At the time of submitting this article, the number of new cases of COVID-19 is still increasing globally. High daily mortality rates continue to be reported in the USA and the UK. The immunocompromised elderly, and individuals with underlying medical conditions continue to predominate the cases. The commonest clinical presentation is fever. Cepheid Xpert Xpress SARS-CoV-2 (California, USA) was the first rapid, point of care molecular test for the Coronavirus.

Background

Accurate and high-throughput genotyping of Mycobacterium tuberculosis complex (MTBC) may be important for understanding the epidemiology and pathogenesis of tuberculosis (TB). In this study, we report the development of a LightCycler® real-time PCR single-nucleotide-polymorphism (LRPS) assay for the rapid determination of MTBC lineages/sublineages in minimally processed sputum samples from TB patients.

Method

Genotyping analysis of 70 MTBC strains was performed using the Long Sequence Polymorphism-PCR (LSP-PCR) technique and the LRPS assay in parallel. For targeted sequencing, 9 MTBC isolates (three isolates per MTBC lineage) were analyzed for lineage-specific single nucleotide polymorphisms (SNPs) in the following three genes to verify LRPS results: Rv004c for MTB Uganda family, Rv2962 for MTB lineage 4, and Rv0129c for MTB lineage 3. The MTBC lineages present in 300 smear-positive sputum samples were then determined by the validated LRPS method without prior culturing.

Results

The LSP-PCR and LRPS assays produced consistent genotyping data for all 70 MTBC strains; however, the LSP-PCR assay was 10-fold less sensitive than the LRPS method and required higher DNA concentrations to successfully characterize the MTBC lineage of certain samples. Targeted sequencing of genes containing lineage-specific SNPs was 100 % concordant with the genotyping results and provided further validation of the LRPS assay. Of the 300 sputum samples analyzed, 58 % contained MTBC from the MTBC-Uganda family, 27 % from the MTBC lineage 4 (excluding MTBC Uganda family), 13 % from the MTBC lineage 3, and the remaining 2 % were of indeterminate lineage.

Conclusion

The LRPS assay is a sensitive, high-throughput technique with potential application to routine genotyping of MTBC in sputum samples from TB patients.

The HIV epidemic in Uganda has highlighted Cryptococcus and Candida infections as important opportunistic fungal infections. However, the burden of other fungal diseases is not well described. We aimed to estimate the burden of fungal infections in Uganda. All epidemiological papers of fungal diseases in Uganda were reviewed. Where there is no Ugandan data, global or East African data were used. Recurrent vaginal candidiasis is estimated to occur in 375 540 Uganda women per year; Candida in pregnant women affects up to 651 600 women per year. There are around 45 000 HIV‐related oral and oesophageal candidosis cases per year. There are up to 3000 cases per year of post‐TB chronic pulmonary aspergillosis. There are an estimated 40 392 people with asthma‐related fungal conditions. An estimated 1 300 000 cases of tinea capitis occur in school children yearly in Uganda. There are approximately 800 HIV‐positive adults with Pneumocystis jirovecii pneumonia (PJP) annually and up to 42 000 children with PJP per year. There are an estimated 4000 cryptococcal cases annually. There are an estimated 2.5 million fungal infections per year in Uganda. Cryptococcus and PJP cause around 28 000 deaths in adults and children per year. We propose replicating the model of research around cryptococcal disease to investigate and development management strategies for other fungal diseases in Uganda.

Background: Clinical practice, for a long time, has dwelt on study and management of pyogenic abscesses without distinction between nosocomial and community-acquired types. This study aimed at identifying the bacteria isolated from community-acquired acute subcutaneous and soft tissue pyogenic abscesses. It also determined their sensitivity to a wide range of antibiotics. Methods: The cross-sectional study was conducted in Mulago hospital, between August and December, 2011. Consecutive, convenient sampling was used to attain a sample size of 130 subjects, with all age groups eligible. They were treated for the abscesses by incision and drainage. The pus was subjected to bacterial culturing and drug sensitivity testing. Data was analysed using STATA version 11.2. Results: The median age was 21.6 years; with females constituting 43.9%, and 10.8% were HIV positive persons. The predominant organism isolated was Staphylococcus aureus (53.9%), followed by coliform organisms (14-1%). Mixed infections, mostly with Staphylococcus aureus, constituted 8.6%. Staphylococcus aureus was most susceptible to ciprofloxacin and showed greatest resistance to chloramphenicol. Coliform organisms were most susceptible amikacin and showed greatest resistance to augmentin. Conclusions: The predominant bacterium isolated from these pyogenic abscesses is Staphylococcus aureus. It is most susceptible to ciprofloxacin and resistant to chloramphenicol. There is benefit in conducting a larger study with more antibiotic sensitivity tests and specific bacterial type dentification. Recommendations can then be made for appropriate antibiotic policies.

