Trends and seasonal variation in gastrointestinal infections in Tanzania: Analysis of 5-year DHIS2 data toward implementing the sampling cycles and metagenomic analyses

Highlights

• •Periodic analyses of DHIS2 data reveal trends and seasonality of diarrheal infection.
• •Climate change influences diarrheal diseases outbreaks in the Great Lakes regions.
• •The seasonal diarrheal infections inform sampling cycles for metagenomic analyses.
• •Seasonal diarrheal sampling and genomics facilitates identification of antimicrobial resistance pathogens.

Abstract

Objectives

Gastrointestinal (GI) infections, such as diarrhea and dysentery, continue to be major contributors of morbidity and mortality in low-resource countries. Determining trends and seasonality of GI infections provides a better understanding of how interventions can be improved to reduce the burden. To this effect, an analysis of data from the District Health Information System 2 (DHIS2) was conducted to determine the trend and seasonal variations of GI infections in regions located in the Great Lakes of Tanzania.

Methods

Data from DHIS2 of 22 districts in Tanzania recorded between January 2018 and December 2022 were analyzed for trends and seasonal variations in GI infections. The data were managed and analyzed by STATA and Microsoft Excel.

Results

A total of 1,511,623 GI cases were recorded between January 2018 and December 2022, with diarrhea leading by 84.4%. Data have shown clear seasonal variations of GI infection: peaks during the rainy season and decline in the dry season.

Conclusion

Results have revealed that there is a significant decrease in GI infections from January to August, and the cases increase from September to December. This confirmed two sampling cycles, the dry and rainy season, within which pathogen characteristics and diversity will be elucidated.

Introduction

Gastrointestinal (GI) infections, such as diarrhea and dysentery, remain major and common public health concerns causing morbidities and mortalities among people of all ages [1]. The common etiologies of GI infections are viruses, bacteria, and protozoans [2]. Bacteria and protozoans are the most common contributors to acute and chronic GI infections and their complications in sub-Saharan Africa [3,4]. This is due to several reasons, among which include weak provisions of water, sanitation, and hygiene and behavioral and environmental factors [4,5]. Typhoid, cholera, and dysentery are common gastroenteric infections caused by Salmonella spp, Vibrio cholerae, Escherichia coli, Bacillus, Shigella, Clostridium, and Campylobacter spp [5,6]. On the other hand, GI parasite infections are typically acquired from ingestion of contaminated food or water. Parasites such as Giardia lamblia and Cryptosporidium are often contracted through drinking untreated stream water [6]. The viruses such as rotavirus, norovirus and adenovirus are notoriously known to cause acute diarrhea in children under the age of 5 years, and adults who are immunocompromised [7]. Rotavirus are one of the most common viral agents that cause acute gastroenteritis, particularly in children under 5 in sub-Saharan Africa [8]. The virus infects and multiplies in the small intestine's mature enterocytes [9], leading to enterocytes’ cell death, and osmotic diarrhea, which end up with watery diarrhea, vomiting, fever, and dehydration [10]. Rotaviruses are mainly transmitted through contaminated water and food. They are significant etiological agent of gastroenteritis, with the presence of a rotavirus vaccine which significantly reducing hospitalizations and mortality [11].

Despite continued improvements in addressing drivers for GI infections, these diseases continue to pose a significant burden and remain among the top 10 causes of morbidity worldwide, with an estimated 550 million people falling ill annually [5,12]. Western sub-Saharan Africa has the highest burden of GI infection, with an age-standardized Disability Adjusted Life Year (DALY) rate of 2769.81 per 100,000 population [5]. In terms of mortality due to GI infections, sub-Saharan Africa leads the other regions with a rate of 6.03-160.95 per 100,000 population, followed by India and the southeast Asian region [5]. The global distribution of GI infection depicts the influence of socio-economic and environmental factors, which jointly drive the infection rate in low- and middle-income countries compared with high-income countries [13].

