Genomic insights of S. aureus associated with bovine mastitis in a high livestock activity region of Mexico.

IMPORTANCE: Bovine mastitis, predominantly associated with gram-positive Staphylococcus aureus, poses a significant threat to dairy cows, leading to a decline in milk quality and volume with substantial economic implications. OBJECTIVE: This study investigated the incidence, virulence, and antibiotic resistance of S. aureus associated with mastitis in dairy cows. METHODS: Fifty milk-productive cows underwent a subclinical mastitis diagnosis, and the S. aureus strains were isolated. Genomic DNA extraction, sequencing, and bioinformatic analysis were performed, supplemented by including 124 S. aureus genomes from cows with subclinical mastitis to enhance the overall analysis. RESULTS: The results revealed a 42% prevalence of subclinical mastitis among the cows tested. Genomic analysis identified 26 sequence types (STs) for all isolates, with Mexican STs belonging primarily to CC1 and CC97. The analyzed genomes exhibited multidrug resistance to phenicol, fluoroquinolone, tetracycline, and cephalosporine, which are commonly used as the first line of treatment. Furthermore, a similar genomic virulence repertoire was observed across the genomes, encompassing the genes related to invasion, survival, pathogenesis, and iron uptake. In particular, the toxic shock syndrome toxin (tss-1) was found predominantly in the genomes isolated in this study, posing potential health risks, particularly in children. CONCLUSION AND RELEVANCE: These findings underscore the broad capacity for antibiotic resistance and pathogenicity by S. aureus, compromising the integrity of milk and dairy products. The study emphasizes the need to evaluate the effectiveness of antibiotics in combating S. aureus infections.

Genomic characteristics of Salmonella Montevideo and Pomona: impact of isolation source on antibiotic resistance, virulence and metabolic capacity.

Salmonella enterica is known for its disease-causing serotypes, including Montevideo and Pomona. These serotypes have been found in various environments, including river water, sediments, food, and animals. However, the global spread of these serotypes has increased, leading to many reported infections and outbreaks. The goal of this study was the genomic analysis of 48 strains of S. Montevideo and S. Pomona isolated from different sources, including clinical. Results showed that environmental strains carried more antibiotic resistance genes than the clinical strains, such as genes for resistance to aminoglycosides, chloramphenicol, and sulfonamides. Additionally, the type 4 secretion system, was only found in environmental strains. .Also many phosphotransferase transport systems were identified and the presence of genes for the alternative pathway Entner-Doudoroff. The origin of isolation may have a significant impact on the ability of Salmonella isolates to adapt and survive in different environments, leading to genomic flexibility and a selection advantage.

Genomic Surveillance of SARS-CoV-2 in México: Three Years since Wuhan, China's First Reported Case.

OBJECTIVE: The aim of this work was to analyze the metadata of the SARS-CoV-2 sequences obtained from samples collected in Mexico from 2020 to 2022. MATERIALS AND METHODS: Metadata of SARS-CoV-2 sequences from samples collected in Mexico up to 31 December 2022 was retrieved from GISAID and manually cured for interpretation. RESULTS: As of December 2022, Mexican health authorities and the scientific community have sequenced up to 81,983 SARS-CoV-2 viral genomes deposited in GISAID, representing 1.1% of confirmed cases. The number of sequences obtained per state corresponded to the gross domestic product (GDP) of each state for the first (Mexico City) and the last (Tlaxcala). Approximately 25% of the sequences were obtained from CoViGen-Mex, an interdisciplinary initiative of health and scientific institutions to collect and sequence samples nationwide. The metadata showed a clear dominance of sequences retrieved by women. A similar variant distribution over time was found in Mexico and overseas, with the Omicron variant predominating. Finally, the age group with the highest representation in the sequences was adults aged 21 to 50 years, accounting for more than 50% of the total. CONCLUSIONS: Mexico presents diverse sociodemographic and economic characteristics. The COVID-19 pandemic has been and continues to be a challenge for collaboration across the country and around the world.

Prevalence and Genomic Diversity of Salmonella enterica Recovered from River Water in a Major Agricultural Region in Northwestern Mexico.

