scholarly journals Investigating the Effect of an Oxytetracycline Treatment on the Gut Microbiome and Antimicrobial Resistance Gene Dynamics in Nile Tilapia (Oreochromis niloticus)

Antibiotics ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1213
Author(s):  
Christopher J. Payne ◽  
James F. Turnbull ◽  
Simon MacKenzie ◽  
Margaret Crumlish
Keyword(s):  
Antimicrobial Resistance ◽  
Antibiotic Treatment ◽  
Resistance Genes ◽  
Gut Microbiome ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Nile Tilapia Oreochromis Niloticus ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
The Impact

Antibiotics play a vital role in aquaculture where they are commonly used to treat bacterial diseases. However, the impact of antibiotic treatment on the gut microbiome and the development of antimicrobial resistance in Nile tilapia (Oreochromis niloticus) over time remains to be fully understood. In this study, fish were fed a single treatment of oxytetracycline (100 mg/kg/day) for eight days, followed by a 14-day withdrawal period. Changes in the distal gut microbiome were measured using 16S rRNA sequencing. In addition, the abundance of antimicrobial resistance genes was quantified using real-time qPCR methods. Overall, the gut microbiome community diversity and structure of Nile tilapia was resilient to oxytetracycline treatment. However, antibiotic treatment was associated with an enrichment in Plesiomonas, accompanied by a decline in other bacteria taxa. Oxytetracycline treatment increased the proportion of tetA in the distal gut of fish and tank biofilms of the treated group. Furthermore, the abundance of tetA along with other tetracycline resistance genes was strongly correlated with a number of microbiome members, including Plesiomonas. The findings from this study demonstrate that antibiotic treatment can exert selective pressures on the gut microbiome of fish in favour of resistant populations, which may have long-term impacts on fish health.

scholarly journals Impact of UV and Peracetic Acid Disinfection on the Prevalence of Virulence and Antimicrobial Resistance Genes in Uropathogenic Escherichia coli in Wastewater Effluents

2014 ◽  
Vol 80 (12) ◽  
pp. 3656-3666 ◽  
Author(s):  
Basanta Kumar Biswal ◽  
Ramzi Khairallah ◽  
Kareem Bibi ◽  
Alberto Mazza ◽  
Ronald Gehr ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Peracetic Acid ◽  
Content Type ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
Municipal Wastewaters ◽  
The Impact

ABSTRACTWastewater discharges may increase the populations of pathogens, includingEscherichia coli, and of antimicrobial-resistant strains in receiving waters. This study investigated the impact of UV and peracetic acid (PAA) disinfection on the prevalence of virulence and antimicrobial resistance genes in uropathogenicEscherichia coli(UPEC), the most abundantE. colipathotype in municipal wastewaters. Laboratory disinfection experiments were conducted on wastewater treated by physicochemical, activated sludge, or biofiltration processes; 1,766E. coliisolates were obtained for the evaluation. The target disinfection level was 200 CFU/100 ml, resulting in UV and PAA doses of 7 to 30 mJ/cm2and 0.9 to 2.0 mg/liter, respectively. The proportions of UPECs were reduced in all samples after disinfection, with an average reduction by UV of 55% (range, 22% to 80%) and by PAA of 52% (range, 11% to 100%). Analysis of urovirulence genes revealed that the decline in the UPEC populations was not associated with any particular virulence factor. A positive association was found between the occurrence of urovirulence and antimicrobial resistance genes (ARGs). However, the changes in the prevalence of ARGs in potential UPECs were different following disinfection, i.e., UV appears to have had no effect, while PAA significantly reduced the ARG levels. Thus, this study showed that both UV and PAA disinfections reduced the proportion of UPECs and that PAA disinfection also reduced the proportion of antimicrobial resistance gene-carrying UPEC pathotypes in municipal wastewaters.

scholarly journals Metagenomics Reveals Impact of Urbanisation in Central India on the Human Gut Microbiome and its Antimicrobial Resistance Profiles

2019 ◽  
Author(s):  
Tanya Monaghan ◽  
Tim J. Sloan ◽  
Stephen R. Stockdale ◽  
Adam M. Blanchard ◽  
Richard D. Emes ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Gut Microbiome ◽  
Human Gut ◽  
Metabolic Potential ◽  
Urban Populations ◽  
Human Gut Microbiome ◽  
Rural And Urban ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
The Impact

