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Scientific Reports Sep 2021Bacterial species and their role in delaying the healing of pressure ulcers (PU) in spinal cord injury (SCI) patients have not been well described. This pilot study...
Bacterial species and their role in delaying the healing of pressure ulcers (PU) in spinal cord injury (SCI) patients have not been well described. This pilot study aimed to characterise the evolution of the cutaneous microbiota of PU in SCI cohort. Twenty-four patients with SCI from a French neurological rehabilitation centre were prospectively included. PU tissue biopsies were performed at baseline (D0) and 28 days (D28) and analysed using 16S rRNA gene-based sequencing analysis of the V3-V4 region. At D0, if the overall relative abundance of genus highlighted a large proportion of Staphylococcus, Anaerococcus and Finegoldia had a significantly higher relative abundance in wounds that stagnated or worsened in comparison with those improved at D28 (3.74% vs 0.05%; p = 0.015 and 11.02% versus 0.16%; p = 0.023, respectively). At D28, Proteus and Morganella genera were only present in stagnated or worsened wounds with respectively 0.02% (p = 0.003) and 0.01% (p = 0.02). Moreover, Proteus, Morganella, Anaerococcus and Peptoniphilus were associated within the same cluster, co-isolated from biopsies that had a poor evolution. This pathogroup could be a marker of wound degradation and Proteus could represent a promising target in PU management.
Topics: Aged; Bacteria; Female; Humans; Male; Microbiota; Middle Aged; Pressure Ulcer; RNA, Ribosomal, 16S; Wound Healing
PubMed: 34531517
DOI: 10.1038/s41598-021-98073-x -
Frontiers in Microbiology 2021Accumulated evidence shows that complex microbial communities resides in the healthy human urinary tract and can change in urological disorders. However, there lacks a...
Accumulated evidence shows that complex microbial communities resides in the healthy human urinary tract and can change in urological disorders. However, there lacks a comprehensive profiling of the genitourinary microbiota in healthy cohort. Here, we performed 16S rRNA gene sequencing of midstream urine specimens from 1,172 middle-aged and elderly healthy individuals. The core microbiota included 6 dominant genera (mean relative abundance >5%), including , , , , , and , and 131 low-abundance genera (0.01-5%), displaying a distinct microbiome profiles to that of host-matched gut microbiota. The composition and diversity of genitourinary microbiome (GM) were distinct between genders and may fluctuate with ages. Several urotypes were identified by the stratification of microbiome profiles, which were mainly dominated by the six most predominant genera. The prevalence of urotypes was disparate between genders, and the male sample additionally harbored other urotypes dominated by , , , or . , , and were co-occurred and co-abundant, and they may play crucial roles as keystone genera and be associated with increased microbial diversity. Our results delineated the microbial structure and diversity landscape of the GM in healthy middle-aged and elderly adults and provided insights into the influence of gender and age to it.
PubMed: 34489882
DOI: 10.3389/fmicb.2021.673969 -
Microorganisms Aug 2021The aim of this multicentre study was to determine the in vitro susceptibility to anti-anaerobic antibiotics of Gram-positive anaerobic cocci (GPAC) isolates responsible...
The aim of this multicentre study was to determine the in vitro susceptibility to anti-anaerobic antibiotics of Gram-positive anaerobic cocci (GPAC) isolates responsible for invasive infections in humans. A total of 133 GPAC isolates were collected in nine French hospitals from 2016 to 2020. All strains were identified to the species level (MALDI-TOF mass spectrometry, 16S rRNA sequencing). Minimum inhibitory concentrations (MICs) of amoxicillin, piperacillin, cefotaxime, imipenem, clindamycin, vancomycin, linezolid, moxifloxacin, rifampicin, and metronidazole were determined by the reference agar dilution method. Main -like genes were detected by PCR. The 133 GPAC isolates were identified as follows: 10 spp., 49 , 33 , 30 spp., and 11 . All isolates were susceptible to imipenem, vancomycin (except 3 ), linezolid and metronidazole. All isolates were susceptible to amoxicillin and piperacillin, except for (54% and 45% susceptibility only, respectively). MICs of cefotaxime widely varied while activity of rifampicin, and moxifloxacin was also variable. Concerning clindamycin, 31 were categorized as resistant (22 (A) subclass (TR), 7 (B), 1 both genes and 1 negative for tested genes) with MICs from 8 to >32 mg/L. Although GPACs are usually susceptible to drugs commonly used for the treatment of anaerobic infections, antimicrobial susceptibility should be evaluated in vitro.