Cryptococcal antigen screening is recommended among people living with AIDS when entering HIV care with a CD4 count of 16 g/ml. We observed an amphotericin B MIC50 of 0.5 g/ml and an MIC90 of 1 g/ml, of which 99.5% of isolates (197 of 198 isolates) were still susceptible. No correlation between MIC and clinical outcome was observed in the context of amphotericin B and fluconazole combination induction therapy. We also analyzed Cryptococcus susceptibility to sertraline, with an MIC50 of 4 g/ml, suggesting that sertraline is a promising oral, low-cost, available, novel medication and a possible alternative to fluconazole. Although the CLSI broth microdilution assay is ideal to standardize results, limit human bias, and increase assay capacity, such assays are often inaccessible in low-income countries. Thus, we also developed and validated an assay that could easily be implemented in a resource-limited setting, with similar susceptibility results (P 0.52).

Background: Urinary tract infections (UTI) are a common medical problem affecting the general population and thus commonly encountered in medical practice, with the global burden of UTIs at about 150 million people. Because uropathogens largely originate from colonic flora, they are easy to predict, and this is the rationale for empirical treatment in Community Acquired-UTI (CA-UTIs). With the increasing prevalence of drug-resistant bacteria among adults with CA-UTI in Uganda, it is no longer adequate to manage CA-UTIs on empiric regimen without revising the susceptibility patterns of common CA-UTI causative agents. Thus in this study we set out to identify: The factors associated with CA-UTIs, the common uropathogens and the drug sensitivity patterns of the common uropathogens cultured.

Methodology: This was a cross-sectional study that was conducted in adults who presented with symptoms of a UTI at Mulago Hospital, assessment center. There were 139 patients who consented to the study and were recruited, an interviewer administered questionnaire was used to collect information from the study participants as regards demographic, social and clinical characteristics and Mid Stream Urine (MSU) samples were collected for urinalysis, culture and antibiotic susceptibility testing using the Kirby-Bauer disc diffusion technique was applied to the isolates.Numeric data were summarized using measures of central tendency while the categorical data was summarized using proportions and percentages.

Results: Age, female sex and marital status were factors that were significantly associated with CA-UTIs. Fifty four (54) cultures were positive for UTI with 26 giving pure growths. The commonest uropathogen isolated was Escherichia coli at 50%, this was followed by Staphylococcus aureus at 15.4%. The sensitivity of Escherichia coli to Ampicillin and Nitrofurantoin were78.6%, 64.3% respectively, and the sensitivity of Staphylococcus aureus to ciprofloxacin, Nitrofurantoin and gentamycin were 100%, 66.7% and 66.7% respectively.

Conclusion: There are known factors associated with CA-UTIs such as age, female sex. There was generally high sensitivity to nitrofurantoin and gentamycin by most of the uropathogens isolated, and high resistance to the common antibiotics such as nalidixic acid and erythromycin thus a need for a bigger study that can be used to effect the change of the current recommendations in the Uganda Clinical Guidelines as regards empirical management of CA-UTIs.

The contribution of fungal infections to the morbidity and mortality of HIV-infected individuals is largely unrecognized. A recent meeting highlighted several priorities that need to be urgently addressed, including improved epidemiological surveillance, increased availability of existing diagnostics and drugs, more training in the field of medical mycology, and better funding for research and provision of treatment, particularly in developing countries.

Candida albicans is a major fungal pathogen of humans, causing approximately 400,000 life-threatening systemic infections world-wide each year in severely immunocompromised patients. An important fungicidal mechanism employed by innate immune cells involves the generation of toxic reactive oxygen species (ROS), such as superoxide and hydrogen peroxide. Consequently, there is much interest in the strategies employed by C. albicans to evade the oxidative killing by macrophages and neutrophils. Our understanding of how C. albicans senses and responds to ROS has significantly increased in recent years. Key findings include the observations that hydrogen peroxide triggers the filamentation of this polymorphic fungus and that a superoxide dismutase enzyme with a novel mode of action is expressed at the cell surface of C. albicans. Furthermore, recent studies have indicated that combinations of the chemical stresses generated by phagocytes can actively prevent C. albicans oxidative stress responses through a mechanism termed the stress pathway interference. In this review, we present an up-date of our current understanding of the role and regulation of oxidative stress responses in this important human fungal pathogen.