Comparison of manual and automated nucleic acid extraction methods from clinical specimens for microbial diagnosis purposes.

The choice of nucleic acids (NAs) extraction method for molecular diagnosis in microbiology is of major importance because of the low microbial load, different nature of microorganisms, and clinical specimens. The NA yield of different extraction methods has been mostly studied using spiked samples. However, information from real human clinical specimens is scarce. The purpose of this study was to compare the performance of a manual low-cost extraction method (Qiagen kit or salting-out extraction method) with the automated high-cost MagNAPure Compact method. According to cycle threshold values for different pathogens, MagNAPure is as efficient as Qiagen for NA extraction from noncomplex clinical specimens (nasopharyngeal swab, skin swab, plasma, respiratory specimens). In contrast, according to cycle threshold values for RNAseP, MagNAPure method may not be an appropriate method for NA extraction from blood. We believe that MagNAPure versatility reduced risk of cross-contamination and reduced hands-on time compensates its high cost.

[Surveillance of carbapenem-resistant enterobacteria in stool cultures in a university hospital in Santiago, Chile]. / Vigilancia de enterobacterias productoras de carbapenemasas en cultivos rectales en un hospital universitario de Santiago, Chile.

BACKGROUND: Clinical cultures detect only one-third of colonized patients with carbapenem-resistant Enterobacteriaceae. Early identification and contact precautions implementation would help to interrupt transmission. In our hospital no carbapenemase-producing enterobacteria infections have been described. AIM: To perform stool surveillance cultures in patients hospitalized in critical care unit with the purpose to detect carbapenemase-producing Enterobacteriacea. MATERIAL AND METHODS: Rectal swabs were obtained of patients after five or more days of hospital stay, on a monthly basis from July to December 2011. Phenotypic assays (modified test Hodge and phenylboronic acid test) and polymerase chain reaction (PCR) searching for six carbapenemases of group A and B of Ambler's classification were performed. RESULTS: During this period, 241 surveillance rectal cultures were performed. Thirty eight enterobacteria isolated from 30 patients presented a decreased susceptibility to carbapenems by agar dilution method. All PCR were negative. CONCLUSION: We found that despite the significant number of resistant isolates, patients hospitalized in our institution are not colonized with carbapenemase-producing Enterobacteriaceae. We highlight the importance of screening before having the problem in place.