Enrichment of potential pathogens in marine microbiomes with different degrees of anthropogenic activity

Cross-environmental cycling of antimicrobial resistance in agricultural areas fertilized with poultry litter: A one health approach

Poultry litter, commonly used as an organic fertilizer, can contain antimicrobial residues, resistant bacteria, and/or antimicrobial resistance genes. After application to soil, these contaminants can reach crops and be transported to aquatic systems through leaching and runoff. Once in water bodies, they can return to soil and crops through irrigation, establishing a cycle that promotes the selection, spread and persistence of antimicrobial resistance. To investigate the hypothesis of a cyclical event, samples of poultry litter, cultivable soil fertilized with this organic residue, rhizosphere soil from Sechium edule (chayote), water, and sediments from irrigation ponds were collected across two agricultural and poultry-producing areas during the dry and rainy seasons. Clinically significant bacteria, especially bacteria belonging to the Enterobacteriaceae family, were isolated. Fifty-three strains exhibited one or more antimicrobial resistance genes, as detected by PCR amplification, including those conferring resistance to sulfonamides (sul1 and sul2), fluoroquinolones (qnrB, qnrA, and qnrS), and β-lactams (blaGES, blaTEM, blaSHV, blaCTX-M-1/2,blaCTX-M-8, and blaCTX-M-14). Genes encoding integrases related to class-1 and 2 integrons (intI1 and intI2) were also observed. A rare occurrence of the blaGES gene was observed in Stenotrophomonas sp. and Brevundimonas sp. Strains of Escherichia sp. were multidrug resistant. Sequencing of the 16S rRNA encoding gene indicated unique operational taxonomic units (OTUs) originating from poultry litter and found in the soil, rhizosphere, water, and sediment, highlighting the dissemination of this material across agricultural substrates. These findings strongly suggest the spread of antimicrobial-resistant bacteria in agricultural environments, posing potential risks to both human and animal health.

Beyond water and soil: Air emerges as a major reservoir of human pathogens

Assessing the risk of human pathogens in the environment is crucial for controlling the spread of diseases and safeguarding human health. However, conducting a thorough assessment of low-abundance pathogens in highly complex environmental microbial communities remains challenging. This study compiled a comprehensive catalog of 247 human-pathogenic bacterial taxa from global biosafety agencies and identified more than 78 million genome-specific markers (GSMs) from their 17,470 sequenced genomes. Subsequently, we analyzed these pathogens' types, abundance, and diversity within 474 shotgun metagenomic sequences obtained from diverse environmental sources. The results revealed that among the four habitats studied (air, water, soil, and sediment), the detection rate, diversity, and abundance of detectable pathogens in the air all exceeded those in the other three habitats. Air, sediment, and water environments exhibited identical dominant taxa, indicating that these human pathogens may have unique environmental vectors for their transmission or survival. Furthermore, we observed the impact of human activities on the environmental risk posed by these pathogens, where greater amounts of human activities significantly increased the abundance of human pathogenic bacteria, especially in water and air. These findings have remarkable implications for the environmental risk assessment of human pathogens, providing valuable insights into their presence and distribution across different habitats.

Contamination status, source analysis and exposure assessments of quinolone antibiotics in the south of Yancheng Coastal Wetland, China

Yancheng coastal wetland, the largest coastal wetland in the west coast of the Pacific Ocean and the margin of the Asian continent, has significant environmental, economic and social effects on local human beings. The extensive contamination and potential risk of quinolone antibiotics (QNs) on local aquaculture and human health are still not clear until now. In this study, 52 surface sediment samples were collected to investigate the contamination status and polluted sources, and evaluate ecological risks of QNs in the south of Yancheng coastal wetland. The total contents of QNs ranged from 0.33 to 21.60 ng/g dw (mean value of 4.51 ng/g dw), following the detection frequencies of QNs ranging from 19.23 to 94.23%. The highest content of QNs occurred around an aquaculture pond dominated by flumequine. The total organic carbon contents of sediment were positively correlated with sarafloxacin and lomefloxacin (p < 0.05), indicating the enhanced absorption of these QNs onto sediments. Partial QNs, such as lomefloxacin, enrofloxacin, sarafloxacin and flumequine, presented the homology features originating from the emission of medical treatment and aquaculture. There was no potential risk of QNs to human beings but a potential risk to aquatic organisms (algae > plant > invertebrate). Totally, the management and protection of Yancheng coastal wetland should be of concern with aquaculture as the important industry.

