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Computational and Structural... 2023Colistin is considered as one of the last-resort antimicrobial agents for treating multidrug-resistant bacterial infections. Multidrug-resistant has been increasingly...
Colistin is considered as one of the last-resort antimicrobial agents for treating multidrug-resistant bacterial infections. Multidrug-resistant has been increasingly isolated from clinical patients, which posed a great challenge for antibacterial treatment. This study aimed to report a and co-carrying clinical isolate 5549 conferred a high-level resistance against colistin. Antibiotic susceptibility testing was performed using the microdilution broth method. Transferability of and -carrying plasmids were investigated by conjugation experiments. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to identify modifications in lipid A. Whole genome sequencing and phylogenetic analysis between strain 5549 and a total of 301 genomes retrieved from NCBI database were performed. The genetic characteristics of and -bearing plasmids were also analyzed. Our study indicated that strain 5549 showed extensively antibiotic-resistant trait, including colistin and carbapenem resistance. The and were carried by IncFIB/IncFII type p5549_mcr-10 (159417 bp) and IncN type p5549_NDM-1 (63489 bp), respectively. Conjugation assays identified that only the -carrying plasmid could be successfully transferred to J53. Interestingly, did not mediate colistin resistance when it was cloned into DH5α. Mass spectrometry analysis showed the lipid A palmitoylation of the C-lacyl-oxo-acyl chain to the chemical structure of lipid A at 2063 in strain 5549. In summary, this study is the first to report a and co-occurrence recovered from China. Our investigation revealed the distribution of different clonal lineage of with epidemiology perspective and the underlying mechanisms of colistin resistance. Active surveillance is necessary to control the further dissemination of multidrug-resistant .
PubMed: 37602227
DOI: 10.1016/j.csbj.2023.08.004 -
Applied and Environmental Microbiology Jul 2022Surface waters are one of the main sources for drinking water production, and thus microbial contamination should be as minimal as possible. However, high concentrations...
Surface waters are one of the main sources for drinking water production, and thus microbial contamination should be as minimal as possible. However, high concentrations of coliform bacteria were detected in reservoirs and lakes used for drinking water production during summer months due to autochthonous proliferation processes. Here, we present the genomic analyses of 17 strains of Enterobacter asburiae and spp. proliferating in reservoirs and lakes with special focus on the hygienic relevance, antibiotic resistance, and adaptations to the oligotrophic environments. The genomes contain neither genes for the type III secretion system nor cytotoxins or hemolysins, which are considered typical virulence factors. Examination of antibiotic resistance genes revealed mainly efflux pumps and β-lactamase class C () genes. Phenotypically, single isolates of Enterobacter asburiae showed resistance to fosfomycin and ceftazidime. The genome analyses further suggest adaptations to oligotrophic and changing environmental conditions in reservoirs and lakes, e.g., genes to cope with low nitrate and phosphate levels and the ability to utilize substances released by algae, like amino acids, chitin, alginate, rhamnose, and fucose. This leads to the hypothesis that the proliferation of the coliform bacteria could occur at the end of summer due to algae die-off. Certain strains of coliform bacteria have been shown to proliferate in the oligotrophic water of drinking water reservoirs and lakes, reaching values above 10 per 100 mL. Such high concentrations challenge drinking water treatment, and occasionally the respective coliform bacteria have been detected in the treated drinking water. Thus, the question of their hygienic relevance is of high importance for water suppliers and authorities. Our genomic analyses suggest that the strains are not hygienically relevant, as typical virulence factors are absent and antibiotic resistance genes in the genomes most likely are of natural origin. Furthermore, their presence in the water is not related to fecal contamination. The proliferation in reservoirs and lakes during stable summer stratification is an autochthonic process of certain E. asburiae and strains that are well adapted to the surrounding oligotrophic environment.
Topics: Anti-Bacterial Agents; Drinking Water; Enterobacter; Enterobacteriaceae; Gram-Negative Bacteria; Lakes; Virulence Factors
PubMed: 35862664
DOI: 10.1128/aem.00471-22 -
Frontiers in Microbiology 2020Sugarcane is a major crop in tropical and subtropical regions of the world. In China, the application of large amounts of nitrogen (N) fertilizer to boost sugarcane...
