Longitudinal analysis of 20 Years of external quality assurance schemes for PCR/NAAT-based bacterial genome detection in diagnostic testing

Background

Quality control (QC), quality assurance, and standardization are crucial for modern diagnostic testing in the field of medical microbiology. The need for efficient QC to ensure accurate laboratory results, treatment, and infection prevention has led to significant efforts in standardizing assay reagents and workflows. External quality assessment (EQA) schemes, like those offered by INSTAND, play a vital role in evaluating in-house and commercial routine diagnostic assays, regarded as mandatory by national and global guidelines. The recent impact of polymerase chain reaction/nucleic acid amplification technology (PCR/NAAT) assays in medical microbiology requires that high-performing assays be distinguished from inadequately performing ones, especially those made by inexperienced suppliers.

Objectives

The study assesses the evolving diagnostic performance trends over 2 decades for the detection of EHEC/STEC, Borrelia (B.) burgdorferi, and MRSA/cMRSA. It explores the historical context of assay utilization, participant engagement, and rates of correct results in EQA schemes. The research seeks to identify patterns in assay preferences, participant proficiency, and the challenges encountered in detecting emerging variants or clinical strains.

Results

The study highlights the decline in in-house PCR assay usage, the emergence of new diagnostic challenges, and educational aspects within EQA schemes. Specific examples, such as the inclusion, in certain EQA surveys, of EHEC strains carrying stx-2f or B. miyamotoi, highlight the role of EQAs in increasing awareness and diagnostic capabilities. Advancements in MRSA detection, especially through the adoption of commercial assays, demonstrate the impact that technology evolution has had on diagnostic performance.

Conclusion

Achieving excellence in diagnostic molecular microbiology involves a multifaceted approach, including well-evaluated assays, careful instrumentation selection, and structured training programs. EQA schemes contribute significantly to this pursuit by providing insights into the evolving diagnostic landscape and identifying areas for improvement in the diagnostic workflow as well as in PCR/NAAT assay design.

Progress toward Health System Readiness for Genome-Based Testing in Canada

(1) Background: Genomic medicine harbors the real potential to improve the health and healthcare journey of patients, care provider experiences, and improve the health system efficiency-even reducing healthcare costs. There is expected to be an exponential growth in medically necessary new genome-based tests and test approaches in the coming years. Testing can also create scientific research and commercial opportunities beyond healthcare decision making. The purpose of this research is to generate a better understanding of Canada's state of readiness for genomic medicine, and to provide some insights for other healthcare systems. (2) Methods: A mixed-methods approach of a review of the literature and key informant interviews with a purposive sample of experts was used. The health system readiness was assessed using a previously published set of conditions. (3) Results: Canada has created some of the established conditions, but further action needs to be taken to improve the state of readiness for genome-based medicine. The important gaps to be filled are the need for linked information systems and data integration; evaluative processes that are timely and transparent; navigational tools for care providers; dedicated funding to facilitate rapid onboarding and support test development and proficiency testing; and broader engagement with innovation stakeholders beyond care providers and patients. These findings highlight the role of the organizational context, social influence, and other factors that are known to affect the diffusion of innovation within health systems.

Full cost of diagnostic pathology for lung carcinoma in Italy: results from four Pathology Units

Objective

To calculate the full cost of diagnostic pathology tests for Non-Small Cell Lung Cancer (NSCLC) across four Italian Pathology Units.

Methods

Pathology Units were located in private (2) and public (2) hospitals distributed across the Italian territory (North: 2; Centre: 1; South: 1). Pathologists provided via questionnaire data on tests on NSCLC samples along with the identification and quantification of the necessary healthcare resources (diagnostic technologies, laboratory instruments and personnel). Resources were valued according to hospital-specific unit, yearly and hourly costs (disposables; technologies; professional clusters).

