Search Results (850)

Background: Antimicrobial resistance is a One Health problem driven by the intricate interactions across human, animal, and environmental interfaces that enable microbial exchange and movement of mobile genetic elements encoding resistance and virulence. This study investigated the genomic epidemiology of ESBL and non-ESBL Escherichia coli across One Health interfaces in Oman. Methods: This prospective cross-sectional study analyzed 295 non-duplicate Escherichia coli isolates derived from 104 clinical, 173 animal [diseased (123) and healthy (50)], 14 sewage and four water sources. Antimicrobial susceptibility testing was performed phenotypically, and a representative subset of 50 ESBL and non-ESBL Escherichia coli from the three interfaces underwent whole genome sequencing to determine MLST, phylogroups, resistance genes, virulence determinants and plasmid replicons. Results: ESBL prevalence was highest in human isolates (73%), followed by sewage (28.6%) and animals (16.3% diseased; 8% healthy). blaCTX-M-15 predominated in humans, whereas blaCTX-M-55 dominated in animals and sewage, suggesting ecological partitioning with partial overlap. Quinolone resistance was lowest in the animal interface. Sewage isolates harbored the most complex resistome, including rmtB and plasmid-mediated quinolone resistance genes. MLST analysis revealed high diversity in human isolates, including globally recognized ExPEC lineages (ST10, ST38, ST73, ST127, ST131), while ST224 dominated in animals with evidence of possible spillover to humans. ST167 was confined to sewage, consistent with environmental maintenance of high-risk clones. Phylogroup structuring showed predominance of A, B2 and D among human isolates and A, B1, and E among animal and sewage isolates. Virulence profiling demonstrated broader virulome diversity in humans, but shared core determinants (fimH, sitA, traT) across all domains. IncFIB(AP001918) was the dominant plasmid replicon, particularly among ESBL isolates, underscoring its role in horizontal gene dissemination. Alarmingly, mutation in pmrB (V161G) was identified in a healthy animal isolate, pointing to a need for greater colistin restriction in animal husbandry. Conclusions: This study highlights plasmid-mediated resistance and shared virulence determinants linking reservoirs; although AMR profile was quite distinct across the three interfaces, human isolates demonstrated greater resistance than animal isolates, suggesting healthcare-driven AMR in Oman. Continued integrated genomic surveillance is essential to monitor gene flow and inform coordinated antimicrobial stewardship strategies. Full article

Background and Objectives: Systemic mastocytosis (SM) is a clonal mast cell disorder characterized by abnormal mast cell accumulation and activation in multiple organs, leading to mediator-related symptoms, including anaphylaxis. Drug hypersensitivity reactions (DHRs) are a major clinical challenge in SM, but their frequency and characteristics remain undefined. This study aimed to evaluate the frequency of drug allergy, identify high-risk drug groups, investigate reaction characteristics, and examine the relationship between drug reactions, baseline serum tryptase levels, and SM subtypes in patients with SM. Materials and Methods: We retrospectively analyzed 34 patients diagnosed with SM between 2009 and 2024 at Ege University Faculty of Medicine. Clinical features, SM subtypes, baseline serum tryptase levels, and DHR characteristics were recorded. Reactions to antibiotics, nonsteroidal anti-inflammatory drugs (NSAIDs), paracetamol, anesthetics, radiocontrast media (RCM), and COVID-19 vaccines were graded using the Ring and Messmer anaphylaxis classification. Results: Among 34 patients, the mean age was 48.6 ± 13.3 years, 53% were male, and 10 (29.4%) had DHRs. The most common culprit drugs were NSAIDs (17.6%) and β-lactam antibiotics (14.7%). Anaphylaxis was the predominant reaction, frequently associated with hypotension. In 5 patients (14.7%), drug-induced anaphylaxis was the initial and only manifestation of SM. No hypersensitivity reactions occurred to quinolones, general anesthetics, or COVID-19 vaccines. Median baseline tryptase was 50.25 µg/L (min–max: 8.59–200.00) overall, and 41.85 µg/L (min–max: 19.00–200.00) among those with DHRs. Conclusions: Patients with SM are at increased risk of severe DHRs, particularly to NSAIDs and beta-lactam antibiotics. In some patients, drug allergy may be the first and only manifestation of SM. Measurement of baseline serum tryptase is essential in patients with drug-induced anaphylaxis. A comprehensive allergy assessment, including tolerance testing and individualized counseling, is crucial to ensure safe pharmacological management. Full article