PubMed: 34442745
DOI: 10.3390/microorganisms9081665 -
American Journal of Translational... 2021To investigate the associations between Vaginal Pathogenic Community with Bacterial vaginosis, Candida vaginitis, and Trichomonas vaginalis in Chinese women.
BACKGROUND
To investigate the associations between Vaginal Pathogenic Community with Bacterial vaginosis, Candida vaginitis, and Trichomonas vaginalis in Chinese women.
METHOD
In this experiment, ten BV, nine VVC, eight TV patients, and four non-infected healthy women were recruited. The vaginal samples were collected from the vaginal orifice, the middle of the vagina, and vaginal fornix from every participant and conducted with next-generation sequencing (NGS). The NGS was based upon the analysis of bacterial 16S rRNA genes by using the Illumina Miseq system.
RESULTS
No significant difference in microbiome community structures was observed for the three sampling sites from the same subject. Compared with the healthy population, patients with BV and TV showed more diverse symptoms and had a lower amount of but a higher number of BV-related bacteria like , and . On the contrary, the species composition of the VVC group is relatively simple, which has a significantly high abundance of . Eight genera, including , and , were closely correlated with BV. Among vaginal pathogenic bacteria, and were more common, with higher copy numbers in the TV group.
CONCLUSIONS
The data outlined the overall structure of vaginal communities, indicating that BV and TV were touching related to a sharp increase in the rich taxonomy and diversity of vaginal microbiota. VVC group presented a lower variety, with a significantly high abundance of .
PubMed: 34306475
DOI: No ID Found -
Gut Microbes 2021To investigate the relationship between intestinal microbiota and SARS-CoV-2-mediated pathogenicity in a United States, majority African American cohort. We...
To investigate the relationship between intestinal microbiota and SARS-CoV-2-mediated pathogenicity in a United States, majority African American cohort. We prospectively collected fecal samples from 50 SARS-CoV-2 infected patients, 9 SARS-CoV-2 recovered patients, and 34 uninfected subjects seen by the hospital with unrelated respiratory medical conditions (controls). 16S rRNA sequencing and qPCR analysis was performed on fecal DNA/RNA. The fecal microbial composition was found to be significantly different between SARS-CoV-2 patients and controls (PERMANOVA FDR- = .004), independent of antibiotic exposure. and were identified as the three most significantly enriched genera in COVID-19 patients compared to controls. Actively infected patients were also found to have a different gut microbiota than recovered patients (PERMANOVA FDR- = .003), and the most enriched genus in infected patients was , with and being enriched in the recovered patients. No difference in microbial community structure between recovered patients and uninfected controls was observed, nor a difference in alpha diversity between the three groups. 24 of the 50 COVID-19 patients (48%) tested positive via RT-qPCR for fecal SARS-CoV-2 RNA. A significant difference in gut microbial composition between SARS-CoV-2 positive and negative samples was observed, with and being enriched in the positive cohort. No significant associations between microbiome composition and disease severity was found. The intestinal microbiota is sensitive to the presence of SARS-CoV-2, with increased relative abundance of genera () associated with gastrointestinal (GI) disease. Further studies are needed to investigate the functional impact of SARS-CoV-2 on GI health.
Topics: Aged; Bacteria; COVID-19; Cohort Studies; Feces; Female; Gastrointestinal Microbiome; Humans; Male; Middle Aged; RNA, Ribosomal, 16S; RNA, Viral; SARS-CoV-2; Severity of Illness Index; United States
PubMed: 34100340
DOI: 10.1080/19490976.2021.1926840 -
The Journal of Allergy and Clinical... Apr 2021Little is known about the relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the respiratory virus responsible for the ongoing...
BACKGROUND
Little is known about the relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the respiratory virus responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic, and the upper respiratory tract (URT) microbiome.
OBJECTIVE
We sought to compare the URT microbiome between SARS-CoV-2-infected and -uninfected adults and to examine the association of SARS-CoV-2 viral load with the URT microbiome during COVID-19.
METHODS
We characterized the URT microbiome using 16S ribosomal RNA sequencing in 59 adults (38 with confirmed, symptomatic, mild to moderate COVID-19 and 21 asymptomatic, uninfected controls). In those with COVID-19, we measured SARS-CoV-2 viral load using quantitative reverse transcription PCR. We then examined the association of SARS-CoV-2 infection status and its viral load with the ⍺-diversity, β-diversity, and abundance of bacterial taxa of the URT microbiome. Our main models were all adjusted for age and sex.
