scholarly journals Covid-19 deaths in Africa: prospective systematic postmortem surveillance study

BMJ ◽  
2021 ◽  
pp. n334 ◽  
Author(s):  
Lawrence Mwananyanda ◽  
Christopher J Gill ◽  
William MacLeod ◽  
Geoffrey Kwenda ◽  
Rachel Pieciak ◽  
...  
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Tertiary Care ◽  
Threshold Value ◽  
University Teaching ◽  
Surveillance Study ◽  
Polymerase Chain ◽  
The University ◽  
The Impact ◽  
Deceased People ◽  
Underlying Risk

Abstract Objective To directly measure the fatal impact of coronavirus disease 2019 (covid-19) in an urban African population. Design Prospective systematic postmortem surveillance study. Setting Zambia’s largest tertiary care referral hospital. Participants Deceased people of all ages at the University Teaching Hospital morgue in Lusaka, Zambia, enrolled within 48 hours of death. Main outcome measure Postmortem nasopharyngeal swabs were tested via reverse transcriptase quantitative polymerase chain reaction (PCR) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Deaths were stratified by covis-19 status, location, age, sex, and underlying risk factors. Results 372 participants were enrolled between June and September 2020; PCR results were available for 364 (97.8%). SARS-CoV-2 was detected in 58/364 (15.9%) according to the recommended cycle threshold value of <40 and in 70/364 (19.2%) when expanded to any level of PCR detection. The median age at death among people with a positive test for SARS-CoV-2 was 48 (interquartile range 36-72) years, and 69% (n=48) were male. Most deaths in people with covid-19 (51/70; 73%) occurred in the community; none had been tested for SARS-CoV-2 before death. Among the 19/70 people who died in hospital, six were tested before death. Among the 52/70 people with data on symptoms, 44/52 had typical symptoms of covid-19 (cough, fever, shortness of breath), of whom only five were tested before death. Covid-19 was identified in seven children, only one of whom had been tested before death. The proportion of deaths with covid-19 increased with age, but 76% (n=53) of people who died were aged under 60 years. The five most common comorbidities among people who died with covid-19 were tuberculosis (22; 31%), hypertension (19; 27%), HIV/AIDS (16; 23%), alcohol misuse (12; 17%), and diabetes (9; 13%). Conclusions Contrary to expectations, deaths with covid-19 were common in Lusaka. Most occurred in the community, where testing capacity is lacking. However, few people who died at facilities were tested, despite presenting with typical symptoms of covid-19. Therefore, cases of covid-19 were under-reported because testing was rarely done not because covid-19 was rare. If these data are generalizable, the impact of covid-19 in Africa has been vastly underestimated.

scholarly journals COVID-19 deaths detected in a systematic post-mortem surveillance study in Africa

2020 ◽  
Author(s):  
Lawrence Mwananyanda ◽  
Christopher J. Gill ◽  
William MacLeod ◽  
Geoffrey Kwenda ◽  
Rachel Pieciak ◽  
...  
Keyword(s):  
Tertiary Care ◽  
University Teaching ◽  
Surveillance Study ◽  
Post Mortem ◽  
Next Of Kin ◽  
African Countries ◽  
The University ◽  
The Impact ◽  
Written Informed Consent ◽  
Underlying Risk

