Li Bai

Background/Objectives: Multidrug resistant (MDR) Salmonella represents a major global public health challenge within the One Health interface. This study aimed to characterize the genomic epidemiology of Salmonella isolates from Colombia and resolve the genetic architecture of novel MDR plasmids identified in foodborne strains. Methods: A total of 90 Salmonella isolates collected between 2002 and 2009 from various food sources and food-producing animals in Colombia were analyzed using whole-genome sequencing (WGS). Bioinformatics tools were employed for serotype prediction, multi-locus sequence typing (MLST), and resistome/virulome profiling. Long-read sequencing was utilized to close the complete sequences of representative MDR plasmids. Results: 45.6% of isolates exhibited antimicrobial resistance, with seven being classified as MDR. The major serotypes identified were Uganda (n = 20), Newport (n = 10), and Braenderup (n = 10). We characterized a novel 229,037 bp IncHI1 plasmid (pCFS0255-1) harboring a copper homeostasis and silver resistance island (CHASRI) integrated with tetracycline and macrolide resistance clusters. Additionally, a 99,288 bp IncI1 plasmid (pCFS0255-2) carrying a unique aminoglycoside resistance module was resolved. Conclusions: Our findings highlight the persistence of specific Salmonella lineages in the Colombian food chain and the role of hybrid plasmids in the co-selection of metal and antibiotic resistance. The study underscores the necessity of implementing WGS-based surveillance to track emerging MDR threats.

We present a fully decentralized MD5 hash-based framework that indexes predicted coding sequences (CDSs) and computes pairwise genomic distances without locus annotation or a central database. The method is implemented in the open-source CoDing Sequence Typer (CDST) pipeline, which delivers reproducible, privacy-preserving and computationally efficient bacterial typing. Applied to 1,961 complete Salmonella enterica genomes, CDST produced distance matrices that were highly concordant with core-genome multilocus sequence typing (cgMLST) and whole-genome MLST (wgMLST), core-genome SNP, Mash and Split Kmer analysis. In a 100-genome benchmark, CDST achieved ~8× faster runtimes than cg/wgMLST workflows and reduced storage to ~4% of the original assembly FASTA size. Unsupervised clustering evaluation identified three optimal resolution levels, HC67 (outbreak-level), HC186 (lineage/serotype-level) and HC441 (global structure-level), that align well with conventional typing schemes. These levels demonstrated high internal cohesion and external consistency with conventional typing schemes. Cross-species validation on Listeria monocytogenes and Escherichia coli genomes confirmed that the pipeline recovers species-specific population structures without parameter adjustment. Collectively, CDST provides a scalable and interoperable framework for bacterial population structure analysis, suitable for surveillance and outbreak investigations across laboratories. The CDST pipeline, along with all evaluation scripts, is openly available on GitHub at https://github.com/l1-mh/CDST .

Cronobacter, a Gram-negative opportunistic pathogen, poses a significant risk to neonates. The taxonomic position of strains CFSA2021A14^T and CFSA2021A84^T, isolated from cereal-based infant noodles in China, was investigated. Phenotypic and genotypic analyses identified both strains as novel subspecies of Cronobacter dublinensis, with dulcitol utilization attributed to the presence of the gatYZABCD gene cluster. Based on ANI analysis, the strains are proposed as Cronobacter dublinensis subsp. beijingensis subsp. nov. and Cronobacter dublinensis subsp. infanticibi subsp. nov. The type strain C. dublinensis subsp. beijingensis CFSA2021A14^T (= CGMCC 1.61450^T, = JCM 35886^T) grew aerobically at 25–41 °C, with negative myo-inositol and amygdalin utilization. Strain CFSA2021A14^T genome size was 4.71 Mbp with a G + C content of 57.2%. The type strain C. dublinensis subsp. infanticibi CFSA2021A84^T (= CGMCC 1.61451^T, = JCM 35887^T) exhibited similar growth conditions to C. dublinensis subsp. beijingensis CFSA2021A14^T, but showed positive myo-inositol and amygdalin utilization. Strain CFSA2021A84^T genome size was 4.73 Mbp with a G + C content of 57.4%.