scholarly journals Antibiotic Treatment Drives the Diversification of the Human Gut Resistome

2019 ◽  
Author(s):  
Jun Li ◽  
Elizabeth A. Rettedal ◽  
Eric van der Helm ◽  
Mostafa Ellabaan ◽  
Gianni Panagiotou ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Antibiotic Treatment ◽  
Resistance Genes ◽  
Community Dynamics ◽  
Antibiotic Resistance Genes ◽  
Strain Level ◽  
Functional Study ◽  
Antibiotic Administration ◽  
Bacterial Community Dynamics ◽  
The Impact

AbstractDespite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that short-term antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ∼3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota.

scholarly journals Honeybees exposure to veterinary drugs: how the gut microbiota is affected

2021 ◽  
Author(s):  
Loredana Baffoni ◽  
Daniele Alberoni ◽  
Francesca Gaggia ◽  
Chiara Braglia ◽  
Catherine Stanton ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Tetracycline Resistance ◽  
Veterinary Drugs ◽  
Antibiotic Administration ◽  
Experimental Conditions ◽  
Β Diversity ◽  
Antimicrobial Resistance Genes ◽  
The Impact

Several studies have outlined that a balanced gut microbiota offers metabolic and protective functions supporting honeybee health and performances. The present work contributes to increasing knowledge on the impact on the honeybee gut microbiota of the administration of three different veterinary drugs (oxytetracicline, sulphonamides and tylosin). The trial was designed with a semi-field approach in micro-hives containing about 500 bees, i.e. in experimental conditions as close as possible to real hives considering the restrictions on the use of antibiotics; 6 replicates were considered for each treatment plus the control. The absolute abundance of the major gut microbial taxa in newly eclosed individuals was studied with qPCR and next generation sequencing. Antimicrobial resistance genes for the target antibiotics were also monitored using a qPCR approach. The results showed that none of the veterinary drugs altered the total amount of gut bacteria, but qualitative variations were observed. Tylosin treatment determined a significant decrease of α- and β-diversity indexes and a strong depletion of the rectum population (lactobacilli and bifidobacteria) while favoring the hindgut population (Gilliamella, Snodgrassella and Frischella spp.). Major changes were also observed in honeybees treated with sulphonamides, with a decrease in Bartonella and Frischella core taxa an increase of Bombilactobacillus spp. and Snodgrassella spp. Conversely, minor effects were observed in oxytetracycline treated honeybees. Monitoring of antibiotic resistance genes confirmed that honeybees represent a great reservoir of tetracycline resistance genes. Tetracycline and sulphonamides resistant genes tended to increase in the gut microbiota population upon antibiotic administration.

scholarly journals Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment

2020 ◽  
Author(s):  
Kang Kang ◽  
Lejla Imamovic ◽  
Maria-Anna Misiakou ◽  
Maria Bornakke Sørensen ◽  
Yoshitaro Heshiki ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gut Microbiota ◽  
Resistance Gene ◽  
Antibiotic Treatment ◽  
Relative Abundance ◽  
Resistance Genes ◽  
Specific Resistance ◽  
Specific Gene ◽  
Antibiotic Administration ◽  
Human Gut

Abstract Background. Oral antibiotics are commonly prescribed to non-hospitalized adults. However, antibiotic-induced changes on the human gut microbiome are often investigated in cohorts with pre-existing health conditions and/or concomitant medication, leaving the effects of antibiotics not completely understood.Results. We used a combination of omic approaches to comprehensively assess the effects of antibiotics on the gut microbiota and particularly the gut resistome of a small cohort of healthy adults. We observed that 3 to 19 species per individual proliferated during antibiotic treatment and Gram-negative species expanded significantly in relative abundance. While the overall relative abundance of antibiotic resistance gene homologues did not significantly change, antibiotic-specific gene homologues with presumed resistance towards the administered antibiotics were common in proliferating species and significantly increased in relative abundance. Virome sequencing and plasmid analysis showed the expansion of antibiotic-specific resistance gene homologues even three months after antibiotic administration, while paired-end read analysis suggested their dissemination among different species.Conclusions. These results suggest that antibiotic treatment can lead to a persistent expansion of antibiotic resistance genes in the human gut microbiota and provide further data in support of good antibiotic stewardship.

