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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.

Abstract 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.

IntroductionHoima, 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.MethodsThis 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.ResultsA 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.ConclusionImmunization 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.

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.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.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.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.

INTRODUCTION: Up to 30% of type-1 diabetes mellitus (T1DM) patients have co-existent thyroid autoimmunity with up to 50% of them having associated thyroid dysfunction. Routine screening for thyroid autoimmunity and dysfunction is recommended in all T1DM patients. However, this was not currently practiced in Ugandan paediatric diabetes clinics. There was also paucity of data regarding thyroid autoimmunity and dysfunction in African children and adolescents with diabetes mellitus. The objective of this study was to quantify the magnitude of thyroid autoimmunity and dysfunction in Ugandan children with TIDM. METHODS: This was a cross sectional descriptive study to determine the prevalence of thyroid autoantibodies and describe thyroid function among children and adolescents aged 1-19 years with diabetes mellitus attending the paediatric diabetes clinic at Mulago National Referral Hospital, Kampala, Uganda. We enrolled and obtained details of clinical history and physical examination. Blood (plasma) was assayed to determine levels of antibodies to thyroid peroxidase (antiTPO), free thyroxine (FT4) and thyrotropin (TSH).

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.