Beta-Lactam Antibiotic Resistance Genes in the Microbiome of the Public Transport System of Quito, Ecuador

Fernanda Hernández-Alomía; Carlos Bastidas-Caldes; Isabel Ballesteros; Gabriela N Tenea; Pablo Jarrín-V; C Alfonso Molina; Pablo Castillejo

doi:10.3390/ijerph20031900

Beta-Lactam Antibiotic Resistance Genes in the Microbiome of the Public Transport System of Quito, Ecuador

Int J Environ Res Public Health. 2023 Jan 20;20(3):1900. doi: 10.3390/ijerph20031900.

Authors

Fernanda Hernández-Alomía¹, Carlos Bastidas-Caldes^{2

3}, Isabel Ballesteros^{1

4}, Gabriela N Tenea⁵, Pablo Jarrín-V⁶, C Alfonso Molina^{7

8}, Pablo Castillejo¹

Affiliations

¹ Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Universidad de Las Américas, Quito 170125, Ecuador.
² One Health Research Group, Universidad de las Américas, Quito 170125, Ecuador.
³ Programa de Doctorado en Salud Pública y Animal, Universidad de Extremadura, 10003 Cáceres, Spain.
⁴ Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain.
⁵ Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Universidad Técnica del Norte, Ibarra 100150, Ecuador.
⁶ Dirección de Innovación, Instituto Nacional de Biodiversidad, Quito 170525, Ecuador.
⁷ Instituto de Investigación en Zoonosis (CIZ), Universidad Central del Ecuador, Quito 170521, Ecuador.
⁸ Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, Quito 170521, Ecuador.

Abstract

Multidrug-resistant bacteria present resistance mechanisms against β-lactam antibiotics, such as Extended-Spectrum Beta-lactamases (ESBL) and Metallo-β-lactamases enzymes (MBLs) which are operon encoded in Gram-negative species. Likewise, Gram-positive bacteria have evolved other mechanisms through mec genes, which encode modified penicillin-binding proteins (PBP2). This study aimed to determine the presence and spread of β-lactam antibiotic resistance genes and the microbiome circulating in Quito's Public Transport (QTP). A total of 29 station turnstiles were swabbed to extract the surface environmental DNA. PCRs were performed to detect the presence of 13 antibiotic resistance genes and to identify and to amplify 16S rDNA for barcoding, followed by clone analysis, Sanger sequencing, and BLAST search. ESBL genes bla_TEM-1 and bla_CTX-M-1 and MBL genes bla_OXA-181 and mecA were detected along QPT stations, blaTEM being the most widely spread. Two subvariants were found for bla_TEM-1, bla_CTX-M-1, and bla_OXA-181. Almost half of the circulating bacteria found at QPT stations were common human microbiota species, including those classified by the WHO as pathogens of critical and high-priority surveillance. β-lactam antibiotic resistance genes are prevalent throughout QPT. This is the first report of bla_OXA-181 in environmental samples in Ecuador. Moreover, we detected a new putative variant of this gene. Some commensal coagulase-negative bacteria may have a role as mecA resistance reservoirs.

Keywords: antibiotic-resistance; blaCTX-M-1; blaOXA-181; blaTEM-1; environmental-DNA; mecA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Anti-Bacterial Agents* / pharmacology
Anti-Bacterial Agents* / therapeutic use
Bacteria / metabolism
Drug Resistance, Multiple, Bacterial
Ecuador
Humans
Microbial Sensitivity Tests
Monobactams
beta-Lactamases* / genetics
beta-Lactamases* / metabolism

Substances

beta-Lactamases
Anti-Bacterial Agents
Monobactams

Grants and funding

The authors extend their gratitude to the Corporación Ecuatoriana para el Desarrollo de la Investigación y Academia (CEDIA) and its CEPRA program for the financial support provided to the project “Microbiome colonization and SARS-CoV-2 detection in the new subway system of Quito”. We also thank Universidad de las Américas for the BIO.PCP.22.04-funding.