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Applied and Environmental Microbiology Jul 2002We isolated a bacterial strain, Agrobacterium radiobacter P230, which can hydrolyze a wide range of organophosphate (OP) insecticides. A gene encoding a protein involved...
We isolated a bacterial strain, Agrobacterium radiobacter P230, which can hydrolyze a wide range of organophosphate (OP) insecticides. A gene encoding a protein involved in OP hydrolysis was cloned from A. radiobacter P230 and sequenced. This gene (called opdA) had sequence similarity to opd, a gene previously shown to encode an OP-hydrolyzing enzyme in Flavobacterium sp. strain ATCC 27551 and Brevundimonas diminuta MG. Insertional mutation of the opdA gene produced a strain lacking the ability to hydrolyze OPs, suggesting that this is the only gene encoding an OP-hydrolyzing enzyme in A. radiobacter P230. The OPH and OpdA proteins, encoded by opd and opdA, respectively, were overexpressed and purified as maltose-binding proteins, and the maltose-binding protein moiety was cleaved and removed. Neither protein was able to hydrolyze the aliphatic OP malathion. The kinetics of the two proteins for diethyl OPs were comparable. For dimethyl OPs, OpdA had a higher k(cat) than OPH. It was also capable of hydrolyzing the dimethyl OPs phosmet and fenthion, which were not hydrolyzed at detectable levels by OPH.
Topics: Amino Acid Sequence; Aryldialkylphosphatase; Cloning, Molecular; Coumaphos; Esterases; Molecular Sequence Data; Phosphoric Monoester Hydrolases; Rhizobium; Sequence Homology, Amino Acid; Structure-Activity Relationship; Substrate Specificity
PubMed: 12089017
DOI: 10.1128/AEM.68.7.3371-3376.2002 -
Antimicrobial Agents and Chemotherapy Nov 2011A total of 10 metallo-β-lactamase-producing isolates of six different species, including Brevundimonas diminuta (n = 3), Rhizobium radiobacter (n = 2), Pseudomonas...
A total of 10 metallo-β-lactamase-producing isolates of six different species, including Brevundimonas diminuta (n = 3), Rhizobium radiobacter (n = 2), Pseudomonas monteilii (n = 1), Pseudomonas aeruginosa (n = 2), Ochrobactrum anthropi (n = 1), and Enterobacter ludwigii (n = 1), were detected in the sewage water of a hospital. The presence of bla(VIM-13) associated with a Tn1721-class 1 integron structure was detected in all but one of the isolates (E. ludwigii, which produced VIM-2), and in two of them (R. radiobacter), this structure was located on a plasmid, suggesting that environmental bacteria represent a reservoir for the dissemination of clinically relevant metallo-β-lactamase genes.
Topics: Agrobacterium tumefaciens; Enterobacter; Hospitals; Integrons; Ochrobactrum anthropi; Plasmids; Pseudomonas; Pseudomonas aeruginosa; Sewage; Water Microbiology; beta-Lactamases
PubMed: 21859934
DOI: 10.1128/AAC.00716-11 -
Journal of Clinical Microbiology Jun 2002The purpose of this study was to determine the bacterial diversity in advanced noma lesions using culture-independent molecular methods. 16S ribosomal DNA bacterial...
