Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota. Nat Commun. 2013;4:2151. [PMID: 23877117 DOI: 10.1038/ncomms3151]

The 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.

Role of pollution on the selection of antibiotic resistance and bacterial pathogens in the environment

There is evidence that human activity causes pollution that contributes to an enhanced selection of bacterial pathogens in the environment. In this review, we consider how environmental pollution can favour the selection of bacterial pathogens in the environment. We specifically discuss pollutants released into the environment by human activities (mainly human waste) that are associated with the selection for genetic features in environmental bacterial populations that lead to the emergence of bacterial pathogens. Finally, we also identify key pollutants that are associated with antibiotic resistance and discuss possibilities of how to prevent their release into the environment.

Shotgun metagenomic analysis reveals the prevalence of antibiotic resistance genes and mobile genetic elements in full scale hospital wastewater treatment plants

Wastewater treatment plants are considered as hotspots of emerging antimicrobial genes and mobile genetic elements. We used a shotgun metagenomic approach to examine the wide-spectrum profiles of ARGs (antibiotic resistance genes) and MGEs (mobile genetic elements) in activated sludge samples from two different hospital trains at the wastewater treatment plants (WWTPs) in Daegu, South Korea. The influent activated sludge and effluent of two trains (six samples in total) at WWTPs receiving domestic sewage wastewater (SWW) and hospital wastewater (HWW) samples collected at multiple periods were subjected to high throughput 16S rRNA metagenome sequencing for microbial community diversity. Cloacibacterium caeni and Lewinella nigricans were predominant in SWW effluents, while Bacillus subtilis and Staphylococcus epidermidis were predominant in HWW effluents based on the Miseq platform. Totally, 20,011 reads and 28,545 metagenomic sequence reads were assigned to 25 known ARG types in the SWW2 and HWW5 samples, respectively. The higher abundance of ARGs, including multidrug resistance (>53%, MDR), macrolide-lincosamide-streptogramin (>9%, MLS), beta-lactam (>3.3%), bacitracin (>4.4%), and tetracycline (>3.4%), confirmed the use of these antibiotics in human medicine. In total, 190 subtypes belonging to 23 antibiotic classes were detected in both SWW2 and HWW5 samples. RpoB2, MacB, and multidrug (MDR) ABC transporter shared the maximum matched genes in both activated sludge samples. The high abundance of MGEs, such as a gene transfer agent (GTA) (four times higher), transposable elements (1.6 times higher), plasmid related functions (3.8 times higher), and phages (two times higher) in HWW5 than in SWW2, revealed a risk of horizontal gene transfer in HWW. Domestic wastewater from hospital patients also influenced the abundance of ARGs and MGEs in the activated sludge process.

Metagenomics analysis revealing the occurrence of antibiotic resistome in salt lakes

Although antimicrobial resistance genes (ARGs) in dozens of environments have been well documented, the distribution of ARGs in salt lake ecosystems has been less intensively investigated. In this study, the broad-spectrum ARG profiles, microbial community composition and the comprehensive associations between microbiome and antimicrobial resistome in four salt lakes were investigated using a metagenomic approach. A total of 175 ARG subtypes affiliated with 19 ARG types were detected, and ARGs conferring resistance to multidrug, bacitracin, and macrolide-lincosamide-streptogramin (MLS) accounted for 71.2% of the total ARG abundance. However, the abundance of ARGs significantly decreased with the increasing salinity in the lakes. Both ARG profiles and microbial community structure presented remarkable discrepancies in different lakes, as well as in different sample types. Microbes such as genera Azoarcus, Aeromonas, Pseudomonas, and Kocuria, significantly co-occurred with multiple ARGs, indicating that these bacteria are potential ARG hosts in salt lake ecosystems. Collectively, this work provides new insights into the occurrence and distribution of ARGs in salt lake ecosystems.

Diverse Bacterial Resistance Genes Detected in Fecal Samples From Clinically Healthy Women and Infants in Australia-A Descriptive Pilot Study

The gut microbiota is an immense reservoir of antimicrobial resistance genes (ARGs), the so-called “resistome.” In Australia, where antibiotic use is high and resistance rates in some common pathogens are increasing, very little is known about the human resistome. To assess the presence and diversity of ARGs in the gut of Australians from south-eastern Victoria, we investigated fecal samples from clinically healthy infants and pregnant women using non-targeted (shotgun metagenomics sequencing or SMS) and targeted sequencing (two Ion Ampliseq^TM panels). All methods detected ARGs in all samples, with the detection overall of 64 unique genes conferring resistance to 12 classes of antibiotics. Predominant ARGs belonged to three classes of antibiotics that are the most frequently prescribed in Australia: tetracycline, β-lactams and MLS_B (macrolide, lincosamide, streptogramin B). The three bacterial Orders commonly identified as carrying ARGs were Clostridiales, Bacteroidales, and Enterobacteriales. Our preliminary results indicate that ARGs are ubiquitously present and diverse among the gut microbiota of clinically healthy humans from south-eastern Victoria, Australia. The observed resistance pattern partly overlaps with antimicrobial usage in human medicine in Australia, but ARGs to tetracycline are more common than could be expected. Our current sample is small and limited to south-eastern Victoria, and more data on healthy individuals will be needed to better depict resistance patterns at the population level, which could guide population and/or environmental monitoring and surveillance of antibiotic resistance on various spatio-temporal scales in Australia. For future studies, we recommend using the Ion Ampliseq^TM Antimicrobial Resistance Research panel, which is sensitive and user-friendly, or combining several methods to increase the detected diversity.

Ecological insights into the elevational biogeography of antibiotic resistance genes in a pristine river: Metagenomic analysis along the Yarlung Tsangpo River on the Tibetan Plateau

Presently, the prevalence of antibiotic resistance genes (ARGs) is regarded as an emerging environmental issue, and many studies have illuminated biogeographical patterns of the antibiotic resistome. However, few studies have investigated elevational biogeography and associated assembly mechanisms of ARGs in natural river systems. Accordingly, in the present study, we used metagenomics approaches to analyze the biogeographical pattern of ARGs along the pristine Yarlung Tsangpo River on the Tibetan Plateau. Our study retrieved the baseline profiles of ARGs in the pristine river and showed that the ARGs were dominated by bacA, which was resistant to bacitracin and represented more than 91% of total ARGs. The diversity and abundance of ARGs in the pristine river were lower than those in the human-impacted area, suggesting that the antibiotic resistome evolved and was promoted in a human-impacted environment. Furthermore, an elevational distance-decay relationship of ARGs was observed along the pristine Yarlung Tsangpo River, which provided strong evidence of ARG dissimilarity under the elevational variation. Elevational gradients could lead to changes in environmental variables and spatial factors, and consequently alter ARG composition. Elevational gradients could influence the assembly processes of ARGs. The deterministic and stochastic assembly processes both played critical roles and equally participated in shaping ARG composition at the watershed scale along the Yarlung Tsangpo River, and with increasing elevational variation along the river, the ecological processes of ARG assembly shifted from deterministic to stochastic. Moreover, abundant and rare ARGs were tentatively separated to investigate the difference and similarity in their distributions. Although abundant and rare ARGs presented similar distance-decay relationships, rare ARGs were more diverse and vulnerable to the dispersal process and mutation. Overall, our study provides valuable ecological insights to profile the large-scale elevational patterns of ARGs in a pristine river system, thereby providing important information for public health and environmental management.

Microbiome Studies from Saudi Arabia over the Last 10 Years: Achievements, Gaps, and Future Directions

In the past ten years, microbiome studies have shown tremendous potentiality for implementation of understanding microbiome structures and functions of various biomes and application of this knowledge for human betterment. Saudi Arabia is full of geographical, ecological, ethnical, and industrial diversities and scientific capacities. Therefore, there is a great potential in Saudi Arabia to conduct and implement microbiome-based research and applications. However, there is no review available on where Saudi Arabia stands with respect to global microbiome research trends. This review highlights the metagenome-assisted microbiome research from Saudi Arabia compared to the global focuses on microbiome research. Further, it also highlights the gaps and areas that should be focused on by Saudi microbiome researchers and the possible initiatives to be taken by Saudi government and universities. This literature review shows that the global trends of microbiome research cover a broad spectrum of human and animal health conditions and diseases, environmental and antimicrobial resistance surveillance, surveillance of food and food processing, production of novel industrial enzymes and bioactive pharmaceutical products, and space applications. However, Saudi microbiome studies are mostly confined to very few aspects of health (human and animal) and environment/ecology in last ten years, without much application. Therefore, Saudi Arabia should focus more on applied microbiome research through government, academic, and industry initiatives and global cooperation to match the global trends.