Beach sand plastispheres are hotspots for antibiotic resistance genes and potentially pathogenic bacteria even in beaches with good water quality

Massive amounts of microplastics are transported daily from the oceans and rivers onto beaches. The ocean plastisphere is a hotspot and a vector for antibiotic resistance genes (ARGs) and potentially pathogenic bacteria. However, very little is known about the plastisphere in beach sand. Thus, to describe whether the microplastics from beach sand represent a risk to human health, we evaluated the bacteriome and abundance of ARGs on microplastic and sand sampled at the drift line and supralittoral zones of four beaches of poor and good water quality. The bacteriome was evaluated by sequencing of 16S rRNA gene, and the ARGs and bacterial abundances were evaluated by high-throughput real-time PCR. The results revealed that the microplastic harbored a bacterial community that is more abundant and distinct from that of beach sand, as well as a greater abundance of potential human and marine pathogens, especially the microplastics deposited closer to seawater. Microplastics also harbored a greater number and abundance of ARGs. All antibiotic classes evaluated were found in the microplastic samples, but not in the beach sand ones. Additionally, 16 ARGs were found on the microplastic alone, including genes related to multidrug resistance (blaKPC, blaCTX-M, tetM, mdtE and acrB_1), genes that have the potential to rapidly and horizontally spread (blaKPC, blaCTX-M, and tetM), and the gene that confers resistance to antibiotics that are typically regarded as the ultimate line of defense against severe multi-resistant bacterial infections (blaKPC). Lastly, microplastic harbored a similar bacterial community and ARGs regardless of beach water quality. Our findings suggest that the accumulation of microplastics in beach sand worldwide may constitute a potential threat to human health, even in beaches where the water quality is deemed satisfactory. This phenomenon may facilitate the emergence and dissemination of bacteria that are resistant to multiple drugs.

Aquaculture bacterial pathogen database: Pathogen monitoring and screening in coastal waters using environmental DNA

Increasingly diverse pathogen occurrence in coastal and mariculture areas demands improved monitoring platforms to prevent economic and public health implications. Accessible databases with up-to-date knowledge and taxonomy are critical for detecting and screening environmental pathogens. Condensed from over 3000 relevant reports in peer reviewed articles, we constructed an aquaculture bacterial pathogen database that provides specialized curation of over 210 bacterial pathogenic species impacting aquaculture. Application of the aquaculture bacterial pathogen database to environmental DNA metabarcoding monitoring data in Hong Kong coastal and mariculture waters effectively characterized regional pathogen profiles over a one-year period and improved identification of new potential pathogen targets. The results highlighted the increase in potential pathogen abundance related to aquaculture activity and the associated inorganic nitrogen load, which was chiefly due to the enrichment of Vibrio during the atypical dry winter season. The value of the aquaculture bacterial pathogen database for empowering environmental DNA-based approaches in coastal marine pathogen surveillance benefits water resource management and aquaculture development on a global scale.

Uncovering the Microbial Diversity of Two Exotic Calcareous Sponges

Sponges-associated microorganisms play important roles in their health and ecology; consequently, they may be crucial in the successful adaptation of exotic species to novel environments. However, few studies have focused on the microbial diversity of exotic sponges, especially those with calcium carbonate spicules (class Calcarea). Therefore, this is the first in situ characterization of the microbiota of the exotic calcareous sponges Sycettusa hastifera and Paraleucilla magna. Our results suggest that S. hastifera has a more stable microbiota than P. magna, as there were no differences in its beta diversity among sampling sites. Conversely, P. magna showed significant differences in its microbial communities, perhaps related to its adhesion to artificial substrate and/or shellfish mariculture activities. Each sponge species presented a single dominant proteobacterial OTU potentially active in the nitrogen cycle, which could help sponge detoxification, especially in polluted areas where exotic species usually establish. Our results show the importance of assessing the microbial diversity to unveil host-microorganism relationships and suggest that these associated nitrogen-cycling microorganisms could favor the success of exotic sponges in new environments.

