Search Results (3,777)

Background: Antimicrobial resistance (AMR) is a growing global health threat, disproportionately affecting low- and middle-income countries such as Sudan. Conflict-related health system disruption has further intensified inappropriate antibiotic use and weakened stewardship capacity. Objective: This narrative review synthesizes contemporary evidence on antibiotic prescribing practices in Sudan, with emphasis on ambulatory care, and examines their implications for AMR control in the context of ongoing conflict. Methods: A non-systematic, structured narrative review was conducted successfully. PubMed, Google Scholar, WHO/EMRO databases, and Sudan’s National Action Plan (NAP) materials were examined for literature published between January 2010 and December 2025. Peer-reviewed research, government guidelines, surveillance reports, and gray literature were among the eligible sources. A total of 78 studies were included after titles, abstracts, and full texts were screened. Two reviewers independently confirmed the data extraction, and the synthesis aligned with SANRA guidelines. Results: Antibiotic prescribing in Sudan is frequently inappropriate, particularly in ambulatory and community settings, where empirical treatment, polypharmacy, and extensive use of Watch antibiotics are common. Alignment with WHO AWaRe recommendations remains suboptimal. Recent clinical and molecular evidence demonstrates increasing multidrug resistance among Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus, including ESBL production and emerging carbapenemase genes (e.g., NDM 1, IMP 1). Conflict-related disruptions—such as reduced laboratory capacity, supply chain breakdown, and unregulated community dispensing—have further accelerated AMR. Pilot stewardship interventions show promise but remain limited in scale. Conclusions: Inappropriate antibiotic use in Sudan is driven largely by ambulatory and community practices and has been exacerbated by conflict. Strengthening stewardship beyond hospitals, enforcing prescription-only regulations, operationalizing the AWaRe framework, and aligning empirical therapy with local resistance patterns are critical for mitigating AMR in Sudan and similar conflict-affected settings. Full article

Background: Colistin- and carbapenem-resistant Acinetobacter baumannii (CRAB) represent a critical threat in intensive care unit (ICU) settings. This study aimed to provide a comprehensive molecular epidemiological characterization of extensively drug-resistant (XDR) A. baumannii clinical isolates from a tertiary-care hospital in Kırşehir, Central Anatolia, a region previously absent from the national surveillance literature. Methods: A total of 43 non-duplicate XDR A. baumannii isolates recovered from ICU patients between November 2021 and December 2023 were included. Antimicrobial susceptibility testing was performed by automated systems and broth microdilution for colistin. Resistance genes, including OXA-type carbapenemases, extended-spectrum β-lactamases (ESBLs), metallo-β-lactamases, plasmid-mediated colistin resistance (mcr-1 to mcr-5), plasmid-mediated quinolone resistance genes (qnr, qepA, oqxAB, aac(6′)-Ib-cr), and class 1 and 2 integrons, were screened by PCR. Integron gene cassettes were characterized by sequencing. Clonal relatedness was assessed by pulsed-field gel electrophoresis (PFGE) using ApaI digestion. Results: All 43 isolates exhibited the XDR phenotype with universal resistance to carbapenems, colistin, fluoroquinolones, aminoglycosides (except amikacin), piperacillin, cephalosporins, and tobramycin. Amikacin susceptibility was retained in 58.1% of isolates. blaOXA-51 was detected in all isolates (100%), and blaOXA-23 was the predominant acquired carbapenemase (90.7%). Notably, blaOXA-48, a carbapenemase typically associated with Enterobacteriaceae, was identified in 3 isolates (7.0%), each belonging to a distinct pulsotype. No blaOXA-24/40, blaOXA-58, or class B metallo-β-lactamase genes were detected. ESBL genes were found in a subset of isolates, with blaCTX-M group 1 being the most prevalent (20.9%). The aac(6′)-Ib-cr gene was detected in 81.4% of isolates, and oqxA/oqxB in 60.5% and 39.5%, respectively. No mcr or classical qnr genes were identified. Class 1 and 2 integrons were detected in 4.7% and 7.0% of isolates, respectively, carrying dfrA12-DUF1010-aadA2 (class 1) and dfrA1-sat-1 (class 2) gene cassettes. PFGE identified 12 pulsotypes among the typeable isolates; PT4 (n = 20, 47.6%) and PT11 (n = 8, 19.0%) were the dominant clonal clusters, together accounting for 65.1% of typeable isolates. Conclusions: This study presents one of the first comprehensive molecular epidemiological analyses of XDR A. baumannii from Central Anatolia. The dominance of OXA-23-carrying clonal lineages, the detection of blaOXA-48 in A. baumannii distributed across three distinct pulsotypes, the high prevalence of aac(6′)-Ib-cr, and the concurrent distribution of resistance determinants across genetically diverse clonal backgrounds indicate that both clonal expansion and possible horizontal gene transfer contribute to resistance dissemination in this setting. These findings underscore the need for systematic molecular surveillance and reinforced infection control strategies in ICU settings, at both the regional and national levels. Full article

