The discovery of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) in Wuhan, Hubei province, China, in December 2019 raised global health warnings. Quickly, in 2020, the virus crossed borders and infected i...The discovery of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) in Wuhan, Hubei province, China, in December 2019 raised global health warnings. Quickly, in 2020, the virus crossed borders and infected individuals across the world, evolving into the COVID-19 pandemic. Notably, early signs of the virus’s existence were observed in various countries before the initial outbreak in Wuhan. As of 12<sup>th</sup> of April, the respiratory disease had infected over 762 million people worldwide, with over 6.8 million deaths recorded. This has led scientists to focus their efforts on understanding the virus to develop effective means to diagnose, treat, prevent, and control this pandemic. One of the areas of focus is the isolation of this virus, which plays a crucial role in understanding the viral dynamics in the laboratory. In this study, we report the isolation and detection of locally circulating SARS-CoV-2 in Kenya. The isolates were cultured on Vero Cercopithecus cell line (CCL-81) cells, RNA extraction was conducted from the supernatants, and reverse transcriptase-polymerase chain reaction (RT-PCR). Genome sequencing was done to profile the strains phylogenetically and identify novel and previously reported mutations. Vero CCL-81 cells were able to support the growth of SARS-CoV-2 in vitro, and mutations were detected from the two isolates sequenced (001 and 002). Genome sequencing revealed the circulation of two isolates that share a close relationship with the Benin isolate with the D614G common mutation identified along the S protein. These virus isolates will be expanded and made available to the Kenya Ministry of Health and other research institutions to advance SARS-CoV-2 research in Kenya and the region.展开更多
Introduction: Visceral leishmaniasis is a severe form of leishmaniasis that affects about 90,000 people annually worldwide. It is mainly transmitted by Leishmania donovani and infantum, which can cause damage to inter...Introduction: Visceral leishmaniasis is a severe form of leishmaniasis that affects about 90,000 people annually worldwide. It is mainly transmitted by Leishmania donovani and infantum, which can cause damage to internal organs, such as the spleen, liver, and bone marrow. If left untreated, severe cases can be fatal, as the disease can lead to severe secondary diseases, mycological and bacterial infections, and hemorrhages. Nutritional deficiencies and concurrent infections increase the incidence of visceral leishmaniasis and the likelihood of lethality. There is limited information about the relationship between the disease and nutrition in endemic areas in Kenya. Objective: The study was to analyze the association of nutritional supplements with the nutritional status and treatment outcomes of visceral leishmaniasis among children aged 5 - 12 years in Baringo and West Counties in Kenya. Methods: A quasi-experimental study design adopting quantitative data collection method was used in this study. A total of 204 children aged 5 - 12 years were included in the study. Data on nutritional status and treatment outcomes for VL was collected using a questionnaire and consent form. Pre- and post-intervention assessments were conducted to compare BMI, fever, spleen size, splenic aspirate after treatment, and the presence of PKDL in a 3-month follow-up. The data was analyzed using R statistical software with descriptive and inferential statistics, including chi-square tests and t-tests. The impact of treatment was estimated using the difference-in-difference method to compare changes in outcomes over time between the intervention and comparison groups. Results: The baseline characteristics assessed in this study were socio-demographics (age, gender, marital status, education and religion), vitamins (A, B, C, D) and minerals (zinc, Iron and Iodine). The results showed that the mean age was 8.72, children aged 5 - 9 years were 64.7%, and those aged 10 - 12 years were 35.3% in the intervention and comparison groups. There were more males than females in the study (53.9% in the intervention and 52.9% in the comparison group respectively). All the children in the study were from a Christian background, were underweight, had enlarged spleen, and were positive for VL by Splenic Aspirate. Those who presented with fever were 88.2% (88% in both intervention and comparison groups). Most children had lower levels of zinc, iron, vitamins A, B12, and D at baseline (54.9%, 91.2%, 54.4%, 57.8%, and 58.8% respectively). The majority (93.1%) were deficient in vitamin C (90.2% in the intervention and 96.1% in the comparison group). Conclusion: According to the study findings, the effect of administering micronutrients is significant at 5% significance level with the intervention having a positive effect. The administration of the nutritional supplement led on average to an increase of the minerals, vitamins and BMI levels in the body.展开更多
In Kenya, food screening exercises mostly applies to bacterial and parasitic agents, with enteric viral detection neglected. The aim of this study was to investigate the prevalence and molecular characterization of ro...In Kenya, food screening exercises mostly applies to bacterial and parasitic agents, with enteric viral detection neglected. The aim of this study was to investigate the prevalence and molecular characterization of rotavirus in beef and pork cuts, as well as among handlers, in four selected abattoirs in Nairobi. Rotavirus was preferred because of its high prevalence rates and its ability to cause pathophysiologic infective gastroenteritis in humans. It has diverse strains characterized as P and G genotypes based on the VP7 and VP4 proteins, respectively. This cross-section study involved the collection of a total of 467, (165) beef/pork cuts and (302) handlers’ fecal samples. Collected samples were prepared before rotavirus identification. Prepared meat and stool suspensions were subjected to direct RNA extraction and EIA detection respectively. All the stool suspensions and RNA extracted meat suspensions subjected to EIA and Two step RT-PCR were all non-reactive respectively. Therefore, there was no VP4 and VP7 genotyping for characterization purposes on confirmed primary PCR products. Eppicollect5 was also used to collect and store the descriptive data of study participants, and the analysis conducted using Power BI statistical software application. The study’s findings, indicating no human viral infections in meat cuts, enhance public health by reassuring consumers, guiding regulatory policies, emphasizing the need for ongoing surveillance, directing resources to pressing concerns, supporting safe food handling campaigns, establishing baseline data for future assessments, and encouraging best practices in both formal and informal markets.展开更多
Pneumcystis jirovecii is a pathogen that causes Pneumocystis pneumonia (PCP), an infection in (HIV/ADS) and other immunocompromised patients. The rare reports of P. jirovecii pneumonia in sub-Saharan Africa are contro...Pneumcystis jirovecii is a pathogen that causes Pneumocystis pneumonia (PCP), an infection in (HIV/ADS) and other immunocompromised patients. The rare reports of P. jirovecii pneumonia in sub-Saharan Africa are controversial due to the high HIV/AIDS seropositivity. The study determined the significance of P. jirovecii in TB smear negative retreatment patients at the Coast General Teaching Referral Hospital-Mombasa. Sputum samples were subjected to toluidine blue O(TBO) stain for microscopy and polymerase chain reaction (PCR). A total of 100 TB smear negative participants were enrolled in the study and expectorated sputum was collected. Out of the 100 patients, 63 men and 37 women. Patients aged 31 to 53 made up 62% of the patients. The patients aged 31 to 53 made up 75% of the patients (Min = 11y, Max = 85y). The median age of the patients was 42 years. Nested PCR has a prevalence of 41% (41 instances). TBO staining has a prevalence of 29% (29 instances). Detecting an additional 13 more patients than toluidine O staining technique. The sensitivity of toluidine blue O staining was 33.82%, which indicates that it correctly identified 33.82% of true positive cases compared to PCR. The specificity of toluidine blue O staining was 97.82%, indicating that it had a high ability to correctly identify true negative cases compared to PCR, suggesting that it was good at ruling out non-P. jirovecii cases. The study confirms that P. jirovecii is as a significant cause of persistent symptoms in TB patients that could be responsible for persistent symptoms despite TB treatment. We recommend fungal diagnostics in such patients before retreatment.展开更多
Background: Acute respiratory infection (ARI) is a leading cause of morbidity and mortality in children under five years of age in developing countries with viruses contributing significantly to this problem. The rece...Background: Acute respiratory infection (ARI) is a leading cause of morbidity and mortality in children under five years of age in developing countries with viruses contributing significantly to this problem. The recently identified parvovirus, Human Bocavirus (HBoV), has also been associated with ARI. Objective: To determine the frequency of HBoV in patients with ARI. Materials and Methods: Samples from 125 consenting patients with influenza like illness signs and symptoms were collected. DNA was extracted from these samples using the QIAamp DNA blood mini kit (Qiagen, Germany). Conventional PCR was carried out and the amplicons were examined in 2% agarose gels stained with ethidium bromide. This was followed by sequencing of the HBoV positive samples. Results: Twenty one (16.8%) patients were found to have HBoV infection. Males (n = 61.9%) were mainly infected with HBoV. Local HBoV strains had 98.9% - 100% similarities and were found to cluster together with other strains obtained elsewhere. Conclusion: These findings suggest that HBoV plays a role in respiratory tract infections in children in Kenya just like it has been found elsewhere. It also sheds light on multiple infections associated with HBoV infections in Kenya.展开更多
