Conjunctival Sac Microbiome in Infectious Conjunctivitis

Abstract Background To determine the conjunctival bacterial community among the infectious conjunctivitis cases attending the outpatient clinic of Khanh Hoa General Hospital in Nha Trang, Vietnam from October 2016 through December 2017. Of all, 50 randomly selected samples using a computer generated random number list were included for microbiome identification. Conjunctival swabs were collected and tested using conventional culture, PCR, and 16S ribosomal RNA sequencing. Results The study included randomly selected 47 patients. More than 98% of all DNA reads represented five bacterial phyla. Three of these phyla constitute 92% of all sequences [Firmicutes (35%), Actinobacteria (31%), and Proteobacteria (26%)]. At the genus level, there were twelve common genera constituted about 61% of all the sequence reads. Seven of those genera were common [Streptococcus (10%), Cutibacterium (10%), Staphylococcus (7%), Nocardioides (7%), Corynebacterium 1 (5%), Anoxybacillus (5%), and Acinetobacter (5%)], which encompassed 49% of all reads. As for diversity analysis, there was no difference in PERMANOVA analysis (Unweighted UniFrac) for sex (P = 0.087), chemosis (P = 0.064) and unclassified eyedrops (P = 0.431). There was no difference in PERMANOVA analysis for pain (P = 0.315) and itching (P = 0.133). There was a statistical significant difference in cases with bilateral conjunctivitis (P = 0.017) and for using antibiotics (P = 0.020). Conclusion Firmicutes among the predominant phyla has the highest abundance in bacterial conjunctivitis in our study. Pseudomonas as a resident commensal microbiota has an important role for prevention of infection.

Download Full-text

Conjunctival Sac Microbiome in Infectious Conjunctivitis

Microorganisms ◽

10.3390/microorganisms9102095 ◽

2021 ◽

Vol 9 (10) ◽

pp. 2095

Author(s):

Yasser Mohamed ◽

Masafumi Uematsu ◽

Yoshitomo Morinaga ◽

Hien-Anh Thi Nguyen ◽

Michiko Toizumi ◽

...

Keyword(s):

Bacterial Community ◽

Ribosomal Rna ◽

Diversity Analysis ◽

Bacterial Conjunctivitis ◽

Prevention Of Infection ◽

Bacterial Phyla ◽

Commensal Microbiota ◽

Conventional Culture ◽

Significant Difference ◽

Unweighted Unifrac

Acute bacterial conjunctival infections are common, and this study identified the conjunctival bacterial community in infectious conjunctivitis cases seen at the outpatient clinic of Khanh Hoa General Hospital in Nha Trang, Vietnam from October 2016 through December 2017. Conjunctival swabs were collected and tested using conventional culture, PCR, and 16S ribosomal RNA sequencing. The study included 47 randomly selected patients. More than 98% of all DNA reads represented five bacterial phyla. Three of these phyla constituted 92% of all sequences (Firmicutes (35%), Actinobacteria (31%), and Proteobacteria (26%)). At the genus level, there were 12 common genera that constituted about 61% of all sequence reads. Seven of those genera were common (Streptococcus (10%), Cutibacterium (10%), Staphylococcus (7%), Nocardioides (7%), Corynebacterium 1 (5%), Anoxybacillus (5%), and Acinetobacter (5%)), which encompassed 49% of all reads. As for diversity analysis, there was no difference on PERMANOVA analysis (unweighted UniFrac) for sex (p = 0.087), chemosis (p = 0.064), and unclassified eyedrops (p = 0.431). There was a significant difference in cases with bilateral conjunctivitis (p = 0.017) and for using antibiotics (p = 0.020). Of the predominant phyla, Firmicutes had the highest abundance in bacterial conjunctivitis in this study. Pseudomonas as a resident commensal microbiota may have an important role in the prevention of infection.