The purpose of this study was to determine the bacterial diversity in advanced noma lesions using culture-independent molecular methods. 16S ribosomal DNA bacterial genes from DNA isolated from advanced noma lesions of four Nigerian children were PCR amplified with universally conserved primers and spirochetal selective primers and cloned into Escherichia coli. Partial 16S rRNA sequences of approximately 500 bases from 212 cloned inserts were used initially to determine species identity or closest relatives by comparison with sequences of known species or phylotypes. Nearly complete sequences of approximately 1,500 bases were obtained for most of the potentially novel species. A total of 67 bacterial species or phylotypes were detected, 25 of which have not yet been grown in vitro. Nineteen of the species or phylotypes, including Propionibacterium acnes, Staphylococcus spp., and the opportunistic pathogens Stenotrophomonas maltophilia and Ochrobactrum anthropi were detected in more than one subject. Other known species that were detected included Achromobacter spp., Afipia spp., Brevundimonas diminuta, Capnocytophaga spp., Cardiobacterium sp., Eikenella corrodens, Fusobacterium spp., Gemella haemoylsans, and Neisseria spp. Phylotypes that were unique to noma infections included those in the genera Eubacterium, Flavobacterium, Kocuria, Microbacterium, and Porphyromonas and the related Streptococcus salivarius and genera Sphingomonas and TREPONEMA: Since advanced noma lesions are infections open to the environment, it was not surprising to detect species not commonly associated with the oral cavity, e.g., from soil. Several species previously implicated as putative pathogens of noma, such as spirochetes and Fusobacterium spp., were detected in at least one subject. However, due to the limited number of available noma subjects, it was not possible at this time to associate specific species with the disease.
Topics: Adolescent; Bacteria; Bacterial Infections; Child; Child, Preschool; DNA, Ribosomal; Dental Plaque; Female; Humans; Male; Molecular Sequence Data; Noma; Periodontal Diseases; Phylogeny; Prevalence; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Tongue
PubMed: 12037085
DOI: 10.1128/JCM.40.6.2187-2191.2002 -
Biochemistry Aug 2020The COVID-19 pandemic threatens to overwhelm healthcare systems around the world. The only current FDA-approved treatment, which directly targets the virus, is the...
The COVID-19 pandemic threatens to overwhelm healthcare systems around the world. The only current FDA-approved treatment, which directly targets the virus, is the ProTide prodrug remdesivir. In its activated form, remdesivir prevents viral replication by inhibiting the essential RNA-dependent RNA polymerase. Like other ProTide prodrugs, remdesivir contains a chiral phosphorus center. The initial selection of the ()-diastereomer for remdesivir was reportedly due to the difficulty in producing the pure ()-diastereomer of the required precursor. However, the two currently known enzymes responsible for the initial activation step of remdesivir are each stereoselective and show differential tissue distribution. Given the ability of the COVID-19 virus to infect a wide array of tissue types, inclusion of the ()-diastereomer may be of clinical significance. To help overcome the challenge of obtaining the pure ()-diastereomer of remdesivir, we have developed a novel chemoenzymatic strategy that utilizes a stereoselective variant of the phosphotriesterase from to enable the facile isolation of the pure ()-diastereomer of the chiral precursor for the chemical synthesis of the ()-diastereomer of remdesivir.
Topics: Adenosine Monophosphate; Alanine; Antiviral Agents; Betacoronavirus; COVID-19; Caulobacteraceae; Coronavirus Infections; Humans; Molecular Structure; Pandemics; Phosphoric Triester Hydrolases; Pneumonia, Viral; RNA-Dependent RNA Polymerase; SARS-CoV-2; Virus Replication
PubMed: 32786401
DOI: 10.1021/acs.biochem.0c00591 -
Biotechnology and Bioengineering Mar 2020The widely used 0.2/0.22 µm polymer sterile filters were developed for small molecule and protein sterile filtration but are not well-suited for the production of...
The widely used 0.2/0.22 µm polymer sterile filters were developed for small molecule and protein sterile filtration but are not well-suited for the production of large nonprotein biological therapeutics, resulting in significant yield loss and production cost increases. Here, we report on the development of membranes with isoporous sub-0.2 μm rectangular prism pores using silicon micromachining to produce microslit silicon nitride (MSN) membranes. The very high porosity (~33%) and ultrathin (200 nm) nature of the 0.2 µm MSN membranes results in a dramatically different structure than the traditional 0.2/0.22 µm polymer sterile filter, which yielded comparable performance properties (including gas and hydraulic permeance, maximum differential pressure tolerance, nanoparticle sieving/fouling behavior). The results from bacteria retention tests, conducted according to the guidance of regulatory agencies, demonstrated that the 0.2 µm MSN membranes can be effectively used as sterile filters. It is anticipated that the results and technologies presented in this study will find future utility in the production of non-protein biological therapeutics and in other biological and biomedical applications.
