Molecular Test Results Research Articles

Characterization of Xanthomonas campestris pv. campestris in Algeria

Xanthomonas campestris pv. campestris (Xcc) causes the black rot of cruciferous plants. This seed-borne bacterium is considered as the most destructive disease to cruciferous crops. Although sources of contamination are various, seeds are the main source of transmission. Typical symptoms of black rot were first observed in 2011 on cabbage and cauliflower fields in the main production areas of Algeria. Leaf samples displaying typical symptoms were collected during 2011 to 2014, and 170 strains were isolated from 45 commercial fields. Xcc isolates were very homogeneous in morphological, physiological and biochemical characteristics similar to reference strains, and gave positive pathogenicity and molecular test results (multiplex PCR with specific primers). This is the first record of Xcc in Algeria. Genetic diversity within the isolates was assessed in comparison with strains isolated elsewhere. A multilocus sequence analysis based on two housekeeping genes (gyrB and rpoD) was carried out on 77 strains representative isolates. The isolates grouped into 20 haplotypes defined with 68 polymorphic sites. The phylogenetic tree obtained showed that Xcc is in two groups, and all Algerian strains clustered in group 1 in three subgroups. No relationships were detected between haplotypes and the origins of the seed lots, the varieties of host cabbage, the years of isolation and agroclimatic regions.

Utility of intraoperative frozen sections of thyroid tissue in the age of molecular testing.

Our study aims to examine the correlation between preoperative ultrasound-guided fine-needle aspiration and intraoperative frozen section and examine the clinical benefit of frozen section in the context of the latest national guidelines on the management of differentiated thyroid cancer. A retrospective review of thyroid frozen section from 2012 to2017 at one institution. Tertiary care centre. Patient demographics, fine-needle aspiration results, molecular testing results, frozen section diagnosis (classified as benign, indeterminate, or malignant), final pathologic diagnosis, initial planned surgery, actual surgery performed, need for additional surgery and complications were recorded. Complications included hematoma formation, hypocalcaemia (requiring readmission, symptomatic, or >24-hour stay post op) and recurrent or superior laryngeal nerve damage. 728 total patients had an intraoperative frozen section performed. A Thy 4/Bethesda V USGFNA diagnosis (n=55) significantly correlated with a clinically important intraoperative frozen section (n=17, P<.01). Intraoperative management was changed by the frozen section 53 times (7.2%). Molecular testing was sent on 92 USGFNA specimens, 80 of which were deemed "suspicious." Of the 49 patients whose management was upstaged intraoperatively, 29 (59%) would not necessitate a completion thyroidectomy under the latest UK and ATA guidelines based on final pathology. Intraoperative frozen sections rarely alter the pre-surgical plan and indeed may result in expanded surgery that could have been avoided based on latest UK and US guidelines. Molecular testing of indeterminate fine-needle aspiration results does not appear to predict meaningful intraoperative frozen section results.

Navigating the Debate on Large (4+cm) Thyroid Nodules: Local Insight on a Persisting Problem

Abstract Background: Thyroid nodules are a common clinical finding, however discordant practice guidelines for managing large nodules may result in unnecessary surgeries and excess costs. Recent data suggest similar false negative rates in fine needle aspiration (FNA) biopsies between small (&amp;lt;4cm) and large (4+ cm) nodules, indicating that monitoring rather than surgery may be appropriate for large nodules. Evaluating current management strategies may reveal insights regarding excess surgeries, costs and opportunities for improvement. Objectives: The goal of this project was to describe the patients at our institution with large thyroid nodules and determine the proportion of potentially unnecessary surgeries and the associated predictors. Methods: This was a retrospective cohort study that included patients who received a FNA of nodule (s) ≥4cm between 11/1/2014 and 10/31/2019 at our tertiary care institution. Patient demographics, sonographic nodule size, fine needle aspiration cytology, molecular testing results, final surgical pathology, history of neck irradiation, family history of thyroid cancer, presence of compressive symptoms or presence of a toxic nodule or toxic multinodular goiter, were compared between patients who had surgery and those who did not. A surgery was considered inappropriate if the FNA result was benign in the absence of any of the following: a suspicious result on molecular testing, compressive symptoms, family history of thyroid cancer in a first degree relative, history of neck irradiation, toxic nodule or toxic multinodular goiter or substernal extension. Continuous variables were evaluated using Wilcoxon rank-sum test while categorical variables were tested using chi-square or Fisher’s exact test. Results: A total of 177 patients had a 4+ cm nodule during the timeframe. Half of patients (54.2%)with 4+ cm nodules had surgery. Patients who underwent surgery were significantly younger (51.5 years vs 62 years; P&amp;lt;0.001), more likely to report obstructive symptoms (34.4% vs 12.1%; P=0.001) and have a larger nodule size (5.0 cm vs 4.7 cm; P=0.26) than patients who did not have surgery. Forty-one patients with benign (Bethesda II) FNA results went on to have surgery. All 41 patients were found to be negative at surgery, yielding a false negative rate of 0.0% in our cohort. Twenty-three surgeries (24.0%) were considered inappropriate and overall 13% (23/177) of patients with 4+cm nodules had unnecessary surgery. The median charge for these surgeries was $13,183. Conclusion: Approximately half of our patients with 4+ cm nodules had surgery, especially patients who are younger, report obstructive symptoms, and have larger nodule sizes. Overall 13% of our patients with 4+cm nodules had unnecessary surgery revealing opportunities for improving care and costs.

