC genes have been shown to alleviate the fitness cost of rpoB:S450L, explaining how RIF resistant strains harbor this mutation can spread so rapidly. Unfortunately, the full set of RIF compensatory mutations is still unknown, particularly those compensating for rarer RIF resistance mutations.

Objectives

We performed an association study on a globally representative set of 4,309 whole genome sequenced clinical M. tuberculosis isolates to identify novel putative compensatory mutations, determine the prevalence of known and previously reported putative compensatory mutations, and determine which RIF resistance markers associate with these compensatory mutations.

Results and conclusions

Of the 1,079 RIF resistant isolates, 638 carried previously reported putative and high-probability compensatory mutations. Our strict criteria identified 46 additional mutations in rpoABC for which no strong prior evidence of their compensatory role exists. Of these, 35 have previously been reported. As such, our independent corroboration adds to the mounting evidence that these 35 also carry a compensatory role. The remaining 11 are novel putative compensatory markers, reported here for the first time. Six of these 11 novel putative compensatory mutations had two or more mutation events. Most compensatory mutations appear to be specifically compensating for the fitness loss due to rpoB:S450L. However, an outbreak of 22 closely related isolates each carried three rpoB mutations, the rare RIFR markers D435G and L452P and the putative compensatory mutation I1106T. This suggests compensation may require specific combinations of rpoABC mutations. Here, we report only mutations that met our very strict criteria. It is highly likely that many additional rpoABC mutations compensate for rare resistance-causing mutations and therefore did not carry the statistical power to be reported here. These findings aid in the identification of RIF resistant M. tuberculosis strains with restored fitness, which pose a greater risk of causing resistant outbreaks.

Mycobacterium Tuberculosis infection of the wrist joint: A current concepts review

Background

Osteoarticular Tuberculosis (TB) of wrist joint is a rare, often misdiagnosed form of site affected by Mycobacterium Tuberculosis infection that can lead to severe disability and morbidity. This review aims to summarize the current literature on the diagnosis and management of Mycobacterium Tuberculosis infection of the wrist joint.

Materials and methods

A comprehensive search strategy using the PEO (Population, Exposure, Outcome) framework was conducted on PubMed, Google Scholar, and Web of Science databases from 1967 to 2022, excluding single case reports and correspondence articles. The keywords used for the search included 'Mycobacterium tuberculosis' 'osteoarticular' and 'wrist'. Clinical presentation, demographic details, complementary investigations undertaken, trends, and complications of different management interventions were recorded to generate this review.

Results

Osteoarticular Tuberculosis (TB) of the wrist joint accounts for fewer than 1% of all skeletal TB cases across a spectrum of age ranges. Magnetic Resonance Imaging (MRI) represents an excellent modality to reveal the extent of the disease at an early stage of the condition. Synovial fluid analysis has been recommended for microbiological diagnosis. Treatment options include anti-tubercular therapy (ATT), incision and drainage, debridement, synovectomy, and arthrodesis.

Conclusion

Early diagnosis and treatment of wrist tuberculosis is crucial for achieving good functional outcomes in patients with this uncommon condition. Polymerase Chain Reaction (PCR) and GeneXpert technology for the detection of Mycobacterium tuberculosis (MTB) have improved diagnostic accuracy in detecting MTB DNA and rifampicin resistance. Anti-Tubercular Therapy (ATT) regime remains a foundation pillar in the overall management of these patients with focused surgical interventions leading to improved clinical outcomes.

Advances in point-of-care genetic testing for personalized medicine applications

Breakthroughs within the fields of genomics and bioinformatics have enabled the identification of numerous genetic biomarkers that reflect an individual's disease susceptibility, disease progression, and therapy responsiveness. The personalized medicine paradigm capitalizes on these breakthroughs by utilizing an individual's genetic profile to guide treatment selection, dosing, and preventative care. However, integration of personalized medicine into routine clinical practice has been limited-in part-by a dearth of widely deployable, timely, and cost-effective genetic analysis tools. Fortunately, the last several decades have been characterized by tremendous progress with respect to the development of molecular point-of-care tests (POCTs). Advances in microfluidic technologies, accompanied by improvements and innovations in amplification methods, have opened new doors to health monitoring at the point-of-care. While many of these technologies were developed with rapid infectious disease diagnostics in mind, they are well-suited for deployment as genetic testing platforms for personalized medicine applications. In the coming years, we expect that these innovations in molecular POCT technology will play a critical role in enabling widespread adoption of personalized medicine methods. In this work, we review the current and emerging generations of point-of-care molecular testing platforms and assess their applicability toward accelerating the personalized medicine paradigm.

SMART: A Swing-Assisted Multiplexed Analyzer for Point-of-Care Respiratory Tract Infection Testing

Respiratory tract infections such as the ongoing coronavirus disease 2019 (COVID-19) has seriously threatened public health in the last decades. The experience of fighting against the epidemic highlights the importance of user-friendly and accessible point-of-care systems for nucleic acid (NA) detection. To realize low-cost and multiplexed point-of-care NA detection, a swing-assisted multiplexed analyzer for point-of-care respiratory tract infection testing (SMART) was proposed to detect multiple respiratory tract pathogens using visible loop-mediated isothermal amplification. By performing hand-swing movements to generate acceleration force to distribute samples into reaction chambers, the design of the SMART system was greatly simplified. By using different format of chips and integrating into a suitcase, this system can be applied to on-site multitarget and multi-sample testing. Three targets including the N and Orf genes of SARS-CoV-2 and the internal control were simultaneously analyzed (limit of detection: 2000 copies/mL for raw sample; 200 copies/mL for extracted sample). Twenty-three clinical samples with eight types of respiratory bacteria and twelve COVID-19 clinical samples were successfully detected. These results indicate that the SMART system has the potential to be further developed as a versatile tool in the diagnosis of respiratory tract infection.

An automated, fully-integrated nucleic acid analyzer based on microfluidic liquid handling robot technique

On-site nucleic acid testing (NAT) plays an important role for disease monitoring and pathogen diagnosis. In this work, we developed an automated and fully-integrated nucleic acid analyzer by combining the automated liquid handling robot technique with the microfluidic droplet-based real-time PCR assay technique. The present analyzer could achieve multiple operations including sample introduction, nucleic acid extraction based on magnetic solid-phase extraction, reverse transcription and, sample droplet generation, PCR amplification, real-time and dual fluorescence detection of droplet array. A strategy of constructing an integrated compact and low-cost system was adopted to minimize the analyzer size to 50 × 45 × 45 cm (length × width × height), and reduce the instrument cost to ca. $900 with a single analysis cost less than $5. A simple chip was also designed to pre-load reagents and carry oil-covered PCR reaction droplets. We applied the analyzer to identify eight types of influenza pathogens in human throat swabs, and the results were consistent with the colloidal gold method.

