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Objective: 1) to compare the QIAreachTM QuantiFERON-TB (QIAreach QFT) vs. QuantiFERON®-TB Gold Plus assay (QFT-Plus) to detect tuberculosis (TB) infection; 2) to evaluate diagnostic sensitivity of QIAreach QFT using active TB as surrogate for TB infection; 3) to preliminarily evaluate QIAreach QFT in immunocompromised individuals. Methods: QIAreach QFT measures the level of interferon-γ (IFN-γ) in plasma specimens from blood stimulated by ESAT-6 and CFP-10 peptides in one blood collection tube (equivalent to the TB2 tube of the QFT-Plus). QIAreach QFT was applied to plasma samples from 41 patients with pulmonary TB and from 42 healthy or low-TB-risk individuals. Results: Sensitivity and specificity of QIAreach QFT vs. QFT-Plus were 100% (41/41) and 97.6% (41/42), respectively; overall concordance was 98.8% (82/83). All samples were measured within 20 min. The time to result of each sample was significantly correlated with IFN-γ level with a natural logarithmic scale (r = -0.913, p

Point-of-care tests for rapid diagnosis and treatment of sexually transmitted infections are useful and highly desirable. Supplemental digital content is available in the text., Background Point-of-care (POC) tests enable immediate diagnosis and targeted treatment of sexually transmitted infections (STIs), which could accelerate control of ongoing epidemics. Although older nucleic acid amplification tests have improved the accuracy of laboratory-based tests for STIs, newer POC tests can facilitate control efforts. We sought to review the performance and time to result of POC assays for STIs in the last 10 years. Methods The authors performed a PubMed, US National Library of Medicine, National Center for Biotechnology Information search for POC tests for STIs or sexually transmitted diseases. Results Diagnostic technology for POC assays for STIs has achieved high sensitivity and specificity (>90%) using recent molecular advances in the last 10 years. Three POC tests for chlamydia and gonorrhea and 2 for trichomonas have been cleared by the Food and Drug Administration and can provide rapid results during the clinical encounter. Two POC assays for syphilis are now cleared by the Food and Drug Administration. Other similar POC assays are in development. These “fast followers” have faster time to result and will extend the diagnostic armamentarium at POC. Conclusions New technology has improved the performance accuracy of STI POC diagnostics. Innovation in device format has resulted in accurate POC assays, which can decrease the time to result and accelerate the detection and treatment of STIs during the clinical encounter. The full implementation potential of these newer tests will depend on the ability of these tests to achieve Clinical Laboratory Improvement Amendments–waived status so they can be performed by nonlaboratorians with no previous training.

In the emergency department, troponin assays are commonly used and essential in the evaluation of chest pain and diagnosis of acute coronary syndrome. This study was designed to assess the potential impact of implementing point-of-care troponin testing by comparing the time to point-of-care laboratory result and time to conventional laboratory result.The study enrolled 60 ED patients deemed to need a troponin test in the evaluation of low-risk chest pain (HEART score4 based on history, electrocardiogram, age, risk factors). Point-of-care troponin testing was performed with the same blood sample obtained for a conventional troponin assay. If the provider determined that the patient required 2 troponin tests, the second laboratory draw was used in the data collection. This was to correlate the time of laboratory result to time of disposition.Of the 60 subjects enrolled, 2 subjects were excluded because of user errors with the point-of-care testing equipment and 2 others for not meeting inclusion criteria on later review. The median times for the point-of-care troponin and conventional troponin assays were 11:00 minutes (interquartile range 10:00-15:30) and 40:00 minutes (interquartile range 31:30-52:30), respectively; P0.001. There were 3 extreme outliers from the conventional troponin assay that significantly skewed the distribution of the mean, making the median the more accurate assessment of the central tendency.Point-of-care troponin testing provided results in a median time 29 minutes quicker than the conventional troponin assay. This result is statistically significant and has the potential to greatly improve time to disposition in all patients with chest pain requiring a troponin assay.

BACKGROUND This review provides a description of how the opioid epidemic has impacted drug testing. METHODS Four major service areas of drug testing were considered, including emergency response, routine clinical care, routine forensics, and death investigations. RESULTS Several factors that the opioid epidemic has impacted in drug testing are discussed, including specimens, breadth of compounds recommended for testing, time to result required for specific applications, analytical approaches, interpretive support requirements, and examples of published practice guidelines. CONCLUSIONS Both clinical and forensic laboratories have adapted practices and developed new testing approaches to respond to the opioid epidemic. Such changes are likely to continue evolving in parallel with changes in both prescription and nonprescription opioid availability and use patterns, as well as emerging populations that are affected by the "waves" of the opioid epidemic.

Increasing contamination of environmental waters with pharmaceuticals represents an emerging threat for the drinking water quality and safety. In this regard, fast and reliable analytical methods are required to allow quick countermeasures in case of contamination. Here, we report the development of a magnetic bead-based immunoassay (MBBA) for the fast and cost-effective determination of the analgesic diclofenac (DCF) in water samples, based on diclofenac-coupled magnetic beads and a robust monoclonal anti-DCF antibody. A novel synthetic strategy for preparation of the beads resulted in an assay that enabled for the determination of diclofenac with a significantly lower limit of detection (400 ng/L) than the respective enzyme-linked immunosorbent assay (ELISA). With shorter incubation times and only one manual washing step required, the assay demands for remarkably shorter time to result (

Molecular markers are becoming increasingly important for cancer diagnosis, proper clinical trial enrollment, and even surgical decision making, motivating ultra-rapid, intraoperative variant detection. Sequencing-based detection is considered the gold standard approach, but typically takes hours to perform. In this work, we present Threshold Sequencing, a methodology for designing protocols for targeted variant detection on real-time sequencers with a minimal time to result. Threshold Sequencing analytically identifies a time-optimal threshold to stop target amplification and begin sequencing. To further reduce diagnostic time, we explore targeted Loop-mediated Isothermal Amplification (LAMP) and design a LAMP-specific bioinformatics tool—LAMPrey—to process sequenced LAMP product. LAMPrey’s concatemer aware alignment algorithm is designed to maximize recovery of diagnostically relevant information leading to a more rapid detection versus standard read alignment approaches. Coupled with time-optimized DNA extraction and library preparation, we demonstrate confirmation of a hot-spot mutation (250x support) from tumor tissue in less than 30 minutes.

