Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods
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 <i>16S rRNA</i> 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 (<i>16S rRNA</i> 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 <i>Gardnerella vaginalis</i>, <i>Lactobacillus iners</i>, and <i>Prevotella timonensis</i> 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.
Authors
- Víctor Hugo Gutiérrez-Muñoz (ORCID: https://orcid.org/0000-0002-0792-4500)
- Clemente Cruz-Cruz (ORCID: https://orcid.org/0000-0003-1555-3102)
- Araceli Rojas‐Bernabé (ORCID: https://orcid.org/0000-0002-3851-5881)
- Mónica Alethia Cureño-Díaz (ORCID: https://orcid.org/0000-0002-4556-637X)
- Graciela Castro‐Escarpulli (ORCID: https://orcid.org/0000-0002-7496-8247)
- Enzo Vásquez-Jiménez (ORCID: https://orcid.org/0000-0003-0205-817X)
- Dulce Milagros Razo Blanco-Hernández (ORCID: https://orcid.org/0000-0003-3869-344X)
- María Elizbeth Álvarez-Sánchez (ORCID: https://orcid.org/0000-0002-9212-4451)
- Juan Carlos Bravata-Alcántara (ORCID: https://orcid.org/0000-0002-3585-0051)
- Omar García-Hernández (ORCID: https://orcid.org/0000-0001-8807-1353)
- Claudia Camelia Calzada‐Mendoza (ORCID: https://orcid.org/0000-0002-5893-8566)
- Emilio Mariano Durán-Manuel (ORCID: https://orcid.org/0000-0001-8985-486X)
- Erika Gómez-Zamora (ORCID: https://orcid.org/0000-0002-0488-7900)
- Miguel Ángel Loyola-Cruz (ORCID: https://orcid.org/0000-0001-5383-8737)
- Juan Manuel Bello–López (ORCID: https://orcid.org/0000-0002-9957-3807)
- Verónica Fernández-Sánchez (ORCID: https://orcid.org/0000-0001-9732-2265)
- Aída Verónica Rodríguez-Tovar (ORCID: https://orcid.org/0000-0002-5514-8972)
- Liliana Nicolás-Sayago (ORCID: https://orcid.org/0000-0002-0417-7896)
- Estibeyesbo Said Plascencia-Nieto (ORCID: https://orcid.org/0009-0002-2949-4924)
- Mireya Ruíz-Valdés
Institutions
- Universidad Autónoma de la Ciudad de México (MX)
- Hospital Juárez de México (MX)
- Instituto Politécnico Nacional (MX)
- Universidad Nacional Autónoma de México (MX)
Publication Details
- Journal
- Microorganisms
- Published
- 2025-01-10
- DOI
- https://doi.org/10.3390/microorganisms13010131
- Primary Topic
- Amoebic Infections and Treatments
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Instituto Politécnico Nacional
- Secretaría de Investigación y Posgrado, Instituto Politécnico Nacional
- Federal Aviation Administration