Search Results (21)

Background/Objectives: Water pollution caused by human activities disrupts ecosystems and promotes the spread of antimicrobial resistance genes (ARGs), posing a public health threat. This study investigated the presence of resistant Gram-negative bacteria and resistance genes in water from two sites occasionally exposed to domestic and hospital effluents, the Carioca River (CR) and Rodrigo de Freitas Lagoon (RFL), both used for recreation. Methods: Physicochemical parameters and coliform levels were measured. Bacterial isolates were identified by Matrix-Assisted Laser Desorption Ionization–Time-of-Flight Mass Spectrometry (MALDI-TOF MS) and tested for antimicrobial susceptibility using disk diffusion. The Minimum Inhibitory Concentration (MIC) was determined using the E-test^® and broth microdilution methods. PCR was used to detect carbapenem resistance and other ARGs from the DNA of bacterial isolates obtained from water samples. Results: CR presented signs of environmental degradation, with low dissolved oxygen and high coliform counts. One Citrobacter braakii isolate showed resistance to all tested antimicrobials, raising concern for untreatable infections. Carbapenem-resistant isolates accounted for 49.4% of the total, harboring bla_KPC (20%), bla_TEM (5%), bla_VIM (5%), and bla_SPM (5%). The intl1 gene was found in 10% of isolates, indicating potential horizontal gene transfer. Conclusions: The findings from a one-day sampling reveal the presence of multidrug-resistant bacteria that carry antimicrobial resistance genes in polluted aquatic systems. These highlight the connection between water contamination and antimicrobial resistance. The evidence underscores the urgent need for environmental monitoring and effective management strategies to reduce public health risks. Full article

Citrobacter braakii is an emerging opportunistic pathogen of escalating clinical significance in animal hosts, though its pathogenic mechanisms remain poorly characterized. This study isolated a C. braakii strain (SCGY-1L) from diseased Siniperca chuatsi and confirmed its identity through integrated morphological, physiological, and molecular analyses. Comprehensive genomic sequencing revealed a 5.75 Mb genome comprising one circular chromosome and two plasmids. A Circos plot was constructed to visualize the genomic architecture of strain SCGY-1L, revealing 5482 protein-coding genes, 25 tRNA genes, and 86 rRNA genes. Additionally, 738 virulence-associated genes and 366 antibiotic resistance determinants were annotated, elucidating multidrug-resistant phenotypes including insensitivity to erythromycin and penicillin. Pathogenicity assessment established an LD₅₀ of 1.28 × 10⁶ CFU/mL in infected hosts, with histopathological analysis showing significant hemorrhage and necrosis in target organs (liver, spleen, kidney). Host transcriptome profiling generated 41.21 Gb of high-quality clean data, identifying 2201 differentially expressed genes post-infection (1568 up-regulated; 633 down-regulated). These were significantly enriched in phagocytosis, cytokine-mediated signaling, and inflammatory regulation pathways. These molecular insights establish C. braakii’s mechanistic framework for pathogenesis and host adaptation, providing critical targets for diagnostics and therapeutics against emerging Citrobacter infections. Full article

The emergence of extensively drug-resistant (XDR) foodborne pathogens poses grave threats to food safety. This study characterizes the genome of an XDR Salmonella Kentucky isolate (Sal23C1) co-harboring cfr, mcr-1 and tet(A) from Shanghai chicken meat in 2022, which was the only isolate co-harboring these three key resistance genes among 502 screened Salmonella isolates. Genomic analysis revealed that the multidrug resistance gene cfr, which confers resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins and streptogramin A, was identified within a Tn3-IS6-cfr-IS6 structure on the transferable plasmid p3Sal23C1 (32,387 bp), showing high similarity to the Citrobacter braakii plasmid pCE32-2 (99% coverage, 99.98% identity). Concurrently, the mcr-1 gene resided in a pap2-mcr-1 structure on the transferable IncI2 plasmid p2Sal23C1 (63,103 bp). Notably, both genes could be co-transferred to recipient bacteria via conjugative plasmids at frequencies of (1.15 ± 0.98) × 10⁻⁶. Furthermore, a novel ~79 kb multidrug resistance region (MRR) chromosomally inserted at the bcfH locus was identified, carrying fosA3, mph(A), rmtB, qnrS1 and bla_CTX-M-55. Additionally, a novel Salmonella Genomic Island 1 variant (SGI1-KI) harbored aadA7, qacEΔ1, sul1 and the tet(A) variant. The acquisition of these antibiotic resistance genes in this isolate enhanced bacterial resistance to 21 antimicrobials, including resistance to the critical last-resort antibiotics tigecycline and colistin, which left virtually no treatment options for potential infections. Taken together, this is the first comprehensive genomic report of an XDR poultry-derived Salmonella Kentucky isolate co-harboring cfr, mcr-1 and the tet(A) variant. The mobility of these resistance genes, facilitated by IS6 elements and conjugative plasmids, underscores significant public health risks associated with such isolates in the food chain. Full article

