The Bacterial Species Behind the Wound and Their Antibacterial Resistant Pattern: A Three-Year Retrospective Study at St. Dominic Hospital, Akwatia, Ghana.

BACKGROUND: Wound infections are often underestimated issues that can lead to chronic illnesses, and since the introduction of antibiotics, wound complications have become less common. However, due to the increased and irrational use of these antibiotics, the resistance in the bacterial isolates has become very common. This has led to reduced treatment options, delay in wound healing, and high treatment costs. This study aimed to investigate bacterial wound infections and their antibiotic resistance at St. Dominic Hospital, Ghana. METHODS: A total of 517 records of wound swab culture and susceptibility testing, and patient demographics from 2020 to 2022 were collected from the microbiology unit of St. Dominic Hospital in the Eastern Region of Ghana. The data were entered into Microsoft Excel 2019, cleaned, and exported into IBM SPSS v26 for the statistical analysis. p < 0.05 was considered statistically significant for all analyses. RESULTS: The overall prevalence of bacteriological agents causing wound infection in individuals who visited the St. Dominic Hospital from 2020 to 2022 was 70.21% (363/517), with S. aureus 79/363 (21.76%) being the most abundant isolate. Out of the 79 S. aureus isolated, 40 (50.63%) and 39 (49.37%) were resistant to ampicillin and cephalexin, respectively. More than 50% of the predominant Gram-negative isolate, K. pneumoniae, were resistant to clindamycin 45/72 (62.50%) but susceptible to levofloxacin 70/72 (97.22%), cefotetan 69/72 (95.83%), and chloramphenicol 67/72 (93.06%). CONCLUSION: Antibacterial susceptibility patterns revealed significant resistance trends, particularly among Gram-negative isolates, emphasizing the urgent need for prudent antibiotic use and ongoing surveillance to combat resistance.

Factors Influencing HIV Status Disclosure to Partners Among Antiretroviral Therapy Clients in the Upper East Region, Ghana.

In Ghana, HIV status disclosure to partners is voluntary. This study sought to determine the factors associated with HIV status disclosure to partners among antiretroviral therapy (ART) clients in the Upper East Region. A matched case-control study (1:1) was carried out in nine ART sites in the Upper East region in which 100 ART sexually active clients who had not disclosed their status to their partners were compared with 100 ART sexually ART clients who had disclosed their status to their partners. To each of the 200 study participants, a structured questionnaire was administered to elicit relevant responses. Discordant pair analysis was done with Mantel-Haenszel matched test to determine associations between variables. The study found persons with informal education more likely to disclose HIV status, whereas persons living apart or not having children with a partner were less likely to disclose their status to their sexual partners. On the other hand, active involvement or participation in ART-related services were more likely going to impact HIV status disclosure. Early initiation of ART, while adherence to ART services and the use of treatment monitors were less associated with disclosure. Active participation in ART related services such as prompt initiation of ART following diagnosis, adherence promotion, and treatment monitoring should be encouraged to promote HIV status disclosure among sexual partners.

Carbapenemase Production and Detection of Colistin-Resistant Genes in Clinical Isolates of Escherichia Coli from the Ho Teaching Hospital, Ghana.

Background: Effective and successful treatment of infectious diseases is a significant gain in clinical settings. However, resistance to antibiotics, especially the last-resort medicines, including carbapenems and colistin is on the rise. Aim: The aim of this study was to detect carbapenemase production and colistin-resistant genes in clinical isolates of Escherichia coli. Method. The study was a cross-sectional study carried out from July 2018 to June 2019. One hundred and thirty-five nonrepetitive E. coli isolates obtained from various clinical samples were screened for carbapenemase production using meropenem (10 µg) and imipenem (10 µg) disks. Screened-positive isolates were further subjected to a confirmatory test using modified carbapenem inhibition method (mCIM). Deoxyribonucleic acid (DNA) was extracted from all the isolates to detect colistin-resistant genes by polymerase chain reaction. Data were analyzed using GraphPad Prism version 8.00 for Windows and IBM SPSS version 26 (IMB Corp. New York, USA). Results: Of the 135 isolates, 2 were screened positive for carbapenemase production but tested negative to mCIM. With the colistin-resistant genes, only mcr-1 and mcr-2_700bp were detected in 3 of the E. coli isolates, representing 2.2%. The mcr-1 was detected in a high vaginal swab sample of a female aged between 65 and 84 years. Mcr-2_700bp was also detected in urine and blood samples of the patients. Conclusion: The study investigated the presence of carbapenemase and colistin-resistant genes in E. coli organisms. The absence of carbapenemase in the isolates and the detection of colistin-genes call for strict infection prevention and control practices to prevent their introduction and spread to other bacterial species, respectively.

