Figures
Abstract
In this study, we investigated the prevalence and abundance of the mercury resistance gene merA in human feces, retail chicken meat, and environmental water samples collected from Japan, Vietnam, and Ghana. A real-time PCR assay developed in this study demonstrated high specificity toward merA sequences from more than 12 bacterial species. Using this assay, merA was detected in 6.8% of human fecal samples in Japan (n = 29), in contrast to significantly higher rates observed in Vietnam (70.2%, n = 47) and Ghana (97.4%, n = 39). Similar geographic trends were evident in the chicken meat samples: 18.5% in Japan (n = 27), 66% in Vietnam (n = 91), and 90% in Ghana (n = 10). Environmental water samples showed a consistently high merA detection rate across all countries (75–100%, n = 21), with substantially higher gene copy numbers in Vietnam and Ghana than in Japan. merA was detected in some water samples, even when total mercury concentrations were below the detection limit, indicating that molecular detection may offer greater sensitivity than traditional physicochemical methods. Mercury-resistant bacteria were successfully isolated and cultured, and Citrobacter freundii was identified as the representative strain. Genomic analysis revealed that merA was located on an IncFIB plasmid, flanked by insertion sequences, suggesting its potential for horizontal gene transfer. These findings highlight merA as a promising biomarker for environmental mercury exposure and support the utility of fecal merA analysis as a proxy for assessing mercury-related public health risks.
Citation: Le YH, Azumah JD, Khong DT, Nguyen TN, Appiah-Kwarteng C, Matsui K, et al. (2026) Comparative prevalence of the mercury resistance gene merA in human feces, food, and environmental water from Japan, Vietnam, and Ghana. PLoS One 21(9): e0357976. https://doi.org/10.1371/journal.pone.0357976
Editor: Ali Hasan, University of Agriculture Faisalabad, PAKISTAN
Received: June 10, 2025; Accepted: August 19, 2026; Published: September 8, 2026
Copyright: © 2026 Le et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All genome sequence files are now available from the DDBJ database (accession numbers AP040138, AP040139). The working links are as follows: https://www.ncbi.nlm.nih.gov/nuccore/AP040138 and https://www.ncbi.nlm.nih.gov/nuccore/AP040139
Funding: This work was supported by the Japan Society for the Promotion of Science (Grant no. 23H00446). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Introduction
Mercury (Hg) is a widespread environmental pollutant due to its ubiquitous presence in nature and continuous release into soil and water. Both anthropogenic activities, such as mining, and natural processes, including volcanic eruptions and wildfires, contribute to Hg contamination of the environment [1]. Small-scale gold mining is a major contributor to global Hg emissions, especially in African countries such as Ghana [2].
In contaminated environments, the predominant inorganic form of Hg is Hg(II), which is highly toxic because of its strong affinity for cellular thiol groups, leading to disruption of essential biological functions. The bacterial merA gene plays a key role in detoxifying Hg(II) by reducing it to the less toxic and volatile elemental Hg (Hg0). In contrast, methylmercury (MeHg) is the Hg species of greatest concern for human health because it readily bioaccumulates and biomagnifies through aquatic and terrestrial food webs. Consequently, humans, as top-level consumers, are particularly vulnerable to MeHg exposure through dietary intake [3–5]. Accordingly, systematic surveillance of Hg contamination across environmental and dietary sources is a critical component of public health protection. Importantly, the World Health Organization (WHO) sets a guideline value of 0.006 mg/L for total Hg in drinking water [6]. However, national standards in both Vietnam [7] and Ghana [8] impose a more stringent maximum permissible concentration of 0.001 mg/L for both drinking and surface water, above which Hg exposure is considered hazardous to human health.
Microbial communities play a crucial role in regulating the Hg cycle [9]. Hg-resistant bacteria are enriched in Hg-contaminated environments due to the strong selective pressure imposed by Hg(II) toxicity [10]. Approximately 1–10% of heterotrophic aerobic microbes from various environments possess mer systems that confer resistance to Hg by detoxifying Hg(II) [11].
