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Microorganisms Jun 2024() is found in water, soil, plants and animals. Even though it has low virulence, it has increasingly been found to cause a number of infectious diseases in people with...
() is found in water, soil, plants and animals. Even though it has low virulence, it has increasingly been found to cause a number of infectious diseases in people with low immunity. The identification of mainly uses biochemical methods, such as the API 20NE or Vitek-2. The typing studies of have mainly utilized PFGE, rep-PCR, AFLP, 16s rDNA sequencing, RecA-PCR RFLP, and MALDI-TOF MS. This study aims to evaluate the polymorphisms of variable-number tandem-repeats (VNTRs) within genomic DNA of strains. The tandem repeats (TRs) in genomic DNA are discovered using Tandem Repeat Finder software (version 4.09). Twelve different VNTRs are designated and assigned to the nomenclature. The primers for PCR of 12 loci are designed. The PCR product size is converted to the number of tandem repeats in every locus. The relatedness of 65 strains from geographically different countries are analyzed by means of 12-variable-number tandem-repeat analysis(MLVA-12). A total of 51 different genotypes are found in 65 strains. These strains, which were collected from the same environmental samples, hospitals, and countries, are clustered within the same or closely genotypes. The MLVA-12 assay has a good discriminatory power for species determination, typing of , and inferring the origin of bacteria.
PubMed: 38930593
DOI: 10.3390/microorganisms12061211 -
Journal of Biological Engineering Feb 2023Aromatic primary amines (APAs) are key intermediates in the chemical industry with numerous applications. Efficient and mild biocatalytic synthesis is an excellent...
BACKGROUND
Aromatic primary amines (APAs) are key intermediates in the chemical industry with numerous applications. Efficient and mild biocatalytic synthesis is an excellent complement to traditional chemical synthesis. Our lab previously reported a whole-cell catalytic system for the synthesis of APAs catalyzed by carboxylic acid reductase from Neurospora crassa (ncCAR) and ω-transaminase from Ochrobactrum anthropi (OATA). However, the accumulation of toxic intermediates (aromatic aldehydes) during biocatalytic synthesis affected yields of APAs due to metabolic imbalance.
RESULTS
In this work, the biocatalytic synthesis of APAs (taking cinnamylamine as an example) was metabolically regulated by the overexpression or knockout of five native global transcription factors (TFs), the overexpression of eight native resistance genes, and optimization of promoters. Transcriptome analysis showed that knockout of the TF arcA increased the fluxes of NADPH and ATP in E. coli, while the rate of pyruvate metabolism was accelerated. In addition, the genes related to stress and detoxification were upregulated with the overexpression of resistance gene marA, which reduced the NADPH level in E. coli. Then, the expression level of soluble OATA increased by promoter optimization. Overall, arcA and marA could regulate the catalytic rate of NADPH- dependent ncCAR, while arcA and optimized promoter could regulate the catalytic rate of OATA. Lastly, the cinnamylamine yield of the best metabolically engineered strain S020 was increased to 90% (9 mM, 1.2 g/L), and the accumulation of cinnamaldehyde was below 0.9 mM. This work reported the highest production of cinnamylamine by biocatalytic synthesis.
CONCLUSION
This regulatory process provides a common strategy for regulating the biocatalytic synthesis of other APAs. Being entirely biocatalytic, our one-pot procedure provides considerable advantages in terms of environmental and safety impacts over reported chemical methods.
PubMed: 36823535
DOI: 10.1186/s13036-023-00334-y -
BMC Research Notes May 2020Di-2-ethylhexyl phthalate (DEHP) pollution is one of the major environmental concerns all over the world. This research aimed at studying the biodegradation kinetics of...
OBJECTIVE
Di-2-ethylhexyl phthalate (DEHP) pollution is one of the major environmental concerns all over the world. This research aimed at studying the biodegradation kinetics of DEHP by a newly isolated bacterial strain. Water and sediment samples were collected from Wuhan South Lake and potent bacterial isolates were screened for DEHP degradation, characterized by biochemical, physiological, morphological and 16S rDNA gene sequencing, and optimized under suitable pH, temperature, NaCl and DEHP concentrations. DEHP and its metabolites were quantified by High Performance Liquid Chromatography and their degradation kinetics were studied.
