TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome

The aim of the study. The aim of the study was to review publication about microbiome of chicken manure, chicken manure compost, as well as soil and crop microbiome after compost addition to soil as a fertilizer. Methodology. A search in the bibliographical data bases PubMed and elibrary.ru was performed using the keywords pertaining to the topic of the article. Main results. The results about the chicken manure microbiome, obtained by high throughput sequencing, showed that the chicken gut microbiome is dominated by bacteria of the Firmicutes and Bacteroidetes phyla; some regional chicken populations were found to have Clostridium, Lactobacillus, Eubacterium, Bacteroides, Escherichia coli, Prevotella, Selenomonas, Streptococcus, Megasphaera, Fusobacterium и Bifidobacterium as the main representatives of the gut microbiome. However, chicken manure can contain bacteria with antibiotic resistance genes, as antibiotics are increasingly used in the poultry industry to stimulate production. In general manure composting can be regarded as environmentally safe method for transforming various organic wastes into organic fertilizers. As increasing output of the poultry industry, which inevitably includes manure, increased the interest to its composting, and recent years have seen unprecedented number of research, dealing with various details of manure composting, such as duration, hydrothermal conditions, added bulking materials, microbiological preparations, abundance of the antibiotic resistance genes, and so on. However, the studies of soil and crop microbiome after soil fertilization with chicken manure compost have so far been rather scarce, resulting in ambiguous conclusions, i.e. about positive or no effect of the compost addition. The effect is determined by species, breed, age, rearing and manure composting technology, as well as by crop and its cultivar, agricultural practices and soil specifics. Conclusions. Chicken manure contains taxonomically diverse microbiome that can be changed during composting. Microbiota of chicken manure and its compost with their great microbial species richness can contain bacteria, carrying antibiotic resistance genes. Dispersal of such components of the compost resistome in environment via compost addition to agricultural soils should be regarded as a growing biological hazard, threatening the efficient use of antibiotics for treating bacterial infections in in veterinary and medicine. Therefore increasing poultry production urges for assessing the risks and evaluating the scope of the threat, as well as estimating and establishing permissible limits of pathomicrobiotic load of the poultry litter manure and compost, using up-to-date metagenomic techniques. The greatest concern is about spreading antibiotic resistance genes into the marketable crop components, consumed raw; consequently, alongside with studying microbiota of the compost-receiving agricultural soil as a source of dust, microbiome research should be also focused crop phytobiome where crops are produced under addition of composts, obtained with manure of the antibiotic-treated poultry during industrial production.

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Antibiotic resistance potential of the healthy preterm infant gut microbiome

PeerJ ◽

10.7717/peerj.2928 ◽

2017 ◽

Vol 5 ◽

pp. e2928 ◽

Cited By ~ 23

Author(s):

Graham Rose ◽

Alexander G. Shaw ◽

Kathleen Sim ◽

David J. Wooldridge ◽

Ming-Shi Li ◽

...

Keyword(s):

Antibiotic Resistance ◽

Preterm Infant ◽

Resistance Genes ◽

Gut Microbiome ◽

Antibiotic Resistance Genes ◽

Taxonomic Diversity ◽

Metagenomic Sequencing ◽

Important Species ◽

Antimicrobial Resistance Genes ◽

Infant Gut Microbiome

Background Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut microbiomes from preterm but healthy infants, characterising the taxonomic diversity identified and frequency of antibiotic resistance genes detected. Results Dominant clinically important species identified within the microbiomes included C. perfringens, K. pneumoniae and members of the Staphylococci and Enterobacter genera. Screening at the gene level we identified an average of 13 antimicrobial resistance genes per preterm infant, ranging across eight different antibiotic classes, including aminoglycosides and fluoroquinolones. Some antibiotic resistance genes were associated with clinically relevant bacteria, including the identification of mecA and high levels of Staphylococci within some infants. We were able to demonstrate that in a third of the infants the S. aureus identified was unrelated using MLST or metagenome assembly, but low abundance prevented such analysis within the remaining samples. Conclusions We found that the healthy preterm infant gut microbiomes in this study harboured a significant diversity of antibiotic resistance genes. This broad picture of resistances and the wider taxonomic diversity identified raises further caution to the use of antibiotics without consideration of the resident microbial communities.

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Joining the resistance

Science Translational Medicine ◽

10.1126/scitranslmed.aar7519 ◽

2018 ◽

Vol 10 (425) ◽

pp. eaar7519

Author(s):

Stephanie A. Christenson

Keyword(s):

Antibiotic Resistance ◽

Preterm Infants ◽

Resistance Genes ◽

Gut Microbiome ◽

Antibiotic Resistance Genes ◽

Antibiotic Administration ◽

Before And After

The effect of antibiotic resistance genes on the gut microbiome is examined in preterm infants before and after antibiotic administration.

