Summary 14Prokaryotes use a mechanism called priming to update their CRISPR immunological memory to rapidly counter 15 revisiting, mutated viruses and plasmids. Here we have determined how new spacers are produced and 16 selected for integration into the CRISPR array during priming. We show that Cas3 couples CRISPR interference 17 to adaptation by producing DNA breakdown products that fuel the spacer integration process in a two-step,

BackgroundBorrelia miyamotoi is a relapsing fever spirochete found in Ixodes ticks in North America, Europe, and Asia, and has recently been found to be invasive in humans. Cultivation of this spirochete has not yet been described, but is important for patient diagnostics and scientific purposes. Host specificity of Borrelia species is dependent on resistance to host complement (serum resistance), and since B. miyamotoi has been identified as a human pathogen we were interested whether B. miyamotoi is resistant to human complement.MethodsWe inoculated B. miyamotoi strains LB-2001 and HT31 in modified-Kelly-Pettenkofer medium with 10% fetal calf serum (MKP-F), and used standard non-laborious Borrelia culture methods to culture the spirochetes. Next, we assessed serum sensitivity by a direct killing assay and a growth inhibition assay.ResultsWe were able to passage B. miyamotoi over 10 times using a standard culture method in MKP-F medium, and found B. miyamotoi to be resistant to human complement. In contrast to B. miyamotoi, Borrelia anserina - a relapsing fever spirochete unrelated to human infection- was serum sensitive.ConclusionsUsing a variation on MKP medium we were able to culture B. miyamotoi, opening the door to in vitro research into this spirochete. In addition, we describe that B. miyamotoi is resistant to human complement, which might play an important role in pathogenesis. We have also found B. anserina to be sensitive to human complement, which might explain why it is not related to human infection. Summarizing, we describe a novel culture method for B. miyamotoi and show it is resistant to human complement.

BackgroundThe specificity of molecular methods for the detection of Streptococcus pneumoniae carriage is under debate. We propose a procedure for carriage surveillance and vaccine impact studies that increases the accuracy of molecular detection of live pneumococci in polymicrobial respiratory samples.MethodsCulture and qPCR methods were applied to detect pneumococcus and pneumococcal serotypes in 1,549 nasopharyngeal samples collected in the Netherlands (n = 972) and England (n = 577) from 946 toddlers and 603 adults, and in paired oropharyngeal samples collected exclusively from 319 Dutch adults. Samples with no live pneumococci isolated at primary diagnostic culture yet generating signal specific for pneumococcus in qPCRs were re-examined with a second, qPCR-guided culture. Optimal Cq cut-offs for positivity in qPCRs were determined via receiver operating characteristic (ROC) curve analysis using isolation of live pneumococci from the primary and qPCR-guided cultures as reference.ResultsDetection of pneumococcus and pneumococcal serotypes with qPCRs in cultured (culture-enriched) nasopharyngeal samples exhibited near-perfect agreement with conventional culture (Cohen’s kappa: 0.95). Molecular methods displayed increased sensitivity of detection for multiple serotype carriage, and implementation of qPCR-guided culturing significantly increased the proportion of nasopharyngeal and oropharyngeal samples from which live pneumococcus was recovered (p < 0.0001). For paired nasopharyngeal and oropharyngeal samples from adults none of the methods applied to a single sample type exhibited good agreement with results for primary and qPCR-guided nasopharyngeal and oropharyngeal cultures combined (Cohens kappa; 0.13–0.55). However, molecular detection of pneumococcus displayed increased sensitivity with culture-enriched oropharyngeal samples when compared with either nasopharyngeal or oropharyngeal primary cultures (p < 0.05).ConclusionThe accuracy of pneumococcal carriage surveillance can be greatly improved by complementing conventional culture with qPCR and vice versa, by using results of conventional and qPCR-guided cultures to interpret qPCR data. The specificity of molecular methods for the detection of live pneumococci can be enhanced by incorporating statistical procedures based on ROC curve analysis. The procedure we propose for future carriage surveillance and vaccine impact studies improves detection of pneumococcal carriage in adults in particular and enhances the specificity of serotype carriage detection.