ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, Mar. 2005, p. 1265–1266 0066-4804/05/$08.00⫹0 doi:10.1128/AAC.49.3.1265–1266.2005 Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Vol. 49, No. 3
Letters to the Editor Hybrid tet Genes and tet Gene Nomenclature: Request for Opinions current tet classes, suggesting that it does indeed originate from a novel class of tet determinant. The naming of tetracycline resistance genes is currently based on the predicted amino acid sequences of the proteins encoded by those genes (1). Amino acid identity of ⱕ80% has been proposed as a cutoff for defining new determinants (1). This cutoff value was established for previously known tet genes varying in sequence over their entire lengths and before the discovery of hybrid tet genes. Based on the 80% cutoff, the tet(32) gene, encoding a protein with an amino acid sequence 78.4% identical to that of C. jejuni Tet(O), should be assigned to a new tet class (3). By this criterion, the three M. elsdenii genes in Fig. 1A to C would be designated tet(W) genes, since their translated proteins are, respectively, 95.8, 89.2, and 92% identical to the Tet(W) protein of Butyrivibrio fibrisolvens (GenBank accession no. AJ222769). In our opinion, the current classification guidelines do not adequately reflect the evolutionary position of these mosaic genes or convey their unique recombinant nature. The nomenclature is also confusing because certain M. elsdenii strains contain nonhybrid tet(W) genes (6). For these reasons, we propose that the guidelines for naming tet genes be expanded
We would like to make our colleagues aware of the existence of naturally occurring recombinant tetracycline resistance genes and also solicit opinions regarding the expansion of current guidelines for naming tetracycline resistance genes. Mosaic tetracycline resistance genes were recently discovered in Megasphaera elsdenii strains from the swine intestine (5, 6). Based on their nucleotide sequences, these genes are interclass hybrids of tet(O) and tet(W) genes (Fig. 1A to C). Although the M. elsdenii mosaic tet genes are novel, they are not unique. The tet(32) gene encodes a ribosomal protection-type protein providing tetracycline resistance to strain K10, a human fecal isolate phylogenetically related to Clostridium (3, 4). Although the tet(32) gene was identified as a new class of tet determinant, a reevaluation of the tet(32) sequence has led us to conclude that this gene is an interclass hybrid formed between tet(O) and an unknown tet gene (Fig. 1D). The tet(32) gene begins and ends with nucleotide sequences highly similar to those of tet(O) (Fig. 1D). A noncoding region (158 nucleotides) upstream of tet(32) is 98% identical to the corresponding sequences upstream of the tet(O) genes from Streptococcus mutans and Campylobacter jejuni (3). The middle of tet(32), however, has low (⬍70%) nucleotide similarity with
FIG. 1. Schematic representation of mosaic tetracycline resistance genes from M. elsdenii strains 25–51 (accession no. AY485122) (A), 7–11 (accession no. AY196921) (B), and 14-14 (accession no. AY196920) (C) and Clostridium-like fecal strain K-10 (accession no. AJ295238) (D). The original strain K10 tet(32) sequence (3) contained an error that introduced a premature stop codon into the sequence. The revised sequence is shown here. Stippled regions represent gene segments sharing high sequence identity with C. jejuni tet(O) (accession no. M18896). Open regions in M. elsdenii genes indicate high sequence identity with B. fibrisolvens tet(W) (accession no. AJ222769). The middle section of the K-10 strain tet(32) sequence (hatched) has a low level of identity with every known tet gene, and the designation tet(O/32/O) is proposed for this gene, as described in text. Mosaic genes produced by recombination between the same tet classes at different crossover positions are differentiated by italicized numbers [tet(O/W/O)-1 and tet(O/W/O)-2]. Nucleotide base positions are indicated above each gene. Identical nucleotides are expressed as percentages below each gene. Values in parentheses represent percentages of identical amino acid sequences based on translated DNA sequences. 1265
