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.

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.

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.

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.

Age at menarche in relation to nutritional status and critical life events among rural and urban secondary school girls in post-conflict northern Uganda.

BACKGROUND: Menarche age is an important indicator of reproductive health of a woman or a community. In industrial societies, age at menarche has been declining over the last 150 years with a secular trend, and similar trends have been reported in some developing countries. Menarche age is affected by genetic and environmental cues, including nutrition. The study was designed to determine the age at menarche and its relation to childhood critical life events and nutritional status in post-conflict northern Uganda. METHODS: This was a comparative cross-sectional study of rural and urban secondary school girls in northern Uganda. Structured questionnaires were administered to 274 secondary school girls, aged 12 - 18 years to determine the age at menarche in relation to home location, nutritional status, body composition and critical life events. RESULTS: The mean age at menarche was 13.6 ± 1.3 for rural and 13.3 ± 1.4 years for urban dwelling girls (t = -1.996, p = 0.047). Among the body composition measures, hip circumference was negatively correlated with the age at menarche (r = -0.109, p = 0.036), whereas height, BMI and waist circumference did not correlate with menarche. Paternal (but not maternal) education was associated with earlier menarche (F = 2.959, p = 0.033). Childhood critical life events were not associated with age at menarche. CONCLUSIONS: Age at menarche differed among urban and rural dwelling school girls and dependent on current nutritional status, as manifested by the hip circumference. It was not associated with extreme stressful childhood critical life events.

Genetic analysis of influenza B viruses isolated in Uganda during the 2009-2010 seasons.

BACKGROUND: Influenza B viruses can cause morbidity and mortality in humans but due to the lack of an animal reservoir are not associated with pandemics. Because of this, there is relatively limited genetic sequences available for influenza B viruses, especially from developing countries. Complete genome analysis of one influenza B virus and several gene segments of other influenza B viruses isolated from Uganda from May 2009 through December 2010 was therefore undertaken in this study. METHODS: Samples were collected from patients showing influenza like illness and screened for influenza A and B by PCR. Influenza B viruses were isolated on Madin-Darby Canine Kidney cells and selected isolates were subsequently sequenced and analyzed phylogenetically. FINDINGS: Of the 2,089 samples collected during the period, 292 were positive by PCR for influenza A or B; 12.3% of the PCR positives were influenza B. Thirty influenza B viruses were recovered and of these 25 that grew well consistently on subculture were subjected to further analysis. All the isolates belonged to the B/Victoria-lineage as identified by hemagglutination inhibition assay and genetic analysis except one isolate that grouped with the B-Yamagata-lineage. The Ugandan B/Victoria-lineage isolates grouped in clade 1 which was defined by the N75K, N165K and S172P substitutions in hemagglutinin (HA) protein clustered together with the B/Brisbane/60/2008 vaccine strain. The Yamagata-like Ugandan strain, B/Uganda/MUWRP-053/2009, clustered with clade 3 Yamagata viruses such as B/Bangladesh/3333/2007 which is characterized by S150I and N166Y substitutions in HA. CONCLUSION: In general there was limited variation among the Ugandan isolates but they were interestingly closer to viruses from West and North Africa than from neighboring Kenya. Our isolates closely matched the World Health Organization recommended vaccines for the seasons.

Molecular epidemiology of influenza A/H3N2 viruses circulating in Uganda.

The increasing availability of complete influenza virus genomes is deepening our understanding of influenza evolutionary dynamics and facilitating the selection of vaccine strains. However, only one complete African influenza virus sequence is available in the public domain. Here we present a complete genome analysis of 59 influenza A/H3N2 viruses isolated from humans in Uganda during the 2008 and 2009 season. Isolates were recovered from hospital-based sentinel surveillance for influenza-like illnesses and their whole genome sequenced. The viruses circulating during these two seasons clearly differed from each other phylogenetically. They showed a slow evolution away from the 2009/10 recommended vaccine strain (A/Brisbane/10/07), instead clustering with the 2010/11 recommended vaccine strain (A/Perth/16/09) in the A/Victoria/208/09 clade, as observed in other global regions. All of the isolates carried the adamantane resistance marker S31N in the M2 gene and carried several markers of enhanced transmission; as expected, none carried any marker of neuraminidase inhibitor resistance. The hemagglutinin gene of the 2009 isolates differed from that of the 2008 isolates in antigenic sites A, B, D, and to a lesser extent, C and E indicating evidence of an early phylogenetic shift from the 2008 to 2009 viruses. The internal genes of the 2009 isolates were similar to those of one 2008 isolate, A/Uganda/MUWRP-050/2008. Another 2008 isolate had a truncated PB1-F2 protein. Whole genome sequencing can enhance surveillance of future seasonal changes in the viral genome which is crucial to ensure that selected vaccine strains are protective against the strains circulating in Eastern Africa. This data provides an important baseline for this surveillance. Overall the influenza virus activity in Uganda appears to mirror that observed in other regions of the southern hemisphere.

