Search Results (52)

Background: Wastewater treatment plants (WWTPs) are hotspots of antimicrobial resistance (AMR) due to inputs from diverse anthropogenic sources. Aeromonas spp., ubiquitous in aquatic environments, often carry clinically relevant antibiotic resistance genes (ARGs) and can persist beyond fecal contamination indicators, making them promising sentinel organisms for AMR dissemination. The aim of this study was to assess the suitability of Aeromonas spp. in this role by characterizing resistance profiles, associated virulence factor genes (VFGs), genetic mobility, and persistence across wastewater and drinking water treatment processes in the Barcelona metropolitan area, Spain. Methods: Isolates were phenotypically characterized and screened for ARGs, VFGs, integrons, and heavy metal tolerance genes, followed by whole-genome sequencing (WGS). Biofilm formation was assessed in vitro. Conjugation assays with Escherichia coli evaluated horizontal gene transfer (HGT) potential. Results: A total of 428 antibiotic-resistant Aeromonas spp., the most abundant antibiotic-resistant bacteria isolated during the 2023 sampling campaigns from two WWTPs and one drinking water treatment plant (DWTP), were characterized. Trimethoprim/sulfamethoxazole (SXT) non-susceptibility was most frequent (72%), followed by cefoxitin resistance (65.4%). The sul1 (57.5%) and bla_MOX (78.6%) genes predominated among SXT- and β-lactam-resistant isolates. The merA gene was detected in 23.6%; 97.9% harbored at least one VFG (aerA, act, fla, alt, or hlyA), and 70.3% carried intI1. Half formed biofilm. Conjugation confirmed bi-directional HGT, and WGS revealed persistent ST3458 clones across treatment stages. Conclusions: WWTPs and DWTPs act as reservoirs of antibiotic-resistant Aeromonas spp., demonstrating persistence and HGT potential. Findings support their use as sentinel organisms for AMR surveillance in aquatic environments and for assessing treatment efficacy, highlighting variability across treatment types and locations, and reinforcing their relevance for urban water reclamation monitoring. Full article

Saxitoxin (STX) is one of the most potent marine neurotoxins, produced by several species of freshwater cyanobacteria and marine dinoflagellates. Although omics-based approaches have advanced our understanding of STX biosynthesis in recent decades, the origin, regulation, and ecological drivers of STX in dinoflagellates remain poorly resolved. Specifically, dinoflagellate STX biosynthetic genes (sxt) are extremely fragmented, inconsistently expressed, and unevenly distributed between toxic and non-toxic taxa. Environmental studies further report inconsistent relationships between abiotic factors and STX production, suggesting regulation across multiple genomic, transcriptional, post-transcriptional, and epigenetic levels. These gaps prevent a comprehensive understanding of STX biosynthesis in dinoflagellates and limit the development of accurate predictive models for harmful algal blooms (HABs) and paralytic shellfish poisoning (PSP). Artificial intelligence (AI), including machine learning and deep learning, offers new opportunities in ecological pattern recognition, molecular annotation, and data-driven prediction. This review explores the current state of knowledge and persistent knowledge gaps in dinoflagellate STX research and proposes an AI-integrated multi-omics framework highlighting recommended models for sxt gene identification (e.g., DeepFRI, ProtTrans, ESM-2), evolutionary reconstruction (e.g., PhyloGAN, GNN, PhyloVAE, NeuralNJ), molecular regulation (e.g., MOFA+, LSTM, GRU, DeepMF), and toxin prediction (e.g., XGBoost, LightGBM, LSTM, ConvLSTM). By integrating AI with diverse biological datasets, this novel framework outlines how AI can advance fundamental understanding of STX biosynthesis and inform future applications in HAB monitoring, seafood safety, and PSP risk management in aquaculture and fisheries. Full article

