Sequence variation within the P1 gene of Mycoplasma pneumoniae.

With interest, we have read the article by Zhao et al. (4), who describe the sequence of the P1 gene from 60 Mycoplasma pneumoniae strains. In their paper, the authors claim to have found novel sequence variants of the P1 gene. However, after comparison of these sequences with published P1 sequences, we found that the “novel” variant P1 sequences from five of the strains (which are referred to in the paper as “2c variants”) are not entirely novel. Although these strains contain a remarkably high number of tandem repeats within the P1 gene, which is indeed a new finding, they do not contain a novel variation within the RepMP4 element of the P1 gene; in fact, the same variation has previously been reported in a study by Spuesens and coworkers (2). As a consequence, only one of the strains described by Zhao et al. (strain MpP053) actually contains “novel” sequences within the P1 gene. Similarly as in the other five strains, the “novel” sequences in strain MpP053 have likely originated from inter-RepMP4 recombination events, as they are identical to (and likely derived from) another RepMP4 element, i.e., RepMP4-g (2) (which is referred to as “RepMP4-7” by the authors). While the finding of novel sequences in the P1 gene of M. pneumoniae is biologically and clinically relevant, the data reported by Zhao et al. again underline the importance of performing careful sequence analyses of seemingly new P1 gene sequences. Moreover, there apparently is still a great deal of confusion in the “M. pneumoniae community” on how (variant) P1 sequences should be interpreted and classified and how variations in the sequence of the P1 gene, as a result of recombination events among RepMP4 or RepMP2/3 elements, are related to the subtype (subtype 1 or 2 [see below]) to which a particular M. pneumoniae strain belongs. We therefore previously introduced a classification system for M. pneumoniae strains that can be employed to unambiguously and objectively classify P1 sequences (1, 3). This system not only is applicable to current M. pneumoniae strains, but also can be used for strains that will be isolated in the future and harbor yet novel P1 sequence variations due to homologous DNA recombination events (3). Also, it is important to clearly distinguish the “subtype” to which an M. pneumoniae strain belongs from the “P1 sequence type” of this strain. M. pneumoniae strains can be classified as subtype 1 or subtype 2 strains; these subtypes can be discriminated on the basis of relatively small sequence differences that are found throughout the bacterial genome. However, the variation of the P1 sequence type is likely determined by homologous DNA recombination events among RepMP4 elements and RepMP2/3 elements, which are subtype-independent processes (and can occur in both subtype 1 and subtype 2 strains). This clear distinction leaves no room for ambiguity and confusion in the molecular typing of M. pneumoniae. More importantly, it leaves no room for the suggestion by Zhao et al. that a subtype 1 variant strain, such as “4817,” would harbor subtype 2-specific sequences. As described previously, the P1 gene sequence variation of this subtype 1 strain is merely the result of a recombination event between RepMP2/3 sequences and is not the result of horizontal DNA transfer between a subtype 1 strain and a subtype 2 strain (3). The presumed donor sequence in this recombination event was found to be invariably present within another RepMP2/3 element of strain 4817; it represents a typical subtype 1 sequence (and is therefore not derived from a subtype 2 strain) (3). Clearly, this recombination event resulted in a new P1 gene sequence in strain 4817 and, thus, a new P1 sequence type, which can be described as “1-P1(4-c;2/3-d[e]d)” according to the sequence classification system of Spuesens et al. (1, 3). In conclusion, it is crucial to describe novel P1 gene variation in a thorough fashion, using a standardized sequence classification method, in order to avoid confusion in the subtyping of M. pneumoniae strains and in the analysis of (subtype-independent) homologous DNA recombination events in the P1 gene.