Vegetable farming plays an important role in urban and peri-urban food systems in West Africa, contributing to the supply of fruits and vegetables, income generation, and food security. However, the intensification of vegetable production is associated with constraints related in particular to access to good-quality irrigation water, sanitation, organic waste management, and the use of inputs of animal origin. These factors may promote the introduction and circulation of pathogenic microorganisms in production environments.

Fruits and vegetables are an essential component of a healthy diet because of their richness in vitamins, minerals, fiber, and other bioactive compounds. However, when consumed raw or minimally processed, they may serve as vehicles for the transmission of microorganisms of fecal origin. Recent FAO and WHO reports emphasize that fresh plant products are regularly implicated in foodborne disease outbreaks and that the control of microbiological hazards should begin at primary production. Key factors to consider include water quality, organic soil amendments, animal and human intrusion, production-site characteristics, as well as harvesting and handling practices [1].

Water used for irrigation is therefore a determining factor in the microbiological safety of vegetable production. Surface water, runoff water, well water, and other water resources may be exposed to various sources of contamination, including animal and human feces, wastewater, and runoff from residential or livestock areas. FAO and WHO therefore recommend a fit-for-purpose approach to water use and the assessment of the microbiological quality of the different water sources used during production [1].

This issue is particularly important in vegetable-growing systems where water resources are limited. Recent international recommendations consider irrigation water as a potential route for the introduction of enteropathogenic bacteria, particularly Salmonella spp. and Shigella spp., into the production environment. The Codex Alimentarius also emphasizes that water may act as a source of microbiological contamination at different stages of fresh produce production, particularly during irrigation, application of water-soluble fertilizers, harvesting, and post-harvest operations [2].

Runoff water deserves particular attention because it may facilitate the transfer of microorganisms present in soil, animal or human fecal matter, and waste into watercourses and agricultural plots. Changes in land use and climate change may also modify runoff, infiltration, and the transport of microbiological contaminants. In this context, monitoring the quality of water resources used for irrigation is an essential component of contamination prevention in vegetable production systems.

In addition, organic fertilizers of animal origin, particularly poultry manure, cattle manure, compost, and humus, may constitute potential reservoirs of enteric microorganisms when they are insufficiently treated or composted. FAO and WHO recommend appropriate treatment of fecal waste, including composting, before its use as organic fertilizer, as well as limiting contact between contaminated amendments and edible parts of plants [1].

Microbiological contamination of plant products therefore results from complex interactions among water quality, soil characteristics, organic amendments, animals, climatic conditions, and agricultural practices. Recent evidence shows that Salmonella can persist in different environmental compartments and that its survival and transmission to plants depend, among other factors, on environmental conditions, plant characteristics, and production practices [3]. A recent meta-analysis of commercially marketed fresh fruits and vegetables further confirmed the persistence of Salmonella as an important food-safety concern and identified irrigation water quality and environmental conditions among the factors associated with its presence. The serotypes S.typhimurium and S.enteritidis were among those most frequently reported [4].

In the Guinean context, recent data also indicate that microbiological contamination of water resources is a concern in Kindia Prefecture. A study published in 2025 on bathing waters in Kindia detected Salmonella spp. at several sites and identified runoff, agriculture, livestock farming, waste, and wastewater as potential sources of environmental contamination [5]. Another recent study conducted in N’Zérékoré highlights the importance of assessing the quality of water used for irrigation of vegetable crops and the need for regular microbiological monitoring [6].

In Kindia, a recent study on the contamination of fruits and vegetables also reported the presence of Salmonella in vegetable products and highlighted the potential role of irrigation water and insufficiently composted organic fertilizers. However, this study specified that the associations between these factors and product contamination had not been subjected to specific statistical analysis [7]. The present manuscript specifically analyzes the “irrigation water” and “organic fertilizer” components of a broader sampling campaign that also supported the study of contamination of vegetable products in Kindia. This work addresses a distinct scientific question by characterizing the detection frequency, distribution according to matrices, and serotypes of Salmonella and Shigella in agricultural inputs.

Accordingly, the present study aimed to assess the microbiological contamination of irrigation water and organic fertilizers used in vegetable farms in Kindia Prefecture by Salmonella spp. and Shigella spp. More specifically, it sought to determine the contamination frequency of different irrigation water sources and different types of organic fertilizers, as well as to identify the Salmonella serotypes and Shigella species/taxa present in these matrices.

As shown in Table 1, a total of 1073 samples were analyzed, including 577 irrigation water samples (53.77%) and 496 organic fertilizer samples (46.23%).

Table 1. Distribution of Samples according to the matrix studied.

