Reliable automated identification and susceptibility testing of clinically relevant bacteria is an essential routine for microbiology laboratories, thus improving patient care. Examples of automated identification systems include the Phoenix (Becton Dickinson) and the VITEK 2 (bioMérieux). However, more and more frequently, microbiologists must isolate "difficult" strains that automated systems often fail to identify. An alternative approach could be the genetic identification of isolates; this is based on 16S rRNA gene sequencing and analysis. The aim of the present study was to evaluate the possible use of MicroSeq 500 (Applera) for sequencing the 16S rRNA gene to identify isolates whose identification is unobtainable by conventional systems. We analyzed 83 "difficult" clinical isolates: 25 gram-positive and 58 gram-negative strains that were contemporaneously identified by both systems-VITEK 2 and Phoenix-while genetic identification was performed by using the MicroSeq 500 system. The results showed that phenotypic identifications by VITEK 2 and Phoenix were remarkably similar: 74% for gram-negative strains (43 of 58) and 80% for gram-positive strains were concordant by both systems and also concordant with genetic characterization. The exceptions were the 15 gram-negative and 9 gram-positive isolates whose phenotypic identifications were contrasting or inconclusive. For these, the use of MicroSeq 500 was fundamental to achieving species identification. In clinical microbiology the use of MicroSeq 500, particularly for strains with ambiguous biochemical profiles (including slow-growing strains), identifies strains more easily than do conventional systems. Moreover, MicroSeq 500 is easy to use and cost-effective, making it applicable also in the clinical laboratory.Since the time when microbial identification (ID) was performed by using tube tests, much progress has been made. Initially, to assist microbiologists, miniaturized ID systems appeared, followed by innovative automatic ID systems such as VITEK 2 (bioMérieux, Marcy l'Étoile, France) and Phoenix (Becton Dickinson Microbiology Systems, Cockeysville, Md.) (1, 9). These are new, fully automated systems that provide accurate and reproducible IDs, as well as antimicrobial susceptibility tests. The systems possess either sophisticated software to identify microorganism phenotypes or "advanced expert systems" able to elaborate and validate the antimicrobial susceptibilities of the isolates (1, 2, 6, 7, 9, 10). In spite of the undoubtedly innovative results obtained with the widespread use of these automated systems, they do have some drawbacks, particularly when microbiologists need to identify microorganisms exhibiting biochemical features that do not fit into any known patterns of genus and species. These unusual isolates are quite common, especially when we consider that more and more strains isolated from patients that have undergone longterm antimicrobial therapy (such as hematological patients and those in intensive care units) can lose their typical b...

No abstract