Sequencing facility and DNA source associated patterns of virus-mappable reads in whole-genome sequencing data.

Numerous viral sequences have been reported in the whole-genome sequencing (WGS) data of human blood. However, it is not clear to what degree the virus-mappable reads represent true viral sequences rather than random-mapping or noise originating from sample preparation, sequencing processes, or other sources. Identification of patterns of virus-mappable reads may generate novel indicators for evaluating the origins of these viral sequences. We characterized paired-end unmapped reads and reads aligned to viral references in human WGS datasets, then compared patterns of the virus-mappable reads among DNA sources and sequencing facilities which produced these datasets. We then examined potential origins of the source- and facility-associated viral reads. The proportions of clean unmapped reads among the seven sequencing facilities were significantly different (P < 2 × 10-16). We identified 260,339 reads that were mappable to a total of 99 viral references in 2535 samples. The majority (86.7%) of these virus-mappable reads (corresponding to 47 viral references), which can be classified into four groups based on their distinct patterns, were strongly associated with sequencing facility or DNA source (adjusted P value <0.01). Possible origins of these reads include artificial sequences in library preparation, recombinant vectors in cell culture, and phages co-contaminated with their host bacteria. The sequencing facility-associated virus-mappable reads and patterns were repeatedly observed in other datasets produced in the same facilities. We have constructed an analytic framework and profiled the unmapped reads mappable to viral references. The results provide a new understanding of sequencing facility- and DNA source-associated batch effects in deep sequencing data and may facilitate improved bioinformatics filtering of reads.

Impact of delays to incubation and storage temperature on blood culture results: a multi-centre study.

BACKGROUND: Blood cultures are one of the most important tests performed by microbiology laboratories. Many hospitals, particularly in low and middle-income countries, lack either microbiology services or staff to provide 24 h services resulting in delays to blood culture incubation. There is insufficient guidance on how to transport/store blood cultures if delays before incubation are unavoidable, particularly if ambient temperatures are high. This study set out to address this knowledge gap. METHODS: In three South East Asian countries, four different blood culture systems (two manual and two automated) were used to test blood cultures spiked with five common bacterial pathogens. Prior to incubation the spiked blood culture bottles were stored at different temperatures (25 °C, in a cool-box at ambient temperature, or at 40 °C) for different lengths of time (0 h, 6 h, 12 h or 24 h). The impacts of these different storage conditions on positive blood culture yield and on time to positivity were examined. RESULTS: There was no significant loss in yield when blood cultures were stored < 24 h at 25 °C, however, storage for 24 h at 40 °C decreased yields and longer storage times increased times to detection. CONCLUSION: Blood cultures should be incubated with minimal delay to maximize pathogen recovery and timely result reporting, however, this study provides some reassurance that unavoidable delays can be managed to minimize negative impacts. If delays to incubation ≥ 12 h are unavoidable, transportation at a temperature not exceeding 25 °C, and blind sub-cultures prior to incubation should be considered.

Reference interval transference of common clinical biomarkers.

Clinical examination has become an important method of disease diagnosis, curative effect evaluation, prognosis judgment and health monitoring, and the biological reference interval is the reference standard to interpret test results and analyses of test information. In clinical tests, the reference interval is often affected by race, sex, age, geographical location and growth and development, so it is very important to establish a suitable reference interval for each laboratory. It is a huge and arduous task for each laboratory to establish its own reference interval. It is unrealistic for different measurement systems to establish reference intervals. According to the C28-A3c guideline from the Clinical and Laboratory Standards Institute (CLSI), clinical laboratories can appropriately transfer the reference intervals provided by other laboratories. This paper reviews whether the biomarkers in multiregional laboratories can transfer reference intervals between different measurement systems to expand the application of reference interval databases and ensure the accuracy and consistency of the test results.

Sigma metrics application for validated and non-validated detecting systems performance assessment.