As shown in Table 2, among the 577 irrigation water samples analyzed, 68 were positive for Salmonella spp., corresponding to a prevalence of 11.79% (95% CI: 9.40 - 14.67). Shigella spp. was detected in only one sample, corresponding to a prevalence of 0.17% (95% CI: 0.03 - 0.98). Overall, 69 samples were positive for at least one of the two bacterial genera, corresponding to an overall prevalence of 11.96%.

Table 2. Prevalence of Salmonella and Shigella in irrigation water.

As shown in Table 3, among the 496 organic fertilizer samples analyzed, 59 were positive for Salmonella spp., corresponding to a prevalence of 11.90% (95% CI: 9.33 - 15.04). No sample was positive for Shigella spp.

Table 3. Prevalence of Salmonella and Shigella in organic fertilizers.

Analysis of the different types of organic fertilizers showed that compost had the highest observed detection frequency of Salmonella (15.07%), followed by cattle manure (12.50%), humus (10.09%), and poultry manure (9.94%). No organic fertilizer sample was positive for Shigella spp. (Table 4).

Table 4. Detection frequency of Salmonella and Shigella according to the type of organic fertilizer.

The prevalence of Salmonella spp. was highest in runoff water (15.94%), followed by river water (11.64%), dam water (10.00%), streams (8.94%), and well water (6.17%) (Table 5).

Table 5. Detection frequency of Salmonella according to irrigation water source.

This descriptive distribution indicates a higher detection frequency in runoff water than in the other sources studied. Well water had the lowest prevalence among the sources investigated.

Serotyping of the isolates identified 128 bacterial isolates, including 127 Salmonella spp. isolates and one Shigelladysenteriae type 1 isolate. These isolates originated from 128 positive samples among the 1073 samples analyzed, corresponding to an overall prevalence of 11.93% (Table 6).

Table 6. Distribution of Salmonella serotypes and Shigella according to sample type.

The predominant serotype was Salmonellaenteritidis, with 75 strains, representing 6.99% of the samples analyzed and 58.59% of the isolated strains. It was followed by Salmonellatyphimurium, with 49 strains, corresponding to 4.57% of the samples analyzed and 38.28% of the isolates. Salmonellatyphi was detected in only three irrigation water samples, representing 0.28% of the samples analyzed and 2.34% of the isolates. Only one strain of Shigelladysenteriae type 1 was isolated from irrigation water, corresponding to 0.09% of the samples analyzed and 0.78% of the isolates.

Irrigation water accounted for 69 samples positive for Salmonella spp. and/or Shigella spp. (11.96%), compared with 59 positive samples among organic fertilizers (11.90%). The isolates were predominantly represented by S.enteritidis (58.59%) and S.typhimurium (38.28%), whereas S.typhi and Shigelladysenteriae type 1 accounted for 2.34% and 0.78% of the isolates, respectively. S.typhi and Shigelladysenteriae type 1 were detected exclusively in irrigation water, whereas S.enteritidis and S.typhimurium were found in both matrices studied.

The prevalence of Salmonella observed in irrigation water was 11.79%, highlighting a non-negligible level of microbiological contamination in this matrix. This observation is consistent with studies reporting that water used for irrigation can constitute a route for the introduction of enteropathogenic bacteria into vegetable production systems [6]. The presence of Salmonella in irrigation water therefore highlights its potential role as a source of exposure for crops, particularly when the water comes into direct contact with edible plant parts. However, since the present study did not investigate vegetable products, the transfer of Salmonella from water to vegetables cannot be directly established.

Contamination of organic fertilizers was also substantial, with a Salmonella prevalence of 11.90%. The bacterium was detected in all four types of fertilizers studied: compost (15.07%), cattle manure (12.50%), humus (10.09%), and poultry manure (9.94%). This distribution indicates that different organic matrices used in vegetable farming may constitute potential sources of microbiological contamination. These findings are consistent with those of [12], which emphasize the importance of treatment, storage, and handling practices for organic amendments in controlling bacterial contamination. However, since the degree of composting or hygienization of the fertilizers was not assessed in our study, it is not possible to directly attribute the observed contamination to inadequate treatment.

The prevalence of Salmonella varied according to the irrigation water source. Runoff water had the highest prevalence (15.94%), followed by river water (11.64%), dam water (10.00%), streams (8.94%), and wells (6.17%). The higher frequency observed in runoff water could be explained by its direct exposure to runoff from different areas of the watershed, which may transport microbiological contaminants originating from domestic, agricultural, or livestock activities [2]. However, this interpretation remains hypothetical because the specific sources of contamination were not characterized in the present study. Similarly, the lower prevalence observed in well water does not allow us to conclude that there is less fecal contamination in the absence of measurements of specific microbiological indicators.

