Tracking severe acute respiratory syndrome coronavirus 2 transmission and co-infection with other acute respiratory pathogens using a sentinel surveillance system in Rift Valley, Kenya

BACKGROUND

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been the most significant public health challenge in over a century. SARS-CoV-2 has infected over 765 million people worldwide, resulting in over 6.9 million deaths. This study aimed to detect community transmission of SARS-CoV-2 and monitor the co-circulation of SARS-CoV-2 with other acute respiratory pathogens in Rift Valley, Kenya.

METHODS

We conducted a cross-sectional active sentinel surveillance for the SARS-CoV-2 virus among patients with acute respiratory infections at four sites in Rift Valley from January 2022 to December 2022. One thousand two hundred seventy-one patients aged between 3 years and 98 years presenting with influenza-like illness (ILI) were recruited into the study. Nasopharyngeal swab specimens from all study participants were screened using a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for SARS-CoV-2, influenza A, influenza B and respiratory syncytial virus (RSV).

RESULTS

The samples that tested positive for influenza A (n = 73) and RSV (n = 12) were subtyped, while SARS-CoV-2 (n = 177) positive samples were further screened for 12 viral and seven bacterial respiratory pathogens. We had a prevalence of 13.9% for SARS-CoV-2, 5.7% for influenza A, 2% for influenza B and 1% for RSV. Influenza A-H1pdm09 and RSV B were the most dominant circulating subtypes of influenza A and RSV, respectively. The most common co-infecting pathogens were Streptococcus pneumoniae (n = 29) and Haemophilus influenzae (n = 19), accounting for 16.4% and 10.7% of all the SARS-CoV-2 positive samples.

CONCLUSIONS

Augmenting syndromic testing in acute respiratory infections (ARIs) surveillance is crucial to inform evidence-based clinical and public health interventions.

Neisseria gonorrhoeae infection in female sex workers in an STI clinic in Nairobi, Kenya

Background

Gonorrhea caused by Neisseria gonorrhoeae is the second most prevalent curable sexually transmitted infection worldwide. Female Sex Workers (FSWs) are at a higher risk of contracting gonorrhea due to their risky sexual behaviors like inconsistent condom use and multiple sexual partners. We determined the prevalence and risk factors associated with gonorrhea and its antimicrobial susceptibility pattern among symptomatic FSWs attending Sexual Workers Outreach Program (SWOP) city clinic in Nairobi, Kenya.

Methods

Using convenience sampling, we recruited 379 female sex workers from SWOP City clinic in Nairobi County. We administered a semi-structured questionnaire to collect data on socio-demographics and behavioral risk factors associated with gonorrhea. We also conducted three focus groups. Two endocervical swabs were collected from each participant by the attending physician for the laboratory identification of Neisseria gonorrhoeae. An antimicrobial susceptibility test was performed using the disc diffusion method.

Results

Twenty-four out of 379 (6.3%) participants tested positive for gonorrhea by PCR. The significant risk factors associated with gonorrhea were having multiple sexual partners in the previous two weeks, primary education, and being in the age group of 38–49 years (p < 0.05).

From the qualitative data, sex work disclosure, and difficulty in engaging protected sex with their partner, and unprotected sex with their clients due to more money from the client, PREP, and alcohol use made the female sex workers vulnerable to gonorrhea exposure and or risky sexual behavior. The culture-positive sample result yielded complete (100%) resistance to all the antimicrobials used.

Conclusion

Neisseria gonorrhoeae infection is prevalent among symptomatic FSWs in Nairobi. Multiple sexual partners, being in age group 38–49 years and having primary education were the factors associated with gonorrhea among the study participants. Based on our identification of a highly resistant isolate, we strongly recommend increasing capacity for culture-based diagnosis and susceptibility testing.