Automated System for Multiplexing Detection of COVID-19 and Other Respiratory Pathogens

OBJECTIVE

Infectious diseases are global health challenge, impacted the communities worldwide particularly in the midst of COVID-19 pandemic. The need of rapid and accurate automated systems for detecting pathogens of concern has always been critical. Ideally, such systems shall detect a large panel of pathogens simultaneously regardless of well-equipped facilities and highly trained operators, thus realizing on-site diagnosis for frontline healthcare providers and in critical locations such as borders and airports.

METHODS & RESULTS

Avalon Automated Multiplex System, AAMST, is developed to automate a series of biochemistry protocols to detect nucleic acid sequences from multiple pathogens in one test. Automated processes include isolation of nucleic acids from unprocessed samples, reverse transcription and two rounds of amplifications. All procedures are carried out in a microfluidic cartridge performed by a desktop analyzer. The system was validated with reference controls and showed good agreement with their laboratory counterparts. In total 63 clinical samples, 13 positives including those from COVID-19 patients and 50 negative cases were detected, consistent with clinical diagnosis using conventional laboratory methods.

CONCLUSIONS

The proposed system has demonstrated promising utility. It would benefit the screening and diagnosis of COVID-19 and other infectious diseases in a simple, rapid and accurate fashion. Clinical and Translational Impact Statement- A rapid and multiplex diagnostic system proposed in this work can clinically help to control spread of COVID-19 and other infectious agents as it can provide timely diagnosis, isolation and treatment to patients. Using the system at remoted clinical sites can facilitate early clinical management and surveillance.

3D Specimen Mapping Expedites Frozen Section Diagnosis of Nonpalpable Ground Glass Opacities

BACKGROUND

Pulmonary ground glass opacities (GGOs) are early-stage adenocarcinoma spectrum lesions that are not easily palpable. Challenges in localizing GGOs during intraoperative pathology can lead to imprecise diagnoses and additional time under anesthesia. To improve localization of GGOs during frozen section diagnosis, we evaluated a novel technique, 3-dimensional near-infrared specimen mapping (3D-NSM).

METHODS

Fifty-five patients with a cT1 GGO were enrolled and received a fluorescent tracer preoperatively. After resection, specimens were inspected to identify lesions. Palpable and nonpalpable nodules underwent 3D-NSM and the area of highest fluorescence was marked with a suture. Time for 3D-NSM, time for frozen section diagnosis, and number of tissue sections examined were recorded. To compare 3D-NSM with standard-of-care techniques, a control cohort of 20 subjects with identical inclusion criteria were enrolled. Specimens did not undergo 3D-NSM and were sent directly to pathology.

RESULTS

3D-NSM localized 54 of 55 lesions with 1 false negative. All 41 palpable lesions were identified by 3D-NSM. Thirteen (92.8%) of 14 nonpalpable lesions were located by 3D-NSM. Time to diagnosis for the 3D-NSM cohort was 23.5 minutes, compared with 26.0 minutes in the control cohort (P = .04). 3D-NSM did not affect time to diagnosis of palpable lesions (23.2 minutes vs 21.4 minutes; P = .10). 3D-NSM significantly reduced time to diagnosis for nonpalpable lesions (23.3 minutes vs 34.4 minutes; P < .0001). 3D-NSM also reduced the number of tissue sections analyzed in nonpalpable lesions (4.50 vs 11.00; P < .0001).

CONCLUSIONS

3D-NSM accurately localizes GGOs and expedites intraoperative diagnosis by reducing the number of tissue sections analyzed for nonpalpable GGOs.

The Revolution of Lateral Flow Assay in the Field of AMR Detection

The global spread of antimicrobial resistant (AMR) bacteria represents a considerable public health concern, yet their detection and identification of their resistance mechanisms remain challenging. Optimal diagnostic tests should provide rapid results at low cost to enable implementation in any microbiology laboratory. Lateral flow assays (LFA) meet these requirements and have become essential tools to combat AMR. This review presents the versatility of LFA developed for the AMR detection field, with particular attention to those directly triggering β-lactamases, their performances, and specific limitations. It considers how LFA can be modified by detecting not only the enzyme, but also its β-lactamase activity for a broader clinical sensitivity. Moreover, although LFA allow a short time-to-result, they are generally only implemented after fastidious and time-consuming techniques. We present a sample processing device that shortens and simplifies the handling of clinical samples before the use of LFA. Finally, the capacity of LFA to detect amplified genetic determinants of AMR by isothermal PCR will be discussed. LFA are inexpensive, rapid, and efficient tools that are easy to implement in the routine workflow of laboratories as new first-line tests against AMR with bacterial colonies, and in the near future directly with biological media.

Passivated Impedimetric Sensors for Immobilization-Free Pathogen Detection by Isothermal Amplification and Melt Curve Analysis

The ongoing SARS-CoV-2 pandemic demonstrates that the capacity of centralized clinical diagnosis laboratories represents a significant limiting factor in the global fight against the newly emerged virus. Scaling up these capacities also requires simple and robust methods for virus diagnosis to be easily driven by untrained personnel in a point-of-care (POC) environment. The use of impedance sensors reduces the complexity and costs of diagnostic instruments and increases automation of diagnosis processes. We present an impedance point-of-care system (IMP-POCS) that uses interdigitated electrodes surrounded by an integrated heating meander to monitor loop-mediated isothermal amplification (LAMP) and melt curve analysis (MCA) consecutively in a short time. MCA permits distinguishing false- from true-positive results and significantly raises the validity of pathogen detection. Conclusively, the herein-developed miniaturized total analysis system (µTAS) represents a powerful and promising tool for providing reliable, low-cost alternatives to standard clinical diagnosis.

