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Antimicrobial Agents and Chemotherapy Dec 2015Nutritionally variant streptococci (NVS) are fastidious Gram-positive cocci comprised of the species Abiotrophia defectiva, Granulicatella adiacens, and Granulicatella...
Nutritionally variant streptococci (NVS) are fastidious Gram-positive cocci comprised of the species Abiotrophia defectiva, Granulicatella adiacens, and Granulicatella elegans. NVS are an important cause of bacteremia and infective endocarditis (IE) associated with significant morbidity and mortality. Antimicrobial susceptibility testing (AST) was performed for 14 antimicrobials using the broth microdilution MIC method described in the Clinical and Laboratory Standards Institute (CLSI) M45 guideline. A total of 132 clinical NVS blood isolates collected from 2008 to 2014 were tested. Species level identification of NVS isolates was achieved by 16S rRNA gene sequencing and/or matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Ninety isolates were identified as G. adiacens, 37 as A. defectiva, and 5 as G. elegans. All isolates were susceptible to vancomycin (MIC90 = 1 μg/ml), and none displayed high-level resistance to aminoglycosides. G. adiacens was considerably more susceptible to penicillin than A. defectiva (38.9% versus 10.8% of isolates susceptible) but was less susceptible to cephalosporins than was A. defectiva (43.3% versus 100% of isolates susceptible to ceftriaxone). Several isolates were resistant to levofloxacin (6%), erythromycin (51%), and clindamycin (10%). The MIC90 for daptomycin was ≥ 4 μg/ml for G. adiacens and A. defectiva. G. elegans isolates were 100% susceptible to all antimicrobials tested, with the exception of erythromycin, to which only 20% were susceptible. This study provides antimicrobial susceptibility data for a recent collection of NVS and demonstrates important NVS species-related differences with respect to susceptibility to penicillin, cephalosporins, carbapenems, and daptomycin. Species-level identification of NVS organisms when susceptibility testing is not readily available may aid in treatment decisions.
Topics: Abiotrophia; Anti-Bacterial Agents; Carnobacteriaceae; Gram-Positive Bacterial Infections; Humans; Los Angeles; Microbial Sensitivity Tests; Molecular Typing; RNA, Ribosomal, 16S; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; beta-Lactams
PubMed: 26666926
DOI: 10.1128/AAC.02645-15 -
Revista Chilena de Infectologia :... Apr 2016
Topics: Abiotrophia; Agar; Culture Media; Gram-Positive Bacterial Infections; Staphylococcus aureus
PubMed: 27314997
DOI: 10.4067/S0716-10182016000200009 -
Frontiers in Bioscience (Elite Edition) Aug 2022spp. and spp. are Gram-positive cocci, formerly known as nutritionally variant or deficient . Their role as causative agents of infective endocarditis (IE) is...
BACKGROUND
spp. and spp. are Gram-positive cocci, formerly known as nutritionally variant or deficient . Their role as causative agents of infective endocarditis (IE) is numerically uncertain, as well as diagnostic and clinical management of this infection. The aim of our study is to describe the clinical, microbiological, therapeutic, and prognosis of patients with IE caused by these microorganisms in a large microbiology department.
METHODS
Retrospective analysis of all the patients with spp. and spp. IE registered in our centre in the period 2004-2021.
RESULTS
Of the 822 IE in the study period, 10 (1.2%) were caused by spp. (7) or spp. (3). The species involved were (7), (2) and (1). Eight patients were male, their mean age was 46 years and four were younger than 21 years. The most frequent comorbidities were congenital heart disease (4; 40%) and the presence of intracardiac prosthetic material (5; 50%). IE occurred on 5 native valves and 5 prosthetic valve or material. Blood cultures were positive in 8/10 patients, within a mean incubation period of 18.07 hours. In the other two patients, a positive 16SPCR from valve or prosthetic material provided the diagnosis. Surgery for IE was performed in seven patients (70%) and in all cases positive PCR and sequencing from valve or prosthetic material was demonstrated. Valves and/or prosthetic removed material cultures were positive in four patients. Nine patients received ceftriaxone (4 in monotherapy and 5 in combination with other antibiotics). The mean length of treatment was 6 weeks and IE-associated mortality was 20% at one year follow-up.
CONCLUSIONS
spp. or spp. IE were infrequent but not exceptional in our environment and particularly affected patients with congenital heart disease or prosthetic material. Blood cultures and molecular methods allowed the diagnosis. Most of them required surgery and the associated mortality, in spite of a mean age of 46 years, was high.