BACKGROUND: Sigma metrics provide an objective and quantitative methodology for analytical quality evaluation of clinical laboratory. This study investigated the testing performance of validated systems and non-validated systems based on sigma metrics, and explored the major parameters affecting the system performance. METHODS: Sigma metrics were evaluated by six biochemistry assays based on Beckman and Mindray validated and non-validated systems through crossing the reagents and analyzers. Imprecision and bias were assessed for all assays based on trueness programs organized by National Centre for Clinical Laboratory. Total error allowance obtained from the Chinese Ministry of Health Clinical Laboratory Centre Industry Standard (WS/T403-2012). RESULTS: The imprecision for all systems meets the quality specifications except TP assay (2.19%) detected by Mindray non-validated system, and the bias for four assays measured by non-validated systems cannot fulfill the criterion, including lactate dehydrogenase (LDH), total protein (TP), triglycerides (TG), and glucose (GLU). Higher biases were detected in six assays at different levels among non-validated and validated systems. Systems performed poorly or unacceptably for TP assay with sigma metrics lower than 3 except Mindray non-validated system. The sigma metrics for other assays with four systems were greater than 3 except the LDH evaluated on Mindray non-validated systems. CONCLUSION: Non-validated systems may introduce performance uncertainty compared with validated systems based on sigma metrics evaluation, and lower bias was provided by validated systems. The performance of non-validated systems should be evaluated thoroughly in the clinical laboratory before they were adopted for routine use.

Research and discussion on the evaluation scheme of reagent lot-to-lot differences in 16 chemiluminescence analytes, established by the EP26-A guidelines of the CLSI.

BACKGROUND: Verification of new reagent lots is a part of the crucial tasks in clinical laboratories. The Clinical and Laboratory Standards Institute (CLSI) EP26-A guideline provides laboratories with an evaluation method for reagent verification. The purpose of this study was to compare the performance of EP26-A with our laboratory reagent lot verification protocol and get the final scheme. METHOD: 16 chemiluminescence analytes including estradiol (E2), progesterone (P), ferritin (FER), cortisol (COR),carbohydrate antigen 153 (CA153), and free prostate-specific antigen (FPSA). were prospectively evaluated in two reagent lots. The laboratory's lot verification process included evaluating 5 patient samples with the current and new lots and acceptability according to a predefined criteria. For EP26-A, method imprecision data and critical differences at medical decision points were important factors affecting the sample size requirements and rejection limits. RESULT: The number of samples required for EP26-A was 3 to 12, of which P, CA153, and FPSA had increased by more than 5 samples compared with the current protocol. Of the 16 chemiluminescence analytes, 11 had higher rejection limits when using EP26-A than the current laboratory scheme. Our current protocol and EP26-A were in agreement in 32 of the 32 (100%) paired verifications. CONCLUSION: The EP26-A protocol is an important tool to find the differences between reagent lots, and it makes up for the loopholes in the statistical efficiency, sample concentration and quantity, and the selection of rejection limits in the current protocol.

EQA/PT scheme to improve the equivalence of enzymatic results between mutual recognition laboratories in Beijing.

BACKGROUND: To utilize the external quality assessment (EQA)/proficiency testing (PT) scheme to evaluate the equivalence of different clinical enzymatic measuring systems in Beijing. METHODS: The Beijing Center for Clinical Laboratory (BCCL) distributed three investigation samples to mutual recognition clinical laboratories in Beijing including alanine aminotransferase (ALT), aspartate aminotransferase (AST), γ-glutamyltransferase (GGT), creatine kinase (CK), and lactate dehydrogenase (LDH). These samples were derived from serum pools with values assigned by the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) enzymatic reference measurement procedures (RMPs). Each laboratory performed duplicate tests of the samples. Then, the samples at level 1 were used to recalibrate individual measuring systems for repeating the tests. BCCL collected data for evaluation of their analytical quality. RESULTS: Before recalibration, the biases of ALT and AST tests were not traceable to the IFCC RMPs, and the bias pass rates of GGT, CK, and LDH tests were only 51.2%, 55.7%, and 48.6% respectively. After recalibration, the pass rates of ALT, AST, GGT, CK, and LDH increased to 95.1%, 82.9%, 95.1%, 97.1%, and 70.0% respectively. The EQA/PT also showed that after recalibration, more than 95% of laboratories met the optimum level specifications of the biological variation for ALT, AST, GGT, and CK tests and the desirable for LDH tests. CONCLUSION: The enzymatic tests in Beijing need to be further standardized by category 1 or 2 EQA/PT scheme for mutual recognition between clinical laboratories. The criteria of biological variation are more relevant for determining the equivalence of clinical enzymatic tests.

