Commercial Laboratory Research Articles

Fungal keratitis culture results from a major commercial laboratory

Fungal keratitis culture results from a major commercial laboratory

Microplastic Volatile Organic Compounds Found within Chrysaora chesapeakei in the Patuxent River, Maryland

Microplastics are tangible particles of less than 0.2 inches in diameter that are ubiquitously distributed in the biosphere and accumulate in water bodies. During the east-coast hot summers (23–29 °C) of 2021 and 2022, June through September, we captured copious amounts of the jellyfish Chrysaora chesapeakei, a predominant species found in the Patuxent River of the Chesapeake Bay in Maryland on the United States East Coast. We determined that their gelatinous bodies trapped many microplastics through fluorescent microscopy studies using Rhodamine B staining and Raman Spectroscopy. The chemical nature of the microplastics was detected using gas chromatography–mass spectroscopy headspace (SPME-GC-MS) and solvent extraction (GC-MS) methods through a professional commercial materials evaluation laboratory. Numerous plastic-affiliated volatile organic compounds (VOCs) from diverse chemical origins and their functional groups (alkanes, alkenes, acids, aldehydes, ketones, ethers, esters, and alcohols) along with other non-microplastic volatile organic compounds were observed. Our findings corroborate data in the available scientific literature, distinguishing our finding’s suitability.

Abstract PO4-08-09: Concordance analysis of paired breast cancer core needle biopsies and surgical excision samples using the Oncotype DX Breast Recurrence Score® assay

Abstract INTRODUCTION: The Oncotype DX Breast Recurrence Score® (RS) assay is validated to predict risk of distant recurrence at 10 years and the benefit of adjuvant chemotherapy in patients with estrogen receptor (ER)+, HER2- early breast cancer who receive 5 years of endocrine therapy. The feasibility of Oncotype DX® testing with diagnostic core needle biopsies (CNB) was demonstrated through analysis of a large commercial laboratory experience. The neoadjuvant ADAPT study showed the clinical utility of deriving the Recurrence Score® (RS) result from CNB as well. However, data are limited on concordance of RS results from paired CNB and surgical samples. Our primary objective was to determine the degree of concordance of RS results between paired tissue samples from the same primary breast tumor of patients with early stage, ER+, HER2- invasive breast cancer who had a CNB and subsequent surgical excision (SE; lumpectomy or mastectomy) without intervening systemic therapy. METHODS: Patients with a commercial RS result on either CNB or subsequent SE were identified through medical record and clinical database review. A pathologist reviewed archival tissue samples to confirm eligibility and selected the other paired CNB or SE block most representative of the tumor tissue for subsequent study Oncotype DX testing. Descriptive statistics were used to summarize patient and tumor characteristics. Wilcoxon signed rank, McNemar’s and Cochran-Mantel-Haenszel tests were used to compare RS between SE and CNB paired samples. Cohen’s Kappa and 95% confidence intervals (CIs) were used to compare the agreement of categorical RS (0-25 and 26-100) result between SE and CNB paired samples. Lin’s concordance correlation and 95% CIs were used to compare agreement of continuous RS between paired samples. RESULTS: A total of 134 patients were identified with paired CNB and SE samples with a median time of 34 (range 5-103) days between collections. Of the 134 patients, a commercial RS result was available for 25 (18.7%) with CNB and 109 (81.3%) with SE. A study RS result was then generated on the other paired sample. Median age was 62 years (range 33-99; 23 patients [17%] were age ≤50 vs. 111 [83%] age >50). Cases were predominantly node negative (107/134 node negative vs. 26/134 node positive; 1/134 unknown) invasive ductal carcinomas (104/134 ductal vs. 18/134 classic lobular vs. 12/134 other). Mean RS results were 15.6 (range 0-56) and 16.6 (range 0-59) for CNB and SE, respectively (p = 0.003), with no statistically significant differences in RS category defined as low vs. high risk (119/134 CNB vs. 114/134 SE for RS 0-25 and 15/134 CNB vs 20/134 SE for RS 26-100; p = 0.13) or low vs. intermediate vs. high risk (85/134 CNB vs. 78/134 SE for RS 0-17 and 43/134 CNB vs. 48/134 SE for RS 18-30 and 6/134 CNB vs. 8/134 SE for RS 31-100; p = 0.19). No differences were observed based on age relative to 50 years or nodal status (data not shown). Cohen’s Kappa statistic k = 0.64 (95% CI, 0.44-0.83) supports substantial agreement between the CNB and SE samples. Lin’s concordance correlation coefficient (CCC) demonstrates similar agreement for the continuous RS result between paired samples (CCC = 0.86 [0.80-0.90]). Overall percent agreement was 91.8% (87.1-96.4%). CONCLUSIONS: Studies evaluating the level of concordance of ER, progesterone receptor, and HER2 biomarker status between CNB and SE samples have found high concordance rates, albeit varied. We now provide data demonstrating high concordance of RS results between CNB and SE specimens obtained from the same breast primary tumor without intervening systemic therapy. This supports use of either biopsy source for testing with a genomic predictor to identify those patients who will most likely benefit from chemotherapy and which patients may be spared. Citation Format: Aziza Nassar, Jodi Carter, Paige Innis, Satish Seerapu, Christy Russell, Helena Hanna, Abigail Lochala, Minetta Liu. Concordance analysis of paired breast cancer core needle biopsies and surgical excision samples using the Oncotype DX Breast Recurrence Score® assay [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-08-09.

