'Streptomyces sp. SK519 was cultivated in the medium containing 0.5% birch wood xylan to produce extracellular xylanase. The xylanase was isolated from the culture supernatant by ammonium sulfate precipitation and partially purified by absorbing on the insoluble xylan. Alkali-extracted kenaf glucuronoylan of which main chain primarily consisting of (1-4)-linked β-D-xylopyranose ... More
Pseudomonas panipatensis sp. nov., isolated from an oil-contaminated site
AuthorsGupta, SK; Kumari, R; Prakash, O; Lal, R
Journal
PubMed ID
'A Gram-negative, motile, rod-shaped, non-sporulating, aerobic bacterial strain (Esp-1(T)) was isolated from oil-contaminated soil of Panipat Oil Refinery, India, and its taxonomic position was determined using a polyphasic approach. Strain Esp-1(T) grew in the presence of 2% NaCl at 30 °C and was characterized chemotaxonomically by having C(16:0) as the ... More
Multilocus DNA sequence comparisons rapidly identify pathogenic molds.
'The increasing incidence of opportunistic fungal infections necessitates rapid and accurate identification of the associated fungi to facilitate optimal patient treatment. Traditional phenotype-based identification methods utilized in clinical laboratories rely on the production and recognition of reproductive structures, making identification difficult or impossible when these structures are not observed. We ... More
Species distribution and antimicrobial resistance of enterococci isolated from surface and ocean water
AuthorsMoore, DF; Guzman, JA; Mcgee, C
Journal
PubMed ID
'Aims: The species identification and antimicrobial resistance profiles were determined for enterococci isolated from Southern California surface and ocean waters. Methods and Results: Species identification was determined for 1413 presumptive Enterococcus isolates from urban runoff, bay, ocean and sewage water samples. The most frequently isolated species were Enterococcus faecalis, Enterococcus ... More
Multicenter evaluation of the new VITEK 2 advanced colorimetric yeast identification card.
AuthorsHata DJ; Hall L; Fothergill AW; Larone DH; Wengenack NL
Journal
PubMed ID
'The performance of the new VITEK 2 Advanced Colorimetry yeast identification (YST) card for use with the VITEK 2 system (bioMerieux, Inc., Hazelwood, MO) was compared to that of the API 20C AUX (API) system (bioMerieux SA, Marcy-l''Etoile, France) in a multicenter evaluation. A total of 12 quality control, 64 ... More
Probiotic bacteria are antagonistic to Salmonella enterica and Campylobacter jejuni and influence host lymphocyte responses in human microbiota-associated immunodeficient and immunocompetent mice
AuthorsWagner, RD; Johnson, SJ; Rubin, DK
Journal
PubMed ID
'A defined human microbiota-associated (HMA) mouse model in BALB/c and immunodeficient Tgε26 mice was used to assess the ability of probiotic lactobacilli and bifidobacteria to enhance colonization resistance to gastrointestinal (GI) tract pathogens. Probiotic bacteria (1 x 10(8) colony forming unit (CFU)/mL) successfully excluded Campylobacter jejuni from both strains of ... More
Lactobacillus taiwanensis sp. nov., isolated from silage
AuthorsWang, LT; Kuo, HP; Wu, YC; Tai, CJ; Lee, FL
Journal
PubMed ID
'Strain FIRDI 006(T), isolated from silage cattle feed, was characterized by using phenotypic and molecular taxonomic methods. The strain was a homofermentative lactic acid bacterium; the cells stained Gram-positive and were catalase-negative, non-motile, facultatively anaerobic rods. 16S rRNA gene sequence analysis revealed that the strain belongs phylogenetically to the genus ... More
Atypical mycobacterial spondylitis in HIV-negative patients identified by genotyping.
AuthorsDanaviah S; Govender S; Gordon ML; Cassol S
Journal
PubMed ID
'Non-tuberculous mycobacterial infections pose a significant diagnostic and therapeutic challenge. We report two cases of such infection of the spine in HIV-negative patients who presented with deformity and neurological deficit. The histopathological features in both specimens were diagnostic of tuberculosis. The isolates were identified as Mycobacterium intracellulare and M. fortuitum ... More
Degradation of 1,4-dioxane and cyclic ethers by an isolated fungus.
AuthorsNakamiya K; Hashimoto S; Ito H; Edmonds JS; Morita M
Journal
PubMed ID
'By using 1,4-dioxane as the sole source of carbon, a 1,4-dioxane-degrading microorganism was isolated from soil. The fungus, termed strain A, was able to utilize 1,4-dioxane and many kinds of cyclic ethers as the sole source of carbon and was identified as Cordyceps sinensis from its 18S rRNA gene sequence. ... More
Forms of phosphorus in bacteria and fungi isolated from two Australian soils
'To understand the origin of organic and condensed forms of phosphorus (P) in soils, detailed information about P forms in microorganisms is required. We isolated 7 bacteria and 8 fungi from two Australian soils and analyzed the P forms in their pure cultures by extraction with NaOH-EDTA followed by (31)P ... More
Phylogenetic analysis of Mycobacterium aurum and Mycobacterium neoaurum with redescription of M. aurum culture collection strains
'We examined American Type Culture Collection (ATCC) strains of Mycobacterium aurum and Mycobacterium neoaurum by using multilocus DNA target sequencing. Apart from the type strain, all 10 ATCC M, aurum strains examined were classified incorrectly, with most being reclassified as belonging to the M. neoaurum-''Mycobacterium lacticola'' relatedness group. All four ... More
Advances in the microbiological diagnosis of sepsis
AuthorsAndrade, SS; Bispo, PJM; Gales, AC
Journal
PubMed ID
'Accurate diagnostic tests are essential for the correct identification of etiologic agents causing sepsis. Conventional microbiology cultures are time consuming and may even yield negative results in many cases of septic shock. In this manner, molecular-based technologies are emerging as promising tests for use into routine clinical laboratories. In this ... More
Automatic identification of large collections of protein-coding or rRNA sequences
AuthorsArigon, AM; Perriere, G; Gouy, M
Journal
PubMed ID
'The number of available genomic sequences is growing very fast, due to the development of massive sequencing techniques. Sequence identification is needed and contributes to the assessment of gene and species evolutionary relationships. Automated bioinformatics tools are thus necessary to carry out these identification operations in an accurate and fast ... More
Tracheal granuloma because of infection with a novel mycobacterial species in an old FIV-positive cat
AuthorsDe Lorenzi, D; Solano-Gallego, L
Journal
PubMed ID
'A 15-year-old domestic shorthair feline immunodeficiency virus-positive cat was presented with a five day history of productive cough and acute respiratory distress. Physical examination revealed inspiratory dyspnoea and diffuse gingivostomatitis. Radiographs showed an intratracheal mass located at the level of the sixth and the seventh cervical vertebrae. Bronchoscopy revealed a ... More
AuthorsFukatsu H; Hashimoto Y; Goda M; Higashibata H; Kobayashi M
Journal
PubMed ID
'N-substituted formamide was produced through the hydration of an isonitrile by isonitrile hydratase in the isonitrile metabolism. The former compound was further degraded by a microorganism, strain F164, which was isolated from soil through an acclimatization culture. The N-substituted formamide-degrading microorganism was identified as Arthrobacter pascens. The microbial degradation was ... More
Histoplasma capsulatum var. duboisii infection in a patient with AIDS: rapid diagnosis using polymerase chain reaction-sequencing
'We describe an original case of disseminated infection with Histoplasma capsulatum (Hc) var. duboisii in an African patient with AIDS who migrated to Switzerland. The diagnosis of histoplasmosis was Suggested using direct examination of tissues and confirmed in 24 h with a panfungal polymerase chain reaction assay. The variety duboisii ... More
Mycobacterium lentiflavum as an emerging causative agent of cervical lymphadenitis.