OBJECTIVES: Many hospitals have transitioned from conventional stool diagnostics to rapid multiplex polymerase chain reaction gastrointestinal panels (GIP). The clinical impact of this testing has not been evaluated in children. In this study, we compare use, results, and patient outcomes between conventional diagnostics and GIP testing. METHODS: This is a multicenter cross-sectional study of children who underwent stool testing from 2013 to 2017. We used bivariate analyses to compare test use, results, and patient outcomes, including length of stay (LOS), ancillary testing, and hospital charges, between the GIP era (24 months after GIP introduction) and conventional diagnostic era (historic control, 24 months before). RESULTS: There were 12 222 tests performed in 8720 encounters. In the GIP era, there was a 21% increase in the proportion of children who underwent stool testing, with a statistically higher percentage of positive results (40% vs 11%), decreased time to result (4 vs 31 hours), and decreased time to treatment (11 vs 35 hours). Although there was a decrease in LOS by 2 days among those who received treatment of a bacterial and/or parasitic pathogen (5.1 vs 3.1; P < .001), this represented only 3% of tested children. In the overall population, there was no statistical difference in LOS, ancillary testing, or charges. CONCLUSIONS: The GIP led to increased pathogen detection and faster results. This translated into improved outcomes for only a small subset of patients, suggesting that unrestricted GIP use leads to low-value care. Similar to other novel rapid diagnostic panels, there is a critical need for diagnostic stewardship to optimize GIP testing.

Synthesis of silver nanoparticles (AgNPs) and analytical development of silver nanoparticles has been done. AgNPs were making by chemical reduction method using trisodium citrate as a reducing agent. AgNPS was Prepared with a variant of silver nitrate concentration, trisodium citrate concentration, and stirring time to result in the best silver nanoparticles. AgNPs were characterized using UV-Vis Spectrophotometer, Particle Size Analyzer (PSA), Transmission Electron Microscopy (TEM). AgNPs was applied as the colorimetric sensor of histamine. The histamine presence can induce the aggregation of silver nanoparticles by a color change from yellow to brown.

The SARS-CoV-2 detection campaign is a key element in the viral pandemic response. Here we present a monocentric study to evaluate a simplified molecular amplification technology alternative to classical RT-qPCR platforms. The test, C4Covid-19 HumanTM makes use of saliva as a starting sample allowing for self, painless collection, avoiding risk of viral transmission for the operator who performs the nasopharyngeal (NP) procedure. Total time to result is 30 minutes. The principle relies on an extraction-free detection of two targets within the viral genomic RNA, RdRp and N genes, by real-time reverse transcription loop mediated isothermal amplification (RT-LAMP). Saliva and NP swabs were collected simultaneously from 1491 symptomatic or contact cases and analyzed in parallel by RT-LAMP and RT-qPCR respectively. The 249 positives RT-qPCR samples had a Ct

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is widely used in clinical microbiology laboratories because it is cost-effective, reliable, and fast. This study is aimed at comparing the identification performance of the recently developed Autof ms1000 (Autobio, China) with that of the Bruker Biotyper (Bruker Daltonics, Germany). From January to June 2020, 205 preserved strains and 302 clinical isolates were used for comparison. Bacteria were tested with duplicates of the direct transfer method, and formic acid extraction was performed if the results were not at the species level. Fungi were tested with formic acid extraction followed by ethanol extraction methods. 16S rRNA or ITS region sequence analysis was performed on isolates that could not be identified by any of the instruments and on isolates that showed inconsistent results. The time to result of each instrument was also compared. Among preserved strains, species-level identification results were obtained in 202 (98.5%) strains by the Autof ms1000 and 200 (97.6%) strains by the Bruker Biotyper. Correct identification at the species/complex level was obtained for 200 (97.6%) strains by the Autof ms1000 and for 199 (97.1%) strains by the Bruker Biotyper. Among clinical isolates, species-level identification results were obtained in 301 (99.7%) strains and 300 (99.3%) strains by the Autof ms1000 and Bruker Biotyper, respectively. Correct identification at the species/complex level was achieved for 299 (99.0%) strains by the Autof ms1000 and for 300 (99.3%) strains by the Bruker Biotyper. The time to analyze 96 spots was approximately 14 min for the Autof ms1000 and approximately 27 min for the Bruker Biotyper. The two instruments showed comparable performance for the routine identification of clinical microorganisms. In addition, the Autof ms1000 has a short test time, making it convenient for use in clinical microbiology laboratories.

Quantitative PCR (qPCR) assays are the gold standard for diagnosis of Pneumocystis jirovecii pneumonia (PCP). However, they are laborious and require skilled personnel. Therefore, execution outside regular working hours of the molecular biology laboratory is limited. The eazyplex P. jirovecii assay (PJA) uses loop-mediated isothermal amplification for detection of P. jirovecii. It is performed directly with respiratory specimens, without the need for special skills, and delivers a result within 3 to 25 min. The goal of our study was to compare the performance of the eazyplex PJA with that of established P. jirovecii qPCR assays. All archived bronchoalveolar lavage fluid (BALF) samples that had previously tested positive for P. jirovecii by qPCR assay and 50 control samples (retrospective part), as well as all BALF samples received for P. jirovecii analysis over a period of 4 months (prospective part), were tested. Forty-nine patients with proven PCP and 126 patients without PCP were included. The sensitivity and specificity of the eazyplex PJA (95.7% and 96.5%, respectively) were comparable to those for three different P. jirovecii qPCR assays. The detection limit of the eazyplex PJA was analogous to 103 copies of the major surface glycoprotein gene per 25 μl of BALF, corresponding to 10 to 20 P. jirovecii cells. The eazyplex PJA reliably discriminated patients with PCP from patients with P. jirovecii colonization. It delivered a positive result within a mean of 9 min 38 s and required a hands-on time of 2 min 45 s. In summary, the eazyplex PJA showed identical performance for the diagnosis of PCP, compared to qPCR assays. However, in terms of time to result, practicability, and robustness, the eazyplex PJA is clearly superior and allows for around-the-clock molecular testing.

Blood stream infections pose a major challenge for clinicians as the immediate application of an appropriate antibiotic treatment is the vital factor to safe the patients' lives. This preliminary study compares three different systems promising fast pathogen identification and susceptibility testing in comparison to conventional blood culture (BC): (i) the rapid antimicrobial susceptibility testing protocol according to EUCAST in combination with the Sepsityper® kit (sRAST), (ii) the direct inoculation method on the VITEK®2 system (dVIT) and (iii) testing with the Accelerate Pheno® system (AccPh). All methods were assessed in terms of accuracy, time to result and usability. Twenty‐three BC samples obtained from patients suffering from proven sepsis were analysed in detail. Pathogen identification was successful in 95·6, 91·3 and 91·3% in sRAST, dVIT and AccPh, respectively. Categorical agreement in antimicrobial susceptibility testing was 89·5, 96 and 96·6%, respectively. Time to result from sample entry to reporting ranged from an average of 4·6 h for sRAST and 6·9 h for AccPh to 10·6 h for dVIT. These results imply a significant shortening of reporting times at considerably high agreement rates for these new diagnostic approaches., Significance and Impact of the Study: Timely reporting of pathogen identification and antimicrobial susceptibility is crucial for patients suffering from sepsis. New approaches promising short turnaround times compared to conventional workup of blood cultures are seeking their way to routine laboratory implementation. This pilot study evaluates novel techniques for pathogen identification and antimicrobial susceptibility testing directly from positive blood cultures. The data indicate a considerable expediting in microbiological sepsis diagnosis without compromising result quality.

