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Metagenomic profiling reveals distinct signatures of pathogens, antibiotic-resistance genes and human viruses in urban river mouths of the north-western Adriatic coast

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Abstract

Coastal ecosystems are increasingly threatened by microbiological risk due to urban wastewater discharges, which might affect public health and have important economic consequences on the blue tourism. Here, we examine the changes in water and sediment microbiomes at the mouths of three urban-draining rivers (Marecchia, Marano, Rio Melo) and at the Santa Giustina wastewater treatment plant, situated in one of the most densely urbanized and touristic areas of the Adriatic Sea. During the peak summer season, water and sediment samples were analysed through 16 S rRNA metabarcoding and shotgun metagenomics to identify the presence of pathogenic bacteria, human viruses, and antibiotic resistance genes (ARGs). Results revealed that impacted river mouths hosted distinct microbial fingerprints, with seawater showing higher levels of pathogenic bacteria (including Vibrio, Enterococcus, Escherichia-Shigella, and Streptococcus) than sediments. Several human viruses of risk groups 2 and 4, such as Adenoviridae, Herpesviridae, Papillomaviridae, Poxviridae, were detected, along with 99 ARGs, 82 of which were classified by the World Health Organization (WHO) as critically important. Our data suggest the persistence of pathogens in treated effluents and reveal a specific combination of bacterial taxa, viruses, and ARGs, with site-specific profiles. Overall, our findings underscore the need for systematic genomic-based monitoring to safeguard bathing water quality and mitigate risks to human and environmental health, in line with One Health principles.

Data availability

High-quality reads from the samples sequenced in this study were deposited in the European Nucleotide Archive under the project accession number ENA: PRJEB104705.

References

  1. Chen, J., McIlroy, S. E., Archana, A., Baker, D. M. & Panagiotou, G. A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments. Microbiome 7, 1–12 (2019).

    Google Scholar 

  2. Jahne, M. A., Schoen, M. E., Garland, J. L. & Ashbolt, N. J. Simulation of enteric pathogen concentrations in locally-collected greywater and wastewater for microbial risk assessments. Microb. Risk Anal. 5, 44–52 (2017).

    Google Scholar 

  3. Neumann, B., Vafeidis, A. T., Zimmermann, J. & Nicholls, R. J. Future coastal population growth and exposure to sea-level rise and coastal flooding-a global assessment. PloS ONE 10 (3), e0118571. (2015).

  4. Trevathan-Tackett, S. M. et al. A horizon scan of priorities for coastal marine microbiome research. Nat. Ecol. Evol. 3 (11), 1509–1520 (2019).

    Google Scholar 

  5. Wambua, S. et al. Cross-sectional variations in structure and function of coral reef microbiome with local anthropogenic impacts on the Kenyan coast of the Indian ocean. Front. Microbiol. 12, 673128 (2021).

    Google Scholar 

  6. Anastasi, E. M., Matthews, B., Stratton, H. M. & Katouli, M. Pathogenic Escherichia coli found in sewage treatment plants and environmental waters. Appl. Environ. Microbiol. 78 (16), 5536–5541 (2012).

    Google Scholar 

  7. Bagi, A. & Skogerbø, G. Tracking bacterial pollution at a marine wastewater outfall site–A case study from Norway. Sci. Total Environ. 829, 154257 (2022).

    Google Scholar 

  8. Basili, M., Campanelli, A., Frapiccini, E., Luna, G. M. & Quero, G. M. Occurrence and distribution of microbial pollutants in coastal areas of the Adriatic Sea influenced by river discharge. Environ. Pollut. 285, 117672 (2021).

    Google Scholar 

  9. Cox, J. A. SOS–save our seaside! The microbiological risks to human health of raw sewage in our coastal waters. Microbiology 171 (2), 001529 (2025).

    Google Scholar 

  10. Frank, E. M. et al. Microbial Contamination in Urban Marine Sediments: Source Identification Using Microbial Community Analysis and Fecal Indicator Bacteria. Microorganisms 13 (5), 983 (2025).

    Google Scholar 

  11. Diamond, M. B. et al. Wastewater surveillance of pathogens can inform public health responses. Nat. Med. 28 (10), 1992–1995 (2022).