Antibiotic residues in aquatic products pose a serious food safety concern, whereas conventional laboratory methods often fail to meet the demand for on-site rapid screening. This study systematically reviews the research progress from 2021 to 2025 on both the risks of antibiotic residues in aquatic products and the development of rapid on-site detection technologies. First, based on a literature survey covering major aquatic products (e.g., fish, shrimp, and shellfish), the widespread occurrence of multiple antibiotics at high concentrations was documented, with quinolones and sulfonamides identified as the most frequently detected classes. To address the need for on-site testing, this review focuses on six rapid detection techniques: fluorescent sensor (FRS), lateral flow immunoassay (LFIA), surface-enhanced Raman scattering (SERS), enzyme-linked immunosorbent assay (ELISA), electrochemical sensor (ECRS), and colorimetric sensor (CRS). The core principles, technical advantages, recent application cases (e.g., integration with smartphones and novel nanomaterials), and development trends for each method are analyzed. Finally, it discusses the current challenges faced by existing on-site detection approaches and their potential solutions. Technology selection strategies tailored to different application scenarios (e.g., aquaculture farms, distribution channels, and consumer-level use) are also proposed. Full article

Background: Reusable tourniquets are widely used across clinical settings, yet their role as reservoirs of microbial contamination and antimicrobial resistance remains poorly characterized. Methods: In this cross-sectional study, 53 polyester–elastane tourniquets were collected from an Emergency Department (SR) and Operating Theater (SBO) over a 28-day period to assess bacterial burden and resistome composition. A 180-target qPCR panel targeting antibiotic and disinfectant resistance determinants was used. qPCR analysis identified 112 distinct resistance genes across all samples, with SR tourniquets harboring significantly richer resistomes than SBO (median 34 vs. 15 genes; p < 0.001). Efflux pump- and disinfectant-associated genes were pervasive, and β-lactamase and quinolone-resistance determinants increased over time in SR samples. Results: Principal component analysis showed clear segregation of resistome profiles by clinical unit and progressive enrichment over time. These findings indicate that reusable, porous tourniquets can accumulate extensive resistance gene profiles under routine clinical use, particularly in high-contact environments. Conclusions: Enhanced decontamination strategies, development of new materials or transition to single-use alternatives may be necessary to mitigate their potential contribution to environmental antimicrobial resistance in hospitals. Full article

Background: Multidrug-resistant (MDR) Escherichia coli in intensive pig production represents a persistent animal health and One Health concern. Here, we integrated quantitative phenotypic susceptibility data with whole-genome sequencing (WGS) to characterize the resistome and its inferred genomic context (chromosomal vs. plasmid-predicted contigs and mobile genetic element (MGE)-proximal regions) in swine-associated MDR E. coli from Hungary. Methods: A total of 203 E. coli isolates from large-scale pig farms were tested by broth microdilution. Based on resistance-oriented screening from an extended-spectrum β-lactamase (ESBL)-screen-positive pool, 116 isolates were subjected to whole-genome sequencing (WGS) as a resistance-enriched subset. Resistance determinants were annotated using the Comprehensive Antibiotic Resistance Database (CARD). Results: Resistance-oriented screening indicated frequent β-lactamase activity and ESBL screening positivity (110/203 and 127/203 isolates, respectively), consistent with strong antimicrobial selection pressure in the source population. Across the full phenotypic panel, 78/203 isolates (38.4%) met the MDR definition (non-susceptible to ≥3 antimicrobial classes), with marked between-farm variation (p < 0.001) but no age-group effect (p = 0.75). Non-β-lactam minimum inhibitory concentration (MIC) distributions showed pronounced, site-dependent high-MIC “tails”, most notably for tetracyclines, trimethoprim–sulfamethoxazole, fluoroquinolones, and colistin. In the WGS cohort (n = 116), we detected 82 distinct resistance determinants (5433 total occurrences), featuring a conserved chromosomal backbone enriched for intrinsic multidrug resistance components and lipid A modification pathways, alongside common plasmid- and MGE-associated acquired ARG modules involving tetracycline (tetA/tetB), sulfonamide/trimethoprim (sul/dfrA), aminoglycoside-modifying enzymes, and phenicol determinants (floR/cat). High-priority mobile determinants were rare but present, including mcr-1 (3/116; plasmid-associated) and plasmid-mediated quinolone resistance qnrB5 (2/116). Conclusions: Importantly, mobility/context inferences are restricted to this ESBL-screen-enriched WGS subset. Swine-associated E. coli from Hungarian large-scale farms harbors complex resistance architectures shaped by co-selection of mobile ARG modules on top of a pervasive chromosomal resistance backbone. Mobility-aware surveillance and stewardship are warranted to mitigate dissemination risks at the animal–environment–human interface. Full article

