Step-by-Step Bacterial Genome Comparison.

Thanks to advancements in genome sequencing and bioinformatics, thousands of bacterial genome sequences are available in public databases. This presents an opportunity to study bacterial diversity in unprecedented detail. This chapter describes a complete bioinformatics workflow for comparative genomics of bacterial genomes, including genome annotation, pangenome reconstruction and visualization, phylogenetic analysis, and identification of sequences of interest such as antimicrobial-resistance genes, virulence factors, and phage sequences.

Protein-Coding Gene Families in Prokaryote Genome Comparisons.

The identification of orthologous genes is relevant for comparative genomics, phylogenetic analysis, and functional annotation. There are many computational tools for the prediction of orthologous groups as well as web-based resources that offer orthology datasets for download and online analysis. This chapter presents a simple and practical guide to the process of orthologous group prediction, using a dataset of 10 prokaryotic proteomes as example.

Analysis of twelve genomes of the bacterium from brown-throated sloths (), the first from a non-human host.

is a Gram-negative bacterium found in various animals, including humans, where it has been associated with various infections. Knowledge of the basic biology of is essential to understand the evolutionary strategies of niche adaptation and how this organism contributes to infectious diseases; however, genomic data about is very limited, especially from non-human hosts. In this work, we sequenced 12 genomes isolated from healthy free-living brown-throated sloths () in the Parque Estadual das Fontes do Ipiranga (São Paulo, Brazil), and compared them with genomes from isolates of human origin, in order to gain insights into genomic diversity, phylogeny, and host specialization of this species.

Possible Spreading of SARS-CoV-2 from Humans to Captive Non-Human Primates in the Peruvian Amazon.

Human-to-animal transmission events of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) have been reported in both domestic and wild species worldwide. Despite the high rates of contagion and mortality during the COVID-19 (Coronavirus Diseases 2019) pandemic in Peru, no instances of natural virus infection have been documented in wild animals, particularly in the Amazonian regions where human-wildlife interactions are prevalent. In this study, we conducted a surveillance investigation using viral RNA sequencing of fecal samples collected from 76 captive and semi-captive non-human primates (NHPs) in the Loreto, Ucayali, and Madre de Dios regions between August 2022 and February 2023.

Genomic insights into ESBL-producing isolated from non-human primates in the Peruvian Amazon.

Introduction: Extended-spectrum beta-lactamase (ESBL)-producing 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 (ESBL-producing ) in NHP from the Peruvian Amazon.

Genomic data of global clones of CTX-M-65-producing Escherichia coli ST10 from South American llamas inhabiting the Andean Highlands of Peru.

Background: The global spread of extended-spectrum β-lactamase (ESβL)-producing Escherichia coli has been considered a One Health issue that demands continuous genomic epidemiology surveillance in humans and non-human hosts.

Objectives: To report the occurrence and genomic data of ESβL-producing E. coli strains isolated from South American llamas inhabiting a protected area with public access in the Andean Highlands of Peru.

Genomic analysis of multidrug-resistant Escherichia coli strains carrying the mcr-1 gene recovered from pigs in Lima-Peru.

Antibiotic resistance is a current problem that significantly impacts overall health. The dissemination of antibiotic resistance genes (ARGs) to urban areas primarily occurs through ARG-carrying bacteria present in the gut microbiota of animals raised in intensive farming settings, such as pig production. Hence, this study aimed to isolate and analyzed 87 Escherichia coli strains from pig fecal samples obtained from intensive farms in Lima Department.

The genomic approach of antimicrobial resistance of Salmonella Typhimurium isolates from guinea pigs in Lima, Peru.

Salmonella Typhimurium is an important agent of foodborne diseases. In Peru, the emergence of multidrug-resistant isolates of S. Typhimurium from the food chain could be linked to guinea pig farming as a potential reservoir and their uncontrolled antibiotic treatment against salmonellosis.

Genomic Characterization of Typhimurium Isolated from Guinea Pigs with Salmonellosis in Lima, Peru.

subsp. serovar Typhimurium ( 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 serotypes.

Carnivore protoparvovirus 1 in Peruvian dogs: Temporal/geographical and evolutionary dynamics of virus.

Canine parvovirus (CPV) has been recognized all around the world as the causal agent of a contagious and highly mortal disease in domestic dogs. In Peru, the infection is endemic and unvaccinated animals and puppies are the most at risk. In order to analyze viral diversity and determine the evolutionary genetic relationships and transmission dynamic of Peruvian CPV-2, were collected during the period of 2016-2017 rectal swabs from puppies with parvovirosis compatible symptoms.