scholarly journals Next-Generation Sequencing for Pathogen Identification in Infected Foot Ulcers

2020 ◽  
Vol 5 (4) ◽  
pp. 2473011420S0002
Author(s):  
Yoonjung Choi ◽  
Irvin Oh
Keyword(s):  
Next Generation Sequencing ◽  
False Positive ◽  
Bacterial Genome ◽  
Rrna Gene ◽  
Next Generation ◽  
Antibiotic Resistant ◽  
Streptococcus Species ◽  
Resistant Genes ◽  
Standard Culture ◽  
Generation Sequencing

Category: Other Introduction/Purpose: Foot infections are often polymicrobial with diverse microbiomes. Accurate identification of the main pathogen in diabetic foot ulcer (DFU) remain challenging due to contamination or negative cultures often leading to ineffective post-surgical antibiotic treatment. Application of molecular diagnostics, such as next generation sequencing (NGS) has been explored as an alternative to standard culture in orthopaedic infections. NGS is highly sensitive and detects an entire bacterial genome along with pharmacologic resistant genes in a given sample. We sought to investigate the potential use of NGS for accurate diagnosis and quantification of various species in infected DFU. We hypothesize that NGS will provide a more accurate means of diagnosing and profiling microorganisms in infected DFU compared to the standard culture method. Methods: We investigated 30 infected DFU patients who underwent surgical treatment by a single academic orthopaedic surgeon from October 2018 to September 2019. The average age of the patient was 60.4 (range 33-82) years-old. Surgical procedures performed were irrigation and debridement (12), toe or ray amputation (13), calcanectomies (4), and below-knee amputation (1). Infected bone specimens were obtained intraoperatively and processed for standard culture and NGS. Quantitative PCR was performed to determine the bacterial burden present in the sample. DNA was amplified by PCR from a highly conserved region of the rRNA gene in the bacteria (16S rRNA). Once a high level of DNA was generated and determined, it was compared against NIH GenBank database. Concordance between the standard culture and NGS was assessed. Results: In 28 of 29 patients, pathogens were identified by both NGS and culture, with complete consistency of organisms in 13 cases (concordance rate: 43.3%). NGS provided relative quantitative measures and the presence of antibiotic resistant genes for each pathogen. In NGS, Anaerococcus species (79.3%) was the most common organism, followed by Streptococcus species (44.8%), Prevotella species (44.8%), Finegoldia magna (44.8%). In culture, S. aureus (58.6%) was the most common, followed by Streptococcus species (34.5%), coagulase-negative Staphylococci (24.1%), Corynebacterium species (20.7%). On average, NGS revealed 5.1 (1-11) number of pathogens, whereas standard culture revealed 2.6 (1-6) pathogens in a given sample. NGS identified 2 cases with false positive standard culture and detected antibiotic resistant organisms in 15 specimens. Conclusion: NGS is an emerging method of microbial identification in orthopedic infection. It is particularly helpful in profiling diverse microbes in polymicrobial infected DFU. It can identify major pathogens and may correct false positive or false negative culture. NGS may allow a faster invitation of postoperative targeted antibiotic therapy. [Table: see text]

scholarly journals 1554. Epidemiology of Adult Bacterial Hand Infections at Two Urban Hospitals

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S777-S778
Author(s):  
Arsheena Yassin ◽  
Christine Stavropoulos ◽  
Krystina L Woods ◽  
Jiashan Xu ◽  
Justin Carale ◽  
...  
Keyword(s):  
New York ◽  
Staphylococcus Aureus ◽  
Antibiotic Regimen ◽  
Gram Positive ◽  
Gram Negative ◽  
Streptococcus Species ◽  
Urban Hospitals ◽  
Haemophilus Parainfluenzae ◽  
Empiric Antibiotic ◽  
Gram Negative Organisms

Abstract Background Hand infections represent a major source of morbidity, which can result in hand stiffness and amputation. Early appropriate empiric antibiotic regimen may reduce the associated morbidity, hence the importance to examine local epidemiology. The aim of this study was to define the current epidemiology of adult hand infections at two urban hospitals in New York City. Methods We performed a double center, retrospective study of adult patients hospitalized from March 2018 to May 2020. Patients with positive cultures associated with the hand infections were included. Retrospectively, 100 patients were reviewed. Data on baseline demographic, clinical, surgical, microbiology, and treatment parameters were collected. Results Of the 100 patients, 76% were male, with median age of 47.5 years (35, 58.25) and average C-reactive protein (CRP) of 50.66 mg/L (± 64.64) on admission (see Table 1). Previous hospitalization within 1 year (38%), previous surgical procedures (39%) and recent IV medication use (26%) were common. 130 bacterial isolates were identified (see Table 2). The most frequent organisms were Gram-positive, with Methicillin susceptible Staphylococcus aureus (MSSA, 25.38%), Streptococcus species (20.08%), and Methicillin resistant Staphylococcus aureus (MRSA, 15.38%) being the most common. Gram-negative organisms were infrequent, with Haemophilus parainfluenzae (3.85%), Enterobacter cloacae (3.85) and Pseudomonas aeruginosa (3.08%) being the most prevalent. Of the 100 patients, 27% had polymicrobial infections, associated with trauma (6%), illicit IV use (6%) and unknown (7%) etiologies. Table 1: Baseline demographics and co-morbid conditions Table 2: Types and numbers of organisms in relation to etiologies Conclusion Within our population, the most common organisms associated with hand infections were Gram-positive, with Staphylococcus aureus and Streptococcus species being the most prevalent. Gram-negative pathogens were infrequently isolated. The results within this study can provide guidance to clinicians on assessing the appropriate empiric antibiotic regimen in patients with hand infections, and can serve as a basis for further studies identifying risk factors associated with isolation of organisms associated with hand infections. Disclosures All Authors: No reported disclosures

