Carbapenem resistance in Bacteroides fragilis: A review of molecular mechanisms

A Review of In Silico and In Vitro Approaches in the Fight Against Carbapenem-Resistant Enterobacterales

OBJECTIVES

The rise in carbapenem-resistant Enterobacterales (CRE) has reinforced the global quest for developing effective therapeutics. Traditional drug discovery approaches have been inadequate in overcoming this challenge due to their resource and time constraints.

METHODS

English literature was searched by structured queries related to our review between January 1, 2020, and December 31, 2024.

RESULTS

The key resistance mechanisms in CRE, such as enzymatic hydrolysis, decreased permeability, and efflux pump overexpression, have been examined in this review. Computational technologies have become pivotal in discovering novel antimicrobial agents with improved accuracy and efficiency. Besides this, the review highlights the advances in structure- and ligand-based drug discovery approaches for identifying potential drugs against CRE. Recent studies demonstrating the use of such in silico techniques to develop targeted drugs against CRE have also been explored. Moreover, this review also underscores the significance of integrating both in silico and in vitro techniques to counter resistance in Enterobacterales, supported by the latest studies. However, these promising computational technologies have a few major drawbacks, such as a lack of standardized parameterization, potentially false positives, and the complexity of effective clinical translations. The drug regulatory barriers also restrict the progress of new antimicrobials for market approval.

CONCLUSION

The use of computational technologies for antimicrobial inhibitor discovery is gaining popularity, and it can be expedited by refining computational techniques and integrating them with reliable in vitro validation. The use of innovative hybrid in silico and in vitro technologies is the need of the hour to tackle CRE and mitigate the global threat of antimicrobial resistance.

Effects of extended anaerobic antibiotic coverage on anaerobic bloodstream infection: A multisite retrospective study

OBJECTIVES

Routine clinical practice with extended anaerobic antibiotic coverage (EAC) has been recently reconsidered for several infections; however, its benefits remain unclear even in patients with anaerobic bacteremia (AB). Here, we aimed to elucidate the effects of EAC on AB prognosis.

METHODS

A multicenter retrospective observational study was conducted in patients with AB. Multivariate logistic regression analysis was performed to assess the effect of EAC on 30-day mortality. Inverse probability of treatment weighting analysis was performed to confirm the robustness of the findings.

RESULTS

In total, 483 patients were included, of whom 387 received EAC and 96 received limited anaerobic antibiotic coverage (LAC). Atypical foci of anaerobic infection, such as urinary tract infection and pneumonia, together with undetectable infection foci, comprised a larger proportion of infection foci in the LAC group than that in the EAC group (46.9% vs 30.5%). The 30-day mortality rates of the EAC and LAC groups were similar (12.5% and 14.2%, respectively; P = 0.664). Primary analysis revealed that EAC was not significantly associated with high mortality (odds ratio [OR], 1.42; 95% confidence interval [CI], 0.7-2.8), whereas source control significantly reduced this risk (OR, 0.28; 95% CI, 0.2-0.5). The sensitivity analysis results were consistent with those of the primary analyses.

CONCLUSION

This study demonstrated a less significant effect of initial EAC on AB compared with source control, particularly on AB with atypical infection foci. These findings would prompt reconsideration of the necessity of an initial EAC in several infections.

Monitoring of Pathogens Carried by Imported Flies and Cockroaches at Shenzhen Ports

