Avian zoonoses in Somalia: a scoping review of evidence gaps and surveillance challenges (2005-2024)

¹Faculty of Veterinary Medicine, Red Sea University, Galkaio, Somalia, ²Department of Veterinary Medicine, Pan African University Institute of Life and Earth Sciences (PAULES), University of Ibadan, Ibadan, Nigeria, ³Department of Pathobiology, School of Veterinary Medicine, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana, ³Faculty of Health Sciences, Red Sea University, Bosaso, Somalia, ⁴Faculty of Veterinary Science, Benadir University, Mogadishu, Somalia

^&Corresponding author
Rahmo Musse Yusuf, Faculty of Veterinary Medicine, Red Sea University, Galkaio, Somalia

Introduction    

Zoonotic diseases, particularly those originating from avian species, represent a significant and often under-recognized global public health threat. The World Health Organization estimates that zoonoses account for over 75% of emerging infectious diseases, yet surveillance efforts remain disproportionately focused on epidemic-prone pathogens like influenza, leaving critical gaps in understanding endemic avian zoonoses [1,2]. While avian influenza has received considerable global attention, other avian-associated pathogens including Chlamydia psittaci (psittacosis), Salmonella spp, Campylobacter spp and avian paramyxoviruses also pose serious risks to human health [3,4]. These diseases can range from self-limiting gastroenteritis to severe pneumonia and systemic infections, with the greatest burden often falling on vulnerable populations in low-resource settings [5]. Across Africa, several factors such as expanding poultry production, the movement of migratory birds, and poor biosecurity have contributed to the emergence of hotspots for avian zoonotic disease transmission [6]. Countries with robust veterinary and public health systems have reported outbreaks of many avian-associated zoonotic diseases among poultry workers as well as the human populace linked to varied factors, especially the presence of backyard poultry flocks [3,7]. However, there is a glaring lack of data from fragile states, particularly those with underdeveloped health infrastructures [8]. Somalia exemplifies this gap, as its poultry sector is dominated by small-scale, free-range backyard systems [9]. Like many other African nations, poultry production in Somalia is a vital part of the livestock sub-sector, contributing to income generation, employment, food and nutrition security, and women's economic empowerment in rural communities [10].

Poultry keeping is widespread among households in Somalia, and commercial poultry farming is on the rise in urban areas. Most poultry are kept by agro-pastoral and peri-urban households [11,12]. Over 90% of Somalia's poultry sector consists of indigenous chicken breeds raised under extensive systems with minimal biosecurity, often cohabiting with household members [13,14]. Poultry flocks typically range from 5 to 20 birds per household, and scavenging is the primary feeding method, which increases the risk of exposure to wild birds and environmental contaminants [10,12]. Moreover, Somalia's position along the East African-West Asian migratory flyway increases the likelihood of the introduction of novel pathogens. In Somalia, cultural practices such as the consumption of raw eggs and the use of poultry faeces in traditional medicine further elevate the risk of zoonotic transmission [15]. Despite these ecological and behavioural risk factors, Somalia lacks a consolidated and accessible evidence base on avian zoonotic diseases. Existing reports indicate major knowledge gaps in poultry health, disease prevalence, and pathogen distribution [16]. The absence of routine surveillance, limited diagnostic capacity, and sparse peer-reviewed publications highlight an urgent need for a systematic synthesis of available information. This scoping review addresses that gap by examining all published evidence on avian zoonotic diseases in Somalia from 2005 to 2024. Specifically, the review aimed to: i) map the extent, nature, and distribution of published evidence on avian zoonotic diseases in Somalia from 2005 to 2024; ii) identify geographic, pathogen-specific, host-specific, and surveillance-level gaps in the existing evidence base; and iii) provide a foundation for improved One Health strategies and national disease control efforts in Somalia.

Methods     

Study design: this study employed a scoping review methodology following the framework proposed by Arksey and O'Malley [17] and later refined by Levac [18]. The review was conducted and reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) guidelines. This methodological approach was chosen due to its suitability for mapping existing literature, particularly in under-researched or fragmented fields such as zoonotic disease surveillance in fragile states like Somalia.

Eligibility criteria: for the purposes of this review, an "avian zoonotic disease" was operationally defined as any infectious disease caused by a pathogen that has documented or plausible potential for transmission between avian species and humans, based on established scientific evidence. This definition encompassed pathogens with confirmed zoonotic transmission (e.g., Salmonella spp, avian influenza) as well as those classified as having zoonotic potential in standard veterinary and public health literature (e.g., Newcastle disease virus, Escherichia coli). Inclusion was not limited to studies with confirmed human cases; rather, studies documenting pathogen presence in avian populations that represent a recognized interface risk were eligible. Studies and reports were included if they; i) were published between January 2005 and December 2024; ii) reported on one or more avian zoonotic pathogens in Somalia; iii) included either human or avian hosts as part of the transmission cycle, and iv) were written in English. Grey literature, including reports from international organisations (e.g., World Health Organization (WHO), Food and Agriculture Organization (FAO), and the World Organisation for Animal Health (WOAH)), government bulletins, non-governmental organization (NGO) publications) were also considered eligible. Studies were excluded if they; i) lacked geographical relevance to Somalia; ii) focused solely on non-zoonotic avian diseases, or iii) provided insufficient information on pathogen identification or transmission pathways.

