Genomic characterization of Achromobacter genogroup 20 and identification of a potential species-specific marker
Objective: To describe the genome of Achromobacter genogroup 20 and explore the presence of resistance determinants. Methods: Isolate 413638 was identified through nrdA and MLST analysis. Antimicrobial susceptibility testing was performed according CLSI 2024. NGS was conducted using Illumina MiSeq,...
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2025-01-01
|
| Series: | Journal of Global Antimicrobial Resistance |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2213716524004545 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1825199461014437888 |
|---|---|
| author | Mariana Papalia Rocio Stucchi Valeria Alexander Liliana Clara Mariángeles Visus Gabriel Gutkind Marcela Radice |
| author_facet | Mariana Papalia Rocio Stucchi Valeria Alexander Liliana Clara Mariángeles Visus Gabriel Gutkind Marcela Radice |
| author_sort | Mariana Papalia |
| collection | DOAJ |
| description | Objective: To describe the genome of Achromobacter genogroup 20 and explore the presence of resistance determinants. Methods: Isolate 413638 was identified through nrdA and MLST analysis. Antimicrobial susceptibility testing was performed according CLSI 2024. NGS was conducted using Illumina MiSeq, on the NextSeq500 platform with 150 bp paired-end reads, and de novo assembly was assessed using Unicycler (Galaxy). Coding sequences were predicted and confirmed with RAST and BLAST, and resistance determinants were evaluated using Resfinder and manual curation. All Achromobacter spp. genomes were obtained from NCBI, and the presence of blaOXA was investigated. Average nucleotide identity (ANI) and tetranucleotide analysis (TETRA) were calculated. Phylogenetic analysis of the new OXA variant was conducted against other species-specific markers in Achromobacter. Results: Isolate 413638 was identified as Achromobacter genogroup 20 ST365, showing resistance to third- and fourth-generation cephalosporins, aminoglycosides, and fluoroquinolones. The genome included coding sequences for three putative β-lactamases (one new OXA type-class D β -lactamase and two new class C), 32 efflux pump proteins, two aminoglycoside-modifying enzymes and a dihydropteroate synthase; also, substitutions in parC and parE were detected. The OXA enzyme, designated OXA-1238 (PP446293), differs from OXA-114a by 85 amino acids, with 69% identity. In silico analysis found OXA-1238 variants in three additional Achromobacter spp. genomes, with 97% identity. Based on ANI and tetra analysis, the three genomes corresponded to Achromobacter genogroup 20. Conclusion: Several resistance markers were found, probably contributing to the resistance profile observed in Achromobacter genogroup 20 ST365. The new OXA variant identified, OXA-1238, could constitute a useful molecular marker for species identification. |
| format | Article |
| id | doaj-art-ed2d6e56c9d84d29a854d84593c50aac |
| institution | Kabale University |
| issn | 2213-7165 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Global Antimicrobial Resistance |
| spelling | doaj-art-ed2d6e56c9d84d29a854d84593c50aac2025-02-08T05:00:26ZengElsevierJournal of Global Antimicrobial Resistance2213-71652025-01-01402628Genomic characterization of Achromobacter genogroup 20 and identification of a potential species-specific markerMariana Papalia0Rocio Stucchi1Valeria Alexander2Liliana Clara3Mariángeles Visus4Gabriel Gutkind5Marcela Radice6Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Laboratorio de Resistencia Bacteriana, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Corresponding author. Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, IBaViM, Laboratorio de Resistencia Bacteriana; Junín 956, 8vo. Piso, Ciudad Autónoma de Buenos Aires, CP 1113, ArgentinaUniversidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Laboratorio de Resistencia Bacteriana, Buenos Aires, ArgentinaHospital Italiano de Buenos Aires, Sección Bacteriología Laboratorio Central, Ciudad Autónoma de Buenos Aires, ArgentinaHospital Italiano de Buenos Aires, Sección Infectología, Servicio de Clínica Médica, Ciudad Autónoma de Buenos Aires, ArgentinaHospital Italiano de Buenos Aires, Sección Bacteriología Laboratorio Central, Ciudad Autónoma de Buenos Aires, ArgentinaUniversidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Laboratorio de Resistencia