The burden of gastrointestinal (GI) illness in developing countries remains significantly high, despite a marked decrease in mortality rates from 4.6 million in 1980 to about 1.5 million annually in 1999.1–3 It is estimated that approximately 1.87 million (CI: 1.56–2.19) children die from diarrhoea before reaching their fifth birthday.4 Diarrhoeal diseases account for 1/5 of all child deaths, 78% of which are concentrated in the African and South East Asian Regions.4,5 Several studies have shown that the burden of GI remain particularly high in the African continent, especially in areas characterized by poverty. Three of the Millennium Development Goals (MDG) are associated with the burden of diarrhoeal diseases. The progress towards achieving the targets of MDG 7- to halve the proportion of people without sustainable access to improved sanitation; MDG 1- to eradicate extreme poverty and hunger and MDG 4- to reduce child deaths by two thirds by 2015, has been slow.6,7
Current trends suggest that many countries in SSA will not reach these target as only about 31% of people have access to improved sanitation,8 leaving a significant proportion of vulnerable people at risk from infectious diseases.7 Infectious organisms can be transmitted through a variety of routes,9,10 the epidemiology of GI illness is influenced by the context in which they are transmitted and differs between developing and developed countries.2,4,11 Recent studies have described a high incidence of pathogenic organisms, especially in children in the SSA region when compared with the rest of the world.2,4,11 Since the African continent is disproportionately affected by a high burden of illness from GI illness, it is important to understand the types and prevalence of pathogens that are responsible in SSA countries and how this can influence planning for prevention and control programmes. The high prevalence and burden of HIV infection in countries in SSA populations have also increased the risk of acute and persistent diarrhoea. There is much value in describing not just a single pathogen, but a range of pathogens, as many are transmitted via similar routes of exposure. The application of prevention and control measures at each route of exposure can impact several pathogens at the same time.12–14 The aim of this paper is to describe the common diarrhoeal pathogens, and discuss their public health implications in the Sub-Saharan African context. A systematic review of studies from the SSA region was done, as it provides empirical information through the appraising and synthesizing of evidence from primary studies, while reducing the reviewer's own bias.15–17
Materials and Methods
Search strategy and selection criteria
A search for studies on diarrhoeal pathogens and associated risk factors conducted in sub-Saharan Africa was performed between September 2009 and December 2010. Several databases including EBSCO host, Academic Search Premier, Scopus, Science Direct, Google scholar and Web of Science, were searched for articles published in the English language. The search strategy used a combination of terms including: infectious intestinal disease, aetiology (etiology) diarrhoea Africa, aetiology (etiology) gastroenteritis Africa, enteric infectious pathogen Africa. Boolean operators (not, and, or) were also used in succession to narrow and widen the searches. Other articles were identified by reviewing the reference list of articles.
Criteria for selecting studies
The primary selection was made based on the major topic of the article. The apriori-decided criteria used were the following:
The age group of the study population must be clearly defined;
The study must define whether the subjects were clinically asymptomatic or symptomatic;
The study must include detailed results of microscopic analysis of stool samples and the number of samples tested must be reported;
The number of study subjects and positive results for both cases/controls must be reported;
Only studies providing adequate information on the actual pathogens identified and prevalence rates for all pathogens identified and tested for three or more (≥3) pathogens were included.
Studies were excluded if they focused on a single pathogen, did not include information on aetiology or did not provide adequate information about methods employed, or was not available in full-text among other reasons presented in Table 1.
Study selection, quality assessment and data extraction
The primary selection included any cross-sectional studies, case controls, and retrospective or prospective cohorts. Studies were selected if they included details of the number of samples tested, laboratory methods, results of analyses, and subjects' HIV status and the period of the study. The outcome of interest was the number and types of pathogens isolated from diarrhoeal and non- diarrhoeal stool specimens. All studies included were screened based on the MOOSE guidelines. Data were summarized based on location, study population and associated risk factors (Table 2). Microbiological analyses of stool specimen are summarized in Table 3.