COVID-19-another influential event impacts on laboratory medicine management.

BACKGROUND: Before public health emergencies became a major challenge worldwide, the scope of laboratory management was only related to developing, maintaining, improving, and sustaining the quality of accurate laboratory results for improved clinical outcomes. Indeed, quality management is an especially important aspect and has achieved great milestones during the development of clinical laboratories. CURRENT STATUS: However, since the coronavirus disease 2019 (COVID-19) pandemic continues to be a threat worldwide, previous management mode inside the separate laboratory could not cater to the demand of the COVID-19 public health emergency. Among emerging new issues, the prominent challenges during the period of COVID-19 pandemic are rapid-launched laboratory-developed tests (LDTs) for urgent clinical application, rapid expansion of testing capabilities, laboratory medicine resources, and personnel shortages. These related issues are now impacting on clinical laboratory and need to be effectively addressed. CONCLUSION: Different from traditional views of laboratory medicine management that focus on separate laboratories, present clinical laboratory management must be multidimensional mode which should consider consolidation of the efficient network of regional clinical laboratories and reasonable planning of laboratories resources from the view of overall strategy. Based on relevant research and our experience, in this review, we retrospect the history trajectory of laboratory medicine management, and also, we provide existing and other feasible recommended management strategies for laboratory medicine in future.

Challenges and Controversies to Testing for COVID-19.

The coronavirus disease (COVID-19) pandemic has placed the clinical laboratory and testing for SARS-CoV-2 front and center in the worldwide discussion of how to end the outbreak. Clinical laboratories have responded by developing, validating, and implementing a variety of molecular and serologic assays to test for SARS-CoV-2 infection. This has played an essential role in identifying cases, informing isolation decisions, and helping to curb the spread of disease. However, as the demand for COVID-19 testing has increased, laboratory professionals have faced a growing list of challenges, uncertainties, and, in some situations, controversy, as they have attempted to balance the need for increasing test capacity with maintaining a high-quality laboratory operation. The emergence of this new viral pathogen has raised unique diagnostic questions for which there have not always been straightforward answers. In this commentary, the author addresses several areas of current debate, including (i) the role of molecular assays in defining the duration of isolation/quarantine, (ii) whether the PCR cycle threshold value should be included on patient reports, (iii) if specimen pooling and testing by research staff represent acceptable solutions to expand screening, and (iv) whether testing a large percentage of the population is feasible and represents a viable strategy to end the pandemic.

Establishment of a WHO Reference Reagent for anti-Mullerian hormone.

BACKGROUND: There is a need for a reference material to support the development and ensure the quality of immunoassays for human AMH. A batch of ampoules, coded 16/190, containing lyophilised recombinant AMH was evaluated in a WHO Collaborative Study. The aims of the study were to determine the AMH content in terms of the calibration of each immunoassay method, to predict long-term stability and to assess the suitability of the preparation to calibrate AMH immunoassays. METHODS: Study participants were asked to report the AMH content of specific dilutions of coded ampoules of 16/190 and a comparator preparation containing approximately half the AMH content. In each assay, participants also reported the AMH content of 22 patient samples to assess commutability. A robust all-laboratory geometric mean of the content estimates was determined using the laboratory geometric mean estimates. Commutability was assessed using a difference in bias approach. Stability was predicted by the measurement of thermally accelerated degradation samples. RESULTS: Seven laboratories performed twenty-one immunoassay method-platform combinations, sixteen of which provided data which met the validity criteria, giving a consensus geometric mean estimate of AMH content of 511 ng/ampoule (95% CI, 426-612, n = 16, GCV 42%) and a robust geometric mean of 489 ng/ampoule. By contrast, the GCV% for the all-laboratory geometric mean of the relative content estimates for the comparator sample to 16/190 was 12%. Commutability was assessed using 20 of the 22 representative patient samples. Of the valid assays, 16/190 was within the limits of acceptable commutability for 6 methods, partially commutable for a further 3 methods and non-commutable when measured by 7 methods. The preparation was predicted to be highly stable when stored at - 20 °C. CONCLUSION: The majority of methods met the validity criteria. Content estimates showed a high between-method variability, yet assays exhibited a similar proportionality of response as demonstrated using the comparator sample. 16/190 was commutable in some but not all methods. On the basis of these results, it was agreed by the WHO Expert Committee on Biological Standardization to establish 16/190 as a WHO Reference Reagent for AMH with a content defined by consensus immunoassay of 489 ng/ampoule.

