AUTHOR=Bazalar-Gonzales Jhonathan , Silvestre-Espejo Thalía , Rodríguez Cueva Carmen , Carhuaricra Huamán Dennis , Ignación León Yennifer , Luna Espinoza Luis , Rosadio Alcántara Raúl , Maturrano Hernández Lenin 

TITLE=Genomic insights into ESBL-producing Escherichia coli isolated from non-human primates in the Peruvian Amazon

JOURNAL=Frontiers in Veterinary Science

VOLUME=10

YEAR=2024

URL=https://www.frontiersin.org/journals/veterinary-science/articles/10.3389/fvets.2023.1340428

DOI=10.3389/fvets.2023.1340428

ISSN=2297-1769

ABSTRACT=<sec id="sec1"><title>Introduction</title><p>Extended-spectrum beta-lactamase (ESBL)-producing <italic>Enterobacteriaceae</italic> are on the WHO priority pathogens list because they are associated with high mortality, health-care burden, and antimicrobial resistance (AMR), a serious problem that threatens global public health and should be addressed through the One Health approach. Non-human primates (NHP) have a high risk of acquiring these antibiotic-resistant bacteria due to their close phylogenetic relationship with humans and increased anthropogenic activities in their natural environments. This study aimed to detect and analyze the genomes of ESBL-producing <italic>Escherichia coli</italic> (ESBL-producing <italic>E. coli</italic>) in NHP from the Peruvian Amazon.</p></sec><sec id="sec2"><title>Materials and methods</title><p>We collected a total of 119 fecal samples from semi-captive <italic>Saguinus labiatus</italic>, <italic>Saguinus mystax</italic>, and <italic>Saimiri boliviensis</italic>, and captive <italic>Ateles chamek</italic>, <italic>Cebus unicolor</italic>, <italic>Lagothrix lagothricha</italic>, and <italic>Sapajus apella</italic> in the Loreto and Ucayali regions, respectively. Subsequently, we isolated and identified <italic>E. coli</italic> strains by microbiological methods, detected ESBL-producing <italic>E. coli</italic> through antimicrobial susceptibility tests following CLSI guidelines, and analyzed their genomes using previously described genomic methods.</p></sec><sec id="sec3"><title>Results</title><p>We detected that 7.07% (7/99) of <italic>E. coli</italic> strains: 5.45% (3/55) from Loreto and 9.09% (4/44) from Ucayali, expressed ESBL phenotype. Genomic analysis revealed the presence of high-risk pandemic clones, such as ST10 and ST117, carrying a broad resistome to relevant antibiotics, including three <italic>bla</italic><sub>CTX-M</sub> variants: <italic>bla</italic><sub>CTX-M-15</sub>, <italic>bla</italic><sub>CTX-M-55</sub>, and <italic>bla</italic><sub>CTX-M-65</sub>. Phylogenomic analysis confirmed the clonal relatedness of high-risk lineages circulating at the human-NHP interface. Additionally, two ESBL-producing <italic>E. coli</italic> strains were identified as EPEC (<italic>eae</italic>) and ExPEC according to their virulence profiles, and one more presented a hypermucoviscous phenotype.</p></sec><sec id="sec4"><title>Discussion</title><p>We report the detection and genomic analysis of seven ESBL-producing <italic>E. coli</italic> strains carrying broad resistome and virulence factors in NHP from two regions of the Peruvian Amazon. Some of these strains are closely related to high-risk pandemic lineages previously reported in humans and domestic animals, highlighting the negative impact of anthropogenic activities on Amazonian wildlife. To our knowledge, this is the first documentation of ESBL-producing <italic>E. coli</italic> in NHP from the Amazon, underscoring the importance of adopting the One Health approach to AMR surveillance and minimizing the potential transmission risk of antibiotic-resistant bacteria at the human-NHP interface.</p></sec>