A fully integrated SNP genotyping system for hereditary hearing-loss detection

Hereditary hearing loss is one of the most common human neurosensory disorders, and there is a great need for early intervention methods such as genetically screening newborns. Single nucleotide polymorphisms (SNPs) are the major genetic targets for hearing-loss screening. In this study, a fully integrated SNP genotyping system was constructed to identify hereditary hearing loss-related genetic markers from human whole blood. The entire detection process, including blood cell lysis, nucleic acid extraction, the reaction mixture distribution, the chambers sealing and the two-colour multiplex competitive allele-specific polymerase chain reaction (KASP), can be automatically conducted in a self-contained cassette within 3 hours. To critically evaluate the performance of the system, its specificity, sensitivity and stability were assessed. Then, 13 clinical samples were genotyped with this fluidic cassette system to detect seven hotspot deafness-associated mutations in three genes (MT-RNR1, GJB2 and SLC26A4). The detection results of the cassette system were 100% concordant with those obtained by Sanger sequencing, proving its accuracy in the genetic screening of inherited hearing loss.

Recent advances and challenges of biosensing in point-of-care molecular diagnosis

Molecular diagnosis, which plays a major role in infectious disease screening with successful understanding of the human genome, has attracted more attention because of the outbreak of COVID-19 recently. Since point-of-care testing (POCT) can expand the application of molecular diagnosis with the benefit of rapid reply, low cost, and working in decentralized environments, many researchers and commercial institutions have dedicated tremendous effort and enthusiasm to POCT-based biosensing for molecular diagnosis. In this review, we firstly summarize the state-of-the-art techniques and the construction of biosensing systems for POC molecular diagnosis. Then, the application scenarios of POCT-based biosensing for molecular diagnosis were also reviewed. Finally, several challenges and perspectives of POC biosensing for molecular diagnosis are discussed. This review is expected to help researchers deepen comprehension and make progresses in POCT-based biosensing field for molecular diagnosis applications.

Multiplexed detection of respiratory pathogens with a portable analyzer in a "raw-sample-in and answer-out" manner

Coronavirus disease 2019 (COVID-19) has emerged, rapidly spread and caused significant morbidity and mortality worldwide. There is an urgent public health need for rapid, sensitive, specific, and on-site diagnostic tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. In this study, a fully integrated and portable analyzer was developed to detect SARS-CoV-2 from swab samples based on solid-phase nucleic acid extraction and reverse transcription loop-mediated isothermal amplification (RT-LAMP). The swab can be directly inserted into a cassette for multiplexed detection of respiratory pathogens without pre-preparation. The overall detection process, including swab rinsing, magnetic bead-based nucleic acid extraction, and 8-plex real-time RT-LAMP, can be automatically performed in the cassette within 80 min. The functionality of the cassette was validated by detecting the presence of a SARS-CoV-2 pseudovirus and three other respiratory pathogens, i.e., Klebsiella pneumoniae, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia. The limit of detection (LoD) for the SARS-CoV-2 pseudovirus was 2.5 copies/μL with both primer sets (N gene and ORF1ab gene), and the three bacterial species were successfully detected with an LoD of 2.5 colony-forming units (CFU)/μL in 800 μL of swab rinse. Thus, the analyzer developed in this study has the potential to rapidly detect SARS-CoV-2 and other respiratory pathogens on site in a “raw-sample-in and answer-out” manner.

rpoB gene mutations in rifampin-resistant Mycobacterium tuberculosis isolates from rural areas of Zhejiang, China

Objective

The aim was to analyze genetic mutations in the rpoB gene of rifampin-resistant Mycobacterium tuberculosis isolates (RIF^R-MTB) from Zhejiang, China.

Methods

We prospectively analyzed RIF^R-associated mutations in 13 rural areas of Zhejiang. Isolates were subjected to species identification, phenotype drug susceptibility testing (DST), DNA extraction, and rpoB gene sequencing.

Results

A total of 103 RIF^R isolates were identified by DST (22 RIF^R only, 14 poly-drug resistant, 49 multidrug resistant, 13 pre-extensively drug resistant [pre-XDR], and 5 extensively drug resistant [XDR]) from 2152 culture-positive sputum specimens. Gene sequencing of rpoB showed that the most frequent mutation was S450L (37.86%, 39/103); mutations P280L, E521K, and D595Y were outside the rifampicin resistance-determining region (RRDR) but may be associated with RIF^R. Mutations associated with poly-drug resistant, pre-XDR, and XDR TB were mainly located at codon 445 or 450 in the RRDR.

Conclusions

The frequency of rpoB RRDR mutation in Zhejiang is high. Further studies are needed to clarify the relationships between RIF^R and the TTC insertion at codon 433 in the RRDR and the P280L and D595Y mutations outside the RRDR.

Droplet-Based Single-Cell Measurements of 16S rRNA Enable Integrated Bacteria Identification and Pheno-Molecular Antimicrobial Susceptibility Testing from Clinical Samples in 30 min

Empiric broad-spectrum antimicrobial treatments of urinary tract infections (UTIs) have contributed to widespread antimicrobial resistance. Clinical adoption of evidence-based treatments necessitates rapid diagnostic methods for pathogen identification (ID) and antimicrobial susceptibility testing (AST) with minimal sample preparation. In response, a microfluidic droplet-based platform is developed for achieving both ID and AST from urine samples within 30 min. In this platform, fluorogenic hybridization probes are utilized to detect 16S rRNA from single bacterial cells encapsulated in picoliter droplets, enabling molecular identification of uropathogenic bacteria directly from urine in as little as 16 min. Moreover, in-droplet single-bacterial measurements of 16S rRNA provide a surrogate for AST, shortening the exposure time to 10 min for gentamicin and ciprofloxacin. A fully integrated device and screening workflow were developed to test urine specimens for one of seven unique diagnostic outcomes including the presence/absence of Gram-negative bacteria, molecular ID of the bacteriaas Escherichia coli, an Enterobacterales, or other organism, and assessment of bacterial susceptibility to ciprofloxacin. In a 50-specimen clinical comparison study, the platform demonstrates excellent performance compared to clinical standard methods (areas-under-curves, AUCs >0.95), within a small fraction of the turnaround time, highlighting its clinical utility.

GeneXpert assay - A cutting-edge tool for rapid tissue diagnosis of tuberculous lymphadenitis

BACKGROUND

The most prevalent clinical entity of extra pulmonary tuberculosis is tuberculous lymphadenitis. However, it resembles other granulomatous conditions pathologically and obtaining tissue for microbiological diagnosis is also difficult. Thus it is a challenging task for diagnosis and early initiation of management. Fine needle aspiration cytology and biopsy are the diagnostic methods generally used to obtain the lymph node samples for histopathological and microbiological diagnosis. Mycobacterium culture on Lowenstein-Jensen medium remains the gold standard for definitive diagnosis, but its major limitations is a prolonged turn-around time of 2-4 weeks. The GeneXpert Mtuberculosis/RIF assay is a novel molecular diagnostic method for rapid diagnosis of tuberculosis and rifampicin resistance in clinical specimens.

