scholarly journals 1018. Bacterial Bioburden Characterization of Infected Diabetic Foot Ulcers in Hospitalized Patients in Association with Clinical Outcomes: Traditional Cultures vs. Molecular Sequencing Methods

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S599-S600
Author(s):  
Hadar Mudrik-Zohar ◽  
Shaqed Carasso ◽  
Tal Gefen ◽  
Anat Zalmanovich ◽  
Michal Katzir ◽  
...  
Keyword(s):  
16S Rrna ◽  
Clinical Outcomes ◽  
16S Rrna Sequencing ◽  
Gram Negative Bacteria ◽  
Metagenomic Sequencing ◽  
Gram Negative ◽  
Rrna Sequencing ◽  
Traditional Cultures ◽  
Molecular Sequencing ◽  
Toe Amputation

Abstract Background Infected diabetic foot ulcers (IDFU) are a major complication of diabetes mellitus. These potentially limb-threatening ulcers are challenging to treat due to the impairment of wound healing in diabetic patients and the complex microbial environment characterizing these ulcers. Our aim was to analyze the microbiome of IDFU in association with clinical outcomes. Methods Wound biopsies from IDFU were obtained from hospitalized patients and were analyzed using traditional microbiology cultures, 16S rRNA sequencing and shotgun metagenomic sequencing. Patients’ characteristics, culture-based results and sequencing data were analyzed in association with clinical outcomes. Study Design Results 31 patients were enrolled. Significantly more anaerobic and Gram-negative bacteria were detected with sequencing methods compared to conventional cultures (59% and 76% were anaerobes according to 16SrRNA and metagenomic respectively vs. 26% in cultures, p=0.001, and 79%, 59% and 54% were Gram negative bacteria respectively, p< 0.001). Culture-based results showed that Staphylococcus aureus was more prevalent among patients who were conservatively treated (p=0.048). In metagenomic analysis the Bacteroides genus was more prevalent among patients who underwent toe amputation (p< 0.001). Analysis of metagenomic-based functional data showed that antibiotic resistance genes and genes related to biofilm production and to bacterial virulent factors were more prevalent in IDFU that resulted in toe amputation (p< 0.001). Occurrences and mean relative abundances of the most prevalent bacteria of IDFU Comparison between [A] traditional cultures, 16S rRNA sequencing and metagenomic sequencing results (genera level - 12 samples) [B] traditional cultures and metagenomic sequencing results (species level – 30 samples) [C] traditional cultures and 16S rRNA sequencing results (genera level - 30 samples) CUL – cultures; 16S - 16S rRNA sequencing; MTG – metagenomic sequencing Bacteroides genus association with toe amputation Bacteroides genera was more common among samples of patients who underwent toe amputation compared with samples of patients who were conservatively treated (p < 0.001). Species level analysis showed that Bacteroides fragilis and Bacteroides xylanisolvens predominated IDFU of patients who underwent toe amputation (p=0.04, p=0.002 respectively). No – conservative treatment; Yes – toe amputation. Functional genes differentiating patients who underwent toe amputation from conservatively treated Yellow stars – indicate genes that were associated with bacterial virulent factors, biofilm formation and resistant mechanisms – all were more prevalent in patients who underwent toe amputation (with p values<> Conclusion Molecular sequencing tools uncover the complex biodiversity of IDFU and emphasize the high prevalence of anaerobes and Gram-negative bacteria in these ulcers. Furthermore, sequencing results highlighted the possible association between certain genera, species, and bacterial functional genes to clinical outcomes Disclosures Yossi Paitan, PhD, Ilex Medical Ltd (Employee, Other Financial or Material Support, As of 01.01.2021 I am the Laboratories Manager of Ilex Labs)

scholarly journals Anaerobiospirillum succiniciproducens bacteraemia in a patient with acute lymphoblastic leukaemia

2009 ◽  
Vol 58 (1) ◽  
pp. 142-143 ◽  
Author(s):  
M. N. Fadzilah ◽  
L. J. Faizatul ◽  
M. S. Hasibah ◽  
I.-C. Sam ◽  
M. Kahar Bador ◽  
...  
Keyword(s):  
16S Rrna ◽  
Acute Lymphoblastic Leukaemia ◽  
Lymphoblastic Leukaemia ◽  
Anaerobic Bacterium ◽  
16S Rrna Sequencing ◽  
Gram Negative ◽  
Anaerobiospirillum Succiniciproducens ◽  
Rrna Sequencing ◽  
Neutropenic Episode