Download Full-text

1005 Antibiotic-Impregnated Calcium Sulfate Beads Are Not Effective in the Primary Prevention of Infection in Open Femur and Tibia Fractures

British Journal of Surgery ◽

10.1093/bjs/znab134.596 ◽

2021 ◽

Vol 108 (Supplement_2) ◽

Author(s):

A Fung ◽

A Ward ◽

K Patel ◽

M Krkovic

Keyword(s):

Primary Prevention ◽

Infection Rate ◽

Calcium Sulfate ◽

Acute Infection ◽

Open Fractures ◽

Prevention Of Infection ◽

Significant Difference ◽

Tibia Fractures ◽

Systemic Antibiotics

Abstract Introduction Infection is a major complication of open fractures. Antibiotic-impregnated calcium sulfate (AICS) beads are widely used as an adjuvant to systemic antibiotics. Whilst their efficacy in the secondary prevention of infection is established, we present the first retrospective study evaluating AICS beads in the primary prevention of infection in open fractures. Method 214 open femur and tibia fractures in 207 patients were reviewed over a seven-year period. 148 fractures received only systemic antibiotic prophylaxis. 66 fractures also received AICS beads. The occurrence of acute infection (wound infection and acute osteomyelitis) was recorded, as well as that of long-term complications (chronic osteomyelitis, non-union and death). Results Fractures that received AICS with systemic antibiotics had an overall acute infection rate of 42% (28/66), compared to 43% (63/148) in fractures that received only systemic antibiotics (p > 0.05). There was no significant difference in infection rate even when fractures were stratified by Gustilo-Anderson grade. There was also no significant difference in the rate of long-term complications. Conclusions Our results indicate that the adjuvant use of AICS beads is not effective for the primary prevention of acute infection or long-term complications in open leg fractures. Further research is needed to elucidate the factors influencing the outcomes of AICS use.

Download Full-text

Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi)

Evolutionary Bioinformatics ◽

10.1177/1176934321996353 ◽

2021 ◽

Vol 17 ◽

pp. 117693432199635

Author(s):

Daoxin Liu ◽

Pengfei Song ◽

Jingyan Yan ◽

Haijing Wang ◽

Zhenyuan Cai ◽

...

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

High Throughput Sequencing ◽

Tibet Plateau ◽

Rrna Gene ◽

Diversity Analysis ◽

Bacterial Phyla ◽

In Captivity ◽

Relative Abundances ◽

Plateau Zokor

Wild-caught animals must cope with drastic lifestyle and dietary changes after being induced to captivity. How the gut microbiome structure of these animals will change in response receives increasing attention. The plateau zokor ( Eospalax baileyi), a typic subterranean rodent endemic to the Qinghai-Tibet plateau, spends almost the whole life underground and is well adapted to the environmental pressures of both plateau and underground. However, how the gut microbiome of the plateau zokor will change in response to captivity has not been reported to date. This study compared the microbial community structure and functions of 22 plateau zokors before (the WS group) and after being kept in captivity for 15 days (the LS group, fed on carrots) using the 16S rRNA gene via high-throughput sequencing technology. The results showed that the LS group retained 973 of the 977 operational taxonomic units (OTUs) in the WS group, and no new OTUs were found in the LS group. The dominant bacterial phyla were Bacteroides and Firmicutes in both groups. In alpha diversity analysis, the Shannon, Sobs, and ACE indexes of the LS group were significantly lower than those of the WS group. A remarkable difference ( P < 0.01) between groups was also detected in beta diversity analysis. The UPGMA clustering, NMDS, PCoA, and Anosim results all showed that the intergroup difference was significantly greater than the intragroup difference. And compared with the WS group, the intragroup difference of the gut microbiota in the LS group was much larger, which failed to support the assumption that similar diets should drive convergence of gut microbial communities. PICRUSt revealed that although some functional categories displayed significant differences between groups, the relative abundances of these categories were very close in both groups. Based on all the results, we conclude that as plateau zokors enter captivity for a short time, although the relative abundances of different gut microbiota categories shifted significantly, they can maintain almost all the OTUs and the functions of the gut microbiota in the wild. So, the use of wild-caught plateau zokors in gut microbial studies is acceptable if the time in captivity is short.

Download Full-text

Environmental Temperatures Affect the Gastrointestinal Microbes of the Chinese Giant Salamander

Frontiers in Microbiology ◽

10.3389/fmicb.2021.543767 ◽

2021 ◽

Vol 12 ◽

Author(s):

Lifeng Zhu ◽

Wei Zhu ◽

Tian Zhao ◽

Hua Chen ◽

Chunlin Zhao ◽

...

