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

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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COVID-19 Lockdowns May Reduce Resistance Genes Diversity in the Human Microbiome and the Need for Antibiotics

International Journal of Molecular Sciences ◽

10.3390/ijms22136891 ◽

2021 ◽

Vol 22 (13) ◽

pp. 6891

Author(s):

João S. Rebelo ◽

Célia P. F. Domingues ◽

Francisco Dionisio ◽

Manuel C. Gomes ◽

Ana Botelho ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Pathogenic Bacteria ◽

Bacterial Resistance ◽

Human Microbiome ◽

Antibiotic Resistance Genes ◽

Public Health Problem ◽

Small World ◽

Physical Contact ◽

Hygiene Measures

Recently, much attention has been paid to the COVID-19 pandemic. Yet bacterial resistance to antibiotics remains a serious and unresolved public health problem that kills hundreds of thousands of people annually, being an insidious and silent pandemic. To contain the spreading of the SARS-CoV-2 virus, populations confined and tightened hygiene measures. We performed this study with computer simulations and by using mobility data of mobile phones from Google in the region of Lisbon, Portugal, comprising 3.7 million people during two different lockdown periods, scenarios of 40 and 60% mobility reduction. In the simulations, we assumed that the network of physical contact between people is that of a small world and computed the antibiotic resistance in human microbiomes after 180 days in the simulation. Our simulations show that reducing human contacts drives a reduction in the diversity of antibiotic resistance genes in human microbiomes. Kruskal–Wallis and Dunn’s pairwise tests show very strong evidence (p < 0.000, adjusted using the Bonferroni correction) of a difference between the four confinement regimes. The proportion of variability in the ranked dependent variable accounted for by the confinement variable was η2 = 0.148, indicating a large effect of confinement on the diversity of antibiotic resistance. We have shown that confinement and hygienic measures, in addition to reducing the spread of pathogenic bacteria in a human network, also reduce resistance and the need to use antibiotics.

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Identification and antibiotic resistance profiling of bacterial isolates from septicaemic soft-shelled turtles (Pelodiscus sinensis)

Veterinární Medicína ◽

10.17221/65/2016-vetmed ◽

2017 ◽

Vol 62 (No. 3) ◽

pp. 169-177 ◽

Cited By ~ 13

Author(s):

TH Chung ◽

SW Yi ◽

BS Kim ◽

WI Kim ◽

GW Shin

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Present Report ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Edwardsiella Tarda ◽

Pelodiscus Sinensis ◽

Class 1 Integron ◽

Class 1 ◽

M 14

The present study sought to identify pathogens associated with septicaemia in the Chinese soft-shelled turtle (Pelodiscus sinensis) and to characterise antibiotic resistance in these pathogens. Twenty-three isolates recovered from the livers of diseased soft-shelled turtles were genetically identified as Aeromonas hydrophila (n = 8), A. veronii (n = 3), Citrobacter freundii (n = 4), Morganella morganii (n = 3), Edwardsiella tarda (n = 2), Wohlfahrtiimonas chitiniclastica (n = 1), Chryseobacterium sp. (n = 1), and Comamonas sp. (n = 1). Most isolates (n = 21) were resistant to ampicillin whereas a low percentage of isolates was susceptible to aminoglycosides (amikacin, gentamicin, and tobramycin). PCR assays and sequence analysis revealed the presence of the qnrS2 and blaTEM antibiotic resistance genes in all isolates. The blaDHA-1, blaCTX-M-14 and blaCMY-2 genes were harboured by 17.4% (n = 4), 13.5% (n = 3) and 8.7% (n = 2) of the strains, respectively. One or more tetracycline resistance genes were detected in 60.9% (n = 14) of the isolates. Four isolates (17.4%) harboured single or multiple class 1 integron cassettes. Collectively, a variety of bacterial pathogens were involved in the occurrence of septicaemia in Chinese soft-shelled turtles and most of the isolates had multi-antibiotic resistant phenotypes. To our knowledge, the present report is the first to identify W. chitiniclastica and Comamonas sp. as causes of septicaemia in soft-shelled turtles and the first to identify Aeromonas spp. with blaCTX-M-14 and blaDHA-1 resistance genes.

