Date Of Collection Research Articles

A new narrower circumscription and a nomenclatural synopsis for Calea subg. Meyeria (Asteraceae: Neurolaeneae)

The studies on Calea subg. Meyeria (Neurolaeneae, Asteraceae), a group from open vegetation in Southeastern South America, recently resulted in the description of novel species and nothospecies. Continued progress on the nomenclatural and taxonomic studies of this subgenus is presented here. A comprehensive bibliography for species described in this section was compiled and revised to allow the proposition of nomenclatural changes. All type specimens were consulted either in person or using high-resolution digital images. Based on these efforts, we propose a narrower circumscription of Calea subg. Meyeria, altering the number of accepted taxa assigned to it from 15 to 9. The subgenus is here proposed to be characterized morphologically by shrubs with a cymose capitulescence, capitula with four or more foliaceous outer phyllaries and cypsela longer than the pappus. As here defined, it comprises eight species (C. funkiana, C. marginata, C. myrtifolia, C. parvifolia, C. phyllolepis, C. pruskiana, C. subintegerrima, and C. triantha) and one nothospecies (C. × parviantha). Altogether, we synonymize four names; propose lectotypifications for two names; recognize three new isolectotypes; and provide corrections for type specimen collection data from six taxa, including collector names, collection date, and locality.

Concordance between human epidermal growth factor receptor 2 (HER2) status by immunohistochemistry (IHC) and next-generation sequencing (NGS) in tissue and blood samples from gastric and gastroesophageal junction cancers (GC/GEJC).

478 Background: An estimated 18% of patients (pts) with GC/GEJC have HER2-positive (HER2+; IHC 3+ or 2+/in situ hybridization–positive [ISH+]) tumors. Although IHC/ISH are the standard testing methods for determining HER2 positivity, NGS can identify HER2 ( ERBB2 ) amplification alongside other biomarkers. This study assessed the concordance of detecting HER2 amplification by tissue/plasma NGS with IHC/ISH HER2 status in pts with GC/GEJC. Methods: Pts were retrospectively identified in the Tempus database. The primary analysis assessed tissue and plasma NGS HER2 copy number (CN) concordance with a HER2+ (IHC 3+ or 2+/ISH+) or HER2− (IHC 0, 1+, or 2+/ISH−) status; NGS samples were collected in ≤30 days of the IHC sample collection date. HER2 amplification was defined as tissue CN ≥8 or plasma log2(CN) ≥0.5; additional amplifications were captured by manual inspection. A secondary analysis assessed the correlation between paired tissue and plasma HER2 log2(CN) in pts with plasma and tissue NGS samples collected ≤30 days apart. The secondary analysis included pts irrespective of IHC sample collection date. Results: Of 1578 pts with GC/GEJC and a curated IHC score evaluated in the primary analysis, 1507 and 305 pts underwent tissue and plasma NGS testing, respectively. Among pts with tissue and plasma NGS results, 902 (59%) and 201 (66%) had primary tumors of the stomach, respectively; all remaining pts had primary tumors of the cardia.According to IHC/ISH, 229 (15%) and 40 (13%) pts were HER2+ among those with tissue and plasma NGS testing, respectively. Of the pts identified as HER2 amplified by tissue and plasma NGS,95% and 92% were HER2+ by IHC/ISH, respectively. Positive percent agreement (PPA) of HER2 amplification by tissue and plasma NGS with IHC/ISH HER2+ status was 70% and 58%, respectively. Concordance rates by PPA, negative PA (NPA), and overall PA (OPA) are summarized in Table. In the secondary analysis, a positive correlation in NGS HER2 log2(CN) was observed in pts with paired tissue and plasma NGS (mutant variant allele frequency >5%; R=0.85; P<2.2e−16; n=307). Conclusions: Based on PPA, we observed moderate concordance between NGS HER2 amplification detection (plasma or tissue) and standard HER2 IHC assessment. NGS is not sufficient to detect all pts with HER2+ GC/GEJC. Further testing is warranted to determine if NGS testing could complement IHC/ISH in identifying pts who may benefit from HER2-directed therapies. IHC 3+ or 2+/ISH+ (HER2+), n IHC 0, 1+, or 2+/ISH− (HER2−), n Total Total 229 1120 Tissue HER2 amplified, n 160 8 168 Tissue HER2 not amplified, n 69 1112 1181 PPA: 69.9% NPA: 99.3% OPA: 94.3% IHC 3+ or 2+/ISH+ (HER2+), n IHC 0, 1+, or 2+/ISH − (HER2 − ), n Total Total 40 233 Plasma HER2 amplified, n 23 2 25 Plasma HER2 not amplified, n 17 231 248 PPA: 57.5% NPA: 99.1% OPA: 93.0%

Fruit Cuticle Thickness and Anatomical Changes in Pedicel Xylem Vessels Influence Fruit Transpiration and Calcium Accumulation in Cranberry Fruit.

Ca is a key nutrient for fruit quality due to its role in bonding with pectin in the cell wall, providing strength through cell-to-cell adhesion, thus increasing fruit firmness and extending post-harvest life. However, Ca accumulation is mostly limited to the initial stages of fruit development due to anatomical and physiological changes that occur as fruits develop. The objective of this study was to evaluate fruit transpiration, cuticle thickness, and pedicel vessel changes during cranberry fruit development and the effect these parameters might have on Ca translocation. 'Stevens' cranberry fruits were collected weekly, starting seven days after full bloom (DAFB) until 70 DAFB. For each collection date, fruit transpiration was evaluated in the field, and samples were taken to analyze total fruit Ca content, stomata density, cuticle thickness, pedicel anatomical changes, and xylem functionality. Ca accumulation in the fruit exhibited a sigmoidal curve, beginning at 0.04 mg per berry at 7 DAFB, increasing to a maximum of 0.1 mg per berry at 28 DAFB, and remaining constant until harvest (70 DAFB). Fruit Ca accumulation was mostly explained by fruit transpiration, which exhibited a similar sigmoidal pattern. The rapid decline in fruit transpiration was largely modulated by increases in cuticle thickness, as well as anatomical changes in the pedicel xylem, thereby reducing the capacity to transport water and nutrients into the fruit. Thus, this research could help cranberry growers maximize fruit Ca content by prioritizing fertilization during the early stages of fruit development.

