Variable effects on virulence of bacteriophage resistance mechanisms in extraintestinal pathogenicEscherichia coli

Abstract

Bacteria exposed to killing agents such as antibiotics or viruses develop resistance. While phage therapy, the use of bacteriophages (phages) for treating bacterial infections, is proposed to answer the antibiotic resistance crisis, bacterial resistance to phages remains poorly characterized during phage treatment. We studied a large population of phage-resistant extra-intestinal pathogenic Escherichia coli 536 clones emerging from both in vitro (non-limited liquid medium) and in vivo (murine pneumonia) conditions. Genome sequencing revealed a mutational convergence of phage resistance mechanisms towards the modification of two cell-wall components, the K15 capsule and the LPS, whatever the condition, showing that their identification could be predicted from the in vitro conditions. The fitness cost of all phage resistant clones was broad in terms of growth rate and resistance to grazing by amoeba and could not discriminate K15 capsule to LPS mutants. By contrast, the virulence of the clones tested in mice showed that K15 capsule mutants were as virulent as the wildtype strain while LPS mutants were strongly attenuated. We also found that resistance to one phage led to the sensitization to other phages. In clinics, to control phage-resistant clones that remains virulent phage cocktail should include phages infecting both phage susceptible and future phage resistant clones.

“This training is bound for glory” : selection by experimental evolution of a bacteriophage with expanded host-range and increased virulence

“…In fact, genes coding for structural part represent a large part of phage genome (about 30%), which offers the possibility to mutations to accumulate at many loci. Previous results have shown that adaptive mutations impacted the host-interaction subunits proteins, such as capsides or spikes proteins for microvirid bacteriophages (Sackman et al, 2017), ΦX174 (Bull et al, 1997; CrillX174 (Bull et al, 1997; Crill et al, 2000; Pepin et al, 2008) and receptor binding proteins in the RNA virus ΦX174 (Bull et al, 1997; Crill6 (Duffy et al, 2006; Ferris et al, 2007) as well as almost hundred Caudoviricetes (Gaborieau et al, 2023). Interestingly, we didn’t observe any adaptive mutation in the gene coding for pb5 the major receptor binding proteins (RBP), that commits the phage to infection, triggering cell wall perforation and DNA ejection through a non-reversible interaction with FhuA, an outer-membrane ferrichrome transporter (Linares et al, 2023).…”