Nucleic acid amplification tests (NAATs) are common in laboratory and clinical settings because of their low time to result and exquisite sensitivity and specificity. Laboratory NAATs include onboard positive controls to reduce false negatives and specialized hardware to enable real-time fluorescence detection. Recent efforts to translate NAATs into at-home tests sacrifice one or more of the benefits of laboratory NAATs, such as sensitivity, internal amplification controls (IACs), or time to result. In this manuscript, we describe a mobile-phone-based strategy for real-time imaging of biplexed NAATs in paper. The strategy consisted of: (1) using mobile phones with multipass excitation and emission filters on the flash and camera to image the signal from distinct fluorophore-labeled probe types in a biplexed NAAT in a glass fiber membrane; and (2) analyzing the differential fluorescence signal between the red and green color channels of phone images to overcome a strong evaporation-induced optical artifact in heated glass fiber pads due to changes in the refractive index. We demonstrated that differential fluorescence imaging enabled low limits of detection (316 copies of methicillin-resistant

We assessed the impact of a rapid molecular assay for influenza detection whether outsourced or performed onsite 24/7 in a University Hospital in Paris, France. Shorter median time-to-results (16.8 vs 2.3 hours, P

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread across the globe. As part of the worldwide response, many molecular diagnostic platforms have been granted emergency use authorization (EUA) by the Food and Drug Administration (FDA) to identify SARS-CoV-2 positive patients. Our objective was to evaluate three sample-to-answer molecular diagnostic platforms (Cepheid Xpert Xpress SARS-CoV-2 [Xpert Xpress], Abbott ID NOW COVID-19 [ID NOW], and GenMark ePlex SARS-CoV-2 Test [ePlex]) to determine analytical sensitivity, clinical performance, and workflow for the detection of SARS-CoV-2 in nasopharyngeal swabs from 108 symptomatic patients., Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread across the globe. As part of the worldwide response, many molecular diagnostic platforms have been granted emergency use authorization (EUA) by the Food and Drug Administration (FDA) to identify SARS-CoV-2 positive patients. Our objective was to evaluate three sample-to-answer molecular diagnostic platforms (Cepheid Xpert Xpress SARS-CoV-2 [Xpert Xpress], Abbott ID NOW COVID-19 [ID NOW], and GenMark ePlex SARS-CoV-2 Test [ePlex]) to determine analytical sensitivity, clinical performance, and workflow for the detection of SARS-CoV-2 in nasopharyngeal swabs from 108 symptomatic patients. We found that Xpert Xpress had the lowest limit of detection (100% detection at 100 copies/ml), followed by ePlex (100% detection at 1,000 copies/ml), and ID NOW (20,000 copies/ml). Xpert Xpress also had highest positive percent agreement (PPA) compared to our reference standard (98.3%) followed by ePlex (91.4%) and ID NOW (87.7%). All three assays showed 100% negative percent agreement (NPA). In the workflow analysis, ID NOW produced the lowest time to result per specimen (∼17 min) compared to Xpert Xpress (∼46 min) and ePlex (∼1.5 h), but what ID NOW gained in rapid results, it lost in analytical and clinical performance. ePlex had the longest time to results and showed a slight improvement in PPA over ID NOW. Information about the clinical and analytical performance of these assays, as well as workflow, will be critical in making informed and timely decisions on testing platforms.

Summary Background The spread of carbapenemase-producing Enterobacterales (CPE) is a global health problem. Gastrointestinal tract carriage makes faeces or rectal swabs the recommended screening methods. Aim To assess the impact of three laboratory screening strategies for CPE on positivity rates and infection prevention and control in a hospital setting in North West England from 2015 to 2017. Methods In a retrospective study, time to CPE-positive and -negative results, number of new CPE-positive patients identified, and number of hospital bed-days lost/wards affected were measured for each of three CPE screening strategies; culture plus phenotypic tests, culture plus polymerase chain reaction (PCR), and PCR only (phases 1, 2 and 3, respectively). Findings The fastest time to CPE results was PCR only (median: 4.0 h), then culture plus PCR (median: 47.6 h), then culture plus phenotypic tests (median: 49.8 h) (P < 0.001). The mean numbers of hospital bed-days lost per month decreased between phases 2 and 3 (P = 0.01). The mean number of wards/units affected by CPE increased from phase 1 (2.57) to phase 2 (7.71), then decreased in phase 3 (3.86). The percentage positivity rate for phases 1, 2, and 3 were 2.01, 1.38, and 1.55 respectively. From May to October, the number of new CPE-positive patients was lower for phases 1 and 3 than for phase 2. During all three phases there was a peak in the number of newly identified CPE carriers in August. Conclusion This study provides evidence that using a rapid PCR to screen rectal or faeces swabs enables more timely infection prevention and control measures when compared with culture-based methods. A reduction in bed-days lost due to CPE was observed when rapid molecular screening was introduced.

The Revogene® Carba C assay is a real-time polymerase chain reaction–based assay that runs on the microfluidic Revogene platform. It was recently designed for the detection of genes encoding the 5 major carbapenemases (NDM, VIM, IMP, KPC, and OXA-48) from various Gram-negatives. A total of 145 clinical Gram-negative strains (96 carbapenemase producers and 49 non–carbapenemase producers) were tested. The overall sensitivity and specificity were 100%. All strains co-producing double carbapenemases have been correctly detected. All non–carbapenemase producers and nontargeted carbapenemase producers gave a negative result. The sample preparation was easy to handle, taking around 5 to 10 min per isolate, with a run time of approximately 70 min. This assay is a rapid, easy-to-perform, reliable tool to detect the most common carbapenemases, with excellent sensitivity and specificity regardless of the host bacteria. Given its user friendliness, simplicity, and short time to result, the Revogene® Carba C assay is suitable for microbiology laboratories.

A novel real-time multiplex PCR assay, BD MAX Check-Points CPO, was evaluated to detect carbapenemase-producing organisms in clinical settings on the BD MAX system. A total of 175 well-characterized isolates (including 123 carbapenemase producers) and 128 rectal swab specimens (including 83 positives) of patients considered at high risk for carriage of carbapenemase producers were included. Bacterial suspensions were used to spike true-negative rectal swabs to mimic a clinical sample. Sample (50 μL), containing either the spiked or the patient's sample, was processed. The BD MAX Check-Points CPO assay detected carbapenemases KPC, VIM/IMP, NDM, and OXA-48–like producers with a high sensitivity and specificity of 97.1% and 98.8%, respectively. Rare variants of the IMP type (IMP-11, IMP-13, and IMP-14) and one rare and distantly related OXA-48 variant (OXA-535) remained undetected. With patients' rectal swabs, sensitivity and specificity were 92.8% and 97.8%, respectively. Failure of detection was due to weak inoculum. The time to result was short: approximately. 2.5 hours for 12 samples (including extraction and PCR). The automated sample-in results-out platform is an efficient, quick, and easy-to-use tool for the detection of the main five carbapenemases. The lack of distinction between producers of VIM and IMP may be limiting in countries where these enzymes are widespread, as in Asia, but not in France, where IMP producers are extremely rare.