Abstract PO5-06-04: EMSY amplification co-occurs with FGF/FGFR axis amplification in Metastatic Breast Cancer

Abstract Background: Amplification of FGFR and its ligands play an important role in breast cancer onset and progression and mutations of this signaling axis are emerging as mechanisms of resistance to targeted treatments. Understanding the molecular landscape of tumors that harbor aberrations in the FGF/FGFR (FGF/R) axis may help define the biology of these tumors and lead to the development of novel personalized approaches for more effective treatments in this group of patients. Using publicly available datasets, this study aimed at identifying genomic alterations co-occurring with amplification (amp) of the FGF/R axis in Metastatic Breast Cancer (mBC) patients. Methods: We utilized data from three cohorts of mBC patients. The first cohort (c1) included 176 patients with mBC from an ongoing precision medicine program sponsored by the Side-Out Foundation where genomic testing was performed, using a targeted gene panel, in real-world settings by commercial labs based predominantly on tumor specimens collected between 2019 and 2023. Whole exome sequencing data was obtained from AACR Genomics Evidence Neoplasia Information Exchange (GENIE) to establish a second cohort (c2) of 301 patients and a third cohort (c3) of 216 patients with mBC. Lastly, we included a fourth cohort (c4, n=122) of patients with early breast cancer (eBC). Chi2 test and Fisher’s Exact test were used to find significant co-occurring events. Python, pandas, and shell scripting were used for data manipulation, analysis and performing statistical tests. Results: Alterations of the FGF/R axis occurred in 26% (n=46) of patients in c1 of which 76% (n=35) were HR+ tumors and 24% (n=11) were Triple Negative Breast Cancers. Specifically, we detected amp of FGF3 (n=24, 52%), FGF4 (n=23, 50%), FGF19 (n=17, 37%), FGFR1 (n=18, 39%). In patients with alteration of the FGF/R axis, the most frequent aberrations were CCND1 (n=22, 48%), ZNF703 (n=12, 26%), MYC (n=9, 20%), and EMSY (n=8, 17%) amp, along with mutations of PIK3CA (n=17, 37%) and TP53 (n=18, 39%). EMSY amp was found in none of the patients without alterations of the FGF/R axis and co-amplified with the FGF/R axis in 8 patients(100%) (p< 0.0001). Similar results were also detected in the two independent cohorts of patients retrieved from the GENIE database. In c2, co-amp of EMSY and FGF/R axis was found in 53 of the 56 patients (95%) harboring EMSY amp (p< 0.0001). In c3, 17 patients (89%) had co-amp of EMSY and FGF/R axis of the 19 patients with EMSY amp (p< 0.0001). However, when we looked at patients with eBC in c4, of the 10 patients with EMSY amp, 7 patients (70%) had co-amp of EMSY and FGF/R axis and this association was not significant (p = 0.09). Conclusion: Amplification of EMSY has been mostly reported in ovarian (~17%) and sporadic breast cancers (~13%). EMSY has been reported to behave as an oncogene and a transcriptional repressor. It is well known that it can interact with the BRCA2 protein and potentially contributes to the “BRCAness” of tumors harboring its amp. Studies have also suggested that EMSY may act as a transcriptional repressor that modulates the expression of antimetastatic microRNAs in breast cancer. In the three mBC cohorts included in this analysis, EMSY amp was detected in 8, 56, and 19 cases, respectively. However, when the analysis was restricted to tumors harboring amps of both EMSY and FGF/R axis, EMSY was amplified in 100%, 95%, and 89% of those cases. While co-amplification of the EMSY gene with members of the FGF/R axis may be explained by its close proximity to the FGF3/4/19, and CCND1 genes on chromosome 11, in our analysis these co-amplifications were significant only in patients with metastatic disease. As dissecting the complex molecular landscape of mBC continues to be an essential step for advancing personalized treatment and better patient care, understanding the phenotypic effects of these co-amplifications may provide unique opportunities for devising combinatorial treatments for these patients. Citation Format: Deepika Prasad, Edik Blais, Rick Dunetz, Emanuel Petricoin, Mariaelena Pierobon. EMSY amplification co-occurs with FGF/FGFR axis amplification in Metastatic Breast Cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-06-04.