scholarly journals Gut Streptococcus species affect persistence and severity of atopic dermatitis during infancy

2018 ◽  
Vol 141 (2) ◽  
pp. AB232
Author(s):  
Park Yoon Mee ◽  
Mi-Jin Kang ◽  
So-Yeon Lee ◽  
Ji-Sun Yoon ◽  
Sungsu Jung ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Streptococcus Species

scholarly journals Synthesis of the lipoteichoic acid of the Streptococcus species DSM 8747

2010 ◽  
Vol 18 (11) ◽  
pp. 3696-3702 ◽  
Author(s):  
Yan Qiao ◽  
Buko Lindner ◽  
Ulrich Zähringer ◽  
Peter Truog ◽  
Richard R. Schmidt
Keyword(s):  
Lipoteichoic Acid ◽  
Streptococcus Species

Streptococcus Species

2003 ◽  
Author(s):  
Barry Gray ◽  
Sylvie Rodriguez Arnavielhe
Keyword(s):  
Streptococcus Species

scholarly journals Clinical Profile and Management of Peritonsillar Abscess in a Sub Saharan Africa

2020 ◽  
Vol 5 (01) ◽  
Author(s):  
Waheed Atilade Adegbiji ◽  
Gabriel Toye Olajide ◽  
Aluko AbdulAkeem Adebayo
Keyword(s):  
Clinical Findings ◽  
Peritonsillar Abscess ◽  
Clinical Profile ◽  
Sub Saharan Africa ◽  
Prehospital Treatment ◽  
Female Ratio ◽  
Streptococcus Species ◽  
Staphyloccocus Aureus ◽  
Sub Saharan ◽  
Nose And Throat

Background: Peritonsillar abscess is a common pathology that presents to an otolaryngologist with poor documentation especially in developing countries. The aim of this study was to describe the clinical profile and management of peritonsillar abscess in our practice. Material and Method: This was a retrospective study of patients presenting to our Ear, Nose and Throat facility with diagnosis of peritonsillar abscess. Information obtained includes detailed demographic characteristics, clinical findings and management of the patients. All obtained data were collated, entered into computer system and analyzed using SPSS version 18.0. Results: Prevalence of peritonsillar abscess was 0.2%. There were 38.9% males and male to female ratio was 1:1.6. Duration of illness at presentation with more than 1 week was 75.9% and single episode occurred in 85.2%. Right peritonsillar abscess accounted for 66.7% and aspirated pus of more than 5 ml was recorded in 48.1%. Majority (87.0%) of the patients was referred and 42.6% of such referral is by family physician. Patients seen in ear, nose and throat outpatient clinic were 83.3%. Common symptoms at presentation were fever, sore throat, odynophagia and otalgia in 100%, 94.4%, 90.7% and 59.3% respectively. All the patients (100%) had enlarged tonsils and with deviated uvula on clinical examination followed by 98.1% exudate on the tonsils and 31.5% trismus. Test aspirate confirmed peritonsillar abscess in 68.5% and all revealed growth of bacteria. Common isolated bacteria were 35.2% Streptococcus species and 11.1% Staphyloccocus aureus. Isolated Streptococcus species and Staphylococcus aureus had 100% sensitivity to cefuroxime, gentamicin, azithromycin, ceftazidine, Amoxicillin and Streptomycin. Prior prehospital treatment was received by 81.5% patients. Hospital treatments were surgical intervention and medical treatment in 90.7% and 100% respectively. Recurrences occurred in 3.7% during followed up. Conclusion: Peritonsillar abscess are common disorder with female preponderance in this study. The prevalence recorded in this study was 0.2%. It usually mimic other causes of fever hence eye index of suspicion is essential. Surgical treatment remains the effective mode of management in our study.

scholarly journals Pneumonia Outbreak Associated with Group A Streptococcus Species at a Military Training Facility

2005 ◽  
Vol 40 (4) ◽  
pp. 511-518 ◽  
Author(s):  
N. F. Crum ◽  
K. L. Russell ◽  
E. L. Kaplan ◽  
M. R. Wallace ◽  
J. Wu ◽  
...  
Keyword(s):  
Group A Streptococcus ◽  
Military Training ◽  
Streptococcus Species ◽  
Training Facility ◽  
Group A