Sugarcane is a major crop in tropical and subtropical regions of the world. In China, the application of large amounts of nitrogen (N) fertilizer to boost sugarcane yield is commonplace, but it causes substantial environmental damages, particularly soil, and water pollution. Certain rhizosphere microbes are known to be beneficial for sugarcane production, but much of the sugarcane rhizosphere microflora remains unknown. We have isolated several sugarcane rhizosphere bacteria, and 27 of them were examined for N-fixation, plant growth promotion, and antifungal activity. 16S rRNA gene sequencing was used to identify these strains. Among the isolates, several strains were found to have a relatively high activity of nitrogenase and ACC deaminase, the enzyme that reduces ethylene production in plants. These strains were found to possess and genes associated with N-fixation and ethylene production, respectively. Two of these strains, -AA7 and -BY4 showed maximum plant growth promotion (PGP) and nitrogenase activity, and thus they were selected for detailed analysis. The results show that they colonize different sugarcane tissues, use various growth substrates (carbon and nitrogen), and tolerate various stress conditions (pH and osmotic stress). The positive effect of AA7 and BY4 strains on and stress-related gene (, , , , and ) expression and the induction of defense-related processes in two sugarcane varieties, GT11 and GXB9, showed their potential for stress amelioration and PGP. Both bacterial strains increased several sugarcane physiological parameters. i.e., plant height, shoot weight, root weight, leaf area, chlorophyll content, and photosynthesis, in plants grown under greenhouse conditions. The ability of rhizobacteria on N-fixing in sugarcane was also confirmed by a N isotope-dilution study, and the estimate indicates a contribution of 21-35% of plant nitrogen by rhizobacterial biological N fixation (BNF). This is the first report of sugarcane growth promotion by N-fixing rhizobacteria and strains. Both strains could be used as biofertilizer for sugarcane to minimize nitrogen fertilizer use and better disease management.
PubMed: 33510724
DOI: 10.3389/fmicb.2020.600417 -
Microbiology Spectrum Mar 2023Carbapenem-resistant strains have emerged as a serious threat to global public health. In recent years, , a carbapenemase gene that drew less attention before, has been...
Carbapenem-resistant strains have emerged as a serious threat to global public health. In recent years, , a carbapenemase gene that drew less attention before, has been increasingly detected in both clinical and environmental settings. However, the environmental distribution and transmission of , especially in aquaculture, require systematic investigation. In this study, the gene was detected in fish ( = 1), sewage ( = 1), river water ( = 1), and aquaculture pond water samples ( = 17) collected from Jiangsu, China, demonstrating a relatively high sample-positive ratio of 12.4% (20/161). Thirteen - or -carrying Enterobacter asburiae strains were isolated from -positive samples of aquatic products and aquaculture ponds. We also identified a novel transposon (Tn) carrying and a conserved region containing several truncated insertion sequence (IS) elements harboring , all of which may play important roles in mobilization. The occurrence of -carrying Enterobacter asburiae in aquaculture-related water samples and fish samples highlights the risk of transmission of -carrying strains through the food chain and the need for effective measures to prevent further dissemination. IMI carbapenemases have been detected in clinical isolates of many bacterial species with systemic infection and cause a further burden on clinical treatment in China, but their source and distribution are still unclear. The study systematically investigated the distribution and transmission of the gene in aquaculture-related water bodies and aquatic products in Jiangsu Province, China, which is famous for its rich water resources and developed aquaculture industry. The relatively high prevalence of in aquaculture samples and the identification of novel mobile elements harboring enhance our knowledge of gene distribution and highlight the public health risk and urgency of surveillance of aquaculture water systems in China.
PubMed: 36877062
DOI: 10.1128/spectrum.02853-22 -
Antimicrobial Agents and Chemotherapy Jul 2021The family was designated in 2017. To date, two alleles have been discovered that are carried by plasmids. Here, we identified a new quinolone resistance gene, , in...