Changes in the Recovery Efficiency, Nutritional and Safety Quality of Dried Sergestid Shrimp (Acetes species) during Commercial Production

The sun-dried method is popular for producing dried Sergestid shrimp in Vietnam, but maintaining consistent product quality across seasons is challenging due to its dependence on weather conditions. A previous study used convection drying at a laboratory scale. In this study, the laboratory scale was upgraded to a commercial scale, and recovery efficiency and Sergestid shrimp images were recorded during production stages. Parameters were adjusted for economic efficiency and convenience. Results showed a decrease in recovery efficiency on the laboratory scale, while the commercial scale improved with washing and blanching. Overall, there was no significant difference in recovery efficiency between the commercial production (15.76 %) and laboratory scale (16.29 %). The commercial-scale dried Sergestid shrimp exhibited better colour than the laboratory-scale product. The product met food safety and quality criteria according to Vietnamese standards. Microorganisms such as Coliforms, E. coli, B. cereus, C. perfringens and salmonella, and total number of yeast and mold spores, were not detected in the product. On the other hand, the product of commercial production contained 256 kcal 100 g−1 of energy and a protein content of 55.50 ± 0.33 %. These findings form a foundation for scaling up production and assessing economic feasibility. Adjusting production parameters using larger equipment contributes to achieving optimal production efficiency and economic benefits.

Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols.

Several studies have documented the significant impact of methodological choices in microbiome analyses. The myriad of methodological options available complicate the replication of results and generally limit the comparability of findings between independent studies that use differing techniques and measurement pipelines. Here we describe the Mosaic Standards Challenge (MSC), an international interlaboratory study designed to assess the impact of methodological variables on the results. The MSC did not prescribe methods but rather asked participating labs to analyze 7 shared reference samples (5 × human stool samples and 2 × mock communities) using their standard laboratory methods. To capture the array of methodological variables, each participating lab completed a metadata reporting sheet that included 100 different questions regarding the details of their protocol. The goal of this study was to survey the methodological landscape for microbiome metagenomic sequencing (MGS) analyses and the impact of methodological decisions on metagenomic sequencing results. A total of 44 labs participated in the MSC by submitting results (16S or WGS) along with accompanying metadata; thirty 16S rRNA gene amplicon datasets and 14 WGS datasets were collected. The inclusion of two types of reference materials (human stool and mock communities) enabled analysis of both MGS measurement variability between different protocols using the biologically-relevant stool samples, and MGS bias with respect to ground truth values using the DNA mixtures. Owing to the compositional nature of MGS measurements, analyses were conducted on the ratio of Firmicutes: Bacteroidetes allowing us to directly apply common statistical methods. The resulting analysis demonstrated that protocol choices have significant effects, including both bias of the MGS measurement associated with a particular methodological choices, as well as effects on measurement robustness as observed through the spread of results between labs making similar methodological choices. In the analysis of the DNA mock communities, MGS measurement bias was observed even when there was general consensus among the participating laboratories. This study was the result of a collaborative effort that included academic, commercial, and government labs. In addition to highlighting the impact of different methodological decisions on MGS result comparability, this work also provides insights for consideration in future microbiome measurement study design.

Maternal red blood cell alloimmunization prevalence in the United States

Hemolytic disease of fetus and newborn (HDFN) is a life-threatening disease mediated by maternal alloimmunization to red blood cell (RBC) antigens. Studies of maternal alloimmunization prevalence in the United States (U.S.) lack national data. This study describes prevalence and trends in alloimmunization in pregnancy in the U.S. RBC antibodies (abs) were identified in a large, nationwide, commercial laboratory database from 2010-2021. The cohort comprised pregnancies for which the year of lab collection and patient's state of residence were available. Data were normalized based on U.S. Centers for Disease Control and Prevention estimates of live births and weighted by year and U.S. Census Division. Cochrane-Armitage tests assessed temporal trends of alloimmunization. Of 9,876,196 pregnancies, 1.5% (147,262) screened positive for RBC abs, corresponding to an estimated prevalence of 1,518/100,000 pregnancies. Of identified RBC abs, anti-D comprised 64.1% (586/100,000 pregnancies). Prevalence of other high-risk RBC abs for HDFN included anti-K (68/100,000) and anti-c (29/100,000). Incidence of all three high-risk abs increased from 2010-21 (all p<0.001). Among almost 10 million pregnancies in the US, comprising an estimated 14.4% of all pregnancies, 1.5% screened positive for RBC abs. Almost three-quarters (74.3%; 683/100,000) of RBC abs identified were high-risk for HDFN. Though prevalence of anti-D is difficult to interpret without the ability to distinguish alloimmunization from passive immunity, it remains problematic in HDFN, ranking second only to anti-K in critical titers. Given the sequelae of HDFN, new initiatives are required to reduce the incidence of alloimmunization in patients of reproductive potential.