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US Immigration Is Associated With Rapid and Persistent Acquisition of Antibiotic Resistance Genes in the Gut

Clinical Infectious Diseases ◽

10.1093/cid/ciz1087 ◽

2019 ◽

Vol 71 (2) ◽

pp. 419-421

Author(s):

Quentin Le Bastard ◽

Pajau Vangay ◽

Eric Batard ◽

Dan Knights ◽

Emmanuel Montassier

Keyword(s):

United States ◽

Antibiotic Resistance ◽

Resistance Gene ◽

Resistance Genes ◽

Gut Microbiome ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

The United States ◽

Human Migration ◽

Metagenomics Analysis

Abstract Little is known about the effect of human migration on gut microbiome antibiotic resistance gene (ARG) carriage. Using deep shotgun stool metagenomics analysis, we found a rapid increase in gut microbiome ARG richness and abundance in women from 2 independent ethnic groups relocating from Thailand to the United States.

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An Orally Delivered Beta-Lactamase Protects the Gut Microbiome from Antibiotic-Mediated Damage and Mitigates the Propagation of Antibiotic-Resistance Genes in a Porcine Dysbiosis Model

Gastroenterology ◽

10.1016/s0016-5085(17)34350-0 ◽

2017 ◽

Vol 152 (5) ◽

pp. S1305-S1306

Author(s):

Sheila Connelly ◽

Christian Furlan Freguia ◽

Poorani Subramanian ◽

Nur A. Hasan ◽

Rita R. Colwell ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Gut Microbiome ◽

Antibiotic Resistance Genes ◽

Beta Lactamase

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Putative mobilized colistin resistance genes in the human gut microbiome

BMC Microbiology ◽

10.1186/s12866-021-02281-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Bruno G. N. Andrade ◽

Tobias Goris ◽

Haithem Afli ◽

Felipe H. Coutinho ◽

Alberto M. R. Dávila ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Gut Microbiome ◽

Antibiotic Resistance Genes ◽

Future Research ◽

Human Populations ◽

Bacterial Strains ◽

Colistin Resistance ◽

Human Gut ◽

Human Gut Microbiome

Abstract Background The high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin, caused by mobilized colistin resistance (mcr) genes, poses an unprecedented threat to human health. Understanding the spread, evolution, and distribution of such genes among human populations will help in the development of strategies to diminish their occurrence. To tackle this problem, we investigated the distribution and prevalence of potential mcr genes in the human gut microbiome using a set of bioinformatics tools to screen the Unified Human Gastrointestinal Genome (UHGG) collection for the presence, synteny and phylogeny of putative mcr genes, and co-located antibiotic resistance genes. Results A total of 2079 antibiotic resistance genes (ARGs) were classified as mcr genes in 2046 metagenome assembled genomes (MAGs), distributed across 1596 individuals from 41 countries, of which 215 were identified in plasmidial contigs. The genera that presented the largest number of mcr-like genes were Suterella and Parasuterella. Other potential pathogens carrying mcr genes belonged to the genus Vibrio, Escherichia and Campylobacter. Finally, we identified a total of 22,746 ARGs belonging to 21 different classes in the same 2046 MAGs, suggesting multi-resistance potential in the corresponding bacterial strains, increasing the concern of ARGs impact in the clinical settings. Conclusion This study uncovers the diversity of mcr-like genes in the human gut microbiome. We demonstrated the cosmopolitan distribution of these genes in individuals worldwide and the co-presence of other antibiotic resistance genes, including Extended-spectrum Beta-Lactamases (ESBL). Also, we described mcr-like genes fused to a PAP2-like domain in S. wadsworthensis. These novel sequences increase our knowledge about the diversity and evolution of mcr-like genes. Future research should focus on activity, genetic mobility and a potential colistin resistance in the corresponding strains to experimentally validate those findings.

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Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota

10.1101/385831 ◽

2018 ◽

Author(s):

Bálint Kintses ◽

Orsolya Méhi ◽

Eszter Ari ◽

Mónika Számel ◽

Ádám Györkei ◽

...

Keyword(s):

Antibiotic Resistance ◽

Gut Microbiota ◽

Resistance Genes ◽

Gut Microbiome ◽

Horizontal Transfer ◽

Bacterial Species ◽

Antibiotic Resistance Genes ◽

Genetic Exchange ◽

Human Gut ◽

Human Gut Microbiota

AbstractThe human gut microbiota has adapted to the presence of antimicrobial peptides (AMPs) that are ancient components of immune defence. Despite important medical relevance, it has remained unclear whether AMP resistance genes in the gut microbiome are available for genetic exchange between bacterial species. Here we show that AMP- and antibiotic-resistance genes differ in their mobilization patterns and functional compatibilities with new bacterial hosts. First, whereas AMP resistance genes are widespread in the gut microbiome, their rate of horizontal transfer is lower than that of antibiotic resistance genes. Second, gut microbiota culturing and functional metagenomics revealed that AMP resistance genes originating from phylogenetically distant bacteria only have a limited potential to confer resistance inEscherichia coli, an intrinsically susceptible species. Third, the phenotypic impact of acquired AMP resistance genes heavily depends on the genetic background of the recipient bacteria. Taken together, functional compatibility with the new bacterial host emerges as a key factor limiting the genetic exchange of AMP resistance genes. Finally, our results suggest that AMPs induce highly specific changes in the composition of the human microbiota with implications for disease risks.

