Biology subjects

Souque, C.

Publications and source records attributed to Souque, C..

5 recordsLinked to original sources

bioRxiv2025

Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species

The ability to detect and reconstruct plasmids from genome assemblies is crucial for studying the evolution and spread of antimicrobial resistance and virulence in bacteria. Though long-read sequencing technologies have made reconstructing plasmids easier, most (97%) of the bacterial genome assemblies in the public domain are generated from short-read data. Work to compare plasmid reconstruction tools has focused primarily on E. coli, leaving gaps in our understanding of how well these tools perform on other, less well-characterized, taxa. Using high quality assemblies as ground truth, we benchmarked 12 plasmid detection tools (which identify plasmid contigs in assemblies) and four plasmid reconstruction tools (which group contigs from the same plasmid together). We tested their ability to characterize diverse plasmids from short-read assemblies representing a wide range of Enterobacterales and Enterococcus species, including newly discovered and poorly characterized species collected from non-human hosts. Plasmer, PlasmidEC, PlaScope, and gplas2 were the highest-scoring plasmid detection tools, performing well for both Enterobacterales and enterococci. The two major determinants of accurate plasmid detection were representation in plasmid databases - with Enterobacterales plasmids being more easily detected than those from enterococci - and assembly contiguity, which was also key for successful plasmid reconstruction. Gplas2 performed best for plasmid reconstruction; however, less than half of plasmids were perfectly reconstructed, suggesting that substantial room for improvement remains in this class of tools. Key MessagesO_LIThe ability to detect and reconstruct plasmids from short-read assemblies is crucial to study the spread of antimicrobial resistance and virulence genes in bacteria. C_LIO_LIMost past comparisons of tools for plasmid detection and reconstruction have focused on plasmids from well-characterized E. coli; therefore, we broadened our benchmarking set to include plasmids from diverse Enterobacterales and Enterococcus species, collected from a wide range of hosts. C_LIO_LIWe compared the predictions of 12 recent plasmid detection and four plasmid reconstruction tools on short read assemblies, against a truth set generated from high-quality hybrid assemblies. C_LIO_LIPlasmer, PlasmidEC, PlaScope, and gplas2 were the highest-scoring plasmid detection tools. C_LIO_LIGplas2 was the highest-scoring tool for plasmid reconstruction; the quality of plasmid reconstruction was mainly determined by assembly fragmentation, with plasmids in more contiguous assemblies being easier to reconstruct. C_LI

bioinformatics↗

bioRxiv2025

RNA-guided nucleases enable a gene drive of insertion sequences in plasmids

Mobile genetic elements (MGEs) are diverse, self-replicating DNA molecules that can reside within cellular hosts and integrate into one another. This co-occurrence imposes distinct evolutionary pressures. Plasmids often contain insertion sequences (ISs). However, the multi-copy nature of plasmids should hinder IS introduction and spread, disfavoring inheritance of nascent plasmid variants through genetic drift. Mechanisms by which ISs overcome these barriers remain unidentified. Here we find that the RNA-guided nuclease TnpB enables such a mechanism to bias its inheritance in plasmids. We show that TnpB, the likely ancestor to Cas12, enables a gene drive to spread the IS within multicopy plasmids and functions as a primitive anti-self defense system in conjugative plasmids. The gene drive between TnpB-bearing ISs and plasmids promotes the spread of both MGEs beyond the ability of either individually. The nested existence between MGEs is not an incidental result of selfish spread, but a driver of it.

