Search Results (325)

The red-claw crayfish Cherax quadricarinatus has been widely introduced and cultured in China and has become a crucial economic freshwater species. However, individuals reared from the same batch of seedlings in uniform aquaculture systems exhibit significant size variation within and between genders, which notably impedes the optimization of both their quality and yield. Gut microbiota plays an important role in the metabolism, development, and immunity of aquatic animals. However, the knowledge on the intestinal microbiota of red-claw crayfish with various sizes and genders is poor. In this study, the intestinal microbiota of red-claw crayfish cultured in consistent farming conditions were separated to larger-sized female (GUBF), larger-sized male (GUBM), smaller-sized female (GUSF), and smaller-sized male (GUSM) groups based on their body size (weight) and gender, before being analyzed via high-throughput 16S rRNA gene sequencing. The intestinal microbiota results showed that alpha diversity tended to generally decrease in the order of GUBF, GUBM, GUSF, and GUSM, indicating that the richness and evenness of the gut flora were gradually improved with the increase in body weight or from male to female. Community richness and diversity were highest in the GUBF group, followed by the GUBM, GUSF, and GUSM groups, respectively. Beta diversity indicated significant differences in gut microbiota between the GUBF and GUSF, GUBM and GUSM, GUBF, and GUBM groups. Further analysis showed that the dominant phyla in the intestine of the red-claw crayfish were Firmicutes, Proteobacteria, Fusobacteriota, Bacteroidota, and Deinococcota, and the dominant genera were Vibrio, Tyzzerella, Candidatus Bacilloplasma, Citrobacter, and Candidatus Hepatoplasma. Moreover, nine phyla and 106 genera were identified to be significantly different in abundance among all four groups. Pairwise comparisons revealed that the phylum Dependentiae and Planctomycetota and genus Babeliaceae_unclassified were significantly abundant in the gut of female crayfishes, regardless of body size. On the other hand, irrespective of genders, the abundance of Novosphingobium, Piscinibacter, and Citrobacter was significantly increased or declined in the larger or smaller crayfishes, respectively. PICRUSt2 analysis based on the KEGG database suggested that the pathway bacterial secretion system, isoflavonoid biosynthesis, and pathway glycerolipid metabolism were significantly up- and down-regulated in female individuals, respectively, regardless of body sizes. Meanwhile, the adipocytokine signaling pathway, pyruvate metabolism, and pathway electron transfer carriers were significantly up- and down-regulated in larger individuals, respectively, regardless of gender. Gender differences may induce gut microbiota to exert a greater impact on hormonal regulation, whereas differences in individual size seem to lead gut microbiota to develop a preference for food intake and energy sources. In summary, this study revealed key differences in the intestinal microbiota of the crayfish with different sizes and genders, even in those which were cultured in the same environment and period, which potentially suggest that the intestinal microbiota may be influenced by some other factors in the culture system, such as hormone secretion, metabolism, and immunity. This study will contribute to improving growth performance and animal quality in the aquaculture of C. quadricarinatus. 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

Background/Objectives: The complementary feeding period is a critical window for shaping infant diet, gut microbiota, and immune development. While allergic symptoms often emerge in the first year of life, the effects of specific foods, such fruits, on infant allergy symptoms, inflammation, immunity and associated microbiota remain unclear. This study aimed to assess the impact of daily blueberry consumption during the complementary feeding period on allergy-related symptoms, immune biomarkers, and gut microbiota in breastfed U.S. infants. Methods: In a double-blind, randomized, placebo-controlled trial, infants from the Denver metro area were assigned to receive up to 10 g/day of freeze-dried blueberry powder or an isocaloric placebo from 5 to 12 months of age. Stool, blood, and caregiver-reported allergy-related symptom data were collected at baseline and study end. Results: Of the 76 infants enrolled, 61 completed the study (Blueberry: n = 30; Placebo: n = 31). While more infants in the blueberry group had allergy-related symptoms at baseline, they had significantly different longitudinal symptom trajectories than the placebo (p = 0.05), showing a greater resolution rate of symptoms by study end. Pro-inflammatory serum IL-13 levels were significantly reduced (p = 0.035) and anti-inflammatory IL-10 levels borderline increased (p = 0.052) in the blueberry group. However, changes in allergy symptoms were not significantly associated with IL-10 or IL-13. The relative abundances of Lacticaseibacillus, Blautia, and Peptostreptococcaceae at 12 months were negatively correlated with IL-10, while Lactobacillus, Clostridiaceae, and Megasphaera were positively associated. IL-13 was positively associated with Citrobacter and negatively associated with Anaerostipes and Blautia. Conclusions: The consumptio9n of blueberries as an early complementary food may improve resolution of allergy symptoms, modulate immune biomarkers, and promote beneficial shifts in gut microbiota during infancy. Future research should aim to identify the specific bioactive components of blueberries responsible for these effects and explore the potential of other complementary foods to favorably influence developing biological systems involved in microbiota and immune development. Full article