Laboratory Quality Management System and Quality Indicators Implementation Status as Perceived by Laboratory Professionals in Preparation for the Accreditation Process from Selected Government Hospitals of Ethiopia.

BACKGROUND: The aim was to produce quality results that clinical laboratories need to implement and maintain continuous quality improvement systems. In recent years, health organizations have increasingly prioritized the quality of laboratory services by implementing quality management systems (QMSs) and building quality improvement activities. Efforts to strengthen laboratory systems in the African region have received increased attention in recent years. Assessing the implementation levels of laboratory quality management system components is important to identify the gaps that need further improvements. METHODS: A cross-sectional study design was used between March and May 2017 in selected government hospitals of Ethiopia, and sample size was determined using a finite population formula, and a proportional sampling technique was employed; a sample size of 184 (62%) was calculated from 295 laboratory professionals. RESULTS: All respondents were informed about the laboratory's experience in the quality management system implementation; of those, only 138 (79%) engaged in the implementation process. From the 18 selected laboratory quality management components, 5 were observed to have the list implementation status, which are: (1) Performance of internal quality control for all tests, (2) Development and communication of a quality manual for all tests, (3) Adequacy of storage space for the supplies, (4) Development of an action plan based on internal audit, and (5) monitoring of environmental conditions. Running quality controls for all types of tests became a headache in almost all laboratories. From 12 selected quality indicators studied in this research, the 5 indicators with either poor or very poor performance outcome were: control of documents 136 (77.7%), control of records 123 (70.3%), development of manuals and policies 122 (69.7%), development of process and procedures 120 (68.6%), and internal communication 114 (65.1%). CONCLUSIONS: This research indicated the top 3 LQMS components with either poor or very poor implementation status: (1) Performance of internal quality controls for all tests, (2) Development and communication of quality manuals for all tests, (3) Adequacy of storage space for the supplies. Of the quality indicators studied, control of documents was perceived to have poor performance outcome by 136 (77.7%) of study participants.

CCMG practice guideline: laboratory guidelines for next-generation sequencing.

PurposeThe purpose of this document is to provide guidance for the use of next-generation sequencing (NGS, also known as massively parallel sequencing or MPS) in Canadian clinical genetic laboratories for detection of genetic variants in genomic DNA and mitochondrial DNA for inherited disorders, as well as somatic variants in tumour DNA for acquired cancers. They are intended for Canadian clinical laboratories engaged in developing, validating and using NGS methods. METHODS OF STATEMENT DEVELOPMENT: The document was drafted by the Canadian College of Medical Geneticists (CCMG) Ad Hoc Working Group on NGS Guidelines to make recommendations relevant to NGS. The statement was circulated for comment to the CCMG Laboratory Practice and Clinical Practice committees, and to the CCMG membership. Following incorporation of feedback, the document was approved by the CCMG Board of Directors. DISCLAIMER: The CCMG is a Canadian organisation responsible for certifying medical geneticists and clinical laboratory geneticists, and for establishing professional and ethical standards for clinical genetics services in Canada. The current CCMG Practice Guidelines were developed as a resource for clinical laboratories in Canada and should not be considered to be inclusive of all information laboratories should consider in the validation and use of NGS for a clinical laboratory service.