Information sources and search strategy: a comprehensive literature search was conducted in the following electronic databases: PubMed, Scopus, Web of Science, and Google Scholar. Additional searches were performed in organizational repositories such as those of the WHO, FAO, and the WOAH. Grey literature was identified through targeted Google searches and manual retrieval from institutional websites and national repositories. The final search was conducted in December 2024. The search strategy combined terms related to zoonotic diseases and avian hosts with terms specific to Somalia and poultry. The full Boolean search string used in PubMed was: (("avian zoonoses" OR "zoonotic disease"OR "avian influenza"OR "Newcastle disease" OR "Salmonella" OR "Campylobacter" OR "psittacosis" "birds"OR "avian" OR "bird-to-human transmission")). Equivalent search strings were adapted for use in Scopus and Web of Science. Grey literature credibility was assessed based on institutional affiliation, relevance to Somalia, and whether the issuing organization (e.g., WHO, FAO, WOAH) was a recognized authority in animal or public health.

Study selection process: all identified records were imported into EndNote reference management software, and duplicates were removed. The selection process followed two screening phases. First, titles and abstracts were independently screened by two reviewers to assess relevance. In the second phase, full texts of potentially eligible studies were retrieved and reviewed in detail against the inclusion criteria. Discrepancies were resolved through consensus, with a third reviewer available for adjudication if necessary. Inter-reviewer agreement was assessed after both screening phases; any disagreements were discussed until consensus was reached, and no formal adjudication by the third reviewer was ultimately required. This review was not prospectively registered in a protocol registry; however, the methodology was pre-specified by the authors prior to data collection. A PRISMA-ScR flow diagram was used to illustrate the study selection process.

Data extraction, charting and analysis: data were extracted using a standardized data charting form developed a priori. Key variables included: author(s), year of publication, type of source (peer-reviewed or grey literature), type of avian pathogen, host species (avian and/or human), geographical location within Somalia, and any identified risk factors or transmission contexts. The data charting process was iterative, with the form refined as new themes emerged during the review process. The extracted data were synthesized using both descriptive statistics and qualitative thematic analysis. The results were organized thematically according to pathogen type, transmission route, and the nature of the reporting source. Tables and summary figures were used to illustrate the distribution of studies over time and by pathogen type. Gaps in surveillance and research were highlighted, with a view to informing national health policy and prioritizing zoonotic diseases for future research and control efforts.

Results     

Overview of included studies: a total of four studies conducted between 2005 and 2024 met the inclusion criteria for this scoping review. The studies were peer-reviewed publications, each documenting the presence of one or more avian zoonotic pathogens in Somalia (Figure 1).

Yearly distribution of publications: it was observed that all four (4) papers identified and included in this review were from 2020 to 2023 (Figure 2).

Types of zoonotic diseases and prevalence: the reviewed studies conducted between 2020 and 2023 provide critical insights into the prevalence of avian zoonotic diseases in Somalia, highlighting a diverse range of pathogens across viral and bacterial categories. Viral infections, particularly Newcastle Disease, were frequently reported, with prevalence ranging from 31.8% to 39.4%, while Avian Influenza was documented at 12.85%. Bacterial pathogens such as Salmonella showed considerable variation, with prevalence rates between 8.9% and 64.9%, alongside Escherichia coli (19.5% and 20.77%) (Table 1).

Geographical distribution and type of avian species regarding zoonotic diseases: the regional analysis of the reviewed studies showed that the Benadir Region had the highest number of studies, with a total of three (3) studies. Lower Jubbada, Bay, and Marodi Jeh each recorded one study, as shown in Figure 3.

Avian species investigated regarding avian zoonotic diseases in Somalia: the reviewed studies consistently focused on poultry as the primary avian species involved in zoonotic disease transmission in Somalia. Most studies investigated indigenous chicken breeds, which are commonly raised under extensive backyard systems, while only two studies included both indigenous and commercial poultry [10,19] (Table 2).