Characterization of putative drug resistant biomarkers in Plasmodium falciparum isolated from Ghanaian blood donors.

BACKGROUND: Plasmodium falciparum parasites, which could harbour anti-malaria drug resistance genes, are commonly detected in blood donors in malaria-endemic areas. Notwithstanding, anti-malaria drug resistant biomarkers have not been characterized in blood donors with asymptomatic P. falciparum infection. METHODS: A total of 771 blood donors were selected from five districts in the Greater Accra Region, Ghana. Each donor sample was screened with malaria rapid diagnostic test (RDT) kit and parasitaemia quantified microscopically. Dried blood spots from malaria positive samples were genotyped for P. falciparum chloroquine resistance transporter (Pfcrt), P. falciparum multi-drug resistance (Pfmdr1), P. falciparum dihydropteroate-synthetase (Pfdhps), P. falciparum dihydrofolate-reductase (Pfdhfr) and Kelch 13 propeller domain on chromosome 13 (Kelch 13) genes. RESULTS: Of the 771 blood donors, 91 (11.8%) were positive by RDT. Analysis of sequence reads indicated successful genotyping of Pfcrt, Pfmdr1, Pfdhfr, Pfdhps and Kelch 13 genes in 84.6, 81.3, 86.8, 86.9 and 92.3% of the isolates respectively. Overall, 21 different mutant haplotypes were identified in 69 isolates (75.8%). In Pfcrt, CVIET haplotype was observed in 11.6% samples while in Pfmdr1, triple mutation (resulting in YFN haplotype) was detected in 8.1% of isolates. In Pfdhfr gene, triple mutation resulting in IRNI haplotype and in Pfdhps gene, quintuple mutation resulting in AGESS haplotype was identified in 17.7% parasite isolates. Finally, five non-synonymous Kelch 13 alleles were detected; C580Y (3.6%), P615L (4.8%), A578S (4.8%), I543V (2.4%) and A676S (1.2%) were detected. CONCLUSION: Results obtained in this study indicated various frequencies of mutant alleles in Pfcrt, Pfmdr1, Pfdhfr, Pfdhps and Kelch 13 genes from P. falciparum infected blood donors. These alleles could reduce the efficacy of standard malaria treatment in transfusion-transmitted malaria cases. Incorporating malaria screening into donor screening protocol to defer infected donors is therefore recommended.

Chronic Noncommunicable Diseases in 6 Low- and Middle-Income Countries: Findings From Wave 1 of the World Health Organization's Study on Global Ageing and Adult Health (SAGE).

In this paper, we examine patterns of self-reported diagnosis of noncommunicable diseases (NCDs) and prevalences of algorithm/measured test-based, undiagnosed, and untreated NCDs in China, Ghana, India, Mexico, Russia, and South Africa. Nationally representative samples of older adults aged ≥50 years were analyzed from wave 1 of the World Health Organization's Study on Global Ageing and Adult Health (2007-2010; n = 34,149). Analyses focused on 6 conditions: angina, arthritis, asthma, chronic lung disease, depression, and hypertension. Outcomes for these NCDs were: 1) self-reported disease, 2) algorithm/measured test-based disease, 3) undiagnosed disease, and 4) untreated disease. Algorithm/measured test-based prevalence of NCDs was much higher than self-reported prevalence in all 6 countries, indicating underestimation of NCD prevalence in low- and middle-income countries. Undiagnosed prevalence of NCDs was highest for hypertension, ranging from 19.7% (95% confidence interval (CI): 18.1, 21.3) in India to 49.6% (95% CI: 46.2, 53.0) in South Africa. The proportion untreated among all diseases was highest for depression, ranging from 69.5% (95% CI: 57.1, 81.9) in South Africa to 93.2% (95% CI: 90.1, 95.7) in India. Higher levels of education and wealth significantly reduced the odds of an undiagnosed condition and untreated morbidity. A high prevalence of undiagnosed NCDs and an even higher proportion of untreated NCDs highlights the inadequacies in diagnosis and management of NCDs in local health-care systems.

Short-term treatment outcomes in human immunodeficiency virus type-1 and hepatitis B virus co-infections.