Quinolone antibiotic (QA) residues in various natural environments have recently received massive scientific attention. Nevertheless, there is limited information on the distribution characteristics and potential hazards of antibiotics in coastal wetlands. Here, the occurrence, spatial and seasonal distribution, and ecological risk assessment of eight QAs including pipemidic acid (PPA), ofloxacin (OFL), enrofloxacin (ENR), ciprofloxacin (CIP), sarafloxacin (SAL), lomefloxacin (LOM), flumequine (FLU), and oxolinic acid (OA) in coastal wetland were investigated through collected water, sediment, benthos, and plant samples along the Jiangsu coastline in four seasons. The results demonstrated that all selected QAs were detected with varying frequencies and degrees, and their mean concentrations in water, sediment, plants, and benthos ranged from n.d. to 6.11 ng L⁻¹, 3.10 μg kg⁻¹, 6.14 μg kg⁻¹, and 17.13 μg kg⁻¹, respectively. The seasonal differences in antibiotic concentration indicated higher values in winter and significantly lower values in summer, while no significant variations were observed between spring and autumn. Based on the risk quotient (RQ) method, the ecological risk assessment revealed medium risks for OFL, ENR, CIP, and LOM, and low or no risks of other QAs. It is suggested that the differences in PNEC values between seasons and toxicity of antibiotic mixtures should be considered in future studies for better illustration of actual risk levels. This research provides fundamental data and an assessment pattern that governments and other scientific groups all over the world could use as reference to evaluate QA residues in coastal wetlands. Full article

Non-O1/non-O139 Vibrio cholerae strains are widely distributed in aquatic environments worldwide and are increasingly recognized as potential reservoirs of antimicrobial resistance and virulence-associated determinants. In this study, we performed an integrated phenotypic and genomic analysis of 116 V. cholerae isolates collected in 2024 from environmental and clinical sources in Jiaxing, China, including 106 non-O1/non-O139 isolates, 9 O1 isolates, and 1 O139 isolate. Antimicrobial susceptibility testing showed that most isolates remained susceptible to β-lactam/β-lactamase inhibitor combinations, third-generation cephalosporins, carbapenems, and tigecycline, whereas resistance was more frequently observed for ampicillin, streptomycin, nalidixic acid, and ciprofloxacin. Based on the non-susceptibility criteria of Maitrakas et al., 19 of 116 isolates (16.4%) were classified as multidrug-resistant, whereas none met the definition of extensively drug-resistant. Genomic analysis identified diverse resistance determinants, including plasmid-mediated quinolone resistance genes (qnrVC variants) and quinolone resistance-determining region mutations in gyrA and parC. Virulence-associated genes showed heterogeneous distributions: core regulatory and hemolysis-related genes were highly prevalent, whereas classical cholera toxin genes were largely absent. Several accessory virulence factors, including the RTX toxin operon, chxA, ninth, and makA, were detected in subsets of isolates. Core genome multilocus sequence typing revealed substantial genetic diversity, with environmental and clinical isolates distributed across multiple lineages and showing no clear clustering by isolation source. Overall, these data demonstrate the diverse antimicrobial resistance, virulence-associated gene repertoires, and population structure of the Jiaxing V. cholerae collection, with particular relevance to the predominant non-O1/non-O139 population. Full article