Use of BRAF immunohistochemistry as a screening test in detecting BRAFV600E mutation in melanomas.

BRAF mutation is detected in 50-70% of melanomas. The molecular methods used to detect BRAF mutations are 80-90% sensitive, specific, and expensive methods. Immunohistochemistry is a relatively common, rapid, relatively inexpensive method in pathology practice compared to molecular techniques. We aimed to compare immunohistochemical and molecular methods in our case of malign melanoma in which we investigated BRAF mutation with "real time PCR" method and to investigate the compatibility of molecular test results of BRAF immunohistochemistry results as a preliminary test. Selected blocks of 30 patients with metastatic melanoma who came to our department for BRAF mutation detection were subjected to real time PCR molecular method and immunohistochemical study was performed with BRAF primer antibody. BRAF mutation was detected by molecular method in 7 of 30 cases (23.33%). In all of these 7 cases, positive immunohistochemical staining was identified (100%). In conclusion, the use of BRAF immunohistochemistry as a screening test in the detection of mutant disease will allow the cost-effective use of molecular testing.

Further delineation of van den Ende‐Gupta syndrome: Genetic heterogeneity and overlap with congenital heart defects and skeletal malformations syndrome

Van den Ende-Gupta syndrome (VDEGS) is a rare autosomal recessive condition characterized by distinctive facial and skeletal features, and in most affected persons, by biallelic pathogenic variants in SCARF2. We review the type and frequency of the clinical features in 36 reported individuals with features of VDEGS, 15 (42%) of whom had known pathogenic variants in SCARF2, 6 (16%) with negative SCARF2 testing, and 15 (42%) not tested. We also report three new individuals with pathogenic variants in SCARF2 and clinical features of VDEGS. Of the six persons without known pathogenic variants in SCARF2, three remain unsolved despite extensive genetic testing. Three were found to have pathogenic ABL1 variants using whole exome sequencing (WES) or whole genome sequencing (WGS). Their phenotype was consistent with the congenital heart disease and skeletal malformations syndrome (CHDSKM), which has been associated with ABL1 variants. Of the three unsolved cases, two were brothers who underwent WGS and targeted long-range sequencing of both SCARF2 and ABL1, and the third person who underwent WES and RNA sequencing for SCARF2. Because these affected individuals with classical features of VDEGS lacked a detectable pathogenic SCARF2 variant, genetic heterogeneity is likely. Our study shows the importance of performing genetic testing on individuals with the VDEGS "phenotype," either as a targeted gene analysis (SCARF2, ABL1) or WES/WGS. Additionally, individuals with the combination of arachnodactyly and blepharophimosis should undergo echocardiography while awaiting results of molecular testing due to the overlapping physical features of VDEGS and CHDSKM.

Use of Predictive Modeling to Tailor Molecular Testing Utilization for Thyroid Nodules.

