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Antibiotics (Basel, Switzerland) May 2024The recognition of the complex (AUC) as an emerging uropathogen has led to growing concerns due to a limited understanding of its disease spectrum and antibiotic...
The recognition of the complex (AUC) as an emerging uropathogen has led to growing concerns due to a limited understanding of its disease spectrum and antibiotic resistance profiles. Here, we investigated the prevalence of macrolide resistance within urinary AUC isolates, shedding light on potential genetic mechanisms. Phenotypic testing revealed a high rate of macrolide resistance: 45%, among a total of 189 urinary AUC isolates. Genomic analysis identified integrative and conjugative elements (ICEs) as carriers of the macrolide resistance gene , suggesting horizontal gene transfer as a mechanism of resistance. Furthermore, comparison with publicly available genomes of related pathogens revealed high ICE sequence homogeneity, highlighting the potential for cross-species dissemination of resistance determinants. Understanding mechanisms of resistance is crucial for developing effective surveillance strategies and improving antibiotic use. Furthermore, the findings underscore the importance of considering the broader ecological context of resistance dissemination, emphasizing the need for community-level surveillance to combat the spread of antibiotic resistance within the urinary microbiome.
PubMed: 38786161
DOI: 10.3390/antibiotics13050433 -
Scientific Reports May 2024Using pooled vaginal microbiota data from pregnancy cohorts (N = 683 participants) in the Environmental influences on Child Health Outcomes (ECHO) Program, we...
Using pooled vaginal microbiota data from pregnancy cohorts (N = 683 participants) in the Environmental influences on Child Health Outcomes (ECHO) Program, we analyzed 16S rRNA gene amplicon sequences to identify clinical and demographic host factors that associate with vaginal microbiota structure in pregnancy both within and across diverse cohorts. Using PERMANOVA models, we assessed factors associated with vaginal community structure in pregnancy, examined whether host factors were conserved across populations, and tested the independent and combined effects of host factors on vaginal community state types (CSTs) using multinomial logistic regression models. Demographic and social factors explained a larger amount of variation in the vaginal microbiome in pregnancy than clinical factors. After adjustment, lower education, rather than self-identified race, remained a robust predictor of L. iners dominant (CST III) and diverse (CST IV) (OR = 8.44, 95% CI = 4.06-17.6 and OR = 4.18, 95% CI = 1.88-9.26, respectively). In random forest models, we identified specific taxonomic features of host factors, particularly urogenital pathogens associated with pregnancy complications (Aerococcus christensenii and Gardnerella spp.) among other facultative anaerobes and key markers of community instability (L. iners). Sociodemographic factors were robustly associated with vaginal microbiota structure in pregnancy and should be considered as sources of variation in human microbiome studies.
Topics: Humans; Female; Pregnancy; Vagina; Microbiota; Adult; RNA, Ribosomal, 16S; Cohort Studies; Young Adult
PubMed: 38782975
DOI: 10.1038/s41598-024-62537-7 -
Scientific Reports May 2024Alterations in the vaginal microbiota, including both species composition and functional pathways, have been associated with HPV infection and progression of dysplasia...
Alterations in the vaginal microbiota, including both species composition and functional pathways, have been associated with HPV infection and progression of dysplasia to cervical cancer. To further explore this, shotgun metagenomic sequencing was used to taxonomically and functionally characterize the vaginal microbiota of women with and without cervical dysplasia. Women with histologically verified dysplasia (n = 177; low grade dysplasia (LSIL) n = 81, high-grade dysplasia (HSIL) n = 94, cancer n = 2) were compared with healthy controls recruited from the cervical screening programme (n = 177). Women with dysplasia had a higher vaginal microbial diversity, and higher abundances of Gardnerella vaginalis, Aerococcus christensenii, Peptoniphilus lacrimalis and Fannyhessea vaginae, while healthy controls had higher relative abundance of Lactobacillus crispatus. Genes involved in e.g. nucleotide biosynthesis and peptidoglycan biosynthesis were more abundant in women with dysplasia. Healthy controls showed higher abundance of genes important for e.g. amino acid biosynthesis, (especially L-lysine) and sugar degradation. These findings suggest that the microbiota may have a role in creating a pro-oncogenic environment in women with dysplasia. Its role and potential interactions with other components in the microenvironment deserve further exploration.
