Biology subjects

Pfeifer, E.

Publications and source records attributed to Pfeifer, E..

6 recordsLinked to original sources

bioRxiv2025

Efficient detection and typing of phage-plasmids

Phage-plasmids are temperate phages that replicate as plasmids during lysogeny. Despite their high diversity, they carry genes similar to phages and plasmids. This leads to gene exchanges, and to the formation of hybrid or defective elements, which limits accurate detection of phage-plasmids. To address this challenge, we present tyPPing, an easy-to-use method that efficiently detects and types phage-plasmids with high accuracy. It searches for distinct frequencies and sets of conserved proteins to separate phage-plasmids from plasmids and phages. tyPPings strength comes from both its precise predictions and its ability to systematically type phage-plasmids, including the assignment of confidence levels. We tested tyPPing on current databases and a collection of incomplete (draft) genomes. While predictions rely on the quality of assemblies, we detected high-quality phage-plasmids and experimentally proved them to be functional. Compared to other classification methods, tyPPing is designed to detect distinct types of phage-plasmids, and surpasses other tools in terms of sensitivity and scalability. Phage-plasmids are highly diverse, making the systematic identification of new types a difficult task. By combining tyPPing with other tools, however, we show a valuable foundation for addressing this challenge.

genomics↗

bioRxiv2023

Phage-plasmids promote genetic exchanges between phages and plasmids and create novel ones.

Phages and plasmids have key roles in bacterial evolution and are usually very different. Yet, they must recombine, since they sometimes carry nearly identical accessory genes. Phage-plasmids are both plasmids and phages and we found they connect them by being at their interface in the network of gene repertoire relatedness. We searched for recombining genes in all three types of elements and found that phage-plasmid exchange rates are between those of plasmids (highest) and phages (lowest). Phage-plasmids drive gene flow between phages and plasmids, including that of antibiotic resistances and defense systems. Genetic exchanges and gene inactivation resulted in P1-like phage-plasmids turning into integrative prophages or just plasmids. The latter acquired conjugation-related functions thereby transitioning from viral to conjugation-driven horizontal transfer. Phage-plasmids have thus a key role in spreading traits across mobile genetic elements and their hosts, while facilitating conversions of one type of element into another.

genomics↗

bioRxiv2022

Phage-plasmids spread antibiotic resistance genes through infection and lysogenic conversion

Antibiotic resistance is rapidly spreading by horizontal transfer of resistance genes in mobile genetic elements. While plasmids are key drivers of this process, very few integrative phages encode antibiotic resistance genes. Here, we find that phage-plasmids, elements that are both phages and plasmids, often carry antibiotic resistance genes. We found 60 phage-plasmids with 184 antibiotic resistance genes, including broad-spectrum-cephalosporins, carbapenems, aminoglycosides, fluoroquinolones and colistin. These genes are in a few hotspots, seem to have been co-translocated with transposable elements, and are often in class I integrons, which had not been previously found in phages. We tried to induce six phage-plasmids with resistance genes (including four with resistance integrons) and succeeded in five cases. Other phage-plasmids and integrative prophages were co-induced in these experiments. As a proof of principle, we focused on a P1-like element encoding an extended spectrum {beta}-lactamase, blaCTX-M-55. After induction, we confirmed that its capable to infect and convert four other E. coli strains. Its re-induction led to further conversion of a sensitive strain, confirming its a fully functional phage. This study shows that phage-plasmids carry a large diversity of clinically relevant antibiotic resistance genes that they transfer across bacteria. As plasmids, these elements seem very plastic and capable of acquiring genes from other plasmids. As phages, they may provide novel paths of transfer for resistance genes, because they can infect bacteria distant in time and space from the original host. As a matter of alarm, they may also eventually mediate transfer to other types of phages. ImportanceDissemination of antimicrobial resistances is a major threat to global health. Here, we show that a group of temperate bacterial viruses (=phages), termed phage-plasmids, commonly encode different and multiple types of resistance genes of high clinical importance, often in integrons. This is unexpected since phages typically do not carry resistance genes and, hence, do not confer their hosts with resistance upon infection and genome integration. Our experiments with phage-plasmids isolated from clinical settings confirmed they infect sensitive strains, rendering them antibiotic resistant. The spread of antibiotic resistance genes by phage-plasmids is worrisome because it dispenses cell-to-cell contact, necessary for the canonical plasmid transfer (=conjugation). Furthermore, their integrons are now genetic platforms for the acquisition of novel resistance genes.

microbiology↗

bioRxiv2020

Bacteria have numerous phage-plasmid families with conserved phage and variable plasmid gene repertoires.

