Restricted accessResearch articleFirst published online 2024-06
Tradeoffs Between Evolved Phage Resistance and Antibiotic Susceptibility in a Highly Drug-Resistant Cystic Fibrosis-Derived Pseudomonas aeruginosa Strain
Multi-drug resistant pathogens pose significant challenges towards the effective resolution of bacterial infections. A promising alternative strategy is phage therapy in which limited applications has afforded lifesaving resolution from drug resistant pathogens. However, adoption of this strategy is hampered by narrow bacteriophage host ranges, and as with antibiotics, bacteria can acquire resistance to phage.
Methods:
To address these issues, we isolated 25 broad-host range phages against multiple cystic fibrosis (CF)-derived P. aeruginosa clinical strains thus promoting their application against conspecific pathogens. To investigate evolved resistance to phage in relation to antibiotic resistance, one CF-derived P. aeruginosa strain was exposed to a lytic phage over a short time scale.
Results:
Trade-offs were observed in which evolved phage resistant P. aeruginosa strains showed decreased resistance to antibiotics. These traits that likely reflect single nucleotide polymorphisms.
Conclusion:
Results suggest phage and antibiotics may be a combined approach to treat bacterial infections.
MagiorakosAP, SrinivasanA, CareyRB, et al.Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: An international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect, 2012; 18(3):268–281; doi: 10.1111/j.1469-0691.2011.03570.x
5.
SchooleyRT, BiswasB, GillJJ, et al.Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection. Antimicrob Agents Chemother, 2017; 61(10); doi: 10.1128/AAC.00954-17
6.
DedrickRM, Guerrero-BustamanteCA, GarlenaRA, et al.Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus. Nat Med, 2019; 25(5):730–733; doi: 10.1038/s41591-019-0437-z
7.
StrathdeeSA, HatfullGF, MutalikVK, et al.Phage therapy: From biological mechanisms to future directions. Cell, 2023; 186(1):17–31; doi: 10.1016/j.cell.2022.11.017
8.
ChanBK, SistromM, WertzJE, et al.Phage selection restores antibiotic sensitivity in MDR Pseudomonas aeruginosa. Sci Rep, 2016; 6(26717; doi: 10.1038/srep26717
9.
BurmeisterAR, TurnerPE. Trading-off and trading-up in the world of bacteria-phage evolution. Curr Biol, 2020; 30(19):R1120–R1124; doi: 10.1016/j.cub.2020.07.036
10.
GurneyJ, PradierL, GriffinJS, et al.Phage steering of antibiotic-resistance evolution in the bacterial pathogen, Pseudomonas aeruginosa. Evol Med Public Health, 2020; 2020(1):148–157; doi: 10.1093/emph/eoaa026
11.
PangZ, RaudonisR, GlickBR, et al.Antibiotic resistance in Pseudomonas aeruginosa: Mechanisms and alternative therapeutic strategies. Biotechnol Adv, 2019; 37(1):177–192; doi: 10.1016/j.biotechadv.2018.11.013
12.
MillerJH.Experiments in Molecular Genetics. Cold Spring Harbor Laboratory: Cold Spring Harbor, New York, USA; 1972.
WiegandI, HilpertK, HancockRE. Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances. Nat Protoc, 2008; 3(2):163–175; doi: 10.1038/nprot.2007.521
15.
Institute CaLS. Performance Standards for Antimicrobial Susceptibility Testing; Nineteenth Informational Supplement. Clinical and Laboratory Standards Institute: Wayne, PA, USA; 2009.
16.
Barreto-VieraDF, BarthOM. Negative and positive staining in transmission electron microscopy for virus diagnosis. In: Microbiology in Agriculture and Human Health. InTech: Croatia; 2015; pp. 45–56.
17.
GurevichA, SavelievV, VyahhiN, et al.QUAST: Quality assessment tool for genome assemblies. Bioinformatics, 2013; 29(8):1072–1075; doi: 10.1093/bioinformatics/btt086
18.
KolmogorovM, YuanJ, LinY, et al.Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol, 2019; 37(5):540–546; doi: 10.1038/s41587-019-0072-8
19.
SchwengersO, JelonekL, DieckmannMA, et al.Bakta: Rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom, 2021; 7(11); doi: 10.1099/mgen.0.000685
20.
DarlingAC, MauB, BlattnerFR, et al.Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res, 2004; 14(7):1394–1403; doi: 10.1101/gr.2289704
21.
MarcaisG, DelcherAL, PhillippyAM, et al.MUMmer4: A fast and versatile genome alignment system. PLoS Comput Biol, 2018; 14(1):e1005944; doi: 10.1371/journal.pcbi.1005944
22.
BasallaJ, ChatterjeeP, BurgessE, et al.Loci encoding compounds potentially active against drug-resistant pathogens amidst a decreasing pool of novel antibiotics. Appl Environ Microbiol, 2019; 85(23):1–17; doi: 10.1128/AEM.01438-19
23.
McNairK, ZhouC, DinsdaleEA, et al.PHANOTATE: A novel approach to gene identification in phage genomes. Bioinformatics, 2019; 35(22):4537–4542; doi: 10.1093/bioinformatics/btz265
24.
TiszaMJ, BelfordAK, Domínguez-HuertaG, et al.Cenote-Taker 2 democratizes virus discovery and sequence annotation. Virus Evol, 2021; 7(1):veaa100; doi: 10.1093/ve/veaa100
25.
LopesA, TavaresP, PetitMA, et al.Automated classification of tailed bacteriophages according to their neck organization. BMC Genom, 2014; 15(1):1027; doi: 10.1186/1471-2164-15-1027
26.
