Tetracycline resistance genes and mobile genetic elements from the oral metagenome

ABSTRACT Horizontal transfer of plasmids encoding antimicrobial resistance and virulence determinants has been instrumental in Staphylococcus aureus evolution, including the emergence of community-associated methicillin-resistant S. aureus (CA-MRSA). In the early 1990s, the first CA-MRSA strain isolated in Western Australia (WA), WA-5, encoded cadmium, tetracycline, and penicillin resistance genes on plasmid pWBG753 (∼30 kb). WA-5 and pWBG753 appeared only briefly in WA; however, fusidic acid resistance plasmids related to pWBG753 were also present in the first European CA-MRSA isolates at the time. Here, we characterize a 72-kb conjugative plasmid, pWBG731, present in multiresistant WA-5-like clones from the same period. pWBG731 was a cointegrant formed from pWBG753 and a pWBG749 family conjugative plasmid. pWBG731 carried mupirocin, trimethoprim, cadmium, and penicillin resistance genes. The stepwise evolution of pWBG731 likely occurred through the combined actions of IS257, IS257-dependent miniature inverted-repeat transposable elements (MITEs), and the BinL resolution system of the β-lactamase transposon Tn552. An evolutionarily intermediate ∼42-kb nonconjugative plasmid, pWBG715, possessed the same resistance genes as pWBG731 but retained an integrated copy of the small tetracycline resistance plasmid pT181. IS257 likely facilitated the replacement of pT181 with conjugation genes on pWBG731, thus enabling autonomous transfer. Like conjugative plasmid pWBG749, pWBG731 also mobilized nonconjugative plasmids carrying oriT mimics. It seems likely that pWBG731 represents the product of multiple recombination events between the WA-5 pWBG753 plasmid and other mobile genetic elements present in indigenous community-associated methicillin-sensitive S. aureus (CA-MSSA) isolates. The molecular evolution of pWBG731 saliently illustrates how diverse mobile genetic elements can together facilitate rapid accrual and horizontal dissemination of multiresistance in S. aureus CA-MRSA.

Download Full-text

Habitat determines the relationships among bacteria, resistance genes and mobile genetic elements in the soil‐plant system

European Journal of Soil Science ◽

10.1111/ejss.13132 ◽

2021 ◽

Author(s):

Ruilin Huang ◽

Jixian Ding ◽

Yuwei Guo ◽

Bo Sun ◽

Yuting Liang

Keyword(s):

Resistance Genes ◽

Mobile Genetic Elements ◽

Plant System ◽

Genetic Elements ◽

Bacteria Resistance

Download Full-text

Shotgun metagenomic analysis reveals the prevalence of antibiotic resistance genes and mobile genetic elements in full scale hospital wastewater treatment plants

Journal of Environmental Management ◽

10.1016/j.jenvman.2021.113270 ◽

2021 ◽

Vol 296 ◽

pp. 113270

Author(s):

Ranjith Kumar Manoharan ◽

Sathiyaraj Srinivasan ◽

Gnanendra Shanmugam ◽

Young-Ho Ahn

Keyword(s):

Antibiotic Resistance ◽

Wastewater Treatment ◽

Resistance Genes ◽

Wastewater Treatment Plants ◽

Antibiotic Resistance Genes ◽

Mobile Genetic Elements ◽

Full Scale ◽

Metagenomic Analysis ◽

Hospital Wastewater ◽

Genetic Elements

Download Full-text

Microevolution within ST11 group Clostridioides difficile isolates through mobile genetic elements based on complete genome sequencing

BMC Genomics ◽

10.1186/s12864-019-6184-1 ◽

2019 ◽

Vol 20 (1) ◽

Author(s):

Yuan Wu ◽

Lin Yang ◽

Wen-Ge Li ◽

Wen Zhu Zhang ◽

Zheng Jie Liu ◽

...