This study tested the efficacy of xenomonitoring using contaminated flies and cockroaches at ports in Shenzhen by analysing sample data from imported flies and cockroaches from October 2023 to April 2024 to identify the pathogens they carried. Among all the samples of flies and cockroaches collected, Musca domestica vicina and Blattella germanica accounted for the highest proportion, 27.59% and 66.47%, respectively. Their positive rates for carrying Staphylococcus aureus were also the most significant, reaching 4.35% and 6.47%, respectively. The imported flies and cockroaches mainly came from Asia, with the highest proportion coming from Hong Kong, at 97.71% and 92.11%, respectively. Metagenomic sequencing indicated that the pathogens carried by the flies and cockroaches from different regions of Asia were generally similar but showed some differences. Flies from Southeast Asia, East Asia, South Asia, and West Asia and cockroaches from Southeast Asia, East Asia, and West Asia harboured unique opportunistic pathogens capable of causing gastrointestinal and respiratory infections in humans. Specifically, flies carried pathogens such as Campylobacter jejuni, Bacillus anthracis, Bacteroides fragilis, and Bordetella bronchiseptica, while cockroaches carried B. fragilis, Clostridium tetani, and Bacillus cereus. Our findings provide data support for future risk assessments of pathogens carried by imported vectors.

Genotypic and phenotypic diversity of carbapenem-resistant Bacteroides fragilis strains collected from different clinical origins

OBJECTIVE

Strains of carbapenem-resistant Bacteroides fragilis have frequently emerged in recent years. In China, data on the genotypic and phenotypic characteristics of these antimicrobial-resistant anaerobic bacteria are scarce. Thus, the aim of this study was to characterize clinical isolates of carbapenem-resistant B. fragilis collected from a tertiary hospital in China using whole genome sequencing (WGS), phenotypic susceptibility tests, and a biofilm formation assay.

METHODS

We analyzed 49 B. fragilis strains with different antimicrobial resistance profiles. Antimicrobial susceptibility was determined using the agar dilution method and biofilm formation using a crystal violet assay. Genomic characteristics were analyzed using WGS, and the transcription level of cfiA, which is responsible for carbapenem resistance, was determined using quantitative reverse transcription polymerase chain reaction (PCR). Carbapenem-sensitive isolates were used as controls.

RESULTS

All 49 B. fragilis isolates were biofilm producers and the percentage of carbapenem-resistant isolates was 42.86 % (21/49). The percentage of carbapenem-resistant isolates with medium-to-strong biofilm production ability was significantly lower than that of carbapenem-sensitive isolates (19.1 % vs. 88.9 %, p < 0.01). None of the carbapenem-resistant B. fragilis isolates carried bft. In contrast, 53.6 % (15/28) of the carbapenem-sensitive isolates carried bft, and all of them were fpn(+). All carbapenem-resistant isolates (21/21, 100 %) harbored cfiA and its upstream insertion sequence (IS) element. Three isolates (BF058, BF059, and BF060) carried the IS613 element, which was not immediately adjacent upstream to cfiA but was separated by a 1000-kb sequence encoding vatD. The quantitative PCR assay results revealed the elevated expression of cfiA mRNA among carbapenem-resistant isolates, although the relative expression levels varied greatly among isolates. However, a significant correlation between the relative expression level of cfiA mRNA and phenotypic carbapenem resistance was observed.

CONCLUSIONS

Carbapenem-resistant B. fragilis isolates carried a low frequency of virulence-related genes and showed weaker biofilm formation ability compared with carbapenem-sensitive B. fragilis isolates. CfiA was the dominant mediator of carbapenem resistance in B. fragilis. This study was the first to identify the structural plasticity of the cfiA-IS element, emphasizing the diverse and complex evolution of carbapenem resistance in B. fragilis, which warrants further investigation.

Metabolomics in the Diagnosis of Bacterial Infections

One of the essential factors in the appropriate treatment of infections is accurate and timely laboratory diagnosis. The correct diagnosis of infections plays a vital role in determining desirable therapy and controlling the spread of pathogens. Traditional methods of infection diagnosis are limited by several factors such as insufficient sensitivity and specificity, being time-consuming and laborious, having a low ability to distinguish infection from non-infectious inflammatory conditions and a low potential to predict treatment outcomes. Therefore, it is necessary to find innovative strategies for detecting specific biomarkers in order to diagnose infections. The rapid advancement of metabolomics makes it possible to determine the pattern of metabolite changes in the both of pathogen and the host during an infection. Metabolomics is a method used to assess the levels and type of metabolites in an organism. Metabolites are of low-molecular-weight compounds produced as a result of metabolic processes and pathways within cells. Metabolomics provides valuable data to detect accurate biomarkers of specific biochemical features directly related to certain phenotypes or conditions. This study aimed to review the applications and progress of metabolomics as a biomarker for the diagnosis of bacterial infections.