P-1951. Incidence of SARS-CoV-2 Infection among those 6 Months to 49 Years of Age in the Cascadia Prospective Cohort Study, Oregon and Washington, United States, July 1, 2022 – March 31, 2024

Abstract Background With the ending of the public health emergency and changes in the testing landscape, less is known about SARS-CoV-2 incidence in the community than earlier in the pandemic. Our goal was to describe SARS-CoV-2 incidence among individuals 6 months to 49 years of age enrolled in the Cascadia prospective community cohort study in Oregon and Washington, USA, by age, sex, and COVID-19 vaccination status. Covid-like illness (CLI) and vaccination status definitions Methods We included Cascadia participants enrolled July 1, 2022 – March 31, 2024. We collected weekly nasal swabs and surveys from participants; more frequently among those with SARS-CoV-2 infection. We defined SARS-CoV-2 infection as a positive or inconclusive swab result and assessed covid-like illness (CLI) symptoms ±7 days from collection date (Fig.1). We followed individuals from receipt of their first nasal swab until the earliest of SARS-CoV-2 infection, loss to follow-up, or the end of the study period. We considered age and COVID-19 vaccination status (Fig. 1) as time-varying variables. We estimated incidence as the number of SARS-CoV-2 infections per 1,000 person-weeks (p-w) of observation, along with robust-error 95% confidence intervals (CI); we considered incidence rates to vary between strata if confidence intervals did not overlap. Table Incidence of SARS-CoV-2 Infection among Cascadia study participants, by sex, age, and vaccination status, July 1, 2022-March 31, 2024 Results We observed 1,495 SARS-CoV-2 infections among 3,464 included individuals with 164,290 p-w of follow-up; overall incidence rate was 9.10 (CI 9.09, 9.11). Incidence was similar by sex, lowest among those 6m-4y, and highest among those 12-17y (Table). Overall SARS-CoV-2 incidence was higher among those previously up-to-date (10.17 [CI 9.24, 11.18]) than among those currently up-to-date with vaccines (8.42 [CI 7.72, 9.19]; Table). A quarter (178/716) of SARS-CoV-2 infections among those < 18y were asymptomatic, compared with 10% (76/785) among those ≥18. The proportions reporting ≥2 CLI symptoms were 54% (49/91) among those 6m–4y, 62% (219/354) among those 5–11y, 69% (184/265) among those 12–17y, and 85% (666/785) among those 18–49y (Fig. 2). Frequency of covid-like illness (CLI) symptoms1 reported among Cascadia study participants, by age, July 1, 2022-March 31, 2024 Conclusion Our study fills a knowledge gap about the incidence of SARS-CoV-2 in the community later in the pandemic. Incidence was lowest among those recently vaccinated. These findings will inform continued discussions about COVID-19 vaccination strategies. Disclosures Mark A. Schmidt, PhD, MPH, HilleVax: Grant/Research Support|Janssen: Grant/Research Support|Moderna: Grant/Research Support|Pfizer: Grant/Research Support|Vir Biotechnology: Grant/Research Support Neil D. Yetz, M.P.H., N/A: Expert Testimony Teresa Kimes, MS, Moderna: Grant/Research Support|Vir Biotechnology: Grant/Research Support Stephen P. Fortmann, MD, Pfizer: Grant/Research Support Holly C. Groom, MPH, Hillevax: Grant/Research Support|Moderna: Grant/Research Support Jennifer L. Kuntz, MS, PhD, Hillevax, Inc: Grant/Research Support Richard A. Mularski, MD, MSHS, MCR, Pfizer, Inc: Grant/Research Support Janet A. Englund, MD, Abbvie: Advisor/Consultant|AstraZeneca: Advisor/Consultant|AstraZeneca: Grant/Research Support|GlaxoSmithKline: Advisor/Consultant|GlaxoSmithKline: Grant/Research Support|Meissa Vaccines: Advisor/Consultant|Merck: Advisor/Consultant|Pfizer: Board Member|Pfizer: Grant/Research Support|Pfizer: Speaker at meeting|SanofiPasteur: Advisor/Consultant|Shinogi: Advisor/Consultant Helen Y. Chu, MD, MPH, Abbvie: Advisor/Consultant|Merck: Advisor/Consultant|Vir: Advisor/Consultant

P-1182. Impact of Standard Infection Prevention Measures, Including Contact Precautions, on Serratia marcescens Outbreaks in the Neonatal ICU

