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Water SA

versión On-line ISSN 1816-7950
versión impresa ISSN 0378-4738

Water SA vol.44 no.3 Pretoria jul. 2018


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Received 21 September 2016
Accepted in revised form 9 October 2017



* To whom all correspondence should be addressed. e-mail:





Table A1 - Click to enlarge



Table A2 - Click to enlarge

^rND^sBÉGA^nS^rND^sBÉGA^nS^rND^sBREDENKAMP^nDB^rND^sDURAND^nJF^rND^sDURAND^nJF^rND^sMEEUVIS^nJ^rND^sFOURIE^nM^rND^sERIKSSON^nPG^rND^sRECZKO^nBFF^rND^sERIKSSON^nPG^rND^sALTERMANN^nW^rND^sHARTZER^nFJ^rND^sFLOREA^nLJ^rND^sVACHER^nHL^rND^sGROENEWALD^nY^rND^sHAMILTON-SMITH^nE^rND^sHOBBS^nPJ^rND^sMILLS^nPJ^rND^sKLIMCHOUK^nA^rND^sMARTINI^nJEJ^rND^sMARTINI^nJ^rND^sKAVALIERIS^nI^rND^sMARTINI^nJEJ^rND^sWILSON^nMGC^rND^sMASONDO^nM^rND^sROBB^nLJ^rND^sROBB^nVM^rND^sSECCOMBE^nA^rND^sWELLS^nJD^rND^sVAN MEURS^nLH^rND^sRABIE^nGF^rND^sMOIR^nF^rND^sRUSSELL^nJ^rND^sWHITE^nWB^rND^1A01 A02^nSylivia^sNabateesa^rND^1A01^nAhamada^sZziwa^rND^1A01^nIsa^sKabenge^rND^1A01^nRobert^sKambugu^rND^1A01^nJoshua^sWanyama^rND^1A01^nAllan John^sKomakech^rND^1A01 A02^nSylivia^sNabateesa^rND^1A01^nAhamada^sZziwa^rND^1A01^nIsa^sKabenge^rND^1A01^nRobert^sKambugu^rND^1A01^nJoshua^sWanyama^rND^1A01^nAllan John^sKomakech^rND^1A01 A02^nSylivia^sNabateesa^rND^1A01^nAhamada^sZziwa^rND^1A01^nIsa^sKabenge^rND^1A01^nRobert^sKambugu^rND^1A01^nJoshua^sWanyama^rND^1A01^nAllan John^sKomakech

Occurrence and survival of pathogens at different sludge depths in unlined pit latrines in Kampala slums



Sylivia NabateesaI, II; Ahamada ZziwaI, *; Isa KabengeI; Robert KambuguI; Joshua WanyamaI; Allan John KomakechI

IDepartment of Agricultural and Bio-systems Engineering, Makerere University, P.O. Box 7062, Kampala, Uganda
IINational Water and Sewerage Corporation. PO Box 7053, Kampala, Uganda




Occurrence and survival of pathogens in faecal sludge was investigated in unlined pit latrines at varying depths in peri-urban areas of Kampala city, Uganda. A total of 55 unlined pit latrines, 7 private and 8 rental unlined pit latrines were sampled in the first and second phases (representing the rainy season) and 40 pits in the third phase (representing dry season), and analysed for indicator organisms and pathogens from 4 pit latrine sludge layers, at depths of 0, 0.5, 1.0 and 1.5 m, following APHA standard methods. Physico-chemical parameters of the faecal sludge were also measured. Three sampling phases were undertaken to determine the effect of seasonal variation. Results indicate that the mean temperature and pH were 25.4 ± 1.14°C and 8.0 ± 1.5, respectively; and moisture content increased with pit sludge depth, except between Depths 3 and 4. Average moisture content was 86.3 ± 3%. The measured parameters varied significantly (P > 0.05) between seasons. The mean reduction in total coliforms, thermo-tolerant coliforms, E. coli, and faecal enterococci with sludge depth was significant at all depths (P < 0.05), but the least significant difference was not significant at depth levels of 1.0 m and 1.5 m. Salmonella was only detected at the top layer of faecal sludge in 60% of Phase 2 samples and in only 20% of the samples in Phase 3. About 200-4 100 eggs/g of strongyles were found in 98% of the samples and 100-1 600 eggs/g of ascarids in 55% of the samples. Temperature, pH and moisture content did not show a significant correlation with observed reductions of indicators and pathogens. With extrapolation of the generated regression models, a pit of 8 m can be recommended for reduction of bacteria. It is recommended that protective field gear be used during pit emptying and that faecal sludge treatment should be done to reduce pathogens before disposal into the environment.

