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Anaerobe Aug 2023The main study objective was to evaluate the correlation between matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rRNA...
Comparative evaluation of MALDI-TOF MS and 16S rRNA gene sequencing for the identification of clinically relevant anaerobic bacteria: critical evaluation of discrepant results.
OBJECTIVES
The main study objective was to evaluate the correlation between matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing results for the identification of anaerobes.
METHODS
A retrospective study was conducted of all anaerobic bacteria isolated from clinically significant specimens. MALDI-TOF (Bruker Byotyper) and 16S rRNA gene sequencing were performed in all strains. Identifications were considered correct when the concordance with gene sequencing was ≥99%.
RESULTS
The study included 364 isolates of anaerobic bacteria: 201 (55.2%) Gram-negative and 163 (44.8%) Gram-positive, mostly belonging to the genus Bacteroides. Isolates were largely obtained from blood cultures (128/35.4%) and intra-abdominal samples (116/32.1%). Overall, 87.3% of isolates were identified at species level using the version 9 database (89.5% of Gram-negative and 84.6% of Gram-positive anaerobic bacteria). All isolates belonging to the species B. fragilis sensu stricto were correctly identified by MALDI-TOF MS, but five cases of Phocaeicola (Bacteroides) dorei were misidentified as Phocaeicola (Bacteroides) vulgatus; all Prevotella isolates were correctly identified at the genus level, and most were correctly identified at the species level. Among Gram-positive anaerobes, 12 Anaerococcus species were not identified by MALDI-TOF MS, while six cases identified as Peptoniphilus indolicus were found to belong to other genera/species.
CONCLUSIONS
MALDI-TOF is a reliable technique for identifying most anaerobic bacteria, although the database needs frequent updating to identify rare, infrequent, and newly discovered species.
Topics: Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Bacteria, Anaerobic; Bacterial Typing Techniques; RNA, Ribosomal, 16S; Genes, rRNA; Retrospective Studies; Gram-Positive Bacteria
PubMed: 37321445
DOI: 10.1016/j.anaerobe.2023.102754 -
MedRxiv : the Preprint Server For... May 2024Recently, associations between recurrent urinary tract infections (UTI) and the urinary microbiome (urobiome) composition have been identified in adults. However, little...
BACKGROUND
Recently, associations between recurrent urinary tract infections (UTI) and the urinary microbiome (urobiome) composition have been identified in adults. However, little is known about the urobiome in children. We aimed to characterize the urobiome of children with species-level resolution and to identify associations based on UTI history.
STUDY DESIGN
Fifty-four children (31 females and 21 males) from 3 months to 5 years of age participated in the study. Catheterized urine specimens were obtained from children undergoing a clinically indicated voiding cystourethrogram. To improve the analysis of the pediatric urobiome, we used a novel protocol using filters to collect biomass from the urine coupled with synthetic long-read 16S rRNA gene sequencing to obtain culture-independent species-level resolution data. We tested for differences in microbial composition between sex and history of UTIs using non-parametric tests on individual bacteria and alpha diversity measures.
RESULTS
We detected bacteria in 61% of samples from 54 children (mean age 40.7 months, 57% females). Similar to adults, urobiomes were distinct across individuals and varied by sex. The urobiome of females showed higher diversity as measured by the inverse Simpson and Shannon indices but not the Pielou evenness index or number of observed species (p = 0.05, p=0.04, p = 0.35, and p = 0.11, respectively). Additionally, several species were significantly overrepresented in females compared to males, including those from the genera , and (p = 0.03, 0.04, and 0.02, respectively). Urobiome diversity increased with age, driven mainly by males. Comparison of children with a history of 1, 2, or 3+ UTIs revealed that urobiome diversity significantly decreases in the group that experienced 3+ UTIs as measured by the Simpson, Shannon, and Pielou indices (p = 0.03, p = 0.05, p = 0.01). Several bacteria were also found to be reduced in abundance.
DISCUSSION
In this study, we confirm that urobiome can be identified from catheter-collected urine specimens in infants as young as 3 months, providing further evidence that the pediatric bladder is not sterile. In addition to confirming variations in the urobiome related to sex, we identify age-related changes in children under 5 years of age, which conflicts with some prior research. We additionally identify associations with a history of UTIs.
CONCLUSIONS
Our study provides additional evidence that the pediatric urobiome exists. The bacteria in the bladder of children appear to be affected by early urologic events and warrants future research.
PubMed: 38798594
DOI: 10.1101/2024.05.16.24307309 -
Waste Management (New York, N.Y.) May 2024Treating food waste using black soldier fly larvae (BSFL) is widely regarded as a promising nature-based measure. This study explored the influence of food waste...