Background/Objectives: Antimicrobial agents have revolutionized disease management in humans and animals; however, their misuse and overuse have accelerated the emergence and spread of antimicrobial resistance (AMR) and antimicrobial resistance genes (ARGs). Dairy farms are recognized as potential hotspots for ARG dissemination, particularly through Escherichia coli, which acts as a reservoir and vector of ARGs, enabling their horizontal transfer via plasmids and other mobile genetic elements. This study aimed to characterize the genomic diversity, ARG profiles, plasmid content, and phylogenetic relationships of E. coli isolated from dairy farm environments and milk using whole-genome sequencing. Methods: A total of 31 E. coli isolates recovered from soil, effluent, cow dung, and milk samples underwent deoxyribonucleic acid extraction, library preparation, and sequencing on the Illumina MiSeq platform, followed by comprehensive bioinformatic analysis. Results: The E. coli isolates exhibited 20 distinct sequence types, including one novel sequence type. Plasmids were detected in 71% of the isolates, with the IncF plasmid family being the most predominant. Furthermore, 12 ARG groups were identified, with β-lactam resistance genes detected in 67.7% of isolates. Notably, blaCTX-M genes were identified in all phenotypically confirmed extended-spectrum β-lactamase-producing isolates. Additional ARGs, including those conferring resistance to tetracyclines (tet(A), tetX4), quinolones (qnrS1), aminoglycosides (aph, aad, ant), and folate pathway inhibitors (dfr and sul), were widely distributed throughout the samples. Phylogenetic analysis revealed clustering of isolates from different sample types, particularly among ST58 isolates, suggesting cross-environmental transmission. Conclusions: This study demonstrates that E. coli from dairy farm environments harbor diverse ARGs and plasmids, confirming their role as reservoirs of AMR. These findings underscore the importance of prudent antimicrobial use, routine genomic surveillance, and enhanced biosecurity measures to limit cross-environmental transmission. Full article

Objectives: We aimed to compare the treatment success and patient compliance of triple therapy with levofloxacin, high-dose dual therapy with amoxicillin, and quadruple therapy with bismuth and levofloxacin as first-line treatment for Helicobacter pylori (H. pylori) eradication using amoxicillin 875 mg + clavulanic acid 125 mg instead of amoxicillin 1 g. Methods: Patients who tested positive for Helicobacter pylori in the histopathological examination of biopsies taken during upper gastrointestinal endoscopy were initially divided into three different treatment groups. There were 179 patients in the first group, 178 patients in the second group, and 182 patients in the third group. A total of 480 patients from these groups who came for follow-up were included in this study, with 160 patients in each group receiving one of three different treatment protocols. The first group received treatment with amoxicillin 875 mg + 125 mg clavulanic acid twice daily, levofloxacin 500 mg once daily, and pantoprazole 40 mg twice daily (Group 1). The second group received treatment with amoxicillin 875 mg + 125 mg clavulanic acid three times a day, along with pantoprazole 40 mg twice daily (Group 2) as treatment. The third group received treatment with amoxicillin 875 mg + 125 mg clavulanic acid, twice daily, levofloxacin 500 mg once daily, pantoprazole 40 mg twice daily, and bismuth subsalicylate 262 mg2 pieces four times a day (Group 3). H. pylori was checked with a stool antigen test 45 days after the 14-day treatment. The groups were compared in terms of treatment success and treatment compliance. Results: In Group 1, 150 (90.6%) of 160 patients tested negative for an H. pylori antigen in stool samples on day 45 after treatment. This rate was 139 (86.9%) in Group 2 and 148 (92.5%) in Group 3. There were no statistically significant differences between the three groups in terms of treatment success (p = 0.233). Side effects were observed in 10 (6.2%) patients in Group 1. Side effects were present in nine (5.6%) patients in Group 2. Side effects were observed in 12 (7.5%) patients in Group 3. There was no significant difference between the groups in terms of patient compliance (p = 0.786). Conclusions: Treatment success and side effects were similar in all three groups, with no statistical difference. The combination of amoxicillin 875 mg + clavulanic acid 125 mg is at least as effective as amoxicillin 1 g alone. Full article

Tularemia is a plague-like, potentially fatal zoonosis caused by the coccobacillus Francisella tularensis. It was discovered at the beginning of the last century in the United States and was soon recognized in Japan and in the former Soviet Union as the cause of clinical conditions that had been known for one and two centuries, respectively. More than 250 animal species are susceptible to infection, with rodents and lagomorphs serving as key reservoirs, and several vectors may transmit the disease, mainly ticks and mosquitoes. Humans are incidental hosts and are infected primarily by two F. tularensis subspecies, tularensis and holarctica: the former is more severe and is found almost exclusively in North America, whereas the latter is distributed throughout the Northern Hemisphere, mainly in Europe and Asia. Tularemia is highly infectious; therefore, diagnostic cultures should be handled in biosafety level 3 laboratories. Nevertheless, interhuman transmission is exceedingly rare. Although tularemia is relatively uncommon, it shows a re-emerging pattern at the global level, particularly in Europe. As with plague, mitigation may be more effectively achieved through a One Health approach. Neither approved vaccines nor therapeutic antibodies are currently available, whereas aminoglycoside, tetracycline, and quinolone antibiotics are effective. Owing to its high infectivity, its ease of transmission by inhalation, its clinical severity, with a prolonged and debilitating course, and its potential lethality, F. tularensis has long been considered a potential biological weapon, particularly if antibiotic-resistant strains were used. Although natural antibiotic resistance has not been described to date, research programs aimed at obtaining resistant strains have been conducted. It has been suggested that the disease was already present in the Middle East during the second millennium BC; should this hypothesis be confirmed by paleogenomic studies, plague and tularemia would have coexisted for more than three millennia, with plague masking the less severe tularemia. Many challenges related to tularemia are still unresolved. Full article