Results

The full cost per NSCLC tissue sample included histopathological immunophenotypic and required molecular analysis. Overall, it reached € 659.77 and it was mainly composed of direct costs (77.69%). The processing of a NSCLC tissue sample was labour intensive, as a relevant share of the full cost (44.98%) was actually due to personnel costs, with laboratory technicians, biologists and pathologist driving this finding (17.09%,12.43% and 10.81%, respectively).

Conclusions

The results of this research can facilitate the negotiation of new dedicated tariffs for NSCLC sample processing with the national or local third party-payers.

Favorable Conditions for the Detection of EGFR T790M Mutation Using Plasma Sample in Patients with Non-Small-Cell Lung Cancer

BACKGROUND

Detection of the epidermal growth factor receptor (EGFR) T790M mutation using plasma samples has been considered simple and non-invasive, but the relatively high false negative results lead to additional tissue sampling in some patients. Until now, the characteristics of patients who prefer liquid biopsy have not yet been established.

METHODS

To evaluate the favorable conditions for the detection of T790M mutations using plasma samples, a multicenter retrospective study was performed between May 2018 and December 2021. Patients whose T790M mutation was detected in a plasma sample were classified as the plasma positive group. Study subjects with a T790M mutation not detected in a plasma sample but only in a tissue sample were grouped as the plasma false negative group.

RESULTS

Plasma positive and plasma false negative groups were found in 74 and 32 patients, respectively. As a result, 40% of patients with one or two metastatic organs at the time of re-biopsy had false negative plasma sample results, and 69% of patients with three or more metastatic organs at the time of re-biopsy had positive plasma results. In multivariate analysis, three or more metastatic organs at initial diagnosis were independently associated with the detection of a T790M mutation using plasma samples.

CONCLUSION

Our results demonstrated that the detection rate of a T790M mutation using plasma samples was related to the tumor burden, particularly to the number of metastatic organs.

Effective and Efficient Delivery of Genome-Based Testing-What Conditions Are Necessary for Health System Readiness?

Health systems internationally must prepare for a future of genetic/genomic testing to inform healthcare decision-making while creating research opportunities. High functioning testing services will require additional considerations and health system conditions beyond traditional diagnostic testing. Based on a literature review of good practices, key informant interviews, and expert discussion, this article attempts to synthesize what conditions are necessary, and what good practice may look like. It is intended to aid policymakers and others designing future systems of genome-based care and care prevention. These conditions include creating communities of practice and healthcare system networks; resource planning; across-region informatics; having a clear entry/exit point for innovation; evaluative function(s); concentrated or coordinated service models; mechanisms for awareness and care navigation; integrating innovation and healthcare delivery functions; and revisiting approaches to financing, education and training, regulation, and data privacy and security. The list of conditions we propose was developed with an emphasis on describing conditions that would be applicable to any healthcare system, regardless of capacity, organizational structure, financing, population characteristics, standardization of care processes, or underlying culture.

Routine next generation sequencing of lymphoid malignancies: clinical utility and challenges from a 3-Year practical experience

Since 2016, a next-generation sequencing (NGS) panel targeting 68 genes frequently mutated in lymphoid malignancies is an accredited part of routine diagnostics at the Institute of Pathology in Basel, Switzerland. Here, we retrospectively evaluate the feasibility and utility of integrating this NGS platform into routine practice on 80 diagnostic cases of lymphoid proliferations. NGS analysis was useful in most instances, yielding a diagnostically, predictively and/or prognostically meaningful result. In 35 out of the 50 cases, in which conventional histopathological evaluation remained indecisive, molecular subtyping with the NGS panel was helpful to either confirm or support the favored diagnosis, enable a differential diagnosis, or seriously question a suspected diagnosis. A total of 61 actionable or potentially actionable mutations in 34 out of 80 cases that might have enabled patient selection for targeted therapies was detected. NGS panel analysis had implications for prognosis in all 15 cases interrogated for risk assessment.

