Spontaneous Phage Resistance in Avian Pathogenic Escherichia coli

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.

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Bacteriophage resistance alters antibiotic mediated intestinal expansion of enterococci

10.1101/531442 ◽

2019 ◽

Author(s):

Anushila Chatterjee ◽

Cydney N. Johnson ◽

Phat Luong ◽

Karthik Hullahalli ◽

Sara W. McBride ◽

...

Keyword(s):

Molecular Mechanisms ◽

Phage Therapy ◽

Selective Pressure ◽

Acquired Resistance ◽

Productive Infection ◽

Phage Resistance ◽

Intestinal Colonization ◽

Intestinal Dysbiosis ◽

Loss Of Resistance ◽

Mutant Strains

AbstractEnterococcus faecalisis a human intestinal pathobiont with intrinsic and acquired resistance to many antibiotics, including vancomycin. Nature provides a diverse and virtually untapped repertoire of bacterial viruses, or bacteriophages (phages), that could be harnessed to combat multi-drug resistant enterococcal infections. Bacterial phage resistance represents a potential barrier to the implementation of phage therapy, emphasizing the importance of investigating the molecular mechanisms underlying the emergence of phage resistance. Using a cohort of 19 environmental lytic phages with tropism againstE. faecalis, we found that these phages require the enterococcal polysaccharide antigen (Epa) for productive infection. Epa is a surface-exposed heteroglycan synthesized by enzymes encoded by both conserved and strain specific genes. We discovered that exposure to phage selective pressure favors mutation in non-conservedepagenes both in culture and in a mouse model of intestinal colonization. Despite gaining phage resistance,epamutant strains exhibited a loss of resistance to the cell wall targeting antibiotics, vancomycin and daptomycin. Finally, we show that anE. faecalis epamutant strain is deficient in intestinal colonization, cannot expand its population upon antibiotic-driven intestinal dysbiosis and fails to be efficiently transmitted to juvenile mice following birth. This study demonstrates that phage therapy could be used in combination with antibiotics to target enterococci within a dysbiotic microbiota. Enterococci that evade phage therapy by developing resistance may be less fit at colonizing the intestine and sensitized to vancomycin preventing their overgrowth during antibiotic treatment.

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Single-Nucleotide Polymorphisms in the Whole-Genome Sequence Data of Shiga Toxin-Producing Escherichia coli O157:H7/H- Strains by Cultivation

Current Microbiology ◽

10.1007/s00284-017-1208-z ◽

2017 ◽

Vol 74 (4) ◽

pp. 425-430 ◽

Cited By ~ 3

Author(s):

Eiji Yokoyama ◽

Shinichiro Hirai ◽

Taichiro Ishige ◽

Satoshi Murakami

Keyword(s):

Escherichia Coli ◽

Single Nucleotide Polymorphisms ◽

Genome Sequence ◽

Shiga Toxin ◽

Sequence Data ◽

Whole Genome Sequence ◽

Whole Genome ◽

Escherichia Coli O157 ◽

Nucleotide Polymorphisms ◽

Single Nucleotide

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Bacteriophage Resistance Alters Antibiotic-Mediated Intestinal Expansion of Enterococci

Infection and Immunity ◽

10.1128/iai.00085-19 ◽

2019 ◽

Vol 87 (6) ◽

Cited By ~ 25

Author(s):

Anushila Chatterjee ◽

Cydney N. Johnson ◽

Phat Luong ◽

Karthik Hullahalli ◽

Sara W. McBride ◽

...

Keyword(s):

Molecular Mechanisms ◽

Phage Therapy ◽

Acquired Resistance ◽

Multidrug Resistant ◽

Productive Infection ◽

Phage Resistance ◽

Intestinal Colonization ◽

Content Type ◽

Intestinal Dysbiosis ◽

Loss Of Resistance

ABSTRACTEnterococcus faecalisis a human intestinal pathobiont with intrinsic and acquired resistance to many antibiotics, including vancomycin. Nature provides a diverse and virtually untapped repertoire of bacterial viruses, or bacteriophages (phages), that could be harnessed to combat multidrug-resistant enterococcal infections. Bacterial phage resistance represents a potential barrier to the implementation of phage therapy, emphasizing the importance of investigating the molecular mechanisms underlying the emergence of phage resistance. Using a cohort of 19 environmental lytic phages with tropism againstE. faecalis, we found that these phages require the enterococcal polysaccharide antigen (Epa) for productive infection. Epa is a surface-exposed heteroglycan synthesized by enzymes encoded by both conserved and strain-specific genes. We discovered that exposure to phage selective pressure favors mutation in nonconservedepagenes both in culture and in a mouse model of intestinal colonization. Despite gaining phage resistance,epamutant strains exhibited a loss of resistance to cell wall-targeting antibiotics. Finally, we show that anE. faecalisepamutant strain is deficient in intestinal colonization, cannot expand its population upon antibiotic-driven intestinal dysbiosis, and fails to be efficiently transmitted to juvenile mice following birth. This study demonstrates that phage therapy could be used in combination with antibiotics to target enterococci within a dysbiotic microbiota. Enterococci that evade phage therapy by developing resistance may be less fit at colonizing the intestine and sensitized to vancomycin, preventing their overgrowth during antibiotic treatment.

Download Full-text