Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms. - Related Documents




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767701.0000Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms. Dairy farms are major reservoirs of zoonotic bacterial pathogens, which harbor antimicrobial resistance genes (ARGs), and raise critical questions about their dissemination on and off the farm environment. Here, we investigated the role of coprophagous muscid flies (Diptera: Muscidae) as carriers of zoonotic pathogens and antimicrobial resistance. We collected cow manure and flies on a dairy farm and used shotgun metagenomics to identify the presence of clinically relevant bacteria, virulence factors, and ARGs in both environments. Our results reveal that, although the fly microbiome is largely composed of manure-associated taxa, they also harbor specific insect-associated bacteria, which may be involved in nutrient provisioning to the host. Furthermore, we identifed shared ARGs, virulence factors, and zoonotic pathogens enriched within the fly gastrointestinal tract (GIT). Our study illustrates the potential flow of pathogenic microorganisms from manure to coprophagous flies, suggesting that flies may pose an important zoonotic threat on dairy farms.202540537478
768410.9997Trophic level and proteobacteria abundance drive antibiotic resistance levels in fish from coastal New England. BACKGROUND: The natural marine environment represents a vast reservoir of antimicrobial resistant bacteria. The wildlife that inhabits this environment plays an important role as the host to these bacteria and in the dissemination of resistance. The relationship between host diet, phylogeny, and trophic level and the microbiome/resistome in marine fish is not fully understood. To further explore this relationship, we utilize shotgun metagenomic sequencing to define the gastrointestinal tract microbiomes of seven different marine vertebrates collected in coastal New England waters. RESULTS: We identify inter and intraspecies differences in the gut microbiota of these wild marine fish populations. Furthermore, we find an association between antibiotic resistance genes and host dietary guild, which suggests that higher trophic level organisms have a greater abundance of resistance genes. Additionally, we demonstrate that antibiotic resistance gene burden is positively correlated with Proteobacteria abundance in the microbiome. Lastly, we identify dietary signatures within the gut of these fish and find evidence of possible dietary selection for bacteria with specific carbohydrate utilization potential. CONCLUSIONS: This work establishes a link between host lifestyle/dietary guild, and microbiome composition and the abundance of antibiotic resistance genes within the gastrointestinal tract of marine organisms. We expand the current understanding of marine organism-associated microbial communities and their role as reservoirs of antimicrobial resistance genes.202336879316
325520.9997Early life dynamics of ARG and MGE associated with intestinal virome in neonatal piglets. The pre- and post-weaning stages for piglets are critical periods for the maturation of intestinal functions and contamination with antibiotic resistant bacterial pathogens will threaten their intestinal health. The presence of bacteriophage can also alter bacterial populations in the intestine but whether transmission of antibiotic resistance genes (ARG) is affected by phage during maturation of the neonatal piglet intestine is not known. We therefore identified the intestinal virome along with ARGs and mobile genetic elements (MGE) from piglet fecal samples collected from 3 to 28 days representing the different growth stages. We found wide fluctuations for the intestinal virome of weaning piglets and most virus - related antibiotic resistance was derived from temperate phage suggesting a reservoir of multidrug resistance was present in the neonatal porcine gut. Our results provide a comprehensive understanding of ARGs associated with the intestinal virome that therefore represents a potential risk for horizontal ARG transfer to pathogenic bacteria.202236191572
669830.9997The risk of transmitting antibiotic resistance through endophytic bacteria. Antibiotic resistance is a global human health threat distributed across humans, animals, plants, and the environment. Under the One-Health concept (humans, animals, and environment), the contamination of water bodies and soil by antibiotic-resistant bacteria cannot be dissociated from its potential transmission to humans. Edible plants can be colonized by a vast diversity of bacteria, representing an important link between the environment and humans in the One-Health triad. Based on multiple examples of bacterial groups that comprise endophytes reported in edible plants, and that have close phylogenetic proximity with human opportunistic pathogens, we argue that plants exposed to human-derived biological contamination may represent a path of transmission of antibiotic resistance to humans.202134593300