Antimicrobial susceptibility patterns of aerobic bacteria isolated from canine urinary samples in South East Queensland, 2013 to 2018.

Urinary tract infections are a common diagnosis in dogs presenting to veterinary practice. Veterinarians often treat suspected infections empirically, either in the absence of culture and susceptibility testing results or whilst waiting for them. This study aimed to identify the bacteria most frequently isolated from canine urinary samples and their antimicrobial susceptibility patterns in South East Queensland (SEQ) to help guide responsible empirical antimicrobial prescription by the veterinary community in this geographical location. Cumulative antibiograms were generated from the results of 1284 culture-positive urinary samples in SEQ, obtained from a commercial veterinary laboratory over a 5-year period. Escherichia coli was the most commonly isolated bacterial species (43%), followed by Staphylococcus spp. (23%), Proteus spp. (21%) and Enterococcus spp. (10%). Of the six most common isolates, 97% had susceptibility to at least one low-importance antimicrobial. Susceptibility to the low-importance and first-line antimicrobial recommendation, amoxicillin, was 81% for E. coli and 24% for Staphylococcus spp. Susceptibility of both E. coli and Staphylococcus spp. to medium-importance and commonly recommended empirical antimicrobials, trimethoprim sulphonamides and amoxicillin-clavulanic acid was ≥85% and >92% for high-importance antimicrobials enrofloxacin and ceftiofur. Of the E. coli and Staphylococcus spp. isolates, 8.8% and 4%, respectively, were considered multidrug resistant. There was no increase in resistance to antimicrobials detected over the study period. Susceptibilities suggest low- and medium-importance antimicrobials remain acceptable first-line empirical treatments. However, this should be continually assessed and updated using local surveillance data.

Retrospective analysis of canine fecal flotation and coproantigen immunoassay hookworm positive results in Greyhounds and other dog breeds

Recent studies demonstrated that Greyhounds are commonly infected with Ancylostoma caninum and these infections have been shown to be resistant to anthelmintics. This study evaluated samples submitted to a commercial reference laboratory (IDEXX Laboratories) for canine fecal flotation zinc sulfate centrifugation and coproantigen immunoassay between January 1, 2019, and July 30, 2023 for evidence that Greyhounds were more often positive for Ancylostoma spp. (hookworms) compared to other breeds. The purpose of the study was to determine if Greyhounds were more likely to be hookworm-positive compared to other breeds, if Greyhounds on preventives with efficacy against hookworm infections are more likely to test positive than other breeds, if their infections take longer to resolve, to estimate how long this takes and to assess whether the proportion of hookworm positive tests for all breeds is increasing over time.Records of 25,440,055 fecal results were obtained representing 17,671,724 unique dogs. Of these, 49,795 (∼0.3%) were Greyhounds. The overall odds ratio (OR) of 15.3 (p < 0.001) suggests that Greyhounds are at significantly higher risk than other breeds for hookworm positive float findings, and the OR of 14.3 (p < 0.001) suggests significantly higher risk for hookworm antigen positive results. The median time to negative testing event from the Turnbull distribution estimate was in the interval of 1–2 days for other breeds and 71–72 days for Greyhounds. These results provide evidence that anthelmintic resistant A. caninum strains may be having population-level impacts on the frequency and duration of infections in Greyhounds. The findings have broader health implications beyond Greyhounds as MADR A. caninum strains could spread to other breeds and even pet owners.

Continuous and Scalable Synthesis of Prussian Blue Analogues with Tunable Structure and Composition in Surfactant-Free Microreactor for Stable Zinc-Ion Storage.

We represent a segmented flow surfactant-free microfluidic strategy for continuous synthesis of Prussian blue analogues (PBAs) with high dispersity and high crystallization. Representative zinc hexacyanoferrate (ZnHCF) nanocubes were successfully synthesized in a microfluidic reactor within a few minutes via the cooperation method and possessed lower contents of crystal water and Fe(CN)63- vacancies than that of synthesis in bulk solution. The nucleation and particle growth process can be precisely controlled by the exploration of different flow rates and reaction temperatures during the formation of ZnHCF nanocubes in segmented flow microfluidic reactors. High crystallinity, low crystal water and vacancies in the ZnHCF structure were presented at relatively high temperatures for the crystal growth process. High-quality ZnHCF with a low content of crystal water showed excellent electrochemical activity and stability towards zinc-ion storage. The continuous and scalable synthesis approach can be extended to the fabrication of other PBAs such as NiHCF, CoHCF, MnHCF, and CuHCF with high dispersity without using any surfactants. The controllable construction of PBAs with tunable properties in microfluidic reactors provides a promising direction to minimize the gap between commercial reality and laboratory research.