Abstract Background The impact of the rapid urbanisation of low- and middle-income countries on the human gut microbiome remains grossly understudied. Whilst the effect of urbanisation on the bacterial populations of the human gut microbiome have been documented, little is known about the influence of diet and antibiotics on the bacteriome, its virome, and antibiotic resistome. Here, we use shotgun metagenomics to comprehensively characterise the bacterial and viral fractions of the human gut microbiome, and their encoded functions, from two divergent Central Indian populations (rural agriculturalists from Melghat and an urban population in Nagpur). Additionally, we investigate cohorts with and without diarrhoea, and the potential burden of Clostridioides difficile, associated with widespread unregulated use of antibiotics in India. Results We observed distinct rural-urban differences in the gut microbiome, including viral diversity and composition, with geography exhibiting a greater influence than diarrhoeal status. Urban microbiomes were enriched in metabolic pathways responsible for degradation of drugs and organic compounds, which were predicted to relate to replacement of rural-enriched Prevotella spp. and fermentative Clostridiales with Enterobacteriaceae and Bacteroides spp. By linking phages present in the microbiome to their bacterial hosts through CRISPR spacers, a shift from Prevotella- and Eubacterium-infecting phages to Bacteroides- and Parabacteroides-infecting phages was observed in rural and urban populations, respectively. Additionally, the auxiliary metabolic potential of rural-associated phage populations was enriched for carbon and amino acid energy harvesting potential, compared to urban-associated phages. A core set of antimicrobial resistance genes was identified in both populations, particularly those conferring resistance to macrolides, tetracyclines and 1stgeneration cephalosporins, with the majority also showing evidence of resistance to fluoroquinolones, aminoglycosides and sulphonamides. In a subgroup of urban subjects with diarrhoea and high antibiotic exposure, most of whom tested positive for C. difficile toxin, evidence of resistance to fosfomycin, glycopeptides, daptomycin, 3rd generation cephalosporins and carbapenems was widespread. Conclusions We report distinct differences in antimicrobial resistance gene profiles as well as a marked variation in the burden of C. difficile disease between rural and urban populations. The key drivers of variation in urban and rural Indian microbiomes are geography, diet, industrial and healthcare exposures.

Formula-fed and Clostridium difficile infected neonatal piglets carry a highly diverse and abundant set of antimicrobial resistance genes

2020 ◽  
Author(s):  
Robert Pieper ◽  
Temesgen Dadi ◽  
Lukasz Grzeskowiak ◽  
Laura Pieper ◽  
Britta Siegmund ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Microbial Colonization ◽  
Metagenomic Data ◽  
Neonatal Piglets ◽  
Gut Colonization ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
Genes Encoding

Abstract Background: Clostridium difficile infection (CDI) is an increasing zoonotic health threat and has also been documented as a cause of enteritis outbreaks in neonatal pigs. Furthermore, CDI in neonatal piglets cause changes in microbial gut colonization. We hypothesized that an imbalanced microbial colonization in piglets with CDI could be associated with an altered abundance of antimicrobial resistance genes. Results: We analyzed fecal metagenomic data of lactating sows (S), their piglets during suckling (SP), the same piglets two weeks after weaning (WP), 5-day old artificially reared and formula-fed siblings (FP) and FP infected with C. difficile (FP-CD) for microbiota composition and antimicrobial resistance gene abundance. FP and FP-CD piglets had an immature-type microbiota and increased abundance of antimicrobial resistance genes. A co-occurrence of genes encoding for resistance against aminoglycosides (e.g. aph(3”)-lb, aph(6)-ld, ant(2”)-la), β-lactams (blaCTX-M, blaTEM), fluoroquinolones (pat(A) macrolides (mph(A)), sulfonamides (sul1, sul2), polypeptides (e.g. pmrB, pmrC, arnA, bac(A)) and tetracyclines (e.g. tet(A-D),) was observed. Conclusion: Increased abundance of antimicrobial resistance genes in formula feeding and concomitant CDI may be associated with therapeutic resistance later in life and warrant further studies.

scholarly journals Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle

2017 ◽  
Author(s):  
Milton Thomas ◽  
Megan Webb ◽  
Sudeep Ghimire ◽  
Amanda Blair ◽  
Kenneth Olson ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Gut Microbiota ◽  
Resistance Genes ◽  
Feedlot Cattle ◽  
Feed Additives ◽  
Gastrointestinal Microbiota ◽  
Finishing Diets ◽  
Antimicrobial Resistance Genes ◽  
Metagenome Sequencing ◽  
The Impact