|Location, author and date of publication||Setting, HIV prevalence, sample source||Participants age, study design||No. of specimen tested||Overall pathogen isolation rates|
|Guinea-Bissau: Bandim II & Belem of Bissau (2003)68||Peri-urban, community based||02 yrs; prospective cohort 2 yrs, follow-up||11987 cases||Pathogens found in 58% of specimen|
|Kenya 2: Kisumu (2009)69||Urban; HIV sero-prevalence was 1 3.6% amongst cases; hospital based||02 yrs; prospective Cohort 2 yrs, follow-up.||630 cases||Pathogens found in 32.2% of specimen.|
|Nigeria (1): Abakaliki (2008)70||Mixed setting; primary health care unit||04 yrs; retrospective study||150 cases 50 controls||Pathogens found in 81.3% of specimen|
|Nigeria (2): East Central State (1997)71||Mixed setting; hospital based||05 yrs; retrospective study||1015 cases 401 controls||Pathogens found in 21.0 % and 3.9% (P<0.001) of cases and control specimen respectively|
|Zambia: Lusaka 1 (1998)72||Peri-urban; hospital based||05 yrs; retrospective study||639||Pathogens found in 29.9% of specimen.|
|Mozambique: Maputo province (2007)73||Rural, hospital based||05 yrs; retrospective study||529 cases||Pathogens found in 42.2% of specimen|
|Cameroon: Yaounde (2008)74||Urban, community based||05 yrs; retrospective study||3034 cases||pathogens found in 59.5% of specimen|
|Tanzania: Ifakara (2004)75||Urban; hospital based||05 yrs; retrospective study||451 cases||Pathogens found in 67.6% of specimen.|
|Ghana: Bulpelia / Tamale (2007)76||Urban, primary health care unit||011 yrs; case control study||243 cases, 124 controls||Pathogens found in 76.5 % and 53.2% (P<0.001) of cases and control specimen, respectively|
|Central African Rep. Bangui (1994)77||Urban, hospital based||015 yrs; retrospective study||1197 cases||Pathogens found in 49.4% of specimen|
|Zaire: Kinshasa (1994)78||Urban; hospital and health centre based||05 years; matched case control||173 cases, 155 controls||Pathogens found in 100% and 94% of cases and control specimen respectively|
|Zaire: Kivu (1983)79||Peri-urban; hospital based||05 years; case control||355 cases; 320 controls||Pathogens found in 40.3% and 14.1% of cases and control specimen respectively.|
|Nigeria: Lagos (1994)80||Urban; hospital and health centre based||05 years; case control||215 cases, 100 controls||Pathogens found in 74.9% and 28% of cases and control specimen respectively|
|Nigeria: Osun State (2003)81||Urban; hospital based||05 years; retrospective study||135||Pathogens found in 100% of cases.|
|Nigeria: Abuja (2008)82||Peri-urban; hospital based||05 years; retrospective study||404||Pathogens found in 68.5% of cases.|
|Burkina Faso: Ouagadougou (2007)83||Peri-urban; HIV sero-prevalence = approx 10.6% amongst cases health centre based||05 years; retrospective study||66||Pathogens found in 42.4% of cases.|
|Ghana: Tamale (2008)84||Peri-urban; health centre based||011 years; case control||243 cases; 124 controls||Pathogens found in 92.6% and 86.3% of cases and control specimen, respectively.|
|Uganda: Kampala (2009)85||Peri-urban; HIV sero-prevalence = approx 24.7% amongst cases hospital based||05 years; retrospective study||190||Pathogens found in 24.7% of specimen.|
|Meta-analysis: random effects mean isolation rate in children: 58.1% (95% CI; 50.165.6%); heterogeneity P<0.046;|
|Malawi: Lilongwe (1996)86||Urban; HIV sero-prevalence = approx 60% amongst controls; hospital based||12 yrs; case control study.||132 cases 73 controls||Pathogens found in 48.3% and 2% of cases and control specimen respectively.|
|Uganda: Entebbe (2002)87||Semi-urban; HIV sero-prevalence = approx 100% amongst cases and controls; community based||Adults (IQR = 2636 yrs) Prospective Cohort, 2 yrs, follow-up||357 cases, 127 controls||Pathogens found in 49% and 39% of cases and control specimen, respectively|
|Zambia: Lusaka (2) (1996)88||Urban; HIV sero-prevalence = approx 97% amongst cases; community based.||1879 yrs; retrospective study||77||Pathogens found in 78% of specimen|
|Zambia, Misisi, Lusaka (3) (2009)89||Urban; HIV sero-prevalence was 31% amongst cases; hospital based||1879 yrs; prospective Cohort, 3 yrs, follow-up||4780||Pathogens found in 99% of specimen|
|Central African Republic, Bangui (1998)90||HIV sero-prevalence = approx 74% and 52% amongst cases and controls, respectively; hospital based||>18 years; case control||290 cases; 140 controls||Pathogens found in 55.5% and 61.4% of cases and control specimen, respectively|
|Meta-analysis: random effects mean isolation rate in adults: 65.6% (95% CI, 26.091.2%); heterogeneity P<0.454|
