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...
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2025-01-01
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| author | 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_facet | 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_sort | Verónica Fernández-Sánchez |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-bc04e994087b4ccebbc7ad8341828541 |
| institution | Kabale University |
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| language | English |
| publishDate | 2025-01-01 |
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| spelling | doaj-art-bc04e994087b4ccebbc7ad83418285412025-01-24T13:42:46ZengMDPI AGMicroorganisms2076-26072025-01-0113113110.3390/microorganisms13010131Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture MethodsVerónica Fernández-Sánchez0Estibeyesbo Said Plascencia-Nieto1Mónica Alethia Cureño-Díaz2Emilio Mariano Durán-Manuel3Aida Verónica Rodríguez-Tovar4Claudia Camelia Calzada-Mendoza5Clemente Cruz-Cruz6Miguel Ángel Loyola-Cruz7María Elizbeth Álvarez-Sánchez8Juan Carlos Bravata-Alcántara9Enzo Vásquez-Jiménez10Víctor Hugo Gutiérrez-Muñoz11Dulce Milagros Razo Blanco-Hernández12Liliana Nicolás-Sayago13Araceli Rojas-Bernabé14Omar García-Hernández15Erika Gómez-Zamora16Mireya Ruíz-Valdés17Graciela Castro-Escarpulli18Juan Manuel Bello-López19Hospital Juárez de México, Mexico City 07760, MexicoSección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, MexicoHospital Juárez de México, Mexico City 07760, MexicoHospital Juárez de México, Mexico City 07760, MexicoEscuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, MexicoSección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, MexicoHospital Juárez de México, Mexico City 07760, MexicoHospital Juárez de México, Mexico City 07760, MexicoLaboratorio de Patogénesis Celular y Molecular Humana y Veterinaria, Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, MexicoHospital Juárez de México, Mexico City 07760, MexicoHospital Juárez de México, Mexico City 07760, MexicoHospital Juárez de México, Mexico City 07760, MexicoHospital Juárez de México, Mexico City 07760, MexicoHospital Juárez de México, Mexico City 07760, MexicoSección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, MexicoDivisión de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 54090, MexicoHospital Juárez de México, Mexico City 07760, MexicoHospital Juárez de México, Mexico City 07760, MexicoEscuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, MexicoHospital Juárez de México, Mexico City 07760, MexicoPyogenic 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.https://www.mdpi.com/2076-2607/13/1/131bioinformaticsDNA sequencingV3-V4 hypervariablepyogenic liver abscesses |
| spellingShingle | 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 Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods Microorganisms bioinformatics DNA sequencing V3-V4 hypervariable pyogenic liver abscesses |
| title | Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods |
| title_full | Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods |
| title_fullStr | Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods |
| title_full_unstemmed | Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods |
| title_short | Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods |
| title_sort | massive sequencing of v3 v4 hypervariable region in pyogenic liver abscesses reveals the presence of unusual bacteria not detected by classical culture methods |
| topic | bioinformatics DNA sequencing V3-V4 hypervariable pyogenic liver abscesses |
| url | https://www.mdpi.com/2076-2607/13/1/131 |
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