Although rates have decreased in middle-income and wealthy nations, shigellosis remains a major public health problem in impoverished settings because of sub-optimal sanitation and hygiene and contaminated water supplies [1], [2], [3]. Annually, Shigella is responsible for >160 million infections in developing countries with an estimated 1.1 million deaths [3]. Most deaths occur in children <5 years of age [3]. Humans are the only natural hosts of Shigella. Persons with diarrhea are primarily responsible for transmission [4], which occurs predominantly through the faecal-oral route via direct contact, fomites, or contaminated food and water [5]. The low infectious dose (as few as 10 organisms) renders Shigella highly infectious [5]. When human feces are not properly disposed of, common houseflies, particularly Musca domestica, may serve as vectors for transmission [6].

Symptoms of shigellosis typically include diarrhea and/or bloody stools with abdominal cramps and tenesmus [7]. Antimicrobial drugs shorten duration of illness and bacterial shedding, and decrease morbidity and mortality [8]. Antimicrobial resistance among Shigellae is increasing worldwide [9], [10], [11], [12]. In sub-Saharan Africa, repeated prolonged outbreaks of drug-resistant Shigella have reduced antimicrobial therapeutic options and increased cost of therapy [13].

Previous estimates of the burden of shigellosis in developing countries may have underestimated its magnitude. Studies present varying incidence and prevalence rates, because of divergent methods and intrinsic disparities among the populations studied [2], [14], [15], [16]. Rapid urbanization in Africa and Asia has increased the number of residents of informal settlements who lack access to basic sanitation and safe drinking water. Continued urbanization in Africa will likely contribute to an even greater burden of enteric diseases including shigellosis.

Since 2005, the Centers for Disease Control and Prevention (CDC) and the Kenya Medical Research Institute (KEMRI) have maintained population-based infectious disease surveillance (PBIDS) in a geographically defined area within an urban informal settlement in Nairobi, Kenya [17], [18]. We used systematically collected data from PBIDS to define the incidence and characterise the epidemiologic, clinical, and microbiologic features of shigellosis within this population.

Our study revealed a high burden of shigellosis within a densely populated urban slum in Kenya. The high crude incidence of shigellosis of 0.29% was slightly higher than that reported in a multicenter population-based study done in six developing countries in Asia; three of the sites were rural/semi rural (in China, Thailand, and Vietnam) and three of the sites were in urban slums (in Bangladesh, Indonesia, and Pakistan), where the overall unadjusted incidence of Shigella in this multicenter study was estimated at 0.2% among patients of all ages [27]. The rates were much higher than that seen in industrialized countries such as the UK and US where the incidence of shigellosis is estimated at 0.027% and 0.0038% respectively [28], [29].

In our study, over 20% of all stool samples yielded Shigella, further confirming the high burden of shigellosis. Similar estimates in other urban slums in Kenya are lacking. However, two studies performed in rural western Kenya also found high Shigella isolation rates of 15% and 16% of stool samples collected from patients presenting with diarrhea or dysentery [30], [31]. While we documented high rates of shigellosis in an urban slum, we do not have conclusive evidence indicating that rates were higher than in rural areas. However, high population density coupled with grossly inadequate sanitary facilities and unregulated water connections with high likelihood of contamination may contribute to the high incidence of shigellosis in this urban slum site.

As expected, patients presenting with dysentery were more likely to have Shigella isolated from stool than patients presenting with non-dysenteric diarrhea [30]. Like in other studies [3], [32], [33], [34], we found relatively low incidence of shigellosis among infants. This may be partially explained by passive induced immunity conferred by breastfeeding, as seen in a study conducted in Dhaka, Bangladesh [34], but may also result from fewer opportunities for exposure to contaminated food or water sources, especially when compared with toddlers. According to the Kenya demographic and health survey, 2008–2009, the mean duration of breastfeeding among Kenyan children is 21 months. It is possible that majority of mothers in our setting breastfed for a period of at least 1 year. Our findings of lowest incidence of shigellosis in people ≥50 years old are also consistent with other studies; while unexplained, it may relate to acquisition of protective immunity or, perhaps, to safer hygiene and/or food preparation practices.