The role of bacterial selenium metabolism in non-polluted environments remains underexplored within the selenium biogeochemical cycle. In this study, selenium-metabolizing bacteria were isolated from urban environmental samples. Among 12 isolates, 10 were identified as Citrobacter spp., while the remaining 2 were Scandinavium hiltneri and Klebsiella aerogenes. The Citrobacter isolates demonstrated high selenium-removal efficiency, removing over 95% of 5 mM selenium from the aqueous phase within one week. In contrast, S. hiltneri K24-1 and K. aerogenes K24-4 removed only 19% and 69%, respectively. A detailed investigation of five representative isolates, C. freundii K21-1, S. hiltneri K24-1, C. braakii K24-2, K. aerogenes K24-4, and C. freundii K24-5, revealed that Citrobacter spp. efficiently reduced selenate directly to elemental selenium, with minimal accumulation of selenite intermediates. These results highlight Citrobacter spp. as key selenium reducers and suggest their potential as bioindicators of selenium metabolic capacity in the environment. Full article

Citrobacter braakii can colonize the intestinal tract of humans and animals and occasionally act as opportunistic pathogen. Although isolated from food and the environment, its potential as a foodborne pathogen remains uncertain. Twenty C. braakii isolates were previously collected from salami and soft cheese artisanal productions. In the present study, the potentialities of C. braakii as a food safety hazard were explored by a genomic comparison of C. braakii newly sequenced genomes with publicly available genomes, including those of clinical relevance, and a pathogenicity assessment in Galleria mellonella as an in vivo infection model. Phylogenomic reconstruction revealed that one salami clone and two C. braakii genomes of the soft cheese production were closely related (from 11 to 28 core SNP differences) to C. braakii publicly available clinical genomes. All genomes carried the chromosomally located bla_CMY and/or qnrB genes and were resistant to cephalosporins and/or had reduced susceptibility to ciprofloxacin. G. mellonella larvae showed 90% mortality after challenge with C. braakii strains carrying the vex and tvi operons coding for the capsular polysaccharide (Vi antigen), in comparison to 40% of strains lacking these two operons. The high mortality rate of vex- and tvi-positive C. braakii isolated from food processing plants suggests C. braakii to be a possible foodborne hazard. Full article

The objective of this research was to assess the effectiveness of three specific dried herbs (rosemary, thyme, and oregano) in combating microbial spoilage in sheep lump cheese. This was achieved by comparing them with a control group and cheeses treated with corresponding 1% essential oils (Rosmarinus officinalis, Origanum vulgare, Thymus vulgaris). All cheese samples were vacuum-sealed and stored at 4 °C for 15 days. Analysis of total viable counts of viable bacteria (TVC), coliform bacteria (CB), lactic acid bacteria (LAB), and microscopic filamentous fungi (MFF) was conducted on days 0, 5, 10, and 15. The results revealed that, at the end of the storage period, dried oregano-treated samples exhibited the lowest TVC count (5.80 log CFU/g), while dried rosemary-treated samples showed the lowest CB count (3.27 log CFU/g). Moreover, the lowest MFF count (2.40 log CFU/g) was observed in oregano essential oil-treated samples. Additionally, dried oregano-treated samples displayed the highest LAB count (4.49 log CFU/g) at the experiment’s conclusion. Furthermore, microorganism identification from sheep cheese was performed using MALDI-TOF MS Biotyper technology, revealing that the most frequently isolated bacteria were Citrobacter braakii and Hafnia alvei (Enterobacteriaceae family), along with Lacticaseibacillus paracasei (Lactobacillaceae family). In summary, all the natural substances examined exhibited inhibitory effects against the studied microorganisms, with oregano essential oil and dried oregano demonstrating the strongest inhibitory effects. This supports their potential use as cost-effective natural preservatives to extend the shelf life of sheep lump cheese. Full article

