Search Results (1,167)

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. Full article

Recently, a strain of Streptococcus agalactiae serotype Ia sequence type 7 clonal complex 1 (SaIa ST7 CC1) has emerged in Latin American tilapia aquaculture as an international threat. This study evaluated outbreaks of acute streptococcosis occurring between 2021 and 2025 on commercial Nile tilapia (Oreochromis niloticus) farms in six Latin American countries, aiming to integrate molecular, clinical, pathological, and environmental data. In total, 360 moribund or recently dead fish at various production stages (larvae/fry, pre-grow-out, and grow-out) were examined, and 25 S. agalactiae isolates were serotyped and subjected to real-time PCR analysis, multilocus sequence typing (MLST), virulence and antimicrobial resistance gene profiling, and antimicrobial susceptibility testing. All isolates belonged to SaIa and shared the same ST7 CC1 MLST profile, forming a highly homogeneous cluster with reference SaIa ST7 CC1 strains previously isolated from tilapia farms in Asia. These results are consistent with the regional spread of a single clonal line. At the larval and fry stages, SaIa ST7 CC1 was associated with hyperacute septicemia, gastrointestinal hemorrhage, and frequent intestinal intussusception, whereas in pre-grow-out and grow-out fish, neurological signs were more prominent, followed by ocular signs, systemic hemorrhages, and coelomic lesions. Histopathological examination showed profuse colonization of the brain, spleen, liver, and intestine by Gram-positive cocci, accompanied by marked acute circulatory and inflammatory lesions and few chronic granulomatous responses, consistent with a rapidly progressing, highly aggressive infectious process. All outbreaks occurred during extended periods of warm water (>32 °C), with large day–night thermal gradients and reduced dissolved oxygen, suggesting that thermal stress may exacerbate disease expression in affected systems. All SaIa ST7 CC1 strains exhibited phenotypic susceptibility to florfenicol and amoxicillin, whereas 84% (21/25) and 100% (25/25) exhibited intermediate susceptibility to oxytetracycline and enrofloxacin, respectively. In total, 5 of the 21 isolates (23.8%) with intermediate susceptibility to oxytetracycline carried tetracycline resistance genes (tetM, tetO). These findings identify SaIa ST7 CC1 as a clinically significant emerging threat associated with thermally facilitated and geographically expanding streptococcosis in tilapia production in Latin America. Immediate priorities include screening imported broodstock using MLST or whole-genome sequencing (WGS), harmonized regional molecular surveillance, climate-adaptive farm management practices, prudent antimicrobial use, and serotype-matched vaccination and breeding strategies that improve both disease and heat resilience. Full article

The increasing volume of plant-based waste generated by the agri-food sector represents both an environmental challenge and an underexploited biotechnological resource. These wastes, rich in lignocellulosic compounds, constitute a natural habitat for specialized microorganisms. The aim of this article is to provide a critical review of the potential use of such wastes—specifically straw, pomace, and manure—in two complementary ways: (1) as a specific source for isolating new microbial strains with high biodegradation capacity and plant-growth-promoting potential, and (2) as a low-cost substrate for their propagation, e.g., in solid-state fermentation processes. This dual perspective represents a novel, integrative approach, as previous reviews typically address these aspects in isolation rather than considering their synergistic potential. The article discusses the relationship between the chemical composition of selected wastes (straw, pomace, manure) and the targeted selection of desirable microbiological traits. Particular emphasis is placed on advanced, integrated approaches for assessing microbial potential, combining phenotyping (zymography, activity assays), genomics (whole-genome sequencing—WGS, identification of CAZyme genes and biosynthetic gene clusters), and metabolomics (metabolite profiling, 3D MSI imaging). The limitations of individual methods are critically evaluated, and key research gaps are identified, including the need for in situ validation of omics-based findings and the development of stable microbial consortia with predictable performance under variable environmental conditions. These gaps are discussed in the broader context of circular bioeconomy and sustainable agriculture, highlighting the strategic relevance of integrating waste valorization with microbiome-based biotechnological innovations. Full article