Background/Objectives: The emergence of colistin resistance mediated by the mcr-1 gene in Salmonella enterica poses a significant public health concern. In 2022, mcr-1 was identified for the first time in Salmonella isolates recovered from chicken meat in Saudi Arabia, prompting the need for further genomic investigation. Methods: Four Salmonella enterica isolates—two serovar Minnesota and two serovar Infantis—underwent antimicrobial susceptibility testing (AST), whole-genome sequencing (WGS), and bioinformatics analyses including antimicrobial resistance genes (ARGs), virulence factors, plasmid replicons, and mcr-1 locations. Results: All isolates exhibited resistance to colistin, polymyxin B, and multiple first-line antibiotics. All four isolates were classified as multidrug-resistant (MDR). The mcr-1 gene was plasmid-borne in all isolates, located on IncI1_1_Alpha plasmids in S. Minnesota and IncFIB(K)_1_Kpn3 plasmids in S. Infantis. Additional antimicrobial resistance genes (ARGs) were detected, including bla_CTX-M-65, qnrB5, ermB, and aminoglycoside-modifying enzymes, alongside multiple efflux pump genes. Virulence gene profiles showed minor differences between serovars, including the presence of the cdtB toxin gene in S. Infantis isolates. Phylogenetic analysis indicated that the isolates clustered within a distinct clade, suggesting a potential common local source or clonal expansion. Conclusions: This study provides the first detailed genomic insight into mcr-1-positive Salmonella isolates from food in Saudi Arabia. The co-existence of resistance and virulence determinants, together with mobile plasmids carrying the mcr-1 gene, emphasizes the risk of dissemination through the food chain. These findings highlight the urgent need for integrated genomic surveillance and strengthened antimicrobial stewardship within a One Health framework. Full article

Poultry is the main reservoir of Campylobacter spp. and most human cases result from consuming undercooked poultry or handling raw meat. In 2022, a total of 55 samples, including neck skin, cecal contents, and processing waters, were collected at two poultry slaughterhouses in Italy and analysed according to ISO 10272-2:2017 at the Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata laboratories. Overall, 51/55 (92.72%) samples tested positive for Campylobacter. Among the isolates, 64.71% were identified as C. coli, and 35.29% as C. jejuni. Phenotypic and genotypic analysis were performed to assess antimicrobial resistance and virulence characteristics. All C. jejuni isolates and 72.72% of C. coli showed resistance to fluoroquinolones. Resistances to tetracycline and carbapenem were observed in 60.78% and 45.09% of isolates, respectively. Genomic analysis confirmed the presence of the tet(O) gene, conferring tetracycline resistance. In addition, OXA-450 and OXA-466 genes, conferring beta-lactam resistance, were detected in 78.43% and 3.92% of isolates. Virulence-associated genes were detected. Specifically, the ciaB gene was found in 50/51 (98.04%) of isolates, whereas jlpA, cdtA, cdtB, and ctdC genes were exclusively identified in C. jejuni strains. The high prevalence of pathogenic and antimicrobial-resistant Campylobacter strains highlights the need for strengthened control measures along the poultry production chain. Full article