Keyword(s):

Drug Resistance ◽

Resistance Genes ◽

Point Mutations ◽

Evolutionary Process ◽

Mobile Genetic Elements ◽

Genetic Elements ◽

Clostridioides Difficile ◽

Hospitalized Elderly ◽

Great Heterogeneity ◽

High Level

Abstract Background Clade 5 Clostridioides difficile diverges significantly from the other clades and is therefore, attracting increasing attention due its great heterogeneity. In this study, we used third-generation sequencing techniques to sequence the complete whole genomes of three ST11 C. difficile isolates, RT078 and another two new ribotypes (RTs), obtained from three independent hospitalized elderly patients undergoing antibiotics treatment. Mobile genetic elements (MGEs), antibiotic-resistance, drug resistance genes, and virulent-related genes were analyzed and compared within these three isolates. Results Isolates 10,010 and 12,038 carried a distinct deletion in tcdA compared with isolate 21,062. Furthermore, all three isolates had identical deletions and point-mutations in tcdC, which was once thought to be a unique characteristic of RT078. Isolate 21,062 (RT078) had a unique plasmid, different numbers of transposons and genetic organization, and harboring special CRISPR spacers. All three isolates retained high-level sensitivity to 11 drugs and isolate 21,062 (RT078) carried distinct drug-resistance genes and loss of numerous flagellum-related genes. Conclusions We concluded that capillary electrophoresis based PCR-ribotyping is important for confirming RT078. Furthermore, RT078 isolates displayed specific MGEs, indicating an independent evolutionary process. In the further study, we could testify these findings with more RT078 isolates of divergent origins.

Download Full-text

Analysis of newly detected tetracycline resistance genes and their flanking sequences in human intestinal bifidobacteria

Scientific Reports ◽

10.1038/s41598-017-06595-0 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 11

Author(s):

Na Wang ◽

Xiaomin Hang ◽

Min Zhang ◽

Xianglong Liu ◽

Hong Yang

Keyword(s):

Resistance Genes ◽

Tetracycline Resistance ◽

Tetracycline Resistance Genes ◽

Flanking Sequences

Download Full-text

Antimicrobial Use and Resistance in Swine Waste Treatment Systems

Applied and Environmental Microbiology ◽

10.1128/aem.01087-06 ◽

2006 ◽

Vol 72 (12) ◽

pp. 7813-7820 ◽

Cited By ~ 74

Author(s):

Archana Jindal ◽

Svetlana Kocherginskaya ◽

Asma Mehboob ◽

Matthew Robert ◽

Roderick I. Mackie ◽

...

Keyword(s):

Resistance Genes ◽

Waste Treatment ◽

Growth Promotion ◽

Tetracycline Resistance ◽

Land Application ◽

Molecular Methods ◽

23S Rrna ◽

Organic Farm ◽

Tetracycline Resistance Genes ◽

Fecal Streptococci

ABSTRACT Chlortetracycline and the macrolide tylosin were identified as commonly used antimicrobials for growth promotion and prophylaxis in swine production. Resistance to these antimicrobials was measured throughout the waste treatment processes at five swine farms by culture-based and molecular methods. Conventional farm samples had the highest levels of resistance with both culture-based and molecular methods and had similar levels of resistance despite differences in antimicrobial usage. The levels of resistance in organic farm samples, where no antimicrobials were used, were very low by a culture-based method targeting fecal streptococci. However, when the same samples were analyzed with a molecular method detecting methylation of a specific nucleotide in the 23S rRNA that results in resistance to macrolides, lincosamides, and streptogramin B (MLSB), an unexpectedly high level of resistant rRNA (approximately 50%) was observed, suggesting that the fecal streptococci were not an appropriate target group to evaluate resistance in the overall microbial community and that background levels of MLSB resistance may be substantial. All of the feed samples tested, including those from the organic farm, contained tetracycline resistance genes. Generally, the same tetracycline resistance genes and frequency of detection were found in the manure and lagoon samples for each commercial farm. The levels of tetracycline and MLSB resistance remained high throughout the waste treatment systems, suggesting that the potential impact of land application of treated wastes and waste treatment by-products on environmental levels of resistance should be investigated further.

Download Full-text