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Peer-reviewedCC BYMemorias do Instituto Oswaldo Cruz

In silico characterisation of lysis and host-recognition modules in Staphylococcus aureus bacteriophage genomes

  • Ivan Armadi Hasugian1
  • Na’ilah Insani Alifiyah1
  1. 1Universitas Terbuka, Faculty of Science and Technology, Department of Biology, Tangerang Selatan, Indonesia
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Abstract

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is a leading human pathogen, and declining antibiotic efficacy has renewed interest in lytic bacteriophages, whose efficacy phenotypic assays predict poorly.

OBJECTIVES: To characterise the lysis and host-recognition modules of lytic S. aureus bacteriophages, and to determine how far the detectability of each module depends on the annotation source rather than on the genomes.

METHODS: Twenty-two S. aureus phage genomes from NCBI GenBank were processed through an identical detection funnel under three annotation sources: the deposited record, Pharokka and Phold. Modules were validated by InterPro, disrupted endolysins resolved by tBLASTn, and each domain aligned separately to measure identity.

FINDINGS: The LysK-type endolysin (CHAP-Amidase-SH3b) was conserved and detected identically under all three sources. Tail fibre/receptor-binding protein (RBP) detection was strongly source-dependent: 14 of 22 genomes from the deposited annotation, 20 of 22 after re-annotation, and 22 of 22 combined. Resolved by domain, conservation was scale-dependent: the amidase domain was invariant within species while SH3b varied by 5.7%.

MAIN CONCLUSIONS: Lysis-module conservation is independent of the annotation source; the apparent variability of host recognition is largely an artefact of incomplete deposited annotation. Module-level surveys require re-annotation before comparative claims.

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Cite

BibTeXRIS
BibTeX
@article{hasugian2026silico,
  title = {{In silico characterisation of lysis and host-recognition modules in Staphylococcus aureus bacteriophage genomes}},
  author = {Ivan Armadi Hasugian and Na’ilah Insani Alifiyah},
  journal = {Memorias do Instituto Oswaldo Cruz},
  year = {2026},
  month = nov,
  doi = {10.1590/0074-02760260245},
  url = {https://europepmc.org/article/PMC/PMC13729910},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - In silico characterisation of lysis and host-recognition modules in Staphylococcus aureus bacteriophage genomes
AU  - Ivan Armadi Hasugian
AU  - Na’ilah Insani Alifiyah
PY  - 2026
DA  - 2026/11/02
JO  - Memorias do Instituto Oswaldo Cruz
DO  - 10.1590/0074-02760260245
UR  - https://europepmc.org/article/PMC/PMC13729910
AB  - BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is a leading human pathogen, and declining antibiotic efficacy has renewed interest in lytic bacteriophages, whose efficacy phenotypic assays predict poorly.  OBJECTIVES: To characterise the lysis and host-recognition modules of lytic S. aureus bacteriophages, and to determine how far the detectability of each module depends on the annotation source rather than on the genomes.  METHODS: Twenty-two S. aureus phage genomes from NCBI GenBank were processed through an identical detection funnel under three annotation sources: the deposited record, Pharokka and Phold. Modules were validated by InterPro, disrupted endolysins resolved by tBLASTn, and each domain aligned separately to measure identity.  FINDINGS: The LysK-type endolysin (CHAP-Amidase-SH3b) was conserved and detected identically under all three sources. Tail fibre/receptor-binding protein (RBP) detection was strongly source-dependent: 14 of 22 genomes from the deposited annotation, 20 of 22 after re-annotation, and 22 of 22 combined. Resolved by domain, conservation was scale-dependent: the amidase domain was invariant within species while SH3b varied by 5.7%.  MAIN CONCLUSIONS: Lysis-module conservation is independent of the annotation source; the apparent variability of host recognition is largely an artefact of incomplete deposited annotation. Module-level surveys require re-annotation before comparative claims.
SN  - 0074-0276
SN  - 1678-8060
ER  -