Molecular detection of Coxiella burnetii in ticks collected from animals and the environment in Uganda.

AIMS: Coxiella burnetii is a highly infectious organism that is easily spread through aerosols causing Q fever in humans. Ticks can harbour and transmit C. burnetii to animals, contributing to disease maintenance. Our aim was to examine the presence of C. burnetii in ticks in Uganda. METHODS AND RESULTS: In this study, ticks were collected from five Ugandan districts and tested by real-time PCR for C. burnetii (Coxiella outer membrane protein 1 gene). A total of 859 tick pools (9602 individual ticks) were tested, and pool positivity for C. burnetii was 5.5% (n = 47). Pooled prevalence differed by district; the highest was Luwero (7.3%), then Gulu (6.6%), and Kasese had the lowest (1.3%). However, district variation was not statistically significant (Fisher's exact = 0.07). Ticks collected from dogs and cats had the highest positivity rates [23/47, (48.9%)] followed by livestock (cattle, goats, sheep, and pigs) [18/47, (38.3%)] and vegetation [6/47, (12.8%)]. Haemaphysalis elliptica had the highest infection rates, followed by Rhipicephalus appendiculatus, Amblyomma variegatum and Rhipicephalus decoloratus had similar prevalence. CONCLUSIONS: Although ticks are not the primary transmitters of C. burnetii to humans, pathogen detection in ticks can be an indirect indicator of risk among animal hosts. Vulnerable populations, including occupations with close animal contact such as farming, butchery, and veterinary practice, have an increased risk of C. burnetii exposure. Veterinarians and clinicians should be aware that C. burnetii may cause human and animal illness in these regions.

Genome Analysis of Klebsiella pneumoniae Reveals International High-Risk Pandemic MDR Clones Emerging in Tertiary Healthcare Settings in Uganda.

Klebsiella pneumoniae is a threat to public health due to its continued evolution. In this study, we investigated the evolution, convergence, and transmission of hypervirulent and multi-drug resistant (MDR) clones of K. pneumoniae within healthcare facilities in Uganda. There was high resistance to piperacillin (90.91%), cefuroxime (86.96%), ceftazidime (84.62%), cefotaxime (84.00%), amoxicillin/clavulanate (75%), nalidixic acid (73.68%), and nitrofurantoin (71.43%) antibiotics among K. pneumoniae isolates. The isolates were genetically diverse, consisting of 20 different sequence types (STs) and 34 K-serotype groups. Chromosomal fosA (for fosfomycin) and oqxAB efflux pump genes were detected in all isolates. Two carbapenem resistance genes, blaNDM-5 and blaOXA-181 plus extended-spectrum beta-lactamase (blaCTX-M-15) gene (68.12%), quinolone-resistant genes qnrS1 (28.99%), qnrB1 (13.04%), and qnrB6 (13.04%) and others were found. All, except three of the isolates, harbored plasmids. While the isolates carried a repertoire of virulence genes, only two isolates carried hypervirulent genes demonstrating a low prevalence (2.90%) of hypervirulent strains. Our study demonstrated genetically diverse populations of K. pneumoniae, low levels of carbapenem resistance among the isolates, and no convergence of MDR and hypervirulence. Emerging high-risk international pandemic clones (ST11, ST14, ST147, ST 86 and ST307) were detected in these healthcare settings which are difficult to treat.

Resistome and virulome of high-risk pandemic clones of multidrug-resistant extra-intestinal pathogenic Escherichia coli (ExPEC) isolated from tertiary healthcare settings in Uganda.