Background: Shigella spp. are critical pathogens causing diarrheal diseases. This study analyzed the epidemiological characteristics, antimicrobial resistance profiles, virulence factor profiles, and molecular patterns of Shigella isolates in Pudong New Area, Shanghai, from 2013 to 2024. Materials and Methods: Antimicrobial susceptibility of Shigella isolates was determined using the broth microdilution method. All molecular characterization analyses were based on whole-genome next-generation sequencing of Shigella strains. Results: A total of 55 Shigella spp. isolates were obtained from 17,670 enrolled diarrheal cases between 2013 and 2024, including 47 S. sonnei and 8 S. flexneri isolates. Resistance rates to sulfamethoxazole-trimethoprim (SXT), streptomycin (STR), nalidixic acid (NAL), ampicillin (AMP), and tetracycline (TET) all exceeded 90.00%. The resistance rate to azithromycin (AZI) increased from 12.50% to 60.00% with a fluctuating upward trend from 2013 to 2019; 97.87% of S. sonnei and 100.00% of S. flexneri isolates were multidrug-resistant. These isolates harbored multiple resistance genes and virulence factors. S. sonnei was dominated by ST152, while S. flexneri was predominantly ST245. These isolates were phylogenetically close to domestic (Beijing) and international (USA) strains of the same sequence typing collected at different time points, suggesting a common origin and stable transmission characteristics. Conclusion: From 2013 to 2024, the prevalent Shigella species in Pudong were S. sonnei and S. flexneri. Shigella isolates exhibited high resistance rates, and the situation of multidrug resistance was severe. Therefore, strengthening antimicrobial resistance monitoring and controlling regional transmission are of great significance. Meanwhile, genomic surveillance of Shigella ST152/ST245 is recommended for Pudong’s enteric pathogen control programs. Full article

Slaughterhouses serve as critical surveillance hubs for identifying subclinical and economically important diseases in food-producing animals. Trueperella (Arcanobacterium) pyogenes, an opportunistic pathogen commonly found on the mucous membranes of livestock, is associated with mastitis, abortion, and suppurative infections such as abscesses. In this study, we investigated 30 pig carcasses fully condemned due to vertebral osteomyelitis (VO) at two slaughterhouses in Gwangju, Republic of Korea, between November 2023 and May 2024. From abscess lesions, 11 T. pyogenes strains were isolated and characterized morphologically, biochemically, and genetically. The hemolytic exotoxin pyolysin (plo gene), a major virulence factor, was detected in five isolates (45.46%). Phylogenetic analysis of partial 16S rDNA sequences confirmed close clustering with known T. pyogenes reference strains. All 11 isolates exhibited multidrug resistance, showing resistance to 8–14 antimicrobial agents per strain. Complete resistance (11/11, 100%) was observed against amikacin (AMI), nalidixic acid (NAL), chloramphenicol (CHL), florfenicol (FFN), and trimethoprim/sulfamethoxazole (SXT). High resistance rates were also detected for erythromycin (ERY) and clindamycin (CLI) (10/11, 90.9%), ceftazidime (TAZ), ceftriaxone (AXO), ciprofloxacin (CIP) (7/11, 63.6%), and tetracycline (TET) and streptomycin (STR) (5/11, 45.5%), while gentamicin (GEN) resistance was found in three isolates (27.3%). In contrast, none of the isolates showed resistance to ampicillin, cefoxitin, or cefotaxime. These findings underscore the epidemiological value of abattoir-based monitoring in detecting emerging pathogens and tracking antimicrobial resistance. The results provide important baseline data to inform disease control strategies, guide antimicrobial stewardship, and support One Health approaches, including the development of preventive measures such as vaccines. Full article

Proteus mirabilis is a significant foodborne opportunistic pathogen associated with various nosocomial infections. Chicken farms may serve as an important reservoir for P. mirabilis. However, research on antibiotic resistance and genomic features of P. mirabilis in China’s poultry industry is limited. This study isolates P. mirabilis from a breeder farm in China and investigates the dissemination of P. mirabilis and clinically significant antibiotic resistance genes (ARGs), including bla_NDM and bla_CTX-M. From 510 samples, 69 isolates were obtained, classified into 11 sequence types (STs), with ST135 and ST175 predominating. A total of 39 ARGs were detected, including fosA3, floR, bla_CTX-M-3, bla_CTX-M-65, and bla_NDM-1. Genetic analysis revealed that bla_NDM-1 was exclusively located on Salmonella genomic island 1 (SGI1), while bla_CTX-M was found in various mobile genetic elements (MGEs), including Tn7, SXT/R391 integrative conjugative elements (ICEs), Proteus mirabilis genomic resistance island 1 (PmGRI1), and SGI1. Notably, many isolates carried multiple MGEs, suggesting frequent horizontal transfer of ARGs in P. mirabilis. These findings underscore the role of P. mirabilis in carrying and spreading antibiotic resistance, posing significant risks to the poultry industry and public health. Full article