Various risk stratification systems for cytologically indeterminate thyroid nodules are available. However, malignancy risk assessment data, such as ultrasound features, are not always used when the decision is to order molecular testing or not. Our aim was to investigate the utility of molecular testing after incorporating an algorithm with ultrasound-based risk of malignancy (ROM) estimation. Diagnostic/prognostic study. Single-institution urban tertiary care center. We performed a single-institution retrospective chart review of all thyroid nodules that had undergone molecular testing. A web-based Malignancy Risk Estimation System for Thyroid Nodules was utilized with ultrasound findings to stratify malignancy risk according to the Korean Thyroid Imaging Reporting and Data System (TI-RADS), French TI-RADS, American Association of Clinical Endocrinology guideline, and American Thyroid Association guideline. A novel algorithm for utilizing molecular testing at our institution was developed with the Korean TI-RADS and with recommendations from the American Thyroid Association and National Comprehensive Cancer Network. The Korean TI-RADS performed best in our population (area under the curve = 0.83). A positive molecular test result had a positive association with a higher ROM according to all 4 models (P < .05). Use of our algorithm prior to molecular testing would have prevented 38% of benign/low-ROM negative nodules (n = 28) from being tested. In patients with indeterminate thyroid nodules, an algorithm built on pre- and posttest probability to guide molecular testing might reduce unnecessary testing of benign and low-risk nodules.

Analysis of FLT3-Activating Mutations in Patients With Acute Myelogenous Leukemia in Jordan: Association With FAB Subtypes and Identification of Subgroups With Poor Prognosis

BackgroundFLT3 mutations are common in acute myeloid leukemia (AML), particularly in French–American–British M2 subtype AML and in cytogenetically normal (CN) AML; however, its incidence in Jordan is poorly studied. An FLT3 mutation implies poor prognosis in AML patients. We aimed to assess the incidence and prognostic value of FLT3 mutations in AML in Jordan. Patients and MethodsOne hundred thirty-two newly diagnosed unselected AML patients were included. Patient data were collected, including demographics as well as morphologic, cytogenetic, and molecular testing results. FLT3 mutations were detected by real-time reverse transcriptase PCR, next-generation sequencing, or both. Survival analysis and comparisons of incidence, remission rate, relapse, and survival outcomes between FLT3-mutated and wild-type groups were done and prognostic factors identified. ResultsFLT3 mutation was detected in 40% of AML patients. The highest incidence was associated with M2 subtype AML (47%) and CN-AML (50%). There was a significant negative association between FLT3 mutations and overall survival (OS), as well as a trend toward improved relapse-free survival, with 3-year OS being 19.17% vs 34.16% (P < .0001) and 33.6% vs 71.0% (P = .085), respectively. Patients with FLT3 mutation had a significantly better complete remission rate after induction (67.9% vs 63.3%, P = .001). Also, OS improved in patients with complete remission (P = .0015) and who then continued to allogeneic hematopoietic cell transplantation compared to FLT3 wild-type patients (P < .001). ConclusionFLT3 mutation is common in Jordanian AML patients, with the highest incidence occurring in patients with M2 or CN disease. It implies a poor prognosis, with poor OS and relapse-free survival, which may be abrogated by early allogeneic transplantation and/or peritransplantation provision of FLT3 inhibitors.

COVID-19 Microbiological and Radiological Diagnostics

The purpose of this paper is to present SARS-CoV-2 diagnostic methods and their optimal implementation. The main routine microbiological diagnostic tools are molecular and serological methods. Sensitivity and utilisation of molecular methods is the best at the disease onset, while serological methods are the best if used at least 5-7 days after disease onset. Positive molecular test result (real-time polymerase chain reaction; RT-PCR) must be interpreted in the clinical presentation context. A sampling site for molecular analysis is based on disease severity; upper and lower respiratory tract samples are used for mild and severe presentations, respectively. Virus cultivation is the only method of proving the existence of a viable virus in a tissue sample, but due to the method complexity, it is not a part of a routine process. Ground glass opacities with or without reticular pattern and/or consolidation are typical findings for COVID-19 pneumonia. Multi-slice computerized tomography (MSCT) is a superior radiological method for performing X-ray of the chests.