Abstract Background Serratia marcescens outbreaks attributed to lapses in hand hygiene, contaminated sinks or drains, and other sources of environmental contamination have been observed in the neonatal intensive care unit (NICU).1S. marcescens outbreaks were identified in the St. Louis Children’s Hospital (SLCH) NICU, a level IV NICU with 150 beds, in 2019 and 2023. NICU Location and Infant Body Sites of Serratia marcescens Infections Proportion of 2019-2024 Quarter 1 Serratia marcescens infections from specific NICU locations (1A) and infant body sites (1B). Methods A detailed review of NICU S. marcescens infections was performed and quarterly infection rates per 1,000 patient-days were followed. The following response measures were implemented in ­­2020: 1. Contact isolation precautions (CP) for infants with S. marcescens infections. 2. Education provided to NICU staff: a. Impact of S. marcescens infections in infants. b. Potential sources of S. marcescens in the NICU. c. Importance of standard infection prevention measures, including hand hygiene, nail hygiene, isolation precautions, and environmental cleaning. 3. Cleaning or exchange of NICU sink aerators. 4. Installation of splash guards next to sinks in medication rooms. The following response measures were implemented in 2023: 5. Steps 1-3 above were re-implemented. 6. Sterile water was substituted for tap water during infant baths. 7. Whole genome sequencing was performed on seven S. marcescens isolates. A cutoff of >30 allelic differences between isolates indicated genetically unrelated strains. Annotated NICU Serratia marcescens Infection Rate Annotated neonatal intensive care unit (NICU) nosocomial Serratia marcescens infection rates per 1,000 patient-days by quarter and selected interventions. The dotted grey line indicates the average annual infection rate. Results Geographic clustering was identified in specific NICU locations (Figure 1A). The most common body site of infection was the respiratory tract, followed by bloodstream (Figure 1B). A sustained decrease in S. marcescens infection rates was observed following 2020 response measures (Figure 2). As such, CP for infants with S. marcescens was paused. In 2023, S. marcescens infection rates again doubled and re-implementation of interventions resulted in decreased infection rates. Isolates were genetically unrelated based on whole genome sequencing (Figure 3). Whole Genome Sequencing Results Minimum Spanning Tree showing patient Serratia marcescens isolates, including NICU room location (and date) of collection in circles and the number of allelic differences on linking lines between the circles. Conclusion Standard infection prevention measures, including CP, and mitigation of potential water exposure sources resulted in decreased S. marcescens infection rates following two separate outbreaks in the NICU. Despite temporal and geographic clustering, isolates were genetically unrelated. Disclosures All Authors: No reported disclosures

P-1358. Understanding Fungal Infections and Trends in Fungal Resistance: A Single Center Evaluation

Abstract Background Invasive fungal infections cost the US health care system billions and are challenging to treat. In 2021 alone, the CDC estimates that fungal infections contributed to over $7 billion in direct medical costs and over 7,000 deaths in the US. The most common agents used to treat clinical fungal infections are azoles. However, antifungal resistance is on the rise. Exposure to agricultural fungicides has been identified as likely contributing to increased resistance to medical azoles, as there has been incidence of infection with azole-resistant fungi in patients who were azole-naïve. Furthermore, in vitro studies have demonstrated that fungi exposed to agricultural azoles develop cross-resistance to medical azoles. This study aims to describe retrospective antifungal susceptibility trends for medical azoles in patients at UCSD Health and agricultural azole use in San Diego and Imperial Counties. Methods Chart review was used to obtain sensitivity data (minimum inhibitory concentrations or MICs) for non-Candida fungal isolates sent for susceptibility testing from UCSD Health patients from January 2016 through February 2024. Data on fungal isolates including species, date of isolate collection, susceptibility data, and patient zip code were collected. Agricultural azole use data is publicly available from the California Department of Pesticide Regulation and was analyzed for azoles applied in San Diego and Imperial Counties from 2016 to 2021. Results 189 fungal isolates from 170 patients were included in the analysis. Fusarium demonstrated high resistance to common medical azoles which did not change over time. A. fumigatus also exhibited minimal change in MICs for itraconazole and posaconazole but showed possible increase in MICs over time for voriconazole and isavuconazole. Imperial County had an 8 to 10-fold higher use of agricultural azoles compared to San Diego County. Conclusion Fusarium demonstrated resistance to all common medical azoles. There may be a possible increase in resistance of A. fumigatus to voriconazole and isavuconazole over time, however this is limited by small sample size. This study highlights the need for increased antifungal susceptibility testing at UCSD Health. Disclosures Nina Haste, PharmD, PhD, Novartis: Spouse is an employee

P-2349. Clinical and genomic epidemiology of coxsackievirus A21 and enterovirus D68 in homeless shelters, King County, Washington, 2019-2021