The family was designated in 2017. To date, two alleles have been discovered that are carried by plasmids. Here, we identified a new quinolone resistance gene, , in the chromosome of Enterobacter mori clinical isolate 08-091 in China. conferred decreased susceptibility to fluoroquinolones, similar to and . To investigate the precise origin of , , and , 79 -bearing strains producing 30 variants were retrieved from the NCBI database. Phylogenetic analysis illustrated two major clusters, QnrE and QnrE, produced mainly by the and strains, respectively. Comparison of the genetic context of alleles demonstrated that and alleles presumably were captured by ISE and mobilized from the and strains to the and Escherichia coli strains, respectively. was proposed to be named , since it has spread to another genus. All the alleles were harbored by the Enterobacter species, except those captured by ISE and mobilized into other species of . is probably the source of to alleles, and is the reservoir of .
Topics: Anti-Bacterial Agents; Enterobacter; Enterobacter cloacae; Humans; Microbial Sensitivity Tests; Phylogeny; Quinolones
PubMed: 34097486
DOI: 10.1128/AAC.00456-21 -
Journal of Microbiology and... Jun 2018In the course of screening for microbes with nematicidal activity, we found that HK169 displayed promising nematicidal activity against the root-knot nematode , along...
In the course of screening for microbes with nematicidal activity, we found that HK169 displayed promising nematicidal activity against the root-knot nematode , along with plant growth-promoting properties. Soil drenching of a culture of HK169 reduced gall formation by 66% while also increasing root and shoot weights by 251% and 160%, respectively, compared with an untreated control. The cell-free culture filtrate of the HK169 culture killed all juveniles of within 48 h. In addition, the nematicidal activity of the culture filtrate was dramatically reduced by a protease inhibitor, suggesting that proteolytic enzymes contribute to the nematicidal activity of HK169. In order to obtain genomic information about the HK169 isolate related to its nematicidal and plant growth-promoting activities, we sequenced and analyzed the whole genome of the HK169 isolate, and the resulting information provided evidence that the HK169 isolate has nematicidal and plant growth-promoting activities. Taken together, these observations enable the future application of HK169 as a biocontrol agent for nematode control and promote our understanding of the beneficial interactions between HK169 and plants.
Topics: Animals; Anthelmintics; Antibiosis; Enterobacter; Genome, Bacterial; Solanum lycopersicum; Plant Growth Regulators; Plant Roots; Plant Shoots; Sequence Analysis, DNA; Tylenchoidea; Whole Genome Sequencing
PubMed: 29642290
DOI: 10.4014/jmb.1801.01021 -
Journal of Genomics 2024is a species of Gram-negative bacteria that is found in soil, water, and sewage. is generally considered to be an opportunistic pathogen, but has also been reported as...
is a species of Gram-negative bacteria that is found in soil, water, and sewage. is generally considered to be an opportunistic pathogen, but has also been reported as a plant growth-promoting bacterium (PGPB), which may have beneficial effects on plant growth and development. However, genetic analysis of has been limited, possibly due to its redundant enzymes that digest exogenous DNA in the cell. Here, an strain i6 was isolated from soil in Nara, Japan. This strain was amenable to transformation and the one-step gene inactivation method based on λ Red recombinase. The transformation efficiency of the i6 strain with the 10 kb plasmid DNA pCF430 was at least four orders of magnitude higher than that of the previously sequenced strain ATCC 35953, which could not be transformed with the same plasmid DNA. A draft genome sequence of the i6 strain was determined and deposited into the database, allowing several factors that may determine transformation efficiency to be perturbed and tested. Together with the amenability of the i6 strain to genetic manipulation, the information from the i6 genome will facilitate characterization and fine-tuning of the beneficial and detrimental traits of this species.
PubMed: 38321998
DOI: 10.7150/jgen.91337 -
Microbial Biotechnology Nov 2023Virulence factor modulating (VFM) is a quorum sensing (QS) signal shared by and specific to Dickeya bacteria, regulating the production of plant cell wall degrading...