BACKGROUND: Co-infection of HIV with HBV is common in West Africa but little information is available on the effects of HBV on short-term therapy for HIV patients. A 28 day longitudinal study was conducted to examine short-term antiretroviral therapy (ART) outcomes in HIV infected individuals with HBV co-infection. METHODS: Plasma from 18 HIV infected individuals co-infected with HBV and matched controls with only HIV infection were obtained at initiation, and 7 and 28 days after ART. HIV-1 viral load changes were monitored. Clinical and demographic data were also obtained from patient folders, and HIV-1 drug resistance mutation and subtype analysis performed. RESULTS: The presence of HBV co-infection did not significantly affect HIV-1 viral load changes within 7 or 28 days. The CD4(+) counts on the other hand of patients significantly affected the magnitude of HIV-1 viral load decline after 7 days (ρ = -0.441, p = 0.040), while the pre-ART HIV-1 VL (ρ = 0.844, p = <0.001) and sex (U = 19.0, p = 0.020) also determined HIV-1 viral load outcomes after 28 days of ART. Even though the geometric sensitivity score of HIV-1 strains were influenced by the HIV-1 subtypes (U = 56.00; p = 0.036), it was not a confounder for ART outcomes. CONCLUSIONS: There may be the need to consider the confounder effects of sex, pre-ART CD4(+), and pre-ART HIV-1 viral load in the discourse on HIV and HBV co-infection.

Genetic landscape for majority and minority HIV-1 drug resistance mutations in antiretroviral therapy naive patients in Accra, Ghana.

Background: The successful detection of drug-resistance mutations (DRMs) in HIV-1 infected patients has improved the management of HIV infection. Next-generation sequencing (NGS) to detect low-frequency mutations is predicted to be useful for efficiently testing minority drug resistance mutations, which could contribute to virological failure. This study employed Sanger sequencing and NGS to detect and compare minority and majority drug resistance mutations in HIV-1 strains in treatment-naive patients from Ghana. Method: From a previous study, 20 antiretroviral therapy (ART)-naive participants were selected for a cross-sectional study. Sanger sequencing and NGS techniques were used to detect the majority and minority HIV drug resistance (HIVDR) mutations, respectively, in the protease (PR) and partial reverse transcriptase (RT) genes. NGS detected mutations at 1 % and 5 % frequencies and Sanger sequencing at ≥20 % frequencies. The sequences obtained from NGS and Sanger sequencing platforms were submitted to the Stanford HIV drug resistance database for subtyping, mutation identification, and interpretations. Results: Sequences from the twenty participants where the CRF02_AG was the predominant strain (16, 80 %) were analyzed. NGS detected 25 mutations in the RT and PR genes, compared to 21 mutations by Sanger sequencing. Minority DRMs were detected at the prevalence of 55.0 % with NGS against 35 % DRMs by Sanger sequencing. One of the patients had eight different HIVDR variants, with two minority variants. These mutations were directed against PI (K20I and D30DN), NNRTI (Y181C, M23LM and V108I) and NRTI (K65R, M184I, and D67N). Conclusion: The study affirms the usefulness of genomic sequencing for drug resistance testing in HIV. It further shows that Sanger sequencing alone may not be adequate to detect mutations and that NGS capacity should be developed and deployed in the Ghanaian clinical settings for patients living with HIV.

Faecal shedding of SARS-CoV-2 from patients with asymptomatic and mild COVID-19 without gastrointestinal symptoms in Ghana.

OBJECTIVE: In this study, we sought to determine whether faecal shedding occurs among SARS-COV-2 positive Ghanaians, as reported elsewhere. Hence we assayed for SARS-COV-2 in the stools of 48 SARS-COV-2 confirmed patients at the Ho Municipal Hospital in Ghana. RESULTS: Of the 48 COVID-19 patients, 45 (93.8%) had positive tests for SARS-CoV-2 faecal shedding. About 60% reported no respiratory symptoms, while only 2% (1 patient) reported gastrointestinal (GI) symptoms in the form of nausea. Other symptoms reported included headache (57.9%), weakness (57.9%), cough (52.6%), blocked/runny nose (47.4%), fever (31.6%), sore throat (31.6%), and shortness of breath (21.1%). One person complained of nausea (5.3%) Semi-quantitative comparison of the SARS COV-2 viral loads in matched respiratory and faecal samples using the cycle threshold (CT) values revealed no statistical differences. Furthermore, the duration between collection of respiratory and faecal samples did not have any direct influence on the differences in the CT values. This suggests that treatment and use of sewage for environmental surveillance of SARS COV-2 could be a potential public health countermeasure.

Knowledge and prevalence of common sexually transmitted infections among patients seeking care at selected health facilities in Southern Ghana.

