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The CIDRZ Research Repository serves as an open-access archive for peer-reviewed publications, conference papers, and other scholarly outputs from CIDRZ researchers. Our goal is to promote the dissemination of knowledge and support evidence-based public health initiatives.
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Item Statistical Modelling of Waning Immunity After Shanchol Vaccination: A Prospective Cohort Study(Vaccines, 2026-01-30) Bosomprah, Samuel; Liswaniso, Fraser; Phiri, Bernard; Chibuye, Mwelwa; Luchen, Charlie C.; Ng’ombe, Harriet; Chibesa, Kennedy; Ngosa, Dennis; Muchimba, Mutinta; Debes, Amanda K.; Chilengi, Roma; Sack, David A.; Chisenga, Caroline C.Abstract Introduction: Cholera remains a major public health threat in endemic settings, and oral cholera vaccine (Shanchol™) campaigns are increasingly used amid constrained global supply. However, practical decisions on revaccination require clearer, setting-specific estimates of how rapidly vaccine-induced vibriocidal antibodies peak and wane. Methods: We conducted a prospective cohort kinetics analysis in Lukanga Swamps (Central Province, Zambia), enrolling adults (18–65 years) stratified by prior Shanchol™ exposure (0, 1, or 2 previous doses). All participants received two Shanchol™ doses 14 days apart, with serum collected at baseline and days 14, 28, 60, and 90 (end of follow-up). Ogawa and Inaba vibriocidal titres were measured using a complement-based assay and analysed on the log10 scale. Serotype-specific mixed-effects models with natural cubic splines for time (knots: 14, 28, 60 days) assessed trajectories by prior-dose strata, adjusting for age, sex, and HIV status. Peak timing and post-peak half-life were derived from model-based predictions with participant-level bootstrap CIs (1000 replications). Results: The analysis included 225 participants: 68 (30.2%) with zero prior doses, 89 (39.6%) with one, and 68 (30.2%) with two; median age was 33 years (IQR 25–49), 56.4% were female, and 19.2% were HIV-positive. Modelled titres for both serotypes rose steeply after vaccination, peaking around day 36–37 across prior-dose strata. Ogawa titres reached half of peak by about day 73–78, corresponding to post-peak half-lives of 37–41 days; Inaba declined more slowly with half-lives of 42–46 days. Confidence intervals overlapped across prior-dose strata, indicating minimal differences by vaccination history. Conclusions: In this cholera-endemic adult population, Shanchol™ induced vibriocidal responses that peaked at ~5 weeks and waned over the following 5–7 weeks, with broadly similar kinetics regardless of prior vaccination and slightly slower decay for Inaba than Ogawa. These parameters can inform booster timing in hotspot settings.Item Rotavirus Prevalence, Genetic Diversity, and Co-Infections during the 2023- 2024 Cholera Outbreak in Zambia: Insights from Multi-Pathogen Diagnostics(2026-02-28) Chauwa, Adriace; Bosomprah, Samuel; Phiri, Bernard; Laban, Natasha M.; Kuntawala, Dhvani H.; Ngosa, Dennis; Ng'ombe, Harriet; Liswaniso, Fraser; Luchen, Chaluma C.; Muchimba, Mutinta; Mwape, Innocent; Nzangwa, Bertha T.; Tigere, Sekayi F.; Chibesa, Kennedy; Silwamba, Suwilanji; Simuyandi, Michelo; Mbewe, Nyuma; Chilengi, Roma; Chisenga, Caroline C.Abstract During cholera outbreaks in Zambia, diagnostic strategies that rely on single-plex or targeted assays risk overlooking concomitant infections with other clinically important enteric pathogens. We estimated the prevalence of rotavirus and described co-detected enteropathogens and rotavirus genotypes among patients admitted with clinically suspected cholera during Zambia’s 2023–2024 cholera outbreak. We conducted a sub-analysis of diarrhoeal specimens collected from patients admitted to five cholera treatment centres who met the syndromic suspected cholera case definition. Stool samples were tested using the Bosphore® Gastroenteritis Panel v2, a multiplex PCR enteric panel, to detect rotavirus and other gastrointestinal pathogens. Rotavirus-positive specimen with sufficient viral load were further characterised by RT-PCR genotyping and Sanger sequencing targeting VP7 and VP4 genes. Among 319 suspected cholera admissions, rotavirus was detected in 18 patients, yielding a prevalence of 5.6% (95% CI 3.4%, 8.8%). Rotavirus detections occurred predominantly in children aged <5 years (87.5%) and 6-15 years (80.0%). Co-infection was common - 93.7%, (15/16) of rotavirus-positive samples showed co-infection with at least one additional enteric pathogen, primarily Campylobacter. Genotyping was successful in five samples and showed heterogenous circulating strains, including G1P[8], G2P[4], G3P[6], G12P[6], and a rare