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To assess the prevalence and abundance of antibiotic resistance genes in human and livestock gut microbiomes, 87 humans (healthy individuals and patients with Clostridioides difficile infection (CDI)) and 108 livestock (swine, cattle, and chickens) were enrolled. Gut microbiomes and fluoroquinolone-resistant Escherichia coli isolates were sequenced, and mobile genetic elements adjacent to the β-lactamase (bla) and transferable quinolone resistance (qnr) genes were compared using metagenomic contigs. Each group of humans and livestock exhibited distinctive microbiota and resistome compositions in the gut. Concerning the resistome of bla and qnr, the prevalence rates between chickens and patients with CDI were the most similar (R2 = 0.46); blaTEM, blaOXA, blaCTX-M, and qnrS were highly prevalent in both groups. According to genomic and phylogenetic analyses, blaCTX-M and blaOXA expressed lineage specificity to either humans or livestock, while qnrS and blaTEM displayed a shared lineage between humans and livestock. A qnrS1 mobilome comprising five genes, including two recombinases, a transposase, and a plasmid gene, is commonly found in human and chicken gut microbiomes. Humans and chickens showed the most similar gut resistomes to β-lactams and quinolones. QnrS and blaTEM displayed especially strong co-occurrence between the guts of humans and livestock. [ABSTRACT FROM AUTHOR]

Objective was to analyse bacterial composition and abundance of Clostridioides difficile in gut microbiome of patients with C. difficile infection (CDI) in association with clinical characteristics. Whole metagenome sequencing of gut microbiome of 26 CDI patients was performed, and the relative abundance of C. difficile and its toxin genes was measured. Clinical characteristics of the patients were obtained through medical records. A strong correlation between the abundance of C. difficile and tcdB genes in CDI patients was found. The relative abundance of C. difficile in the gut microbiome ranged from undetectable to 2.8% (median 0.089). Patients with fever exhibited low abundance of C. difficile in their gut, and patients with fewer C. difficile organisms required long-term anti-CDI treatment. Abundance of Bifidobacterium and Bacteroides negatively correlated with that of C. difficile at the genus level. CDI patients were clustered using the bacterial composition of the gut: one with high population of Enterococcus (cluster 1, n = 12) and another of Bacteroides or Lactobacillus (cluster 2, n = 14). Cluster1 showed significantly lower bacterial diversity and clinical cure at the end of treatment. Additionally, patients with CDI exhibited increased ARGs; notably, blaTEM, blaSHV and blaCTX-M were enriched. C. difficile existed in variable proportion of the gut microbiome in CDI patients. CDI patients with Enterococcus-rich microbiome in the gut had lower bacterial diversity and poorer clinical cure. [ABSTRACT FROM AUTHOR]

Plastic products contain numerous additive chemicals, which are present in large amount, and can be transferred to the marine environment. In this study, we quantified chemical additives and persistent organic pollutants (POPs) in marine plastic debris, along with their corresponding new plastic products (e.g., fishing gear, packaging material, and cigarette butts). The levels of chemical additives were significantly higher than those of conventional POPs in plastic samples, which was indicative of the widespread utilization of additives in plastics. New plastic products contained significantly higher additive concentrations than plastic debris, implying potential leaching during use or after disposal in the marine environment. In fishing gear materials, buoys generally contained high concentrations of antioxidants (280–91,000 ng/g). Polyvinyl chloride (PVC) rope used in aquaculture had the highest phthalate and bisphenol A (BPA) concentrations, and the second-highest ultraviolet radiation stabilizers. Rubber bars from the tire recycling used in aquaculture contained the highest 6PPD-quinone concentration, which is known to be responsible for salmon death. This is the first quantitative analysis of 6PPD-quinone in recycling tire, suggesting a need for chemical analysis of the tires itself, not only in environmental matrices. Compared to fishing gear materials, concentrations of the targeted chemical additives were relatively low in packaging material and cigarette butts, except for plastic bags. The concentration difference between new and debris was largest in PVC rope for aquaculture farm. It was estimated that 340–470 kg of phthalates and 140–194 kg of BPA are released into the sea from this PVC rope in Korean marine aquaculture. The study indicates that aquaculture fishing gear represents a significant source of chemical additives in the marine environment. It also suggests that exercising caution is crucial when considering the use of recycled plastics in aquaculture gear due to potential chemical contamination of the marine environment. [Display omitted] • First comprehensive quantification of plastic additives in fishing gears from Korea. • New products contained significantly higher additive contents than debris samples. • Fishing gears displayed greater additive contents compared to other plastic items. • High levels of hazardous chemicals in aquaculture gear with recycled plastic. • Fishing gear is a significant source of chemical additives in the marine environment. [ABSTRACT FROM AUTHOR]

To characterize the carriage of antibiotic resistance genes (ARGs) in the gut microbiome of healthy individuals. Fecal carriage of ARGs was investigated in 61 healthy individuals aged 30 to 59 years through whole metagenome sequencing of the gut microbiome and a targeted metagenomic approach. The number of ARGs in the gut microbiome was counted and normalized per million predicted genes (GPM). In the Korean population, the resistome ranged from 49.7 to 292.5 GPM (median 89.7). Based on the abundance of ARGs, the subjects were categorised into high (> 120 GPM), middle (60‒120 GPM), and low (< 60 GPM) ARG groups. Individuals in the high ARG group tended to visit hospitals more often (P = 0.065), particularly for upper respiratory tract infections (P = 0.066), and carried more blaCTX-M (P = 0.008). The targeted metagenome approach for bla and plasmid-mediated quinolone resistance (PMQR) genes revealed a high fecal carriage rate; 23% or 13.1% of the subjects carried blaCTX-M or blaCMY-2, respectively. Regarding PMQR genes, 59% of the subjects carried PMQR, and 83% of them harboured 2‒4 PMQR genes (qnrB 44.3%, qnrS 47.5% etc.). The presence of blaCTX-M correlated with ARG abundance in the gut resistome, whereas PMQR genes were irrelevant to other ARGs (P = 0.176). Fecal carriage of blaCTX-M and PMQR genes was broad and multiplexed among healthy individuals. [ABSTRACT FROM AUTHOR]

