Search Results (39)

Background: Klebsiella variicola is a Gram-negative, capsulated, nonmotile, facultative anaerobic rod. It is one of the species belonging to the K. pneumoniae complex. The objective of this study was to gain insights into the antimicrobial resistance and virulence of K. variicola strains isolated from clinical samples from oncologic patients. Methods: Strain identification was performed using a mass spectrometry method. Whole genome sequencing was conducted for all analyzed strains. Antimicrobial susceptibility was determined using an automated method. The presence of antimicrobial resistance mechanisms and genes encoding extended-spectrum beta-lactamases (ESBL) was assessed using the double-disc synergy test and genotypic methods. Results: All isolates were identified as K. variicola using mass spectrometry and whole genome sequencing (WGS). All isolates were ESBL-positive, and two of them harbored the bla_CTX-M-15 gene. In our study, the bla_LEN-17 gene was detected in all strains. Genome sequence analysis of the K. variicola isolates revealed the presence of virulence factor genes, including entAB, fepC, ompA, ykgK, and yagWXYZ. Two different plasmids, IncFIB(K) and IncFII, were identified in all of the analyzed K. variicola strains. The detected virulence factors suggest the ability of the bacteria to survive in the environment and infect host cells. All isolates demonstrated in vitro susceptibility to carbapenems. Conclusions: Further studies are needed to confirm whether multidrug-resistant K. variicola strains represent an important pathogen in infections among oncologic patients. Full article

Klebsiella variicola strains are Gram-negative rod-shaped bacteria that usually cause bloodstream, urinary and respiratory tract infections. The aim of the study was to identify K. variicola strains, evaluate the susceptibility of strains to selected antimicrobials, and detect their resistance mechanisms to β-lactams. Strain identification was performed using the mass spectrometry method. DNA sequencing was performed for selected strains. Susceptibility to selected antimicrobials was assessed using an automated method. The presence of an antimicrobial resistance mechanism and genes encoding ESβL was determined using the double-disc synergy test and genotypic methods. Most of the 108 analyzed strains were susceptible to imipenem (99.1%), meropenem (96.3%) and amikacin (96.3%). Over 12% of strains produced ESβL and were multidrug-resistant. Although K. variicola strains remain susceptible to antibiotics, there is a constant need to monitor their susceptibility to selected antimicrobials. The isolation of multidrug-resistant K. variicola strains underscores the critical importance of accurate species identification. This species may be clinically significant, as certain strains can also produce enzymes that pose significant threats today. Full article

Background and Clinical Significance: Klebisella variicola belongs to the Klebsiella pneumoniae complex. It is a Gram-negative, facultative anaerobic, and nonmotile bacillus, mainly isolated in plants. However, as an emerging human pathogen, it has been isolated in immunocompromised patients with urinary tract infections, pneumonia, and bacteremia. K. variicola infection in pregnancy, responsible for acute chorioamnionitis, has never been reported. Case Presentation: We present a case of a twin pregnancy at 17 + 5 weeks in which chorioamnionitis and fetal inflammatory responses such as funisitis and chorionic vasculitis were due to an ascending infection of K. variicola. The pathogen was isolated postmortem in fetal blood and tissues and the placenta using MALDI-ToF mass spectrometry (MALDI-ToF MS). The accuracy of this microbiological diagnosis sheds further light on the epidemiology and virulence of K. variicola in the prenatal setting. Conclusions: In the case of miscarriage, microbiological investigations on the fetus should always be recommended to identify the exact microorganism in order to target the medical treatment and manage subsequent pregnancies. Full article

Phosphorus is a macronutrient crucially important for plant growth and development; its limited amount in soil and water poses bewildering concerns amongst agronomists. Externally applied phosphorus fertilizers can fulfil crops’ phosphorus needs throughout essential growth stages; however, the overapplication of phosphorus fertilizers leads to diminished phosphorus acquisition efficiency (PAE), disrupts the delicate balance of nutrients in soil and water, leads to deficiencies in other essential elements, poses significant environmental risks, and accelerates the loss of phosphorus mineral supplies. Moreover, much of the applied phosphorus may become fixed as insoluble phosphates by combining with calcium, iron, aluminum, manganese, etc., present in soil, making it unavailable for the plants. Phosphate solubilizing bacteria (PSB) can render insoluble phosphate accessible to plants by solubilization and mineralization, hence enhancing crop yields while ensuring environmental sustainability. Earthworms are vital soil invertebrates that interact continuously with soil and soil microorganisms and play an essential role in maintaining soil fertility. The present study aims to screen and identify potential phosphate solubilizing bacteria from the intestinal tract of the earthworm Aporrectodea rosea. The experimental results indicate that the strain PSEG-1 was effective in phosphate solubilization, with a solubilization index of 1.6 in Pikovskaya (PVK)’s medium. The strain produced organic acid in the National Botanical Research Institute (NBRIP)’s medium. Phenotypic and genotypic studies of the isolate showed that the strain PSEG-1 belongs to Klebsiella variicola. Our results suggest that the vermi-bacterial strain Klebsiella variicola PSEG-1 possesses intrinsic abilities to solubilize phosphate, which could be exploited for formulating potential microbial biofertilizers to enhance crop production. Full article