Serotyping revealed a predominance of Salmonellaenteritidis, with 75 isolates representing 58.59% of the 128 isolates obtained, followed by S.typhimurium with 49 isolates (38.28%). S.typhi accounted for 2.34% of the isolates (3/128), while a single strain of Shigelladysenteriae type 1 was identified, representing 0.78%. The predominance of S.enteritidisand S.typhimurium is consistent with their frequently reported importance in food contamination and agricultural environments [4]. The presence of these serotypes in irrigation water and organic fertilizers highlights their circulation within the matrices studied. However, in the absence of molecular characterization and analyses capable of tracing contamination sources, the animal, human, or environmental origin of the isolates cannot be established with certainty.

Overall, the detection of Salmonella in irrigation water and organic fertilizers demonstrates the presence of this bacterium in two important matrices of vegetable production systems in Kindia Prefecture. These findings highlight the need to strengthen microbiological monitoring of irrigation water and improve the treatment, storage, and handling practices of organic fertilizers. Further studies incorporating microbiological analysis of vegetable products, molecular characterization of isolates, and assessment of seasonal variations would help better determine contamination pathways and estimate the potential risk to consumers.

The purposive selection of sites limits the generalizability of the results to all vegetable farms in Guinea.The study was conducted in only one prefecture.There was no additional molecular characterization of the isolates, particularly for genetic typing and analysis of phylogenetic relationships.No specific indicator of fecal contamination, particularly E.coli, was measured.Other enteric pathogens (E.coli O157, Campylobacter, Listeria) were not investigated.Although the study period covered part of both the rainy and dry seasons, no season-stratified analysis was performed.No quantitative health risk assessment for consumers was conducted.The degree of maturation, composting, or hygienization of the fertilizers was not documented.

The results of this study demonstrate the detection of Salmonella and/or Shigella in some of the irrigation water and organic fertilizers used on the market garden holdings surveyed. Runoff water showed the highest detection rates among the irrigation sources examined, while the use of inadequately treated poultry manure was identified as a potential source of microbial hazards. These findings indicate that certain production inputs may constitute reservoirs of enteric pathogens and therefore represent potential upstream sources of contamination within the production environment.

However, the detection of pathogens in irrigation water or organic fertilizers does not, in itself, demonstrate their transfer to the surfaces or internal tissues of vegetables. Nor does it establish the magnitude of contamination of harvested produce or provide a direct estimate of the microbiological or health risk to consumers. Demonstration of such transfer and assessment of consumer health risk would require direct microbiological examination of the vegetables, together with information on pathogen concentrations, environmental persistence, irrigation and harvesting practices, post-harvest handling, and the amount of contaminated produce potentially consumed.

Accordingly, the findings should be interpreted primarily as evidence of the presence of potential microbial hazards in production inputs, rather than as evidence of confirmed contamination of vegetables or demonstrated illness risk among consumers. Nevertheless, the presence of these pathogens in inputs provides a scientific basis for preventive measures aimed at reducing the possibility of their transfer to crops and limiting potential downstream exposure.

The results therefore support the strengthening of preventive agricultural hygiene measures, particularly the improvement of irrigation-water quality and the proper treatment and management of organic fertilizers. Routine monitoring of relevant production inputs, combined with training in Good Agricultural Practices (GAP), may help reduce the occurrence of microbial hazards at the production stage. Future studies should include direct microbiological testing of vegetables and, where appropriate, quantitative assessment of pathogen levels and exposure pathways in order to determine whether contamination of produce occurs and to better characterize any associated consumer health risk.

Based on the findings of this study, the following recommendations are proposed primarily to control potential microbial hazards identified in production inputs and to prevent their possible transfer to fresh produce. These recommendations should not be interpreted as evidence that contamination of vegetables or adverse health effects in consumers were demonstrated by the present study.

Conceptualization: BAH Mariama, KOLIÉ Bonaventure, DIALLO Souleymane, BAH Boubacar Sidy Sily.

Data curation: BAH Mariama, KOLIÉ Bonaventure.

Formal analysis: BAH Mariama, KOLIÉ Bonaventure, DIALLO Souleymane.

Investigation: BAH Mariama, KOLIÉ Bonaventure, DIALLO Souleymane, DIALLO Amadou Tidia.

Methodology: KOLIÉ Bonaventure, BAH Mariama.

Project administration: BAH Boubacar Sidy Sily.

Supervision: BAH Boubacar Sidy Sily, KOLIÉ Bonaventure.

Visualization: BAH Mariama, KOLIÉ Bonaventure.

Writing—original draft: BAH Mariama, KOLIÉ Bonaventure, DIALLO Souleymane, DIALLO Amadou Tidia.

Writing—review and editing: BAH Mariama, KOLIÉ Bonaventure, DIALLO Souleymane, DIALLO Amadou Tidia, MANSARE Aly Nènè.

The authors would like to thank the Government of the Republic of Guinea, particularly the Ministry of Higher Education, Scientific Research and Innovation, the University of Kindia (UK), and the Institute for Applied Biological Research of Guinea (IRBAG/Kindia) for their support.