Multi-drug resistant (MDR) globally disseminated extraintestinal pathogenic high-risk Escherichia coli (ExPEC) clones are threatening the gains in bacterial disease management. In this study, we evaluated the genomic structure including the resistome and virulome of the E. coli isolates from extraintestinal infections using whole genome sequencing (WGS). The results highlight that isolates were highly resistant (≥ 90.0%) to commonly used antibiotics (Ampicillin, Trimethoprim-Sulfamethoxazole, Nalidixic acid, and Piperacillin) and were less (<14%) resistant to last resort antibiotics; Imipenem (10.94%) and Meropenem (10.20%). A greater proportion of the E. coli isolates belonged to phylogroup B2 (30.52%) and phylogroup A (27.37%). The sequence types ST131 of phylogroup B2 (21.05%) and ST648 of phylogroup F (9.3%) were the dominant pandemic high-risk clones identified in addition to the ST1193, ST410, ST69, ST38, ST405, and ST10. Many of the isolates were MDR and most (64.58%) carried the blaCTX-M-15 gene for extended-spectrum ß-lactamases. There was a high correlation between phylogroups and the occurrence of both antimicrobial resistance and virulence genes. The cephalosporin-resistance gene blaEC-5 was only found in phylogroup B2 while blaEC-8 and blaEC-19, were only found within phylogroup D and phylogroup F respectively. Aminoglycoside gene (aadA1) was only associated with phylogroups D and C. The isolates were armed with a broad range of virulence genes including adhesins, toxins, secreted proteases, iron uptake genes, and others. The yfcv, chuA, and kpsE genes preferentially occurred among isolates of phylogroup B2. The study underlines the predominance of MDR internationally disseminated high-risk ExPEC clones with a broad range of virulence genes known to be highly transmissible in healthcare and community settings.

Whole Genome Sequencing Reveals High Genetic Diversity, Diverse Repertoire of Virulence-Associated Genes and Limited Antibiotic Resistance Genes among Commensal Escherichia coli from Food Animals in Uganda.

Commensal Escherichia coli with broad repertoire of virulence and antimicrobial resistance (AMR) genes pose serious public health risks as reservoirs of AMR and virulence. This study undertook whole genome characterization of commensal E. coli from food-producing animals in Uganda to investigate their genome variability (resistome and virulome). We established that the E. coli had high genomic diversity with 38 sequence types, 24 FimH types, and 33 O-antigen serotypes randomly distributed within three phylogroups (A, B1, and E). A greater proportion (≥93.65%) of the E. coli were resistant to amoxicillin/clavulanate and ampicillin antibiotics. The isolates were AmpC beta-lactamase producers dominated by blaEC-15 (71.88%) and tet(A) (20.31%) antimicrobial resistant genes besides a diverse armory of virulence-associated genes in the class of exotoxin, adhesins, iron uptake, and serine protease autotransporters which varied by host species. Cattle were found to be the major source of E. coli carrying Shiga toxin genes, whereas swine was the main source of E. coli carrying colicin-like Usp toxin gene. The study underscores the importance of livestock as the carrier of E. coli with antimicrobial resistance and a large repertoire of virulence traits with a potential of causing disease in animals and humans by acquiring more genetic traits.

Wide distribution of Mediterranean and African spotted fever agents and the first identification of Israeli spotted fever agent in ticks in Uganda.

Rickettsia microorganisms are causative agents of several neglected emerging infectious diseases in humans transmitted by arthropods including ticks. In this study, ticks were collected from four geographical regions of Uganda and pooled in sizes of 1-179 ticks based on location, tick species, life stage, host, and time of collection. Then, they were tested by real-time PCR for Rickettsia species with primers targeting gltA, 17kDa and ompA genes, followed by Sanger sequencing of the 17kDa and ompA genes. Of the 471 tick pools tested, 116 (24.6%) were positive for Rickettsia spp. by the gltA primers. The prevalence of Rickettsia varied by district with Gulu recording the highest (30.1%) followed by Luwero (28.1%) and Kasese had the lowest (14%). Tick pools from livestock (cattle, goats, sheep, and pigs) had the highest positivity rate, 26.9%, followed by vegetation, 23.1%, and pets (dogs and cats), 19.7%. Of 116 gltA-positive tick pools, 86 pools were positive using 17kDa primers of which 48 purified PCR products were successfully sequenced. The predominant Rickettsia spp. identified was R. africae (n = 15) in four tick species, followed by R. conorii (n = 5) in three tick species (Haemaphysalis elliptica, Rhipicephalus appendiculatus, and Rh. decoloratus). Rickettsia conorii subsp. israelensis was detected in one tick pool. These findings indicate that multiple Rickettsia spp. capable of causing human illness are circulating in the four diverse geographical regions of Uganda including new strains previously known to occur in the Mediterranean region. Physicians should be informed about Rickettsia spp. as potential causes of acute febrile illnesses in these regions. Continued and expanded surveillance is essential to further identify and locate potential hotspots with Rickettsia spp. of concern.

