Biology subjects

Ceyssens, P.-J.

Publications and source records attributed to Ceyssens, P.-J..

6 recordsLinked to original sources

bioRxiv2026

Genomic epidemiology of Ukraine conflict-associated Klebsiella pneumoniae reveals the emergence of a high-risk clone with a hybrid virulence-resistance plasmid vulnerable to lytic phages

As antimicrobial resistance continues to rise and the development of new antimicrobials lags, we face an urgent threat where routine infections could become life-threatening. Armed conflicts, like Russias war on Ukraine, intensify this crisis by accelerating the emergence and spread of resistant organisms across regions and borders. Phage Support Ukraine (Phage Sp UKR) is a collaborative effort to provide phages targeting circulating pathogens in Ukraine for delivery of personalized phage therapies. Within this context, we received multidrug-resistant bacterial isolates belonging to a number of different species. We here focus on Klebsiella pneumoniae, the most concerning pathogen with regard to prevalence, virulence and antibiotic resistance. Among the K. pneumoniae isolates, we identified sequence types (ST) 39, 101, 147, 307 and 395, as well as a predominating clonal group--CG10146 (ST23 KL57), first detected in Moscow--carrying a hybrid virulence-resistance plasmid encoding NDM-1 and aerobactin. Over two years (2023-2025), this clonal group expanded and acquired pan-resistance. When tested in virulence assays, only one isolate (ST395) displayed hypervirulence in a Galleria mellonella though not in a mouse infection model. Several phages isolated from Ukrainian sewage were able to lyse these K. pneumoniae strains, including strains obtained from soldiers displaced in Belgium, Germany, and Latvia. Bacterial resistance was observed during in vitro testing. However, some phage-resistant isolates had mutations in virulence factors, including one that completely lost its hybrid plasmid, resulting in restored antibiotic susceptibility. Strategies like Phage Sp UKR are essential to prevent the selection, persistence, and global spread of these MDR clones.

microbiology↗

bioRxiv2022

Targeted chromosomal barcoding establishes direct genotype-phenotype associations for antibiotic resistance in Mycobacterium abscessus

A bedaquiline resistant Mycobacterium abscessus isolate was sequenced and a candidate mutation in the atpE gene was identified as responsible for the antibiotic resistance phenotype. To establish a direct genotype-phenotype relationship of this D29A mutation, we developed a recombineering-based method consisting of the specific replacement of the desired mutation in the bacterial chromosome. As surrogate bacteria, we used two M. abscessus antibiotic susceptible strains: ATCC19977, and the SL541 clinical isolate. The allelic exchange substrates used in recombineering carried either the sole D29A mutation, or a genetic barcode of silent mutations in codons flanking the D29A mutation. After selection of bedaquiline resistant M. abscessus colonies, transformed with both substrates, we obtained equivalent numbers of recombinants. These resistant colonies were analyzed by allele-specific PCR, and Sanger sequencing, demonstrating that the presence of the genetic barcode is linked to the targeted incorporation of the desired mutation in its chromosomal location. All recombinants displayed the same minimal inhibitory concentration to bedaquiline than the original isolate, from which the D29A mutation was identified. Finally, to demonstrate the broad applicability of this method, we confirmed the association of bedaquiline resistance with the atpE A64P mutation, performed in independent M. abscessus strains and by independent researchers.

microbiology↗

bioRxiv2022

The paradoxical relationship between CRISPR-Cas and phage susceptibility in Pseudomonas aeruginosa

CRISPR-Cas systems are part of the pan-immune system of Pseudomonas aeruginosa and have been shown to limit horizontal gene transfers in that species. Indeed, isolates equipped with these systems tend to have smaller genomes and CRISPR spacers targeting integrative conjugative elements, phages, and plasmids. In this work, we investigate the genomic effects and phenotypic consequences of CRISPR-Cas systems in P. aeruginosa. First, we establish that the population structure is a confounding factor of the relation between genome sizes and the presence of CRISPR-Cas systems in P. aeruginosa as isolates from group II are, on average, 200 kbp larger than those from group I, and have a lower likelihood of possessing CRISPR-Cas systems. Second, we show that the impact on the genome size of CRISPR deactivation by anti-CRISPR proteins differs between the various CRISPR-Cas types found in this species (I-C, I-E, and I-F). Finally, we highlight a paradoxical, positive correlation between the presence of CRISPR-Cas systems and the chances of the host being infected by a set of distinct, strictly virulent Pseudomonas phages. We propose that this increased phage susceptibility in the presence of CRISPR-Cas is linked to a depletion of other accessory defense system genes in isolates with CRISPR-Cas systems. Note: This manuscript was published as a chapter in the doctoral dissertation of Cedric Lood [72]

microbiology↗

bioRxiv2019

Host metabolic reprogramming of Pseudomonas aeruginosa by phage-based quorum sensing modulation

