Nomenclature for New Tetracycline Resistance Determinants

Abstract

Letters of the English alphabet have heretofore been used to name tetracycline resistance determinants. Since all 26 letters have now been used, a nomenclature employing numerals is recommended for future determinants, and one laboratory has offered to coordinate the assignment of numerals.

In 1989, a Note describing the nomenclature for tetracycline resistance determinants which employed letters of the English alphabet was published in this journal (14). Since no letters now remain for designating additional determinants, we propose that new determinants be hereafter designated by Arabic numerals. The new system is patterned on the previous letter-based one, with a numeral used instead of a letter to name a determinant. Since 30 determinants have been described (most, but not all, according to the 1989 nomenclature, with the new 1999 nomenclature being used for Tet 30) (Table 1), the next determinant would receive number 31, with no renaming of the earlier determinants. Following the previous system used with letters, the class would be 31, and the determinant would be designated Tet 31 (with a space between “Tet” and “31”). If there were only a single gene in the determinant, it would be designated tet(31). If there were more than one structural gene, the first would be designated tetA(31) and the second would be tetB(31), etc. A regulatory gene would be designated tetR(31). Note that the class designation, 31, is not italicized. The names of the corresponding proteins would be Tet(31) or TetA(31), etc. An allele of a gene would be designated by a hyphen followed by an italicized allele number; for example, tetA(31)-1 would be allele number 1 of the tetA gene of class 31. If the class designation is not needed within a single communication, it could be omitted.

TABLE 1.

Known tetracycline resistance determinants^a

Tet determinant (or gene, if no determi-nant name was given)	Mechanism	GenBank accession no.	Refer-ence
Tet A	Efflux	X00006	33
Tet B	Efflux	J01830	11
Tet C	Efflux	J01749	23
Tet D	Efflux	X65876	2
Tet E	Efflux	L06940	1
Tet F	Efflux (ineffective?)	Unsequenced	22, 30
Tet G	Efflux	S52437	34
Tet H	Efflux	U00792	10
Tet I	Efflux (?)	Unsequenced	25
Tet J	Efflux	AF038993	16
Tet K	Efflux	M16217	20
Tet L (plasmid)b	Efflux	M11036	13
Tet L (chromosomal)b	Efflux	X08034	26
Tet M	Ribosomal protection	X04388	17
(Tet N)	(Withdrawn)		12
Tet O	Ribosomal protection	M18896c	28
Tet P	Efflux, ribosomal pro-tection (two genes)	L20800	27
Tet Q	Ribosomal protection	X58717	19
Tet S	Ribosomal protection	L09756	4
Tet T	Ribosomal protection	L42544	5
Tet U	Unknown	U01917	24
Tet V	Efflux	AF030344	7;1)
Tet W	Ribosomal protection	AJ222769	3
Tet X	Modification	M37699	29
Tet Y	Efflux	AF070999	32
Tet Z	Efflux	AF121000	31
otrA	Ribosomal protection	X53401	9
otrB	Efflux	AF079900	18
otrC	Unknown	Unsequenced	21, 25
tcr3 (tcrC)	Efflux	D38215	6
tet	Ribosomal protection	M74049	8
Tet 30 [originally unnamed determinant; protein is 46% identical to TetA(A)]	Efflux	AF090987 (wild type)	15

^aIn most cases, we cite the first publication to report the sequence for one or both genes of a determinant. In cases where major (but not minor) errors were later corrected, we cite the later publication. The sequences of many variants of some determinants (particularly Tet L and Tet M) are available but are not given here. Four different unnamed and unsequenced but presumed ribosomal protection determinants (5) are not included. 

^bThe proteins encoded by these two Tet L determinants are only 81% identical. 

^cThe original sequence is not available electronically, so another is substituted. 

This system employs some of the conventions from the previous communication (14) and is summarized in Table 2. Usage for previously described determinants should continue to conform to the prior recommendations (14).

TABLE 2.

Proposed nomenclature for new tetracycline resistance determinants

Classa	Determinantb	Structuralcd		Regulatory (repressor)d
		Gene	Protein	Gene	Protein
n	Tet n	tet(n)	Tet(n)	tetR(n)	TetR(n)

^aClass n is used as an example, where n is an Arabic numeral (31, 32, 33, etc.), numbered in approximate order of public dissemination. 

^bNote the space between Tet and n. 

^cIn the case of multiple structural genes, use the following format: tetA(n), tetB(n), etc. 

^dAfter an introductory use, “n” may be omitted where no ambiguity exists. 

Recently, there have been several situations in which tetracycline resistance determinants discovered in different laboratories were nearly given the same designation. To avoid such a problem in the future, we offer the S. B. Levy group to coordinate the naming of new determinants. Such a determinant can be defined as a naturally occurring unit of one or more adjacent genes involved primarily in tetracycline resistance (as opposed to multidrug resistance or other known function) having a sequence significantly different from sequences of currently known determinants. We suggest ≤80% amino acid identity as the dividing line, based on previous usage. Class L has been defined as a single class even though it contains two subgroups in which the single proteins only are 81% identical (25, 26), while the proteins of two different classes, M and S, are 79% identical (4, 25). To confirm that a number proposed for a newly discovered tetracycline resistance determinant has not been used, please contact S. B. Levy.

Finally, we note that when looking in databases for a name containing parentheses or a space, such as “tet(X)” or “Tet X”, quotation marks should be used around the name, as shown, to retrieve the term intact.