Characteristic dysbiosis in gout and the impact of a uric acid-lowering treatment, febuxostat on the gut microbiota

Gut dysbiosis is suggested to play a critical role in the pathogenesis of gout. The aim of our study was to identify the characteristic dysbiosis of the gut microbiota in gout patients and the impact of a commonly used uric acid-lowering treatment, febuxostat on gut microbiota in gout. 16S ribosomal RNA sequencing and metagenomic shotgun sequencing was performed on fecal DNA isolated from 38 untreated gout patients, 38 gout patients treated with febuxostat, and 26 healthy controls. A restriction of gut microbiota biodiversity was detected in the untreated gout patients, and the alteration was partly restored by febuxostat. Biochemical metabolic indexes involved in liver and kidney metabolism were significantly associated with the gut microbiota composition in gout patients. Functional analysis revealed that the gut microbiome of gout patients had an enriched function on carbohydrate metabolism but a lower potential for purine metabolism, which was comparatively enhanced in the febuxostat treated gout patients. A classification microbial model obtained a high mean area under the curve up to 0.973. Therefore, gut dysbiosis characterizings gout could potentially serve as a noninvasive diagnostic tool for gout and may be a promising target of future preventive interventions.

Genome-resolved metagenomics using environmental and clinical samples

Recent advances in high-throughput sequencing technologies and computational methods have added a new dimension to metagenomic data analysis i.e. genome-resolved metagenomics. In general terms, it refers to the recovery of draft or high-quality microbial genomes and their taxonomic classification and functional annotation. In recent years, several studies have utilized the genome-resolved metagenome analysis approach and identified previously unknown microbial species from human and environmental metagenomes. In this review, we describe genome-resolved metagenome analysis as a series of four necessary steps: (i) preprocessing of the sequencing reads, (ii) de novo metagenome assembly, (iii) genome binning and (iv) taxonomic and functional analysis of the recovered genomes. For each of these four steps, we discuss the most commonly used tools and the currently available pipelines to guide the scientific community in the recovery and subsequent analyses of genomes from any metagenome sample. Furthermore, we also discuss the tools required for validation of assembly quality as well as for improving quality of the recovered genomes. We also highlight the currently available pipelines that can be used to automate the whole analysis without having advanced bioinformatics knowledge. Finally, we will highlight the most widely adapted and actively maintained tools and pipelines that can be helpful to the scientific community in decision making before they commence the analysis.

Anthropogenic disturbances on antibiotic resistome along the Yarlung Tsangpo River on the Tibetan Plateau: Ecological dissemination mechanisms of antibiotic resistance genes to bacterial pathogens

Human activities can accelerate the antibiotic resistome prevalence and pose threats to ecological safety and public health globally. However, antibiotic resistance gene (ARG) mobility and dissemination into bacterial pathogens under anthropogenic disturbances are still poorly understood. Here, we used a metagenomic approach to profile the biogeography of ARGs and pathogenic antibiotic resistant bacteria (PARB) under anthropogenic disturbances along the Yarlung Tsangpo River. Results showed the ARGs was dominated by bacA gene along the Yarlung Tsangpo River on the Tibetan Plateau. The ARG composition was differently impacted by rapid urbanization and dam construction, which urbanization could promote ARGs resistant to sulfonamide and tetracycline, whereas dam construction could elevate the resistance to chloramphenicol and aminoglycoside. Land use pattern was identified as a critical factor influencing ARG composition under anthropogenic disturbances, as it could directly reflect the land degradation level and indicate the inputs of ARG-selective chemicals of different human activities. Moreover, despite of the lack of variation in ARG relative abundance, PARB were highly promoted by anthropogenic activities, indicating increasing ARG dissemination to pathogen. We found that human-impacted environments harbored high proportion of mobile genetic elements (MGEs), and the MGE carrying ARGs also increased under anthropogenic disturbances in the pathogenic hosts, which confirmed that anthropogenic activities could promote ARG horizontal gene transfer. Furthermore, anthropogenic activities could influence PARB assembly processes. Basically, stochastic processes dominated PARB assembly along the river, and with increasing level of anthropogenic activities, these processes shifted from undominated stochastic processes to dispersal limitation. In summary, this study provides useful strategies in watershed resistome management and reduction of ARG dissemination to pathogens, which should consider the mode and intensity of human activity and its potential influence on horizontal gene transfer and assembly processes.

Artificial sweeteners stimulate horizontal transfer of extracellular antibiotic resistance genes through natural transformation

Antimicrobial resistance has emerged as a global threat to human health. Natural transformation is an important pathway for horizontal gene transfer, which facilitates the dissemination of antibiotic resistance genes (ARGs) among bacteria. Although it is suspected that artificial sweeteners could exert antimicrobial effects, little is known whether artificial sweeteners would also affect horizontal transfer of ARGs via transformation. Here we demonstrate that four commonly used artificial sweeteners (saccharin, sucralose, aspartame, and acesulfame potassium) promote transfer of ARGs via natural transformation in Acinetobacter baylyi ADP1, a model organism for studying competence and transformation. Such phenomenon was also found in a Gram-positive human pathogen Bacillus subtilis and mice faecal microbiome. We reveal that exposure to these sweeteners increases cell envelope permeability and results in an upregulation of genes encoding DNA uptake and translocation (Com) machinery. In addition, we find that artificial sweeteners induce an increase in plasmid persistence in transformants. We propose a mathematical model established to predict the long-term effects on transformation dynamics under exposure to these sweeteners. Collectively, our findings offer insights into natural transformation promoted by artificial sweeteners and highlight the need to evaluate these environmental contaminants for their antibiotic-like side effects.

Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes

BACKGROUND

Therapeutic and growth-promoting antibiotics are frequently used in broiler production. Indirect evidence indicates that these practices are linked to the proliferation of antimicrobial resistance (AMR), the spread of antibiotic-resistant bacteria from food animals to humans, and the environment, but there is a lack of comprehensive experimental data supporting this. We investigated the effects of growth promotor (bacitracin) and therapeutic (enrofloxacin) antibiotic administration on AMR in broilers for the duration of a production cycle, using a holistic approach that integrated both culture-dependent and culture-independent methods. We specifically focused on pathogen-harboring families (Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae).

RESULTS

Antibiotic-resistant bacteria and antibiotic resistance genes were ubiquitous in chicken cloaca and litter regardless of antibiotic administration. Environment (cloaca vs. litter) and growth stage were the primary drivers of variation in the microbiomes and resistomes, with increased bacterial diversity and a general decrease in abundance of the pathogen-harboring families with age. Bacitracin-fed groups had higher levels of bacitracin resistance genes and of vancomycin-resistant Enterococcaceae (total Enterococcaceae counts were not higher). Although metagenomic analyses classified 28-76% of the Enterococcaceae as the commensal human pathogens E. faecalis and E. faecium, culture-based analysis suggested that approximately 98% of the vancomycin-resistant Enterococcaceae were avian and not human-associated, suggesting differences in the taxonomic profiles of the resistant and non-resistant strains. Enrofloxacin treatments had varying effects, but generally facilitated increased relative abundance of multidrug-resistant Enterobacteriaceae strains, which were primarily E. coli. Metagenomic approaches revealed a diverse array of Staphylococcus spp., but the opportunistic pathogen S. aureus and methicillin resistance genes were not detected in culture-based or metagenomic analyses. Camphylobacteriaceae were significantly more abundant in the cloacal samples, especially in enrofloxacin-treated chickens, where a metagenome-assembled C. jejuni genome harboring fluoroquinolone and β-lactam resistance genes was identified.

CONCLUSIONS

Within a "farm-to-fork, one health" perspective, considering the evidence that bacitracin and enrofloxacin used in poultry production can select for resistance, we recommend their use be regulated. Furthermore, we suggest routine surveillance of ESBL E. coli, vancomycin-resistant E. faecalis and E. faecium, and fluoroquinolone-resistant C. jejuni strains considering their pathogenic nature and capacity to disseminate AMR to the environment. Video Abstract.

Metagenomics-Based Analysis of the Age-Related Cumulative Effect of Antibiotic Resistance Genes in Gut Microbiota

Antibiotic resistance in bacteria has become a major global health problem. One of the main reservoirs of antibiotic resistance genes is the human gut microbiota. To characterise these genes, a metagenomic approach was used. In this study, a comprehensive antibiotic resistome catalog was established using fecal samples from 246 healthy individuals from world's longevity township in Jiaoling, China. In total, 606 antibiotic resistance genes were detected. Our results indicated that antibiotic resistance genes in the human gut microbiota accumulate and become more complex with age as older groups harbour the highest abundance of these genes. Tetracycline resistance gene type tetQ was the most abundant group of antibiotic resistance genes in gut microbiota, and the main carrier of antibiotic resistance genes was Bacteroides. Antibiotic efflux, inactivation, and target alteration were found to be the dominant antimicrobial resistance mechanisms. This research may help to establish a comprehensive antibiotic resistance catalog that includes extremely long-lived healthy people such as centenarians, and may provide potential recommendations for controlling the use of antibiotics.