Molecular characterization and antibiotic resistance of clinical Bacteroides and related genera from a tertiary care center in Türkiye (Turkey)

OBJECTIVES

This study was conducted to measure the prevalence of antibiotic resistance, and corresponding resistance genes among Bacteroides and related genera in a tertiary hospital.

METHODS

We examined 138 clinical strains of Bacteroides, Phocaeicola and Parabacteroides species isolated between July 2018 and June 2022. Antibiotic susceptibility tests were conducted using agar dilution. The bft gene and antibiotic resistance genes were targeted by real-time PCR.

RESULTS

Resistance rates of all strains against ampicillin, cefoxitin, piperacillin-tazobactam, meropenem, imipenem, clindamycin, metronidazole, and tigecycline were 97.8 %, 28.3 %, 11.6 %, 7.9 %, 5.1 %, 47.8 %, 0 % and 4.3 %, respectively. Non-fragilis Bacteroidales spp. (NFB) exhibited lower susceptibility rates compared to B. fragilis for cefoxitin, clindamycin, and piperacillin-tazobactam. The prevalence of meropenem resistance was higher in B. fragilis (15.5 %) than in NFB (0 %). Among all strains, the rates of cepA, cfxA, cfiA, ermF, ermG, ermB, nim, linA, mefA, msrSA, tetQ, tetX, tetX1 and bft genes were 42.8 %, 44.9 %, 8.7 %, 44.2 %, 10.9 %, 2.2 %, 0.7 %, 29.0 %, 17.4 %, 7.2 %, 76.1 %, 8.0 %, 37.7 % and 16.7 %, respectively. In five B. fragilis strains, insertion sequences [IS1187(n = 3), ISBf6(n = 1), IS612B(n = 1)] were detected in the upstream region of cfiA. NimE with ISBf6 on plasmid pBFM29b was detected in one B. fragilis strain, intermediate to metronidazole (MIC = 16 μg/mL). ErmF was the most abundant gene responsible for clindamycin resistance. TetQ and tetX1 genes exhibited a higher frequency in strains that were not susceptible to tigecycline (MIC ≥8 μg/ml).

CONCLUSIONS

Monitoring the resistance trends of Bacteroides and related genera is crucial given the observed resistance to all classes of antibiotics and the presence of various resistance mechanisms.

Overview of anaerobic infections in children and their treatment

Anaerobic bacteria can cause many infections in children. Because they predominant in the normal human skin and mucous membranes bacterial flora, they are often associated with bacterial infections that originate from these sites. They are difficult to isolate from infectious sites, and are frequently missed. Anaerobic infections can occur in all body sites, including the central nervous system, oral cavity, head and neck, chest, abdomen, pelvis, skin, and soft tissues. Anaerobes colonize the newborn after birth and have been isolated in several types of neonatal infections. These include cellulitis of the site of fetal monitoring, neonatal aspiration pneumonia, bacteremia, conjunctivitis, omphalitis, and infant botulism. Management of anaerobic infection is challenging because of the slow growth of these bacteria, by their polymicrobial nature and by the growing antimicrobial resistance of anaerobic. Antimicrobial therapy may be the only treatment required, and may also be an adjunct to a surgical approach. Polymicrobial aerobic-anaerobic infection generally requires delivering antimicrobial therapy effective against all pathogens. The antibiotics with the greatest activity against anaerobes include carbapenems, beta-lactam/beta-lactamase inhibitor combinations, metronidazole, and chloramphenicol. Antimicrobial resistance is growing among anaerobic bacteria. The major increased in resistance have been reported with clindamycin, cephamycins, and moxifloxacin against Bacteroides fragilis group and related strains. Resistance patterns vary between different geographic areas and medical facilities.