Background/Objectives: Despite a significant reduction in diphtheria incidence and mortality due to vaccination, antitoxin therapy and antibiotic treatments, a concerning resurgence is occurring in Europe. Resistance to penicillins and macrolides is emerging, resulting in a growing challenge for diphtheria management. This retrospective study aims to evaluate and compare antibiotic susceptibilities of both toxigenic Corynebacterium diphtheriae and C. ulcerans. Methods: Susceptibilities were assessed using broth microdilution—the gold standard—disk diffusion and the gradient method, and analyzed on the basis of the EUCAST breakpoint tables for the interpretation of MICs and zone diameters. Antimicrobial resistance genes and mutations were detected by analyzing whole-genome sequences (WGS). Results: A small number of C. diphtheriae isolates were resistant to the first-choice antimicrobial classes, penicillins and macrolides, while higher resistance rates were observed for ciprofloxacin (29%), tetracycline (38%) and trimethoprim-sulfamethoxazole (SXT, 85%). A good correlation was found with resistance genes and mutations detected by WGS. C. ulcerans isolates were susceptible to all tested antibiotics, except clindamycin, to which this species is naturally resistant, and a few ciprofloxacin resistances not confirmed by WGS. Diffusion techniques were found to be acceptable alternatives, but false susceptible results were detected for ciprofloxacin and tetracycline by disk diffusion and ciprofloxacin and SXT by gradient diffusion. Conclusions: Penicillins and macrolides remain the first-choice antibiotics for the treatment of diphtheria. However, antimicrobial susceptibility testing is needed for all toxigenic C. diphtheriae and C. ulcerans isolates, as resistance is emerging. Antimicrobial susceptibility testing should not be limited to penicillins and macrolides, but be extended to other antibiotics. When WGS is performed for epidemiological purposes, resistance genes and mutations should be looked for. Full article

The irrational use of antimicrobials has led to the emergence of resistance, impacting not only pathogenic bacteria but also commensal bacteria. Resistance against colistin, a last-resort antibiotic, mediated by globally disseminated plasmid-borne mobile colistin resistance (mcr) genes, has raised significant global concerns. This cross-sectional study aimed to investigate the antimicrobial resistance patterns of colistin-resistant Escherichia coli (E. coli) and mobilised colistin resistance (mcr 1–5) genes from broiler meat. A total of 570 broiler samples (285 liver and 285 muscle) were collected from 7 supermarkets and 11 live bird markets (LBMs) in Chattogram metropolitan areas of Bangladesh. The isolation and identification of E. coli were carried out using standard bacteriological and molecular techniques. Antimicrobial susceptibility testing (AST) was performed using the Kirby–Bauer disc diffusion method, and colistin’s minimum inhibitory concentration (MIC) was determined by the broth microdilution (BMD) method. Colistin-resistant isolates were further tested for the presence of mcr (1–5) genes using polymerase chain reaction (PCR). Out of the 570 samples, 311 (54.56%; 95% confidence interval: 50.46–58.60) were positive for E. coli. AST results showed the highest resistance to sulphamethoxazole–trimethoprim (89.39%), while the highest susceptibility was observed for cefalexin (62.70%). A total of 296 isolates (95.18%) were found to be multidrug-resistant (MDR), with the multiple antibiotic resistance (MAR) index ranging from 0.38 to 1. Additionally, 41 isolates (13.18%) exhibited resistance to five antimicrobial classes, with resistance patterns of CIP + SXT + AMP + DO + TE + CT. A total of 233 isolates (74.92%) were resistant to colistin (MIC > 2 mg/L). A strong correlation between colistin resistance and the presence of the mcr-1 gene was observed (r = 1). All phenotypic colistin-resistant E. coli isolates carried the mcr-1 gene, while no isolates were positive for mcr (2–5). The detection of mcr genes in E. coli strains from poultry sources poses a significant risk, as these resistance genes can be transferred to humans through the food chain. The prevalence of multidrug-resistant Escherichia coli and the mcr-1 gene in poultry products in Bangladesh presents a significant public health and food safety concern. Full article