Risk factors for zoonotic transmission: the reviewed studies identified a range of risk factors contributing to the transmission of avian zoonotic diseases across various regions in Somalia. In the Benadir region, several studies reported critical issues, including bird age [20], poor body condition, suboptimal housing and management systems, as well as poor vaccine quality and inadequate hygiene practices on farms. One study highlighted concerns specific to egg handling and the lack of quality control as major contributors to bacterial transmission risks [19]. In Jubbada Hoose and Bay, risk factors were inferred but not distinctly specified [10]. Meanwhile, in the Marodi Jeh region, age and sex of birds were identified as key epidemiological variables [21] (Table 3).

Discussion     

This study focused on reviewing avian zoonotic diseases that have been reported or published in Somalia in the last two decades (2005-2024). The temporal pattern observed in this review, with all four included studies published between 2020 and 2023 despite covering a broader period from 2005 to 2024, reveals a striking gap in the historical attention given to avian zoonotic diseases in Somalia. This recent clustering of research reflects a late but significant shift in national and regional focus toward poultry health and zoonotic disease surveillance. For over a decade, avian zoonoses were largely overlooked in both research and policy domains, likely due to longstanding systemic challenges such as limited veterinary infrastructure, protracted conflict, weak institutional capacity, and inadequate funding mechanisms. Compounding this neglect, Somalia's livestock sector has traditionally prioritized species such as camels, cattle, sheep, and goats, which hold greater economic and cultural value [10], while poultry, mostly reared under traditional backyard systems, received minimal attention [12]. As a result, critical data on poultry disease dynamics and associated zoonotic risks remained undocumented, rendering the sub-sector particularly vulnerable. The emergence of studies from 2020 onwards suggests growing momentum in poultry health research, likely driven by rising urban demand, expanding poultry production, and increased awareness of zoonotic threats under the global One Health agenda in the country [15,16]. Notably, the rise of semi-commercial and commercial poultry enterprises, especially around Mogadishu in southern Somalia, has brought new attention to the health and economic implications of poultry rearing [12,22]. While this trend is promising, the small number of studies underscores that Somalia remains in the early stages of developing a coordinated and evidence-based poultry health surveillance system. Continued progress will depend on sustained investment in research, broader geographic coverage, and the integration of poultry health into national development and public health strategies.

Newcastle Disease Virus (NDV) emerged as the most commonly reported viral pathogen, with prevalence ranging from 31.8% to 39.4%. These findings are consistent with reports from across sub-Saharan Africa, where NDV remains endemic in backyard flocks due to insufficient vaccination, weak cold-chain systems, and limited veterinary outreach [5,23]. The persistent presence of NDV in poultry populations results in high mortality, productivity losses, and economic setbacks, particularly for smallholder farmers who depend on poultry as a primary source of income and nutrition [24]. Although avian influenza was reported less frequently (12.85%), its presence in Somalia is notable given the country's location along the East African-West Asian migratory flyway [25]. This geographic positioning increases the risk of disease introduction via migratory birds, highlighting the importance of long-term, risk-based surveillance, especially in high-risk ecological zones [26,27]. Bacterial pathogens demonstrated a wide range of prevalence values, with Salmonella spp ranging from 8.9% to 64.9%, Escherichia coli reported at 19.5%, and 20.77%. Such variability reflects differences in production systems, biosecurity, and sampling protocols. These results are comparable to findings from poultry farms where Salmonella prevalence was associated with poor sanitation, inadequate waste management, and mixed-species rearing [28,29]. In Somalia, bacterial infections in poultry pose dual challenges: they contribute to productivity losses and serve as potential zoonotic threats to humans through contaminated meat and eggs [15]. This is particularly concerning in urban markets and informal food systems where food safety standards are poorly enforced. Although none of the four included studies directly measured antimicrobial resistance (AMR) prevalence, the widespread empirical use of antibiotics in informal poultry systems raises concerns about AMR as a contextual risk, consistent with patterns documented across low- and middle-income countries [30]. Geographically, the studies were disproportionately concentrated in the Benadir region, with only one study each conducted in Jubbada Hoose, Bay, and Marodi Jeh. This uneven distribution points to a research and surveillance bias toward urban and peri-urban centers, leaving vast rural areas where poultry is extensively kept underrepresented. These data gaps hinder national planning and outbreak preparedness, particularly in a fragile state context where timely interventions are crucial. The review also found that all studies focused on poultry, primarily indigenous chickens reared in backyard systems.