Methodology for high-performance liquid chromatography detection of latanoprost and latanoprost free acid

AbstractA gradient high-performance liquid chromatography (HPLC) method has been developed to determine the concentrations of latanoprost (LP) and latanoprost free acid (LPA) in aqueous solutions. It is novel due to a combination of its simplicity, speed, and detection capability in aqueous solutions for both active drug (LPA) and prodrug (LP). This method is applicable for the research and development of novel drug delivery devices and quality control assays for experimental and commercial laboratory settings, as it allows for a high sample throughput. Samples were chromatographed across a C18 + 2.7 µm 4.6 × 7.5 mm reversed-phase column with gradient elution using a mobile phase of aqueous acetic acid (pH 3.1) and acetonitrile with 0.1% acetic acid. UV spectrophotometry was used to monitor the eluents at 210 nm. Drug concentrations from 1.0 to 150 μg mL−1 were tested, with good linearity observed across the range. LPA had a signature peak at approximately 4.82 min (SD &lt; 0.08) and LP at 9.27 min (SD &lt; 0.07). For both drug and pro-drug, LOD and LOQ were 1.0 and 2.5 μg mL−1, respectively. This assay which accurately measures both prodrug and drug in a single injection, has significant applicability in determining the release kinetics of novel LP drug delivery systems.

[Overview on utility of in-house tests for detection of systemic infectious diseases in dogs].

For detection of infectious diseases, several point-of-care (POC) tests are on the market in addition to methods performed in commercial laboratories. These POC tests are based on enzyme-linked immunosorbent assay (ELISA) or other immunochromatographic technologies and present results within few minutes in veterinary practice. This article gives an overview of the utility of numerous POC tests of different manufacturers for detection of parvovirus antigen in feces, Dirofilaria (D.) immitis antigen in blood as well as antibodies against Borrelia (B.) burgdorferi, Anaplasma (A.) spp., Ehrlichia (E.) spp., Leptospira (L.) spp. and Leishmania (L.) infantum in blood (single or in different combinations). Sensitivity and specificity of these tests are important for their usefulness in veterinary practice. Furthermore, presence of antibodies or detection of antigen has to correlate with the presence of clinical signs. POC tests for detection of canine parvovirus antigen have a very high specificity, the sensitivity of all evaluated POC tests, however, is very low. POC tests for detection of D. immitis antigen have a very high sensitivity and specificity. As they detect antigen from the uterus of female adult parasites, test results are negative when only very few female or only male adults are present. POC tests for detection of antibodies against B. burgdorferi only indicate contact with Borrelia spp. and do not prove clinical Lyme disease, as the infection only extremely rarely causes clinical signs. POC tests for detection of antibodies against A. phagocytophilum are also not suitable for diagnosis of clinical anaplasmosis. Infections with A. phagocytophilum only lead to clinical disease in very rare cases and in these, clinical signs occur before the development of antibodies. POC tests for detection of antibodies against E. canis have a very high sensitivity as well as specificity. POC tests for detection of antibodies against L. infantum and Leptospira species (spp.) show a very high specificity and a high sensitivity. However, Leptospira spp. antibody-positive results may occur following vaccination, as the POC tests cannot distinguish between field and vaccination strains.

Isolation of aerobic bacteria from abscesses and wounds in rabbits and antibiotic susceptibility testing of Staphylococcus spp. and Pseudomonas spp. isolates

BackgroundWound infections and abscesses in rabbits are a common problem in veterinary practice and their treatment can be challenging. Bacterial culture and antimicrobial susceptibility testing are important tools in these cases. While some studies are available on bacteria associated with wound infections and abscesses in rabbits, the numbers of animals included is generally limited. Monitoring of antibiotic resistance in clinical practice is also an important part of good antibiotic stewardship. Multiple antibiotic resistances are frequently encountered in Staphylococcus and Pseudomonas spp., two groups of bacteria commonly associated with abscesses in rabbits. MethodsThis retrospective study evaluated the results of aerobic bacterial cultures and antibiotic susceptibility tests in swabs from abscesses (A) (n=541) and from skin and wounds (SW) (n=308) submitted to a commercial diagnostic laboratory. Samples submitted between January 2017 and October 2020 were included in the study. Antimicrobial susceptibility testing for Staphylococcus and Pseudomonas spp. was evaluated and compared. ResultsIn A, 465 bacterial isolates including 35 different species were isolated while 394 bacterial isolates, including 35 different species, were found in SW. The most frequently isolated bacteria were Staphylococcus spp. (A = 21.7%, SW = 36.5%) followed by Pasteurella spp. in A (13.3%) and aerobic spore-forming bacteria in SW (11.2%). Pseudomonas spp. was the third most commonly isolated genus in both sample types (A = 11.6%, SW = 8.9%). Pseudomonas aeruginosa isolated from A were more often resistant to the tested antibiotics than other Pseudomonas species. These results support the need for bacterial culture and antibiotic susceptibility testing in small mammal practice.