AuthorsPiersimoni C; Goteri G; Nista D; Mariottini A; Mazzarelli G; Bornigia S
Journal
PubMed ID
'A lymph node excision was performed on a 45-year-old woman with left cervical swelling. The disorder which developed after the patient had undergone oral surgery for a severe periodontal disease failed to respond to antimicrobial chemotherapy. A mycobacterial strain subsequently identified by high-performance liquid chromatography analysis of cell wall mycolic ... More
Clostridium glycolicum bacteremia in a bone marrow transplant patient.
AuthorsElsayed S; Zhang K
Journal
PubMed ID
'We describe a case of Clostridium glycolicum bacteremia and septic shock in an adult woman with a recent bone marrow transplant for relapsed Hodgkin''s disease. The bacterium was identified by 16S rRNA gene sequencing. This is the first published report of the recovery of this organism from human clinical material.' ... More
Fungal Molecular Diagnostics
AuthorsWengenack, NL; Binnicker, MJ
Journal
PubMed ID
'This article summarizes the current state of the art in molecular diagnostic methods for the detection and identification of fungi as performed in the mycology laboratory. The advantages and limitations of current molecular testing methods are evaluated, with examples provided from the recent literature. Finally, commentary is provided on the ... More
Species-specific identification of Vibrio fluvialis by PCR targeted to the conserved transcriptional activation and variable membrane tether regions of the toxR gene.
Authors
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PubMed ID
Evaluation of VITEK 2 and RapID yeast plus systems for yeast species identification: experience at a large clinical microbiology laboratory.
AuthorsSanguinetti M; Porta R; Sali M; La Sorda M; Pecorini G; Fadda G; Posteraro B
Journal
PubMed ID
'A total of 750 clinical yeast isolates were evaluated by two identification systems, VITEK 2 and RapID Yeast Plus, using sequence analysis of the rRNA gene internal transcribed spacer regions as the reference method. The VITEK 2 and RapID systems correctly identified 737 (98.2%) and 716 (95.5%) isolates, respectively.' ... More
Molecular diagnostic tools in mycobacteriology
AuthorsNeonakis, IK; Gitti, Z; Krambovitis, E; Spandidos, DA
Journal
PubMed ID
'Although the diagnosis of mycobacteriosis and susceptibility testing are still primarily based on conventional methods (staining, culture, biochemical analysis, proportional method), a series of molecular assays are increasingly introduced and incorporated in the workflow of clinical mycobacteriology laboratories worldwide. These assays are rapid and offer high sensitivities and specificities. In ... More
Molecular characterization of isoniazid resistance in Mycobacterium tuberculosis: identification of a novel mutation in inhA.
AuthorsLeung ET; Ho PL; Yuen KY; Woo WL; Lam TH; Kao RY; Seto WH; Yam WC
Journal
PubMed ID
'Multiplex allele-specific PCRs detecting katG codon 315 and mabA (bp -15) mutations could specifically identify 77.5% of isoniazid-resistant Mycobacterium tuberculosis strains in the South China region. One clinical isolate harboring InhA Ile194Thr was characterized to show strong association with isoniazid resistance in Mycobacterium tuberculosis.' ... More
Biofilm Formation by Lactic Acid Bacteria and Resistance to Environmental Stress
AuthorsKubota, H; Senda, S; Nomura, N; Tokuda, H; Uchiyama, H
Journal
PubMed ID
'We investigated the formation of biofilms by 3 type strains of lactic acid bacteria (LAB), Lactobacillus plantarum, Lactobacillus brevis and Lactobacillus fructivorans, as representatives of LAB that cause food deterioration or contamination. Lactobacillus plantarum subsp. plantarum JCM1149 and Lactobacillus brevis JCM1059 appeared to adhere and accumulate on glass cover slips. ... More
A paradigm for the molecular identification of Mycobacterium species in a routine diagnostic laboratory.
