Identification and Characterization of Two Novel IS
 CR1
 -Associated Genes,
 dfrA42
 and
 dfrA43
 , Encoding Trimethoprim-Resistant Dihydrofolate Reductases

Li, Ling; Zhang, Mengge; Wang, Wenjia; Xia, Ruirui; Ma, Yong; Xin, Wei; Wang, Xinhua; Sun, Xiaomin; Xie, Xiulan; Xie, Shiling; Wang, Mingyu; Xu, Hai

doi:10.1128/aac.02010-20

Cited by 2 publications

(1 citation statement)

References 19 publications

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“…Importantly, the most abundant ARGs encoded in gut phages across seven pig breeds were the DfrA42 that accounted for 75.47% of total ARGs, followed by DfrA4 . The DfrA42 and DfrA43 are novel genes identified from trimethoprim-resistant Proteus strains and confer diaminopyrimidine resistance [ 62 ]. Our data also suggested a larger spread risk of diaminopyrimidine resistance in gut phages in commercial DLY pigs than those in Chinese native pigs.…”

Section: Discussionmentioning

confidence: 99%

Characterizing the gut phageome and phage-borne antimicrobial resistance genes in pigs

Hu,

Chen,

Nie

et al. 2024

Microbiome

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Background Mammalian intestine harbors a mass of phages that play important roles in maintaining gut microbial ecosystem and host health. Pig has become a common model for biomedical research and provides a large amount of meat for human consumption. However, the knowledge of gut phages in pigs is still limited. Results Here, we investigated the gut phageome in 112 pigs from seven pig breeds using PhaBOX strategy based on the metagenomic data. A total of 174,897 non-redundant gut phage genomes were assembled from 112 metagenomes. A total of 33,487 gut phage genomes were classified and these phages mainly belonged to phage families such as Ackermannviridae, Straboviridae, Peduoviridae, Zierdtviridae, Drexlerviridae, and Herelleviridae. The gut phages in seven pig breeds exhibited distinct communities and the gut phage communities changed with the age of pig. These gut phages were predicted to infect a broad range of 212 genera of prokaryotes, such as Candidatus Hamiltonella, Mycoplasma, Colwellia, and Lactobacillus. The data indicated that broad KEGG and CAZy functions were also enriched in gut phages of pigs. The gut phages also carried the antimicrobial resistance genes (ARGs) and the most abundant antimicrobial resistance genotype was diaminopyrimidine resistance. Conclusions Our research delineates a landscape for gut phages in seven pig breeds and reveals that gut phages serve as a key reservoir of ARGs in pigs.

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Section: Discussionmentioning

confidence: 99%

Characterizing the gut phageome and phage-borne antimicrobial resistance genes in pigs

Hu,

Chen,

Nie

et al. 2024

Microbiome

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dfrA trimethoprim resistance genes found in Gram-negative bacteria: compilation and unambiguous numbering

Ambrose

Hall

2021

Journal of Antimicrobial Chemotherapy

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To track the spread of antibiotic resistance genes, accurate identification of individual genes is essential. Acquired trimethoprim resistance genes encoding trimethoprim-insensitive homologues of the sensitive dihydrofolate reductases encoded by the folA genes of bacteria are increasingly found in genome sequences. However, naming and numbering in publicly available records (journal publications or entries in the GenBank non-redundant DNA database) has not always been unambiguous. In addition, the nomenclature has evolved over time. Here, the changes in nomenclature and the most commonly encountered problems and pitfalls affecting dfrA gene identification arising from historically incorrect or inaccurate numbering are explained. The complete set of dfrA genes/DfrA proteins found in Gram-negative bacteria for which readily searchable sequence information is currently available has been compiled using less than 98% identity for both the gene and the derived protein sequence as the criteria for assignment of a new number. In most cases, trimethoprim resistance has been demonstrated. The gene context, predominantly in a gene cassette or near the ori end of CR1 or CR2, is also covered. The RefSeq database that underpins the programs used to automatically identify resistance genes in genome data sets has been curated to assign all sequences listed to the correct number. This led to the assignment of corrected or new gene numbers to several mis-assigned sequences. The unique numbers assigned for the dfrA/DfrA set are now listed in the RefSeq database, which we propose provides a way forward that should end future duplication of numbers and the confusion that causes.

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Identification and Characterization of Two Novel IS CR1 -Associated Genes, dfrA42 and dfrA43 , Encoding Trimethoprim-Resistant Dihydrofolate Reductases

Cited by 2 publications

References 19 publications

Characterizing the gut phageome and phage-borne antimicrobial resistance genes in pigs

Characterizing the gut phageome and phage-borne antimicrobial resistance genes in pigs

dfrA trimethoprim resistance genes found in Gram-negative bacteria: compilation and unambiguous numbering

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