Abstract Background Congregate homeless shelters are disproportionately affected by infectious disease outbreaks. Although outbreaks of SARS-CoV-2 and influenza viruses have been reported in homeless shelters, there are minimal data describing enterovirus transmission among people experiencing homelessness.Figure 1. Nasal swab specimens and enterovirus detection in homeless shelters, October 2019 - February 2020, King County, Washington, USANOTE: No coxsackievirus A21 or enterovirus D68 positive specimens were detected between March 2020 - May 2021 Methods We describe the epidemiology of enteroviruses across 23 adult and family shelters in King County, Washington from October 2019 through May 2021, using repeated cross-sectional respiratory illness and environmental surveillance. Genomic sequencing was used to describe the molecular diversity of enteroviruses within and across shelter sites.Figure 2. Phylogenetic trees of sequenced participant coxsackievirus A21 shelter specimens. A) Tree containing all shelter coxsackievirus A21 and all coxsackievirus A21 genomes deposited in Genbank. Tips representing study specimens are colored according to shelter. Light gray tips represent coxsackievirus A21 genomes downloaded from Genbank. The x-axis represents number of nucleotide changes in the genome relative to a coxsackievirus A21 reference genome (AF465515.1). B) Tree containing all shelter coxsackievirus A21 genomes. Internal nodes with >90% bootstrap support are labeled on tree. C) Tree containing all shelter coxsackievirus A21 genomes with x-axis corresponding to sample collection date. Results Of 3,281 participants aged ≥3 months, coxsackievirus A21 (CVA21) was identified in 39 adult residents (3.0% detection, 95% CI: 1.9%-4.8%) across seven shelters from October 2019-February 2020 (Figure 1). Enterovirus D68 (EV-D68) was identified in five adult residents in two shelters October-November 2019. The most commonly reported signs or symptoms of both CVA21 and EV-D68 included runny nose and cough. Of 812 environmental samples, one was EV-D68-positive and five were CVA21-positive. Other enteroviruses detected among residents, but not in environmental samples, included coxsackievirus A6/A4 (n=3 children). No enteroviruses were detected from April 2020-May 2021. Closely related CVA21 and EV-D68 cases occurred in some shelters (Figures 2-3). Some shelters also hosted multiple CVA21 lineages (Figure 2). Figure 3. Phylogenetic tree of sequenced participant enterovirus D68 shelter specimens. Tips representing study specimens are colored according to shelter. Light gray tips represent enterovirus D68 genomes downloaded from Genbank. The inset shows a detailed view of the relationship among the study genomes. The x-axis represents the number of nucleotide changes in the genome relative to an enterovirus D68 reference genome (NC_038308.1). Conclusion This study provides critical information on clinical features and transmission patterns of enteroviruses in congregate homeless shelters. Surveillance of enteroviruses in shelters and other congregate settings may be warranted for early detection and implementation of control measures to reduce outbreaks. Disclosures Eric J. Chow, MD, MS, MPH, IDWeek: Travel Grant|Providence Regional Health Everett: Honoraria Michael J. Boeckh, MD PhD, Allovir: Advisor/Consultant|Allovir: Grant/Research Support|AstraZeneca: Advisor/Consultant|AstraZeneca: Grant/Research Support|Merck: Advisor/Consultant|Merck: Grant/Research Support|Moderna: Advisor/Consultant|Moderna: Grant/Research Support|Symbio: Advisor/Consultant Janet A. Englund, MD, Abbvie: Advisor/Consultant|AstraZeneca: Advisor/Consultant|AstraZeneca: Grant/Research Support|GlaxoSmithKline: Advisor/Consultant|GlaxoSmithKline: Grant/Research Support|Meissa Vaccines: Advisor/Consultant|Merck: Advisor/Consultant|Pfizer: Board Member|Pfizer: Grant/Research Support|Pfizer: Speaker at meeting|SanofiPasteur: Advisor/Consultant|Shinogi: Advisor/Consultant Helen Y. Chu, MD, MPH, Abbvie: Advisor/Consultant|Merck: Advisor/Consultant|Vir: Advisor/Consultant

P-1907. Comparing Multisystem Inflammatory Syndrome in Children (MIS-C) Case Characteristics Across Periods of SARS-CoV-2 (SC2) Variant Predominance in Los Angeles County (LAC): 2020-2023

Abstract Background MIS-C is a rare condition in children associated with prior SC2 infection. Limited data show the impact of SC2 variants on the presentation of MIS-C. This study analyzes differences in the presentation of MIS-C cases in LAC when different variants were circulating. Characteristics of Multisystem Inflammatory Syndrome in Children (MIS-C) Cases, -- Los Angeles County*, California March 1, 2020- December 31, 2023 Methods This analysis includes MIS-C cases in people < 21 years of age reported to LAC with onset from 3/1/2020-12/31/2023. We defined confirmed SC2 infection as having a documented positive SC2 test with specimen collection date < 60 days prior to MIS-C symptom onset. Where SC2 positive results were not available, we imputed SC2 infection as occurring 30 days prior to MIS-C onset. Infection dates were used to classify cases by variant predominant periods, defined as weeks where > 50% of sequenced specimens reported to LAC were a particular variant as defined by the WHO as a variant of concern. Case demographics and clinical characteristics were compared across variant periods. Analyses were conducted for all reported MIS-C cases and for cases with confirmed SC2 infection. Statistical significance was tested with the Kruskal-Wallis test and chi-squared test [α=0.05]. Results 349 MIS-C cases were reported between 2020-2023 (Table 1). Of these, 102 (29.2%) had a documented SC2 infection. Median age at onset was 7.8 years. 168 (48.1%) had ≥ 1 comorbidity, 124 (35.5%) were admitted to the ICU, and median hospital length of stay (LOS) was 5 days. 18 cases were vaccinated prior to MIS-C onset. The most SC2 infections occurred during the Pre-Delta period (230, 65.9%), while the fewest occurred during the Delta period (57, 16.3%) (Table 2). Median age and proportion of children with ≥ 1 comorbidity decreased across variant periods (p < 0.0001, p=0.0102; respectively). The median LOS was lowest when SC2 infection occurred during the Omicron period (p=0.0370). ICU admission was not statistically different across variant periods. Conclusion The LOS, median age, and proportion of cases with comorbidities decreased when SC2 infection occurred during the Omicron period. This may be due to differences in variant pathogenicity, natural immunity decreasing the MIS-C susceptible pool, and younger children being the last group to be eligible for vaccination during later variant periods. Disclosures All Authors: No reported disclosures

P-695. Analysis of Seasonal Influenza Activity in Los Angeles County throughout the COVID-19 Pandemic

Abstract Background COVID-19 pandemic restrictions impacted flu transmission, leading to lower incidence and high influenza activity outside of the typical respiratory season. Los Angeles County (LAC) Department of Public Health (DPH) typically defines flu season in LAC as the first week of October through the end of March. Because positive flu results became reportable in LAC via electronic laboratory reporting (ELR) in October 2019, this analysis uses this new data source to describe flu positive tests from the current and previous four flu seasons to understand how flu activity in LAC changed throughout the pandemic. Methods This analysis includes influenza positive test results for LAC residents reported to DPH via ELR with specimen collection dates from October 2019 to March 2024. Results were deduplicated at the specimen level. Descriptive statistics were used to analyze positive tests. Results During the 2023-24 flu season from October 2023 through March 2024, 39,412 positive influenza results were reported (87% flu A; 13% flu B), with the greatest number of positive results for flu A observed in December 2023 and flu B observed in February 2024. During the same months of previous seasons, the number of positive tests ranged from 217 tests in the 2020-21 season to 40,843 tests in the 2022-23 season. Peak months of flu activity ranged from November in the 2022-23 season to May in the 2021-22 season. For all tests reported during the study period, subtyping was reported for 8% of positive flu A specimens. Lineage typing was reported for 0.04% of positive flu B specimens. During the current flu season, at least 1 positive test has been reported for flu A/H1, flu A/H3, and flu B/Victoria. The last recent positive flu B/Yamagata specimen was reported in January 2020. Conclusion Results show that flu activity in LAC during the current flu season appears to be returning to pre-COVID-19 pandemic seasonality; flu B activity peaked later in the season, which has been described for previous flu seasons. During the pandemic, peak months of flu activity varied from what is usually observed. No positive flu B/Yamagata tests since 2020 may support ongoing efforts to assess flu B/Yamagata extinction during the COVID-19 pandemic, prompting the World Health Organization to recommend excluding flu B/Yamagata from flu vaccines. Disclosures All Authors: No reported disclosures