BACKGROUND Meningitis and Encephalitis are potentially fatal infections. When suspected, empirical treatment is started, and only safely discontinued once excluded. The impact of current CSF investigations is prolonged inpatient stay, and exposure to broad-spectrum antimicrobials. Biofire Filmarray is a point-of-care PCR system. Our aim was to assess time to BioFire result, and its impact on clinical management. METHOD BioFire was implemented, in addition to current practice, on CSF samples with WCC ≥10 and all neonatal samples processed between November 2018 and February 2019. Data was collected prospectively for: patient demographics, sampling time, time to result of BioFire and current PCR, antimicrobial regime, and early discharge. Percentage agreement between BioFire and current PCR, mean time to result, percentage cases with reduction in antimicrobials, and mean length of stay for those discharged based on BioFire, were calculated. RESULTS There were 22 samples analysed. There was an 86.4% agreement between BioFire and current PCR. In cases of disagreement, BioFire identified pathogens where standard PCR had not. One sample was insufficient for virology PCR however, a full array was obtained from BioFire. Mean time to BioFire result authorization was 17.8 hours, compared to 316 for virology PCR and 331.2 for bacteriology PCR. BioFire allowed narrowing of antimicrobial therapy in 22.7% of patients, discontinuation in 41.0%, and early discharge in 27.3%. CONCLUSION BioFire provides comparable diagnosis of meningo-encephalitis faster than current practice. With the current focus on rising bed pressures and antimicrobial stewardship, BioFire allows targeted therapy and safe early discharge where infection is excluded.

Due to the congestion of emergency wards, a rapid and accurate method for flu diagnosis is required. However, the first evaluations of the ID NOW® influenza AB performances were heterogeneous. We aimed to (i) assess the performance of the second generation of the ID NOW® influenza AB 2 and (ii) compare the ID NOW® to the GeneXpert® use when performed within a central laboratory. (i) Analytical performances of ID NOW® were assessed using a collection of 112 clinical samples in comparison with a reference multiplex PCR (Seegene®); (ii) Invalid rate per operator and time to result were calculated for the GeneXpert® Xpress Flu/RSV and the ID NOW® influenza AB 2® during 2017-2018 and 2018-2019 flu outbreaks respectively. ID NOW® reaches an overall sensitivity and specificity of 96.6% and 96.1% respectively. Most of the false-negative display a CT 37. For both instruments, a single operator was involved in about a half of all invalid results. Excluding this operator involved in most invalid result, the invalid rate was about 1% for both instruments. Time to result from sampling was significantly shorter in the ID NOW® versus the GeneXpert® group (33 vs 97 min, P 0.01). The second generation of the ID NOW® influenza AB 2 displays high performances, comparable with conventional PCR method. In order to prevent invalid results, we highlight the need for adequate training of operators. Also, when implemented in a central laboratory, the location of the instrument could have a strong impact on the time-to-results.

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

The rapid detection of blood stream infections (BSI) by carbapenemase-producing Enterobacterales (CPE) is indispensable to early optimize antibiotic treatment and to improve survival. While phenotypic tests are time-consuming and PCR is expensive and not available in many routine laboratories, colorimetric tests (e.g., Carba NP test) can provide rapid results at moderate cost. However, up to now, the detection of CPE-BSI requires a further 3-h incubation in broth supplemented with zinc sulfate and imipenem after a blood culture has become positive, thereby causing delay and additional hands-on time. The purpose of this study was to develop and evaluate a new method for the detection of CPE directly from positive blood culture without the need for incubation in broth, based on the commercially available colorimetric β-CARBA test. For the evaluation, blood cultures spiked with 140 different Enterobacterales isolates producing diverse beta-lactamases were tested with the new method. Of these, 70 were CPE (OXA-48-like, NDM, KPC, VIM, and GIM). After blood cultures turned positive, blood culture fluid was drawn, and erythrocytes were hemolyzed with SDS, washed, and equilibrated before the β-CARBA was performed on the bacterial pellet. All carbapenemases were reliably detected, including weak carbapenemases of the OXA-48 group. The sensitivity was 100% (95% CI 94.9-100) and the specificity 94.3% (95% CI 89.2-99.4). The time to result was 20 to 45 min. Carbapenemases can rapidly and reliably be detected directly from blood cultures using the new method, which could help to improve the outcome of these difficult-to-treat infections.

Background Administration of appropriate antimicrobial therapy is one of the key factors in surviving bloodstream infections. Blood culture is currently the reference standard for diagnosis, but conventional practices have long turnaround times while diagnosis needs to be faster to improve patient care. Phenotypic methods offer an advantage over genotypic methods in that they can identify a wide range of taxa, detect the resistance currently expressed, and resist genetic variability in resistance detection. Aims We aimed to discuss the wide array of phenotypic methods that have recently been developed to substantially reduce the time to result from identification to antibiotic susceptibility testing. Sources A literature review focusing on rapid phenotypic methods for improving the diagnosis of bloodstream infection was the source. Content Rapid phenotypic bacterial identification corresponds to Matrix-assisted laser-desorption/ionization time of flight mass spectrometry (MALDI-TOF), and rapid antimicrobial susceptibility testing methods comprised of numerous different approaches, are considered and critically assessed. Particular attention is also paid to emerging technologies knocking at the door of routine microbiology laboratories. Finally, workflow integration of these methods is considered. Implications The broad panel of phenotypic methods currently available enables healthcare institutions to draw up their own individual approach to improve bloodstream infection diagnosis but requires a thorough evaluation of their workflow integration. Clinical microbiology will probably move towards faster methods while maintaining a complex multi-method approach as there is no all-in-one method.

Urine cultures are among the most common specimens received by clinical laboratories and generate a major share of the laboratory workload. Chromogenic agar can expedite culture results, but technologist review is still needed. In this study, we evaluated the ability of the WASPLab software to interpret urine specimens plated onto chromID CPS Elite (CPSE) agar. Urine specimens submitted for bacterial culture were plated onto CPSE agar with a 1-μl loop using the WASP., Urine cultures are among the most common specimens received by clinical laboratories and generate a major share of the laboratory workload. Chromogenic agar can expedite culture results, but technologist review is still needed. In this study, we evaluated the ability of the WASPLab software to interpret urine specimens plated onto chromID CPS Elite (CPSE) agar. Urine specimens submitted for bacterial culture were plated onto CPSE agar with a 1-μl loop using the WASP. Each plate was imaged after 0 and 18 h of incubation, and colonies were enumerated by color using the WASPLab software and a technologist’s reading from a high-definition (HD) monitor. The results were reported as negative if 50 CFU (n = 11). The use of both CPSE agar and the WASPLab software improved the time to result for urine culture, reducing the average time to result by 4 h 42 min for negative specimens and 3 h 28 min for positive specimens compared to that with standard-of-care testing. These data demonstrate that the use of CPSE agar and automated plate reading has the potential to improve turnaround time while maintaining high sensitivity and reducing urine culture workload.