Klebsiella variicola is an opportunistic pathogen often misidentified as Klebsiella pneumoniae, leading to misdiagnoses and inappropriate treatment in clinical settings. The genetic and molecular characteristics of clinically isolated K. variicola remain largely unexplored. We aim to fill this knowledge gap by examining the genomic properties of and evolutionary relationships between clinical isolates of K. variicola. The genomic data of 70 K. variicola strains were analyzed using whole-genome sequencing. A phylogenetic tree was generated based on the gene sequences from these K. variicola strains and public databases. Among the K. variicola strains, the drug resistance genes with the highest carrying rates were beta-lactamase and aminoglycoside. Locally isolated strains had a higher detection rate for virulence genes than those in public databases, with yersiniabactin genes being the most prevalent. The K locus types and MLST subtypes of the strains exhibited a dispersed distribution, with O3/O3a being the predominant subtype within the O category. In total, 28 isolates carried both IncFIB(K)_Kpn3 and IncFII_pKP91 replicons. This study underscores the importance of developing more effective diagnostic tools and therapeutic strategies for K. variicola infections. The continued surveillance and monitoring of K. variicola strains is essential for understanding the epidemiology of infections and informing public health strategies. Full article

Outbreaks of bacterial diseases occur in farmed Chinese longsnout catfish (Leiocassis longirostris). Due to limited information on aquatic Klebsiella variicola-infected animals, this study aimed to identify strain LL2208 isolated from diseased L. longirostris, determine its biological features, and evaluate its risk to public health. Strain LL2208 was tested for molecular identification, challenge, string, biofilm formation, and antimicrobial susceptibility. Furthermore, the whole genome of the strain was sequenced and analyzed. Based on molecular identification, strain LL2208 was identified as K. variicola. Artificial infection showed that this strain was moderately virulent to L. longirostris with an LD₅₀ = 7.92 × 10⁷ CFU/mL. Antibiotic sensitivity tests showed that this strain was resistant to penicillins, macrolides, aminoglycosides, amphenicols, glycopeptides, and lincosamide, indicating multidrug resistance. Strain LL2208 has a genome size of 5,557,050 bp, with a GC content of 57.38%, harboring 30 antimicrobial resistance genes and numerous virulence-related genes. Its molecular type was ST595-KL16-O5. Collinearity analysis showed that strain LL2208 was highly similar to the human-derived K. variicola strain. In conclusion, the multidrug-resistant and virulent K. variicola strain LL2208 was isolated from fish and may have originated from humans. These results provide a foundation for further studies on the transmission of K. variicola between humans and aquatic animals. Full article

The emergence and spread of antimicrobial resistance (AMR) among Enterobacteriaceae pose significant threats to global public health. In this study, we conducted a short-term surveillance effort in Southern Thailand hospitals to characterize the genomic diversity, AMR profiles, and virulence factors of Enterobacteriaceae strains. We identified 241 carbapenem-resistant Enterobacteriaceae, of which 12 were selected for whole-genome sequencing (WGS) and genome analysis. The strains included Proteus mirabilis, Serratia nevei, Klebsiella variicola, Klebsiella aerogenes, Klebsiella indica, Klebsiella grimontii, Phytobacter ursingii, Phytobacter palmae, Kosakonia spp., and Citrobacter freundii. The strains exhibited high levels of multidrug resistance, including resistance to carbapenem antibiotics. Whole-genome sequencing revealed a diverse array of antimicrobial resistance genes (ARGs), with strains carrying genes for ß-lactamase, efflux pumps, and resistance to other antibiotic classes. Additionally, stress response, metal tolerance, and virulence-associated genes were identified, highlighting the adaptability and pathogenic potential of these strains. A plasmid analysis identified several plasmid replicons, including IncA/C2, IncFIB(K), and Col440I, as well as several plasmids identical to those found globally, indicating the potential for the horizontal gene transfer of ARGs. Importantly, this study also identified a novel species of Kosakonia spp. PSU27, adding to the understanding of the genetic diversity and resistance mechanisms of Enterobacteriaceae in Southern Thailand. The results reported in this study highlight the critical importance of implementing effective antimicrobial management programs and developing innovative treatment approaches to urgently tackle AMR. Full article