The prevalence of potential pathogens in ballast water and sediments of oceangoing vessels and implications for management

Ballast water and sediments can serve as prominent vectors for the widespread dispersal of pathogens between geographically distant areas. However, information regarding the diversity and distribution of the bacterial pathogens in ballast water and sediments is highly limited. In this study, using high-throughput sequencing and quantitative PCR, we investigated the composition and abundance of potential pathogens, and their associations with indicator microorganisms. We accordingly detected 48 potential bacterial pathogens in the assessed ballast water and sediments, among which there were significant differences in the compositions and abundances of pathogenic bacterial communities characterizing ballast water and sediments. Rhodococcus erythropolis, Bacteroides vulgatus, and Vibrio campbellii were identified as predominant pathogens in ballast water, whereas Pseudomonas stutzeri, Mycobacterium paragordonae, and Bacillus anthracis predominated in ballast sediments. Bacteroidetes, Vibrio alginolyticus, Vibrio parahaemolyticus, and Escherichia coli were generally detected with median values of 8.54 × 10³-1.22 × 10⁷ gene copies (GC)/100 mL and 1.16 × 10⁷-3.97 × 10⁹ GC/100 g in ballast water and sediments, respectively. Notably, the concentrations of Shigella sp., Staphylococcus aureus, and V. alginolyticus were significantly higher in ballast sediments than in the water. In addition, our findings tend to confirm that the indicator species specified by the International Maritime Organization (IMO) might underestimate the pathogen risk in the ballast water and sediments, as these bacteria were unable to predict some potential pathogens assessed in this study. In summary, this study provides a comprehensive insight into the spectrum of the potential pathogens that transferred by ship ballast tanks and emphasizes the need for the implementation of IMO convention on ballast sediment management.

Irrigation Ponds as Sources of Antimicrobial-Resistant Bacteria in Agricultural Areas with Intensive Use of Poultry Litter

Poultry litter is widely used worldwide as an organic fertilizer in agriculture. However, poultry litter may contain high concentrations of antibiotics and/or antimicrobial-resistant bacteria (ARB), which can be mobilized through soil erosion to water bodies, contributing to the spread of antimicrobial resistance genes (ARGs) in the environment. To better comprehend this kind of mobilization, the bacterial communities of four ponds used for irrigation in agricultural and poultry production areas were determined in two periods of the year: at the beginning (low volume of rainfall) and at the end of the rainy season (high volume of rainfall). 16S rRNA gene sequencing revealed not only significantly different bacterial community structures and compositions among the four ponds but also between the samplings. When the DNA obtained from the water samples was PCR amplified using primers for ARGs, those encoding integrases (intI1) and resistance to sulfonamides (sul1 and sul2) and β-lactams (blaGES, blaTEM and blaSHV) were detected in three ponds. Moreover, bacterial strains were isolated from CHROMagar plates supplemented with sulfamethoxazole, ceftriaxone or ciprofloxacin and identified as belonging to clinically important Enterobacteriaceae. The results presented here indicate a potential risk of spreading ARB through water resources in agricultural areas with extensive fertilization with poultry litter.

Tracking bacterial pollution at a marine wastewater outfall site - A case study from Norway

Coastal marine environments are increasingly affected by anthropogenic impacts, such as the release of sewage at outfall sites and agricultural run-off. Fecal pollution introduced to the sea through these activities poses risks of spreading microbial diseases and disseminating antibiotic resistant bacteria and their genes. The study area of this research, Bore beach, is situated between two such point sources, an outfall site where treated sewage is released 1 km off the coast and a stream that carries run-off from an agricultural area to the northern end of the beach. In order to investigate whether and to what extent fecal contamination from the sewage outfall reached the beach, we used microbial source tracking, based on whole community analysis. Samples were collected from sea water at varying distances from the sewage outfall site and along the beach, as well as from the sewage effluent and the stream. Amplicon sequencing of 16S rRNA genes from all the collected samples was carried out at two time points (June and September). In addition, the seawater at the sewage outfall site and the sewage effluent were subject to shotgun metagenomics. To estimate the contribution of the sewage effluent and the stream to the microbial communities at Bore beach, we employed SourceTracker2, a program that uses a Bayesian algorithm to perform such quantification. The SourceTracker2 results suggested that the sewage effluent is likely to spread fecal contamination towards the beach to a greater extent than anticipated based on the prevailing sea current. The estimated mixing proportions of sewage at the near-beach site (P4) were 0.22 and 0.035% in June and September, respectively. This was somewhat below that stream's contribution in June (0.028%) and 10-fold higher than the stream's contribution in September (0.004%). Our analysis identified a sewage signal in all the tested seawater samples.

