Isolation and characterization of Escherichia colipathotypes and factors associated with well and boreholes water contamination in Mombasa County

Introduction: Safe water for human consumption is important, but there is a limited supply. Mombasa County has water shortages making residences rely on other sources of water including boreholes and wells. Microbiological evaluation of drinking water is important to reduce exposure to water borne enteric diseases. This cross sectional study aimed at determining the frequency and characterization of Escherichia coli (E. coli) pathotypes from water samples collected from wells and boreholes in Mombasa County. Methods: One hundred and fifty seven (157) water samples were collected from four divisions of the county and a questionnaire administered. The samples were inoculated to double strength MacConkey broth and incubated at 370C for up to 48 hours. Positive results were compared to the 3 tube McCrady MPN table. The E. coli were confirmed by Eijkman's test and antibiotic susceptibility carried out. Using polymerase chain reaction (PCR), the E. coli were characterized to establish pathotypes. Results: One hundred and thirty one (n=131; 83.4%) samples had coliform bacteria with only 79 (60.3%) samples having E. coli. Significant values (<0.05) were noted when coliforms were compared to variables with E. Coli showing no significance when compared to similar variables. E. coli (n = 77; 100%) tested were sensitive to Gentamicin, while all (n = 77; 100%) isolates were resistant to Ampicillin. PCR typed isolates as enteroinvasive E. Coli (EIEC). Conclusion: Findings suggest that coliforms and E. coli are major contaminants of wells and boreholes in Mombasa County. The isolates have a variety of resistant and sensitivity patterns to commonly used antibiotics.Pan African Medical Journal 2016; 2

Etiology of Persistent Tubo-Ovarian Abscess in Nairobi, Kenya

Objective To study the microbial etiology of tubo-ovarian abscess (TOA). Methods We recruited 11 women in Nairobi, Kenya who failed antibiotic therapy alone and required surgical drainage of a presumptive TOA. Pus from the nine abscesses and two pyosalpinges were collected and cultured for aerobic, facultative and anaerobic microorganisms. Results Eleven women suspected of having a TOA were hospitalized and treated for a median of 6 days (range 3–14 days) prior to surgical drainage of the abscess. Nine (82%) specimens were culture positive. Aerobes were present in all nine specimens. Seven of the nine positive cultures (78%) were polymicrobial and five of the polymicrobial cultures contained both anaerobes and aerobes. Anaerobic Gram-negative bacilli (Prevotella sp., Porphyromonas sp. and Bacteroides sp., Escherichia coli ) and Streptococcus sp. ( S. viridans and S. agalactiae) were the most common microorganisms isolated. Neisseria gonorrhoeae and Chlamydia trachomatis were not isolated by culture or detected by polymerase chain reaction. Conclusions In Kenya, persistent TOAs are associated with endogenous flora similar to that normally found in the gastrointestinal tract

Whole genome phylogenetic investigation of a West Nile virus strain isolated from a tick sampled from livestock in north eastern Kenya

BACKGROUND:West Nile virus (WNV) has a wide geographical distribution and has been associated to cause neurological disease in humans and horses. Mosquitoes are the traditional vectors for WNV; however, the virus has also been isolated from tick species in North Africa and Europe which could be a means of introduction and spread of the virus over long distances through migratory birds. Although WNV has been isolated in mosquitoes in Kenya, paucity of genetic and pathogenicity data exists. We previously reported the isolation of WNV from ticks collected from livestock and wildlife in Ijara District of Kenya, a hotspot for arbovirus activity. Here we report the full genome sequence and phylogenetic investigation of their origin and relation to strains from other regions. METHODS: A total of 10,488 ticks were sampled from animal hosts, classified to species and processed in pools of up to eight ticks per pool. Virus screening was performed by cell culture, RT-PCR and sequencing. Phylogenetic analysis was carried out to determine the evolutionary relationships of our isolate. RESULTS: Among other viruses, WNV was isolated from a pool of Rhipicephalus pulchellus sampled from cattle, sequenced and submitted to GenBank (Accession number: KC243146). Comparative analysis with 27 different strains revealed that our isolate belongs to lineage 1 and clustered relatively closely to isolates from North Africa and Europe, Russia and the United States. Overall, Bayesian analysis based on nucleotide sequences showed that lineage 1 strains including the Kenyan strain had diverged 200years ago from lineage 2 strains of southern Africa. Ijara strain collected from a tick sampled on livestock was closest to another Kenyan strain and had diverged 20years ago from strains detected in Morocco and Europe and 30years ago from strains identified in the USA. CONCLUSION: To our knowledge, this is the first characterized WNV strain isolated from R. pulchellus. The epidemiological role of this tick in WNV transmission and dissemination remains equivocal but presents tick verses mosquito virus transmission has been neglected. Genetic data of this strain suggest that lineage 1 strains from Africa could be dispersed through tick vectors by wild migratory birds to Europe and beyond