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Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China

mSystems ◽

10.1128/msystems.00206-19 ◽

2019 ◽

Vol 4 (6) ◽

Cited By ~ 5

Author(s):

Chunlai Wang ◽

Peng Li ◽

Qiulong Yan ◽

Liping Chen ◽

Tiantian Li ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Gut Microbiome ◽

Human Microbiome ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Aminoglycoside Resistance ◽

Pig Production ◽

Resistance Proteins ◽

Gene Catalogue

ABSTRACT To characterize the diversity and richness and explore the function and structure of swine gut microbiome and resistome in common pig-farming feedlots, we sampled and metagenomic sequenced the feces of pigs from four different industrialized feedlots located in four distant provinces across China. Surprisingly, more than half of the nonredundant genes (1,937,648, 54.3%) in the current catalogue were newly found compared with the previously published reference gene catalogue (RGC) of the pig gut microbiome. Additionally, 16 high-completeness draft genomes were obtained by analyzing the dominant species on each feedlot. Notably, seven of these species often appeared in the human body sites. Despite a smaller number of nonredundant genes, our study identified more antibiotic resistance genes than those available in the RGC. Tetracycline, aminoglycoside, and multidrug resistance genes accounted for nearly 70% of the relative abundance in the current catalogue. Slightly higher sharing ratios were shown between the industrialized feedlot pig gut microbiomes and human gut microbiomes than that between the RGC and human counterpart (14.7% versus 12.6% in genes and 94.1% versus 87.7% in functional groups, respectively). Furthermore, a remarkably high number of the antibiotic resistance proteins (n =141) were identified to be shared by the pig, human, and mouse resistome, indicating the potential for horizontal transfer of resistance genes. Of the antibiotic resistance proteins shared by pigs and humans, 50 proteins were related to tetracycline resistance, and 49 were related to aminoglycoside resistance. IMPORTANCE The gut microbiota is believed to be closely related to many important physical functions in the host. Comprehensive data on mammalian gut metagenomes has facilitated research on host-microbiome interaction mechanisms, but less is known about pig gut microbiome, especially the gut microbiome in industrialized feedlot pigs, compared with human microbiome. On the other hand, pig production, as an important source of food, is believed to exacerbate the antibiotic resistance in humans due to the abuse of antibiotics in pig production in various parts of the world. This study delineates an intricate picture of swine gut microbiome and antibiotic resistome in industrialized feedlots and may provide insight for the pig producing industry.

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Metagenomic analysis revealed a wide distribution of antibiotic resistance genes and biosynthesis of antibiotics in the gut of giant pandas

BMC Microbiology ◽

10.1186/s12866-020-02078-x ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Ghulam Raza Mustafa ◽

Caiwu Li ◽

Siyue Zhao ◽

Lei Jin ◽

Xueping He ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Gut Microbiome ◽

Antibiotic Resistance Genes ◽

Positive Association ◽

Wide Distribution ◽

Functional Characteristics ◽

Kegg Pathways ◽

Occurrence Pattern ◽

Metagenome Sequencing

Abstract Background The gut microbiome is essential for the host’s health and serves as an essential reservoir of antibiotic resistance genes (ARGs). We investigated the effects of different factors, including the dietary shifts and age, on the functional characteristics of the giant panda’s gut microbiome (GPs) through shotgun metagenome sequencing. We explored the association between gut bacterial genera and ARGs within the gut based on network analysis. Results Fecal samples (n=60) from captive juvenile, adult, and geriatric GPs were processed, and variations were identified in the gut microbiome according to different ages, the abundance of novel ARGs and the biosynthesis of antibiotics. Among 667 ARGs identified, nine from the top ten ARGs had a higher abundance in juveniles. For 102 ARGs against bacteria, a co-occurrence pattern revealed a positive association for predominant ARGs with Streptococcus. A comparative KEGG pathways analysis revealed an abundant biosynthesis of antibiotics among three different groups of GPs, where it was more significantly observed in the juvenile group. A co-occurrence pattern further revealed a positive association for the top ten ARGs, biosynthesis of antibiotics, and metabolic pathways. Conclusion Gut of GPs serve as a reservoir for novel ARGs and biosynthesis of antibiotics. Dietary changes and age may influence the gut microbiome’s functional characteristics; however, it needs further studies to ascertain the study outcomes.

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