Topics: Abiotrophia; Anti-Bacterial Agents; Carnobacteriaceae; Ceftriaxone; Endocarditis; Endocarditis, Bacterial; Female; Humans; Male; Middle Aged; RNA, Ribosomal, 16S; Retrospective Studies; Streptococcus
PubMed: 36137991
DOI: 10.31083/j.fbe1403023 -
Scientific Reports May 2022Undernutrition is a public health challenge in sub-Saharan countries, including Uganda. In a previous randomized controlled trial (RCT) with a nutrition, hygiene and... (Randomized Controlled Trial)
Randomized Controlled Trial
Undernutrition is a public health challenge in sub-Saharan countries, including Uganda. In a previous randomized controlled trial (RCT) with a nutrition, hygiene and stimulation education intervention among mothers of 6 months' old children, we found less caries in the intervention group when the children were 36 months of age. We now examined the effects of (i) the intervention on the microbiota, (ii) microbiota on caries, and (iii) the intervention and microbiota on caries. The original RCT comprised 511 mother/child pairs whereas in the current study we had access to data from 344/511 (67%) children aged 36 months. The saliva microbiota was determined using 16S rRNA gene sequencing. Carious lesions (a proxy for dental health) were identified using close-up intra-oral photographs of the upper front teeth. Statistical models were used to determine host-microbiota associations. The intervention had a significant effect on the microbiota, e.g. an increase in Streptococcus abundance and decreases in Alloprevotella and Tannerella. Significant associations between the microbiota and dental caries were identified: Positive associations of Capnocytophaga and Tannerella suggest that these taxa may be deleterious to dental health while negative associations of Granulicatella, Fusobacterium, and Abiotrophia suggest taxa potentially beneficial or benign contributors to dental health. Based on taxonomic profiles, the effects of the intervention and microbiota on dental health may be independent of one another. Educational interventions with emphasis on nutrition and oral hygiene may provide a feasible strategy to decrease progression of childhood caries in low-resource settings.
Topics: Carnobacteriaceae; Child; Dental Caries; Dental Caries Susceptibility; Female; Humans; Microbiota; RNA, Ribosomal, 16S; Saliva; Streptococcus; Uganda
PubMed: 35552492
DOI: 10.1038/s41598-022-11979-y -
Medicine Dec 2023This study used metagenomic next-generation sequencing (mNGS) technology to explore the changes of the microbial characteristics in the lower respiratory tract in...
This study used metagenomic next-generation sequencing (mNGS) technology to explore the changes of the microbial characteristics in the lower respiratory tract in patients with acute exacerbations of bronchiectasis (noncystic fibrosis) to guide clinical treatment and improve patients' quality of life and prognosis. This prospective study included 54 patients with acute exacerbation and 46 clinically stable patients admitted to the Respiratory and Critical Care Medicine Center of the People's Hospital of Xinjiang Uygur Autonomous Region from January 2020 to July 2022. Sputum was subjected to routine microbiological tests, and bronchoalveolar lavage fluid (BALF) samples were subjected to microbiological tests and mNGS of BALF before empirical antibiotic therapy. Serum inflammatory markers (white blood cell count, interleukin-6, procalcitonin, and C-reactive protein) were measured. In addition, we evaluated the pathogen of mNGS and compared the airway microbiome composition of patients with acute exacerbation and control patients. The mean age of our cohort was 56 ± 15.2 years. Eighty-nine patients had positive results by mNGS. There was a significant difference in the detection of viruses between the groups (χ2 = 6.954, P < .01). The fungal species Candida albicans, Pneumocystis jirovecii, and Aspergillus fumigatus were significantly more common in patients with acute exacerbations (χ2 = 5.98, P = .014). The bacterial species Acinetobacter baumannii, Mycobacterium tuberculosis, Haemophilus influenzae, Haemophilus parahaemolyticus, Abiotrophia defectiva, and Micromonas micros were significantly more prevalent in patients with acute exacerbations (χ2 = 4.065, P = .044). The most common bacterial species isolated from the sputum and BALF samples of patients with acute exacerbation was A. baumannii. Chlamydia psittaci was found in 4 patients. In addition, of 77 patients with negative sputum culture, 66 had positive results by mNGS, demonstrating the increased sensitivity and accuracy of mNGS. Patients with acute exacerbation of bronchiectasis tend to have mixed infections in the lower respiratory tract. The frequency of viruses, fungi, and Mycoplasma was higher in these patients. Our findings suggest that mNGS could be used to identify pathogenic microorganisms in these patients, increasing the effectiveness of antibiotic therapy.