Recently advances in miniaturization and automation have been utilized to rapidly decrease the time to result for microbiology testing in the clinic. These advances have been made due to the limitations of conventional culture-based microbiology methods, including agar plate and microbroth dilution, which have long turnaround times and require physicians to treat patients empirically with antibiotics before test results are available. Currently, there exist similar limitations in pharmaceutical sterility and bioburden testing, where the long turnaround times associated with standard microbiology testing drive costly inefficiencies in workflows. These include the time lag associated with sterility screening within drug production lines and the warehousing cost and time delays within supply chains during product testing. Herein, we demonstrate a proof-of-concept combination of a rapid microfluidic assay and an efficient cell filtration process that enables a path toward integrating rapid tests directly into pharmaceutical microbiological screening workflows. We demonstrate separation and detection of Escherichia coli directly captured and analyzed from a mammalian (i.e., CHO) cell culture with a 3.0 h incubation. The demonstration is performed using a membrane filtration module that is compatible with sampling from bioreactors, enabling in-line sampling and process monitoring.

As the complexity and interconnect density of advanced semiconductor packages increase, failure analysis and root cause determination are also facing new challenges and higher requirements. The 3-D X-ray microscopy, enabling nondestructive defect imaging and enhanced navigation for failure analysis, is considered a key method to fulfill these requirements. This technique results in a short time to result and high success failure analysis yield. After a short introduction into the basic principles of laboratory-based X-ray tomography, two different approaches of X-ray investigations are discussed. The author demonstrates the capabilities of the individual techniques and gives an outlook into future failure analysis opportunities. This includes the recently developed application using 3-D X-ray imaging for back-end-of-line and chip-package-interaction features.

Cartridge-based multiplex panels covering numerous pathogens offer an advantage of minimal hands-on-time and short time to result to commercial RT-PCR assays. In this study, we evaluated the performance of the ePlex respiratory pathogen panel (RPP) compared to the Fast Track Diagnostics Respiratory pathogens 21 multiplex RT-PCR assay (FTD21) using 400 clinical respiratory samples. Discrepant results were further analysed by a reference nucleic acid amplification testing (NAT) and a composite reference approach was used for final interpretation. Discordant results were observed in 56 targets corresponding to 54 samples. Sensitivities and specificities were 85.5% and 99.9% for the ePlex RPP and 95.8% and 99.7% for the FTD21 system, respectively. Altogether, the ePlex RPP is a valuable tool for the rapid detection of a number of different respiratory viruses with the exception of the coronavirus family (low sensitivity ranging from 50-80%) and samples with a low pathogen load (Ct values >33).

The article contains the results of the research, which set two main goals. The first is the determination of the actual indicators of the effectiveness of noninvasive prenatal studies and the development of counseling tools about the predictability of a positive outcome, taking into account certain clinical indicators and the a priori age risk of the mother. The second is the assessment of changes in the clinical and demographic population after the introduction of testing. Objective : The primary goal of this study was to provide clinically relevant information for appropriate patient counseling. Method : Demographics and test metrics were reviewed for 86 658 clinical cases. Outcome information was requested for samples reported as aneuploidy detected or suspected for chromosomes 21, 18, or 13; voluntary outcome reporting was encouraged for all discordant outcomes. Results : Of 86 658 cases, 85 298 (98.4%) met inclusion criteria for result reporting. Of the 1360 (1.6%) cancellations, only 101 (0.1%) were for technical reasons. Average time to result was 3.3 business days. Aneuploidy was detected or suspected in 2142 (2.5%) samples. For aneuploidy detected cases with known clinical outcomes, the overall positive predictive value was 83.5% (608/728); observed positive predictive values for trisomies 21, 18, and 13 ranged from 50.0 to 92.8%. As individual positive predictive values are determined by a patient’s prior risk, we developed a chart for counseling patients on positive predictive value based on maternal age. Conclusion : This large-scale report reinforces that noninvasive prenatal testing is a highly accurate screen for fetal aneuploidy in the general obstetric population. Test improvements have facilitated a reduction in failure rates, time to result, and borderline results/unclassifiable results. We have developed a positive predictive value counseling tool to ensure appropriate patient education, counseling, and clinical utilization. Funding sources : This study was funded by Illumina. Conflicts of interest : Authors of article are employees of and hold equity in Illumina.

Early identification of infections caused by carbapenemase-producing Enterobacterales (CPE) can help to optimize patient treatment and improve outcome. In this study, protocols for rapid detection of carbapenemase production directly from positive blood cultures were developed applying a concentration and hemolysis step before a test for carbapenemase production was performed. Four different methods (three modified colorimetric assays [β-Carba, bcCarba NP, and NeoRapid Carb] and a variation of the carbapenem inactivation method [CIM] test with blood cultures [bcCIM]) were assessed on blood cultures spiked with 185 different molecularly characterized Enterobacterales isolates. The challenge collection included 81 carbapenemase-negative isolates and 104 CPEs (OXA-48 [n = 25], NDM [n = 20], KPC [n = 18], VIM [n = 25], GIM [n = 5], OXA-48-like [n = 9], and OXA-48-like plus NDM [n = 2]). The sensitivity/specificity was 99.0%/95.1% for bcCarba NP, 99.0%/91.4% for NeoRapid Carb, 100%/95.1% for β-Carba and 100%/100% for bcCIM. Weakly hydrolyzing carbapenemases (e.g., OXA-48-like) were also well detected by the assays. The time to result was 20 to 45 min for β-Carba, 2 to 3 h for bcCarba NP, 2.5 to 2 h for NeoRapid Carb, and 18 to 24 h for bcCIM. In conclusion, all assays demonstrated good detection of CPE. The protocols can be easily implemented in any clinical microbiology laboratory and could help to optimize therapy early in bloodstream infections by CPE.

With expanding global population, there is now an urgent need to produce more food, more efficiently with the available existing finite resources. Concerning dairy production, bovine diseases negatively impact animal welfare, while decreasing farm efficiency and profitability through wasted feed, reduced milk production and increased veterinary costs. New digital technologies that provide veterinarians with immediate test results on-farm will enable early clinical interventions, thereby ensuring food security and reduce loses. To address this challenge, we present an impedimetric biosensor platform that enables rapid identification of bovine immunoglobulin G and bovine Liver Fluke antibodies in complex blood plasma with time to result of 15 mins.

