Biology subjects

Cardenas, P. A.

Publications and source records attributed to Cardenas, P. A..

7 recordsLinked to original sources

bioRxiv2023

Distribution of blaCTX-M-gene variants in E. coli from different origins in Ecuador

The increasing abundance of extended spectrum {beta}-lactamase (ESBL) genes in E. coli, and other commensal and pathogenic bacteria, endangers the utility of third or more recent generation cephalosporins, which are major tools for fighting deadly infections. The role of domestic animals in the transmission of ESBL carrying bacteria has been recognized, especially in low- and middle-income countries, however the horizontal gene transfer of these genes is difficult to assess. Here we investigate blaCTX-M gene diversity (and flanking nucleotide sequences) in E. coli from chicken and humans, in an Ecuadorian rural community and from chickens in another location in Ecuador. The blaCTX-M associated sequences in isolates from humans and chickens in the same remote community showed greater similarity from those found in E. coli in a chicken industrial operation 200 km away. Our study may provide evidence of blaCTX-M transfer between chickens and humans in the community.

microbiology↗

bioRxiv2022

Multi-omic analysis along the gut-brain axis points to a functional architecture of autism

Autism is a highly heritable neurodevelopmental disorder characterized by heterogeneous cognitive, behavioral and communication impairments. Disruption of the gut-brain axis (GBA) has been implicated in autism, with dozens of cross-sectional microbiome and other omic studies revealing autism-specific profiles along the GBA albeit with little agreement in composition or magnitude. To explore the functional architecture of autism, we developed an age and sex-matched Bayesian differential ranking algorithm that identified autism-specific profiles across 10 cross-sectional microbiome datasets and 15 other omic datasets, including dietary patterns, metabolomics, cytokine profiles, and human brain expression profiles. The analysis uncovered a highly significant, functional architecture along the GBA that encapsulated the overall heterogeneity of autism phenotypes. This architecture was determined by autism-specific amino acid, carbohydrate and lipid metabolism profiles predominantly encoded by microbial species in the genera Prevotella, Enterococcus, Bifidobacterium, and Desulfovibrio, and was mirrored in brain-associated gene expression profiles and restrictive dietary patterns in individuals with autism. Pro-inflammatory cytokine profiling and virome association analysis further supported the existence of an autism-specific architecture associated with particular microbial genera. Re-analysis of a longitudinal intervention study in autism recapitulated the cross-sectional profiles, and showed a strong association between temporal changes in microbiome composition and autism symptoms. Further elucidation of the functional architecture of autism, including of the role the microbiome plays in it, will require deep, multi-omic longitudinal intervention studies on well-defined stratified cohorts to support causal and mechanistic inference.

microbiology↗

bioRxiv2022

A Longitudinal Study of Dominant E. coli Lineages and Antimicrobial Resistance in the Gut of Children Living in an Upper Middle-income Country

The gastrointestinal tract constitutes a complex and diverse ecosystem. Escherichia coli is one of the most frequently studied and characterized species in the gut ecosystem, nevertheless, there has been little research to determine their diversity and population dynamics in the intestines of children over time. In this prospective study, a fresh fecal sample was obtained from children longitudinally over one year (30 fecal samples at sampling period 1 and 22 fecal samples at sampling periods 2 and 3). From each stool sample, five E. coli colonies were randomly selected (n = 405 E. coli isolates total) in order to characterize the genotype and phenotypic antimicrobial resistance patterns. We found that all numerically dominant E. coli lineages in childrens intestines were transient colonizers, and antimicrobial resistance phenotypes of these strains varied significantly over time without any apparent selective force. Whole-genome sequencing of 3 isolates belonging to ST131 found in one child during the sampling period I and II indicated that isolates were three different ST 131 clones that carried extended-spectrum {beta}-lactamase (ESBL) genes. IMPORTANCEThe length of residency and numeric dominance of antimicrobial-resistant E. coli may affect the extent to which an isolate contributes to the dissemination of antimicrobial resistance in a community. We studied the persistence of numerically dominant and antimicrobial-resistant lineages of E. coli in the human intestine. We found that E. coli lineages in the children's gut change considerably and rapidly over time. This study suggests that some phenotypic resistance patterns may result from the random distribution of genes in E. coli populations over time and may not be associated with differential exposure to antimicrobials.

microbiology↗

bioRxiv2021

Urbanization and altitude impact on gut microbiome of an Andean frog (Pristimantis unistrigatus)

