Water quality is a critical element for human health and the balance of ecosystems, as indicated by the World Health Organization (WHO, 2003). However, microbiological contamination of water represents a global challenge, with the risk of serious or even fatal waterborne diseases, as highlighted by Tulchinsky (2018). Therefore, understanding the genetic diversity of contaminants present in water is fundamental to assessing the risks associated with its consumption or use (Allix-Béguec et al., 2014). Moreover, seasonal conditions significantly influence water quality and the presence of contaminants (Adjemian et al., 2012; Bojarczuk et al., 2018).

In the aforementioned context, it is crucial to emphasize that while M. ulcerans is generally recognized as the etiological agent responsible for ulcerations, some studies have revealed the presence of other mycobacteria involved in skin infections (Cox, 1981; Frisk et al., 2003; George, 2023; Ichiki et al., 1997). This discovery highlights the imperative to understand the genetic diversity of mycobacteria present in the aquatic environment, given that they could potentially represent a risk to human health. To effectively characterize this genetic diversity, specific markers such as the IS2404 sequences and MIRU VNTRs play a central role (Vakou et al., 2016). These genetic markers allow for the differentiation of mycobacterial strains and provide a better understanding of their distribution in the aquatic environment. Additionally, studies conducted in Côte d’Ivoire have also highlighted the genetic diversity of mycobacteria, both in environmental and clinical samples (Tchan et al., 2023; Zeukeng et al., 2021).

The real-time PCR analysis aimed at detecting IS2404 insertion sequences in M. ulcerans has yielded significant results, providing crucial information regarding the presence of this bacterium in the studied aquatic ecosystems within each endemic city. The prevalence of the IS2404 sequence in the samples observed both during the dry and rainy seasons highlights the ubiquity of Mycobacterium in the examined sites. Notable sites where the sequence was found include station 5 in Abidjan, station 1 in Daloa, station 5 in Tiassalé, as well as stations 4 and 5 in Yamoussoukro. These observations reinforce the notion of a constant presence of the bacterium in these regions.

These results shed light on a possible correlation between M. ulcerans and aquatic environments. The omnipresence of the IS2404 sequence in the sampled sites suggests complex interactions between M. ulcerans and its environment, while raising questions about the biotic and abiotic reservoirs of this bacterium. These findings support the idea that Mycobacterium can survive and proliferate in various types of environments, especially in aquatic settings (Singh et al., 2019). The presence of Mycobacterium ulcerans in water samples from all cities could also result from environmental transmission of Buruli ulcer through various vectors and reservoirs. Although previous consensus leaned towards contact with contaminated soil or ulcerated wounds as the primary mode of transmission, the research Konan et al. (2019) examined social and environmental risk factors that may expose populations to mycobacterial infections. After analyzing the dynamics of local knowledge transfer and practices related to Buruli ulcer in two endemic localities in Côte d’Ivoire, namely Taabo and Daloa, it was found that the etiology of the disease was linked to natural causes such as water and insects.

The presence of the IS2404 sequence in samples from all sampled cities reveals the ubiquity of the bacterium, which results from its adaptation to specific conditions. When environmental conditions become unfavorable, especially in terms of resources and growth factors, M. ulcerans responds by altering its cellular processes. This adaptive response aims to enable its survival in hostile conditions, explaining its presence in most of the sampled waters. Studies by Ayerakwa et al. (2023) have shown that one survival strategy adopted by M. ulcerans in response to unfavorable conditions is the production of endospores. Research led by Halstrom et al. (2015) established that the genetic presence of mycobacterial species, including Mycobacterium ulcerans, in aquatic and humid environments could result from their ability to form biofilms (Steed & Falkinham, 2006). This conclusion is supported by the research conducted by Mullis and Falkinham (2013), which focused on the adhesion and biofilm formation of mycobacteria. Their work revealed that M. avium, M. intracellular, and M. abscessus adhered to and created biofilms on various materials, suggesting this is a survival mechanism in moist environments (Pereira et al., 2020). Furthermore, the mobility associated with this sequence over time could have significant implications for the diversity and distribution of mycobacteria within aquatic and humid ecosystems.