scholarly journals Impact of Ciprofloxacin and Clindamycin Administration on Gram-Negative Bacteria Isolated from Healthy Volunteers and Characterization of the Resistance Genes They Harbor

2015 ◽  
Vol 59 (8) ◽  
pp. 4410-4416 ◽  
Author(s):  
Roderick M. Card ◽  
Muriel Mafura ◽  
Theresa Hunt ◽  
Miranda Kirchner ◽  
Jan Weile ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Bacterial Species ◽  
Antibiotic Resistance Genes ◽  
Antibiotic Administration ◽  
Healthy Human ◽  
Gram Negative ◽  
Content Type ◽  
The Impact

ABSTRACTThe aim of this study was to assess the impact of ciprofloxacin, clindamycin, and placebo administration on culturable Gram-negative isolates and the antibiotic resistance genes they harbor. Saliva and fecal samples were collected from healthy human volunteers before and at intervals, up to 1 year after antibiotic administration. Samples were plated on selective and nonselective media to monitor changes in different colony types or bacterial species. Following ciprofloxacin administration, there was a decrease ofEscherichia coliin feces and after clindamycin administration a decrease ofBacteroidesin feces andLeptotrichiain saliva, which all returned to pretreatment levels within 1 to 4 months. Ciprofloxacin administration also resulted in an increase in ciprofloxacin-resistantVeillonellain saliva, which persisted for 12 months. Additionally, 949 aerobic and anaerobic isolates purified from ciprofloxacin- and clindamycin-containing plates were screened for the presence of resistance genes. Resistance gene carriage was widespread in isolates from all three treatment groups, and no association was observed between genes and antibiotic administration. Although the anaerobic component of the microbiota was not a major reservoir of aerobe-associated antimicrobial resistance (AMR) genes, we detected the sulfonamide resistance genesul2in anaerobic isolates. The longitudinal nature of the study allowed identification of distinctEscherichia coliclones harboring multiple resistance genes, including one carrying an extended-spectrum β-lactamaseblaCTX-Mgroup 9 gene, which persisted in the gut for up to 4 months. This study provided insight into the effects of antibiotic administration on healthy microbiota and the diversity of resistance genes harbored therein.

scholarly journals Honeybee Exposure to Veterinary Drugs: How Is the Gut Microbiota Affected?

2021 ◽  
Author(s):  
Loredana Baffoni ◽  
Daniele Alberoni ◽  
Francesca Gaggìa ◽  
Chiara Braglia ◽  
Catherine Stanton ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gut Microbiota ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Veterinary Drugs ◽  
The Impact

This study investigates the impact of the three most widely used antibiotics in the beekeeping sector (oxytetracycline, tylosin, and sulfonamides) on the honeybee gut microbiota and on the spread of antibiotic resistance genes. The research represents an advance to the present literature, considering that the tylosin and sulfonamides effects on the gut microbiota have never been studied.

scholarly journals Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment

2020 ◽  
Author(s):  
Morten Sommer ◽  
Kang Kang ◽  
Lejla Imamovic ◽  
Maria-Anna Misiakou ◽  
Maria Bornakke Sørensen ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gut Microbiota ◽  
Resistance Gene ◽  
Antibiotic Treatment ◽  
Relative Abundance ◽  
Resistance Genes ◽  
Specific Resistance ◽  
Specific Gene ◽  
Antibiotic Administration ◽  
Human Gut