The analysis of the intestinal microbiome in amphibians provides insights of the anthropogenic environmental impact. Pristimantis unistrigatus is an Andean amphibian species whose distribution has been recorded in Ecuador and Colombia, ranging from endemic elfin forests to urban gardens. In this study, we focus on the analysis of the P. unistrigatus microbiome 16S rRNA gene sequencing. A total of 32 specimens of P. unistrigatus were collected and analyzed from 4 locations in the Valley of Quito, Ecuador, characterized by several urban environments and altitudes. The results show that the relative abundance of bacteria is significantly different amongst groups. Clostridiales are proportionally more abundant in rural and lower altitude locations, while Erysipelotrichaceae, Desulfovibrionaceae, Enterobacteriaceae, Bacteroidaceae and Lachnospiraceae are found at higher elevations. These results highlight the importance of the evolution of the microbiome as a tool of adaptation and survival of amphibians in the present-day changing ecosystems undergoing anthropogenic stresses. ImportanceAmphibians constitutes one of the groups most vulnerable to environmental alterations. Due to their sophisticated reproductive and breeding requirements and their permeable skins to breathe, amphibians are compulsively studied as ecological indicators. The destruction of pristine habitats occurred all over the planet in recent decades has caused a catastrophic decline in amphibian populations for many species everywhere. Ecuador, being one of the most biodiverse country on Earth, hosts a huge variety of amphibians, thus offering a unique possibility of studying the biology of the amphibian species living in its ecosystems, and how they adapt to changing habitats. A direct way to diagnose the status of an amphibian population is to study the gut microbiome of the individual specimens. The gut microbiome is closely related to the hosts health and so to its ability to adapt and survive. An important output of this study is to offer indications and tools useful to conservation programs before irreversible damages are caused to the habitats and the amphibians populations still thriving in them.

ecology↗

bioRxiv2020

A longitudinal study of E. coli lineages and antimicrobial resistance in Ecuadorian children

The gastrointestinal tract (GIT) constitutes a complex and diverse ecosystem. Escherichia coli is one of the most frequently studied and characterized species in the gut ecosystem. Nevertheless, there has been little research to determine their diversity and population dynamics in the intestines of children over time. Many intestinal E. coli lineages carry antimicrobial resistance and virulence genes, which have implications in disease and public health. In this one-year prospective study, a fresh fecal sample was obtained from 30 children longitudinally for one year (n = 82 fecal samples). From each stool sample, five Escherichia coli colonies were randomly selected to characterize their genotype and phenotypic antimicrobial resistance pattern (n = 405 E. coli isolates). We found that the most numerically dominant E. coli lineages in childrens intestines were transient colonizers, and phenotypic antimicrobial resistance varied significantly over time, however, ST131 a multi-drug resistant pathogen, and 3 additional STs persisted in a childs intestine for 3 months or more. IMPORTANCEThe length of residency and numeric dominance of antimicrobial-resistant E. coli may affect the extent to which an isolate contributes to the dissemination of antimicrobial resistance. We studied the persistence of numerically dominant and antimicrobial-resistant lineages of E. coli in the human intestine and found that E. coli lineages in the gut of children change rapidly over time.

microbiology↗

bioRxiv2019

Diverse commensal E. coli clones and plasmids disseminate antimicrobial resistance genes in domestic animals and children in a semi-rural community in Ecuador

The increased prevalence of antimicrobial resistance (AMR) among Enterobacteriaceae has had major clinical and economic impacts in human medicine. Many of the multi-drug resistant (MDR) Enterobacteriaceae found in humans are community-acquired and linked to food animals (i.e. livestock raised for meat and dairy products). In this study, we examined whether numerically dominant, commensal Escherichia coli strains from humans (n=63 isolates) and domestic animals (n=174 isolates) in the same community and with matching phenotypic AMR patterns, were clonally related or shared the same plasmids. We identified 25 multi-drug resistant isolates (i.e. resistant to 3 or more antimicrobial classes) that shared identical phenotypic resistance patterns. We then investigated the diversity of E. coli clones, AMR genes and plasmids carrying the AMR genes using conjugation, replicon typing and whole genome sequencing. None of the MDR E. coli isolates (from children and domestic animals) analyzed were clonal. While the majority of isolates shared the same antimicrobial resistance genes and replicons, DNA sequencing indicated that these genes and replicons were found on different plasmid structures. Our findings suggest that nonclonal resistance gene dissemination is common in this community and that diverse plasmids carrying AMR genes presents a significant challenge for understanding the movement of AMR in a community.\n\nIMPORTANCEEven though Escherichia coli strains may share nearly identical AMR profiles, AMR genes, and overlap in space and time, the diversity of clones and plasmids challenges to research that aims to identify sources of AMR. Horizontal gene transfer appears to play a much larger role than clonal expansion in the spread of AMR in the community.

microbiology↗

bioRxiv2019

Evolutionary changes of an intestinal Lactobacillus reuteri during probiotic manufacture

Probiotic bacteria are frequently used to treat intestinal (and other types of diseases) or to improve health, however little is known about the evolutionary changes of these bacteria during probiotic manufacture. It has been observed that when bacteria adapt to a new environment, they lose the skills to thrive in the original niche. In this study, a strain of Lactobacillus reuteri was isolated from the duodenum of a mouse and subjected to 150 serial passes in milk to simulate industrial propagation of probiotic bacteria. The strain adapted to milk outperformed its ancestor in milk, but it showed reduced aptitude to grow culture media, and possibly in mouse intestines. Bacterial adaptation to milk seemed to select a number of non-synonymous mutations in metabolic genes.\n\nIMPORTANCEBacteria in the microbiota must endure hostile conditions including antagonism from other members of the microbial community. Little is known about the evolution of probiotic bacteria in the dairy industry. We show that repeated growth of L. reuteri in milk results in reduced ability to grow in culture medium and possibly colonize the mammalian intestine. Our results contribute to the notion that probiotic bacteria colonize only transiently intestines.

evolutionary biology↗