    Google Scholar 

  12. Ostoich, M. et al. Biologic impact on the coastal belt of the province of Venice (Italy, Northern Adriatic Sea): preliminary analysis for the characterization of the bathing water profile. Environ. Sci. Pollut. Res. 18 (2), 247–259 (2011).

    Google Scholar 

  13. Wongprommoon, A., Chomkatekaew, C. & Chewapreecha, C. Monitoring pathogens in wastewater. Nat. Rev. Microbiol. 22 (5), 261–261 (2024).

    Google Scholar 

  14. Xiao, K. & Zhang, L. Wastewater pathogen surveillance based on One Health approach. Lancet Microbe. 4 (5), e297 (2023).

    Google Scholar 

  15. Fresia, P. et al. Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters. Microbiome 7 (1), 35 (2019).

    Google Scholar 

  16. Read, D. S. et al. Dissemination and persistence of antimicrobial resistance (AMR) along the wastewater-river continuum. Water Res. 264, 122204 (2024).

    Google Scholar 

  17. Corinaldesi, C. et al. The paradox of an unpolluted coastal site facing a chronically contaminated industrial area. Front. Mar. Sci. 8, 813887 (2022).

    Google Scholar 

  18. Danovaro, R. Pollution threats in the Mediterranean Sea: an overview. Chem. Ecol. 19 (1), 15–32 (2003).

    Google Scholar 

  19. Schmid, C., Cozzarini, L. & Zambello, E. A critical review on marine litter in the Adriatic Sea: Focus on plastic pollution. Environ. Pollut. 273, 116430 (2021).

    Google Scholar 

  20. Trapella, G. et al. Signature of the anthropogenic impacts on the epipelagic microbiome of the North-Western Adriatic Sea (Mediterranean Sea). Front. Mar. Sci. 11, 1340088 (2024).

    Google Scholar 

  21. Zuccato, E. et al. Pharmaceuticals in the environment in Italy: causes, occurrence, effects and control. Environ. Sci. Pollut. Res. 13, 15–21 (2006).

    Google Scholar 

  22. Drius, M. et al. Tackling challenges for Mediterranean sustainable coastal tourism: An ecosystem service perspective. Sci. Total Environ. 652, 1302–1317 (2019).

    Google Scholar 

  23. Piante, C. & Ody, D. Blue growth in the Mediterranean Sea: the challenge of good environmental status. MedTrends Project WWF France 192 (2015).

  24. Andolina, C., Signa, G., Tomasello, A., Mazzola, A. & Vizzini, S. Environmental effects of tourism and its seasonality on Mediterranean islands: the contribution of the Interreg MED BLUEISLANDS project to build up an approach towards sustainable tourism. Environ. Dev. Sustain. 23 (6), 8601–8612 (2021).

    Google Scholar 

  25. Malham, S. K. et al. The interaction of human microbial pathogens, particulate material and nutrients in estuarine environments and their impacts on recreational and shellfish waters. Environ. Science: Processes Impacts. 16 (9), 2145–2155 (2014).

    Google Scholar 

  26. World Health Organization. Critically important antimicrobials for human medicine: 6th revision. https://www.who.int/publications/i/item/9789241515528 (2018).

  27. Scicchitano, D. et al. Microbiome network in the pelagic and benthic offshore systems of the northern Adriatic Sea (Mediterranean Sea). Sci. Rep. 12 (1), 16670 (2022).

    Google Scholar 

  28. Campbell, A. M., Fleisher, J., Sinigalliano, C., White, J. R. & Lopez, J. V. Dynamics of marine bacterial community diversity of the coastal waters of the reefs, inlets, and wastewater outfalls of southeast Florida. MicrobiologyOpen 4 (3), 390–408 (2015).

    Google Scholar 

  29. Sadik, N. J. et al. Quantification of multiple waterborne pathogens in drinking water, drainage channels, and surface water in Kampala, Uganda, during seasonal variation. GeoHealth 1 (6), 258–269 (2017).

    Google Scholar 

  30. Su, H. C. et al. Persistence of antibiotic resistance genes and bacterial community changes in drinking water treatment system: from drinking water source to tap water. Sci. Total Environ. 616, 453–461 (2018).

    Google Scholar 

  31. Musella, M. et al. Tissue-scale microbiota of the Mediterranean mussel (Mytilus galloprovincialis) and its relationship with the environment. Sci. Total Environ. 717, 137209 (2020).

