scholarly journals “Flexispira rappini” Bacteremia in a Child with Pneumonia

1998 ◽  
Vol 36 (6) ◽  
pp. 1679-1682 ◽  
Author(s):  
Wee Tee ◽  
Karin Leder ◽  
Elena Karroum ◽  
Michael Dyall-Smith
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Middle Lobe ◽  
Base Substitution ◽  
Rrna Gene ◽  
Invasive Infection ◽  
Biochemical Tests ◽  
History Of ◽  
Chest X Ray ◽  
Right Middle Lobe ◽  
Rrna Gene Sequencing

We describe a case of “Flexispira rappini” bacteremia from a 9-year-old girl who presented with a 5-day history of fever, productive cough, and malaise. A chest X-ray result was compatible with right middle lobe pneumonia. Blood culture grew a gram-negative spiral fusiform bacterium 2 days after the inoculation. Biochemical tests showed the organism to be catalase negative, oxidase positive, sodium hippurate hydrolysis negative, and urea hydrolysis negative. 16S rRNA gene sequencing identified this organism as “F. rappini,” showing a six-base substitution from the type strain. This is the first report of “F. rappini” bacteremia in a human, suggesting that this organism has the potential of causing invasive infection, but its role in pneumonia is uncertain and could be unrelated to the bacteremia.

scholarly journals Case report: pulmonary nocardiosis caused by Nocardia exalbida in an immunocompetent patient

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Seitaro Abe ◽  
Yoshinari Tanabe ◽  
Takeshi Ota ◽  
Fumio Fujimori ◽  
Akira Youkou ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Immunocompromised Host ◽  
Immunocompetent Patient ◽  
Middle Lobe ◽  
Response To Treatment ◽  
Rrna Gene ◽  
Pulmonary Nocardiosis ◽  
First Case ◽  
History Of ◽  
Right Middle Lobe

Abstract Background Nocardiosis is known as an opportunistic infection in immunocompromised hosts, but it occasionally has been reported in immunocompetent patient. The Nocardia exalbida is first-reported in 2006 from Japan, and a few cases of have been reported in only immunocompromised host, and the characteristic is still unclear. We herein describe the first case of pulmonary nocardiosis caused by N. exalbida in an immunocompetent patient. Case presentation A77 -year-old Japanese man was admitted to our hospital on November 2, 2018. He was a lifelong non-smoker with no childhood history of respiratory disease. He had a medical history of dyslipidemia. One month before this admission fevers, sputum, mild cough were developed and he was evaluated in a clinic near our hospital. His diagnosis was community acquired pneumonia within his right middle lobe. He was treated with ceftriaxone 1 g/day intravenously for a week, however his symptoms relapsed a few days later. So, the physician retried ceftriaxone for another 3 days, but his symptoms did not improve. He was referred to our hospital. He was treated with sitafloxacin as an outpatient for a week, however his symptoms got worse. The chest CT showed consolidation and atelectasis in his right middle lobe. Low density area was scattered in consolidation, and right pleural effusion was observed. The patient was diagnosed with pulmonary abscess and he was admitted. Administration of piperacillin/tazobactam improved his condition. We switched antibiotics to amoxicillin/clavulanate, and he was discharged. After 2 weeks, he relapsed and was admitted again. After administration of piperacillin/tazobactam for 3 weeks, we perform bronchoscopy and Nocardia species were cultured from samples of the bronchial wash. The isolates were identified as N. exalbida using 16S rRNA gene sequencing. We prescribed Trimethoprim / Sulfamethoxazole (TMP/SMX) for 4 months. Then we switched to minocycline for renal dysfunction caused from TMP-SMX for 1 more month. After 5 months therapy, Consolidation on CT disappeared, and Nocardiosis was cured. Conclusion we reported the first case of pulmonary nocardiosis caused by N. exalbida in an immunocompetent patient. N. exalbida infection might be associated with a good response to treatment.

scholarly journals Molecular Identification and Epidemiological Tracing of Pasteurella multocida Meningitis in a Baby

2000 ◽  
Vol 38 (3) ◽  
pp. 1235-1237 ◽  
Author(s):  
Patrick Boerlin ◽  
Hans H. Siegrist ◽  
André P. Burnens ◽  
Peter Kuhnert ◽  
Purita Mendez ◽  
...  
Keyword(s):  
Pasteurella Multocida ◽  
Close Contact ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Source Of Infection ◽  
Subspecies Level ◽  
History Of ◽  
Rrna Gene Sequencing ◽  
The One