Human activity is thought to affect the abundance and contamination characteristics of microplastics (MPs) in the environment, which may in turn affect aquatic species. However, few studies have examined the impact of coastal area use pattern on characteristics of MPs in coastal regions. In this study, we investigated MP contamination of abiotic matrices (seawater and sediment) and biotic matrices (bivalves and polychaetes) in three coastal regions characterized by different types of human activity, covering urban, aquafarm, and rural areas. MP abundance was higher in sediment from the urban site than in that from the rural site, but similar to that from the aquafarm site. In the abiotic matrices, different MP polymer compositions were observed among the three sites. Diverse polymers were found in marine matrices from the urban site, implying diverse MP sources in highly populated and industrialized areas. Polystyrene was more abundant in the aquafarm site, reflecting the wide use of expanded polystyrene aquaculture buoys. Polypropylene was more abundant at the rural site, probably due to the use of polypropylene ropes and nets in fishing activity. MP accumulation profiles in marine invertebrates showed trends similar to those exhibited by abiotic matrices, reflecting coastal area use patterns. These results indicate that marine MPs are generated from both land- and marine-based sources, and that the abiotic and biotic marine matrices reflect the MP characteristics. Image 1 • Microplastic (MP) contamination was compared in urban, aquafarm, and rural areas. • MP shape, size, and polymer type were examined in various marine matrices. • Coastal area use pattern and MP contamination were found to be closely related. • Diverse polymers were found in marine matrices, creek, and road dust from urban. • Marine-based activities are important contributors to MP contamination. [ABSTRACT FROM AUTHOR]

This is the first report to evaluate the potential effects of microplastics (MPs) on wild wharf roaches (Ligia exotica) in a shoreline habitant. L. exotica is an important plastic detritus consumer in coastal area. A survey was conducted from May to June in the years 2019 and 2020 in two South Korean nearshore sites: Nae-do (as MPs-uncontaminated) and Maemul-do (as MPs-contaminated). MPs (>20 μm in size) were detected highly in gastrointestinal tracts of the L. exotica from Maemul-do, at an average level of 50.56 particles/individual. They were detected in much lower levels in the L. exotica from Nae-do. at an average rate of 1.00 particles/individual. The polymer type and shape were dominated by expanded polystyrene (EPS, 93%) and fragment (99.9%) in L. exotica from Maemul-do. Especially, Hexabromocyclododecanes, brominated flame retardants added to EPS, have been detected highly in L. exotica from Maemul-do (630.86 ± 587.21 ng/g l. w.) than those of Nae-do (detection limit: 10.5 ng/g l. w). Genome-wide transcriptome profiling revealed altered expression of genes associated with fatty acid metabolic processes, the innate-immune response-activating system and vesicle cytoskeletal trafficking in L. exotica from Maemul-do. The activation of the p53 signaling pathway (which is related to proteasome, ER regulation and cell morphogenesis) is likely to be involved in the EPS-uptake of wild L. exotica. Four neurosteroids were also detected in head tissue, and cortisol and progesterone concentrations differed significantly in L. exotica from Maemul-do. Our findings also suggest that resident plastic detritus consumer might be a useful indicator organism for evaluating pollution and potential effects of environmental microplastics. [Display omitted] • This is the first study to clarify the toxic effects derived from MP contamination in L. exotica. • MP contamination was higher in L. exotica from Maemul-do (50.56 particles/individual). • Composition of MP was dominated by the expanded polystyrene in L. exotica from Maemul-do (93%). • Abundant MP concentration altered the metabolic and immune system. • Significant variated neurosteroids also might be caused by MP contamination. [ABSTRACT FROM AUTHOR]

Background Antibiotics administered to farm animals have led to increasing prevalence of resistance genes in different microbiomes and environments. While antibiotic treatments help cure infectious diseases in farm animals, the possibility of spreading antibiotic resistance genes into the environment and human microbiomes raises significant concerns. Through long-term evolution, antibiotic resistance genes have mutated, thereby complicating the resistance problems. Results In this study, we performed deep sequencing of the gut microbiomes of 36 swine and 41 cattle in Korean farms, and metagenomic analysis to understand the diversity and prevalence of antibiotic resistance genes. We found that aminoglycoside, β-lactam, lincosamide, streptogramin, and tetracycline were the prevalent resistance determinants in both swine and cattle. Tetracycline resistance was abundant and prevalent in cattle and swine. Specifically, tetQ, tetW, tetO, tet32 , and tet44 were the 5 most abundant and prevalent tetracycline resistance genes. Their prevalence was almost 100% in swine and cattle. While tetQ was similarly abundant in both swine and cattle, tetW was more abundant in swine than in cattle. Aminoglycoside was the second highest abundant resistance determinant in swine, but not in cattle. In particular, ANT(6) and APH(3′′) were the dominant resistance gene families in swine. β-lactam was also an abundant resistance determinant in both swine and cattle. Cfx was the major contributing gene family conferring resistance against β-lactams. Conclusions Antibiotic resistome was more pervasive in swine than in cattle. Specifically, prevalent antibiotic resistance genes (prevalence >50%) were found more in swine than in cattle. Genomic investigation of specific resistance genes from the gut microbiomes of swine and cattle in this study should provide opportunities to better understand the exchange of antibiotic resistance genes in farm animals. [ABSTRACT FROM AUTHOR]