    Google Scholar 

  32. Palladino, G. et al. Impact of marine aquaculture on the microbiome associated with nearby holobionts: the case of Patella caerulea living in proximity of Sea Bream aquaculture cages. Microorganisms 9 (2), 455 (2021).

    Google Scholar 

  33. Klindworth, A. et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41 (1), e1–e1 (2013).

    Google Scholar 

  34. Palladino, G. et al. Metagenomic shifts in mucus, tissue and skeleton of the coral Balanophyllia europaea living along a natural CO2 gradient. ISME Commun. 2 (1), 65 (2022).

    Google Scholar 

  35. Masella, A. P., Bartram, A. K., Truszkowski, J. M., Brown, D. G. & Neufeld, J. D. PANDAseq: paired-end assembler for illumina sequences. BMC Bioinform. 13, 1–7 (2012).

    Google Scholar 

  36. Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37 (8), 852–857 (2019).

    Google Scholar 

  37. Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26 (19), 2460–2461 (2010).

    Google Scholar 

  38. Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: a versatile open-source tool for metagenomics. PeerJ 4 e2584. (2016).

  39. Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41 (D1), D590–D596 (2012).

    Google Scholar 

  40. Oksanen, J. et al. Vegan community ecology package version 2.6-2. (2022).

  41. Culhane, A. C., Thioulouse, J., Perrière, G. & Higgins, D. G. MADE4: an R package for multivariate analysis of gene expression data. Bioinformatics 21 (11), 2789–2790 (2005).

    Google Scholar 

  42. Martinez Arbizu, P. pairwiseAdonis: Pairwise multilevel comparison using adonis. R package version 0.4, 1. (2020).

  43. Neuwirth, E. & Neuwirth, M. E. Package ‘rcolorbrewer’. ColorBrewer palettes. 991, 1296 (2014).

    Google Scholar 

  44. Wickham, H. ggplot2: Elegant Graphics for Data Analysis. https://ggplot2.tidyverse.org (Springer, 2016).

  45. Wood, M. J. Package ‘RcppBigIntAlgos’. (2025).

  46. Maechler, M. et al. Package ‘cluster’’ 980 (Dosegljivo, 2013).

  47. Bengtsson, H. et al. Package ‘matrixStats’. (2025).

  48. Kolde, R. Pheatmap: pretty heatmaps. R package version 1.0.13. https://github.com/raivokolde/pheatmap (2025).

  49. Dragulescu, A. & Arendt, C. Package “XLSX”. Version, 0.6.5. (2020).

  50. Wickham, H., François, R., Henry, L., Müller, K. & Vaughan, D. dplyr: A Grammar of Data Manipulation. R package version 1.1.4. https://dplyr.tidyverse.org (2025).

  51. Müller, K. & Wickham, H. tibble: Simple Data Frames. R package version 3.3.0.9002. https://github.com/tidyverse/tibble (2025).

  52. Wickham, H., Vaughan, D. & Girlich, M. tidyr: Tidy Messy Data. R package version 1.3.1. https://tidyr.tidyverse.org (2025).

  53. Warnes, G. R. et al. gplots: Various R Programming Tools for Plotting Data. R package version 3.3.0. (2025).

  54. Rampelli, S. et al. ViromeScan: a new tool for metagenomic viral community profiling. BMC Genom. 17, 1–9 (2016).

    Google Scholar 

  55. European Commission Directive 2000/54/EC of the European Parliament and of the Council of 18 September 2000 on the protection of workers from risks related to exposure to biological agents at work (seventh individual directive within the meaning of Article 16(1) of Directive 89/391/EEC). Official J. L 262. 17/10/2000, P0021–0045 (2000).

    Google Scholar 

  56. Birch, O. N., Garza, F. M. & Greaves, J. C. Wastewater Surveillance for Group A Streptococcus pyogenes in a Small City. Pathogens 14 (7), 658 (2025).

    Google Scholar 

  57. Fiore, E., Van Tyne, D. & Gilmore, M. S. Pathogenicity of enterococci. Microbiol. Spectr. 7 (4), 10–1128 (2019).

    Google Scholar 

  58. Kaper, J. B., Nataro, J. P. & Mobley, H. L. Pathogenic escherichia coli. Nat. Rev. Microbiol. 2 (2), 123–140 (2004).

    Google Scholar 

  59. Manini, E. et al. Assessment of spatio-temporal variability of faecal pollution along coastal waters during and after rainfall events. Water 14 (3), 502 (2022).