Molecular characterisation of human adenoviruses associated with respiratory infections in Uganda.

Human adenoviruses (HAdV) are a diverse group of viruses causing a broad range of infections of the respiratory, urogenital and gastrointestinal tracts and keratoconjunctivitis. There are seven species of human adenoviruses with 113 genotypes which may contain multiple genetic variants. This study characterised respiratory human adenoviruses and associated factors in samples collected from selected hospitals in Uganda. A total of 2,298 nasopharyngeal samples were collected between the period of 2008 to 2016 from patients seeking health care at tertiary hospitals for influenza-like illness. They were screened by polymerase chain reaction (PCR) to determine the prevalence of HAdV. HAdV was cultured in A549 cell lines and the hexon gene was sequenced for genotyping. Of the 2,298 samples tested, 225 (9.8%) were adenovirus-positive by PCR. Age was found to be significantly associated with HAdV infections (p = 0.028) with 98% (220/225) of the positives in children aged 5 years and below and none in adults above 25 years of age. The sequenced isolates belonged to species HAdV-B and HAdV-C with most isolates identified as genotype B3. The results showed a high prevalence and genetic diversity in respiratory HAdV circulating in Ugandan population. Deeper genomic characterization based on whole genome sequencing may be necessary to further elucidate possible transmission and impact of current adenovirus-vectored vaccines in Africa.

Genetic Evolution of Avian Influenza A (H9N2) Viruses Isolated from Domestic Poultry in Uganda Reveals Evidence of Mammalian Host Adaptation, Increased Virulence and Reduced Sensitivity to Baloxavir.

A (H9N2) avian influenza A viruses were first detected in Uganda in 2017 and have since established themselves in live bird markets. The aim of this study was to establish the subsequent genetic evolution of H9N2 viruses in Uganda. Cloacal samples collected from live bird market stalls in Kampala from 2017 to 2019 were screened by RT-PCR for influenza A virus and H9N2 viruses were isolated in embryonated eggs. One hundred and fifty H9N2 isolates were subjected to whole genome sequencing on the Illumina MiSeq platform. The sequence data analysis and comparison with contemporary isolates revealed that the virus was first introduced into Uganda in 2014 from ancestors in the Middle East. There has since been an increase in nucleotide substitutions and reassortments among the viruses within and between live bird markets, leading to variations in phylogeny of the different segments, although overall diversity remained low. The isolates had several mutations such as HA-Q226L and NS-I106M that enable mammalian host adaptation, NP-M105V, PB1-D3V, and M1-T215A known for increased virulence/pathogenicity and replication, and PA-E199D, NS-P42S, and M2-S31N that promote drug resistance. The PA-E199D substitution in particular confers resistance to the endonuclease inhibitor Baloxavir acid, which is one of the new anti-influenza drugs. Higher EC50 was observed in isolates with a double F105L+E199D substitution that may suggest a possible synergistic effect. These H9N2 viruses have established an endemic situation in live bird markets in Uganda because of poor biosecurity practices and therefore pose a zoonotic threat. Regular surveillance is necessary to further generate the needed evidence for effective control strategies and to minimize the threats.

Seroprevalence of human coronaviruses among patients visiting hospital-based sentinel sites in Uganda.