Cyanobacteria are adaptable and dominant organisms that exist in many harsh and extreme environments due to their great ecological tolerance. They produce various secondary metabolites, including cyanotoxins. While cyanobacteria are well studied in surface waters and some aerial habitats, numerous other habitats and niches remain underexplored. We collected 61 samples of: (i) biofilms from springs, (ii) aerial microbial mats from buildings and subaerial mats from caves, and (iii) water from borehole wells, caves, alkaline, saline, sulphidic, thermal, and iron springs, rivers, seas, and melted cave ice from five countries (Croatia, Georgia, Italy, Serbia, and Slovenia). We used (q)PCR to detect cyanobacteria (phycocyanin intergenic spacer—PC-IGS and cyanobacteria-specific 16S rRNA gene) and cyanotoxin genes (microcystins—mcyE, saxitoxins—sxtA, cylindrospermopsins—cyrJ), as well as amplicon sequencing and morphological observations for taxonomic identification. Cyanobacteria were detected in samples from caves, a saline spring, and an alkaline spring. While mcyE or sxtA genes were not observed in any sample, cyrJ results showed the presence of a potential cylindrospermopsin producer in a biofilm from a sulphidic spring in Slovenia. This study contributes to our understanding of cyanobacteria occurrence in diverse habitats, including rare and extreme ones, and provides relevant methodological considerations for future research in such environments. Full article

Dinoflagellate species that form some of the most frequent toxic blooms are also bioluminescent, yet the two traits are rarely linked when studying bloom development and persistence. P. bahamense is a toxic, bioluminescent dinoflagellate that previously bloomed in Florida with no known record of saxitoxin (STX) production. Over the past 20 years, STX was identified in P. bahamense populations. The goal of this study was to examine toxin dynamics and associated molecular mechanisms in spatially and temporally distinct P. bahamense populations from the Indian River Lagoon, FL. SxtA4 is a key gene required for toxin biosynthesis. SxtA4 genotype analysis was performed on individual cells from multiple sites. Cell abundance, toxin quota cell⁻¹, and sxtA4 and RubisCo (rbcL) transcript abundance were also measured. There was a significant negative correlation between cell abundance and toxin quota cell⁻¹. While the sxtA4+ genotype was dominant at all sites, its frequency varied, but it occurred at 90–100% in many samples. The underlying mechanism for toxin decrease with increased cell abundance remains unknown. However, a strong, statistically significant negative correlation was found between stxA4 transcripts and the sxtA4/rbcL ratio, suggesting cells make fewer sxtA4 transcripts as a bloom progresses. However, the influence of sxtA4− cells must also be considered. Future plans include bioluminescence measurements, normalized to a per cell basis, at sites when toxicity is measured along with concomitant quantification of sxtA4 gene and transcript copy numbers as a means to elucidate whether changes in bloom toxicity are driven more at the genetic (emergence of sxtA4− cells) or transcriptional (repression of sxtA4 in sxtA4+ cells) level. Based on the results of this study, a model is proposed that links the combined traits of toxicity and bioluminescence in P. bahamense bloom development. Full article

The marine dinoflagellate Alexandrium is known to form harmful algal blooms (HABs) and produces saxitoxin (STX) and its derivatives (STXs) that cause paralytic shellfish poisoning (PSP) in humans. Cell growth and cellular metabolism are affected by environmental conditions, including nutrients, temperature, light, and the salinity of aquatic systems. Abiotic factors not only engage in photosynthesis, but also modulate the production of toxic secondary metabolites, such as STXs, in dinoflagellates. STXs production is influenced by a variety of abiotic factors; however, the relationship between the regulation of these abiotic variables and STXs accumulation seems not to be consistent, and sometimes it is controversial. Few studies have suggested that abiotic factors may influence toxicity and STXs-biosynthesis gene (sxt) regulation in toxic Alexandrium, particularly in A. catenella, A. minutum, and A. pacificum. Hence, in this review, we focused on STXs production in toxic Alexandrium with respect to the major abiotic factors, such as temperature, salinity, nutrients, and light intensity. This review informs future research on more sxt genes involved in STXs production in relation to the abiotic factors in toxic dinoflagellates. Full article