G1P[6] reassortant. During a large 2023–2024 cholera outbreak in Zambia, rotavirus accounted for a modest but clinically important fraction of the suspected cholera admissions and was typically identified within mixed enteric infections. These findings highlight the limitations of syndromic diagnosis in outbreak settings and support integrating multi-pathogen diagnostics and sustained molecular surveillance to improve case management, antimicrobial stewardship, and vaccine-era monitoring.Item Faecal Coliforms and Escherichia coli Contamination in Drinking Water Sources in Cholera Hotspot Areas of Lusaka District, Zambia: A Cross-Sectional Study(Microorganisms, 2026-02-11) Ng’ombe, Harriet; Luchen, Charlie C.; Phiri, Bernard; Ngosa, Dennis; Kapikila, Robby; Sakanya, Sydney; Sakala, Chikondi; Mbewe, Nyuma; Liswaniso, Fraser; Chilengi, Roma; Wilkinson, Eduan; Liebenberg, Lenine; Khan, Wesaal; Thomson, Nicholas R; Sack, David; Bosomprah, Samuel; Chisenga, Caroline C.Abstract The October 2023 to 2024 cholera outbreak demonstrates significant challenges related to water quality and sanitation, especially in peri-urban areas with limited access to clean water. This study assesses the presence of faecal coliforms and Escherichia coli (E. coli) in drinking water sources across five townships, identified as cholera transmission hotspots, two months post the cholera outbreak in the Lusaka District. A total of 169 water samples were collected from protected sources, treated piped water, and unprotected sources, including dams and shallow wells. Faecal coliforms and E. coli were detected across all source types. Among unprotected sources, 92.3% (12/13) of samples contained ≥100 CFU/100 mL of both faecal coliforms and E. coli. Protected sources showed variable contamination, with 18.3% exceeding ≥100 CFU/100 mL for faecal coliforms and 15.4% for E. coli. Treated water sources showed the lowest contamination, with 88.5% of samples having no detectable faecal coliforms and 90.4% having no detectable E. coli. Zero-inflated negative binomial regression showed that treated water sources were associated with substantially lower faecal coliform counts compared with protected sources (PR = 0.11, 95% CI: 0.03–0.35), while unprotected sources exhibited higher contamination intensity (PR = 1.77, 95% CI: 0.94–3.31). Treated sources were significantly more likely to be structurally free of contamination, whereas unprotected sources had an extremely low probability of yielding zero counts. These findings indicate that current water safety conditions in Lusaka’s cholera hotspot areas remain inadequate for preventing faecal-oral transmission.Item Genomic Analysis and Antimicrobial Resistance of Vibrio Cholerae Isolated During Zambia’s 2023 Cholera Epidemic(2025-12-02) Ng'ombe, Harriet; Luchen, Charlie C.; Bote, Lia; Kasonde, Mpanga; Musonda, Kunda; Mwape, Kapambwe K.; Kuntawala, Dhvani H.; Silwamba, Suwilanji; Chibuye, Mwelwa; Chibesa, Kennedy; Mbewe, Nyuma; Bosomprah, Samuel; Khan, Wesaal; Liebenberg, Lenine; Oliveira, Tulio de; Wilkinson, Eduan; Dorman, Matthew J.; Coghlan, Avril; Simuyandi, Michelo; Chilengi, Roma; Chisenga, Caroline; Thomson, Nicholas R.Introduction. Cholera, caused by Vibrio cholerae, remains a priority public health concern, particularly in developing countries. The first cholera outbreak in Zambia was documented in the 1970s, with recurring epidemics reported since then. In 2023, a cholera outbreak affected Zambia, particularly in districts bordering Malawi, Mozambique and the Democratic Republic of Congo, with significant cases reported in these neighbouring countries. This study aims to analyse cholera cases and isolates obtained during the 2023 epidemic, focusing on geographical distribution, genetic relatedness of isolates and their antibiotic resistance profiles. Methods. Stool samples were collected from patients presenting with cholera-like symptoms across three provinces of Zambia. A total of 98 samples were cultured on thiosulphate citrate bile salts sucrose agar, resulting in 32 sequenced V. cholerae isolates. Whole-genome sequencing was performed using Oxford Nanopore Technology, and phylogenetic inference was also achieved by the analysis of SNPs. Phenotypic antimicrobial resistance testing was conducted following Clinical and Laboratory Standards Institute guidelines. The genomic data were analysed for virulence factors and antimicrobial resistance profiles. Results. Of the 98 stool samples tested, 38 confirmed cholera cases were identified. A subset of 32 confirmed V. cholerae isolates, predominantly from the Eastern Province of Zambia (n=21), was selected for whole-genome sequencing. Genomic analysis revealed that all isolates belonged to the seventh pandemic El Tor