The gut microbiota plays a pivotal role in developing colorectal cancer (CRC) through interactions with host immunity, metabolism, and inflammation. However, microbiome-based studies remain scarce in Middle Eastern populations, limiting regional insights into microbial signatures associated with CRC. This study aimed to characterize the gut microbiota profiles of Jordanian CRC patients using 16S rRNA gene sequencing and compare them to those of healthy controls from the GutFeeling KnowledgeBase (GutFeelingKB). Stool samples from 50 CRC patients were analyzed using Illumina iSeq targeting the V3–V4 region. Taxonomic profiling was conducted with a standardized 16S metagenomics pipeline and compared with GutFeelingKB reference data. CRC samples were enriched in Streptococcus, Enterococcus, Klebsiella, Escherichia, Citrobacter, Veillonella, Megamonas, and Eggerthella, while beneficial butyrate-producing genera such as Roseburia, Ruminococcus, Akkermansia, Faecalibacterium, and Bacteroides were significantly depleted. The absence of Fusobacterium nucleatum and Bacteroides fragilis—commonly seen in global studies—suggests region-specific microbial patterns. This study is the first metagenomic study profiling CRC-associated microbiota in Jordan. The findings reveal a dysbiotic microbial signature that reflects both global changes associated with CRC and local ecological influences. This research emphasizes the importance of population-specific microbiome studies and highlights the need to include appropriately matched controls in future investigations. Full article

Background: The Citrobacter genus harbors class C (AmpC) and class A β-lactamases. Citrobacter freundii produces an inducible AmpC β-lactamase controlled by the LysR-type transcriptional regulator AmpR and cytosolic amidase AmpD. Citrobacter sedlakii produces the class A β-lactamase Sed-1, whose expression is believed to be regulated by the transcriptional regulator SedR and AmpD. Objectives:C. sedlakii NR2807, isolated in Japan, is resistant to third-generation cephalosporins and displays extended-spectrum β-lactamase characteristics. Here, we sought to understand the mechanism for successful resistance to third-generation cephalosporins by investigating the regulators controlling Sed-1 production. Methods: Plasmids containing bla_Sed-1 and sedR (pCR2807) or truncated sedR (pCR2807ΔSedR) were constructed and introduced into Escherichia coli. Antibiotic-resistant mutants of NR2807 were obtained, and enzyme kinetics were assessed. Results: The AmpD mutant (pCR2807/ML4953) showed an 8-fold increase in cefotaxime MIC and an 8.46-fold increase in Sed-1 activity compared to the wild-type (pCR2807/ML4947). However, induction of pCR2807/ML4947 also led to a 1.32-fold higher Sed-1 activity, indicating semi-inducibility. Deletion of sedR (pCR2807ΔSedR/ML4947) led to a 4-fold decrease in cefotaxime MIC and 1.93-fold lower Sed-1 activity, confirming SedR as an activator. While wild-type C. sedlakii ATCC51115 is susceptible to third-generation cephalosporins, the AmpD mutation in NR2807 led to Sed-1 overproduction and resistance to this class of antibiotics. Finally, mutagenesis revealed that amino acid substitution in Sed-1 conferred resistance to ceftazidime and extended-spectrum β-lactamase characteristics. Conclusions: Sed-1 producers, though usually susceptible to third-generation cephalosporins, may develop extended-spectrum β-lactamase traits due to AmpD or Sed-1 mutations, thereby requiring careful monitoring. Full article