microbiology↗

bioRxiv2025

Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics

Antibiotic resistance is frequently observed shortly after the clinical introduction of an antibiotic. Whether and how frequently that resistance occurred before the introduction is harder to determine, as isolates could not have been tested for resistance before an antibiotic was discovered. Historical collections, like the British National Collection of Type Cultures (NCTC), stretching back to 1885, provide a window into this history. Here we match 1,817 sequenced high-quality genomes from the NCTC collection to their respective year of isolation to study resistance genes before and concurrent with the age of antibiotics. Concordant with previous work, we find resistance genes in both pathogens and environmental samples before the age of antibiotics. While generally rare before the introduction of an antibiotic, we find an associated increase in frequency with antibiotic introduction. Finally, we observe a trend of resistance elements becoming both increasingly mobile and nested within multiple mobile elements as time goes on. More broadly, our findings suggest that likely-functional antibiotic resistance genes were circulating in clinically relevant isolates before the age of antibiotics, but human usage is associated with increasing both their overall prevalence and mobility. DATA SUMMARYGenome assemblies downloaded and analyzed are in Supplementary Table 1, and computational tools used are found in the Methods. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. Impact statementHistorical collections of microbial isolates enable researchers to both investigate the past and identify interesting trends over time. In this study, we queried over 1,800 isolate genomes in one such collection for genomic variation linked to antibiotic resistance. We show that numerous isolates cultured before the introduction of a given antibiotic contain genomic variation linked to antibiotic resistance; however, this phenomenon remained relatively rare. We demonstrate a strong association between the year a given antibiotic was clinically introduced and a rise in prevalence of genomic resistance to that antibiotic. Finally, we show that while mobile elements are common throughout the isolates and timeframe analyzed, genomic resistance has become increasingly mobile as time has gone on. This study shows that as expected, the clinical introduction of a given antibiotic is correlated with an increase in resistance to that antibiotic but also was linked with increased mobility of genes and alleles conferring resistance. However, we note that the effect of deposition bias in the collection cannot be excluded. Our work also indicates that numerous microbial pangenomes of pathogens naturally contained genomic resistance to a given antibiotic even before anthropogenic use of that antibiotic. Taken together, we demonstrate that although human use may affect the prevalence and mobility of genomic resistance in clinical isolates; for most antibiotics, genomic resistance existed within the pangenomes of sampled pathogens prior to clinical introduction. Quantifying and understanding the impact of antibiotic introduction in the past helps us understand how the introduction of novel antibiotics can impact bacteria; allowing better reaction to novel resistant infections as they arise.

microbiology↗

bioRxiv2022

Off-target integron activity leads to rapid plasmid compensatory evolution in response to antibiotic selection pressure

Integrons are mobile genetic elements that have played an important role in the dissemination of antibiotic resistance. Under stress, the integron can generate combinatorial variation in resistance cassette expression by cassette re-shuffling, accelerating the evolution of resistance. However, the flexibility of the integron integrase site recognition motif hints at potential off-target effects of the integrase on the rest of the genome that may have important evolutionary consequences. Here we test this hypothesis by selecting for increased piperacillin resistance populations of P.aeruginosa with a mobile integron containing a hard-to-mobilise beta-lactamase cassette to minimize the potential for adaptive cassette re-shuffling. We found that integron activity can both decrease overall survival rate but also improve the fitness of the surviving populations. Off-target inversions mediated by the integron accelerated plasmid adaptation by disrupting costly conjugative genes otherwise mutated in control populations lacking a functional integrase. Plasmids containing integron-mediated inversions were associated with lower plasmid costs and higher stability than plasmids carrying mutations, albeit at a cost of reduced conjugative ability. These findings highlight the potential for integrons to create structural variation that can drive bacterial evolution, and they provide an interesting example showing how antibiotic pressure can drive the loss of conjugative genes.

evolutionary biology↗

bioRxiv2020

Integron activity accelerates the evolution of antibiotic resistance

Mobile integrons are widespread genetic platforms that allow bacteria to modulate the expression of antibiotic resistance cassettes by shuffling their position from a common promoter. Antibiotic stress induces the expression of an integrase that excises and integrates cassettes, and this unique recombination and expression system is thought to allow bacteria to evolve on demand in response to antibiotic pressure. To test this hypothesis, we inserted a custom three cassette integron into P. aeruginosa, and used experimental evolution to measure the impact of integrase activity on adaptation to gentamicin. Crucially, integrase activity accelerated evolution by increasing the expression of a gentamicin resistance cassette through duplications and by eliminating redundant cassettes. Importantly, we found no evidence of deleterious off-target effects of integrase activity. In summary, integrons accelerate resistance evolution by rapidly generating combinatorial variation in cassette composition while maintaining genomic integrity.

microbiology↗