Keyword(s):

Potential Effect ◽

Shannon Index ◽

Effect Of Temperature ◽

Sample Type ◽

Gastrointestinal Microbiome ◽

Unifrac Distance ◽

Alpha And Beta Diversity ◽

Significant Difference ◽

Unweighted Unifrac ◽

Sample Time

An increasing number of studies have shown that warming also influences the animal gut microbiome (altering the community structure and decreasing its diversity), which might further impact host fitness. Here, based on an analysis of the stomach and gut (the entire intestine: from the anterior intestine to the cloaca) microbiome in laboratory larva of giant salamanders (Andrias davidianus) under different living water temperatures (5, 15, and 25°C) at two sample time points (80 and 330 days after the acclimation), we investigated the potential effect of temperature on the gastrointestinal microbiome community. We found the significant Interaction between sampling time and temperature, or type (stomach and gut) on Shannon index in the gastrointestinal microbiome of the giant salamanders. We also found the significant difference in Shannon index among temperature groups within the same sample type (stomach or gut) at each sample time. 10% of variation in microbiome community could be explained by temperature alone in the total samples. Both the stomach and gut microbiomes displayed the highest similarity in the microbiome community (significantly lowest pairwise unweighted Unifrac distance) in the 25-degree group between the two sampling times compared to those in the 5-degree and 15-degree groups. Moreover, the salamanders in the 25°C treatment showed the highest food intake and body mess compared to that of other temperature treatments. A significant increase in the abundance of Firmicutes in the gastrointestinal microbiome on day 330 with increasing temperatures might be caused by increased host metabolism and food consumption. Therefore, we speculate that the high environmental temperature might indirectly affect both alpha and beta diversity of the gastrointestinal microbiome.

Download Full-text

High-throughput isolation and sorting of gut microbes reduce biases of traditional cultivation strategies

10.1101/759969 ◽

2019 ◽

Cited By ~ 1

Author(s):

William J. Watterson ◽

Melikhan Tanyeri ◽

Andrea R. Watson ◽

Candace M. Cham ◽

Yue Shan ◽

...

Keyword(s):

Ribosomal Rna ◽

Fold Increase ◽

Taxonomic Composition ◽

Biased Sampling ◽

Human Gut ◽

Rare Taxa ◽

Conventional Culture ◽

16S Ribosomal Rna Gene ◽

Slow Growing ◽

New Strategies

AbstractTraditional cultivation approaches in microbiology are labor-intensive, low-throughput, and often yield biased sampling of taxa due to ecological and evolutionary factors. New strategies are needed to enable ample representation of rare taxa and slow-growers that are outcompeted by fast-growing organisms. We developed a microfluidic platform that anaerobically isolates and cultivates microbial cells in millions of picoliter droplets and automatically sorts droplets based on colony density. We applied our strategy to mouse and human gut microbiomes and used 16S ribosomal RNA gene amplicons to characterize taxonomic composition of cells grown using different media. We found up to 4-fold increase in richness and larger representation of rare taxa among cells grown in droplets compared to conventional culture plates. Automated sorting of droplets for slow-growing colonies further enhanced the relative abundance of rare populations. Our method improves the cultivation and analysis of diverse microbiomes to gain deeper insights into microbial functioning and lifestyles.

Download Full-text

Mortalité du sapin baumier défolié par la tordeuse des bourgeons de l'épinette dans la région de la Gatineau au Québec

The Forestry Chronicle ◽

10.5558/tfc58213-5 ◽

1982 ◽

Vol 58 (5) ◽

pp. 213-219 ◽

Cited By ~ 4

Author(s):

Jean Beaulieu ◽

Yvan J. Hardy

Keyword(s):

Linear Regression ◽

Multiple Linear Regression ◽

Least Squares ◽

Random Number ◽

Least Squares Method ◽

Random Number Generator ◽

Balsam Fir ◽

Number Generator ◽

Profit Analysis ◽

Significant Difference

This paper presents a method of analysis which differentiates between spruce budworm caused mortality and regular mortality on balsam fir in the Gatineau region in Quebec. A first attempt was made using multiple linear regression and a uniform random number generator. In order to overcome the bias inherent to the least squares method when dealing with a binary (0,1) dependent variable, a profit analysis was also conducted. In this case, the parameters and their variance were estimated using likehood method. These two approaches proved to be equivalent when percent budworm caused mortality was compared within the 1958 to 1979 period covered by the data at hand, while the outbreak lasted from 1968 to 1975.In 1979, approximately 55% of the stems had been killed by the budworm, accounting for 53% of the volume. Maple-yellow birch associations were more affected than fir associations although no significant difference was found. Fir mortality was delayed by aerial spraying of insecticides but this advantage disappeared as soon as the spray operations came to an end.