PD-BAT: A novel approach of pooling basophil donors for expansion of commercial laboratory testing of Chronic Spontaneous Urticaria

The type II autoimmune subtype of Chronic Spontaneous Urticaria (CSU) is characterized by the presence of IgG autoantibodies targeting IgE or the IgE high-affinity receptor (FcεRI) on mast cells and basophils. In evaluation of CSU patients, indirect basophil activation testing (BAT), has been utilized, involving the mixing of patient serum with heterologous peripheral blood donors, followed by flow cytometric assessment of basophil markers. However, the reliability of the indirect BAT results hinges on the quality of the donor basophils utilized. In this study, we introduce an innovative approach where multiple potential basophil donors undergo rigorous BAT characterization alongside control samples. By selecting and pooling donors with optimal performance, we significantly enhance the inter-assay reproducibility of the indirect BAT test.

Implications of Measles Inclusion by Commercial Syndromic Polymerase Chain Reaction Panels - United States, May 2022-April 2023.

Syndromic polymerase chain reaction (PCR) panels are used to test for pathogens that can cause rash illnesses, including measles. Rash illnesses have infectious and noninfectious causes, and approximately 5% of persons experience a rash 7-10 days after receipt of a measles, mumps, and rubella (MMR) vaccine. MMR vaccine includes live attenuated measles virus, which is detectable by PCR tests. No evidence exists of person-to-person transmission of measles vaccine virus, and illness does not typically result among immunocompetent persons. During September 2022-January 2023, the Tennessee Department of Health received two reports of measles detected by syndromic PCR panels. Both reports involved children (aged 1 and 6 years) without known risk factors for measles, who were evaluated for rash that occurred 11-13 days after routine MMR vaccination. After public health responses in Tennessee determined that both PCR panels had detected measles vaccine virus, six state health departments collaborated to assess the frequency and characteristics of persons receiving a positive measles PCR panel test result in the United States. Information was retrospectively collected from a commercial laboratory testing for measles in syndromic multiplex PCR panels. During May 2022-April 2023, among 1,548 syndromic PCR panels, 17 (1.1%) returned positive test results for measles virus. Among 14 persons who received a positive test result and for whom vaccination and case investigation information were available, all had received MMR vaccine a median of 12 days before specimen collection, and none had known risk factors for acquiring measles. All positive PCR results were attributed to detection of measles vaccine virus. Increased awareness among health care providers about potential measles detection by PCR after vaccination is needed. Any detection of measles virus by syndromic PCR testing should be immediately reported to public health agencies, which can use measles vaccination history and assessment of risk factors to determine the appropriate public health response. If a person recently received MMR vaccine and has no risk factors for acquiring measles, additional public health response is likely unnecessary.

Abstract 4972: Bioinformatic analysis of an annotated genomic database is clinically useful in a private cancer center

Abstract Background: Sequencing of patient solid tumor tissue is not a common service provided by community cancer centers. Our community cancer center has collected and sequenced over 5,000 tumor tissue samples from patients with various types of cancer. Since April 2019, we have conducted whole-exome and whole-transcriptome sequencing and stored this data in an internal genomics database. To analyze large patient cohorts, we must first optimize bioinformatic workflows on a smaller scale, which can then be applied to studies of larger populations. Previous studies have shown BRAF mutations are associated with an increased activation of the mitogen-activated protein kinase (MAPK) pathway. We analyzed transcriptomes of a cohort of 30 patients with thyroid cancer, 15 with V600E BRAF mutations and 15 wild-type for BRAF, for MAPK Pathway Activation Scores (MPAS). MPAS serves as a transcriptomic measure of the activation state of the MAPK pathway and has been shown to be a reliable prognostic biomarker of MAPK activity. Method: We conducted a retrospective analysis of data from FFPE tumor samples sent to a commercial CLIA-certified laboratory from April 2019 to October 2023. Samples were profiled by whole exome, whole transcriptome sequencing and immunohistochemistry (IHC). Whole transcriptome sequencing (WTS) was executed using Illumina NovaSeq along with the Agilent SureSelect Human All Exon V7 bait panel. Resulting data were reported in transcripts per million (TPM) using the Salmon expression pipeline. MPAS was calculated using the expression profile of 10 MAPK-associated genes. Results: There was no significant difference in BRAF expression levels or MAPK activation between patients with BRAF mutant and BRAF wild-type thyroid cancer (median MPAS scores: -0.09 vs. 0.11, p=0.9). This analysis workflow will be repeated with a larger patient population of patients with melanoma in the future; however, the consistency of expression between the groups, the rank-order, and the low variability per group suggest that expression changes related to this BRAF mutation may occur upstream or via differential regulation of an indirect pathway. Rank-order statistics and percentiles become more precise as data per tumor type grows. Conclusions: Our community cancer center began building an internal genomics database including whole-exome and whole-transcriptome sequencing since 2019. This resource facilitates analysis of patient samples for tumor mutational burden, gene fusions, transcriptomic data, and other important characteristics which could reveal patterns or trends that inform cancer diagnosis and prognosis of other patients. Analysis of expression data for patients with advanced solid tumors who have mutations in genes of interest could inform on potential targeted treatments in the future. This study represents a single example of the potential of our internal clinically annotated genomics database. Citation Format: Carlos E. Zuazo, Sourat Darabi, David R. Braxton, Phillip Stafford, Michael J. Demeure. Bioinformatic analysis of an annotated genomic database is clinically useful in a private cancer center [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4972.