In Tanzania, as with other low- and middle-income countries, the burden of GI is appreciably high; in the year 2022, diarrhea ranked fifth (3.7%) of the top 10 diseases presented at the outpatient departments (OPDs). Equally, diarrhea cases among children under 5 years are equally high; in the same period, it ranked third recording 8.45% of OPD involving children <5 years old [14]. Most GI diseases are self-monitored; however, severe cases may occur in high-risk groups, such as children aged <5 years, the elderly, and immunocompromised persons, resulting in high morbidity and mortality [15]. On the other hand, Tanzania has been experiencing a recurrence of cholera outbreaks across different regions annually [16]. For example, in 2023 and 2024, regions along the great lakes namely Kigoma, Songwe, Katavi, Rukwa, Kigoma, Mwanza, Simiyu, Rukwa, and Mbeya have been grappling with the cycles of cholera outbreaks [17]. Generally, the districts located within great lakes ecosystems and along the boarders with western and southern boarders exhibit a unique patterns of GI infections due to several factors, including cross-border socio-ecological systems, environmental, socio-economic, behavior, and cultural issues [18,19]. In addition, the demographic and epidemiological changes, host-related elements, environmental determinants, and climate change have a huge influence on the trend of GI diseases [20,21].

Although there have been improvements in the access to clean and safe water and sustained health promotion, rapid transmission of GI infections has often been associated with predisposing factors such as inadequate personal hygiene, substandard sanitation practices, limited access to safe and clean water, and attitudes toward food hygiene [16]. These factors contribute to the vulnerability of the community to GI infections. Thus, understanding the epidemiology of GI infections in the selected districts can be useful for developing targeted public health interventions, active surveillance, and strengthening of the response system.

This study aimed to determine the trends and patterns of GI diseases within a specific time interval in specific geographical localities as an important step toward informing planning for preventive and curative interventions. The analysis covers DHIS2 data from 22 districts located along the Great Lake regions, posted between 2018 and 2022 as a milestone toward understanding the trend and seasonality of GI infections across the study areas. Furthermore, the analytical outputs will serve as a baseline and determinant of the sampling cycles and metagenomics for the study titled “Linking Infectious Disease Front-liners’ Control Efforts with Central Public Health Authorities in the African Great Lakes Region (GREAT LIFE)” and other upcoming projects focusing on GI infections, pathogen diversity, and antimicrobial resistance.

Materials and methods

Study area and population

The study population included patient records on GI disease cases reported between January 2018 and December 2022. The data from 11 regions in Tanzania that border the Great Lakes and neighboring countries were extracted. These regions include Mara, Kagera, Mwanza, Kigoma, Rukwa, Katavi, Songwe, Mbeya, Ruvuma, Njombe, and Mtwara. From each region, two districts were randomly selected to make a total of 22 districts (Figure 1), where their corresponding GI disease recorded cases were extracted from the District Health Information System 2 (DHIS2) (Figure 1).

Figure 1.

Map of Tanzania showing districts that border major lakes in Tanzania and international boundaries colored according to their contribution to GI incidence rates.

GI, gastrointestinal.

Data source, management, and analysis

The district-level routine data from the selected districts were extracted from DHIS2 between 2018 and 2022. The DHIS2 is a routine health facility–level database that provides a monthly reporting platform for disease cases across all districts in Tanzania.

Patient data, such as the number of GI infection cases and the number of outpatients attending the OPD by month in each district for the period between January 2018 and December 2022, included urban and rural populations from the district to ensure that a representative study population was obtained. The extracted data from DHIS2 were managed and analyzed via Stata version 17 software and visualized via Microsoft Excel, whereas a Tanzanian map was sketched via ArcGIS version 10.8 software.

The OPD attendance data were used to calculate the incidence rate for each year. The incidence rate was determined by the ratio between the “number of new cases” and “number of persons in the population at risk” times 10^n, where n is any number that a researcher wants to express the rate per population as outlined by the Centers for Disease Control [22]. That is,

$$\text{Incidence}\text{rate}=\frac{\text{Number}\text{of}\text{GI}\text{disease}\text{cases}}{\text{Number}\text{of}\text{persons}\text{in}\text{the}\text{population}\text{at}\text{risk}}*1000$$

The growth rate estimate was determined by the ratio between “present and past disease cases” power over time duration between present and records minus 1 [21]. That is,

$$\mathrm{r}={\left(\frac{{\mathrm{N}}_{\mathrm{t}}}{{\mathrm{N}}_0}\right)}^{\frac{1}{\mathrm{t}}}-1$$

here r = growth rate, N_t = present GI disease cases, and N₀ = past GI disease cases.