METHODS

This was a cross sectional analytical study conducted on 67 cases of suspected tubercular lymphadenitis at R.L Jalappa Hospital and Research Centre, Tamaka, Kolar. The study was carried out between December 2017 to June 2019. The samples were collected using excision biopsy and subjected to GeneXpert Mtuberculosis/RIF assay and histopathology. Further, sensitivity, specificity, positive predictive value and negative predictive value was measured and compared with histopathology.

RESULTS

The average age of the patients was 37.04 ± 19.27 and majority was males. The lymph nodes were predominantly present in cervical region. Histopathology analysis reveals 46 positive cases of tuberculosis Lymphadenitis and GeneXpert Mtuberculosis/RIF assay detects 42 cases of tuberculosis Lymphadenitis. In the present study, GeneXpert Mtuberculosis/RIF assay had a sensitivity of 82.60% and specificity of 85% when compared to histopathology. Further the PPV and NPV was found to be 92.68% and 68% respectively. GeneXpert Mtuberculosis/RIF showed 2 cases of rifampicin resistance out of 67 cases. In this study, the GeneXpert Mtuberculosis/RIF showed the results in 0.79 days.

CONCLUSION

The present study showed that GeneXpert Mtuberculosis/RIF is a simple and reliable technique for diagnosing tuberculosis Lymphadenitis with high specificity and sensitivity as compared histopathology. Further, the methods elicit rapid diagnosis and also detected rifampicin resistance. It is thus a reliable and useful diagnostic modality in rapid detection of the causative agent and initiation of appropriate category anti-tubercular therapy when necessary.

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.

Fully Automated Molecular Diagnostic System "Simprova" for Simultaneous Testing of Multiple Items

Nucleic acid amplification-based diagnostics is known as one of the molecular diagnostic systems that allows higher sensitive detection of pathogens than test methods such as immunoassay. However, it has not been widely used because it is complicated to use and takes a long time to generate results. On the other hand, development of fully automated molecular diagnostic systems has been growing around the world as demand for such systems from physicians and laboratory technicians has increased. To meet this demand, we have developed the "Simprova" fully automated molecular diagnostic system, which takes advantage of LAMP (Loop-mediated Isothermal Amplification), a method Eiken Chemical Co., Ltd. invented. Simprova comprises a master unit that controls the entire system and a test unit that extracts and purifies nucleic acid from samples (pretreatment), and uses the LAMP method to detect and amplify nucleic acid. Users can obtain test results automatically by simply installing a pretreatment cartridge, a multi-well testing chip and the sample in the test unit. The multi-well testing chip has 25 reaction wells connected by channels and enables simultaneous testing of multiple targets with one sample. Turnaround time for one test is approximately 30 minutes. Since a conventional extraction and purification method using magnetic-bead separation is used for the pretreatment, nucleic acid can be extracted from serum, plasma, whole blood, urine, and sputum, for example. In addition, the system can perform random-access testing by connecting four test units to the master unit to realize near-the-patient testing. Simprova is therefore a robust and useful system for a wide variety of applications.

Extract from used Xpert MTB/RIF Ultra cartridges is useful for accurate second-line drug-resistant tuberculosis diagnosis with minimal rpoB-amplicon cross-contamination risk

Xpert MTB/RIF Ultra (Ultra) detects Mycobacterium tuberculosis and rifampicin resistance. Follow-on drug susceptibility testing (DST) requires additional sputum. Extract from the diamond-shaped chamber of the cartridge (dCE) of Ultra's predecessor, Xpert MTB/RIF (Xpert), is useful for MTBDRsl-based DST but this is unexplored with Ultra. Furthermore, whether CE from non-diamond compartments is useful, the performance of FluoroType MTBDR (FT) on  CE, and rpoB cross-contamination risk associated with the extraction procedure are unknown. We tested MTBDRsl, MTBDRplus, and FT on CEs from chambers from cartridges (Ultra, Xpert) tested on bacilli dilution series. MTBDRsl on Ultra dCE on TB-positive sputa (n = 40) was also evaluated and, separately, rpoB amplicon cross-contamination risk . MTBDRsl on Ultra dCE from dilutions ≥103 CFU/ml (CTmin <25, >"low semi-quantitation") detected fluoroquinolone (FQ) and second-line injectable (SLID) susceptibility and resistance correctly (some SLIDs-indeterminate). At the same threshold (at which ~85% of Ultra-positives in our setting would be eligible), 35/35 (100%) FQ and 34/35 (97%) SLID results from Ultra dCE were concordant with sputa results. Tests on other chambers were unfeasible. No tubes open during 20 batched extractions had FT-detected rpoB cross-contamination. False-positive Ultra rpoB results was observed when dCE dilutions ≤10-3 were re-tested. MTBDRsl on Ultra dCE is concordant with isolate results. rpoB amplicon cross-contamination is unlikely. These data mitigate additional specimen collection for second-line DST and cross-contamination concerns.

A self-contained and fully integrated fluidic cassette system for multiplex nucleic acid detection of bacteriuria

The gold standard for diagnosing infectious diseases is culture-based identification of bacterial pathogens, which is time-consuming and labour-intensive. Current advances in molecular diagnostics and microfluidic technologies have made the rapid detection of bacteria or viruses in clinical specimens possible. However, the need for rapid, sensitive and multiplex detection of pathogens in a "sample-in and answer-out" manner has not been fully satisfied. In this study, a self-contained and fully integrated fluidic cassette and its supporting analyser were constructed for multiplex detection of bacteria to accelerate the diagnosis of urinary tract infections (UTIs). The fully integrated cassette contains all the necessary components and reagents for bacterial analysis. All of the bacterial analysis processes, including bacterial lysis, magnetic silica bead-based DNA extraction, DNA elution and multiplex loop-mediated amplification (LAMP), are automatically conducted in the cassette. This cassette was successfully applied for the detection of four major pathogenic bacteria in UTIs, i.e., Escherichia coli, Proteus mirabilis, Salmonella typhimurium and Staphylococcus aureus. The first three were successfully detected with a limit of detection (LoD) of 1 colony-forming unit (CFU) μL^-1 and the last was with a LoD of 10 CFU μL^-1 in urine samples, demonstrating that the cassette has similar sensitivity compared to that of the manual protocol, which is lower than that required by UTIs. The turnaround time for this cassette-based sample-to-answer system was approximately 100 minutes, and the detection is sensitive, fully automated, and accurate, demonstrating the potential to be a useful diagnostic tool for UTIs.