Few studies assess the utility of rapid multiplex molecular respiratory panels in adult patients. Previous multiplex PCR assays took hours to days from order time to result. We analyze the clinical impact of switching to a molecular assay with a 3-h test-turnaround-time (TAT)., Few studies assess the utility of rapid multiplex molecular respiratory panels in adult patients. Previous multiplex PCR assays took hours to days from order time to result. We analyze the clinical impact of switching to a molecular assay with a 3-h test-turnaround-time (TAT). We performed a retrospective review of adult patients who presented to our emergency departments with respiratory symptoms and had a respiratory viral panel (xTAG RVP; RVP) or respiratory pathogen panel (ePlex RP; RPP) within 48 h of presentation. The average TATs for the RVP and RPP were 27.9 and 3.0 h, respectively (P < 0.0001). In RVP-positive and RPP-positive patients, 68.9 and 44.5% of those with normal chest imaging received antibiotics (P = 0.013), while 95.4 and 89.6% of those with abnormal imaging received antibiotics, respectively (P = 0.187). There was no difference in antibiotic duration in RVP-positive and RPP-positive patients with abnormal chest imaging (6.2 and 6.0 days, respectively; P = 0.923) and normal chest imaging (4.5 and 4.3 days, respectively; P = 0.922). Fewer patients were admitted in the RPP-positive compared to the RVP-positive group (76.9 and 88.6%, respectively; P = 0.013), while the proportion of admissions were similar among RPP-negative and RVP-negative patients (85.3 and 87.1%, P = 0.726). Switching to a multiplex respiratory panel with a clinically actionable TAT is associated with reduced hospital admissions and, in admitted adults without focal radiographic findings, reduced antibiotic initiation. Opportunities to further mitigate inappropriate antibiotic use may be realized by combining rapid multiplex PCR with provider education, clinical decision-care algorithms, and active antibiotic stewardship.

Diarrheal illness is a major cause of morbidity and mortality throughout the world, yet the etiologic agent of many cases of gastrointestinal illness remains unspecified, often due to the lack of convenient, timely, and sensitive diagnostic testing. Although bulk fecal specimens remain the recommended specimen type for enteric culture, rectal swabs may be an option preferred by clinicians and patients due to the convenience and timing of collection. However, the lack of data evaluating the sensitivity of rectal swabs compared to fecal specimens for detection of enteric pathogens precludes this specimen type from being recommended by national guidelines. In this study, we retrospectively reviewed 480 paired rectal swab and fecal specimens submitted for enteric culture to the Barnes-Jewish Hospital and St. Louis Children’s Hospital microbiology laboratories in St. Louis, MO, from 2002 to 2017. We report 32% positivity of paired specimens with an overall agreement of 93% and Cohen's κ of 0.84 (95% confidence interval, 0.78 to 0.89). Additionally, we evaluated the time to result from the time of patient presentation to the health care setting and demonstrate that rectal swabs have a significantly shorter time to an actionable result than bulk fecal specimens (median, 67.4 h versus 78.4 h, respectively; P

The diagnosis of tuberculous meningitis (TBM) is difficult and poses a significant challenge to physicians worldwide. Recently, nucleic acid amplification (NAA) tests have shown promise for the diagnosis of TBM, although their performance has been variable. We undertook a systematic review and meta-analysis to evaluate the diagnostic accuracy of NAA tests with cerebrospinal fluid (CSF) samples against that of culture as the reference standard or a combined reference standard (CRS) for TBM. We searched the Embase, PubMed, Web of Science, and Cochrane Library databases for the relevant records. The QUADAS-2 tool was used to assess the quality of the studies. Diagnostic accuracy measures (i.e., sensitivity and specificity) were pooled with a random-effects model. All statistical analyses were performed with STATA (version 14 IC; Stata Corporation, College Station, TX, USA), Meta-DiSc (version 1.4 for Windows; Cochrane Colloquium, Barcelona, Spain), and RevMan (version 5.3; The Nordic Cochrane Centre, the Cochrane Collaboration, Copenhagen, Denmark) software. Sixty-three studies comprising 1,381 cases of confirmed TBM and 5,712 non-TBM controls were included in the final analysis. These 63 studies were divided into two groups comprising 71 data sets (43 in-house tests and 28 commercial tests) that used culture as the reference standard and 24 data sets (21 in-house tests and 3 commercial tests) that used a CRS. Studies which used a culture reference standard had better pooled summary estimates than studies which used CRS. The overall pooled estimates of sensitivity, specificity, positive likelihood ratio (PLR), and negative likelihood ratio (NLR) of the NAA tests against culture were 82% (95% confidence interval [CI], 75 to 87%), 99% (95% CI, 98 to 99%), 58.6 (95% CI, 35.3 to 97.3), and 0.19 (95% CI, 0.14 to 0.25), respectively. The pooled sensitivity, specificity, PLR, and NLR of NAA tests against CRS were 68% (95% CI, 41 to 87%), 98% (95% CI, 95 to 99%), 36.5 (95% CI, 15.6 to 85.3), and 0.32 (95% CI, 0.15 to 0.70), respectively. The analysis has demonstrated that the diagnostic accuracy of NAA tests is currently insufficient for them to replace culture as a lone diagnostic test. NAA tests may be used in combination with culture due to the advantage of time to result and in scenarios where culture tests are not feasible. Further work to improve NAA tests would benefit from the availability of standardized reference standards and improvements to the methodology.

In this work, we describe a fully automated cytokinesis-block micronucleus (CBMN) assay with a significantly shortened time to result, motivated by the need for rapid high-throughput biodosimetric estimation of radiation doses from small-volume human blood samples. The Rapid Automated Biodosimetry Tool (RABiT-II) currently consists of two commercial automated systems: a PerkinElmer cell::explorer Workstation and a GE Healthcare IN Cell Analyzer 2000 Imager. Blood samples (30 μl) from eight healthy volunteers were gamma-ray irradiated ex vivo with 0 (control), 0.5, 1.5, 2.5, 3.5 or 4.5 Gy and processed with full automation in 96-well plates on the RABiT-II system. The total cell culture time was 54 h and total assay time was 3 days. DAPI-stained fixed samples were imaged on an IN Cell Analyzer 2000 with fully-automated image analysis using the GE Healthcare IN Cell Developer Toolbox version 1.9. A CBMN dose-response calibration curve was established, after which the capability of the system to predict known doses was assessed. Various radiation doses for irradiated samples from two donors were estimated within 20% of the true dose (±0.5 Gy below 2 Gy) in 97% of the samples, with the doses in some 5 Gy irradiated samples being underestimated by up to 25%. In summary, the findings from this work demonstrate that the accelerated CBMN assay can be automated in a high-throughput format, using commercial biotech robotic systems, in 96-well plates, providing a rapid and reliable bioassay for radiation exposure.