Download Full-text

Actinobacillus (Haemophilus) Pleuropneumoniae: Use of Coagglutination and Complement Fixation to Determine the Relationship between Presence of Organism and Antibody Titer in Slaughterhouse Pigs

Journal of Veterinary Diagnostic Investigation ◽

10.1177/104063878900100105 ◽

1989 ◽

Vol 1 (1) ◽

pp. 12-15 ◽

Cited By ~ 5

Author(s):

Lorraine J. Hoffman

Keyword(s):

Respiratory Disease ◽

Complement Fixation ◽

Culture Method ◽

Respiratory Problems ◽

Conventional Culture ◽

Significant Difference ◽

Positive Threshold ◽

Standard Culture ◽

History Of ◽

The Difference

The conventional culture method was compared to coagglutination for detection of Actinobacillus (Haemophilus) pleuropneumoniae in 425 sets of pig lungs. Sera from the same animals were evaluated for antibodies to A. pleuropneumoniae by the complement fixation (CF) test. All samples were collected at 2 packing plants in Iowa. In 2 nonvaccinated herds with no history of respiratory disease, the difference between standard culture results and coagglutination was highly significant ( P < 0.001). None of the 57 pigs in this group were positive for A. pleuropneumoniae by conventional culture, but 7 were positive by the coagglutination test. There were 15 animals with CF titers between 1:8 and 1:32. Animals from 6 herds vaccinated for A. pleuropneumoniae and without recent respiratory problems were evaluated. One out of 118 animals tested was positive for A. pleuropneumoniae by standard culture as compared to 9 positive by coagglutination. The difference in positive results between culture and coagglutination was highly significant ( P < 0.001). Twenty-eight animals had CF titers to A. pleuropneumoniae (1:4 to ≥ 1: 128). Two hundred fifty lungs and sera samples were collected from 7 herds which had recently experienced varying degrees of respiratory disease. Thirty-nine lungs were positive for A. pleuropneumoniae by culture and 182 were positive by coagglutination. The number of positives detected by coagglutination was significantly different ( P < 0.001) from the number positive by culture. There were 172 animals with antibody titers ranging from suspect to ≥ 1:128. There were significantly fewer positive animals detected by standard culture than with the CF test ( P < 0.001). There was no significant difference between coagglutination results and CF titers when a titer of 1:4 was used as the positive threshold.

Download Full-text

Fermentation profile, microbial populations, taxonomic diversity and aerobic stability of total mixed ration silages based on Cactus and Gliricidia

The Journal of Agricultural Science ◽

10.1017/s0021859620000805 ◽

2020 ◽

Vol 158 (5) ◽

pp. 396-405

Author(s):

F. N. S. Santos ◽

E. M. Santos ◽

J. S. Oliveira ◽

G. R. Medeiros ◽

A. M. Zanine ◽

...

Keyword(s):

Interaction Effect ◽

Diversity Index ◽

Taxonomic Diversity ◽

Gliricidia Sepium ◽

Microbial Populations ◽

Total Mixed Ration ◽

Bacterial Phyla ◽

Aerobic Stability ◽

Significant Difference ◽

Fermentation Profile

AbstractThe aim of this study was to investigate the effects of Cactus (Opuntia spp) levels in total mixed ration silages based on Cactus and Gliricidia (Gliricidia sepium (Jacq.) Steud) on the fermentation profile, microbial populations, aerobic stability and taxonomic diversity. The completely randomized design was used in a 4 × 4 factorial design with four replications, being four rations with different levels of Cactus (15, 30, 45, 60% based on the dry matter) and four opening periods (0, 15, 30 and 60 days of fermentation). An interaction effect (P < 0.050) was observed among the diets and opening times for mould and yeast populations. An interaction effect for the levels of acetic acid was observed, where the diets 15, 30, 45 and 60% showed higher values at 60 days (0.44, 0.41, 0.35 and 0.40 g/kg DM, respectively). A significant difference was observed for the richness and diversity index (Chao1 and Shannon). The most abundant bacterial phyla were Proteobacteria and Firmicutes and the genera Lactobacillus and Weissella. Cactus can be added in total mixed ration silages up to the level of 60% in a way that it positively affects the qualitative indicators of the silages, modulating the taxonomic communities and allowing the predominance of important groups for preservation of the ensiled mass.