The bacterial mer operon is a well-characterized genetic system involved in Hg detoxification. It includes genes responsible for Hg transport, regulation, and reduction. Within this operon, merA encodes mercuric reductase, which catalyzes the NADPH-dependent reduction of Hg(II) to Hg0, thereby decreasing intracellular Hg toxicity [5]. Some mer operon variants also contain merB, which enables the degradation of organomercury compounds such as MeHg. However, merA-mediated reduction of inorganic Hg(II) remains the core mechanism of bacterial Hg resistance [12,13]. Horizontal gene transfer (HGT) plays a significant role in the dissemination of Hg resistance genes in aquatic ecosystems. Previous studies have documented the transfer of mer operon via conjugative plasmids and transposon among diverse bacterial taxa in freshwater and marine environments [27], highlighting the potential for rapid spread of Hg resistance determinants in response to environmental selection pressure.
Hg contamination can be detected through direct physicochemical analysis or by ascertaining indirect biological indicators, such as the prevalence of Hg-resistant bacteria. The abundance of Hg resistant bacteria may reflect the increased presence of bioavailable Hg [14,15]. The quantification of merA in microbial communities, including human gut microbiota, food-contaminating bacteria, and environmental microorganisms, offers valuable insight into environmental Hg exposure and the associated potential health risks. Indeed, a study in an aquatic environment has successfully used merA expression, measured by mRNA production, as a direct indicator of bioavailable Hg [16].
In this study, we focused on the Hg resistance gene merA as a biomarker for regional environmental Hg contamination. We investigated the prevalence and abundance of merA in fecal samples from local residents, food, and environmental water across three countries (Japan, Vietnam, and Ghana). Furthermore, we evaluated its potential utility as an indicator of Hg contamination.
Materials and methods
Ethical approval
Clinical specimens were collected from study participants following the approval of the institutional ethics committees at Gifu University (no. 2019–164), Thai Binh University of Medicine and Pharmacy (no. 1264/HDDD), and the University of Ghana (no. ECBAS 051/22–23). Written informed consent was obtained from all participants and/or their legal guardians.
Sample collection
This study utilized fecal samples provided by local residents, commercially available chicken meat, and environmental water obtained from public water bodies. The collection of small quantities of retail chicken meat and environmental water for research purposes is not subject to regulatory restrictions. The use of human fecal specimens was conducted with the approval of the ethics committee of the relevant local research institution.
This study was conducted using newly collected samples from Ghana and Vietnam in addition to previously reported samples from Vietnam and Japan. Details are provided in Tables 1–3.
Human fecal samples
Human fecal samples were procured for the experiment in this study. A total of 47 participants were recruited from Thai Binh Province (Red River Delta), Vietnam; 29 participants from Gifu Prefecture (Central Japan), Japan; and 39 participants from Kumasi (the Kumasi Metropolitan Assembly in a rainforest region), Ghana. Characteristics of participants and sampling date are depicted in Table 1. One fecal sample was collected from each participant. All samples were collected as previously described [17].
Food samples
Retail chicken meat was used as a food sample. A total of 91 chicken meat samples were collected from meat retailers in four regions of Vietnam (Hanoi, Thai Binh, Nghe An, and Ho Chi Minh City). Additionally, 10 samples were obtained from meat retailers in Kumasi, Ghana, and 27 samples were collected from meat retailers in Gifu City, Japan. All chicken meat examined was locally raised. In each case, a single sample was collected from each retailer. Details of meat sample collection have been described in our previous reports [18,19]. An overview of meat samples is provided in Table 2.
Environmental water samples
Environmental water samples were collected from local water sources in the target regions. Approximately 50 mL of each water sample was collected in a sterile container at the sampling site. A total of 21 environmental water samples were assessed in this study.
The samples were initially centrifuged at 211 × g for 1 min to remove insoluble residues. The supernatant was then subjected to high-speed centrifugation at 15,000 × g for 5 min, and the resulting pellet was collected. The obtained pellet was used for DNA extraction and isolation of Hg-resistant bacteria. Table 3 provides the characteristics of the environmental water samples.
Mercury concentrations
In accordance with the official analytical method published by the Ministry of the Environment, Japan [20], the total Hg levels in environmental water samples were measured using cold vapor atomic absorption spectrophotometry (CV-AAS). Hg concentrations were measured in 11 environmental water samples from Vietnam and Japan. The sampling locations are listed in Table 3.