During the COVID-19 pandemic carbapenem-resistant Acinetobacter baumannii (CRAB) were found to be the major pathogen associated with ventilator-associated pneumonia in mechanically ventilated patients. This prompted us to analyze the post-pandemic mechanisms of carbapenem resistance, antibiotic resistance trends, and molecular epidemiology of CRAB in Croatia. In total, 94 CRAB isolates from two hospital centers, including outpatient settings, were investigated. Antimicrobial susceptibility testing was performed by broth microdilution. PCR was used to detect genes encoding carbapenemases of group A, B and D and extended-spectrum β-lactamases (ESBL). Randomly selected isolates were subjected to whole resistome analysis by Inter-array CarbaResist Kit and whole-genome sequencing (WGS). Phylogenetic tree and sequence types (STs) were retrieved from WGS. Plasmid incompatibility groups were determined by PCR-based replicon typing (PBRT). All isolates were extensively drug resistant (XDR), showing resistance to ceftazidime, cefepime, piperacillin–tazobactam, imipenem, meropenem, gentamicin, amikacin and ciprofloxacin, and 13% (n = 12) were also resistant to colistin. The Hodge and CIM test exhibited poor sensitivity with only 32 and 30% of isolates being identified as carbapenemase producers, respectively. PCR identified bla_OXA-23 as the dominant carbapenemase gene in both hospitals, found in 71% of the isolates (67/94). In an outpatient setting, bla_OXA-24/40 was dominant. bla_OXA-23 and bla_OXA-72 were the only allelic variants. The Inter-array CarbaResist Kit and whole-genome sequencing (WGS) identified a variety of aminoglycoside (armA, ant(3″)-IIa, aph(3″)-Ib, aph(6)-Id) and sulphonamide resistance (sul1 and sul2) genes. The representative bla_OXA-23-positive isolates belonged to ST2, while bla_OXA-72-positive isolates were allocated to ST492. These data show that there are different populations of XDR A. baumannii between hospital and outpatients. Full article

Background/Objectives: Multidrug-resistant tuberculosis (MDR-TB) remains a major public health challenge in the WHO European Region, which reports the highest global proportion of rifampicin-resistant and MDR-TB cases. Whole-genome sequencing (WGS) has emerged as a key tool for improving drug-resistance detection and supporting molecular surveillance. However, the level of genomic implementation across Central and Eastern Europe (CEE) remains insufficiently characterized. This scoping review aimed to evaluate the use of WGS for MDR-TB in CEE countries and to classify implementation maturity using a predefined framework (L0–L4). Methods: A structured search of PubMed/MEDLINE and Web of Science identified original studies published in English between 2015 and 2026 reporting genomic applications in MDR-TB across 13 predefined CEE countries. Data were extracted on sequencing approaches, resistance prediction, transmission analysis, monitoring of new or repurposed drugs, bioinformatic pipelines, and programmatic integration. Countries were categorized according to a five-level maturity model based on documented capacity, scope of application, and integration into national tuberculosis programs (NTPs). Results: Twenty-eight studies were included. WGS was used in 23/28 studies (82.1%), predominantly for genomic resistance prediction (25/28). Transmission analysis was reported in 19/28 studies, with heterogeneous single nucleotide polymorphism (SNP) thresholds and clustering methodologies. Monitoring of resistance to new or repurposed drugs was described in 8/28 studies. No country achieved Level L4 (formally integrated genomic surveillance). Four countries were classified as L3 and nine as L2, while no L0 or L1 settings were identified. Conclusions: Countries in Central and Eastern Europe demonstrate increasing operational use of WGS for MDR-TB, primarily driven by clinical resistance prediction. However, the lack of formal integration into national surveillance systems highlights a persistent gap between technological adoption and structured public health implementation. Strengthening programmatic integration and methodological standardization is essential for advancing genomic surveillance of MDR-TB in the region. Full article