BACKGROUND: Human coronaviruses are causative agents of respiratory infections with several subtypes being prevalent worldwide. They cause respiratory illnesses of varying severity and have been described to be continuously emerging but their prevalence is not well documented in Uganda. This study assessed the seroprevalence of antibodies against the previously known human coronaviruses prior 2019 in Uganda. METHODS: A total 377 serum samples collected from volunteers that showed influenza like illness in five hospital-based sentinel sites and archived were analyzed using a commercial Qualitative Human Coronavirus Antibody IgG ELISA kit. Although there is no single kit available that can detect the presence of all the circulating coronaviruses, this kit uses a nucleoprotein, aa 340-390 to coat the wells and since there is significant homology among the various human coronavirus strains with regards to the coded for proteins, there is significant cross reactivity beyond HCoV HKU-39849 2003. This gives the kit a qualitative ability to detect the presence of human coronavirus antibodies in a sample. RESULTS: The overall seroprevalence for all the sites was 87.53% with no significant difference in the seroprevalence between the Hospital based sentinel sites (p = 0.8). Of the seropositive, the age group 1-5 years had the highest percentage (46.97), followed by 6-10 years (16.67) and then above 20 (16.36). An odds ratio of 1.6 (CI 0.863-2.97, p = 0.136) showed that those volunteers below 5 years of age were more likely to be seropositive compared to those above 5 years. The seropositivity was generally high throughout the year with highest being recorded in March and the lowest in February and December. CONCLUSIONS: The seroprevalence of Human coronaviruses is alarmingly high which calls for need to identify and characterize the circulating coronavirus strains so as to guide policy on the control strategies.

Prevalence, factors associated and treatment outcome of hyperbilirubinaemia in neonates admitted to St Francis hospital, Nsambya, Uganda: a descriptive study.

BACKGROUND: With targeted management of neonatal hyperbilirubinaemia in high-income countries, there has been a drastic drop in both the prevalence and mortality. On the contrary, over two-thirds of the global burden of neonatal hyperbilirubinaemia is in Sub-saharan Africa and South East Asia with a high mortality risk of 16-35%. Neonatal hyperbilirubinaemia is not a leading global cause of neonatal mortality, however leads to irreversible neurological damage and death when managed poorly. Three-quarters of the babies admitted to the national referral hospital in Uganda had significant hyperbilirubinaremia; 16.6% of these babies died. We aimed at determining the prevalence, treatment outcome and describing factors associated with hyperbilirubinaemia in neonates admitted to St Francis hospital, Nsambya. METHODS: A cross sectional study was carried out. A total of 242 files of babies with a preliminary diagnosis of hyperbilirubinaemia were retrieved retrospectively. Relevant data was extracted from the files and analysed using STATA version 14.0. RESULTS: The prevalence of significant hyperbillirubinaemia was 22.7% (55/242). Seventy-seven percent of the babies admitted did not require treatment for hyperbilirubinaemia. No factors were found to be significantly associated with significant hyperbilirubinaemia. The case fatality for severe hyperbilirubinaemia was 20% (6/30); half of these babies had haemolytic disease of the newborn. CONCLUSION: Establishment of local guidelines will prevent unnecessary admissions and ensure timely treatment is administered. Longitudinal studies are required to discover factors associated with neonatal hyperbilirubinaemia in this region.

Barriers to effective uptake and provision of immunization in a rural district in Uganda.

INTRODUCTION: Hoima, one of the largest districts in mid- western Uganda, has persistently performed poorly with low immunization coverage, high immunization drop outs rates and repeated outbreaks of vaccine preventable diseases especially measles. The objectives of this study were to evaluate the state of immunization services and to identify the gaps in immunization health systems that contribute to low uptake and completion of immunization schedules in Hoima District. METHODS: This was a cross sectional mixed methods study, utilizing both qualitative and quantitative approaches. A situation analysis of the immunization services was carried out using in-depth interviews with vaccinators, focus group discussions and key informant interviews with ethno-videography. Secondary data was sourced from records at headquarters and vaccination centres within Hoima District. The quantitative component utilized cluster random sampling with sample size estimated using the World Health Organization's 30 cluster sampling technique. RESULTS: A total of 311 caretaker/child pairs were included in the study. Immunization completion among children of age at least 12 months was 95% for BCG, 96% for OPV0, 93% for DPT1, 84.5% for DPT2, 81% for DPT3 and 65.5% for measles vaccines. Access to immunization centres is difficult due to poor road terrain, which affects effectiveness of outreach program, support supervision, mentorship and timely delivery of immunization program support supplies especially refrigerator gas and vaccines. Some facilities are under-equipped to effectively support the program. Adverse Events Following Immunization (AEFI) identification, reporting and management is poorly understood. CONCLUSION: Immunization services in Hoima District require urgent improvement in the following areas: vaccine supply, expanding service delivery points, more health workers, transport and tailored mechanisms to ensure adequate communication between health workers and caretakers.