Subinhibitory concentrations of meropenem stimulate membrane vesicle production and modulate immune response in Bacteroides fragilis infection

This study explores an adaptation mechanism of Bacteroides fragilis to subinhibitory concentrations of meropenem, characterized by an alteration in the production of membrane vesicles (MVs) and modulation of the host inflammatory response. Using a rat model of infection, we demonstrated a significant increase in the size of MVs accompanied by a nonsignificant increase in their number in the meropenem-treated group compared to the infected control. Both infected groups showed significantly altered hematological parameters and shifts in monocyte on day 8 (average increase of 21.5 %). At the same time, significant changes in neutrophils (decrease by 26 %) and eosinophils (increase by 3 %) were observed only in the infected group but not in the infected meropenem-treated group. On day 16, increased macrophage activation, neovascularization, and fibrosis were observed in the tissues of the antibiotic-treated group. Immunological profile analysis revealed a slight increase in the levels of pro-inflammatory cytokines (IL-5, IL-6, IFN-γ and G-CSF) on day 8 of the experiment, followed by a sharp decrease on day 16 in both infected groups compared to the negative control. At the same time, network analysis of correlations between these immunological factors showed complex changes in response to subinhibitory concentrations of meropenem. The bacterial load did not differ between the infected groups on days 8 and 16, but only in the meropenem-free group a significant decrease in the number of bacteria was observed on day 16 in all samples. These findings suggest that subinhibitory antibiotic concentrations can influence the pathophysiological progression of B. fragilis infection, modulating both the bacterial response and the host immune reaction, potentially leading to a more complex and chronic disease course.

Multi-omics approach for understanding the response of Bacteroides fragilis to carbapenems

Background

The prevalence of Bacteroides fragilis isolates resistant to first-line beta-lactam drugs is increasing, resulting in reduced treatment efficacy. Investigating the bacterial transcriptome and proteome can uncover links between bacterial genes and resistance mechanisms. In this study, we experimentally assessed in vitro the transcriptional and proteomic profiles of B. fragilis exposed to SICs of meropenem, an effective antimicrobial agent, collected from patients with intra-abdominal diseases at Astana City Hospital, Kazakhstan.

Methods

B. fragilis was cultured in brain heart infusion broth and sub-cultured every 48 h for 8 days in media with and without meropenem. Total RNA was extracted from the liquid cultures using a commercial RNeasy mini kit, and strand-specific RNA sequencing (RNA-seq) was performed on the DNBSEQ platform. Raw RNA-seq data were retrieved from BioProject No. PRJNA531645 and uploaded to the NCBI Sequence Read Archive (accession no. SRX22081155). Proteins of B. fragilis were extracted and separated using sodium dodecyl sulphate-polyacrylamide gel electrophoresis, followed by analysis of the eluted peptides using liquid chromatography-tandem mass spectrometry. Cluster analysis utilised the Database for Annotation, Visualisation, and Integrated Discovery.

Results

The subinhibitory concentration (SIC) of meropenem was determined to be 0.5 μg/L (minimum inhibitory concentration: 1). Mapping of reads to the reference genome identified 2477 expressed genes in all B. fragilis BFR KZ01 samples. Ten differentially expressed genes (DEGs) were common across comparison groups during and post-antibiotic exposure (wMEM vs. MEM2 and MEM2 vs. rMEM8); however, no substantially enriched Gene Ontology terms were identified. The cluster analysis highlighted a significant enrichment cluster (W-0560 oxidoreductase) of DEGs following antibiotic withdrawal. In total, 859 B. fragilis proteins were identified, with the expressions of three proteins, 3-oxoacyl-[acyl carrier protein] reductase, acetyl-CoA carboxylase biotin carboxylase subunit, and beta-ketoacyl-ACP synthase III, being upregulated in the enriched protein folding category. Notably, chaperone proteins such as FKBP-type peptidyl-prolyl cis-trans isomerases (involved in the cis-trans isomerisation of prolyl peptide bonds) and GroES (a co-chaperone functioning with GroEL) were also identified.