RESULTS
The observed species index was significantly higher in SARS-CoV-2-infected than in -uninfected adults (β linear regression coefficient = 7.53; 95% CI, 0.17-14.89; P = .045). In differential abundance testing, 9 amplicon sequence variants were significantly different in both of our comparisons, with Peptoniphilus lacrimalis, Campylobacter hominis, Prevotella 9 copri, and an Anaerococcus unclassified amplicon sequence variant being more abundant in those with SARS-CoV-2 infection and in those with high viral load during COVID-19, whereas Corynebacterium unclassified, Staphylococcus haemolyticus, Prevotella disiens, and 2 Corynebacterium_1 unclassified amplicon sequence variants were more abundant in those without SARS-CoV-2 infection and in those with low viral load during COVID-19.
CONCLUSIONS
Our findings suggest complex associations between SARS-CoV-2 and the URT microbiome in adults. Future studies are needed to examine how these viral-bacterial interactions can impact the clinical progression, severity, and recovery of COVID-19.
Topics: Adult; Biodiversity; COVID-19; Case-Control Studies; Female; Host Microbial Interactions; Humans; Male; Microbiota; Middle Aged; Pandemics; RNA, Ribosomal, 16S; Respiratory System; SARS-CoV-2; Species Specificity; Viral Load
PubMed: 33577896
DOI: 10.1016/j.jaci.2021.02.001 -
Frontiers in Public Health 2020Persistent infection with the carcinogenic human papillomavirus (HPV) is a prerequisite for the progression of cervical lesions and cancer. A growing body of research...
Persistent infection with the carcinogenic human papillomavirus (HPV) is a prerequisite for the progression of cervical lesions and cancer. A growing body of research has focused on the functional role of the vaginal microbiota in the persistence of HPV infection. Understanding the microbial composition and structure in women with high-risk (hr)-HPV infection may help reveal associations between the vaginal microbiota and HPV infection, and identify potential biomarkers. Our study investigated the vaginal microbial community in women with and without hr-HPV infection, by using rRNA gene sequencing. We found that microbial perturbations occurred in the early phase of hr-HPV infection. and were decreased, while bacteria related to bacterial vaginosis (BV), such as , and were increased. Our results could offer insights into the correlations between hr-HPV and the vaginal microbiota in the early infection period, and provide indications that the predominance of some BV-associated bacteria during hr-HPV infection may increase the risk for cervical neoplasia.
Topics: Female; Humans; Microbiota; Papillomaviridae; Papillomavirus Infections; RNA, Ribosomal, 16S; Vagina
PubMed: 33490017
DOI: 10.3389/fpubh.2020.587298 -
International Journal of Surgery Case... Feb 2021Peptoniphilus indolicus is not usually seen in the eye or paranasal sinuses but is a commensal of the human vagina and gut. However, with COVID-19, eye infections and...
BACKGROUND
Peptoniphilus indolicus is not usually seen in the eye or paranasal sinuses but is a commensal of the human vagina and gut. However, with COVID-19, eye infections and other unusual complications are possible with such unsuspected bacteria.
CASE PRESENTATION
The patient is a 76-year-old white male from a nursing home tested positive for COVID-19 and was sent from a nursing facility for left eye drainage and psychiatric evaluation. Upon presentation, the patient was not fully oriented and could not provide a history of the eye drainage. CT scan showed sinusitis with left orbital and periorbital abscess formation, cellulitis, and extensive osteomyelitis. He underwent endoscopic transnasal drainage and orbiotomy. Cultures returned positive for methicillin-resistant Stapholococcus aureus (MRSA), Streptococcus constellatus, and Peptoniphilus indolicus. He was maintained on several days of IV antibiotics and returned to the nursing home. He then presented 2 months later and required enucleation of his globe, due to the presence of multiple scleral perforations in the setting of orbital abscess, as well as removal of necrotic orbital bone.
CONCLUSIONS
Given the concomitant infection with COVID-19 and unusual presentation, the patient's sinus cultures support the notion that COVID-19 can affect the presence of bacteria within certain anatomical regions. Specifically, Peptoniphilus indolicus is not normally found outside of the vagina or gut biome. Avascular, pale mucosa and bone of the nasal cavity was noted during surgery of this COVID-19 infected patient, which is in contrast to the friable and edematous tissue typically found in acutely infected sinuses. Our patient's orbital abscess began to drain spontaneously through the skin, which is rare for orbital abscesses. Also uncommon with orbital abscesses is the need for enucleation, which in this case was deemed necessary given that the abscess had perforated the sclera in multiple locations.