Partitioning and sources of microbial pollution in the Venice Lagoon

Microbial pollutants are a serious threat to human and environmental health in coastal areas. Based on the hypothesis that pollution from multiple sources may produce a distinct microbial signature and that microbial pollutants seem to distribute between a free-living and a particle-attached fraction, we investigated the occurrence, partitioning and sources of microbial pollutants in water samples collected in the Venice Lagoon (Italy). The area was taken as a case study of an environment characterized by a long history of industrial pollution and by growing human pressure. We found a variety of pollutants from several sources, with sewage-associated and faecal bacteria accounting for up to 5.98% of microbial communities. Sewage-associated pollutants were most abundant close to the city centre. Faecal pollution was highest in the area of the industrial port and was dominated by human inputs, whereas contamination from animal faeces was mainly detected at the interface with the mainland. Microbial pollutants were almost exclusively associated with the particle-attached fraction. The samples also contained other potential pathogens. Our findings stress the need for monitoring and managing microbial pollution in highly urbanized lagoon and semi-enclosed systems and suggest that management plans to reduce microbial inputs to the waterways should include measures to reduce particulate matter inputs to the lagoon. Finally, High-Throughput Sequencing combined with computational approaches proved critical to assess water quality and appears to be a valuable tool to support the monitoring of waterborne diseases.

Metagenomic Characterization of Microbial Pollutants and Antibiotic- and Metal-Resistance Genes in Sediments from the Canals of Venice

The spread of fecal pollutants and antibiotic resistance in the aquatic environment represents a major public health concern and is predicted to increase in light of climate change consequences and the increasing human population pressure on the lagoon and coastal areas. The city of Venice (Italy) is affected by diverse microbial pollution sources, including domestic wastewaters that, due to the lack of modern sewage treatment infrastructure in the historical city center, are released into canals. The outflowing jets of its tidal inlets thus represent a source of contamination for the nearby beaches on the barrier island separating the lagoon from the sea. Metagenomic analyses of DNA extracted from sediment samples from six sites in the canals of the city’s historic center were undertaken to characterize the microbial community composition, the presence of fecal microbes as well as other non-enteric pathogens, and the content of genes related to antibiotic (AB) and heavy metal (HM) resistance, and virulence. The six sites hosted similar prokaryotic communities, although variations in community composition likely related to oxygen availability were observed. All sites displayed relatively high levels of fecal contamination, including the presence of Fecal Indicator Bacteria, sewage- and alternative feces-associated bacteria. Relatively high levels of other potential pathogens were also found. About 1 in 500 genes identified at these sites are related to AB and HM resistance; conversely, genes related to virulence were rare. Our data suggest the existence of widespread sediment microbial pollution in the canals of Venice, coupled with the prevalence of ARGs to antibiotics frequently used in humans as well as of HMRGs to toxic metals that still persists in the lagoon. All of this evidence raises concerns about the consequences on the water quality of the lagoon and adjacent marine areas and the potential risks for humans, deserving further studies.

Investigation of polyethylene terephthalate (PET) drinking bottles as marine reservoirs for fecal bacteria and phytoplankton

Polyethylene terephthalate (PET) is frequently used in the food and beverage industry and therefore contributes greatly to plastic marine debris. The fecal pollution indicator bacteria Enterococcus is used for marine water contamination assessments and is regularly found in storm water discharge. In order to examine if PET drinking bottles act as refuges for Enterococcus, a study was conducted within euhaline tidal waters of Wrightsville Beach, NC, USA via the deployment of bottle floats positioned nearby two stormwater outfall pipes. Bottles were retrieved weekly to assess the accumulation of fecal bacteria and phytoplankton. Each bottle was analyzed for the presence of Enterococcus on plastic surfaces and within water inside the bottle. Abundance of Enterococcus and planktonic chlorophyll α was found to be significantly greater in association with PET bottles versus the surrounding waters. Bottles were observed to act as reservoirs for both Enterococcus and phytoplankton with concentrations well above the state, federal, and WHO standards.