Short-term cold stress can reduce the abundance of antibiotic resistance genes in the cecum and feces in a pig model

Comprehensive studies on the effects of cold stress on antibiotic resistance genes (ARGs) in the intestines and feces remain scarce. In this study, pigs were selected as the animal model and divided into a normal temperature group and a 48-h short-term cold stress group. The ARG profiles in fecal, cecal content and cecal mucosa samples were analyzed. The results showed that the normalized abundance of ARGs in the cecal mucosa samples in the cold stress group was significantly higher than that in the normal temperature group, while the normalized ARG abundances in the fecal and cecal content samples were significantly lower than those in the normal temperature group (P < 0.05). The bacterial community composition (especially Firmicutes) was the major driver impacting the ARG profile and accounted for 32.2% of the variation in the ARG profile, followed by metabolites (especially creatinine and oxypurinol) and mobile genetic elements (MGEs) (especially plasmids and insertion elements). And it was found that creatinine and oxypurinol can reduce the abundance of ARGs and Firmicutes in the in vitro experiment. The results indicate that short-term cold stress can reduce the abundance of ARGs in the cecum and feces of pigs, providing reference data for environmental safety.

The gut microbiome of healthy Vietnamese adults and children is a major reservoir for resistance genes against critical antimicrobials

Antimicrobials are a key group of therapeutic agents. Given the animal/human population density and high antimicrobial consumption rate in Southeast Asia, the region is a focal area for monitoring antimicrobial resistance (AMR). Hypothesizing that the gastrointestinal tract of healthy individuals in Vietnam is a major source of AMR genes that may be transferred to pathogens, we performed shotgun metagenomic sequencing on fecal samples from 42 healthy Vietnamese people (21 children and 21 adults). We compared their microbiome profiles by age group and determined the composition of AMR genes. An analysis of the taxonomic profiles in the gut microbiome showed a clear differentiation by age, with young children (age <2 years) exhibiting a unique structure in comparison to adults and older children. We identified a total of 132 unique AMR genes, with macrolide, lincosamide, and streptogramin class resistance genes (ermB and lnuC) and tetracycline resistance genes being almost ubiquitous across the study population. Notably, samples from younger children were significantly associated with a greater number of AMR genes than other age groups, including key signature genes associated with AMR pathogens (eg, bla_CTX-M, mphA). Our data suggest that the gut microbiome of those living in Vietnam, particularly young children, is a substantial reservoir of AMR genes, which can be transferred to circulating enteric pathogens. Our data support the generation of longitudinal cohort studies of those living in urban and rural areas of developing countries to understand the behavior of these AMR reservoirs and their role in generating multidrug-resistant and extensively drug-resistant pathogens.

More diversified antibiotic resistance genes in chickens and workers of the live poultry markets

BACKGROUND

Poultry farms and LPMs are a reservoir of antimicrobial resistant bacteria and resistance genes from feces. The LPM is an important interface between humans, farm animals, and environments in a typical urban environment, and it is considered a reservoir for ARGs and viruses. However, the antibiotic resistomes shared between chicken farms and LPMs, and that of LPM workers and people who have no contact with the LPMs remains unknown.

METHODS

We characterized the resistome and bacterial microbiome of farm chickens and LPMs and LPM workers and control subjects. The mobile ARGs identified in chickens and the distribution of the mcr-family genes in publicly bacterial genomes and chicken gut metagenomes was analyzed, respectively. In addition, the prevalence of mcr-1 in LPMs following the ban on colistin-positive additives in China was explored.

RESULTS

By profiling the microbiomes and resistomes in chicken farms, LPMs, LPM workers, and LPM environments, we found that the bacterial community composition and resistomes were significantly different between the farms and the LPMs, and the LPM samples possessed more diversified ARGs (59 types) than the farms. Some mobile ARGs, such as mcr-1 and tet(X3), identified in chicken farms, LPMs, LPM workers, and LPM environments were also harbored by human clinical pathogens. Moreover, we found that the resistomes were significantly different between the LPM workers and those who have no contact with the LPMs, and more diversified ARGs (188 types) were observed in the LPM workers. It is also worth noting that mcr-10 was identified in both human (5.2%, 96/1,859) and chicken (1.5%, 14/910) gut microbiomes. Although mcr-1 prevalence decreased significantly in the LPMs across the eight provinces in China, from 190/333 (57.1%) samples in September 2016-March 2017 to 208/544 (38.2%) samples in August 2018-May 2019, it is widespread and continuous in the LPMs.

CONCLUSION

Live poultry trade has a significant effect on the diversity of ARGs in LPM workers, chickens, and environments in China, driven by human selection with the live poultry trade. Our findings highlight the live poultry trade as ARG disseminators into LPMs, which serve as an interface of LPM environments even LPM workers, and that could urge Government to have better control of LPMs in China. Further studies on the factors that promote antibiotic resistance exchange between LPM environments, human commensals, and pathogens, are warranted.

Comparative microbial antibiotic resistome between urban and deep forest environments

A paradoxical result of using antibiotics to eradicate microbial pathogens is the emergence of a vast number of resistant microbes in various environments. The concern that environmental microbes will inevitably become resistant to virtually every clinically usable antibiotics has been exacerbated by the spread of these resistance genes across different environments and the emergence of multidrug resistant phenotypes. Here, we provide metagenomic insights into the microbiomes and resistomes of 16 soil samples collected from hospitals, residential areas, and forest parks in the megacity of Beijing and deep forests in the Yunnan province. Using Illumina HiSeq sequencing, we investigated the microbial diversity within the metagenomic shotgun reads and identified 486 antibiotic-resistant genes (ARGs) classified into 30 types from these samples, among which multidrug resistance genes were the most abundant. Our results present an important reference and direct comparison of microbial antibiotic resistomes of soil samples from a megacity and deep forests and extend our understanding of the spread of ARGs in modern urban and natural environments.

Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

Gut microbial communities can respond to antibiotic perturbations by rapidly altering their taxonomic and functional composition. However, little is known about the strain-level processes that drive this collective response. Here, we characterize the gut microbiome of a single individual at high temporal and genetic resolution through a period of health, disease, antibiotic treatment, and recovery. We used deep, linked-read metagenomic sequencing to track the longitudinal trajectories of thousands of single nucleotide variants within 36 species, which allowed us to contrast these genetic dynamics with the ecological fluctuations at the species level. We found that antibiotics can drive rapid shifts in the genetic composition of individual species, often involving incomplete genome-wide sweeps of pre-existing variants. These genetic changes were frequently observed in species without obvious changes in species abundance, emphasizing the importance of monitoring diversity below the species level. We also found that many sweeping variants quickly reverted to their baseline levels once antibiotic treatment had concluded, demonstrating that the ecological resilience of the microbiota can sometimes extend all the way down to the genetic level. Our results provide new insights into the population genetic forces that shape individual microbiomes on therapeutically relevant timescales, with potential implications for personalized health and disease.

Impact of Chronic Tetracycline Exposure on Human Intestinal Microbiota in a Continuous Flow Bioreactor Model

Studying potential dietary exposure to antimicrobial drug residues via meat and dairy products is essential to ensure human health and consumer safety. When studying how antimicrobial residues in food impact the development of antimicrobial drug resistance and disrupt normal bacteria community structure in the intestine, there are diverse methodological challenges to overcome. In this study, traditional cultures and molecular analysis techniques were used to determine the effects of tetracycline at chronic subinhibitory exposure levels on human intestinal microbiota using an in vitro continuous flow bioreactor. Six bioreactor culture vessels containing human fecal suspensions were maintained at 37 °C for 7 days. After a steady state was achieved, the suspensions were dosed with 0, 0.015, 0.15, 1.5, 15, or 150 µg/mL tetracycline, respectively. Exposure to 150 µg/mL tetracycline resulted in a decrease of total anaerobic bacteria from 1.9 × 10⁷ ± 0.3 × 10⁷ down to 2 × 10⁶ ± 0.8 × 10⁶ CFU/mL. Dose-dependent effects of tetracycline were noted for perturbations of tetB and tetD gene expression and changes in acetate and propionate concentrations. Although no-observed-adverse-effect concentrations differed, depending on the traditional cultures and the molecular analysis techniques used, this in vitro continuous flow bioreactor study contributes to the knowledge base regarding the impact of chronic exposure of tetracycline on human intestinal microbiota.

Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains

Plasmid-mediated dissemination of antibiotic resistance among fecal Enterobacteriaceae in natural ecosystems may contribute to the persistence of antibiotic resistance genes in anthropogenically impacted environments. Plasmid transfer frequencies measured under laboratory conditions might lead to overestimation of plasmid transfer potential in natural ecosystems. This study assessed differences in the conjugative transfer of an IncP-1 (pKJK5) plasmid to three natural Escherichia coli strains carrying extended-spectrum beta-lactamases, by filter mating. Matings were performed under optimal laboratory conditions (rich LB medium and 37°C) and environmentally relevant temperatures (25, 15 and 9°C) or nutrient regimes mimicking environmental conditions and limitations (synthetic wastewater and soil extract). Under optimal nutrient conditions and temperature, two recipients yielded high transfer frequencies (5 × 10-1) while the conjugation frequency of the third strain was 1000-fold lower. Decreasing mating temperatures to psychrophilic ranges led to lower transfer frequencies, albeit all three strains conjugated under all the tested temperatures. Low nutritive media caused significant decreases in transconjugants (-3 logs for synthetic wastewater; -6 logs for soil extract), where only one of the strains was able to produce detectable transconjugants. Collectively, this study highlights that despite less-than-optimal conditions, fecal organisms may transfer plasmids in the environment, but the transfer of pKJK5 between microorganisms is limited mainly by low nutrient conditions.

Investigation of the Genomic and Pathogenic Features of the Potentially Zoonotic Streptococcus parasuis

Recently, Streptococcus suis reference strains of serotype 20, 22, and 26 were reclassified as Streptococcus parasuis. The public health significance of S. parasuis is underestimated due to the lack of clinical isolates. In the present study, we first reported two sporadic S. parasuis infections in humans, after using full-length 16S rRNA and housekeeping genes' phylogeny and ANI values of genome sequence comparisons to determine the species of their isolates BS26 and BS27. Compared to highly pathogenic S. suis strain P1/7, S. parasuis strains BS26 and BS27 possessed a delayed capacity to initiate lethal infection, which may attribute to the later production of higher level of pro-inflammatory cytokines. Differed to S. suis strain P1/7, S. parasuis strains did not induce significant inflammatory response in the brain of mice. Histopathological changes in liver and lungs were widely present in mice infected with S. parasuis strains. Our data indicated that the pathogenic mechanism of S. parasuis may be different from that of S. suis. Three lineages in the core-genome phylogenetic tree and ten types of cps gene cluster were found in 13 S. parasuis genomes, indicating high heterogeneity of this species. The similarity of CPS structure and antibiotic-resistant genes relative to S. suis indicated the evolutionary affinity between the two species. Our data suggested S. parasuis is a potential zoonotic pathogen and poses severe threat to health of susceptible people. Further study on the epidemiology and public health significance of S. parasuis is urgently necessary.

The infant gut resistome is associated with E. coli and early-life exposures

BACKGROUND

The human gut microbiome harbors a collection of bacterial antimicrobial resistance genes (ARGs) known as the resistome. The factors associated with establishment of the resistome in early life are not well understood. We investigated the early-life exposures and taxonomic signatures associated with resistome development over the first year of life in a large, prospective cohort in the United States. Shotgun metagenomic sequencing was used to profile both microbial composition and ARGs in stool samples collected at 6 weeks and 1 year of age from infants enrolled in the New Hampshire Birth Cohort Study. Negative binomial regression and statistical modeling were used to examine infant factors such as sex, delivery mode, feeding method, gestational age, antibiotic exposure, and infant gut microbiome composition in relation to the diversity and relative abundance of ARGs.

RESULTS

Metagenomic sequencing was performed on paired samples from 195 full term (at least 37 weeks' gestation) and 15 late preterm (33-36 weeks' gestation) infants. 6-week samples compared to 1-year samples had 4.37 times (95% CI: 3.54-5.39) the rate of harboring ARGs. The majority of ARGs that were at a greater relative abundance at 6 weeks (chi-squared p < 0.01) worked through the mechanism of antibiotic efflux. The overall relative abundance of the resistome was strongly correlated with Proteobacteria (Spearman correlation = 78.9%) and specifically Escherichia coli (62.2%) relative abundance in the gut microbiome. Among infant characteristics, delivery mode was most strongly associated with the diversity and relative abundance of ARGs. Infants born via cesarean delivery had a trend towards a higher risk of harboring unique ARGs [relative risk = 1.12 (95% CI: 0.97-1.29)] as well as having an increased risk for overall ARG relative abundance [relative risk = 1.43 (95% CI: 1.12-1.84)] at 1 year compared to infants born vaginally.

CONCLUSIONS

Our findings suggest that the developing infant gut resistome may be alterable by early-life exposures. Establishing the extent to which infant characteristics and early-life exposures impact the resistome can ultimately lead to interventions that decrease the transmission of ARGs and thus the risk of antibiotic resistant infections.

Nonnutritive sweeteners can promote the dissemination of antibiotic resistance through conjugative gene transfer

Antimicrobial resistance (AMR) poses a worldwide threat to human health and biosecurity. The spread of antibiotic resistance genes (ARGs) via conjugative plasmid transfer is a major contributor to the evolution of this resistance. Although permitted as safe food additives, compounds such as saccharine, sucralose, aspartame, and acesulfame potassium that are commonly used as nonnutritive sweeteners have recently been associated with shifts in the gut microbiota similar to those caused by antibiotics. As antibiotics can promote the spread of antibiotic resistance genes (ARGs), we hypothesize that these nonnutritive sweeteners could have a similar effect. Here, we demonstrate for the first time that saccharine, sucralose, aspartame, and acesulfame potassium could promote plasmid-mediated conjugative transfer in three established conjugation models between the same and different phylogenetic strains. The real-time dynamic conjugation process was visualized at the single-cell level. Bacteria exposed to the tested compounds exhibited increased reactive oxygen species (ROS) production, the SOS response, and gene transfer. In addition, cell membrane permeability increased in both parental bacteria under exposure to the tested compounds. The expression of genes involved in ROS detoxification, the SOS response, and cell membrane permeability was significantly upregulated under sweetener treatment. In conclusion, exposure to nonnutritive sweeteners enhances conjugation in bacteria. Our findings provide insight into AMR spread and indicate the potential risk associated with the presence of nonnutritive sweeteners.

Distribution of antibiotic resistance genes and their association with bacteria and viruses in decentralized sewage treatment facilities

The distribution of antibiotic resistance genes (ARGs) has been intensively studied in large-scale wastewater treatment plants and livestock sources. However, small-scale decentralized sewage treatment facilities must also be explored due to their possible direct exposure to residents. In this study, six wastewater treatment facilities in developed rural areas in eastern China were investigated to understand their risks of spreading ARGs. Using metagenomics and network analysis tools, ARGs and bacterial and viral communities were identified in the influent (INF) and effluent (EFF) samples. The dominant ARGs belonged to the bacitracin class, which are different from most of municipal wastewater treatment plants (WWTPs). The dominant hosts of ARGs are Acidovorax in bacterial communities and Prymnesiovirus in viral communities. Furthermore, a positive relationship was found between ARGs and phages. The ARGs significantly correlated with phages were all hosted by specific genera of bacteria, indicating that phages had contributed to the ARG's proliferation in sewage treatment facilities. Paying significant concern on the possible enhanced risks caused by bacteria, viruses and their related ARGs in decentralized sewage treatment facilities is necessary.

ELECTRONIC SUPPLEMENTARY MATERIAL

Supplementary material is available in the online version of this article at 10.1007/s11783-021-1469-4 and is accessible for authorized users.

Systematic review and meta-analysis of integrated studies on antimicrobial resistance genes in Africa-A One Health perspective

Background

Increasing antimicrobial resistance (AMR) raises serious health and financial concerns. However, the main drivers of the emergence, spread and subsequent colonisation of resistant bacterial strains between humans, animals and the environment are still poorly understood.

Objective

The aim of this review was to identify molecular studies on AMR in One Health settings in Africa and to determine the prevalence of antimicrobial resistance genes in humans, animals and the environment. Due to the very low number of studies including environmental samples, the meta‐analysis only includes data obtained from animals and humans.

Methods

The PubMed, Web of Science and Scopus databases were searched, identifying 10 464 publications on AMR in Africa from January 1st, 2000 until June 1st, 2020. Inclusion criteria were: (i) Integrated studies assessing AMR simultaneously in an animal‐human, animal‐environment, human‐environment or animal‐human‐environment context, (ii) Genotypic characterisation of AMR and (iii) temporal and spatial relationship between samples from humans and animals. Statistical random‐effects model meta‐analysis was performed.

Results

Overall, 18 studies met our eligibility criteria and were included in this review. Six studies investigated Escherichia coli and Salmonella spp. (N = 6). The most prevalent AMR genes in animals included sul1 (36.2%), sul2 (32.0%), tetA (31.5%), strB (30.8%) and blaTEM (30.0%), whereas sul2 (42.4%), tetA (42.0%), strB (34.9%), blaTEM (28.8%) and sul1 (27.8%) were most prevalent in humans. We observed no clear pattern for a higher prevalence in either the animal or the human reservoir.

Conclusion

To date, data on AMR in a One Health perspective in Africa are scarce. Prospective and longitudinal studies using an integrated One Health approach assessing the environment, animals and humans at the same time are needed to better understand the main drivers of AMR sharing in Africa.