Urinary Tract Infections (UTIs) during pregnancy are among the most common infections worldwide and can lead to poor perinatal and maternal outcomes. This study determined the prevalence of UTIs during pregnancy, asso...Urinary Tract Infections (UTIs) during pregnancy are among the most common infections worldwide and can lead to poor perinatal and maternal outcomes. This study determined the prevalence of UTIs during pregnancy, associated risk factors and antimicrobial susceptibility profiles of associated bacterial pathogens. A cross-sectional study was conducted among 210 pregnant women attending antenatal clinic at Pumwani Maternity hospital. Their social-demographic profiles were obtained using a structured questionnaire. Cultures were done from midstream urine and antimicrobial susceptibility testing determined using the disc diffusion test. The overall prevalence of UTI was 15.7% regardless of the women’s age, parity and stage of gestation. Prevalence of asymptomatic and symptomatic bacteriuria was 4.3% and 11.4% respectively. Material of undergarment and frequency of changing the undergarments were found to contribute significantly to the acquisition of UTI (P < 0.05). E. coli was the most predominant UTI organism at (44.5%) followed by K. pneumoniae (21.2%) and S. aureus (15.1%). Almost a half (over 49%) of all Gram-negative organisms showed resistance prevalence against third generation cephalosporins, fluoroquinolones, Sulfamethoxazole-Trimethoprim, Cefoxitin, Nitrofurantoin and Amoxicillin-clavulanic acid. Gram-positive strains were susceptible to Amoxicillin-clavulanic acid, Nitrofurantoin, Linezolid and Ofloxacin. The prevalence of multi-drug resistance (MDR) in all study isolates was 96%. Our data suggest a serious resistance trend among UTI strains and more should be done to slow down this trend. Pregnant women should be screened by urine culture and treatment be guided by the antimicrobial susceptibility data.展开更多
Background: Screening for cancer of the cervix at Kenyatta National Hospital (KNH), follows the recommended three-step strategy;Papanicolaou (Pap) smear, colposcopy/biopsy and loop electrosurgical excision procedure (...Background: Screening for cancer of the cervix at Kenyatta National Hospital (KNH), follows the recommended three-step strategy;Papanicolaou (Pap) smear, colposcopy/biopsy and loop electrosurgical excision procedure (LEEP)/biopsy. This approach poses the following challenges: multiple clinic visits, costly, time consuming, long turnaround time to treatment, non-compliance and loss-to-follow-up. Objective: To determine the agreement between histologies following colposcopy and LEEP amongst women in KNH as a forerunner for opportunity to shift from the three-step approach to the two-step “see and treat” (same-day colposcopy and LEEP) approach. Methods: This was a retrospective descriptive cohort of Women who underwent LEEP procedure between January 2008 and 31st December 2010 following the three-step approach at KNH, Kenya. Results: A total of 124 patients out of the 132 patients who underwent LEEP were included in the analysis. The 8 patients excluded had missing files. HIV infected, uninfected or unknown women are similar socio-demographically. The mean (SD) age for the HIV infected, uninfected and unknown is 37 (6), 33 (10) and 35 (9) years respectively. Colposcopic and LEEP biopsy histology within patients demonstrated a high weighted kappa statistics agreement of 84%. LEEP increased diagnosis of invasive cancer. Patients had a median (IQR) 5 (4 - 6) clinic visits from Pap smear to LEEP treatment. It took median (IQR) 55 (27 - 116) days between Pap smear to colposcopy result and 167 (101 - 276) days between Pap smear results to LEEP treatment. If a LEEP procedure were to be performed in this cohort of women on the same day of the colposcopy biopsy a median (IQR) 77 (55 - 137) days could have been saved. Conclusion: There is a high agreement between colposcopy and LEEP biopsies in our setting offering a window of opportunity to perform “See and Treat” same-day colposcopy and LEEP treatment procedure, skipping the colposcopy biopsy stage.展开更多
Aflatoxin M1 (AFM1) is a major carcinogenic compound that may be found in milk and dairy products resulting from ingestion of aflatoxin B1 by dairy animals. The study aimed at determining the level of aflatoxin M1 in ...Aflatoxin M1 (AFM1) is a major carcinogenic compound that may be found in milk and dairy products resulting from ingestion of aflatoxin B1 by dairy animals. The study aimed at determining the level of aflatoxin M1 in milk and milk products from Bomet County. A total of 185 samples (150 raw milk and 35 processed milk and milk products) were randomly collected from milk collection sites and randomly selected milk kiosks respectively. The AFM1 was analyzed using a commercial ELISA kit (Ridascreen, aflatoxin M1 R-Biopharm, Product code, R5812, Darmstadt, Germany). Out of 185 samples investigated, 156 samples were positive for AFM1, an overall contamination rate of 84.32%. The samples with levels higher than the tolerance limit of 0.05 μg/l recommended by Food and Agriculture Organization (FAO) and World Health Organization (WHO) limits were 43.8% mainly contributed by the raw milk compared to processed milk (52.0% versus 8.6%). Processed milk had insignificant level of contamination with aflatoxin M1 (Median 0.00 (IQR: 0.00, 0.00 μg/l) with a minimum of 0.00 μg/l and a maximum of 0.69 μg/l. Raw milk showed significant contamination, median 0.09 (IQR: 0.00, 0.50) μg/l with a minimum of 0.00 μg/l and a maximum of 2.93 μg/l. Although there was no significant differences in AFM1 levels with study sites (P = 0.217);the median levels of aflatoxin M1 was high in sites 1, 3, and 7. The sites that had median aflatoxin M1 levels below the WHO/FAO acceptable limits of 0.05 μg/l were sites 2, 4 and 6. Due to high incidence of AFM1 contamination of milk and milk samples in Bomet County, there is need for regular monitoring and regulation of AFM1 contamination in milk and its products in the County.展开更多
The prevalence of TB in sub-Sahara Africa has been reported as 511 per 100,000 populations and a mortality of 74 per 100,000 in year 2009. In the same period, incidence was estimated at 350 cases per 100,000. In this ...The prevalence of TB in sub-Sahara Africa has been reported as 511 per 100,000 populations and a mortality of 74 per 100,000 in year 2009. In the same period, incidence was estimated at 350 cases per 100,000. In this regard, the health system requires strengthening to respond to the rising cases of infection, drug resistance and quality of life lost while continuing to seek interventions that improve adherence to medication and case detection among those infected. Methods: This study sought to determine factors that are associated with sputum positivity after intensive phase of chemotherapy in people with tuberculosis. It was a retrospective case-control study conducted in Rhodes chest clinic, a City Council health unit in Nairobi that specializes in treatment of chest infections. The participants were sampled from clinic attendants who had completed two months of intensive phase TB chemotherapy and met inclusion criteria. Results: Seventy participants of whom 25 (36%) were sputum positive at the end of two (2) months intensive phase were included in the study. Skipping medication doses was significantly associated with sputum positivity (p = 0.01). Patients who were sputum positive at the end of the two-month period were more likely to have taken longer time before seeking treatment compared to those who were sputum negative by median (IQR) 8 (3 - 12) and 4 (3 - 8) weeks respectively although this difference was not significant (p = 0.09). Patients who had not disclosed their infection status had a two-fold possibility of remaining sputum positive at the end of intensive phase. Conclusion: Early diagnosis and treatment of TB, and adherence to medication were important factors that affect sputum conversion during intensive phase of TB treatment. Therefore, public health practitioners should advise patients to seek prompt diagnosis and treatment of signs and symptoms of tuberculosis.展开更多
Objective： This study compared the performance of the immunochromatographic strip （ICS） to the Venereal Disease Research Laboratory （VDRL） test and Treponema pallidum haemagglutination assay （TPHA） at a primary...Objective： This study compared the performance of the immunochromatographic strip （ICS） to the Venereal Disease Research Laboratory （VDRL） test and Treponema pallidum haemagglutination assay （TPHA） at a primary health care setting. Methods： The study group was comprised of 150 females randomly drawn from a population of pregnant women attending their first antenatal visit or follow-up visits at West Maternity Hospital in Eldoret Kenya, but without a previous syphilis test during that pregnancy. On-site VDRL, ICS and TPHA tests were performed and immediate treatment provided where appropriate. The performance of the three tests was compared, Results： The sero-prevalence of syphilis as determined by the VDRL test was 3%. There was no significant difference between the ICS and the VDRL test （P 〉 0.05）. The sensitivity and specificity of the ICS test were 80% and 98.6% respectively, while the negative predictive value （NPV） and positive predictive value （PPV） were both 100%. On the other hand, the sensitivity and specificity of the VDRL test were 66.7% and 99.3%, while the NPV and PPV were 80% and 98.6% respectively. The Treponema pallidum haemagglutination assay was used as a reference test and had sensitivity, specificity, NPV and PPV of 100%. Conclusion： The diagnostic accuracy of the ICS compared favorably with theVDRL gold standard. The use of the ICS in Kenya can improve the diagnosis of syphilis in health facilities both with and without laboratories and allow community health care workers to make a rapid diagnosis of the disease, and consequently make immediate therapeutic decisions.展开更多