Topics: Biological Products; Caulobacteraceae; Drug Contamination; Equipment Design; Filtration; Membranes, Artificial; Nanostructures; Porosity; Silicon Compounds
PubMed: 31784974
DOI: 10.1002/bit.27240 -
Medicina (Kaunas, Lithuania) Nov 2021is rarely described in clinical specimens, never at the umbilical stump. Most of the reported cases are in patients with underlying pathologies. We must integrate this...
is rarely described in clinical specimens, never at the umbilical stump. Most of the reported cases are in patients with underlying pathologies. We must integrate this microorganism in the etiological agents of nosocomial infections, but much remains to be understood about its virulence. We present a case of umbilical stump infection (omphalitis) caused by , in a preterm and hypotrophic new-born and discuss the diagnosis of this bacterium and its role as responsible of nosocomial neonatal infections.
Topics: Caulobacteraceae; Cross Infection; Democratic Republic of the Congo; Humans; Infant, Low Birth Weight; Infant, Newborn
PubMed: 34833445
DOI: 10.3390/medicina57111227 -
American Journal of Health-system... Aug 2015Specific deviations from United States Pharmacopeia standards were analyzed to investigate the factors allowing an outbreak of Serratia marcescens bloodstream infections...
PURPOSE
Specific deviations from United States Pharmacopeia standards were analyzed to investigate the factors allowing an outbreak of Serratia marcescens bloodstream infections in patients receiving compounded amino acid solutions.
METHODS
Filter challenge experiments using the outbreak strain of S. marcescens were compared with those that used the filter challenge organism recommended by ASTM International (Brevundimonas diminuta ATCC 19162) to determine the frequency and degree of organism breakthrough. Disk and capsule filters (0.22- and 0.2-μm nominal pore size, respectively) were challenged with either the outbreak strain of S. marcescens or B. diminuta ATCC 19162. The following variables were compared: culture conditions in which organisms were grown overnight or cultured in sterile water (starved), solution type (15% amino acid solution or sterile water), and filtration with or without a 0.5-μm prefilter.
RESULTS
Small-scale, syringe-driven, disk-filtration experiments of starved bacterial cultures indicated that approximately 1 in every 1,000 starved S. marcescens cells (0.12%) was able to pass through a 0.22-μm nominal pore-size filter, and about 1 in every 1,000,000 cells was able to pass through a 0.1-μm nominal pore-size filter. No passage of the B. diminuta ATCC 19162 cells was observed with either filter. In full-scale experiments, breakthrough was observed only when 0.2-μm capsule filters were challenged with starved S. marcescens in 15% amino acid solution without a 0.5-μm prefiltration step.
CONCLUSION
Laboratory simulation testing revealed that under certain conditions, bacteria can pass through 0.22- and 0.2-μm filters intended for sterilization of an amino acid solution. Bacteria did not pass through 0.2-μm filters when a 0.5-μm prefilter was used.
Topics: Bacteremia; Disease Outbreaks; Drug Compounding; Filtration; Humans; Parenteral Nutrition; Pharmacy Service, Hospital; Serratia Infections; Serratia marcescens; United States
PubMed: 26195654
DOI: 10.2146/ajhp150141 -
PeerJ 2019Increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, and thus it is hypothesized that interactions between...
Increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, and thus it is hypothesized that interactions between bacteria and alien plants might play an important role in plant invasions. However, the diversity of the bacterial communities associated with invasive plants is poorly understood. We therefore investigated the diversity of rhizospheric and endophytic bacteria associated with the invasive annual plant L. (Asteraceae) based on 16S rRNA gene data obtained from 57 samples of four populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Specifically, the rhizosphere harbored many more bacterial operational taxonomic units and showed higher alpha diversity than the leaf and root endospheres. The relative abundance profiles of the bacterial community composition differed substantially between the compartments and populations, especially at the phylum and family levels. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria) accounted for more than 90% of all the bacterial communities. Moreover, similar endophytic communities with a shared core set of bacteria were observed from different populations. Heavy-metal-resistant, phosphate-solubilizing bacteria (), nitrogen-fixing bacteria (), and cold-resistant bacteria () were present in the endosphere at relatively high abundance. This study, which reveals the structure of bacterial communities and their putative function in invasive plants, is the first step in investigating the role of plant-bacteria interactions in the invasion of this species in China.