Long-term temporal and seasonal trends of infective endocarditis

Abstract Background Over the past two decades, the epidemiology of infective endocarditis (IE) has changed significantly with the increase of life expectancy, use of cardiac implantable devices, and more invasive procedures. There is an ongoing shift in the incidence of IE, but a temporal/seasonal association with specific pathogens is yet to be investigated. Aims In this study, we aimed to assess (1) whether there is a temporal trend / increase in IE incidence in recent years, and (2) if there is a seasonality among specific IE-related pathogens. Methods We conducted a single center retrospective study of all consecutive patients in a 6-year period between 2017 and 2022, with a diagnosis of definite infective endocarditis as assessed by the modified Duke criteria. All electronic medical records were reviewed for demographics, blood cultures dates and results, and echocardiographic results were analyzed. The blood cultures collection date was used to define the time of the year for IE. Seasons were defined according to the northern hemisphere as Winter (January to March), Spring (April to June), Summer (July to September) and Autumn (October to December). If blood cultures were negative, the date of the first echocardiography with signs of infective endocarditis was noted. Results A total of 103 cases of IE were identified over a 6-year period. Mean age of IE patients was 70±13 years, 31.1% were female (n=32). No significant difference was found over the years. Overall, 76.7% had one isolated pathogen (n=79), 3.9% had 2 different pathogens (n=4), and 19.4% had persistent negative blood cultures (n=20). The most predominant infective agent was Streptococcus species (30.1% of cases, n=31), followed by Staphylococcus species (29.1%, n=30) and Enterococcus species (18.4%, n=19). The most affected valve was native aortic valve (35.9%, n=37), followed by native mitral valve (30.1%, n=31) and biological prosthetic aortic valve (17.5%, n=18). Summer had the fewer cases of IEs (18.4%), while Spring is the season with more IEs (32.0%). Negative blood cultures were more frequent in the Spring (24.2%). In Autumn, the proportion of Staphylococcus IE increases to 36% of all infections in this season. The most frequent pathogen in Winter and Spring is Streptococcus, representing 34.6% and 36.4% of IEs in these seasons. Conclusion In our population, there was no significant increase in the incidence of IEs over the years. However, there was a seasonal trend both in frequency and in specific pathogens: Summer had fewer IEs and Spring was the season with the highest frequency; Streptococcus is the most frequent pathogen in both Winter and Spring. These results may not represent the reality nationwide, and further epidemiological studies would be necessary to establish a trend.

Studies on C-Reactive Protein, Erythrocyte Sedimentation Rate, White Blood Cell and Differential White Cell Counts in Patients Diagnosed with Rheumatoid Arthritis in Owerri, Nigeria

Background: Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disease characterized by persistent synovial inflammation, joint pain, and progressive joint damage. It affects approximately 1% of the global population, disproportionately impacts women and is associated with significant morbidity, reduced quality of life, and economic burden. Aim: This study was aimed at determining the changes in some haematological parameters and C-reactive protein in rheumatoid arthritis patients attending Federal University Teaching Hospital, Owerri, Imo State, Nigeria. Methods: A cross-sectional study was carried out from the month of June to August, 2023, and all subjects who gave a written informed consent were enrolled in the study. The study population consisted of 50 rheumatoid arthritis and an equivalent number of age matched apparently healthy patients who served as controls. The procedure was carried out at the Federal University Teaching Hospital, Owerri, and standard operating procedures were followed. The results of the tests were analyzed using SPSS version 21. Eight millilitres of venous blood sample was collected at the ante-cubital vein aseptically, 4ml was dispensed into ethylenediaminetetraacetic acid containers for the estimations of erythrocyte sedimentation rate (ESR), white blood cell (WBC) and differential white cell counts, while the remaining 4ml was dispensed into plain containers for the determination of C-Reactive Proteins. The EDTA and plain containers were properly labeled with the subject’s name, sample number and date of collection. The blood sample dispensed into the EDTA containers were stored in a refrigerator at 40C while the serum was stored in a freezer at -200C prior to use. Results: The mean values of TWBC, (15.04 ± 13.98) cells/μl, neutrophils (62.67 ± 16.08) %, eosinophils (5.47 ± 3.39)%, and monocytes (4.70 ± 3.12)% were significantly raised in rheumatoid arthritis patients when compared to controls (8.93 ± 2.35) cells/μl, (51.52 ± 10.79)%, (28.07 ± 10.12)%, (3.28 ± 2.54)% and (1.80±1.29)% (p = 0.031, p= 0.000, p= 0.001, p= 0.002 and p=0.000). The mean values of lymphocytes (28.07 ± 10.12) %, was significantly reduced in rheumatoid arthritis patients when compared to controls (40.48±10.92) %. The mean value of ESR (50.16 ± 40.87) mm/hr and C-reactive protein (79.16 ± 55.55) mg/dl were significantly increased in rheumatoid arthritis patients when compared to controls (6.89 ± 2.09) mm/hr and (8.32 ± 3.03) mg/dl respectively (p= 0.000 and p=0.001). There were no significant differences in the mean values of WBC, neutrophils, lymphocytes, eosinophils, monocytes, ESR and C-reactive protein in male rheumatoid arthritis compared to female rheumatoid arthritis patients (p=0.886, p=0.695, p=0.881, p=0.652, p=0.341, p=0.516 and p=0.434). A significant positive correlation of C-reactive protein occurred with ESR, WBC and neutrophils in rheumatoid arthritis patients (r=0.32, p=0.011, r=0.44 and p=0.021, r=0.54, p=0.043), and a non-significant positive correlation with lymphocytes, monocytes and eosinophils (r=0.87, p=0.179, r=0.96, p=0.317 and r=1.06, p=0.398). Conclusion: Rheumatoid arthritis is associated with increase in total white blood cell, neutrophils, eosinophils, monocytes counts, ESR and C-reactive protein. Lymphocytopenia is linked to rheumatoid arthritis. Therefore, monitoring the parameters in rheumatoid arthritis is essential for diagnosis, disease activity assessment, and management.

