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Combined CRISPRi chemical genetics and comparative genomics reveal Mycobacterium tuberculosis drug resistance mechanisms and a potential opportunity to repurpose clarithromycin to treat tuberculosis due to inactivation of the whiB7 resistance factor in an entire Mtb sublineage.
A platform developed for rapid isolation of SARS-CoV-2 variants also facilitates the characterization of variant immune evasion and viral fitness. The platform enabled rapid detection of the Omicron variant in samples of the first cases in Australia.
Characterization of bacterial microbiomes associated with >1,000 microscopic marine invertebrates reveals that phylosymbiosis is rare across animal lineages.
Evolution experiments using sequential Acinetobacter baumannii lung infections in immunocompetent and immunocompromised mice treated with ciprofloxacin reveal that neutrophil-depleted hosts enable the outgrowth of drug persisters and serve as reservoirs for antibiotic resistance variants.
An analysis of memory T cells induced by messenger RNA vaccination reveals that they maintain polyfunctionality in response to the Omicron spike protein.
A machine learning framework for integrating multi-omic high-dimensional datasets identified disease-specific and shared host gene–microbiome associations across three gastrointestinal diseases.
A phenotypic screen based on a conditional Cas9-system identifies two Toxoplasma gondii genes, revealing conoid gliding protein (CGP) and signalling linking factor (SLF) that act at different steps in host cell egress.
The gut bacterium Clostridium sporogenes uses reductive Stickland reactions for energy and consequently produces metabolites that circulate in the host.
Multi-omics analyses of faecal, urine and blood samples from women with and without recurrent urinary tract infections reveal that gut dysbiosis and differential immune responses may play a role in risk of infection via the gut–bladder axis.
A comparison of the repertoire of SARS-CoV-2-specific epitopes targeted by T cells induced by vaccination or natural infection reveals that T cells predominantly target non-spike epitopes in convalescent individuals, while there is a broader spike-specific CD8+ T-cell response in vaccinees. Despite differences in T-cell response, the targeted T-cell epitopes were conserved between the wild-type and Omicron variants in both groups.
The development of a high-throughput tagging platform to screen kinases of the parasite Toxoplasma gondii led to the identification of a kinase regulating invasion of and egress from host cells.
A longitudinal analysis of viral expansion and clearance rates in 60 individuals sampled daily during acute infection reveals high inter-individual variation in infectious virus shedding, which may contribute to superspreading.
β-glucuronidases produced by gut microbiota members mediate proteolytic activity in the gut via the production of unconjugated bilirubin, which is dysregulated in irritable bowel syndrome.
An inhibitor of the SARS-CoV-2 main protease (Mpro), Y180, showed therapeutic efficacy against wild-type SARS-CoV-2 and its variants including Omicron after oral administration and improved survival in a humanized mouse model.
Whole-genome sequencing and population genomics of 218 Aspergillus fumigatus environmental and clinical isolates reveals strong genetic clustering and the occurrences of near-identical genotypes, indicating the infection of patients with resistant isolates from the environment.
Gut virome analysis of preterm infants at risk of developing necrotizing enterocolitis identifies a conserved viral signature that precedes disease onset.
The mosquito gut resident bacterium Pseudomonas alcaligenes protects the integrity of the mosquito peritrophic matrix by catabolizing 3-hydroxykynurenine, thereby contributing to protection against Plasmodium infection.