Topics: Humans; Adult; Middle Aged; Aged; Prospective Studies; Quality of Life; Bronchiectasis; Microbiota; Respiratory System; Anti-Bacterial Agents; High-Throughput Nucleotide Sequencing; Sensitivity and Specificity
PubMed: 38115299
DOI: 10.1097/MD.0000000000036519 -
Scientific Reports Apr 2021To explore the changes in oral flora in people with functional dyspepsia (FD). Unstimulated saliva was collected from 21 FD patients diagnosed according to the Rome IV...
To explore the changes in oral flora in people with functional dyspepsia (FD). Unstimulated saliva was collected from 21 FD patients diagnosed according to the Rome IV criteria and from 12 healthy controls (HCs) for 16SrRNA sequencing. The pH of saliva samples and community periodontal index (CPI) were tested. The prevalence of small intestinal bacterial overgrowth (SIBO) was obtained by the methane-and hydrogen-based breath test. At the phylum level, FD patients had a higher relative abundance of Spirochaetes and a lower relative abundance of Fusobacteria, TM7 and Proteobacteria than HCs (p < 0.01). In the saliva, Kingella and Abiotrophia genus levels showed significant changes between the FD and HC groups (p < 0.01). Salivary species level marker Intermedia was significantly different between FD and HC groups (p < 0.01). The oral pH of FD patients was higher than that of HCs (p < 0.01). The mean CPI of the FD group was 1.52 and that of the HC group was 0.17 (p < 0.01). Moreover, 71.4% of the FD group was positive for SIBO. The oral flora of FD patients was different from that of HCs. Spirochaetes, Kingella, Abiotrophia, and Intermedia may be diagnostic indicators of FD.
Topics: Adult; Case-Control Studies; Dyspepsia; Humans; Male; Microbiota; Middle Aged; Prevalence
PubMed: 33850203
DOI: 10.1038/s41598-021-87600-5 -
Frontiers in Cellular and Infection... 2021Supragingival dental plaque samples were collected from 40 Swedish adolescents, including 20 with caries lesions (CAR) and 20 caries-free (CF). Fresh plaque samples were...
Supragingival dental plaque samples were collected from 40 Swedish adolescents, including 20 with caries lesions (CAR) and 20 caries-free (CF). Fresh plaque samples were subjected to an acid tolerance (AT) test where the proportion of bacteria resistant to an acid shock was evaluated through confocal microscopy and live/dead staining, and the metabolites produced were quantified by H Nuclear Magnetic Resonance (H NMR). In addition, DNA was extracted and the 16S rRNA gene was sequenced by Illumina sequencing, in order to characterize bacterial composition in the same samples. There were no significant differences in AT scores between CAR and CF individuals. However, 7 out of the 10 individuals with highest AT scores belonged to the CAR group. Regarding bacterial composition, , and were found at significantly higher levels in CAR individuals (p=0.0085, 0.026 and 0.04 respectively) and and at significantly higher levels in CF individuals (p=0.026 and 0.003). The caries pathogen was found at low frequencies and was absent in 60% of CAR individuals. Random-forest predictive models indicate that at least 4 bacterial species or 9 genera are needed to distinguish CAR from CF adolescents. The metabolomic profile obtained by NMR showed a significant clustering of organic acids with specific bacteria in CAR and/or high AT individuals, being the species with strongest associations. A significant clustering of ethanol and isopropanol with health-associated bacteria such as or was also found. Accordingly, several relationships involving these compounds like the Ethanol : Lactate or Succinate : Lactate ratios were significantly associated to acid tolerance and could be of predictive value for caries risk. We therefore propose that future caries risk studies would benefit from considering not only the use of multiple organisms as potential microbial biomarkers, but also their functional adaptation and metabolic output.
Topics: Actinobacteria; Adolescent; Dental Caries; Dental Plaque; Humans; Metabolomics; Microbiota; RNA, Ribosomal, 16S; Streptococcus mutans
PubMed: 34395316
DOI: 10.3389/fcimb.2021.716493 -
Journal of Translational Medicine Feb 2023Alterations in oral microbiota in patients with systemic lupus erythematosus (SLE) is less evaluated. The aim of this study was to compare the characteristics of the...
BACKGROUND
Alterations in oral microbiota in patients with systemic lupus erythematosus (SLE) is less evaluated. The aim of this study was to compare the characteristics of the oral microbiome in SLE patients and healthy controls, and construct an SLE classifier based on the oral microbiota.
