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Enterobacter

Enterobacter is a genus of Gram-negative, rod-shaped bacteria commonly found in the environment and human gastrointestinal tract.
These opportunistic pathogens can cause a variety of infections, including pneumonia, bacteremia, and urinary tract infections, particularly in immunocompromised individuals.
Enterobacter species are known for their ability to develop antibiotic resistance, making them a significant challenge in clinical settings.
Researchers studying Enterobacter can leverage PubCompare.ai to optimize research protocols, improve reproducibility, and identify the most effective methods by analyzing the latest literature, preprints, and patent information.
This AI-driven tool can help streamline the research process and elevate the accuracy and impact of Enterobacter-related findings.

Most cited protocols related to «Enterobacter»

MLST databases for Staphylococcus aureus, Streptococcus pneumoniae, Salmonella enterica, Escherichia coli, Enterococcus faecium, Listeria monocytogenes and Enterobacter cloaceae were downloaded from pubmlst.org using the getmlst.py script included with SRST2 (June 2014).
Antimicrobial resistance gene detection was performed using the ARG-Annot database of acquired resistance genes [18 (link)]. Allele sequences (DNA) were downloaded in fasta format [43 ] (May, 2014). Sequences were clustered into gene groups with ≥80% identity using CD-hit [44 (link)] and the headers formatted for use with SRST2 using the scripts provided (cdhit_to_csv.py, csv_to_gene_db.py). A copy of the formatted sequence database used in this study is included in the SRST2 github repository [35 ].
Representative sequences for 18 plasmid replicons were extracted from GenBank using the accessions and primer sequences specified by Carattoli et al. [45 (link)]. A copy of the formatted sequence database used in this study is included in the SRST2 github repository [35 ].
Publication 2014
Alleles Enterobacter Enterococcus faecium Escherichia coli Genes Listeria monocytogenes Microbicides Oligonucleotide Primers Plasmids Replicon Salmonella enterica Staphylococcus aureus Streptococcus pneumoniae
The HiSeq and MiSeq metagenomes were built using 20 sets of bacterial whole-genome shotgun reads. These reads were found either as part of the GAGE-B project [21 (link)] or in the NCBI Sequence Read Archive. Each metagenome contains sequences from ten genomes (Additional file 1: Table S1). For both the 10,000 and 10 million read samples of each of these metagenomes, 10% of their sequences were selected from each of the ten component genome data sets (i.e., each genome had equal sequence abundance). All sequences were trimmed to remove low quality bases and adapter sequences.
The composition of these two metagenomes poses certain challenges to our classifiers. For example, Pelosinus fermentans, found in our HiSeq metagenome, cannot be correctly identified at the genus level by Kraken (or any of the other previously described classifiers), because there are no Pelosinus genomes in the RefSeq complete genomes database; however, there are seven such genomes in Kraken-GB’s database, including six strains of P. fermentans. Similarly, in our MiSeq metagenome, Proteus vulgaris is often classified incorrectly at the genus level because the only Proteus genome in Kraken’s database is a single Proteus mirabilis genome. Five more Proteus genomes are present in Kraken-GB’s database, allowing Kraken-GB to classify reads better from that genus. In addition, the MiSeq metagenome contains five genomes from the Enterobacteriaceae family (Citrobacter, Enterobacter, Klebsiella, Proteus and Salmonella). The high sequence similarity between the genera in this family can make distinguishing between genera difficult for any classifier.