lineage and the O1 serogroup, with two distinct clades identified corresponding to the 10th (T10) and 15th (T15) transmission events. Geographical analysis indicated a predominance of Ogawa serotypes in Eastern Province and Inaba in Northern Province. The virulence gene analysis confirmed the presence of key cholera toxin genes (ctxA and ctxB) and intestinal colonization factors. All isolates carried genes or mutations predicted to confer resistance to multiple antibiotics, including decreased susceptibility to ciprofloxacin, recommended for the treatment of cholera by the World Health Organization. Conclusion. The findings highlight the critical need for enhanced surveillance and targeted interventions to mitigate cholera outbreaks in Zambia. The emergence of resistant V. cholerae strains necessitates innovative strategies, including improved water sanitation, vaccination efforts and novel therapeutic approaches to combat this enduring public health threat.Item Prevalence and Patterns of Enteric Co-Infections Among Individuals Presenting with Cholera-like Diarrheal Disease During Seasonal Cholera Outbreaks(Pathogens, 2025-11-30) Kuntawala, Dhvani H.; Bosomprah, Samuel; Phiri, Bernard; Ng’ombe, Harriet; Liswaniso, Fraser; Muchimba, Mutinta; Silwamba, Suwilanji; Chibesa, Kennedy; Nzangwa, Bertha T.; Luchen, Charlie C.; Mwape, Innocent; Tigere, Sekayi F.; Simuyandi, Michelo; Mbewe, Nyuma; Chilengi, Roma; Debes, Amanda K.; Thomson, Nicholas R.; Sack, David A.; Chisenga, Caroline C.Abstract Cholera remains a major public health challenge, and co-infections can complicate clinical outcomes. In a cross-sectional study, we investigated the prevalence and patterns of enteric co-infections during Zambia’s 2023–2024 cholera outbreak and evaluated their implications for disease severity. 240 suspected cholera patients were enrolled from five healthcare facilities in Lusaka. Stools were tested for 11 enteric pathogens using the Bosphore® Gastroenteritis Panel Kit v2 on the QuantStudio 5 qPCR, with Vibrio cholerae confirmed by real-time PCR (quantitative PCR). Co-infections were highly prevalent, affecting 79.2% of participants. Campylobacter was the most frequently detected pathogen (70.0%), followed by Norovirus GI/GII (20.0%). Persons living with HIV were significantly more likely to present with co-infections than their counterparts (adjusted PR 1.27, 95% CI: 1.07–1.51; p = 0.008). Participants with confirmed V. cholerae + coinfections (N = 62) were less likely to developed moderate to severe disease compared to those with mono-infections (adjusted PR 0.59, 95% CI: 0.38–0.90; p = 0.014). These findings highlight the high prevalence and complexity of co-infections during cholera outbreaks, potentially contributing to antimicrobial resistance. They also highlight the need for targeted clinical management, particularly among persons living with HIV.Item Systematic review of associations between gut microbiome composition and stunting in under-five children.(2024-May-23) Chibuye, Mwelwa; Mende, Daniel R.; Spijker, Rene; Simuyandi, Michelo; Luchen, Chaluma C.; Bosomprah, Samuel; Chilengi, Roma; Schultsz, Constance; Harris, Vanessa C.Childhood stunting is associated with impaired cognitive development and increased risk of infections, morbidity, and mortality. The composition of the enteric microbiota may contribute to the pathogenesis of stunting. We systematically reviewed and synthesized data from studies using high-throughput genomic sequencing methods to characterize the gut microbiome in stunted versus non-stunted children under 5 years in LMICs. We included 14 studies from Asia, Africa, and South America. Most studies did not report any significant differences in the alpha diversity, while a significantly higher beta diversity was observed in stunted children in four out of seven studies that reported beta diversity. At the phylum level, inconsistent associations with stunting were observed for Bacillota, Pseudomonadota, and Bacteroidota phyla. No single genus was associated with stunted children across all 14 studies, and some associations were incongruent by specific genera. Nonetheless, stunting was associated with an abundance of pathobionts that could drive inflammation, such as Escherichia/Shigella and Campylobacter, and a reduction of butyrate producers, including Faecalibacterium, Megasphera, Blautia, and increased Ruminoccoccus. An abundance of taxa thought to originate in the oropharynx was also reported in duodenal and fecal samples of stunted children, while metabolic pathways, including purine and pyrimidine biosynthesis, vitamin B biosynthesis, and carbohydrate and amino acid degradation pathways, predicted linear growth. Current studies show that stunted children can have distinct microbial patterns compared to non-stunted children, which could contribute to the pathogenesis of stunting.Item Lessons learnt from the first controlled human malaria infection study conducted in Nairobi, Kenya.