Benzo[a]pyrene and phenanthrene hemoglobin adducts as biomarkers of longer-term air pollution exposure.

Urinary hydroxylated-polycyclic aromatic hydrocarbons (PAHs), with half-life less than 2 days, are established biomarkers of short-term exposure to PAHs, a ubiquitous constituent of air pollution mixture. In this study, we explore the use of PAHs-hemoglobin adducts as biomarkers of longer-term exposure to air pollution by leveraging an extant resource of blood samples collected from 235 pregnant women residing in Rochester, NY. We measured red blood cells for benzo[a]pyrene-tetrols (BaPT) and phenanthrene-tetrols (PHET), both of which are hydrolysis products of PAH-hemoglobin adduct. We utilized previously estimated PM2.5 and NO2 concentrations within the 1 km2 grid surrounding each participant's residence, calculated for up to 20 weeks before the blood collection date. Associations between PAHs tetrols and cumulative exposures to ambient PM2.5 or NO2 over different time periods were examined using a linear mixed-effects model with participant-specific random intercepts adjusting for season, gestation age, maternal age, maternal income level, and pre-pregnancy BMI. We observed positive associations between PHET concentration and cumulative PM2.5 exposure over gestational weeks 12-17, and between BaPT concentration and cumulative PM2.5 exposure over gestational weeks 3-16 prior to sample collection. Each interquartile range (IQR) increase in 14 week PM2.5 exposure (1.26 μg m-3) was associated with a 9.02% (95% CI: 0.30%, 17.7%) increase in PHET and a 12.8% (95% CI: 1.09%, 23.5%) increase in BaPT levels. In contrast, no associations were observed between either biomarker and cumulative NO2 exposures. These findings underscore the potential of PAH-hemoglobin adducts as longer-term (weeks to 4 months) exposure biomarkers of ambient PM2.5.

Amino acid substitution patterns in the <i>E6</i> and <i>E7</i> Proteins of HPV type 16: Phylogeography and Evolution

The E6 and E7 proteins of human papillomavirus (HPV) play a key role in the oncogenesis of papillomavirus infection. Data on the variability of these proteins are limited, and the factors affecting their variability are poorly understood. We analyzed the variability of the currently known sequences of HPV type 16 (HPV16) E6 and E7 proteins, taking into account their geographic origin and year of sample collection, as well as the direction of their evolution in major geographic regions of the world. All sequences belonging to HPV16 genome fragments encoding E6 and E7 oncoproteins were downloaded from the NCBI GenBank database on October 6, 2022. Samples were filtered according to the following parameters: the sequence includes at least one of the two whole open reading frames, the collection date and the country of origin are known. A total of 3,651 full-genome nucleotide sequences encoding the E6 protein and 4,578 full-genome nucleotide sequences encoding the E7 protein were sampled. The nucleotide sequences obtained after sampling and alignment were converted to amino acid sequences and analyzed using MEGA11, R, RStudio, Jmodeltest 2.1.20, BEAST v1.10.4, Fastcov, and Biostrings software. The highest variability in E6 protein structure was recorded at positions 17, 21, 32, 85, and 90, while in E7, positions 28, 29, 51, and 77 were the most variable. The samples were divided geographically into 5 heterogeneous groups: African, European, American, Southwest and South Asia and Southeast Asia. Unique amino acid substitutions (AA-substitutions) in the E6/E7 proteins of HPV16, presumably characteristic of certain ethnic groups, were identified for a number of countries. They are mainly localized in sites of known B- and T-cell epitopes and relatively rarely in structural and functional domains. The revealed differences in AA-substitutions in different ethnic groups and their colocalization with clusters of B- and T-cell epitopes suggest their possible relationship with the geographical distribution of alleles and haplotypes of the major histocompatibility complex (HLA). This may lead to the recognition of a different set of B- and T-cell epitopes of the virus, resulting in regional differences in the direction of epitope drift. Phylogenetic analysis of the nucleotide sequences encoding the E6 protein of HPV16 revealed a common ancestor, confirmed regional clustering of the E6 protein gene sequences by the set of the most common AA-substitutions, and identified cases of reversion of individual AA-substitutions when the virus distribution region changed. For the E7 protein, a similar analysis was not possible due to high sequence homology. Covariance analysis of the pooled sample revealed that there was no relationship between amino acid residues in the E6 protein, in the E7 protein, and between E6 and E7. Data obtained are important for the development of therapeutic vaccines against HPV of high carcinogenic risk.

Extremely elevated erythrocyte sedimentation rates: Associations with patients' diagnoses and clinical characteristics.