Treating food waste using black soldier fly larvae (BSFL) is widely regarded as a promising nature-based measure. This study explored the influence of food waste particle sizes on substrate properties and its subsequent effects on bioconversion efficiency and gut microbiota. The results indicated that particle sizes mainly ranging from 4 mm to 10 mm (T1) significantly increased the weight loss rate of food waste by 35 % and larval biomass by 38 % compared to those in T4 (particle sizes mostly less than 2 mm) and promoted the bioconversion of carbon and nitrogen into larvae and gases. Investigation of substrates properties indicated that the final pH value of T1 was 7.79 ± 0.10, with Anaerococcus as the predominant substrate microorganism (relative abundance: 57.4 %), while T4 exhibited a final pH value of 5.71 ± 0.24, with Lactobacillus as the dominant microorganism (relative abundance: 95.2 %). Correlation analysis between substrate chemical properties and microbial community structure unveiled a strong relationship between substrate pH and the relative abundance of Anaerococcus and Lactobacillus. Furthermore, beneficial microorganisms such as Lactobacillus and Enterococcus colonized the BSFL gut of T1, while pathogenic bacterium Morganella, detrimental to BSFL gut function, was enriched in T4 (relative abundance: 60.9 %). Nevertheless, PCA analysis indicated that alterations in the gut microbial community structure may not be attributed to the substrate microorganisms. This study establishes particle size as a crucial parameter for BSFL bioconversion and advances understanding of the relationship between gut microbiota and substrate microbiota.
Topics: Animals; Larva; Gastrointestinal Microbiome; Food; Refuse Disposal; Diptera
PubMed: 38564911
DOI: 10.1016/j.wasman.2024.03.030 -
BMC Microbiology Jan 2024Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification...
Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing.
BACKGROUND
Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot be characterized by conventional identification procedures MALDI-TOF MS and partial 16 S rRNA gene sequencing using Whole Genome Sequencing (WGS).
RESULTS
We identified a total of 35 bacterial strains that represent potentially novel species. Corynebacterium sp. (n = 6) and Schaalia sp. (n = 5) were the predominant genera. Two strains each were identified within the genera Anaerococcus, Clostridium, Desulfovibrio, and Peptoniphilus, and one new species was detected within Citrobacter, Dermabacter, Helcococcus, Lancefieldella, Neisseria, Ochrobactrum (Brucella), Paenibacillus, Pantoea, Porphyromonas, Pseudoclavibacter, Pseudomonas, Psychrobacter, Pusillimonas, Rothia, Sneathia, and Tessaracoccus. Twenty-seven of 35 strains were isolated from deep tissue specimens or blood cultures. Seven out of 35 isolated strains identified were clinically relevant. In addition, 26 bacterial strains that could only be identified at the species level using WGS analysis, were mainly organisms that have been identified/classified very recently.
CONCLUSION
Our new algorithm proved to be a powerful tool for detection and identification of novel bacterial organisms. Publicly available clinical and genomic data may help to better understand their clinical and ecological role. Our identification of 35 novel strains, 7 of which appear to be clinically relevant, shows the wide range of undescribed pathogens yet to define.
Topics: Bacteria; Whole Genome Sequencing; Corynebacterium; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; RNA, Ribosomal, 16S; Bacterial Typing Techniques
PubMed: 38178003
DOI: 10.1186/s12866-023-03163-7 -
Journal of Pediatric Urology May 2024Recently, associations between recurrent urinary tract infections (UTI) and the urinary microbiome (urobiome) composition have been identified in adults. However, little...
BACKGROUND
Recently, associations between recurrent urinary tract infections (UTI) and the urinary microbiome (urobiome) composition have been identified in adults. However, little is known about the urobiome in children. We aimed to characterize the urobiome of children with species-level resolution and to identify associations based on UTI history.
STUDY DESIGN
Fifty-four children (31 females and 21 males) from 3 months to 11 years of age participated in the study. Catheterized urine specimens were obtained from children undergoing a clinically indicated voiding cystourethrogram. To improve the analysis of the pediatric urobiome, we used a novel protocol using filters to collect biomass from the urine coupled with synthetic long-read 16S rRNA gene sequencing to obtain culture-independent species-level resolution data. We tested for differences in microbial composition between sex and history of UTIs using non-parametric tests on individual bacteria and alpha diversity measures.