334240.9996Marine sediment bacteria harbor antibiotic resistance genes highly similar to those found in human pathogens. The ocean is a natural habitat for antibiotic-producing bacteria, and marine aquaculture introduces antibiotics into the ocean to treat infections and improve aquaculture production. Studies have shown that the ocean is an important reservoir of antibiotic resistance genes. However, there is a lack of understanding and knowledge about the clinical importance of the ocean resistome. We investigated the relationship between the ocean bacterial resistome and pathogenic resistome. We applied high-throughput sequencing and metagenomic analyses to explore the resistance genes in bacterial plasmids from marine sediments. Numerous putative resistance determinants were detected among the resistance genes in the sediment bacteria. We also found that several contigs shared high identity with transposons or plasmids from human pathogens, indicating that the sediment bacteria recently contributed or acquired resistance genes from pathogens. Marine sediment bacteria could play an important role in the global exchange of antibiotic resistance.201323370726
736550.9996A case study on the distribution of the environmental resistome in Korean shrimp farms. Hundreds of tons of antibiotics are widely used in aquaculture to prevent microbial infections and promote fish growth. However, the overuse of antibiotics and chemical products can lead to the selection and spreading of antibiotic-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs), which are of great concern considering the threat to public health worldwide. Here, in-depth metagenome sequencing was performed to explore the environmental resistome and ARB distribution across farming stages in shrimp farms and examine anthropogenic effects in nearby coastal waters. A genome-centric analysis using a metagenome binning approach allowed us to accurately investigate the distribution of pathogens and ARG hosts in shrimp farms. The diversity of resistomes was higher in shrimp farms than in coastal waters, and the distribution of resistomes was dependent on the farming stage. In particular, the tetracycline resistance gene was found mainly at the early post-larval stage regardless of the farm. The metagenome-assembled genomes of Vibrio spp. were dominant at this stage and harbored tet34, which is known to confer resistance to oxytetracycline. In addition, opportunistic pathogens such as Francisella, Mycoplasma, Photobacterium, and Vibrio were found in abundance in shrimp farms, which had multiple virulence factors. This study highlights the increased resistance diversity and environmental selection of pathogens in shrimp farms. The use of environmental pollutants on farms may cause an increase in resistome diversity/abundance and the transmission of pathogens to the surrounding environment, which may pose future risks to public health and aquatic organisms.202134653940
334160.9996The shared resistome of human and pig microbiota is mobilized by distinct genetic elements. The extensive use of antibiotics in hospitals and in the animal breeding industry has promoted antibiotic resistance in bacteria, which resulted in the emergence of a large number of antibiotic resistance genes in the intestinal tract of human and farmed animals. Genetic exchange of resistance genes between the two ecosystems is now well documented for pathogenic bacteria, but the repertoire of shared resistance genes in the commensal bacterial community and by which genetic modules they are disseminated are still unclear. By analyzing metagenomics data of human and pig intestinal samples both collected in Shenzhen, China, a set of 27 highly prevalent antibiotic resistance genes was found to be shared between human and pig intestinal microbiota. The mobile genetic context for 11 of these core antibiotic resistance genes could be identified by mining their carrying scaffolds constructed from the two datasets, leading to the detection of seven integrative and conjugative/mobilizable elements and two IS-related transposons. The comparison of the relative abundances between these detected mobile genetic elements and their associated antibiotic resistance genes revealed that for many genes, the estimated contribution of the mobile elements to the gene abundance differs strikingly depending on the host. These findings indicate that although some antibiotic resistance genes are ubiquitous across microbiota of human and pig populations, they probably relied on different genetic elements for their dissemination within each population.IMPORTANCE There is growing concern that antibiotic resistance genes could spread from the husbandry environment to