Biotechnological research increasingly focuses on developing new drugs to counter the rise of antibiotic-resistant strains in hospitals. This study aimed to create bacterial lysates from antibiotic-resistant pathogens isolated from patients and medical instruments across hospital departments. Identification was performed based on morphological, cultural, and biochemical characteristics, as well as 16S rRNA gene sequencing using the BLAST algorithm. Strain viability was assessed using the Miles and Misra method, while sensitivity to eight antibacterial drug groups and biosafety between cultures were evaluated using agar diffusion. From 15 clinical sources, 25 pure isolates were obtained, and their phenotypic and genotypic properties were studied. Carbohydrate fermentation testing confirmed that the isolates belonged to the genera Escherichia, Citrobacter, Klebsiella, Acinetobacter, Pseudomonas, Staphylococcus, Haemophilus, and Streptococcus. The cultures exhibited good viability (10⁹–10¹⁰ CFU/mL) and compatibility with each other. Based on prevalence and clinical significance, three predominant hospital pathogens (Klebsiella pneumoniae 12 BL, Pseudomonas aeruginosa 3 BL, and Acinetobacter baumannii 24 BL) were selected to develop a bacterial lysate consortium. Lysates were prepared with physical disruption using a French press homogenizer. The resulting product holds industrial value and may stimulate the immune system to combat respiratory pathogens prevalent in Kazakhstan’s healthcare settings. Full article

Klebsiella pneumoniae carbapenemases (KPCs) are a group of class A β-lactamases of Gram-negative bacteria leading to difficult-to-treat infections. We evaluated the global epidemiology of KPC-producing Gram-negative clinical isolates. A systematic search of six databases (Cochrane Library, Embase, Google Scholar, PubMed, Scopus, and Web of Science) was conducted. Extracted data were tabulated and evaluated. After screening 1993 articles, 119 were included in the study. The included studies originated from Asia (n = 49), Europe (n = 29), North America (n = 14), South America (n = 11), and Africa (n = 3); 13 studies were multicontinental. The most commonly reported KPC-producing species were Klebsiella pneumoniae (96 studies) and Escherichia coli (52 studies), followed by Enterobacter cloacae (31), Citrobacter spp. (24), Klebsiella oxytoca (23), Serratia spp. (15), Enterobacter spp. (15), Acinetobacter baumannii complex (13), Providencia spp. (11), Morganella spp. (11), Klebsiella aerogenes (9), Pseudomonas aeruginosa (8), Raoultella spp. (8), Proteus spp. (8), and Enterobacter aerogenes (6). Among the studies with specific bla_KPC gene detection, 52/57 (91%) reported the isolation of bla_KPC-2 and 26/57 (46%) reported bla_KPC-3. The antimicrobial resistance of the studied KPC-producing isolates was the lowest for ceftazidime–avibactam (0–4%). Resistance to polymyxins, tigecycline, and trimethoprim–sulfamethoxazole in the evaluated studies was 4–80%, 0–73%, and 5.6–100%, respectively. Conclusions: The findings presented in this work indicate that KPC-producing Gram-negative bacteria have spread globally across all continents. Implementing proper infection control measures, antimicrobial stewardship programs, and enhanced surveillance is crucial. 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

Colistin has re-emerged as a last-resort antibiotic for treating infections caused by multidrug-resistant (MDR) Gram-negative bacilli (GNB). However, increasing resistance threatens its efficacy. This study aimed to evaluate colistin resistance trends among clinical isolates of Gram-negative bacilli isolated over a five-year period at a large Emergency Hospital in North-Eastern Romania. A total of 23,143 GNB strains were isolated during the study period, including 14,531 Enterobacterales and 8294 non-fermenting Gram-negative bacilli. The percentage of colistin-resistant strains among those analyzed was 3.98%. Species-specific analysis focused on Klebsiella spp., Escherichia coli, Enterobacter spp., Citrobacter spp., Pseudomonas spp., and Acinetobacter spp. Klebsiella spp. exhibited the highest prevalence of colistin resistance, accounting for over 80% of all colistin-resistant strains, with annual resistance rates fluctuating between 12.97% and 21.64%. Colistin resistance among E. coli was low (0.18–1.25%). Citrobacter spp. showed no resistance in the last three years of the study, and Enterobacter spp. maintained relatively stable resistance (3–5%). Resistance in Pseudomonas spp. remained below 1%, while Acinetobacter spp. showed a resistance rate of 5.43%. Several distinct resistance phenotypes were identified among Klebsiella spp., Pseudomonas spp., and Acinetobacter spp. strains, reflecting both endemic and sporadic circulation patterns. The study highlights a persistent presence of colistin resistance, especially in Klebsiella spp., underlining the importance of ongoing surveillance. Despite low resistance in other species, the emergence of resistant strains underscores the need for robust antimicrobial stewardship and infection control policies. Full article