Keywords: pathogens, indicator organisms, faecal sludge, unlined pit latrine, water contamination




Access to appropriate sanitation facilities is a major global challenge today, with over a third of the world's population still lacking access to improved sanitation (WHO and UNICEF, 2015). Uganda has a population of 34.5 million, growing at an estimated rate of 3.25% per annum (UBOS, 2014). Kampala, Uganda's capital city, hosts a third of the country's urban population (Trading Economics Statistics, 2012). Kampala, being an urban agglomeration with a daytime population of over 2.5 million people (UBOS, 2014), suffers health and environmental problems related to the increasing population pressure. In the peri-urban communities with informal settlements, land is subdivided into very small plots of less than 300 m2, leading to several households sharing pit latrines of shallow depths owing to limited space. It has also been reported that some on-site sanitary interventions have become a threat to groundwater-derived domestic supplies, mainly because of pollution and contamination (Sorensen et al., 2016). This is also the case in Kampala slums, with inadequate water and sanitation facilities resulting in people using poorly-constructed shared pit latrines which are a pollution risk to groundwater, especially where the water table is high. Hence poor sanitation and faecal sludge management have negative impacts on human health through contamination and pollution of water sources and food sources (Rose et al., 2015). The risk of groundwater contamination is even higher in the densely populated areas (Dzwairo et al., 2006). This has resulted in water and sanitation related diseases being among the top 10 killers in Uganda, especially in urban informal settlements (Kibikyo and Kakembo, 2010), and this has been partly attributed to use of contaminated groundwater.

It is evident that access to effective sanitation in Kampala is limited and it does not cope with urbanization and industrial development in the city. Less than 8% of Kampala residents are currently served by the public sewer system (African Water Facility, 2012) with the majority relying on various forms of on-site sanitation - that is 51.7% use septic tanks while 38.2% rely on pit latrines (Zziwa et al., 2014). The situation is compounded by weak national policies and regulatory frameworks regarding faecal sludge management, a common feature in most sub-Saharan African countries (Holm et al. 2015).

Pit latrines are used as anaerobic accumulation systems for stabilizing faecal matter, urine and other added materials (Chaggu, 2004), but they also serve as containment for digestion of fresh faeces and storage of the digested faecal solids (Mara, 1996). In addition, pits fill at different rates owing to user diets and behaviour (Brouckaert et al., 2013). For instance, most pits in Kampala double as faecal and waste disposal points. Due to the functionality of on-site sanitation facilities, there is a challenge of pit latrines filling prematurely; yet the limited size of residential plots, particularly in Kampala, does not allow for a new pit to be dug (Zziwa et al., 2016).

This scenario necessitates emptying of the existing pits and finding safe means of disposing of the sludge (Yoke et al., 2009). However, the emptying and disposal of pit sludge has become a challenge, partly due to the congestion of slum settlements, inaccessibility of residences due to poorly-planned access-road networks and unplanned sanitation systems (Thye et al., 2009; Radford and Fenner, 2013). The most common practice is disposal of the sludge to wastewater treatment plants using vacuum trucks. However, introduction of pit sludge into wastewater works and waste stabilization ponds increases the risk of wastewater treatment plant failure. The fact that pit latrines display incomplete anaerobic digestion (Nwaneri, 2009), the non-homogeneity in pits within the same locality and incomplete pathogen die-off (Buckley et al., 2008), imply that there are still water- and sanitation-related challenges which necessitate scientific research and development. Investing in and developing scientific research in pit latrine content characterization is therefore a pivotal contribution towards sustainable handling and disposal of sludge. Therefore, this paper investigated the factors which influence safe pit latrine emptying, particularly the occurrence and survival of pathogens at different sludge depths in unlined pit latrines of Kampala slums.



Description of the study area

Kampala is located on hilly terrain at an altitude of about 1 300 m amsl, on the north shore of Lake Victoria, and receives a mean annual rainfall of 1 200 mm. The climate is tropical wet (April to June and September to December) and dry (January to March and July to August) (UN-Habitat, 2010). The topography of the city is characterized by a series of low-lying hills with flat hilltops. These hills are surrounded by a network of wetlands which have been developed into informal settlements. As a consequence, these areas have no access to the central sewerage system and thus experience many sanitation challenges. Sanitation-related diseases such as diarrhoea, dysentery and cholera are common in the area, with the highest prevalence occurring in children below 5 years (Katukiza et al., 2010). However, these opportunistic diseases could be prevented with good hygiene and sanitation practices (Kulabako et al., 2010). Administratively, Kampala is divided into 5 divisions: Kawempe, Rubaga, Makindye, Nakawa and Central (Fig. 1).