WuJ, LiuQ, LiM, et al.PhaGAA: An integrated web server platform for phage genome annotation and analysis. Bioinformatics, 2023; 39(3); doi: 10.1093/bioinformatics/btad120
27.
TerzianP, Olo NdelaE, GaliezC, et al.PHROG: Families of prokaryotic virus proteins clustered using remote homology. NAR Genom Bioinform, 2021; 3(3):lqab067; doi: 10.1093/nargab/lqab067
28.
KelleyLA, MezulisS, YatesCM, et al.The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc, 2015; 10(6):845–858; doi: 10.1038/nprot.2015.053
29.
ZimmermannL, StephensA, NamSZ, et al.A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J Mol Biol, 2018; 430(15):2237–2243; doi: 10.1016/j.jmb.2017.12.007
30.
NishimuraY, YoshidaT, KuronishiM, et al.ViPTree: The viral proteomic tree server. Bioinformatics, 2017; 33(15):2379–2380; doi: 10.1093/bioinformatics/btx157
31.
MoraruC, VarsaniA, KropinskiAM. VIRIDIC- a novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. Viruses, 2020; 12(11); doi: 10.3390/v12111268
32.
HuloC, de CastroE, MassonP, et al.ViralZone: A knowledge resource to understand virus diversity. Nucleic Acids Res, 2011; 39(Database issue):D576–D582; doi: 10.1093/nar/gkq901
33.
MillerES, HeidelbergJF, EisenJA, et al.Complete genome sequence of the broad-host-range vibriophage KVP40: Comparative genomics of a T4-related bacteriophage. J Bacteriol, 2003; 185(17):5220–5233; doi: 10.1128/jb.185.17.5220-5233.2003
34.
NakayamaK, KanayaS, OhnishiM, et al.The complete nucleotide sequence of phi CTX, a cytotoxin-converting phage of Pseudomonas aeruginosa: Implications for phage evolution and horizontal gene transfer via bacteriophages. Mol Microbiol, 1999; 31(2):399–419; doi: 10.1046/j.1365-2958.1999.01158.x
35.
CeyssensPJ, MiroshnikovK, MattheusW, et al.Comparative analysis of the widespread and conserved PB1-like viruses infecting Pseudomonas aeruginosa. Environ Microbiol, 2009; 11(11):2874–2883; doi: 10.1111/j.1462-2920.2009.02030.x
36.
KornienkoM, KuptsovN, GorodnichevR, et al.Contribution of Podoviridae and Myoviridae bacteriophages to the effectiveness of anti-staphylococcal therapeutic cocktails. Sci Rep, 2020; 10(1):18612; doi: 10.1038/s41598-020-75637-x
37.
GuoY, ChenP, LinZ, et al.Characterization of two Pseudomonas aeruginosa viruses vB_PaeM_SCUT-S1 and vB_PaeM_SCUT-S2. Viruses, 2019; 11(4); doi: 10.3390/v11040318
38.
TurnerD, KropinskiAM, AdriaenssensEM. A roadmap for genome-based phage taxonomy. Viruses, 2021; 13(3); doi: 10.3390/v13030506
39.
KimJ, LinnS. The mechanisms of action of E. coli endonuclease III and T4 UV endonuclease (endonuclease V) at AP sites. Nucleic Acids Res, 1988; 16(3):1135–1141; doi: 10.1093/nar/16.3.1135
40.
KurnasovO, JablonskiL, PolanuyerB, et al.Aerobic tryptophan degradation pathway in bacteria: Novel kynurenine formamidase. FEMS Microbiol Lett, 2003; 227(2):219–227; doi: 10.1016/s0378-1097(03)00684-0
41.
PenningtonJM, KempM, McGarryL, et al.Siroheme synthase orients substrates for dehydrogenase and chelatase activities in a common active site. Nat Commun, 2020; 11(1):864; doi: 10.1038/s41467-020-14722-1
42.
van StaalduinenLM, NovakowskiSK, JiaZ. Structure and functional analysis of YcfD, a novel 2-oxoglutarate/Fe2+-dependent oxygenase involved in translational regulation in Escherichia coli. J Mol Biol, 2014; 426(9):1898–1910; doi: 10.1016/j.jmb.2014.02.008
43.
CabezónT, HerzogA, PetreJ, et al.Ribosomal assembly deficiency in an Escherichia coli thermosensitive mutant having an altered L24 ribosomal protein. J Mol Biol, 1977; 116(3):361–374; doi: 10.1016/0022-2836(77)90075-4
44.
TavaresIM, JollyL, PompeoF, et al.Identification of the Pseudomonas aeruginosa glmM gene, encoding phosphoglucosamine mutase. J Bacteriol, 2000; 182(16):4453–4457; doi: 10.1128/jb.182.16.4453-4457.2000
45.
KandiahE, CarrielD, PerardJ, et al.Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA. Sci Rep, 2016; 6(24601; doi: 10.1038/srep24601
46.
KawaiF, ShodaM, HarashimaR, et al.Cardiolipin domains in Bacillus subtilis marburg membranes. J Bacteriol, 2004; 186(5):1475–1483; doi: 10.1128/jb.186.5.1475-1483.2004
47.
DouglassMV, CléonF, TrentMS. Cardiolipin aids in lipopolysaccharide transport to the gram-negative outer membrane. Proc Natl Acad Sci, 2021; 118(15):e2018329118; doi: 10.1073/pnas.2018329118
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