Nutritional rickets among children admitted with severe pneumonia at Mulago hospital, Uganda: a cross-sectional study.

BACKGROUND: There's abundant sunshine in the tropics but severe rickets is still observed. Nutritional rickets is associated with an increased risk of acute lower respiratory infections. Pneumonia is the leading cause of death in the under 5 -year old children with the highest burden in developing countries. Both Pneumonia and rickets are common in the developing countries and may affect clinical presentation and outcome. This study aimed to determine the prevalence and associated factors of nutritional rickets in children admitted with severe pneumonia. METHODS: This was a cross-sectional study of children aged 2-59 months presenting with severe pneumonia at an emergency unit. We enrolled 221 children between February and June 2012 after consent. A pre-coded questionnaire was used to collect data on socio-demographic, nutritional and past medical history. Physical exam was done for signs of rickets and anthropometric measurements. Serum calcium, phosphorus, and alkaline phosphatase (ALP) were assessed. Children with any physical signs of rickets or biochemical rickets (ALP > 400 IU); had a wrist x-ray done. Nutritional rickets was defined as the presence of radiological changes of cupping or fraying and/ or metaphyseal thickening. Severe pneumonia was defined using the WHO criteria. Statistical analysis was performed using the Stata 10 statistical package. P- value < 0.05 was significant. RESULTS: The prevalence of nutritional rickets among children with severe pneumonia is 9.5%. However, 14.5% had raised ALP (biochemical rickets). The factors independently associated with rickets was an elevated alkaline phosphatase; p-value < 0.001, or 32.95 95% CI (10.54-102.93). Other factors like breastfeeding, big family size, birth order were not significantly associated with rickets. Low serum calcium was detected in 22 (9.9%) of the 221 participants. Overall few children with rickets had typical clinical features of rickets on physical examination. CONCLUSION: Rickets is a common problem in our setting despite ample sunshine. Clinicians should actively assess children for rickets in this setting and screen for rickets in those children at high risk even without clinical features.

Incidence and short term outcomes of neonates with hypoxic ischemic encephalopathy in a Peri Urban teaching hospital, Uganda: a prospective cohort study.

BACKGROUND: Hypoxic Ischemic Encephalopathy carries high case fatality rates ranging between 10-60%, with 25% of survivors have an adverse long-term neurodevelopment outcome. Despite the above, there is paucity of data regarding its magnitude and short term outcomes in a low resource setting like Uganda. Therefore we set out to determine the incidence and short term outcomes of Newborns with Hypoxic Ischemic Encephalopathy at St.Francis Hospital, Nsambya. METHODS: This was a Prospective Cohort study conducted between October 2015 and January 2016 at St. Francis Hospital, Nsambya, Kampala- Uganda. Term Newborn babies were enrolled. Umbilical cord arterial blood gas analysis was done for Newborns with low Apgar scores at 5 min. Clinical examination was done on all newborns within 48 h of life, for features of encephalopathy. Neonates with Hypoxic Ischemic Encephalopathy were followed up by a daily clinical examination and a short term outcome was recorded on day seven. RESULTS: The incidence of Hypoxic Ischemic Encephalopathy was 30.6 cases per 1000 live births. The majority, 10 (43.5%) had mild Hypoxic Ischemic Encephalopathy, followed by 8 (34.8%), 5 (21.7%) that had moderate and severe Hypoxic Ischemic Encephalopathy respectively. A total of (6) 26% died, and (15) 65.2% were discharged within 1 week. Lack of a nutritive suckling reflex (nasogastric feeding), poor Moro reflex, and requirement for respiratory support (oxygen therapy by nasal prongs) were the common complications by day seven. CONCLUSIONS: The burden of Hypoxic Ischemic Encephalopathy is high with a case fatality rate of 26%. There is need to conduct a longitudinal study to determine the long term complications of HIE.