GeneXpert in stool: Diagnostic yield in Intestinal Tuberculosis

Background

Diagnosing intestinal (Luminal) tuberculosis is challenging due to limited yield of diagnostic modalities like CT scan, colonoscopy with blind ileal biopsies. GeneXpert MTB/RIF (Xpert) assays for diagnosing tuberculosis have been performed in the body secretions with excellent results. Its yield in stool is tested in this study.

Objective

The study aims to evaluate the yield of GeneXpert assay in stool of suspected cases of intestinal tuberculosis.

Methods

Hundred patients with suspected intestinal tuberculosis underwent routine biochemical tests, radiological investigations, colonoscopy with caecal and blind ileal biopsies for histopathology. Fresh stool samples were collected, processed for DNA extraction, tested using 2:1 ratio of GeneXpert reagent to sample to give positive or negative results for Mycobacterium tuberculosis and Rifampicin resistance.

Results

Out of hundred participants, 52% were female. Mean age was 28.21 ± 12.13. CT scan and colonoscopy findings suggestive of TB were present in 47% and 43% participants respectively. GeneXpert in stool was positive in 20% cases. Considering mucosal biopsy with histopathology of intestinal specimens as diagnostic of abdominal Tuberculosis, sensitivity and specificity of GeneXpert was 39.1% and 85.7% respectively.

Conclusion

Stool GeneXpert assay offers an alternative approach to detect intestinal tuberculosis rapidly with good diagnostic accuracy. Although it cannot replace the AFB culture and histopathology but contribute for early diagnosis and management.

Developments in Transduction, Connectivity and AI/Machine Learning for Point-of-Care Testing

We review some emerging trends in transduction, connectivity and data analytics for Point-of-Care Testing (POCT) of infectious and non-communicable diseases. The patient need for POCT is described along with developments in portable diagnostics, specifically in respect of Lab-on-chip and microfluidic systems. We describe some novel electrochemical and photonic systems and the use of mobile phones in terms of hardware components and device connectivity for POCT. Developments in data analytics that are applicable for POCT are described with an overview of data structures and recent AI/Machine learning trends. The most important methodologies of machine learning, including deep learning methods, are summarised. The potential value of trends within POCT systems for clinical diagnostics within Lower Middle Income Countries (LMICs) and the Least Developed Countries (LDCs) are highlighted.

Diagnostic tools for tackling febrile illness and enhancing patient management

Most patients with acute infectious diseases develop fever, which is frequently a reason to visit health facilities in resource-limited settings. The symptomatic overlap between febrile diseases impedes their diagnosis on clinical grounds. Therefore, the World Health Organization promotes an integrated management of febrile illness. Along this line, we present an overview of endemic and epidemic etiologies of fever and state-of-the-art diagnostic tools used in the field. It becomes evident that there is an urgent need for the development of novel technologies to fulfill end-users' requirements. This need can be met with point-of-care and near-patient diagnostic platforms, as well as e-Health clinical algorithms, which co-assess test results with key clinical elements and biosensors, assisting clinicians in patient triage and management, thus enhancing disease surveillance and outbreak alerts. This review gives an overview of diagnostic technologies featuring a platform based approach: (i) assay (nucleic acid amplification technologies are examined); (ii) cartridge (microfluidic technologies are presented); (iii) instrument (various detection technologies are discussed); and at the end proposes a way that such technologies can be interfaced with electronic clinical decision-making algorithms towards a broad and complete diagnostic ecosystem.

HIV-associated opportunistic CNS infections: pathophysiology, diagnosis and treatment

Nearly 30 years after the advent of antiretroviral therapy (ART), CNS opportunistic infections remain a major cause of morbidity and mortality in HIV-positive individuals. Unknown HIV-positive disease status, antiretroviral drug resistance, poor drug compliance, and recreational drug abuse are factors that continue to influence the morbidity and mortality of infections. The clinical and radiographic pattern of CNS opportunistic infections is unique in the setting of HIV infection: opportunistic infections in HIV-positive patients often have characteristic clinical and radiological presentations that can differ from the presentation of opportunistic infections in immunocompetent patients and are often sufficient to establish the diagnosis. ART in the setting of these opportunistic infections can lead to a paradoxical worsening caused by an immune reconstitution inflammatory syndrome (IRIS). In this Review, we discuss several of the most common CNS opportunistic infections: cerebral toxoplasmosis, progressive multifocal leukoencephalopathy (PML), tuberculous meningitis, cryptococcal meningitis and cytomegalovirus infection, with an emphasis on clinical pearls, pathological findings, MRI findings and treatment. Moreover, we discuss the risk factors, pathophysiology and management of IRIS. We also summarize the challenges that remain in management of CNS opportunistic infections, which includes the lack of phase II and III clinical trials, absence of antimicrobials for infections such as PML, and controversy regarding the use of corticosteroids for treatment of IRIS.

Towards lab-on-a-chip diagnostics for malaria elimination

Malaria continues to be one of the most devastating diseases impacting global health. Although there have been significant reductions in global malaria incidence and mortality rates over the past 17 years, the disease remains endemic throughout the world, especially in low- and middle-income countries. The World Health Organization has put forth ambitious milestones moving toward a world free of malaria as part of the United Nations Millennium Goals. Mass screening and treatment of symptomatic and asymptomatic malaria infections in endemic regions is integral to these goals and requires diagnostics that are both sensitive and affordable. Lab-on-a-chip technologies provide a path toward sensitive, portable, and affordable diagnostic platforms. Here, we review and compare currently-available and emerging lab-on-a-chip diagnostic approaches in three categories: (1) protein-based tests, (2) nucleic acid tests, and (3) cell-based detection. For each category, we highlight the opportunities and challenges in diagnostics development for malaria elimination, and comment on their applicability to different phases of elimination strategies.

Development of a panel of recombinase polymerase amplification assays for detection of common bacterial urinary tract infection pathogens

AIMS

To develop and evaluate the performance of a panel of isothermal real-time recombinase polymerase amplification (RPA) assays for detection of common bacterial urinary tract infection (UTI) pathogens.

METHODS AND RESULTS

The panel included RPAs for Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa and Enterococcus faecalis. All five RPAs required reaction times of under 12 min to reach their lower limit of detection of 100 genomes per reaction or less, and did not cross-react with high concentrations of nontarget bacterial genomic DNA. In a 50-sample retrospective clinical study, the five-RPA assay panel was found to have a specificity of 100% (95% CI, 78-100%) and a sensitivity of 89% (95% CI, 75-96%) for UTI detection.

