Genomic-wide analysis approach revealed genomic similarity for environmental Mexican S. Oranienburg genomes.

As the human population grows, an increase in food trade is needed. This elevates the risk of epidemiological outbreaks. One of the prevalent pathogens associated with food production in Mexico has been Salmonella Oranienburg. Effective surveillance systems require microbial genetic knowledge. The objective of this work is to describe the genetic composition of Mexican S. Oranienburg genomes. For that, 53 strains from different environmental sources were isolated and sequenced. Additionally, 109 S. Oranienburg genomes were downloaded. Bioinformatic analyses were used to explore the clonal complex and genomic relatedness. A major clonal group formed by ST23 was identified comprising four STs. 202 SNPs were found the maximum difference among isolates. Virulence genes for host invasion and colonization as rpoS, fimbria type 1, and, T3SS were found common for all isolates. This study suggests that Mexican S. Oranienburg strains are potential pathogens circulating continuously in the region between host and non-host environments.

Norovirus and human adenovirus occurrence and diversity in recreational water in a karst aquifer in the Yucatan Peninsula, Mexico.

AIMS: To determine the seasonal occurrence and diversity of norovirus (NoV) and human adenovirus (HAdV) in groundwater from sinkholes, and brackish water used for recreational activities in the karst aquifer of the Yucatan Peninsula, Mexico. METHODS AND RESULTS: Hollow fibre ultrafiltration was used to concentrate viruses and standard plaque assay methods were used to enumerate somatic and F+ specific coliphages as viral indicators. Real-time quantitative polymerase chain reaction assays were used to estimate the number of genome copies for NoV strains GI, and GII, and HAdVs. The predominant NoV genotypes and HAdV serotypes were identified by comparative sequence analysis. Somatic and male F+ specific coliphages were detected at concentrations up to 94 and 60 plaque-forming units per 100 ml respectively. The NoV genogroup I (GI) was associated with 50% of the sampled sites during the rainy season only, at concentrations ranging from 120 to 1600 genome copies per litre (GC l-1 ). The NoV genogroup II (GII) was detected in 30 and 40% of the sampled sites during the rainy and dry seasons, respectively, at concentrations ranging from 10 to 290 GC l-1 . During the rainy and dry seasons, HAdVs were detected in 20% of the sites, at concentrations ranging from 24 to 690 GC l-1 . Identification of viral types revealed the presence of NoV GI.2, GII.Pe, GII.P16 and GII.P17, and HAdV F serotypes 40 and 41. CONCLUSIONS: These findings demonstrate that NoVs and HAdVs are prevalent as virus contaminants in the karst aquifer, representing potential health risks particularly during the rainy season, in one of the most important areas used for tourism in Mexico. SIGNIFICANCE AND IMPACT OF THE STUDY: This is one of the few studies conducted in karst aquifers that provide a foundational baseline of the distribution, concentrations and diversity of NoVs and HadVs in these particular environments.

Molecular sequence typing reveals genotypic diversity among Escherichia coli isolates recovered from a cantaloupe packinghouse in Northwestern Mexico.

The increase in the consumption of fresh produce has correlated with a rise in the number of reported foodborne illnesses. To identify potential risk factors associated with postharvest practices, the present study employed multilocus sequence typing (MLST) for the genotypic classification of Escherichia coli isolates recovered from three sources sampled at seven operational stages in a cantaloupe packinghouse in Northwestern Mexico. The MLST analysis results indicated that the E. coli isolates were classified into 18 different sequence types (ST), and 11 of these STs were found to be novel. ST-171 was the predominant type and was found in 19% (7/36) of the recovered isolates. Interestingly, the novel ST-827 was found to be significantly associated with isolates recovered from workers' hands, sampled during final postwash stages. Further phylogenetic analyses to examine the relatedness of the STs revealed genetic heterogeneity. Fourteen of the identified STs were assigned to known clonal groups, while the remaining four novel STs were distinct and did not cluster with any clonal group. The present study has provided the first evidence indicating that several sources from distinct operational stages in a cantaloupe packinghouse may contribute to a genotypic and phylogenetic diverse set of E. coli isolates. SIGNIFICANCE AND IMPACT OF THE STUDY: Packinghouses can be considered as a potential source of microbial contamination. Using multilocus sequence typing, this study identified a genotypic and phylogenetic diverse set of Escherichia coli isolates recovered from the surfaces of cantaloupes, workers' hands and processing equipment at a cantaloupe packinghouse. A total of 61% of the sequence types identified were novel, and a distinct sequence type, ST-827, was significantly associated with worker's hands, sampled during the final postwash operational stages in the packinghouse. These findings serve as a baseline to identify potential sources of microbial contamination at distinct operational stages in a cantaloupe packinghouse.

Genomic signatures of adaptation to natural settings in non-typhoidal Salmonella enterica Serovars Saintpaul, Thompson and Weltevreden.

Salmonella enterica is a pathogenic bacterium responsible for intestinal illness and systemic diseases such as typhoid and paratyphoid fevers. Among clinical manifestation classification, non-typhoidal Salmonella is mainly known as foodborne pathogen associated with the consumption of fecal contaminated food and water. Even though Salmonella hosts include humans and warm-blooded animals, it has been found in non-host environments as river water where the bacteria use different strategies to fitness the environment persisting and establishment. Now with the availability of WGS and bioinformatics tools, we can explore bacterial genomes with higher resolution to increase our understanding of specific genetic signatures among environmental and clinical isolates, being the goal of this work. Pangenome construction allowed the detection of specific environmental and clinical gene clusters related to metabolism and secretion systems as the main signature respectively. Specifically, D-galactonate degradation pathway was observed mainly in environmental genomes while T3SS and flagellum genes were detected for all clinical but not for all environmental isolates. Gene duplication and pseudogenes accumulation were detected as the main adaptation strategy for environmental isolates; thus, isolation source may play an important role in genome plasticity, conferring a selective advantage to survive and persist for environmental Salmonella isolates. Intact prophage sequences with cargo genes were observable for both isolation sources playing an important role in virulence contribution.

Closed Genome Sequences of Three Salmonella enterica Strains Belonging to Serovars Saintpaul, Weltevreden, and Thompson, Isolated from Mexico.

Here, we report the genome sequences of three Salmonella enterica strains belonging to serovars Weltevreden (CFSAN047349), Saintpaul (CFSAN047351), and Thompson (CFSAN047352), isolated from river water in Sinaloa, Mexico. The genomes were closed by a combination of long-read and short-read sequencing. The strain sequence types (STs) are ST365, ST50, and ST26, respectively.