In medicine, parasitic cysts (e.g., brain cysticerci) are believed to be sterile, and are primarily treated with antiparasitic medications, not antibiotics, which could prevent abscess formation and localized inflammation. This study quantified the microbial composition of parasitic cysts in a wild rodent, using multi-kingdom metagenomics to comprehensively assess if parasitic cysts are sterile, and further understand gut microbial translocation and adaptation in wildlife confined environments, outside the gut. Analysis was conducted on DNA from two hepatic parasitic cysts from a feline tapeworm, Hydatigera (Taenia) taeniaeformis, affecting a wild vole mouse (Microtus pennsylvanicus), and from feces, liver and peritoneal fluid of this and two other concurrent individual wild voles trapped during pest control in one of our university research vegetable gardens. Bacterial metagenomics revealed the presence of gut commensal/opportunistic species, Parabacteroides distasonis, Bacteroides (Bacteroidota); Klebsiella variicola, E. coli (Enterobacteriaceae); Enterococcus faecium and Lactobacillus acidophilus (Bacillota) inhabiting the cysts, and peritoneal fluid. Remarkably, viral metagenomics revealed various murine viral species, and unexpectedly, a virus from the insect armyworm moth (Pseudaletia/Mythimna unipuncta), known as Mythimna unipuncta granulovirus A (MyunGV-A), in both cysts, and in one fecal and one peritoneal sample from the other non-cyst voles, indicating the survival and adaption potential of the insect virus in voles. Metagenomics also revealed a significantly lower probability of fungal detection in cysts compared to that in peritoneal fluid/feces (p < 0.05), with single taxon detection in each cyst (Malassezia and Pseudophaeomoniella oleicola). The peritoneal fluid had the highest probability for fungi. In conclusion, metagenomics revealed that bacteria/viruses/fungi coexist within parasitic cysts supporting the potential therapeutic benefits of antibiotics in cystic diseases, and in inflammatory microniches of chronic diseases, such as Crohn’s disease gut wall cavitating micropathologies, from which we recently isolated similar synergistic pathogenic Bacteroidota and Enterobacteriaceae, and Bacillota. Full article

Ironwood trees, which are of great importance for the economy and environment of tropical areas, were first discovered to suffer from a slow progressive dieback in Guam in 2002, later referred to as ironwood tree decline (IWTD). A variety of biotic factors have been shown to be associated with IWTD, including putative bacterial pathogens Ralstonia solanacearum and Klebsiella species (K. variicola and K. oxytoca), the fungus Ganoderma australe, and termites. Due to the soilborne nature of these pathogens, soil microbiomes have been suggested to be a significant factor influencing tree health. In this project, we sequenced the microbiome in the soil collected from the root region of healthy ironwood trees and those showing signs of IWTD to evaluate the association between the bacterial community in soil and IWTD. This dataset contains 4,782,728 raw sequencing reads present in soil samples collected from thirty-nine ironwood trees with varying scales of decline severity in Guam obtained via sequencing the V1–V3 region of the 16S rRNA gene on the Illumina NovaSeq (2 × 250 bp) platform. Sequences were taxonomically assigned in QIIME2 using the SILVA 132 database. Firmicutes and Actinobacteria were the most dominant phyla in soil. Differences in soil microbiomes were detected between limestone and sand soil parent materials. No putative plant pathogens of the genera Ralstonia or Klebsiella were found in the samples. Bacterial diversity was not linked to parameters of IWTD. The dataset has been made publicly available through NCBI GenBank under BioProject ID PRJNA883256. This dataset can be used to compare the bacterial taxa present in soil associated with ironwood trees in Guam to bacteria communities of other geographical locations to identify microbial signatures of IWTD. In addition, this dataset can also be used to investigate the relationship between soil microbiomes and the microbiomes of ironwood trees as well as those of the termites which attack ironwood trees. Full article