CONCLUSIONS

The analytical and clinical validity of RPA for the rapid and sensitive detection of common UTI pathogens was established.

SIGNIFICANCE AND IMPACT OF THE STUDY

Rapid identification of the causative pathogens of UTIs can be valuable in preventing serious complications by helping avoid the empirical treatment necessitated by traditional urine culture's 48-72-h turnaround time. The routine and widespread use of RPA to supplement or replace culture-based methods could profoundly impact UTI management and the emergence of multidrug-resistant pathogens.

Lab-on-capillary: a rapid, simple and quantitative genetic analysis platform integrating nucleic acid extraction, amplification and detection

In this work, we describe for the first time a genetic diagnosis platform employing a polydiallyldimethylammonium chloride (PDDA)-modified capillary and a liquid-based thermalization system for rapid, simple and quantitative DNA analysis with minimal user interaction. Positively charged PDDA is modified on the inner surface of the silicon dioxide capillary by using an electrostatic self-assembly approach that allows the negatively charged DNA to be separated from the lysate in less than 20 seconds. The capillary loaded with the PCR mix is incorporated in the thermalization system, which can achieve on-site real-time PCR. This system is based on the circulation of pre-heated liquids in the chamber, allowing for high-speed thermalization of the capillary and fast amplification. Multiple targets can be simultaneously analysed with multiplex spatial melting. Starting with live Escherichia coli (E. coli) cells in milk, as a realistic sample, the current method can achieve DNA extraction, amplification, and detection within 40 min.

An in vitro diagnostic certified point of care single nucleotide test for IL28B polymorphisms

Numerous genetic polymorphisms have been identified as associated with disease or treatment outcome, but the routine implementation of genotyping into actionable medical care remains limited. Point-of-care (PoC) technologies enable rapid and real-time treatment decisions, with great potential for extending molecular diagnostic approaches to settings with limited medical infrastructure (e.g., CLIA certified diagnostic laboratories). With respect to resource-limited settings, there is a need for simple devices to implement biomarker guided treatment strategies. One relevant example is chronic hepatitis C infection, for which several treatment options are now approved. Single nucleotide polymorphisms (SNPs) in the IL-28B / IFNL3 locus have been well described to predict both spontaneous clearance and response to interferon based therapies. We utilized the Genedrive® platform to develop an assay for the SNP rs12979860 variants (CC, CT and TT). The assay utilizes a hybrid thermal engine, permitting rapid heating and cooling, enabling an amplification based assay with genetic variants reported using endpoint differential melting cure analysis in less than 60 minutes. We validated this assay using non-invasive buccal swab sampling in a prospective study of 246 chronic HCV patients, achieving 100% sensitivity and 100% specificity (95% exact CI: 98.8-100%)) in 50 minutes as compared to conventional lab based PCR testing. Our results provide proof of concept that precision medicine is feasible in resource-limited settings, offering the first CE-IVD (in vitro diagnostics) validated PoC SNP test. We propose that IL-28B genotyping may be useful for directing patients towards lower cost therapies, and rationing use of costly direct antivirals for use in those individuals showing genetic risk.

PCR Technologies for Point of Care Testing: Progress and Perspectives

Since the Human Genome Project completed in 2000, the sequencing of the first genome, massive progress has been made by medical science in the early diagnosis and personalized therapies based on nucleic acids (NA) analysis. To allow the extensive use of these molecular methods in medical practice, scientific research is nowadays strongly focusing on the development of new miniaturized and easy-to-use technologies and devices allowing fast and low cost NA analysis in decentralized environments. It is now the era of so-called genetic "Point-of-Care" (PoC). These systems must integrate and automate all steps necessary for molecular analysis such as sample preparation (extraction and purification of NA) and detection based on PCR (Polymerase Chain Reaction) technology in order to perform, by unskilled personnel, in vitro genetic analysis near the patient (in hospital, in the physician office, clinic, or home), with rapid answers and low cost. In this review, the recent advances in genetic PoC technologies are discussed, including the extraction and PCR amplification chemistry suitable for PoC use and the new frontiers of research in this field.

Performance Evaluation of the New HIV-1 Quantification Assay, Xpert HIV-1 Viral Load, on a Wide Panel of HIV-1 Variants

OBJECTIVE

To evaluate the quantification performance of the new Cepheid GeneXpert HIV-1 viral load assay, on a wide panel of HIV-1 variants.

METHODS

Clinical performance was evaluated relative to the Abbott RealTime HIV-1 assay on 285 HIV-1 seropositive samples selected to cover the assays quantification range (40 copies/mL-10,000,000 copies/mL), and included RNA undetectable or detected seropositive samples. The panel comprised 120 subtype B, 150 non-B, and 15 nontypable clinical samples; serial dilutions of 18 viral supernatants representative of the divergent viruses of HIV-1 groups N, O, and P were also tested.

RESULTS

Based on samples selected according to the Abbott assay viral loads (VL), the Cepheid assay detected or quantified 222/285 (78%) samples and the Abbott assay 240/285 (84%). Xpert yielded VLs for 162 (76%) of the 213 quantifiable samples with Abbott. This difference corresponded to 51 samples with VL >40 copies/mL by the Abbott assay (all below 200 copies/mL) but detected (n = 40) or undetectable (n = 11) by the Cepheid assay. VL of samples quantifiable by both assays (n = 162) showed very strong correlation, with a Spearman correlation coefficient of 0.985 and a Bland-Altman's mean of differences of -0.01. Performance for quantification of the non-M samples showed very good correlation, with significantly higher values with Cepheid for the group N and 2 group O samples.

CONCLUSIONS

Our study showed that the Xpert HIV-1 VL assay offered very good performance for detection and quantification of the current HIV-1 genetic diversity; differences reported at the threshold could be an issue and requires further evaluations. The practicability of this new assay makes it suitable for low-income countries, where it could facilitate and improve follow-up of patients, as well as for high-income regions.

Evaluation of rapid GeneXpert MTB/RIF method using DNA tissue specimens of vertebral bones in patients with suspected spondylitis TB

PURPOSE

To detect Mycobacterium tuberculosis DNA and rifampicin resistance in vertebral bone tissue specimens from spondylitis TB suspects.