A 17-year-old man with acute lymphoblastic leukaemia had fever and diarrhoea during a febrile neutropenic episode. A spiral-shaped, Gram-negative anaerobic bacterium was isolated from blood, and confirmed as Anaerobiospirillum succiniciproducens by 16S rRNA sequencing. The patient responded to imipenem.

scholarly journals Repeated Courses of Orally Administered Fecal Microbiota Transplantation for the Treatment of Steroid Resistant and Steroid Dependent Intestinal Acute Graft Vs. Host Disease: A Pilot Study (NCT 03214289)

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2121-2121 ◽  
Author(s):  
Roni Shouval ◽  
Ilan Youngster ◽  
Mika Geva ◽  
Adi Eshel ◽  
Ivetta Danylesko ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Diversity ◽  
Stool Sample ◽  
Fecal Microbiota Transplantation ◽  
Complete Response ◽  
Fecal Microbiota ◽  
16S Rrna Sequencing ◽  
Metagenomic Sequencing ◽  
Steroid Dependent ◽  
Rrna Sequencing

Abstract Background: Steroid-resistant (SR) intestinal acute graft versus host disease (aGVHD) is a devastating complication of allogeneic hematopoietic stem cell transplantation. Preliminary reports suggest that fecal microbiota transplantation (FMT) administered through a nasogastric tube or colonoscopy may be an effective treatment. We report the results of a single-arm pilot study (NCT 03214289) using FMT in capsules to treat SR or steroid dependent (SD) intestinal aGVHD. Methods: The primary outcome was the occurrence of severe adverse events (SAEs) at 28 days post last FMT course. Secondary outcomes included GVHD response. Complete response (CR) was defined as resolution of gastrointestinal symptoms or reduction of steroid dose to 5 mg of prednisone. Partial response was defined as a decrease in severity of GVHD by at least one stage or a ≥40% reduction in steroid dose. Patients were eligible if they had SR or SD gut aGVHD without active infection or neutropenia. Per-protocol, participants received a course of 30 frozen capsules of fecal matter over two consecutive days. FMT courses could be repeated from the same or a different donor, at the treating physician's discretion. Capsules are produced from healthy unrelated donors who underwent vigorous screening. They are taken orally and are flavorless and odor-free. To characterize the impact of the FMT on the gut microbiota, stool samples of recipients were serially collected and underwent 16s rRNA sequencing. Results: To date, we have enrolled 7 patients with intestinal aGVHD (6 SR, 1 SD) (Table). The median dose of methylprednisolone (MP) was 1 mg/kg (interquartile range [IQR] 0.8-1.3 mg/kg). FMT was administered at a median of 39 days (IQR 21-58 days) from aGVHD diagnosis. A total of 15 courses of FMT were given. Patients received a range of 1-3 FMT courses (median 2). The capsules were well tolerated. Patient #1 developed Enterococcus Faecium bacteremia 2 days following the second FMT. To track the source of bacteremia, we performed targeted metagenomic sequencing. The enterococcus strain from the blood culture was identified in the recipient's pre-FMT stool sample but not in the FMT inoculum (i.e., capsule), confirming that the bacteremia was not an FMT complication. Similarly, patient #6 developed Pseudomonas aeruginosa bacteremia 3 days after the 2nd FMT. 16s rRNA sequencing of the donor capsule failed to demonstrate Pseudomonas taxa. No other SAEs suspected to be related to the FMT were observed. Two patients achieved a CR with complete resolution of GVHD symptoms. Patient #6 had a partial improvement following the 1st FMT, with a reduction of MP from 2 mg/kg to 1.3 mg/kg. Three days after the 2nd FMT, she developed fatal pseudomonas bacteremia, not related to the FMT as detailed above. At last follow-up (median 61 days, IQR 40-99), 3/7 patients were alive. Three patients died from consequences of active GVHD, while one patients who responded to FMT and was free of GVHD, succumbed to an invasive Aspergillus infection of the brain. 16s rRNA sequencing of stool samples revealed bacterial domination (i.e., occupation of at least 40% of the microbiota by a single predominating taxon) of Escherichia(E) coli in four patients before FMT, with a major reduction following therapy. FMT was associated with the introduction of new bacteria and an increase in bacterial diversity in the recipient's stool (Figure). Conclusions: We demonstrate for the first time the utility of fecal microbiota transplantation in orally administered capsules for the treatment of severe intestinal acute GVHD. The capsules were well tolerated and safe. Metagenomic sequencing proved that a bacterial infection following FMT was not related to the procedure. Sequencing of the stool sample revealed bacterial domination with E.coli in 4/7 patients prior to the first FMT. Following FMT, bacterial diversity increased. Finally, 2/7 patients attained a complete response following therapy, suggesting a potential role of FMT in patient management. Figure. (A) Heatmap of operational taxonomics units (OTU). Each column marks a sequenced stool sample at a specific time point and rows individual taxas. The color code indicates relative abundance. Dotted lines represent an FMT course. Before FMT all patients, aside from patient #6, had markedly reduced diversity, with enrichment of OTUs following treatment. (B). Change of bacterial diversity, measured by the Shanon diversity index before and after FMTs. Figure. Figure. Disclosures No relevant conflicts of interest to declare.