AbstractIn North America, antibiotic feed additives such as monensin and tylosin are added to the finishing diets of feedlot cattle to counter the ill-effects of feeding diets with rapidly digestible carbohydrates. While these feed additives have been proven to improve feed efficiency, and reduce liver abscess incidence, how these products impact the gastrointestinal microbiota is not completely understood. Furthermore, there are concerns that antibiotic feed additives may expand the antibiotic resistome of feedlot cattle by enriching antimicrobial resistance genes in pathogenic and nonpathogenic bacteria in the gut microbiota. In this study, we analyzed the impact of providing antibiotic feed additives to feedlot cattle using metagenome sequencing of treated and untreated animals. Our results indicate that use of antibiotic feed additives does not produce discernable changes at the phylum level however treated cattle had reduced the abundance of gram-positive bacteria at the genus level. The abundance of Ruminococcus, Erysipelotrichaceae and Lachanospira in the gut of treated steers was reduced. This may impact the ability of these animals to exclude pathogens from the gut. However, our results did not show any correlation between the presence of antimicrobial resistance genes in the gut microbiota and the administration of antibiotic feed additives.

scholarly journals Antimicrobial resistance gene prevalence in a population of patients with advanced dementia is related to specific pathobionts

2019 ◽  
Author(s):  
Aislinn D. Rowan-Nash ◽  
Rafael Araos ◽  
Erika M.C. D’Agata ◽  
Peter Belenky
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
High Frequency ◽  
Multidrug Resistant ◽  
Advanced Dementia ◽  
Dementia Patients ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
Multidrug Resistant Organisms

ABSTRACTBackgroundThe issue of antimicrobial resistance continues to grow worldwide, and long-term care facilities are significant reservoirs of antimicrobial-resistant organisms, in part due to high frequency of antimicrobial use. Patients with advanced dementia are particularly vulnerable to multidrug-resistant organism acquisition and antimicrobial overuse, which has negative consequences for the gut microbiome and can contribute to the selection and propagation of antimicrobial resistance genes. In this study, we longitudinally examined a group of advanced dementia patients treated with the fluoroquinolone antimicrobial levofloxacin, finding a correlation between abundance of pathogens and antimicrobial resistance genes, which we confirmed in a larger cohort of subjects with advanced dementia.ResultsWe observed significant inter- and intra-subject heterogeneity in the composition of the microbiota of the longitudinal levofloxacin cohort, suggesting temporal instability. Within this dataset, we did not find significant impacts of levofloxacin on the diversity, composition, function, or resistome of the gut microbiota of this population. However, we were able to link the antimicrobial resistance gene burden in a sample with the relative abundance of several pathobionts – particularly Escherichia coli, Proteus mirabilis, and Enterococcus faecalis, as well as less-prevalent species including Providencia stuartii and Staphylococcus haemolyticus. Furthermore, we used metagenomic assembly and binning to demonstrate that these species had higher genomic resistance gene levels than common gut commensals, and we were able to predict antimicrobial resistance gene burden from the relative abundances of these species in a separate, larger cohort from the same population.ConclusionsWe found that the relative abundances of several pathobionts were correlated with and were even predictive of the level of antimicrobial resistance genes in corresponding samples, and that these species carried high levels of resistances genes in their assembled genomes. In order to test this observation, we utilized a larger metagenomics dataset from a similar population and confirmed the association between pathobiont abundance and antimicrobial resistance genes. Given the high frequency with which these species were found at high levels in this population and the underlying vulnerability to infection with multidrug resistant organisms of advanced dementia patients, attention to microbial blooms of these species may be warranted. Additionally, in this study, we were able to utilize genomic assembly from metagenomic data to more definitively associate antimicrobial resistance gene levels with specific assembled species; as this technology continues to develop, assembly could prove to be a valuable method to monitor both specific resistance genes and blooms of multidrug-resistant organisms.

scholarly journals Antimicrobial resistance gene surveillance in the receiving waters of an upgraded wastewater treatment plant

FACETS ◽  
2018 ◽  
Vol 3 (1) ◽  
pp. 128-138 ◽  
Author(s):  
Claire N. Freeman ◽  
Lena Scriver ◽  
Kara D. Neudorf ◽  
Lisbeth Truelstrup Hansen ◽  
Rob C. Jamieson ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Antimicrobial Resistance ◽  
Wastewater Treatment Plants ◽  
Treatment Plant ◽  
Nutrient Content ◽  
Rrna Gene ◽  
Treated Effluent ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
The Impact