Ticks harbor multiple pathogens, most of which can be transmitted to humans. The ensuing zoonoses display non-specific symptoms that make definitive diagnosis difficult. We report here the development and evaluation o...Ticks harbor multiple pathogens, most of which can be transmitted to humans. The ensuing zoonoses display non-specific symptoms that make definitive diagnosis difficult. We report here the development and evaluation of multiplex real time polymerase chain reaction (qPCR) assays for eight tick-borne zoonoses (TBZ). The assays were organized in duo formats of 4-plex each. Format 1 was optimized for Anaplasma phagocytophilum, Coxiella burnetii, Borrelia burgdoferi and Ehrlichia chaffeensis. Format 2 was optimized for Rickettsia species (spp.), Bartonella spp., Borrelia spp. other than B. burgdoferi and Babesia spp. Synthetic plasmids were used to show that the assays can specifically detect all target sequences in the same reaction tube. Assays were assayed eight times to determine assay performance and the limit of detection was determined as the lowest plasmid concentration that was amplified for all the targets. Standard curves of threshold cycle (Ct) versus copy numbers were generated and used to determine linearity and efficiency of the assays. Pairwise comparison of singleplex and multiplex assays was done using Bland-Altman plots. Prevalence was calculated as overall percentage of positive patients to each TBZ tested Assay 1 had a limit of detection of 2 copy numbers for all targets. Assay 2 was less sensitive and on average had a limit of detection of 18 gene copies. In replicate tests, both assays had intra-assay variation of less than two cycles. Multiplex assays performance was comparable to respective singleplex assays. Evaluation of 512 clinical samples collected between 2008 and 2016 from acute febrile illness patients attending hospitals in different counties in Kenya revealed a 20% prevalence of tick-borne pathogens comprising B. burgdorferi (6%), non B. burgdorferi Borrelia spp. (3%), C. burnetii (5%), A. phagocytophilum (5%), Rickettsia spp. (2%), E. chaffeensis (0.8%), Bartonella spp. (0.8%), and Babesia spp. (0.4%). The high analytical sensitivity suggests potential for the duo 4-plex qPCR for detection of common TBZ.展开更多
Pseudomonas aeruginosa is a leading cause of hospital infections and is intrinsically resistant to most antibiotics. Emergence of multidrug resistant (MDR) strains has been reported in the world and poses a great chal...Pseudomonas aeruginosa is a leading cause of hospital infections and is intrinsically resistant to most antibiotics. Emergence of multidrug resistant (MDR) strains has been reported in the world and poses a great challenge in the management of infections associated with this species. While a substantial amount of research has been done on strains from most of other infection caused by this species in developed countries, little is known about the susceptibility profiles of strains recovered from African countries in general and Kenya in particular. Furthermore, there is paucity of data regarding strain, phenotype and genetic diversity of strains recoverable from wounds among patients in Kenya. The possible risk factors for acquisition of MDR strains and possible factors that could fuel clonal expansion in hospital and community settings remain undetermined. This cross-sectional study conducted in Tigoni Hospital, a rural area in Central Kenya sought to determine risk factors associated with carriage of MDR Pseudomonas aeruginosa in wounds among rural population. We also analyzed antimicrobial resistance profiles among these isolates. Prevalence of P. aeruginosa in wounds was 28% with 85 isolates recovered from wounds of 299 participants. Most antimicrobial resistance prevalence was recorded towards Ceftazidime (64%) and Cefepime (52%) while Piperacillin-tazobactam was the most effective antimicrobial agent with a resistance prevalence rate of 20%. Resistance towards new classes of aminoglycosides such as Gentamicin was at 45% while that towards Amikacin was at 40%. Compared to other related studies, relatively lower resistance towards Ciprofloxacin (25%) and Meropenem (40%) were recorded. Some of the risk factors identified for carriages of MDR strains were self-medication (p: 0.001, C.I: 3.01 - 8.86, O.R: 5.17) and non-completion of dosage (p: 0.12, C.I: 0.9 - 2.5, O.R: 1.5).展开更多
Ticks are reservoirs of a variety of pathogens including bacteria, viruses and protozoa. We used PCR to detect pathogens of public health importance in ticks collected from diverse regions of Kenya. 503 tick pools wer...Ticks are reservoirs of a variety of pathogens including bacteria, viruses and protozoa. We used PCR to detect pathogens of public health importance in ticks collected from diverse regions of Kenya. 503 tick pools were collected from 982 cattle, 300 sheep and 379 goats that were presented for slaughter at major abattoirs in Nairobi and Mombasa. Tick DNA was screened by qPCR optimized for single-plex detection of Babesia microti, two-plex Coxiella burnetii/Ehrlichia chaffeensis or Bartonella henselae/Borrelia recurrentis or three-plex for the non-human Babesia spp/Anaplasma phagocytophylum/Borrelia burgdorferi. Pathogen prevalence was calculated against tick type and the geographical origin. Computational analysis was performed with Graphpad prism 5. Out of 503 tick analyzed, 21% (106) were positive for at least one pathogen. C. burnetii was the most abundant at 70% (74/106), followed by non-human Babesia at 17% (18/106), 5% (5/106) for B. burgdorferi, 7% (7/106) for other Borrelia species and <1% (1/106) for E. chaffeensis and A. phagocytophylum. B. henselae and the human infective B. microti were not detected. Rh. pulchellus was the most promiscuous one in carrying pathogens: C. burnetti, Babesia, B. burgdorferi, E. chaffeensis and A. phagocytophylum. Non-human infective Babesia were detected in all ticks except Amblyomma. Four counties had 70% of the infected ticks: Marsabit 25% (n = 26/106), Kajiado 17% (18/106), Wajir 16% (17/106) and Narok 11% (12/106). This study identified a number of tick-borne pathogens that cause febrile infections often confused with malaria. Follow-up research will be needed to determine prevalence in humans.展开更多
Wastewater surveillance has been applied in various parts of the world to monitor the introduction and transmissions of SARS-CoV-2 variants in a population. The knowledge of SARS-CoV-2 variants circulating in a popula...Wastewater surveillance has been applied in various parts of the world to monitor the introduction and transmissions of SARS-CoV-2 variants in a population. The knowledge of SARS-CoV-2 variants circulating in a population is critical to COVID-19 management and timing of the application of public health countermeasures. Contrary to the routine clinical surveillance of SARS-CoV-2 where cases from asymptomatic patients are often underreported, wastewater surveillance offers an unbiased tool for monitoring the extent of SARS-CoV-2 transmissions in a community. The present study aimed to characterize SARS-CoV-2 variants that circulated in Nairobi County, Kenya, between April 2021 and August 2021 utilizing wastewater samples. Viral RNA was extracted from wastewater samples, followed by SARS-CoV-2 screening by real-time RT-qPCR before targeted sequencing of the Spike gene. Forty samples were analyzed, of which 50% (n = 20) tested positive for SARS-CoV-2 by real-time RT-qPCR. Of these, 45% (n = 9) were successfully amplified by RT-PCR and sequenced. The majority (78%, 7/9) of the viruses belonged to the Delta (B.1.617.2) lineage of SARS-CoV-2, while a minority (22%) belonged to the Alpha (B.1.1.7) and Alpha-Delta lineages. Phylogenetic analysis of the SARS-COV-2 delta lineage strains revealed scattered clustering of the Kenyan viruses among the global strains included in the analysis, suggesting different introductory routes into the country. On the whole, our results confirm previous clinical findings that SARS-CoV-2 variants belonging to the Alpha (B.1.1.7) and Delta (B.1.617.2) lineages circulated in Nairobi County, Kenya during the study period, with the latter predominating. This is the first study to describe the diversity of SARS-CoV-2 variants circulating in Kenya, through wastewater analysis.展开更多