Conclusions

Under the influence of low doses of antibiotics defense mechanisms are activated which contribute to the emergence of resistance. These results provide insight into the response of B. fragilis to meropenem exposure, mainly at the SIC, contributing to the understanding bacterial survival strategies under stress conditions.

Metabolic changes associated with polysaccharide utilization reduce susceptibility to some β-lactams in Bacteroides thetaiotaomicron

Antibiotic therapy alters bacterial abundance and metabolism in the gut microbiome, leading to dysbiosis and opportunistic infections. Bacteroides thetaiotaomicron (Bth) is both a commensal in the gut and an opportunistic pathogen in other body sites. Past work has shown that Bth responds to β-lactam treatment differently depending on the metabolic environment both in vitro and in vivo. Studies of other bacteria show that an increase in respiratory metabolism independent of growth rate promotes susceptibility to bactericidal antibiotics. We propose that Bth enters a protected state linked to an increase in polysaccharide utilization and a decrease in the use of simple sugars. Here, we apply antibiotic susceptibility testing, transcriptomic analysis, and genetic manipulation to characterize this polysaccharide-mediated tolerance (PM tolerance) phenotype. We found that a variety of mono- and disaccharides increased the susceptibility of Bth to several different β-lactams compared to polysaccharides. Transcriptomics indicated a metabolic shift from reductive to oxidative branches of the tricarboxylic acid cycle on polysaccharides. Accordingly, supplementation with intermediates of central carbon metabolism had varying effects on PM tolerance. Transcriptional analysis also showed a decrease in the expression of the electron transport chain (ETC) protein NQR and an increase in the ETC protein NUO, when given fiber versus glucose. Deletion of NQR increased Bth susceptibility while deletion of NUO and a third ETC protein NDH2 had no effect. This work confirms that carbon source utilization modulates antibiotic susceptibility in Bth and that anaerobic respiratory metabolism and the ETC play an essential role.IMPORTANCEAntibiotics are indispensable medications that revolutionized modern medicine. However, their effectiveness is challenged by a large array of resistance and tolerance mechanisms. Treatment with antibiotics also disrupts the gut microbiome which can adversely affect health. Bacteroides are prevalent in the gut microbiome and yet are frequently involved in anaerobic infections. Thus, understanding how antibiotics affect these bacteria is necessary to implement proper treatment. Recent work has investigated the role of metabolism in antibiotic susceptibility in distantly related bacteria such as Escherichia coli. Using antibiotic susceptibility testing, transcriptomics, and genetic manipulation, we demonstrate that polysaccharides reduce β-lactam susceptibility when compared to monosaccharides. This finding underscores the profound impact of metabolic adaptation on the therapeutic efficacy of antibiotics. In the long term, this work indicates that modulation of metabolism could make Bacteroides more susceptible during infections or protect them in the context of the microbiome.

The wound microbiota: microbial mechanisms of impaired wound healing and infection

The skin barrier protects the human body from invasion by exogenous and pathogenic microorganisms. A breach in this barrier exposes the underlying tissue to microbial contamination, which can lead to infection, delayed healing, and further loss of tissue and organ integrity. Delayed wound healing and chronic wounds are associated with comorbidities, including diabetes, advanced age, immunosuppression and autoimmune disease. The wound microbiota can influence each stage of the multi-factorial repair process and influence the likelihood of an infection. Pathogens that commonly infect wounds, such as Staphylococcus aureus and Pseudomonas aeruginosa, express specialized virulence factors that facilitate adherence and invasion. Biofilm formation and other polymicrobial interactions contribute to host immunity evasion and resistance to antimicrobial therapies. Anaerobic organisms, fungal and viral pathogens, and emerging drug-resistant microorganisms present unique challenges for diagnosis and therapy. In this Review, we explore the current understanding of how microorganisms present in wounds impact the process of skin repair and lead to infection through their actions on the host and the other microbial wound inhabitants.