METHODS
We sequenced tongue-coating samples of individuals in treatment-naïve SLE (n = 182) and matched healthy controls (n = 280). We characterized the oral microbiome and constructed a microbial classifier in the derivation cohort and validated the results in the validation cohorts. Furthermore, the oral microbiome of posttreatment SLE (n = 73) was characterized.
RESULTS
The oral microbial diversity of SLE was increased, and the microbial community was different between SLE and healthy controls. The genera Prevotella and Veillonella were enriched, while Streptococcus and Porphyromonas were reduced in SLE. In addition, an increase was noted in 27 predicted microbial functions, while a decrease was noted in 34 other functions. Thirty-nine operational taxonomy units (OTUs) were identified to be related with seven clinical indicators. Two OTUs were identified to construct a classifier, which yielded area under the curve values of 0.9166 (95% CI 0.8848-0.9483, p < 0.0001), 0.8422 (95% CI 0.7687-0.9157, p < 0.0001), and 0.8406 (95% CI 0.7677-0.9135, p < 0.0001) in the derivation, validation, and cross-regional validation groups, respectively. Moreover, as disease activity increased, Abiotrophia and Lactobacillales increased, while Phyllobacterium and unclassified Micrococcusaceae decreased. Finally, nine OTUs were selected to construct a classifier distinguishing posttreatment SLE patients from healthy controls, which achieved a diagnostic efficacy of 0.9942 (95% CI 0.9884-1, p < 0.0001).
CONCLUSIONS
Our study comprehensively characterizes the oral microbiome of SLE and shows the potential of the oral microbiota as a non-invasive diagnostic biomarker in SLE.
Topics: Humans; Microbiota; Lupus Erythematosus, Systemic
PubMed: 36755319
DOI: 10.1186/s12967-023-03892-3 -
Frontiers in Cellular and Infection... 2023Early childhood caries (ECC) is the most common chronic infectious oral disease in preschool children worldwide. It is closely related to the caries activity (CA) of...
Early childhood caries (ECC) is the most common chronic infectious oral disease in preschool children worldwide. It is closely related to the caries activity (CA) of children. However, the distribution characteristics of oral saliva microbiomes in children with different CA are largely underexplored. The aim of this study was to investigate the microbial community in saliva of preschool children with different CA and caries status, and to analyze the difference of microbial community in saliva of children with different CA and its correlation with ECC. Subjects were divided into 3 groups based on the Cariostat caries activity test: Group H, high CA (n=30); Group M, medium CA (n = 30); Group L, low CA (n=30). Questionnaire survey was used to explore the related influencing factors of CA. According to the caries status (on the basis of decayed mising filled teeth), these subjects were divided into caries-free group (dmft=0, n=19), caries-low group (0 < dmft ≤ 4, n=27) and caries-high group (dmft > 4, n=44). Microbial profiles of oral saliva were analyzed using 16S rRNA gene sequencing. There were significant differences in the microbial structure ( < 0.05). and were the biomarkers of both H group and high caries group. The genus and were the biomarkers of both the L group and the low caries group, while the and spp. were significantly enriched in the M group. The area under the ROC curve of the combined application of dmft score, age, frequency of sugary beverage intake, and the genus , , and in screening children with high CA was 0.842. Moreover, function prediction using the MetaCyc database showed that there were significant differences in 11 metabolic pathways of salivary microbiota among different CA groups. Certain bacteria genera in saliva such as and may be helpful in screening children with high CA.
Topics: Humans; Child, Preschool; RNA, Ribosomal, 16S; Bacteria; Actinobacteria; Microbiota; Saliva; Dental Caries
PubMed: 37113131
DOI: 10.3389/fcimb.2023.1141474 -
Cureus Mar 2022A 71-year-old Caucasian male with a past medical history of Charcot-Marie-Tooth disease type 2 presented to our rural hospital for left knee pain, swelling, and...
A 71-year-old Caucasian male with a past medical history of Charcot-Marie-Tooth disease type 2 presented to our rural hospital for left knee pain, swelling, and difficulty walking. The patient had prior bilateral total knee replacements with a subsequent left knee revision due to infection. Joint aspiration was culture-positive and 16S recombinant DNA (rDNA) sequence positive for . The patient underwent a left total knee extraction with a temporary antibiotic spacer insertion. On discharge, the patient received an initial six weeks of ceftriaxone 2g IV. At the outpatient six-week follow-up, the patient was cleared of the infection. However, later complications and a subsequent infection arose.
PubMed: 35399397
DOI: 10.7759/cureus.22801