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Last Posted: Aug 10, 2022
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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.

Disclaimer: Articles listed in the Public Health Genomics and Precision Health Knowledge Base are selected by the CDC Office of Public Health Genomics to provide current awareness of the literature and news. Inclusion in the update does not necessarily represent the views of the Centers for Disease Control and Prevention nor does it imply endorsement of the article's methods or findings. CDC and DHHS assume no responsibility for the factual accuracy of the items presented. The selection, omission, or content of items does not imply any endorsement or other position taken by CDC or DHHS. Opinion, findings and conclusions expressed by the original authors of items included in the update, or persons quoted therein, are strictly their own and are in no way meant to represent the opinion or views of CDC or DHHS. References to publications, news sources, and non-CDC Websites are provided solely for informational purposes and do not imply endorsement by CDC or DHHS.