'The aim of this study was to improve the identification of Mycobacterium species in the context of a UK teaching hospital. Real-time PCR assays were established to enable the rapid differentiation between Mycobacterium tuberculosis (MTB) complex and Mycobacterium species other than tuberculosis (MOTT), followed by 16S rRNA gene sequencing for ... More
Construction of a Biofilter Immobilized with Rhodococcus sp. B261 for Removal of H(2)S Gas Generated by Livestock
AuthorsYun, SI
Journal
PubMed ID
'To explore the optimal conditions for the removal of H(2)S gas by biofiltration, various conditions, including inlet H(2)S concentration, flow rate, moisture, and cell number, were examined. Heterotrophic bacteria were isolated from the compost of the animal excreta. A strain that effectively removed H(2)S was selected and identified as Rhodococcus ... More
Evaluation of 16S rRNA sequencing and reevaluation of a short biochemical scheme for identification of clinically significant Bacteroides species.
AuthorsSong Y; Liu C; Bolanos M; Lee J; McTeague M; Finegold SM
Journal
PubMed ID
'Sequence analysis of the 16S rRNA gene represents a highly accurate and versatile method for bacterial classification and identification, even when the species in question is notoriously difficult to identify by phenotypic means. In this study, we evaluated the utility of 16S rRNA gene sequencing as a means of identifying ... More
Guidelines for interpretation of 16S rRNA gene sequence-based results for identification of medically important aerobic Gram-positive bacteria
'This study is believed to be the first to provide guidelines for facilitating interpretation of results based on full and 527 bp 16S rRNA gene sequencing and MicroSeq databases used for identifying medically important aerobic Gram-positive bacteria. Overall, full and 527 bp 16S rRNA gene sequencing can identify 24 and ... More
Inflammatory pseudotumor of the heart caused by Listeria monocytogenes infection
'Inflammatory pseudotumor (IPT) of the heart is rare and of unknown etiology. We present a case of cardiac IPT caused by Listeria monocytogenes that evolved following gastroenteritis in a previously healthy child. L. monocytogenes, known to cause acute invasive infections, has not been reported previously as a cause of cardiac ... More
Long-term respiratory tract infection with canine-associated Pasteurella dagmatis and Neisseria canis in a patient with chronic bronchiectasis.
AuthorsAllison K; Clarridge JE 3rd
Journal
PubMed ID
'Pasteurella dagmatis and Neisseria canis were repeatedly isolated from the sputum of a poodle-owning patient with chronic bronchiectasis. Commercially available systems failed to identify these unusual organisms: identification was made by 16S rRNA gene sequencing. Difficulties identifying these and five other canine-associated isolates (P. dagmatis [n = 2], Pasteurella canis ... More
Acute pyelonephritis caused by Aerococcus urinae in a 12-year-old boy
'Aerococcus urinae are Gram-positive cocci that cause urinary tract infections in adults with underlying genitourinary (GU) tract disease. We report a case of pyelonephritis caused by A. urinae in a 12-year-old boy with a history of pyeloplasty and GU reflux.' ... More
Isolation and Identification of a Newly Isolated Alternaria sp. ND-16 and Characterization of Xylanase
'Alternaria sp. ND-16, a bacterium isolated from soil sample, was identified as a strain of Alternaria mali based on the morphology and comparison of internal transcribed spacer rDNA gene sequence studies. Furthermore, it is demonstrated that this strain has xylanase activity, and the activity can be optimized under suitable growing ... More
Interpretive criteria for use of AccuProbe for identification of Mycobacterium avium complex directly from 7H9 broth cultures.
AuthorsCloud JL; Carroll KC; Cohen S; Anderson CM; Woods GL
Journal
PubMed ID
'Rapid identification of Mycobacterium avium complex (MAC) is possible by use of AccuProbe (Gen-Probe, San Diego, Calif.). To evaluate the reliability of the MAC AccuProbe for testing 7H9 cultures inoculated with broth from MGIT cultures positive for acid-fast bacilli or growth on a solid medium, we compared probe results to ... More
Adsorption of tributyltin by tributyltin resistant marine Pseudoalteromonas sp. cells
AuthorsMimura, H; Sato, R; Furuyama, Y; Taniike, A; Yagi, M; Yoshida, K; Kitamura, A
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PubMed ID
'The isolate, Pesudoalteromonas sp. TBT1, could grow to overcome the toxicity of tributyltin chloride (TBTCl) up to 30 μM in the absence of Cl(-) in the medium until the cells reached an exponential phase of growth. The viability, however, was reduced after the cells reached a stationary phase. The degradation ... More
Asaia lannaensis bloodstream infection in a child with cancer and bone marrow transplantation
AuthorsAbdel-Haq, N; Savasan, S; Davis, M; Asmar, BI; Painter, T; Salimnia, H
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PubMed ID
An unusual case of prosthetic joint infection due to Arcanobacterium bernardiae
Human bloodstream infection caused by Staphylococcus pettenkoferi
AuthorsSong, SH; Park, JS; Kwon, HR; Kim, SH; Kim, HB; Chang, HE; Park, KU; Song, J; Kim, EC
Journal
PubMed ID
Staphylococcus pettenkoferi is a recently isolated human pathogen with only a few reported cases of infection. We report a case of bloodstream infection caused by S. pettenkoferi in a patient with pulmonary tuberculosis. ... More
Sepsis associated with a new Atopobium species, provisionally named Atopobium detroiti: Case report and review of the current status of the species Atopobium
This paper reports a case of sepsis associated with a previously unknown Atopobium species and highlights the role of 16S ribosomal subunit sequencing in the rapid identification of slow-growing or atypical organisms in the clinical laboratory. ... More
Bacteremia caused by Clostridium intestinale.
AuthorsElsayed S; Zhang K
Journal
PubMed ID
We describe a case of Clostridium intestinale bacteremia in a previously healthy adolescent female presenting with fever and abdominal pain. The bacterium was definitively identified via 16S rRNA gene sequencing. This is the first report, in the world literature, of human infection caused by this microorganism. ... More
Nocardia ignorata, a new agent of human nocardiosis isolated from respiratory specimens in Europe and soil samples from Kuwait.
AuthorsRodriguez-Nava V; Couble A; Khan ZU; Perouse de Montclos M; Brasme L; Villuendas C; Molinard C; Boiron P; Laurent F
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PubMed ID
Nocardia ignorata is a recently described species identified on the basis of a single isolate of unknown origin. Here we describe the epidemiological, phenotypic, and phylogenetic characteristics of this new species, based on five new clinical and soil isolates. ... More
Clostridium tetani Is a phospholipase (lecithinase)-producing bacterium.