Gut microbes are important for saproxylophagous insects, but little is known about the specific types of microbes that we can grow in the lab and how their diet affects them. We characterized aerobic culturable microbes from the superworm Zophobas atratus larvae reared on a standard diet (SD) and a fungal-based diet (FD) using the selective plating and 16S rRNA sequencing of isolates. Five functional groups were cultured: amino acid autotrophs, enterobacteria, yeasts, cellulolytic bacteria, and molds. A quantitative assessment revealed distinct diet-dependent patterns: SD-fed larvae showed the dominance of enterobacteria and amino acid autotrophs, while FD-fed larvae exhibited a higher abundance of enterobacteria and yeasts. Mold populations remained minimal under both diets. A phylogenetic analysis of bacterial isolates showed four core bacterial phyla (Pseudomonadota, Actinobacteria, Bacillota, and Bacteroidota) with diet-sensitive genus-level variations. Pseudomonadota dominated both diets, but certain genera were associated with different diets: Micrococcus and Brucella in the SD versus Citrobacter and Pseudomonas in the FD. Shared genera (Klebsiella, Enterobacter, and Bacillus) may represent a core culturable community. These findings demonstrate the influence of diet on culturable gut microbes while highlighting the need for complementary molecular approaches to study unculturable taxa. The isolated strains provide resources for investigating microbial functions in insect nutrition. Full article

Background: The combination of aztreonam (ATM) and avibactam (AVI) presents an important therapeutic option for carbapenem-resistant Enterobacterales, particularly the NDM-producing Enterobacterales. In 2024, both the CLSI and EUCAST published their methods in antimicrobial susceptibility testing for this combination of agents. Materials and Methods: Forty carbapenem-resistant Enterobacterales isolates, including Escherichia coli (n = 35), Enterobacter cloacae complex (n = 2), Klebsiella pneumoniae complex (n = 2), and Citrobacter freundii complex (n = 1) were included in this study. All isolates harbored the NDM carbapenemase except one, which had no known detected carbapenemases. Four antimicrobial susceptibility testing methods of the combination of ATM and AVI were evaluated on these isolates, including the CLSI broth disk elution (BDE) method, the disk diffusion (DD) method of aztreonam–avibactam (AZA) following the EUCAST breakpoints, the MIC test strip (MTS) method of AZA following the EUCAST breakpoints, and the gradient strip stacking (SS) method. BDE was used as the standard of comparison. Results: Using BDE as the standard of comparison, the AZA DD, AZA MTS, and SS methods had 100% categorical agreement (CA), 0% very major error (VME), and 0% major error (ME). The essential agreement (EA) between the AZA MTS and SS method was 57.5%. Conclusions: The AZA DD, AZA MTS, and the SS methods showed complete concordance with the BDE method. However, the MICs obtained from the AZA MTS and SS were not comparable. Full article

Regarding the trout microbiota, most information is focused on lactic acid bacteria, which can show beneficial properties. However, in trout farming, mostly pathogenic Gram-positive species were reported, such as Staphylococcus aureus, Listeria monocytogenes, and/or Clostridium spp. In this study, free-living trout were analyzed for Gram-negative microbiota that can cause loss as disease-stimulating agents. Bacteriocin postbiotics should be one of the approaches used to eliminate these agents. In total, 21 strains of different species isolated from the intestinal tract of 50 trout in Slovakia (Salmo trutta and Salmo gairdnerii) were taxonomically allotted into 13 species and 9 genera. This method showed variability in microbiota identified using MALDI-TOF mass spectrometry with the following species: Acinetobacter calcoaceticus, Citrobacter gillenii, Citrobacter freundii, Escherichia coli, Hafnia alvei, Kluyvera cryocrescens, K. intermedia, Leclercia adecarboxylata, Raoultella ornithinolytica, Pseudomonas fragi, Ps. putida, Ps. lundensis, Ps. teatrolens, and Serratia fonticola. Most strains were susceptible to the antibiotics used, reaching inhibitory zones up to 29 mm. On the other hand, 3 out of 21 strains (14%) were susceptible to nine enterocins- postbiotics (Hafnia alvei Hal281, Pseudomonas putida Pp391, and Ps. fragi Pf 284), with inhibitory activity in the range of 100–6400 AU/mL. Full article