To establish a reliable and accurate solid-phase extraction (SPE) pretreatment method for multi-class antibiotics in water and achieve simultaneous determination of 20 antibiotics, including tetracyclines, quinolones, and sulfonamides, key pretreatment parameters were optimized via single-factor experiments in this study. The optimized parameters included pH of acidified water samples, Na₂EDTA dosage, SPE cartridge type, operational conditions, and the type and volume of elution solvent. The validated method was further applied to analyze surface water samples collected from 16 sampling sites in Poyang Lake and its three typical tributaries (Ganjiang River, Jinjiang River, and Yuanhe River) to verify its practicability, reliability, and applicability. Results showed that the optimal pretreatment conditions were as follows: water samples were acidified to pH 3.0, added with 0.2 g Na₂EDTA for metal ion chelation, enriched using Oasis^® HLB cartridges at a loading flow rate of 8–10 mL/min, and dried for 5–30 min until no obvious liquid dripped from the cartridge tip, followed by elution with 12 mL of 0.1% (V:V) formic acid in methanol. Under these conditions, the spiked recoveries of 20 antibiotics in ultrapure water were generally above 80%, and most antibiotics exhibited recoveries exceeding 90%. In addition, the spatial distribution of antibiotic concentrations in the Poyang Lake watershed followed the following order: Jinjiang River > Yuanhe River > Ganjiang River > Poyang Lake. Sulfonamides, especially sulfamethoxazole with a maximum concentration of 250.08 ng·L⁻¹, were identified as the predominant pollutants in this basin. Full article

Quinolone antibiotics (QNs) are widely used in animal production and may pose potential health risks through dietary exposure. A total of 1612 animal-derived food samples covering 10 food categories were collected in Guangzhou, China, from 2016 to 2023. Residues of six QNs were determined using ultra-performance liquid chromatography coupled with tandem mass spectrometry. Dietary exposure among different age groups was assessed using a probabilistic approach based on local food consumption data, and non-carcinogenic health risks were characterized using hazard quotient (HQ) and hazard index (HI) methods. QN residues were detected in 7.75% of samples, with an exceedance rate of 2.23%. Aquatic products, particularly fish and crustaceans, exhibited the highest detection frequencies and contributed most to overall dietary exposure. Enrofloxacin (ENR) was the most frequently detected compound, while sporadic samples showed extremely high residue concentrations (1003 unit/g in eggs). Children aged 3–6 years had the highest HI (mean is 1.94 × 10⁻²). All HQ and HI values were below 1, indicating low non-carcinogenic health risks under current exposure scenarios. Although dietary exposure to QNs among Guangzhou residents is unlikely to pose appreciable non-carcinogenic health risks, elevated exposure in children and sporadic high-residue events highlight the need for continued risk-based monitoring and targeted food safety management. Full article