Abstract Background. Oral antibiotics are commonly prescribed to non-hospitalized adults. However, antibiotic-induced changes on the human gut microbiome are often investigated in cohorts with pre-existing health conditions and/or concomitant medication, leaving the effects of antibiotics not completely understood. Results. We used a combination of omic approaches to comprehensively assess the effects of antibiotics on the gut microbiota and particularly the gut resistome of a small cohort of healthy adults. We observed that 3 to 19 species per individual proliferated during antibiotic treatment and Gram-negative species expanded significantly in relative abundance. While the overall relative abundance of antibiotic resistance gene homologs did not significantly change, antibiotic-specific gene homologs with presumed resistance towards the administered antibiotics were common in proliferating species and significantly increased in relative abundance. Virome sequencing and plasmid analysis showed the expansion of antibiotic-specific resistance gene homologs even three months after antibiotic administration, while paired-end read analysis suggested their dissemination among different species. Conclusions. These results suggest that antibiotic treatment can lead to a persistent expansion of antibiotic resistance genes in the human gut microbiota and provide further data in support of good antibiotic stewardship.

scholarly journals Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Ishi Keenum ◽  
Robert K. Williams ◽  
Partha Ray ◽  
Emily D. Garner ◽  
Katharine F. Knowlton ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Land Application ◽  
Multidimensional Analysis ◽  
Small Scale ◽  
Antibiotic Administration ◽  
Metagenomic Sequencing ◽  
Combined Effects ◽  
Bacterial Microbiota

Abstract Background Research is needed to delineate the relative and combined effects of different antibiotic administration and manure management practices in either amplifying or attenuating the potential for antibiotic resistance to spread. Here, we carried out a comprehensive parallel examination of the effects of small-scale (> 55 °C × 3 days) static and turned composting of manures from dairy and beef cattle collected during standard antibiotic administration (cephapirin/pirlimycin or sulfamethazine/chlortetracycline/tylosin, respectively), versus from untreated cattle, on “resistomes” (total antibiotic resistance genes (ARGs) determined via shotgun metagenomic sequencing), bacterial microbiota, and indicator ARGs enumerated via quantitative polymerase chain reaction. To gain insight into the role of the thermophilic phase, compost was also externally heated to > 55 °C × 15 days. Results Progression of composting with time and succession of the corresponding bacterial microbiota was the overarching driver of the resistome composition (ANOSIM; R = 0.424, p = 0.001, respectively) in all composts at the small-scale. Reduction in relative abundance (16S rRNA gene normalized) of total ARGs in finished compost (day 42) versus day 0 was noted across all conditions (ANOSIM; R = 0.728, p = 0.001), except when externally heated. Sul1, intI1, beta-lactam ARGs, and plasmid-associated genes increased in all finished composts as compared with the initial condition. External heating more effectively reduced certain clinically relevant ARGs (blaOXA, blaCARB), fecal coliforms, and resistome risk scores, which take into account putative pathogen annotations. When manure was collected during antibiotic administration, taxonomic composition of the compost was distinct according to nonmetric multidimensional analysis and tet(W) decayed faster in the dairy manure with antibiotic condition and slower in the beef manure with antibiotic condition. Conclusions This comprehensive, integrated study revealed that composting had a dominant effect on corresponding resistome composition, while little difference was noted as a function of collecting manure during antibiotic administration. Reduction in total ARGs, tet(W), and resistome risk suggested that composting reduced some potential for antibiotic resistance to spread, but the increase and persistence of other indicators of antibiotic resistance were concerning. Results indicate that composting guidelines intended for pathogen reduction do not necessarily provide a comprehensive barrier to ARGs or their mobility prior to land application and additional mitigation measures should be considered.