Using ISO/TS 20914:2019 to calculate the measurement uncertainty of immunosuppressive drugs in a clinical laboratory.

According to the standard ISO 15189 clinical routine laboratories shall estimate measurement uncertainty (MU) of patient results of their provided measurands. Up to now there was no accepted description on how to perform. Recently, the ISO technical standard ISO/TS 20914 was published giving a practical guide for uncertainty estimation. The immunosuppressive drugs Everolimus, Ciclosporin, Sirolimus and Tacrolimus have narrow therapeutic windows. Hence, their MU should be considered for deducing clinical decisions. Here, a pathway is presented in detail on how to estimate MU measuring immunosuppressants using a widespread CE certified assay via LC-MS/MS technology. Namely, the expanded measurement uncertainties are from 13% to 27% depending on analyte and concentration. The calculation based on n > 2000 measurements each of four control levels within one year. Lower uncertainties were observed if the material was native pooled blood (13% to 17%, n > 300 measurements, one year).

Addition of Efficiency Measures to Current Accuracy Measures in the Vascular Laboratory Can Be Used for Future Accreditation and Payment Models.

BACKGROUND: The Medicare Access and CHIP Reauthorization Act (MACRA) brings with it increased regulatory requirements not traditionally addressed by standard vascular laboratory accreditation, which is based on accuracy. The new quality improvement project of the Intersocietal Accreditation Commission (IAC) may satisfy an improvement activity (IA) of the MACRA. We hypothesize that other IAs in the MACRA such as timeliness of test results or patient care quality performance requirements can be met by analyzing data already being collected by the vascular laboratory. After a process improvement strategy, we chose to review progress in our vascular laboratory related to time to interpretation (TI), patient check-in to study completion (study time), wait time for first available outpatient venous duplex scan (wait time), technologist productivity, and critical results reporting. METHODS: Data from our hospital-based vascular laboratory were collected from 2010 to 2016. TI was collected through our reporting software VascuPro (Consensus Medical), and study time and wait time were obtained from electronic medical records (EMR) (Epic). Technologist productivity was calculated by commercially available productivity tools, and compliance with critical results reporting was calculated quarterly as per our quality assurance program. Appropriateness of carotid duplex scan testing was performed by expert review of International Classification of Disease codes used to request the test. RESULTS: TI analysis comprised 91,352 studies with a mean of 3.3 hr between test completion and final interpretation. The TI improved from 5.0 to 2.1 hr on weekdays and was longer on weekends (4.9 hr; P < 0.001). The study time improved from 29.8 to 27.2 min and was 14.9 min shorter on the weekends (P < 0.001). The wait time ranged from a mean of 1-2.08 days. Technologist productivity improved from 90.7% to 93.6%. Critical results reporting quarterly audits showed a 100% compliance rate. On expert review, the International Classification of Disease code on carotid duplex scan requests in the EMR was deemed inaccurate in 17.4% of cases. CONCLUSIONS: TI and study time improved; wait time and critical results reporting remained steady. Most of the data are readily available in a vascular laboratory standard EMR. The plan-do-study-act (PDSA or Shewhart Cycle) principle is critical to process improvement and needed as we transition from traditional accreditation mostly based on test accuracy to one demanding efficiency, timeliness, patient satisfaction, productivity, accountability, and appropriateness of testing. Process improvement studies will improve patient care and satisfaction, increase efficiency and throughput, while satisfying changing IAC standards and preparing for upcoming regulatory requirements of the MACRA.

FACSCanto II and LSRFortessa flow cytometer instruments can be synchronized utilizing single-fluorochrome-conjugated surface-dyed beads for standardized immunophenotyping.

