Centre for Infectious Disease Research in Zambia
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Recent Submissions
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.
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.
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.
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.
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.