Females in the 35–49 year age group had a higher incidence of shigellosis, than males in the same age group. It is not clear why women in this age group were at increased risk of being infected with Shigella; however, it is conceivable that they had a greater risk of being infected by young children.

Our adjusted rates suggest that over 0.4% of people living in urban slum settings are stricken with shigellosis annually. Like other developing countries, Kenya is experiencing rapid urbanization (>3%/year) and migrants from rural to urban areas tend to settle in slums [35]. Extrapolating population-based incidence rates presented in this paper to the estimated 4.3 million Kenyans living in urban informal settlements similar to Kibera [25], we estimate that over 17,000 cases of shigellosis occur in Kenyan urban slums each year. Easy access to high quality health care and a relatively small surveillance population likely account for the occurrence of only one death related to shigellosis during the study period. However, given global estimates of shigellosis-associated case-fatality rates of 0.67% [3], it is reasonable to assume that approximately 117 deaths from Shigella may occur annually in Kenyan urban slums.

As in other developing countries S. flexneri was the most common species of Shigella identified in our study population [3]. While this information is important in guiding vaccine development, further subtyping is necessary to identify the most common serotypes.

Shigella was isolated throughout the year. This may be explained by the lack of adequate sanitary facilities and raw sewage flowing all year round in open drainage channels to which children are exposed potentially providing constant exposure to Shigella.

Many of the Shigella isolates were resistant to commonly available and affordable antibiotics, consistent with findings of previous studies from Africa [30], [36], [37], [38], [39]. Nearly all isolates were susceptible to ceftriaxone, nalidixic acid and ciprofloxacin. While current susceptibility to fluoroquinolone drugs is reassuring, rapid emergence of nalidixic acid and ciprofloxacin resistance elsewhere [10], highlights the importance of judicious use of these drugs to preserve their effectiveness for treating severe shigellosis and other life-threatening infections. Surveillance during the same study period in Kibera has shown emergence of nalidixic acid-resistant Salmonella strains [18], [40], which likely heralds decreased utility of fluoroquinolones for treating invasive salmonellosis [41].

While this study was unique in terms of its active surveillance for shigellosis and for providing reliable basis for rate adjustments, limitations may have led to underestimates or overestimates of the burden of disease. Because of transport requirements to the Kisumu laboratory, some stool specimens were processed >24 hours after collection. Cary-Blair solution preserves viability of Shigella [42]; however, ideally specimens should be processed within 6 hours of collection. Thus, there may have been loss of viable Shigella during shipping and storage.

In calculating, adjusted incidence rates, we assumed that persons with diarrhea who reported visiting any clinic had similar shigellosis incidence rates as those seen in the study field clinic. This assumption could be erroneous if there was a systematic bias in which persons with shigellosis tended to go to the designated study clinic at different rates than persons with other causes of diarrhea or dysentery. We believe that use of non-study field clinics occurred primarily because the study clinic was open only Monday-through-Friday during daylight hours; thus, we do not think that there would be intrinsic biases in the way we adjusted the incidence rates. We did not adjust the incidence rates based on the proportion of patients who met the case definition and did not provide a stool specimen. This is because a relatively small proportion of patients meeting our diarrhea case definitions provided stool specimen, which would have made further adjustments imprecise, potentially exaggerating the adjusted incidence rates. On the other hand, opting not to make this adjustment likely led to underestimation of incidence rates. In addition, patients with dysentery were more likely to provide a stool sample for culture and sensitivity studies compared to patients presenting with non-bloody diarrhea. This led to a higher adjustment factor among patients with diarrhea (without dysentery), which may over estimate the burden of shigellosis in this category of patients.

Drinking water, sanitation, and hygiene improvements within the rapidly multiplying and expanding informal settlements in Kenya, and elsewhere in Africa, are needed to reduce the risk of shigellosis and other enteric infections. Health education, including a focus on hand washing with soap, provision of safe drinking water and proper waste disposal are feasible strategies for containing the burden of shigellosis [43]. Given the slow progress of improving living conditions in informal settlements, these high incidence rates highlight the need to hasten the development of effective vaccines to control shigellosis in resource-limited settings.