BACKGROUND: Multiparameter flow cytometry is the preferred method to determine immunophenotypic features of cells present in a wide variety of sample types. Standardization is key to avoid inconsistencies and subjectivity of interpretations between clinical diagnostic laboratories. Among these standardization requirements, synchronization between different flow cytometer instruments is indispensable to obtain comparable results. This study aimed to investigate whether two widely used flow cytometers, the FACSCanto II and LSRFortessa, can be effectively synchronized utilizing calibration bead-based synchronization. METHOD: Two FACSCanto II and two LSRFortessa flow cytometers were synchronized with both multicolor hard-dyed and single-fluorochrome-conjugated surface-dyed beads according to the manufacturer's instructions. Cell staining was performed on five whole-blood samples obtained from healthy controls and were analyzed upon synchronization with the respective synchronization protocols. RESULTS: Comparability criteria (defined as <15% deviation from the reference instrument) were met with both bead sets when synchronizing different FACSCanto II or LSRFortessa instruments. However, we observed that the criteria could not be met when synchronizing FACSCanto II with LSRFortessa instruments with multicolor hard-dyed beads. By utilizing single-fluorochrome-conjugated surface-dyed beads to determine and adjust PMT voltages, the accepted comparability criteria were successfully met. The protocol has been validated using five different eight-parameter stained samples. CONCLUSION: We show that FACSCanto II and LSRFortessa instruments can effectively be synchronized using single-fluorochrome-conjugated surface-dyed beads in case deviation criteria cannot be met using multicolor hard-dyed beads. Synchronization with single-fluorochrome-conjugated surface-dyed beads results in decreased deviations between instruments, allowing comparability criteria to become stricter.

Practical Guidance for Clinical Microbiology Laboratories: Implementing a Quality Management System in the Medical Microbiology Laboratory

This document outlines a comprehensive practical approach to a laboratory quality management system (QMS) by describing how to operationalize the management and technical requirements described in the ISO 15189 international standard. It provides a crosswalk of the ISO requirements for quality and competence for medical laboratories to the 12 quality system essentials delineated by the Clinical and Laboratory Standards Institute. The quality principles are organized under three main categories: quality infrastructure, laboratory operations, and quality assurance and continual improvement. The roles and responsibilities to establish and sustain a QMS are outlined for microbiology laboratory staff, laboratory management personnel, and the institution's leadership. Examples and forms are included to assist in the real-world implementation of this system and to allow the adaptation of the system for each laboratory's unique environment. Errors and nonconforming events are acknowledged and embraced as an opportunity to improve the quality of the laboratory, a culture shift from blaming individuals. An effective QMS encourages "systems thinking" by providing a process to think globally of the effects of any type of change. Ultimately, a successful QMS is achieved when its principles are adopted as part of daily practice throughout the total testing process continuum.

Benefits and risks of standardization, harmonization and conformity to opinion in clinical laboratories.

Large laboratory systems that include facilities with a range of capabilities and capacity are being created within consolidated healthcare systems. This paradigm shift is being driven by administrators and payers seeking to achieve resource efficiencies and to conform practice to the requirements of computerization as well as the adoption of electronic medical records. Although standardization and harmonization of practice improves patient care outcomes and operational efficiencies, administratively driven practice conformity (conformity to opinion) also has serious drawbacks and may lead to significant system failure. Juxtaposition of the distinct philosophical approaches of physicians and scientists (i.e. "professionalism") versus administrators and managers (i.e. "managerialism") towards bringing about conformity of the laboratory system inherently creates conflict. Despite an administrative edict to "perform all tests using the same methods" regardless of available "best practice" evidence to do so, medical/scientific input on these decisions is critical to ensure quality and safety of patient care. Innovation within the laboratory system, including the adoption of advanced technologies, practices, and personalized medicine initiatives, will be enabled by balancing the relentless drive by non-medical administration to meet "business" requirements, the medical responsibility to provide the best care possible, and customizing practice to meet individual patient care needs.

Delta Checks in the clinical laboratory.