Listeria monocytogenes poses a threat to both human and animal health. This work describes an L. monocytogenes outbreak in a Portuguese rabbit farm, detailing the isolates’ clinical manifestations, necropsy findings, and phenotypic and genomic profiles. Clinical signs, exclusively observed in does, included lethargy and reproductive signs. Post-mortem examination of does revealed splenomegaly, hepatomegaly with a reticular pattern, pulmonary congestion, and haemorrhagic lesions in the uterus, with thickening of the uterine wall and purulent greyish exudates. Positive L. monocytogenes samples were identified in fattening and maternity units across different samples, encompassing does and environmental samples. Core-genome Multi Locus Sequence Typing (cgMLST) analysis confirmed the outbreak, with the 16 sequenced isolates (lineage II, CC31, and ST325) clustering within a ≤2 allelic difference (AD) threshold. Antimicrobial susceptibility testing for five antibiotics revealed that 15 out of 19 outbreak isolates were resistant to sulfamethoxazole-trimethoprim (SXT). Concordantly, all SXT-resistant sequenced isolates were found to exclusively harbour a plasmid containing a trimethoprim-resistance gene (dfrD), along with loci linked to resistance to lincosamides (lnuG), macrolides (mphB), and polyether ionophores (NarAB operon). All sequenced outbreak isolates carried the antibiotic resistance-related genes tetM, fosX, lin, norB, lmrB, sul, and mprF. The outbreak cluster comprises isolates from does and the environment, which underscores the ubiquitous presence of L. monocytogenes and emphasizes the importance of biosecurity measures. Despite limited data on listeriosis in rabbit farming, this outbreak reveals its significant impact on animal welfare and production. Full article

Stenotrophomonas maltophilia is an opportunistic pathogen that produces respiratory infections in immunosuppressed and cystic fibrosis patients. The therapeutic options to treat S. maltophilia infections are limited since it exhibits resistance to a wide variety of antibiotics such as β-lactams, aminoglycosides, tetracyclines, cephalosporins, macrolides, fluoroquinolones, or carbapenems. The antibiotic combination trimethoprim/sulfamethoxazole (SXT) is the treatment of choice to combat infections caused by S. maltophilia, while ceftazidime, ciprofloxacin, or tobramycin are used in most SXT-resistant infections. In the current study, experimental evolution and whole-genome sequencing (WGS) were used to examine the evolutionary trajectories of S. maltophilia towards resistance against tobramycin, ciprofloxacin, and SXT. The genetic changes underlying antibiotic resistance, as well as the evolutionary trajectories toward that resistance, were determined. Our results determine that genomic changes in the efflux pump regulatory genes smeT and soxR are essential to confer resistance to ciprofloxacin, and the mutation in the rplA gene is significant in the resistance to tobramycin. We identified mutations in folP and the efflux pump regulator smeRV as the basis of SXT resistance. Detailed and reliable knowledge of ciprofloxacin, tobramycin, and SXT resistance is essential for safe and effective use in clinical settings. Herein, we were able to prove once again the extraordinary ability that S. maltophilia has to acquire resistance and the importance of looking for alternatives to combat this resistance. Full article

Harmful cyanobacterial blooms (HCBs) are of growing global concern due to their production of toxic compounds, which threaten ecosystems and human health. Saxitoxins (STXs), commonly known as paralytic shellfish poison, are a neurotoxic alkaloid produced by some cyanobacteria. Although many field studies indicate a widespread distribution of STX, it is understudied relative to other cyanotoxins such as microcystins (MCs). In this study, we assessed eleven U.S. urban lakes using qPCR, sxtA gene-targeting sequencing, and 16S rRNA gene sequencing to understand the spatio-temporal variations in cyanobacteria and their potential role in STX production. During the blooms, qPCR analysis confirmed the presence of the STX-encoding gene sxtA at all lakes. In particular, the abundance of the sxtA gene had a strong positive correlation with STX concentrations in Big 11 Lake in Kansas City, which was also the site with the highest quantified STX concentration. Sequencing analysis revealed that potential STX producers, such as Aphanizomenon, Dolichospermum, and Raphidiopsis, were present. Further analysis targeting amplicons of the sxtA gene identified that Aphanizomenon and/or Dolichospermum are the primary STX producer, showing a significant correlation with sxtA gene abundances and STX concentrations. In addition, Aphanizomenon was associated with environmental factors, such as conductivity, sulfate, and orthophosphate, whereas Dolichospermum was correlated with temperature and pH. Overall, the results herein enhance our understanding of the STX-producing cyanobacteria and aid in developing strategies to control HCBs. Full article