|South Africa: Venda region (2003)91||Rural; community based||All age groups; retrospective study||401 cases||Pathogens found in >95.3% of specimen (totals not given)|
|Burkina Fasa: Ouagadougou (2002)92||Rural; hospital based||All age groups; retrospective study||4131 (protozoa) 826 (bacteria)||Pathogens found in 8% of specimen, respectively|
|Kenya 1: Asembo Bay (2006)93||Rural, community based||070 years; retrospective surveillance type||3445 cases||Pathogens found in 31.7% of specimen|
|Kenya 1: Asembo Bay (2003)94||Rural, health centre based||070 years; retrospective surveillance type||451 cases||Pathogens found in 51.% of specimen|
|Location and date of publication||Bacteriology methods||Virology methods||Parasitological methods|
|Guinea-Bissau: Bandim II & Belem of Bissau (2003)68||Standard culture methods, DNA-DNA hybridization||ELISA||Microscopy|
|Kenya 2: Kisumu (2009)69||Standard culture methods & bright-field microscopy||ELISA||Microscopy & IFA|
|Nigeria (1): Abakaliki (2008)70||Standard culture methods & direct microscopy||ELISA||Microscopy|
|Nigeria (2): East Central State (1997)71||Standard culture methods||N/A||N/A|
|Zambia: Lusaka 1 (1998)72||Standard culture methods||N/A||N/A|
|Mozambique: Maputo Province (2007)73||Standard culture methods & direct microscopy||N/A||Direct observation & microscopy|
|Cameroon: Yaounde (2008)74||Standard culture methods||ELISA||Microscopy|
|Tanzania: Ifakara (2004)75||Standard culture methods & direct microscopy||Agglutination test||Direct observation|
|Ghana: Bulpelia / Tamale (2007)76||Standard culture methods||RT-PCR||Microscopy|
|Central African Rep. Bangui (1994)77||Standard culture methods||ELISA||Microscopy|
|Zaire: Kinshasa (1994)78||Standard culture & direct microscopy||Latex agglutination test||Direct observation & microscopy|
|Zaire: Kivu (1983)79||Standard culture methods||ELISA||Direct microscopy.|
|Nigeria: Lagos (1994)80||Standard culture methods||ELISA||Direct microscopy iron haemotoxylin staining for Cryptosporidium sp.|
|Nigeria: Osun State (2003)81||Standard culture methods and plate dilution technique for antibiotic susceptibility testing.||N/A||N/A|
|Nigeria: Abuja (2008)82||Standard culture and slide agglutination technique; modified disc diffusion technique for antibiotic susceptibility testing.||EIA||Light microscopy & Ziehl-Neelsen (Kinyoun's) stain for Cryptosporidium.|
|Burkina Faso: Ouagadougou (2007)83||N/A||Immunochromatographic tests.||Direct microscopy|
|Ghana: Tamale (2008)84||Standard culture methods and breakpoint microdilution test for antibiotic susceptibility.||N/A||N/A|
|Uganda: Kampala (2009)85||Standard culture methods and disc diffusion technique for antibiotic susceptibility.||N/A||N/A|
|Malawi: Lilongwe (1996)86||Standard culture methods & direct microscopy.||N/A||N/A|
|Uganda: Entebbe (2002)87||Standard culture methods & direct microscopy.||N/A||Microscopy|
|Zambia: Lusaka (2) (1996)88||N/A||N/A||Light microscopy, electron microscopy and PCR|
|Zambia, Misisi, Lusaka (3) (2009)89||Standard culture methods & direct microscopy.||N/A||Microscopy|
|Central African Republic, Bangui (1998)90||Standard culture methods and disc diffusion technique for antibiotic susceptibility.||Latex agglutination test||Dark-field microscopy with staining|
|South Africa: Venda region (2003)91||Standard culture.||ELISA||N/A|
|Burkina Faso: Ouagadougou (2002)92||Standard culture methods & direct microscopy.||N/A||N/A|
|Kenya 1: Asembo Bay (2006)93||Standard culture and PCR for E. coli sp.||ELISA||Microscopy|
|Kenya 1: Asembo Bay (2003)94||Standard culture methods and disc diffusion technique for antibiotic susceptibility.||N/A||N/A|
Pooled data was analysed using the Comprehensive Meta-analysis programme,95 based on the random effects (RE) model. This model assumes that the impact of covariates capture some but not all of the true variation among effects, hence the RE model is designed to take these differences into account and makes the assumption that the effect size (pooled prevalence) is the mean of the true effect sizes for all studies with a given value of the co-variates.96
Pooled data was stratified by age groups for analysis. Prevalence was reported with 95% confidence interval (CI), and odds ratios (OR) given where applicable. The random-effect method97 was used in meta-analysis and heterogeneity between studies was calculated on the basis of the Cochran's Q-test. Heterogeneity among studies was considered significant if the P value of Cochran's Q-test was less than 0.05. The findings were interpreted in light of current knowledge and practice based on the previously outlined aims of the study.