Barriers to the Digitization of Health Information: A Qualitative and Quantitative Study in Kenya and Lao PDR Using a Cloud-Based Maternal and Child Registration System

Digitalization of health information can assist patient information management and improve health services even in low middle-income countries. We have implemented a mother and child health registration system in the study areas of Kenya and Lao PDR to evaluate barriers to digitalization. We conducted in-depth interviews with 20 healthcare workers (HCWs) who used the system and analyzed it qualitatively with thematic framework analysis. Quantitatively, we analyzed the quality of recorded data according to missing information by the logistic regression analysis. The qualitative analysis identified six themes related to digitalization: satisfaction with the system, mothers’ resistance, need for training, double work, working environment, and other resources. The quantitative analysis showed that data entry errors improved around 10% to 80% based on odds ratios in subsequent quarters compared to first quarter periods. The number of registration numbers was not significantly related to the data quality, but the motivation, including financial incentives among HCWs, was related to the registration behavior. Considering both analysis results, workload and motivation to maintain high performance were significant obstacles to implementing a digital health system. We recommend enhancing the scope and focus on human needs and satisfaction as a significant factor for digital system durability and sustainability.

Leishmaniasis recidivans by Leishmania tropica in Central Rift Valley Region in Kenya

OBJECTIVES

This study sought to determine the endemic Leishmania species, the clinical features of cutaneous leishmaniasis (CL) in the Central Rift Valley in Kenya and to give an account on unresponsiveness to treatment in the region.

METHODS

Participants were clinically identified and grouped into untreated, classical and recidivate based on clinical manifestation and clinical data. Leishmaniasis recidivans lesions were scaly hyperemic papules that appeared before the classic lesion had healed or after healing. The demographics and socio-economic data were recorded and lesion scraping samples screened through microscopy and Internal Transcribed Spacer 1-PCR. Leishmania species were identified using Restriction Fragment Length Polymorphism.

RESULTS

A total of 52 participants were sampled, of which, 44.2% of the cases were recidivate and L. tropica the only species identified. All patients had been treated using sodium stibogluconate (SSG) which is the recommended first-line drug in Kenya. 60% of the patients experienced prolonged exposure to the drug (>30 days).

CONCLUSION

L. tropica is the endemic Leishmania species for CL leading to classical and leishmaniasis recidivans. Treatment of CL in the area is not effective hence, alternative measures/therapy should be considered to cope with the unresponsiveness.

Development of multiplex serological assay for the detection of human African trypanosomiasis

Human African trypanosomiasis (HAT) is a disease caused by Kinetoplastid infection. Serological tests are useful for epidemiological surveillance. The aim of this study was to develop a multiplex serological assay for HAT to assess the diagnostic value of selected HAT antigens for sero-epidemiological surveillance. We cloned loci encoding eight antigens from Trypanosoma brucei gambiense, expressed the genes in bacterial systems, and purified the resulting proteins. Antigens were subjected to Luminex multiplex assays using sera from HAT and VL patients to assess the antigens' immunodiagnostic potential. Among T. b. gambiense antigens, the 64-kDa and 65-kDa invariant surface glycoproteins (ISGs) and flagellar calcium binding protein (FCaBP) had high sensitivity for sera from T. b. gambiense patients, yielding AUC values of 0.871, 0.737 and 0.858 respectively in receiver operating characteristics (ROC) analysis. The ISG64, ISG65, and FCaBP antigens were partially cross-reactive to sera from Trypanosoma brucei rhodesiense patients. The GM6 antigen was cross-reactive to sera from T. b. rhodesiense patients as well as to sera from VL patients. Furthermore, heterogeneous antibody responses to each individual HAT antigen were observed. Testing for multiple HAT antigens in the same panel allowed specific and sensitive detection. Our results demonstrate the utility of applying multiplex assays for development and evaluation of HAT antigens for use in sero-epidemiological surveillance.

Species-Specific Serological Detection for Schistosomiasis by Serine Protease Inhibitor (SERPIN) in Multiplex Assay

BACKGROUND

Both Schistosoma mansoni and Schistosoma haematobium cause schistosomiasis in sub-Saharan Africa. We assessed the diagnostic value of selected Schistosoma antigens for the development of a multiplex serological immunoassay for sero-epidemiological surveillance.