PubMed: 33477076
DOI: 10.1016/j.ijscr.2021.01.043 -
European Journal of Clinical... Jun 2021The present study focused on the characteristics of the vaginal microbiomes in prepubertal girls with and without vulvovaginitis. We collected 24 vaginal samples and 16... (Comparative Study)
Comparative Study
The present study focused on the characteristics of the vaginal microbiomes in prepubertal girls with and without vulvovaginitis. We collected 24 vaginal samples and 16 fecal samples from 10 girls aged 3-9 years with vulvovaginitis and 16 healthy girls of the same age. The samples were divided into three groups: fecal swabs from healthy controls (HF), vaginal swabs from healthy controls (HVS), and vaginal swabs from girls with vulvovaginitis (VVS). Sequencing of the V3-V4 region of the 16S rDNA gene was performed with the NovaSeq PE250 platform to reveal the vaginal microbial community structure in healthy prepubertal girls and vulvovaginitis-associated microbiota. The intestinal microbiomes of healthy children were also analyzed for comparison. This study revealed that the healthy vaginal tract in prepubertal girls was dominated by Prevotella, Porphyromonas, Ezakiella, and Peptoniphilus species, with a high diversity of microbiota. The vulvovaginitis-associated microbiota were dominated by Streptococcus, Prevotella, Haemophilus, and Granulicatella, with lower diversity than that in healthy girls. Furthermore, the compositions of the vaginal and intestinal microbiomes were completely different. ANOSIM, MRPP, Adonis, and AMOVA were used to analyze the beta diversity, and the results showed that there were significant differences in the microbial communities among the three groups. Lactobacillus deficiency and high bacterial diversity were characteristics of the vaginal microbiome in healthy prepubertal girls; this is inconsistent with that in reproductive-age women. The vulvovaginitis-associated vaginal microbiota differed dramatically from normal microbiota, and the main causative agents were not fecal in origin.
Topics: Bacteria; Child; Child, Preschool; Female; Humans; Microbiota; Phylogeny; Vagina; Vulvovaginitis
PubMed: 33452946
DOI: 10.1007/s10096-021-04152-2 -
PloS One 2021The etiology of vulvar lichen sclerosus (LS) remains unclear; however, alterations in cutaneous and gut microbiota may be contributing to the pathogenesis of this...
The etiology of vulvar lichen sclerosus (LS) remains unclear; however, alterations in cutaneous and gut microbiota may be contributing to the pathogenesis of this inflammatory condition. To explore this hypothesis, we conducted a pilot case-control study, obtaining dermal swab and stool samples from prepubertal girls with vulvar LS (n = 5), girls with nonspecific vulvovaginitis (n = 5), and healthy controls (n = 3). Samples (n = 56) were subjected to total DNA extractions. Resulting DNA was purified, subjected to PCR (targeting the V3V4 region of the 16S rRNA gene), sequenced, and analyzed using QIIME, MetagenomeSeq, and DESeq2 software packages. Our findings showed that there were significant differences in the cutaneous and gut microbiotas of girls with LS compared to controls. On the skin, girls with LS had a statistically significantly higher relative abundance of Porphyromonas spp., Parvimonas spp., Peptoniphilus spp., Prevotella spp., Dialister spp., and Peptostreptococcus spp., but a lower relative abundance of Cornyebacterium compared to the control group. In the gut samples, girls with LS had a significantly higher relative abundance of Dialister spp., Clostridiales spp., Paraprevotella spp., Escherichia coli, Bifidobacterium adolescentis, and Akkermansia muciniphila, and a lower relative abundance of Roseburia faecis and Ruminococcus bromii compared to controls. These results suggest a potential association between cutaneous and gut dysbiosis and pediatric vulvar LS. Future studies involving larger samples sizes are warranted to further evaluate this association.
Topics: Biodiversity; Case-Control Studies; Child; Female; Gastrointestinal Microbiome; Humans; Lichen Sclerosus et Atrophicus; Menarche; Phylogeny; Pilot Projects; Skin
PubMed: 33444404
DOI: 10.1371/journal.pone.0245243