$$\mathrm{r}={\left(\frac{264,828}{345,571}\right)}^{\frac{1}{5}}-1,\mathrm{r}=-5.18\%$$

Ethical issues

Approval of the use of DHIS2 data was obtained from the Ministry of Health through the Department of Monitoring and Evaluation. The analysis of the 5-year GI data was part of the periodic review of the DHIS2 data to inform decision-making and implementation of strategic interventions addressing GI infections. In addition, this work was performed under the GREAT LIFE project, with an ethical approval certificate Ref. No. NIMR/HQ/R.8a/Vol.IX/4596 provided by the National Health Research Ethics Committee (NatHREC).

Results

A total of 1,511,623 GI disease cases were recorded between January 2018 and December 2022. Most reported GI infection cases in the 5 years were attributed to diarrhea, followed by typhoid disease (Table 1). The results show fluctuations in the incidence rates of GI infections with their corresponding Z scores and P-values. The overall GI infections and incidence of diarrhea diseases significantly decreased over the 5 years (Z-value: −3.6, P = 0.003). Similarly, dysentery, typhoid, and cholera showed a decreasing trend (with negative z-values) but were not statistically significant (P >0.05) (Table 1).

Table 1.

Average annual incidence rates of GI infections in Tanzania (per 1000 persons) from 2018 to 2022.

Disease	Year					Z-value	P-value
	2018	2019	2020	2021	2022
Overall (GI)	95.03	101.07	85.88	74.01	87.80	-3.62	0.0003
Diarrhea	78.00	83.36	70.38	58.80	73.11	-3.61	0.0003
Dysentery	5.34	4.85	3.68	3.67	3.55	-1.02	0.3078
Typhoid	11.60	12.82	11.66	11.48	11.07	-0.53	0.5946
Cholera	0.09	0.05	0.16	0.07	0.06	-0.14	0.8930

GI, gastrointestinal.

Trends of reported gastrointestinal infections for the 5 years across the study districts

There was an overall decrease in GI infection incidences from 2018 through 2022 (z-score: −3.62, P <0.01). The results indicate that the incidence of GI disease increased from 95 per 1000 persons in 2018 to 101 per 1000 persons in 2019, then, it sharply decreased to 74 per 1000 persons in 2021 and increased to approximately 88 per 1000 persons in 2022 (Figure 2). Compared with any other disease, the 5-year situation of GI infections was highly associated with diarrhea disease, followed by typhoid, whereas the lowest contributor was cholera (Figure 2). Regarding the trends of GI infections at the district level, Tunduma district had the highest incidence for almost all 5 years, with the highest rate (238 per 1000 persons) recorded in 2021. The Mtwara district recorded the lowest incidence rate of GI infections during the same period with the lowest rate being 33 per 1000 persons recorded in 2018 (Figure 3). The GI infection incidence over the 5 years revealed an increasing trend in the six districts, namely, the Tunduma, Kyela, Nyasa, Kyerwa, Tarime, and Masasi districts, whereas a decreasing trend was observed in the four districts of Misenyi, Ludewa, Makambako, and Rorya (Figure 3).

Figure 2.

Trends of GI infections over 5 years in Tanzania.

GI, gastrointestinal.

Figure 3.

Distributions of GI disease incidence by district over 5 years.

GI, gastrointestinal.

Seasonal variation gastrointestinal infection incidence from 2018 to 2022

In the context of Tanzania, seasonal variations can be classified as either unimodal (regions that receive rain once a year) or bimodal (regions that receive rain twice a year) rainy and dry seasons. The bimodal rain season lasts from March to May, and the second season lasts from November to December. The bimodal dry season lasts from June to October and from January to February. The unimodal rainy season lasts from November to April, and the dry season lasts from May to October [23]. Research shows that seasonal variations, dry and rainy seasons, contribute to infectious disease cycles, including GI-related diseases [24]. In this study, results have revealed that at the end of the dry season and the beginning of the main rainy season (September through November), the incidence of GI infections was high across the study period (Figure 4). The incidence of GI infections increased in the dry season across all 5 years between July and October, with the lowest (74 per 1000 persons) incidence recorded in August 2021 and the highest (100 per 1000 persons) in October 2022 (Figure 4). Furthermore, within 4 years from 2018 to 2021, the incidence of GI disease decreased during the start of the rainy season (November and December), with a recorded incidence of approximately 97 per 1000 persons from November 2020 to approximately 80 per 1000 persons in December 2021. However, in December 2022, the incidence of GI infections appeared to increase (Figure 4).

