Public health implementation of pathogen genomics: the role for accreditation and application of ISO standards

Pathogen genomics has transitioned rapidly from the research setting into a powerful tool now routinely used in public health microbiology, for surveillance, outbreak investigations and disease control. As these investigations can have significant public health, treatment and legal impacts, we must ensure the accuracy of these results through validation of testing processes. For laboratories working in this space, it is important to approach this work with a quality and accreditation framework in mind, working towards implementation of quality systems and test validation that meet international regulatory standards. Here we outline the key international standards and processes that lead toward accreditation for pathogen genomics.

A pilot study of on-site evaluation as external quality assessment for ISO 15189 accreditation of laboratories performing next-generation sequencing oncology tests

BACKGROUND

As next-generation sequencing (NGS) oncology tests vary by platform, application, and target of genes, specific methods for external quality assessment (EQA) have not been universally applied. Hence, we have attempted to implement on-site evaluation as EQA in the accreditation program under ISO 15189 for laboratories that perform NGS oncology tests.

METHODS

A total of 10 laboratories that performed NGS oncology tests were enrolled. Two types of EQA samples were prepared (Acrometrix Oncology Hotspot Control DNA and OncoSpan gDNA DNA samples), and the variant allele frequency of targeted genes was assigned. The samples were subjected to NGS oncology tests in participant laboratories according to their routine protocols. Based on the result reports, auditors visited the participant laboratories to perform on-site evaluations and provided feedback regarding possible laboratory process improvement.

RESULTS

The participant laboratories identified the targeted variants in the Acrometrix Oncology Hotspot Control DNA and OncoSpan gDNA samples with a success rate of 31-100% and 9.5-100%, respectively, compared with reference information, depending on their sequencing systems, and reported a few lower-variant allele frequencies. Six of the eight evaluated laboratories failed to report at least three pathogenic variants due to errors in wet-lab and/or dry-lab processes. Based on the feedback reports and self-assessment, auditors and laboratory staff discussed potential improvements to processes during on-site evaluations for laboratory accreditations.

CONCLUSIONS

On-site evaluation as EQA for NGS oncology tests in the laboratory accreditation program under ISO 15189 was successfully implemented and proved applicable to a broad spectrum of NGS tests.

Survey on the Construction Status of Forensic Virtual Autopsy Laboratory and the Applicability of Laboratory Accreditation

OBJECTIVES

To survey the development status and actual needs of virtual autopsy technology in China and to clarify the applicability of forensic virtual autopsy laboratory accreditation.

METHODS

The questionnaire was set up included three aspects：(1) the current status of virtual autopsy technology development; (2) the accreditation elements such as personnel, equipment, entrustment and acceptance, methods, environmental facilities; (3) the needs and suggestions of practicing institutions. A total of 130 forensic pathology institutions were surveyed by online participation through the Questionnaire Star platform.

RESULTS

Among the 130 institutions, 43.08% were familiar with the characteristics of virtual autopsy technology, 35.38% conducted or received training in virtual autopsy, and 70.77% have establishment needs (including maintenance). Relevant elements were suitable for laboratory accreditation.

CONCLUSIONS

Virtual autopsy identification has gained social recognition. There is a demand for accreditation of forensic virtual autopsy laboratory. After the preliminary assessment, considering the characteristics and current situation of this technology, China National Accreditation Service for Conformity Assessment (CNAS) can first carry out the accreditation pilot of virtual autopsy project at large comprehensive forensic institutions with higher identification capability, and then CNAS can popularize the accreditation in a wide range when the conditions are suitable.

Repository of intra- and inter-run variations of quantitative autoantibody assays: a European multicenter study

OBJECTIVES

No reference data are available on repositories to measure precision of autoantibody assays. The scope of this study was to document inter- and intra-run variations of quantitative autoantibody assays based on a real-world large international data set.

METHODS

Members of the European Autoimmunity Standardisation Initiative (EASI) group collected the data of intra- and inter-run variability obtained with assays quantifying 15 different autoantibodies in voluntary participating laboratories from their country. We analyzed the impact on the assay performances of the type of immunoassay, the number of measurements used to calculate the coefficient of variation (CVs), the nature and the autoantibody level of the internal quality control (IQC).