ABSTRACTObjectivesLimited SARS CoV 2 testing in many African countries has constrained availability of data on the impact of COVID-19 (CV19). To address this gap, we conducted a systematic post-mortem surveillance study to directly measure the fatal impact of CV19 in an urban African population.DesignWe enrolled deceased individuals at the University Teaching Hospital (UTH) Morgue in Lusaka, Zambia. We obtained nasopharyngeal swabs for testing via reverse-transcriptase quantitative PCR (RT-qPCR) against the SARS-2 Coronavirus. We stratified deaths by CV19 status, by location, age, sex, and underlying risk factors.SettingUTH is Zambia’s largest tertiary care referral hospital and its morgue registers ∼80% of Lusaka’s deaths.ParticipantsParticipants of all ages were enrolled if within 48 hours of death and if the next of kin or representative provided written informed consent.ResultsWe enrolled 372 participants between June and September 2020, and had PCR results for 364 (99.5%). CV19 was detected in 70/364 (19.2%). The median age for CV19+ deaths was 48 years (IQR 36-72 years) and 70% were male. Most CV19+ deaths (51/70, 72.8%) occurred in the community; none had been tested for CV19 antemortem. Among the 19/70 facility deaths, six were tested antemortem. Among the 52/70 CV19 deaths with symptoms data, 44/52 had typical symptoms of CV19 (cough, fever, shortness of breath), of whom only five were tested antemortem. We identified CV19 among seven children; only one had been tested antemortem. The proportion of CV19+ deaths increased with age, but 75.7% of CV19+ deaths were aged <60 years. The five most common co-morbidities among CV19+ deaths were: tuberculosis (31.4%); hypertension (27.1%); HIV/AIDS (22.9%); alcohol use (17.1%); and diabetes (12.9%).ConclusionsContrary to expectations, CV19+ deaths were common in Lusaka. The majority occurred in the community where testing capacity is lacking. Yet few who died at facilities were tested, despite presenting with typical symptoms of CV19. Therefore, CV19 cases were under reported because testing was rarely done, not because CV19 was rare. If our data are generalizable, the impact of CV19 in Africa has been vastly underestimated.

Antimicrobial Resistance in Staphylococcus aureus at the University of Chicago Hospitals: A 15-Year Longitudinal Assessment in a Large University-Based Hospital

2003 ◽  
Vol 24 (6) ◽  
pp. 403-408 ◽  
Author(s):  
John B. Seal ◽  
Beatriz Moreira ◽  
Cindy D. Bethel ◽  
Robert S. Daum
Keyword(s):  
Staphylococcus Aureus ◽  
Methicillin Resistance ◽  
Tertiary Care ◽  
University Teaching ◽  
Annual Rate ◽  
University Of Chicago ◽  
Longitudinal Assessment ◽  
Beta Lactam ◽  
The University ◽  
The Impact

AbstractObjectives:To describe a longitudinal profile of resistance to beta-lactam antimicrobials among isolates of Staphylococcus aureus at a large university teaching hospital and to evaluate the impact of the methicillin resistance phenotype on resistance trends for non-beta-lactam antimicrobials.Design:Retrospective evaluation of antimicrobial susceptibility data for all 17,287 S. aureus isolates obtained from January 1986 through December 2000.Setting:The University of Chicago Hospitals, a family of tertiary-care, university-affiliated hospitals in Chicago, Illinois, consisting of 547 adult and pediatric beds.Results:The annual rate of resistance to methicillin increased from 13% in 1986 to 28% in 2000 (P < .001) and has not plateaued. For each non-beta-lactam antimicrobial tested, the annual rates of resistance were far higher among methicillinresistant S. aureus (MRSA) isolates than among methicillin-susceptible S. aureus (MSSA) isolates. The annual rates of resistance to the macrolide, lincosamide, and streptogramin (MLS) antimicrobials erythromycin and clindamycin increased among MSSA isolates (P < .01), but remained lower than 20%. Resistance to the MLS antimicrobials was higher among MRSA isolates (higher than 60%), but the annual rate decreased significantly during the study (P < .01).Conclusion:The prevalence of methicillin resistance among S. aureus isolates has continued to increase; resistance to non-beta-lactam antimicrobials is far more common among MRSA isolates. Recent decreases in the proportion of MRSA isolates resistant to non-beta-lactam antimicrobials suggest important changes in the epidemiology of this pathogen.

scholarly journals COVID-19 Conversion after Exposure in a Semiprivate Room at a Tertiary Care Center in Iowa, July–December 2020

2021 ◽  
Vol 1 (S1) ◽  
pp. s20-s21
Author(s):  
Alexandra Trannel ◽  
Takaaki Kobayashi ◽  
Oluchi Abosi ◽  
Kyle Jenn ◽  
Holly Meacham ◽  
...  
Keyword(s):  
Exposure Time ◽  
Care Center ◽  
Tertiary Care ◽  
Tertiary Care Center ◽  
University Of Iowa ◽  
Subsequent Conversion ◽  
Risk Of Exposure ◽  
Polymerase Chain ◽  
The University

