Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections
PH Serpa et al, Genome Medicine, July 12, 2022
Antimicrobial resistance (AMR) is rising at an alarming rate and complicating the management of infectious diseases including lower respiratory tract infections (LRTI). Metagenomic next-generation sequencing (mNGS) is a recently established method for culture-independent LRTI diagnosis, but its utility for predicting AMR has remained unclear. We aimed to assess the performance of mNGS for AMR prediction in bacterial LRTI and demonstrate proof of concept for epidemiological AMR surveillance and rapid AMR gene detection using Cas9 enrichment and nanopore sequencing.
Tracing the origins of antibiotic resistance
CMJE vandenbrook et al, Nature Medicine, March 22, 2022
It has long been known that resistance exists to every single type of antibiotic in clinical use, without exception, though the origins and mechanisms of this resistance have long remained elusive. It was thought that the development of resistance was driven by the use of antibiotics in the clinic and in farming. We now understand that, as most antibiotic compounds are derived from nature, resistance is the result of ongoing evolution and that there is a constant flow of resistance genes between different ecological niches — not only human and animal, but also environmental.
Exploiting genomics to mitigate the public health impact of antimicrobial resistance
C Waddington et al, Genome Medicine, February 16, 2022
This review explores how WGS techniques have advanced global, national, and local AMR surveillance, and how this improved understanding is being applied to inform solutions, such as novel diagnostic methods that allow antimicrobial use to be optimized and vaccination strategies for better controlling AMR. We highlight some future opportunities for AMR control informed by genomic sequencing, along with the remaining challenges that must be overcome to fully realise the potential of WGS approaches for international AMR control.
Whole genome sequencing-based classification of human-related Haemophilus species and detection of antimicrobial resistance genes
M Diricks et al, Genome Medicine, February 9, 2022
A gene presence/absence-based classification algorithm was developed, which employs the open-source gene-detection tool SRST2 and a new classification database comprising 36 genes, including capsule loci for serotyping. The newly developed algorithm can differentiate between clinically relevant Haemophilus species including, but not limited to, H. influenzae, H. haemolyticus, and H. parainfluenzae.