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OBJECTIVE: this study aims to identify and characterise genomic and phylogenetically isolated SARS-CoV-2 viral isolates in patients from Lambayeque, Peru. METHODS: Nasopharyngeal swabs were taken from patients from the Almanzor Aguinaga Asenjo Hospital, Chiclayo, Lambayeque, Peru, which had been considered mild, moderate, and severe cases of COVID-19. Patients had to have tested positive for COVID-19, using a positive RT-PCR for SARS-CoV-2. Subsequently, the SARS-CoV-2 complete viral genome sequencing was carried out using Illumina MiSeq®. The sequences obtained from the sequence were analysed in Nextclade V1.10.0 to assign the corresponding clades, identify mutations in the SARS-CoV-2 genes and perform quality control of the sequences obtained. All sequences were aligned using MAFFT v7.471. The SARS-CoV-2 isolate Wuhan NC 045512.2 was used as a reference sequence to analyse mutations at the amino acid level. The construction of the phylogenetic tree model was achieved with IQ-TREE v1.6.12. RESULTS: It was determined that during the period from December 2020 to January 2021, the lineages s C.14, C.33, B.1.1.485, B.1.1, B.1.1.1, and B.1.111 circulated, with lineage C.14 being the most predominant at 76.7% (n = 23/30). These lineages were classified in clade 20D mainly and also within clades 20B and 20A. On the contrary, the variants found in the second batch of samples of the period from September to October 2021 were Delta (72.7%), Gamma (13.6%), Mu (4.6%), and Lambda (9.1%), distributed between clades 20J, 21G, 21H, 21J, and 21I. CONCLUSIONS: This study reveals updated information on the viral genomics of SARS-CoV-2 in the Lambayeque region, Peru, which is crucial to understanding the origins and dispersion of the virus and provides information on viral pathogenicity, transmission and epidemiology.
RESUMO
Introducción: Las Enterobacteriaceae productoras de betalactamasas de espectro extendido están presentes en las heces de los individuos de la comunidad. En Perú, la automedicación, el tipo de alimentación, condiciones sanitarias podrían asociarse a esta colonización. Objetivo: determinar la frecuencia de colonización rectal por EP-BLEE en pacientes de consulta externa del Hospital Regional Lambayeque, así como los factores asociados a la misma, durante los meses de julio 2018 a febrero 2019. Material y métodos: 331 pacientes participantes fueron entrevistados, de los cuales se obtuvieron tres muestras seriadas de heces recién emitidas. Las muestras fueron cultivadas en agar McConkey. Las EP-BLEE se confirmaron con la prueba de disco combinado (método americano). Resultados: el 85,8 % de los pacientes estuvieron colonizados por EP-BLEE, siendo Escherichia coli el aislamiento más frecuente (87,7 %). El análisis bivariado asoció el consumo de carne de cerdo (RP=1,15 IC 95%: 1,07 - 1,24), caprino (RP=1,18, IC 95%: 1,10 - 1,25) y el consumo de ensaladas frecuentemente (RP=1,15, IC 95 %: 1,05 - 1,28) con una mayor probabilidad de ser portador rectal de EP-BLEE. La automedicación presentó valores cercanos al límite de validez (p=0,051, RP 1,12, IC 95% 0,98 - 1,26). Conclusiones: Consumir carne de cerdo, caprino y ensaladas aumentan la probabilidad de ser portador de EP-BLEE, mientras que la automedicación podría estar asociada, por lo que es necesario seguir investigando, ya que se desconocen las razones de este hallazgo en pacientes de la comunidad.
Background:Extended-spectrumbeta-lactamase-producing Enterobacteriaceae(EP-BLEE) are present in the feces of individuals in the community. In Peru, self-medication, type of diet and sanitary conditions could be associated with this colonization. Objective:to determine the frequency of rectal colonization by EP-BLEE in outpatients of the "Hospital Regional Lambayeque", as well as the factors associated with it, during the months of July 2018 to February 2019. 331 participating patients Material and methods:were interviewed, and three serial samples of freshly emitted stool were obtained from them. The samples were cultured on McConkey agar. EP-BLEE were confirmed with the combined disc test (American method). 85.8% of patients were colonized by EP-BLEE, and Escherichia coliwas the most frequent isolate (87.7%). Bivariate Results:analysis associated the consumption of pork (RP=1.15, 95% CI: 1.07 - 1.24), goat (RP=1.18, 95% CI: 1.10 - 1.25) and frequent consumption of salads (RP=1.15, 95% CI: 1.05 - 1.28) with a higher probability of being a rectal carrier of EP-BLEE. Self-medication presented values close to the limit of validity (p=0.051, RP1.12, 95% CI 0.98 - 1.26). Consuming pork, goat meat and salads increase the probability Conclusions:of being a carrier of EP-BLEE, while self-medication could be associated, so further research is needed, since the reasons for this finding are unknown.