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Horizontal transfer of antibiotic resistance genes in the human gut microbiome

Current Opinion in Microbiology ◽

10.1016/j.mib.2020.02.002 ◽

2020 ◽

Vol 53 ◽

pp. 35-43 ◽

Cited By ~ 13

Author(s):

Ross S McInnes ◽

Gregory E McCallum ◽

Lisa E Lamberte ◽

Willem van Schaik

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Gut Microbiome ◽

Horizontal Transfer ◽

Antibiotic Resistance Genes ◽

Human Gut ◽

Human Gut Microbiome

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Characterization of antibiotic resistance genes in the species of the rumen microbiota

Nature Communications ◽

10.1038/s41467-019-13118-0 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 9

Author(s):

Yasmin Neves Vieira Sabino ◽

Mateus Ferreira Santana ◽

Linda Boniface Oyama ◽

Fernanda Godoy Santos ◽

Ana Júlia Silva Moreira ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Animal Health ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

Ruminal Bacteria ◽

Genes Encoding

AbstractInfections caused by multidrug resistant bacteria represent a therapeutic challenge both in clinical settings and in livestock production, but the prevalence of antibiotic resistance genes among the species of bacteria that colonize the gastrointestinal tract of ruminants is not well characterized. Here, we investigate the resistome of 435 ruminal microbial genomes in silico and confirm representative phenotypes in vitro. We find a high abundance of genes encoding tetracycline resistance and evidence that the tet(W) gene is under positive selective pressure. Our findings reveal that tet(W) is located in a novel integrative and conjugative element in several ruminal bacterial genomes. Analyses of rumen microbial metatranscriptomes confirm the expression of the most abundant antibiotic resistance genes. Our data provide insight into antibiotic resistange gene profiles of the main species of ruminal bacteria and reveal the potential role of mobile genetic elements in shaping the resistome of the rumen microbiome, with implications for human and animal health.

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Intra- and Interspecies Conjugal Transfer of Tn916-Like Elements from Lactococcus lactis In Vitro and In Vivo

Applied and Environmental Microbiology ◽

10.1128/aem.00470-09 ◽

2009 ◽

Vol 75 (19) ◽

pp. 6352-6360 ◽

Cited By ~ 25

Author(s):

Joanna Boguslawska ◽

Joanna Zycka-Krzesinska ◽

Andrea Wilcks ◽

Jacek Bardowski

Keyword(s):

Antibiotic Resistance ◽

Lactococcus Lactis ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Raw Milk ◽

M Gene ◽

Transfer Resistance

ABSTRACT Tetracycline-resistant Lactococcus lactis strains originally isolated from Polish raw milk were analyzed for the ability to transfer their antibiotic resistance genes in vitro, using filter mating experiments, and in vivo, using germfree rats. Four of six analyzed L. lactis isolates were able to transfer tetracycline resistance determinants in vitro to L. lactis Bu2-60, at frequencies ranging from 10−5 to 10−7 transconjugants per recipient. Three of these four strains could also transfer resistance in vitro to Enterococcus faecalis JH2-2, whereas no transfer to Bacillus subtilis YBE01, Pseudomonas putida KT2442, Agrobacterium tumefaciens UBAPF2, or Escherichia coli JE2571 was observed. Rats were initially inoculated with the recipient E. faecalis strain JH2-2, and after a week, the L. lactis IBB477 and IBB487 donor strains were introduced. The first transconjugants were detected in fecal samples 3 days after introduction of the donors. A subtherapeutic concentration of tetracycline did not have any significant effect on the number of transconjugants, but transconjugants were observed earlier in animals dosed with this antibiotic. Molecular analysis of in vivo transconjugants containing the tet(M) gene showed that this gene was identical to tet(M) localized on the conjugative transposon Tn916. Primer-specific PCR confirmed that the Tn916 transposon was complete in all analyzed transconjugants and donors. This is the first study showing in vivo transfer of a Tn916-like antibiotic resistance transposon from L. lactis to E. faecalis. These data suggest that in certain cases food lactococci might be involved in the spread of antibiotic resistance genes to other lactic acid bacteria.

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The human microbiome harbors a diverse reservoir of antibiotic resistance genes

Virulence ◽

10.4161/viru.1.4.12010 ◽

2010 ◽

Vol 1 (4) ◽

pp. 299-303 ◽

Cited By ~ 109

Author(s):

Morten O.A. Sommer ◽

George M. Church ◽

Gautam Dantas

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Human Microbiome ◽

Antibiotic Resistance Genes

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Incidence, Distribution, and Spread of Tetracycline Resistance Determinants and Integron-Associated Antibiotic Resistance Genes among Motile Aeromonads from a Fish Farming Environment

Applied and Environmental Microbiology ◽

10.1128/aem.67.12.5675-5682.2001 ◽

2001 ◽

Vol 67 (12) ◽

pp. 5675-5682 ◽

Cited By ~ 178

Author(s):

Anja S. Schmidt ◽

Morten S. Bruun ◽

Inger Dalsgaard ◽

Jens L. Larsen

Keyword(s):

Antibiotic Resistance ◽

Resistance Gene ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Class 1 Integron ◽