Topics: Humans; Female; Vagina; Microbiota; Adult; Uterine Cervical Dysplasia; Middle Aged; Case-Control Studies; Metagenomics; Bacteria
PubMed: 38755259
DOI: 10.1038/s41598-024-61942-2 -
International Journal of Food Science 2024Indonesia has abundant traditional fermented food with various lactic acid bacteria (LAB), which can be developed into probiotics for pharmaceutical and functional food...
Indonesia has abundant traditional fermented food with various lactic acid bacteria (LAB), which can be developed into probiotics for pharmaceutical and functional food and feed products. This research is aimed at (1) obtaining and identifying LAB isolates and (2) studying the microbiome (bacterial diversity and abundance) of spontaneously-fermented traditional foods of Kalimantan Island, Cincalok, Tempoyak, and Mandai. To obtain LAB isolates, food samples were serially diluted and inoculated on MRS agar that contained 1% CaCO (MRSA). Isolates forming clear zones were purified and identified by DNA barcoding. The microbiome was studied using genomic-sequencing techniques and analysed for taxonomic composition. Seven pure isolates were obtained from Cincalok, two Tempoyak, and one Mandai. DNA barcoding revealed that the Cincalok seven isolates were (strain HSP-S16), (FSB201), , (SS1995), (S11-6), (C01), and (P3.1); two from Tempoyak, (E1D3BL1) and (UMCC-2996); and one from Mandai, (XAAS.x13; non-LAB). The , , , , and belong to LAB. The from Cincalok and non-LAB in these three fermented foods were the first documented report. The microbiome revealed the dominance of phyla in the fermented foods, with 93% in Cincalok, 89.94% in Tempoyak, and 60.32% in Mandai. On the genus level, Cincalok was dominated by 40.33%, 23.29%, 9.27%, and 6.84%. Meanwhile, Tempoyak was dominated only by 89.94%. Mandai were dominated by 31.97%, 17.14%, 16.85%, 15.15%, and 6.2%. However, Mandai's microbiome LAB was not culturable/isolated on MRSA. The plausibility is that those unculturable LAB require coculturing with other bacteria and additional media components to grow on MRSA. This study is the first report regarding the microbiome of Cincalok, Tempoyak, and Mandai, along with their culturable LAB isolates.
PubMed: 38715571
DOI: 10.1155/2024/6589766 -
Journal of Food Protection Apr 2024Beverage innovation is a growing trend with a reliance on comanufacturing relationships to launch products quickly. A recent comanufacturing relationship is the...
Beverage innovation is a growing trend with a reliance on comanufacturing relationships to launch products quickly. A recent comanufacturing relationship is the utilization of dairy processing facilities to process plant-based beverages using high-temperature short-time (HTST) pasteurization. While the shelflife of HTST bovine milk is well established at 21 days, retailers are expecting new refrigerated beverages to achieve a 60-day shelflife. Little is known about the microbial stability of these new beverages, particularly those with complex formulations. Our objective was to identify bacterial taxa leading to the spoilage of four coconut-based creamers and their potential sources (raw ingredients or packaging). We used a multifaceted approach including plate counting and 16S rRNA metabarcoding to monitor microbial growth in products throughout shelflife (60 d, 4 °C), and cold enrichment (7 °C, 11 d) of ingredients and packaging. Nearly all product units (25/26) had elevated microbial loads (>4.3 log CFU/mL) prior to the 60-d target, with early spoilage detected at 21 d. Key spoilage taxa included Pseudomonas, Streptococcus, Aerococcus, Paenibacillus, Sphingomonas, and Oceanobacillus. Pseudomonas were responsible for "early" product spoilage (21-32 d), whereas Oceanobacillus were important in products with very "late" spoilage (60-62 d). All key spoilage taxa were identified in cold enrichments of multiple units of waxboard cartons. Paenibacillus was the dominant bacterium in 47% (10/21) of product units. In addition to carton samples, Paenibacillus was also identified in one raw ingredient (mushroom extract). Metabarcoding identified Listeria sensu stricto as a dominant taxon in three individual product units from three distinct production lots. Listeria was also found in 31% (5/16) of cold enrichments of individual cartons. Taxa responsible for spoilage of plant-based beverages were identified as well as demonstrating packaging as an important contamination source.