The burden of Sexually transmitted infections (STIs) remains a public health problem that should be addressed considering its effect on society and close association with HIV. This study aimed to determine the knowledge and prevalence of common STIs and associated risk factors among adult patients seeking STI care in health facilities in Ho Municipality. This was an analytical cross-sectional study involving 178 adult clients seeking treatment for suspected STIs, from November 2020 to April 2021. Data on participants' demographic characteristics, knowledge and health-seeking behaviour for STI therapy was obtained. Urine and blood samples were also taken from each participant for microbiological screening to identify the infecting pathogen and the specific STI. Multiple logistic regression and chi-square analyses were used to test the significance of associations. Of the 178 participants, 71.91% (n = 128) were women and 61.24% (n = 109) were unmarried. About 13% (n = 23) had poor knowledge of STIs. Prevalence of the STIs was 24.72% (n = 44) of which gonorrhoea was the highest 11.24% (n = 20), followed by chlamydia 10.11% (n = 18) and syphilis 7.30% (n = 13). Of all the participants, 3.37% (n = 6) had co-infections with at least 2 pathogens. Infection with all three pathogens was observed in a single participant. Participants who were married were associated with 61% reduced odds of sexually transmitted infection compared to participants who were unmarried (AOR = 0.39; Cl = 0.17-0.89). Participants who smoked had 6.5 times increased odds of the infection compared to nonsmoking participants (AOR = 6.51; Cl = 1.07-39.56). Although knowledge of STIs was high, it did not appear to contribute to lowering of the prevalence. This suggests there may be other factors other than awareness or knowledge driving STIs. There is an urgent need for further studies to ascertain the drivers of STIs beyond knowledge and awareness in the public.

The use of the WHO criteria to detect severe malaria among patients clinically diagnosed with uncomplicated malaria.

The World Health Organization (WHO) strict defining criteria were used to identify severe malaria among Ghanaian patients clinically diagnosed as uncomplicated malaria. From each study participant, blood haemoglobin (Hb) and plasma bilirubin levels were estimated using automated analyzers. According to the WHO, the criteria for diagnosing severe malaria among children (< 12 years) was assessed using Hb < 5 g/dL and among other patients ≥ 12 years, Hb < 7 g/dL with parasitemia > 10,000/µL, plasma bilirubin > 50 µmol/L amidst parasitemia > 100,000/µL and P. falciparum hyperparasitaemia (> 500,000 parasites/µL). Patients initially diagnosed with asymptomatic malaria (n = 347) were recruited. The parasitemia range was 540-863,402 parasite/µL. Overall, 86.2% of the patients had uncomplicated malaria while 13.8% of the patients were diagnosed with severe malaria of various origins. In children < 12 years, 10.8% (17/157) had Hb < 5g/dL with parasitaemia < 10,000 parasites/µL and in other patients (≥ 12 years), 6.3% (12/190) of them recorded Hb < 7g/dL with parasitaemia < 10,000 parasites/µL. Furthermore, 13.8% (48/347) had serum bilirubin levels > 50 µmol/L with parasitemia > 100,000/µL. In all the patients with hyperbilirubinemia, Hb levels fell below either 5g/dL or 7g/dL, for patients less than and 12 years or more, respectively. Finally, 1.7% (6/347) of the patients with malaria had parasite counts (> 500,000 parasites/µL). Irrespective of the etiology, patients diagnosed with severe malaria presented with pallor, vomiting, diarrhea, chills, fever and nausea, concurrently. Without comprehensive laboratory evaluation, patients with severe malaria could be misdiagnosed. Therefore, healthcare facilities need adequate human and logistical resources to be able to diagnose severe malaria for appropriate management to avert any untoward outcomes.

Co-infections of SARS-CoV-2 with respiratory syncytial virus and human influenza A in patients with symptoms of COVID-19 in Ghana: A retrospective study.

Background: During the COVID-19 pandemic the aetiology of respiratory illnesses were narrowed to SARS-CoV-2. This prevented diagnosis of other pathogens and patients were not notified of the accurate diagnosis of their illnesses when SARS-CoV-2 was absent. It is therefore important to look back and determine what else was present but was missed. Objective: This retrospective study sought to gain insights into prevalence of respiratory syncytial virus (RSV) and influenza A alongside SARS-CoV-2 in patients who reported with clinical symptoms of respiratory illnesses. Methods: Samples from patients who had reported of respiratory symptoms were selected at random from a pool. RNA was extracted and RT-PCR was performed for SARS-CoV-2, RSV and Influenza A in parallel. Data on the clinical symptoms was extracted from case-base forms and analysed. Results: Of the 400 symptomatic samples tested, prevalence of SARS-CoV-2, influenza A and RSV was 20.3 %, 2.0 % and 0.5 % respectively. Only one sample tested positive for SARS-CoV-2 and influenza A. About 77 % of the symptomatic cases did not test positive for any of the three agents. Cough (79 %) was the most common symptom followed by fever and chills, headache, sore throat and runny nose. Conclusion: The large proportion of symptomatic cases that tested negative for all three respiratory viruses raises a flag and a need for more investigations into the actual burden of respiratory aetiologic agents during the pandemic. With the low levels of co-infections, parallel testing may not be needed however, a strong case for multiplex tests for respiratory agents exists.