We report a case of Pasteurella multocida meningitis in a 1-month-old baby exposed to close contact with two dogs and a cat but without any known history of injury by these animals. 16S rRNA gene sequencing of the isolate from the baby allowed identification at the subspecies level and pointed to the cat as a possible source of infection. Molecular typing of Pasteurella isolates from the animals, from the baby, and from unrelated animals clearly confirmed that the cat harbored the same P. multocidasubsp. septica strain on its tonsils as the one isolated from the cerebrospinal fluid of the baby. This case stresses the necessity of informing susceptible hosts at risk of contracting zoonotic agents about some basic hygiene rules when keeping pets. In addition, this study illustrates the usefulness of molecular methods for identification and epidemiological tracing ofPasteurella isolates.

scholarly journals Streptococcus ursoris sp. nov., isolated from the oral cavities of bears

2011 ◽  
Vol 61 (1) ◽  
pp. 40-44 ◽  
Author(s):  
Noriko Shinozaki-Kuwahara ◽  
Kazuko Takada ◽  
Masatomo Hirasawa
Keyword(s):  
Type Strain ◽  
16S Rrna Gene Sequencing ◽  
Extracellular Polysaccharide ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Sequencing Studies ◽  
Streptococcal Species ◽  
Rrna Gene Sequencing ◽  
Streptococcus Ratti

Three Gram-positive, catalase-negative, coccus-shaped organisms were isolated from the oral cavities of bears. The isolates were tentatively identified as a streptococcal species based on the results of biochemical tests. Comparative 16S rRNA gene sequencing studies confirmed that the organisms were members of the genus Streptococcus, but they did not correspond to any recognized species of the genus. The nearest phylogenetic relative of the new isolates was Streptococcus ratti ATCC 19645T (98.6 %), however, DNA–DNA hybridization analysis showed that the isolates displayed less than 15 % DNA–DNA relatedness with the type strain of S. ratti. Colonies of the novel strains grown on mitis salivarius agar showed an extracellular polysaccharide-producing colony morphology. Based on phenotypic and phylogenetic evidence, it is proposed that the novel isolates are classified in the genus Streptococcus as Streptococcus ursoris sp. nov. The type strain of S. ursoris is NUM 1615T (=JCM 16316T=DSM 22768T).

scholarly journals Nocardia amamiensis sp. nov., isolated from a sugar-cane field in Japan

2007 ◽  
Vol 57 (7) ◽  
pp. 1599-1602 ◽  
Author(s):  
Hideki Yamamura ◽  
Tomohiko Tamura ◽  
Yayoi Sakiyama ◽  
Shigeaki Harayama
Keyword(s):  
Sugar Cane ◽  
16S Rrna Gene Sequencing ◽  
Treatment Method ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Sequencing Studies ◽  
Actinomycete Strain ◽  
Pre Treatment ◽  
Rrna Gene Sequencing ◽  
Type Strains

An actinomycete, strain TT 00-78T, was isolated from soil from a sugar-cane field on Amami Island in Japan, using an SDS/yeast extract pre-treatment method, and the taxonomy was studied using a polyphasic approach. The chemotaxonomic and morphological characterizations clearly demonstrated that the strain belongs to the genus Nocardia. 16S rRNA gene sequencing studies showed that the strain was closely related to the type strains of Nocardia pneumoniae (98.6 %), Nocardia araoensis (98.1 %), Nocardia arthritidis (97.9 %) and Nocardia beijingensis (97.7 %). However, the results of DNA–DNA hybridization and physiological and biochemical tests showed that strain TT 00-78T could be differentiated from its closest phylogenetic relatives both genotypically and phenotypically. Therefore this strain represents a novel species of the genus Nocardia, for which the name Nocardia amamiensis sp. nov. is proposed. The type strain is TT 00-78T (=NBRC 102102T=DSM 45066T=KCTC 19208T).

scholarly journals Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov.

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1486-1490 ◽  
Author(s):  
Dominique Clermont ◽  
Laurence Motreff ◽  
Virginie Passet ◽  
José-Carlos Fernandez ◽  
Chantal Bizet ◽  
...  
Keyword(s):  
Type Species ◽  
16S Rrna Gene Sequencing ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Separate Species ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Rrna Gene Sequencing

Strains originating from various sources and classified as members of the genus Citrobacter within the family Enterobacteriaceae were characterized by sequencing internal portions of genes rpoB, fusA, pyrG and leuS, 16S rRNA gene sequencing, average nucleotide identity (ANI) of genomic sequences and biochemical tests. Phylogenetic analysis based on the four housekeeping genes showed that the 11 species of the genus Citrobacter with validly published names are well demarcated. Strains CIP 55.13T and CIP 55.9 formed a distinct branch associated with Citrobacter youngae . The ANI between CIP 55.9 and CIP 55.13T was 99.19 %, whereas it was 94.75 % between CIP 55.13T and strain CIP 105016T of the species C. youngae , the most closely related species. Biochemical characteristics consolidated the fact that the two isolates represent a separate species, for which the name Citrobacter pasteurii sp. nov. is proposed. The type strain is CIP 55.13T ( = DSM 28879T = Na 1aT).