The simBA-5 metagenome was created by simulating reads from the set of complete bacterial and archaeal genomes in RefSeq. Replicons from those genomes were used if they were associated with a taxon that had an entry associated with the genus rank, resulting in a set of replicons from 607 genera. We then used the Mason read simulator [22 ] with its Illumina model to produce 10 million 100-bp reads from these genomes. First we created simulated genomes for each species, using a SNP rate of 0.1% and an indel rate of 0.1% (both default parameters), from which we generated the reads. For the simulated reads, we multiplied the default mismatch and indel rates by five, resulting in an average mismatch rate of 2% (ranging from 1% at the beginning of reads to 6% at the ends) and an indel rate of 1% (0.5% insertion probability and 0.5% deletion probability). For the simBA-5 metagenome, the 10,000 read set was generated from a random sample of the 10 million read set.
Publication 2014
Bacteria Citrobacter Deletion Mutation Enterobacter Enterobacteriaceae Genome Genome, Archaeal Genome, Bacterial Genome Components INDEL Mutation Klebsiella Metagenome Pelosinus fermentans Proteus Proteus mirabilis Proteus vulgaris Replicon Salmonella Strains
We have expanded the Reference Gene Catalog8 (link) to include genetic elements related to stress response and virulence genes; these expansions can be visualized in the Reference Gene Catalog Browser (https://www.ncbi.nlm.nih.gov/pathogens/refgene/). One reason we expanded AMRFinderPlus is to understand the linkages between AMR genes and stress response and virulence genes in food-borne pathogens; thus, the stress response and virulence genes included in the Reference Gene Catalog are composed primarily of E. coli-related genes derived primarily from González-Escalona et al.23 (link) as well as BacMet24 (link), but also have been supplemented by manual curation efforts for other taxa. Stx gene nomenclature adopts the system of Scheutz et al.25 (link) and the intimin (eae) gene nomenclature uses existing designations in the literature26 (link),27 (link). Genes are incorporated only if there is literature supporting the function of that protein or closely related sequences that meet the identification criteria. As a major focus of our work is to improve NCBI’s Pathogen Detection system16 (link), we excluded genes that belonged to organisms not deemed clinically relevant. To remove ‘housekeeping’ proteins that were universally found in one or more taxa in the Pathogen Detection system, sequences were not included if they were found at a frequency of greater than 95% in a survey of 58,531 RefSeq bacterial assemblies belonging to any of the following species: Acinetobacter, Campylobacter, Citrobacter, Enterococcus, Enterobacter, Escherichia/Shigella, Klebsiella, Listeria, Salmonella, Staphylococcus, Pseudomonas, and Vibrio. If genes of particular interest in foodborne pathogens exceeded this threshold, they were excluded in the taxa where they appear to be nearly universal (see “Identifying genomic elements” below). In addition, genes with misidentified functions, such as copper-binding proteins that use copper as a co-factor yet do not confer resistance to copper, also were excluded. As we continue to expand the database, we use similar criteria when adding genes.
Publication 2021