Point-of-care circulating cathodic antigen positivity and associated factors in school children one year after mass praziquantel administration in an endemic district in Ghana.

Background: Mass drug administration of praziquantel is expected to reduce Schistosome carriage in treated children in endemic communities. However, the effectiveness of this annual exercise has not been assessed in Ghana. Therefore, this study aimed to detect viable Schistosoma mansoni infection using point-of-care circulating cathodic antigen (POC-CCA) positivity as proxy and associated factors in children previously treated with praziquantel in an endemic municipality in Ghana. Materials and methods: This cross-sectional study was done in the Assin Central municipality in the Central Region of Ghana. School children, less than 16 years of age, treated with 40 mg/kg of praziquantel (treatment period: February-March 2019), provided early morning urine (∼40 mL) and stool (∼4 g) samples. Immediately, POC-CCA (ICT International, South Africa) was done, while S. mansoni ova were detected in formalin fixed samples using microscopy later. Additionally, participant's socio-demographic information and factors associated with S, mansoni infection transmission were collected from each child. Results: A total of 520 children participated in the study (males-51.9%, majority age range [9-11 years, 34.4%]). Overall, 244 (46.9%) were positive for urinary CCA with no S. mansoni detected by microscopy. POC-CCA positivity was higher in females (48.4%), children with 2-3 siblings (49.3%), children aged 6-8-year range (55.4%) and residents of Brofoyedur (52%). However, age (x2 = 16.1, p = 0.0003) and town of residence (x2 = 11.7, p = 0.019) associated with CCA positivity. Further, location of water body (x2 = 16.4, p = 0.008), frequency of water contact (x2 = 12.3, p = 0.015) and handling of the Biomphalaria intermediate host (x2 = 5.1, p = 0.024) associated with POC-CCA outcome. Conclusion: About 47% of the school children were positive for CCA, one year after mass praziquantel administration in the Assin Central municipality. Varied factors associated with the post-praziquantel administration POC-CCA positivity. This study should be replicated in other endemic areas to identify groups at risk of parasite persistence or reinfection to inform modification of control and preventive measures.

Pre-vaccination seroprevalence of SARS-CoV-2 antibodies in the Volta Region, Ghana.

Objectives: Before administration of the first dose of the AstraZeneca 2019 SARS-CoV-2 vaccine to selected prioritized groups in the Volta regional capital of Ghana, we determined the pre-vaccination status of prospective recipients and established the baseline exposure status 1 year after the first case was reported. Methods: After informed consent, blood samples were collected for the detection of SARS-CoV-2 immunoglobulin (Ig) M/IgG antibodies using rapid diagnostic test kits. A total of 409 individuals (mean age 27 years) consented and participated in the study, comprising 70% students and others were health staff and educators who presented themselves for vaccination. Results: The overall exposure rate of SARS-CoV-2 was 12.7% (95% confidence interval [CI] 9.6-16.3). The prevalence of SARS-CoV-2 IgM and IgG were 4.2% (95% CI 2.4-6.6) and 5.6% (95% CI 3.6-8.3), respectively. IgM and IgG were detected in 2.9% (95% CI 1.5-5.1) of the respondents. The exposure rates were higher in participants over 40 years old (15.5%). Participants without a history of COVID-19-like symptoms had an exposure rate of 13.0% and those without any chronic diseases was 13.2%. Conclusion: Pre-vaccination exposure was relatively low and underscored the need for vaccination i to increase protection in communities and disease outcomes.

Association between Interleukin-6 Gene Polymorphism (rs1800795 and rs1800796) and Type 2 Diabetes Mellitus in a Ghanaian Population: A Case-Control Study in the Ho Municipality.