Background: Hospital semiprivate rooms may lead to coronavirus disease 2019 (COVID-19) patient exposures. We investigated the risk of COVID-19 patient-to-patient exposure in semiprivate rooms and the subsequent risk of acquiring COVID-19. Methods: The University of Iowa Hospitals & Clinics is an 811-bed tertiary care center. Overall, 16% of patient days are spent in semiprivate rooms. Most patients do not wear masks while in semiprivate rooms. Active COVID-19 surveillance included admission and every 5 days nasopharyngeal SARS-CoV-2 polymerase chain reaction (PCR) testing. We identified inpatients with COVID-19 who were in semiprivate rooms during their infectious periods during July–December 2020. Testing was repeated 24 hours after the first positive test. Cycle threshold (Ct) values of the two tests (average Ct <30), SARS-CoV-2 serology results, clinical assessment, and COVID-19 history were used to determine patient infectiousness. Roommates were considered exposed if in the same semiprivate room with an infectious patient. Exposed patients were notified, quarantined (private room), and follow-up testing was arranged (median seven days). Conversion was defined as having a negative test followed by a subsequent positive within 14 days after exposure. We calculated the risk of exposure: number of infectious patients in semiprivate rooms/number of semiprivate patient-days (hospitalization days in semiprivate rooms). Results: There were 16,427 semiprivate patient days during July–December 2020. We identified 43 COVID-19 inpatients who roommates during their infectious periods. Most infectious patients (77%) were male; the median age was 67 years; and 22 (51%) were symptomatic. Most were detected during active surveillance: admission testing (51%) and serial testing (28%). There were 57 exposed roommates. The risk of exposure was 3 of 1,000 semiprivate patient days. In total, 16 roommates (28%) did not complete follow-up testing. Of 41 exposed patients with follow-up data, 8 (20%) converted following their exposure. Median time to conversion was 5 days. The risk of exposure and subsequent conversion was 0.7 of 1,000 semiprivate patient days. Median Ct value of the source patient was 20 for those who converted and 23 for those who did not convert. Median exposure time was 45 hours (range, 3–73) for those who converted and 12 hours (range, 1–75) for those who did not convert. Conclusions: The overall risk of exposure in semiprivate rooms was low. The conversion rate was comparable to that reported for household exposures. Lower Ct values and lengthier exposures may be associated with conversion. Active COVID-19 surveillance helps early detection and decreases exposure time.Funding: NoDisclosures: None

Immunological Stability ofClostridium difficileToxins in Clinical Specimens

2018 ◽  
Vol 39 (4) ◽  
pp. 434-438 ◽  
Author(s):  
Donna M. Schora ◽  
Lance R. Peterson ◽  
Elena A. Usacheva
Keyword(s):  
Clostridium Difficile ◽  
Detrimental Effect ◽  
Quantitative Polymerase Chain Reaction ◽  
Storage Conditions ◽  
Toxin Detection ◽  
Discernible Effect ◽  
Stool Specimens ◽  
Polymerase Chain ◽  
The Impact ◽  
Good Detection

OBJECTIVEThe impact of storage on stability and detection ofClostridium difficiletoxins in feces is poorly understood. The objective of this study was to investigate the immunological stability ofC. difficiletoxins in clinical stool specimens under different storage conditions by evaluating this stability using toxin detection by enzyme immunoassay (EIA).METHODSStool specimens positive forC. difficileinfection (CDI) by quantitative polymerase chain reaction (qPCR) were used for EIA testing with theC. difficileTox A/B II kit. The EIA-positive specimens were stored aerobically under refrigerated (4–10°C) and frozen (−30°C and −80°C) conditions. Measurement of toxin quantity was conducting using optical density (OD) on days 0, 14, 30, 60, 90, and 120 of storage.RESULTSClostridium difficiletoxins demonstrated good detection in undiluted stool specimens by EIA up to 120 days of storage. Good detection of the toxins was observed in diluted samples at refrigerated and −80°C temperatures. Dilution detrimentally affected toxin detection at −30°C.CONCLUSIONStorage of undiluted clinical stool specimens at refrigerated, −30°C, and −80°C temperatures for up to 120 days has no discernible effect on the immunological stability ofC. difficilecytotoxins. However, storage at −30°C has a detrimental effect onC. difficiletoxin stability in diluted specimens.Infect Control Hosp Epidemiol2018;39:434–438

scholarly journals TEL-AML1 regulation of survivin and apoptosis via miRNA-494 and miRNA-320a