Macleaya cordata extract, an antibiotic alternative, does not contribute to antibiotic resistance gene dissemination

The abuse of antibiotics and their associated health risks are receiving global attention. The use of antibiotic additives in fodder has been banned in the European Union since 2006 and in China since 2020. Antibiotic alternatives are being developed, but their risks to the soil ecosystem remain poorly understood. Here, we compared the effects of the antibiotic oxytetracycline (OTC10, 10 mg/kg) with those of a Macleaya cordata extract (MCE, 10 and 100 mg/kg), the major antibiotic substitute. All tested concentrations of MCE and OTC10 exerted slight effects on the soil microbiome, but OTC10 and MCE100 could interfere with the structures and functions of the gut microbiome and might thus affect the soil ecological functions of Enchytraeus crypticus. Furthermore, OTC10 exposure inevitably increased the antibiotic resistance gene (ARG) abundance by 213%, whereas MCE did not induce ARG dissemination, which explains why MCE is considered to be associated with a low ecological risk. Our research provides the first demonstration of the risks posed by antibiotic alternatives to soil animals from the perspective of environmental toxicology and explores the potential development of antibiotic alternatives associated with a low ecological risk from a new perspective.

Black Soldier Fly Larvae Can Effectively Degrade Oxytetracycline Bacterial Residue by Means of the Gut Bacterial Community

Antibiotic bacterial residue is a unique hazardous waste, and its safe and effective disposal has always been a concern of pharmaceutical enterprises. This report presents the effective treatment of hazardous waste-antibiotic bacterial residue-by black soldier fly larvae (larvae), oxytetracycline bacterial residue (OBR), and soya meal with mass ratios of 0:1 (soya), 1:20 (OBRlow), and 1:2 (OBRhigh), which were used as substrates for larval bioconversion. Degradation of OBR and oxytetracycline, the bacterial community, the incidence of antibiotic resistance genes (ARGs) and the bacterial function in the gut were examined. When the larvae were harvested, 70.8, 59.3, and 54.5% of the substrates had been consumed for soya, OBRlow and OBRhigh; 65.9 and 63.3% of the oxytetracycline was degraded effectively in OBRlow and OBRhigh, respectively. The larval bacterial communities were affected by OBR, abundant and various ARGs were discovered in the gut, and metabolism was the major predicted function of the gut. These findings show that OBR can be digested and converted by larvae with gut bacteria, and the larvae can be used as a bioremediation tool for the treatment of hazardous waste. Finally, the abundant ARGs in the gut deserve further attention and consideration in environmental health risk assessments.

Colistin Selection of the Mcr-1 Gene in Broiler Chicken Intestinal Microbiota

Colistin has a long story of safe use in animals for the treatment and prevention of certain bacterial diseases. Nevertheless, the first description of the mcr-1 gene showed that colistin resistance can spread by horizontal gene transfer and changed the landscape. This study aimed to assess the effect of colistin administration on the dispersion of resistance in the microbiota of day-old broiler chicks and how the presence of mcr-1 genes influences the spread of colistin resistance determinants. In this study, 100 one-day-old chicks were divided into four groups of 25 animals (G1, G2, G3, and G4). Animals from G3/G4 were challenged with mcr-1-carrying Salmonella (day 7), while colistin (600 mg/L) was administered daily to G2/G4 animals through drinking water (from day 8 to day 15). Two quantitative PCR assays were performed to compare the amount of Salmonella and mcr-1 that were present in the caecal samples. We observed that levels of mcr-1 were higher in G3/G4 animals, especially G4, due to the spread of mcr-1-carrying Salmonella. On day 21, Salmonella levels decreased in G4, reaching similar values as those for G3, but mcr-1 levels remained significantly higher, suggesting that colistin may accelerate the spreading process when mcr-1-carrying bacteria reach the gut.

Technologies towards antibiotic resistance genes (ARGs) removal from aquatic environment: A critical review

Antibiotic resistance genes (ARGs) have been recognized as emerging pollutants that are widely distributed and accumulated in most of aquatic environment. Although many ARGs-removal technologies are employed, a corresponding discussion of merits and limitations of known technologies is still currently lacking. More importantly, the removal mechanisms of ARGs remain unclear, hindering their ecological feasibility. Thus, further in-depth studies are highly required. In this review, the occurrence and risk of ARGs in aquatic environment are introduced, and the main routes and potential impacts of ARGs dissemination are enumerated. In addition, several novel ARGs detection methods are critically reviewed. Notably, to ensure greater applicability of these technologies, systematic information on how recent technologies impact the ARGs removal and control are comprehensively compared and summarized. Finally, future research directions to alleviate the risk of ARGs in aquatic environment are briefly introduced. Taken together, this review provides useful information to facilitate the development of innovative and feasible ARGs removal technologies and increase their economic viability and ecological sustainability.

The Beta-Lactam Resistome Expressed by Aerobic and Anaerobic Bacteria Isolated from Human Feces of Healthy Donors

Antibiotic resistance is a major health problem worldwide, causing more deaths than diabetes and cancer. The dissemination of vertical and horizontal antibiotic resistance genes has been conducted for a selection of pan-resistant bacteria. Here, we test if the aerobic and anaerobic bacteria from human feces samples in health conditions are carriers of beta-lactamases genes. The samples were cultured in a brain–heart infusion medium and subcultured in blood agar in aerobic and anaerobic conditions for 24 h at 37 °C. The grown colonies were identified by their biochemical profiles. The DNA was extracted and purified by bacterial lysis using thermal shock and were used in the endpoint PCR and next generation sequencing to identify beta-lactamase genes expression (OXA, VIM, SHV, TEM, IMP, ROB, KPC, CMY, DHA, P, CFX, LAP, and BIL). The aerobic bacterias Aeromonas hydrophila, Citrobacter freundii, Proteus mirabilis, Providencia rettgeri, Serratia fonticola, Serratia liquefaciens, Enterobacter aerogenes, Escherichia coli, Klebsiella pneumoniae, Pantoea agglomerans, Enterococcus faecalis, and Enterobacter cloacae, the anaerobic bacteria: Capnocytophaga species, Bacteroides distasonis, Bifidobacterium adolescentis, Bacteroides ovatus, Bacteroides fragilis, Eubacterium species, Eubacterium aerofaciens, Peptostreptococcus anaerobius, Fusobacterium species, Bacteroides species, and Bacteroides vulgatus were isolated and identified. The results showed 49 strains resistant to beta-lactam with the expression of blaSHV (10.2%), blaTEM (100%), blaKPC (10.2%), blaCYM (14.3%), blaP (2%), blaCFX (8.2%), and blaBIL (6.1%). These data support the idea that the human enteric microbiota constitutes an important reservoir of genes for resistance to beta-lactamases and that such genes could be transferred to pathogenic bacteria.

Gut Microbial SNPs Induced by High-Fiber Diet Dominate Nutrition Metabolism and Environmental Adaption of Faecalibacterium prausnitzii in Obese Children

Dietary intervention is effective in human health promotion through modulation of gut microbiota. Diet can cause single-nucleotide polymorphisms (SNPs) to occur in the gut microbiota, and some of these variations may lead to functional changes in human health. In this study, we performed a systematic SNP analysis based on metagenomic data collected from children with Prader–Willi syndrome (PWS, n = 17) and simple obese (SO) children (n = 19), who had better healthy conditions after receiving high-fiber diet intervention. We found that the intervention increased the SNP proportions of Faecalibacterium, Bifidobacterium, and Clostridium and decreased those of Bacteroides in all children. Besides, the PWS children had Collinsella increased and Ruminococcus decreased, whereas the SO had Blautia and Escherichia decreased. There were much more BiasSNPs in PWS than in SO (4,465 vs 303), and only 81 of them appeared in both groups, of which 78 were from Faecalibacterium prausnitzii, and 51 were nonsynonymous mutations. These nonsynonymous variations were mainly related to pathways of environmental adaptation and nutrition metabolism, particularly to carbohydrate and nucleotide metabolism. In addition, dominant strains carrying BiasSNPs in all children shifted from F. prausnitzii AF32-8AC and F. prausnitzii 942/30-2 to F. prausnitzii SSTS Bg7063 and F. prausnitzii JG BgPS064 after the dietary intervention. Furthermore, although the abundance of Bifidobacterium increased significantly by the intervention and became dominant strains responsible for nutrition metabolism, they had less BiasSNPs between the pre- and post-intervention group in comparison with Faecalibacterium. The finding of F. prausnitzii as important functional strains influenced by the intervention highlights the superiority of applying SNP analysis in studies of gut microbiota. This study provided evidence and support for the effect of dietary intervention on gut microbial SNPs, and gave some enlightenments for disease treatment.

