Mosaic tetracycline resistance genes encoding ribosomal protection proteins

ABSTRACT Phylogenetic analysis of tetracycline resistance genes encoding the ribosomal protection proteins (RPPs) revealed the monophyletic origin of these genes. The most deeply branching class, exemplified bytet and otrA, consisted of genes from the antibiotic-producing organisms Streptomyces rimosus andStreptomyces lividans. With a high degree of confidence, the corresponding genes of the other seven classes (Tet M, Tet S, Tet O, Tet W, Tet Q, Tet T, and TetB P) formed phylogenetically distinct separate clusters. Based on this phylogenetic analysis, a set of PCR primers for detection, retrieval, and sequence analysis of the corresponding gene fragments from a variety of bacterial and environmental sources was developed and characterized. A pair of degenerate primers targeted all tetracycline resistance genes encoding RPPs except otrA and tet, and seven other primer pairs were designed to target the specific classes. The primers were used to detect the circulation of these genes in the rumina of cows, in swine feed and feces, and in swine fecal streptococci. Classes Tet O and Tet W were found in the intestinal contents of both animals, while Tet M was confined to pigs and Tet Q was confined to the rumen. The tet(O) and tet(W) genes circulating in the microbiota of the rumen and the gastrointestinal tract of pigs were identical despite the differences in animal hosts and antibiotic use regimens. Swine fecal streptococci uniformly possessed thetet(O) gene, and 22% of them also carriedtet(M). This population could be considered one of the main reservoirs of these two resistance genes in the pig gastrointestinal tract. All classes of RPPs except Tet T and TetB P were found in the commercial components of swine feed. This is the first demonstration of the applicability of molecular ecology techniques to estimation of the gene pool and the flux of antibiotic resistance genes in production animals.

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Detection of a Novel, and Likely Ancestral, Tn916-Like Element from a Human Saliva Metagenomic Library

Genes ◽

10.3390/genes11050548 ◽

2020 ◽

Vol 11 (5) ◽

pp. 548

Author(s):

Liam J. Reynolds ◽

Muna F. Anjum ◽

Adam P. Roberts

Keyword(s):

Resistance Genes ◽

Metagenomic Library ◽

Tetracycline Resistance ◽

Human Saliva ◽

Fusion Event ◽

Tetracycline Resistance Genes ◽

Antimicrobial Resistance Genes ◽

Genes Encoding ◽

Gene Fusion Event ◽

Metagenomic Approach

Tn916 is a conjugative transposon (CTn) and the first reported and most well characterised of the Tn916/Tn1545 family of CTns. Tn916-like elements have a characteristic modular structure and different members of this family have been identified based on similarities and variations in these modules. In addition to carrying genes encoding proteins required for their conjugation, Tn916-like elements also carry accessory, antimicrobial resistance genes; most commonly the tetracycline resistance gene, tet(M). Our study aimed to identify and characterise tetracycline resistance genes from the human saliva metagenome using a functional metagenomic approach. We identified a tetracycline-resistant clone, TT31, the sequencing of which revealed it to encode both tet(M) and tet(L). Comparison of the TT31 sequence with the accessory, regulation, and recombination modules of other Tn916-like elements indicated that a partial Tn916-like element encoding a truncated orf9 was cloned in TT31. Analysis indicated that a previous insertion within the truncated orf9 created the full length orf9 found in most Tn916-like transposons; demonstrating that orf9 is, in fact, the result of a gene fusion event. Thus, we hypothesise that the Tn916-like element cloned in TT31 likely represents an ancestral Tn916.

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Development, Validation, and Application of PCR Primers for Detection of Tetracycline Efflux Genes of Gram-Negative Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.68.4.1786-1793.2002 ◽

2002 ◽

Vol 68 (4) ◽

pp. 1786-1793 ◽

Cited By ~ 146

Author(s):

R. I. Aminov ◽

J. C. Chee-Sanford ◽

N. Garrigues ◽

B. Teferedegne ◽

I. J. Krapac ◽

...

Keyword(s):

Resistance Genes ◽

Production Systems ◽

Animal Feed ◽

Antibiotic Resistance Gene ◽

Tetracycline Resistance ◽

Pcr Primers ◽

Tetracycline Resistance Genes ◽

Common Structure ◽

Waste Lagoons ◽

Genes Encoding

ABSTRACT Phylogenetic analysis of tetracycline resistance genes, which confer resistance due to the efflux of tetracycline from the cell catalyzed by drug:H+ antiport and share a common structure with 12 transmembrane segments (12-TMS), suggested the monophyletic origin of these genes. With a high degree of confidence, this tet subcluster unifies 11 genes encoding tet efflux pumps and includes tet(A), tet(B), tet(C), tet(D), tet(E), tet(G), tet(H), tet(J), tet(Y), tet(Z), and tet(30). Phylogeny-aided alignments were used to design a set of PCR primers for detection, retrieval, and sequence analysis of the corresponding gene fragments from a variety of bacterial and environmental sources. After rigorous validation with the characterized control tet templates, this primer set was used to determine the genotype of the corresponding tetracycline resistance genes in total DNA of swine feed and feces and in the lagoons and groundwater underlying two large swine production facilities known to be impacted by waste seepage. The compounded tet fingerprint of animal feed was found to be tetCDEHZ, while the corresponding fingerprint of total intestinal microbiota was tetBCGHYZ. Interestingly, the tet fingerprints in geographically distant waste lagoons were identical (tetBCEHYZ) and were similar to the fecal fingerprint at the third location mentioned above. Despite the sporadic detection of chlortetracycline in waste lagoons, no auxiliary diversity of tet genes in comparison with the fecal diversity could be detected, suggesting that the tet pool is generated mainly in the gut of tetracycline-fed animals, with a negligible contribution from selection imposed by tetracycline that is released into the environment. The tet efflux genes were found to be percolating into the underlying groundwater and could be detected as far as 250 m downstream from the lagoons. With yet another family of tet genes, this study confirmed our earlier findings that the antibiotic resistance gene pool generated in animal production systems may be mobile and persistent in the environment with the potential to enter the food chain.

