Retrieval of the Complete Coding Sequence of the UK-Endemic Tatenale Orthohantavirus Reveals Extensive Strain Variation and Supports Its Classification as a Novel Species

©2020 by the authors. Licensee MDPI, Basel, Switzerland. Orthohantaviruses are globally distributed viruses, associated with rodents and other small mammals. However, data on the circulation of orthohantaviruses within the UK, particularly the UK-endemic Tatenale virus, is sparse. In this study, 531 animals from five rodent species were collected from two locations in northern and central England and screened using a degenerate, pan- orthohantavirus RT-PCR assay. Tatenale virus was detected in a single field vole (Microtus agrestis) from central England and twelve field voles from northern England. Unbiased high-throughput sequencing of the central English strain resulted in the recovery of the complete coding sequence of a novel strain of Tatenale virus, whilst PCR-primer walking of the northern English strain recovered almost complete coding sequence of a previously identified strain. These findings represented the detection of a third lineage of Tatenale virus in the United Kingdom and extended the known geographic distribution of these viruses from northern to central England. Furthermore, the recovery of the complete coding sequence revealed that Tatenale virus was sufficiently related to the recently identified Traemersee virus, to meet the accepted criteria for classification as a single species of orthohantavirus

Utilising cumulative antibiogram data to enhance antibiotic stewardship capacity in the Cape Coast Teaching Hospital, Ghana

Background: Antimicrobial resistance (AMR) is a major public health challenge with its impact felt disproportionately in Western Sub-Saharan Africa. Routine microbiology investigations serve as a rich source of AMR monitoring and surveillance data. Geographical variations in susceptibility patterns necessitate regional and institutional tracking of resistance patterns to aid in tailored Antimicrobial Stewardship (AMS) interventions to improve antibiotic use in such settings. This study focused on developing a cumulative antibiogram of bacterial isolates from clinical samples at the Cape Coast Teaching Hospital (CCTH). This was ultimately to improve AMS by guiding empiric therapy. Methods: A hospital-based longitudinal study involving standard microbiological procedures was conducted from 1st January to 31st December 2020. Isolates from routine diagnostic aerobic cultures were identified by colony morphology, Gram staining, and conventional biochemical tests. Isolates were subjected to antibiotic susceptibility testing using Kirby-Bauer disc diffusion. Inhibitory zone diameters were interpreted per the Clinical and Laboratory Standards Institute guidelines and were entered and analysed on the WHONET software using the “first isolate only” principle. Results: Overall, low to moderate susceptibility was observed in most pathogen-antibiotic combinations analysed in the study. Amikacin showed the highest susceptibility (86%, n = 537/626) against all Gram-negatives with ampicillin exhibiting the lowest (6%, n = 27/480). Among the Gram-positives, the highest susceptibilities were exhibited by gentamicin (78%, n = 124/159), with clindamycin having the lowest susceptibility (27%, n = 41/154). Among the Gram-negatives, 66% (n = 426/648) of the isolates were identified phenotypically as potential extended-spectrum beta-lactamase producers. Multiple multidrug-resistant isolates were also identified among both Gram-positive and Gram-negative isolates. Low to moderate susceptibility was found against first- and second-line antibiotics recommended in the National standard treatment guidelines (NSTG). Laboratory quality management deficiencies and a turnaround time of 3.4 days were the major AMS barriers identified. Conclusions: Low to moderate susceptibilities coupled with high rates of phenotypic resistance warrant tailoring NSTGs to fit local contexts within CCTH even after considering the biases in these results. The cumulative antibiogram proved a key AMS programme component after its communication to clinicians and subsequent monitoring of its influence on prescribing indicators. This should be adopted to enhance such programmes across the country

Additional file 4 of Utilising cumulative antibiogram data to enhance antibiotic stewardship capacity in the Cape Coast Teaching Hospital, Ghana

Additional file 4. Gram-negative multidrug-resistant isolates raw data. Total number of Gram-negative isolates classified as multidrug-resistant together with the number of classes of antibiotics they were tested against and zone diameters against antibiotics tested

Additional file 1 of Utilising cumulative antibiogram data to enhance antibiotic stewardship capacity in the Cape Coast Teaching Hospital, Ghana

Additional file 1. Gram-negative Cumulative Antibiogram Raw Data. Total number of Gram-negative isolates tested against each antibiotic to produce cumulative antibiogram percentage susceptibilities

Additional file 5 of Utilising cumulative antibiogram data to enhance antibiotic stewardship capacity in the Cape Coast Teaching Hospital, Ghana

Additional file 5. Inpatient and outpatient raw data for Chi-square analysis. Raw inpatient and outpatient data used in E. coli Chi-square statistical analysis against amikacin, ceftriaxone, cefotaxime, and ciprofloxacin

Probing SARS-CoV-2-positive plasma to identify potential factors correlating with mild COVID-19 in Ghana, West Africa.