Selection of antibiotic resistance genes on biodegradable and non-biodegradable microplastics

Growing evidence have demonstrated that microplastics in the marine ecosystem can provide novel substrates for biofilm formation, potentially facilitating the spread of antibiotic resistance. However, the occurrence of antibiotic resistance genes (ARGs) in the biofilm on microplastics has not been fully explored. This study used the metagenomic data of biodegradable and non-biodegradable microplastics staged at a coastal lagoon in the northern Gulf of Mexico to profile the ARGs and their bacterial hosts. The abundance and Shannon diversity of ARGs on biodegradable poly hydroxy alkanoate (PHA) and non-biodegradable polyethylene terephthalate (PET) have no significant differences. Nevertheless, the abundance of multidrug resistance genes on PET (3.05 copies per 16S rRNA) was statistically higher than that on PHA (2.05). Beta diversity showed that the overall pattern of resistome on PHA was significantly distinct with that on PET. Procrustes analysis suggested a good-fit correlation between ARG profiles and bacterial community composition. The host-tracking analysis identified that Pseudomonas was always the major host for glycopeptide and multidrug resistance genes in PET and PHA biofilms, whereas the primary host for macrolide-lincosamide-streptogramin (MLS) changed to Desulfovibrio on PET. This study provided the first metagenomic insights into the ARGs and their hosts on biodegradable and non-biodegradable microplastics, suggesting that both two types of plastics harbor ARGs with preferences.

Insights into Emergence of Antibiotic Resistance in Acid-Adapted Enterohaemorrhagic Escherichia coli

The emergence of multidrug-resistant pathogens presents a global challenge for treating and preventing disease spread through zoonotic transmission. The water and foodborne Enterohaemorrhagic Escherichia coli (EHEC) are capable of causing intestinal and systemic diseases. The root cause of the emergence of these strains is their metabolic adaptation to environmental stressors, especially acidic pH. Acid treatment is desired to kill pathogens, but the protective mechanisms employed by EHECs cross-protect against antimicrobial peptides and thus facilitate opportunities for survival and pathogenesis. In this review, we have discussed the correlation between acid tolerance and antibiotic resistance, highlighting the identification of novel targets for potential production of antimicrobial therapeutics. We have also summarized the molecular mechanisms used by acid-adapted EHECs, such as the two-component response systems mediating structural modifications, competitive inhibition, and efflux activation that facilitate cross-protection against antimicrobial compounds. Moving beyond the descriptive studies, this review highlights low pH stress as an emerging player in the development of cross-protection against antimicrobial agents. We have also described potential gene targets for innovative therapeutic approaches to overcome the risk of multidrug-resistant diseases in healthcare and industry.

Antibiotic resistance in the environment: a critical insight on its occurrence, fate, and eco-toxicity

The overuse, misuse, and underuse of antibiotics tend to increase the antibiotic burden in the environment resulting into the evolution in microbial community to possess resistance that renders antibiotics ineffective against them. The current review recapitulates the present state of knowledge about the occurrence and fate of antibiotics in various environmental matrices. Also, the prevalence of antibiotic-resistant bacteria/antibiotic-resistant genes (ARB/ARGs) in various biological and non-biological systems, eco-toxicity of antibiotics on non-target organisms, and remediation methods for antibiotics and ARB/ARGs removal were critically reviewed. Furthermore, a comparison of various technologies for their efficiency to eliminate antibiotic residues and ARB/ARGs is made. The study identified gaps in the investigation of toxic effects of low concentration of antibiotics and the mixture of multiple antibiotics on non-target organisms. The study of antibiotics' phytotoxicity and toxicity towards sediment and soil-dwelling organisms are also recognized as a knowledge gap. The review also details policies implemented across the globe to fight against antibiotic resistance, and the scarcity of data on lab to land transferred remediation technology was identified. The present study entails a critical review of literature providing guidelines for the articulation of policies for prudent use of antibiotics, limits on the amount of antibiotics in pharmaceutical formulations, and regular surveillance in the Indian context.

Abundance and Diversity of Phages, Microbial Taxa, and Antibiotic Resistance Genes in the Sediments of the River Ganges Through Metagenomic Approach

In this study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community, and antibiotic resistance genes (ARGs). Utilizing data from Illumina platform, 4,174 (∼0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3,602 reads, ∼86.3%). Among all, Microcystis (782 hits), Haemophilus (403), Synechococcus (386), Pseudomonas (279), Enterococcus (232), Bacillus (196), Rhodococcus (166), Caulobacter (163), Salmonella (146), Enterobacteria (143), Mycobacterium and (128) phages show the highest abundance and account for ∼90% of the total identified phages. In addition, we have also identified corresponding host pertaining to these phages. Mainly, Proteobacteria (∼69.3%) dominates the microbial population structure. Primarily, orders such as Caulobacterales (∼28%), Burkholderiales (∼13.9%), Actinomycetales (∼13.7%), and Pseudomonadales (∼7.5%) signify the core section. Furthermore, 21,869 (∼0.00695%) reads were classified in 20 ARG types (classes) and 240 ARGs (subtypes), among which 4 ARG types, namely multidrug resistance (12,041 reads, ∼55%), bacitracin (3,202 reads, ∼15%), macrolide-lincosamide-streptogramin (1,744 reads, ∼7.98%), and fosmidomycin (990 reads, ∼4.53%), have the highest abundance. Simultaneously, six resistance mechanisms were also recognized with the dominance of antibiotic efflux (72.8%, 15,919 reads). The results unveil the distribution of (pro)-phages; microbial community; and various ARGs in the Ganges river sediments.

Integrating Metagenomic and Bayesian Analyses to Evaluate the Performance and Confidence of CrAssphage as an Indicator for Tracking Human Sewage Contamination in China

Recently, crAssphage has been proposed as a human-specific marker for tracking fecal contamination. However, its performance has always been validated in a limited number of host samples, which may obscure our understanding of its utility. Furthermore, few studies have quantified confidence of fecal contamination when using crAssphage. Here, we evaluate the performance and confidence of crAssphage by analyzing a large panel of metagenomic data sets combined with Bayesian analyses. Results demonstrate that crAssphage exhibits superior performance with high host sensitivity and specificity, indicating its suitability for tracking human fecal sources. With the marker, a high confidence (>90%) can be obtained and particularly, multiple samples with positive results provide a near certainty of confidence. The application of crAssphage in the sediments of three Chinese urban rivers shows a high confidence of >97% of human fecal contamination, suggesting the serious challenge of sewage pollution in these environments. Additionally, significant correlation is observed between crAssphage and antibiotic resistance genes (ARGs), expanding the utilization of crAssphage for pollution management of ARGs. This study highlights the benefit of using metagenomic-based analysis for evaluating the performance and confidence of microbial source tracking markers in the coming era of big data with increasing resources in available metagenomic data.

Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life

Caesarean section delivery (CSD) disrupts mother-to-neonate transmission of specific microbial strains and functional repertoires as well as linked immune system priming. Here we investigate whether differences in microbiome composition and impacts on host physiology persist at 1 year of age. We perform high-resolution, quantitative metagenomic analyses of the gut microbiomes of infants born by vaginal delivery (VD) or by CSD, from immediately after birth through to 1 year of life. Several microbial populations show distinct enrichments in CSD-born infants at 1 year of age including strains of Bacteroides caccae, Bifidobacterium bifidum and Ruminococcus gnavus, whereas others are present at higher levels in the VD group including Faecalibacterium prausnitizii, Bifidobacterium breve and Bifidobacterium kashiwanohense. The stimulation of healthy donor-derived primary human immune cells with LPS isolated from neonatal stool samples results in higher levels of tumour necrosis factor alpha (TNF-α) in the case of CSD extracts over time, compared to extracts from VD infants for which no such changes were observed during the first year of life. Functional analyses of the VD metagenomes at 1 year of age demonstrate a significant increase in the biosynthesis of the natural antibiotics, carbapenem and phenazine. Concurrently, we find antimicrobial resistance (AMR) genes against several classes of antibiotics in both VD and CSD. The abundance of AMR genes against synthetic (including semi-synthetic) agents such as phenicol, pleuromutilin and diaminopyrimidine are increased in CSD children at day 5 after birth. In addition, we find that mobile genetic elements, including phages, encode AMR genes such as glycopeptide, diaminopyrimidine and multidrug resistance genes. Our results demonstrate persistent effects at 1 year of life resulting from birth mode-dependent differences in earliest gut microbiome colonisation.