Background: Herpes simplex virus Type 2 (HSV-2) has been associated with HIV infection. More recently, HSV-2 incidence has been linked to HIV acquisition. A few studies have suggested that the fishing communities have...Background: Herpes simplex virus Type 2 (HSV-2) has been associated with HIV infection. More recently, HSV-2 incidence has been linked to HIV acquisition. A few studies have suggested that the fishing communities have a high HSV-2 prevalence but there is limited knowledge on HSV-2 incidence and associated risk factors among fishermen. Methods: Three hundred fishermen were consented, and evaluated for baseline HSV-2 serology status and again after 12 months among those negative at baseline. Sexual behavior and socio-demographic data were collected at enrolment and exit visits using a structured questionnaire. Baseline HIV serology and Human papillomavirus (HPV) DNA genotyping were also performed. Multivariate logistic regression was used to determine independent factors associated with HSV-2 acquisition. Results: Baseline HSV-2 prevalence was 56.3% (95% CI: 50.7 - 62.0). Factors associated with HSV-2 prevalence were, older age (aOR = 1.96;95% CI: 1.16 - 2.85), history of STI (aOR 2.12;95% CI: 1.19 - 3.91), infection with HIV (aOR 2.22;95% CI: 1.17 - 4.22), ever married (aOR = 3.80;95% CI: 1.42 - 11.90), most recent sexual act with sex worker/casual partner (OR= 3.56;95% CI: 1.49 - 8.62) and inconsistent condom use with new sexual partner (aOR = 6.34;95% CI: 2.24 - 13.04). The HSV-2 incidence was 23.6 (95% CI = 15.4 - 31.8)/100 pyr. Infection with persistent high-risk (HR) HPV (aIRR = 3.35;95% CI: 1.21 - 11.37), multiple (≥2) partners in 12 months prior to study participation (aIRR = 4.77;95% CI: 1.12 - 11.38), inconsistent condom use with new partner (aIRR =2.53;95% CI: 1.12 - 7.38) and most recent sexual act with sex worker/casual partner (OR = 3.03;95% CI: 1.17 - 8.58) were independent risk factors for HSV-2 acquisition. Conclusion: The incidence of HSV-2 is very high among fishermen. It is associated with persistent HR HPV infection and high-risk sexual behavior. Intervention strategies targeting these men with high risk sexual behavior are urgently needed to stop new HSV-2 acquisition and subsequently prevent HIV infection.展开更多
In areas of sub-Saharan Africa where malaria is endemic, pregnant women are at a greater risk of malaria than non-pregnant women leading to significant adverse consequences including anemia, intrauterine growth retard...In areas of sub-Saharan Africa where malaria is endemic, pregnant women are at a greater risk of malaria than non-pregnant women leading to significant adverse consequences including anemia, intrauterine growth retardation, low birth weight (LBW), and pre-term delivery. The Kenya Ministry of Health adopted Intermittent Preventive Treatment (IPT) and use of insecticide-treated nets (ITN) as a National strategy for malaria prevention in pregnancy. In this report, we evaluated the prevalence of malaria, the anthropometric measures of birth outcomes and the reasons for loss to follow up among pregnant women participating in an ongoing cohort study in Western Kenya. A total of 175 HIV-negative pregnant women enrolled at antenatal clinic of Chulaimbo sub-District hospital were longitudinally evaluated in a monthly follow-up visits through antenatal visits (up to 4 per mother) and delivery. Thirty three percent and 15% of the pregnant women were malaria positive by real-time quantitative (Q)-PCR and microscopy respectively at enrolment, while 54% and 23% of the pregnant women had malaria by Q-PCR and microscopy respectively at any time during follow-up. Of the enrolled study participants, 65% delivered at Chulaimbo hospital. Overall, 39% (69) of the pregnant women were lost to follow-up. The major reasons for loss to follow up were relocation from the study area (26%) and delivery at alternative health facilities (25%). The mean birth weight of the newborn infants was 3202 g (range, 2000 g - 4000 g). Only 5.3% of the infants weighed less than 2500 g (low birth weight). The mean head circumference was 34 cm (range, 30 cm - 39 cm) with mean Apgar score (at 10 minutes) ± S.D. of 9.8 ± 0.97. In conclusion, we observed decreased adverse pregnancy outcomes among our study population. We recommend a larger study of all pregnant women attending the Chulaimbo hospital so as to assess whether effectiveness of malaria and anemia control programs lead to improved birth outcomes.展开更多
Antimicrobial drug resistance is a rising concern in the treatment of infectious diseases and necessitates the need for discovery of novel, potent antimicrobial compounds to combat antibiotic resistance. Since natural...Antimicrobial drug resistance is a rising concern in the treatment of infectious diseases and necessitates the need for discovery of novel, potent antimicrobial compounds to combat antibiotic resistance. Since natural environment remains a potential source of novel antimicrobial products, this preliminary study was performed to test the potential of soils from Kericho County for antibiotic-producing Actinomycetes. Soil samples (214) were randomly collected from virgin soils of Kipkelion East, Kipkelion West, Belgut, Ainamoi, Sigowet and Bureti sub-counties in Kericho County from a depth of between 11 cm - 16 cm from the surface of the soil profile. A total of 107 Actinomycetes were isolated and screening was done using modified agar disc diffusion method of which only 39 (36.4%) showed antimicrobial activity against five of the six test isolates that included reference strains Staphylococcus aureus (ATCC 25923), Escherichia coli (ATCC 25922) and Candida albicans (ATCC 90028) and three clinical strains Trichophyton mentagrophyte, Microsporum gypseum and Methicillin Resistant Staphylococcus aureus. Two of the isolates showed activity against MRSA and four isolates showed a higher potency than the standard drug Chloramphenicol (30 μg) against S. aureus. Most of the isolates (41.0%) also showed good antimicrobial activity against T. mentagrophyte, though they lower than the control drug Itraconazole (2 μg/ml), they were statistically significant. DNA from the isolates was extracted and the 16S rRNA gene was amplified using primers specific for Actinomycetes. The amplified gene was sequenced and phylogeny analysis was done. The 16S rRNA gene was able to be amplified in only 15 of these isolates. Sequencing showed that 93.3% were of the genus Streptomyces while 6.7% were of the genus Rhodococcus. From the results, the soils from this region harbour Actinomycetes that may have good potential of producing novel antibiotics against gram positive bacteria and dermatophytes.展开更多
Hepatitis B Virus (HBV) infections affect about 400 million people globally and cause about 1.4 million deaths annually. The virus displays high levels of genetic variations/mutations, some of which are immune escape ...Hepatitis B Virus (HBV) infections affect about 400 million people globally and cause about 1.4 million deaths annually. The virus displays high levels of genetic variations/mutations, some of which are immune escape mutants. The prevalence of HBV infection in Kenya is high at about 8%. This study aimed at identifying and characterizing HBV immune escape mutants in Kenya. From 547 HBV sequences available in Kenya in NCBI, and HBVdb databases in July 2021, 120 full sequences were retrieved. The S gene sequences at position 1-225, which included the “a” determinant region of the gene were analyzed using various bioinformatics tools such as Bioedit software, and Emboss Cons. The clinical significance was flagged from the search of peer-reviewed journals. Forty-six HBV-positive blood donor samples were obtained from the Kenya National Blood Transfusion Services without personal identifiers, DNA extracted, and sequenced targeting positions 1 to 520 of S genes. Mutations were similarly identified from seventeen sequences after cleaning and analysis. Out of 120 sequences that were extracted from databases and analyzed, 79 different mutations were identified. Fifteen of them were of clinical importance with an occurrence frequency of at least 5% were obtained. The majority (64.6%, n = 51), with S207N and A194V being most dominant, could result in immune escape and reduced HBsAg detection signals while 24.1% (n = 19) could result in immune escape/reduced HBsAg detection signals and high probability of hepatocellular carcinoma. Most likely to occur on the amino acids Alanine, Lysine, Serine, Asparagine, and Valine in decreasing order. The most dominant genotype was found to be Genotype A (N = 10), while four sequences were Genotype D. In contrast to the in-silico studies, the sequences from HBV samples from blood donors did not demonstrate the presence of S207N and A194V mutations and all the genotypes were type A1. Only two (13.3%) samples showed the same mutations of sK122R and sT143S for both in-silico analysis and actual sequenced samples. This study did not identify G145R mutation which is the commonest mutation within the HBsAg immunodominant “a” determinant that is associated with immune escape. The concordance of mutations in “a” determinant region of HBsAg gene among various studies is minimal. The study identified new mutations (sA194Y, sS207, sA194S, sS207I, sP46A, sA194T, sS207I, sP46R, and sT143P) that had not been published before. Four (20%) of the mutations were clinically significant. These included sS207R, sT143S, sC76F and sK122R.展开更多
The 2016 Olympic Games happened at the time of heightened fears of Zika virus (ZIKV) that was causing microcephaly in newborns in Brazil. To avert or track introduction of ZIKV in Kenya, the Ministry of Health develop...The 2016 Olympic Games happened at the time of heightened fears of Zika virus (ZIKV) that was causing microcephaly in newborns in Brazil. To avert or track introduction of ZIKV in Kenya, the Ministry of Health developed a public health response that involved screening of the Kenyan contingent before and after traveling to Brazil. Of the 92 team members that were screened, all but one tested negative for ZIKV IgM and IgG. The sero-positive individual had high IgM serum titers before and after travel to Brazil. When tested for potential antibody cross-reactivity to other flaviviruses that have been reported in Kenya, the sample showed high IgM cross-reactivity to West Nile, Tick-Borne Encephalitis and Yellow Fever Virus. Our data support the low risk predictions of acquiring ZIKV that were made before the Games and will help inform risk assessments for personnel traveling to endemic regions under similar circumstances in the future.展开更多