Background/Objectives: Genetic generalized epilepsies (GGE) often remit in childhood, yet a subset of adults remain pharmacoresistant with substantial morbidity. The genetic basis of adult pharmacoresistant GGE is poorly defined. This descriptive study used whole-genome sequencing (WGS) to identify recurrent coding variants and pathways associated with pharmacoresistant adult GGE. Methods: WGS was performed in ten racially diverse adults (mean age 37.2 years; range 20–52) with electroencephalographically confirmed, pharmacoresistant GGE (mean onset 13.7 years). Analysis prioritized variants present in at least 80% of participants and which were either (i) missense variants predicted deleterious with ANNOVAR or (ii) loss-of-function variants predicted high-impact from snpEff. Pathway enrichment and overlap with a commercial clinical epilepsy gene panel were assessed. Results: Filtering identified 133 unique, deleterious coding variants across 69 genes shared by at least eight participants. Four genes (APOL4, KMT2C, SON, VDR) overlapped a clinical epilepsy panel, supporting the capacity of WGS to recover clinically relevant loci. Prioritized loci implicated gastrointestinal and metabolic regulators (e.g., MUC6, PNLIPRP2), chemosensory receptors (OR10D3, OR8U1, TAS2R19), neuroimmune mediators (LILRA2, SIGLEC12, OAS2), and ion transporters (KCNJ12, P2RX5, RHBG), consistent with multifactorial mechanisms of pharmacoresistance. Conclusions: This exploratory WGS study focused exclusively on adults with pharmacoresistant GGE, revealing shared high-impact variants and convergent pathways spanning absorption/metabolism, vitamin D signaling, immunity, and ion transport. Findings broaden the genetic landscape of pharmacoresistant GGE while motivating validation in larger, multiethnic cohorts. Full article

Background: Evaluation of gene-level copy number variants (CNVs) for diagnosis and therapeutic decision making has become standard of care with next-generation sequencing (NGS), immunohistochemistry (IHC), and/or fluorescence in situ hybridization (FISH) being used to detect gene amplifications/deletions in tumor tissue. In contrast to most solid tumors, CNS cancers are challenging to evaluate by resection and/or biopsy due to the associated risks with invasive brain surgery that can also result in death or associated morbidity and therefore alternate methods are required.Methods: This study presents the analytical validation of using quantitative PCR (qPCR) to detect gene CNVs directly from cerebrospinal fluid (CSF)-derived DNA and from the Ascent^TM low-pass whole genome sequencing (LP-WGS) libraries, demonstrating concordance with the gold standard of NGS/IHC/FISH used in tumor tissue. Results: The analytical sensitivity of qPCR to detect gene amplification calls for ERBB2 (erb-b2 receptor tyrosine kinase 2) was demonstrated to be 100% and that of EGFR (epidermal growth factor receptor) was 83%, with specificities of 96% and 100%, respectively. The analytical sensitivity of qPCR to detect gene deletions for CDKN2A/2B (cyclin-dependent kinase inhibitor 2A/2B) was 60% and that for MTAP (methylthioadenosine phosphorylase) was 100% with a specificity of 100% for all three genes. Ascent^TM was demonstrated to have a higher sensitivity (100%) when compared to qPCR for the same genes evaluated and demonstrated 100% positive agreement and 100% negative agreement with known CNV status. Conclusions: The results demonstrate that given the paucity of cells in CSF limiting the use of IHC and FISH, qPCR and Ascent^TM provide highly sensitive, novel, minimally invasive methods for the evaluation of gene copy number (CN) status to inform the diagnosis and management of CNS cancers. Full article

Bacteria associated with unhatched sea turtle eggs remain poorly characterized at the genomic level. This study provides genome-scale characterization of bacterial isolates recovered from unhatched green sea turtle (Chelonia mydas) eggs at Akyatan Beach—a critical nesting site in the Eastern Mediterranean. Sampling 30 nests during the nesting season, we isolated bacteria from infected eggshells and dead embryos. Following Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry(MALDI-TOF MS) identification and 16S rRNA validation, we performed whole-genome sequencing (WGS) on Citrobacter farmeri and Enterobacter cloacae, two opportunistic pathogens of significant clinical and ecological concern. High-quality draft genomes revealed remarkable metabolic versatility, particularly within carbon and nitrogen pathways. Most notably, we identified extensive resistomes including resistance to $\beta$-lactams, fluoroquinolones, and aminoglycosides, alongside virulence factors for adhesion and iron acquisition. ANI analysis confirmed high genomic similarity to clinical reference strains, comparative genomic analysis revealed a substantial accessory gene pool, suggesting potential genomic flexibility between the two isolates. These findings provide the first genome-scale insight into these pathogens in C. mydas nests, and highlighting their genomic potential for opportunistic pathogenicity. Our results advocate for integrating genomic microbial surveillance into nesting beach management through a ‘One Health’ lens. Full article