RESULTS

Data were obtained from 64 laboratories from 15 European countries between February and October 2021. We analyzed 686 and 1,331 values of intra- and inter-run CVs, respectively. Both CVs were significantly dependent on: the method of immunoassay, the level of IQC with higher imprecision observed when the antibody levels were lower than 2-fold the threshold for positivity, and the nature of the IQC with commercial IQCs having lower CVs than patients-derived IQCs. Our analyses also show that the type of autoantibody has low impact on the assay' performances and that 15 measurements are sufficient to establish reliable intra- and inter-run variations.

CONCLUSIONS

This study provides for the first time an international repository yielding values of intra- and inter-run variation for quantitative autoantibody assays. These data could be useful for ISO 15189 accreditation requirements and will allow clinical diagnostic laboratories to assure quality of patient results.

Strengthening Medical Laboratory Systems in Kenya: An Innovative Biosafety Training Model

Background: With increased rates of laboratory-acquired infections from clinical and research laboratories globally, efforts have been made to improve awareness of modern practices and pursue innovations in biosafety to manage risks and laboratory exposures arising from infectious agents and other hazards. Objectives: This article demonstrates a sustainable biosafety training model developed to enhance laboratory quality and support accreditation in health facilities in Kenya. Methods: A biosafety technical working group was formed, and sensitization meetings held with health managers. Trainings were then conducted for training of trainers (TOTs) who then cascaded trainings in health facilities. This was followed by mentorships and monitoring for implementation. Results: Five sensitization meetings were carried out for 264 health managers. TOTs was done for 48 trained trainers and 1044 laboratory workers in 216 facilities covering 44 counties. Site visits were done in 51 facilities, with biosafety achievements measured in 21 (41%), respectively. Achievements in 21 facilities included the following: improvised eye wash stations in 16 facilities (76%), biological spill kits in 17 (81%), buckets of sand in 15 (71%), fire extinguishers in 12 (57%), hepatitis B vaccination in 14 (66%), establishment of phlebotomy areas in 18 facilities (85%), material safety data sheets in 18 (85%), documentation of incidents and exposures in 16 (76%), and proper waste segregation in 17 (81%). Conclusion: This model ensured rapid scale-up to multiple counties and enabled learners to understand biosafety principles. Due to management buy-in, resources were availed to implement interventions, and this was demonstrated by remarkable achievements across all assessed facilities.

Managing Deviating EQA Results: A Survey to Assess the Corrective and Preventive Actions of Medical Laboratories Testing for Oncological Biomarkers

Laboratories testing predictive biomarkers in lung and colorectal cancer are advised to participate in external quality assessment (EQA) schemes. This study aimed to investigate which corrective actions were taken by laboratories if predetermined performance criteria were not met, to ultimately improve current test practices. EQA participants from the European Society of Pathology between 2014 and 2018 for lung and colorectal cancer were contacted, if they had at least one analysis error or test failure in the provided cases, to complete a survey. For 72.4% of 514 deviating EQA results, an appropriate action was performed, most often including staff training (15.2%) and protocol revisions (14.6%). Main assigned persons were the molecular biologist (40.0%) and pathologist (46.5%). A change in test method or the use of complex techniques, such as next-generation sequencing, required more training and the involvement of dedicated personnel to reduce future test failures. The majority of participants adhered to ISO 15189 and implemented suitable actions by designated staff, not limited to accredited laboratories. However, for 27.6% of cases (by 20 laboratories) no corrective action was taken, especially for pre-analytic problems and complex techniques. The surveys were feasible to request information on results follow-up and further recommendations were provided.

The association of imaging equipment age with other quality metrics and successful laboratory accreditation by the Intersocietal Accreditation Commission

BACKGROUND

Intersocietal Accreditation Commission (IAC) accreditation is granted or delayed depending on the fulfillment of several quality metrics. Investing in up-to-date equipment might reflect a commitment to quality.

