Occurrence and Genomic Characterization of <i>mcr-1</i>-Harboring <i>Escherichia coli</i> Isolates from Chicken and Pig Farms in Lima, Peru

• Main Authors: Dennis Carhuaricra (Author), Carla G. Duran Gonzales (Author), Carmen L. Rodríguez Cueva (Author), Yennifer Ignacion León (Author), Thalia Silvestre Espejo (Author), Geraldine Marcelo Monge (Author), Raúl H. Rosadio Alcántara (Author), Nilton Lincopan (Author), Luis Luna Espinoza (Author), Lenin Maturrano Hernández (Author)
• Format: Book
• Published: MDPI AG, 2022-12-01T00:00:00Z.
• Subjects: article
• Online Access: Connect to this object online.

Summary

Resistance to colistin generated by the <i>mcr-1</i> gene in <i>Enterobacteriaceae</i> is of great concern due to its efficient worldwide spread. Despite the fact that the Lima region has a third of the Peruvian population and more than half of the national pig and poultry production, there are no reports of the occurrence of the <i>mcr-1</i> gene in <i>Escherichia coli</i> isolated from livestock. In the present work, we studied the occurrence of <i>E. coli</i> carrying the <i>mcr-1</i> gene in chicken and pig farms in Lima between 2019 and 2020 and described the genomic context of the <i>mcr-1</i> gene. We collected fecal samples from 15 farms in 4 provinces of Lima including the capital Lima Metropolitana and recovered 341 <i>E. coli</i> isolates. We found that 21.3% (42/197) and 12.5% (18/144) of the chicken and pig strains were <i>mcr-1</i>-positive by PCR, respectively. The whole genome sequencing of 14 <i>mcr-1</i>-positive isolates revealed diverse sequence types (e.g., ST48 and ST602) and the presence of other 38 genes that confer resistance to 10 different classes of antibiotics, including beta-lactamase <i>bla</i>_CTX-M-55. The <i>mcr-1</i> gene was located on diverse plasmids belonging to the IncI2 and IncHI1A:IncHI1B replicon types. A comparative analysis of the plasmids showed that they contained the <i>mcr-1</i> gene within varied structures (<i>mikB</i>-<i>mcr1</i>-<i>pap2,</i> IS<i>Apl1</i>-<i>mcr1</i>-<i>pap2,</i> and Tn6330). To the best of our knowledge, this is the first attempt to study the prevalence of the <i>mcr-1</i> gene in livestock in Peru, revealing its high occurrence in pig and chicken farms. The genetic diversity of <i>mcr-1</i>-positive strains suggests a complex local epidemiology calling for a coordinated surveillance under the One-Health approach that includes animals, retail meat, farmers, hospitals and the environment to effectively detect and limit the spread of colistin-resistant bacteria.

Item Description

10.3390/antibiotics11121781
2079-6382