For each sample (29–52 mL), the debris and suspended solids were first removed by centrifugation at 211 × g for 1 min. Hg in the water samples was then reduced to its vapor phase for quantification, following the official analytical method. The analysis was conducted by a commercial vendor (Tokai Technical Center, Nagoya, Japan).
Detection of the mercury resistance gene (merA)
The merA gene was detected in DNA extracted from each sample using real-time PCR. Briefly, DNA was extracted from the sample pellets using the Kaneka Easy DNA Extraction Kit version 2 in accordance with the manufacturer’s instructions. Specifically, 1 g of fecal matter, 10 g of chicken meat, and 50 mL of environmental water were used for DNA extraction, respectively. DNA concentrations varied depending on the sample type and extraction efficiency, typically ranging from 10-50 ng/μL for fecal samples, 5–30 ng/μL for chicken meat samples, and 0.5-10 ng/μL for environmental water samples. Approximately 100 μL of DNA solution was obtained from each extraction. A portion of the extracted DNA was then subjected to multiplex real-time PCR using a TaqMan probe-based assay on the Mic qPCR Cycler (BioMolecular Systems, Queensland, Australia). The merA-specific primers and probe sequences, as well as the PCR conditions, are detailed in S1 and S2 Tables. The merA-specific primers and probe were designed using Geneious Prime software (Geneious, Boston, MA, USA). For the merA-positive control, genomic DNA was extracted from Escherichia coli strain 22–245 (DDBJ accession no. AP038811) using the NucleoSpin Microbial DNA Kit (Marchery-Nagel, Düren, Germany) according to the manufacturer’s instructions. The concentration of merA in the samples was preliminarily quantified and expressed as E. coli DNA-equivalent copy numbers using the copy number calculation tool [21]. The PCR Cq values below the detection range of the standard curve were calculated by extrapolating the curve.
Isolation of mercury-resistant bacteria
Hg-resistant bacteria were isolated from sediments derived from environmental water samples through centrifugation, following the protocol described above. The sediment was spread onto Luria-Bertani (LB) agar supplemented with 60 μM HgCl2 and incubated at 30°C for 20 h. The HgCl2 concentration was selected based on preliminary culturing experiments and previous studies using micromolar HgCl2 concentrations as selective pressure for isolating Hg-resistant bacteria [22]. Colonies developed on the plates were subjected to further subculturing on LB agar to obtain the isolates. The presence of the merA gene in the isolated colonies was detected using real-time PCR, and the bacterial species was identified using Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS, Bruker Japan, Kanagawa, Japan).
Genome analysis
Genomic DNA was extracted from the Hg-resistant bacterial isolate Citrobacter freundii TB25-009W-60–9, which was recovered from an environmental water sample collected in Vietnam during the selective isolation described above, using the NucleoBond HMW DNA kit (Macherey-Nagel, Germany) according to the manufacturer’s protocol. Whole-genome sequences were obtained using a NovaSeq X Plus (Illumina, CA, USA) and MinION Mk1C sequencer (Oxford Nanopore Technologies, London, UK). Short-read sequencing was performed using the NovaSeq X Plus high-throughput sequencing set by a commercial vendor (Genome-Lead, Takamatsu, Japan). For long-read sequencing, performed using MinION with an R10.4.1 flow cell, and the high molecular weight DNA of each isolate was barcoded using a Rapid Barcoding kit (Oxford Nanopore Technologies). The MinION library was prepared without fragmentation and cleaned using AMPure beads (Beckman Coulter, CA, USA). To obtain the complete genome of the isolate, a de novo hybrid assembly of both short and long reads was conducted using Unicycler 0.5.1, with default settings, and CLC Genomics Workbench 25.0.1.
The completely assembled sequences were annotated by uploading the FASTA files to the DNA Data Bank of Japan Fast Annotation and Submission Tool v.1.6.0. [23]. To investigate antimicrobial resistance genes, the assembled sequences were screened and confirmed using the ResFinder 4.7.0 database [24]. Plasmid replicons were detected using PlasmidFinder 2.1 [25]. The sequences were further analyzed and visualized in Genious Prime v.2025.0.3, which was used to examine the organization and structure of the merA gene and to support comparative genomic analysis.