The important role of antibiotics cannot be overestimated, as human health relies heavily on them for the treatment of infectious diseases. In this study, the antimicrobial susceptibility profiles of pathogens isolated from spinach (Spinacia oleracea) and cabbage (Brassica oleracea) collected from Free State Province were investigated. A total of 38 isolates representing 10 species, Enterobacter cloacae (5.3%), Staphylococcus aureus (13.2%), Micrococcus luteus (5.3%), Staphylococcus sciuri (5.3%), Acinetobacter haemolyticus (5.3%), Burkholderia cepacia (15.8%), Pseudomonas luteola (15.8%), Escherichia coli (18.4%), Citrobacter freundii (5.3%), and Serratia marcescens (10.5%), were confirmed by the Analytical Profile Index (API). We evaluated antibiotic resistance patterns of 38 unduplicated isolates using the disk diffusion method. As a result, E. coli (18.4%), B. cepacia (15.8%), P. luteola (15.8%), S. aureus (13.2%), and S. marcescens (10.5%), as well as 5.3% each for E. cloacae, M. luteus, S. sciuri, A. haemolyticus, and C. freundii, showed resistance to tested antibiotics. The majority (84%) of the isolates showed resistance to tetracycline, and penicillin had a value of 71%. A total of 79% of the antibiotic-resistant isolates demonstrated multidrug resistance (MDR) to several classes such as β-lactams, chloramphenicol, tetracycline, aminoglycosides, and macrolides. The results highlight the importance of monitoring the microbiological quality of leafy greens as they contain antibiotic-resistant bacteria that could affect human health when consumed. Full article

Background: Cow-milk-induced allergic proctocolitis (CMIAP) is a non-IgE-mediated food hypersensitivity that often resolves spontaneously but may predispose infants to IgE-mediated allergies and eosinophilic gastrointestinal disorders. Understanding its pathophysiology is crucial for microbiota-based interventions. Methods: We enrolled 32 exclusively breastfed infants—16 with confirmed cases of CMIAP and 16 age-matched healthy controls. The cohorts were sex-balanced (8 F/8 M), term-born (gestational age ± SD: 40 ± 1.2 vs. 39 ± 1.3 weeks), vaginally delivered, and sampled at a mean age of 2.0 ± 0.44 months (range 1.5–3.0) vs. 2.4 ± 0.66 months (range 1.5–3.5). Faecal samples underwent 16S rRNA gene sequencing on the Illumina NovaSeq platform, with diversity and differential abundance analyses. Results: The maternal dairy intake was similar (total dairy: 250 ± 80 vs. 240 ± 75 mL/day; yoghurt: 2.3 ± 1.0 vs. 2.5 ± 1.2 days/week; p = 0.72). Bray–Curtis dissimilarity assessments revealed distinct microbiota in infants with CMIAP. Infants with CMIAP had a lower abundance of Bifidobacterium (log₂FC−2.27; q = 0.022; ANCOM-BC), Collinsella (−29.35; padj < 0.0001; DESeq2), and Limosilactobacillus (−8.01; padj = 0.0285; DESeq2; q < 0.0001; ANCOM-BC) compared with controls. In contrast, Hungatella (+24.99; padj < 0.0001; DESeq2), Veillonella (+4.73; padj = 0.0221; DESeq2), Citrobacter (+10.44; padj = 0.0124; DESeq2), and Ruminococcus gnavus (+2.69; q < 0.0001; ANCOM–BC) were more abundant in the CMIAP group. Conclusions: Infants with CMIAP exhibit gut dysbiosis, which is characterised by the depletion of beneficial commensals and the enrichment of potential pathogens, independent of maternal dairy intake. Further studies should establish whether these microbiota alterations are causal or consequential in CMIAP. Full article

Background: Chronic rhinosinusitis (CRS) affects 5.5–28% of the population and is primarily an inflammatory disease, with microbiota potentially playing a key role. Understanding microbial pathogens and resistance patterns is crucial for effective management. This study aimed to evaluate the incidence of Gram-negative rods in CRS in adults as a part of a prospective microbiological study. Methods: Over one year, paranasal sinus mucosa samples from CRS patients and nasal concha samples from controls were analyzed. Cultivable bacterial flora was assessed using culture-based methods. Biofilm formation was evaluated via a microtiter-plate assay, and antibiotic susceptibility was tested using the disk diffusion method. Results: Tissue samples from 74 CRS patients and 47 controls yielded 198 bacterial strains. Gram-positive cocci dominated, while Gram-negative rods accounted for 17.6%, with Escherichia coli, Klebsiella oxytoca, and Citrobacter spp. being most common. All Gram-negative rods formed biofilms in vitro. They were susceptible to cefotaxime, aztreonam, ciprofloxacin, and meropenem but showed varying sensitivity to ampicillin (20–67%), tigecycline (40–57%), and amoxicillin/clavulanic acid (73–83%). Conclusions: The result of this study underlines that treatment of CRS should be based on the result of drug susceptibility testing of the isolated microorganism. Full article