AuthorsElsayed S; Zhang K
Journal
PubMed ID
We describe a case of Clostridium intestinale bacteremia in a previously healthy adolescent female presenting with fever and abdominal pain. The bacterium was definitively identified via 16S rRNA gene sequencing. This is the first report, in the world literature, of human infection caused by this microorganism. ... More
Thumb Infection Caused by Streptococcus pseudoporcinus
AuthorsMahlen, SD; Clarridge, JE III
Journal
PubMed ID
Streptococcus pseudoporcinus, a recently described organism found in the genitourinary tract of women, was isolated from a thumb wound in a male patient subsequent to trauma. This case describes a rarely reported non-genitourinary tract clinical isolate of S. pseudoporcinus. ... More
Organisms designated as Nocardia asteroides drug pattern type VI are members of the species Nocardia cyriacigeorgica.
AuthorsConville PS; Witebsky FG
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PubMed ID
Nocardia cyriacigeorgica has recently been described as an ""emerging"" pathogen. However, DNA-DNA hybridization results confirm that Nocardia asteroides drug pattern type VI, which has long been recognized as a common and significant pathogen in the United States, belongs to the species N. cyriacigeorgica. ... More
Necrotizing fasciitis from Vibrio vulnificus in a patient with undiagnosed hepatitis and cirrhosis.
AuthorsMuldrew KL; Miller RR; Kressin M; Tang YW; Stratton C
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PubMed ID
Necrotizing fasciitis due to Vibrio vulnificus may result in overwhelming sepsis, leading to death in some patients. Significant risk factors for severe disease include preexisting liver disease. We report a case of Vibrio vulnificus necrotizing fasciitis in a patient with previously undiagnosed chronic hepatitis and cirrhosis. ... More
Identification of bacteria in formalin-fixed, paraffin-embedded heart valve tissue via 16S rRNA gene nucleotide sequencing.
AuthorsImrit K; Goldfischer M; Wang J; Green J; Levine J; Lombardo J; Hong T
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PubMed ID
We applied 16S rRNA gene sequencing to identify bacterial species present in formalin-fixed, paraffin-embedded heart valve tissue. In 40% (12/30) of the cases, we were able to identify the bacterium to the species-genus level. For more recent cases (<or=4 years), the success rate was significantly improved, to 70% (P<0.001). ... More
Bacteremia caused by Janibacter melonis.
AuthorsElsayed S; Zhang K
Journal
PubMed ID
We report a case of bacteremia caused by Janibacter melonis, a recently described aerobic actinomycete originally isolated from a spoiled oriental melon. Our patient's blood culture isolate was identified by partial 16S rRNA gene sequencing. This is the first report of the recovery of Janibacter species from humans. ... More
Disseminated coinfection with Actinomyces graevenitzii and Mycobacterium tuberculosis: case report and review of the literature.
AuthorsTietz A; Aldridge KE; Figueroa JE
Journal
PubMed ID
We report the first case of disseminated infection with both Actinomyces graevenitzii and Mycobacterium tuberculosis and review the medical literature. Concomitant actinomycosis and tuberculosis is very rare. The potential of the facultatively aerobic, newly described A. graevenitzii for disseminated invasive infection needs to be evaluated. ... More
Lactobacillus delbrueckii as the Cause of Urinary Tract Infection
AuthorsDarbro, BW; Petroelje, BK; Doern, GV
Journal
PubMed ID
Lactobacilli are part of the normal bacterial flora of the vagina and are typically considered contaminants when cultured from urine specimens of female patients. Here we describe the case of a female patient with chronic pyuria and urinary tract symptoms in which Lactobacillus delbrueckii was determined to be the causative ... More
Oral Abscess Caused by Campylobacter rectus: Case Report and Literature Review
AuthorsMahlen, SD; Clarridge, JE III
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PubMed ID
Campylobacter rectus was isolated under routine anaerobic conditions (no additional hydrogen gas in the atmosphere) from an oral, nonperiodontal abscess from a patient with gastroesophageal adenocarcinoma. We report the first case of a palate abscess caused by C. rectus and review the literature and atmospheric requirements of this organism. ... More
Cell-cell influences on bacterial community development in aquatic biofilms.
AuthorsMcLean RJ; Barnes MB; Windham MK; Merchant M; Forstner MR; Fuqua C
Journal
PubMed ID
Dialysis tubing containing spent culture media, when placed in a lake, was colonized by a low diversity of bacteria, whereas abiotic controls had considerable diversity. Changes were seen in the presence and absence of acylated homoserine lactones, suggesting that these molecules and other factors may influence adherent-population composition. ... More
Sequence-based identification of new bacteria: a proposition for creation of an orphan bacterium repository.
AuthorsDrancourt M; Raoult D
Journal
PubMed ID
Dialysis tubing containing spent culture media, when placed in a lake, was colonized by a low diversity of bacteria, whereas abiotic controls had considerable diversity. Changes were seen in the presence and absence of acylated homoserine lactones, suggesting that these molecules and other factors may influence adherent-population composition. ... More
Bacteremia caused by Solobacterium moorei in a patient with acute proctitis and carcinoma of the cervix.
AuthorsLau SK; Teng JL; Leung KW; Li NK; Ng KH; Chau KY; Que TL; Woo PC; Yuen KY
Journal
PubMed ID
We describe a case of Solobacterium moorei bacteremia in a 43-year-old woman presenting with acute proctitis complicating radiotherapy for cervical carcinoma. Phenotypic tests failed to identify the bacterium, which was subsequently identified by 16S rRNA gene sequencing. 16S rRNA gene sequencing could help better define the pathogenicity of S. moorei. ... More
Nocardia nova as the causative agent in spondylodiscitis and psoas abscess.
