Peru has become one of the countries with the highest mortality rate from the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. To investigate early transmission event and genomic diversity of SARS-CoV-2 isolates circulating in Peru, we analyzed a total of 3472 SARS-CoV-2 genomes, from which 149 ones were from Peru to investigate how this novel virus became established in the country and to dissect the spread of the one in this area. Phylogenomic analysis revealed multiple, independent introductions of the virus mainly from Europe and Asia. In addition, we found evidence for community-driven transmission of SARS-CoV-2 as suggested by clusters of related viruses found in patients living in different Peru regions.

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Peru has become one of the countries with the highest mortality rates from the current coronavirus disease 2019 (COVID‐19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). To investigate early transmission events and the genomic diversity of SARS‐CoV‐2 isolates circulating in Peru in the early COVID‐19 pandemic, we analyzed 3472 viral genomes, of which 149 were from Peru. Phylogenomic analysis revealed multiple and independent introductions of the virus likely from Europe and Asia and a high diversity of genetic lineages circulating in Peru. In addition, we found evidence for community‐driven transmission of SARS‐CoV‐2 as suggested by clusters of related viruses found in patients living in different regions of Peru.

The draft genome sequences of two strains of Escherichia coli, isolated from alpacas in Peru, are reported here. ECA1 has been determined to be a strain of enterohemorrhagic E. coli and ECB1 a strain of enteropathogenic E. coli. These pathogens are responsible for hemolytic-uremic syndrome in humans and diarrhea in different mammals, respectively.

El objetivo del estudio fue evaluar la expresión relativa de las citoquinas involucradas en la respuesta inmune Th1 (IL-2, IL-12, IFN-γ, TNF-α), Th2 (IL-4, IL-10 y TGF-β) y Th17 (IL-17) en 21 cuyes (Cavia porcellus) inoculados experimentalmente con una cepa aislada de campo de Salmonella Typhimurium a una dosis de 102 UFC/ml, vía intraperitoneal, y comparados con un grupo control de siete cuyes (inoculados con una cepa tratada térmicamente). Se tomaron muestras de sangre los días 1, 3, 5, 7, 9, 15 y 30 pos-inoculación (p.i.). Se extrajo el ARN total de las células linfocitarias y se desarrolló la RT-PCR en tiempo real usando cebadores específicos para las citoquinas. La expresión relativa fue determinada por el método comparativo 2-ΔΔCt a fin de evaluar la expresión de los ARNm de las citoquinas respecto al calibrador (cuy sano), y usando como gen constitutivo de referencia al GAPDH como normalizador. Las expresiones de los genes de las citoquinas en el grupo Tratamiento mostraron un aumento con respecto al grupo Control y una cinética ascendente con respecto a los días p.i. Los primeros días hubo predominio de las expresiones Th1 sobre Th2, posteriormente ambos aumentaron, con predominio de IL-4 e IL-17 a partir del día 15 p.i. La inoculación de S. Typhimurium estimuló una expresión mayoritaria de IL-12 respecto a las otras citocinas, lo cual induciría en los cuyes una respuesta de tipo celular o Th1.

Pasteurella multocida is a multi-host pathogen that infects a wide spectrum of domestic and wild animals including humans. Despite its impact on health and economics, P. multocida is considered an enigmatic pathogen and the genetic basis of its pathogenicity and host adaptation still remains unclear. Here we present a detailed genomic framework based on 336 whole-genome sequences of P. multocida isolates from different animal species and countries. Our data provide genomic support of the existence of two very divergent phylogroups (PmI and PmII), which present a barrier to homologous recombination suggesting genetic isolation. Additionally, a torCAD operon, which reduces TMAO (trimethylamine N-oxide) to produce energy during bacterial anaerobic respiration, is present only in PmI and can act as a hypothetical driver of niche segregation between phylogroups. The PmI phylogroup harbors strains that infect a wider range of hosts than PmII, and shows a highly diverse phylogeny and accessory genome. We identified nine clonal lineages for PmI, seven of which are associated with specific hosts or diseases and contain distinct accessory gene pools that can confer ecologically relevant phenotypes. We found differential presence of a trehalose metabolism operon in the bovine lineage associated with pneumonic pasteurellosis; while, citrate, L-arabinose, L-fucose, and D-allose operons are only present in avian lineages. These findings suggest that alternative metabolic pathways may facilitate the establishment of P. multocida during host colonization in the early stages of infection promoting the adaptation of P. multocida lineages to certain hosts.

El presente estudio tuvo como objetivo evaluar la actividad inmunogénica de tres cepas vivas atenuadas de Salmonella Typhimurium aislados de cuy, mediante la evaluación de la excreción de IgA fecal en ratones. El estudio se realizó con 28 ratones hembra de la cepa Balb/c de cuatro semanas de edad, divididos en cuatro grupos (siete ratones por grupo): cepa 1, cepa 2, cepa 3 y grupo control (PBS). Cada ratón fue inoculado con 109 UFC/100 µl de las cepas atenuadas por vía oral mediante el uso de una sonda orogástrica. Se recolectaron muestras de heces frescas a los días 1, 9, 15 y 21 días pos-inmunización. La cuantificación de IgA fecal fue realizada mediante una prueba de ELISA in house indirecto. Los resultados indican que los ratones inoculados con las cepas 1 y 2 presentaron una mayor actividad inmunogénica (IgA fecal) frente al grupo control.

Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is one of the most important foodborne pathogens that infect humans globally. The gastrointestinal tracts of animals like pigs, poultry or cattle are the main reservoirs of Salmonella serotypes. Guinea pig meat is an important protein source for Andean countries, but this animal is commonly infected by S. Typhimurium, producing high mortality rates and generating economic losses. Despite its impact on human health, food security, and economy, there is no genomic information about the S. Typhimurium responsible for the guinea pig infections in Peru. Here, we sequence and characterize 11 S. Typhimurium genomes isolated from guinea pigs from four farms in Lima-Peru. We were able to identify two genetic clusters (HC100_9460 and HC100_9757) distinguishable at the H100 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing (HierCC-cgMLST) scheme with an average of 608 SNPs of distance. All sequences belonged to sequence type 19 (ST19) and HC100_9460 isolates were typed in silico as monophasic variants (1,4,[5],12:i:-) lacking the fljA and fljB genes. Phylogenomic analysis showed that human isolates from Peru were located within the same genetic clusters as guinea pig isolates, suggesting that these lineages can infect both hosts. We identified a genetic antimicrobial resistance cassette carrying the ant(3)-Ia, dfrA15, qacE, and sul1 genes associated with transposons TnAs3 and IS21 within an IncI1 plasmid in one guinea pig isolate, while antimicrobial resistance genes (ARGs) for β-lactam (blaCTX-M-65) and colistin (mcr-1) resistance were detected in Peruvian human-derived isolates. The presence of a virulence plasmid highly similar to the pSLT plasmid (LT2 reference strain) containing the spvRABCD operon was found in all guinea pig isolates. Finally, seven phage sequences (STGP_Φ1 to STGP_Φ7) were identified in guinea pig isolates, distributed according to the genetic lineage (H50 clusters level) and forming part of the specific gene content of each cluster. This study presents, for the first time, the genomic characteristics of S. Typhimurium isolated from guinea pigs in South America, showing particular diversity and genetic elements (plasmids and prophages) that require special attention and also broader studies in different periods of time and locations to determine their impact on human health.