scholarly journals Gut Microbiota as Prognosis Markers for Patients with HBV-Related Acute-on-Chronic Liver Failure

2020 ◽  
Author(s):  
Ke Wang ◽  
Zhao Zhang ◽  
Zhi-Shuo Mo ◽  
Xiao-Hua Yang ◽  
Bing-Liang Lin ◽  
...  
Keyword(s):  
Hepatitis B ◽  
16S Rrna ◽  
Gut Microbiota ◽  
Liver Failure ◽  
Chronic Liver ◽  
16S Rrna Sequencing ◽  
Metagenomic Sequencing ◽  
Healthy Individuals ◽  
Chronic Liver Failure ◽  
Rrna Sequencing

Abstract Background The gut microbiota in the hepatitis B virus related acute-on-chronic liver failure (HBV-ACLF) is poorly defined. We aim to uncover the characteristics of the gut microbiota in HBV-ACLF and in other HBV associated pathologies. Methods We analyzed the gut microbiome in patients with HBV-ACLF or other HBV associated pathologies and healthy individuals by 16S rRNA sequencing and metagenomic sequencing of fecal samples. 212 patients with HBV-ACLF, 252 with chronic hepatitis B (CHB), 162 with HBV-associated cirrhosis (HBV-LC) and 877 healthy individuals were recruited for the study. CHB and HBV-LC patients are grouped as HBV-Other. Results We discovered striking differences in the microbiome diversity between the HBV-ACLF, HBV-Other and healthy groups using 16S rRNA sequencing. The ratio of cocci to bacilli was significantly elevated in the HBV-ACLF group compared with healthy group. Further analysis within the HBV-ACLF group identified 52 genera showing distinct richness within the group where Enterococcus was enriched in the progression group whilst Faecalibacterium was enriched in the regression group. Metagenomic sequencing validated these findings and further uncovered an enrichment of Lactobacillus casei paracasei in progression group, while Alistipes senegalensis, Faecalibacterium prausnitzii and Parabacteroides merdae dominated the regression group. Importantly, our analysis revealed that there was a rapid increase of Enterococcus faecium during the progression of HBV-ACLF. Conclusions The gut microbiota displayed distinct composition at different phases of HBV-ACLF. High abundance of Enterococcus is associated with progression while that of Faecalibacterium is associated with regression of HBV-ACLF. Therefore the microbiota features hold promising potential as prognostic markers for HBV-ACLF.

scholarly journals Uncovering Symbionts Across the Psyllid Tree of Life and the Discovery of a New Liberibacter Species, “Candidatus” Liberibacter capsica

2021 ◽  
Vol 12 ◽  
Author(s):  
Younghwan Kwak ◽  
Penglin Sun ◽  
Venkata RamaSravani Meduri ◽  
Diana M. Percy ◽  
Kerry E. Mauck ◽  
...  
Keyword(s):  
16S Rrna ◽  
Plant Pathogens ◽  
Severe Disease ◽  
16S Rrna Sequencing ◽  
Metagenomic Sequencing ◽  
Rrna Sequencing ◽  
Potential Pathogen ◽  
Sap Feeding ◽  
Phylogenomic Analyses ◽  
Clade 1

