WGS Pulse

Prospective enrolment across four intensive care units, sequencing human-depleted DNA from positive blood culture broths on MinION, with cloud-based in silico susceptibility prediction from assembled contigs. Species agreement was 94.2%, rising to 100% in monomicrobial infections, and results were reportable 8–16 h from bottle positivity.

Rather than waiting for the bottle to flag, this workflow samples blood cultures drawn before positivity, depletes host DNA by saponin lysis and benzonase, then amplifies and sequences on MinION with real-time taxonomic classification. Across 48 clinical samples it gave species-level identification within 1.5 h of starting sequencing, around 7 h end to end, and resolved both fungal–fungal and fungal–bacterial co-infections.

A global assembly of 712 dog- and cat-derived K. pneumoniae genomes from 25 countries, compared against 38,106 human-associated isolates. The animal isolates spanned 263 sequence types but kept returning to the same high-risk lineages — ST307, ST11, ST15, ST147. ESBL genes were present in 42.9% and carbapenemase genes in 13.9%, and 71.1% of companion-animal sequence types were also found in people.

Nineteen P. aeruginosa isolates from Brussels intensive care units, already sequenced on Illumina, were re-sequenced with a Nanopore-only workflow on V14 chemistry and put through two analysis platforms. Both agreed closely with the Illumina data; Ridom Typer came within a maximum of one cgMLST allele and confirmed every previously identified transmission cluster.

Plasmids fragment in short-read assemblies because they are full of repeats, which leaves resistance genes catalogued but not placed. plsMD guides reconstruction using replicon and full-plasmid reference databases on top of Unicycler assemblies. On an established benchmark it reached 91.3% recall, 95.5% precision and an F1 of 92.0%, outperforming existing tools; on a freshly sequenced set the same figures were 77.6%, 88.9% and 74.5%.

Host DNA swamps conventional metagenomic sequencing in low-biomass samples. This compared probe-capture enrichment against conventional mNGS on 282 clinical specimens — lavage fluid, blood, CSF — then looked at 621 paired lavage-and-blood samples from sepsis patients with pulmonary infection. Probe capture detected pathogens in 66.67% of samples against 57.10%, and the gain was largest in blood: 66.67% against 47.52%.

A review tracing H5N1 from the 1878 description of fowl plague to the continued global circulation of clade 2.3.4.4b, built around the molecular features that let the virus cross species — the polybasic cleavage site in haemagglutinin, and the “1+7” ribonucleoprotein arrangement of a single polymerase core with seven RNA segments. Its pivot is 2024, when H5N1 appeared in US dairy cattle.

A selection scan across 157 P. falciparum whole genomes from Uganda. Extended haplotypes did appear around the known Kelch13 C469Y and A675V mutations — but the strongest signal of recent selection sat somewhere else entirely, on a stretch of chromosome 7 encoding a phosphoinositide-binding protein, PX1. The haplotype was first seen in 2008 and passed 50% prevalence in northern Uganda by 2016 and eastern Uganda by 2023.

A chromogenic assay that detects extended-spectrum β-lactamase and carbapenemase activity in one workflow, and separates the carbapenemase classes by adding relebactam as a selective class A inhibitor. It comes from the University of Fribourg and NARA, the Swiss national reference centre for emerging antibiotic resistance, with a co-author at the Belgian diagnostics manufacturer D-Tek. The isolates used to validate it had resistance mechanisms already defined by whole-genome sequencing: ESBL detection reached 97.8% sensitivity at one hour (n = 67) and carbapenemase activity 100% at twenty minutes (n = 92), both at 100% specificity, for under a dollar a sample and about three minutes of hands-on time.