The aim of the study was to assess the etiological distribution of patients with an erythrocyte sedimentation rate (ESR) over 100 mm/hour and to evaluate differences in demographic, comorbidity, laboratory characteristics, and clinical outcomes. This retrospective observational clinical study included patients aged 18 years and older who were admitted to the internal medicine inpatient clinic between May 1, 2015 and June 1, 2021 and had ESR values above 100 mm/h. Demographic data, comorbidities, laboratory parameters, imaging studies, histopathological findings, microbiological and serological data, along with in-hospital and post-discharge mortality, were collected from the hospital's electronic database. Two independent clinicians evaluated the data to identify diagnoses associated with elevated ESR. Patients were divided into six categories based on the most likely diagnosis. The study included 441 patients, 52.6% of whom were female, and the mean age was 72.6 years. The etiological distribution was as follows: infectious diseases (34%), malignancies (31.5%), undiagnosed cases (15.9%), renal diseases (9.8 %), other causes (5 %), and rheumatologic diseases (3.8%). Etiological distributions did not differ by gender, age, or ESR ranges. The in-hospital mortality rate was 3.6%, and the overall mortality rate from hospitalization to the data collection date was 64.4%. Mortality was higher in patients with malignancies (81.3%) compared to other etiologies (p<0.001). Patients who died had higher mean age, ferritin levels, having diabetes mellitus, heart failure, or malignancy, and lower hemoglobin and lymphocyte levels compared to survivors (p<0.05 for all). Most patients with an ESR over 100 mm/hour had significant underlying medical conditions, with infectious diseases and malignancies comprising two-thirds of the cases.

SARS-CoV-2 introductions to the island of Ireland: a phylogenetic and geospatiotemporal study of infection dynamics

BackgroundIreland’s COVID-19 response combined extensive SARS-CoV-2 testing to estimate incidence, with whole genome sequencing (WGS) for genome surveillance. As an island with two political jurisdictions―Northern Ireland (NI) and Republic of Ireland (RoI)―and access to detailed passenger travel data, Ireland provides a unique setting to study virus introductions and evaluate public health measures. Using a substantial Irish genomic dataset alongside global data from GISAID, this study aimed to trace the introduction and spread of SARS-CoV-2 across the island.MethodsWe recursively searched for 29,518 SARS-CoV-2 genome sequences collected in Ireland from March 2020 to June 2022 within the global SARS-CoV-2 phylogenetic tree and identified clusters based on shared last common non-Irish ancestors. A maximum parsimony approach was used to assign a likely country of origin to each cluster. The geographic locations and collection dates of the samples in each introduction cluster were used to map the spread of the virus across Ireland. Downsampling was used to model the impact of varying levels of sequencing and normalisation for population permitted comparison between jurisdictions.ResultsSix periods spanning the early introductions and the emergence of Alpha, Delta, and Omicron variants were studied in detail. Among 4439 SARS-CoV-2 introductions to Ireland, 2535 originated in England, with additional cases largely from the rest of Great Britain, United States of America, and Northwestern Europe. Introduction clusters ranged in size from a single to thousands of cases. Introductions were concentrated in the densely populated Dublin and Belfast areas, with many clusters spreading islandwide. Genetic phylogeny was able to effectively trace localised transmission patterns. Introduction rates were similar in NI and RoI for most variants, except for Delta, which was more frequently introduced to NI.ConclusionsTracking individual introduction events enables detailed modelling of virus spread patterns and clearer assessment of the effectiveness of control measures. Stricter travel restrictions in RoI likely reduced Delta introductions but not infection rates, which were similar across jurisdictions. Local and global sequencing levels influence the information available from phylogenomic analyses and we describe an approach to assess the ability of a chosen WGS level to detect virus introductions.

Pseudomonas aeruginosa bloodstream infections in children in Queensland, Australia, 2000-2019.

To investigate the incidence, risk factors and outcomes of Pseudomonas aeruginosa bloodstream infections (P-BSI) in Queensland children aged 0-18 years. A retrospective data-linkage study was conducted of P-BSI identified by Pathology Queensland laboratories from resident Queensland children admitted to publicly-funded Queensland Hospitals between 2000 and 2019. We estimated age-standardised incidence of P-BSI and case fatality ratios (48 h, 7-, 30- and 90-day all-cause mortality from the date of the blood culture collection). Data on underlying co-morbidities related to the episode of P-BSI were collected from statewide databases. Overall, 297 episodes of P-BSI were identified in 265 children, with an overall incidence of 1.14 infections/100 000 child-years. The median age of children with P-BSI was 3.7 years [interquartile range 1.2-10.7 years]. Almost 90% (n = 266/297) of infections were healthcare-associated. There were 36 (36 episodes) neonates (31 preterm <37 weeks gestation), of whom 12 (33.3%) and 15 (41.7%) neonates died within 48 h and 7 days of the P-BSI, respectively. The remaining 229 (261 episodes) children were aged 1 month to 18 years, and 234/261 (89.7%) episodes were associated with underlying co-morbidities, especially haematological malignancies. Eleven, 15 and 24 of the 229 children beyond the neonatal age group died within 48 h (4.8%), 7 days (6.6%) and 30 days (10.5%), respectively of the index blood culture. Neonates, healthcare-associated hospital onset infections, cardiovascular co-morbidity, and multi-drug resistance were significantly associated with early mortality. P-BSI occurs predominantly in vulnerable, hospitalised children with underlying comorbidities, especially in preterm neonates and those with haematological malignancies, and is associated with substantial mortality.