Background: Herpes simplex virus type-2 (HSV-2) and human papillomavirus (HPV) are common sexually transmitted infections (STIs) among fishing communities and are associated with high HIV prevalence in this underserve...Background: Herpes simplex virus type-2 (HSV-2) and human papillomavirus (HPV) are common sexually transmitted infections (STIs) among fishing communities and are associated with high HIV prevalence in this underserved population. However, there is limited knowledge on HIV incidence among fishermen. This study aimed at determining prevalence, incidence and risk factors associated with HIV infection among fishermen in Kisumu Kenya. Methods: Three hundred fishermen were evaluated for baseline HIV, HSV-2, HPV infection and a structured questionnaire administered. HIV incidence was assessed after 12 months among those initially HIV negative. HIV incidence rate in person-years and prevalence were estimated. Multivariate logistic regression was used to determine factors independently associated with HIV acquisition. Results: HIV prevalence was 23.3% (95% CI: 18.5 - 28.1). Risk factors for baseline HIV prevalence were older age (aOR = 2.13;95% CI: 1.25 - 5.07), history of STI (aOR 4.21;95% CI: 2.07 - 9.34), baseline HPV infection (aOR 2.13;95% CI: 1.05 - 4.77), number of lifetime sexual partners (>5) aOR = 5.76 (95% CI: 1.41 - 13.57) and transactional sex (aOR = 10.98;95% CI: 1.86 - 19.34). Condom uses with new sexual partner (aOR 0.21, 95% CI: 0.08 - 0.55) and during most recent sexual act (aOR 0.09, 95% CI: 0.03 - 0.61), were negatively associated with HIV prevalence. HIV incidence was 4.2 (95% CI = 1.3 - 7.1) per 100 person-years with being single (aIRR = 8.32;95% CI: 1.27 - 54.67) as an independent risk factor. Condom use with new sexual partner (aIRR = 0.11;95% CI: 0.01 - 0.89) and recent sex with wife/regular girlfriend (compared to sex worker/casual partner;aIRR = 0.03;95% CI: 0.01 - 0.35) were associated with reduced risk of HIV acquisition. Conclusion: Inconsistent condom use and transactional/casual sexual partnerships were the main high-risk sexual behaviors in addition to marital status explaining the high HIV acquisition rate among fishermen. Intensified safer sex promotion is urgently needed in this subpopulation to avert new HIV infections.展开更多
文摘The discovery of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) in Wuhan, Hubei province, China, in December 2019 raised global health warnings. Quickly, in 2020, the virus crossed borders and infected individuals across the world, evolving into the COVID-19 pandemic. Notably, early signs of the virus’s existence were observed in various countries before the initial outbreak in Wuhan. As of 12<sup>th</sup> of April, the respiratory disease had infected over 762 million people worldwide, with over 6.8 million deaths recorded. This has led scientists to focus their efforts on understanding the virus to develop effective means to diagnose, treat, prevent, and control this pandemic. One of the areas of focus is the isolation of this virus, which plays a crucial role in understanding the viral dynamics in the laboratory. In this study, we report the isolation and detection of locally circulating SARS-CoV-2 in Kenya. The isolates were cultured on Vero Cercopithecus cell line (CCL-81) cells, RNA extraction was conducted from the supernatants, and reverse transcriptase-polymerase chain reaction (RT-PCR). Genome sequencing was done to profile the strains phylogenetically and identify novel and previously reported mutations. Vero CCL-81 cells were able to support the growth of SARS-CoV-2 in vitro, and mutations were detected from the two isolates sequenced (001 and 002). Genome sequencing revealed the circulation of two isolates that share a close relationship with the Benin isolate with the D614G common mutation identified along the S protein. These virus isolates will be expanded and made available to the Kenya Ministry of Health and other research institutions to advance SARS-CoV-2 research in Kenya and the region.
文摘Introduction: Visceral leishmaniasis is a severe form of leishmaniasis that affects about 90,000 people annually worldwide. It is mainly transmitted by Leishmania donovani and infantum, which can cause damage to internal organs, such as the spleen, liver, and bone marrow. If left untreated, severe cases can be fatal, as the disease can lead to severe secondary diseases, mycological and bacterial infections, and hemorrhages. Nutritional deficiencies and concurrent infections increase the incidence of visceral leishmaniasis and the likelihood of lethality. There is limited information about the relationship between the disease and nutrition in endemic areas in Kenya. Objective: The study was to analyze the association of nutritional supplements with the nutritional status and treatment outcomes of visceral leishmaniasis among children aged 5 - 12 years in Baringo and West Counties in Kenya. Methods: A quasi-experimental study design adopting quantitative data collection method was used in this study. A total of 204 children aged 5 - 12 years were included in the study. Data on nutritional status and treatment outcomes for VL was collected using a questionnaire and consent form. Pre- and post-intervention assessments were conducted to compare BMI, fever, spleen size, splenic aspirate after treatment, and the presence of PKDL in a 3-month follow-up. The data was analyzed using R statistical software with descriptive and inferential statistics, including chi-square tests and t-tests. The impact of treatment was estimated using the difference-in-difference method to compare changes in outcomes over time between the intervention and comparison groups. Results: The baseline characteristics assessed in this study were socio-demographics (age, gender, marital status, education and religion), vitamins (A, B, C, D) and minerals (zinc, Iron and Iodine). The results showed that the mean age was 8.72, children aged 5 - 9 years were 64.7%, and those aged 10 - 12 years were 35.3% in the intervention and comparison groups. There were more males than females in the study (53.9% in the intervention and 52.9% in the comparison group respectively). All the children in the study were from a Christian background, were underweight, had enlarged spleen, and were positive for VL by Splenic Aspirate. Those who presented with fever were 88.2% (88% in both intervention and comparison groups). Most children had lower levels of zinc, iron, vitamins A, B12, and D at baseline (54.9%, 91.2%, 54.4%, 57.8%, and 58.8% respectively). The majority (93.1%) were deficient in vitamin C (90.2% in the intervention and 96.1% in the comparison group). Conclusion: According to the study findings, the effect of administering micronutrients is significant at 5% significance level with the intervention having a positive effect. The administration of the nutritional supplement led on average to an increase of the minerals, vitamins and BMI levels in the body.
文摘In Kenya, food screening exercises mostly applies to bacterial and parasitic agents, with enteric viral detection neglected. The aim of this study was to investigate the prevalence and molecular characterization of rotavirus in beef and pork cuts, as well as among handlers, in four selected abattoirs in Nairobi. Rotavirus was preferred because of its high prevalence rates and its ability to cause pathophysiologic infective gastroenteritis in humans. It has diverse strains characterized as P and G genotypes based on the VP7 and VP4 proteins, respectively. This cross-section study involved the collection of a total of 467, (165) beef/pork cuts and (302) handlers’ fecal samples. Collected samples were prepared before rotavirus identification. Prepared meat and stool suspensions were subjected to direct RNA extraction and EIA detection respectively. All the stool suspensions and RNA extracted meat suspensions subjected to EIA and Two step RT-PCR were all non-reactive respectively. Therefore, there was no VP4 and VP7 genotyping for characterization purposes on confirmed primary PCR products. Eppicollect5 was also used to collect and store the descriptive data of study participants, and the analysis conducted using Power BI statistical software application. The study’s findings, indicating no human viral infections in meat cuts, enhance public health by reassuring consumers, guiding regulatory policies, emphasizing the need for ongoing surveillance, directing resources to pressing concerns, supporting safe food handling campaigns, establishing baseline data for future assessments, and encouraging best practices in both formal and informal markets.
文摘Pneumcystis jirovecii is a pathogen that causes Pneumocystis pneumonia (PCP), an infection in (HIV/ADS) and other immunocompromised patients. The rare reports of P. jirovecii pneumonia in sub-Saharan Africa are controversial due to the high HIV/AIDS seropositivity. The study determined the significance of P. jirovecii in TB smear negative retreatment patients at the Coast General Teaching Referral Hospital-Mombasa. Sputum samples were subjected to toluidine blue O(TBO) stain for microscopy and polymerase chain reaction (PCR). A total of 100 TB smear negative participants were enrolled in the study and expectorated sputum was collected. Out of the 100 patients, 63 men and 37 women. Patients aged 31 to 53 made up 62% of the patients. The patients aged 31 to 53 made up 75% of the patients (Min = 11y, Max = 85y). The median age of the patients was 42 years. Nested PCR has a prevalence of 41% (41 instances). TBO staining has a prevalence of 29% (29 instances). Detecting an additional 13 more patients than toluidine O staining technique. The sensitivity of toluidine blue O staining was 33.82%, which indicates that it correctly identified 33.82% of true positive cases compared to PCR. The specificity of toluidine blue O staining was 97.82%, indicating that it had a high ability to correctly identify true negative cases compared to PCR, suggesting that it was good at ruling out non-P. jirovecii cases. The study confirms that P. jirovecii is as a significant cause of persistent symptoms in TB patients that could be responsible for persistent symptoms despite TB treatment. We recommend fungal diagnostics in such patients before retreatment.