RESULTS
The newly isolated bacterium was identified as Ochrobactrum anthropi strain L1-W with 99.63% similarity to Ochrobactrum anthropi ATCC 49188. It was capable of utilizing DEHP as the carbon source. The optimum growth temperature, pH, DEHP and NaCl concentration for the strain L1-W were 30 °C, 6, 400 mg/L and 10 g/L respectively. Strain L1-W was capable of degrading almost all (98.7%) of DEHP when the initial concentration was 200 mg/L within a period of 72 h. Besides, it was also found capable of degrading five other phthalates, thus making it a possible candidate for bioremediation of phthalates in the environmental settings.
Topics: Biodegradation, Environmental; China; Chromatography, High Pressure Liquid; Diethylhexyl Phthalate; Humans; Hydrogen-Ion Concentration; Kinetics; Ochrobactrum anthropi; Phylogeny; RNA, Ribosomal, 16S; Soil; Temperature
PubMed: 32448295
DOI: 10.1186/s13104-020-05096-0 -
Journal of Infection and Public Health 2017The human stomach is colonized by diverse bacterial species. The presence of non-Helicobacter pylori bacteria in urease-positive biopsies of individuals has been...
The human stomach is colonized by diverse bacterial species. The presence of non-Helicobacter pylori bacteria in urease-positive biopsies of individuals has been reported. Bacteria belonging to the Ochrobactrum genus have been documented in the human gastric niche. The co-occurrence of Ochrobactrum spp. with H. pylori was previously reported in an antral biopsy of a non-ulcer dyspeptic (NUD) subject from Northern India. There is no information on the genetic diversity of Ochrobactrum spp. isolated from the gastric niche in the stomach. We aimed to study the species distribution and diversity of Ochrobactrum spp. with and without H. pylori in urease-positive biopsies across three different geographical regions in India. Sixty-two Ochrobactrum isolates recovered from patients with an upper gastric disorder (n=218) were subjected to molecular identification and multilocus sequence typing. H. pylori DNA was found in the majority of biopsies, which had a variable degree of Ochrobactrum spp present. Interestingly, some of the urease-positive biopsies only had Ochrobactrum without any H. pylori DNA. Based on phylogenetic analysis, the Ochrobactrum isolates were distributed into the O. intermedium, O. anthropi and O. oryzae groups. This indicates there are multiple species in the gastric niche irrespective of the presence or absence of H. pylori. Antibiotyping based on colistin and polymyxin B could differentiate between O. intermedium and O. anthropi without revealing the resistance-driven diversity. Considering the prevalence of multiple Ochrobactrum spp. in the human gastric niche, it is important to evaluate the commensal and/or pathogenic nature of non-H. pylori bacteria with respect to their geographical distribution, lifestyle and nutrition needs.
Topics: Adolescent; Adult; Aged; Aged, 80 and over; Biopsy; Female; Gastric Mucosa; Gastritis; Genetic Variation; Genotype; Gram-Negative Bacterial Infections; Helicobacter pylori; Humans; India; Male; Microbial Sensitivity Tests; Middle Aged; Multilocus Sequence Typing; Ochrobactrum; Phylogeny; Young Adult
PubMed: 27287730
DOI: 10.1016/j.jiph.2016.04.013 -
Scientific Reports Apr 2023In a survey conducted during the period of March-May 2019 in nurseries, warehouses, and shops at three governorates (Alexandria, El-Behera, and Giza governorates,...