METHODOLOGY/PRINCIPAL FINDINGS

Diagnostic ability of recombinant antigens from S. mansoni and S. haematobium was assessed by Luminex multiplex immunoassay using plasma from school children in two areas of Kenya, endemic for different species of schistosomiasis. S. mansoni serine protease inhibitor (SERPIN) and Sm-RP26 showed significantly higher reactivity to patient plasma as compared to the control group. Sm-Filamin, Sm-GAPDH, Sm-GST, Sm-LAP1, Sm-LAP2, Sm-Sm31, Sm-Sm32 and Sm-Tropomyosin did not show difference in reactivity between S. mansoni infected and uninfected pupils. Sm-RP26 was cross-reactive to plasma from S. haematobium patients, whereas Sm-SERPIN was species-specific. Sh-SEPRIN was partially cross-reactive to S. mansoni infected patients. ROC analysis for Sm-RP26, Sm-SERPIN and Sh-SERPIN showed AUC values of 0.833, 0.888 and 0.947, respectively. Using Spearman's rank correlation coefficient analysis, we also found significant positive correlation between the number of excreted eggs and median fluorescence intensity (MFI) from the multiplex immunoassays for Sm-SERPIN (ρ = 0.430, p-value = 0.003) and Sh-SERPIN (ρ = 0.433, p-value = 0.006).

CONCLUSIONS/SIGNIFICANCE

Sm-SERPIN is a promising species-specific diagnostic antigen. Sh-SEPRIN was partially cross-reactive to S. mansoni infected patients. SERPINs showed correlation with the number of excreted eggs. These indicate prospects for inclusion of SERPINs in the multiplex serological immunoassay system.

Serological surveillance development for tropical infectious diseases using simultaneous microsphere-based multiplex assays and finite mixture models

Background

A strategy to combat infectious diseases, including neglected tropical diseases (NTDs), will depend on the development of reliable epidemiological surveillance methods. To establish a simple and practical seroprevalence detection system, we developed a microsphere-based multiplex immunoassay system and evaluated utility using samples obtained in Kenya.

Methods

We developed a microsphere-based immuno-assay system to simultaneously measure the individual levels of plasma antibody (IgG) against 8 antigens derived from 6 pathogens: Entamoeba histolytica (C-IgL), Leishmania donovani (KRP42), Toxoplasma gondii (SAG1), Wuchereria bancrofti (SXP1), HIV (gag, gp120 and gp41), and Vibrio cholerae (cholera toxin). The assay system was validated using appropriate control samples. The assay system was applied for 3411 blood samples collected from the general population randomly selected from two health and demographic surveillance system (HDSS) cohorts in the coastal and western regions of Kenya. The immunoassay values distribution for each antigen was mathematically defined by a finite mixture model, and cut-off values were optimized.

Findings

Sensitivities and specificities for each antigen ranged between 71 and 100%. Seroprevalences for each pathogen from the Kwale and Mbita HDSS sites (respectively) were as follows: HIV, 3.0% and 20.1%; L. donovani, 12.6% and 17.3%; E. histolytica, 12.8% and 16.6%; and T. gondii, 30.9% and 28.2%. Seroprevalences of W. bancrofti and V. cholerae showed relatively high figures, especially among children. The results might be affected by immunological cross reactions between W. bancrofti-SXP1 and other parasitic infections; and cholera toxin and the enterotoxigenic E. coli (ETEC), respectively.

Interpretation

A microsphere-based multi-serological assay system can provide an opportunity to comprehensively grasp epidemiological features for NTDs. By adding pathogens and antigens of interest, optimized made-to-order high-quality programs can be established to utilize limited resources to effectively control NTDs in Africa.

Monitoring the distribution of neglected tropical diseases (NTDs) is a key to controlling their spread in Africa. Currently, such surveillance is conducted independently for each NTD. To tackle this problem, we developed a microsphere-based system to permit simultaneous measurement of IgG antibody levels for antigens from six infectious diseases: Entamoeba histolytica, Leishmania donovani, Toxoplasma gondii, Wuchereria bancrofti, HIV, and Vibrio cholerae. Using this system, we conducted a serological survey using two health and demographic surveillance system (HDSS) areas in coastal and western Kenya. We randomly selected 4,600 individuals according to sex and age group, of whom 3411 agreed to participate in the study. Mathematical analyses of the distributions of the participants' reactivity to each antigen and the reactivity of the sero-positive and -negative controls indicated that this system could be used to monitor infections, especially, those associated with HIV, filariasis, toxoplasmosis, leishmaniasis, and amebiasis. For the practical development and eventual implementation of actual programs in Africa, pathogens and antigens of interest can be added to optimize made-to-order monitoring programs.