RESULTS
We detected bacteria in 61% of samples from 54 children (mean age 40.7 months, 57% females). Similar to adults, urobiomes were distinct across individuals and varied by sex. The urobiome of females showed higher diversity as measured by the inverse Simpson and Shannon indices but not the Pielou evenness index or number of observed species (p = 0.05, p = 0.04, p = 0.35, and p = 0.11, respectively). Additionally, several species were significantly overrepresented in females compared to males, including those from the genera Anaerococcus, Prevotella, and Schaalia (p = 0.03, 0.04, and 0.02, respectively). Urobiome diversity increased with age, driven mainly by males. Comparison of children with a history of 1, 2, or 3+ UTIs revealed that urobiome diversity significantly decreases in the group that experienced 3+ UTIs as measured by the Simpson, Shannon, and Pielou indices (p = 0.03, p = 0.05, p = 0.01). Several bacteria were also found to be reduced in abundance.
DISCUSSION
In this study, we confirm that urobiome can be identified from catheter-collected urine specimens in infants as young as 3 months, providing further evidence that the pediatric bladder is not sterile. In addition to confirming variations in the urobiome related to sex, we identify age-related changes in children under 5 years of age, which conflicts with some prior research. We additionally identify associations with a history of UTIs.
CONCLUSIONS
Our study provides additional evidence that the pediatric urobiome exists. The bacteria in the bladder of children appear to be affected by early urologic events and warrants future research.
PubMed: 38862292
DOI: 10.1016/j.jpurol.2024.05.016 -
Diagnostic Microbiology and Infectious... May 2024Prosthetic joint infections (PJIs) are commonly diagnosed via culture-based methods, which may miss hard-to-grow pathogens. This study contrasts amplicon metagenomic...
Prosthetic joint infections (PJIs) are commonly diagnosed via culture-based methods, which may miss hard-to-grow pathogens. This study contrasts amplicon metagenomic sequencing (16S AS) with traditional culture techniques for enhanced clinical decision-making. We analyzed sonicate fluid from 27 patients undergoing revision arthroplasty using both methods, emphasizing the distinction between contaminants and true positives. Our findings show moderate agreement between the two methods, with a Cohen's kappa of 0.490, varying across bacterial genera (Cohen's kappa -0.059 to 1). The sensitivity of 16S AS compared to culture was 81% (95% CI, 68% to 94%). Sequencing revealed greater microbial diversity, including anaerobic genera like Anaerococcus and Citrobacter. Interestingly, several culture-negative PJI samples showed diverse bacteria via 16S AS. Despite rigorous controls and algorithms to eliminate contaminants, confirming bacteria presence with 16S AS remains a challenge. This highlights the need for improved PJI diagnostic methods, while also pointing out the limitations of next-generation sequencing (NGS) as a clinical diagnostic tool.
Topics: Humans; Arthritis, Infectious; Bacteria; Prostheses and Implants; Arthroplasty; High-Throughput Nucleotide Sequencing; Prosthesis-Related Infections; Sensitivity and Specificity; RNA, Ribosomal, 16S
PubMed: 38340614
DOI: 10.1016/j.diagmicrobio.2024.116188 -
New Microbes and New Infections Jun 2024
PubMed: 38799826
DOI: 10.1016/j.nmni.2024.101252 -
Scientific Reports May 2024The presence of dysbiotic cervicovaginal microbiota has been observed to be linked to the persistent development of cervical carcinogenesis mediated by the human... (Meta-Analysis)
Meta-Analysis
The presence of dysbiotic cervicovaginal microbiota has been observed to be linked to the persistent development of cervical carcinogenesis mediated by the human papillomavirus (HPV). Nevertheless, the characteristics of the cervical microbiome in individuals diagnosed with cervical cancer (CC) are still not well understood. Comprehensive analysis was conducted by re-analyzing the cervical 16S rRNA sequencing datasets of a total of 507 samples from six previously published studies. We observed significant alpha and beta diversity differences in between CC, cervical intraepithelial neoplasia (CIN) and normal controls (NC), but not between HPV and NC in the combined dataset. Meta-analysis revealed that opportunistic pernicious microbes Streptococcus, Fusobacterium, Pseudomonas and Anaerococcus were enriched in CC, while Lactobacillus was depleted compared to NC. Members of Gardnerella, Sneathia, Pseudomonas, and Fannyhessea have significantly increased relative abundance compared to other bacteria in the CIN group. Five newly identified bacterial genera were found to differentiate CC from NC, with an area under the curve (AUC) of 0.8947. Moreover, co-occurrence network analysis showed that the most commonly encountered Lactobacillus was strongly negatively correlated with Prevotella. Overall, our study identified a set of potential biomarkers for CC from samples across different geographic regions. Our meta-analysis provided significant insights into the characteristics of dysbiotic cervicovaginal microbiota undergoing CC, which may lead to the development of noninvasive CC diagnostic tools and therapeutic interventions.