Supporting and retaining Village Health Teams: an assessment of a community health worker program in two Ugandan districts.

BACKGROUND: Uganda's national community health worker program involves volunteer Village Health Teams (VHTs) delivering basic health services and education. Evidence demonstrates their positive impact on health outcomes, particularly for Ugandans who would otherwise lack access to health services. Despite their impact, VHTs are not optimally supported and attrition is a growing problem. In this study, we examined the support needs and existing challenges of VHTs in two Ugandan districts and evaluated specific factors associated with long-term retention. We report on findings from a standardized survey of VHTs and exploratory interviews with key stakeholders and draw conclusions that inform efforts to strengthen and sustain community health care delivery in Uganda. METHODS: A mixed-methods approach was employed through a survey of 134 individual VHT members and semi-structured interviews with six key stakeholders. Descriptive and bivariate regression analysis of quantitative survey data was performed along with thematic analysis of qualitative data from surveys and interviews. In the regression analysis, the dependent variable is 10-year anticipated longevity among VHTs, which asked respondents if they anticipate continuing to volunteer as VHTs for at least 10 more years if their current situation remains unchanged. RESULTS: VHTs desire additional support primarily in the forms of money (e.g. transportation allowance) and material supplies (e.g. rubber boots). VHTs commonly report difficult working conditions and describe a lack of respect from their communities and other health workers. If their current situation remains unchanged, 57% of VHTs anticipate remaining in their posts for at least 10 years. Anticipated 10-year longevity was positively associated with stronger partnerships with local health center staff and greater ease in home visiting. CONCLUSIONS: Supporting and retaining Uganda's VHTs would be enhanced by building stronger partnerships between VHTs and other health workers and regularly providing supplies and transportation allowances. Pursuing such measures would likely improve equity in access to healthcare for all Ugandans.

Pre-referral Rectal Artesunate Treatment by Community-Based Treatment Providers in Ghana, Guinea-Bissau, Tanzania, and Uganda (Study 18): A Cluster-Randomized Trial.

BACKGROUND: If malaria patients who cannot be treated orally are several hours from facilities for injections, rectal artesunate prior to hospital referral can prevent death and disability. The goal is to reduce death from malaria by having rectal artesunate treatment available and used. How best to do this remains unknown. METHODS: Villages remote from a health facility were randomized to different community-based treatment providers trained to provide rectal artesunate in Ghana, Guinea-Bissau, Tanzania, and Uganda. Prereferral rectal artesunate treatment was provided in 272 villages: 109 through community-based health workers (CHWs), 112 via trained mothers (MUMs), 25 via trained traditional healers (THs), and 26 through trained community-chosen personnel (COMs); episodes eligible for rectal artesunate were established through regular household surveys of febrile illnesses recording symptoms eligible for prereferral treatment. Differences in treatment coverage with rectal artesunate in children aged <5 years in MUM vs CHW (standard-of-care) villages were assessed using the odds ratio (OR); the predictive probability of treatment was derived from a logistic regression analysis, adjusting for heterogeneity between clusters (villages) using random effects. RESULTS: Over 19 months, 54 013 children had 102 504 febrile episodes, of which 32% (31 817 episodes) had symptoms eligible for prereferral therapy; 14% (4460) children received treatment. Episodes with altered consciousness, coma, or convulsions constituted 36.6% of all episodes in treated children. The overall OR of treatment between MUM vs CHW villages, adjusting for country, was 1.84 (95% confidence interval [CI], 1.20-2.83; P = .005). Adjusting for heterogeneity, this translated into a 1.67 higher average probability of a child being treated in MUM vs CHW villages. Referral compliance was 81% and significantly higher with CHWs vs MUMs: 87% vs 82% (risk ratio [RR], 1.1 [95% CI, 1.0-1.1]; P < .0001). There were more deaths in the TH cluster than elsewhere (RR, 2.7 [95% CI, 1.4-5.6]; P = .0040). CONCLUSIONS: Prereferral episodes were almost one-third of all febrile episodes. More than one-third of patients treated had convulsions, altered consciousness, or coma. Mothers were effective in treating patients, and achieved higher coverage than other providers. Treatment access was low. CLINICAL TRIALS REGISTRATION: ISRCTN58046240.

