The flood water as well as residues placed by water and integrated with the topsoil after water retention may constitute difficult to estimate risk for human health without laboratory testing. Flood water often includes different types of bacteria, sewage and unknown chemical substances, therefore any contact or exposure may constitute risk due to unidentified source of contamination. In a special area of science interests are microorganisms, responsible for water-borne diseases, when even unexpected contact with contaminated water may result in disease outbreak. Difficult to gauge is however also the time of the microbiological risk maintenance, because retention of organic substances within soil (SOM soil organic matter) may favour certain microorganisms and eliminate others, shaping bacterial diversity. Flood water may also affect interactions between physicochemical properties of soil and bacterial communities in flooded areas [16].
In our study, more bacteria with pathogenic potential were detected in flooded areas, whereas only application of proposed methods like MALDI-TOF allow for in-depth analysis with accurate identification of the detected bacterial species [17]. Unlike traditional methods, MALDI-TOF MS requires minimal sample preparation and can accurately identify a wide range of bacteria by analyzing their unique protein profiles. It’s a scalable tool ideal also for microbial diagnostics and environmental studies, and direct transfer method is used for 90–95% recommended protocols [7, 18]. Nithimongkolchai et al. [19] demonstrated that MALDI-TOF MS analysis effectively identifies and differentiates related bacterial species in soil and water samples and provides results comparable to whole genome sequencing (WGS). The identification accuracy using MALDI-TOF up to species level is above 90% [7]. It is important to note that, in the present study, during the initial phase of the analysis, bacteria were cultivated on nutrient media to promote their growth prior to identification. This indicates that the collected microorganisms were viable in their natural environment.
The challenge and critical for human health is to identify potentially pathogenic bacteria in the affected areas, which was the aim of our study. The wide spectrum of possible infections after the flood disaster was summarised by Paterson et al. [20]. Special attention should be paid to cutaneous and soft-tissue infections associated with Shewanella putrefaciens, Shewanella algae, Leclercia adecarboxylata, Chromobacterium violaceum, Staphylococcus aureus, and Streptococcus pyogenes as well as Aeromonas spp., identified in about 22% cultured isolates of clinical patients. Our study confirmed the presence of 11 species of Aeromonas in flooded locations, compared to seven species identified in non-flooded areas. In the flooded sites, variations in the confidence levels of identification among the selected Aeromonas species suggest the presence of heterogeneous strains within the same species. The Aeromonas species recognized as potential human pathogens include A. hydrophila, A. caviae, and A. veronii, which are associated with clinical manifestations such as gastrointestinal disorders, wound and soft tissue infections, and septicemia [21]. All the above mentioned species were detected in the present study. Based on the clinical reports, A. caviae has been linked to gastrointestinal issues characterized by hemorrhagic symptoms [22]. Severe complications like septicemia, liver cirrhosis and renal failure may be associated with A. veronii, especially in immunocompromised patients [23]. Although Aeromonas encheleia is considered non-pathogenic in mice, which are often used as a model for human risk [24], A. media, commonly found in aquatic environments, and A. eucrenophila, primarily associated with diarrhea in humans, have also been identified as pathogens [25, 26]. Potentially pathogenic may be also microorganisms constituting Bacillus cereus group (B. cereus, B. thuringiensis, B. mycoides, B. pseudomycoides, B. cytotoxicus), which can cause both local and systemic infections [27]. Microorganisms within the Bacillus cereus group (including B. cereus, B. thuringiensis, B. mycoides, B. pseudomycoides, and B. cytotoxicus) are also considered potentially pathogenic [27]. An important question arises regarding the extent to which flooding may alter the normal composition of soil bacteria. Conversely, the genus Bacillus may serve as an indicator of typical soil composition, as it is one of the predominant bacterial groups found in diverse ecological niches [28]. Soil-associated Bacillus species contribute to the maintenance of homeostasis within soil ecosystems due to their ability to produce natural polypeptide antibiotics, which are effective against pathogenic bacterial species [29,30,31]. In this study, we noted that Bacillus cereus and Bacillus thuringensis—a typical soil microorganisms— were found in all non-flooded locations but disappeared in some flooded places. The lower frequency of identification of soil microorganisms described above may be associated with the washing-out of the top-soil layer by long-lasting flood waters that remained in the examined area for four days, with a flow of about 2000 m3/s. Therefore, the evaluation of soil composition after flooding with special attention paid to its natural residents, may be also increasingly important to discover shifts in residual bacterial soil composition and natural soil biocontrol. A 2013 study in Germany examined the effects of severe flooding on soil processes, particularly focusing on microbial activity in grasslands [32]. The study found that microbial biomass significantly decreased in highly flooded areas, but only in plots with higher plant functional diversity. Flooding also alleviated nitrogen limitation, likely due to nutrient-rich sediment deposition. Interestingly, a study in a controlled environment investigated the effects of increased flooding on soil microbial communities. Frequent flooding altered community composition, significantly raising species alpha-diversity (Shannon index). The Bacteria ratio increased, especially after one flood event [33, 34]. The methods employed in this study enabled the reliable detection of difficult-to-recognize pathogens from the Enterobacter group. With high confidence of