Salmonella enterica is a leading cause of human gastrointestinal disease worldwide. Given that Salmonella is persistent in aquatic environments, this study examined the prevalence, levels and genotypic diversity of Salmonella isolates recovered from major rivers in an important agricultural region in northwestern Mexico. During a 13-month period, a total of 143 river water samples were collected and subjected to size-exclusion ultrafiltration, followed by enrichment, and selective media for Salmonella isolation and quantitation. The recovered Salmonella isolates were examined by next-generation sequencing for genome characterization. Salmonella prevalence in river water was lower in the winter months (0.65 MPN/100 mL) and significantly higher in the summer months (13.98 MPN/100 mL), and a Poisson regression model indicated a negative effect of pH and salinity and a positive effect of river water temperature (p = 0.00) on Salmonella levels. Molecular subtyping revealed Oranienburg, Anatum and Saintpaul were the most predominant Salmonella serovars. Single nucleotide polymorphism (SNP)-based phylogeny revealed that the detected 27 distinct serovars from river water clustered in two major clades. Multiple nonsynonymous SNPs were detected in stiA, sivH, and ratA, genes required for Salmonella fitness and survival, and these findings identified relevant markers to potentially develop improved methods for characterizing this pathogen.

Phenotypic traits of carbon source utilization in environmental Salmonella strains isolated from river water.

Salmonella in the environment have evolved genetically to maintain a stable cell metabolism. Nevertheless, a lack of common nutrients (such as glucose) causes these strains to metabolize alternative carbon sources. In this study, 21 strains of Salmonella Oranienburg isolated from subtropical river water were evaluated to compare their adaptation and preconditioning abilities for the consumption of environmental carbon sources (ECS). The results obtained in this study attributed important biological characteristics to the adaptation of the metabolism of Salmonella strains to diverse ECS; these characteristics include but are not limited to variations in plasticity and natural preconditioning in closely related microorganisms, such as environmental isolates belonging to the serotype Oranienburg.

Metabolic plasticity of Salmonella enterica as adaptation strategy in river water.

The survival of Salmonella in subtropical river water depends on genetic and metabolic reorganization for the expression of alternative metabolic pathways in response to starvation, which allows Salmonella to use environmental carbon sources (C-sources). However, knowledge regarding the metabolic plasticity of Salmonella serotypes for C-source utilization when exposed to these conditions remains unclear. The aim of this study was to evaluate the metabolic response and level of environmental C-source consumption by environmental Salmonella (Oranienburg and Saintpaul) and clinical Salmonella (Typhi) serotypes by comparing laboratory growth against exposure to river water conditions. Metabolic characterization was performed using a Biolog® EcoPlateTM containing 31 C-sources. The results obtained under laboratory growth conditions showed that environmental serotypes used 74.1% of the C-sources, whereas the clinical serotype used 45.1%. In contrast, in river water, all strains used up to 96.7% of the C-sources. Salmonella exposure to river water increases its capacity to use environmental C-sources.

Characterization of biofilm formation by Salmonella enterica at the air-liquid interface in aquatic environments.

Survival of bacterial pathogens in different environments is due, in part, to their ability to form biofilms. Four wild-type Salmonella enterica strains, two Oranienburg and two Saintpaul isolated from river water and animal feces, were tested for biofilm formation at the air-liquid interface under stressful conditions (pH and salinity treatments such as pH 3, NaCl 4.5 w/v; pH 7, NaCl 4.5 w/v; pH 10, NaCl 4.5 w/v; pH 3, Nacl 0.5 w/v; pH 7, NaCl 0.5 w/v; and pH 10, NaCl 0.5 w/v); Salmonella Typhimurium DT104 was used as a control strain. Salmonella Oranienburg and Saintpaul from feces were moderately hydrophobic and motile, while S. Saintpaul from water and the control strain S. Typhimurium showed high hydrophobicity, which helped them form more resistant biofilms than S. Oranienburg. Under stressful conditions, all strains experienced difficulties in forming biofilms. Salmonella Saintpaul and Typhimurium expressed the red dry and rough (RDAR) morphotype and were able to form biofilm at air-liquid interface, contrarily to Oranienburg that showed incomplete rough morphology. This study contributes to the knowledge of biofilm formation as a survival strategy for Salmonella in aquatic environments.

Effect of river water exposition on adhesion and invasion abilities of Salmonella Oranienburg and Saintpaul.

This study was performed to evaluate in vitro the adherence and invasiveness capacity of Salmonella Oranienburg and Saintpaul (isolated from river water) exposed to laboratory and river water growth conditions and inoculated into epithelial HEp-2 cell. Results showed that Salmonella Oranienburg and Salmonella Saintpaul showed lower ability to adhere and invade epithelial HEp-2 cells under both growth conditions as compared to Salmonella Typhimurium reference strain. S. Oranienburg adhesion capacity was not affected by the growth conditions, while S. Saintpaul exposed to river water significantly (p < 0.05) decreased its adhesion capacity by 75.7 %. On the contrary, S. Oranienburg exposed to river water reduced its invasion efficiency by 80 %, whereas S. Saintpaul showed no differences between growth conditions. In conclusion, this study suggests that the exposure to non-host conditions, such as river water, adversely affects the adhesion and invasiveness of Salmonella serotypes differently, impacting on their ability to re-enter a new host.