Topics: Humans; Female; Uterine Cervical Neoplasms; RNA, Ribosomal, 16S; Dysbiosis; Microbiota; Bacteria; Carcinogenesis; Uterine Cervical Dysplasia; Vagina; Cervix Uteri
PubMed: 38773342
DOI: 10.1038/s41598-024-62531-z -
International Orthopaedics Feb 2024It has been suggested that low-grade infections could be the cause of arthrofibrosis. However, this hypothesis has not been conclusively proven. The aim of this study is...
PURPOSE
It has been suggested that low-grade infections could be the cause of arthrofibrosis. However, this hypothesis has not been conclusively proven. The aim of this study is to assess the incidence of unexpected positive cultures (UPC) in patients undergoing revision total joint arthroplasty for a diagnosis of arthrofibrosis.
METHODS
A retrospective single-centre review was performed. All patients who underwent an aseptic revision due to histologically confirmed arthrofibrosis (based on the synovial-like interface membrane (SLIM) criteria) were included. The incidence of UPC was then calculated.
RESULTS
A total of 147 patients were included. Of these, 100 underwent a total knee arthroplasty (TKA) procedure and 46 a total hip arthroplasty (THA) surgery. One patient had a periprosthetic joint infection and was therefore excluded. Of the 146 included patients, 6 had confirmed UPC (4.08%). The following bacteria were identified: Anaerococcus octavius, Staphylococcus epidermidis, Enterobacter cloacae, Staphylococcus hominis, Streptococcus pluranimalium, Staphylococcus pettenkoferi.
CONCLUSIONS
Our results suggest that the incidence of UPC in patients with arthrofibrosis is low. It is lower than that of UPC in patients that undergo a revision for other causes. There is no proven relationship between histologically confirmed arthrofibrosis following total joint arthroplasty and prosthetic joint infection.
Topics: Humans; Arthroplasty, Replacement, Knee; Retrospective Studies; Arthroplasty, Replacement, Hip; Arthritis, Infectious; Staphylococcus; Reoperation; Prosthesis-Related Infections
PubMed: 37755469
DOI: 10.1007/s00264-023-05990-9 -
Frontiers in Microbiology 2024Human papilloma virus (HPV) is the most common sexually transmitted infection worldwide. Cervicovaginal microbiota plays an important role in HPV infection and is...
INTRODUCTION
Human papilloma virus (HPV) is the most common sexually transmitted infection worldwide. Cervicovaginal microbiota plays an important role in HPV infection and is associated with the development of squamous intraepithelial lesions (SIL). The natural history of cervical cancer involves reversible changes in the cervical tissue from a normal state, in which no neoplastic changes are detected in the squamous epithelium, to varying states of cellular abnormalities that ultimately lead to cervical cancer. Low-grade SIL (LSIL), like another cytological category - atypical squamous cells of undetermined significance (ASCUS), may progress to high-grade SIL (HSIL) and invasive cervical cancer or may regress to a normal state.
METHODS
In this work, we studied cervical canal microbiome in 165 HPV-positive and HPV-negative women of a reproductive age with ASCUS [HPV(+) = 29; HPV(-) = 11], LSIL [HPV(+) = 32; HPV(-) = 25], HSIL [HPV(+) = 46], and the control group with negative for intraepithelial lesion malignancy (NILM) [HPV(-) = 22].
RESULTS AND DISCUSSION
HPV16 is the most prevalent HPV type. We have not found any differences between diversity in studied groups, but several genus [like Prevotella (-value = 0.026), Gardnerella (-value = 0.003), Fannyhessea (-value = 0.024)] more often occurred in HSIL group compared by NILM or LSIL regardless of HPV. We have found statistically significant difference in occurrence or proportion of bacterial genus in studied groups. We also identified that increasing of the ratio of or age of patient lead to higher chance to HSIL, while increasing of the ratio of lead to higher chance to LSIL. Patients with a moderate dysbiosis equally often had either of three types of vaginal microbial communities (CST, Community State Type) with the prevalence of (CST I), (CST II), and (CST III); whereas severe dysbiosis is linked with CST IV involving the microorganisms genera associated with bacterial vaginosis and aerobic vaginitis: , , and .
PubMed: 38550866
DOI: 10.3389/fmicb.2024.1334502