Sap-feeding insects in the order Hemiptera associate with obligate endosymbionts that are required for survival and facultative endosymbionts that can potentially modify resistance to stress, enemies, development, and reproduction. In the superfamily Psylloidea, the jumping plant lice (psyllids), less is known about the diversity and prevalence of their endosymbionts compared to other sap-feeding pests such as aphids (Aphididae). To address this knowledge gap, using 16S rRNA sequencing we identify symbionts across divergent psyllid host lineages from around the world. Taking advantage of a new comprehensive phylogenomic analyses of Psylloidea, we included psyllid samples from 44 species of 35 genera of five families, collected from 11 international locations for this study. Across psyllid lineages, a total of 91 OTUs were recovered, predominantly of the Enterobacteriaceae (68%). The diversity of endosymbionts harbored by each psyllid species was low with an average of approximately 3 OTUs. Two clades of endosymbionts (clade 1 and 2), belonging to Enterobacteriaceae, were identified that appear to be long term endosymbionts of the psyllid families Triozidae and Psyllidae, respectively. We also conducted high throughput metagenomic sequencing on three Ca. Liberibacter infected psyllid species (Russelliana capsici, Trichochermes walkeri, and Macrohomotoma gladiata), initially identified from 16S rRNA sequencing, to obtain more genomic information on these putative Liberibacter plant pathogens. The phylogenomic analyses from these data identified a new Ca. Liberibacter species, Candidatus Liberibacter capsica, that is a potential pathogen of solanaceous crops. This new species shares a distant ancestor with Ca. L. americanus, which occurs in the same range as R. capsici in South America. We also detected the first association between a psyllid specializing on woody hosts and the Liberibacter species Ca. L. psyllaurous, which is a globally distributed pathogen of herbaceous crop hosts in the Solanaceae. Finally, we detected a potential association between a psyllid pest of figs (M. gladiata) and a Ca. Liberibacter related to Ca. L. asiaticus, which causes severe disease in citrus. Our findings reveal a wider diversity of associations between facultative symbionts and psyllids than previously reported and suggest numerous avenues for future work to clarify novel associations of ecological, evolutionary, and pathogenic interest.

scholarly journals Assessment of the Spoilage Microbiota during Refrigerated (4 °C) Vacuum-Packed Storage of Fresh Greek Anthotyros Whey Cheese without or with a Crude Enterocin A-B-P-Containing Extract

Foods ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2946
Author(s):  
Nikoletta Sameli ◽  
Eleni Sioziou ◽  
Loulouda Bosnea ◽  
Athanasia Kakouri ◽  
John Samelis
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
16S Rrna ◽  
Leuconostoc Mesenteroides ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Spoilage Bacteria ◽  
Rrna Sequencing ◽  
Leuconostoc Lactis ◽  
Enterocin A

Although fresh whey cheeses are prone to rapid deterioration, mainly by psychrotrophic Gram-negative bacteria and lactic acid bacteria (LAB), data on the specific spoilage species in traditional Greek whey cheeses are scarce. Therefore, this study quantified growth and characterized the primary spoilage bacteria in fresh Anthotyros whey cheeses stored at 4 °C in a vacuum for 40 days, without or with an added 5% (v/w) of an enterocin A-B-P crude extract (CEntE). Psychrotrophic Pseudomonas spp., Aeromonas spp., Hafnia spp. and Serratia spp. grew faster than LAB during early storage. However, LAB outgrew the Gram-negative bacteria and prevailed by mid to late storage in all cheese batches, causing a strong or milder batch-dependent natural acidification. Two major non-slime-producing and two minor biotypes of Leuconostoc-like bacteria, all identified as Leuconostoc mesenteroides by 16S rRNA sequencing, dominated the LAB association (76.7%), which also included four subdominant Carnobacterium maltaromaticum biotypes (10.9%), one Leuconostoc lactis biotype (3.3%) and few Lactococcus (1.6%), mesophilic Lactobacillus (0.8%) and Enterococcus (0.8%). Growth and distribution of LAB and Gram-negative species were strongly batch-dependent and plant-dependent. The CEntE neither retarded growth nor altered the whey cheese spoilage association but enhanced LAB growth and the declines of Gram-negative bacteria by late storage.

scholarly journals Salivary Microbiome in Adenoid Cystic Carcinoma Detected by 16S rRNA Sequencing and Shotgun Metagenomics

2021 ◽  
Vol 11 ◽  
Author(s):  
Qian Jiang ◽  
Xing Liu ◽  
Qifen Yang ◽  
Liang Chen ◽  
Deqin Yang
Keyword(s):  
16S Rrna ◽  
Adenoid Cystic Carcinoma ◽  
16S Rrna Sequencing ◽  
Metagenomic Sequencing ◽  
Healthy Controls ◽  
Human Beings ◽  
Shotgun Metagenomics ◽  
Adenoid Cystic ◽  
Significant Difference ◽  
Rrna Sequencing

