scholarly journals Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes

mSystems ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Pablo Tsukayama ◽  
Manish Boolchandani ◽  
Sanket Patel ◽  
Erica C. Pehrsson ◽  
Molly K. Gibson ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gut Microbiota ◽  
Microbial Communities ◽  
Resistance Genes ◽  
Fecal Microbiota ◽  
Lifestyle Changes ◽  
Past Century ◽  
Agricultural Practice ◽  
Culture Independent ◽  
And Function

ABSTRACT Environmental microbes have harbored the capacity for antibiotic production for millions of years, spanning the evolution of humans and other vertebrates. However, the industrial-scale use of antibiotics in clinical and agricultural practice over the past century has led to a substantial increase in exposure of these agents to human and environmental microbiota. This perturbation is predicted to alter the ecology of microbial communities and to promote the evolution and transfer of antibiotic resistance (AR) genes. We studied wild and captive baboon populations to understand the effects of exposure to humans and human activities (e.g., antibiotic therapy) on the composition of the primate fecal microbiota and the antibiotic-resistant genes that it collectively harbors (the “resistome”). Using a culture-independent metagenomic approach, we identified functional antibiotic resistance genes in the gut microbiota of wild and captive baboon groups and saw marked variation in microbiota architecture and resistomes across habitats and lifeways. Our results support the view that antibiotic resistance is an ancient feature of gut microbial communities and that sharing habitats with humans may have important effects on the structure and function of the primate microbiota. IMPORTANCE Antibiotic exposure results in acute and persistent shifts in the composition and function of microbial communities associated with vertebrate hosts. However, little is known about the state of these communities in the era before the widespread introduction of antibiotics into clinical and agricultural practice. We characterized the fecal microbiota and antibiotic resistomes of wild and captive baboon populations to understand the effect of human exposure and to understand how the primate microbiota may have been altered during the antibiotic era. We used culture-independent and bioinformatics methods to identify functional resistance genes in the guts of wild and captive baboons and show that exposure to humans is associated with changes in microbiota composition and resistome expansion compared to wild baboon groups. Our results suggest that captivity and lifestyle changes associated with human contact can lead to marked changes in the ecology of primate gut communities.

scholarly journals Metagenomics Analysis Reveals the Microbial Communities, Antimicrobial Resistance Gene Diversity and Potential Pathogen Transmission Risk of Two Different Landfills in China

Diversity ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 230
Author(s):  
Shan Wan ◽  
Min Xia ◽  
Jie Tao ◽  
Yanjun Pang ◽  
Fugen Yu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Communities ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Gene Diversity ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Pathogen Transmission ◽  
Transmission Risk ◽  
Antimicrobial Resistance Gene

In this study, we used a metagenomic approach to analyze microbial communities, antibiotic resistance gene diversity, and human pathogenic bacterium composition in two typical landfills in China. Results showed that the phyla Proteobacteria, Bacteroidetes, and Actinobacteria were predominant in the two landfills, and archaea and fungi were also detected. The genera Methanoculleus, Lysobacter, and Pseudomonas were predominantly present in all samples. sul2, sul1, tetX, and adeF were the four most abundant antibiotic resistance genes. Sixty-nine bacterial pathogens were identified from the two landfills, with Klebsiella pneumoniae, Bordetella pertussis, Pseudomonas aeruginosa, and Bacillus cereus as the major pathogenic microorganisms, indicating the existence of potential environmental risk in landfills. In addition, KEGG pathway analysis indicated the presence of antibiotic resistance genes typically associated with human antibiotic resistance bacterial strains. These results provide insights into the risk of pathogens in landfills, which is important for controlling the potential secondary transmission of pathogens and reducing workers’ health risk during landfill excavation.

scholarly journals 655. Detection of Antibiotic Resistance Genes in Clinical Samples using T2 Magnetic Resonance

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S301-S301
Author(s):  
Jessica L Snyder ◽  
Brendan Manning ◽  
Robert Shivers ◽  
Daniel Gamero ◽  
Heidi Giese ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Magnetic Resonance ◽  
Species Identification ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Resistance Testing ◽  
Clinical Samples ◽  
Antibiotic Resistant ◽  
Blood Samples ◽  
Culture Independent

Abstract Background Antibiotic-resistant bacteria are spread through selective pressure from the use of broad-spectrum empirical therapies, mobile genetic elements that pass resistance genes between species, and the inability to rapidly and appropriately respond to their presence. Resistance gene identification is often performed with post culture molecular diagnostic tests. The T2Resistance Panel, which detects methicillin resistance genes mecA/C; vancomycin resistance genes vanA/B; carbapenemases blaKPC, blaOXA-48,blaNDM, blaVIM, and blaIMP; AmpC β-lactamases blaCMY and blaDHA; and extended-spectrum β-lactamases blaCTX-M directly from patient blood samples, is based on T2 magnetic resonance (T2MR), an FDA-cleared technology with demonstrated high sensitivity and specificity for culture-independent bacterial and fungal species identification. Here we report the clinical performance of T2MR detection of resistance genes directly from patient blood samples. Methods Patients with a clinical diagnosis of sepsis and an order for blood culture (BC) were enrolled in the study at two sites. BCs were managed using standard procedures and MALDI-TOF for species identification. Resistance testing with the T2MR assay was performed on a direct patient draw and compared with diagnostic test results from concurrent BC specimen and BC specimen taken at other points in time. The potential impact on therapy was evaluated through patient chart review. Results T2MR detected the same resistance genes as detected by post culture diagnostics in 100% of samples from concurrent blood draws. Discordant results occurred when T2MR was taken ≥48 hours after BC for patients on antimicrobial therapy. The average time to positive result was 5.9 hours with T2MR vs. 30.6 hours with post-culture molecular testing. Conclusion The T2Resistance Panel detected antibiotic resistance genes in clinical samples and displayed agreement with post culture genetic testing. T2MR results were achieved faster than culture-dependent diagnostic testing results and may allow for an earlier change from empiric to directed therapy. The use of culture-independent diagnostics like T2MR could enable a quicker response to antibiotic-resistant organisms for individual patients and developing outbreaks. Disclosures All authors: No reported disclosures.