Acinetobacter Bacteria Bears Campylobacter Citrobacter Copper copper-binding protein Enterobacter Enterococcus Escherichia Escherichia coli factor A Food Gene Components Genome Components Klebsiella Linkage, Genetic Listeria Operator, Genetic Pathogenicity Proteins Pseudomonas Salmonella Shigella Staphylococcus Vibrio Virulence
Five E. cloacae strains the complete genome sequences of which have been determined (ATCC 13047, NCTC 9394, ENHKU 01, SCF1, and EcWSU 1; hereafter, genome strains) were used to design PCR primers. One hundred one clinical isolates collected at National Center for Global Health and Medicine Hospital and a commercial clinical laboratory (BML inc, Saitama, Japan) during 2007–2013 were used to evaluate the performance of the MLST scheme developed in the present study (Table 1).
Publication 2013
Clinical Laboratory Services Enterobacter Genome Oligonucleotide Primers Pharmaceutical Preparations Strains
Experimental procedures and animal management protocols were carried out in accordance with the detailed unified requirements of the Local Ethics Committee on Animal Experimentation, which also meet the EU standards.
Commercial brown layers at 20 weeks that were serologically negative for MS and M. gallisepticum (MG) infection were bought from a poultry farm. They had been vaccinated against Newcastle disease virus (ND), infectious bronchitis virus (IBV) and metapneumovirus. Birds were tested before infection for MG, MS, IBV, ND, avian influenza (AI) and adenoviruses by PCR methods. After 2 weeks’ acclimatization, at the age of 22 weeks the birds were divided into three experimental groups. Each group (n = 11) was housed in our experimental infection facility in a different room and maintained with HEPA-filtered air under negative pressure. The room temperature range was 18–20 °C, birds were exposed to 14 h of light per day, and food and drinking water were provided ad libitum.The three experimental groups were inoculated via trachea. The first group (n = 11) was inoculated with 0.4 ml of broth culture containing 104 colony-forming units (CFU)/ml of the MS strain GK1/15PL isolated from tracheal swabs. The second group (n = 11) was inoculated with 0.4 ml of broth culture containing 104 CFU /ml of the MS strain PL146/3-J/15 isolated from oviduct tissue. The third group (control group n = 11) was given 0.4 ml of sterile modified Frey Medium.
Tracheal and cloacal swabs were collected from all chickens on days 0, 7, 14, 21, 28, 35, 42, 49, and 56. Blood samples were taken from all birds on the same days for MS serology. Over 8 weeks eggs were collected daily from the control and infected groups and weighed and candled. At the end of the experiment the birds were euthanized, necropsies performed and samples collected as described below. Trachea and infundibulum, magnum and uterus were collected post mortem from both infected groups and randomly selected birds from group III (control group). Tissue taken from trachea and oviduct was cut into small pieces (2 g ± 0.1) and placed in 10 ml of PBS (pH 7.4 ± 0.2) and homogenized. Part of the homogenized tissues were taken for mycoplasma culture and DNA extraction.
Swabs taken from birds were used for general bacteriology and mycoplasma culture. DNA extracted from the MS cultures was used for molecular typing. The shells of unaffected and EAA-affected eggs were examined by FF OCT.
Publication 2019
Acclimatization Adenoviruses Animals Autopsy Aves BLOOD Chickens Eggs Enterobacter Food Fowls, Domestic Infection Infectious bronchitis virus Influenza in Birds Light Metapneumovirus Mycoplasma Newcastle disease virus Oviducts Pituitary Stalk Pressure Regional Ethics Committees Sterility, Reproductive Strains Tissues Trachea Uterus