Acinetobacter baumannii (A. baumannii) is a major cause of multidrug-resistant infections, yet resistance is often interpreted from a gene-centered perspective that does not explain inconsistent treatment outcomes. This narrative review redefines resistance as a treatment-associated phenotype arising from interactions among molecular resistance mechanisms, bacterial physiology, and the infection environment. Unlike previous reviews that examine determinants in isolation, this work integrates efflux, permeability, enzymatic activity, and target modification with phenotypic states such as structured growth, metabolic adaptation, and stress response within a unified framework. Within this framework, bacterial elimination depends on whether antibiotics maintain sufficient target engagement under infection conditions. Antibiotic performance varies with local environment, population diversity, and cellular activity, which explains the gap between laboratory susceptibility results and clinical response. Antimicrobial failure therefore results from the combined effects of impaired drug exposure, adaptive bacterial physiology, and resistance mechanisms within the infection environment. Based on this framework, therapeutic strategies are reconsidered with emphasis on enhancing drug access, modulating cellular behavior, and disrupting population structures that sustain persistence. The review also highlights key gaps, including limited representation of infection environments in experimental models, insufficient resolution of population diversity, and weak integration between pharmacokinetics and bacterial physiology. This framework supports a mechanistic interpretation of resistance and therapeutic response in A. baumannii. Full article

Background/Objectives: Probiotic feed additives are increasingly used in livestock production as antimicrobial-sparing tools, yet viable microbial products should not introduce clinically relevant antimicrobial resistance genes (ARGs) into the intestinal resistome. This study evaluated farm-animal probiotic products using an integrated phenotypic, metagenomic and mobilome-aware safety framework. Methods: Seven commercially available products intended for poultry, pigs, cattle or horses were assessed using product metadata, culture-based recovery, broth microdilution minimum inhibitory concentration (MIC) profiling and Illumina short-read sequencing as a screening-level resistome approach. Reads were quality controlled, assembled, screened using the Comprehensive Antibiotic Research Database (CARD)/Resistance Gene Identifier (RGI) workflow and interrogated for plasmid-, phage- and insertion sequence/mobile genetic element-associated genomic context. Results: MIC profiles were generated for viable bacterial isolates representing Enterococcus faecium, Pediococcus acidilactici, Pediococcus pentosaceus and Bacillus subtilis. One labelled Lactobacillus plantarum component was not recovered as viable culture, and one labelled P. acidilactici component was recorded as P. pentosaceus. Sequencing-based resistome screening identified 30 antimicrobial resistance (AMR)-associated CARD antibiotic-resistant organism (ARO) hits belonging to 13 determinants across six ARG-positive coded products, while one coded product had no retained CARD/RGI hit. Profiles were dominated by recurrent Enterococcus-associated background determinants, including aac(6′)-Ii, msrC and eatAv. Plasmid prediction was positive for five hits, whereas no iMGE- or phage-associated ARG context was detected. No vanA/vanB, mcr, optrA, poxtA, cfr, extended-spectrum β-lactamase (ESBL) or carbapenemase gene was detected. Conclusions: The investigated products did not show evidence of high-priority mobile ARG carriage. Nevertheless, AMR-associated determinants and occasional predicted mobile contexts support routine integrated MIC-sequencing-based resistome–mobilome assessment of veterinary probiotic products. Because short-read assemblies do not fully resolve plasmid architecture or transferability, mobile-context predictions should be considered screening-level indicators requiring confirmatory long-read or functional testing for higher-priority findings. Full article

Antimicrobial resistance (AMR) is a global health threat that continues to concern scientists because it can be driven not only by antibiotic misuse but also by environmental factors. Mining-related heavy metal pollution can apply strong selective pressure on microbial communities, leading to a significant increase and spread of antibiotic resistance genes (ARGs) in the environmental ecosystems. Here, we critically review the emerging role of mining environments as hotspots of environmental resistomes and the mechanisms by which heavy metal contamination drives co-selection of antibiotic resistance. There is also evidence that mining environments, such as AMD systems, mine tailings, contaminated sediments, and mining-impacted soils, harbor highly diverse microbiomes enriched with different resistance determinants. Heavy metals such as copper, zinc, cadmium, mercury, and arsenic promote ARG co-selection through co-resistance, cross-resistance, and co-regulation mechanisms. Widespread co-occurrence of metal- and antibiotic-resistance genes on mobile genetic elements such as plasmids, integrons, and transposons has been demonstrated in metagenomic studies. Environmental dissemination pathways, such as water systems, agricultural soils, wildlife interactions, and occupational exposure, may promote the spread of resistance genes outside mining sites. Mining ecosystems are underrecognized and potentially important reservoirs of antimicrobial resistance. This review highlights the importance of integrating environmental resistome surveillance into existing global AMR monitoring frameworks to understand underlying ecological drivers of resistance evolution. Tackling metal-driven antibiotic resistance requires innovative, solution-based interdisciplinary research, enhanced environmental screening and soil and water testing practices, and sustainable mining practices within the One Health paradigm. Full article