These birds are typically raised in proximity to humans with minimal biosecurity, making them key reservoirs for zoonotic transmission. The inclusion of commercial poultry in two studies reflects a gradual shift toward semi-intensive farming in urban and peri-urban areas. However, in the absence of adequate regulation and disease control, such intensification could lead to higher pathogen loads, faster transmission cycles, and greater economic losses during outbreaks. Common risk factors identified across the studies included the age and physical condition of birds, inadequate housing, poor hygiene, and the absence or misuse of vaccines. One study also highlighted unsafe egg handling and lack of quality control in egg production as major contributors to Salmonella transmission. These findings are supported by regional literature indicating that flock density, contaminated feed and water, and poor waste management are strongly associated with zoonotic pathogen circulation [31,32]. Importantly, these risk factors are all modifiable and thus present strategic entry points for intervention. The implications of these findings are multifaceted. Economically, the presence of documented zoonotic pathogens threatens the viability of Somalia's poultry sector, which plays a critical role in food security, income generation, and women's economic empowerment. Public health risks are equally significant, particularly in urban markets where informal slaughter, poor hygiene, and the sale of unregulated poultry products are common. These conditions create pathways for zoonotic transmission to the human population, increasing the likelihood of localised outbreaks or even larger-scale public health events.

A structured summary of evidence gaps identified by this review is warranted. Geographically, research has been almost entirely confined to the Benadir region, leaving the majority of Somalia's territory, including pastoral and agro-pastoral regions in the south and northwest, with no published data on avian zoonoses. Pathogen-specifically, Newcastle Disease Virus and Salmonella spp. account for almost all reported findings; other recognized avian zoonotic pathogens such as Campylobacter spp., Chlamydia psittaci, and avian influenza subtypes beyond H5N1 remain entirely undocumented in the Somali literature. At the host level, all studies focused exclusively on poultry, with no data from wild birds or migratory species despite Somalia's location on a major flyway. At the surveillance level, no study employed prospective, systematic national surveillance; all were localized cross-sectional studies with heterogeneous designs, limiting temporal and spatial comparability. These gaps collectively represent the most critical priorities for future research and targeted investment in Somalia's One Health infrastructure. This study was limited by the small number of available publications on avian zoonotic diseases in Somalia, which restricts the depth of analysis and may not fully represent the national situation. The included studies were concentrated in only a few regions and used varying methods, reducing comparability and generalizability. Additionally, the scarcity of accessible grey literature and national surveillance reports means some relevant data may not have been captured as they were not available for scrutiny. These limitations reflect broader gaps in Somalia's veterinary and public health reporting systems.

Conclusion     

In conclusion, this study provides a consolidated overview of avian zoonotic diseases reported in Somalia between 2005 to 2024, highlighting the presence of viral and bacterial pathogens with varying prevalence across regions. Newcastle Disease Virus and Salmonella spp. were among the most frequently reported pathogens, predominantly affecting poultry kept under backyard systems. The findings reveal a concentration of research in the Benadir region and underscore significant geographic, pathogen-specific, and surveillance-level gaps. Given that only four studies were identified and these were geographically concentrated, the review does not allow conclusions about the national burden of avian zoonoses. Instead, the primary contribution lies in mapping what is currently unknown, highlighting where surveillance systems are absent or inadequate, and identifying the most pressing research priorities needed to build a reliable evidence base for Somalia. Building on the findings of this review, targeted and coordinated interventions are crucial to reduce the burden of avian zoonotic diseases in Somalia. Expanding national disease surveillance systems is essential to capture accurate data across all regions and enable early detection of outbreaks. Strengthening veterinary infrastructure, particularly through improved access to quality vaccines and trained personnel, will support effective disease control. Enhancing biosecurity and hygiene practices at the farm level, especially in smallholder and backyard systems, can significantly lower the risk of transmission. Equally important is the implementation of farmer education programs to promote awareness and adoption of preventive measures. These efforts should be embedded within a One Health framework to ensure integrated action across human, animal, and environmental health sectors.

Competing interests     

The authors declare competing interests.

Authors' contributions     

All authors made significant contributions to this work. Rahmo Musse Yusuf: conceptualised, analyzed, and interpreted the data regarding the avian zoonotic diseases, and drafted the manuscript. Derrick Adu Asare: conceptualised, extracted the data, reviewed the data, analysed, interpreted the data, and drafted the manuscript. Ahmed Said Mohamud and Omar Harsi Warsame performed technical reviews of the first draft of the manuscript and were major contributors in writing the final manuscript. All authors have read and approved the final version of this manuscript.

Acknowledgments     

The authors of this research want to acknowledge Dr. Farha Isse Mumin for his immense support and contributions in guiding and fine-tuning this research work and its outcome.

Tables and figures     

Table 1: reported avian zoonotic diseases in Somalia by pathogen type

Table 2: avian species investigated in reviewed studies on avian zoonotic diseases in Somalia

Table 3: reported risk factors for avian zoonotic disease transmission by region and study

Figure 1: prisma flow diagram showing the number of publications in Somalia screened, reviewed against the inclusion and exclusion criteria, and selected for data extraction on avian zoonoses

Figure 2: distribution of studies focused on avian zoonotic diseases according to years

Figure 3: map of Somalia showing geographical distribution of studies focused on avian zoonotic diseases according to regions

References