Gene Cassettes ◽

Class 1 Integrons ◽

Resistance Determinants ◽

Class 1

ABSTRACT A collection of 313 motile aeromonads isolated at Danish rainbow trout farms was analyzed to identify some of the genes involved in high levels of antimicrobial resistance found in a previous field trial (A. S. Schmidt, M. S. Bruun, I. Dalsgaard, K. Pedersen, and J. L. Larsen, Appl. Environ. Microbiol. 66:4908–4915, 2000), the predominant resistance phenotype (37%) being a combined oxytetracycline (OTC) and sulphadiazine/trimethoprim resistance. Combined sulphonamide/trimethoprim resistance (135 isolates) appeared closely related to the presence of a class 1 integron (141 strains). Among the isolates containing integrons, four different combinations of integrated resistance gene cassettes occurred, in all cases including a dihydrofolate reductase gene and a downstream aminoglycoside resistance insert (87 isolates) and occasionally an additional chloramphenicol resistance gene cassette (31 isolates). In addition, 23 isolates had “empty” integrons without inserted gene cassettes. As far as OTC resistance was concerned, only 66 (30%) out of 216 resistant aeromonads could be assigned to resistance determinant class A (19 isolates), D (n = 6), or E (n = 39); three isolates contained two tetracycline resistance determinants (AD, AE, and DE). Forty OTC-resistant isolates containing large plasmids were selected as donors in a conjugation assay, 27 of which also contained a class 1 integron. Out of 17 successful R-plasmid transfers to Escherichia coli recipients, the respective integrons were cotransferred along with the tetracycline resistance determinants in 15 matings. Transconjugants were predominantly tetApositive (10 of 17) and contained class 1 integrons with two or more inserted antibiotic resistance genes. While there appeared to be a positive correlation between conjugative R-plasmids andtetA among the OTC-resistant aeromonads, tetEand the unclassified OTC resistance genes as well as class 1 integrons were equally distributed among isolates with and without plasmids. These findings indicate the implication of other mechanisms of gene transfer besides plasmid transfer in the dissemination of antibiotic resistance among environmental motile aeromonads.

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Antibiotic Resistance Characteristics of Environmental Bacteria from an Oxytetracycline Production Wastewater Treatment Plant and the Receiving River

Applied and Environmental Microbiology ◽

10.1128/aem.02964-09 ◽

2010 ◽

Vol 76 (11) ◽

pp. 3444-3451 ◽

Cited By ~ 174

Author(s):

Dong Li ◽

Tao Yu ◽

Yu Zhang ◽

Min Yang ◽

Zhen Li ◽

...

Keyword(s):

Antibiotic Resistance ◽

River Water ◽

Resistance Genes ◽

Treatment Plant ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Production Plant ◽

Bacterial Strains ◽

High Concentration ◽

Receiving River

ABSTRACT We characterized the bacterial populations in surface water receiving effluent from an oxytetracycline (OTC) production plant. Additional sampling sites included the receiving river water 5 km upstream and 20 km downstream from the discharge point. High levels of OTC were found in the wastewater (WW), and the antibiotic was still detectable in river water downstream (RWD), with undetectable levels in river water upstream (RWU). A total of 341 bacterial strains were isolated using nonselective media, with the majority being identified as Gammaproteobacteria. The MICs were determined for 10 antibiotics representing seven different classes of antibiotics, and the corresponding values were significantly higher for the WW and RWD isolates than for the RWU isolates. Almost all bacteria (97%) from the WW and RWD samples demonstrated multidrug-resistant (MDR) phenotypes, while in RWU samples, these were less frequent (28%). The WW and RWD isolates were analyzed for the presence of 23 tetracycline (tet) resistance genes. The majority of isolates (94.2% and 95.4% in WW and RWD, respectively) harbored the corresponding genes, with tet(A) being the most common (67.0%), followed by tet(W), tet(C), tet(J), tet(L), tet(D), tet(Y), and tet(K) (in the range between 21.0% and 40.6%). Class I integrons were detected in the majority of WW and RWD isolates (97.4% and 86.2%, respectively) but were not associated with the tet genes. We hypothesize that the strong selective pressure imposed by a high concentration of OTC contributes to the wide dissemination of tetracycline resistance genes and other antibiotic resistance genes, possibly through mobile genetic elements.

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Soil and crop microbiome under soil amendment with poultry manure compost

Почвы и окружающая среда ◽

10.31251/pos.v4i1.141 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Natalia B. Naumova ◽

Helen N. Ruchko ◽

Oleg A. Savenkov ◽

Valentina I. Pleshakova

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Gut Microbiome ◽

High Throughput Sequencing ◽

Antibiotic Resistance Genes ◽

Organic Fertilizers ◽

Chicken Manure ◽

Poultry Production ◽

Poultry Industry ◽

Manure Compost

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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