PubMed: 38692353
DOI: 10.1016/j.jfp.2024.100284 -
Microbiology Resource Announcements Jun 2024Previously identified under the single designation of , three distinct taxonomic species have been distinguished as and . Here, we present the complete genome sequences...
Previously identified under the single designation of , three distinct taxonomic species have been distinguished as and . Here, we present the complete genome sequences of the type strains of these species assembled via a combination of short-read and long-read sequencing techniques.Registered at ClinicalTrials.gov (NCT01166438).
PubMed: 38651909
DOI: 10.1128/mra.00156-24 -
Cureus Mar 2024() infection, primarily observed in elderly patients, is a rare yet emerging occurrence in the pediatric population. Advances in laboratory techniques have facilitated...
() infection, primarily observed in elderly patients, is a rare yet emerging occurrence in the pediatric population. Advances in laboratory techniques have facilitated the increased identification of these bacteria in human infections. There have been only a few recent cases reported among children. The scarcity of literature on the clinical presentation and management of such infections in children presents a challenge for pediatricians. Here, we present the case of a 15-month-old male child with Down syndrome who presented with malodorous urine but lacked other typical symptoms of urinary tract infection. Upon investigation, urine analysis revealed pyuria, and urine culture confirmed infection. The patient also exhibited underlying bilateral mild to moderate hydronephrosis. Successful treatment was achieved with a three-day course of amoxicillin, leading to symptom resolution. This case underscores the significance of promptly identifying infection in pediatric patients presenting with malodorous urine, as a timely intervention with a short course of treatment may avert more severe and invasive infections.
PubMed: 38586679
DOI: 10.7759/cureus.55635 -
Clinical Chemistry and Laboratory... Jun 2024The EFLM Task and Finish Group Urinalysis has updated the ECLM European Urinalysis Guidelines (2000) on urinalysis and urine bacterial culture, to improve accuracy of...
BACKGROUND
The EFLM Task and Finish Group Urinalysis has updated the ECLM European Urinalysis Guidelines (2000) on urinalysis and urine bacterial culture, to improve accuracy of these examinations in European clinical laboratories, and to support diagnostic industry to develop new technologies.
RECOMMENDATIONS
Graded recommendations were built in the following areas.
MEDICAL NEEDS AND TEST REQUISITION
Strategies of urine testing are described to patients with complicated or uncomplicated urinary tract infection (UTI), and high or low-risk to kidney disease.
SPECIMEN COLLECTION
Patient preparation, and urine collection are supported with two quality indicators: contamination rate (cultures), and density of urine (chemistry, particles).
CHEMISTRY
Measurements of both urine albumin and α1-microglobulin are recommended for sensitive detection of kidney disease in high-risk patients. Performance specifications are given for urine protein measurements and quality control of multiproperty strip tests.
PARTICLES
Procedures for microscopy are reviewed for diagnostic urine particles, including urine bacteria. Technologies in automated particle counting and visual microscopy are updated with advice how to verify new instruments with the reference microscopy.
BACTERIOLOGY
Chromogenic agar is recommended as primary medium in urine cultures. Limits of significant growth are reviewed, with an optimised workflow for routine specimens, using leukocyturia to reduce less important antimicrobial susceptibility testing. Automation in bacteriology is encouraged to shorten turn-around times. Matrix assisted laser desorption ionization time-of-flight mass spectrometry is applicable for rapid identification of uropathogens. and are taken into the list of uropathogens. A reference examination procedure was developed for urine bacterial cultures.
PubMed: 38534005
DOI: 10.1515/cclm-2024-0070 -
Molecular and Cellular Probes Jun 2024The effects of mesenchymal stem cells (MSCs) and MSC-derived exosomes (MSC-exos) on serum metabolites and intestinal microbiota in rats after liver trauma were discussed.
OBJECTIVE
The effects of mesenchymal stem cells (MSCs) and MSC-derived exosomes (MSC-exos) on serum metabolites and intestinal microbiota in rats after liver trauma were discussed.