Background/Objectives: Escherichia coli is the predominant pathogen in community-onset urinary tract infections (UTIs) requiring hospitalization. This study characterized antimicrobial resistance profiles, biofilm formation, extended-spectrum β-lactamase (ESBL) gene distribution, and phylogenetic background of E. coli isolates from hospitalized UTI patients in Western Mexico. Methods: Seventy isolates (September 2023–September 2024) underwent susceptibility testing (CLSI M100, 35th edition), multiplex PCR for blaTEM, blaCTX-M, and blaSHV genes, crystal violet biofilm quantification, and Clermont quadruplex PCR phylotyping. Associations were evaluated by Fisher’s exact test with Benjamini–Hochberg FDR (BH-FDR) correction. Results: ESBL phenotype and MDR were detected in 57.1% and 58.6% of isolates. After BH-FDR correction, ESBL production was significantly associated with amikacin (OR = 5.55; 95% CI: 1.80–18.74; q = 0.002) and TMP-SMX non-susceptibility (OR = 3.00; 95% CI: 1.02–9.23; q = 0.036); ciprofloxacin non-susceptibility was linked to MDR status (OR = 7.21; 95% CI: 1.28–75.66; q = 0.017) but not ESBL phenotype. Biofilm was detected in 77.1% of isolates. blaTEM predominated among ESBL producers (85.0%). Phylogroup B2 (51.4%) was inversely associated with recurrent UTI on both univariate (OR = 0.17; 95% CI: 0.03–0.73; p = 0.008) and adjusted analysis (adjusted OR = 0.19; 95% CI: 0.05–0.81; p = 0.025). Phylogroup C (22.9%) exhibited the highest MDR prevalence (81.3%) and the highest biofilm formation rate among phylogroups (87.5%). Conclusions: The high prevalence of ESBL-producing and MDR E. coli, combined with an unexpected predominance of blaTEM, reveals a distinctive local resistance landscape diverging from regional trends. The inverse association of phylogroup B2 with recurrence and TMP-SMX resistance reinforces the clinical value of phylogenetic surveillance in guiding UTI management strategies. Full article

Antimicrobial resistance is a major threat to modern society and healthcare, as it severely compromises the efficacy of standard antibiotic treatments. To meet the ever-increasing demand for novel antimicrobial drugs, it is crucial to develop new strategies for screening antimicrobial compounds and improve existing high-throughput techniques. Reporter systems that employ specific genetic markers are powerful tools not only for detecting antimicrobial activity of the substance being studied, but also for identifying the potential mechanism of its action. Among other metabolic pathways, RNA biosynthesis machinery is considered a promising molecular target as it remains underutilized in current antimicrobial therapy and therefore is rarely exposed to drug pressure. However, there is no suitable biomarker for identifying compounds that inhibit the transcription in Gram-negative bacteria. Combining bioinformatic search and RT-qPCR experimental validation, we have established the overexpression of the spermidine synthase gene (speE) as a biomarker associated with impaired transcription in Escherichia coli. Monitoring the expression level of speE in antibiotic-treated cells enables reliable detection of compounds that inhibit bacterial RNA-polymerase, such as rifampicin and fidaxomicin. Moreover, our screening system was successfully applied in practice to analyze chromatography fractions from fermentation broth of antibiotic producers, with compounds of the rifamycin family being identified as hits and isolated. The proposed method has the potential to be used in sequential screening procedures to reveal active antimicrobial compounds that inhibit bacterial transcription process, giving the world novel antimicrobials with minimal risk of resistance development. Full article