human pathogens through dissemination mediated by mobile genetic elements. In this study, we investigated the contribution of mobile genetic elements to the abundance of highly prevalent antibiotic resistance genes found in commensal bacteria of both human and pig intestinal microbiota originating from the same region. Our results reveal that for most of these antibiotic resistance genes, the abundance is not explained by the same mobile genetic element in each host, suggesting that the human and pig microbial communities promoted a different set of mobile genetic carriers for the same antibiotic resistance genes. These results deepen our understanding of the dissemination of antibiotic resistance genes among and between human and pig gut microbiota.202133310720
324170.9996Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms. Anthropogenic environments have been implicated in enrichment and exchange of antibiotic resistance genes and bacteria. Here we study the impact of confined and controlled swine farm environments on temporal changes in the gut microbiome and resistome of veterinary students with occupational exposure for 3 months. By analyzing 16S rRNA and whole metagenome shotgun sequencing data in tandem with culture-based methods, we show that farm exposure shapes the gut microbiome of students, resulting in enrichment of potentially pathogenic taxa and antimicrobial resistance genes. Comparison of students' gut microbiomes and resistomes to farm workers' and environmental samples revealed extensive sharing of resistance genes and bacteria following exposure and after three months of their visit. Notably, antibiotic resistance genes were found in similar genetic contexts in student samples and farm environmental samples. Dynamic Bayesian network modeling predicted that the observed changes partially reverse over a 4-6 month period. Our results indicate that acute changes in a human's living environment can persistently shape their gut microbiota and antibiotic resistome.202032188862
325380.9996Metagenome-assembled genomes indicate that antimicrobial resistance genes are highly prevalent among urban bacteria and multidrug and glycopeptide resistances are ubiquitous in most taxa. INTRODUCTION: Every year, millions of deaths are associated with the increased spread of antimicrobial resistance genes (ARGs) in bacteria. With the increasing urbanization of the global population, the spread of ARGs in urban bacteria has become a more severe threat to human health. METHODS: In this study, we used metagenome-assembled genomes (MAGs) recovered from 1,153 urban metagenomes in multiple urban locations to investigate the fate and occurrence of ARGs in urban bacteria. Additionally, we analyzed the occurrence of these ARGs on plasmids and estimated the virulence of the bacterial species. RESULTS: Our results showed that multidrug and glycopeptide ARGs are ubiquitous among urban bacteria. Additionally, we analyzed the deterministic effects of phylogeny on the spread of these ARGs and found ARG classes that have a non-random distribution within the phylogeny of our recovered MAGs. However, few ARGs were found on plasmids and most of the recovered MAGs contained few virulence factors. DISCUSSION: Our results suggest that the observed non-random spreads of ARGs are not due to the transfer of plasmids and that most of the bacteria observed in the study are unlikely to be virulent. Additional research is needed to evaluate whether the ubiquitous and widespread ARG classes will become entirely prevalent among urban bacteria and how they spread among phylogenetically distinct species.202336760505
769490.9996The Human Gut Resistome up to Extreme Longevity. Antibiotic resistance (AR) is indisputably a major health threat which has drawn much attention in recent years. In particular, the gut microbiome has been shown to act as a pool of AR genes, potentially available to be transferred to opportunistic pathogens. Herein, we investigated for the first time changes in the human gut resistome during aging, up to extreme longevity, by analyzing shotgun metagenomics data of fecal samples from a geographically defined cohort of 62 urban individuals, stratified into four age groups: young adults, elderly, centenarians, and semisupercentenarians, i.e., individuals aged up to 109 years. According to our findings, some AR genes are similarly represented in all subjects regardless of age, potentially forming part of the core resistome. Interestingly, aging was found to be associated with a higher burden of some AR genes, including especially proteobacterial genes encoding multidrug efflux pumps. Our results warn of possible health implications and pave the way for further investigations aimed at containing AR accumulation, with the ultimate goal of promoting healthy aging. IMPORTANCE Antibiotic resistance is widespread among different ecosystems, and in humans it plays a key role in shaping the composition of the gut microbiota, enhancing the ecological fitness of certain bacterial populations when exposed to antibiotics. A considerable component of the definition of healthy aging and longevity is associated with the structure of the gut microbiota, and, in this regard, the presence of antibiotic-resistant bacteria is critical to many pathologies that come about with aging. However, the structure of the resistome has not yet been sufficiently elucidated. Here, we show distinct antibiotic resistance assets and specific microbial consortia characterizing the human gut resistome through aging.202134494880