Blood ◽  
2010 ◽  
Vol 116 (23) ◽  
pp. 4885-4893 ◽  
Author(s):  
Christofer Diakos ◽  
Sheng Zhong ◽  
Yuanyuan Xiao ◽  
Mi Zhou ◽  
Gisele M. Vasconcelos ◽  
...  
Keyword(s):  
Fusion Protein ◽  
Mirna Expression ◽  
Childhood Leukemia ◽  
Lymphoblastic Leukemia ◽  
Quantitative Polymerase Chain Reaction ◽  
Survivin Expression ◽  
Bioinformatic Analysis ◽  
Expression Arrays ◽  
Polymerase Chain ◽  
The Impact

Abstract There is increasing evidence that miRNA and transcription factors interact in an instructive fashion in normal and malignant hematopoiesis. We explored the impact of TEL-AML1 (ETV6-RUNX1), the most common fusion protein in childhood leukemia, on miRNA expression and the leukemic phenotype. Using RNA interference, miRNA expression arrays, and quantitative polymerase chain reaction, we identified miRNA-494 and miRNA-320a to be up-regulated upon TEL-AML1 silencing independently of TEL expression. Chromatin immunoprecipitation analysis identified miRNA-494 as a direct miRNA target of the fusion protein TEL-AML1. Using bioinformatic analysis as well as functional luciferase experiments, we demonstrate that survivin is a target of the 2 miRNAs. miRNA-494 and miRNA-320a were introduced to the cells by transfection and survivin expression determined by Western blot analysis. These miRNAs blocked survivin expression and resulted in apoptosis in a similar manner as TEL-AML1 silencing by itself; this silencing was also shown to be Dicer-dependent. miRNAs-494 and -320a are expressed at lower levels in TEL-AML1+ leukemias compared with immunophenotype-matched nonTEL-AML1 acute lymphoblastic leukemia subtypes, and within TEL-AML1+ leukemias their expression is correlated to survivin levels. In summary our data suggest that TEL-AML1 might exert its antiapoptotic action at least in part by suppressing miRNA-494 and miRNA-320a, lowering their expression causing enhanced survivin expression.

scholarly journals Healthcare Workers Hospitalized with COVID-19: Outcomes from the Burden of COVID-19 study at the University of Louisville Center of Excellence for Research in Infectious Diseases [CERID]

2020 ◽  
Vol 4 (1) ◽  
Author(s):  
Ruth Carrico ◽  
Keyword(s):  
Healthcare Workers ◽  
Small Population ◽  
Long Term Effects ◽  
University Of Louisville ◽  
The Mean ◽  
Polymerase Chain ◽  
The University ◽  
Epidemiological Characteristics ◽  
The Impact