Đặc điểm vi sinh và điều trị kháng sinh trong bệnh lý áp xe trung thất do thủng thực quản trong cấp cứu tại Bệnh viện Việt Đức

2021 ◽  
Vol 16 (2) ◽  
Author(s):  
Phạm Vũ Hùng ◽  
Nguyễn Đức Chính ◽  
Trần Tuấn Anh ◽  
Nguyễn Minh Ky ◽  
Đào Văn Hiếu ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Klebsiella Pneumoniae ◽  
Enterococcus Faecalis ◽  
Type I ◽  
Acinetobacter Baumanii ◽  
Streptococcus Species

Mục tiêu: Tìm hiểu đặc điểm vi sinh được phân lập và việc điều trị kháng sinh. Đối tượng và phương pháp: Nghiên cứu tiến cứu các trường hợp áp xe trung thất do thủng thực quản được điều trị tại Bệnh viện Việt Đức từ tháng 1/2016 đến tháng 3/2019, bao gồm các trường hợp tử vong. Chẩn đoán áp xe trung thất theo tiêu chuẩn của Estrera (1983). Kết quả: Tổng số 40 ca, tỷ lệ nam: nữ = 4,7:1, tuổi từ 36 - 60 tuổi chiếm 60%. Chấn thương: 70%, bệnh lý: 30%. Do hóc xương chiếm 88,5%. Thủng ở 1/3 trên thực quản là 57,5%, 1/3 giữa thực quản là 22,5%, và 1/3 dưới thực quản là 20%. Type I chiếm 55%, type IIb chiếm 45%, không có type Iia. Vi sinh: 24/40 (60%) phân lập được vi khuẩn, 100% kết hợp cả ái khí và kỵ khí, trong đó Gram (+) ái khí chiếm đa số 75,9%, nhiều nhất là Streptococcus species 37,5%, Enterococcus faecalis 20,8%, Acinetobacter baumanii 20,8%; Gram (-) ái khí chiếm 17,2%, nhiều nhất là Klebsiella pneumoniae chiếm 12,5%, Pseudomonas aeruginosa 12%; Kỵ khí Gram (+): Peptostreptococcus chiếm 8,3%, kháng sinh: Cephalosporin (thế hệ 3) và carbapenem phù hợp kết quả kháng sinh đồ, kết hợp 100% với metronidazole. Kết quả: Biến chứng 7 (17,5%) trường hợp, tử vong: 3 trường hợp (7,5%) do chảy máu, suy đa tạng. Kết luận: Nghiên cứu cho thấy vi khuẩn kết hợp ái khí và kỵ khí chiếm 100%, ái khí Gram (+) chiếm đa số trong đó nhiều nhất là Streptococcus species, Gram (-) ái khí nhiều nhất là Klebsiella pneumoniae và Pseudomonas aeruginosa; kỵ khí Gram (+) duy nhất Peptostreptococcus. Kháng sinh dùng theo kinh nghiệm với loại mạnh, phổ rộng là cephalosporin (thế hệ 3) và carbapenem phù hợp kết quả kháng sinh đồ, kết hợp metronidazole.

scholarly journals Microbial Diversity Associated with Gwell, a Traditional French Mesophilic Fermented Milk Inoculated with a Natural Starter

2020 ◽  
Vol 8 (7) ◽  
pp. 982
Author(s):  
Lucas von Gastrow ◽  
Marie-Noëlle Madec ◽  
Victoria Chuat ◽  
Stanislas Lubac ◽  
Clémence Morinière ◽  
...  
Keyword(s):  
Microbial Community ◽  
Fermentation Process ◽  
Fermented Milk ◽  
Geotrichum Candidum ◽  
Microbial Composition ◽  
Streptococcus Species ◽  
Culture Independent ◽  
History Of ◽  
Points Of View ◽  
Culture Dependent

Gwell is a traditional mesophilic fermented milk from the Brittany region of France. The fermentation process is based on a back-slopping method. The starter is made from a portion of the previous Gwell production, so that Gwell is both the starter and final product for consumption. In a participatory research framework involving 13 producers, Gwell was characterized from both the sensory and microbial points of view and was defined by its tangy taste and smooth and dense texture. The microbial community of typical Gwell samples was studied using both culture-dependent and culture-independent approaches. Lactococcus lactis was systematically identified in Gwell, being represented by both subspecies cremoris and lactis biovar diacetylactis which were always associated. Geotrichum candidum was also found in all the samples. The microbial composition was confirmed by 16S and ITS2 metabarcoding analysis. We were able to reconstruct the history of Gwell exchanges between producers, and thus obtained the genealogy of the samples we analyzed. The samples clustered in two groups which were also differentiated by their microbial composition, and notably by the presence or absence of yeasts identified as Kazachstania servazii and Streptococcus species.

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