New Species for Regional Mycobiotas of Russia. 9. Report: 2024

A total of 81 fungal species including ten ascomycete and 71 basidiomycete species have been recorded for the first time from 19 administrative regions of Russia: Kabardino-Balkarian Republic (6), Republic of Crimea (6), Republic of Tyva (2), Perm Krai (8), Primorsky Krai (2), Arkhangelsk Oblast (2), Bryansk Oblast (1), Irkutsk Oblast (3), Murmansk Oblast (6), Novosibirsk Oblast (1), Oryol Oblast (1), Pskov Oblast (2), Tula Oblast (27), Tyumen Oblast (5), Ulyanovsk Oblast (1), Yaroslavl Oblast (1), Saint Petersburg Federal City (1), Sevastopol Federal City (3), and Khanty-Mansi Autonomous Okrug (4 species). An annotated species list containing the data on locality, substrate, habitat type, date of collection, and voucher numbers is provided. Berkleasmium conglobatum, Biporispora europaea, Heydenia arietina, Lopadostoma pouzarii, Navicella pileata, Trizodia acrobia (Ascomycota), and Callistosporium pseudofelleum, Coltricia confluens, Melanoleuca monticola (Basidiomycota) are reported as the first records in Russia. Clitopilus geminus, Crepidotus stenocystis, Flammulina populicola, Mycena luteovariegata, and Pholiotina longistipitata are recorded in Russia for the second time. Among them, Clitopilus geminus is a new species to European Russia, and Crepidotus stenocystis is a new one to the Asian part of Russia. Amanita mairei, Cortinarius integerrimus, Flammulina elastica, and Infundibulicybe gigas are reported for the third time. New data on rare and little-collected species Purpureodiscus subisabellinus and Hydnellum gracilipes is presented. Complete sequences of ITS1–5.8S–ITS2 nuclear ribosomal DNA for nine species reported have been generated and submitted to the GenBank database.

Macrofungi Determined in Aluçdağı Nature Park (Çamlıdere, Ankara) and its Close Environs

The study is based on the macrofungi samples collected from Aluçdağı Nature Park and its environs between 2021 and 2024. As a result of field and laboratory studies, 124 macrofungi species belonging to 2 divisions, 4 classes, 15 orders, 50 families and 86 genera were determined. All of the determined species are new for the region, and 68 are new for Ankara province. The list of the species is presented together with their localities, habitats or substrates, collection dates and voucher numbers.

Comparative analysis of evapotranspiration (ET), crop water stress index (CWSI), and normalized difference vegetation index (NDVI) to delineate site-specific irrigation management zones in almond orchards

Management zones are an important aspect of precision agriculture as they help to define spatiotemporal areas that share homogenous attributes for site-specific management such as irrigation. In this study, we evaluated the potential of delineating irrigation management zones in almond (Prunus dulcis) orchards using three different variables: evapotranspiration (ET), crop water stress index (CWSI), and normalized difference vegetation index (NDVI). Multispectral and thermal images were collected on 11 days in June and July of 2020 using an instrumented aircraft flown over an almond orchard in the Central Valley of California. Obtained images were used to compute ET, CWSI, and NDVI. An unsupervised k-means clustering algorithm was used to delineate the field into management zones, and silhouette width was used to determine the optimum number of zones. Regardless of the input variable and collection date, the optimum number of irrigation management zones was identified as two. ET- and CWSI-based management zones addressed higher spatial variability in the field (up to 73.6 %) than NDVI (up to 68 %). Similarly, the level of agreement between management zones delineated using ET and CWSI was strong (kappa coefficient: 0.84 to 1.00). ET- and CWSI-based management zones also showed a trend (p < 0.1) in distinguishing the difference in the irrigation application and almond yield between the two delineated zones. This study shows that CWSI can be as effective as ET in delineating irrigation management zones, and both inputs sensitive to capture the vegetation responses to irrigation management during the summer growing season. Results from this study can be useful for growers and decision makers to practice precision irrigation management in woody perennial cropping systems.

Short and medium-term effects of the COVID-19 lockdowns on child and parent accelerometer-measured physical activity and sedentary time: a natural experiment

Abstract Background The COVID-19 pandemic has resulted in marked impacts on children’s physical activity, with large reductions in moderate-to-vigorous physical activity (MVPA) reported during lockdowns. Previous evidence showed children’s activity levels were lower and sedentary time higher immediately post-COVID lockdown, while there was little change in parental physical activity. We need to know if these patterns persist. Methods Active-6 is a natural experiment using repeated cross-sectional data conducted in two waves. Accelerometer data were collected on 393 children aged 10–11 and their parents from 23 schools in Wave 1 (June 2021-December 2021), and 436 children and parents from 27 schools in Wave 2 (January 2022-July 2022). These were compared to a pre-COVID-19 comparator group (March 2017-May 2018) of 1,296 children and parents in the same schools. Mean minutes of accelerometer-measured MVPA and sedentary time were derived for week- and weekend-days and compared across waves via linear multilevel models. We also analysed the date of data collection as a time series, to explore temporal patterns via generalised additive mixed models. Results There was no difference in children’s mean MVPA in Wave 2 (weekdays: -2.3 min; 95% CI: -5.9, 1.3 and weekends: 0.6 min; 95% CI: -3.5, 4.6) when compared to the pre-COVID-19 data. Sedentary time remained higher than pre-pandemic by 13.2 min (95% CI:5.3, 21.1) on weekdays. Differences compared to pre-COVID-19 changed over time, with children’s MVPA decreasing over winter, coinciding with COVID-19 outbreaks, and only returning to pre-pandemic levels towards May/June 2022. Parents’ sedentary time and weekday MVPA was similar to pre-COVID-19 levels, with MVPA higher than pre-pandemic by 7.7 min (95% CI: 1.4, 14.0) on weekends. Conclusion After an initial drop, children’s MVPA returned to pre-pandemic levels by July 2022, while sedentary time remained higher. Parents’ MVPA remained higher, especially at weekends. The recovery in physical activity is precarious and potentially susceptible to future COVID-19 outbreaks or changes in provision, and so robust measures to protect against future disruptions are needed. Furthermore, many children are still inactive, with only 41% meeting UK physical activity guidelines, and so there is still a need to increase children’s physical activity.