Improved detection of microbiological pathogens: role of partner and non-governmental organizations.

BACKGROUND: Proper detection of disease-causing organisms is very critical in controlling the course of outbreaks and avoiding large-scale epidemics. Nonetheless, availability of resources to address these gaps have been difficult due to limited funding. This report sought to highlight the importance of in-country partners and non-governmental organizations in improving detection of microbiological organisms in Ghanaian Public Health Laboratories (PHLs). METHODS/CONTEXT: This study was conducted between June, 2018 to August, 2019. U. S CDC engaged the Centre for Health Systems Strengthening (CfHSS) through the Association of Public Health Laboratories to design and implement strategies for strengthening three PHLs in Ghana. An assessment of the three PHLs was done using the WHO/CDS/CSR/ISR/2001.2 assessment tool. Based on findings from the assessments, partner organizations (CfHSS/APHL/CDC) serviced and procured microbiological equipment, laboratory reagents and logistics. CfHSS provided in-house mentoring and consultants to assist with capacity building in detection of epidemic-prone infectious pathogens by performing microbiological cultures and antimicrobial susceptibility tests. RESULTS: A total of 3902 samples were tested: blood (1107), urine (1742), stool (249) and cerebrospinal fluid (CSF) (804). All-inclusive, 593 pathogenic bacteria were isolated from blood cultures (70; 11.8%); urine cultures (356; 60%); stool cultures (19; 3.2%) and from CSF samples (148; 25%). The most predominant pathogens isolated from blood, urine and stool were Staphylococcus aureus (22/70; 31%), Escherichia coli (153/356; 43%) and Vibrio parahaemolyticus (5/19; 26.3%), respectively. In CSF samples, Streptococcus pneumoniae was the most frequent pathogen detected (80/148; 54.1%). New bacterial species such as Pastuerella pneumotropica, Klebsiella oxytoca, Vibrio parahaemolyticus, and Halfnia alvei were also identified with the aid of Analytical Profile Index (API) kits that were introduced as part of this implementation. Streptococcus pneumoniae and Neisseria meningitidis detections in CSF were highest during the hot dry season. Antimicrobial susceptibility test revealed high rate of S. aureus, K. pneumoniae and E. coli resistance to gentamicin (35-55%). In urine, E. coli was highly resistant to ciprofloxacin (39.2%) and ampicillin (34%). CONCLUSION: Detection of epidemic-prone pathogens can be greatly improved if laboratory capacity is strengthened. In-country partner organizations are encouraged to support this move to ensure accurate diagnosis of diseases and correct antimicrobial testing.

Genetic diversity of SARS-CoV-2 infections in Ghana from 2020-2021.

The COVID-19 pandemic is one of the fastest evolving pandemics in recent history. As such, the SARS-CoV-2 viral evolution needs to be continuously tracked. This study sequenced 1123 SARS-CoV-2 genomes from patient isolates (121 from arriving travellers and 1002 from communities) to track the molecular evolution and spatio-temporal dynamics of the SARS-CoV-2 variants in Ghana. The data show that initial local transmission was dominated by B.1.1 lineage, but the second wave was overwhelmingly driven by the Alpha variant. Subsequently, an unheralded variant under monitoring, B.1.1.318, dominated transmission from April to June 2021 before being displaced by Delta variants, which were introduced into community transmission in May 2021. Mutational analysis indicated that variants that took hold in Ghana harboured transmission enhancing and immune escape spike substitutions. The observed rapid viral evolution demonstrates the potential for emergence of novel variants with greater mutational fitness as observed in other parts of the world.

Performance of COVID-19 associated symptoms and temperature checking as a screening tool for SARS-CoV-2 infection.

INTRODUCTION: Coronavirus disease-19 (COVID-19), which started in late December, 2019, has spread to affect 216 countries and territories around the world. Globally, the number of cases of SARS-CoV-2 infection has been growing exponentially. There is pressure on countries to flatten the curves and break transmission. Most countries are practicing partial or total lockdown, vaccination, massive education on hygiene, social distancing, isolation of cases, quarantine of exposed and various screening approaches such as temperature and symptom-based screening to break the transmission. Some studies outside Africa have found the screening for fever using non-contact thermometers to lack good sensitivity for detecting SARS-CoV-2 infection. The aim of this study was to determine the usefulness of clinical symptoms in accurately predicting a final diagnosis of COVID-19 disease in the Ghanaian setting. METHOD: The study analysed screening and test data of COVID-19 suspected, probable and contacts for the months of March to August 2020. A total of 1,986 participants presenting to Tamale Teaching hospital were included in the study. Logistic regression and receiver operator characteristics (ROC) analysis were carried out. RESULTS: Overall SARS-CoV-2 positivity rate was 16.8%. Those with symptoms had significantly higher positivity rate (21.6%) compared with asymptomatic (17.0%) [chi-squared 15.5, p-value, <0.001]. Patients that were positive for SARS-CoV-2 were 5.9 [3.9-8.8] times more likely to have loss of sense of smell and 5.9 [3.8-9.3] times more likely to having loss of sense of taste. Using history of fever as a screening tool correctly picked up only 14.8% of all true positives of SARS-CoV-2 infection and failed to pick up 86.2% of positive cases. Using cough alone would detect 22.4% and miss 87.6%. Non-contact thermometer used alone, as a screening tool for COVID-19 at a cut-off of 37.8 would only pick 4.8% of positive SARS-CoV-2 infected patients. CONCLUSION: The use of fever alone or other symptoms individually [or in combination] as a screening tool for SARS-CoV-2 infection is not worthwhile based on ROC analysis. Use of temperature check as a COVID-19 screening tool to allow people into public space irrespective of the temperature cut-off is of little benefit in diagnosing infected persons. We recommend the use of facemask, hand hygiene, social distancing as effective means of preventing infection.

Field evaluation of specificity and sensitivity of a standard SARS-CoV-2 antigen rapid diagnostic test: A prospective study at a teaching hospital in Northern Ghana

BackgroundThe testing capacity for SARS-CoV-2 in Africa is rather limited. Antigen-detection rapid diagnostic tests (Ag-RDTs) are a cheap and rapid alternative to reverse transcriptase-polymerase chain reaction (RT-PCR) tests, but there is little data about their performance under real life conditions in tropical countries. ObjectiveTo evaluate the performance of a standard Ag-RDT in a population of a major hospital in northern Ghana. MethodsProspective, cross-sectional, blinded verification of the performance of the SD Biosensor Standard Q SARS-CoV-2 Ag-RDT under real life conditions in 135 symptomatic patients and 58 contacts of RT-PCR positives at Tamale Teaching Hospital in February 2021. Nasopharyngeal samples were taken under standard conditions and tested against RT-PCR in the hospital laboratory. Results193 participants (median age 35 years, 109 male) were included into the study for which both RT-PCR test and Ag-RDT results were available. A total of 42 (22%) were RT-PCR positive. Of the 42 RT-PCR positives, 27 were Ag-RDT positive, resulting in a sensitivity of 64% (95% CI 49-79). Sensitivity among symptomatic patients was 58% (95% CI 38-78). 123 were identified Ag-RDT negatives of the 151 RT-PCR negatives, resulting in a specificity of 81% (95% CI 75-87). ConclusionsSARS-CoV-2 Ag-RDTs appear to have a rather low sensitivity and particularly a low specificity under real life conditions in Africa. The role of existing Ag-RDTs in countries with high-temperature climates and limited resources still needs more data and discussion.