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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 -
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 -
Journal of Bacteriology Aug 2011Ochrobactrum anthropi is a common soil alphaproteobacterium that colonizes a wide spectrum of organisms and is being increasingly recognized as an opportunistic human...
Ochrobactrum anthropi is a common soil alphaproteobacterium that colonizes a wide spectrum of organisms and is being increasingly recognized as an opportunistic human pathogen. Potentially life-threatening infections, such as endocarditis, are included in the list of reported O. anthropi infections. These reports, together with the scant number of studies and the organism's phylogenetic proximity to the highly pathogenic brucellae, make O. anthropi an attractive model of bacterial pathogenicity. Here we report the genome sequence of the type strain O. anthropi ATCC 49188, which revealed the presence of two chromosomes and four plasmids.
Topics: Animals; Genome, Bacterial; Gram-Negative Bacterial Infections; Humans; Molecular Sequence Data; Ochrobactrum anthropi; Symbiosis
PubMed: 21685287
DOI: 10.1128/JB.05335-11 -
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 -
BMC Genomics Aug 2009Using a combination of pyrosequencing and conventional Sanger sequencing, the complete genome sequence of the recently described novel Brucella species, Brucella...
BACKGROUND
Using a combination of pyrosequencing and conventional Sanger sequencing, the complete genome sequence of the recently described novel Brucella species, Brucella microti, was determined. B. microti is a member of the genus Brucella within the Alphaproteobacteria, which consists of medically important highly pathogenic facultative intracellular bacteria. In contrast to all other Brucella species, B. microti is a fast growing and biochemically very active microorganism with a phenotype more similar to that of Ochrobactrum, a facultative human pathogen. The atypical phenotype of B. microti prompted us to look for genomic differences compared to other Brucella species and to look for similarities with Ochrobactrum.
RESULTS
The genome is composed of two circular chromosomes of 2,117,050 and 1,220,319 base pairs. Unexpectedly, we found that the genome sequence of B. microti is almost identical to that of Brucella suis 1330 with an overall sequence identity of 99.84% in aligned regions. The most significant structural difference between the two genomes is a bacteriophage-related 11,742 base pairs insert only present in B. microti. However, this insert is unlikely to have any phenotypical consequence. Only four protein coding genes are shared between B. microti and Ochrobactrum anthropi but impaired in other sequenced Brucella. The most noticeable difference between B. microti and other Brucella species was found in the sequence of the 23S ribosomal RNA gene. This unusual variation could have pleiotropic effects and explain the fast growth of B. microti.
CONCLUSION
Contrary to expectations from the phenotypic analysis, the genome sequence of B. microti is highly similar to that of known Brucella species, and is remotely related to the one of O. anthropi. How the few differences in gene content between B. microti and B. suis 1330 could result in vastly different phenotypes remains to be elucidated. This unexpected finding will complicate the task of identifying virulence determinants in the Brucella genus. The genome sequence of B. microti will serve as a model for differential expression analysis and complementation studies. Our results also raise some concerns about the importance given to phenotypical traits in the definition of bacterial species.
Topics: Base Sequence; Brucella; Comparative Genomic Hybridization; DNA, Bacterial; Genes, Bacterial; Genome, Bacterial; Molecular Sequence Data; Ochrobactrum anthropi; Phenotype; Phylogeny; Pseudogenes; RNA, Ribosomal, 23S; Sequence Alignment; Sequence Analysis, DNA
PubMed: 19653890
DOI: 10.1186/1471-2164-10-352 -
Applied and Environmental Microbiology Aug 2009Most studies of bacterial denitrification have used nitrate (NO3-) as the first electron acceptor, whereas relatively less is understood about nitrite (NO2-)...
