Background: Timely diagnostic investigation to establish the microbial etiology of pneumonia is essential to ensure the administration of effective antibiotic therapy to individual patients. Methods: We evaluated a multiplex PCR assay panel, the FilmArrayâ pneumonia panel (Fil-mArray PP, BioFire Diagnostics), for detection of 35 respiratory pathogens and resistance determinants and compared the performance of the standard-of-care test in intensive care unit patients with lower respiratory tract infections. Results: Among the 59 endotracheal aspirates and bronchoalveolar lavage specimens obtained from 51 adult patients, FilmArray PP was effective in detecting respiratory bacterial pathogens with an overall positive percent agreement of 90% (95% confidence interval [CI], 73.5e97.9%) and negative percent agreement of 97.4% (95% CI, 96.0 e98.4%). FilmArray PP semiquantitative reporting demonstrated a concordance rate of 53.6% for the culture-positive specimens and 86.3% for the culture-negative specimens. FilmArray PP detected 16 viral Journal of Microbiology, Immunology and Infection (2019) 52, 920e928 targets, whereas the conventional viral isolation failed, except influenza A, which showed 100% concordance with PCR. Coinfections were detected in 42.3% of the specimens. Substantial discrepancies were observed in identifying antimicrobial resistance gene targets and in the susceptibility testing. However, FilmArray PP may still be useful at the early stage of pneumonia before culture and susceptibility test reports are available. Consequently, the results of FilmArray PP might alter the antibiotic prescription in 40.7% of the patients. Conclusions: FilmArray PP offers a rapid and sensitive diagnostic method for lower respiratory tract infections. However, clinical correlation is advised to determine its significance in interpreting multiple pathogens and detection of genes involved in antimicrobial resistance.

We assessed the accuracy of species-level identification of two commercially available matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems (Bruker Biotyper and Vitek MS) and two conventional phenotypic methods (Phoenix 100 YBC and Vitek 2 Yeast ID) with that of rDNA gene sequencing analysis among 200 clinical isolates of commonly encountered yeasts. The correct identification rates of the 200 yeast isolates to species or complex (Candida parapsilosis complex, C. guilliermondii complex and C. rugosa complex) levels by the Bruker Biotyper, Vitek MS (using in vitro devices [IVD] database), Phoenix 100 YBC and Vitek 2 Yeast ID (Sabouraud's dextrose agar) systems were 92.5%, 79.5%, 89%, and 74%, respectively. An additional 72 isolates of C. parapsilosis complex and 18 from the above 200 isolates (30 in each of C. parapsilosis, C. metapsilosis, and C. orthopsilosis) were also evaluated separately. Bruker Biotyper system could accurately identify all C. parapsilosis complex to species level. Using Vitek 2 MS (IVD) system, all C. parapsilosis but none of C. metapsilosis, or C. orthopsilosis could be accurately identified. Among the 89 yeasts misidentified by the Vitek 2 MS (IVD) system, 39 (43.8%), including 27 C. orthopsilosis isolates, could be correctly identified Using the Vitek MS Plus SARAMIS database for research use only. This resulted in an increase in the rate of correct identification of all yeast isolates (87.5%) by Vitek 2 MS. The two species in C. guilliermondii complex (C. guilliermondii and C. fermentati) isolates were correctly identified by cluster analysis of spectra generated by the Bruker Biotyper system. Based on the results obtained in the current study, MALDI-TOF MS systems present a promising alternative for the routine identification of yeast species, including clinically commonly and rarely encountered yeast species and several species belonging to C. parapsilosis complex, C. guilliermondii complex, and C. rugosa complex.

Among 36 Mycobacterium masilliense and 22 M. abscessus isolates identified by erm(41) PCR and sequencing analysis of rpoB and 23S rRNA genes, the rate of accurate differentiation between these two subspecies was 100% by cluster analysis of spectra generated by Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry. Mycobacterium abscessus complex, a rapidly growing mycobacterium, is the cause of an increasing number of community-and health care-associated infections in humans (1). The isolation of M. abscessus complex from patients with various clinical infections has been reported in many countries, including Taiwan (2-7). The M. abscessus complex comprises three closely related subspecies, namely, M. massiliense, M. bolletii, and M. abscessus (sensu stricto) (4,5,(7)(8)(9). Identification of M. abscessus complex members to the species level depends on sequencing analysis of several genes, including the erm(41) gene, the 23S rRNA gene, and several housekeeping genes (e.g., rpoB and hsp65) (7,(9)(10)(11)(12). A previous report found that erm(41) PCR can differentiate M. massiliense from M. abscessus and M. bolletii but that sequencing analysis of rpoB and hsp65 was less reliable at differentiating between the two (9). M. abscessus subsp. bolletti is now the recommended taxonomic name for M. massiliense (4, 12). Differences of in vitro susceptibilities to clarithromycin between M. massiliense (M. abscessus subsp. Bolletti) and M. abscessus (sensu stricto) isolates and of treatment response rates of lung diseases caused by these two species with clarithromycin-based antibiotic therapy have been reported (7-12). However, the use of molecular methods to differentiate among these subspecies is not possible in many routine microbiology laboratories.The use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is relatively new in the field of microbiology for species identification of yeasts and bacteria, including mycobacteria (13-17). Although MALDI-TOF MS has been shown to be a highly accurate method for identifying M. abscessus complex isolates to the species level, this method has not been shown to be able to differentiate between subspecies of the M. abscessus complex, i.e., M. massiliense (M. abscessus subsp. bolletti) and M. abscessus (sensu stricto) (15,16).In this study, we evaluated a total of 58 isolates of the M. abscessus complex obtained from various clinical specimens from patients treated during the period from January 2011 to December 2012 at the National Taiwan University Hospital, a 2,900-bed tertiary-care medical center in northern Taiwan. The isolates were presumptively identified as M. abscessus complex based on conventional biochemical methods as previously described (4-6).These isolates were further identified to the subspecies level by sequencing the erm(41) gene and by performing sequence analysis techniques targeting the rpoB and 23S rRNA genes. The following primer pairs were used: ermF (5=-GAC CGG GGC CTT CTT C...

fWe evaluated whether the Bruker Biotyper matrix-associated laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system provides accurate species-level identifications of 147 isolates of aerobically growing Gram-positive rods (GPRs). The bacterial isolates included Nocardia (n ‫؍‬ 74), Listeria (n ‫؍‬ 39), Kocuria (n ‫؍‬ 15), Rhodococcus (n ‫؍‬ 10), Gordonia (n ‫؍‬ 7), and Tsukamurella (n ‫؍‬ 2) species, which had all been identified by conventional methods, molecular methods, or both. In total, 89.7% of Listeria monocytogenes, 80% of Rhodococcus species, 26.7% of Kocuria species, and 14.9% of Nocardia species (n ‫؍‬ 11, all N. nova and N. otitidiscaviarum) were correctly identified to the species level (score values, >2.0). A clustering analysis of spectra generated by the Bruker Biotyper identified six clusters of Nocardia species, i.e., cluster 1 (N.