Billings, E. B. | bioRxiv Science

bioRxiv2025

Resistance and heteroresistance as a consequence of colistin therapy during Acinetobacter baumannii murine pneumonia

Acinetobacter baumannii is an ESKAPE pathogen linked to healthcare-associated diseases. Due to evolved resistance, last-resort antibiotics such as the lipooligosaccharide (LOS)-targeting colistin are increasingly used to treat multidrug-resistant isolates. To track the evolution of colistin resistance within a host, we performed sequential oropharyngeal infections in immunocompetent or immune-depleted mice in the presence of inhaled colistin. Both resistant and heteroresistant A. baumannii strains emerged with pmrB mutations that efficiently competed with the susceptible parent in the presence of colistin. These pmrB mutants had a fitness cost in the absence of colistin treatment but retained their ability to colonize the host. In contrast, LOS-deficient A. baumannii mutants removed the target of colistin, but such mutants were unable to colonize the lung. The two pathogenic pmrB mutants showed clear evidence of LOS modification, which was linked to increased transcription of LOS modification enzymes, including the product of the cryptic eptA gene. Spontaneous insertion mutations that caused hyperexpression of eptA allowed the heteroresistant mutant to develop clinically-significant colistin resistance. Insertion mutations upstream of the eptA gene or those disrupting hns, which encodes a small histone-like protein, resulted in increased eptA transcript, linking expression of this protein to clinically significant resistance. A resistant variant derived from the heteroresistant parent was stable in the absence of drug, but continued passaging selected for colistin-resensitized pseudorevertants that were largely due to disruption of the LOS modification enzymes. Therefore, colistin heteroresistance is an early stage in the stepwise acquisition of stable colistin resistance in A. baumannii. SignificanceThe mutational pathways leading to antibiotic-resistant infections and the role of the immune system in preventing them are poorly understood. Here we employed a colistin-treated mouse pneumonia model of Acinetobacter baumannii and observed the evolution of colistin-resistant and heteroresistant mutants in immune-depleted and immunocompetent hosts, respectively. We show that mutations that result in alteration of colistins target drive evolutionary pathways to resistance, whereas removal of the target is unlikely to be clinically significant. We demonstrated that the heteroresistant mutant generates subpopulations with higher levels of resistance through insertion mutations in specific gene regions. This study furthers our understanding of how resistance emerges during infection and provides a genetic explanation for the transition from colistin heteroresistance to full resistance.

microbiology↗

bioRxiv2022

Two canonically aerobic foraminifera express distinct peroxisomal and mitochondrial metabolisms

Certain benthic foraminifera are known to thrive in marine sediments with low oxygen or even without detectable oxygen. Potential survival avenues used by these supposedly aerobic protists include fermentation and anaerobic respiration, although details on their adaptive mechanisms remain somewhat elusive. To better understand the metabolic versatility of foraminifera, we studied two benthic species that thrive in oxygen-depleted marine sediments. Here we detail, via transcriptomics and metatranscriptomics, differential gene expression of Nonionella stella and Bolivina argentea, collected from Santa Barbara Basin, California, USA, in response to varied oxygenation and chemical amendments. Organelle-specific metabolic reconstructions revealed that these two species utilize adaptable mitochondrial and peroxisomal metabolism that reflect their differing lifestyles. N. stella, most abundant in anoxia and characterized by the lack of food vacuoles and the abundance of intracellular lipid droplets, was predicted to couple the putative peroxisomal beta-oxidation and glyoxylate cycle with a versatile electron transport system and a partial TCA cycle running in the reductive direction. In contrast, B. argentea, most abundant in hypoxia and contains food vacuoles, was predicted to utilize the putative peroxisomal gluconeogenesis and a full TCA cycle but lacks the expression of key beta-oxidation and glyoxylate cycle genes. These metabolic adaptations likely confer ecological success while encountering deoxygenation and illuminate the importance of metabolic modifications and interactions between mitochondria and peroxisomes in protists. ImportanceForaminiferan protists are nearly ubiquitous in todays oceans and likely were major components of the Neoproterozoic protistan community. While largely considered aerobic, certain foraminifera demonstrate surprising adaptability to hypoxia and anoxia, contributing to biogeochemical cycling in benthic environments. The analyses of Rhizarian adaptive metabolism set the stage for studying other microeukaryotes under increasing ocean deoxygenation. Revealing the metabolic roles of foraminifera in anaerobic biogeochemical cycling should spur reassessments of existing paleoecological datasets as well as new perspectives on the metabolic evolution of eukaryotic cells.

microbiology↗