6589100.9996Differential Overlap in Human and Animal Fecal Microbiomes and Resistomes in Rural versus Urban Bangladesh. Low- and middle-income countries (LMICs) bear the largest mortality burden of antibiotic-resistant infections. Small-scale animal production and free-roaming domestic animals are common in many LMICs, yet data on zoonotic exchange of gut bacteria and antibiotic resistance genes (ARGs) in low-income communities are sparse. Differences between rural and urban communities with regard to population density, antibiotic use, and cohabitation with animals likely influence the frequency of transmission of gut bacterial communities and ARGs between humans and animals. Here, we determined the similarity in gut microbiomes, using 16S rRNA gene amplicon sequencing, and resistomes, using long-read metagenomics, between humans, chickens, and goats in a rural community compared to an urban community in Bangladesh. Gut microbiomes were more similar between humans and chickens in the rural (where cohabitation is more common) than the urban community, but there was no difference for humans and goats in the rural versus the urban community. Human and goat resistomes were more similar in the urban community, and ARG abundance was higher in urban animals than rural animals. We identified substantial overlap of ARG alleles in humans and animals in both settings. Humans and chickens had more overlapping ARG alleles than humans and goats. All fecal hosts from the urban community and rural humans carried ARGs on chromosomal contigs classified as potentially pathogenic bacteria, including Escherichia coli, Campylobacter jejuni, Clostridioides difficile, and Klebsiella pneumoniae. These findings provide insight into the breadth of ARGs circulating within human and animal populations in a rural compared to urban community in Bangladesh. IMPORTANCE While the development of antibiotic resistance in animal gut microbiomes and subsequent transmission to humans has been demonstrated in intensive farming environments and high-income countries, evidence of zoonotic exchange of antibiotic resistance in LMIC communities is lacking. This research provides genomic evidence of overlap of antibiotic resistance genes between humans and animals, especially in urban communities, and highlights chickens as important reservoirs of antibiotic resistance. Chicken and human gut microbiomes were more similar in rural Bangladesh, where cohabitation is more common. Incorporation of long-read metagenomics enabled characterization of bacterial hosts of resistance genes, which has not been possible in previous culture-independent studies using only short-read sequencing. These findings highlight the importance of developing strategies for combatting antibiotic resistance that account for chickens being reservoirs of ARGs in community environments, especially in urban areas.202235862660
3924110.9996Antimicrobial resistance determinants in silage. Animal products may play a role in developing and spreading antimicrobial resistance in several ways. On the one hand, residues of antibiotics not adequately used in animal farming can enter the human body via food. However, resistant bacteria may also be present in animal products, which can transfer the antimicrobial resistance genes (ARG) to the bacteria in the consumer's body by horizontal gene transfer. As previous studies have shown that fermented foods have a meaningful ARG content, it is indicated that such genes may also be present in silage used as mass feed in the cattle sector. In our study, we aspired to answer what ARGs occur in silage and what mobility characteristics they have? For this purpose, we have analyzed bioinformatically 52 freely available deep sequenced silage samples from shotgun metagenome next-generation sequencing. A total of 16 perfect matched ARGs occurred 54 times in the samples. More than half of these ARGs are mobile because they can be linked to integrative mobile genetic elements, prophages or plasmids. Our results point to a neglected but substantial ARG source in the food chain.202235347213
