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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 Preterm birth among women with HIV: impact of preconception cART initiation.(2024-Oct-01) Duffy, Cassandra R.; Herlihy, Julie M.; Zulu, Ethan; Mwananyanda, Lawrence ; Forman, Leah; Heeren, Tim; Gill, Christopher J.; Harper, Megan; Chilengi, Roma; Chavuma, Roy; Payne-Lohman, Barbara; Thea, Donald M.OBJECTIVE: To examine the risk of preterm birth (PTB) and small for gestational age (SGA) among women with HIV compared to women without HIV. Secondary objectives were to explore the role of maternal immune activation (IA) and effect of cART timing on these outcomes. DESIGN: Prospective observational cohort. SETTING: Urban government-run clinic at Chawama Hospital in Lusaka, Zambia. PARTICIPANTS: A total of 1481 women with and without HIV with singleton pregnancies enrolled before 26 weeks' gestation by ultrasound dating. METHODS: From August 2019 to November 2022, pregnant women were enrolled in a 1 : 1 ratio of HIV infection. Maternal baseline clinical factors were collected, as well as CD4 + , viral load and CD8 + T-cell IA in women with HIV. Birth outcomes were also collected. The association of HIV-exposure and cART timing on outcomes was assessed by multivariable logistic regression. The independent role of IA was determined by mediation analysis. MAIN OUTCOME MEASURES: PTB (<37 weeks) and SGA. RESULTS: There were 38 fetal deaths and 1230 singleton live births. Maternal HIV infection was associated with PTB [adjusted odds ratio (AOR) 1.60, 95% confidence interval (CI) 1.11-2.32] and to a lesser extent SGA (AOR 1.29, 95% CI 0.98-1.70). Maternal cART timing impacted these associations, with highest risk in women who started cART after conception (PTB AOR 1.77, 95% CI 1.09-2.87, SGA AOR 1.52, 95% CI 1.04-2.22). Maternal IA was not associated with PTB independent of HIV infection. CONCLUSIONS: HIV is associated with PTB. Risk of PTB and SGA was highest in women with HIV who started cART in pregnancy, a modifiable risk factor.Item Reimagining community mental health: adapting interventions for culturally rich, low-resource settings.(2024-Dec) Dalal, Naeem; Chambwe, Chikumbi; Maila, Brian; Chilengi, RomaItem Managing multiple funding streams and agendas to achieve local and global health and research objectives: lessons from the field.(2014-Jan-01) Holmes, Charles B.; Sikazwe, Izukanji; Raelly, Roselyne L.; Freeman, Bethany L.; Wambulawae, Inonge; Silwizya, Geoffrey; Topp, Stephanie M.; Chilengi, Roma; Henostroza, German; Kapambwe, Sharon; Simbeye, Darius; Sibajene, Sheila; Chi, Harmony; Godfrey, Katy; Chi, Benjamin H.; Bolton-Moore, CarolynMultiple funding sources provide research and program implementation organizations a broader base of funding and facilitate synergy, but also entail challenges that include varying stakeholder expectations, unaligned grant cycles, and highly variable reporting requirements. Strong governance and strategic planning are essential to ensure alignment of goals and agendas. Systems to track budgets and outputs, as well as procurement and human resources are required. A major goal of funders is to transition leadership and operations to local ownership. This article details successful approaches used by the newly independent nongovernmental organization, the Centre for Infectious Disease Research in Zambia.Item A mobile phone-based, community health worker program for referral, follow-up, and service outreach in rural Zambia: outcomes and overview.(2014-Aug) Schuttner, Linnaea; Sindano, Ntazana; Theis, Matthew; Zue, Cory; Joseph, Jessica; Chilengi, Roma; Chi, Benjamin H.; Stringer, Jeffrey S.; Chintu, NamwingaBACKGROUND: Mobile health (m-health) utilizes widespread access to mobile phone technologies to expand health services. Community health workers (CHWs) provide first-level contact with health facilities; combining CHW efforts with m-health may be an avenue for improving primary care services. As part of a primary care improvement project, a pilot CHW program was developed using a mobile phone-based application for outreach, referral, and follow-up between the clinic and community in rural Zambia. MATERIALS AND METHODS: The program was implemented at six primary care sites. Computers were installed at clinics for data entry, and data were transmitted to central servers. In the field, using a mobile phone to send data and receive follow-up requests, CHWs conducted household health surveillance visits, referred individuals to clinic, and followed up clinic patients. RESULTS: From January to April 2011, 24 CHWs surveyed 6,197 households with 33,304 inhabitants. Of 15,539 clinic visits, 1,173 (8%) had a follow-up visit indicated and transmitted via a mobile phone to designated CHWs. CHWs performed one or more follow-ups on 74% (n=871) of active requests and obtained outcomes on 63% (n=741). From all community visits combined, CHWs referred 840 individuals to a clinic. CONCLUSIONS: CHWs completed all planned aspects of surveillance and outreach, demonstrating feasibility. Components of this pilot project may aid clinical care in rural settings and have potential for epidemiologic and health system applications. Thus, m-health has the potential to improve service outreach, guide activities, and facilitate data collection in Zambia.