PubMed: 30643678
DOI: 10.7717/peerj.6162 -
Astrobiology Apr 2010The microbial burden of the Phoenix spacecraft assembly environment was assessed in a systematic manner via several cultivation-based techniques and a suite of...
The microbial burden of the Phoenix spacecraft assembly environment was assessed in a systematic manner via several cultivation-based techniques and a suite of NASA-certified, cultivation-independent biomolecule-based detection assays. Extremotolerant bacteria that could potentially survive conditions experienced en route to Mars or on the planet's surface were isolated with a series of cultivation-based assays that promoted the growth of a variety of organisms, including spore formers, mesophilic heterotrophs, anaerobes, thermophiles, psychrophiles, alkaliphiles, and bacteria resistant to UVC radiation and hydrogen peroxide exposure. Samples were collected from the clean room where Phoenix was housed at three different time points, before (1P), during (2P), and after (3P) Phoenix's presence at the facility. There was a reduction in microbial burden of most bacterial groups, including spore formers, in samples 2P and 3P. Analysis of 262 isolates from the facility demonstrated that there was also a shift in predominant cultivable bacterial populations accompanied by a reduction in diversity during 2P and 3P. It is suggested that this shift was a result of increased cleaning when Phoenix was present in the assembly facility and that certain species, such as Acinetobacter johnsonii and Brevundimonas diminuta, may be better adapted to environmental conditions found during 2P and 3P. In addition, problematic bacteria resistant to multiple extreme conditions, such as Bacillus pumilus, were able to survive these periods of increased cleaning.
Topics: Adaptation, Physiological; Bacteria; Biodiversity; Environment, Controlled; Equipment Contamination; Exobiology; Phylogeny; Spacecraft
PubMed: 20446872
DOI: 10.1089/ast.2009.0396 -
International Journal of Environmental... Jun 2016Animal manure is commonly used as fertilizer for agricultural crops worldwide, even though it is believed to contribute to the spread of antibiotic resistance from...
Animal manure is commonly used as fertilizer for agricultural crops worldwide, even though it is believed to contribute to the spread of antibiotic resistance from animal intestines to the soil environment. However, it is unclear whether and how there is any impact of manure fertilization on populations and community structure of antibiotic-resistant endophytic bacteria (AREB) in plant tissues. To investigate the effect of manure and organic fertilizer on endophytic bacterial communities, pot experiments were performed with pakchoi grown with the following treatments: (1) non-treated; (2) chicken manure-treated and (3) organic fertilizer-treated. Manure or organic fertilizer significantly increased the abundances of total cultivable endophytic bacteria (TCEB) and AREB in pakchoi, and the effect of chicken manure was greater than that of organic fertilizer. Further, 16S rDNA sequencing and the phylogenetic analysis indicated that chicken manure or organic fertilizer application increased the populations of multiple antibiotic-resistant bacteria (MARB) in soil and multiple antibiotic-resistant endophytic bacteria (MAREB) in pakchoi. The identical multiple antibiotic-resistant bacterial populations detected in chicken manure, manure- or organic fertilizer-amended soil and the vegetable endophytic system were Brevundimonas diminuta, Brachybacterium sp. and Bordetella sp., suggesting that MARB from manure could enter and colonize the vegetable tissues through manure fertilization. The fact that some human pathogens with multiple antibiotic resistance were detected in harvested vegetables after growing in manure-amended soil demonstrated a potential threat to human health.
Topics: Animals; Anti-Bacterial Agents; Bacteria; Chickens; Crops, Agricultural; DNA, Ribosomal; Drug Resistance, Multiple, Bacterial; Fertilizers; Humans; Manure; Phylogeny; Soil Microbiology; Vegetables
PubMed: 27376311
DOI: 10.3390/ijerph13070662