(2015-Apr-28) Hodgson, Susanne H.; Juma, Elizabeth; Salim, Amina; Magiri, Charles; Njenga, Daniel; Molyneux, Sassy; Njuguna, Patricia; Awuondo, Ken; Lowe, Brett; Billingsley, Peter F.; Cole, Andrew O.; Ogwang, Caroline; Osier, Faith; Chilengi, Roma; Hoffman, Stephen L.; Draper, Simon J.; Ogutu, Bernhards; Marsh, KevinBACKGROUND: Controlled human malaria infection (CHMI) studies, in which healthy volunteers are infected with Plasmodium falciparum to assess the efficacy of novel malaria vaccines and drugs, have become a vital tool to accelerate vaccine and drug development. CHMI studies provide a cost-effective and expeditious way to circumvent the use of large-scale field efficacy studies to deselect intervention candidates. However, to date few modern CHMI studies have been performed in malaria-endemic countries. METHODS: An open-label, randomized pilot CHMI study was conducted using aseptic, purified, cryopreserved, infectious P. falciparum sporozoites (SPZ) (Sanaria® PfSPZ Challenge) administered intramuscularly (IM) to healthy Kenyan adults (n = 28) with varying degrees of prior exposure to P. falciparum. The purpose of the study was to establish the PfSPZ Challenge CHMI model in a Kenyan setting with the aim of increasing the international capacity for efficacy testing of malaria vaccines and drugs, and allowing earlier assessment of efficacy in a population for which interventions are being developed. This was part of the EDCTP-funded capacity development of the CHMI platform in Africa. DISCUSSION: This paper discusses in detail lessons learnt from conducting the first CHMI study in Kenya. Issues pertinent to the African setting, including community sensitization, consent and recruitment are considered. Detailed reasoning regarding the study design (for example, dose and route of administration of PfSPZ Challenge, criteria for grouping volunteers according to prior exposure to malaria and duration of follow-up post CHMI) are given and changes other centres may want to consider for future studies are suggested. CONCLUSIONS: Performing CHMI studies in an African setting presents unique but surmountable challenges and offers great opportunity for acceleration of malaria vaccine and drug development. The reflections in this paper aim to aid other centres and partners intending to use the CHMI model in Africa.Item Prevalence of hypertension and its treatment among adults presenting to primary health clinics in rural Zambia: analysis of an observational database.(2015-Sep-21) Yan, Lily D.; Chi, Benjamin H.; Sindano, Ntazana; Bosomprah, Samuel; Stringer, Jeffrey S.; Chilengi, RomaBACKGROUND: Hypertension constitutes a growing burden of illness in developing countries like Zambia. Adequately screening and treating hypertension could greatly reduce the complications of stroke and coronary disease. Our objective was to determine the prevalence of hypertension and identify current treatment practices among adult patients presenting for routine care to rural health facilities in the Better Health Outcomes through Mentoring and Assessments (BHOMA) project. METHODS: We conducted a retrospective analysis of routinely collected clinical data from 46 rural government clinics in Zambia. Our analysis cohort comprised patients ≥ 25 years with recorded blood pressure measurements, who sought care at primary health centers. Consistent with prior research, in our primary analysis, we only included data from first visits. Hypertension was defined as a systolic blood pressure ≥140 mmHg, or diastolic blood pressure ≥90 mmHg, or reported use of antihypertensive medication. A sensitivity analysis was performed using median blood pressure for individuals with multiple visits. RESULTS AND DISCUSSION: From January 2011 to December 2014, 116,130 first visits by adult patients met eligibility criteria. The crude prevalence of hypertension by onsite measurement or reported use of antihypertensive medication was 23.1% [95% CI: 22.8-23.3] (23.6% in females, 22.3% in males). The age standardized prevalence of hypertension across participating sites was 28.0 [95% CI: 27.7-28.3] (29.7% in females, 25.8% in males). Sensitivity analysis revealed a similar prevalence using data from all visits. Only 5.6% of patients had a diagnosis of hypertension documented in their medical record. Among patients with hypertension, only 18.0% had any antihypertensive drug prescribed, with nifedipine (8.9%), furosemide (8.3%), and propranolol (2.4%) as the most common. CONCLUSIONS: Age standardized prevalence of hypertension in rural primary health clinics in Zambia was high compared to other studies in rural Africa; however, we diagnosed hypertension with only one measurement and this may have biased our findings. Future efforts to improve hypertension control should focus on population preventive care and primary healthcare provider education on individual management.Item Premature adult mortality in urban Zambia: a repeated population-based cross-sectional study.