Background: Extended-spectrum β-lactamase (ESBL)-producing E. coli are a major One Health concern because they compromise critically important cephalosporins and may spread via mobile genetic elements, including plasmids and transposon-associated modules, within food-animal production systems. Objectives: The aim of this study was to characterize cefotaxime (CTX)/clavulanic acid (CLA) inhibitor-positive phenotype profiles in pig-associated multidrug-resistant (MDR) E. coli and resolve their genetic basis using whole-genome sequencing, with emphasis on ESBL determinants and their predicted mobility context. Methods: MDR E. coli isolates (n = 203) from four large-scale pig farms in Hungary were tested by broth microdilution minimum inhibitory concentration (MIC) determination and Clinical and Laboratory Standards Institute (CLSI) inhibitor-based ESBL confirmation using cefotaxime with/without clavulanic acid. CTX/CLA inhibitor-positive isolates (inhibitor-positive phenotype) were subjected to whole-genome sequencing (WGS; n = 116) and resistome profiling; antimicrobial resistance genes (ARGs) were called against the Comprehensive Antibiotic Resistance Database (CARD) and mobility context was inferred using plasmid-origin and MGE-proximity prediction. Results: Overall, 127/203 isolates (62.6%) showed a CTX/CLA inhibitor-positive phenotype with a pronounced inhibitory effect (median cefotaxime/cefotaxime–clavulanate ratio: 33.3). In the sequenced subset (n = 116), 5427 ARG hits were identified (82 unique ARGs in the export), including frequent acquired determinants affecting tetracyclines, sulfonamides/trimethoprim, aminoglycosides, and phenicols; plasmid-mediated quinolone resistance (qnrB5) and mobilizable colistin resistance (mcr-1) were detected at low frequency. Classical β-lactamase genes were detected, including CTX-M (ESBL genes) and TEM alleles. CTX-M and/or TEM were detected in 47/116 genomes (40.5%), dominated by CTX-M-32 (11.2%) and TEM-1 (23.3%); detected ESBL determinants were predominantly predicted to be located on contigs predicted to be of plasmid origin, with a subset showing signatures consistent with transposition-associated mobilization. Conclusion: The high burden of inhibitor-positive phenotype, together with an inferred plasmid-/MGE-associated context for a subset of ESBL genes, and substantial phenotype–genotype heterogeneity, supports integrated phenotypic–genomic surveillance to refine AMR risk assessment and guide targeted stewardship and biosecurity interventions in pig production. Full article

Knowledge about the potential roles of pets as reservoirs for plasmid-mediated quinolone resistance is still limited in Türkiye. Thus, in our study, the presence of plasmid-mediated quinolone genes (qnrA, qnrB and qnrS) was examined by multiplex Polymerase Chain Reaction (PCR) in 101 fecal Escherichia coli (Escherichia coli) strains isolated from healthy dogs. Moreover, the relationship between the presence of qnr genes and prevalence of quinolone resistance, extended spectrum beta-lactamase (ESBL) and plasmid replicon types, mostly detected among fecal E. coli isolates (F, K, FIB, N, FIA, FIC, and Y) were investigated. A total of 41 strains (40.6%) carried at least one qnr gene. Qnr genes were found in 38.8% of quinolone-resistant and 40.9% of quinolone-susceptible strains. ESBL production was detected in 27 strains, 10 of which also harbored a qnr gene. Among qnr-positive strains, 19 (46.3%) carried both IncK and IncF plasmids (p < 0.001). IncF plasmids were significantly more prevalent in quinolone-resistant strains than in susceptible ones (p < 0.001), suggesting a potential link between qnr carriage, quinolone resistance, and IncF plasmids. To our knowledge, this is the first study investigating the relationship between qnr genes and specific plasmid replicon types in E. coli from healthy dogs in Türkiye. Our findings suggest that domestic animals may serve as reservoirs for antibiotic-resistant E. coli, underscoring the importance of a One Health approach. Full article

Background and Aims: Sepsis drives mortality in cirrhosis, yet the gut antimicrobial resistance (AMR) landscape remains unmapped in high-burden settings like India. This study aimed to integrate shotgun metagenomics with deep immunophenotyping to define the gut–immune–resistome axis and correlate specific microbial and genetic signatures with clinical outcomes in decompensated cirrhosis. Methods: We analysed 78 hospitalized patients with cirrhosis using stool shotgun metagenomics, multiplex cytokine arrays, and flow cytometry. The microbiome and resistome (AMR genes) were mapped and correlated with disease severity, immune function (monocyte HLA-DR, neutrophil CD64), and clinical endpoints including mortality. Results: Disease severity was characterized by a “Gram-negative bloom” (Klebsiella) alongside pathogenic Enterococcus expansion and novel markers: Clostridium sp. C5-48 (severe decompensation) and Sutterella (ascites). A specific, dense resistome predicted adverse outcomes; the quinolone-resistance gene QnrB4 correlated with mortality and immune paralysis, while the carbapenemase OXA-833 gene was linked to gastrointestinal bleeding. Notably, the commensal Ligilactobacillus salivarius was associated with systemic inflammatory cytokines. Conclusions: This study reveals a “pathogenic ecosystem” in Indian decompensated cirrhosis where the resistome is intrinsically linked to host immune failure. The identification of specific prognostic markers (QnrB4, OXA-833) and inflammatory associations with L. salivarius challenges generic probiotic use and underscores the urgent need for precision, resistome-targeted therapies. Full article