Study detects multidrug-resistant KPC-producing bacteria in Chilean wastewater for the first time

A team of Chilean researchers has identified, for the first time in the country, the presence of KPC-type carbapenemase-producing bacteria in wastewater samples from the Greater Concepción Metropolitan Area. The finding, published in the journal Biological Research, raises concerns about the environmental circulation of microorganisms with high levels of resistance to critical clinically used antibiotics and reinforces the need for surveillance within the framework of "One Health."

The research, which was part of Franco Ilabaca's Master's thesis in Microbiology, was led by Dr. Gerardo González-Rocha, director of the Antibacterial Agents Research Laboratory at the University of Concepción and thesis advisor, Dr. Andrés Opazo-Capurro, director of the FONDEF IDeA project, and Dr. Helia Bello-Toledo, thesis co-advisor, in collaboration with the MELISA Institute and other institutions. The research consisted of the collection and microbiological and genomic analysis of wastewater samples taken during 2022 at a treatment plant that serves more than 950,000 people in the Biobío Region. “The idea is to see how antibiotic resistance is not only present in bacteria found in hospitals, but can also be present in wastewater or the environment, and to emphasize that the research approach to antibiotic resistance cannot be limited to human health alone, but can also include environmental and animal health, which is known today as a One Health approach. So, the main objective was to see if we can find these resistance mechanisms that are so common in hospitals in wastewater,” explained Dr. González-Rocha.

Of a total of 205 bacterial isolates, three strains were identified as producers of the KPC enzyme, a type of carbapenemase that confers resistance to last-line antibiotics. These strains corresponded to the species Klebsiella pasteurii, Klebsiella pneumoniae subsp. pneumoniae, and Citrobacter freundii sensu stricto, all with multiple antibiotic resistance profiles and carrying the blaKPC-2 gene.

Genomic analysis also revealed that these strains contained plasmids associated with the dissemination of resistance genes and, in some cases, class 1 integrons, which increase the bacteria's ability to acquire new resistance determinants. In evolutionary terms, two of the strains analyzed showed genetic similarities with others previously identified in Asia and Europe, suggesting their possible introduction from abroad and adaptation to local contexts.

Regarding these analyses, performed using the Illumina NextSeq 500 platform, complemented by bioinformatics tools such as FastQC, Unicycler, and Bakta for genome evaluation, assembly, and annotation, along with specialized software to identify resistance genes and plasmids involved in their dissemination, Mauricio Hernández, Laboratory Head at the MELISA Institute, explained, "It was a pleasant experience for us to collaborate with Dr. González's group and support genome sequencing. This also contributes to research into multidrug resistance to antibiotics, which has become a global health problem and requires a significant increase in research."

The researchers warn that, although the detected prevalence is low (1.5%), the presence of carbapenem-resistant bacteria in urban environments represents a warning sign. Early identification allows for anticipating public health risks and implementing timely preventive measures. Therefore, it is essential to analyze wastewater and study whether treatment plants are capable of eliminating both bacteria and resistance genes.

For his part, Dr. Elard Koch, Chairman of the MELISA Institute, emphasized the importance of collaboration and knowledge dissemination: "Studies like this reinforce the vital need for strong scientific collaborations. They allow us to generate and share knowledge on topics of high relevance to society. Collaborative research is undoubtedly essential not only for scientific dissemination, but also for fostering a deeper public understanding of complex phenomena such as antimicrobial resistance."

The study was funded by the National Research and Development Agency (ANID) through the FONDEF IDeA fund and represents a concrete advance in genomic surveillance applied to the control of antimicrobial resistance in Chile.

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This work was funded by the FONDEF IDeA Grant No. ID23I10264 awarded to A. O.-C.

Participating Researchers:

Franco Ilabaca‑Carrasco (1, 2, 3), Carlos Peña‑Raddatz (1), Claudia Torres‑Bustos (1), Mauricio Hernández‑Cea (4), Guillermo Nourdin‑Galindo (4), Pablo Saldivia‑Flandez (4), Cristian Vargas (4), Elard Koch (4), Helia Bello‑Toledo (1, 2), Gerardo González‑Rocha (1,2) and Andrés Opazo‑Capurro (1, 2).

(1) Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile; (2) Grupo de Estudio en Resistencia Antimicrobiana (GRAM), Universidad de Concepción, Concepción, Chile; (3) Laboratorio de Biología, Departamento de Ciencias Biológicas, Facultad de Ciencias de La Vida, Universidad Andrés Bello Sede Concepción, Talcahuano, Chile; (4) Division of Biotechnology, MELISA Institute, Concepción, Chile.

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