Microbiology Research

The genus Kocuria includes Gram-positive and environmentally versatile bacteria, which are of biotechnological interest due to their ability to synthesize secondary metabolites. In this study, the genome of Kocuria sp. KH4, isolated from alkaline mine tailings (southeastern Mexico), was sequenced and analyzed to determine its taxonomic affiliation and explore its metabolic and adaptive potential. The assembled genome showed a size of 3.89 Mb, a GC content of 73.2%, and 3609 coding genes. Phylogenomic analyses and genomic relationship indices (ANI, AAI, and dDDH) confirmed that strain KH4 represents a novel genomospecies within the genus Kocuria. Functional analysis revealed broad metabolic diversity, with genes associated with the transport and metabolism of amino acids, carbohydrates, and inorganic ions. A total of 165 genes linked to metal resistance and homeostasis mechanisms were identified, including ABC-type transport systems and ATPases, as well as specific genes for Fe, Ni, Zn, Cu, As, and Hg. Forty-eight genomic islands were also identified, encoding a wide variety of functions and mobile genetic elements (MGEs). Furthermore, six biosynthetic gene clusters (BGCs) involved in the production of nonribosomal peptides, type III polyketides, terpenes, and siderophores were detected, suggesting a remarkable potential for the synthesis of bioactive compounds. Taken together, the results highlight this strain as a promising source of secondary metabolites with potential applications in environmental, pharmaceutical, and industrial biotechnology, underscoring the importance of Kocuria genomes as natural reservoirs of new biosynthetic pathways.

Escherichia coli (E. coli) pathotypes present in contaminated food, street food, or water are major contributors to foodborne illnesses. Polymerase chain reaction (PCR) methods are widely applied to detect and confirm E. coli pathotypes in food samples, thereby supporting outbreak prevention efforts. The objective of this study was to provide a comprehensive and reliable review of the molecular identification of E. coli isolated from street foods and to examine its public health implications. The review followed the “Preferred Reporting Items for Systematic Reviews and Meta-Analyses” (PRISMA) guidelines and included data retrieved from seven electronic scientific databases covering the period from 1 January 2015, to 15 August 2025. Relevant full-text articles were identified using the search string (“Street food”) AND (Escherichia coli), and only those that met established inclusion and exclusion criteria were selected. A total of 23 studies from Asia, Africa, Europe, and Latin America were included. These studies analyzed a wide range of street foods and beverages. MacConkey Agar and Eosin Methylene Blue Agar were the primary culture media used for the growth and isolation of E. coli. PCR was employed in 50% of the studies to amplify specific DNA segments, enabling the identification of eight E. coli pathotypes: EHEC, ETEC, EAEC (Eagg), EIEC, EPEC, UPEC, DAEC, and APEC. Additionally, a few studies reported phylogroups such as A, B1, B2, C, D, E, and Clade 1. The prevalence of E. coli in street foods varied widely, ranging from 0.5% in Chile to 100% in Mexico. Overall, this systematic review provides an updated scientific overview highlighting persistent challenges in street food safety and E. coli contamination. Across studies, three recurring issues were identified: (1) inadequate and unhygienic vending locations, (2) poor quality of food, and (3) inappropriate food preparation practices. These findings underscore the need for strategic interventions. The evidence presented could support governments and the scientific community in advancing research on E. coli in street foods and implementing corrective measures at local or regional scales, such as educational campaigns for vendors and consumers.

Intensive aquaculture and animal farming along riverbanks have emerged as significant drivers of downstream public health risks, facilitating the transmission of zoonotic pathogens and antimicrobial resistance (AMR) genes from farm effluents into natural water systems. In this study, we conducted a comprehensive 12-week water monitoring program at the Wei River in Shandong, China, using a combination of rapid detection techniques (RPA-LFD) and whole-genome sequencing to trace the origins of detected pathogens. RPA-LFD screening revealed the sequential appearance of Vibrio parahaemolyticus, Aeromonas veronii, norovirus GII, and Brucella spp. in surface water from March onward, coinciding with documented wastewater discharge events from upstream shrimp and fox farms. Subsequent isolation efforts confirmed the presence of V. parahaemolyticus and A. veronii in both river water and shrimp samples, while Brucella abortus was isolated from fox feces and water samples. Whole-genome sequencing of bacterial isolates revealed that V. parahaemolyticus strains from water and shrimp shared identical sequence types (ST150 and ST809) and resistance gene profiles, indicating a clonal relationship. Similarly, B. abortus isolates from water and fox feces differed by fewer than five SNPs, confirming farm-to-water transmission. Norovirus GII.3 and GII.6 sequences from water and fecal samples clustered phylogenetically with regional clinical strains, suggesting local circulation and environmental dissemination. Our findings highlight the critical role of river water monitoring as an early warning system for pathogen spread, emphasizing the need for integrated surveillance systems that monitor both water quality and the health of upstream farms and wildlife populations. The combined use of RPA-LFD and whole-genome sequencing provides a robust framework for real-time detection and source tracing of zoonotic pathogens, offering valuable insights for future environmental monitoring and public health interventions.