Download Full-text

An intact gut microbiome protects genetically predisposed mice against leukemia

Blood ◽

10.1182/blood.2019004381 ◽

2020 ◽

Vol 136 (18) ◽

pp. 2003-2017 ◽

Cited By ~ 3

Author(s):

Carolina Vicente-Dueñas ◽

Stefan Janssen ◽

Marina Oldenburg ◽

Franziska Auer ◽

Inés González-Herrero ◽

...

Keyword(s):

Ribosomal Rna ◽

Genetic Predisposition ◽

Gut Microbiome ◽

Large Scale ◽

Bone Marrow Cells ◽

Bacterial Species ◽

Gas Chromatography Mass Spectrometry ◽

Commensal Microbiota ◽

Successful Prevention ◽

Hematopoietic Bone Marrow

Abstract The majority of childhood leukemias are precursor B-cell acute lymphoblastic leukemias (pB-ALLs) caused by a combination of prenatal genetic predispositions and oncogenic events occurring after birth. Although genetic predispositions are frequent in children (>1% to 5%), fewer than 1% of genetically predisposed carriers will develop pB-ALL. Although infectious stimuli are believed to play a major role in leukemogenesis, the critical determinants are not well defined. Here, by using murine models of pB-ALL, we show that microbiome disturbances incurred by antibiotic treatment early in life were sufficient to induce leukemia in genetically predisposed mice, even in the absence of infectious stimuli and independent of T cells. By using V4 and full-length 16S ribosomal RNA sequencing of a series of fecal samples, we found that genetic predisposition to pB-ALL (Pax5 heterozygosity or ETV6-RUNX1 fusion) shaped a distinct gut microbiome. Machine learning accurately (96.8%) predicted genetic predisposition using 40 of 3983 amplicon sequence variants as proxies for bacterial species. Transplantation of either wild-type (WT) or Pax5+/– hematopoietic bone marrow cells into WT recipient mice revealed that the microbiome is shaped and determined in a donor genotype–specific manner. Gas chromatography-mass spectrometry (GC-MS) analyses of sera from WT and Pax5+/– mice demonstrated the presence of a genotype-specific distinct metabolomic profile. Taken together, our data indicate that it is a lack of commensal microbiota rather than the presence of specific bacteria that promotes leukemia in genetically predisposed mice. Future large-scale longitudinal studies are required to determine whether targeted microbiome modification in children predisposed to pB-ALL could become a successful prevention strategy.

Download Full-text

Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia

10.1101/2020.06.02.20118489 ◽

2020 ◽

Author(s):

Vilas Navapurkar ◽

Josefin Bartholdson Scott ◽

Mailis Maes ◽

Ellen Higginson ◽

Sally Forrest ◽

...

Keyword(s):

Clinical Decision Making ◽

Severe Pneumonia ◽

High Sensitivity ◽

Study Cohort ◽

Microbial Culture ◽

Respiratory Pathogens ◽

Metagenomic Sequencing ◽

Conventional Culture ◽

Comparator Group ◽

Significant Difference

AbstractRationaleThe diagnosis of infectious diseases has been hampered by reliance on microbial culture. Cultures take several days to return a result and organisms frequently fail to grow. In critically ill patients this leads to the use of empiric, broad-spectrum antimicrobials and compromises effective stewardship.ObjectivesTo establish the performance and clinical utility of a syndromic diagnostic for severe pneumonia.MethodsSingle ICU observational cohort study with contemporaneous comparator group. We developed and implemented a TaqMan array card (TAC) covering 52 respiratory pathogens in ventilated patients with suspected pneumonia. The time to result was compared against conventional culture, and sensitivity compared to conventional microbiology and metagenomic sequencing. We observed the clinician decisions in response to array results, comparing antibiotic free days (AFD) between the study cohort and comparator group.Results95 patients were enrolled with 71 forming the comparator group. TAC returned results 61 hours (IQR 42-90) faster than culture. The test had an overall sensitivity of 93% (95% CI 88-97%) compared to a combined standard of conventional culture and metagenomic sequencing, with 100% sensitivity for most individual organisms. In 54% of cases the TAC results altered clinical management, with 62% of changes leading to deescalation, 30% to an increase in spectrum, and investigations for alternative diagnoses in 9%. There was a significant difference in the distribution of AFDs with more AFDs in the TAC group (p=0.02).ConclusionsImplementation of a customised syndromic diagnostic for pneumonia led to faster results, with high sensitivity and measurable impact on clinical decision making.

Download Full-text