BACKGROUND: West Africa has recorded a relatively higher proportion of asymptomatic coronavirus disease 2019 (COVID-19) cases than the rest of the world, and West Africa-specific host factors could play a role in this discrepancy. Here, we assessed the association between COVID-19 severity among Ghanaians with their immune profiles and ABO blood groups. METHODS: Plasma samples were obtained from Ghanaians PCR-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-positive individuals. The participants were categorized into symptomatic and asymptomatic cases. Cytokine profiling and antibody quantification were performed using Luminex™ multiplex assay whereas antigen-driven agglutination assay was used to assess the ABO blood groups. Immune profile levels between symptomatic and asymptomatic groups were compared using the two-tailed Mann-Whitney U test. Multiple comparisons of cytokine levels among and between days were tested using Kruskal-Wallis with Dunn's post hoc test. Correlations within ABO blood grouping (O's and non-O's) and between cytokines were determined using Spearman correlations. Logistic regression analysis was performed to assess the association of various cytokines with asymptomatic phenotype. RESULTS: There was a trend linking blood group O to reduced disease severity, but this association was not statistically significant. Generally, symptomatic patients displayed significantly (p < 0.05) higher cytokine levels compared to asymptomatic cases with exception of Eotaxin, which was positively associated with asymptomatic cases. There were also significant (p < 0.05) associations between other immune markers (IL-6, IL-8 and IL-1Ra) and disease severity. Cytokines' clustering patterns differ between symptomatic and asymptomatic cases. We observed a steady decrease in the concentration of most cytokines over time, while anti-SARS-CoV-2 antibody levels were stable for at least a month, regardless of the COVID-19 status. CONCLUSIONS: The findings suggest that genetic background and pre-existing immune response patterns may in part shape the nature of the symptomatic response against COVID-19 in a West African population. This study offers clear directions to be explored further in larger studies

Additional file 6 of Probing SARS-CoV-2-positive plasma to identify potential factors correlating with mild COVID-19 in Ghana, West Africa

Additional file 6. Coronavirus disease 2019’s fatality rate in the world and Africa. The data was retrieved from WHO COVID-19 dashboard ( https://covid19.who.int/ ). The COVID-19 vaccine was rolled out in December 2020 worldwide and in February/March 2021 in Africa

Additional file 8 of Probing SARS-CoV-2-positive plasma to identify potential factors correlating with mild COVID-19 in Ghana, West Africa

Additional file 8: Table S1. The median cytokine levels of healthy individuals (n = 124). Table S2. Heathy control samples used in the study

Additional file 4 of Probing SARS-CoV-2-positive plasma to identify potential factors correlating with mild COVID-19 in Ghana, West Africa

Additional file 4. Cytokine concentration levels in COVID-19 patients. Comparison of cytokine concentration levels between COVID-19 symptomatic, asymptomatic patients, pre-COVID-19 health participants, COVID-19 pandemic health individuals and COVID-19 non-survivors. The cytokine concentration levels were measured from plasma of COVID-19 symptomatic (n = 29) and asymptomatic (n = 29), individuals, pre-COVID-19 health participants (100), COVID-19 pandemic health individuals (33) and COVID-19 non-survivors (2). The median quantity of the cytokines is shown by a horizontal line across the scatter plot while the lower and upper dotted lines represent the 25th and 75th percentiles, respectively. Statistical significance between symptomatic and asymptomatic patients were determined by a Kruskal-Wallis test with Dunn’s post hoc. (*: p 0.05)

Additional file 2 of Probing SARS-CoV-2-positive plasma to identify potential factors correlating with mild COVID-19 in Ghana, West Africa

Additional file 2. Change on cytokine concentration levels over time in COVID-19 positive individuals. The cytokine concentration levels analysed from plasma of COVID-19 asymptomatic (n = 3), monthly for four months. The quantity of the cytokines for each sampling month is shown by the line graph