7678120.9996Viral Metagenomics Reveals Widely Diverse Viral Community of Freshwater Amazonian Lake. Despite the importance of understanding the ecology of freshwater viruses, there are not many studies on the subject compared to marine viruses. The microbiological interactions in these environments are still poorly known, especially between bacteriophages and their host bacteria and between cyanophages and cyanobacteria. Lake Bologna, Belém, capital of the Brazilian State of Pará, is a water source that supplies the city and its metropolitan region. However, it remains unexplored regarding the contents of its virome and viral diversity composition. Therefore, this work aims to explore the taxonomic diversity of DNA viruses in this lake, especially bacteriophages and cyanophages, since they can act as transducers of resistance genes and reporters of water quality for human consumption. We used metagenomic sequencing data generated by previous studies. We analyzed it at the taxonomic level using the tools Kraken2, Bracken, and Pavian; later, the data was assembled using Genome Detective, which performs the assembly of viruses. The results observed here suggest the existence of a widely diverse viral community and established microbial phage-regulated dynamics in Lake Bolonha. This work is the first ever to describe the virome of Lake Bolonha using a metagenomic approach based on high-throughput sequencing, as it contributes to the understanding of water-related public health concerns regarding the spreading of antibiotic resistance genes and population control of native bacteria and cyanobacteria.202235548089
7478130.9996Global analysis of the metaplasmidome: ecological drivers and spread of antibiotic resistance genes across ecosystems. BACKGROUND: Plasmids act as vehicles for the rapid spread of antibiotic resistance genes (ARGs). However, few studies of the resistome at the community level distinguish between ARGs carried by mobile genetic elements and those carried by chromosomes, and these studies have been limited to a few ecosystems. This is the first study to focus on ARGs carried by the metaplasmidome on a global scale. RESULTS: This study shows that only a small fraction of the plasmids reconstructed from 27 ecosystems representing 9 biomes are catalogued in public databases. The abundance of ARGs harboured by the metaplasmidome was significantly explained by bacterial richness. Few plasmids with or without ARGs were shared between ecosystems or biomes, suggesting that plasmid distribution on a global scale is mainly driven by ecology rather than geography. The network linking plasmids to their hosts shows that these mobile elements have thus been shared between bacteria across geographically distant environmental niches. However, certain plasmids carrying ARGs involved in human health were identified as being shared between multiple ecosystems and hosted by a wide variety of hosts. Some of these mobile elements, identified as keystone plasmids, were characterised by an enrichment in antibiotic resistance genes (ARGs) and CAS-CRISPR components which may explain their ecological success. The ARGs accounted for 9.2% of the recent horizontal transfers between bacteria and plasmids. CONCLUSIONS: By comprehensively analysing the plasmidome content of ecosystems, some key habitats have emerged as particularly important for monitoring the spread of ARGs in relation to human health. Of particular note is the potential for air to act as a vector for long-distance transport of ARGs and accessory genes across ecosystems and continents. Video Abstract.202540108678
3222140.9996Differences in gut metagenomes between dairy workers and community controls: a cross-sectional study. BACKGROUND: As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens as they undergo evolution prior to a spillover event. In light of this, we are interested in characterizing the microbiome and resistome of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases. RESULTS: Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of the human gut microbiome of 10 dairy farm workers and 6 community controls, supplementing these samples with additional publicly available gut metagenomes. We observed greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes in dairy workers' metagenomes, and lower average gene diversity. We also found evidence of commensal organism association with plasmid-mediated tetracycline resistance genes in both dairy workers and community controls (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii). However, we did not find significant differences in the prevalence of resistance genes or virulence factors overall, nor differences in the taxonomic composition of dairy worker and community control metagenomes. CONCLUSIONS: This study presents the first metagenomics analysis of United States dairy workers, providing insights into potential risks of exposure to antibiotics and pathogens in animal farming environments. Previous metagenomic studies of livestock workers in China and Europe have reported increased abundance and carriage of antibiotic resistance genes in livestock workers. While our investigation found no strong evidence for differences in the abundance or carriage of antibiotic resistance genes and virulence factors between dairy worker and community control gut metagenomes, we did observe patterns in the abundance of tetracycline resistance genes and the prevalence of cephamycin resistance genes that is consistent with previous work.202337215025
