We report the emergence of a novel lineage of SARS-CoV-2 in South America, termed C.37. It presents a deletion in the ORF1a gene (Δ3675-3677), also found in variants of concern (VOCs) Alpha, Beta, and Gamma, and seven non-synonymous mutations in the Spike gene (Δ247-253, G75V, T76I, L452Q, F490S, T859N). Initially reported in Lima, Peru, in late December 2020, it now accounts for almost 100% of Peruvian genomes in April 2021. It is expanding in Chile and Argentina, and there is evidence of onward transmission in Colombia, Mexico, the USA, Germany, and Israel. On June 15, 2021, the World Health Organization designated C.37 as Variant of Interest (VOI) Lambda.
The widespread and poorly regulated use of antibiotics in animal production in low- and middle-income countries (LMICs) is increasingly associated with the emergence and dissemination of antibiotic resistance genes (ARGs) in retail animal products. Here, we compared Escherichia coli from chickens and humans with varying levels of exposure to chicken meat in a low-income community in the southern outskirts of Lima, Peru. We hypothesize that current practices in local poultry production result in highly resistant commensal bacteria in chickens that can potentially colonize the human gut. E. coli was isolated from cloacal swabs of non-organic (n = 41) and organic chickens (n = 20), as well as from stools of market chicken vendors (n = 23), non-vendors (n = 48), and babies (n = 60). 315 E. coli isolates from humans (n = 150) and chickens (n = 165) were identified, with chickens showing higher rates of multidrug-resistant and extended-spectrum beta-lactamase phenotypes. Non-organic chicken isolates were more resistant to most antibiotics tested than human isolates, while organic chicken isolates were susceptible to most antibiotics. Whole-genome sequencing of 118 isolates identified shared phylogroups between human and animal populations and 604 ARG hits across genomes. Resistance to florfenicol (an antibiotic commonly used as a growth promoter in poultry but not approved for human use) was higher in chicken vendors compared to other human groups. Isolates from non-organic chickens contained genes conferring resistance to clinically relevant antibiotics, including mcr-1 for colistin resistance, blaCTX-M ESBLs, and blaKPC-3 carbapenemase. Our findings suggest that E. coli strains from market chickens are a potential source of ARGs that can be transmitted to human commensals.
El objetivo del estudio fue caracterizar 20 cepas de Salmonella enterica a nivel molecular y de resistencia antimicrobiana. De estas, 15 fueron obtenidas de cuyes infectados y cinco de cuyes clínicamente sanos, procedentes de dos centros de producción intensiva ubicados en Lima, Perú. Mediante una técnica de PCR múltiple se detectaron los genes invA, prot6E y fliC, correspondientes al género Salmonella y serovares Enteritidis y Typhimurium, respectivamente. Se detectó la variabilidad genética mediante la técnica BOX-PCR utilizando el primer BOXA1R. La resistencia fue evaluada utilizando la técnica de Kirby Bauer en base a eritromicina, nitrofurantoína, estreptomicina, penicilina, enrofloxacina, fosfomicina, amoxicilina con ácido clavulánico, sulfatrimetoprim y ciprofloxacina. Se determinó la serovariedad Typhimurium en el 100% de los aislados. La evaluación de los perfiles electroforéticos obtenidos por la técnica de BOX-PCR demostró alta homogeneidad, con patrones de bandas de ADN similares. Se detectaron cepas resistentes a eritromicina 60% (12/20), nitrofurantoína 40% (8/20), estreptomicina 30% (6/ 20), penicilina 25% (5/20), y enrofloxacina 10% (2/20). La detección de cepas resistentes puede ocasionar problemas en el tratamiento de salmonelosis en cuyes y la presencia de un solo grupo genético sugiere una dispersión clonal.
The role of domestic cats in the dynamics of SARS-CoV-2 remains poorly characterized, especially in epidemiologic contexts of countries with high viral transmission. Here, we report the first evidence of SARS-CoV-2 Lambda variant of interest in symptomatic domestic cats whose owners were diagnosed with COVID-19 in Lima, Peru, providing evidence that transmission of this new variant in domestic cats is occurring. More epidemiological studies are required to further characterize the role of domestic animals in the transmission dynamics of SARS-CoV-2.
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