METHODS AND RESULTS

The rapid GeneXpert MTB/RIF and MGIT 960 liquid culture methods have been used in the specimens. Results from 70 suspects with spondylitis TB shown that 31.42% identified positive for spondylitis TB using culture method, while 88.57% shown positive results using rapid GeneXpert MTB/RIF method. The validity of GeneXpert MTB/RIF shown sensitivity value of 100%, specificity value of 16.6%, PPV of 35.48%, and NPV of 100%.

CONCLUSION

GeneXpert has a high sensitivity but low specificity value in this study.

Evaluation of the GeneXpert MTB/RIF assay on extrapulmonary and respiratory samples other than sputum: a low burden country experience

The aim of this study was to assess the performance of the GeneXpert MTB/RIF assay on extrapulmonary (EP) and respiratory (non-sputum) clinical samples of patients suspected of having tuberculosis (TB) from Queensland, Australia. A total of 269 EP and respiratory (non-sputum) clinical samples collected from Qld patients who were suspected of having TB were subjected to the GeneXpert MTB/RIF analysis, Ziehl-Neelsen (ZN) staining, Mycobacterium tuberculosis (MTB) culture and drug susceptibility testing. Phenotypic and genotypic data were compared. The overall performance analysis of the GeneXpert MTB/RIF assay for detection of MTB complex demonstrated sensitivity of 89%, specificity of 95%, PPV of 89% and NPV of 95% using culture as a reference standard. The GeneXpert MTB/RIF analysis of acid-fast bacilli (AFB) smear positive samples and AFB smear negative samples showed sensitivities of 100% and 77%, respectively. Looking at individual EP and respiratory (non-sputum) sample types, the sensitivity ranged from 60% to 100% although the specificity ranged from 33% to 100% with the specificity of lymph node tissue biopsy being the lowest. The GeneXpert MTB/RIF assay detected 11% more TB cases than culture and 27% more cases than ZN microscopy. Due to insufficient numbers of presenting rifampicin resistance cases, performance analysis of the GeneXpert MTB/RIF assay on rifampicin resistance could not be carried out. The GeneXpert MTB/RIF assay is potentially valuable for TB diagnosis in the majority of the EP and respiratory (other than sputum) samples in our setting. Although the GeneXpert MTB/RIF assay provides rapid diagnostic results, the overall sensitivity to rule out the disease is suboptimal for some specimen types. Performance varied according to specimen type and AFB smear status. The sensitivity and specificity of lymph node tissue was 63% and 33%. Care must be taken when using the GeneXpert MTB/RIF assay for detection of MTB in lymph node tissue samples. All samples should be cultured regardless of the GeneXpert MTB/RIF assay result.

MALDI-TOF MS based carbapenemase detection from culture isolates and from positive blood culture vials

Background

Antibiotic resistance in bacteria leads to massive health problems. Incidence of carbapenem and multidrug resistance in Gram-negative bacteria are increasing globally and turn out to be a very urgent challenge in health care. Resistant bacteria play an important clinical role during hospital outbreaks as well as in sepsis. Rapid diagnostic tests are necessary to provide immediate information for antimicrobial treatment and infection control measures.

Methods

Our mass spectrometry-based assay was validated with 63 carbapenemase-producing Gram-negative bacterial isolates, and 35 carbapenem-resistant Gram-negative species with no carbapenemase production. These were analyzed from solid culture media and positive blood culture vials. After 4 h of incubation the carbapenemase products were analyzed with the MALDI-TOF MS. All the isolates were genotyped for carbapenemase genes by PCR and sequencing.

Results

For culture isolates the concordance of hydrolysis assay to genetic results was 98 % for OXA variants, KPC, VIM, IMP, GIM, and NDM. In contrast, only 14 of 29 Acinetobacter baumannii isolates carrying the OXA and NDM genes could be identified from blood culture. However, from blood culture vials our method allowed the detection of carbapenemases in 98 % of Pseudomonas and Enterobacteriaceae isolates harboring different genes.

Conclusions

This MALDI-TOF MS–based assay permitted the detection of carbapenemases either from solid culture media (98–100 %) or blood culture vials (96 %) for all non-A. baumannii isolates within 4 h. In case of A. baumannii isolates the assay was highly sensitive for the detection of carbapenemases directly from solid culture media.

Analytical Performance Characteristics of the Cepheid GeneXpert Ebola Assay for the Detection of Ebola Virus

BACKGROUND

The recently developed Xpert® Ebola Assay is a novel nucleic acid amplification test for simplified detection of Ebola virus (EBOV) in whole blood and buccal swab samples. The assay targets sequences in two EBOV genes, lowering the risk for new variants to escape detection in the test. The objective of this report is to present analytical characteristics of the Xpert® Ebola Assay on whole blood samples.

METHODS AND FINDINGS

This study evaluated the assay's analytical sensitivity, analytical specificity, inclusivity and exclusivity performance in whole blood specimens. EBOV RNA, inactivated EBOV, and infectious EBOV were used as targets. The dynamic range of the assay, the inactivation of virus, and specimen stability were also evaluated. The lower limit of detection (LoD) for the assay using inactivated virus was estimated to be 73 copies/mL (95% CI: 51-97 copies/mL). The LoD for infectious virus was estimated to be 1 plaque-forming unit/mL, and for RNA to be 232 copies/mL (95% CI 163-302 copies/mL). The assay correctly identified five different Ebola viruses, Yambuku-Mayinga, Makona-C07, Yambuku-Ecran, Gabon-Ilembe, and Kikwit-956210, and correctly excluded all non-EBOV isolates tested. The conditions used by Xpert® Ebola for inactivation of infectious virus reduced EBOV titer by ≥6 logs.

CONCLUSION

In summary, we found the Xpert® Ebola Assay to have high analytical sensitivity and specificity for the detection of EBOV in whole blood. It offers ease of use, fast turnaround time, and remote monitoring. The test has an efficient viral inactivation protocol, fulfills inclusivity and exclusivity criteria, and has specimen stability characteristics consistent with the need for decentralized testing. The simplicity of the assay should enable testing in a wide variety of laboratory settings, including remote laboratories that are not capable of performing highly complex nucleic acid amplification tests, and during outbreaks where time to detection is critical.

Diagnosis of Mycobacterium tuberculosis using molecular biology technology

OBJECTIVE

To present an integrated molecular biology dedicated system for tuberculosis diagnosis.