Stenotrophomonas maltophilia is a multidrug-resistant Gram-negative bacillus associated with nosocomial infections in intensive care units, and nowadays, its acquired resistance to trimethoprim–sulfamethoxazole (SXT) by sul genes within class 1 integrons is a worldwide health problem. Biofilm and motility are two of the major virulence factors in this bacterium and are auto-induced by the diffusible signal factor (DSF). In recent studies, retinoids have been used to inhibit (Quorum Quenching) these virulence factors and for their antimicrobial effect. The aim was to reduce biofilm formation and motility with retinoic acid (RA) in S. maltophilia SXT-resistant strains. Eleven SXT-resistant strains and two SXT-susceptible strains were tested for biofilm formation/reduction and planktonic/sessile cell viability with RA and SXT-MIC₅₀/RA; motility (twitching, swimming, swarming) was measured with/without RA; and MLST typing was determined. The biofilm formation of the strains was classified as follows: 15.38% (2/13) as low, 61.54% (8/13) as moderate, and 23.08% (3/13) as high. It was significantly reduced with RA and SXT-MIC₅₀/RA (p < 0.05); cell viability was not significantly reduced with RA (p > 0.05), but it was with SXT-MIC₅₀/RA (p < 0.05); and swimming (p < 0.05) and swarming (p < 0.05) decreased significantly. MLST typing showed the first and novel strains of Mexican S. maltophilia registered in PubMLST (ST479-485, ST497, ST23, ST122, ST175, ST212, and ST300). In conclusion, RA reduced biofilm formation and motility without affecting cell viability; furthermore, antimicrobial synergism with SXT-MIC₅₀/RA in different and novel STs of S. maltophilia was observed. Full article

Shiga toxin-producing Escherichia coli (STEC) is one of the most prominent food-borne pathogens in humans. The current study aims to detect and to analyze the virulence factors, antibiotic resistance, and plasmid profiles for forty-six STEC strains, isolated from clinical and food strains. Pulsed-field gel electrophoresis (PFGE) was used to determine the genetic relatedness between different serotypes and sources of samples. The clinical samples were found to be resistant to Nb (100%), Tet (100%), Amp (20%), SXT (15%), and Kan (15%) antibiotics. In contrast, the food strains were found to be resistant to Nb (100%), Tet (33%), Amp (16.6%), and SXT (16.6%) antibiotics. The PFGE typing of the forty-six isolates was grouped into more than ten clusters, each with a similarity between 30% and 70%. Most of the isolates were found positive for more than five virulence genes (eae, hlyA, stx1, stx2, stx2f, stx2c, stx2e, stx2, nelB, pagC, sen, toxB, irp, efa, and efa1). All the isolates carried different sizes of the plasmids. The isolates were analyzed for plasmid replicon type by PCR, and 72.5% of the clinical isolates were found to contain X replicon-type plasmid, 50% of the clinical isolates contained FIB replicon-type plasmid, and 17.5% of the clinical isolates contained Y replicon-type plasmid. Three clinical isolates contained both I1 and Hi1 replicon-type plasmid. Only two food isolates contained B/O and W replicon-type plasmid. These results indicate that STEC strains have diverse clonal populations among food and clinical strains that are resistant to several antimicrobials. In conclusion, our findings indicate that food isolates of STEC strains harbor virulence, antimicrobial resistance, plasmid replicon typing determinants like those of other STEC strains from clinical strains. These results suggest that these strains are unique and may contribute to the virulence of the isolates. Therefore, surveillance and characterization of STEC strains can provide useful information about the prevalence of STEC in food and clinical sources. Furthermore, it will help to identify STEC serotypes that are highly pathogenic to humans and may emerge as a threat to public health. Full article