Introduction Whole Genome Sequencing (WGS) for the identification and resistance prediction of mycobacterium tuberculosis (MTB) has been developed and validated by Public Health England with the aim to improve patient management by providing faster more accurate diagnosis of tuberculosis (TB) from clinical samples and to quickly identify linked TB cases. WGS has been used in clinical practice in Birmingham, UK since December 2016. Here we present the results of the first year of WGS results used in clinical practice. Methods Consecutive cases of culture positive TB diagnosed at a hospital in Birmingham in 2014 prior to WGS implementation were compared to cases diagnosed in 2017 following WGS implementation. Time to culture and time to sensitivity profile were compared. Results 100 consecutive controls from 2014 and 82 cases from 2017 were included. The median time from the sample being taken to culture was 18 days (12–26) for controls and 19 days (13–23) for cases. Overall for phenotypic results there were 147 fully sensitive samples, 24 resistant samples and 10 fails. Amongst the WGS results there were 48 sensitive results, 24 unknowns, 4 resistant and 6 fails. The median time to a phenotypic result was 55 days (40–81) for controls and 55 days (39–79) for cases. The median time for a WGS result from taking the sample was 27 days (19–37), the median time from culture positivity to a WGS result was 7 days (5–11). For resistant samples median time to phenotypic result was 31 (21–52) days for sensitive samples and 45 (38–72) days for resistant samples. With WGS mean time to result for sensitive samples was 7 days (6–9) and for resistant samples 19 (7–24) days. Conclusion Early experience with WGS results has shown that results are quicker compared to phenotypic results especially where the MTB sample is resistant. Importantly in this real life setting resistance profiles were available whilst patients were still on initiation phase treatment with 4 drugs. WGS results include relatedness information allowing TB transmission to be detected and investigated. The WGS results are quicker than the previous typing methods which gave results long after phenotypic results and often after patients had competed treatment.

Pathogen identification and antimicrobial susceptibility testing (AST) should be available as soon as possible for patients with bloodstream infections. We investigated whether a lysis-centrifugation (LC) blood culture (BC) method, combined with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification and Vitek 2 AST, provides a time advantage in comparison with the currently used automated broth-based BC system. Seven bacterial reference strains were added each to 10 mL human blood in final concentrations of 100, 10 and 1 CFU/mL. Inoculated blood was added to the Isolator 10 tube and centrifuged at 3000 g for 30 min, then 1.5 mL sediment was distributed onto five 150-mm agar plates. Growth was observed hourly and microcolonies were subjected to MALDI-TOF MS and Vitek 2 as soon as possible. For comparison, seeded blood was introduced into an aerobic BC bottle and incubated in the BACTEC 9240 automated BC system. For all species/concentration combinations except one, successful identification and Vitek 2 inoculation were achieved even before growth detection by BACTEC. The fastest identification and inoculation for AST were achieved with Escherichia coli in concentrations of 100 CFU/mL and 10 CFU/mL (after 7 h each, while BACTEC flagged respective samples positive after 9.5 h and 10 h). Use of the LC-BC method allows skipping of incubation in automated BC systems and, used in combination with rapid diagnostics from microcolonies, provides a considerable advantage in time to result. This suggests that the usefulness of direct BC on solid medium should be re-evaluated in the era of rapid microbiology.

Gas Chromatography-Flame Ionization Detection (GC-FID) analysis for quantitation of residual solvents in drugs and synthetic intermediates is one of the most important and frequently used tests in the pharmaceutical industry. However, as currently practiced, the technique requires significant sample preparation time, in addition to having a very poor ‘green factor’ (Analytical Method Volume Intensity, or AMVI). In this study, a simple and fast protocol using multi-solvent standard mixtures combined with a seven minute universal GC-FID method (using either He or H2 as carrier gas) and Empower™ data analysis is presented. We demonstrate that standard mixtures containing solvents commonly used in process chemistry workflows can be stored in crimped HPLC vials at −10 °C for at least 31 months. The 31 months stability data showed over 97% recovery for all 25 solvents, with overall relative standard deviation below 5%. Our approach simplifies tremendously the tedious task of residual solvent quantitation, resulting in significantly less labor, greater reliability, faster time to result and at least a 290 fold reduction in solvent consumption and hazardous waste disposal.

Background & Aim Cell and Gene Therapies are currently being developed to treat different diseases. By design, those therapies have very short shelf lives compared to traditional sterile pharmaceutical drugs. Besides, Cell and Gene Therapies can not be sterilized by filtration, therefore the historical compendial sterility test methods that takes 14 days to complete as defined in USP : “Sterility Tests” is not compatible. In order to assess the sterility of these therapies prior to transfusion, the BacT/ALERT Dual-T, an automated and more rapid technology, has been developed to reduce the time to result while keeping the highest level of perfomance and compliance. This method has now been recognized as compendial and can be used in lieu of the traditional 14 day sterility test to assess the sterility of cell-based products as defined in the EP Chapter 2.6.27 "Microbiological Examination Of Cell-Based Preparations". The objective of this work is to present the pathway to making an alternative test compendial for the specific cellular products. Methods, Results & Conclusion Method: The BacT/ALERT Dual-T will be presented and discussed as a compendial test replacing the traditional culture-based 14 day incubation sterility test, and other alternative technologies will also be discussed in comparison to compendial testing. A review of all major litteratrue and scientific articles will be presented that demonstrates the use and applicability of the BacT/ALERT Dual-T to assess the sterility of cell-based products. Different real-cases of implementation of the BacT/ALERT Dual-T within the Cell and Gene Therapies field and the biotechnology industry will be discussed, with recently adopted implementation strategies for different type therapies. And finally a regulatory update will be given, specifically on the recent advancements in several regulations and Pharmacopoeia Chapters, encouraging the use of more Modern, Rapid and Automated Sterility Testing solutions. Conclusion: Several validation studies have provided data comparing the BacT/Alert System to the compendial sterility test method and enabled the adoption of this technology as a compendial method for sterility testing of cell-based therapies. This enables the industry to replace the historical 14 day incubation historical compenidal sterility test by a much more modern and rapid automated method, which results in greater patient safety by providing final sterility results in less than 14 days.

BackgroundNewborn screening (NBS) aims to achieve early identification and treatment of affected infants prior to onset of symptoms. The timely completion of each step (i.e., specimen collection, transport, testing, result reporting), is critical for early diagnosis. Goals developed by the Secretary of Health and Human Services' Advisory Committee on Heritable Disorders in Newborns and Children (ACHDNC) for NBS timeliness were adopted (time-critical results reported by five days of life, and non-time-critical results reported by day seven), and implemented into a multi-year quality improvement initiative (NewSTEPS 360) aimed to decrease the time to result reporting and intervention.MethodsThe NBS system from specimen collection through reporting of results was assessed (bloodspot specimen collection, specimen shipping, sample testing, and result reporting). Annual data from 25 participating NBS programs were analyzed; the medians (and interquartile range, IQR) of state-specific percent of specimens that met the goal are presented.ResultsThe percent of specimens collected before 48 hours of life increased from 95% (88-97%) in 2016 to 97% (IQR 92-98%) in 2018 for the 25 states, with 20 (80%) of programs collecting more than 90% of the specimens within 48 hours of birth. Approximately 41% (IQR 29-57%) of specimens were transported within one day of collection. Time-critical result reporting in the first five days of life improved from 49% (IQR 26-74%) in 2016 to 64% (42%-71%) in 2018, and for non-time critical results from 64% (IQR 58%-78%) in 2016 to 81% (IQR 68-91%) in 2018. Laboratories open seven days a week in 2018 reported 95% of time-critical results within five days, compared to those open six days (62%), and five days (45%).ConclusionNBS programs that participated in NewSTEPs 360 made great strides in improving timeliness; however, ongoing quality improvement efforts are needed in order to ensure all infants receive a timely diagnosis.