Sensory attributes strongly influence consumers’ preferences for products. The inoculation of the Klebsiella variicola H8 strain in a reconstituted tobacco leaf concentrate (RTLC) solution increased neutral aroma-enhancing compound (NAEC) production by 45%, decreased the nicotine level by 25%, decreased the water-soluble total sugar content by ~36%, and improved the sensory quality by 5.71%. The production of NAECs such as dihydrokiwi lactone (DHKL: 192.86%), 1,2,3,4-tetrahydro-1,1,6-trimethylnaphthalene (THTMN: 177.77%), 2,4-di-tert-butylphenol (DTBP: 25%), 4-oxoisofolkone (OIFK: 116.66%,) 1,9-heptadecadiene-4,6-diyn-3-ol (HDD: 116.67%), β-damastrone (BDS: 116.67), and megastigmatrienone A (MSTA: 116.67%) was increased. A metagenomics analysis of the microbial community in the fermented RTLC (FRTLC) was performed to elucidate the mechanism by which NAECs were produced. As a result, 24 groups of functional genes were identified, and among them, five families of carbohydrate-active enzymes, (i) glycoside hydrolase (GH), (ii) glycosyltransferase (GT), (iii) polysaccharide lyase (PL), (iv) carbohydrate esterase (CE), and (v) auxiliary active enzyme (AA), were found to be positively correlated with the production of NAECs. However, among the GHs, the GHs annotated from the H8 strain chromosome displayed the highest relative abundance and a positive correlation with the production of NAECs. Specifically, the GH13-14, GH13-20, GH13-38, GH13-25, GH13-10, GH42, and GH28 genes of the H8 strain were relatively more abundant and were key contributors to the production of NAECs. The correlation analyses revealed that the H8 strain plays a leading role among all the microorganisms in FRTLC in the production of NAECs. Our findings support the application of Klebsiella variicola in NAEC production and a reduction in nicotine content in tobacco products. Full article

The Klebsiella pneumoniae complex is a commonly isolated bacteria in human infections. These opportunistic pathogens pose a serious threat to public health due to their potential transmission to the human population. Resistance to carbapenems is a significant antimicrobial resistance mechanism, leading to limited therapeutic options. Therefore, the aim of this study was to evaluate the in vitro activity of fosfomycin, colistin, ceftazidime–avibactam, and meropenem–vaborbactam against multidrug-resistant K. pneumoniae complex strains. This study involved 160 strains of Gram-negative rods, comprising 138 K. pneumoniae and 22 K. variicola. The minimal inhibitory concentration of fosfomycin was estimated using the agar dilution method, and for colistin, the microdilution method was employed. Susceptibility to ceftazidime–avibactam and meropenem–vaborbactam was determined using the gradient strip method. All analyzed K. pneumoniae complex isolates produced extended-spectrum β-lactamases, and 60.0% exhibited carbapenemases. The majority of the analyzed strains were susceptible to fosfomycin and colistin (62.5%). Among pandrug-resistant K. pneumoniae complex isolates, the highest susceptibility was observed with colistin (43.9%). Fosfomycin demonstrated good activity against ESβLs- and VIM-positive isolates from this complex. Colistin also exhibited satisfactory in vitro activity against VIM- and KPC-positive isolates from the K. pneumoniae complex. Ceftazidime–avibactam displayed good activity against K. pneumoniae complex strains producing ESβLs, KPC, and OXA enzymes. Additionally, meropenem–vaborbactam showed satisfactory in vitro activity against ESβLs- and KPC-positive isolates from this complex. Full article

Bioindicator species are used to assess the damage and magnitude of possible impacts of anthropic origin on the environment, such as the reckless consumption of antimicrobials. Chelonia mydas has several characteristics that make it a suitable bioindicator of marine pollution and of the presence of pathogens that cause diseases in humans. This study aimed to investigate the green sea turtle as a reservoir of resistant bacteria, mainly because C. mydas is the most frequent sea turtle species in Brazilian coastal regions and, consequently, under the intense impact of anthropic factors. Free-living green sea turtles ranging from 42.8 to 92 cm (average = 60.7 cm) were captured from Itaipú Beach, Brazil. Cloaca samples (characterizing the gastrointestinal tract) and neck samples (representing the transient microbiota) were collected. Bacterial species were identified, and their was resistance associated with the antimicrobials cephalothin, ciprofloxacin, gentamicin, tetracycline, and vancomycin. Citrobacter braaki, Klebsiella oxytoca, K. variicola and Proteus mirabilis were found resistant to cephalothin and Morganella morganii and Enterococcus faecalis tetracycline-resistant isolates in cloaca samples. In neck samples, species resistant to tetracycline were Salmonella sp., Serratia marcescens, S. ureylitica and Proteus mirabilis. This data reinforces that the green turtle is a bioindicator of antimicrobial resistance (AMR). Full article