Food safety systems are undergoing a profound and urgent transformation, shifting from traditional end-product inspection models toward integrated, preventive, and predictive approaches supported by digital, genomic and data-driven technologies. Conventional frameworks face increasing limitations in the context of globalized supply chains, climate variability, emerging hazards, and growing sustainability demands. This structured narrative review critically examines the technological and governance trends driving the transition toward digital and predictive food safety systems, with particular emphasis on their implications for sustainability. Key enabling technologies (including artificial intelligence (AI), whole-genome sequencing (WGS), Internet of Things (IoT)-based monitoring, blockchain-enabled traceability, and predictive analytics) are analyzed in terms of their capacity to enhance early hazard detection, real-time surveillance, and risk anticipation across the food supply chain. Beyond a descriptive overview, this review integrates technological, regulatory, and governance dimensions to identify convergence points, implementation barriers, and sustainability trade-offs, with particular attention to small and medium-sized enterprises and low- and middle-income countries. Furthermore, a four-level Digital Maturity Framework is proposed to conceptualize progressive stages of technological integration, providing a structured pathway for the evolution from reactive to predictive food safety systems. While digital and predictive approaches offer significant potential to reduce food losses, improve transparency, and strengthen evidence-based decision-making, their effective implementation remains constrained by infrastructure gaps, data governance challenges, regulatory fragmentation, and unequal access to digital capabilities. Achieving resilient and sustainability-oriented food safety systems will therefore require coordinated innovation, regulatory harmonization, and inclusive digital transformation strategies. Full article

The reproductive traits of sheep are very important characteristics influencing productivity. Among these, gestation length (GL) is an important trait with positive or negative influences on birth weight, lamb survival, lambing intervals, ease of lambing, and the dam’s health. This review evaluates the existing knowledge of genetic and environmental factors influencing reproductive traits, with a focus on GL in sheep, and the potential of this knowledge to inform effective molecular breeding programs. The mean GL for sheep is 147 days, generally ranging from 142 to 152 days. Both extremely long and extremely short GL may have either positive or negative effects on sheep rearing. Variations among breeds and within populations arise from complex interactions between nature and nurture. GL has a moderate level of heritability, indicating that genetic factors contribute to phenotypic variation in this trait. The GL is a result of gene-regulatory pathway interactions, hormonal signaling, placental, and fetal–maternal communication. Three stages of gestation are characterized by distinct patterns of gene expression, hormonal regulation, and physiological functions. Advances in genomic technologies, including whole-genome sequencing (WGS) and genome-wide association studies (GWAS), have enhanced the ability to identify the genetic determinants of GL and facilitate their incorporation into molecular breeding strategies. In addition, the invention of molecular biology in the discovery of single-nucleotide polymorphisms (SNPs), insertion/deletion (InDels), and copy number of variants (CNVs) has created new opportunities to uncover the molecular basis of GL. In general, this review offers a comprehensive framework that identifies genetic and environmental determinants of GL and describes their practical implications for sustainable sheep breeding. Full article

Background/Objectives: Acinetobacter baumannii is a critical opportunistic pathogen causing severe healthcare-associated infections, particularly in intensive care units. The global dissemination of carbapenem-resistant A. baumannii (CRAB) and its environmental persistence necessitate continuous genomic surveillance to monitor high-risk clones. Methods: We conducted whole-genome sequencing (WGS), core genome multi-locus sequence typing (cgMLST), and phylogenomic analyses on 26 CRAB isolates collected at the National Institute for Infectious Diseases (INMI) “Lazzaro Spallanzani” IRCCS (September 2023–September 2024). Antimicrobial resistance determinants, virulence-related genes, and capsular (KL) and lipooligosaccharide outer core (OCL) loci were characterized by interrogation of comprehensive bioinformatic pipelines. Results: All CRAB isolates displayed an extensively drug-resistant (XDR) phenotype, with a shared resistance pattern to carbapenems, aminoglycosides, fluoroquinolones, fosfomycin, and sulfonamides, while being susceptible only to colistin and cefiderocol. The carbapenemase gene bla_OXA-23 was detected in all CRAB isolates, together with clone-specific bla_OXA-51-like variants. For all isolates, the resistome profile fully matched the observed resistance phenotype. All isolates belonged to the International Clonal Lineage II (ICL II), Pasteur Sequence Type (ST) 2, and Oxford ST369, ST208, and ST455. Integration of cgMLST data with phylogenomic analyses and genome-based classification of KL and OCL loci revealed five distinct clusters, each one including nearly identical isolates, indicating both intra-hospital dissemination and possible inter-hospital transmission. Virulome profiling revealed heterogeneous repertoires of virulence-associated genes, resulting in cluster-specific patterns, while patristic analysis identified phylogenetic clusters linking the study isolates to other Italian and other European lineages. Conclusions: This study underscores the complex genomic landscape of CRAB in our setting, driven by the circulation of different ICL II clonal types, and reinforces the urgency of integrated genomic surveillance and robust antimicrobial stewardship to mitigate the spread of high-risk XDR A. baumannii clones. Full article