文摘Background: Acute respiratory infection (ARI) is a leading cause of morbidity and mortality in children under five years of age in developing countries with viruses contributing significantly to this problem. The recently identified parvovirus, Human Bocavirus (HBoV), has also been associated with ARI. Objective: To determine the frequency of HBoV in patients with ARI. Materials and Methods: Samples from 125 consenting patients with influenza like illness signs and symptoms were collected. DNA was extracted from these samples using the QIAamp DNA blood mini kit (Qiagen, Germany). Conventional PCR was carried out and the amplicons were examined in 2% agarose gels stained with ethidium bromide. This was followed by sequencing of the HBoV positive samples. Results: Twenty one (16.8%) patients were found to have HBoV infection. Males (n = 61.9%) were mainly infected with HBoV. Local HBoV strains had 98.9% - 100% similarities and were found to cluster together with other strains obtained elsewhere. Conclusion: These findings suggest that HBoV plays a role in respiratory tract infections in children in Kenya just like it has been found elsewhere. It also sheds light on multiple infections associated with HBoV infections in Kenya.
文摘Urinary Tract Infections (UTIs) during pregnancy are among the most common infections worldwide and can lead to poor perinatal and maternal outcomes. This study determined the prevalence of UTIs during pregnancy, associated risk factors and antimicrobial susceptibility profiles of associated bacterial pathogens. A cross-sectional study was conducted among 210 pregnant women attending antenatal clinic at Pumwani Maternity hospital. Their social-demographic profiles were obtained using a structured questionnaire. Cultures were done from midstream urine and antimicrobial susceptibility testing determined using the disc diffusion test. The overall prevalence of UTI was 15.7% regardless of the women’s age, parity and stage of gestation. Prevalence of asymptomatic and symptomatic bacteriuria was 4.3% and 11.4% respectively. Material of undergarment and frequency of changing the undergarments were found to contribute significantly to the acquisition of UTI (P < 0.05). E. coli was the most predominant UTI organism at (44.5%) followed by K. pneumoniae (21.2%) and S. aureus (15.1%). Almost a half (over 49%) of all Gram-negative organisms showed resistance prevalence against third generation cephalosporins, fluoroquinolones, Sulfamethoxazole-Trimethoprim, Cefoxitin, Nitrofurantoin and Amoxicillin-clavulanic acid. Gram-positive strains were susceptible to Amoxicillin-clavulanic acid, Nitrofurantoin, Linezolid and Ofloxacin. The prevalence of multi-drug resistance (MDR) in all study isolates was 96%. Our data suggest a serious resistance trend among UTI strains and more should be done to slow down this trend. Pregnant women should be screened by urine culture and treatment be guided by the antimicrobial susceptibility data.
文摘Background: Screening for cancer of the cervix at Kenyatta National Hospital (KNH), follows the recommended three-step strategy;Papanicolaou (Pap) smear, colposcopy/biopsy and loop electrosurgical excision procedure (LEEP)/biopsy. This approach poses the following challenges: multiple clinic visits, costly, time consuming, long turnaround time to treatment, non-compliance and loss-to-follow-up. Objective: To determine the agreement between histologies following colposcopy and LEEP amongst women in KNH as a forerunner for opportunity to shift from the three-step approach to the two-step “see and treat” (same-day colposcopy and LEEP) approach. Methods: This was a retrospective descriptive cohort of Women who underwent LEEP procedure between January 2008 and 31st December 2010 following the three-step approach at KNH, Kenya. Results: A total of 124 patients out of the 132 patients who underwent LEEP were included in the analysis. The 8 patients excluded had missing files. HIV infected, uninfected or unknown women are similar socio-demographically. The mean (SD) age for the HIV infected, uninfected and unknown is 37 (6), 33 (10) and 35 (9) years respectively. Colposcopic and LEEP biopsy histology within patients demonstrated a high weighted kappa statistics agreement of 84%. LEEP increased diagnosis of invasive cancer. Patients had a median (IQR) 5 (4 - 6) clinic visits from Pap smear to LEEP treatment. It took median (IQR) 55 (27 - 116) days between Pap smear to colposcopy result and 167 (101 - 276) days between Pap smear results to LEEP treatment. If a LEEP procedure were to be performed in this cohort of women on the same day of the colposcopy biopsy a median (IQR) 77 (55 - 137) days could have been saved. Conclusion: There is a high agreement between colposcopy and LEEP biopsies in our setting offering a window of opportunity to perform “See and Treat” same-day colposcopy and LEEP treatment procedure, skipping the colposcopy biopsy stage.
文摘Aflatoxin M1 (AFM1) is a major carcinogenic compound that may be found in milk and dairy products resulting from ingestion of aflatoxin B1 by dairy animals. The study aimed at determining the level of aflatoxin M1 in milk and milk products from Bomet County. A total of 185 samples (150 raw milk and 35 processed milk and milk products) were randomly collected from milk collection sites and randomly selected milk kiosks respectively. The AFM1 was analyzed using a commercial ELISA kit (Ridascreen, aflatoxin M1 R-Biopharm, Product code, R5812, Darmstadt, Germany). Out of 185 samples investigated, 156 samples were positive for AFM1, an overall contamination rate of 84.32%. The samples with levels higher than the tolerance limit of 0.05 μg/l recommended by Food and Agriculture Organization (FAO) and World Health Organization (WHO) limits were 43.8% mainly contributed by the raw milk compared to processed milk (52.0% versus 8.6%). Processed milk had insignificant level of contamination with aflatoxin M1 (Median 0.00 (IQR: 0.00, 0.00 μg/l) with a minimum of 0.00 μg/l and a maximum of 0.69 μg/l. Raw milk showed significant contamination, median 0.09 (IQR: 0.00, 0.50) μg/l with a minimum of 0.00 μg/l and a maximum of 2.93 μg/l. Although there was no significant differences in AFM1 levels with study sites (P = 0.217);the median levels of aflatoxin M1 was high in sites 1, 3, and 7. The sites that had median aflatoxin M1 levels below the WHO/FAO acceptable limits of 0.05 μg/l were sites 2, 4 and 6. Due to high incidence of AFM1 contamination of milk and milk samples in Bomet County, there is need for regular monitoring and regulation of AFM1 contamination in milk and its products in the County.
文摘The prevalence of TB in sub-Sahara Africa has been reported as 511 per 100,000 populations and a mortality of 74 per 100,000 in year 2009. In the same period, incidence was estimated at 350 cases per 100,000. In this regard, the health system requires strengthening to respond to the rising cases of infection, drug resistance and quality of life lost while continuing to seek interventions that improve adherence to medication and case detection among those infected. Methods: This study sought to determine factors that are associated with sputum positivity after intensive phase of chemotherapy in people with tuberculosis. It was a retrospective case-control study conducted in Rhodes chest clinic, a City Council health unit in Nairobi that specializes in treatment of chest infections. The participants were sampled from clinic attendants who had completed two months of intensive phase TB chemotherapy and met inclusion criteria. Results: Seventy participants of whom 25 (36%) were sputum positive at the end of two (2) months intensive phase were included in the study. Skipping medication doses was significantly associated with sputum positivity (p = 0.01). Patients who were sputum positive at the end of the two-month period were more likely to have taken longer time before seeking treatment compared to those who were sputum negative by median (IQR) 8 (3 - 12) and 4 (3 - 8) weeks respectively although this difference was not significant (p = 0.09). Patients who had not disclosed their infection status had a two-fold possibility of remaining sputum positive at the end of intensive phase. Conclusion: Early diagnosis and treatment of TB, and adherence to medication were important factors that affect sputum conversion during intensive phase of TB treatment. Therefore, public health practitioners should advise patients to seek prompt diagnosis and treatment of signs and symptoms of tuberculosis.
文摘Objective： This study compared the performance of the immunochromatographic strip （ICS） to the Venereal Disease Research Laboratory （VDRL） test and Treponema pallidum haemagglutination assay （TPHA） at a primary health care setting. Methods： The study group was comprised of 150 females randomly drawn from a population of pregnant women attending their first antenatal visit or follow-up visits at West Maternity Hospital in Eldoret Kenya, but without a previous syphilis test during that pregnancy. On-site VDRL, ICS and TPHA tests were performed and immediate treatment provided where appropriate. The performance of the three tests was compared, Results： The sero-prevalence of syphilis as determined by the VDRL test was 3%. There was no significant difference between the ICS and the VDRL test （P 〉 0.05）. The sensitivity and specificity of the ICS test were 80% and 98.6% respectively, while the negative predictive value （NPV） and positive predictive value （PPV） were both 100%. On the other hand, the sensitivity and specificity of the VDRL test were 66.7% and 99.3%, while the NPV and PPV were 80% and 98.6% respectively. The Treponema pallidum haemagglutination assay was used as a reference test and had sensitivity, specificity, NPV and PPV of 100%. Conclusion： The diagnostic accuracy of the ICS compared favorably with theVDRL gold standard. The use of the ICS in Kenya can improve the diagnosis of syphilis in health facilities both with and without laboratories and allow community health care workers to make a rapid diagnosis of the disease, and consequently make immediate therapeutic decisions.