Most recents protocols related to «Enterobacter»

This study was conducted in Damietta Governorate on the Egyptian Mediterranean coast (northern east Nile Delta), Egypt through the period from October 2021 to March 2022. A total of 200 cloacal swabs were collected from migratory and broiler chicken birds. Broiler chickens were selected from poultry farms and live bird markets near which the migratory birds were hunted at the similar time points. One hundred samples were obtained from migratory birds and 100 from broiler chickens; 50 from 5 poultry farms (10 for each farm) with deep litter system and 50 from 3 live bird markets located in different regions inside Damietta Governorate. Five broiler poultry farms were chosen on the basis of their owners’ willingness to permit the samples collection. Broiler chicken birds from the farms and live bird markets were selected randomly. The map of Damietta Governorate was constructed to highlight the location of the selected broiler chicken farms and live bird markets in relation to the rest of Damietta (Supplementary Fig. 9). The migratory birds that were found near to the examined farms and live bird markets were trapped by net traps, sampled, marked (to ensure that each bird was only sampled once) and photographed to detect its species. The cotton swabs were aseptically collected on 2 ml of Bolton broth (Oxoid, UK) then labeled and transported within 1 h in an ice box at 4 °C to the Reference Laboratory for Veterinary Quality control on Poultry production to perform further examinations. All samples were incubated at 42 °C for 48 h under microaerophilic conditions. Isolation and identification of Campylobacter spp.
Each enriched sample was streaked onto modified charcoal cefoperazone deoxycholate agar (Oxoid, UK) with antibiotic solution (cefoperazone sodium salt; 0.032 g, amphotericin B; 0.01 g and water; 5 ml) and incubated at 42 °C for 48 h. The suspected colonies were identified by morphological characteristics and Gram staining [45 ]. The suspected isolates were subjected to standard biochemical procedures, including tests for hippurate, acetate hydrolysis and catalase [46 ].
Publication 2023
Acetate Agar Amphotericin B Antibiotics Aves Campylobacter Catalase Cefoperazone Charcoal Chickens Deoxycholate Enterobacter Fowls, Domestic Gossypium Hartnup Disease hippurate Hydrolysis isolation Physical Examination Sodium, Cefoperazone Specimen Collection
Individual sharks were captured by using a handline or drumline and secured alongside the boat. Handling time was limited to 30 min, at which point the sharks were released safely back to the water. Microbiome samples were taken from three distinct anatomical locations (skin, gills, and cloaca) by gently rubbing a sterile swab (COPAN Diagnostics, United States) against the shark’s organs. In addition, an environmental sample (1.5-L surrounding seawater) was collected near each shark captured. The swabs and the seawater samples were kept sterile in a cool box until arrived at the laboratory. At the laboratory, environmental samples were filtered using a single use “Nalgene RapidFlow Filters” 0.2 μm (Thermo Scientific, cat no. 566–0020, Israel). All swabs and filtered environmental samples were stored at −20°C for further work. In total, 27 sharks (15 female dusky and 12 male sandbar sharks) were sampled, including 77 shark microbiome samples and 12 environmental samples (Supplementary Table S1). Mean ambient seawater temperature was measured in 10 m intervals by four acoustic receivers (Thelma Biotel, Norway) positioned around the power and desalination plant’s warm water plume.
Publication 2023
Acoustics Diagnosis Enterobacter Females Gills Males Microbiome Plants Sharks Skin Sterility, Reproductive
A total of 1,270 oropharyngeal and cloacal swabs were collected from chickens, ducks, geese and pigeons in a live-poultry market between 2018 and 2021. Each sample was placed in 1 mL of cold phosphate-buffered saline (PBS) containing penicillin (5,000 U/mL) and streptomycin (5,000 U/mL). After mixing and centrifugation at 10,000 × g/min for 5 min, 0.2 mL of supernatant was used to inoculate 9-day-old specific-pathogen-free chicken embryos via the allantoic cavity, followed by incubation at 37°C for 48–72 h. We then harvested the allantoic fluid, and a total of 29 viruses were isolated (Supplementary Table 3).
Publication 2023
Allantois Centrifugation Chickens Columbidae Common Cold Dental Caries Ducks Embryo Enterobacter Fowls, Domestic Geese Oropharynxs Penicillins Phosphates Saline Solution Specific Pathogen Free Streptomycin Virus
A balloon catheter (MILA Anal Sac Balloon Catheter 4fr × 17.5 cm) was advanced 3 cm through the cloaca to the urethra and connected to a second pressure transducer (ADInstruments MLT844 with a MEMSCAP 844-28 disposable dome coupler) to measure Pura. Both pressure transducers were calibrated before insertion using a pressure gauge between 0 and 20 mmHg and recorded (1 kHz) simultaneously during stimulation using an acquisition system (ADInstruments PowerLab 4/26 and two ADInstruments bridge amplifiers) via the ADInstruments LabChart™ Software.
Publication 2023
Anal Sacs Catheters Enterobacter Pressure Pus Transducers, Pressure Urethra
The experiments were carried out between April and May 2018 (Spring season). This experiment was carried out on non-hibernating adult male Dabb lizards (U. aegyptia; n = 24) of age of 18–24 months. The main site of captive Dabb lizards from Talaba Abdel Halim farm, Abu Rawash village, Kerdasa Center, Giza Governorates, Egypt. The Dabb lizards were individually housed in glass terraria with sandy substrate, large rock for basking, resin rock Cave for hiding, overhead lamps (MIXJOY UV-A/UV-B Sun Lamp, 160 watts) that gave both heat/light that turned off at night and were set for a light/dark cycle of 12 h and fed on corn seeds and leaf lettuces, as well as bits of zucchini and carrots. Water was provided ad libitum. They were given two weeks for acclimation prior to start the experiment (Fig. 1).

It represented experimental design and measuring parameters.

