Santiago Redondo-Salvo

The bacterial accessory genome, comprised of plasmids, phages, and other mobile elements, underpins the adaptability of bacterial populations. Pangenome (core and accessory) analysis of pathogens can reveal epidemiological relatedness missed by using core-genome methods alone. Employing a k -mer-based Jaccard Index approach to compute pangenome relatedness, we explore the population structure and epidemiology of Salmonella enterica serotype Hadar (Hadar), an emerging zoonotic pathogen in the United States (U.S.) linked to both commercial and backyard poultry. A total of 3384 U.S. Hadar genomes collected between 1990 and 2023 are analyzed here. Hadar populations underwent substantial shifts between 2019 and 2020 in the U.S., driven by the expansion of a lineage carrying a previously uncommon prophage-like element. Phylogenetic and pangenomic relatedness, coupled with epidemiological data, suggest this lineage emerged from extant populations circulating in commercial poultry, with subsequent dissemination into backyard poultry environments. We demonstrate the utility of pangenomic approaches for mapping vertical and horizontal diversity and informing complex dynamics of zoonotic bacterial pathogens.

The bacterial accessory genome, comprised of plasmids, phages, and other mobile elements, underpins the adaptability of bacterial populations. Pangenome (core and accessory) analysis of pathogens can reveal epidemiological relatedness missed by using core-genome methods alone. Employing a k -mer-based Jaccard Index approach to compute pangenome relatedness, we explored the population structure and epidemiology of Salmonella enterica serotype Hadar (Hadar), an emerging zoonotic pathogen in the United States (U.S.) linked to both commercial and backyard poultry. Hadar populations underwent substantial shifts between 2019 and 2020 in the U.S., driven by the expansion of a lineage carrying a previously uncommon prophage-like element. Phylogenetic and pangenomic relatedness, coupled with epidemiological data, suggest this lineage emerged from extant populations circulating in commercial poultry, with subsequent dissemination into backyard poultry environments. We demonstrate the utility of pangenomic approaches for mapping vertical and horizontal diversity and informing complex dynamics of zoonotic bacterial pathogens.

Plant-associated microorganisms, particularly endophytes, are essential for plant health and development. Endophytic microbiota is intimately associated with host plants colonizing various tissues, including seeds. Seed endophytes are particularly noteworthy because of their potential for vertical transmission. This pathway may play a role in the long-term establishment and evolution of stable bacteria-host interactions across plant generations. Hundreds of seed-bacteria associations have been recently uncovered; however, most seem to be transient or unspecific. While it is known that microorganisms can be transmitted from plant tissues to seeds and from seeds to seedlings, the experimental confirmation of bacterial transfer through successive plant generations remains unreported. In this study, we identified Pantoea as the unique core endophytic bacteria inhabiting the endosperms of 24 wheat seed samples originally harvested in different worldwide locations. Remarkably, Pantoea is the genus with the highest relative average abundance in wheat seeds (61%) and also in germinated seedlings grown under gnotobiotic conditions (30%). In the field, it was the only genus dwelling roots, shoots, spikes and seeds of 4 different wheat varieties tested and its abundance progressively increased across these tissues. This genuine pattern of vertical enrichment, which was not found in other common wheat-associated taxa, suggests a role in the transfer of these endophytic bacteria through the seeds. To confirm intergenerational transmission, parental plants were inoculated with labelled Pantoea isolates, which specifically colonized the next generations of Poaceae plants, experimentally demonstrating bacterial vertical inheritance to the offspring generations and suggesting transmission specificity.

Public health genomic surveillance systems typically measure genome relatedness and infer molecular epidemiological relationships using chromosomal loci alone – an approximation of vertical evolution, or homology-by-descent. The accessory genome, composed of plasmids and other mobile genetic elements, reflects horizontal gene transfer and serves as an important mechanism of bacterial evolution, enabling rapid adaptation. Measuring homology in the accessory genome – homology-by-admixture – could offer important molecular epidemiological information for public health application. We applied Jaccard Index and a novel genome length distance metric to compute pangenome relatedness for the globally-important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both homology-by-descent and homology-by-admixture in a reticulate network. Jaccard Index Network Analysis revealed structure in the Typhi pangenome that can be harnessed to enhance discriminatory power for surveillance, track antimicrobial resistance, and refine our understanding of homology for outbreak management and prevention. This offers a more intricate, multidimensional framework for understanding pathogen evolution. Significance Statement: Bacterial relatedness is often measured and visualized using chromosomal comparison and phylogenetic trees. While valuable, this approach captures only the vertical evolutionary dimension and excludes genetic material acquired or lost through horizontal gene transfer. We present an approach for measuring and visualizing bacterial relatedness using all core and accessory genetic material and discuss the interpretation of resulting reticulate networks of bacterial genomes. In application to Salmonella Typhi, Jaccard Index Network Analysis revealed structure in populations of this pathogen that may be harnessed for public health applications. This approach captures both vertical and horizontal evolutionary dimensions, offering an intricate genetic framework for exploring pathogen evolution.