In a survey conducted during the period of March-May 2019 in nurseries, warehouses, and shops at three governorates (Alexandria, El-Behera, and Giza governorates, Egypt), symptoms of root rot, basal stem rot, and wilt disease complex were observed in the lucky bamboo (Dracaena sanderiana hort. ex. Mast.). The highest disease infection percentage was found in lucky bamboo collected from Alexandria City (47.67%), while the highest disease severity was in lucky bamboo collected from El-Behera Governorate (35.19%). Rhizoctonia solani, Fusarium oxysporum, F. solani, Aspergillus niger, and Alternaria alternate were isolated and identified in the infected lucky bamboo samples. R. solani isolates were the most dominant among the recovered fungal species with a percentage of 80.89% of the total isolates (246). Pathogenicity tests showed that R. solani was the most pathogen with 100% disease infection and 76.67% disease severity. Molecular identification characterized R. solani isolate as R. solani AUMC 15120, MZ723906. Meanwhile, four biological control agents (bioagents) were isolated from the healthy lucky bamboo samples and identified based on cultural, morphological, microscopic characteristics, and the molecular phylogenetic analysis as Clonostachys rosea AUMC 15121, OL461708; Bacillus circulans TAG1, MW441316; B. siamensis TAP1, MW441318 and Ochrobactrum anthropi TAM1, MW441317. The four bioagents showed potential inhibition of R. solani in vitro as well as in vivo on lucky bamboo plants in vase treatments compared to the untreated inoculated control as well as certain fungicides and biocides used (Moncut, Rizolex-T, Topsin-M, Bio-Zeid, and Bio-Arc). The bioagent O. anthropi showed the highest inhibition growth (85.11%) of the in vitro R. solani colony, which was not significantly different from the biocide Bio-Arc (83.78%). However, C. rosea, B. siamensis and B. circulans showed inhibition values of 65.33, 64.44, and 60.44%, respectively. On the other hand, the biocide Bio-Zeid showed less inhibitory effect (43.11%), while the lowest growth inhibition was recorded by Rizolex-T (34.22%) and Topsin-M (28.67%). Furthermore, the in vivo experiment supported the in vitro results for the most effective treatments, where all the treatments significantly decreased the percentage of infection and disease severity compared to the inoculated untreated control. Additionally, the bioagent O. anthropi showed the highest effect, i.e., the lowest disease incidence and disease severity being 13.33% and 10%, compared to 100% and 75%, respectively, in the untreated inoculated control. This was not significantly different from the fungicide Moncut (13.33% and 21%) and from the bioagent C. rosea (20% and 15%) treatments for both parameters, respectively. In conclusion, the bioagents O. anthropi MW441317 at 1 × 10 CFU/ml as well as C. rosea AUMC15121 at 1 × 10/ml proved to be efficient to control R. solani causing root rot, and basal stem rot on lucky bamboo, compared to fungicide Moncut and can be used for disease management without the negative impact of the chemical control. Furthermore, this is the first report of the isolation and identification of Rhizoctonia solani, a pathogenic fungus, and four biocontrol agents (Bacillus circulans, B. siamensis, Ochrobactrum anthropi and Clonostachys rosea) associated with the healthy lucky bamboo plants.
Topics: Dracaena; Phylogeny; Fungicides, Industrial
PubMed: 37095150
DOI: 10.1038/s41598-023-33628-8 -
Journal of Orthopaedic Case Reports Mar 2022Ochrobactrum anthropi is an unusual low virulence emerging pathogen that rarely causes orthopedic infection and its clinical picture is not well described. It usually...
INTRODUCTION
Ochrobactrum anthropi is an unusual low virulence emerging pathogen that rarely causes orthopedic infection and its clinical picture is not well described. It usually causes infection in immunocompromised hosts with indwelling catheters or foreign bodies, such as the central venous catheters.
CASE REPORT
We reported a case of O. anthropi pyomyositis in a 22-year-old immunocompetent male patient not on any invasive procedure presented with raised temperature, left shoulder pain, and restriction of movements. Diagnosis was confirmed with the help of MRI and biopsy. He was successfully managed with surgical debridement and appropriate antibiotics.
CONCLUSION
Our case highlights the ability of O. anthropi to cause pyomyositis in immunocompetent individuals and its relevance in the field of orthopaedic infection.
PubMed: 36199917
DOI: 10.13107/jocr.2022.v12.i03.2700 -
ACS Chemical Biology Aug 2021Pantothenic acid is an essential metabolite found throughout all branches of life. Although the enzymes responsible for pantothenic biosynthesis have been characterized,...
Pantothenic acid is an essential metabolite found throughout all branches of life. Although the enzymes responsible for pantothenic biosynthesis have been characterized, those leading to its biodegradation remain poorly understood. In the study described herein, we showed that use of a "genomic enzymology" strategy enabled identification of four biodegradation pathway genes, which were then confirmed by using kinetic analysis of the purified recombinant enzymes encoded in . The reconstituted pathway converts pantothenic acid to β-alanine and ()-pantoate, and then ()-pantoate to aldopentoate, which is transformed to ()-3,3-dimethylmalate and hence to α-ketoisovalerate. The pathway genes are common to Proteobacterial genomes in which they are not colocated.
Topics: Amidohydrolases; Genes, Bacterial; Genomics; Multigene Family; NAD (+) and NADP (+) Dependent Alcohol Oxidoreductases; Ochrobactrum anthropi; Pantothenic Acid
PubMed: 34313416
DOI: 10.1021/acschembio.1c00492 -
Journal of Ophthalmic Inflammation and... Feb 2024To describe a puzzling case of endophthalmitis caused by three unusual bacteria after intravitreal injection, its outcome, and underlying questions.