scholarly journals Longitudinal Characterization of the Tumoral Microbiome during Radiotherapy in HPV-associated Oropharynx Cancer

2020 ◽  
Author(s):  
Houda Bahig ◽  
Clifton D Fuller ◽  
Aparna Mitra ◽  
Travis Solley ◽  
Sweet Ping Ng ◽  
...  
Keyword(s):  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Concurrent Chemotherapy ◽  
Rrna Gene ◽  
Entire Cohort ◽  
Oropharynx Cancer ◽  
History Of ◽  
Rrna Gene Sequencing ◽  
Never Smokers

ABSTRACTPurposeTo describe the baseline and serial tumor microbiome in HPV-associated oropharynx cancer (OPC) over the course of radiotherapy (RT).MethodsPatients with newly diagnosed HPV-associated OPC treated with definitive radiotherapy +/- concurrent chemotherapy were enrolled in this prospective study. Using 16S rRNA gene sequencing, dynamic changes in tumor microbiome during RT were investigated. Surface tumor samples were obtained before RT and at week 1, 3 and 5 of RT. Radiological primary tumor response at mid-treatment was categorized as complete (CR) or partial (PR).ResultsTen patients were enrolled. Mean age was 63 years (range: 51-71). As per AJCC 8th Ed, 50%, 20% and 30% of patients had stage I, II and III, respectively. At 4-weeks, 7 patients had CR and 3 patients had PR; at follow-up imaging post treatment, all patients had CR. Baseline diversity of tumoral and buccal microbiomes was not statistically different. For the entire cohort, alpha diversity was significantly decreased over the course of treatment (p=0.02). There was a significant alteration in the bacterial community within the first week of radiation. Baseline tumor alpha diversity of patients with CR was significantly higher than those with PR (p=0.03). While patients with CR had significant reduction in diversity over the course of radiation (p=0.02), the diversity remained unchanged in patients with PR. Patients with history of smoking had significantly increased abundance of Granulicatella (p=0.04), and Kingella (0.05) and lower abundance of Alloprevotella (p=0.04) compared to never smokers.ConclusionsThe tumor microbiome of HPV-associated OPC exhibits reduced alpha diversity and altered taxa abundance over the course of radiotherapy. The baseline bacterial profiles of smokers vs. non-smokers were inherently different. Baseline tumor alpha diversity of patients with CR was higher than patients with PR, suggesting that the microbiome as a biomarker of radiation response deserves further investigation.

scholarly journals Analysis of Vaginal and Endometrial Microbiota Communities in Infertile Women With a History of Repeated Implantation Failure

2020 ◽  
Author(s):  
Takuhiko Ichiyama ◽  
Keiji Kuroda ◽  
Yoko Nagai ◽  
Daichi Urushiyama ◽  
Motoharu Ono ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Implantation Failure ◽  
Repeated Implantation Failure ◽  
Infertile Women ◽  
Healthy Women ◽  
History Of ◽  
Rrna Gene Sequencing ◽  
Clinical Trials Registry

Abstract Background: Repeated implantation failure (RIF) is estimated to occur in 15%–20% of infertile women undergoing in vitro fertilization-embryo transfer (IVF-ET). Molecular identification recently confirmed that the uterine microbiota may have implications for reproductive and obstetrical outcomes. One hundred forty-five women who had been diagnosed with RIF were enrolled in the study. Twenty-one healthy women were also enrolled as controls. We investigated their vaginal and endometrial microbiotas using 16S rRNA gene sequencing and compared the microbiota profiles in the patients with RIF and controls.Results: The endometrial microbiotas had higher α-diversities than did the vaginal microbiotas (p<0.001 in both patients with RIF and healthy women). The microbiota profiles showed that vaginal and endometrial samples in patients with RIF had significantly higher levels of 5 and 14 bacterial genera, respectively, than those in healthy women. These genera included Atopobium, Gardnerella, Prevotella and Megasphaera. Vaginal Lactobacillus rates in patients with RIF were significantly lower at 76.4 ± 38.9% compared with those of the controls at 91.8 ± 22.7% (p=0.018), but endometrial Lactobacillus rates did not significantly differ between the RIF patients and controls (56.2 ± 36.4% and 58.8 ± 37.0%, respectively, p=0.79) Conclusions: Impaired microbiota communities containing specific bacteria in both the endometrium and vagina were associated with implantation failure. The Lactobacillus rate in the vagina, but not the endometrium, may be a biomarker for RIF.Trial registration: UMIN Clinical Trials Registry, UMIN000031731, Registered 15 March 2018; https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000036121

scholarly journals Nocardia takedensis sp. nov., isolated from moat sediment and scumming activated sludge