    Google Scholar 

  60. Mueller, M. & Tainter, C. R. Escherichia coli infection. In: StatPearls. (StatPearls Publishing, 2023).

  61. Okabe, S. & Shimazu, Y. Persistence of host-specific Bacteroides–Prevotella 16S rRNA genetic markers in environmental waters: effects of temperature and salinity. Appl. Microbiol. Biotechnol. 76 (4), 935–944 (2007).

    Google Scholar 

  62. Pinto, B., Pierotti, R., Canale, G. & Reali, D. Characterization of ‘faecal streptococci’as indicators of faecal pollution and distribution in the environment. Lett. Appl. Microbiol. 29 (4), 258–263 (1999).

    Google Scholar 

  63. Shin, J. H. et al. Bacteroides and related species: The keystone taxa of the human gut microbiota. Anaerobe 85, 102819 (2024).

    Google Scholar 

  64. Shrestha, S., Malla, B. & Haramoto, E. Group A Streptococcus pyogenes in wastewater: Applicability of wastewater-based epidemiology for monitoring the prevalence of GAS pharyngitis during the late COVID-19 pandemic phase. Sci. Total Environ. 928, 172447 (2024).

    Google Scholar 

  65. Tett, A., Pasolli, E., Masetti, G., Ercolini, D. & Segata, N. Prevotella diversity, niches and interactions with the human host. Nat. Rev. Microbiol. 19 (9), 585–599 (2021).

    Google Scholar 

  66. Wexler, H. M. Bacteroides: the good, the bad, and the nitty-gritty. Clin. Microbiol. Rev. 20 (4), 593–621 (2007).

    Google Scholar 

  67. Zaidi, M. B. & Estrada-García, T. Shigella: a highly virulent and elusive pathogen. Curr. Trop. Med. Rep. 1 (2), 81–87 (2014).

    Google Scholar 

  68. Brinkwirth, S., Ayobami, O., Eckmanns, T. & Markwart, R. Hospital-acquired infections caused by enterococci: a systematic review and meta-analysis, WHO European Region, 1 January 2010 to 4 February 2020. Eurosurveillance 26 (45), 2001628 (2021).

    Google Scholar 

  69. Ferede, Z. T., Tullu, K. D., Derese, S. G. & Yeshanew, A. G. Prevalence and antimicrobial susceptibility pattern of Enterococcus species isolated from different clinical samples at Black Lion Specialized Teaching Hospital, Addis Ababa, Ethiopia. BMC Res. Notes. 11 (1), 793 (2018).

    Google Scholar 

  70. Baker-Austin, C. et al. Vibrio spp. infections. Nat. Reviews Disease Primers. 4 (1), 1–19 (2018).

    Google Scholar 

  71. Celina, S. S. & Cerný, J. Coxiella burnetii in ticks, livestock, pets and wildlife: a mini-review. Front. Veterinary Sci. 9, 1068129 (2022).

    Google Scholar 

  72. Chai, Q., Zhang, Y. & Liu, C. H. Mycobacterium tuberculosis: an adaptable pathogen associated with multiple human diseases. Front. Cell. Infect. Microbiol. 8, 158 (2018).

    Google Scholar 

  73. Chauhan, D. & Shames, S. R. Pathogenicity and Virulence of Legionella: Intracellular replication and host response. Virulence 12 (1), 1122–1144 (2021).

    Google Scholar 

  74. Coleman, M., Martinez, L., Theron, G., Wood, R. & Marais, B. Mycobacterium tuberculosis transmission in high-incidence settings—new paradigms and insights. Pathogens 11 (11), 1228 (2022).

    Google Scholar 

  75. Collingro, A., Köstlbacher, S. & Horn, M. Chlamydiae in the environment. Trends Microbiol. 28 (11), 877–888 (2020).

    Google Scholar 

  76. Dragan, A. L. & Voth, D. E. Coxiella burnetii: international pathogen of mystery. Microbes Infect. 22 (3), 100–110 (2020).

    Google Scholar 

  77. Hennebique, A., Boisset, S. & Maurin, M. Tularemia as a waterborne disease: a review. Emerg. microbes infections. 8 (1), 1027–1042 (2019).