Contributions of Lactobacillus plantarum PC170 administration on the recovery of gut microbiota after short-term ceftriaxone exposure in mice

2020 ◽  
Vol 11 (5) ◽  
pp. 489-509
Author(s):  
R. Cheng ◽  
H. Liang ◽  
Y. Zhang ◽  
J. Guo ◽  
Z. Miao ◽  
...  
Keyword(s):  
Body Weight ◽  
Gut Microbiota ◽  
Lactobacillus Plantarum ◽  
Antibiotic Treatment ◽  
Recovery Phase ◽  
The Body ◽  
Faecal Microbiota ◽  
Short Term ◽  
Host Animal ◽  
The Impact

This study aimed to determine the impact of Lactobacillus plantarum PC170 concurrent with antibiotic treatment and/or during the recovery phase after antibiotic treatment on the body weight, faecal bacterial composition, short-chain fatty acids (SCFAs) concentration, and splenic cytokine mRNA expression of mice. Orally administrated ceftriaxone quantitatively and significantly decreased body weight, faecal total bacteria, Akkermansia muciniphila, and Lactobacillus plantarum, and faecal SCFAs concentration. Ceftriaxone treatment also dramatically altered the faecal microbiota with an increased Chao1 index, decreased species diversities and Bacteroidetes, and more Firmicutes and Proteobacteria. After ceftriaxone intervention, these changes all gradually started to recover. However, faecal microbiota diversities were still totally different from control by significantly increased α- and β-diversities. Bacteroidetes all flourished and became dominant during the recovery process. However, mice treated with PC170 both in parallel with and after ceftriaxone treatment encouraged more Bacteroidetes, Verrucomicrobia, and Actinobacteria, and the diversity by which to make faecal microbiota was very much closer to control. Furthermore, the expression of splenic pro-inflammatory cytokine tumour necrosis factor-α mRNA in mice supplemented with PC170 during the recovery phase was significantly lower than natural recovery. These results indicated that antibiotics, such as ceftriaxone, even with short-term intervention, could dramatically damage the structure of gut microbiota and their abilities to produce SCFAs with loss of body weight. Although such damages could be partly recovered with the cessation of antibiotics, the implication of antibiotics to gut microbiota might remain even after antibiotic treatment. The selected strain PC170 might be a potential probiotic because of its contributions in helping the host animal to remodel or stabilise its gut microbiome and enhancing the anti-inflammatory response as protection from the side effects of antibiotic therapy when it was administered in parallel with and after antibiotic treatment.

Enrichment of antibiotic resistance genes in soil receiving composts derived from swine manure, yard wastes, or food wastes, and evidence for multiyear persistence of swine Clostridium spp.

2018 ◽  
Vol 64 (3) ◽  
pp. 201-208 ◽  
Author(s):  
Andrew Scott ◽  
Yuan-Ching Tien ◽  
Craig F. Drury ◽  
W. Daniel Reynolds ◽  
Edward Topp
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Swine Manure ◽  
Organic Amendments ◽  
Antibiotic Resistance Genes ◽  
Gene Target ◽  
Soil Dna ◽  
Yard Waste ◽  
The Impact ◽  
Clostridium Spp

The impact of amendment with swine manure compost (SMC), yard waste compost (YWC), or food waste compost (FWC) on the abundance of antibiotic resistance genes in soil was evaluated. Following a commercial-scale application of the composts in a field experiment, soils were sampled periodically for a decade, and archived air-dried. Soil DNA was extracted and gene targets quantified by qPCR. Compared with untreated control soil, all 3 amendment types increased the abundance of gene targets for up to 4 years postapplication. The abundance of several gene targets was much higher in soil amended with SMC than in soil receiving either YWC or FWC. The gene target ermB remained higher in the SMC treatment for a decade postapplication. Clostridia were significantly more abundant in the SMC-amended soil throughout the decade following application. Eight percent of Clostridium spp. isolates from the SMC treatment carried ermB. Overall, addition of organic amendments to soils has the potential to increase the abundance of antibiotic resistance genes. Amendments of fecal origin, such as SMC, will in addition entrain bacteria carrying antibiotic resistance genes. Environmentally recalcitrant clostridia, and the antibiotic resistance genes that they carry, will persist for many years under field conditions following the application of SMC.

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