International standards and practice guidelines recommend the use of delta check alerts for laboratory test result interpretation and quality control. The value of contemporary applications of simple univariate delta checks determined as an absolute change, percentage change, or rate of change to recognize specimen misidentification or other laboratory errors has not received much study. This review addresses these three modes of calculation, but in line with the majority of published work, most attention is focused on the identification of specimen misidentification errors. Investigation of delta check alerts are time-consuming and the yield of identified errors is usually small compared to the number of delta check alerts; however, measured analytes with low indices of individuality frequently perform better. While multivariate approaches to delta checks suggest improved usefulness over simple univariate delta check strategies, some of these are complex and not easily applied in contemporary laboratory information systems and middleware. Nevertheless, a simple application of delta checks may hold value in identifying clinically significant changes in several clinical situations: for acute kidney injury using changes in serum creatinine, for risk of osmotic demyelination syndrome using rapid acute changes in serum sodium levels, or for early triage of chest pain patients using high sensitivity troponin assays. A careful and highly selective approach to identifying delta check analytes, calculation modes, and thresholds before putting them into practice is warranted; then follow-up with careful monitoring of performance and balancing true positives, false negatives, and false positives among delta check alerts is needed.

Delivering modern, high-quality, affordable pathology and laboratory medicine to low-income and middle-income countries: a call to action.

Modern, affordable pathology and laboratory medicine (PALM) systems are essential to achieve the 2030 Sustainable Development Goals for health in low-income and middle-income countries (LMICs). In this last in a Series of three papers about PALM in LMICs, we discuss the policy environment and emphasise three crucial high-level actions that are needed to deliver universal health coverage. First, nations need national strategic laboratory plans; second, these plans require adequate financing for implementation; and last, pathologists themselves need to take on leadership roles to advocate for the centrality of PALM to achieve the Sustainable Development Goals for health. The national strategic laboratory plan should deliver a tiered, networked laboratory system as a central element. Appropriate financing should be provided, at a level of at least 4% of health expenditure. Financing of new technologies such as molecular diagnostics is challenging for LMICs, even though many of these tests are cost-effective. Point-of-care testing can substantially reduce test-reporting time, but this benefit must be balanced with higher costs. Our research analysis highlights a considerable deficiency in advocacy for PALM; pathologists have been invisible in national and international health discourse and leadership. Embedding PALM in LMICs can only be achieved if pathologists advocate for these services, and undertake leadership roles, both nationally and internationally. We articulate eight key recommendations to address the current barriers identified in this Series and issue a call to action for all stakeholders to come together in a global alliance to ensure the effective provision of PALM services in resource-limited settings.

Microbiology Investigation Criteria for Reporting Objectively (MICRO): a framework for the reporting and interpretation of clinical microbiology data.

BACKGROUND: There is a pressing need to understand better the extent and distribution of antimicrobial resistance on a global scale, to inform development of effective interventions. Collation of datasets for meta-analysis, mathematical modelling and temporo-spatial analysis is hampered by the considerable variability in clinical sampling, variable quality in laboratory practice and inconsistencies in antimicrobial susceptibility testing and reporting. METHODS: The Microbiology Investigation Criteria for Reporting Objectively (MICRO) checklist was developed by an international working group of clinical and laboratory microbiologists, infectious disease physicians, epidemiologists and mathematical modellers. RESULTS: In keeping with the STROBE checklist, but applicable to all study designs, MICRO defines items to be included in reports of studies involving human clinical microbiology data. It provides a concise and comprehensive reference for clinicians, researchers, reviewers and journals working on, critically appraising, and publishing clinical microbiology datasets. CONCLUSIONS: Implementation of the MICRO checklist will enhance the quality and scientific reporting of clinical microbiology data, increasing data utility and comparability to improve surveillance, grade data quality, facilitate meta-analyses and inform policy and interventions from local to global levels.

Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing.

Metagenomic sequencing for infectious disease diagnostics is an important tool that holds promise for use in the clinical laboratory. Challenges for implementation so far include high cost, the length of time to results, and the need for technical and bioinformatics expertise. However, the recent technological innovation of nanopore sequencing from Oxford Nanopore Technologies (ONT) has the potential to address these challenges. ONT sequencing is an attractive platform for clinical laboratories to adopt due to its low cost, rapid turnaround time, and user-friendly bioinformatics pipelines. However, this method still faces the problem of base-calling accuracy compared to other platforms. This review highlights the general challenges of pathogen detection in clinical specimens by metagenomic sequencing, the advantages and disadvantages of the ONT platform, and how research to date supports the potential future use of nanopore sequencing in infectious disease diagnostics.