    Google Scholar 

  78. Héry, M. et al. Diversity and geochemical structuring of bacterial communities along a salinity gradient in a carbonate aquifer subject to seawater intrusion. FEMS Microbiol. Ecol. 90 (3), 922–934 (2014).

    Google Scholar 

  79. Ibangha, I. A. I. et al. Wastewater treatment plants as reservoirs for Vibrio species: an assessment of the Abuja wastewater treatment plant in Nigeria. Discover Water. 5 (1), 1–12 (2025).

    Google Scholar 

  80. Mtetwa, H. N., Amoah, I. D., Kumari, S., Bux, F. & Reddy, P. The source and fate of Mycobacterium tuberculosis complex in wastewater and possible routes of transmission. BMC Public. Health. 22 (1), 145 (2022a).

    Google Scholar 

  81. Mtetwa, H. N., Amoah, I. D., Kumari, S., Bux, F. & Reddy, P. Molecular surveillance of tuberculosis-causing mycobacteria in wastewater. Heliyon 8 (2). (2022).

  82. Robi, D. T., Demissie, W. & Temteme, S. Coxiellosis in livestock: epidemiology, public health significance, and prevalence of Coxiella burnetii infection in Ethiopia. Vet. Med. Res. Rep. 145–158 (2023).

  83. Walker, J. T. The influence of climate change on waterborne disease and Legionella: a review. Perspect. public. health. 138 (5), 282–286 (2018).

    Google Scholar 

  84. Zhou, H. et al. Seawater-associated highly pathogenic Francisella hispaniensis infections causing multiple organ failure. Emerg. Infect. Dis. 26 (10), 2424 (2020).

    Google Scholar 

  85. Keim, P., Johansson, A. & Wagner, D. M. Molecular epidemiology, evolution, and ecology of Francisella. Ann. N. Y. Acad. Sci. 1105 (1), 30–66 (2007).

    Google Scholar 

  86. Van Hoek, M. L. Biofilms: an advancement in our understanding of Francisella species. Virulence 4 (8), 833–846 (2013).

    Google Scholar 

  87. Hooper, D. C. Mechanisms of action of antimicrobials: focus on fluoroquinolones. Clin. Infect. Dis. 32 (Supplement 1), S9–S15 (2001).

    Google Scholar 

  88. Kohanski, M. A., Dwyer, D. J. & Collins, J. J. How antibiotics kill bacteria: from targets to networks. Nat. Rev. Microbiol. 8 (6), 423–435 (2010).

    Google Scholar 

  89. Sarkar, P., Yarlagadda, V., Ghosh, C. & Haldar, J. A review on cell wall synthesis inhibitors with an emphasis on glycopeptide antibiotics. Medchemcomm 8 (3), 516–533 (2017).

    Google Scholar 

  90. Adegoke, A. A., Madu, C. E., Reddy, P., Stenström, T. A. & Okoh, A. I. Prevalence of vancomycin resistant Enterococcus in wastewater treatment plants and their recipients for reuse using PCR and MALDI-ToF MS. Front. Environ. Sci. 9, 797992 (2022).

    Google Scholar 

  91. Alexander, J., Bollmann, A., Seitz, W. & Schwartz, T. Microbiological characterization of aquatic microbiomes targeting taxonomical marker genes and antibiotic resistance genes of opportunistic bacteria. Sci. Total Environ. 512, 316–325 (2015).

    Google Scholar 

  92. Cahill, N. et al. Hospital effluent: A reservoir for carbapenemase-producing Enterobacterales? Sci. Total Environ. 672, 618–624 (2019).

    Google Scholar 

  93. Khan, F. A., Söderquist, B. & Jass, J. Prevalence and diversity of antibiotic resistance genes in Swedish aquatic environments impacted by household and hospital wastewater. Front. Microbiol. 10, 688 (2019).

    Google Scholar 

  94. Mutuku, C., Gazdag, Z. & Melegh, S. Occurrence of antibiotics and bacterial resistance genes in wastewater: resistance mechanisms and antimicrobial resistance control approaches. World J. Microbiol. Biotechnol. 38 (9), 152 (2022).

    Google Scholar 

  95. Szczepanowski, R. et al. Detection of 140 clinically relevant antibiotic-resistance genes in the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to selected antibiotics. Microbiology 155 (7), 2306–2319 (2009).