Invasive breast cancer: Current perspectives and emerging views

Invasive breast cancer constitutes a heterogeneous group of tumors. They comprise various histological types that differ in clinical presentation, imaging features, histopathological characteristics, biomarker profiles, prognostic and predictive parameters. The current classification of invasive breast cancer is based primarily on histopathological features. Invasive carcinoma of no special type accounts for the majority, with some rare entities also being described. With recent research and advances, there are emerging concepts, including new genetic insights of invasive breast cancer and the role of the stromal microenvironment. With greater understanding of the pathogenesis of invasive breast cancer, changes based on the correlation of histologic and genetic findings have been incorporated in the latest World Health Organization classification of breast tumors. Medullary carcinomas are subsumed as invasive carcinoma of no special type with basal-like and medullary features, regarded as part of the spectrum of tumor infiltrating lymphocyte-rich breast cancers. Tall cell carcinoma with reversed polarity is proposed as a distinct entity in recognition of unique IDH2 mutations. This article reviews conventional prognostic parameters, new histological entities, and updates on breast cancer classification, with inclusion of some genetic insights into breast cancer and the role of tumor infiltrating lymphocytes.

Histomorphological and molecular profiling: friends not foes! Morpho-molecular analysis reveals agreement between histological and molecular profiling

AIMS

Whereas current cancer diagnosis largely relies on the well-established organ and tissue typing of tumours, partially complemented by molecular properties, the comprehensive molecular profiling efforts of recent years have stimulated proposals for molecular reclassifications of tumours independently of anatomical origin. Proposals based only on mutational profiles show the least concordance with histotypes, whereas greater concordance is achieved when various genomic and proteomic data are included.

METHODS AND RESULTS

The most comprehensive molecular reclassification of tumours, by Hoadley et  al (Cell, 158, 2014; 929) and Hoadley et  al (Cell, 173, 2018; 291), integrated multi-omics data, and proposes novel molecular tumour classes. To investigate the relationship between the proposed molecular classes and the original histological tumour types, we re-examined the histomorphology of molecularly reclassified cases. Our results show that the claimed molecular reclassification is associated with and explainable by specific histological subtypes in 70% of the reclassified cases.

CONCLUSION

Therefore, in contrast to the proclaimed reclassification and independence of molecular and histological tumour types, our analysis demonstrates that comprehensive molecular profiling, which includes gene expression and methylation as well as proteomic profiling in addition to mutational analyses, is largely consistent with histomorphological tumour properties.

Understanding the pathophysiology behind chairside diagnostics and genetic testing for IL-1 and IL-6

In order for chairside diagnostic testing to make an impact on dental therapy, practitioners require a better understanding of genetic mutations contributing to the pathophysiology of periodontal disease. Commensal and pathogenic bacterial colonization in oral cavity tissues produces a cascade of proinflammatory signaling pathways ultimately detrimental to host tissues. Resolving inflammation is a multifactorial process involving the downregulation of proinflammatory cytokines while allowing commensal bacterial levels to return to normal. Because of the complicated nature of commensal bacteria and oral health homeostasis, the emphasis of dental therapy should place renewed focus on limiting destructive inflammation rather than solely eliminating bacteria. Salivary diagnostics are an easy, non-invasive way to assess inflammatory markers. Inflammatory cytokine levels can help determine the subclinical health of a patient, showing the transition from health to gingivitis, or periodontitis, prior to clinical presentation. Single nucleotide polymorphism mutations can aid in determining increased risk of developing periodontitis. Taken together, and alongside regular clinical evaluations, chairside diagnostics help individualize treatment plans to slow, or halt, the progression of disease-before tissue destruction can take place. While more studies are needed analyzing specific mutations across periodontal categories, chairside diagnostics present an exciting adjunct to improve patient care.

