A Comprehensive Study of Historical Detection Data for Pathogen Isolates from U.S. Cattle

Foodborne pathogens pose substantial health hazards and result in considerable economic losses in the U.S. Fortunately, the National Center for Biotechnology Information Pathogen Detection Isolates Browser (NPDIB) provides valuable access to antimicrobial resistance (AMR) genes and antimicrobial assay data. This study aimed to conduct the first comprehensive investigation of AMR genes in pathogens isolated from U.S. cattle over the past decade, driven by the urgent need to address the dangers of AMR specifically originating in pathogens isolated from U.S. cattle. In this study, around 28,000 pathogen isolate samples were extracted from the NPDIB and then analyzed using multivariate statistical methods, mainly principal component analysis (PCA) and hierarchical clustering (H-clustering). These approaches were necessary due to the high dimensions of the raw data. Specifically, PCA was utilized to reduce the dimensions of the data, converting it to a two-dimensional space, and H-clustering was used to better identify the differences among data points. The findings from this work highlighted Salmonella enterica and Escherichia coli as the predominant pathogens among the isolates, with E. coli being the more concerning pathogen due to its increasing prevalence in recent years. Moreover, tetracycline was observed as the most commonly resistant antimicrobial, with the resistance genes mdsA, mdsB, mdtM, blaEC, and acrF being the most prevalent in pathogen isolates from U.S. cattle. The occurrence of mdtM, blaEC, acrF, and glpT_E448k showed an increase in pathogens isolated from U.S. cattle in recent years. Furthermore, based on the data collected for the locations of AMR cases, Texas, California, and Nebraska were the major areas carrying major AMR genes or antimicrobials with detected resistance. The results from this study provide potential directions for targeted interventions to mitigate pathogens' antimicrobial resistance in U.S. cattle.

Hybrid Genomic Analysis of Salmonella enterica Serovar Enteritidis SE3 Isolated from Polluted Soil in Brazil

In Brazil, Salmonella enterica serovar Enteritidis is a significant health threat. Salmonella enterica serovar Enteritidis SE3 was isolated from soil at the Subaé River in Santo Amaro, Brazil, a region contaminated with heavy metals and organic waste. Illumina HiSeq and Oxford Nanopore Technologies MinION sequencing were used for de novo hybrid assembly of the Salmonella SE3 genome. This approach yielded 10 contigs with 99.98% identity with S. enterica serovar Enteritidis OLF-SE2-98984-6. Twelve Salmonella pathogenic islands, multiple virulence genes, multiple antimicrobial gene resistance genes, seven phage defense systems, seven prophages and a heavy metal resistance gene were encoded in the genome. Pangenome analysis of the S. enterica clade, including Salmonella SE3, revealed an open pangenome, with a core genome of 2137 genes. Our study showed the effectiveness of a hybrid sequence assembly approach for environmental Salmonella genome analysis using HiSeq and MinION data. This approach enabled the identification of key resistance and virulence genes, and these data are important to inform the control of Salmonella and heavy metal pollution in the Santo Amaro region of Brazil.

Production of (2S)-sakuranetin from (2S)-naringenin in Escherichia coli by strengthening methylation process and cell resistance

(2S)-Sakuranetin is a 7-O-methylflavonoid that has anticancer, antiviral, and antimicrobial activities. Methylation process is involved in biosynthesizing (2S)-sakuranetin from (2S)-naringenin, in which S-adenosylmethionine (SAM) serves as the methyl donor. In this study, after methyl donor and substrate inhibition were identified as limiting factors for (2S)-sakuranetin biosynthesis, an efficient (2S)-sakuranetin-producing strain was constructed by enhancing methyl donor supply and cell tolerance to (2S)-naringenin. Firstly, PfOMT3 from Perilla frutescens was selected as the optimal flavonoid 7-O-methyltransferase (F7-OMT) for the conversion of (2S)-naringenin to (2S)-sakuranetin. Then, the methylation process was upregulated by regulating pyridoxal 5′-phosphate (PLP) content, key enzymes in methionine synthesis pathway, and the availability of ATP. Furthermore, genes that can enhance cell resistance to (2S)-naringenin were identified from molecular chaperones and sRNAs. Finally, by optimizing the fermentation process, 681.44 mg/L of (2S)-sakuranetin was obtained in 250-mL shake flasks. The titer of (2S)-sakuranetin reached 2642.38 mg/L in a 5-L bioreactor, which is the highest titer ever reported. This work demonstrates the importance of cofactor PLP in methylation process, and provides insights to biosynthesize other O-methylated flavonoids efficiently in E. coli.

Investigation of the Genes Involved in the Outbreaks of Escherichia coli and Salmonella spp. in the United States

Salmonella spp. and Escherichiacoli (E. coli) are two of the deadliest foodborne pathogens in the US. Genes involved in antimicrobial resistance, virulence, and stress response, enable these pathogens to increase their pathogenicity. This study aims to examine the genes detected in both outbreak and non-outbreak Salmonella spp. and E. coli by analyzing the data from the National Centre for Biotechnology Information (NCBI) Pathogen Detection Isolates Browser database. A multivariate statistical analysis was conducted on the genes detected in isolates of outbreak Salmonella spp., non-outbreak Salmonella spp., outbreak E. coli, and non-outbreak E. coli. The genes from the data were projected onto a two-dimensional space through principal component analysis. Hierarchical clustering was then used to quantify the relationship between the genes in the dataset. Most of the outlier genes identified in E. coli isolates are virulence genes, while outlier genes identified in Salmonella spp. are mainly involved in stress response. Gene epeA, which encodes a high-molecular-weight serine protease autotransporter of Enterobacteriaceae (SPATE) protein, along with subA and subB that encode cytotoxic activity, may contribute to the pathogenesis of outbreak E. coli. The iro operon and ars operon may play a role in the ecological success of the epidemic clones of Salmonella spp. Concurrent relationships between esp and ter operons in E. coli and pco and sil operons in Salmonella spp. are found. Stress-response genes (asr, golT, golS), virulence gene (sinH), and antimicrobial resistance genes (mdsA and mdsB) in Salmonella spp. also show a concurrent relationship. All these findings provide helpful information for experiment design to combat outbreaks of E. coli and Salmonella spp.