    Google Scholar 

  96. Waśko, I., Kozińska, A., Kotlarska, E. & Baraniak, A. Clinically relevant β-lactam resistance genes in wastewater treatment plants. Int. J. Environ. Res. Public Health. 19 (21), 13829 (2022).

    Google Scholar 

  97. Young, S. et al. Vancomycin-resistant enterococci and bacterial community structure following a sewage spill into an aquatic environment. Appl. Environ. Microbiol. 82 (18), 5653–5660 (2016).

    Google Scholar 

  98. Ullmann, I. F. et al. Detection of aminoglycoside resistant bacteria in sludge samples from Norwegian drinking water treatment plants. Front. Microbiol. 10, 487 (2019).

    Google Scholar 

  99. Zhang, Y. et al. The prevalence and distribution of aminoglycoside resistance genes. Biosaf. Health. 5 (01), 14–20 (2023).

    Google Scholar 

  100. Cetinkaya, Y., Falk, P. & Mayhall, C. G. Vancomycin-resistant enterococci. Clin. Microbiol. Rev. 13 (4), 686–707 (2000).

    Google Scholar 

  101. World Health Organization. Global antimicrobial resistance and use surveillance system (GLASS) report. https://www.who.int/publications/i/item/9789240062702 (2022).

  102. Munoz-Price, L. S. et al. Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases. Lancet. Infect. Dis. 13 (9), 785–796 (2013).

    Google Scholar 

  103. Nordmann, P., Cuzon, G. & Naas, T. The real threat of Klebsiella pneumoniae carbapenemase-producing bacteria. Lancet. Infect. Dis. 9 (4), 228–236 (2009).

    Google Scholar 

  104. Nordmann, P., Naas, T. & Poirel, L. Global spread of carbapenemase-producing Enterobacteriaceae. Emerg. Infect. Dis. 17 (10), 1791 (2011).

    Google Scholar 

  105. Poirel, L., Héritier, C., Tolün, V. & Nordmann, P. Emergence of oxacillinase-mediated resistance to imipenem in Klebsiella pneumoniae. Antimicrob. Agents Chemother. 48 (1), 15–22 (2004).

    Google Scholar 

  106. Ferraro, G. B. et al. Global quantification and distribution of antibiotic resistance genes in oceans and seas: Anthropogenic impacts and regional variability. Sci. Total Environ. 955, 176765 (2024).

    Google Scholar 

  107. Kvesić, M. et al. Microbiome and antibiotic resistance profiling in submarine effluent-receiving coastal waters in Croatia. Environ. Pollut. 292, 118282 (2022).

    Google Scholar 

  108. Kumar, S. & Jena, L. Understanding rifampicin resistance in tuberculosis through a computational approach. Genomics Inf. 12 (4), 276 (2014).

    Google Scholar 

  109. Hou, J. et al. Detection of the plasmid-encoded fosfomycin resistance gene fosA3 in Escherichia coli of food-animal origin. J. Antimicrob. Chemother. 68 (4), 766–770 (2013).

    Google Scholar 

  110. Menck-Costa, M. F. et al. High-Frequency Detection of fosA3 and bla CTX–M–55 Genes in Escherichia coli From Longitudinal Monitoring in Broiler Chicken Farms. Front. Microbiol. 13, 846116 (2022).

    Google Scholar 

  111. Ribeiro, V. S. T. et al. In vitro susceptibility to fosfomycin in clinical and environmental extended-spectrum beta-lactamase producing and/or ciprofloxacin-non-susceptible Escherichia coli isolates. Revista Instituto Med. Trop. São Paulo 66 e5. (2024).

  112. Javvadi, Y. & Mohan, S. V. Understanding the distribution of antibiotic resistance genes in an urban community using wastewater-based epidemiological approach. Sci. Total Environ. 868, 161419 (2023).

    Google Scholar 

  113. Suzuki, S. et al. Macrolide resistance genes and mobile genetic elements in waterways from pig farms to the sea in Taiwan. J. global Antimicrob. Resist. 29, 360–370 (2022).

    Google Scholar 

  114. Nonaka, L., Maruyama, F., Suzuki, S. & Masuda, M. Novel macrolide-resistance genes, mef (C) and mph (G), carried by plasmids from Vibrio and Photobacterium isolated from sediment and seawater of a coastal aquaculture site. Lett. Appl. Microbiol. 61 (1), 1–6 (2015).