Salmonella enterica serovar Enteritidis is a leading cause of foodborne zoonoses worldwide. The rapid emergence of multidrug-resistant (MDR) strains has compromised traditional antimicrobial therapies, necessitating the development of biosafe alternatives such as bacteriophages. This study aimed to isolate and comprehensively characterize novel lytic bacteriophages targeting multidrug-resistant Salmonella enterica subspecies enterica serovar Enteritidis isolates from Lebanon. In this study, four novel Salmonella phages, EDA02, EDA03, EDA05, and EDA06, were isolated from wastewater and poultry effluents in Lebanon. The isolates were characterized using host range profiling, one-step growth kinetics, and physicochemical stability assays. Comprehensive whole-genome sequencing (WGS) and phylogenetic analyses were performed to assess their genomic safety and taxonomic placement. Phages EDA03 and EDA06 exhibited the broadest intra-serovar lytic activity within the tested panel, infecting up to 72% and 67% of the MDR isolates, respectively. One-step growth analysis revealed latent periods of 30–40 min, with burst sizes ranging from 6.0 to 150 phages/infected cell. All four phages demonstrated robust stability across pH 4.7–10.3 and temperatures from 4 °C to 50 °C. WGS revealed genome sizes ranging from 42.3 kb to 108.8 kb, with no identified genes associated with lysogeny, virulence, or antimicrobial resistance. Phylogenomic analysis assigned all isolates to the family Straboviridae, with <95% intergenomic similarity to their closest RefSeq relatives, supporting their classification as novel species. The isolated phages demonstrate substantial lytic activity and environmental resilience under the tested conditions. Their complementary lytic profiles, environmental resilience, and genomic safety support their further evaluation as biocontrol candidates. This study represents the first genomic and phenotypic characterization of anti-Salmonella Enteritidis phages from Lebanon. These findings support the development of phage-based interventions for food safety and antimicrobial resistance mitigation in resource-limited settings. Full article

Describing novel microbial species opens access to uncharted biosynthetic gene clusters and their associated secondary metabolites, offering fresh opportunities in the search for new antibiotics urgently needed to combat multidrug resistance. In this study, we describe a new species of Streptomyces, S. marxii sp. nov. (type strain VKM Ac-3100), an actinobacterium isolated from soil in the Yaroslavl Region of Russia. Using a polyphasic taxonomic approach that included whole-genome sequencing (WGS), we found that the strain’s average nucleotide identity (ANI) and digital DNA–DNA hybridisation (dDDH) values relative to its closest relative, S. maoxianensis, were 92.53% and 47.9%, respectively. Both values fell significantly below the species delimitation thresholds. Functional screening using the pDualrep2 dual fluorescent reporter system identified a unique SOS-silent antimicrobial profile characterised by growth inhibition without induction of the SOS response or translation stress. High-resolution mass spectrometry (HRMS) and genomic mining revealed that this activity is linked to the production of kinanthraquinone B ([M+H]⁺ m/z 275.0550), a rare polycyclic aromatic polyketide. Genomic analysis identified a specialised type II polyketide synthase (T2PKS) biosynthetic gene cluster (BGC) with evidence of acquisition via horizontal gene transfer (HGT). Our findings characterise S. marxii as a promising natural producer of rare catalytic inhibitors of DNA topoisomerases II and IV, offering a scaffold for the development of antibiotics with potentially lower genotoxicity. Full article

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a significant pathogen for both hospital-acquired and community-acquired infections, characterized by its strong epidemic potential and high mortality rate, posing a severe threat to global public health. CRKP spreads widely across the globe through the horizontal transfer of plasmid-mediated resistance genes such as *blaKPC*, *blaNDM*, and *blaOXA-48*. The clinical treatment options for this bacterium are limited, and its resistance has been increasing year by year, urgently necessitating the development of new antimicrobial drugs or alternative strategies. In recent years, the CRISPR-Cas system has shown great potential in the diagnosis and treatment of CRKP, including rapid detection and identification, gene editing, antimicrobial strategies, and resistance inhibition. For instance, CRISPR-Cas12a/13a can be used for the rapid detection and identification of CRKP, while CRISPR-Cas9/Cas3 can target resistance genes to reverse the resistance of strains. With the advancement of delivery and biotechnologies, the CRISPR-Cas system is expected to become an important tool against drug-resistant CRKP. This review focuses on the application of the CRISPR-Cas system in the detection and treatment of CRKP, analyzing its technical advantages, limitations, and future development directions. Full article