Statistical analysis
Statistical comparisons of variables among the three countries were conducted using the Chi-square test with StatFlex version 7 (Artech Co., Ltd., Osaka, Japan). When expected samples in category were less than 5, Fisher’s exact test was applied. A p-value of <0.05 was considered indicative of statistical significance.
Results
Specificity of merA detection primers and probe
The specificity of the merA primers and probe used in this study was evaluated using BLAST analysis against genome sequences registered in GenBank. The results showed 100% identity with merA sequences from over 12 bacterial species (S3 Table), including Escherichia, Morganella, Citrobacter, and Pseudomonas.
Validation of the method for merA detection
Using DNA from the merA-standard strain, a detection sensitivity of 0.3 pg DNA per reaction was achieved using the method (S1Fig). The quantifiable DNA range was 0.3 pg to 3 ng per reaction, corresponding to approximately 10⁴ to 10⁸ copies of merA.
Prevalence of the merA gene in collected samples
The prevalence of the merA gene in human fecal samples from residents of multiple countries was assessed using merA-specific real-time PCR. The results are summarized in Table 4. In Japan, only 6.8% of the individuals tested positive for merA, whereas the prevalence was significantly higher in Vietnam (70.2%) and Ghana (97.4%) (p < 0.001).
A similar detection assay conducted on retail chicken meat samples revealed merA in 18.5% of samples in Japan, compared to 66% in Vietnam and 90% in Ghana (p < 0.001).
In contrast to the variation observed in human and chicken samples, environmental water samples (mainly from small local canals) collected from the same regions exhibited consistently high merA detection rates across all countries, ranging from 75% to 100%, with no significant differences (p = 0.337), as shown in Table 4.
Abundance of merA across environmental, food, and human samples
The quantitative results of merA gene copies detected in various sample types are shown in Fig 1. In human fecal samples from Vietnamese residents, the number of merA gene copies per gram of feces varied widely between individuals, ranging from 10³ to as high as 108 copies (median copy numbers: 1.578 × 106). Similar variations were observed among Ghanaian residents, with copy numbers ranging from 104 to 109 copies/g (median copy numbers: 3.656 × 106). In contrast, among Japanese residents, only two individuals tested positive for merA, with copy numbers limited to 10³ and 10⁵ (median copy numbers: 1.02 × 105), respectively.
The dots in the figure indicate the merA level of each sample. Samples with copy numbers below 10³ are not shown. Red horizontal bars indicate the median.
Comparable trends were observed in the retail chicken meat samples. In Japan, merA was detected in only 5 of 27 chicken samples, with copy numbers close to the detection limit (~10³). In sharp contrast, chicken samples from Vietnam and Ghana exhibited significantly higher copy numbers (p < 0.001), ranging from 10⁴ up to 10⁸ in Ghana.
A similar pattern was observed in environmental water samples. Although the detection rate of merA was comparably high across all three countries, the copy numbers showed notable differences: Japanese samples contained merA at levels of approximately 10³, whereas samples from Vietnam and Ghana reached up to 10⁷ copies, indicating substantially higher environmental burdens in those regions.
Mercury concentrations in environmental water samples
The total Hg concentrations in eleven environmental water samples collected in Vietnam and Japan, as shown in Table 3, were measured using CV-AAS, and all samples contained <0.0005 mg/L of Hg.
Isolation and characterization of mercury-resistant bacteria
From environmental water samples in Vietnam and Ghana exhibiting high merA abundance, Hg-resistant bacteria were selectively isolated and characterized. The aim was to obtain representative isolates for species identification and genomic analysis, rather than to culture all merA-positive samples. Numerous colonies of Hg-resistant bacteria were growing even in the presence of a high Hg concentration (60 μM). Species identification of these colonies revealed a diverse range of bacterial species (Table 5). A representative strain, C. freundii TB25-009W-60–9, was chosen for genomic analysis to investigate the localization and structure of the merA gene. As a result, merA was localized on an IncFIB plasmid, and the structure of the mer operon, composed of other mer genes, was nearly identical to that of the reference strain Klebsiella pneumoniae 1_GR_13 [26] (Fig 2). This mer operon was flanked by two insertion sequences (ISs). No homology was found with most other genes, including the antimicrobial resistance genes, on the plasmid of the reference strain (S2Fig).