Hemagglutination is a specific form of agglutination that involves red blood cells (RBCs). It has a limitation in view of emergency and point-of-care diagnoses (POCD) due to the requirement of large scale equipment and long time to result. In this study, a plastic microfluidic chip (P-μFC) included dried antibody-embedded was introduced. The hemagglutination reaction was enhanced by increasing amount of antibody dissolved in a reaction chamber. Within 2 minutes, the blood agglutination reaction was evaluated quantitatively by image processing. Moreover, a protein stabilizers of sugars were employed to increase the solubility of dried antibody so that the reaction with dried antibody was equivalent to which with fresh antibody.

BackgroundThe field of medicine is rapidly becoming digitised, and in the process passively amassing large volumes of healthcare data. Machine learning and data analytics are advancing rapidly, but these have been slow to be taken up in the day-to-day delivery of healthcare. We present an application of machine learning to optimise a laboratory testing programme as an example of benefiting from these tools.MethodsCanterbury District Health Board has recently implemented a system for urgent lab sample processing in the community, reducing unnecessary emergency presentations to hospital. Samples are transported from primary care facilities to a central laboratory. To improve the efficiency of this service, our team built a prototype transport scheduling platform using machine learning techniques and simulated the efficiency and cost impact of the platform using historical data.ResultsOur simulation demonstrated procedural efficiency and potential for annual savings between 5% and 14% from implementing a real-time lab sample transport scheduling platform. Advantages included providing a forward job list to the laboratory, an expected time to result and a streamlined transport request process.ConclusionThere are a range of opportunities in healthcare to use large datasets for improved delivery of care. We have described an applied example of using machine learning techniques to improve the efficiency of community patient lab sample processing at scale. This is with a view to demonstrating practical avenues for collaboration between clinicians and machine learning engineers.

Background Growth-based drug susceptibility testing (DST) is the reference standard for diagnosing drug-resistant tuberculosis (TB), but standard time to result (TTR) is typically ≥ 3 weeks. Rapid tests can reduce that TTR to days or hours, but accuracy may be lowered. In addition to the TTR and test accuracy, the cost of a diagnostic test may affect whether it is adopted in clinical settings. We examine the cost-effectiveness of rapid diagnostics for extremely drug-resistant TB (XDR-TB) in three different high-prevalence settings. Methods 1128 patients with confirmed TB were enrolled at clinics in Mumbai, India; Chisinau, Moldova; and Port Elizabeth, South Africa. Patient sputum samples underwent DST for first and second line TB drugs using 2 growth-based (MGIT, MODS) and 2 molecular (Pyrosequencing [PSQ], line-probe assays [LPA]) assays. TTR was the primary measure of effectiveness. Sensitivity and specificity were also evaluated. The cost to perform each test at each site was recorded and included test-specific materials, personnel, and equipment costs. Incremental cost-effectiveness ratios were calculated in terms of $/day saved. Sensitivity analyses examine the impact of batch size, equipment, and personnel costs. Results Our prior results indicated that the LPA and PSQ returned results in a little over 1 day. Mean cost per sample without equipment or overhead was $23, $28, $33, and $41 for the MODS, MGIT, PSQ, and LPA, respectively. For diagnosing XDR-TB, MODS was the most accurate, followed by PSQ, and LPA. MODS was quicker and less costly than MGIT. PSQ and LPA were considerably faster but cost more than MODS. Batch size and personnel costs were the main drivers of cost variation. Conclusions Multiple factors must be weighed when selecting a test for diagnosis of XDR-TB. Rapid tests can greatly improve the time required to diagnose drug-resistant TB, potentially improving treatment success, and preventing the spread of XDR-TB. Faster time to result must be weighed against the potential for reduced accuracy, and increased costs. Trial registration ClinicalTrials.gov Identifier: NCT02170441. Electronic supplementary material The online version of this article (10.1186/s12879-018-3013-0) contains supplementary material, which is available to authorized users.

Bloodstream infections caused by carbapenemase-producing Enterobacteriaceae (CPE) are associated with treatment failure and increased mortality. Detection of CPE from blood cultures (BC) by standard methods takes 16–72 hours, which can delay the initiation of appropriate antimicrobial therapy and compromise patient outcome. In the present study, we developed and evaluated a new method for the rapid detection of carbapenemases directly from positive BC using a new multiplex immunochromatographic test (ICT). The new ICT was assessed using 170 molecularly characterized Enterobacteriaceae clinical isolates including 126 CPE (OXA-48-like (N = 79), KPC (N = 18) and NDM (N = 29)). After spiking with bacteria and incubation in a BC system, blood from positive BC bottles was hemolyzed, bacteria concentrated by centrifugation and lysed. The lysate was transferred to the RESIST-3 O.K.N. ICT (Coris BioConcept, Gembloux, Belgium), which detects OXA-48-like, KPC and NDM carbapenemases. The final results of the ICT were read when they became positive, at the latest after 15 min. All CPE isolates (126/126) were correctly detected with the new protocol (100% sensitivity, 100% specificity). There was perfect concordance between ICT results and molecular characterization. Total time to result was 20–45 min. Conclusions: This proof-of-principle study demonstrates that with the newly developed method, OXA-48-like, KPC and NDM carbapenemases can be reliably detected directly from positive BC bottles. The new method is more rapid than other currently available assays and can be performed in any routine microbiology laboratory. This can help to rapidly identify patients with CPE BSI and optimize the management of patients with these difficult-to-treat infections. Further studies are needed to assess the performance of the ICT in routine diagnostics.

Multiplexed nucleic acid-based tests for infectious disease have become a standard part of clinical laboratory practice. These tests provide a comprehensive syndrome-based approach to determine the etiological agent of disease. The technology underlying these different systems is reviewed here with a special focus on the BioFire FilmArray® platform. The literature on the clinical utility and cost-effectiveness of these platforms for respiratory, blood culture, and gastrointestinal infections is discussed. Although there are reports showing a clear benefit to the patient or to the healthcare system from adopting a syndromic molecular approach, it is also apparent that clinical laboratories and healthcare providers are still learning how to take full advantage of the new systems. Finally, some improvements to this technology that should appear in the next few years are discussed. These include automated pathogen-specific surveillance based on aggregating the data from these systems, a move toward point-of-care syndromic testing, and further decreases in time to result of the tests.