Microorganisms are confirmed to be closely related to the occurrence and development of cancers in human beings. However, there has been no published report detailing relationships between the oral microbiota and salivary adenoid cystic carcinoma (SACC). In this study, unstimulated saliva was collected from 13 SACC patients and 10 healthy controls. The microbial diversities, compositions and functions were comprehensively analyzed after 16S rRNA sequencing and whole-genome shotgun metagenomic sequencing. The alpha diversity showed no significant difference between SACC patients and healthy controls, while beta diversity showed a separation trend. The SACC patients showed higher abundances of Streptococcus and Rothia, while Prevotella and Alloprevotella were more abundant in healthy controls. The prevalent KEGG pathways, carbohydrate-active enzymes, antibiotic resistances and virulence factors as well as the biomarkers in SACC were determined by functional gene analysis. Our study preliminarily investigated the salivary microbiome of SACC patients compared with healthy controls and might be the basis for further studies on novel diagnostic and treatment strategies.

Haemophilus parainfluenzaeInfective Endocarditis Diagnosed by Direct 16S rRNA Sequencing of Vegetation

2012 ◽  
Vol 2 (2) ◽  
pp. 111
Author(s):  
Sung-Hee Oh ◽  
Min-Chul Cho ◽  
Jae-Wook Kim ◽  
Dongheui An ◽  
Mun-Hui Jeong ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Sequencing ◽  
Rrna Sequencing

Full-length versus short amplicon 16S rRNA sequencing: benefits, drawbacks and risks

2020 ◽  
Author(s):  
Isabel Abellan-Schneyder ◽  
Andrea Janina Bayer ◽  
Sandra Reitmeier ◽  
Klaus Neuhaus
Keyword(s):  
16S Rrna ◽  
Full Length ◽  
16S Rrna Sequencing ◽  
Rrna Sequencing

Full-length versus short amplicon 16S rRNA sequencing: benefits, drawbacks and risks

2020 ◽  
Author(s):  
Andrea Janina Bayer ◽  
Sandra Reitmeier ◽  
Klaus Neuhaus ◽  
Isabel Abellan-Schneyder
Keyword(s):  
16S Rrna ◽  
Full Length ◽  
16S Rrna Sequencing ◽  
Rrna Sequencing

scholarly journals Phenotypic and phylogenetic characterization of Lactobacillus species isolated from traditional Lighvan cheese

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Haleh Forouhandeh ◽  
Sepideh Zununi Vahed ◽  
Hossein Ahangari ◽  
Vahideh Tarhriz ◽  
Mohammad Saeid Hejazi
Keyword(s):  
16S Rrna ◽  
Random Amplified Polymorphic Dna ◽  
Bacterial Species ◽  
16S Rrna Sequencing ◽  
Lactobacillus Species ◽  
Culture Methods ◽  
Phylogenetic Characterization ◽  
Rrna Sequencing ◽  
Specific Culture ◽  
Lighvan Cheese

Abstract Lighvan cheese (Lighvan panir) is among the most famous traditional cheese in Iran for its desired aroma and flavor. Undoubtedly, the lactic acid bacteria especially the genus Lactobacillus are the critical factors in developing the aroma, flavor, and texture in Lighvan cheese. In this study, the Lactobacillus population of the main Lighvan cheese was investigated. The Lactobacillus of the main Lighvan cheese was isolated using specific culture methods according to previously published Guidelines. Then, the phylogenetic features were investigated and the phenotypic characteristics were examined using specific culture methods. Twenty-eight Gram-positive bacterial species were identified belonged to the genus Lactobacillus. According to the same sequences as each other, three groups (A, B, and C) of isolates were categorized with a high degree of similarity to L. fermentum (100%) and L. casei group (L. casei, L. paracasei, and L. rhamnosus) (99.0 to 100%). Random amplified polymorphic DNA (RAPD) fingerprint analysis manifested the presence of three clusters that were dominant in traditional Lighvan cheese. Cluster І was divided into 4 sub-clusters. By the result of carbohydrate fermentation pattern and 16S rRNA sequencing, isolates were identified as L. rhamnosus. The isolates in clusters II and III represented L. paracasei and L. fermentum, respectively as they were identified by 16S rRNA sequencing and fermented carbohydrate patterns. Our result indicated that the specific aroma and flavor of traditional Lighvan cheese can be related to its Lactobacillus population including L. fermentum, L. casei, L. paracasei, and L. rhamnosus. Graphical abstract

Sign in / Sign up

Export Citation Format

Share Document