Most studies of bacterial denitrification have used nitrate (NO3-) as the first electron acceptor, whereas relatively less is understood about nitrite (NO2-) denitrification. We isolated novel bacteria that proliferated in the presence of high levels of NO2- (72 mM). Strain YD50.2, among several isolates, was taxonomically positioned within the alpha subclass of Proteobacteria and identified as Ochrobactrum anthropi YD50.2. This strain denitrified NO2-, as well as NO3-. The gene clusters for denitrification (nar, nir, nor, and nos) were cloned from O. anthropi YD50.2, in which the nir and nor operons were linked. We confirmed that nirK in the nir-nor operon produced a functional NO2- reductase containing copper that was involved in bacterial NO2- reduction. The strain denitrified up to 40 mM NO2- to dinitrogen under anaerobic conditions in which other denitrifiers or NO3- reducers such as Pseudomonas aeruginosa and Ralstonia eutropha and nitrate-respiring Escherichia coli neither proliferated nor reduced NO2-. Under nondenitrifying aerobic conditions, O. anthropi YD50.2 and its type strain ATCC 49188(T) proliferated even in the presence of higher levels of NO2- (100 mM), and both were considerably more resistant to acidic NO2- than were the other strains noted above. These results indicated that O. anthropi YD50.2 is a novel denitrifier that has evolved reactive nitrogen oxide tolerance mechanisms.
Topics: Aerobiosis; Anaerobiosis; Bacterial Proteins; DNA, Bacterial; DNA, Ribosomal; Molecular Sequence Data; Nitrates; Nitrogen Oxides; Ochrobactrum anthropi; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Water Microbiology
PubMed: 19542343
DOI: 10.1128/AEM.00604-09 -
The Science of the Total Environment Feb 2021Previous studies have provided evidence that bioremediation deals a novel approach to graffiti removal, thereby overcoming well-known limitations of current cleaning...
Previous studies have provided evidence that bioremediation deals a novel approach to graffiti removal, thereby overcoming well-known limitations of current cleaning methods. In the present study eight bacteria aerobic, mesophilic and culturable from the American ATCC and the German DSMZ collections of microorganisms, some isolated from car paint waste, colored deposits in a pulp dryer and wastewater from dye works, were tested in the removal of silver and black graffiti spray paints using immersion strategies with glass slides. Absorbance at 600 nm and live/dead assays were performed to estimate bacterial density and activity in all samples. Also, pH and dissolved organic carbon (DOC) and inorganic carbon (DIC) measurements in the liquid media were made, as well as, thickness, colorimetric and infrared (FTIR) spectroscopy measurements in graffiti paint layers were used to evaluate the presence of the selected bacteria in the samples and the graffiti bioremoval capacity of bacteria. Data demonstrated that of the eight bacteria studied, Enterobacter aerogenes, Comamonas sp. and a mixture of Bacillus sp., Delftia lacustris, Sphingobacterium caeni, and Ochrobactrum anthropi were the most promising for bioremoval of graffiti. According to significant changes in FTIR spectra, indicating an alteration of the paint polymeric structure, coupled with the presence of a consistent quantity of live bacteria in the medium as well as a significant increase of DIC (a measure of metabolic activity) and a change in paint color.
Topics: Bacteria; Biodegradation, Environmental; Delftia; Sphingobacterium
PubMed: 33280882
DOI: 10.1016/j.scitotenv.2020.144075 -
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 -
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 -
International Journal of Environmental... Jan 2022The phenylurea herbicides are persistent in soil and water, making necessary the de-velopment of techniques for their removal from the environment. To identify new...
The phenylurea herbicides are persistent in soil and water, making necessary the de-velopment of techniques for their removal from the environment. To identify new options in this regard, bacterial strains were isolated from a soil historically managed with pesticides. CD3 showed the ability to remove completely herbicides such as diuron, linuron, chlorotoluron and fluometuron from aqueous solution, and up to 89% of isoproturon. In the case of diuron and linuron, their main metabolite, 3,4-dichloroaniline (3,4-DCA), which has a higher toxicity than the parent compounds, was formed, but remained in solution without further degradation. CD3 was also tested for bioremediation of two different agricultural soils artificially contaminated with diuron, employing bioremediation techniques: (i) biostimulation, using a nutrient solution (NS), (ii) bioaugmentation, using CD3, and iii) bioavailability enhancement using 2-hydroxypropyl-β-cyclodextrin (HPBCD). When bioaugmentation and HPBCD were jointly applied, 50% of the diuron initially added to the soil was biodegraded in a range from 4.7 to 0.7 d. Also, 3,4-DCA was degraded in soil after the strain was inoculated. At the end of the soil biodegradation assay an ecotoxicity test confirmed that after inoculating CD3 the toxicity was drastically reduced.
Topics: Biodegradation, Environmental; Diuron; Feasibility Studies; Herbicides; Ochrobactrum; Soil; Soil Microbiology; Soil Pollutants
PubMed: 35162387
DOI: 10.3390/ijerph19031365