PURPOSE
To describe a puzzling case of endophthalmitis caused by three unusual bacteria after intravitreal injection, its outcome, and underlying questions.
FINDINGS
A 70-year-old female patient was diagnosed with acute endophthalmitis following intravitreal aflibercept injection for age-related macular degeneration. A standard tap and inject procedure was performed. Microbiological analyses on the anterior chamber and vitreous samples yielded the presence of three non-fermenting Gram-negative rods: Pseudomonas stutzeri, Stenotrophomonas maltophilia, and Ochrobactrum anthropi. The outcome was favorable after intravitreal injections of vancomycin and ceftazidime, with an almost complete recovery of the visual acuity to its baseline level. No potential source of infection was identified.
CONCLUSION
Endophthalmitis following intravitreal injection can be caused by a wide variety of bacteria, including some rare Gram-negative species. They can sometimes co-exist in a single patient, but their virulence may vary greatly. Due to the variable antibiotic susceptibility and frequent multiresistance associated with non-fermenting Gram-negative rods, a prompt microbiological approach is required. Favorable outcome can be achieved with standard management.
PubMed: 38334879
DOI: 10.1186/s12348-023-00376-9 -
IDCases 2018is a Gram-negative bacillus widely distributed in nature. It is a low virulence and low pathogenic microorganism and human infection by this agent is considered rare....
is a Gram-negative bacillus widely distributed in nature. It is a low virulence and low pathogenic microorganism and human infection by this agent is considered rare. This microorganism can cause bacteremia and in some cases can lead to osteomyelitis and endocarditis. Included in family, this bacterium is phenotypically and genetically closely related to the genus and may be misidentified by rapid identification systems. The authors describe a patient admitted to the Infectious Diseases Department with vertebral osteomyelitis initially identified as . Despite appropriate antimicrobial therapy, the blood cultures remained positive and there were no signs of clinical improvement. This raised suspicion of a possible misidentification. It was decided to initiate antimicrobial therapy to include the genus, with slow but progressive clinical improvement. Samples were sent to Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA) for genotyping, confirming the initial suspicion of misidentification and identifying as the causal agent. Timely diagnosis of brucellosis is essential for the correct management and prevention of its consequences for the patient and for safe handling of the laboratory samples, preventing laboratory-acquired infection.
PubMed: 29619327
DOI: 10.1016/j.idcr.2018.01.010 -
Genomics Sep 2020Ochrobactrum genus is comprised of soil-dwelling Gram-negative bacteria mainly reported for bioremediation of toxic compounds. Since last few years, mainly two species...
Ochrobactrum genus is comprised of soil-dwelling Gram-negative bacteria mainly reported for bioremediation of toxic compounds. Since last few years, mainly two species of this genus, O. intermedium and O. anthropi were documented for causing infections mostly in the immunocompromised patients. Despite such ubiquitous presence, study of adaptation in various niches is still lacking. Thus, to gain insights into the niche adaptation strategies, pan-genome analysis was carried out by comparing 67 genome sequences belonging to Ochrobactrum species. Pan-genome analysis revealed it is an open pan-genome indicative of the continuously evolving nature of the genus. The presence/absence of gene clusters also illustrated the unique presence of antibiotic efflux transporter genes and type IV secretion system genes in the clinical strains while the genes of solvent resistance and exporter pumps in the environmental strains. A phylogenomic investigation based on 75 core genes depicted better and robust phylogenetic resolution and topology than the 16S rRNA gene. To support the pan-genome analysis, individual genomes were also investigated for the mobile genetic elements (MGE), antibiotic resistance genes (ARG), metal resistance genes (MRG) and virulence factors (VF). The analysis revealed the presence of MGE, ARG, and MRG in all the strains which play an important role in the species evolution which is in agreement with the pan-genome analysis. The average nucleotide identity (ANI) based on the genetic relatedness between the Ochrobactrum species indicated a distinction between individual species. Interestingly, the ANI tool was able to classify the Ochrobactrum genomes to the species level which were assigned till the genus level on the NCBI database.
Topics: Drug Resistance, Bacterial; Environmental Microbiology; Genes, Bacterial; Genome, Bacterial; Genomics; Humans; Interspersed Repetitive Sequences; Molecular Sequence Annotation; Ochrobactrum; Phylogeny; Virulence Factors
PubMed: 32428556
DOI: 10.1016/j.ygeno.2020.04.030