Salivary SARS-CoV-2 antigen rapid detection: A prospective cohort study

Background and aimSARS-CoV-2 quick testing is relevant for the containment of new pandemic waves. Antigen testing in self-collected saliva might be useful. We compared salivary and naso-pharyngeal swab (NPS) SARS-CoV-2 antigen detection by a rapid chemiluminescent assay (CLEIA) and two different point-of-care (POC) immunochromatographic assays, with results of molecular testing. Methods234 patients were prospectively enrolled. Paired self-collected saliva (Salivette) and NPS were obtained to perform rRT-PCR, chemiluminescent (Lumipulse G) and POC (NPS: Fujirebio and Abbott; saliva: Fujirebio) for SARS-CoV-2 antigen detection. ResultsThe overall agreement between NPS and saliva rRT-PCR was 78.7%, reaching 91.7% at the first week from symptoms. SARS-CoV-2 CLEIA antigen was highly accurate in distinguishing positive and negative NPS (ROC-AUC = 0.939, 95%CI:0.903–0.977), with 81.6% sensitivity and 93.8% specificity. This assay on saliva reached the optimal value within 7 days from symptoms onset (Sensitivity: 72%; Specificity: 97%). Saliva POC antigen was limited in sensitivity (13%), performing better in NPS (Sensitivity: 48% and 66%; Specificity: 100% and 99% for Espline and Abbott respectively), depending on viral loads. ConclusionsSelf-collected saliva is a valid alternative to NPS for SARS-CoV-2 detection by molecular, but also by CLEIA antigen testing, which is therefore potentially useful for large scale screening.

Pathologists at the Leading Edge of Optimizing the Tumor Tissue Journey for Diagnostic Accuracy and Molecular Testing.

ObjectivesTumor biomarker analyses accompanying immuno-oncology therapies are coupled with a tumor tissue journey aiming to guide tissue procurement and allow for accurate diagnosis and delivery of test results. The engagement of pathologists in the tumor tissue journey is essential because they are able to link the preanalytic requirements of this process with pathologic evaluation and clinical information, ultimately influencing treatment decisions for patients with cancer. The aim of this review is to provide suggestions on how cancer diagnosis and the delivery of molecular test results may be optimized, based on the needs and available resources of institutions, by placing the tumor tissue journey under the leadership of pathologists.MethodsLiterature searches on PubMed and personal experience provided the necessary material to satisfy the objectives of this review.ResultsPathologists are usually involved across many steps of the tumor tissue journey and have the requisite knowledge to ensure its efficiency.ConclusionsThe expansion of oncology diagnostic testing emphasizes the need for pathologists to acquire a leadership role in the multidisciplinary effort to optimize the accuracy, completeness, and delivery of diagnoses guiding personalized treatments.

Molecular Characterization and Therapeutic Targeting of Colorectal Cancers Harboring Receptor Tyrosine Kinase Fusions.

Receptor tyrosine kinase fusions in colorectal cancers are rare, but potentially therapeutically relevant. We describe clinical, molecular, and pathologic attributes of RTK fusion-associated colorectal cancer. We identified all cases with RTK fusions in patients with colorectal cancer seen at Dana-Farber Cancer Institute (Boston, MA) who underwent OncoPanel testing between 2013 and 2018. Clinical, histologic, and molecular features were extracted from the patient charts and molecular testing results. We identified 12 driver oncogenic fusions in various RTKs. These fusions occurred exclusively in BRAF and RAS wild-type tumors and were enriched in right-sided and mismatch repair-deficient (MMR-D) colorectal cancers. All of the MMR-D colorectal cancers with RTK fusions were found in tumors with acquired MMR-D due to MLH1 promoter hypermethylation and one was associated with a sessile serrated polyp. Molecular profiles of MMR-D colorectal cancer with RTK fusions largely resembled BRAF V600E-mutated MMR-D colorectal cancer, rather than those secondary to Lynch syndrome. We describe two patients with fusion-associated microsatellite stable (MSS) colorectal cancer who derived clinical benefit from therapeutic targeting of their translocation. The first harbored an ALK-CAD fusion and received sequential crizotinib and alectinib therapy for a total of 7.5 months until developing an ALK L1196Q gatekeeper mutation. The second patient, whose tumor contained an ROS1-GOPC fusion, continues to benefit from entrectinib after 9 months of therapy. RTK fusions in colorectal cancer are a rare, but important disease subgroup that occurs in RAS and BRAF wild-type tumors. Despite enrichment in acquired MMR-D tumors, RTK fusions also occur in MSS colorectal cancer and provide an important therapeutic target.

Genomics-based precision medicine in hematology/oncology

Precision medicine refers to a medical model wherein treatments are customized for the patients according to their lifestyles, genetic background, and other molecular and physiological test results. Herein, I discuss the utility of comprehensive genomic profiling of hematologic malignancies and provide a perspective on the future of genomics-based precision medicine in the field of hematology/oncology.