Introduction: On March 6, 2020, the current ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also known as COVID-19 reached the commonwealth of Kentucky. Within days the first cases of infection and hospitalization were identified among healthcare workers (HCW) in Kentucky, other states in the U.S., and around the world. There is little information available regarding the impact of COVID-19 on the HCW population within this area. The objective of this study is to describe the baseline characteristics of hospitalized HCWs infected with COVID-19. Methods: Data collection was performed as part of a retrospective study of patients hospitalized with COVID-19 in any of nine acute care hospitals in Louisville. COVID-19 infection was confirmed using Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR). Descriptive statistics were performed on clinical and epidemiological characteristics of hospitalized patients with COVID-19 who had indicated healthcare as their occupation. Results: Of the 700 adults hospitalized with COVID-19 from March 7 through July 1, 2020, 23 were HCWs. The mean age was 51 years and 78% were female. The majority of hospitalized HCWs had comorbidities including obesity (70%), hypertension (57%), hyperlipidemia (35%) and diabetes (26%). Common symptoms reported were fever (70%), dyspnea (78%), cough (78%) and fatigue (57%). Nine HCWs (39%) were admitted to the intensive care unit (ICU) and 6 (26%) developed acute respiratory distress syndrome (ARDS). Two (9%) patients developed a new, serious arrhythmia, two sustained cardiac arrest (9%), and two (9%) died in-hospital. Conclusions: Older adult HCWs with underlying health conditions such as obesity and hypertension were more likely to be hospitalized and have severe in-hospital complications. One HCW death due to COVID-19 was identified in this small population. These findings can help to identify and strengthen approaches to protect HCWs from SARS-CoV-2 infection and from long term effects of COVID-19.

scholarly journals Incidence of Asiatic Citrus Canker on Trifoliate Orange and Its Hybrid Accessions in a Florida Field Planting

HortScience ◽  
2021 ◽  
pp. 1-7
Author(s):  
Ed Stover ◽  
Chandrika Ramadugu ◽  
Mikeal Roose ◽  
Joseph Krystel ◽  
Richard F. Lee ◽  
...  
Keyword(s):  
Sweet Orange ◽  
Quantitative Polymerase Chain Reaction ◽  
Citrus Canker ◽  
Chain Reaction ◽  
Department Of Agriculture ◽  
Randomized Design ◽  
Consistent Manner ◽  
Polymerase Chain ◽  
Completely Randomized Design ◽  
The University

Asiatic citrus canker (ACC) foliar lesions were evaluated on progenies of 84 seed-source genotypes (“parent genotypes”) from the Citrus Variety Collection (CVC) of the University of California at Riverside (UCR) of Citrus trifoliata and hybrids between C. trifoliata and other Citrus species and hybrids. Trees were planted Aug. 2013 in a completely randomized design at the Fort Pierce U.S. Department of Agriculture (USDA) grove. Plants were assessed visually Aug. 2017, Sept. 2019, and Sept. 2020 for distinctive ACC lesion incidence and severity. Progeny were compared by parent genotypes using nonparametric analysis. Incidence of ACC [percentage of leaves displaying symptoms, verified by quantitative polymerase chain reaction (qPCR) to be associated with Xanthomonas citri pv. citri] across parent genotypes ranged from 8% to 80% (mean, 49%) of leaves affected in 2017, from 4% to 58% (mean, 29%) in 2019, and 8% to 46% (mean, 25%) in 2020. In 2017, of 49 C. trifoliata parent genotypes, only four separated from the two highest ACC-incidence statistical categories [Citrus Research Center (CRC) 3345, 3484, 3888, and 4017]. whereas 29 of the 35 C. trifoliata hybrids displayed lower ACC incidence, which separated from the two highest statistical categories. In 2019, of the C. trifoliata, only six separated from the highest ACC-incidence statistical category (CRC 3330, 3484, 3547, 3549, 3876, and 3888), whereas all 35 C. trifoliata hybrids displayed lower ACC incidence and separated from the highest statistical category, and 26 hybrids separated from 18 of the C. trifoliata. In 2020, only three C. trifoliata separated from the highest ACC-incidence statistical category (CRC 2861, 3549, and 3888) and 20 hybrids separated from 18 of the C. trifoliata. By parent genotype, ACC incidence correlated substantially between each pair of the 3 years, with r2 values of 0.39, 0.57, and 0.65. Of 34 hybrids validated, similar numbers had C. trifoliata, grapefruit (C. ×aurantium var. racemosa), and sweet orange (C. ×aurantium var. sinensis) chloroplasts. Chloroplast type affected ACC incidence and severity, but not in a consistent manner. Near-isogenic groups within C. trifoliata, as determined by DNA markers, were associated with some statistically different ACC sensitivity. Overall, hybrids of C. trifoliata with other citrus types displayed markedly reduced ACC sensitivity compared with C. trifoliata, indicating that this trait is readily overcome through breeding.

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