Gatermann, S. | bioRxiv Science

bioRxiv2021

Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae

Genomic surveillance can inform effective public health responses to pathogen outbreaks. However, integration of non-local data is rarely done. We investigate two large hospital outbreaks of a carbapenemase-carrying Klebsiella pneumoniae strain in Germany and show the value of contextual data. By screening more than ten thousand genomes, 500 thousand metagenomes, and two culture collections using in silico and in vitro methods, we identify a total of 415 closely related genomes reported in 28 studies. We identify the relationship between the two outbreaks through time-dated phylogeny, including their respective origin. One of the outbreaks presents extensive hidden transmission, with descendant isolates only identified in other studies. We then leverage the genome collection from this meta-analysis to identify genes under positive selection. We thereby identify an inner membrane transporter (ynjC) with a putative role in colistin resistance. Contextual data from other sources can thus enhance local genomic surveillance at multiple levels and should be integrated by default when available.

microbiology↗

bioRxiv2019

Comparison of Vitek(R) 2, three different gradient strip tests and broth microdilution for detecting vanB-positive Enterococcus faecium isolates with low vancomycin MICs

ObjectivesIn 2018, EUCAST issued a warning regarding unreliable results of gradient strip tests for confirming vancomycin resistance in enterococci. We compared the performance of various diagnostic standard and confirmatory tests to identify and determine vanB-type vancomycin resistance.\n\nMethodsWe analysed a collection of vanB-positive E. faecium isolates (n = 68) with low level vancomycin minimal inhibitory concentrations (MICs) and compared the performance of Vitek(R) 2 (bioMerieux), of broth microdilution and of three different gradient strip test providers (Oxoid, Liofilchem, bioMerieux). For the latter we compared the standard procedure vs. a protocol with increased inoculum, a rich agar medium and a longer incubation time (\"macromethod\").\n\nResultsThe sensitivity of Vitek(R) 2 was 81% of vanB-isolates compared to 72% for broth microdilution and 61 - 63% for the three gradient strip tests using standard conditions. The \"macromethod\" substantially improved performance of all strip tests resulting in a sensitivity of 89 - 96% at 48h readout.\n\nConclusionsThe \"macromethod\" provided the overall best performance for recognition of vanB E. faecium. We therefore propose to adapt the EUCAST warning and to recommend the \"macromethod\" with an additional 48h readout or a confirmation by a vanB-specific PCR from culture.

microbiology↗