METHODS

Data from echocardiography (n = 3079) and nuclear cardiology (n = 1835) accreditation applications submitted between 2012 and 2014 were evaluated to determine the mean age of laboratory equipment. Laboratory quality was assessed by the number of missing quality metrics, and a composite quality score was calculated as the sum of missing quality metrics. A lower score thus represented better laboratory quality. The relationship between equipment age and quality was explored as an interaction term between equipment age and the composite quality score and was incorporated into regression models for prediction of accreditation status.

RESULTS

During the study period, 49% of echocardiography and 42% of nuclear laboratories were granted accreditation without delay. For both echocardiography and nuclear laboratories, there was a statistically significant trend toward an increasing number of missing quality metrics with increasing quartiles of equipment age. The interaction between equipment age and the composite quality score was a significant predictor of delay of accreditation for both echocardiography and nuclear cardiology laboratories, with a stronger association for 1st-time applicants. Among sites applying for accreditation in both modalities simultaneously, accreditation in one modality predicted the accreditation decision for the other.

CONCLUSIONS

Laboratory quality is an important determinant of IAC accreditation, and equipment age is an effect modifier of this relationship. Contemporary equipment likely reflects a commitment to quality, for both echocardiography and nuclear laboratories.

Global harmonization of food safety regulations: perspectives from Japan after the Fukushima nuclear accident

Japanese food self-sufficiency was only 39% on the basis of kcal in 2012, so Japan relies heavily on imported food. Hence the necessity of having international rules on the regulation of food contaminants is important especially for countries like Japan that depend on food imports. A One-Stop-Testing system is desired, in which the test result obtained from a single testing laboratory is accepted as valid worldwide. To establish this system, laboratory accreditation under international standards is a necessary step. Furthermore, the importance of supply of reference materials for internal quality control and proficiency testing for external quality control of each laboratory's analytical system is reviewed in connection with the experience of radioactive nuclide contamination resulting from the Fukushima nuclear power plant accident in March 2011.

Middle East food safety perspectives

Food safety and quality assurance are increasingly a major issue with the globalisation of agricultural trade, on the one hand, and intensification of agriculture, on the other. Consumer protection has become a priority in policy-making amongst the large economies of the Middle East and North Africa (MENA) countries following a number of food safety incidents. To enhance food safety, it is necessary to establish markets underpinned by knowledge and resources, including analysis of international rejections of food products from MENA countries, international laboratory accreditation, improved reporting systems and traceability, continued development and validation of analytical methods, and more work on correlating sensory evaluation with analytical results. MENA countries should develop a national strategy for food safety based on a holistic approach that extends from farm-to-fork and involves all the relevant stakeholders. Accordingly, food safety should be a regional programme, raising awareness among policy- and decision-makers of the importance of food safety and quality for consumer protection, food trade and economic development.

MODS accreditation process for regional reference laboratories in Peru: validation by GenoType® MTBDRplus

SETTING

Although considerable effort has been put into the development and evaluation of new diagnostics for tuberculosis (TB) and multidrug-resistant TB (MDR-TB), little attention has thus far been paid to the technical aspects of initiating quality-assured routine service use. For implementation of the microscopic-observation drug susceptibility (MODS) methodology in the Peruvian reference laboratory network, a laboratory accreditation process was devised; MODS results from an expert reference laboratory (Universidad Peruana Cayetano Heredia [UPCH]) were used as the standard against which implementing laboratory MODS results were judged to ensure that, prior to use for patient care, implementing laboratories achieved the same high performance with MODS as previously demonstrated in the research laboratory.

OBJECTIVE

To evaluate the validity of MODS-based accreditation and the concordance of MODS drug susceptibility testing (DST) with molecular testing.

DESIGN

Head-to-head comparison of MODS DST results from implementing Peruvian regional reference laboratories and the accrediting expert MODS laboratory (UPCH) with GenoType® MTBDRplus DST.

RESULTS

The concordance of phenotypic MODS rifampicin (RMP) DST with GenoType MTBDRplus was respectively 97.4%, 97.9% and 97.1% for the two implementing regional laboratories and UPCH, and respectively 94.7%, 95.7% and 94.6% for isoniazid (INH) DST.

CONCLUSION

High and consistent levels of MODS/MTBDRplus concordance for INH and RMP DST confirm the validity of the use of rapid methods as reference standards for accreditation.