Prevalence and factors associated with rotavirus infection among children admitted with acute diarrhea in Uganda.

BACKGROUND: Rotavirus remains the commonest cause of severe dehydrating diarrhea among children worldwide. Children in developing countries die more because of several factors including poorer access to hydration therapy and greater prevalence of malnutrition. Hitherto, the magnitude of rotavirus disease in Uganda has remained unknown. This study was therefore done to determine the prevalence and factors associated with rotavirus infection among children aged 3-59 months admitted with acute diarrhea to paediatric emergency ward of Mulago Hospital, Uganda METHODS: Three hundred and ninety children, aged between 3-59 months with acute diarrhoea were recruited. The clinical history, socio-demographic characteristics, physical examination findings and laboratory investigations were recorded. Stool samples were tested for rotavirus antigens using the DAKO IDEIA rotavirus EIA detection kit. RESULTS: The prevalence of rotavirus infection was 45.4%. On multivariate analysis rotavirus was significantly associated with a higher education (above secondary) level of the mother [OR 1.8; 95% CI 1.1-2.7]; dehydration [OR 1.8; 95% CI 1.1-3.0] and breastfeeding [OR 2.6; 95% CI 1.4-4.0]. Although age was significantly associated with rotavirus on bivariate analysis; this association disappeared on multivariate analysis. No significant association was found between rotavirus infection and nutritional status, HIV status and attendance of day care or school. CONCLUSIONS: Rotavirus infection is highly prevalent among children with acute diarrhoea admitted to Mulago Hospital in Uganda.

The clinical pattern, prevalence, and factors associated with immune reconstitution inflammatory syndrome in Ugandan children.

OBJECTIVE: To determine clinical pattern, prevalence, and factors associated with pediatric immune reconstitution inflammatory syndrome (IRIS) in Uganda. DESIGN: A prospective, multicenter cross-sectional study. METHODS: We enrolled HIV-infected children receiving antiretroviral therapy (ART) between 0.5 and 6 months duration from December 2006 to October 2007 at three pediatric clinics in Uganda. Children were evaluated for IRIS at a one-time study visit by a standardized pediatric case definition. RESULTS: The IRIS prevalence was 38% [95% confidence interval (CI) 31-46] among 162 children (57% female) with a median age of 6 years (interquartile range 2.5-11 years). Of the IRIS events, 77% were unmasking of a new opportunistic infection and 23% were probable paradoxical IRIS events toward prior opportunistic infections. The majority of IRIS events (55%) occurred in the first month of ART. The clinical events were diverse, with tuberculosis-IRIS (29%) being the most frequent presentation. Independent risk factors for IRIS were pre-ART CD4(+) cell percentage below 15% (odds ratio = 3.1, 95% CI 1.2-8.4, P = 0.027), current CD8(+) cell absolute count below 1000 cells/microl (odds ratio = 4.3, 95% CI 1.8-10.4, P = 0.001), male sex (odds ratio = 2.6, 95% CI 1.06-8.4, P = 0.01), and a cough of more than 1 week duration at the current clinic visit (odds ratio = 4.3, 95% CI 1.7-10.7, P = 0.002). A more than 25 CD4(+) T-cells increase at current study visit from the pre-ART baseline was associated with IRIS by univariate (P = 0.005) but not multivariate analysis. CONCLUSION: IRIS events commonly occur early after ART initiation in children with advanced immunosuppression, as commonly seen in resource-limited areas. Both healthcare providers and caregivers of the children need awareness of IRIS to minimize ART nonadherence.