scholarly journals Chloramphenicol Resistance in Clostridium difficile Is Encoded on Tn4453 Transposons That Are Closely Related to Tn4451 from Clostridium perfringens

1998 ◽  
Vol 42 (7) ◽  
pp. 1563-1567 ◽  
Author(s):  
Dena Lyras ◽  
Christine Storie ◽  
Andrea S. Huggins ◽  
Paul K. Crellin ◽  
Trudi L. Bannam ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Clostridium Difficile ◽  
Transposable Elements ◽  
Clostridium Perfringens ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Nucleotide Sequencing ◽  
Chloramphenicol Resistance ◽  
Circular Form ◽  
And Function

ABSTRACT The chloramphenicol resistance gene catD fromClostridium difficile was shown to be encoded on the transposons Tn4453a and Tn4453b, which were structurally and functionally related to Tn4451 fromClostridium perfringens. Tn4453a and Tn4453b excised precisely from recombinant plasmids, generating a circular form, as is the case for Tn4451. Evidence that this process is mediated by Tn4453-encodedtnpX genes was obtained from experiments which showed that in trans these genes complemented a Tn4451tnpXΔ1 mutation for excision. Nucleotide sequencing showed that the joint of the circular form generated by the excision of Tn4453a and Tn4453b was similar to that from Tn4451. These results suggest that the Tn4453-encoded TnpX proteins bind to similar DNA target sequences and function in a manner comparable to that of TnpX from Tn4451. Furthermore, it has been shown that Tn4453a and Tn4453b can be transferred to suitable recipient cells by RP4 and therefore are mobilizable transposons. It is concluded that, like Tn4451, they must encode a functional tnpZ gene and a targetoriT or RSA site. The finding that related transposable elements are present in C. difficile andC. perfringens has implications for the evolution and dissemination of antibiotic resistance genes and the mobile elements on which they are found within the clostridia.

Rare earth oxide nanoparticles promote soil microbial antibiotic resistance by selectively enriching antibiotic resistance genes

2019 ◽  
Vol 6 (2) ◽  
pp. 456-466 ◽  
Author(s):  
Lin Qi ◽  
Yuan Ge ◽  
Tian Xia ◽  
Ji-Zheng He ◽  
Congcong Shen ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Rare Earth ◽  
Microbial Communities ◽  
Resistance Genes ◽  
Soil Microbial Communities ◽  
Antibiotic Resistance Genes ◽  
Rare Earth Oxide ◽  
Oxide Nanoparticles ◽  
Soil Microbial

This study demonstrates that rare earth oxide nanoparticles can enhance soil microbial antibiotic resistance by inducing the enrichment and spread of antibiotic resistance genes in soil microbial communities.

scholarly journals Fecal Microbiota Transplant in Cirrhosis Reduces Gut Microbial Antibiotic Resistance Genes: Analysis of Two Trials

2020 ◽  
Author(s):  
Jasmohan S. Bajaj ◽  
Amirhossein Shamsaddini ◽  
Andrew Fagan ◽  
Richard K. Sterling ◽  
Edith Gavis ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Fecal Microbiota ◽  
Fecal Microbiota Transplant

scholarly journals Variability of the Ability of Complex Microbial Communities to Exclude Microbes Carrying Antibiotic Resistance Genes in Rabbits

2019 ◽  
Vol 10 ◽  
Author(s):  
Caroline Stéphanie Achard ◽  
Véronique Dupouy ◽  
Suzanne Siviglia ◽  
Nathalie Arpaillange ◽  
Laurent Cauquil ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Communities ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes

scholarly journals Antibiotics as Major Disruptors of Gut Microbiota

2020 ◽  
Vol 10 ◽  
Author(s):  
Jaime Ramirez ◽  
Francisco Guarner ◽  
Luis Bustos Fernandez ◽  
Aldo Maruy ◽  
Vera Lucia Sdepanian ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Adaptive Immune System ◽  
Antibiotic Use ◽  
Negative Effects ◽  
Antibiotic Resistant ◽  
Childhood Exposure ◽  
Clostridioides Difficile ◽  
Culture Independent ◽  
Health And Disease ◽  
And Function

Advances in culture-independent research techniques have led to an increased understanding of the gut microbiota and the role it plays in health and disease. The intestine is populated by a complex microbial community that is organized around a network of metabolic interdependencies. It is now understood that the gut microbiota is vital for normal development and functioning of the human body, especially for the priming and maturation of the adaptive immune system. Antibiotic use can have several negative effects on the gut microbiota, including reduced species diversity, altered metabolic activity, and the selection of antibiotic-resistant organisms, which in turn can lead to antibiotic-associated diarrhea and recurrent Clostridioides difficile infections. There is also evidence that early childhood exposure to antibiotics can lead to several gastrointestinal, immunologic, and neurocognitive conditions. The increase in the use of antibiotics in recent years suggests that these problems are likely to become more acute or more prevalent in the future. Continued research into the structure and function of the gut microbiota is required to address this challenge.

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