文摘Ticks harbor multiple pathogens, most of which can be transmitted to humans. The ensuing zoonoses display non-specific symptoms that make definitive diagnosis difficult. We report here the development and evaluation of multiplex real time polymerase chain reaction (qPCR) assays for eight tick-borne zoonoses (TBZ). The assays were organized in duo formats of 4-plex each. Format 1 was optimized for Anaplasma phagocytophilum, Coxiella burnetii, Borrelia burgdoferi and Ehrlichia chaffeensis. Format 2 was optimized for Rickettsia species (spp.), Bartonella spp., Borrelia spp. other than B. burgdoferi and Babesia spp. Synthetic plasmids were used to show that the assays can specifically detect all target sequences in the same reaction tube. Assays were assayed eight times to determine assay performance and the limit of detection was determined as the lowest plasmid concentration that was amplified for all the targets. Standard curves of threshold cycle (Ct) versus copy numbers were generated and used to determine linearity and efficiency of the assays. Pairwise comparison of singleplex and multiplex assays was done using Bland-Altman plots. Prevalence was calculated as overall percentage of positive patients to each TBZ tested Assay 1 had a limit of detection of 2 copy numbers for all targets. Assay 2 was less sensitive and on average had a limit of detection of 18 gene copies. In replicate tests, both assays had intra-assay variation of less than two cycles. Multiplex assays performance was comparable to respective singleplex assays. Evaluation of 512 clinical samples collected between 2008 and 2016 from acute febrile illness patients attending hospitals in different counties in Kenya revealed a 20% prevalence of tick-borne pathogens comprising B. burgdorferi (6%), non B. burgdorferi Borrelia spp. (3%), C. burnetii (5%), A. phagocytophilum (5%), Rickettsia spp. (2%), E. chaffeensis (0.8%), Bartonella spp. (0.8%), and Babesia spp. (0.4%). The high analytical sensitivity suggests potential for the duo 4-plex qPCR for detection of common TBZ.
文摘Pseudomonas aeruginosa is a leading cause of hospital infections and is intrinsically resistant to most antibiotics. Emergence of multidrug resistant (MDR) strains has been reported in the world and poses a great challenge in the management of infections associated with this species. While a substantial amount of research has been done on strains from most of other infection caused by this species in developed countries, little is known about the susceptibility profiles of strains recovered from African countries in general and Kenya in particular. Furthermore, there is paucity of data regarding strain, phenotype and genetic diversity of strains recoverable from wounds among patients in Kenya. The possible risk factors for acquisition of MDR strains and possible factors that could fuel clonal expansion in hospital and community settings remain undetermined. This cross-sectional study conducted in Tigoni Hospital, a rural area in Central Kenya sought to determine risk factors associated with carriage of MDR Pseudomonas aeruginosa in wounds among rural population. We also analyzed antimicrobial resistance profiles among these isolates. Prevalence of P. aeruginosa in wounds was 28% with 85 isolates recovered from wounds of 299 participants. Most antimicrobial resistance prevalence was recorded towards Ceftazidime (64%) and Cefepime (52%) while Piperacillin-tazobactam was the most effective antimicrobial agent with a resistance prevalence rate of 20%. Resistance towards new classes of aminoglycosides such as Gentamicin was at 45% while that towards Amikacin was at 40%. Compared to other related studies, relatively lower resistance towards Ciprofloxacin (25%) and Meropenem (40%) were recorded. Some of the risk factors identified for carriages of MDR strains were self-medication (p: 0.001, C.I: 3.01 - 8.86, O.R: 5.17) and non-completion of dosage (p: 0.12, C.I: 0.9 - 2.5, O.R: 1.5).
文摘Ticks are reservoirs of a variety of pathogens including bacteria, viruses and protozoa. We used PCR to detect pathogens of public health importance in ticks collected from diverse regions of Kenya. 503 tick pools were collected from 982 cattle, 300 sheep and 379 goats that were presented for slaughter at major abattoirs in Nairobi and Mombasa. Tick DNA was screened by qPCR optimized for single-plex detection of Babesia microti, two-plex Coxiella burnetii/Ehrlichia chaffeensis or Bartonella henselae/Borrelia recurrentis or three-plex for the non-human Babesia spp/Anaplasma phagocytophylum/Borrelia burgdorferi. Pathogen prevalence was calculated against tick type and the geographical origin. Computational analysis was performed with Graphpad prism 5. Out of 503 tick analyzed, 21% (106) were positive for at least one pathogen. C. burnetii was the most abundant at 70% (74/106), followed by non-human Babesia at 17% (18/106), 5% (5/106) for B. burgdorferi, 7% (7/106) for other Borrelia species and <1% (1/106) for E. chaffeensis and A. phagocytophylum. B. henselae and the human infective B. microti were not detected. Rh. pulchellus was the most promiscuous one in carrying pathogens: C. burnetti, Babesia, B. burgdorferi, E. chaffeensis and A. phagocytophylum. Non-human infective Babesia were detected in all ticks except Amblyomma. Four counties had 70% of the infected ticks: Marsabit 25% (n = 26/106), Kajiado 17% (18/106), Wajir 16% (17/106) and Narok 11% (12/106). This study identified a number of tick-borne pathogens that cause febrile infections often confused with malaria. Follow-up research will be needed to determine prevalence in humans.
文摘Wastewater surveillance has been applied in various parts of the world to monitor the introduction and transmissions of SARS-CoV-2 variants in a population. The knowledge of SARS-CoV-2 variants circulating in a population is critical to COVID-19 management and timing of the application of public health countermeasures. Contrary to the routine clinical surveillance of SARS-CoV-2 where cases from asymptomatic patients are often underreported, wastewater surveillance offers an unbiased tool for monitoring the extent of SARS-CoV-2 transmissions in a community. The present study aimed to characterize SARS-CoV-2 variants that circulated in Nairobi County, Kenya, between April 2021 and August 2021 utilizing wastewater samples. Viral RNA was extracted from wastewater samples, followed by SARS-CoV-2 screening by real-time RT-qPCR before targeted sequencing of the Spike gene. Forty samples were analyzed, of which 50% (n = 20) tested positive for SARS-CoV-2 by real-time RT-qPCR. Of these, 45% (n = 9) were successfully amplified by RT-PCR and sequenced. The majority (78%, 7/9) of the viruses belonged to the Delta (B.1.617.2) lineage of SARS-CoV-2, while a minority (22%) belonged to the Alpha (B.1.1.7) and Alpha-Delta lineages. Phylogenetic analysis of the SARS-COV-2 delta lineage strains revealed scattered clustering of the Kenyan viruses among the global strains included in the analysis, suggesting different introductory routes into the country. On the whole, our results confirm previous clinical findings that SARS-CoV-2 variants belonging to the Alpha (B.1.1.7) and Delta (B.1.617.2) lineages circulated in Nairobi County, Kenya during the study period, with the latter predominating. This is the first study to describe the diversity of SARS-CoV-2 variants circulating in Kenya, through wastewater analysis.
文摘Background: Herpes simplex virus Type 2 (HSV-2) has been associated with HIV infection. More recently, HSV-2 incidence has been linked to HIV acquisition. A few studies have suggested that the fishing communities have a high HSV-2 prevalence but there is limited knowledge on HSV-2 incidence and associated risk factors among fishermen. Methods: Three hundred fishermen were consented, and evaluated for baseline HSV-2 serology status and again after 12 months among those negative at baseline. Sexual behavior and socio-demographic data were collected at enrolment and exit visits using a structured questionnaire. Baseline HIV serology and Human papillomavirus (HPV) DNA genotyping were also performed. Multivariate logistic regression was used to determine independent factors associated with HSV-2 acquisition. Results: Baseline HSV-2 prevalence was 56.3% (95% CI: 50.7 - 62.0). Factors associated with HSV-2 prevalence were, older age (aOR = 1.96;95% CI: 1.16 - 2.85), history of STI (aOR 2.12;95% CI: 1.19 - 3.91), infection with HIV (aOR 2.22;95% CI: 1.17 - 4.22), ever married (aOR = 3.80;95% CI: 1.42 - 11.90), most recent sexual act with sex worker/casual partner (OR= 3.56;95% CI: 1.49 - 8.62) and inconsistent condom use with new sexual partner (aOR = 6.34;95% CI: 2.24 - 13.04). The HSV-2 incidence was 23.6 (95% CI = 15.4 - 31.8)/100 pyr. Infection with persistent high-risk (HR) HPV (aIRR = 3.35;95% CI: 1.21 - 11.37), multiple (≥2) partners in 12 months prior to study participation (aIRR = 4.77;95% CI: 1.12 - 11.38), inconsistent condom use with new partner (aIRR =2.53;95% CI: 1.12 - 7.38) and most recent sexual act with sex worker/casual partner (OR = 3.03;95% CI: 1.17 - 8.58) were independent risk factors for HSV-2 acquisition. Conclusion: The incidence of HSV-2 is very high among fishermen. It is associated with persistent HR HPV infection and high-risk sexual behavior. Intervention strategies targeting these men with high risk sexual behavior are urgently needed to stop new HSV-2 acquisition and subsequently prevent HIV infection.
