Factors associated with the number of drugs in darunavir/cobicistat regimens

Persistence of resistance: a panel data analysis of the effect of antibiotic usage on the prevalence of resistance

The use of antibiotics promotes the emergence of resistant bacteria in the patient and the environment. The extent of this well-documented biological relationship is, however, not well characterized at an ecological level. To make good policy around antibiotic use, it is important to understand the empirical connection between usage and resistance. We provide a consistent approach to estimate this relationship using national-level surveillance data. This paper estimates the effect of antibiotic usage on antibiotic resistance using an 11-year panel of data on both usage and resistance for 26 antibiotic-bacteria combinations in 26 European countries. Using distributed-lag models and event-study specifications, we provide estimates of the rate at which increases in antibiotic usage at the national level affect antibiotic resistance nationally and internationally. We also calculate the persistence of resistance and analyze how resistance behaves asymmetrically with respect to increases and decreases in usage. Our analysis finds the prevalence of resistant bacteria increases immediately after usage and continues to increase for at least 4 years after usage. We show that a decrease in usage has little identifiable impact on resistance over the same period. Usage in neighboring countries increases resistance in a country, independent of usage in that country. Trends in usage-related resistance vary across European regions and across bacterial classifications.

Putative mobilized colistin resistance genes in the human gut microbiome

BACKGROUND

The high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin, caused by mobilized colistin resistance (mcr) genes, poses an unprecedented threat to human health. Understanding the spread, evolution, and distribution of such genes among human populations will help in the development of strategies to diminish their occurrence. To tackle this problem, we investigated the distribution and prevalence of potential mcr genes in the human gut microbiome using a set of bioinformatics tools to screen the Unified Human Gastrointestinal Genome (UHGG) collection for the presence, synteny and phylogeny of putative mcr genes, and co-located antibiotic resistance genes.

RESULTS

A total of 2079 antibiotic resistance genes (ARGs) were classified as mcr genes in 2046 metagenome assembled genomes (MAGs), distributed across 1596 individuals from 41 countries, of which 215 were identified in plasmidial contigs. The genera that presented the largest number of mcr-like genes were Suterella and Parasuterella. Other potential pathogens carrying mcr genes belonged to the genus Vibrio, Escherichia and Campylobacter. Finally, we identified a total of 22,746 ARGs belonging to 21 different classes in the same 2046 MAGs, suggesting multi-resistance potential in the corresponding bacterial strains, increasing the concern of ARGs impact in the clinical settings.

CONCLUSION

This study uncovers the diversity of mcr-like genes in the human gut microbiome. We demonstrated the cosmopolitan distribution of these genes in individuals worldwide and the co-presence of other antibiotic resistance genes, including Extended-spectrum Beta-Lactamases (ESBL). Also, we described mcr-like genes fused to a PAP2-like domain in S. wadsworthensis. These novel sequences increase our knowledge about the diversity and evolution of mcr-like genes. Future research should focus on activity, genetic mobility and a potential colistin resistance in the corresponding strains to experimentally validate those findings.

Factors associated with the use and composition of two-drug regimens in a large single-centre HIV cohort

OBJECTIVES

We aimed to assess the clinical characteristics associated with the use of two-drug regimens (2DRs) and the factors associated with specific antiretrovirals in 2DRs in a large single-centre HIV cohort.

METHODS

Retrospective analysis of demographics, HIV characteristics and AIDS events, antiretroviral prescription, virological failure and genotypic resistance testing, and laboratory results from all adult people with HIV (PWH) prospectively followed at the Hospital Clinic of Barcelona who were receiving a 3DR or a 2DR in January 2020. We assessed factors associated with the probability of receiving 2DRs relative to three-drug regimens (3DRs) using a logistic regression model, controlling for age, sex and year of HIV diagnosis. The same methodology was applied to identify factors associated with the prescription of integrase inhibitor-based regimens or PI-based regimens among PWH receiving 2DRs.

RESULTS

There were 3432 (88%) PWH receiving 3DRs and 463 (12%) receiving 2DRs. In the final adjusted model, ≥2 previous virological failures, previous resistance mutations, previous AIDS diagnosis, longer time on current regimen, higher total cholesterol or triglycerides and lower baseline haemoglobin were independent factors associated with 2DRs. The majority of 2DRs included an integrase inhibitor or/and a PI. We identified independent factors associated with the inclusion of integrase inhibitors (lower HDL cholesterol) or PIs (prior AIDS, prior genotypic resistance mutations and lower CD4/CD8 ratio) in the 2DR.

CONCLUSIONS

In this large single-centre HIV cohort, a worse cardiometabolic status or more archived resistance were key factors associated with inclusion of integrase inhibitors or PIs, respectively, in 2DRs.