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Jan 10, 2025;13 (1):

Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods.

Verónica Fernández-Sánchez, Estibeyesbo Said Plascencia-Nieto, Mónica Alethia Cureño-Díaz, Emilio Mariano Durán-Manuel, Aida Verónica Rodríguez-Tovar, Claudia Camelia Calzada-Mendoza, Clemente Cruz-Cruz, Miguel Ángel Loyola-Cruz, María Elizbeth Álvarez-Sánchez, Juan Carlos Bravata-Alcántara, Enzo Vásquez-Jiménez, Víctor Hugo Gutiérrez-Muñoz, Dulce Milagros Razo Blanco-Hernández, Liliana Nicolás-Sayago, Araceli Rojas-Bernabé, Omar García-Hernández, Erika Gómez-Zamora, Mireya Ruíz-Valdés, Graciela Castro-Escarpulli, Juan Manuel Bello-López
Author Information
  1. Verónica Fernández-Sánchez: Hospital Juárez de México, Mexico City 07760, Mexico. ORCID
  2. Estibeyesbo Said Plascencia-Nieto: Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico.
  3. Mónica Alethia Cureño-Díaz: Hospital Juárez de México, Mexico City 07760, Mexico. ORCID
  4. Emilio Mariano Durán-Manuel: Hospital Juárez de México, Mexico City 07760, Mexico. ORCID
  5. Aida Verónica Rodríguez-Tovar: Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico. ORCID
  6. Claudia Camelia Calzada-Mendoza: Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico. ORCID
  7. Clemente Cruz-Cruz: Hospital Juárez de México, Mexico City 07760, Mexico. ORCID
  8. Miguel Ángel Loyola-Cruz: Hospital Juárez de México, Mexico City 07760, Mexico. ORCID
  9. María Elizbeth Álvarez-Sánchez: Laboratorio de Patogénesis Celular y Molecular Humana y Veterinaria, Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, Mexico. ORCID
  10. Juan Carlos Bravata-Alcántara: Hospital Juárez de México, Mexico City 07760, Mexico. ORCID
  11. Enzo Vásquez-Jiménez: Hospital Juárez de México, Mexico City 07760, Mexico. ORCID
  12. Víctor Hugo Gutiérrez-Muñoz: Hospital Juárez de México, Mexico City 07760, Mexico. ORCID
  13. Dulce Milagros Razo Blanco-Hernández: Hospital Juárez de México, Mexico City 07760, Mexico.
  14. Liliana Nicolás-Sayago: Hospital Juárez de México, Mexico City 07760, Mexico.
  15. Araceli Rojas-Bernabé: Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico. ORCID
  16. Omar García-Hernández: División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 54090, Mexico.
  17. Erika Gómez-Zamora: Hospital Juárez de México, Mexico City 07760, Mexico. ORCID
  18. Mireya Ruíz-Valdés: Hospital Juárez de México, Mexico City 07760, Mexico.
  19. Graciela Castro-Escarpulli: Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico. ORCID
  20. Juan Manuel Bello-López: Hospital Juárez de México, Mexico City 07760, Mexico. ORCID
PMID: 39858899 DOI: 10.3390/microorganisms13010131

Abstract

Pyogenic liver abscesses (PLAs) are serious infections in which doctors often fail in identifying the causative agent due to microbiological limitations. These limitations in detecting uncommon pathogens complicate the treatment and recovery. Molecular techniques, like massive sequencing, enable the detection of uncommon pathogens and highlight the shortcomings of traditional cultures. The aim of this work was to characterise the bacterial composition of PLAs through massive sequencing of the V3-V4 hypervariable region of the gene in cases where conventional culture methods were negative. Purulent material was collected from three patients with PLAs at Hospital Juárez de México. Classical and molecular microbiological cultures were performed in parallel. Metagenomic DNA was extracted and massively sequenced ( gene) using the Illumina MiSeq platform. A bioinformatic analysis was performed to determine the diversity at six different taxa levels and the relative abundances. The culture methods were not sufficient to detect the causative agent of the PLAs. However, the massive sequencing revealed the causative agents of the monomicrobial and polymicrobial infectious foci, with , , and as the dominant bacteria. The massive sequencing revealed the presence of unusual pathogens that traditional culture failed to detect. There is an immediate need for molecular or comprehensive microbiological culture techniques to search for unusual bacteria in the diagnosis of PLAs.

Keywords

DNA sequencing V3-V4 hypervariable bioinformatics pyogenic liver abscesses

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