Thus, the conclusions drawn from the study by Ngazoa Kakou et al. (2015) suggest that the recurrence of the IS2404 sequence in clinical samples may result from the continuous spread of these genetic sequences in the environment. Moreover, the results obtained in this study demonstrated that all clinical samples taken from Buruli ulcer patients reacted positively to molecular tests targeting IS2404. The main objective of this research was to conduct an analysis of molecular diversity using the MIRU/VNTR method on clinical samples from patients affected by this disease in Côte d’Ivoire. In addition to this study, the work Tchan et al. (2023) also identified the IS2404 sequence in samples from various endemic areas. Taking into account the research conducted by Ngazoa-Kakou et al. (2019), it is increasingly plausible to consider that the frequent recurrence of the IS2404 sequence in samples may reflect a continuous dissemination of genetic strains in the environment. This highlights the potential impact of this ongoing dissemination on the diversity and distribution of mycobacteria within aquatic and humid ecosystems, possibly promoting their adaptation and evolution.

The absence of detection of VNTR sequences, particularly at locus 6, in the analyzed samples raises questions. This absence may be related to specific characteristics of Mycobacterium in these cities, indicating genetic differences among bacterial populations. Additionally, numerous studies in the literature have reported that mycobacteria in their environments may influence the detection of VNTR sequences, especially locus 6, in environmental samples (Dassi, 2016; Djouaka et al., 2018; Gyamfi et al., 2022; Lavender et al., 2008; Ngazoa Kakou et al., 2015; Vakou, 2017; Zeukeng et al., 2021). It is also important to emphasize that changes in microbial composition, nutrient availability, or climatic conditions could contribute to fluctuations in the distribution of VNTR sequences.

The absence of locus 6 in the samples could also be explained by a specific mutation or deletion. Bacterial strains, including Mycobacterium, can undergo genetic alterations over time. In the context of our study, these alterations could potentially lead to a modification of the locus 6 sequence. This situation could result in a different reference sequence being used for identification. Mutations can occur spontaneously due to the accumulation of random genetic changes, but they can also be induced by factors such as exposure to environmental mutagens.

It is also possible to speculate that the absence of locus 6 could stem from the adaptability of mycobacteria to their environment. Jackson (2014) had already highlighted that Mycobacterium ulcerans had developed several resistance mechanisms to persist in hostile environmental conditions. This adaptability even includes the production of photoprotective compounds aimed at enhancing its survival (Robledo et al., 2011). Furthermore, deletions, which correspond to the loss of a portion of genetic material, could also occur in locus 6. If the key region of locus 6 has been deleted, it could prevent its detection by the methods used. Mutations and deletions can be influenced by adaptation to environmental changes. In the environment, deletions and insertions exist, affecting bacteria such as M. ulcerans and M. marinum, which share 98% of their genome and similar genetic markers. However, genomic similarities hide distinct molecular characteristics resulting from various insertions and deletions. These genetic variations demonstrate the bacteria’s ability to adapt and evolve, reflecting changes in their genome and ecology (Stinear et al., 2000).

Inter-strain genetic variability should also be considered to explain the observed absence of locus 6. Mycobacterium strains are extremely diverse, even within the same species. This variability can result from the accumulation of mutations, genetic recombination, and other evolutionary processes. Therefore, it is possible that the locus 6 strain in the sample naturally differs from the reference sequence used for identification.

The study of the MIRU 1 locus offers important insights into the genetic adaptation of mycobacteria to seasonal variations in aquatic environments. In this context, we have analyzed the genetic profiles of Mycobacterium in detail, with a focus on the MIRU 1 locus, during two distinct seasonal periods: the dry season and the rainy season. Our results highlight significant differences in the number of copies of the MIRU 1 tandem sequence between these two seasons. This observation raises questions about the underlying mechanisms behind these variations.

This study provides an in-depth analysis of the genetic adaptation mechanisms and responses of mycobacteria to seasonal variations in aquatic environments. It underscores the importance of considering not only the interactions between bacteria and their environment but also the underlying genetic mechanisms that influence their survival and spread. These findings have significant implications for our understanding of mycobacterial adaptation mechanisms and for the management of their impact on public health and aquatic ecosystems.