Figure 4.

Seasonal variation in the incidence rates of specific GI diseases by month from 2018 to 2022.

GI, gastrointestinal.

In terms of GI disease specificity, diarrhea had the highest incidence rate in the dry season, which peaked in October throughout the study period, with the highest incidence recorded in October 2022 (88 per 1000 persons), whereas the lowest (54 per 1000 persons) was reported at the end of the main rainy season in May across the study period. Typhoid incidence rates were reported to be almost constant throughout the study period, except for 2 months, which showed a sharp increase in typhoid incidence in January 2021 (16 per 1000 persons) and April 2021 (15 per 1000 persons) (Figure 4). Dysentery has the highest incidence rate (21 per 1000 persons) during the rainy season in February and March 2021 (Figure 4). The rate in the other months appeared to remain constant throughout the study period, except for the observed sharp increase from January to February 2021, which remained constant until March 2021 before a sharp decrease in April 2021, when it remained constant throughout the study period (Figure 4). The incidence of cholera was the lowest and remained constant throughout the study period.

Discussion

This work aimed to understand the trends and seasonal variations of GI infections in Tanzania, particularly, in regions located within proximity to the Great Lakes and along borders with east and south African countries. The focus was on four GI infections, namely, diarrhea, dysentery, typhoid, and cholera, across the 22 selected districts along the Great Lakes in Tanzania and those bordering neighboring countries. This study highlights the potential of aggregating and analyzing routinely collected DHIS2 data to enhance a better understanding of the drivers of GI infections and inform the public health decision-making processes on the prevention and response strategies, as well as promote surveillance systems.

Overall, approximately 1.5 million cases of GI infections were recorded between January 2018 and December 2022, with an annual decrease of 5.18%. Specifically, diarrhea decreased by 5.54%, dysentery by 5.24%, typhoid by 1.56%, and cholera by 64.44%. The decreasing trend of GI infections is highly commendable and desirable within the health system. It is important to explore predisposing factors, including seasonal variations, that contributed to this trend and devise mechanisms for strengthening the health system response to achieve further decrease in the incidence of GI disease.

The seasonal variation was noted as an important factor driving the GI disease burden in the studied areas. The variations necessitate area-specific strategies for prevention and response to these diseases. A circle of seasonal variation in the overall GI infections was found, with an increasing rate during the end of the dry season (September and October) and the start of the rainy season (November and December) across the study period. Moreover, we observed a decreasing rate of GI infections during the rainy season (December through February), with a slight increase in the end months of the rainy season (April to May) and a decrease during the dry season from June to August before a sharp increase in September. This might be because, during the dry season, GI-causing pathogens grow and replicate in zoonotic areas, including ground surfaces, and on unpreserved food [25]. Therefore, drinking water/eating from unprotected sources/unpreserved food may lead to any of these types of GI infections [26,27]. In addition, during the rainy season, the pathogens that accumulate during the dry season are flushed into the water sources and underground water, and, when ingested without treatment, it leads to GI infections [28]. These findings correspond to studies reported elsewhere, including studies done in the southern hemisphere region with four distinct seasons of summer, winter, autumn, and spring, and indicates that GI infections peaks in the winter seasons (June-August) [29], which overlaps with Tanzania’s dry season months (June-October). In addition, when it comes to specific condition, it has been reported that typhoid fever and other enteric diseases increases during the rainy season after dry periods [28]. Furthermore, diarrhea was found to be the leading GI infection across all areas covered in this analysis. The cases appeared to peak from July to November every year and began to decline from December to May of the subsequent year (Figure 4). This interesting incident cycle provides an opportunity to investigate the drivers as to whether it is due to poor water, sanitation and hygiene (WASH) provisions, weather factors, and/or pathogen characteristics.