Nontuberculous mycobacteria testing and culture positivity in the United States

BackgroundNontuberculous mycobacteria (NTM) are environmental bacteria which may cause chronic lung disease. The prevalence of NTM pulmonary infection and disease has been increasing in the United States and globally. The predominant clinically relevant species of NTM in the United States are Mycobacterium avium complex (MAC) species and Mycobacterium abscessus. With the development of rapid species identification methods for NTM (e.g. PCR probes), more testing for NTM is being conducted through commercial labs, such as Laboratory Corporation of America (Labcorp), which provides deidentified real-time testing data to the Centers for Disease Control (CDC) pursuant to a data sharing agreement. Because NTM lung infections are not reportable in most states, other data sources are key to understanding NTM testing patterns, positivity rates, and species distributions to track infection trends and identify clinical care needs.MethodsWe obtained national Labcorp data for the period January 2019 through mid-April 2022. We subset the data to only respiratory samples sent for Acid Fast Bacilli (AFB) cultures. NTM positive results were defined as those which identified an NTM species and are not Mycobacterium tuberculosis, Mycobacterium bovis, or Mycobacterium gordonae.ResultsOverall, 112,528 respiratory samples were sent for AFB testing during the study period; 26.3% were from the Southeast U.S., identified as HSS Region IV in the Labcorp dataset, and 23.0% were from the Pacific and South Pacific region (Region IX). The culture positive prevalence ranged from 20.2% in the Southeast to 9.2% in the East North Central region (Region V). In the Southeast US, M. abscessus prevalence was 4.0%. For MAC, the highest prevalence was observed in the Mountain region (Region VII) (13.5%) and the lowest proportion was in the East South Central region (7.3%, Region III). Among positive tests, the proportion which was MAC varied from 61.8% to 88.9% and was highest in the Northeast U.S. The proportion of positive samples which were M. abscessus ranged from 3.8% to 19.7% and was highest in the Southeast.ConclusionsThe Southeastern region of the U.S. has the highest rate of culture positivity in Labcorp tests for total NTM and, of all positive tests, the highest proportion of M.abscessus. These estimates may underrepresent the true number of M.abscessus infections because M. absesscus-specific probes are not commercially available and not all NTM testing in the United States is done by Labcorp. Analysis of real-time testing data from commercial laboratories may provide insights into risk factors for NTM culture positivity in ‘hotspot’ areas.

86 Evaluation of dietary Saccharomyces cerevisiae fermentation product on markers of joint inflammation in young, exercising horses following an intra-articular lipopolysaccharide challenge

Abstract Including Saccharomyces cerevisiae fermentation product (SCFP) into the diets of young, exercising horses may prolong their performance career by optimizing the intra-articular environment. Our objective was to evaluate the effect of dietary SCFP on joint inflammation in yearlings undergoing regular exercise, challenged with intra-articular lipopolysaccharide (LPS). Thirty Quarter Horse yearlings (374 ± 25 kg BW; 562 ± 16 d of age; 15 fillies and 15 geldings) were used in a 60-d study to test the hypothesis that dietary SCFP (TruEquine C, Diamond V Mills, Inc.) ameliorates joint inflammation following an acute inflammatory insult. Horses were stratified by BW, age, sex, and randomly assigned to dietary treatments (n = 10/treatment): Control (0), 46, or 92 mg/kg BW SCFP. Treatments were top-dressed onto a custom-formulated concentrate void of added microbials offered at 1% BW/d (as-fed) every 12 h. Horses were individually stalled (3.6 m × 7.3 m) and offered ad libitum Coastal bermudagrass hay. Using a free-stall exerciser, horses were exercised following a progressive workload regimen for 30 min/d, 5 d/wk. On d 46, all horses underwent an intra-articular LPS challenge where each horse had one radial carpal joint randomly assigned to receive either 0.8 mL of a 0.5 ng LPS solution or sterile lactated Ringer’s solution (LRS) as a contralateral control. Synovial fluid samples were obtained pre-injection (h 0) and at 6, 12, 24, and 336 h post-injection and analyzed for prostaglandin E2 (PGE2), a pro-inflammatory prostaglandin via commercial ELISA, and for chemokine-concentration (signaling proteins that direct immune cells; CCL2, and CCL11) and cytokines (inflammatory mediators; TNFα and IL-10) using a multiplex platform via commercial laboratory. Non-normal data (PGE2, IL-10, and CCL2) were log transformed, and all markers were analyzed using MIXED procedure of SAS v9.4. Mean separation was achieved with orthogonal contrasts, and contralateral control carpi were used as a covariate across all hours. There was no effect of SCFP on synovial logPGE2 (P = 0.42), logCCL2 (P = 0.90), CCL11 (P = 0.26), or logIL-10 (P = 0.23). However, there was a treatment × hour interaction for CCL11 (P = 0.04) where the Control had increased concentrations compared with SCFP treatment groups at 6 h post-injection. Furthermore, logIL-10 also had a treatment × hour interaction (P = 0.05) where the 46mg/kg BW group had decreased concentrations at h 12 compared with the Control and 92mg/kg BW group. The main effect of treatment for TNFα (P = 0.04) revealed that the 92mg/kg BW group had less concentrations than the 46mg/kg BW group and tended to have less concentrations than the Control group across all hours. Results indicate that SCFP may help mitigate inflammation markers following an acute intra-articular inflammatory insult.