The double-crested cormorant (Nannopterum auritum), a piscivorous bird endemic to North America, frequently forages in aquaculture ponds during migration and wintering, contributing to economic losses in catfish-producing regions of the southern United States. While interactions between cormorants and aquaculture systems are well documented, their associated microbial communities and genetic elements remain less characterized. In this exploratory study, Hi-C-enabled metagenomics was applied to fecal samples from two cormorants to generate a genome-resolved, descriptive analysis of gut microbial composition and to associate bacterial genomes with mobile genetic elements (MGEs), antimicrobial resistance genes (ARGs), and putative virulence-associated genes. Metagenome-assembled genomes (MAGs) included taxa reported in aquatic or animal-associated environments, including Edwardsiella tarda, Plesiomonas shigelloides, Clostridium perfringens, and Campylobacter volucris. ARGs were detected across multiple MAGs, with E. tarda harboring the greatest diversity. Hi-C-enabled linkage of plasmids and phages to putative hosts, providing structural insight into microbial organization. Analyses are descriptive (n = 2) and do not include statistical comparisons or diversity metrics. These findings demonstrate the utility of Hi-C for resolving gene–host associations and provide a framework for future studies of microbial connectivity in One Health contexts. Full article

Chronic ulcers are characterized by impaired tissue repair and frequently harbor antimicrobial-resistant microorganisms, worsening clinical outcomes. The objective of this study is to identify microbial agents in chronic ulcers treated at the Lauro de Souza Lima Institute Wound Care Outpatient Clinic and to evaluate their antimicrobial susceptibility profiles and β-lactamase production. Samples (swab and biopsy) from patients treated at the Lauro de Souza Lima Institute were analyzed. Susceptibility was assessed by disk diffusion. ESBL and AmpC production were confirmed by PCR targeting blaTEM, blaSHV, blaCTX-M1, and blaCMY-2. In Staphylococcus spp., oxacillin and clindamycin resistance were evaluated and confirmed by mecA and ermAC. From 33 patients (mean age 63.4 years), 116 isolates were obtained, mainly Pseudomonas aeruginosa (27%), Proteus mirabilis (18%), and Staphylococcus aureus (13%). P. aeruginosa showed high resistance, with 48% MDR and 29% PDR. Among Enterobacterales, 19% were ESBL producers and 17% AmpC, with 56% carrying blaCMY-2. In Staphylococcus, 33% were oxacillin-resistant and 50% expressed MLSb phenotype. P. aeruginosa was identified as the most prevalent pathogen, with frequent MDR/PDR phenotypes. Resistance genes exhibited a discrepancy between genotypic and phenotypic profiles, suggesting the presence of unexpressed resistance that may be inducible during treatment. Full article

Coagulase-negative staphylococci (CoNS) and mammaliicocci (MA) are common in food-derived samples and may act as antimicrobial resistance (AMR) reservoirs. A previous study reported a high S. aureus prevalence in poultry meat. The objective of this study was to characterize the species diversity, antimicrobial resistance, and biofilm-forming capacity of CoNS/MA from the same food samples. Species identification, antimicrobial susceptibility testing, resistance gene detection, molecular typing, and biofilm formation assays were performed. One hundred and forty-eight non-repetitive CoNS/MA isolates were detected in 85% of samples, and 14 species were identified. The most prevalent species were S. epidermidis (18.2%), S. simulans (12.8%), S. saprophyticus (12.2%), S. warneri (11.5%), and M. lentus (10.1%). Most samples harbored one or two different species, although some showed higher diversity. Although 27.0% of isolates were pan-susceptible, 22.3% were multidrug-resistant (MDR), significantly associated with M. lentus and S. epidermidis. Methicillin resistance was found in 10 isolates, mainly in S. epidermidis (lineages ST9, ST59, ST88 and ST640). Biofilm formation was observed in 24.3% of isolates (some of them MDR) and was significantly associated with S. pasteuri and S. xylosus and with samples from supermarkets. No methicillin-resistant isolates were biofilm producers. These findings highlight the diversity of CoNS/MA in poultry meat and their role as AMR reservoirs and persistence factors, emphasizing their relevance in food safety. Full article