Co-occurrence of the cephalosporinase cepA and carbapenemase cfiA genes in a Bacteroides fragilis division II strain, an unexpected finding

BACKGROUND

Bacteroides fragilis, an anaerobic gut bacterium and opportunistic pathogen, comprises two genetically divergent groups (or divisions) at the species level. Differences exist both in the core and accessory genomes and the beta-lactamase genes, with the cephalosporinase gene cepA represented only in division I and the carbapenemase gene cfiA only in division II.

METHODS

Multidrug resistance in a clinical B. fragilis strain was examined by whole-genome sequencing.

RESULTS

Strain CNM20200260 carried the antimicrobial resistance genes cepA, cfiA2, ant(6'), erm(F), mef(En2), est(T), tet(Q) and cat(A), along with 82-Phe mutation in gyrA (together with 47 amino acid changes in gyrA/B and parC/parE). bexA/B and other efflux pump genes were also observed. None of the detected insertion sequences was located upstream of cfiA2. The genome-based taxonomy coefficients (average nucleotide identity, DNA-DNA hybridization similarity and difference in genomic G + C%) with respect to genomes of the strains of B. fragilis division II and the novel species Bacteroides hominis (both cfiA-positive) met the criteria for CNM20200260 to belong to either species (>95%, >70% and <1%, respectively). No such similarity was seen with type strain NCTC 9343 or the representative genome FDAARGOS 1225 of B. fragilis (division I, cfiA-negative). Strain CNM20200260 harboured four out of nine Kyoto Encyclopedia of Genes and Genomes orthologues defined for division I and one of two defined for division II.

CONCLUSIONS

This is the first description of the co-occurrence of cepA and cfiA in a Bacteroides strain, confirming the complexity of the taxonomy of this species.

Novel and rare β-lactamase genes of Bacteroides fragilis group species: Detection of the genes and characterization of their genetic backgrounds

OBJECTIVES

This study screened the prevalence of rare β-lactamase genes in Bacteroides fragilis group strains from clinical specimens and normal microbiota and examined the genetic properties of the strains carrying these genes.

METHODS

blaHGD1, blaOXA347, cblA, crxA, and pbbA were detected by real-time polymerase chain reaction in collections of Bacteroides strains from clinical (n = 406) and fecal (n = 184) samples. To examine the genetic backgrounds of the samples, end-point PCR, FT-IR, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were used.

RESULTS

All B. uniformis isolates were positive for cblA in both collections. Although crxA was B. xylanisolvens-specific and associated with carbapenem resistance, it was only found in six fecal and three clinical B. xylanisolvens strains. Moreover, the crxA-positive strains were not clonal among B. xylanisolvens (contrary to cfiA in B. fragilis), implicating a rate of mobility or emergence by independent evolutionary events. The Phocaeicola (B.) vulgatus/P. dorei-specific gene blaHGD1 was detected among all P. vulgatus/P. dorei isolates from fecal (n = 36) and clinical (n = 26) samples. No blaOXA347-carrying isolate was found from European collections, but all US samples (n = 6) were positive. For three clinical isolates belonging to B. thetaiotaomicron (n = 2) and B. ovatus (n = 1), pbbA was detected on mobile genetic elements, and pbbA-positive strains displayed non-susceptibility to piperacillin or piperacillin/tazobactam phenotypically.