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Prevalence of Tetracycline Resistance Genes in Oral Bacteria

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.47.3.878-882.2003 ◽

2003 ◽

Vol 47 (3) ◽

pp. 878-882 ◽

Cited By ~ 94

Author(s):

A. Villedieu ◽

M. L. Diaz-Torres ◽

N. Hunt ◽

R. McNab ◽

D. A. Spratt ◽

...

Keyword(s):

Resistance Genes ◽

Tetracycline Resistance ◽

Oral Bacteria ◽

Healthy Adults ◽

Resistant Bacteria ◽

First Report ◽

Tetracycline Resistance Genes ◽

Oral Microflora ◽

Genes Encoding ◽

Ribosomal Protection Protein

ABSTRACT Tetracycline is a broad-spectrum antibiotic used in humans, animals, and aquaculture; therefore, many bacteria from different ecosystems are exposed to this antibiotic. In order to determine the genetic basis for resistance to tetracycline in bacteria from the oral cavity, saliva and dental plaque samples were obtained from 20 healthy adults who had not taken antibiotics during the previous 3 months. The samples were screened for the presence of bacteria resistant to tetracycline, and the tetracycline resistance genes in these isolates were identified by multiplex PCR and DNA sequencing. Tetracycline-resistant bacteria constituted an average of 11% of the total cultivable oral microflora. A representative 105 tetracycline-resistant isolates from the 20 samples were investigated; most of the isolates carried tetracycline resistance genes encoding a ribosomal protection protein. The most common tet gene identified was tet(M), which was found in 79% of all the isolates. The second most common gene identified was tet(W), which was found in 21% of all the isolates, followed by tet(O) and tet(Q) (10.5 and 9.5% of the isolates, respectively) and then tet(S) (2.8% of the isolates). Tetracycline resistance genes encoding an efflux protein were detected in 4.8% of all the tetracycline-resistant isolates; 2.8% of the isolates had tet(L) and 1% carried tet(A) and tet(K) each. The results have shown that a variety of tetracycline resistance genes are present in the oral microflora of healthy adults. This is the first report of tet(W) in oral bacteria and the first report to show that tet(O), tet(Q), tet(A), and tet(S) can be found in some oral species.

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Diversity of tet resistance genes in tetracycline-resistant bacteria isolated from a swine lagoon with low antibiotic impact

Canadian Journal of Microbiology ◽

10.1139/w07-104 ◽

2007 ◽

Vol 53 (12) ◽

pp. 1307-1315 ◽

Cited By ~ 22

Author(s):

John J Macauley ◽

Craig D. Adams ◽

Melanie R. Mormile

Keyword(s):

Resistance Genes ◽

Tetracycline Resistance ◽

Antibiotic Use ◽

Resistant Bacteria ◽

Concentrated Animal Feeding Operations ◽

Animal Feeding Operations ◽

Tetracycline Resistance Genes ◽

Animal Feeding ◽

Ribosomal Protection Protein ◽

Ribosomal Protection

Tetracycline resistance has been extensively studied and shown to be widespread. A number of previous studies have clearly demonstrated that a variety of tetracycline resistance genes are present in swine fecal material, treatment lagoons, and the environments surrounding concentrated animal feeding operations (CAFOs). The diversity of tetracycline resistance within a swine lagoon located at a CAFO that used only bacitricin methylene disalicylate as an antibiotic was evaluated by screening 85 tetracycline-resistant isolates for the presence of 18 different genes by performing PCR with primers that target tetracycline efflux genes of Gram-negative bacteria and ribosomal protection proteins. In addition, partial 16S rRNA sequences from each of these isolates were sequenced to determine the identity of these isolates. Of the 85 isolates examined, 17 may represent potential novel species based on BLAST results. Greater than 50% of the isolates (48 out of 85) were found to not contain targeted tet efflux genes. Though minimum inhibitory concentrations ranged widely (16 – >256 mg/L), these values did not give an indication of the tet genes present. Ten new genera were identified that contain at least one tet efflux gene. Five other genera possessed tet efflux genes that were not found in these organisms previously. Interestingly, none of the isolates possessed any of the selected ribosomal protection protein genes. Though tetracycline resistance was found in bacteria isolated from a swine CAFO lagoon, it appears that the limited antibiotic use at this CAFO might have impacted the presence and diversity of tetracycline resistance genes.

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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

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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.

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