METHODS
Adult Wistar Albino rats were assigned into control, model (liver trauma), MSCs, and MSC-exos groups (n = 6). The study examined changes in the inflammatory environment in liver tissues were analyzed by histological examination and analysis of macrophage phenotypes. Alterations in serum metabolites were determined by untargeted metabonomics, and gut microbiota composition was characterized by 16S rDNA sequencing. Correlations between specific gut microbiota, metabolites, and inflammatory response were calculated using Spearman correlation analysis.
RESULTS
Rats with liver trauma after MSCs and MSC-exos treatment exhibited attenuated inflammatory infiltration and necrosis in liver tissues. MSCs and MSC-exos treatment reduced the proportion of M1 macrophages, accompanied by a decrease in inducible nitric oxide synthase (iNOS) and tumor necrosis factor-alpha (TNF-α) levels. Furthermore, MSCs and MSC-exos treatment expanded the proportion of M2 macrophages, accompanied by an increase in arginase-1 (Arg-1) and interleukin-10 (IL-10) levels. The beneficial effects of MSC-exo treatment on rats with liver trauma were superior to those of MSC treatment. The composition and abundance of the gut microbiota and metabolites were altered in pathological rats, whereas MSC and MSC-exo intervention partially restored specific gut microbiota and metabolite alterations. At the phylum level, alterations in Bacteroidota, Proteobacteria, and Verrucomicrobiota were observed after MSC and MSC-exo intervention. At the genus level, Intestinimonas, Alistipes, Aerococcus, Faecalibaculum, and Lachnospiraceae_ND3007_group were the main differential microbiota. 6-Methylnicotinamide, N-Methylnicotinamide, Glutathione, oxidized, ISOBUTYRATE, ASCORBATE, EICOSAPENTAENOATE, GLYCEROL 3-PHOSPHATE, and Ascorbate radical were selected as important differential metabolites. There was a clear correlation between Ascorbate, Intestinimonas/Faecalibaculum and inflammatory cytokines.
CONCLUSION
MSC-exos promoted the repair of tissue damage in rats with liver trauma by regulating serum metabolites and intestinal microbiota, providing new insights into how MSC-exos reduced inflammation in rats with liver trauma.
Topics: Animals; Exosomes; Gastrointestinal Microbiome; Mesenchymal Stem Cells; Liver; Rats, Wistar; Rats; Male; Wound Healing; Macrophages; Inflammation
PubMed: 38518900
DOI: 10.1016/j.mcp.2024.101958 -
Frontiers in Microbiology 2024Traditional Chinese medicine (TCM) is widely used in humans and animals, which is very important for health. TCM affects the body 's immunity and changes in intestinal...
BACKGROUND
Traditional Chinese medicine (TCM) is widely used in humans and animals, which is very important for health. TCM affects the body 's immunity and changes in intestinal flora. This study was conducted to investigate the effects of dietary Hong-bailanshen (HBLS) supplementation in horses on serum biochemical profile, antioxidant enzymes and gut microbiota.
METHODS
In this study, five horses were selected. On day 0, 14, 28, blood samples and feces were collected on days 0, 14, and 28 to analyse gut microbiota, serum biochemical and redox indexes.
RESULTS
The results showed that the addition of HBLS to horse diets significantly decreased the level of alanine aminotransferase, alkaline phosphatase, creatine kinase and malondialdehyde ( < 0.05, < 0.01) and significantly increased the activity of total antioxidant capacity, superoxide dismutase and catalase ( < 0.05, < 0.01). Compared with day 14, the levels of alanine aminotransferase, alkaline phosphatase and creatine kinase were significantly decreased; however, the level of catalase was significantly increased in the horses continuously fed with HBLS for 28 days ( < 0.05, < 0.01). Alpha diversity analysis was performed that chao1 ( < 0.05), observed_specicies, faith'pd and goods_coverage upregulated in the horses fed HBLS. A total of 24 differential genera were detected adding HBLS to diet increased the abundance of and , while reduced and ( < 0.05, < 0.01).
CONCLUSION
Adding HBLS to the diet could be a potentially effective strategy to improve horses' health.
PubMed: 38444806
DOI: 10.3389/fmicb.2024.1327210