METHODS

One hundred and five sputum specimens from patients strongly suspected by clinical parameters of tuberculosis were studied by Ziehl-Neelsen staining, by cultivation on solid medium and by a balanced heminested fluorometric PCR system (Orange G3TB) that could preserve worker safety and produce a rather pure material free of potential inhibitors. DNA amplification was performed in a low cost tuberculosis termocycler-fluorometer. Produced double stranded DNA was flurometrically detected. The whole reaction was conducted in one single tube which would not be opened after adding the processed sample in order to minimize the risk of cross contamination with amplicons.

RESULTS

The assay was able to detect 30 bacillus per sample mL with 99.8% interassay variation coefficient. PCR was positive in 23 (21.9%) tested samples (21 of them were smear negative). In our study it showed a preliminary sensitivity of 94.5% for sputum and an overall specificity of 98.7%.

CONCLUSIONS

Total run time of the test is 4 h with 2.5 real working time. All PCR positive samples are also positive by microbiological culture and clinical criteria. Results show that it could be a very useful tool to increase detection efficiency of tuberculosis disease in low bacilus load samples. Furthermore, its low cost and friendly using make it feasible to run in poor regions.

DNA/RNA preparation for molecular detection

BACKGROUND

Effective upstream preparation of nucleic acid (NA) is important for molecular techniques that detect unique DNA or RNA sequences. The isolated NA should be extracted efficiently and purified away from inhibitors of a downstream molecular assay.

CONTENT

Many NA sample preparation techniques and commercial kits are available. Techniques for cell lysis and isolation or purification of NA were discovered in early NA characterization studies, evolved in the 20th century with molecular techniques, and still serve as the foundation for current methods. Advances in solid phase extraction methods with nonhazardous chemicals and automated systems have changed the way NA is prepared. Factors to consider when selecting NA preparation methods for molecular detection include lysis (from sources as diverse as human cells, viruses, bacterial spores, or protozoan oocysts), DNA vs RNA, sample background, appropriate preparation chemicals, and required detection limits. Methods are also selected on the basis of requirements for a particular application, such as sample volume or removal of inhibitors. Sometimes tradeoffs are made.

SUMMARY

Good automated and manual methods are available to effectively prepare NA for molecular detection in under an hour. Numerous systems are available for various applications, including techniques that are flexible for multiple sample types, are capable of processing large batches, can be performed in <10 min, or that can yield high-purity NA. When methods are selected using the most applicable combination of lysis isolation efficiency and concentration, NA preparation can be very effective, even for molecular detection of multiple targets from the same sample.

Classical and new assays for detecting drug resistance in tuberculosis

Tuberculosis is a public health concern worldwide. Particularly worrying is the emergence of severe forms of drug resistance, such as extensively drug resistant and totally drug resistant tuberculosis, with few treatment options for the afflicted patients. To avoid further spread of drug resistance, its early detection is extremely important. Conventional phenotypic procedures to detect drug resistance depended on the in vitro slow growth of the bacteria. More recent molecular approaches such as reverse-hybridization assays and real-time PCR tests have been introduced. Newer options proposed include, faster culture-based methods and whole-genome sequencing and nanotechnology. Not yet available is a real point-of-care test, applied directly in clinical samples and reliable enough for guiding a treatment option.

Development and validation of rapid magnetic particle based extraction protocols

Background

In order to control and eradicate transboundary animal diseases, early diagnosis and reaction is essential for the implementation of control activities. Thus, mobile diagnostic units which allow analytical testing close to the site of occurrence could provide valuable support for centralized laboratories. Consequently, the availability of diagnostic tests using mobile amplification and detection technologies has been increasing over the past years. However, methods enabling rapid and simple nucleic acid extraction also under resource-limited settings are still scarce.

Methods

In the present study rapid extraction protocols based on magnetic particle technology have been developed. For this purpose, the two open extraction platforms KingFisher™ Duo (Thermo Fisher Scientific) and BioSprint® 15 (Qiagen) as well as the fully automated EZ1® advanced XL instrument (Qiagen) were used. All protocols were validated in comparison to standard manual extraction using blood and serum samples from animals infected with Schmallenberg virus or bovine viral diarrhea virus.

Results

All newly developed protocols allowed a complete extraction within 30 minutes of time. The fully automated EZ1-extraction yielded the highest reproducibility, whereas slightly higher intra- and inter-assay variations were observed using the open platforms. Compared to the manual procedure, the analytical sensitivity of all the rapid protocols was 1 log₁₀ step reduced for extraction from blood samples. For sera a reduced dynamic range could only be observed using the maximally shortened BioSprint 15 protocol. Validation using clinical samples showed an excellent concordance of all the rapid extraction protocols to the standard manual extraction procedure, independent of sample materials and target viruses.

Conclusions

The results of this study show that the speed-optimized novel extraction protocols allow rapid and simple nucleic acid extractions for a variety of target viruses without significant loss of sensitivity compared to standard procedures. For this reason they represent valuable tools to accelerate magnetic particle based automated extraction.

Point-of-care system for detection of Mycobacterium tuberculosis and rifampin resistance in sputum samples

Early detection of Mycobacterium tuberculosis complex (MTBC) and markers conveying drug resistance can have a beneficial impact on preventive public health actions. We describe here a new molecular point-of-care (POC) system, the Genedrive, which is based on simple sample preparation combined with PCR to detect MTBC and simultaneously detect mutation markers in the rpoB gene directly from raw sputum sample. Hybridization probes were used to detect the presence of the key mutations in codons 516, 526, and 531 of the rpoB gene. The sensitivities for MTBC and rpoB detection from sputum samples were assessed using model samples spiked with known numbers of bacteria prepared from liquid cultures of M. tuberculosis. The overall sensitivities were 90.8% (95% confidence interval [CI], 81, 96.5) for MTBC detection and 72.3% (95% CI, 59.8, 82.7) for rpoB detection. For samples containing ≥1,000 CFU/ml, the sensitivities were 100% for MTBC and 85.7% for rpoB detection, while for samples containing ≤100 CFU/ml, the sensitivities were 86.4% and 65.9% for MTBC and rpoB detection, respectively. The specificity was shown to be 100% (95% CI, 83.2, 100) for MTBC and rpoB. The clinical sputum samples were processed using the same protocol and showed good concordance with the data generated from the model. Tuberculosis-infected subjects with smear samples assessed as scanty or negative were detectable by the Genedrive system. In these paucibacillary patients, the performance of the Genedrive system was comparable to that of the GeneXpert assay. The characteristics of the Genedrive platform make it particularly useful for detecting MTBC and rifampin resistance in low-resource settings and for reducing the burden of tuberculosis disease.