Similar GI infection cycles have been reported in other countries. For instance, in Kenya, cholera cases peak during the rainy season, particularly, after dry spells [30], and the trend has been reported from Guinea-Bissau [23]. Regarding GI-specific diseases, the present study has revealed that diarrhea cases increased during the dry season (June) and peaked at the onset of the rainy season (November). On the other hand, typhoid and dysentery remained constantly low throughout the study period, except in 2021, when typhoid cases peaked in January and April, and dysentery cases peaked in February and March 2021, which are the rainy months. The cholera cases were generally low (less than two per 1000 persons) and remained constant throughout the study period.

The influence of COVID-19 preventive measures, such as strengthening of infection prevention and control (IPC) and improved sanitation and hygiene practices was observed in 2020 and 2021. The analysis has further revealed that the incidence of GI infections decreased sharply in 2021, registering the lowest incidence rate (65.8 per 1000), exemplifying a positive impact of COVID-19 preventive interventions on GI infections across the country. The positive impact was felt more in Misenyi, Buhigwe, Ludewa, Makambako, and Magu districts. This observation corroborates other reports on the impact of COVID-19 preventive intervention on other infectious diseases [31,32]. Despite this interesting trend, there were two districts, namely, Kyela and Nyasa DC, which had the opposite trend, where GI infection cases increased during the COVID-19 pandemic. This is irrespective of the hand hygiene and sanitation practices that were promoted and enforced widely across the country. This might be due to seasonal variability, a low response of the community to IPC, reduced access to clean and safe water, and behavioral reasons. A similar observation was reported from Ethiopia, where there was an increase in diarrheal disease cases during the COVID-19 pandemic, with one of the contributing factors being seasonal fluctuations, with more cases during spring and winter than during the summer season [33].

Dysentery, which is caused by Shigella in particular, showed mixed trends during the pandemic. In some regions, there was a decrease in the transmission of shigellosis, whereas, in other regions, the cases increased. Similarly, dysentery incidences increased in February and March 2021, again raising interesting questions about what the drivers were.

Special attention should be given to Sumbawanga, Momba, and Tunduma DC, which had relatively large shares of the GI disease burden across the study period compared with the other districts. It is important to explore reasons beyond seasonal variations, WASH, IPC practices, and other factors such as antimicrobial resistance, which may be responsible for such high morbidity. Deliberate efforts, particularly, in investigating the genomes of pathogens responsible for GI infections and environmental and socio-ecological factors in these districts may reveal important details to guide the delivery of appropriate interventions.

The current study has determined the trend and cycles for GI infections in the districts located along the Great Lake regions. This provides an opportunity for strengthening the health system’s efforts focusing on surveillance strategies at the primary health care level, where most of the patients seek services. The trends and cycles of GI revealed here will guide the development and promotion of preventive interventions, as well as sampling cycles for metagenomic analyses.

Conclusion

We identified localities with GI burdens that fluctuated with seasonality. A significant decrease in the GI disease burden was observed within the 5 years studied. We found an increasing rate during the end of the dry season (September and October) and the start of the rainy season (November and December) across the study period. Sumbawanga, Momba, and Tunduma DC accounted for a relatively high share of the GI disease burden, which needs special attention. A focus on specific diseases showed that diarrhea is the most prevalent GI infection in all the 22 districts studied. Typhoid fever was the second and the last was cholera. All of these are diseases of poverty caused by limited provision of safe and clean water, poor sanitation and hygiene at the individual and household levels, behavioral issues, and environmental factors. The analysis has clearly revealed the best sampling months for the GREAT LIFE project studying pathogens diversity and characteristics responsible infections and drug resistance. This will provide a better understanding of pathogens characteristics and diversity to inform the delivery of interventions and case management.

Limitations

The fact that DHIS2 does not collect disaggregated data, such as demographic characteristics and other socio-economic statuses, poses an important limitation in this study because it lacks inferential statistical analysis and modeling to predict and identify specific factors or drivers influencing differential GI burdens and distributions.

Declarations of competing interest

The authors have no competing interests to declare.