Acinetobacter baumannii is a Gram-negative coccoid rod species, clinically relevant as a human pathogen, included in the ESKAPE group. Carbapenem-resistant A. baumannii (CRAB) are considered by the World Health Organization (WHO) as a critical priority pathogen for the research and development of new antibiotics. Some of the most relevant features of this pathogen are its intrinsic multidrug resistance and its ability to acquire rapid and effective new resistant determinants against last-resort clinical antibiotics, mostly from other ESKAPE species. The presence of plasmids and mobile genetic elements in their genomes contributes to the acquisition of new antimicrobial resistance determinants. However, although A. baumannii has arisen as an important human pathogen, information about these elements is still not well understood. Current genomic analysis availability has increased our ability to understand the microevolution of bacterial pathogens, including point mutations, genetic dissemination, genomic stability, and pan- and core-genome compositions. In this work, we deeply studied the genomes of four clinical strains from our hospital, and the reference strain ATCC^®19606^TM, which have shown a remarkable ability to survive and maintain their effective capacity when subjected to long-term stress conditions. With that, our aim was presenting a detailed analysis of their genomes, including antibiotic resistance determinants and plasmid composition.

The Plasmid Taxonomic Unit (PTU) concept is an initial step for a natural classification of plasmids. Here we present COPLA, a software for plasmid assignation to existing PTUs. To assess its performance, we used a sample of 1,000 plasmids missing from its current database. Overall, 41% of samples could be assigned an existing PTU (63% within the most abundant order, Enterobacterales ), while 4% of samples could help to define new PTUs once COPLA database was updated.

Plasmids can mediate horizontal gene transfer of antibiotic resistance, virulence genes, and other adaptive factors across bacterial populations. Here, we analyze genomic composition and pairwise sequence identity for over 10,000 reference plasmids to obtain a global map of the prokaryotic plasmidome. Plasmids in this map organize into discrete clusters, which we call plasmid taxonomic units (PTUs), with high average nucleotide identity between its members. We identify 83 PTUs in the order Enterobacterales, 28 of them corresponding to previously described archetypes. Furthermore, we develop an automated algorithm for PTU identification, and validate its performance using stochastic blockmodeling. The algorithm reveals a total of 276 PTUs in the bacterial domain. Each PTU exhibits a characteristic host distribution, organized into a six-grade scale (I–VI), ranging from plasmids restricted to a single host species (grade I) to plasmids able to colonize species from different phyla (grade VI). More than 60% of the plasmids in the global map are in groups with host ranges beyond the species barrier.

Objective: Compare the numbers of CD14+/CD105+, plasma levels of TGF‐beta1, apoptosis and induced CD105 expression in atherosclerotic patients (bypass surgery) and control ones (valvular patients). Methods: Blood was taken from our patients and CD34+/CD144+, CD34+/KDR+ and CD14+/CD105+ cells were assessed by flow cytometry (R=0.8908). Plasma was added to peripheral blood mononuclear cells. CD105 expression was assessed by Western blot (day 4). Apoptosis was measured as DNA fragmentation (day 7). Results: By‐pass patients had a higher number of CD14+/CD105+ (5.357 vs 2.829% lymphocytes, p=0.04; 87.13 vs 49.77 cells/mcL, p=0.0339) and a higher level of plasmatic TGF‐beta1 (72.01 vs 48.33, p=0.0033). When plasma from by‐pass and valvular was added to cell (day 7), valvular plasma triggered apoptosis (0.9998 vs 1.599, p=0.0078), an effect mimicked when plasma from by‐pass was coincubated with the TGF‐beta1 blockers SIS3 (0.9998 vs 1.624, p=0.0034) and SB‐431542 (0.9998 vs 1.802, p=0.0108). In Western blot, a trend was found towards higher CD105 expression with plasma from bypass (0.94 vs. 0.57, p=0.18). Conclusion: Plasma from by‐pass patients deregulates the effect of TGF‐beta1, which correlates to increased plasmatic TGF‐beta1 levels and CD14+/CD105+ cells and a trend towards higher in vitro expression of CD105. Disclosure: Funded by FISS PI041018 (Spanish Ministry of Health).