The Pseudomonas quinolone signal (PQS) is a multifunctional quorum sensing molecule of key importance to the P. aeruginosa metabolism. We here describe that the lytic Pseudomonas bacterial virus LUZ19 targets this population-density-dependent signaling system by expressing quorum sensing-associated acyltransferase (Qst) during early infection. Qst interacts with a key biosynthesis pathway enzyme PqsD, resulting in decreased metabolites levels of PQS and its precursor 2-heptyl-4(1H)-quinolone. The lack of a functional PqsD enzyme impairs the normal LUZ19 infection but is restored by external supplementation of 2-heptyl-4(1H)-quinolone, showing that LUZ19 exploits PQS to successfully achieve its infection. A functional interaction network, which includes enzymes of the central carbon metabolism (CoaC/ThiD) and a novel non-ribosomal peptide synthetase pathway (PA1217), suggests a broader functional context for Qst, which blocks P. aeruginosa cell division. Qst represents an exquisite example of intricate reprogramming of the bacterium, which may be exploited towards antibiotic target discovery for this bacterial pathogen.

microbiology↗

bioRxiv2019

Global phylogenomics of multidrug resistant Salmonella enterica serotype Kentucky ST198

Salmonella enterica serotype Kentucky (S. Kentucky) can be a common causative agent of salmonellosis, usually associated with consumption of contaminated poultry. Antimicrobial resistance (AMR) to multiple drugs, including ciprofloxacin, is an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 S. Kentucky ST198 isolates from five continents. Population structure was inferred using phylogenomic analysis and whole genomes were compared to investigate changes in gene content, with a focus on acquired AMR genes. Our analysis showed that multidrug resistant (MDR) S. Kentucky isolates belonged to a single lineage, which we estimate emerged circa 1989 following the acquisition of the AMR-associated Salmonella genomic island 1 (variant SGI1-K) conferring resistance ampicillin, streptomycin, gentamicin, sulfamethoxazole, and tetracycline. Phylogeographic analysis indicates this clone emerged in Egypt before disseminating into Northern, Southern and Western Africa, then to the Middle East, Asia and the European Union. The MDR clone has since accumulated various substitution mutations in the quinolone resistance determining regions (QRDR) of DNA gyrase (gyrA) and DNA topoisomerase (parC), such that most strains carry three QRDR mutations which together confer resistance to ciprofloxacin. The majority of AMR genes in the S. Kentucky genomes were carried either on plasmids or SGI structures. Remarkably, each genome carried a different SGI1-K derivative structure; this variation could be attributed to IS26-mediated insertions and deletions, which appear to have hampered previous attempts to trace the clone's evolution using sub-WGS resolution approaches. Several different AMR plasmids were also identified, encoding resistance to chloramphenicol, third-generation cephalosporins, carbapenems, and/or azithromycin. These results indicate that most MDR S. Kentucky circulating globally result from the clonal expansion of a single lineage that acquired chromosomal AMR genes 30 years ago, and has continued to diversify and accumulate additional resistances to last-line oral antimicrobials.

microbiology↗

bioRxiv2018

Comparative transcriptomics reveals a conserved Bacterial Adaptive Phage Response (BAPR) to viral predation

Intrinsic and acquired defenses against bacteriophages, including Restriction/Modification, CRISPR/Cas, and Toxin/Anti-toxin systems have been intensely studied, with profound scientific impacts. However, adaptive defenses against phage infection analogous to adaptive resistance to antimicrobials have yet to be described. To identify such mechanisms, we applied an RNAseq-based, comparative transcriptomics approach in different Pseudomonas aeruginosa strains after independent infection by a set of divergent virulent bacteriophages. A common host-mediated adaptive stress response to phages was identified that includes the Pseudomonas Quinolone Signal, through which infected cells inform their neighbors of infection, and what may be a resistance mechanism that functions by reducing infection vigor. With host transcriptional machinery left intact, we also observe phage-mediated differential expression caused by phage-specific stresses and molecular mechanisms. These responses suggest the presence of a conserved Bacterial Adaptive Phage Response mechanism as a novel type of host defense mechanism, and which may explain transient forms of phage persistence.

microbiology↗