Epidemiology and Surveillance of Influenza Viruses in Uganda between 2008 and 2014.

INTRODUCTION: Influenza surveillance was conducted in Uganda from October 2008 to December 2014 to identify and understand the epidemiology of circulating influenza strains in out-patient clinic attendees with influenza-like illness and inform control strategies. METHODOLOGY: Surveillance was conducted at five hospital-based sentinel sites. Nasopharyngeal and/or oropharyngeal samples, epidemiological and clinical data were collected from enrolled patients. Real-time reverse transcription polymerase chain reaction (RT-PCR) was performed to identify and subtype influenza strains. Data were double-entered into an Epi Info 3.5.3 database and exported to STATA 13.0 software for analysis. RESULTS: Of the 6,628 patient samples tested, influenza virus infection was detected in 10.4% (n = 687/6,628) of the specimens. Several trends were observed: influenza circulates throughout the year with two peaks; the major one from September to November and a minor one from March to June. The predominant strains of influenza varied over the years: Seasonal Influenza A(H3) virus was predominant from 2008 to 2009 and from 2012 to 2014; Influenza A(H1N1)pdm01 was dominant in 2010; and Influenza B virus was dominant in 2011. The peaks generally coincided with times of higher humidity, lower temperature, and higher rainfall. CONCLUSION: Influenza circulated throughout the year in Uganda with two major peaks of outbreaks with similar strains circulating elsewhere in the region. Data on the circulating strains of influenza and its patterns of occurrence provided critical insights to informing the design and timing of influenza vaccines for influenza prevention in tropical regions of sub-Saharan Africa.

Whole-genome analysis of influenza A(H1N1)pdm09 viruses isolated in Uganda from 2009 to 2011.

We report a whole-genome analysis of 19 influenza A(H1N1)pdm09 isolates from four Ugandan hospitals between 2009 and 2011. The isolates differed from the vaccine strain A/California/07/2009 by three amino acid substitutions P100S, S220T, and I338V in the hemagglutinin and by two amino acid substitutions V106I and N248D in the neuraminidase proteins with consistent mutations in all gene segments distinguishing isolates from the 2009/2010 to 2010/2011 seasons. Phylogenetic analysis showed low genetic evolution, with genetic distances of 0%-1.3% and 0.1%-1.6% for HA and NA genes, respectively. The amino acid substitutions did not lead to antigenic differences from the reference strains.

High prevalence of antibiotic resistance in nasopharyngeal bacterial isolates from healthy children in rural Uganda: A cross-sectional study.

BACKGROUND: In Uganda, the main causes of death in children under 5 years of age are malaria and pneumonia--often due to delayed diagnosis and treatment. In preparation for a community case management intervention for pneumonia and malaria, the bacterial composition of the nasopharyngeal flora and its in vitro resistance were determined in children aged five or under to establish baseline resistance to commonly used antibiotics. METHODS: In a population-based survey in April 2008, nasopharyngeal specimens were collected from 152 randomly selected healthy children under 5 years of age in the Iganga/Mayuge Health and Demographic Surveillance Site (HDSS). Medical history and prior treatment were recorded. Demographic characteristics and risk factors for carriage of resistant strains were obtained from the HDSS census. Bacteria were isolated and analysed for antibiotic susceptibility using disk diffusion and E test. RESULTS: Streptococcus pneumoniae (S. pneumoniae) carriage was 58.6%, and, while most (80.9%) isolates had intermediate resistance to penicillin, none was highly resistant. Whereas no isolate was resistant to erythromycin, 98.9% were resistant to trimethoprim-sulphamethoxazole (co-trimoxazole). CONCLUSIONS: In vitro resistance in S. pneumoniae to co-trimoxazole treatment was high, and the majority of isolates had intermediate resistance to penicillin. To inform treatment policies on the clinical efficacy of current treatment protocols for pneumonia in health facilities and at the community level, routine surveillance of resistance in pneumonia pathogens is needed as well as research on treatment efficacy in cases with resistant strains. Improved clinical algorithms and diagnostics for pneumonia should be developed.