    Google Scholar 

  115. Sugimoto, Y. et al. The novel mef (C)–mph (G) macrolide resistance genes are conveyed in the environment on various vectors. J. global Antimicrob. Resist. 10, 47–53 (2017).

    Google Scholar 

  116. González-Plaza, J. J. et al. Functional repertoire of antibiotic resistance genes in antibiotic manufacturing effluents and receiving freshwater sediments. Front. Microbiol. 8, 2675 (2018).

    Google Scholar 

  117. Amin, M. B. et al. High prevalence of plasmid-mediated quinolone resistance (PMQR) among E. coli from aquatic environments in Bangladesh. PLoS ONE 16 (12), e0261970. (2021).

  118. Pauli, G. et al. Orthopox viruses: infections in humans. Transfus. Med. Hemotherapy. 37 (6), 351 (2010).

    Google Scholar 

  119. Shchelkunov, S. N. Orthopoxvirus genes that mediate disease virulence and host tropism. Adv. Virol. 2012 (1), 524743 (2012).

    Google Scholar 

  120. Shchelkunov, S. N. An increasing danger of zoonotic orthopoxvirus infections. PLoS Pathog. 9 (12), e1003756 (2013).

    Google Scholar 

  121. Ahmed, W. et al. Occurrence of multiple respiratory viruses in wastewater in Queensland, Australia: potential for community disease surveillance. Sci. Total Environ. 864, 161023 (2023).

    Google Scholar 

  122. Di Bonito et al. A large spectrum of alpha and beta papillomaviruses are detected in human stool samples. J. Gen. Virol. 96 (3), 607–613 (2015).

    Google Scholar 

  123. La Rosa, G. et al. Mucosal and cutaneous human papillomaviruses detected in raw sewages. PloS ONE 8 (1), e52391. (2013).

  124. McCall, C., Wu, H., Miyani, B. & Xagoraraki, I. Identification of multiple potential viral diseases in a large urban center using wastewater surveillance. Water Res. 184, 116160 (2020).

    Google Scholar 

  125. Miyani, B., McCall, C. & Xagoraraki, I. High abundance of human herpesvirus 8 in wastewater from a large urban area. J. Appl. Microbiol. 130 (5), 1402–1411 (2021).

    Google Scholar 

  126. Oghuan, J. et al. Wastewater analysis of Mpox virus in a city with low prevalence of Mpox disease: an environmental surveillance study. Lancet Reg. Health Am. 28 (2023).

  127. Omatola, C. A., Ogunsakin, R. E., Olaniran, A. O. & Kumari, S. Monkeypox Virus Occurrence in Wastewater Environment and Its Correlation with Incidence Cases of Mpox: A Systematic Review and Meta-Analytic Study. Viruses 17 (3), 308 (2025).

    Google Scholar 

  128. Shi, L. D. et al. A mixed blessing of viruses in wastewater treatment plants. Water Res. 215, 118237 (2022).

    Google Scholar 

  129. Tiwari, A. et al. Monkeypox outbreak: Wastewater and environmental surveillance perspective. Sci. Total Environ. 856, 159166 (2023).

    Google Scholar 

  130. Gibson, K. E. Viral pathogens in water: occurrence, public health impact, and available control strategies. Curr. Opin. Virol. 4, 50–57 (2014).

    Google Scholar 

  131. Griffin, D. W., Donaldson, K. A., Paul, J. H. & Rose, J. B. Pathogenic human viruses in coastal waters. Clin. Microbiol. Rev. 16 (1), 129–143 (2003).

    Google Scholar 

  132. Kaas, L. et al. Detection of human enteric viruses in French Polynesian wastewaters, environmental waters and giant clams. Food Environ. Virol. 11 (1), 52–64 (2019).

    Google Scholar 

  133. Block, J. C. Viruses in environmental waters. In Viral Plution of the Environment. 117–145. (CRC, 2018).

  134. Lanrewaju, A. A., Enitan-Folami, A. M., Sabiu, S., Edokpayi, J. N. & Swalaha, F. M. Global public health implications of human exposure to viral contaminated water. Front. Microbiol. 13, 981896 (2022).