The initial search identified 198 articles, 66 of which were reviewed for inclusion, with 39 rejected for various reasons (Figure 1 and Table 1). After critical review, 27 articles were selected for this review. The methodology and summary of findings for each study,68–94,98–101 are summarized in Table 2. The studies represented 14 countries in SSA. Different study designs were employed in the studies, including cross-sectional, case control and prospective follow-up cohort designs. The samples were obtained from persons seen in hospitals, primary health care centres or recruited in community cohorts, in urban, peri-urban and rural settings. Seventeen of the studies looked at children, six looked at adults (12–80+ years) and four looked at mixed age groups.
Stool samples were examined using standard parasitological (microscopy or direct observation), bacteriology (cultures), and virology techniques [mainly the enzyme-linked immunosorbent assay (ELISA) for rotavirus screening], presented in Table 3.
Pathogen isolation rates
The rate of isolating pathogens from cases varied widely between countries and between age groups, with an overall isolation rate of 55.7% (95% CI, 48.2–62.9%). Isolation of pathogens was highest amongst adult cases (mean 65.6%; 95% CI, 26.0%–91.2%) followed by children, (mean 58.1%; 95% CI, 50.1–65.6%) and mixed aged groups showed the lowest rates (26.8% (95% CI, 11.3%–51.3%) (Figure 2). Heterogeneity testing suggests slight differences between age groups (Q=5.806; df=2), but this was not significant (P=0.055). Eight studies reported HIV sero-prevalence rates ranging from 10.6%–100% amongst adult participants. When these studies were removed from the analysis the overall isolation rate was not significantly different (54.3%; 95% CI, 43.5%–64.7%). In ten studies where comparable asymptomatic controls were tested, there were significantly more pathogens isolated from cases than controls with a mean overall odds ratio (OR) of 4.93 (95% CI, 1.99–12.23), ranging from 0.52 to 72.05. Very large differences between cases and controls of over 20 times higher isolation rates were observed in Malawi (39), OR 20.52 (95% CI, 2.73–154.24, Nigeria (42), OR 50.0 (95% CI, 16.63–150.36), and Central Africa Rep. (31) OR 72.05 (95% CI, 38.21–135.85).
Etiology data by category was collated from the details reported in each study (Figure 3). Bacterial pathogens (39.82%) were the most common group isolated in a majority of studies followed by parasites (27.11%) and viruses (21.95%).
On average, other diarrheagenic E. coli spp., (29.95%), ETEC (15.37%), Shigella spp. (10.49%), Salmonella spp. (8.36%), and Campylobacter spp. (8.33%), were the most common bacterial pathogens reported by 12, 9, 22, 21 and 17 studies, respectively. Non-cholera Vibrio spp., Staphylococcus aureus and C. difficile were reported by one study each (Table 4).
Rotavirus was by far the most common viral agent isolated in an average of 19.51% of cases, in 13 studies; with nearly half of these studies isolating it from 20% or more of cases (Figure 4). Adenovirus (9.2%) was reported by five studies, while astroviruses (5%) and norovirus (9.5%) were only reported in the Ghana 2005–2006 study. Intestinal parasites were isolated from an average of 25.9% of cases. The enteric protozoa Cryptosporidium spp. (21.52%), Cyclospora spp. (18%), Entamoeba spp. (13.8%), Blastocystis hominis (11.0%) were the most common. Ascaris lumbricoides was the most common helminthic infection reported in an average of 9.14% of cases, while several other pathogenic and non-pathogenic parasites reported in a few studies. In the study from Zambia (1994) which only tested for parasites in HIV positive adults, up to 78% of specimen were positive with a high prevalence of intracellular protozoa (Cryptosporidium parvum, Cystoisospora (isospora) belli and microsporidia).
Diarrhoea continues to affect children and adults in African countries.2,4,11 Increases in diarrhoea rates over the period 1967 to 1997 have been seen in Kenya (6%–18%) and Uganda (16–21%), but reduction seen in Tanzania (11–8%)12 and Malawi (20–14%) from 1992–2000.56 While some countries have attempted to determine the prevalence and etiology of GI, most have looked at single pathogens.102 This review has confirmed and strengthened the view that there is a high rate of illness due to pathogenic enteric microorganisms affecting the region.