Fecal Microbiome and Resistome Profiling of Healthy and Diseased Pakistani Individuals Using Next-Generation Sequencing

In this paper, we aimed to characterize the fecal microbiome and its resistomes of healthy and diseased subjects infected with multidrug-resistant Escherichia coli using next-generation sequencing (NGS). After initial screening, 26 stools samples belonging to healthy (n = 13) and diseased subjects (n = 13) were selected and subjected to NGS. A total of 23 and 42 antibiotic-resistant genes (ARGs) conferring resistance to 6 and 9 classes of antibiotics were identified in the resistomes of healthy and diseased subjects, respectively. Bacteroidetes were found to be the major phylum in both healthy and diseased subjects; however, Proteobacteria was predominantly present in the diseased subjects only. Microbial dysbiosis and predominance of various ARGs in the resistome of diseased subjects reflect the excessive usage of antibiotics in Pakistan and warrants immediate attention to regulate the use of various antimicrobials.

Influence of Human Eating Habits on Antimicrobial Resistance Phenomenon: Aspects of Clinical Resistome of Gut Microbiota in Omnivores, Ovolactovegetarians, and Strict Vegetarians

The use of xenobiotics in food production and how food intake is carried out in different cultures, along with different eating habits (omnivorism (ON), ovolactovegetarianism (VT), and strict vegetarianism (VG)) seem to have implications for antimicrobial resistance, especially in the human gut microbiota. Thus, the aim of this study was to evaluate aspects of the clinical resistome of the human gut microbiota among healthy individuals with different eating habits. Volunteers were divided into 3 groups: n = 19 omnivores (ON), n = 20 ovolactovegetarians (VT), and n = 19 strict vegetarians (VG), and nutritional and anthropometric parameters were measured. Metagenomic DNA from fecal samples was used as a template for PCR screening of 37 antimicrobial resistance genes (ARG) representative of commonly used agents in human medicine. The correlation between eating habits and ARG was evaluated. There were no significant differences in mean caloric intake. Mean protein intake was significantly higher in ON, and fiber and carbohydrate consumption was higher in VG. From the screened ARG, 22 were detected. No clear relationship between diets and the occurrence of ARG was observed. Resistance genes against tetracyclines, β-lactams, and the MLS group (macrolides, lincosamides, and streptogramins) were the most frequent, followed by resistance genes against sulfonamides and aminoglycosides. Vegetables and minimally processed foods seem to be the main source of ARG for the human gut microbiota. Although eating habits vary among individuals, the open environment and the widespread ARG from different human activities draw attention to the complexity of the antimicrobial resistance phenomenon which should be addressed by a One Health approach.

Abundance, diversity and mobility potential of antibiotic resistance genes in pristine Tibetan Plateau soil as revealed by soil metagenomics

Widespread occurrence of antibiotic resistance genes (ARGs) has become an important clinical issue. Studying ARGs in pristine soil environments can help to better understand the intrinsic soil resistome. In this study, 10 soil samples were collected from a high elevation and relatively pristine Tibetan area, and metagenomic sequencing and bioinformatic analyses were conducted to investigate the microbial diversity, the abundance and diversity of ARGs and the mobility potential of ARGs as indicated by different mobile genetic elements (MGEs). A total of 48 ARG types with a relative abundance of 0.05-0.28 copies of ARG/copy of 16S rRNA genes were detected in Tibetan soil samples. The observed ARGs were mainly associated with antibiotics that included glycopeptide and rifamycin; the most abundant ARGs were vanRO and vanSO. Low abundance of MGEs and potentially plasmid-related ARGs indicated a low horizontal gene transfer risk of ARGs in the pristine soil. Pearson correlation and redundancy analyses showed that temperature and total organic carbon were the major environmental factors controlling both microbial diversity and ARG abundance and diversity.

Impact of a Novel Nano-Protectant on the Viability of Probiotic Bacterium Lactobacillus casei K17

Probiotics are considered as desirable alternatives to antibiotics because of their beneficial effects on the safety and economy of farm animals. The protectant can ensure the viability of probiotics, which is the prerequisite of the beneficial effects. The objective of this study was to evaluate the effects of a novel nano-protectant containing trehalose, skim milk powder, phytoglycogen nanoparticles, and nano-phytoglycogen Pickering emulsions on the viability of Lactobacillus casei K17 under different conditions. The results indicated that the optimal concentration of the carbohydrate substrate was determined to be 10% skim milk powder (w/w) instead of trehalose. The combination of 10% skim milk powder (w/w), 1% phytoglycogen nanoparticles (w/w), and 10% Pickering emulsions (w/w) was selected as the optimal component of the protectant. Trilayer protectants with an optimal component had a more significant protective effect on the bacteria than that of the monolayer and bilayer protectants, or the control in feed storage, freeze-drying, and simulated gastrointestinal environment. A scanning electron microscope was used to monitor the morphological characteristics of the protectants for different layers on L. casei. In conclusion, the trilayer protectant exhibited a substantial effect on L. casei during storage and consumption, which could be used in the feed and functional food.

Antibiotic resistome from the One-Health perspective: understanding and controlling antimicrobial resistance transmission

The concept of the antibiotic resistome was introduced just over a decade ago, and since then, active resistome studies have been conducted. In the present study, we describe the previously established concept of the resistome, which encompasses all types of antibiotic resistance genes (ARGs), and the important findings from each One-Health sector considering this concept, thereby emphasizing the significance of the One-Health approach in understanding ARG transmission. Cutting-edge research methodologies are essential for deciphering the complex resistome structure in the microbiomes of humans, animals, and the environment. Based on the recent achievements of resistome studies in multiple One-Health sectors, future directions for resistome research have been suggested to improve the understanding and control of ARG transmission: (1) ranking the critical ARGs and their hosts; (2) understanding ARG transmission at the interfaces of One-Health sectors; (3) identifying selective pressures affecting the emergence, transmission, and evolution of ARGs; and (4) elucidating the mechanisms that allow an organism to overcome taxonomic barriers in ARG transmission.

PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data

BACKGROUND

Pathogenic microorganisms cause disease by invading, colonizing, and damaging their host. Virulence factors including bacterial toxins contribute to pathogenicity. Additionally, antimicrobial resistance genes allow pathogens to evade otherwise curative treatments. To understand causal relationships between microbiome compositions, functioning, and disease, it is essential to identify virulence factors and antimicrobial resistance genes in situ. At present, there is a clear lack of computational approaches to simultaneously identify these factors in metagenomic datasets.

RESULTS

Here, we present PathoFact, a tool for the contextualized prediction of virulence factors, bacterial toxins, and antimicrobial resistance genes with high accuracy (0.921, 0.832 and 0.979, respectively) and specificity (0.957, 0.989 and 0.994). We evaluate the performance of PathoFact on simulated metagenomic datasets and perform a comparison to two other general workflows for the analysis of metagenomic data. PathoFact outperforms all existing workflows in predicting virulence factors and toxin genes. It performs comparably to one pipeline regarding the prediction of antimicrobial resistance while outperforming the others. We further demonstrate the performance of PathoFact on three publicly available case-control metagenomic datasets representing an actual infection as well as chronic diseases in which either pathogenic potential or bacterial toxins are hypothesized to play a role. In each case, we identify virulence factors and AMR genes which differentiated between the case and control groups, thereby revealing novel gene associations with the studied diseases.

CONCLUSION

PathoFact is an easy-to-use, modular, and reproducible pipeline for the identification of virulence factors, bacterial toxins, and antimicrobial resistance genes in metagenomic data. Additionally, our tool combines the prediction of these pathogenicity factors with the identification of mobile genetic elements. This provides further depth to the analysis by considering the genomic context of the pertinent genes. Furthermore, PathoFact's modules for virulence factors, toxins, and antimicrobial resistance genes can be applied independently, thereby making it a flexible and versatile tool. PathoFact, its models, and databases are freely available at https://pathofact.lcsb.uni.lu . Video abstract.

The 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.

Reponses of microbial community and antibiotic resistance genes to the selection pressures of ampicillin, cephalexin and chloramphenicol in activated sludge reactors

High concentrations of antibiotics can exert strong selection pressures on the microbial community and promote the emergence and dissemination of antibiotic resistance genes (ARGs). The activated sludge reactors treating ampicillin, cephalexin and chloramphenicol production wastewater were established to investigate the responses of microbial community, ARGs and mobile genetic elements (MGEs) to antibiotics. Antibiotic selection pressures significantly declined the microbial diversity and changed microbial community structures. Based on metagenomic analysis, a total of 500 ARG subtypes affiliated with 18 ARG types were identified and 63 ARGs were shared by all samples. The substantial increase of ARG abundance and the shifts of ARG profiles were significantly correlated with antibiotic types and concentrations. The evident enrichment of non-corresponding ARG types suggested the strong co-selection effects of the target antibiotics. Additionally, metagenomic analysis revealed the occurrence of 104 MGEs belonging to various types and the five dominant MGEs were tnpA, intI1, tniA, tniB and IS91. The ARG-MGE co-occurrence associations implied the potential mobility of ARGs. Network analysis also demonstrated that five ARG types (aminoglycoside, beta-lactam, chloramphenicol, multidrug and tetracycline resistance genes) tended to co-occur internally and the obvious co-occurrence patterns among different ARG types indicated the potential for resistance co-selection. Moreover, 15 bacterial genera were speculated as the hosts of diverse ARGs. This study provides a comprehensive overview of the occurrence of ARGs and MGEs and is valuable for the risk assessment and management of antibiotic resistance.