Plasmids and temperate phages are mobile genetic elements driving bacterial evolution. They are usually regarded as very distinct. However, some elements, termed phage-plasmids, are known to be both plasmids and phages, e.g. P1, N15 or SSU5. The number, distribution, relatedness and characteristics of these phage-plasmids are poorly known. Here, we screened for these elements among ca. 14000 phages and plasmids and identified 780 phage-plasmids across very diverse bacterial phyla. We grouped 92% of them by similarity of gene repertoires to define 8 families and 18 other broader communities of elements. The existence of these large groups suggests that phage-plasmids are ancient. Their gene repertoires are large, the average element is larger than an average phage or plasmid, and they include slightly more homologs to phages than to plasmids. We analyzed the pangenomes and the genetic organization of each group of phage-plasmids and found the key phage genes to be conserved and co-localized within families, whereas genes with homologs in plasmids are much more variable and include most accessory genes. Phage-plasmids are a sizeable fraction of all phages and plasmids and could have key roles in bridging the genetic divide between phages and other mobile genetic elements.

genomics↗

bioRxiv2020

Cancer-associated hypersialylated MUC1 drives the differentiation of monocytes into macrophages with a pathogenic phenotype

The tumour microenvironment plays a crucial role in the growth and progression of cancer and the presence of tumour-associated macrophages (TAMs) is associated with poor prognosis. Recent studies show that TAMs show transcriptomic, phenotypic, functional and geographical diversity. Here we show that a sialylated tumour-associated glycoform of the mucin MUC1, MUC1-ST, through the engagement of Siglec-9 can specifically and independently induce the differentiation of monocytes into TAMs with a unique phenotype. These TAMs can recruit and maintain neutrophils, inhibit the function of T cells, degrade basement membrane allowing for invasion, are inefficient at phagocytosis, and can induce plasma clotting. This novel macrophage phenotype is enriched in the stroma at the edge of breast cancer nests and their presence is associated with poor prognosis in breast cancer patients.

cancer biology↗

bioRxiv2020

Genome diversification via genetic exchanges between temperate and virulent bacteriophages

Bacteriophages (phages) evolve rapidly by acquiring genes from other phages leading to mosaic genomes. Here, we identify numerous genetic transfers between distantly related phages and aim at understanding their frequency, consequences and the conditions favoring them. Gene flow tends to occur between phages that are enriched for recombinases, transposases and non-homologous end joining, suggesting that both homologous and illegitimate recombination contribute to gene flow. Phage family and host phyla are strong barriers to gene exchange, but phage lifestyle is not. We observe more exchanges between temperate phages even if they tend to have smaller genomes. These acquisitions often include transcription regulators and lysins. Yet, there is also extensive gene flow between temperate and virulent phages, or between the latter. These predominantly involve virulent phages with large genomes previously classed as low gene flux, and lead to the preferential transfer of genes encoding functions involved in cell energetics, nucleotide metabolism, DNA packaging and injection, and virion assembly. Such exchanges may explain the acquisition of genes in virulent phages, which tend to have the largest genomes. We used genetic transfers, which occur upon co-infection of a host, to compare phage host range. We found that virulent phages have broader host ranges and mediate genetic exchanges between narrow host range temperate phages infecting distant bacterial hosts, thus contributing to gene flow between virulent phages, as well as between temperate phages. This gene flow drastically expands the gene repertoires available for phage and bacterial evolution, including the transfer of functional innovations across taxa.

microbiology↗