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Genetic diversity and evolutionary analysis of human respirovirus type 3 strains isolated in Kenya using complete hemagglutinin-neuraminidase (HN) gene.

Human respirovirus type 3 (HRV3) is a leading etiology of lower respiratory tract infections in young children and ranks only second to the human respiratory syncytial virus (HRSV). Despite the public health importance of HRV3, there is limited information about the genetic characteristics and diversity of these viruses in Kenya. To begin to address this gap, we analyzed 35 complete hemagglutinin-neuraminidase (HN) sequences of HRV3 strains isolated in Kenya between 2010 and 2013. Viral RNA was extracted from the isolates, and the entire HN gene amplified by RT-PCR followed by nucleotide sequencing. Phylogenetic analyses of the sequences revealed that all the Kenyan isolates grouped into genetic Cluster C; sub-clusters C1a, C2, and C3a. The majority (54%) of isolates belonged to sub-cluster C3a, followed by C2 (43%) and C1a (2.9%). Sequence analysis revealed high identities between the Kenyan isolates and the HRV3 prototype strain both at the amino acid (96.5-97.9%) and nucleotide (94.3-95.6%) levels. No amino acid variations affecting the catalytic/active sites of the HN glycoprotein were observed among the Kenyan isolates. Selection pressure analyses showed that the HN glycoprotein was evolving under positive selection. Evolutionary analyses revealed that the mean TMRCA for the HN sequence dataset was 1942 (95% HPD: 1928-1957), while the mean evolutionary rate was 4.65x10-4 nucleotide substitutions/site/year (95% HPD: 2.99x10-4 to 6.35x10-4). Overall, our results demonstrate the co-circulation of strains of cluster C HRV3 variants in Kenya during the study period. This is the first study to describe the genetic and molecular evolutionary aspects of HRV3 in Kenya using the complete HN gene

Epidemiology and Molecular Characterization of Influenza Viruses Isolated From Children Admitted At the Kenyatta National Hospital in April-July 2008

Background: 20% of deaths in children are caused by respiratory infections. Acute respiratory infections (ARIs), have both bacterial and viral aetiologies. Influenza viruses cause highly contagious respiratory diseases. In Kenya, three studies focusing on influenza-like-illness and severe acute respiratory illness are ongoing. Despite these surveillance programmes, little is known regarding the epidemiology and molecular characteristics of influenza viruses found in children at the KenyattaNational Hospital (KNH). Objective: To determine the epidemiology and molecular characteristics of influenza viruses from children at the Kenyatta National Hospital during the April-July 2008 period. Methodology: Throat swabs were collected from 388 consenting patients. Swabs were inoculated onto monolayers of cultured MDCK cellsto isolate influenza viruses. The virus isolates were identified by HA/HAI assays. Viral RNA was extracted from isolates followed by RT-PCR amplification of the haemagglutinin gene.Nucleotide sequences were determined by the Sanger dideoxy termination method on an ABI 3500xL genetic analyzer. The nucleotide sequences were aligned to similar sequences from GenBank, and phylogeny inferred using Bayesian methods. Results: Twenty viruses consisting of 19 (95%) influenza B viruses and 1 (5%) seasonal influenza A/H1N1 were detected from the 388 patient samples. HAI titres for both A and B viruses ranged between 320-1280 with both vaccine strains showing a titre of 320. Viruses were detected mostly in 1year olds (11; 55%), patients with LRTI (14; 70%) and in the month of June (9; 45%). The nucleotide sequences displayed had 97-98%similarities to other 2008 influenza sequences. Phylogenetic analyses of seasonal influenza A/H1N1 clustered together with 2008 regional sequences while influenza B also clustered with 2008 sequences. Influenza A sequence showed substitutions at one antigenic site (198-Sb), while 3 antigenic sites (150loop, 160loop and 190 – Helix) on influenza B also had substitutions when compared to the 2008 vaccine strains. Conclusion: In 2008, influenza viruses were common in 1year oldsat KNH. Infection rates were highest in the month of June. Viruses isolated in the study period were genetically similar to those isolated elsewhere. Amino acid changes in the Kenyan isolates did not adversely affect the immunogenicity of the 2008 vaccine

Etiology of persistent tubo-ovarian abscess in Nairobi, Kenya.