These Dabb lizards were divided into four equal groups; control group, low temperature exposed group, moderate temperature exposed group and high temperature exposed group. Each group (n = 6) of them (n = 24) were kept at glass terraria. Control group was exposed to Terrarium temperature (38–39 °C) and kept as control group. The animals in low, moderate and high temperature exposed Dabb lizards’ groups were exposed to low (12–14 °C), moderate (41–43 °C), and high (43–45 °C) temperatures, respectively, for one week. Low and high temperatures were chosen based on seasonal changes in the winter, and summer seasons in their natural range.
At low temperatures (12–14 °C), blood sampling was performed after the lizards were kept for a week on a laboratory refrigerator (PHCbi, formerly Panasonic, MPR-722R-PA, Series 23.7 Cu. Ft., its temperature range: 2–23 °C) with temperature of 12–14 °C. At moderate temperature, the glass terraria containing the lizards were introduced in a water bath (Gallenkemp BKS-350-010Q) at 41–43 °C. At high temperature, the glass terraria with the lizards were again introduced in a water bath but at a temperature of 43–45 °C.
In the laboratory, the body temperature of the lizards was monitored using ultra-thin thermocouple probes that were linked to tele-thermometer (YSI Tele-thermometer, Model 44-Twelve channel, Yellow Springs Instrument Co., Inc., Ohio) alongside an Omni scribe Houston Instrument B5217-1 chart recorded for keeping track of inner body temperature. The thermocouple probes (Temperature sensors) were embedded within the cloaca of lizards during the run. The length of the wire attached was long enough to allow the lizards to move freely in the laboratory at a given temperature stated above.
Publication 2023
Acclimatization Adult Animals Bath Cold Temperature Daucus carota Enterobacter Fever Lactuca sativa Light Lizards Maize Males Natural Springs Plant Embryos Plant Leaves Resins, Plant Thermometers

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E. cloacae is a laboratory strain of the bacterium Enterobacter cloacae, a Gram-negative, rod-shaped, facultatively anaerobic bacterium commonly found in the environment and human gastrointestinal tract. This strain is used for research and quality control purposes in various microbiological applications.
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More about "Enterobacter"

Enterobacter, a genus of Gram-negative, rod-shaped bacteria, is a common inhabitant of the environment and human gastrointestinal tract.
These opportunistic pathogens are known for their ability to cause a variety of infections, including pneumonia, bacteremia, and urinary tract infections, particularly in immunocompromised individuals.
Enterobacter species, such as Enterobacter cloacae (E. cloacae), are particularly concerning due to their propensity for developing antibiotic resistance, posing a significant challenge in clinical settings.
Researchers studying Enterobacter can leverage advanced analytical tools like MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry) and the Vitek 2 system to accurately identify and characterize these bacteria.
These techniques, combined with traditional microbiological methods like Buffered peptone water enrichment, can provide valuable insights into the epidemiology, virulence factors, and antimicrobial resistance profiles of Enterobacter isolates.
To further enhance Enterobacter research, scientists can utilize AI-driven platforms like PubCompare.ai.
This tool can help optimize research protocols, improve reproducibility, and identify the most effective methods by analyzing the latest literature, preprints, and patent information.
By leveraging PubCompare.ai, researchers can streamline their workflow, enhance the accuracy of their findings, and contribute to the broader understanding of this opportunistic pathogen.
In addition to Enterobacter, other closely related Gram-negative bacteria, such as Klebsiella pneumoniae (K. pneumoniae) and Pseudomonas aeruginosa (P. aeruginosa), are also of great interest to the scientific community.
Techniques like OneStep RT-PCR kits and the QIAamp Viral RNA Mini Kit can be employed to detect and characterize these pathogens, further expanding the arsenal of tools available to researchers studying Enterobacter and related microorganisms.
By combining the insights gained from the MeSH term description, the Metadescription, and the incorporation of relevant terms and techniques, researchers can develop a comprehensive understanding of Enterobacter and its role in clinical settings.
This knowledge can lead to the development of more effective prevention, diagnosis, and treatment strategies, ultimately improving patient outcomes and public health.