(2016-Mar-03) Rathod, Sujit D.; Timæus, Ian M.; Banda, Richard; Thankian, Kusanthan; Chilengi, Roma; Banda, Andrew; Lemba, Musonda; Stringer, Jeffrey S.; Chi, Benjamin H.OBJECTIVES: To measure the sex-specific and community-specific mortality rates for adults in Lusaka, Zambia, and to identify potential individual-level, household-level and community-level correlates of premature mortality. We conducted 12 survey rounds of a population-based cross-sectional study between 2004 and 2011, and collected data via a structured interview with a household head. SETTING: Households in Lusaka District, Zambia, 2004-2011. PARTICIPANTS: 43,064 household heads (88% female) who enumerated 123,807 adult household members aged between 15 and 60 years. PRIMARY OUTCOME: Premature adult mortality. RESULTS: The overall mortality rate was 16.2/1000 person-years for men and 12.3/1000 person-years for women. The conditional probability of dying between age 15 and 60 (45q15) was 0.626 for men and 0.537 for women. The top three causes of death for men and women were infectious in origin (ie, tuberculosis, HIV and malaria). We observed an over twofold variation of mortality rates between communities. The mortality rate was 1.98 times higher (95% CI 1.57 to 2.51) in households where a family member required nursing care, 1.44 times higher (95% CI 1.22 to 1.71) during the cool dry season, and 1.28 times higher (95% CI 1.06 to 1.54) in communities with low-cost housing. CONCLUSIONS: To meet Zambia's development goals, further investigation is needed into the factors associated with adult mortality. Mortality can potentially be reduced through focus on high-need households and communities, and improved infectious disease prevention and treatment services.Item Theory-based formative research on oral rehydration salts and zinc use in Lusaka, Zambia.(2016-Apr-12) Greenland, Katie; Chipungu, Jenala; Chilengi, Roma; Curtis, ValerieBACKGROUND: A theoretically grounded formative research study was carried out to investigate behaviour related to the use of Oral Rehydration Salts (ORS) and zinc tablets. The purpose was to inform the design of the behaviour change component of the Programme for Awareness and Elimination of Diarrhoea in Lusaka Province, Zambia, which aims to reduce childhood morbidity and mortality from diarrhoeal disease. METHODS: Fourteen behaviour trials were conducted among caregivers of children under-five with diarrhoea. Caregivers were recruited from two clinics situated in rural and peri-urban Lusaka. Trials took ten days and data were captured using video, observation and repeated interviews. Additional data were collected through focus group discussions with mothers, observations in clinics and pharmacies and interviews with clinic and pharmacy staff. Findings were organised according to categories of behavioural determinants from Evo-Eco theory. RESULTS: Participants were all familiar with ORS and most knew its purpose. ORS use was motivated by symptoms of dehydration, rather than the start of a diarrhoea episode, and was stopped when the child had visibly recovered energy. Only four of 14 behaviour trial participants were observed to correctly prepare ORS. Errors were mainly associated with measurement, resulting in a solution that was too concentrated. ORS was not observed to be given to children at clinics. Although zinc was unknown in this population, it was positively received by mothers keen to learn whether zinc would work better than alternative treatments to stop diarrhoea. CONCLUSIONS: ORS was sub-optimally prepared and used at home. It was not used while waiting to be seen at a clinic. In homes, the behaviour change intervention should promote early and continued use of correctly prepared ORS. In the longer-term, these behaviours may best be encouraged by changing the product design or sachet size. Despite its unfamiliarity, this population was well disposed to the use of zinc as a treatment for diarrhoea; when zinc is new to a population, promoting zinc as a solution to stopping diarrhoea, which mothers seek, may drive initial trial. Ensuring the availability of zinc in public clinics and private pharmacies prior to commencement of any promotion activities is crucial.
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