Bloodstream infections – etiology and current microbiological diagnostics

Introduction: Bloodstream infections (BSI) and sepsis constitute an important clinical problem worldwide, with a high mortality rate. A fast and reliable determination of BSI etiology is necessary for administration of targeted antibiotic therapy and improvement in survival rates of patients with BSI. Aim: To present the possibilities for optimal laboratory diagnostics of BSI, in the aspect of epidemiology, available research methods and current diagnostic recommendations. Material and methods: A review of literature concerning recommendations in diagnosis and peer-reviewed publications using the following keywords ‘bloodstream infection,’ ‘bacteremia,’ ‘epidemiology,’ and ‘diagnostics.’ Results and discussion: Etiology of BSI depends on several factors, such as origin of microorganisms, the location of the primary source of infection, immunocompetence of the host, and possible contact of the patient with the healthcare. Blood culture has status of the ‘gold standard,’ which inables susceptibility testing of the isolated pathogen. Non-culture methods based on detection of microbial genetic material or proteins are increasingly used in laboratory diagnostics of BSI. They constitute the methods of choice in detection of uncultivable or difficult to culture microorganisms. New diagnostic solutions are urgently needed for rapid detection of multidrug-resistant strains of microorganisms. Conclusions: Blood culture remains the reference method in laboratory diagnostics of BSI, while molecular techniques available at present are a valuable addition to it. However, the clinical relevance of the results of molecular tests which do not correlate with clinical symptoms needs to be solved.

1534. Gonorrhea Testing and Ceftriaxone Resistance in the Department of Veterans Affairs (VA), 2010-2019

BackgroundGonorrhea (GC) infections caused by Neisseria gonorrhoeae are an ongoing public health issue and have shown resistance to nearly all antibiotic classes, including cephalosporins which are a CDC recommended treatment. We investigated national GC testing and Ceftriaxone resistance in VA.MethodsGC cases identified from VA data sources from 1/1/2010-12/15/2019 by either molecular laboratory testing or GC culture with sensitivity testing. Patients were reviewed for positive results, whether culture testing was performed after 2 positive molecular GC results in < 90 days, and sensitivity patterns.Results10,642 of 644,968 (2%) GC molecular results were positive with annual number of positive cases (1,365 to 3,225), number of tests performed (97,636 to 164,085) and percent positive for GC (1.4% to 2%) increasing over the time period studied. 2,358/10,642 (22%) of positive molecular test results had repeat testing < 3mo with 351 (15%) positive on repeat testing which is concerning for possible resistance. 2,624 GC cultures were performed with 2,179 (83%) positive. 1,480/2,179 (68%) positive GC culture tests had some sensitivity testing performed. Culture testing remained stable with 287 in 2010 to 289 in 2019 with percent positive ranging from 78-89%. Of the 351 patients with repeat positive GC molecular testing done < 3mo from their positive molecular test, only 18 (5%) had GC culture testing performed proximal to the second positive test. Among all cultured isolates, resistance to Ceftriaxone was noted in 1 sample in 2017 in Missouri (also intermediate resistance to Tetracycline) and 1 in 2019 in New Jersey (also resistant to Penicillin, Tetracycline, and Ciprofloxacin).ConclusionIn VA, GC infections have increased from 2010 to 2019 and GC culture testing has remained stable despite increasing molecular testing. Only 2 samples were identified with Ceftriaxone resistance. However, the low percentage of GC culture testing after persistent positive molecular testing in VA could mask treatment failures and possible resistance. Culture testing with sensitivity testing should be increased in VA in cases where patients may have resistance to initial treatments (i.e., – repeat positive testing less than 3 months after a positive test).Disclosures All Authors: No reported disclosures

Outcomes of Indeterminate Thyroid Nodules Managed Nonoperatively after Molecular Testing.

Molecular testing to refine the diagnosis of cytologically indeterminate thyroid nodules has become increasingly popular, but data on long-term durability of test results and the rate of delayed operation are limited. Determine the delayed rate of surgical resection in indeterminate nodules with benign/negative molecular testing and the risk of false-negative molecular test results. Prospective follow-up of the Gene Expression Classifier vs Targeted Next-Generation Sequencing in the Management of Indeterminate Thyroid Nodules randomized controlled trial comparing the diagnostic test performance of Afirma Gene Expression Classifier and ThyroSeq v2. University of California, Los Angeles. Patients who underwent thyroid biopsy with indeterminate (Bethesda III/IV) cytology (April 2016 to July 2017). Ultrasound surveillance. False-negative rate of molecular testing. Of 95 indeterminate nodules with negative/benign molecular test results, 12 nodules underwent immediate resection (11 benign nodules, 1 noninvasive follicular thyroid neoplasm nodule with papillary-like nuclear features). Nonoperative management was pursued for 83 (87.4%) nodules. The median surveillance was 26.7 months. Ten nodules were resected during surveillance and malignancy was identified in 4 nodules (overall false-negative rate of 5.8%). In the 4 malignant nodules that underwent delayed operation, surgery was prompted by sonographic changes during surveillance. The majority of indeterminate nodules with negative molecular testing have a stable clinical course over 3 years of follow-up, but our finding of a 6% false-negative rate highlights the importance of continuing sonographic surveillance. Long-term studies are needed to determine the optimal length of follow-up.