3256150.9996Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition. BACKGROUND: In environmental bacteria, the selective advantage of antibiotic resistance genes (ARGs) can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes, and virulence genes (VGs). The gut microbiome of infants has been shown to contain numerous ARGs, however, co-localization related to ARGs is unknown during early life despite frequent exposures to biocides and metals from an early age. RESULTS: We conducted a comprehensive analysis of genetic co-localization of resistance genes in a cohort of 662 Danish children and examined the association between such co-localization and environmental factors as well as gut microbial maturation. Our study showed that co-localization of ARGs with other resistance and virulence genes is common in the early gut microbiome and is associated with gut bacteria that are indicative of low maturity. Statistical models showed that co-localization occurred mainly in the phylum Proteobacteria independent of high ARG content and contig length. We evaluated the stochasticity of co-localization occurrence using enrichment scores. The most common forms of co-localization involved tetracycline and fluoroquinolone resistance genes, and, on plasmids, co-localization predominantly occurred in the form of class 1 integrons. Antibiotic use caused a short-term increase in mobile ARGs, while non-mobile ARGs showed no significant change. Finally, we found that a high abundance of VGs was associated with low gut microbial maturity and that VGs showed even higher potential for mobility than ARGs. CONCLUSIONS: We found that the phenomenon of co-localization between ARGs and other resistance and VGs was prevalent in the gut at the beginning of life. It reveals the diversity that sustains antibiotic resistance and therefore indirectly emphasizes the need to apply caution in the use of antimicrobial agents in clinical practice, animal husbandry, and daily life to mitigate the escalation of resistance. Video Abstract.202438730321
4024160.9996Potential influence of antimicrobial resistance gene content in probiotic bacteria on the gut resistome ecosystems. Antimicrobial resistance (AMR) poses a substantial threat to human health. The commensal bacteria of the gut microbiome were shown to serve as a reservoir of antibiotic resistance genes (ARGs), termed the gut resistome, which has the potential to transfer horizontally to pathogens and contribute to the emergence of drug-resistant bacteria. Namely, AMR traits are generally linked with mobile genetic elements (MGEs), which apart from disseminating vertically to the progeny, may cross horizontally to the distantly related microbial species. On the other hand, while probiotics are generally considered beneficiary to human health, and are therefore widely consumed in recent years most commonly in conjunction with antibiotics, the complexities and extent of their impact on the gut microbiome and resistome have not been elucidated. By reviewing the latest studies on ARG containing commercial probiotic products and common probiotic supplement species with their actual effects on the human gut resistome, this study aims to demonstrate that their contribution to the spread of ARGs along the GI tract merits additional attention, but also indicates the changes in sampling and profiling of the gut microbiome which may allow for the more comprehensive studying of the effects of probiotics in this part of the resistome.202336819705
3259170.9996Prevalence of antibiotic resistance genes and bacterial pathogens along the soil-mangrove root continuum. Plants roots are colonised by soil bacteria that are known to be the reservoir of antibiotic resistance genes (ARGs). ARGs can transfer between these microorganisms and pathogens, but to what extent these ARGs and pathogens disseminate from soil into plant is poorly understood. Here, we examined a high-resolution resistome profile along the soil-root continuum of mangrove saplings using amplicon and metagenomic sequencing. Data revealed that 91.4% of total ARGs were shared across four root-associated compartments (endosphere, episphere, rhizosphere and unplanted soil). Rather than compartment-selective dynamics of microbiota, the resistome was disseminated in a continuous fashion along the soil-root continuum. Such dissemination was independent of underlying root-associated bacterial and fungal microbiota, but might be facilitated by a multiplicity of mobile genetic elements. As the multiple-drug resistant pathogens, Vibrio vulnificus, pathogenic Escherichia coli and Klebsiella pneumoniae consistently predominated across four compartments, indicating the potential dissemination of antibiotic pathogens along the soil-root continuum. Through deciphering the profile and dynamics of the root-associated resistome and pathogens, our study identified the soil-root continuum as an interconnected sink through which certain ARGs and pathogens can flow from soil into the plant.202133421848