The numbers in the figure indicate the size of mer operon.
Discussion
The primer–probe set targeting merA demonstrated high sequence homology with a wide spectrum of merA gene sequences from diverse bacterial taxa, as revealed using BLAST analysis against GenBank. However, at least seven merA determinants have been documented [27], and the application of multiple primer–probe sets will be essential in future studies to ensure more comprehensive detection. Although the current approach is not exhaustive, it provides meaningful insights into the geographical distribution and prevalence of merA-harboring bacteria.
The detection of merA in fecal samples from residents and in retail domestic chicken meat suggests the presence of merA-harboring bacteria in the human gut microbiota and the food supply, respectively. These findings support the hypothesis that Hg-resistant bacteria may be transmitted through the food chain and may circulate through both environmental and dietary pathways. In this context, the presence of merA may serve as a potential microbiological indicator associated with Hg exposure via ingestion or environmental contact. However, merA should be interpreted not as a direct quantitative biomarker of individual Hg burden, but rather as an ecological marker reflecting environmental Hg exposure and the dissemination of Hg-resistant bacteria.
The prevalence of merA was higher in Ghana and Vietnam, but significantly lower in Japan. This disparity likely reflects differences in environmental Hg contamination, influenced by local industrial activities, mining practices, and regulatory frameworks. Although merA levels varied between individuals, overall fecal merA gene abundance was comparable between Vietnamese and Ghanaian residents. In contrast, only two low-level positives were detected among Japanese residents. A similar pattern was observed in chicken meat samples, suggesting shared exposure pathways between environmental and dietary sources.
While merA prevalence in environmental water was consistently high across all countries (75–100%), detection rates in human stools and chicken meat varied. For example, although 75% of Japanese water samples were merA-positive, the prevalence in human (6.8%) and chicken (18.5%) samples remained low. Conversely, in Ghana and Vietnam, high water prevalence corresponded with elevated detection rates in both human and chicken samples. These discrepancies suggest that, although aquatic environments may serve as reservoirs of merA-positive bacteria, their transmission into the food chain and human gut microbiota is modulated by additional factors. These may include dietary exposure pathways, environmental contamination levels, farming practices, food processing, and host-specific microbiome dynamics.
Thus, high merA prevalence in water may indicate a reservoir of potential risk, but its downstream impact on humans and food products likely depends on a complex interplay of ecological, cultural, and behavioral factors beyond environmental contamination alone.
Although Hg is a naturally occurring element and the merA gene is widely distributed, its relative abundance may act as an indicator of bioavailable Hg in the environment. Accordingly, the elevated levels of merA observed in Vietnam and Ghana are likely attributable to anthropogenic Hg contamination. In Ghana, artisanal and small-scale gold mining have been linked to Hg pollution [28], whereas in Vietnam, coal combustion and industrial discharge are probable contributors [29]. The lack of stringent regulatory controls and inadequate waste management in these countries may have exacerbated this issue. It is important to note that the WHO and national regulation in both Vietnam and Ghana specify a maximum permissible Hg concentration of 0.001 mg/L in drinking and surface water. In this study, all Vietnamese water samples contained total Hg levels below this regulatory threshold (<0.0005 mg/L). Nevertheless, the frequent detection of merA in these samples underscore the potential value of microbial indicators as complementary tools, since merA prevalence may reflect both current low-level exposure and historical Hg contamination even when physicochemical measurements fall below detection limits.
merA was detected in several samples where Hg was undetectable, suggesting that merA gene detection offers superior sensitivity for assessing environmental Hg exposure. Prior research supports this notion, highlighting that merA-positive bacteria may persist in environments with trace or undetectable levels of Hg, reflecting historical contamination or low-level chronic exposure [30].