The role of bats in the global microbial ecology no doubt is significant due to their unique immune responses, ability to fly, and long lifespan, all contributing to pathogen spread. Some of these animals hibernate during winter, which results in the altering of their physiology. However, gut microbiota shifts during hibernation is little studied. In this research, we studied cultivable gut microbiota composition and diversity of Nyctalus noctula before, during, and after hibernation in a bat rehabilitation center. Gut microorganisms were isolated on a broad spectrum of culture media, counted, and identified with mass spectrometry. Linear modeling was used to investigate associations between microorganism abundance and N. noctula physiological status, and alpha- and beta-diversity indexes were used to explore diversity changes. As a result, most notable changes were observed in Serratia liquefaciens, Hafnia alvei, Staphylococcus sciuri, and Staphylococcus xylosus, which were significantly more highly abundant in hibernating bats, while Citrobacter freundii, Klebsiella oxytoca, Providencia rettgeri, Citrobacter braakii, and Pedicoccus pentosaceus were more abundant in active bats before hibernation. The alpha-diversity was the lowest in hibernating bats, while the beta-diversity differed significantly among all studied periods. Overall, this study shows that hibernation contributes to changes in bat cultivable gut microbiota composition and diversity. Full article

Beta-lactam resistance can lead to increased mortality, higher healthcare expenses, and limited therapeutic options. The primary mechanism of beta-lactam resistance is the production of extended-spectrum beta-lactamases (ESBL) and AmpC beta-lactamases. The spread of beta-lactamase-producing Enterobacterales via the food chain may create a resistance reservoir. The aims of this study were to determine the prevalence of ESBL/AmpC-producing Enterobacterales in vegetables, to examine the association between EBSL/AmpC-producing bacteria and types of vegetables, packaging, and markets, and to investigate the genetic features of ESBL-producing isolates. The antibiotic susceptibilities were determined using VITEK. Phenotypic ESBL/AmpC production was confirmed using disk diffusion. ESBL-producing isolates were subjected to Fourier-transform infrared (FT-IR) spectroscopy and to whole genome sequencing using Oxford Nanopore sequencing technology. Of the 301 vegetable samples, 20 (6.6%) were positive for ESBL producers (16 Klebsiella pneumoniae and 4 Escherichia coli), and 63 (20.9%) were positive for AmpC producers (56 Enterobacter cloacae complex, 4 Enterobacter aerogenes/cancerogenus, and 3 Pantoea spp., Aeromonas hydrophila, and Citrobacter braakii). The blaCTX-M and blaSHV genes were most common among ESBL-producing isolates. The beta-lactamase genes of the ESBL producers were mainly carried on plasmids. Multilocus sequence typing and FT-IR typing revealed high diversity among the ESBL producers. AmpC producers were significantly more common in leafy greens and ESBL producers were significantly less common in climbing vegetables. The presence of ESBL/AmpC-producing Enterobacterales in raw vegetables may contribute to the dissemination of resistance genes in the community. Full article

Introduction: Due to the high load of pathogens in sewage, seeking for effective treatments became a priority. In this regard, testing the sensitivity of microorganisms isolated from sewage against essential oils (EOs) is suggested. In Lebanon, little evidence supports bacteria isolated from sewage reveals a sensitivity to EOs. Due to this fact, the present investigation aims at determining the sensitivity of microbes isolated from sewage sludge to three EOs: lettuce, coconut, and almond. Methods: Bacterial isolates were identified by VITEK screening. Yeast was identified by germ tube assay. The chemical components of the oils were identified by gas chromatography – mass spectrometry (GC-MS). Susceptibility of the microbial isolates was assessed by the agar well diffusion assay. Bacteriostatic and bactericidal effects of EOs were detected by minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) broth microdilution assay. The activity of EOs on biofilms was detected by antibiofilm screening. Results: The identified microorganisms include Gram-negative isolates (Escherichia coli, Citrobacter freundii, Citrobacter braakii, Leclercia adecarboxylata, and Stenotrophomonas maltophilia), Gram-positive isolates (Enterococcus faecium, Streptococcus intermedius, Staphylococcus aureus, Staphylococcus capitis, and Staphylococcus haemolyticus), and Candida albicans. Thirty oils’ chemical components were identified. Among the antibiotics, doxycycline exhibited the best inhibitory effect. The three EOs were effective against bacterial isolates and yeast at concentrations ranging between 3.125% and 50%. They exhibited a bacteriostatic activity. Lettuce and coconut oils were effective against biofilm formation and the three oils were effective on pre-formed biofilms. Conclusions: The results reflected the significant antimicrobial and antibiofilm activities of the oils, thus suggesting their potential antimicrobial applications. Full article