We describe here the first case of Nocardia nova spondylodiscitis accompanied by a psoas abscess due to spreading from pulmonary nocardiosis. Nocardia was cultured from all affected sites. After 1 year of an appropriate antimicrobial therapy and a surgical drainage of the abscess that was required, the patient's clinical condition ... More
Life-threatening invasive Helcococcus kunzii infections in intravenous-drug users and ermA-mediated erythromycin resistance.
AuthorsWoo PC; Tse H; Wong SS; Tse CW; Fung AM; Tam DM; Lau SK; Yuen KY
Journal
PubMed ID
We report the first two cases of life-threatening invasive Helcococcus kunzii infection, with primary bacteremia and empyema thoracis, respectively. Gram smears of both H. kunzii isolates showed a mixture of gram-positive and gram-negative cocci. The isolate from the first patient, resistant to erythromycin and clindamycin, possessed an ermA gene. ... More
Burkholderia pseudomallei Misidentified by Automated System
AuthorsWeissert, C; Dollenmaier, G; Rafeiner, P; Riehm, J; Schultze, D
Journal
PubMed ID
After returning from Thailand, a 35-year-old man from Switzerland was hospitalized with an abscess of the head. Material cultured from the abscess and adjacent bone grew a gram-negative rod, which was misidentified by an automated microbiology system as Burkholderia cepacia. The organism was eventually identified by molecular methods as B. ... More
Etiological misidentification by routine biochemical tests of bacteremia caused by Gordonia terrae infection in the course of an episode of acute cholecystitis.
Gordonia terrae has been reported to be a rare cause of bacteremia. We report the first case of bacteremia associated with acute cholecystitis. Commercial biochemical testing was not able to identify the strain at the genus level, classifying it instead as Rhodococcus sp. Definitive identification was obtained by sequencing of ... More
Peripartum bacteremias due to Leptotrichia amnionii and Sneathia sanguinegens, rare causes of fever during and after delivery.
We report three cases of delivery and postpartum bacteremia due to unusual anaerobic bacteria in healthy young women. Leptotrichia amnionii bacteremia occurred during delivery in two mothers and was associated with fetal distress during labor. Conversely, Sneathia sanguinegens bacteremia occurred postpartum, 2 days after delivery, without consequence for the neonate. ... More
Comparative studies and identification of camptothecin produced by an endophyte at shake flask and bioreactor
The fungus showing homology with Nodulisporium by 28S ribosomal gene sequencing, which has been discovered as an endophyte on medicinal plant Nothapodytes foetida, was found to produce 45 and 5.5 μg of camptothecin (CPT) per gram of mycelia at bioreactor and at shake flask, respectively, which was further quantified and ... More
Multicenter evaluation of a Candida albicans peptide nucleic acid fluorescent in situ hybridization probe for characterization of yeast isolates from blood cultures.
AuthorsWilson DA; Joyce MJ; Hall LS; Reller LB; Roberts GD; Hall GS; Alexander BD; Procop GW
Journal
PubMed ID
We evaluated aliquots from 244 clinical blood culture bottles that demonstrated yeasts on Gram stain using a Candida albicans peptide nucleic acid (PNA) fluorescent in situ hybridization (FISH) probe. The sensitivity, specificity, positive predictive value, and negative predictive value of the C. albicans PNA FISH test in this study were ... More
Comparison of DNA pyrosequencing with alternative methods for identification of mycobacteria
AuthorsHeller, LC; Jones, M; Widen, RH
Journal
PubMed ID
Identification of mycobacterial clinical isolates by pyrosequencing within the hypervariable A region of the 16S rRNA gene was compared to other identification methods. For >90% of isolates, these identifications correlated to the level of complex or species. For identification of many mycobacteria, pyrosequencing offers an inexpensive alternative to traditional sequencing. ... More
Microsphaerins A-D, four novel benzophenone dimers with activity against MRSA from the fungus Microsphaeropsis sp.
Bioassay-guided isolation using an MRSA whole cell assay yielded four novel benzophenone dimers, microsphaerins A-D (1-4), from two Singapore isolates of the soil anamorph Microsphaeropsis sp. The structures of 1-4 were elucidated on the basis of spectral data and the structures of 1 and 4 were confirmed by X-ray crystallographic ... More
Evaluation of decontamination methods and growth media for primary isolation of Mycobacterium ulcerans from surgical specimens.
We evaluated four decontamination methods and one nondecontamination procedure in combination with four egg-based media for the primary isolation of Mycobacterium ulcerans from tissue specimens. With mycobacterial recovery and contamination rates of 75.6 and 2.4%, respectively, the combination of the oxalic acid decontamination method with Lowenstein-Jensen medium supplemented with glycerol ... More
Bordetella hinzii septicemia in association with Eppstein-Barr virus viremia and an Epstein-Barr virus-associated diffuse large B-cell lymphoma
AuthorsHristov, AC; Auwaerter, PG; Romagnoli, M; Carroll, KC
Journal
PubMed ID
We report the 1st case of Bordetella hinzii septicemia associated with Epstein-Barr virus viremia and lymphoma. B. hinzii identification necessitated cellular fatty acid analysis by gas-liquid chromatography and 16S rRNA gene sequencing. Isolates were resistant to many antimicrobials. Resistance and diagnostic challenges complicated management and contributed to mortality. © 2008 ... More
Identification of an emerging pathogen, Mycobacterium massiliense, by rpoB sequencing of clinical isolates collected in the United States.
