Biology subjects

Delgado-Suarez, E. J.

Publications and source records attributed to Delgado-Suarez, E. J..

3 recordsLinked to original sources

bioRxiv2025

Uncharacterized Acetilactobacillus-like genera represent the most abundant microorganisms in honeys produced by native stingless bee

Pot honey, the honey produced by stingless bees, is valued for its antimicrobial capacity, which may be influenced by its microbial content. While Lactobacillaceae species are commonly associated with honeybees and honey microbiomes, most studies have focused on Apis mellifera, leaving pot honey microbial diversity largely unexplored. We present the first pot honey shotgun metagenomic analysis from bee species Melipona beecheii and Scaptotrigona mexicana. We reconstructed 24 metagenome-assembled genomes (MAGs), 15 of which lacked close matches to any described species, showing[≤] 81% Average Nucleotide Identity (ANI) to available reference genomes. Phylogenetic analyses resolved these MAGs into four well-defined clades (intraclade ANI > 99%, interclade ANI[≤] 81%), consistent with four novel species within the family Lactobacillaceae. GTDB-Tk classification placed MAG clades 1 and 2 closest to Nicoliella, and clades 3 and 4 closest to Acetilactobacillus. We validated the presence of these lineages in honey by sequencing three isolates that clustered within MAG clade 2. Aminoacid similarity (AAI/cAAI) indicates the presence of two genus-level lineages: one occupying a transitional genomic space near Nicoliella, and a second representing an undescribed genus. The genomic similarity of our MAGs and isolates to those from pot honey or larval food in Malaysia, Brazil, and Australia suggests these taxa are closely associated with stingless bees and may contribute to honey properties. By reducing the genomic underrepresentation of evolutionarily divergent sister clades related to Nicoliella and Acetilactobacillus, our genome-resolved analyses reveal a globally distributed, phylogenetically cohesive Lactobacillaceae species complex dominating pot honey.

ecology↗

bioRxiv2024

Healthy carriage of Salmonella within cattle lymph nodes is a key source of ground beef contamination with strains of clinical significance

This study assessed the genetic relatedness, evolutionary dynamics, and virulence profile of Salmonella isolated from lymph nodes and ground beef from apparently healthy cattle over two years. For this purpose, we used a set of isolates of nine different serovars: Anatum (n=23), Reading (n=22), Typhimurium (n=10), London (n=9), Kentucky (n=6), Fresno (n=4), Give, Muenster, and monophasic 1,4,[5],12:i- (n=1 each). These isolates were subjected to whole genome sequencing, and assembled and annotated genomes were used for downstream bioinformatic analyses. Although lymph nodes and ground beef were collected and analyzed separately, we still observed clonality between isolates from both sources. This finding suggests that some Salmonella circulating in the gut may reach the lymphatic system, creating a dual reservoir for ground beef contamination. We also found evidence of Salmonella persistence across cattle cohorts, as we observed clonality between isolates collected in different years. Variation in the virulence and pathogenicity island profiles was limited, with minor differences that could not be associated with attenuated virulence in the bovine host. Conversely, isolates of all serovars, except Fresno, were genetically close to strains involved in human salmonellosis in different countries, highlighting the risk to public health posed by strains associated with the carrier state in cattle. Further research is needed to reveal the mechanisms by which Salmonella causes subclinical infections in cattle and persists for long periods within farm environments.

genomics↗

bioRxiv2020

Genomic surveillance of antimicrobial resistance shows cattle are a moderate source of multi-drug resistant non-typhoidal Salmonella in Mexico

Multi-drug resistant (MDR) non-typhoidal Salmonella (NTS) is a major public health concern globally. This study reports antibiotic susceptibility testing and genotypic antimicrobial resistance (AMR) profiles of NTS isolates from bovine lymph nodes (n=48) and ground beef (n=29). Furthermore, we compared genotypic AMR data of our isolates with those of publicly available NTS genomes from Mexico (n=1637). The probability of finding MDR isolates was higher in ground beef as compared to lymph nodes: {chi}2=12.0, P=0.0005. The most common resistant phenotypes involved tetracycline (40.3%), carbenicillin (26.0%), amoxicillin-clavulanic acid (20.8%), chloramphenicol (19.5%) and trimethoprim-sulfamethoxazole (16.9%), while over 55% of the isolates showed decreased susceptibility to ciprofloxacin and 26% were MDR. Occurrence of MDR isolates was strongly associated with NTS serovar ({chi}2=24.5, P<0.0001), with Typhimurium accounting for 40% of MDR strains. Most of these (9/10), carried Salmonella genomic island 1, which harbors multiple AMR genes (aadA2, blaCARB-2, floR, sul1, tetG) that confer a penta-resistant phenotype. Moreover, 100% of MDR isolates had mutations in the ramR gene. Among public NTS isolates from foods and clinical cases in Mexico to date, those from cattle had the highest proportion of MDR genotypes. Our results suggest attaining significant improvements in AMR meat safety may require the identification and removal (or treatment) of product harboring MDR NTS, instead of screening for Salmonella spp. or for isolates showing resistance to individual antibiotics. In that sense, massive integration of whole genome sequencing (WGS) technologies in AMR surveillance provides the shortest path to accomplish these goals.

genomics↗