3884180.9996Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non-agricultural metagenomes. There is concern that antibiotic resistance can potentially be transferred from animals to humans through the food chain. The relationship between specific antibiotic resistant bacteria and the genes they carry remains to be described. Few details are known about the ecology of antibiotic resistant genes and bacteria in food production systems, or how antibiotic resistance genes in food animals compare to antibiotic resistance genes in other ecosystems. Here we report the distribution of antibiotic resistant genes in publicly available agricultural and non-agricultural metagenomic samples and identify which bacteria are likely to be carrying those genes. Antibiotic resistance, as coded for in the genes used in this study, is a process that was associated with all natural, agricultural, and human-impacted ecosystems examined, with between 0.7 to 4.4% of all classified genes in each habitat coding for resistance to antibiotic and toxic compounds (RATC). Agricultural, human, and coastal-marine metagenomes have characteristic distributions of antibiotic resistance genes, and different bacteria that carry the genes. There is a larger percentage of the total genome associated with antibiotic resistance in gastrointestinal-associated and agricultural metagenomes compared to marine and Antarctic samples. Since antibiotic resistance genes are a natural part of both human-impacted and pristine habitats, presence of these resistance genes in any specific habitat is therefore not sufficient to indicate or determine impact of anthropogenic antibiotic use. We recommend that baseline studies and control samples be taken in order to determine natural background levels of antibiotic resistant bacteria and/or antibiotic resistance genes when investigating the impacts of veterinary use of antibiotics on human health. We raise questions regarding whether the underlying biology of each type of bacteria contributes to the likelihood of transfer via the food chain.201223133629
7693190.9996Prevalence of Antibiotic Resistance Genes among Human Gut-Derived Bifidobacteria. The microbiota of the human gastrointestinal tract (GIT) may regularly be exposed to antibiotics, which are used to prevent and treat infectious diseases caused by bacteria and fungi. Bacterial communities of the gut retain a reservoir of antibiotic resistance (AR) genes, and antibiotic therapy thus positively selects for those microorganisms that harbor such genetic features, causing microbiota modulation. During the first months following birth, bifidobacteria represent some of the most dominant components of the human gut microbiota, although little is known about their AR gene complement (or resistome). In the current study, we assessed the resistome of the Bifidobacterium genus based on phenotypic and genotypic data of members that represent all currently recognized bifidobacterial (sub)species. Moreover, a comparison between the bifidobacterial resistome and gut metagenome data sets from adults and infants shows that the bifidobacterial community present at the first week following birth possesses a reduced AR arsenal compared to that present in the infant bifidobacterial population in subsequent weeks of the first year of life. Our findings reinforce the concept that the early infant gut microbiota is more susceptible to disturbances by antibiotic treatment than the gut microbiota developed at a later life stage. IMPORTANCE: The spread of resistance to antibiotics among bacterial communities has represented a major concern since their discovery in the last century. The risk of genetic transfer of resistance genes between microorganisms has been extensively investigated due to its relevance to human health. In contrast, there is only limited information available on antibiotic resistance among human gut commensal microorganisms such as bifidobacteria, which are widely exploited by the food industry as health-promoting microorganisms or probiotic ingredients. In the current study, we explored the occurrence of antibiotic resistance genes in the genomes of bifidobacteria and evaluated their genetic mobility to other human gut commensal microorganisms.201727864179