Quantification was based on provisional copy number estimates using E. coli genomic DNA as a reference. Because merA is distributed across diverse bacterial taxa [31], with variable genomic localization (e.g., plasmid-borne or chromosomal) and copy numbers, the estimated values should be regarded as relative indices rather than absolute gene copy numbers. Furthermore, although an equal amount of each fecal sample was used for DNA extraction, no sample-specific normalization (e.g., to the 16S rRNA gene) was performed. Therefore, the present data are suitable for relative comparisons among samples and populations rather than for determining absolute merA abundance. Nevertheless, this approach provides a practical and consistent basis for cross-sample and cross-country comparisons.
The successful isolation and cultivation of merA-positive bacteria from water samples supports the validity of the molecular detection methods. Furthermore, the diversity of isolated Hg-resistant strains highlights the broad taxonomic range of merA-bearing organisms in aquatic systems.
In this study, C. freundii was isolated as a representative Hg-resistant bacterium, and its genome was analyzed to investigate the localization and structural characteristics of the mer operon, including merA. A comparative analysis revealed that the mer operon observed on the IncFIB plasmid of the isolated strain was nearly identical to that of the previously characterized K. pneumoniae 1_GR_13 [26]. The presence of insertion sequences flanking the mer operon further supports the potential for HGT. These findings are consistent with previous reports that mer operon is frequently associated with mobile genetic elements, facilitating their dissemination across diverse bacterial taxa and environmental niches [27]. The detection of nearly identical mer operon structures on plasmid IncFIB plasmids from different bacterial species suggested that plasmid-mediated HGT may play a significant role in the spread of Hg resistance determinants in aquatic environments.
The results of this study demonstrated that merA is a valuable biomarker for assessing Hg contamination. Furthermore, the application of this method to compare regional Hg pollution in Ghana and Vietnam with that in Japan highlights the potential of evaluating human fecal samples as a proxy for Hg exposure. From a public health standpoint, the hypothesis that human exposure to Hg or ingestion of Hg-resistant bacteria via food may lead to an increased prevalence of Hg-resistant bacteria within the gut microbiota represents a potentially sensitive and informative biomarker for assessing environmental health risks. This approach is supported by studies in wildlife, which have demonstrated correlations between fecal Hg levels and the composition of gut microbiota [32]. Future challenges include conducting qualitative assessments of the sources and historical progression of environmental Hg contamination in areas. Such assessments may be achieved through detailed analysis of the bacterial species composition of Hg-resistant strains and structural characterization of the mer operon, including the presence and types of associated ISs.
Limitations
This study has several limitations. First, the limited sample size and restricted sampling area may limit the generalizability of the findings. Second, the primers and probe used may not detect all merA subtypes, potentially underestimating the overall prevalence of mercury-resistant bacteria. In addition, merA prevalence reflects bacterial adaptation to Hg selection pressure rather than Hg concentration itself. Hg-resistant bacteria may persist after Hg levels have declined following historical contamination or chronic low-level exposure; therefore, merA should be interpreted as an ecological indicator of Hg selection pressure rather than a direct proxy for the current Hg burden. The absence of direct Hg measurements in stool and meat samples also prevented quantitative assessment of the relationship between merA abundance and Hg concentrations. Future studies should include larger and more diverse sample sets, broader detection of merA subtypes, and paired analyses of Hg concentrations and merA prevalence to clarify the relationship among environmental exposure, bacterial resistance, and potential human health risks.
Supporting information
S3 Table. merA-carrying bacterial species that showed 100% homology with the primers and probes used in this study.
https://doi.org/10.1371/journal.pone.0357976.s003
(XLSX)
S1 Fig. (A) Standard curve of merA detected using real-time PCR.
Cq, cycle threshold. (B) Real-time PCR amplification fluorescence curves of standard positive controls.
https://doi.org/10.1371/journal.pone.0357976.s004
(PDF)
S2 Fig. Comparative analysis of IncFIB plasmids between Citrobacter freundii TB25-009W-60–9 and reference Klebsiella pneumoniae 1_GR_13.
Plasmid size: C. freundii200,468 bp; K. pneumoniae (reference)168,873 bp.
https://doi.org/10.1371/journal.pone.0357976.s005
(PDF)
Acknowledgments
We thank the staff of Gifu University, Thai Binh University of Medicine and Pharmacy, and the University of Ghana for their technical assistance.
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