CONCLUSIONS

Based on these observations, β-lactamases produced by rare β-lactamase genes in B. fragilis group strains should not be overlooked because they could encode important resistance phenotypes.

Fifty years devoted to anaerobes: historical, lessons, and highlights

Renew interest and enthusiasm for anaerobes stem from both technological improvements (culture media, production of an adequate anaerobic atmosphere, identification methods) and greater awareness on the part of clinicians. Anaerobic infections were historically treated empirically, targeting the species known to be involved in each type of infection. Prevotella, fusobacteria, and Gram-positive cocci (GPAC) were considered responsible for infections above the diaphragm whereas for intra-abdominal infections, Bacteroides of the fragilis group (BFG), GPAC and clostridia were predominantly implicated. The antibiotic susceptibility of anaerobes was only taken into consideration by the clinician in the event of treatment failure or when faced with infections by multidrug-resistant bacteria (MDR). The evolution of antibiotic resistance together with clinical failures due to the absence of detection of hetero-resistant clones has resulted in a greater need for accessible antibiotic susceptibility testing (AST) and disc diffusion method. Improved isolation and identification of anaerobes, along with the availability of accessible and robust methods for performing AST, will ensure that treatment, whether empirical or guided by an antibiogram, will lead to better outcomes for anaerobic infections.

Genomic analyses of Bacteroides fragilis: subdivisions I and II represent distinct species

Introduction. Bacteroides fragilis is a Gram-negative anaerobe that is a member of the human gastrointestinal microbiota and is frequently found as an extra-intestinal opportunistic pathogen. B. fragilis comprises two distinct groups - divisions I and II - characterized by the presence/absence of genes [cepA and ccrA (cfiA), respectively] that confer resistance to β-lactam antibiotics by either serine or metallo-β-lactamase production. No large-scale analyses of publicly available B. fragilis sequence data have been undertaken, and the resistome of the species remains poorly defined.Hypothesis/Gap Statement. Reclassification of divisions I and II B. fragilis as two distinct species has been proposed but additional evidence is required.Aims. To investigate the genomic diversity of GenBank B. fragilis genomes and establish the prevalence of division I and II strains among publicly available B. fragilis genomes, and to generate further evidence to demonstrate that B. fragilis division I and II strains represent distinct genomospecies.Methodology. High-quality (n=377) genomes listed as B. fragilis in GenBank were included in pangenome and functional analyses. Genome data were also subject to resistome profiling using The Comprehensive Antibiotic Resistance Database.Results. Average nucleotide identity and phylogenetic analyses showed B. fragilis divisions I and II represent distinct species: B. fragilis sensu stricto (n=275 genomes) and B. fragilis A (n=102 genomes; Genome Taxonomy Database designation), respectively. Exploration of the pangenome of B. fragilis sensu stricto and B. fragilis A revealed separation of the two species at the core and accessory gene levels.Conclusion. The findings indicate that B. fragilis A, previously referred to as division II B. fragilis, is an individual species and distinct from B. fragilis sensu stricto. The B. fragilis pangenome analysis supported previous genomic, phylogenetic and resistome screening analyses collectively reinforcing that divisions I and II are two separate species. In addition, it was confirmed that differences in the accessory genes of B. fragilis divisions I and II are primarily associated with carbohydrate metabolism and suggest that differences other than antimicrobial resistance could also be used to distinguish between these two species.

The Abnormal Accumulation of Lipopolysaccharide Secreted by Enriched Gram-Negative Bacteria Increases the Risk of Rotavirus Colonization in Young Adults