2005 ◽  
Vol 55 (1) ◽  
pp. 433-436 ◽  
Author(s):  
Hideki Yamamura ◽  
Masayuki Hayakawa ◽  
Youji Nakagawa ◽  
Tomohiko Tamura ◽  
Tetsuro Kohno ◽  
...  
Keyword(s):  
Activated Sludge ◽  
Reference Strain ◽  
16S Rrna Gene Sequencing ◽  
Morphological Characterization ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing ◽  
Physiological And Biochemical

Chemotaxonomic and morphological characterization of two actinomycete strains, MS1-3T and AS4-2, respectively isolated from moat sediment and scumming activated sludge, was carried out. This characterization clearly demonstrated that strains MS1-3T and AS4-2 belong to the genus Nocardia. 16S rRNA gene sequencing studies showed that these isolates are most closely related to Nocardia beijingensis (98·1–98·3 % similarity), Nocardia brasiliensis (97·9–98·0 %) and Nocardia tenerifensis (97·8–97·9 %). However, the results of DNA–DNA hybridizations and physiological and biochemical tests showed that strains MS1-3T and AS4-2 could be differentiated from their closest phylogenetic relatives both genotypically and phenotypically. It is proposed that the two isolates be classified as representatives of a novel species of Nocardia, Nocardia takedensis sp. nov. The type strain is MS1-3T (=NBRC 100417T=DSM 44801T); AS4-2 (=NBRC 100418=DSM 44802) is a reference strain.

scholarly journals Genetic and Biochemical Diversity ofPaenibacillus larvaeIsolated from Tunisian Infected Honey Bee Broods

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Chadlia Hamdi ◽  
Jihène Essanaa ◽  
Luigi Sansonno ◽  
Elena Crotti ◽  
Khaoula Abdi ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
16S Rrna Gene Sequencing ◽  
Intraspecific Diversity ◽  
Economic Losses ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Phenotypic Differences ◽  
Ecological Aspects ◽  
Rrna Gene Sequencing

Paenibacillus larvaeis the causative agent of American foulbrood (AFB), a virulent disease of honeybee (Apis mellifera) larvae. In Tunisia, AFB has been detected in many beekeeping areas, where it causes important economic losses, but nothing is known about the diversity of the causing agent. Seventy-five isolates ofP. larvae, identified by biochemical tests and 16S rRNA gene sequencing, were obtained from fifteen contaminated broods showing typical AFB symptoms, collected in different locations in the northern part of the country. Using BOX-PCR, a distinct profile ofP. larvaewith respect to relatedPaenibacillusspecies was detected which may be useful for its identification. SomeP. larvae-specific bands represented novel potential molecular markers for the species. BOX-PCR fingerprints indicated a relatively high intraspecific diversity among the isolates not described previously with several molecular polymorphisms identifying six genotypes on polyacrylamide gel. Polymorphisms were also detected in several biochemical characters (indol production, nitrate reduction, and methyl red and oxidase tests). Contrary to the relatively high intraspecies molecular and phenotypic diversity, thein vivovirulence of three selectedP. larvaegenotypes did not differ significantly, suggesting that the genotypic/phenotypic differences are neutral or related to ecological aspects other than virulence.

scholarly journals Pseudomonas simiae sp. nov., isolated from clinical specimens from monkeys (Callithrix geoffroyi)

2006 ◽  
Vol 56 (11) ◽  
pp. 2671-2676 ◽  
Author(s):  
Ana I. Vela ◽  
María C. Gutiérrez ◽  
Enevold Falsen ◽  
Eduardo Rollán ◽  
Isabel Simarro ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Molecular Genetic ◽  
16S Rrna Gene Sequencing ◽  
Clinical Samples ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing ◽  
Callithrix Geoffroyi

An unusual Gram-negative, catalase- and oxidase-positive, rod-shaped bacterium isolated from different clinical samples from two monkeys (Callithrix geoffroyi) was characterized by phenotypic and molecular genetic methods. The micro-organism was tentatively identified as a Pseudomonas species on the basis of the results of cellular morphological and biochemical tests. Fatty acid studies confirmed this generic placement and comparative 16S rRNA gene sequencing studies demonstrated that the unknown isolates were phylogenetically closely related to each other (100 % sequence similarity) and were part of the ‘Pseudomonas fluorescens intrageneric cluster’. The novel bacterium, however, was distinguished from other phylogenetically related species of Pseudomonas by DNA–DNA hybridization studies and biochemical tests. On the basis of both phenotypic and phylogenetic findings, it is proposed that the novel Pseudomonas isolates are classified as Pseudomonas simiae sp. nov. The type strain of P. simiae is OLiT (=CCUG 50988T=CECT 7078T).

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