文摘In areas of sub-Saharan Africa where malaria is endemic, pregnant women are at a greater risk of malaria than non-pregnant women leading to significant adverse consequences including anemia, intrauterine growth retardation, low birth weight (LBW), and pre-term delivery. The Kenya Ministry of Health adopted Intermittent Preventive Treatment (IPT) and use of insecticide-treated nets (ITN) as a National strategy for malaria prevention in pregnancy. In this report, we evaluated the prevalence of malaria, the anthropometric measures of birth outcomes and the reasons for loss to follow up among pregnant women participating in an ongoing cohort study in Western Kenya. A total of 175 HIV-negative pregnant women enrolled at antenatal clinic of Chulaimbo sub-District hospital were longitudinally evaluated in a monthly follow-up visits through antenatal visits (up to 4 per mother) and delivery. Thirty three percent and 15% of the pregnant women were malaria positive by real-time quantitative (Q)-PCR and microscopy respectively at enrolment, while 54% and 23% of the pregnant women had malaria by Q-PCR and microscopy respectively at any time during follow-up. Of the enrolled study participants, 65% delivered at Chulaimbo hospital. Overall, 39% (69) of the pregnant women were lost to follow-up. The major reasons for loss to follow up were relocation from the study area (26%) and delivery at alternative health facilities (25%). The mean birth weight of the newborn infants was 3202 g (range, 2000 g - 4000 g). Only 5.3% of the infants weighed less than 2500 g (low birth weight). The mean head circumference was 34 cm (range, 30 cm - 39 cm) with mean Apgar score (at 10 minutes) ± S.D. of 9.8 ± 0.97. In conclusion, we observed decreased adverse pregnancy outcomes among our study population. We recommend a larger study of all pregnant women attending the Chulaimbo hospital so as to assess whether effectiveness of malaria and anemia control programs lead to improved birth outcomes.
文摘Antimicrobial drug resistance is a rising concern in the treatment of infectious diseases and necessitates the need for discovery of novel, potent antimicrobial compounds to combat antibiotic resistance. Since natural environment remains a potential source of novel antimicrobial products, this preliminary study was performed to test the potential of soils from Kericho County for antibiotic-producing Actinomycetes. Soil samples (214) were randomly collected from virgin soils of Kipkelion East, Kipkelion West, Belgut, Ainamoi, Sigowet and Bureti sub-counties in Kericho County from a depth of between 11 cm - 16 cm from the surface of the soil profile. A total of 107 Actinomycetes were isolated and screening was done using modified agar disc diffusion method of which only 39 (36.4%) showed antimicrobial activity against five of the six test isolates that included reference strains Staphylococcus aureus (ATCC 25923), Escherichia coli (ATCC 25922) and Candida albicans (ATCC 90028) and three clinical strains Trichophyton mentagrophyte, Microsporum gypseum and Methicillin Resistant Staphylococcus aureus. Two of the isolates showed activity against MRSA and four isolates showed a higher potency than the standard drug Chloramphenicol (30 μg) against S. aureus. Most of the isolates (41.0%) also showed good antimicrobial activity against T. mentagrophyte, though they lower than the control drug Itraconazole (2 μg/ml), they were statistically significant. DNA from the isolates was extracted and the 16S rRNA gene was amplified using primers specific for Actinomycetes. The amplified gene was sequenced and phylogeny analysis was done. The 16S rRNA gene was able to be amplified in only 15 of these isolates. Sequencing showed that 93.3% were of the genus Streptomyces while 6.7% were of the genus Rhodococcus. From the results, the soils from this region harbour Actinomycetes that may have good potential of producing novel antibiotics against gram positive bacteria and dermatophytes.
文摘Hepatitis B Virus (HBV) infections affect about 400 million people globally and cause about 1.4 million deaths annually. The virus displays high levels of genetic variations/mutations, some of which are immune escape mutants. The prevalence of HBV infection in Kenya is high at about 8%. This study aimed at identifying and characterizing HBV immune escape mutants in Kenya. From 547 HBV sequences available in Kenya in NCBI, and HBVdb databases in July 2021, 120 full sequences were retrieved. The S gene sequences at position 1-225, which included the “a” determinant region of the gene were analyzed using various bioinformatics tools such as Bioedit software, and Emboss Cons. The clinical significance was flagged from the search of peer-reviewed journals. Forty-six HBV-positive blood donor samples were obtained from the Kenya National Blood Transfusion Services without personal identifiers, DNA extracted, and sequenced targeting positions 1 to 520 of S genes. Mutations were similarly identified from seventeen sequences after cleaning and analysis. Out of 120 sequences that were extracted from databases and analyzed, 79 different mutations were identified. Fifteen of them were of clinical importance with an occurrence frequency of at least 5% were obtained. The majority (64.6%, n = 51), with S207N and A194V being most dominant, could result in immune escape and reduced HBsAg detection signals while 24.1% (n = 19) could result in immune escape/reduced HBsAg detection signals and high probability of hepatocellular carcinoma. Most likely to occur on the amino acids Alanine, Lysine, Serine, Asparagine, and Valine in decreasing order. The most dominant genotype was found to be Genotype A (N = 10), while four sequences were Genotype D. In contrast to the in-silico studies, the sequences from HBV samples from blood donors did not demonstrate the presence of S207N and A194V mutations and all the genotypes were type A1. Only two (13.3%) samples showed the same mutations of sK122R and sT143S for both in-silico analysis and actual sequenced samples. This study did not identify G145R mutation which is the commonest mutation within the HBsAg immunodominant “a” determinant that is associated with immune escape. The concordance of mutations in “a” determinant region of HBsAg gene among various studies is minimal. The study identified new mutations (sA194Y, sS207, sA194S, sS207I, sP46A, sA194T, sS207I, sP46R, and sT143P) that had not been published before. Four (20%) of the mutations were clinically significant. These included sS207R, sT143S, sC76F and sK122R.
文摘The 2016 Olympic Games happened at the time of heightened fears of Zika virus (ZIKV) that was causing microcephaly in newborns in Brazil. To avert or track introduction of ZIKV in Kenya, the Ministry of Health developed a public health response that involved screening of the Kenyan contingent before and after traveling to Brazil. Of the 92 team members that were screened, all but one tested negative for ZIKV IgM and IgG. The sero-positive individual had high IgM serum titers before and after travel to Brazil. When tested for potential antibody cross-reactivity to other flaviviruses that have been reported in Kenya, the sample showed high IgM cross-reactivity to West Nile, Tick-Borne Encephalitis and Yellow Fever Virus. Our data support the low risk predictions of acquiring ZIKV that were made before the Games and will help inform risk assessments for personnel traveling to endemic regions under similar circumstances in the future.
文摘Background: Herpes simplex virus type-2 (HSV-2) and human papillomavirus (HPV) are common sexually transmitted infections (STIs) among fishing communities and are associated with high HIV prevalence in this underserved population. However, there is limited knowledge on HIV incidence among fishermen. This study aimed at determining prevalence, incidence and risk factors associated with HIV infection among fishermen in Kisumu Kenya. Methods: Three hundred fishermen were evaluated for baseline HIV, HSV-2, HPV infection and a structured questionnaire administered. HIV incidence was assessed after 12 months among those initially HIV negative. HIV incidence rate in person-years and prevalence were estimated. Multivariate logistic regression was used to determine factors independently associated with HIV acquisition. Results: HIV prevalence was 23.3% (95% CI: 18.5 - 28.1). Risk factors for baseline HIV prevalence were older age (aOR = 2.13;95% CI: 1.25 - 5.07), history of STI (aOR 4.21;95% CI: 2.07 - 9.34), baseline HPV infection (aOR 2.13;95% CI: 1.05 - 4.77), number of lifetime sexual partners (>5) aOR = 5.76 (95% CI: 1.41 - 13.57) and transactional sex (aOR = 10.98;95% CI: 1.86 - 19.34). Condom uses with new sexual partner (aOR 0.21, 95% CI: 0.08 - 0.55) and during most recent sexual act (aOR 0.09, 95% CI: 0.03 - 0.61), were negatively associated with HIV prevalence. HIV incidence was 4.2 (95% CI = 1.3 - 7.1) per 100 person-years with being single (aIRR = 8.32;95% CI: 1.27 - 54.67) as an independent risk factor. Condom use with new sexual partner (aIRR = 0.11;95% CI: 0.01 - 0.89) and recent sex with wife/regular girlfriend (compared to sex worker/casual partner;aIRR = 0.03;95% CI: 0.01 - 0.35) were associated with reduced risk of HIV acquisition. Conclusion: Inconsistent condom use and transactional/casual sexual partnerships were the main high-risk sexual behaviors in addition to marital status explaining the high HIV acquisition rate among fishermen. Intensified safer sex promotion is urgently needed in this subpopulation to avert new HIV infections.