The distribution of antibiotic resistance genes in chicken gut microbiota commensals

Antibiotic resistance in bacterial pathogens or several indicator bacteria is commonly studied but the extent of antibiotic resistance in bacterial commensals colonising the intestinal tract is essentially unknown. In this study, we aimed to investigate the presence of horizontally acquired antibiotic resistance genes among chicken gut microbiota members in 259 isolates with known whole genomic sequences. Altogether 124 isolates contained at least one gene coding for antibiotic resistance. Genes coding for the resistance to tetracyclines (detected in 101 isolates), macrolide-lincosamide-streptogramin B antibiotics (28 isolates) and aminoglycosides (25 isolates) were the most common. The most frequent tetracycline resistance genes were tet(W), tet(32), tet(O) and tet(Q). Lachnospiraceae and Ruminococcaceae frequently encoded tet(W). Lachnospiraceae commonly coded also for tet(32) and tet(O). The tet(44) gene was associated with Erysipelotrichaceae and tet(Q) was detected in the genomes of Bacteroidaceae and Porphyromonadaceae. Without any bias we have shown that antibiotic resistance is quite common in gut commensals. However, a comparison of codon usage showed that the above-mentioned families represent the most common current reservoirs but probably not the original host of the detected resistances.

Occupational Exposure and Carriage of Antimicrobial Resistance Genes (tetW, ermB) in Pig Slaughterhouse Workers

Objectives

Slaughterhouse staff is occupationally exposed to antimicrobial resistant bacteria. Studies reported high antimicrobial resistance gene (ARG) abundances in slaughter pigs. This cross-sectional study investigated occupational exposure to tetracycline (tetW) and macrolide (ermB) resistance genes and assessed determinants for faecal tetW and ermB carriage among pig slaughterhouse workers.

Methods

During 2015–2016, 483 faecal samples and personal questionnaires were collected from workers in a Dutch pig abattoir, together with 60 pig faecal samples. Human dermal and respiratory exposure was assessed by examining 198 carcass, 326 gloves, and 33 air samples along the line, next to 198 packed pork chops to indicate potential consumer exposure. Samples were analyzed by qPCR (tetW, ermB). A job exposure matrix was created by calculating the percentage of tetW and ermB positive carcasses or gloves for each job position. Multiple linear regression models were used to link exposure to tetW and ermB carriage.

Results

Workers are exposed to tetracycline and macrolide resistance genes along the slaughter line. Tetw and ermB gradients were found for carcasses, gloves, and air filters. One packed pork chop contained tetW, ermB was non-detectable. Human faecal tetW and ermB concentrations were lower than in pig faeces. Associations were found between occupational tetW exposure and human faecal tetW carriage, yet, not after model adjustments. Sampling round, nationality, and smoking were determinants for ARG carriage.

Conclusion

We demonstrated clear environmental tetracycline and macrolide resistance gene exposure gradients along the slaughter line. No robust link was found between ARG exposure and human faecal ARG carriage.

Microbiomes and Resistomes in Biopsy Tissue and Intestinal Lavage Fluid of Colorectal Cancer

Aim: The gut microbiome plays a crucial role in colorectal cancer (CRC) tumorigenesis, but compositions of microorganisms have been inconsistent in previous studies due to the different types of specimens. We investigated the microbiomes and resistomes of CRC patients with colonic biopsy tissue and intestinal lavage fluid (IVF). Methods: Paired samples (biopsy tissue and IVF) were collected from 20 patients with CRC, and their gut microbiomes and resistomes were measured by shotgun metagenomics. Clinical and laboratory data were recorded. Bioinformatics (KneadData, Kraken2, and FMAP) and statistical analysis were done using the R (v4.0.2) software. Results: Bacterial diversity in IVF was higher than in tissue samples, and bacterial operational taxonomic units (OTUs) were 2,757 in IVF vs. 197 in tissue. β-diversity showed distinct clusters in paired samples. The predominant bacteria in IVF were phylum Proteobacteria, while the predominant bacteria of tissue were phylum Actinobacteria. Twenty-seven representative bacteria were selected to form six bacterial clusters, which showed only Firmicutes Cluster 1, and the Bacteroidetes Cluster 1 were significantly more abundant in the IVF group than those in the tissue group (p < 0.05). The Firmicutes Cluster 2, Bacteroidetes Cluster 2, Pathogen Cluster, and Prevotella Cluster were not significantly different between IVF and tissue (p > 0.05). Correlation analysis revealed that some bacteria could have effects on metabolic and inflammatory parameters of CRC patients. A total of 1,295 antibiotic resistance genes (ARGs) were detected in the gut microbiomes, which conferred multidrug resistance, as well as resistance to tetracycline, aminoglycoside, and more. Co-occurrence patterns revealed by the network showed mainly ARG-carrying bacteria to be similar between IVF and tissue, but leading bacteria located in the hub differed between IVF and tissue. Conclusion: Heterogeneity of microbiota is particularly evident when studied with IVF and tissue samples, but bacterial clusters that have close relationships with CRC carcinogenesis are not significantly different, using IVF as an alternative to tissue for gut microbiome, and resistome assessment may be a feasible method.

Dietary supplementation with Bacillus subtilis and xylo-oligosaccharides improves growth performance and intestinal morphology and alters intestinal microbiota and metabolites in weaned piglets

The present study was conducted to investigate the effects of dietary supplementation with Bacillus subtilis (BS) and xylo-oligosaccharides (XOS) on growth performance, intestinal morphology, intestinal microbial community, and metabolites of weaned piglets. One hundred and twenty-eight piglets were randomly allocated to one of four groups, including a control group (basal diet), BS group (basal diet + 500 g t-1 BS), XOS group (basal diet + 250 g t-1 XOS), and BS + XOS group (basal diet + 500 g t-1 BS + 250 g t-1 XOS). Dietary BS and XOS were mixed with the basal diet. All groups had eight replicates with four piglets per replicate. The experiment lasted for 42 days. The results showed that dietary XOS supplementation increased the ADFI and ADG, while decreasing the F/G. Dietary BS or XOS supplementation improved the intestinal morphology of weaned piglets by increasing the villus height and the ratio of villus height to crypt depth in the ileum. In addition, dietary XOS supplementation increased the concentrations of butyrate in the ileum and tryptamine and spermidine in the colon, while decreasing the concentration of indole in the colon compared with the control group. Dietary BS supplementation increased the colonic concentrations of butyrate, tryptamine, and cadaverine, while decreasing the concentration of skatole compared with the control group. The LEfSe analysis identified 16 biomarkers in the ileum of the BS group. The intestinal microbiota alterations of weaned piglets indicated that dietary BS or XOS supplementation could improve intestinal health by increasing the gut microbial diversity and altering the relative abundances of different bacterial species. Moreover, Spearman's correlation analysis revealed the potential link between gut microbiota alterations and metabolite changes of weaned piglets. These findings suggest that dietary XOS supplementation could alone improve the growth performance, while dietary BS or XOS and BS with XOS supplementation could influence intestinal health by altering the intestinal morphology, microbial community, and metabolites of weaned piglets. Meanwhile, there were interactions between BS and XOS in intestinal metabolites.

Significant higher airborne antibiotic resistance genes and the associated inhalation risk in the indoor than the outdoor

Inhalation of airborne antibiotic resistance genes (ARGs) can lead to antimicrobial resistance and potential health risk. In modern society, increasing individuals stay more indoors, however, studies regarding the exposure to airborne ARGs in indoor environments and the associated risks remain limited. Here, we compared the variance of aerosol-associated ARGs, bacterial microbiomes, and their daily intake (DI) burden in dormitory, office, and outdoor environments in a university in Tianjin. The results indicated that compared to outdoor aerosols, indoors exhibited significantly higher absolute abundance of both ARG subtypes and mobile genetic elements (MGEs) (1-7 orders of magnitude), 16S rRNA genes (2-3 orders), and total culturable bacteria (1-3 orders). Furthermore, we observed that significantly different airborne bacterial communities are the major drivers contributing to the variance of aerosol-associated ARGs in indoor and outdoor aerosols. Notably, the high abundances of total bacteria, potential pathogenic genera, and ARGs (particularly those harbored by pathogens) in indoor and outdoor aerosols, especially in indoors, may pose an increased exposure risk via inhalation. The successful isolation of human pathogens such as Elizabethkingia anopheles, Klebsiella pneumonia, and Delftia lacustris resistant to the "last-resort" antibiotics carbapenems and polymyxin B from indoor aerosols further indicated an increased exposure risk in indoors. Together, this study highlights the potential risks associated with ARGs and their inhalation to human health in indoor environments.