Wastewater treatment plants (WWTPs) have been identified as hotspots for antimicrobial resistance genes (ARGs) and thus represent a critical point where patterns in ARG abundances can be monitored prior to their release into the environment. The aim of the current study was to measure the impact of the release of the final treated effluent (FE) on the abundance of ARGs in the receiving water of a recently upgraded WWTP in the Canadian prairies. Sample nutrient content (phosphorous and nitrogen species) was measured as a proxy for WWTP functional performance, and quantitative PCR (qPCR) was used to measure the abundance of eight ARGs, the intI1 gene associated with class I integrons, and the 16S rRNA gene. The genes ermB, sul1, intI1, blaCTX-M, qnrS, and tetO all had higher abundances downstream of the WWTP, consistent with the genes with highest abundance in the FE. These findings are consistent with the increasing evidence suggesting that human activity affects the abundances of ARGs in the environment. Although the degree of risk associated with releasing ARGs into the environment is still unclear, understanding the environmental dimension of this threat will help develop informed management policies to reduce the spread of antibiotic resistance and protect public health.

scholarly journals Occurrence of Virulence and Antimicrobial Resistance Genes in Escherichia coli Isolates from Different Aquatic Ecosystems within the St. Clair River and Detroit River Areas

2006 ◽  
Vol 73 (2) ◽  
pp. 477-484 ◽  
Author(s):  
Katia Hamelin ◽  
Guillaume Bruant ◽  
Abdel El-Shaarawi ◽  
Stephen Hill ◽  
Thomas A. Edge ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Surface Waters ◽  
Aquatic Ecosystems ◽  
Urban Site ◽  
Detroit River ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene

ABSTRACT Although the number of Escherichia coli bacteria in surface waters can differ greatly between locations, relatively little is known about the distribution of E. coli pathotypes in surface waters used as sources for drinking or recreation. DNA microarray technology is a suitable tool for this type of study due to its ability to detect high numbers of virulence and antimicrobial resistance genes simultaneously. Pathotype, phylogenetic group, and antimicrobial resistance gene profiles were determined for 308 E. coli isolates from surface water samples collected from diverse aquatic ecosystems at six different sites in the St. Clair River and Detroit River areas. A higher frequency (48%) of E. coli isolates possessing virulence and antimicrobial resistance genes was observed in an urban site located downstream of wastewater effluent outfalls than in the other examined sites (average of 24%). Most E. coli pathotypes were extraintestinal pathogenic E. coli (ExPEC) pathotypes and belonged to phylogenetic groups B2 and D. The ExPEC pathotypes were found to occur across all aquatic ecosystems investigated, including riverine, estuarine, and offshore lake locations. The results of this environmental study using DNA microarrays highlight the widespread distribution of E. coli pathotypes in aquatic ecosystems and the potential public health threat of E. coli pathotypes originating from municipal wastewater sources.

scholarly journals Vertical Transmission of Gut Microbiome and Antimicrobial Resistance Genes in Infants Exposed to Antibiotics at Birth

2020 ◽  
Author(s):  
Weizhong Li ◽  
Terhi Tapiainen ◽  
Lauren Brinkac ◽  
Hernan A Lorenzi ◽  
Kelvin Moncera ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Vertical Transmission ◽  
Gut Microbiome ◽  
Treated Group ◽  
Control Group ◽  
Gut Colonization ◽  
Antimicrobial Resistance Genes ◽  
Major Route ◽  
Group 10 ◽  
The Impact

Abstract Vertical transmission of maternal microbes is a major route for establishing the gut microbiome in newborns. The impact of perinatal antibiotics on vertical transmission of microbes and antimicrobial resistance is not well understood. Using a metagenomic approach, we analyzed the fecal samples from mothers and vaginally delivered infants from a control group (10 pairs) and a treatment group (10 pairs) receiving perinatal antibiotics. Antibiotic-usage had a significant impact on the main source of inoculum in the gut microbiome of newborns. The control group had significantly more species transmitted from mothers to infants (P = .03) than the antibiotic-treated group. Approximately 72% of the gut microbial population of infants at 3–7 days after birth in the control group was transmitted from their mothers, versus only 25% in the antibiotic-treated group. In conclusion, perinatal antibiotics markedly disturbed vertical transmission and changed the source of gut colonization towards horizontal transfer from the environment to the infants.

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