Global lessons from Nigeria's ebolavirus control strategy.

The current Ebola virus disease outbreak challenged medical and public health systems in West Africa. In Nigeria, the existing infrastructure of the polio surveillance system was leveraged rapidly to contain the spread of Ebola virus. We highlight important lessons learnt from the successful implementation of Ebola virus disease surveillance strategies, which should be amplified further to prepare the ground for successful vaccination programs. Close collaboration between national and international stakeholders as well as public/private partnerships will be instrumental in future Ebola virus immunization strategies.

Alpha thalassemia among sickle cell anaemia patients in Kampala, Uganda.

BACKGROUND: Sickle cell anaemia is prevalent in sub Saharan Africa. While α+-thalassaemia is known to modulate sickle cell anaemia, its magnitude and significance in Uganda have hitherto not been described. OBJECTIVES: To determine the prevalence of α+thalassaemia among sickle cell anaemia patients in Mulago Hospital and to describe the clinical and laboratory findings in these patients. METHODS: A cross sectional study was carried out on patients with sickle cell anaemia in Kampala. Dried blood spots were used to analyze for the deletional α+ thalassaemia using multiplex polymerase chain reaction. RESULTS: Of the 142 patients with sickle cell anaemia, 110 (77.5%) had the αα+thalassaemia deletion. The gene frequency of (-α) was 0.425. Ninety one percent (100/110) of those with α+thalassaemia were heterozygous (αα/α-). Amongst the patients older than 60 months, 15 (83.3%) of those without αα+thalassaemia had significant hepatomegaly of greater than 4 cm compared to 36 (45.6%) of those with α+thalassaemia (p=0.003). CONCLUSION: The gene frequency of (-α) of 0.425 noted in this study is higher than that reported from many places in Africa. Concurrent alpha thalassemia might be a protective trait against significant hepatomegaly in sickle cell anaemia patients more than 60 months of age at Mulago hospital.

Malariometric indices from Iganga, Uganda: baseline characterization in preparation of GMZ2 vaccine trial.

BACKGROUND: Malaria still remains the leading cause of childhood morbidity and mortality in Uganda. Interventions like malaria vaccines which reduce the malaria burden are needed in malaria endemic communities. There is need to establish baseline characteristics in vaccine trial study sites. This study determined the following baseline malariometric indices: spleen rates, bed net use, malaria parasitaemia and malaria episodes in an inception cohort of children aged 12 - 60 months in Iganga district, Uganda. METHODS: In a longitudinal cohort study, 748 children were enrolled with 397 in an active follow up arm and 351 in a passive arm. The children in the two arms were followed for 6 months to determine the incidence of malaria episodes. RESULTS: The overall baseline spleen rate was 8.2% (61/748) among the study participants. Of the households surveyed, about 36% reported using bed nets and almost 30% of the users had insecticide-treated nets. 274 (36.6%) of the study participants had a history of fever in the past 24 hrs at the time of the baseline survey. All participants had a peripheral blood smear for malaria parasites done at enrollment with 76.8% having the asexual form of malaria parasites. The malaria episodes per child per year were 1.5 and 0.79 in the active and passive follow up arms respectively. CONCLUSIONS: There is a high prevalence of malaria asexual parasitaemia in children below five years. The bed net usage still remains low among this population. These baseline malariometric indices have important implication for malaria control interventions.