ObjectiveTo study the microbial etiology of tubo-ovarian abscess (TOA).MethodsWe recruited 11 women in Nairobi, Kenya who failed antibiotic therapy alone and required surgical drainage of a presumptive TOA. Pus from the nine abscesses and two pyosalpinges were collected and cultured for aerobic, facultative and anaerobic microorganisms.ResultsEleven women suspected of having a TOA were hospitalized and treated for a median of 6 days (range 3-14 days) prior to surgical drainage of the abscess. Nine (82%) specimens were culture positive. Aerobes were present in all nine specimens. Seven of the nine positive cultures (78%) were polymicrobial and five of the polymicrobial cultures contained both anaerobes and aerobes. Anaerobic Gram-negative bacilli (Prevotella sp., Porphyromonas sp. and Bacteroides sp., Escherichia coli) and Streptococcus sp. (S. viridans and S. agalactiae) were the most common microorganisms isolated. Neisseria gonorrhoeae and Chlamydia trachomatis were not isolated by culture or detected by polymerase chain reaction.ConclusionsIn Kenya, persistent TOAs are associated with endogenous flora similar to that normally found in the gastrointestinal tract

Diagnostic performance of a colorimetric RT -LAMP for the identification of SARS-CoV-2: A multicenter prospective clinical evaluation in sub-Saharan Africa

Management and control of the COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus SARS-CoV-2 is critically dependent on quick and reliable identification of the virus in clinical specimens. Detection of viral RNA by a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a simple, reliable and cost-effective assay, deployable in resource-limited settings (RLS). Our objective was to evaluate the intrinsic and extrinsic performances of RT-LAMP in RLS

Clinical epidemiology of COVID-19 among hospitalized children in rural western Kenya.

The epidemiology of pediatric COVID-19 in sub-Saharan Africa and the role of fecal-oral transmission in SARS-CoV-2 are poorly understood. Among children and adolescents in Kenya, we identify correlates of COVID-19 infection, document the clinical outcomes of infection, and evaluate the prevalence and viability of SARS-CoV-2 in stool. We recruited a prospective cohort of hospitalized children aged two months to 15 years in western Kenya between March 1 and June 30 2021. Children with SARS-CoV-2 were followed monthly for 180-days after hospital discharge. Bivariable logistic regression analysis was used to identify the clinical and sociodemographics correlates of SARS-CoV-2 infection. We also calculated the prevalence of SARS-CoV-2 detection in stool of confirmed cases. Of 355 systematically tested children, 55 (15.5%) were positive and were included in the cohort. The commonest clinical features among COVID-19 cases were fever (42/55, 76%), cough (19/55, 35%), nausea and vomiting (19/55, 35%), and lethargy (19/55, 35%). There were no statistically significant difference in baseline sociodemographic and clinical characteristics between SARS-CoV-2 positive and negative participants. Among positive participants, 8/55 (14.5%, 95%CI: 5.3%-23.9%) died; seven during the inpatient period. Forty-nine children with COVID-19 had stool samples or rectal swabs available at baseline, 9 (17%) had PCR-positive stool or rectal swabs, but none had SARS-CoV-2 detected by culture. Syndromic identification of COVID-19 is particularly challenging among children as the presenting symptoms and signs mirror other common pediatric diseases. Mortality among children hospitalized with COVID-19 was high in this cohort but was comparable to mortality seen with other common illnesses in this setting. Among this small set of children with COVID-19 we detected SARS-CoV-2 DNA, but were not able to culture viable SARs-CoV-2 virus, in stool. This suggests that fecal transmission may not be a substantial risk in children recently diagnosed and hospitalized with COVID-19 infection