Eight of the studies reported HIV seroprevalence rates amongst patients. The HIV sero-prevalence in some SSA countries is high and infected persons may have been included in some studies, but was not reported. All adult studies included HIV positive cases, but when these were removed from the analysis, there was no apparent difference in prevalence. While immuno-compromised persons are more susceptible to diarrhoeal illness, the pathogens are similar to those in immunocompetent persons, with differences mainly seen with opportunistic parasitic infections.87,103,104 Where higher rates are seen in immuno-compromised patients this may be due to the higher likelihood of seeking medical attention for their symptoms, and are more likely to be tested for pathogens.105
Bacteria were the main pathogens identified by a majority of studies, and the high rates of diarrhoeagenic E. coli spp., Shigella, Salmonella spp., and Campylobacter spp., is consistent with the prevailing risk factors,9,11,106,107 and likely reflects the availability of bacteriological diagnostic techniques. Our study like many others confirm that pathogenic E. coli and Shigella dominate in developing countries,68,72,77,108 compared with Salmonella, Shigella, and Campylobacter in industrialized countries.109–111 These pathogens are transmitted through mainly fecal oral route,112–115 and contaminated food or water.115–123 In eleven studies, only one category of pathogen was investigated, which is a limitation of such studies in estimating the overall burden of infectious pathogens.71,72,81,82,84,85,88,92–94,117
Rotavirus was the most common virus isolated and reported in SSA. Worldwide, norovirus, rotavirus, and other caliciviruses represent over 80% of acute GI from known causes, affecting young children and the elderly.107,115,124–127 In both developing and developed countries rotavirus is the leading cause of viral gastroenteritis.68,74,77,108–110 A majority of children become infected with rotavirus by their third birthday,68,76,77,112,125,126,128 with the average age of onset in developing countries being lower than in children in developed countries.112 Waterborne transmission is common, but risk of nosocomial infections in infants and newborns and in childcare settings increases once infection occurs.108,115 The epidemiology of norovirus on the other hand is different as it affects persons of all age groups and has become notorious for causing epidemics on ships, hotels and large gatherings.125,126,129
High rates of parasitic infections have been found in SSA with Cryptosporidium, Cyclospora spp., and Entamoeba spp implicated as common parasites, and is consistent with findings from other developing settings, where sanitation and access to clean water is compromised.25,60,102,130 Blastocystis hominis was frequently isolated from diarrhoeal stools, but there are conflicting views about its role as a pathogen, and some laboratories may not place priority on looking for this parasite.131–133 In addition, limited diagnostic capacity for protozoan pathogens may have influenced what is reported, and the true prevalence may be higher.25,133,134 Advanced biotechnological methods such as PCR will improve the diagnosis and understanding of intestinal parasites.132,134,135 The presence of multiple parasite species is also common and this has further implications for diarrhoea related malnutrition and stunting.23,60,136–138
Prevention and control
Many enteric pathogens are transmitted through similar exposures routes, hence community based multi-stage prevention measures will control several at the same time. Improved sanitation, drinking water quality and hygiene measures have proven to decrease the incidence of diarrhoeal disease by at least 1/3.8,139 There is evidence that hand hygiene alone can reduce incidence by 31–47%,140,141 while low cost household treatment, safe storage and improved water quality can reduce incidence by about 25–35%.139 Except some protozoa, the enteric pathogens are easily controlled by chlorination of water, which can be done at the household level,14,142 supplemented by safe storage and use.139
Public Health significance
The high prevalence of gastrointestinal pathogens in SSA suggests the presence and high risk of exposure to environmental risk factors. Risk factors must therefore be tackled head-on, if countries in SSA are to achieve the target of reducing child deaths by two thirds by the year 2015. Public health programmes must therefore be given priority by governments, with policies supported by sufficiently well trained personnel, modern equipment and legislation. Many countries have the will, but with diarrheal diseases competing with other programmes for scarce resources, the degree of the impact of small interventions can hardly be felt. Currently, less than 5% of funding for research and development goes into diarrhoeal disease.143–145
This review is the first looking at the range of infectious enteric pathogens circulating in SSA, and confirms high rates of isolation of pathogens from diarrhoeal cases; while age related differences were observed and some looked at one category of pathogen, the quality of those included was assured by the peer review process.
Further studies are needed to quantify the prevalence and types of pathogens in circulation in SSA. Public health practitioners can use this information to understanding the challenges related to GI pathogens and set priorities for prevention programmes, and develop multi-stage prevention strategies for increased overall effectiveness.