AuthorsSimmon KE; Pounder JI; Greene JN; Walsh F; Anderson CM; Cohen S; Petti CA
Journal
PubMed ID
Mycobacterium massiliense is a rapidly growing mycobacterium that is indistinguishable from Mycobacterium chelonae/M. abscessus by partial 16S rRNA gene sequencing. We sequenced rpoB, sodA, and hsp65 genes from isolates previously identified as being M. chelonae/M. abscessus and identified M. massiliense from isolates from two patients with invasive disease representing the ... More
Lactococcus garvieae Endocarditis with Initial Presentation of Acute Cerebral Infarction in a Healthy Immunocompetent Man
AuthorsLi, WK; Chen, YS; Wann, SR; Liu, YC; Tsai, HC
Journal
PubMed ID
Lactococcus garvieae is considered a rare, opportunistic pathogen with low virulence in human infection. There are only scattered case reports of L. garvieae-related infection in humans in the past 20 years. The majority of them were reported to be infective endocarditis. We present a case study of a 41-year-old man ... More
Lobomycosis in Offshore Bottlenose Dolphins (Tursiops truncatus), North Carolina
Lacazia loboi, a cutaneous fungus, is found in humans and dolphins from transitional tropical (Florida) and tropical (South America) regions. We report 2 cases of lobomycosis in stranded bottlenose dolphins (Tursiops truncatus), and 1 case of lobomycosis-like disease in 1 free-swimming, pelagic, offshore bottlenose dolphin from North Carolina, where no ... More
Identification and phylogeny of Enterobacter sakazakii relative to Enterobacter and Citrobacter Species.
AuthorsIversen C; Waddington M; On SL; Forsythe S
Journal
PubMed ID
The phylogenetic relationships of Enterobacter sakazakii strains were investigated using 16S ribosomal DNA (rDNA) and hsp60 sequencing. Each analysis distributed E. sakazakii strains among four clusters, indicating substantial taxonomic heterogeneity. The E. sakazakii type strain 16S rDNA sequence was 97.8% similar to that of Citrobacter koseri but 97.0% similar to ... More
Prosthetic valve endocarditis is an uncommon manifestation of infection with Bartonella species. Herein, we report a case of Bartonella henselae endocarditis involving prosthetic mitral and aortic valves. The patient had a favorable outcome with combined medical and surgical therapy. Concomitant crescentic glomerulonephritis led to an initial mistaken diagnosis of Wegener's ... More
Duplex PCR Assay Simultaneously Detecting and Differentiating Bartonella quintana, B. henselae, and Coxiella burnetii in Surgical Heart Valve Specimens
AuthorsTang, YW
Journal
PubMed ID
A duplex PCR (dPCR) assay was developed to simultaneously detect and differentiate Bartonella quintana, Bartonella henselae, and Coxiella burnetii from surgical heart valve tissue specimens with an analytic sensitivity of 10 copies/reaction. Among 17 specimens collected from patients with a clinical diagnosis of culture-negative endocarditis, 2, 4, and 2 were ... More
We report on a patient with an abdominal wall abscess that developed after an inguinal hernia repair that utilized synthetic mesh. Mycobacterium goodii, a recently recognized, rapidly growing mycobacterium related to M. smegmatis, was isolated both from the abdominal wall aspirate and from surgically drained material. Infection resolved following thorough ... More
Multifocal osteomyelitis due to Mycobacterium szulgai in a patient with chronic lymphocytic leukemia
AuthorsMeyer, JJ; Gelman, SS
Journal
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Mycobacterium szulgai is a pathogenic organism that most frequently causes pulmonary infection and may rarely result in disseminated disease in immunocompromised individuals. We report a case of multifocal osteomyelitis and cutaneous lesions due to M. szulgai in a patient with chronic Lymphocytic Leukemia. The successful treatment of multifocal osteomyelitis was ... More
Acute cholecystitis accompanied by acute pancreatitis potentially caused by Dolosigranulum pigrum.
AuthorsLin JC; Hou SJ; Huang LU; Sun JR; Chang WK; Lu JJ
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We report a case of acute cholecystitis accompanied by acute pancreatitis and caused by Dolosigranulum pigrum in a 76-year-old male with gallstones. D. pigrum was isolated from a blood culture and confirmed by biochemistry tests and 16S rRNA sequencing. The isolate was susceptible to the beta-lactams ampicillin, penicillin, cephalothin, ceftriaxone, ... More
Gemella morbillorum: an underestimated aetiology of central nervous system infection?
AuthorsBenedetti, P; Rassu, M; Branscombe, M; Sefton, A; Pellizzer, G
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A case is reported of cerebellar abscess and diffuse cerebritis due to Gemella morbillorum. The clinical course was 'biphasic', developing with an acute meningeal infection followed shortly afterwards by suppuration in the cerebellar and cerebral parenchyma; this pattern seemed to suggest a latent survival of the aetiological agent, probably within ... More
The other group G Streptococcus: increased detection of Streptococcus canis ulcer infections in dog owners.
AuthorsLam MM; Clarridge JE 3rd; Young EJ; Mizuki S
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beta-Hemolytic Lancefield group G Streptococcus dysgalactiae and Streptococcus canis cannot be distinguished when only Lancefield typing is performed. Phenotypic testing and 16S rRNA gene sequencing identified S. canis associated with ulcer infections in dog owners. Because S. canis may be incorrectly identified (published biochemical descriptions are inconsistent), there may be ... More
Use of PCR-restriction enzyme pattern analysis and sequencing database for hsp65 gene-based identification of Nocardia species.
Nocardia identification required laborious and time-consuming phenotypic and chemotaxonomic methods until molecular methods were developed in the mid-1990s. Here we reassessed the capacity of PCR-restriction enzyme pattern analysis (PRA) of the hsp65 gene to differentiate Nocardia species, including 36 new species. Our results confirm that hsp65 PRA must no longer ... More
Distribution of nocardia species in clinical samples and their routine rapid identification in the laboratory.