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to recognize hybrid tet genes. A simple, descriptive approach would be to incorporate the designations of the known tet gene classes forming the hybrid into the nomenclature, e.g., tet(O/ W), tet(O/W/O) for M. elsdenii (Fig. 1). Consistent with a previous guideline for naming alleles of a resistance gene (1), italicized numbers would be used to differentiate hybrid genes produced from the same genes recombining at different crossover points, e.g., tet(O/W/O)-1 and tet(O/W/O)-2 genes (Fig. 1). Existing guidelines for naming regulators and protein products of tet genes (2) would incorporate the hybrid denotation, for example, TetA(O/W/O)-2 or TetO/W/O-2 for the protein encoded by tet(O/W/O)-2. For taxonomic consistency and to avoid name duplications, designations for new tet genes should be referred to S. B. Levy prior to publication (1). This proposed nomenclature guideline covers hybrid genes of known tet classes. What about tet(32)-like genes, hybrids of both known and unknown tet classes? We propose giving a new, specific designation to the unknown gene (portion) of the hybrid, e.g., tet(O/32/O), where the letter O refers to regions matching tet(O) and the number 32 indicates an unknown tet gene. We recognize that there are additional issues and details regarding mosaic tet gene nomenclature, more than can be fully considered here. Our intent is to open a dialog on these matters and to encourage a collegial solution. We expect that analyses of tet genes among diverse bacterial species in complex microbial ecosystems, such as the mammalian digestive tract, will uncover new tet gene classes, reveal additional examples of hybrid genes, and ultimately lead to a greater understanding of how resistance genes evolve and disseminate among bacteria in those ecosystems.
ANTIMICROB. AGENTS CHEMOTHER. REFERENCES 1. Levy, S. B., L. M. McMurry, T. M. Barbosa, V. Burdett, P. Courvalin, W. Hillen, M. C. Roberts, J. I. Rood, and D. E. Taylor. 1999. Nomenclature for new tetracycline resistance determinants. Antimicrob. Agents Chemother. 43:1523–1524. 2. Levy, S. B., L. M. McMurry, V. Burdett, P. Courvalin, W. Hillen, M. C. Roberts, and D. E. Taylor. 1989. Nomenclature for tetracycline resistance determinants. Antimicrob. Agents Chemother. 33:1373–1374. 3. Melville, C. M., K. P. Scott, D. K. Mercer, and H. J. Flint. 2001. Novel tetracycline resistance gene, tet(32), in the Clostridium-related human colonic anaerobe K10 and its transmission in vitro to the rumen anaerobe Butyrivibrio fibrisolvens. Antimicrob. Agents Chemother. 45:3246–3249. 4. Scott, K. P., C. M. Melville, T. M. Barbosa, and H. J. Flint. 2000. Occurrence of the new tetracycline resistance gene tet(W) in bacteria from the human gut. Antimicrob. Agents Chemother. 44:775–777. 5. Stanton, T. B., and S. B. Humphrey. 2003. Isolation of tetracycline-resistant Megasphaera elsdenii strains with novel mosaic gene combinations of tet(O) and tet(W) from swine. Appl. Environ. Microbiol. 69:3874–3882. 6. Stanton, T. B., J. S. McDowall, and M. A. Rasmussen. 2004. Diverse tetracycline-resistant genotypes of Megasphaera elsdenii strains selectively cultured from swine feces. Appl. Environ. Microbiol. 70:3754–3757.
Thad B. Stanton* Samuel B. Humphrey Pre-Harvest Food Safety and Enteric Diseases Research Unit National Animal Disease Center USDA, Agricultural Research Service Ames, Iowa 50010–0070 Karen P. Scott Harry J. Flint Microbial Genetics Group Rowett Research Institute Aberdeen AB21 9SB, United Kingdom *Phone: (515) 663–7495 Fax: (515) 663–7458 E-mail:
[email protected].