Glyphosate is a non-selective herbicide that is used to control perennial weeds in agriculture. However, its vast application may result in glyphosate residues in the food chain. Due to its toxicity to non-target organisms, glyphosate-contaminated soils needed to be remediated, and bioremediation is a conventional remedial method. The success of this depends on the isolation of bacteria with the ability to degrade glyphosate. The goal of this study was to isolate glyphosate-degrading bacteria from the rhizosphere of maize and wheat with a repeated application history of glyphosate for 5–10 years and test their roles in promoting the growth of maize (Zea mays) and glyphosate degradation in vitro. Eleven isolated bacteria were inoculated, and their role in plant growth was compared at different levels (100 and 200 mg/kg) of glyphosate. The results revealed that E. ludwigii improved the highest shoot length by 26% and the root length by 34% compared to the control at 100 mg/kg. The relative water contents in leaves significantly improved by 58% using P. aeruginosa at 100 mg/kg. The maximum electrolyte leakage from leaves significantly reduced by 73% using E. ludwigii at 100 mg/kg compared to the control (uninoculated). A high-pressure liquid chromatography instrument was used to assess the glyphosate concentrations. The highest degradation of glyphosate was observed in treatments inoculated with E. ludwigii (99 and 40%), P. aeruginosa (95 and 39%), K. variicola, (91 and 38%) E. cloacae (92 and 38%), and S. liquefaciens (87 and 36%), respectively, at 100 and 200 mg/kg within 28 days. These five strains demonstrated a great potential for degrading glyphosate and promoting the growth of maize in vitro, and they will be further exploited for the biodegradation of glyphosate and the growth promotion of broader crop species in situ in the near future. Full article

Functional oligosaccharides exert obesity-reducing effects by acting at various pathological sites responsible for the development of obesity. In this study, tamarind xyloglucan oligosaccharides (TXOS) were used to attenuate metabolic disorders via the gut–liver axis in mice with high-fat-diet (HFD)-induced obesity, as determined through LC/MS-MS and 16S rRNA sequencing technology. A TXOS dose equivalent to 0.39 g/kg/day in humans restored the gut microbiota in obese mice, which was in part supported by the key microflora, particularly Bifidobacterium pseudolongum. Moreover, TXOS reduced the abundance of opportunistic pathogen species, such as Klebsiella variicola and Romboutsia ilealis. The bodyweight and weight gain of TXOS-treated (4.8 g/kg per day) mice began to decrease at the 14th week, decreasing by 12.8% and 23.3%, respectively. Sixteen fatty acids were identified as potential biomarkers in the liver, and B. pseudolongum and caprylic acid were found to tightly regulate each other. This was associated with reduced inflammation in the liver, circulation, and adipose tissue and protection from metabolic disorders. The findings of this study indicate that TXOS can significantly increase the gut microbiota diversity of obese mice and restore the HFD-induced dysbiosis of gut microbiota. Full article

The establishment of the Yellow River wetland nature reserves improves the local soil structure and fertility through the long-term succession of microorganisms. However, little is known about which indigenous microbial resources can accelerate the process of soil improvement and ecology restoration. To fill this gap, exopolysaccharides-producing bacteria and phosphate-solubilizing bacteria were isolated from soil samples of the wetland nature reserve with higher soil organic matter, available phosphorus, and available nitrogen content. 16S rRNA nucleotide sequence homology analysis and physiological-biochemical assay showed that the strain PD12 with the highest phosphate solubilization activity and higher EPS production was identified as Klebsiella variicola, and other high yield EPS-producing strains (EPS12, EPS15, EPS18, and EPS19) were identified as Pseudomonas migulae, Pseudomonas frederiksbergensis, Aeromonas media, and Pseudomonas vancouverensis, respectively. These results provided new potential microbial resources for the research and development of biofertilizers and added new insights into accelerating the restoration of physical, chemical, and biological properties of soil in the Yellow River basin. Full article