A surfeit of YATMs?

I have become increasingly distressed by the number of YATMs described in recent years in the Journal of Clinical Microbiology. Although tradition has dictated comment on specific articles, this letter addresses articles too numerous to mention individually and summarizes the limitations and benefits of YATMs, TATBSTMs, and TBCAs. Examples of accepted TATBSTMs are the serogrouping schemes based on the serology of capsular polysaccharides or lipopolysaccharides of numerous bacterial pathogens, which are often linked with certain disease syndromes. TATBSTMs have been implemented in many national reference laboratories, and in some cases, commerical kits enable their universal use. Such typing results described in different articles are universally comprehensible. Many TATBSTMs are not particularly discriminatory for epidemiological purposes, and genetically unrelated bacteria can share common serological properties. Some TATBSTMs, such as phage typing, have negligible value from the point of view of population genetics. TBCAs based on multilocus enzyme electrophoresis (MLEE) have revealed the broad genetic structure of numerous bacterial species. For Escherichia coli, Salmonella enterica, and serogroup A and C Neisseria meningitidis, reference strain collections enable the extension of these schemes to untested bacteria. Fewer reference laboratories implement these methods than implement TATBSTMs, but enough such laboratories exist to allow typing of unknown organisms within a reasonable time. TBCAs yield digital signatures, which can be analyzed retrospectively, for each strain tested and allow estimates of genetic distance based on cluster analyses. However, MLEE is time-consuming and primarily worthwhile for testing larger number of strains. YATMs are generally based on DNA technology (e.g., ribotyping, random amplified polymorphic DNA analysis, or pulsed-field gel electrophoresis polymorphism) and are designed to rapidly distinguish clonal epidemic outbreaks from hyperendemic disease levels caused by concurrent multiplication of unrelated strains. In many cases in which the results from YATMs were compared with those from TBCAs, the TBCA was as discriminatory as the YATM or the YATM was based on genetically hypervariable properties. Most YATMs have been applied to limited numbers of isolates isolated locally within a short time. Only rarely have globally relevant collections spanning decades been tested, and provisions for the comparison of results between independent laboratories are often neglected. Many YATMs are based on the assumption that all detectable genetic variation is suitable for fine typing, but data on the longitudinal stability of such variants in nature are needed before such an assumption is warranted. Lacking clonal analysis of a bacterial species, it is impossible to predict either its genetic heterogeneity or the genetic stability of epidemic clones. Some bacterial species are subjected to horizontal genetic exchange sufficient that fine typing methods may split bacteria of relatively recent common ancestral descent into apparently distantly related groupings. Other bacterial species are so homogeneous that the search for fine typing methods may focus on the use of hypervariable genes or insertion sequences; probably, the resulting classifications will not be applicable to any other collection of these organisms, as the sequences tested are likely to vary with time. Thus, the better YATMs will continue to be useful for rapid analyses of potential outbreaks, but it seems unlikely that any YATM will be able to replace TATBSTMs or TBCAs for describing extensive changes in bacterial distribution and spread.