    Google Scholar 

  135. Pinon, A. & Vialette, M. Survival of viruses in water. Intervirology 61 (5), 214–222 (2019).

    Google Scholar 

  136. Guerra, V., Guerra, C. & Nesci, O. Geomorphology of the town of Rimini and surrounding areas (Emilia-Romagna, Italy). J. Maps. 17 (4), 113–123 (2021).

    Google Scholar 

  137. Cacace, D. et al. Antibiotic resistance genes in treated wastewater and in the receiving water bodies: A pan-European survey of urban settings. Water Res. 162, 320–330 (2019).

    Google Scholar 

  138. Girón-Guzmán, I. et al. Survival of viruses in water microcosms. Sci. Total Environ. 963, 178416 (2025).

    Google Scholar 

  139. Singer, A. C., Shaw, H., Rhodes, V. & Hart, A. Review of antimicrobial resistance in the environment and its relevance to environmental regulators. Front. Microbiol. 7, 1728 (2016).

    Google Scholar 

  140. Venier, S. Waste Water Management in Seaside Tourism Areas: The Rimini Seawater Protection Plan. In: The Italian Water Industry: Cases of Excellence. 225–235. Cham: Springer International Publishing. (2018).

    Google Scholar 

Download references

Acknowledgements

We would like to thank the Yacht Club Rimini for their assistance with the sampling, in particular for providing a boat for the collection of marine samples. The research leading to these results has been conceived under the International PhD Program Innovative Technologies and Sustainable Use of Mediterranean Sea Fishery and Biological Resources (www.FishMed-PhD.org; last access: 30 September 2025). This study represents partial fulfilment of the requirements for the PhD thesis of L. Foresto, E. Radaelli and D. Leuzzi at the FishMed-PhD course.

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Authors and Affiliations

  1. Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy

    Lucia Foresto, Elena Radaelli, Daniela Leuzzi, Giorgia Palladino, Daniel Scicchitano, Semeh Bejaoui, Silvia Turroni, Simone Rampelli & Marco Candela

  2. Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy

    Lucia Foresto, Elena Radaelli, Daniela Leuzzi, Giorgia Palladino, Daniel Scicchitano, Simone Rampelli & Marco Candela

  3. Fondazione Cetacea Onlus, Riccione, Italy

    Carlotta Santolini & Alice Pari

  4. Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy

    Francesca Marcellini & Roberto Danovaro

  5. Dipartimento di Scienze e Ingegneria della Materia, dell’Ambiente ed Urbanistica, Università Politecnica delle Marche, Ancona, Italy

    Cinzia Corinaldesi

Authors

  1. Lucia Foresto
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  2. Elena Radaelli
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  3. Daniela Leuzzi
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  4. Giorgia Palladino
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  5. Daniel Scicchitano
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  6. Semeh Bejaoui
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  7. Silvia Turroni
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  8. Simone Rampelli
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  9. Carlotta Santolini
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  10. Alice Pari
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  11. Francesca Marcellini
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  12. Roberto Danovaro
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  13. Cinzia Corinaldesi
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  14. Marco Candela
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Contributions

R.D., C.C. and M.C.: conceptualization. L.F., E.R., D.L., G.P., D.S. and F.M.: data curation. L.F., E.R., D.L. and D.S.: formal analysis. C.C. and M.C.: funding acquisition and project administration. G.P., D.S. and S.B.: visualization. L.F., R.D., C.C. and M.C.: writing – original draft. G.P., D.S., S.B., S.T., S.R., C.S., A.P. and F.M.: writing – review and editing.

Corresponding author

Correspondence to
Marco Candela.

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The authors declare no competing interests.

Ethical statement

This study did not involve human participants, vertebrate animals, or any other organisms requiring ethical approval. All samples consisted solely of non-living environmental materials (i.e., seawater and sediment). Therefore, ethical review and approval were not required for the collection or analysis of these inorganic biological specimens.

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Foresto, L., Radaelli, E., Leuzzi, D. et al. Metagenomic profiling reveals distinct signatures of pathogens, antibiotic-resistance genes and human viruses in urban river mouths of the north-western Adriatic coast.
Sci Rep (2026). https://doi.org/10.1038/s41598-026-45229-2

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  • DOI: https://doi.org/10.1038/s41598-026-45229-2

Keywords

  • Coastal environments
  • One Health
  • Metagenomics
  • Pathogens
  • Antibiotic resistance genes
  • Human virus

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