Chassard, A. | bioRxiv Science

bioRxiv2026

Calcium signals natural transformation in Acinetobacter baumannii

The acquisition of resistance to antibiotics in the opportunistic pathogen Acinetobacter baumannii may be linked to its capacity to undergo natural transformation. This mode of horizontal gene transfer relies on the import of extracellular DNA and its chromosomal integration by homologous recombination. Type IV pilus activity initiates the capture of extracellular DNA, which is then transported to the cytoplasm for recombination in the chromosome. While most Acinetobacter baumannii strains are transformable, the conditions allowing the expression of type IV pilus and other transformation genes remain largely unexplored. By investigating transformation-permissive conditions, we uncovered that calcium is a potent inducer of natural transformation. Type IV pilus genes and other transformation-specific genes (comEA, dprA) are upregulated by submillimolar concentrations of calcium ions, in a growth phase-dependent manner. In contrast, sodium chloride represses expression of pilA, counteracting the calcium-dependent induction, explaining the reported absence of transformation in NaCl-containing medium (such as LB). Independently of transcriptional induction, calcium ions also directly bind the type IV pilus through the calcium-dependent adhesin PilY1. Our data support a model in which calcium strengthens the interaction of PilY1 with the minor pilin complex, increasing pilus dynamics and subsequent pilus-dependent DNA capture. Hence, calcium signals natural transformation through both transcriptional and structural activation of type IV pilus. In addition to providing new insights into the regulation of natural transformation in A. baumannii this work led us to establish a protocol for genetic engineering of A. baumannii by natural transformation. ImportanceAcinetobacter baumannii is a nosocomial pathogen considered a critical research priority due to its resistance to last resort antibiotics. Understanding how A. baumannii evolves and acquires resistance to antibiotics is thus of prime importance. This species is capable of natural transformation, a means to acquire and spread genetic information, including antibiotic resistance genes. However, the conditions under which this process is active in this species remain elusive. We identify calcium ions as potent inducers of natural transformation and propose a model of the signaling of natural transformation by calcium ions. This opens the way for further investigations into the contribution of natural transformation to acquisition of antibiotic resistance. In addition, it provides an efficient way to genetically manipulate most A. baumannii strains.

microbiology↗

bioRxiv2024

Host shapes microevolution of MDR Acinetobacter baumannii during long-term infection

Acinetobacter baumannii is a nosocomial pathogen associated with various infections, including urinary tract infections (UTIs). In the course of an infection, A. baumannii is known to rapidly become resistant to antibiotic therapy, but much less is known about possible adaptation without antibiotic pressure. Through a retrospective study, we investigated within-host genetic diversity during a subclinical five-year UTI in an animal-patient after withdrawal of colistin treatment. We conducted whole-genome sequencing and phenotypic assays on seventeen clonally related isolates from the Sequence Type 25 lineage. Phylogenomic analysis revealed their proximity with animal and human strains from the same country suggesting zoonotic transmission (France). In this case study, the clonally related strains presented variations in genome sizes and nucleotide sequences. Over the course of the infection, A. baumannii underwent genome reduction through insertion sequence (IS) recombination, phage excision, or plasmid curing. Alongside this global genome reduction, we observed an expansion of IS17, initially located on the endogenous large plasmid. Genetic variations were mainly located in biofilm formation and metabolism genes. We observed repeated variation affecting three biofilm genes and two adhesion operons associated with weak biofilm-forming capacity. Conversely, only two metabolic genes were recurrently affected and phenotypic assays indicated a rather stable metabolism profile between the isolates suggesting minor adaptations to its host. Lastly, an overall decreased antibiotic resistance - expected in the absence of antibiotic treatment - contrasted with a conserved colistin resistance due to a pmrB mutation among the isolates. Impact statementThis study brings a new insight on the genome evolution of the opportunistic pathogen Acinetobacter baumannii during a five-year urinary tract infection in the absence of antibiotic treatment. It relies on genomic and phenotypic analyses of multiple isolates from the same animal-patient highlighting the necessity of studying bacterial diversity as opposed to solely on single-isolate approaches. Over the course of the infection, we observed a reduction in genome size, resulting however in a limited loss of metabolism flexibility, but we observed recurrent loss in adhesion capacities and antibiotic resistance. However, this study stands out by the unexpected conserved colistin resistance of the study isolates in the absence of treatment. Data summaryThe newly sequenced genomes are listed in Table S1, these genomes have been submitted to the NCBI and their BioProject number is PRJNA1100485. The publicly available genomes of bacteria from human and animal origin used in this study are listed in Table S2 All the supplementary tables are available in the Supplementary Material File.

microbiology↗