The effects of increasing doses of bacterial phytase (Citrobacter braakii) on performance and carcass characteristics of growing-finishing pigs was evaluated. A total of 120 barrows weighing 25.16 ± 2.80 kg and 68 days old were submitted to five treatments: positive control diet (PC) containing inorganic phosphorus (P) and limestone (Ca); negative control (NC) with reductions in P (by 0.13%) and Ca (by 0.11%); and three NC diets supplemented with 1500 (NC15), 3000 (NC30) and 4500 (NC45) units of phytase (FYT)/kg. The daily weight gain (DWG) in growth phase I (68–91 days) was higher in the PC, NC15 and NC30, compared to the NC (1.06, 1.06, 1.06 vs. 0.95, respectively). The DWG in finishing phase II (141–156 days) was higher in the NC15 (1.20 kg) and NC30 (1.14 kg) than in the NC45 (0.94 kg). The final weights (LW156) in the NC15 (122.95 kg LW) were higher than NC (116.47 kg LW) and NC45 (114.43 kg LW). Over the entire period, a quadratic effect (2012 FYT) was observed for the DWG. The increasing levels of phytase in corn and soybean meal-based diets improved the DWG and carcass traits; however, the addition of more than 3000 FYT/kg of feed should be carefully studied to determine enzyme viability. Full article

Background: antimicrobial resistance is a global problem in human and veterinary medicine. We aimed to investigate the extended spectrum β-lactamase-producing Enterobacterales (ESBL-PE) gut colonization in healthy community dogs in Israel. Methods: Rectal swabs were sampled from 145 healthy dogs, enriched, plated on selective plates, sub-cultured to obtain pure cultures, and ESBL production was confirmed. Bacterial species and antibiotic susceptibility profiles were identified. WGS was performed on all of the ESBL-PE isolates and their resistomes were identified in silico. Owners’ questionnaires were collected for risk factor analysis. Results: ESBL-PE gut colonization rate was 6.2% (n = 9/145, 95% CI 2.9–11.5). Overall, ten isolates were detected (one dog had two isolates); the main species was Escherichia coli (eight isolates), belonging to diverse phylogenetic groups—B1, A and C. Two isolates were identified as Citrobacter braakii, and C. portucalensis. A phylogenetic analysis indicated that all of the isolates were genetically unrelated and sporadic. The isolates possessed diverse ESBL genes and antibiotic-resistance gene content, suggesting independent ESBL spread. In a multivariable risk factor analysis, coprophagia was identified as a risk factor for ESBL-PE gut colonization (p = 0.048, aOR = 4.408, 95% CI 1.014–19.169). Conclusions: healthy community dogs may be colonized with ESBL-PE MDR strains, some of which were previously reported in humans, that carry wide and diverse resistomes and may serve as a possible source for AMR. Full article

The aim of this study was to screen for extended spectrum cephalosporin-, carbapenem- and colistin-resistant Gram-negative bacteria in fresh vegetables in Batna, Algeria. A total of 400 samples of fresh vegetables were collected from different retail stores. Samples were immediately subjected to selective isolation, then the representative colonies were identified using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF–MS). Phenotypic and genotypic analyses were carried out in terms of species identification and relative antibiotic resistance. Transferability of the carbapenemase and mcr-bearing plasmids was verified by conjugation. The clonal relationships of carbapenemase and mcr-positive Escherichia coli isolates were studied by multi-locus sequence typing (MLST). Sixty-seven isolates were characterised and were mostly isolated from green leafy vegetables, where the dominant species identified included Citrobacter freundii, Klebsiella pneumoniae, Enterobacter cloacae, Stenotrophomona maltophilia, E. coli and Citrobacter braakii. PCR and sequencing results showed that E. coli was the bacterial species presenting the highest antibiotic resistance level in parallel to bla_TEM (n = 16) and bla_CTX-M-15 (n = 11), which were the most detected genes. Moreover, five isolates carried carbapenemase genes, including the bla_OXA-48 and/or bla_VIM-4 genes. The mcr-1 gene was detected in two E. coli isolates. MLST analysis revealed three different E. coli sequence types: ST101 (n = 1), ST216 (n = 1) and ST2298 (n = 1). Conjugation assays confirmed the transferability of the bla_OXA-48 and mcr-1 genes. In this study we report, for the first time, the detection of the bla_OXA-48 gene in E. coli and C. braakii isolates and the bla_VIM-4 gene in vegetables. To the best of our knowledge, this is the first report on the detection of mcr-1 genes from vegetables in Algeria. Full article