Background: There is no conclusive evidence on the association between interleukin- (IL-) 6 gene polymorphism and type 2 diabetes mellitus (type 2 DM). Thus, this study is aimed at evaluating the role of rs1800795 and rs1800796 polymorphisms in the pathogenesis of type 2 DM among Ghanaians in the Ho Municipality. Materials and Methods: We recruited into this hospital-based case-control study 174 patients with type 2 DM (75 DM alone and 99 with DM+HTN) and 149 healthy individuals between 2018 and 2020. Demographic, lifestyle, clinical, anthropometric, and haemodynamic variables were obtained. Fasting blood samples were collected for haematological, biochemical, and molecular analyses. Genomic DNA was extracted, amplified using Tetra-primer amplification refractory mutation system-polymerase chain reaction (T-ARMS-PCR) technique, and genotyped for IL-6 gene polymorphism. Logistic regression analyses were performed to assess the association between IL-6 gene polymorphism and type 2 DM. Results: The minor allele frequency (MAF) of the rs1800795 and rs1800796 polymorphisms was higher in DM alone (57.5%, 62.0%) and DM with HTN groups (58.3%, 65.3%) than controls (33.1%, 20.0%). Carriers of the rs1800795GC genotype (aOR = 2.35, 95% CI: 1.13-4.90, p = 0.022) and mutant C allele (aOR = 2.41, 95% CI: 1.16-5.00, p = 0.019) as well as those who carried the rs1800796GC (aOR = 8.67, 95% CI: 4.00-18.90, p < 0.001) and mutant C allele (aOR = 8.84, 95% CI: 4.06-19.26, p = 0.001) had increased odds of type 2 DM. For both polymorphisms, carriers of the GC genotype had comparable levels of insulin, HOMA-IR, and fasting blood glucose (FBG) with those who carried the GG genotype. IL-6 levels were higher among carriers of the rs1800796GC variant compared to carriers of the rs1800796GG variant (p = 0.023). The rs1800796 polymorphism, dietary sugar intake, and exercise status, respectively, explained approximately 3% (p = 0.046), 3.2% (p = 0.038, coefficient = 1.456), and 6.2% (p = 0.004, coefficient = -2.754) of the variability in IL-6 levels, suggesting weak effect sizes. Conclusion: The GC genotype and mutant C allele are risk genetic variants associated with type 2 DM in the Ghanaian population. The rs1800796 GC variant, dietary sugar intake, and exercise status appear to contribute significantly to the variations in circulating IL-6 levels but with weak effect sizes.

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.

The SARS-CoV-2 genome occupies a unique place in infection biology - it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. As a result, these phylogenetic data are an incredibly valuable resource for science and public health. However, the vast majority of the data was sequenced by tiling amplicons across the full genome, with amplicon schemes that changed over the pandemic as mutations in the viral genome interacted with primer binding sites. In combination with the disparate set of genome assembly workflows and lack of consistent quality control (QC) processes, the current genomes have many systematic errors that have evolved with the virus and amplicon schemes. These errors have significant impacts on the phylogeny, and therefore over the last few years, many thousands of hours of researchers time has been spent in "eyeballing" trees, looking for artefacts, and then patching the tree. Given the huge value of this dataset, we therefore set out to reprocess the complete set of public raw sequence data in a rigorous amplicon-aware manner, and build a cleaner phylogeny. Here we provide a global tree of 3,960,704 samples, built from a consistently assembled set of high quality consensus sequences from all available public data as of March 2023, viewable at https://viridian.taxonium.org. Each genome was constructed using a novel assembly tool called Viridian (https://github.com/iqbal-lab-org/viridian), developed specifically to process amplicon sequence data, eliminating artefactual errors and mask the genome at low quality positions. We provide simulation and empirical validation of the methodology, and quantify the improvement in the phylogeny. Phase 2 of our project will address the fact that the data in the public archives is heavily geographically biased towards the Global North. We therefore have contributed new raw data to ENA/SRA from many countries including Ghana, Thailand, Laos, Sri Lanka, India, Argentina and Singapore. We will incorporate these, along with all public raw data submitted between March 2023 and the current day, into an updated set of assemblies, and phylogeny. We hope the tree, consensus sequences and Viridian will be a valuable resource for researchers.

Detection of cytological abnormalities in urothelial cells from individuals previously exposed or currently infected with Schistosoma haematobium.