identification, bacteria from the Enterobacter cloacae complex, such as Enterobacter asburiae, E. bugandensis, E. ludwigii, and E. roggencampii, were selectively detected in the flooded areas, all of which participate in nosocomial infection outbreaks [33]. Enterobacter bugandensis was described as a life-threatening microorganism associated with nosocomial infections in neonates and immunocompromised patients [34]. Also Enterobacter ludwigii is an opportunistic human pathogen [35]. Additionally, Enterobacter asburiae has been identified as a common contaminant on hospital surfaces, potentially contributing to respiratory infections [36]. Therefore, the Enterobacter cloacae complex is clinically substantial due to its role as an opportunistic pathogen and its potential for antibiotic resistance [37]. In our study, Enterococcus hirae was associated with flooded meadows. Although E. hirae has been implicated in severe human diseases, including pyelonephritis, infective endocarditis, and biliary tract infections, reported cases remain scarce, largely due to challenges in accurately identifying the bacterium. For instance, Piccini et al. [38] documented E. hirae isolates from clinical samples obtained in Switzerland, where it was associated with various conditions: gallbladder disorders (42.9%), urinary tract infections (21.4%), wound or peritoneal infections (14.3%), as well as documented cases of E. hirae bacteremia. The emerging pathogen identified in one of the flooded locations was Klebsiella oxytoca, which is known to cause hospital-acquired infections in adults. This organism exhibits multidrug resistance to several commonly used antibiotics [39]. We also confirmed the presence of Leclercia adecarboxylata, a human pathogen commonly acquired through wounds and contact with aquatic environments [40]. Notably, this bacterium was detected in both flooded and non-flooded areas. Among other water-associated pathogens Basri et al. [41] identified Shigella flexneri and Salmonella typhimurium in floodwater in Malaysia, neither of which were found in this study. Additionally, we did not detect emerging Vibrio species, such as the highly virulent Vibrio vulnificus, V. parahaemolyticus, or V. cholerae, which were reported with high frequency by the CDC in the USA in 2005 [42]. The isolation of Raoultella ornithinolytica and Raoultella planticola from flooded areas in the Wrocław agglomeration poses a substantial threat of serious complications, as these emerging bacteria are primarily associated with gastrointestinal and hepatobiliary infections. However, their prevalence may be underestimated in medical reports due to challenges in identification using traditional culture methods [43].
Our findings indicate that the risk to human health is considerably associated with the flood disaster in Wrocław (2024), particularly in flooded recreational areas. However, some potentially pathogenic bacteria were also identified in non-flooded zones within the same locations in the present study. In our opinion, the most likely explanation for the presence of these bacteria in non-flooded areas is their connection to other locations where the bacteria may persist in the environment for extended periods. Analyzing the remaining sampling points, the direction of river flow, and the location of other potential sources influencing bacterial identification, it appears that certain areas within the Wrocław agglomeration may meet the criteria of reservoir locations. One such area could be the Odra’s tributary, the Ślęza River, where periodic flooding occurs, particularly during the spring or following heavy rainfall, when the river is swollen. Moreover, the nearby former irrigation fields, which functioned for over a hundred years (until 2013) as a natural sewage treatment plant for the agglomeration, as well as one of the city’s largest necropolises—the municipal cemetery, where burials, including earth burials, have been carried out since 1867—may also play a role. This suggests that contamination in recreational areas warrants more comprehensive monitoring under typical conditions. Both Figs. 4 and 5 imply that microbial diversity is significant at sites on the Odra River upstream from Wrocław (sites 9 and 11), whereas it shows less variation in locations within the city limits (sites 1, 2, and 3) and downstream (site 5). An exception is site 4, where a large difference in the Menhinick index (0.9) is observed, located at the inlet of the Ślęza River into the Odra. Sites situated away from the Odra River, on tributaries, show almost no difference in microbial diversity: sites 6 and 7 on the Bystrzyca River, and site 8 on the Ślęza River. This suggests that not all tributary waters carried microbiological contaminants.
This study has potential limitations. Although MALDI-TOF is a high-throughput method of identification, limitations of our study may be associated with environmental microorganisms, as routine application of the described methods in microbiology that not correspond with databases linked to bacterial soil composition. Failures in microorganisms identification could be also due to the unknown spectrum attributed to the new species that have insufficient quality for recognition. MALDI-TOF does not enable quantitative identification of determined risks. Another issue may arise from the similarity between certain species, such as those within the Citrobacter freundii complex (Citrobacter braakii, C. freundii, C. gillenii, C. murliniae, C. rodentium, C. sedlakii, C. werkmannii, C. youngae), as well as Escherichia coli and Shigella. However, according to Elbehiry et al. [44], MALDI-TOF achieves high separation scores between species for categorization, with the exception of Aeromonas. Investigation on Leptospira spp. (an important waterborne pathogen) was not included in the study thus there was no possibility to determine the leptospirosis infection risk for human health in the examined areas.
In conclusion, to the best of our knowledge, this study is the first to assess the impact of the 2024 flood on soil bacterial communities in the Wrocław agglomeration (Poland), with a focus on the potential human health risks posed by bacteria isolated from the topsoil layer. Post-disaster research is critical for understanding the recovery of the natural environment and its implications for public health.