Background: High infectious disease burden and uncontrolled antibiotic usage across human, animal, and environmental contaminants make antimicrobial resistance (AMR) a growing public health problem in Africa. Mobile genetic elements (MGEs) such plasmids, transposons, integrons, conjugative elements, and phages help spread AMR via horizontal gene transfer (HGT) across human, animal, food, and environmental sources. Despite growing evidence for antibiotic resistance genes (ARGs), Africa lacks a one-health-focused synthesis of mobile genetic element-mediated AMR. Objective: This systematic review and meta-analysis aimed to consolidate information on MGEs and ARGs in AMR dissemination throughout Africa’s one health interface. Methods: The literature was searched using PubMed, Scopus, and ScienceDirect. Observational. molecular epidemiology, whole genome sequencing (WGS), and metagenomic investigations of MGE-associated AMR in Africa were eligible. The study selection, data extraction, and quality assessment were performed by two independent reviewer and quality was graded using ROBVIS 2 utilizing Rayyan software. Narrative synthesis, random-effect meta-analysis, subgroup analysis, and meta-regression were utilized. Results: A total of 109 studies were included, with 91 studies contributing to the meta-analysis. MGEs reported were plasmids (71.7%) and integrons (54.8%). ARGs carried by MGEs were blaCTMX-M-15 (78.6%), Sul2 (69.6%), blaTEM (59.1%), and tetA (49.9%). Horizontal gene transfer was seen in 259 instances; however, transmission was unclear. In 442 observations, transmission pathways across human, animal, and environmental interfaces showed AMR prevalence of 75.1% in human, 98.0% in human–animal, and 61.3% in one health interface. Whole-genome sequencing was the most frequently used method for detecting MGEsThe pooled pathogen and AMR prevalence rates were 73.3% (95% CI: 60.5–83.7%) and 94% (95% CI: 85–98%), with significant heterogeneity (I² = 97.8% and 97.4%, respectively). The prevalence of Escherichia coli was 93% and Salmonella enterica 85% in subgroup analysis. Fluoroquinolones, aminoglycosides, and beta-lactams were prevalent in humans (89.7%) and human–animal interactions (98.0%) according to AMR Class. Conclusions: Horizontal gene transfer has propagated MGE-mediated antimicrobial resistance across human, animal, and environmental interfaces in Africa. To combat AMR in Africa, coordinated, genomics-informed One Health surveillance and antibiotic stewardship are needed. Due to variability and publication bias, these data should be considered cautiously. Pooled data may only show descriptive patterns, and not necessarily precise continent-wide prevalence estimates. Full article

Hereditary breast cancer (BC) remains unexplained in a substantial proportion of families who test negative for BRCA1/2 and other known susceptibility genes. To contribute to the genomic characterization of these unresolved cases, we generated a whole-genome sequencing (WGS) dataset from six women belonging to two unrelated high-risk families, each comprising three sisters diagnosed with BC. All participants had previously received negative results in conventional multigene panel testing. WGS was performed on peripheral blood DNA using the Illumina NovaSeq platform, followed by variant calling against GRCh38 and the comprehensive annotation of single-nucleotide variants, indels, and structural variants. For each family, we identified shared ClinVar-annotated variants, rare exonic or splice-site alterations, and intronic variants located within a curated set of 286 cancer-related genes. The dataset includes per-patient VCF files, copy number variation annotations, and family-level variant summaries. Raw and processed data are publicly available through the Sequence Read Archive and Zenodo. This resource supports variant reinterpretation, exploration of regulatory and intronic regions, and methodological benchmarking in the study of familial BC beyond established susceptibility genes. Full article