Urinary schistosomiasis has long been associated with bladder cancer, but it is still not clear the mechanisms involved. Schistosoma haematobium causes injury and disruptions in the integrity of the urothelium. The cellular and immunologic responses to the infection lead to the formation of granulomata. The ability to use cellular morphological changes to predict the risk of developing bladder cancer following S. haematobium infection is thus important. This study assessed the cellular changes in the urine associated with schistosomiasis and the potential of routine urine being used as a risk predictor of the development of bladder cancer. Urine samples (160) were screened for the presence of S. haematobium ova. Smears stained with the Papanicolaou method were evaluated using light microscopy to determine the cell populations. A high prevalence (39.9%) of urinary schistosomiasis and haematuria (46.9%) was found among the participants. Polymorphonuclear cells, normal and reactive urothelial cells and lymphocytes were characteristic of S. haematobium infection. Squamous metaplastic cells (SMCs) were found in 48% and 47.1% of participants who have had past or current S. haematobium infection respectively, but were not found in participants who had no exposure to S. haematobium. These squamous metaplastic cells are in transition and are prone to malignant transformation when exposed to a carcinogenic agent. There is still a high burden of schistosomiasis in endemic communities in Ghana. by examining urine, one can find metaplastic cells and? dysplastic cells and thus predict cancer in SH-infested patients. Thus, routine urine cytology as a tool to monitor the risk of bladder cancer development is recommended.

Management of sexually transmitted infections: a qualitative assessment of community pharmacy practices in the Ho Municipality, Ghana.

BACKGROUND: Effective management of sexually transmitted infections (STIs) is crucial in the control and spread of these infections in health systems. Community pharmacies are usually the first port of call in Ghana for most people who contract STIs for therapy. Delayed and inappropriate treatment contributes significantly to treatment failures, drug resistance and complications. However, the community pharmacies may not have diagnostic tools and trained personnel for prompt case detection and appropriate therapeutic action. Thus, posing a higher risk for inappropriate therapy with consequences of worsening symptoms and poor treatment outcomes. This study explored the STI management practices in community pharmacies in the Ho Municipality. METHODS: Purposively selected study participants were community pharmacy staff including Pharmacists (n = 6), Pharmacy Technicians (n = 2) and Dispensing Assistants (n = 10) in outlets in Ho Municipality of the Volta region, Ghana. Data collection was carried out from December 2020 to January 2021. In-depth interviews of the participants using a semi-structured interview guide were conducted and recorded. Data obtained was transcribed and analyzed using NVivo version 12 using the thematic framework. RESULTS: Some of the pharmacy staff were unaware of National Standard Treatment Guidelines (STG) and its recommendations for STI management. More than half of the participants believed the STG recommendations were important for therapy but few thought the STG recommendations were ineffective sometimes. Appropriate STI management practices observed included infection treatment based on laboratory data, and STG protocols that recommend syndromic approach. Negative STI management practices included disregarding the presence of possible mixed infections and treating all symptoms observed empirically as a single infection without laboratory confirmation. CONCLUSION: The STI management practices in the community pharmacies had many gaps that risk infective therapy, treatment failures, STI complications, and antibiotic resistance. Efforts should be invested into the training of practitioners in community pharmacies for safe and effective practices for STI management, and encouraged to have diagnostic kits or work with laboratory facilities for testing to inform definitive therapy for optimal outcomes.

Performance of Body Adiposity Index and Relative Fat Mass in Predicting Bioelectric Impedance Analysis-Derived Body Fat Percentage: A Cross-Sectional Study among Patients with Type 2 Diabetes in the Ho Municipality, Ghana.

Objective: The study sought to determine the diagnostic accuracy of body adiposity index (BAI) and relative fat mass (RFM) to predict BIA-derived BFP among patients with type 2 diabetes in the Ho municipality. Materials and Method. This hospital-based cross-sectional study involved 236 patients with type 2 diabetes. Demographic data, including age and gender were obtained. Height, waist circumference (WC), and hip circumference (HC) were measured using standard methods. BFP was estimated on a bioelectrical impedance analysis (BIA) scale. The validity of BAI and RFM as alternative estimates for BIA-derived BFP was evaluated based on mean absolute percentage error (MAPE), Passing-Bablok regression, Bland-Altman plots, receiver-operating characteristic curve (ROC), and kappa statistics analyses. A p value less than 0.05 was considered statistically significant. Results: BAI showed systematic bias in estimating BIA-derived BFP in both genders, but this was not evident between RFM and BFP among females (t = -0.62; p = 0.534). While BAI showed "good" predictive accuracy in both genders, RFM exhibited "high" predictive accuracy for BFP (MAPE: 7.13%; 95% CI: 6.27-8.78) among females according to MAPE analysis. From the Bland-Altman plot analysis, the mean difference between RFM and BFP was acceptable among females [0.3 (95% LOA: -10.9 to 11.5)], but both BAI and RFM recorded large limits of agreement and low Lin's concordance correlation coefficient with BFP (Pc < 0.90) in the two gender populations. The optimal cut-off, sensitivity, specificity, and Youden index for RFM were >27.2, 75%, 93.75%, and 0.69, respectively, while those of BAI were >25.65, 80%, 84.37%, and 0.64, respectively, among males. Among females, the values for RFM were >27.26, 92.57%, 72.73%, and 0.65, whereas those of BAI were >29.4, 90.74%, 70.83%, and 0.62, respectively. The accuracy of discriminating between BFP levels was higher among females [BAI (AUC: 0.93) and RFM (AUC: 0.90)] compared to males [BAI (AUC: 0.86) and RFM (AUC: 0.88)]. Conclusion: RFM had a better predictive accuracy of BIA-derived BFP in females. However, both RFM and BAI failed as valid estimates for BFP. Furthermore, gender-specific performance in the discrimination of BFP levels for RFM and BAI was observed.