The frequency of point mutations associated with resistance to isoniazid and rifampin among clinical isolates of multidrug-resistant Mycobacterium tuberculosis in the west of Iran

Global increasing broad-spectrum resistance to many antibiotics established Tuberculosis (TB) infections as worldwide health issue. The rising prevalence of multidrug-resistant (MDR) Mycobacterium tuberculosis (MTB) isolates around the world is a therapeutic challenge. Monitoring of resistance to anti-TB drugs is essential to implement the strategies to control tuberculosis.This study was aimed to identify the point mutations associated with resistance to isoniazid (INH) and rifampin (RIF) antibiotics by Polymerase chain reaction (PCR) and reverse hybridization methods in clinical isolated samples of MDR Mycobacterium tuberculosis in the west of Iran.Phenotypic and biochemical methods were used for the identification of TB strains. Then proportion and GeneXpert methods were used to determine resistance isolates. The DNA was extracted, and finally, PCR and reverse hybridization methods were performed to identify the mutations.Among 54 isolates of MTB, 22 isolates were INH and RIF susceptible, and 32 isolates were diagnosed as MDR isolates. Of 32 MDR isolates, 22 cases (%70) had a mutation in katG codon of 315, 1 case inhA (%3) and 9 (%28) isolated had no detectable mutation. About rifampin, the mutations associated with rpoB gene in codons 531, 516 and 626 comprised (n = 21, %66), (n = 7, %22) and (n = 1, %3) respectively and in 3 (%9) isolates no mutations were found. The sensitivity, specificity and accuracy for INH (%71, %100, %83) and rifampin (%91, %100, %94) obtained, also PPV and NPV were determined for INH (%100, %70), RIF (%100, %88) respectively.Our results showed that MDR isolates with mutations in the katG 315 and rpoB 531 regions are epidemic strains in our study area. Also, our results suggest that TB Resistance line probe assay (AID) method has high sensitivity for detection of point mutations among isoniazid- and rifampin- resistant TB isolates. However, gold-standard phenotypic methods must always confirm the molecular drug susceptibility test results.

The combination of left ventricular non-compaction and hypertrophic cardiomyopathy in one family with a pathogenic variant in the MYBPC3 gene (rs397516037)

The article presents the results of clinical, instrumental and molecular genetic tests of three generations of a family with inherited cardiomyopathy caused by a new variant in the MYBPC3 gene. A specific feature of this case is the phenotypic heterogeneity of the mutation — a combination of hypertrophic cardiomyopathy and left ventricular non-compaction in family members. Attention is drawn to the various severity of clinical manifestations in relatives of carriers of mutation: from asymptomatic to severe heart failure and acute cerebrovascular accident.

Accuracy of endoscopic ultrasound-guided needle aspiration specimens for molecular diagnosis of non-small-cell lung carcinoma.