Bacteriana, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, ArgentinaUniversidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Laboratorio de Resistencia Bacteriana, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, ArgentinaObjective: To describe the genome of Achromobacter genogroup 20 and explore the presence of resistance determinants. Methods: Isolate 413638 was identified through nrdA and MLST analysis. Antimicrobial susceptibility testing was performed according CLSI 2024. NGS was conducted using Illumina MiSeq, on the NextSeq500 platform with 150 bp paired-end reads, and de novo assembly was assessed using Unicycler (Galaxy). Coding sequences were predicted and confirmed with RAST and BLAST, and resistance determinants were evaluated using Resfinder and manual curation. All Achromobacter spp. genomes were obtained from NCBI, and the presence of blaOXA was investigated. Average nucleotide identity (ANI) and tetranucleotide analysis (TETRA) were calculated. Phylogenetic analysis of the new OXA variant was conducted against other species-specific markers in Achromobacter. Results: Isolate 413638 was identified as Achromobacter genogroup 20 ST365, showing resistance to third- and fourth-generation cephalosporins, aminoglycosides, and fluoroquinolones. The genome included coding sequences for three putative β-lactamases (one new OXA type-class D β -lactamase and two new class C), 32 efflux pump proteins, two aminoglycoside-modifying enzymes and a dihydropteroate synthase; also, substitutions in parC and parE were detected. The OXA enzyme, designated OXA-1238 (PP446293), differs from OXA-114a by 85 amino acids, with 69% identity. In silico analysis found OXA-1238 variants in three additional Achromobacter spp. genomes, with 97% identity. Based on ANI and tetra analysis, the three genomes corresponded to Achromobacter genogroup 20. Conclusion: Several resistance markers were found, probably contributing to the resistance profile observed in Achromobacter genogroup 20 ST365. The new OXA variant identified, OXA-1238, could constitute a useful molecular marker for species identification.http://www.sciencedirect.com/science/article/pii/S2213716524004545Achromobacter genogroup 20Achromobacter spp.OXA-1238β-lactamaseSpecies-specific marker |
| spellingShingle | Mariana Papalia Rocio Stucchi Valeria Alexander Liliana Clara Mariángeles Visus Gabriel Gutkind Marcela Radice Genomic characterization of Achromobacter genogroup 20 and identification of a potential species-specific marker Journal of Global Antimicrobial Resistance Achromobacter genogroup 20 Achromobacter spp. OXA-1238 β-lactamase Species-specific marker |
| title | Genomic characterization of Achromobacter genogroup 20 and identification of a potential species-specific marker |
| title_full | Genomic characterization of Achromobacter genogroup 20 and identification of a potential species-specific marker |
| title_fullStr | Genomic characterization of Achromobacter genogroup 20 and identification of a potential species-specific marker |
| title_full_unstemmed | Genomic characterization of Achromobacter genogroup 20 and identification of a potential species-specific marker |
| title_short | Genomic characterization of Achromobacter genogroup 20 and identification of a potential species-specific marker |
| title_sort | genomic characterization of achromobacter genogroup 20 and identification of a potential species specific marker |
| topic | Achromobacter genogroup 20 Achromobacter spp. OXA-1238 β-lactamase Species-specific marker |
| url | http://www.sciencedirect.com/science/article/pii/S2213716524004545 |
| work_keys_str_mv | AT marianapapalia genomiccharacterizationofachromobactergenogroup20andidentificationofapotentialspeciesspecificmarker AT rociostucchi genomiccharacterizationofachromobactergenogroup20andidentificationofapotentialspeciesspecificmarker AT valeriaalexander genomiccharacterizationofachromobactergenogroup20andidentificationofapotentialspeciesspecificmarker AT lilianaclara genomiccharacterizationofachromobactergenogroup20andidentificationofapotentialspeciesspecificmarker AT mariangelesvisus genomiccharacterizationofachromobactergenogroup20andidentificationofapotentialspeciesspecificmarker AT gabrielgutkind genomiccharacterizationofachromobactergenogroup20andidentificationofapotentialspeciesspecificmarker AT marcelaradice genomiccharacterizationofachromobactergenogroup20andidentificationofapotentialspeciesspecificmarker |