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Avian pathogenic Escherichia coli (APEC) is one of the most important bacterial pathogens affecting poultry worldwide. The emergence of multidrug-resistant pathogens has renewed the interest in the therapeutic use of bacteriophages (phages). However, a major concern for the successful implementation of phage therapy is the emergence of phage-resistant mutants. The understanding of the phage-host interactions, as well as underlying mechanisms of resistance, have shown to be essential for the development of a successful phage therapy. Here, we demonstrate that the strictly lytic Escherichia phage vB_EcoM-P10 rapidly selected for resistance in the APEC ST95 O1 strain AM621. Whole-genome sequence analysis of 109 spontaneous phage-resistant mutant strains revealed 41 mutants with single-nucleotide polymorphisms (SNPs) in their core genome. In 32 of these, a single SNP was detected while two SNPs were identified in a total of nine strains. In total, 34 unique SNPs were detected. In 42 strains, including 18 strains with SNP(s), gene losses spanning 17 different genes were detected. Affected by genetic changes were genes known to be involved in phage resistance (outer membrane protein A, lipopolysaccharide-, O- antigen-, or cell wall-related genes) as well as genes not previously linked to phage resistance, including two hypothetical genes. In several strains, we did not detect any genetic changes. Infecting phages were not able to overcome the phage resistance in host strains. However, interestingly the initial infection was shown to have a great fitness cost for several mutant strains, with up to ∼65% decrease in overall growth. In conclusion, this study provides valuable insights into the phage-host interaction and phage resistance in APEC. Although acquired resistance to phages is frequently observed in pathogenic E. coli, it may be associated with loss of fitness, which could be exploited in phage therapy.

The therapeutic use of bacteriophages (phage therapy) represents a promising alternative to antibiotics to control bacterial pathogens. However, the understanding of the phage–bacterium interactions and population dynamics seems essential for successful phage therapy implementation. Here, we investigated the effect of three factors: phage species (18 lytic E. coli-infecting phages); bacterial strain (10 APEC strains); and multiplicity of infection (MOI) (MOI 10, 1, and 0.1) on the bacterial growth dynamics. All factors had a significant effect, but the phage appeared to be the most important. The results showed seven distinct growth patterns. The first pattern corresponded to the normal bacterial growth pattern in the absence of a phage. The second pattern was complete bacterial killing. The remaining patterns were in-between, characterised by delayed growth and/or variable killing of the bacterial cells. In conclusion, this study demonstrates that the phage–host dynamics is an important factor in the capacity of a phage to eliminate bacteria. The classified patterns show that this is an essential factor to consider when developing a phage therapy. This methodology can be used to rapidly screen for novel phage candidates for phage therapy. Accordingly, the most promising candidates were phages found in Group 2, characterised by growth dynamics with high bacterial killing.

Antimicrobial resistance has been described in all ecosystems, including wildlife. Here we investigated the presence of methicillin-resistant and susceptible staphylococci in both colony-born and wild vervet monkeys (Chlorocebus sabaeus). Through selective isolation, PCR, MALDI-TOF, and whole-genome sequencing, methicillin-resistant and susceptible Staphylococcus spp. isolated from vervet monkeys were characterized. We obtained putatively methicillin-resistant staphylococci from 29 of the 34 nasal samples collected. Strains were identified by MALDI-TOF analysis. Staphylococcus cohnii (n = 15) was the most commonly isolated species, while nine other species were isolated one or two times. PCR analysis indicated that eight [28%] strains were mecA positive. The whole-genome sequencing [WGS] included eight methicillin-resistant strains (S. epidermidis (n = 2), S. cohnii (n = 3), S. arlettae (n = 2) and S. hominis (n = 1)), nine additional S. cohnii strains and two strains that could not be identified by MALDI-TOF, but genetically characterized as one S. cohnii and one S. warneri. Different resistance genes carried by different mobile genetic elements, mainly blaZ (n = 10) and tet(K) (n = 5) were found, while msr(A), cat, fosB, dfrG, erm(C), mph(C) and str were identified in one to three strains. Phylogenetic analysis of the S. cohnii strains based on SNPs indicated four clusters associated with colony born or wild. In addition, one singleton S. cohnii isolated did not form a separate group and clustered within other S. cohnii strains submitted to the NCBI. In this study, we demonstrated the presence of AMR and mobile genetic elements to both colony-born and wild vervet monkeys. We also identified a previously undescribed prevalence of S. cohnii in the nasal flora of these monkeys, which merits further investigation.