Study design

This study was carried out in 3 phases to capture the impact of season on the parameters investigated. A total of 15 unlined pit latrines were sampled in the rainy season and 40 in the dry season. In September 2014 (first phase), 15 unlined pit latrines were selected and sampled: 8 rental pit latrines (single pit used by several households but limited to only those households) and 7 private pit latrines (used by single household). This number of latrines was adopted from previous studies by Nwaneri, (2009), Buckley et al. (2008) and Bakare et al. (2012), who characterized pit latrine sludge from 16 lined and unlined pit latrines. To make a comparison within the season, these same pit latrines were re-sampled in December 2014 (second phase). The average monthly rainfall between September and December 2014 was 84.4 mm (Accessed at In February and March 2015 (Phase 3), 40 more pit latrines were sampled to make a total of 55 unlined pit latrines. The average monthly rainfall between February and March 2015 was 39.4 mm (Accessed at The sampled pit latrines were located in low-lying areas of Kampala ( 1 200 m amsl) because it is these areas that face the biggest challenge with sanitation.

Sample collection

Ethical clearance and research approval were obtained from Kampala Capital City Authority and Uganda National Council for Science and Technology prior to sample collection. Samples were collected from slums most affected with sanitation challenges at spatially distributed locations within Kampala (Fig. 1). A specially designed sludge sampler (Fig. 2) was used to collect sludge samples. Four samples were collected from each pit latrine at four sludge depths (0.0 m, 0.5 m, 1.0 m, and 1.5 m). Temperature and pH of samples were determined on-site by inserting the probe into the sample immediately after sampling. Samples were wrapped in black polyethylene bags to mimic dark conditions of a pit latrine and later put in a portable ice chest for transportation to the laboratory. Samples were tested within 1 day after sampling to avoid re-growth of some bacteria (Sherpa et al., 2009).



Physico-chemical parameters

The physico-chemical parameters measured in this study were temperature, moisture and pH, because these are the major determinants of pathogen survival. Temperature and pH readings were taken at the time of sample collection for each layer using a digital pH meter (HI 98128 Hanna Instruments Limited, Bedfordshire, UK). Moisture content was determined using the oven-dry method following APHA (1999).

Indicator organisms and pathogen analysis

Total coliforms (TC), thermo-tolerant coliforms (TTC), E. coli, faecal enterococci and Salmonella were determined to infer bacterial pathogen die-off patterns in pit latrine sludge. From a well-homogenized sample, 5 g was weighed into a sterile stomacher and 45 mL of peptone water was added and blended. Serial dilutions up to 106 were performed. E. coli and TC were cultured on chromocult coliform agar (CCA, Merck Dermstadt, Germany), and enterococci on Slanetz and Bartley agar (Oxoid, England), thermo-tolerant coliforms on violet red bile agar (Pronadisa, Spain), and Salmonella on xylose lysine dextrose (XLD) agar. Enumeration of E. coli, TC, TTC, enterococci, and Salmonella colonies was performed according to Byamukama et al. (2005). For Salmonella, bio-chemical tests were performed; 5 g of pit sludge was weighed from a well-mixed sample using an analytical balance and transferred to 45 mL of peptone water in a stomacher for blending and incubated at 37°C for 24 h. On Day 2, 1 mL from the pre-enriched sample was transferred to 9 mL of Selenite Broth at 42°C for 24 h.

On Day 3, a loop full was striped on the XLD agar and incubated at 37°C for 24 h and formed pink colonies with a dark centre. On Day 4, biochemical tests were performed with urease while on Days 5 and 6; TSI and citrate were used. Urea agar slant (slope) was inoculated and incubated at 37°C for 1-4 h following APHA (1999). The urease-negative samples were inoculated on TSI slant and on Day 5 incubated at 37°C for 24 h, and thereafter inoculated on citrate. Helminth ova were determined following criteria used by Hawksworth et al. (2005). Approximately 3 g of faecal sludge was weighed and dissolved into 45 mL of distilled water in a beaker. The solution was filtered using a sieve to make a filtrate into a 45 mL conical centrifuge tube. The tube was then centrifuged at 2 000 r/min for 2 min and the supernatant discarded. The sediment was topped up with a saturated solution of sodium chloride to the mark of 45 mL while vortexing. The saturated solution of sodium chloride has a high specific gravity which allows all of the viable eggs to float. The solution obtained was pipetted onto a MacMaster microscope slide for examination using the compound microscope at objective magnification 10 and the eggs were counted.

Statistical analysis

GenStat Discovery Edition 4 was used for statistical analysis. One way analysis of variance (ANOVA) was used to determine the statistical differences in the concentration of various parameters in the pit latrine sludge at different depths at a 95% confidence level. Following analysis of variance, multiple comparisons using least significant difference (LSD) were done to establish which parameters were significantly different based on the LSD. The correlation between the physico-chemical properties and the bacterial load reduction was also established. Linear regression of log-transformed data for the bacterial load was also performed to show the trends of reduction in bacteria.


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