AuthorsWauters G; Avesani V; Charlier J; Janssens M; Vaneechoutte M; Delmee M
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Eighty-six Nocardia strains isolated from clinical samples in Belgium were identified by 16S rRNA gene sequencing. Eighty-three (96%) strains belonged to only six Nocardia species: N. farcinica (38 [44%]), N. nova (19 [22%]), N. cyriacigeorgica (13 [15%]), N. brasiliensis (6 [6.9%]), N. abscessus (5 [5.8%]), and N. paucivorans (2 [2.3%]). ... More
Sphingomonas paucimobilis bacteraemia and septic arthritis in a diabetic patient presenting with septic pulmonary emboli
Sphingomonas paucimobilis, a yellow-pigmented, aerobic, glucose non-fermenting, Gram-negative bacillus, is a rare cause of human infection normally associated with immunocompromised hosts. We report a case of bacteraemia. and septic arthritis in a 47-year-old diabetic man who presented with septic pulmonary emboli due to S. paucimobilis. The patient had an initial ... More
Comparison of in-house and commercial 16S rRNA sequencing with high-performance liquid chromatography and genotype AS and CM for identification of nontuberculous mycobacteria
AuthorsDaley, P; Petrich, A; May, K; Luinstra, K; Rutherford, C; Chedore, P; Jamieson, F; Smieja, M
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Sequencing of the 16S gene or other targets and line probe assay are in wide use for the identification of nontuberculous mycobacteria. We compared in-house and commercial sequencing with 3 sequence databases against high-performance liquid chromatography (HPLC) and line probe assay (HAIN Genotype AS and CM) for the identification of ... More
Identification of two distinct hybridization groups in the genus Hafnia by 16S rRNA gene sequencing and phenotypic methods.
AuthorsJanda JM; Abbott SL; Bystrom S; Probert WS
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A collection of 52 strains belonging to the Hafnia alvei complex were subjected to molecular (16S rRNA gene sequencing) and biochemical analysis. Based upon 16S rRNA gene sequencing results, two genetic groups were identified which correspond with previously recognized DNA hybridization group 1 (ATCC 13337(T) and ATCC 29926; n = ... More
A case of endocarditis caused by the yeast Pichia fabianii with biofilm production and developed in vitro resistance to azoles in the course of antifungal treatment
AuthorsHamal, P; Ostransky, J; Dendis, M; Horvath, R; Ruzicka, F; Buchta, V; Vejsova, M; Sauer, P; Hejnar, P; Raclavsky, V
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Pichia fabianii, a yeast rarely causing human infections, was isolated from the blood of a patient with aortic valve endocarditis. The isolates were initially identified biochemically as Candida pelliculosa, but based on direct sequencing of the ITS2 region of rRNA, they were subsequently reidentified as P. fabianii. Antifungal therapy with ... More
Molecular tools for the detection and characterization of bacterial infections: A review
AuthorsMuthukumar, A; Zitterkopf, NL; Payne, D
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Bacterial infections, especially drug-resistant infections, continue to cause public health problems. While culture methods currently serve as the reference methods for detecting and charcterizing most bacterial and characterizing most bacterial infections, new molecular techniques provide the means for rapid, specific, and sensitive detection of pathogenic bacteria. Previoulsy, molecular detection of ... More
Xanthan and gellan degradation by bacteria of activated sludge
AuthorsMuchova, M; Ruzicka, J; Julinova, M; Dolezalova, M; Houser, J; Koutny, M; Bunkova, L
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Owing to increasing amounts of xanthan and gellan in food, cosmetics and pharmaceuticals, as well as in some technical spheres, studies were carried out on the xanthan and gellan degrading bacteria present in activated sludge. The activated sludge used in the study was able to degrade both carbohydrates over 7 ... More
ANTINEOPLASTIC AGENTS. 575. THE FUNGUS Aspergillus phoenicis.
AuthorsPettit, GR; Du, J; Pettit, RK; Knight, JC; Doubek, DL
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Cancer cell line bioassay-guided separation of an extract from the fungus Aspergillus phoenicis collected in Saskatchewan, Canada, resulted in the isolation of three new constituents designated asperlactone (1), aspergillol A (2), and aspergillol B (3), accompanied by four previously known constituents: asperic acid (4), hexylitaconic acid (5), methyl 2-hydroxyphenylacetate (6), ... More
Comparison of the MicroScan, VITEK 2, and Crystal GP with 16S rRNA sequencing and MicroSeq 500 v2.0 analysis for coagulase-negative Staphylococci
AuthorsKim, M; Heo, SR; Choi, SH; Kwon, H; Park, JS; Seong, MW; Lee, DH; Park, KU; Song, J; Kim, EC
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Background: Three phenotypic identification systems (MicroScan, VITEK 2, and Crystal GP) were evaluated for their accuracy to identify coagulase-negative staphylococci (CNS). A total of 120 clinical isolates confirmed to be CNS via 16S rRNA sequencing and analysis with the MicroSeq 500 v2.0 database were assessed. Results: The MicroScan, VITEK ... More
Degradation of Rutin by Thermoactinomyces vulgaris and Other Thermophilic Compost Isolates
AuthorsYang, CH; Huang, YC; Chen, CY
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The mutagenic effects of rutin and quercetin have aroused the interest of many investigators. To develop the microbial degradation of rutin, a thermophilic actinomycete, which could hydrolyze rutin, was isolated from compost soil. The taxonomical characteristics of this thermophilic actinomycete were examined and identified as Thermoactinomyces vulgaris PU18-2. After cultivation ... More
Performances of VITEK 2 colorimetric cards for identification of gram-positive and gram-negative bacteria.
The purpose of this study was to evaluate the new VITEK 2 identification cards that use colorimetric reading to identify gram-positive and gram-negative bacteria (GP and GN cards, respectively) in comparison to fluorimetric cards (ID-GPC and ID-GNB, respectively). A total of 580 clinical isolates and stock collection strains belonging to ... More
The Progress of Protein Quality Control Methods in Shotgun Proteomics
AuthorsLi, N; Wu, SF; Zhu, YP; Yang, XM
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The shotgun strategy applying tandem mass spectrometry to identify proteins has been widely used in proteomics for its high reliability and efficiency. However, protein deduction is ambiguous due to uncorrected identified peptides and erased correlated information between peptides and their source proteins. Protein quality control methods can be divided into ... More
Analysis of multiple differing copies of the 16S rRNA gene in five clinical isolates and three type strains of Nocardia species and implications for species assignment.
AuthorsConville PS; Witebsky FG
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Five clinical isolates of Nocardia that showed ambiguous bases within the variable region of the 16S rRNA gene sequence were evaluated for the presence of multiple copies of this gene. The type strains of three Nocardia species, Nocardia concava, Nocardia ignorata, and Nocardia yamanashiensis, which also showed ambiguous bases in ... More
Bacillus velezensis is a later heterotypic synonym of Bacillus amyloliquefaciens.