Histamine is a toxic biogenic amine commonly found in seafood products or their derivatives. This metabolite is produced by histamine-producing bacteria (HPB) such as Proteus vulgaris, P. mirabilis, Enterobacter aerogenes, E. cloacae, Serratia fonticola, S. liquefaciens, Citrobacter freundii, C. braakii, Clostridium spp., Raoultella planticola, R. ornithinolytica, Vibrio alginolyticus, V. parahaemolyticus, V. olivaceus, Acinetobacter lowffi, Plesiomonas shigelloides, Pseudomonas putida, P. fluorescens, Aeromonas spp., Photobacterium damselae, P. phosphoreum, P. leiognathi, P. iliopiscarium, P. kishitanii, and P. aquimaris. In this review, the role of these bacteria in histamine production in fish and seafood products with consequences for human food poisoning following consumption are discussed. In addition, methods to control their activity in countering histamine production are proposed. Full article

Background: Companion animal clinics contribute to the spread of antimicrobial resistant microorganisms (ARM) and outbreaks with ARM of public health concern have been described. Methods: As part of a project to assess infection prevention and control (IPC) standards in companion animal clinics in Switzerland, a total of 200 swabs from surfaces and 20 hand swabs from employees were collected during four days in a medium-sized clinic and analyzed for extended spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E), carbapenemase-producing Enterobacteriaceae (CPE), vancomycin-resistant enterococci (VRE), and methicillin-resistant staphylococci (MRS). Results: A total of 22 (11.0%) environmental specimen yielded CPE, 14 (7.0%) ESBL-E, and 7 (3.5%) MRS; MR Staphylococcus aureus were isolated from two (10.0%) hand swabs. The CPE isolates comprised Escherichia coli, Klebsiella pneumoniae, Enterobacter hormaechei, Citrobacter braakii, and Serratia marcescens. Whole genome sequencing revealed that all CPE carried closely related bla_OXA-48 plasmids, suggesting a plasmidic spread within the clinic. The clinic exhibited major deficits in surface disinfection, hand hygiene infrastructure, and hand hygiene compliance. CPE were present in various areas, including those without patient contact. The study documented plasmidic dissemination of bla_OXA-48 in a companion animal clinic with low IPC standards. This poses a worrisome threat to public health and highlights the need to foster IPC standards in veterinary clinics to prevent the spread of ARM into the community. Full article

Antimicrobial-resistant bacteria causing intractable and even fatal infections are a major health concern. Resistant bacteria residing in the intestinal tract of healthy individuals present a silent threat because of frequent transmission via conjugation and transposition. Plasmids harboring quinolone resistance genes are increasingly detected in clinical isolates worldwide. Here, we investigated the molecular epidemiology of plasmid-mediated quinolone resistance (PMQR) in Gram-negative bacteria from healthy service trade workers. From 157 rectal swab samples, 125 ciprofloxacin-resistant strains, including 112 Escherichia coli, 10 Klebsiella pneumoniae, two Proteus mirabilis, and one Citrobacter braakii, were isolated. Multiplex PCR screening identified 39 strains harboring the PMQR genes (including 17 qnr,19 aac(6′)-Ib-cr, and 22 oqxA/oqxB). The genome and plasmid sequences of 39 and 31 strains, respectively, were obtained by short- and long-read sequencing. PMQR genes mainly resided in the IncFIB, IncFII, and IncR plasmids, and coexisted with 3–11 other resistance genes. The high PMQR gene carriage rate among Gram-negative bacteria isolated from healthy individuals suggests the high-frequency transmission of these genes via plasmids, along with other resistance genes. Thus, healthy individuals may spread antibiotic-resistant bacterial, highlighting the need for improved monitoring and control of the spread of antibiotic-resistant bacteria and genes in healthy individuals. Full article