Burden of Fluoroquinolone Resistance in Clinical Isolates of Escherichia coli at the Ho Teaching Hospital, Ghana.

BACKGROUND: The growing burden of antibiotic resistance is a threat to the management of infections. Infections by Escherichia coli are routinely treated with fluoroquinolone antimicrobial agents. Due to their frequent use, there has been increasing resistance to these drugs. We set out to determine the burden of fluoroquinolone resistance among clinical E. coli isolates at the Ho Teaching Hospital, Ghana. METHODS: This was a cross-sectional study conducted from July 2018 to June 2019. One hundred and thirty-five E. coli isolates were cultured from various clinical samples. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method with discs of nalidixic acid (NAL), ciprofloxacin (CIP), norfloxacin (NOR) and levofloxacin (LEV). Deoxyribonucleic acid (DNA) was extracted from the resistant isolates for the detection of fluoroquinolone resistant genes by polymerase chain reaction. RESULTS: Ninety of the 135 isolates (66.7%) were resistant to at least one of the four fluoroquinolone drugs investigated. Resistance to NAL, CIP, NOR, and LEV was 51.0%, 51.1%, 38.8% and 35.7% respectively. Out of the fluoroquinolone resistant isolates, 69 carried one or more fluoroquinolone resistant genes. The predominant resistant genes were aac(6')-Ib-cr (48.9%) and qnrD (25.6%). Seven of the isolates carried both qnrS and aac(6')-Ib-cr genes. Two isolates carried 5 different fluoroquinolone resistant genes. CONCLUSION: High prevalence of resistance to 4 fluoroquinolone drugs was recorded with associated resistant genes. This is a threat to current efforts to control the spread of antibiotic resistance and calls for concerted efforts to curb the spread of these resistant organisms.

Intestinal Parasitic Infection and Associated Risk Factors among HIV-Infected Patients Seeking Healthcare in a Rural Hospital in Ghana.

Background: Parasitic infections among human immunodeficiency virus (HIV)-infected patients are common in various regions and populations across the world and have since remained a persistent public health challenge. Sub-Saharan Africa harbors the greatest burden of the infections due to sociodemographic and behavioral factors. However, the prevalence of gastrointestinal parasitic infections among HIV-infected persons has been poorly investigated in Ghana. Aim: This study sought to determine the prevalence of gastrointestinal parasitic infections and associated factors in HIV-infected individuals attending the antiretroviral therapy (ART) clinic in St. Mary Theresa Hospital, Dodi Papase. Methods: A cross-sectional study was conducted from June 2021 to September 2021 among three hundred and thirty-five HIV-infected individuals in the study area. Sociodemographic and behavioral factors were collected with the aid of a close-ended structured questionnaire. Furthermore, stool samples were collected from each participant and examined for the presence of intestinal parasites by microscopy using direct wet mount, formol-ether concentration, and modified Ziehl-Neelsen (Zn) techniques. Data obtained were analyzed using Statistical Package for Social Sciences (SPSS) version 22.0 and Graphpad Prism version 8. Results: The prevalence of gastrointestinal parasitic infections was 5.97%. Species-specific prevalence was found to be 2.99% for Giardia lamblia, 1.19% for Ascaris lumbricoides, and 0.90% each for Entamoeba histolytica/dispar and Trichuris trichiura. There was a significant association between participants' educational level and intestinal parasitic infection. In addition, gastrointestinal parasitic infections were not found to be associated with age. Unemployed participants, those with a lower frequency of deworming, and those who do not use water closet toilet facilities were at a higher risk of getting infected. Conclusion: The lower infection rate recorded in this study suggests that public health interventions put in place are yielding significant results. Even though the prevalence is low, routine screening of all HIV-infected patients for parasitic infection is recommended to ensure timely, effective treatment and comprehensive care.