AuthorsWang LT; Lee FL; Tai CJ; Kuo HP
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Strain BCRC 14193, isolated from soil, shared more than 99 % 16S rRNA gene sequence similarity with Bacillus amyloliquefaciens BCRC 11601(T) and Bacillus velezensis BCRC 17467(T). This strain was previously identified as B. amyloliquefaciens, based on DNA-DNA hybridization, but its DNA relatedness value with B. velezensis BCRC 17467(T) was 89 ... More
In silico analysis of 16S ribosomal RNA gene sequencing-based methods for identification of medically important anaerobic bacteria.
AuthorsWoo PC; Chung LM; Teng JL; Tse H; Pang SS; Lau VY; Wong VW; Kam KL; Lau SK; Yuen KY
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This study is the first study that provides useful guidelines to clinical microbiologists and technicians on the usefulness of full 16S rRNA sequencing, 5'-end 527-bp 16S rRNA sequencing and the existing MicroSeq full and 500 16S rDNA bacterial identification system (MicroSeq, Perkin-Elmer Applied Biosystems Division, Foster City, California, USA) databases ... More
Rapid identification of bacterial isolates from aqueous kava (Piper methysticum) extracts by polymerase chain reaction and DNA sequencing
AuthorsKandukuru, P; Huang, AS; Dong, J; Bittenbender, HC; Li, Y
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Aim: Fresh kava beverages have a limited shelf life under refrigerated conditions. The objective of this study was to isolate and identify bacteria in aqueous extracts of kava rhizome. Methods and Results: The internal part of kava rhizome was used to minimize soil contamination. Three kava extracts were ... More
Molecular biology in clinical microbiology in 2007 - Part 1
AuthorsLamoril, J; Bogard, M; Ameziane, N; Deybach, JC; Bouizegardene, P
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Molecular biology is omnipresent in medical biology especially in microbiology. Many papers report studies on its importance in diagnosis, prognosis, therapeutic field, epidemiology, natural (or not) biological risks alike. The important sum of reports on this subject does not always bring an obvious answer to the part that molecular biology ... More
icaA is not a useful diagnostic marker for prosthetic joint infection.
AuthorsFrank KL; Hanssen AD; Patel R
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A collection of 99 staphylococcal isolates associated with prosthetic joint infection and 23 coagulase-negative staphylococci isolated from noninfected arthroplasty-associated specimens were screened in order to determine whether the presence of icaA could be used to distinguish between pathogens and nonpathogens. All Staphylococcus aureus prosthetic joint infection isolates (n = 55) ... More
Nocardia cyriacigeorgica, an emerging pathogen in the United States.
AuthorsSchlaberg R; Huard RC; Della-Latta P
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Nocardia cyriacigeorgica is recognized as an emerging pathogen in many parts of the world. We present the first case description of invasive N. cyriacigeorgica pulmonary infection in the United States identified to the species level by 16S rRNA and hsp65 sequence analysis. A subsequent retrospective molecular screening of recent Nocardia ... More
High Catalase Production by Rhizobium radiobacter Strain 2-1
AuthorsNakayama, M; Nakajima-Kambe, T; Katayama, H; Higuchi, K; Kawasaki, Y; Fuji, R
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To promote the application of catalase for treating wastewater containing hydrogen peroxide, bacteria exhibiting high catalase activity were screened. A bacterium, designated strain 2-1, with high catalase activity was isolated from the wastewater of a beverage factory that uses hydrogen peroxide. Strain 2-1 was identified as Rhizobium radiobacter (formerly known ... More
Molecular biology in clinical microbiology in 2007 - Part 2
AuthorsLamoril, J; Bogard, M; Ameziane, N; Deybach, JC; Bouizegarene, P
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Molecular biology is omnipresent in medical biology especially in microbiology. Many papers report studies on its importance in diagnosis, prognosis, therapeutic field, epidemiology, natural (or not) biological risks alike. The important sum of reports on this subject does not always bring an obvious answer to the part that molecular biology ... More
First isolation of Nocardia crassostreae from pacific oyster Crassostrea gigas in Europe
AuthorsEngelsma, MY; Roozenburg, I; Joly, JP
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In summer 2006 an extensive mortality of Pacific oysters Crassostrea gigas occurred in Lake Grevelingen, the Netherlands. A sample of Pacific oysters was investigated for the presence of shellfish pathogens as potential causes of the mortality. Yellow-green lesions were observed in several oysters upon clinical inspection. Histopathology showed that 6 ... More
A novel dichloromethane-degrading Lysinibacillus sphaericus strain wh22 and its degradative plasmid
AuthorsWu, SJ; Hu, ZH; Zhang, LL; Yu, X; Chen, JM
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Dichloromethane (DCM)-degrading bacterium strain wh22 (GenBank accession number FJ418643) was isolated and identified as Lysinibacillus sphaericus based on standard morphological and physiological properties, cellular fatty acid composition, mole percent guanine-cytosine content, and nucleotide sequence analysis of enzymatically amplified 16S ribosomal deoxyribonucleic acid. The strain also grew on many other halocarbons ... More
Current status and future perspectives on molecular and serological methods in diagnostic mycology
AuthorsLau, A; Chen, S; Sleiman, S; Sorrell, T
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Invasive fungal infections are an important cause of infectious morbidity, Nonculture-based methods are increasingly used for rapid, accurate diagnosis to improve patient outcomes. New and existing DNA amplification platforms have high sensitivity and specificity for direct detection and identification of fungi in clinical specimens. Since laboratories are increasingly reliant on ... More
Cytotoxic and cell vacuolating activity of Vibrio fluvialis isolated from paediatric patients with diarrhoea.
Vibrio fluvialis is a halophilic Vibrio species associated with acute diarrhoeal illness in humans. It has the potential to cause outbreaks and has an association with paediatric diarrhoea. In this study, 11 V. fluvialis strains isolated from hospitalized patients with acute diarrhoea at the Infectious Diseases Hospital, Kolkata were extensively ... More