Virulence factor modulating (VFM) is a quorum sensing (QS) signal shared by and specific to Dickeya bacteria, regulating the production of plant cell wall degrading enzymes (PCWDEs) and virulence of Dickeya. High polarity and trace of VFM signal increase the difficulty of signal separation and structure identification, and thus limit the development of quorum quenching strategy to biocontrol bacterial soft rot diseases caused by Dickeya. In order to high-throughput screen VFM quenching bacteria, a vfmE-gfp biosensor VR2 (VFM Reporter) sensitive to VFM signal was first constructed. Subsequently, two bacterial strains with high quenching efficiency were screened out by fluorescence intensity measurement and identified as Pseudomonas chlororaphis L5 and Enterobacter asburiae L95 using multilocus sequence analysis (MLSA). L5 and L95 supernatants reduced the expression of vfm genes, and both strains also decreased the production of PCWDEs of D. zeae MS2 and significantly reduced the virulence of D. oryzae EC1 on rice seedlings, D. zeae MS2 on banana seedlings, D. dadantii 3937 on potato and D. fangzhongdai CL3 on taro. Findings in this study provide a method to high-throughput screen VFM quenching bacteria and characterize novel functions of P. chlororaphis and E. asburiae in biocontrolling plant diseases through quenching VFM QS signal.
Topics: Virulence Factors; Dickeya; Quorum Sensing; Pseudomonas chlororaphis; Enterobacteriaceae; Plant Diseases
PubMed: 37815509
DOI: 10.1111/1751-7915.14351 -
Acta Medica Iranica Jan 2016Enterobacter asburiae (E. asburiae) is a facultative anaerobic, non-spore-forming gram-negative rod-shaped bacterium belonging to the family of Enterobacteriaceae. It is...
Enterobacter asburiae (E. asburiae) is a facultative anaerobic, non-spore-forming gram-negative rod-shaped bacterium belonging to the family of Enterobacteriaceae. It is an opportunistic pathogen that its strains are isolated from a variety of clinical and environmental specimens. Since powdered infant formula milk (PIF) is not a sterile product, it is an excellent medium for bacterial growth. The aim of this study was to isolate and identify E. asburiae from PIF in the neonatal intensive care unit (NICU) and determine antimicrobial susceptibility patterns of this bacterium. A total 125 PIF samples were purchased from drug stores between June 2011 to March 2012. E. asburiae was isolated according to FDA method. For final confirmation, biochemical tests embedded in the API-20E system were used. The drug susceptibility test was performed using the disc diffusion method according to CLSI recommendations. Out of the 125 PIF samples investigated, 2 (1.6%) samples were positive for E. asburiae. All isolated strains were uniformly susceptible to aztreonam, cefotaxim, amikacin, streptomycin, nalidixic acid, meropenem, tetracycline, ceftazidime, and colistin. Variable susceptibility was seen to the some antimicrobial agents tested. Each country should categorize its own designed guidelines for the preparation and handling of PIF adapted to the local environment. Moreover, the pathogenesis of the E. asburiae in infants hospitalized in NICU and other groups such as immunosuppressed patients and HIV infected individuals is uncertain and requires further study.
Topics: Animals; Anti-Bacterial Agents; Enterobacter; Food Microbiology; Humans; Infant; Infant Formula; Infant, Newborn; Intensive Care Units, Neonatal; Milk
PubMed: 26853289
DOI: No ID Found -
F1000Research 2018The predominant species in clinical isolates is . Many articles, clinicians, and GenBank submissions misname these strains as . The lack of sequenced type strains or...
The predominant species in clinical isolates is . Many articles, clinicians, and GenBank submissions misname these strains as . The lack of sequenced type strains or named species/subspecies for some clades in the complex complicate the issue. The genomes of the type strains for subsp. , . subsp. , and , and two strains from Hoffmann clusters III and IV of the complex were sequenced. These genomes, the . subsp. type strain, and other available type strains were analysed in conjunction with all extant genomes in NCBI's RefSeq using Average Nucleotide Identity (ANI). There were five recognizable subspecies of : subsp. subsp. nov., subsp. comb. nov., and the three previously known subspecies. One of the strains sequenced from the complex was not a novel subspecies but rather a member of a clade of a novel species: sp. nov.. was determined to be a later heterotypic synonym of which should take precedence. The phylogeny of the genus, particularly the complex, was re-evaluated based on the type strain genome sequences and all other available genomes in RefSeq.
Topics: Bacterial Typing Techniques; Computational Biology; Enterobacter; Genome, Bacterial; Phylogeny; RNA, Ribosomal, 16S; Species Specificity
PubMed: 30430006
DOI: 10.12688/f1000research.14566.2