103 Goats complement cattle in a woody-plant encroached, diverse Cross Timbers rangeland

Abstract Our objectives were to 1) determine diet selection of goats and cattle grazing woody plant-encroached tallgrass prairie, and, 2) determine the effect of the presence of goats on cattle diet selection. In 2019, pastures (n = 6) were allocated to 1 of 2 experimental grazing treatments. Pastures (n = 3) grazed by cattle only (crossbred Angus yearling heifers) were moderately grazed year-round at 4.2 ha per heifer. Pastures (n = 3) grazed by cattle (similar heifers) and goats (Boer x Spanish crossbred mature does) were moderately grazed year-round at 4.7 ha per heifer and 2.3 ha per goat simultaneously. Each pasture was burned in 6 patches (2 patches per year) to facilitate range management objectives. Every 35 d from May 2022 until June 2023, fecal samples were collected from all animals and stored frozen and later composited into 2 composites per animal species per pasture. Composites were then analyzed by a commercial lab with DNA barcoding and high-throughput sequencing. For statistical analysis, the top 50 Exact Sequence Variants (ESVs), representing species of forage, across all treatments were used for analysis. Each ESV was georeferenced to eliminate plants that did not grow in the study area, and assigned to a representative functional group: graminoid, forb, legume, and woody plant. Analysis of variance and Tukey’s post-hoc separation of estimated marginal means were performed to assess the effects of season, grazer species, and the interaction. The interaction of season and grazer species was significant (P &amp;lt; 0.01) for the percentage of diet selected from each functional group of plants. As expected, goats selected a greater percentage of their diet as woody plants in summer (57%) and winter (74%) compared with cattle (27%). Cattle selected more grass in winter (34%) than goats (11%). Goats selected more forbs in spring (33%) than cattle (10%). However, goats selected a lesser percentage of their diet as legumes in summer (16%) than cattle (58%), which was unexpected. Overall, these results indicate that both species of grazers select a diverse diet from these diverse pastures, and selection is dynamic over time. Goat presence in a pasture does not seem to drastically alter cattle selection, actually complementing cattle in these pastures where goats can be used to target species cattle do not prefer.

Rapid response to a COVID-19 outbreak at a nightclub in Kagoshima prefecture, Japan, in the early phase of the COVID-19 pandemic, June and July 2020: A descriptive epidemiological study

IntroductionDuring COVID-19 pandemic in Japan, nightclubs were identified as high-risk locations for COVID-19 outbreaks, but an outbreak investigation in this setting is challenging because of the anonymous and opportunistic nature of interactions. MethodsThe joint rapid response team collected epidemiological data, conducted descriptive epidemiology to determine the characteristics of cases associated with the nightclub, and implemented countermeasures. Polymerase chain reaction (PCR) tests were performed by the Local Institute of Public Health, Kagoshima University, and several commercial laboratories. ResultsBetween June 15 and July 20, 2020, 121 individuals tested positive for SARS-CoV-2 (59 confirmed and 62 asymptomatic) of whom 8 were nightclub staff who had no travel history of outside Kagoshima, 66 were guests, and 47 were subsequent contacts. The median age was 32 years (interquartile range: 24–43 years). One individual showed severe symptoms but there were no fatal. The epidemic curve showed one peak on June 30 and July 1 with a limited number of cases subsequently. Of the 121 cases, 116 and 5 were in individuals living in and outside Kagoshima Prefecture, respectively. Haplotype network analysis showed 5 genome-wide single-nucleotide variants between the isolates before and during this outbreak. ConclusionsThere is a possibility that unidentified guests from outside Kagoshima Prefecture could infect staff who could subsequently spread the virus to guests and other staff, who were mainly a younger population. The rapid outbreak response enabled onward transmission in the community to be minimized. This outbreak investigation could provide insights for effective responses to challenging situations in future pandemic.