Talía Berruga-Fernández defends thesis on how bacteria build hybrid chromosomes

Talía Berruga-Fernández successfully defended her PhD thesis, "Chromosomal Hybrids. A source of globally-spread antibiotic-resistant pathogens," at Uppsala University on 4 September 2026. Talías is the eighth member of the second cohort of UAC’s research school to defend.

Bacteria can swap more than a gene or acquire a mutation

Bacteria acquire resistance in two well-known ways: mutations in their own genome, and horizontal genetic transfer of mobile elements, picking up already-available resistance genes carried on elements such as plasmids.

Nevertheless, some of the most successful drug-resistant pathogens do not fit that picture completely. Klebsiella pneumoniae ST258 and Escherichia coli ST1193 are multidrug-resistant pathogens that are highly virulent and have spread worldwide. Both are shown to carry more than a megabase of chromosomal DNA, which amounts to around 20 percent of their genome, that came from a foreign strain. These are hybrids: strains whose chromosome is a mosaic of two parents. How such strains can form in nature was until now unknown, and Talía's thesis set out to answer that question.

From method to mechanism in four projects

Clinical E. coli readily generate hybrids driven by conjugative elements. Talía designed a selection method that recovers hybrids from populations of more than 10 billion cells. Screening 118 clinical E. coli isolates from urinary tract infections as DNA donors, she obtained hybrids from 39% of them. Whole-genome sequencing showed transferred segments of different lengths, some of them covering almost the whole chromosome. More than half recombined the donor DNA into multiple separate segments, closely resembling the architecture of E. coli ST1193. In 56% of hybrids the transferred DNA carried resistance or virulence genes, and 90% also picked up a conjugative mobile element from the donor. Every individual plasmid and integrative and conjugative element (ICE) she isolated was sufficient on its own to mobilize the chromosome. Her results show that transfer proceeded progressively around the chromosome from the element's insertion site, rather than by excision of adjacent DNA.

Hybrids can form across species, and they are stable. Talía tested whether clinical K. pneumoniae bacteria could donate chromosomal DNA to E. coli. Several were able to, and sequencing of the hybrids revealed two main routes: integration of donor DNA into the recipient chromosome, and transfer of an F'-like plasmid carrying donor chromosomal genes. Acquired DNA had a diverse range of lenghts, and several hybrids gained resistance- or virulence-associated genes, including a type VI secretion system, siderophores and fimbrial genes. After 30 generations without selection, every chromosomal hybrid retained its new capability, while most F'-like carriers lost it. Relative fitness ranged from 0.73 to 1.03, showing that interspecies chromosomal hybrids could persist in competition with other bacteria around.

The barrier to hybrid formation is conjugation, not recombination of the transferred segment. Talias third project showed that hybrid frequencies depend heavily on which strain receives the DNA. Using the clinical reference strain ATCC25922 instead of the standard laboratory recipient reduced hybrid formation 10 to 1000 times. Selecting for plasmid transfer alone showed the same reduction, placing the barrier at conjugation itself. Inserting a transposon in a small gene of unknown function on a plasmid could recover 500 times more transconjugants and up to 1000 times more hybrids than the strain carrying an untouched plasmid, pointing to a yet unknown important role for this gene in conjugation and hybrid formation.

Without transfer, some lost functions could never be recovered. E. coli can synthesise every compound it needs to grow, using roughly 60 genes for amino acid synthesis, an essential component for bacterial life. Talía asked whether cells could recover from irreversible loss of one of those genes without outside DNA. Across 59 knockout mutants for these aminoacid genes, spontaneous suppressors emerged for only ten, through different mechanisms. Genome-internal rescue is available to a minority of these pathways. This points out to the importance of maintaining the full metabolic repertoire through horizontal transfer.

Why this work matters for AMR

Talía's work reframes how quickly a susceptible bacterium can become an untreatable one. Full fluoroquinolone resistance requires several specific mutations. Waiting for a cell to acquire all of them independently and in a sequence is, in evolutionary terms, waiting forever. But in her experiments, hybrids picked up two of those mutations, which are sitting far apart on the chromosome, in a single transfer event, alongsde hundreds of other genes.

The conditions that might make conugation events likely are the ones where there can be a strong selection, and plenty of donor DNA close at hand.

If hybrids can only be identified when both parent genomes are available for comparison, then many strains already sitting in sequence databases may be hybrids that nobody has yet recognized. As Talía concludes, the exchange of chromosomal DNA between bacteria is less of an anomaly and more a basic characteristic of how they live and evolve, with implications still yet to be uncovered.

We warmly congratulate Talía on a thesis that changes how we should read the genomes of resistant pathogens, and we look forward to following her next steps.