Background/Objectives: Multidrug-resistant (MDR) Escherichia coli resistant to third-generation cephalosporins are a growing One Health concern, but data on extraintestinal pathogenic E. coli (ExPEC) from wildlife in North Africa remain scarce. We aimed to characterize ESBL/AmpC-producing ExPEC from captive wild mammals in Tunisia and to situate these isolates in a global genomic context. Methods: In 2018, 30 fecal samples from 14 captive wild mammals in a private farm were screened on cefotaxime agar. Four cefotaxime-resistant E. coli isolates were recovered from a llama, lion, hyena, and tiger. Antimicrobial susceptibility testing and Illumina whole-genome sequencing were combined with in silico typing, resistome and virulome profiling, plasmid and mobile element analysis, human pathogenicity prediction and core-genome MLST-based minimum-spanning trees. Results: All isolates were MDR but remained susceptible to carbapenems, colistin and tigecycline. Two ST162/B1 isolates from the llama and tiger carried bla_CMY-2, whereas two ST69/D isolates from the lion and hyena harbored bla_CTX-M-15 and qnrS1. Genomes encoded 61–68 antimicrobial resistance genes and 114–131 virulence-associated genes, together with IncF-, IncI1- and IncY-type plasmids and IS26-rich insertion sequence profiles. Mating-out assays yielded cefotaxime-resistant transconjugants, supporting plasmid transferability of bla_CMY-2 or bla_CTX-M-15. PathogenFinder predicted a ≥0.93 probability of human pathogenicity for all isolates. cgMLST-based trees showed that Tunisian ST69 and ST162 clustered within internationally disseminated lineages containing human, animal and food isolates, rather than forming wildlife-restricted branches. Conclusions: Captive wild mammals in Tunisia can harbor high-risk ExPEC lineages combining ESBL/AmpC production, multidrug resistance and extensive virulence and mobility gene repertoires. These findings highlight captive wildlife as potential reservoirs and sentinels of clinically relevant E. coli and underscore the need for integrated WGS-based One Health surveillance at the human–animal–environment interface in North Africa. Full article

Tocosh, an ancestral fermented potato product, relies on spontaneous processes near freshwater springs under extreme high-altitude conditions and represents an underexplored reservoir of microbial diversity with significant potential for the discovery of probiotics. This study provides, for the first time, a comprehensive probiogenomic characterization of 19 lactic acid bacteria (LAB) isolated from tocosh, in the Peruvian Andes, at three distinct altitudes—2992, 3882, and 4451 m above sea level (m.a.s.l.)—using whole genome sequencing (WGS) and bioinformatic profiling. A total of six species were identified: Lactiplantibacillus plantarum and Levilactobacillus brevis at all three study sites, Lacticaseibacillus paracasei and Lentilactobacillus buchneri at the lowest altitude (2992 m.a.s.l.), and Latilactobacillus curvatus and Latilactobacillus sakei at the highest altitudes (3882 and 4451 m.a.s.l.). Our results reveal that the extreme Andean environment is associated with stability in L. plantarum (genome sizes from 3.36 to 3.38 Mb) across all altitudinal levels. Functional analysis using CAZymes determined that L. brevis and L. buchneri act as primary degraders (high percentage of glycosyl hydrolases/carbohydrate binding) while L. curvatus and L. sakei function as primary builders through exopolysaccharide biosynthesis, likely a cryoprotective adaptation preventing cell damage during cold temperatures at high altitudes. Additionally, L. sakei and L. plantarum exhibited unique auxiliary activity (AA) enzymes, suggesting an oxidative mechanism to breach recalcitrant starch surfaces. All isolates were confirmed as genomically safe, lacking transferable antibiotic resistance genes and virulence factors. Pathogenic risk potential scores (PPRS) were consistently ≤2.0, fulfilling qualified presumption of safety (QPS) criteria. These findings provide the first genomic characterization of tocosh-associated LAB, establishing a basis for tocosh standardization, enabling the rational design of starter cultures that preserve ancestral traits and ensure microbiological safety in modern food applications. Full article