BACKGROUNDEndoscopic ultrasonography-guided fine-needle aspiration (EUS-FNA) and endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) are highly sensitive for diagnosing and staging lung cancer. In recent years, targeted therapy has shown great significance in the treatment of non-small cell lung carcinoma (NSCLC). Using these minimally invasive techniques to obtain specimens for molecular testing will provide patients with a more convenient diagnostic approach.AIMTo evaluate the feasibility and accuracy of tissue samples obtained using EUS-FNA and EBUS-TBNA for molecular diagnosis of NSCLC.METHODSA total of 83 patients with NSCLC underwent molecular testing using tissues obtained from EUS-FNA or EBUS-TBNA at the Tianjin Medical University Cancer Hospital from January 2017 to June 2019. All enrolled patients underwent chest computed tomography or positron emission tomography/computed tomography prior to puncture. We detected abnormal expression of EGFR, KRAS, MET, HER2, ROS1 and anaplastic lymphoma kinase protein. Two patients failed to complete molecular testing due to insufficient tumor tissue. The clinical features, puncture records, molecular testing results and targeted treatment in the remaining 81 patients were summarized.RESULTSIn a total of 99 tissue samples obtained from 83 patients, molecular testing was successfully completed in 93 samples with a sample adequacy ratio of 93.9% (93/99). Biopsy samples from two patients failed to provide test results due to insufficient tumor tissue. In the remaining 81 patients, 62 cases (76.5%) were found to have adenocarcinoma, 11 cases (13.6%) had squamous cell carcinoma, 3 cases (3.7%) had adenosquamous carcinoma and 5 cases (6.2%) had NSCLC-not otherwise specified. The results of molecular testing showed EGFR mutations in 21 cases (25.9%), KRAS mutations in 9 cases (11.1%), ROS-1 rearrangement in 1 case (1.2%) and anaplastic lymphoma kinase-positive in 5 cases (6.2%). Twenty-four patients with positive results received targeted therapy. The total effectiveness rate of targeted therapy was 66.7% (16/24), and the disease control rate was 83.3% (20/24).CONCLUSIONTissue samples obtained by EUS-FNA or EBUS-TBNA are feasible for the molecular diagnosis of NSCLC and can provide reliable evidence for clinical diagnosis and treatment.

Spatial variability of SARS-CoV-2 infection in the Silesian voivodeship, Poland.

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) and related to infection COVID-19 (coronavirus disease 2019) remain a new and global challenge for public health. Due to the location, specifics of employment, and the high density of population in the Silesia voivodeship it is appropriate to study the available epidemiological data in a region with a potentially higher risk of infection. In the descriptive model of the study, data on the number of infected, hospitalized, and dead people due to SARS-CoV-2 infection were analyzed. The source of information was daily reports conducted by the Provincial Sanitary and Epidemiological Station in Katowice, in the period from March 5 to August 18, 2020. Results of antigenic molecular tests for SARS-CoV-2 infection in the Silesian voivodeship indicate that in the first half of 2020, the infection rate was approximately 5% and the symptomatic form of the disease was approximately 20%. The analysis of the frequency of infection and mortality in the poviats reveals a large variation in the occurrence of both phenomena, but the explanation of this difference is not possible due to the descriptive nature of the analysis and the secondary form of epidemiological data.

Assessment of early mitigation measures against COVID-19 in Puerto Rico: March 15-May 15, 2020.

On March 15, 2020 Puerto Rico implemented non-pharmaceutical interventions (NPIs), including a mandatory curfew, as part of a state of emergency declaration to prevent the community transmission of the SARS-CoV-2 virus. The strict enforcement of this curfew was extended through May 25, with a gradual relaxation beginning on May 1. This report summarizes an assessment of these early mitigation measures on the progression of the COVID-19 pandemic in the island. From March 15 to May 15, 2020, 70,656 results of molecular (RT-PCR) tests were reported to the Puerto Rico Department of Health. Of these, 1,704 were positive, corresponding to 1,311 individuals with COVID-19 included in the study. We derived the epidemic growth rates (r) and the corresponding reproductive numbers (R) from the epidemic curve of these 1,311 individuals with laboratory-confirmed diagnosis of COVID-19 using their date of test collection as a proxy for symptoms onset. Through May 31, 2020, there were 143 COVID-19 associated deaths in Puerto Rico, for a case fatality risk of 10.9%. We compared the observed cases and deaths with Gompertz model projections had the mitigation measures not been implemented. The number of daily RT-PCR-confirmed cases peaked on March 30 (85 cases), showing a weekly cyclical trend, with lower counts on weekends and a decreasing secular trend since March 30. The initial exponential growth rate (r) was 15.87% (95% CI: 7.59%, 24.15%), corresponding to R of 1.82 (95% CI:1.37, 2.30). After March 30, the r value reverted to an exponential decay rate (negative) of -2.95% (95% CI: -4.99%, -0.92%), corresponding to R of 0.93 (95% CI: 0.86, 0.98). We estimate that, had the initial growth rate been maintained, a total of 6,155 additional COVID-19 cases would have occurred by May 15, with 211 additional COVID-19 deaths by May 31. These findings are consistent with very effective implementation of early NPIs as mitigation measures in Puerto Rico. These results also provide a baseline to assess the impact of the transition from mitigation to subsequent containment stages in Puerto Rico.