Lymphoproliferative Tumors of the Ocular Adnexa

The ocular adnexa include the eyelids, conjunctiva, lacrimal apparatus, and orbital soft tissue. One percent of all lymphomas and approximately 8% of all extranodal lymphomas arise in the ocular adnexa and their incidence is increasing. Reactive lymphoid hyperplasia comprises 16% of all lymphoproliferative tumors of the ocular adnexa. The relative frequencies of ocular adnexal lymphoma presentation are in the orbit, 37%; conjunctiva, 29%; lacrimal apparatus, 20%; and eyelid, 14%. The most frequent primary lymphoma types of the ocular adnexa are extranodal marginal zone lymphoma, 62%; follicular lymphoma, 17%; and diffuse large B-cell lymphoma, 10%. The eyelids show the highest proportion of secondary lymphoma involvement, 49% of all eyelid lymphoproliferative lesions, compared with 24% in all ocular adnexa. The specific aspects of the site, histologic, immunohistochemical, cytogenetic, and molecular findings of the most relevant lymphoma types occurring in the various parts of the ocular adnexa will be discussed in relation to clinical parameters and relevance for therapy choice. Furthermore, the implications of the updated version of the World Health Organization Classification of Tumours of Haematopoietic and Lymphoid Tissues in relation to ocular adnexal lymphoma are reviewed.

Abdominal monophasic synovial sarcoma is a morphological and immunohistochemical mimic of gastrointestinal stromal tumour

AIMS

Synovial sarcomas may arise within retroperitoneal or pelvic tissues or, more rarely, within the luminal gastrointestinal tract. This case series aims to demonstrate how such primary abdominal synovial sarcomas may particularly mimic gastrointestinal stromal tumour (GIST) on both morphological and immunohistochemical grounds.

METHODS AND RESULTS

Four cases of primary abdominal synovial sarcoma were reviewed morphologically and with immunohistochemistry, fluorescence in-situ hybridization with an SS18 break-apart probe, and KIT/PDGFRA mutation analysis. The four patients comprised two males and two females, with a median age of 42 years (range: 17-59 years). Two synovial sarcomas arose within the stomach, one within the small-intestine mesentery, and the fourth within the retroperitoneum. All four tumours showed only a monophasic spindle cell component in the tissues available for review. All four tumours showed DOG1 immunopositivity, and three coexpressed CD117. Three tested cases did not show activating KIT or PDGFRA mutations, whereas all four cases showed chromosomal rearrangement of SS18.

CONCLUSIONS

A diagnosis of synovial sarcoma should be considered particularly if an abdominal spindle cell neoplasm shows a haemangiopericytomatous pattern and diffuse CD99 and CD56 immunopositivity. A confident distinction between abdominal synovial sarcoma and GIST requires KIT/PDGFRA mutation analyses and specific molecular testing for synovial sarcoma.

Practicing pathology in the era of big data and personalized medicine

The traditional task of the pathologist is to assist physicians in making the correct diagnosis of diseases at the earliest possible stage to effectuate the optimal treatment strategy for each individual patient. In this respect surgical pathology (the traditional tissue diagnosis) is but a tool. It is not, of itself, the purpose of pathology practice; and change is in the air. This January 2014 issue of Applied Immunohistochemistry and Molecular Morphology (AIMM) embraces that change by the incorporation of the agenda and content of the journal Diagnostic Molecular Morphology (DMP). Over a decade ago AIMM introduced and promoted the concept of "molecular morphology," and has sought to publish molecular studies that correlate with the morphologic features that continue to define cancer and many diseases. That intent is now reinforced and extended by the merger with DMP, as a logical and timely response to the growing impact of a wide range of genetic and molecular technologies that are beginning to reshape the way in which pathology is practiced. The use of molecular and genomic techniques already demonstrates clear value in the diagnosis of disease, with treatment tailored specifically to individual patients. Personalized medicine is the future, and personalized medicine demands personalized pathology. The need for integration of the flood of new molecular data, with surgical pathology, digital pathology, and the full range of pathology data in the electronic medical record has never been greater. This review describes the possible impact of these pressures upon the discipline of pathology, and examines possible outcomes. There is a sense of excitement and adventure. Active adaption and innovation are required. The new AIMM, incorporating DMP, seeks to position itself for a central role in this process.