Human rotavirus (HRV) is an enteric virus that causes infantile diarrhea. However, the risk factors contributing to HRV colonization in young adults have not been thoroughly investigated. Here, we compared the differences in dietary habits and composition of gut microbiota between asymptomatic HRV-infected young adults and their healthy counterparts and investigated potential risk factors contributing to HRV colonization. Our results indicated that asymptomatic HRV-infected adults had an excessive intake of milk and dairy and high levels of veterinary antibiotics (VAs) and preferred veterinary antibiotic (PVAs) residues in urine samples. Their gut microbiota is characterized by abundant Gram-negative (G-) bacteria and high concentrations of lipopolysaccharide (LPS). Several opportunistic pathogens provide discriminatory power to asymptomatic, HRV-infected adults. Finally, we observed an association between HRV colonization and disrupted gut microbiota caused by the exposure to VAs and PVAs. Our study reveals the traits of disrupted gut microbiota in asymptomatic HRV-infected adults and provides a potential avenue for gut microbiota-based prevention strategies for HRV colonization.

Antimicrobial Effects of Mouse Adipose-Derived Mesenchymal Stem Cells Encapsulated in Collagen-Fibrin Hydrogel Scaffolds on Bacteroides fragilis Wound Infection in vivo

Background

Anaerobes are the causative agents of many wound infections. B. fragilis is the most prevalent endogenous anaerobic bacterium causes a wide range of diseases, including wound infections. This study aimed to assess the antibacterial effect of mouse adipocyte derived-mesenchymal stem cell (AD-MSCs) encapsulated in collagen-fibrin (CF) hydrogel scaffolds on B. fragilis wound infection in an animal model.

Methods

Stem cells were extracted from mouse adipose tissue and confirmed by surface markers using flow cytometry analysis. The possibility of differentiation of stem cells into osteoblast and adipocyte cells was also assessed. The extracted stem cells were encapsulated in the CF scaffold. B. fragilis wound infection was induced in rats, and then following 24 h, collagen and fibrin-encapsulated mesenchymal stem cells (MSCs) were applied to dress the wound. One week later, a standard colony count test monitored the bacterial load in the infected rats.

Results

MSCs were characterized as positive for CD44, CD90, and CD105 markers and negative for CD34, which were able to differentiate into osteoblast and adipocyte cells. AD-MSCs encapsulated with collagen and fibrin scaffolds showed ameliorating effects on B. fragilis wound infection. Additionally, AD-MSCs with a collagen scaffold (54 CFU/g) indicated a greater effect on wound infection than AD-MSCs with a fibrin scaffold (97 CFU/g). The combined CF scaffold demonstrated the highest reduction in colony count (the bacteria load down to 29 CFU/g) in the wound infection.

Conclusion

Our findings reveal that the use of collagen and fibrin scaffold in combination with mouse AD-MSCs is a promising alternative treatment for B. fragilis.

Antimicrobial susceptibility of Bacteroides fragilis group organisms in Hong Kong, 2020-2021

OBJECTIVES

This retrospective study analyzed the susceptibility levels of Bacteroides fragilis group (BFG) in a hospital-based laboratory where disk diffusion test (DDT) was routinely performed. Isolates non-susceptible to imipenem and metronidazole by DDT were further investigated using a gradient method.

METHODS

The DDT and MIC susceptibility data of clindamycin, metronidazole, moxifloxacin and imipenem obtained on Brucella blood agar for 1264 non-duplicated isolates during 2020-2021 were analyzed. Species identification was obtained by matrix-assisted laser desorption ionization time-of-flight mass spectrometry and 16S rRNA sequencing. Interpretative agreement of DDT results using the 2015 EUCAST tentative and 2021 CA-SFM breakpoints was compared against MIC as the reference.

RESULTS

The dataset included 604 B. fragilis (483 division I, 121 division II isolates), 415 non-fragilis Bacteroides, 177 Phocaeicola and 68 Parabacteroides. Susceptibility rates for clindamycin (22.1-62.1%) and moxifloxacin (59.9-80.9%) were low and many had no inhibition zones. At the EUCAST and CA-SFM breakpoints, 83.0 and 89.4% were imipenem-susceptible, and 89.6% and 97.4 were metronidazole-susceptible. MIC testing confirmed 11.4% and 2.8% isolates as imipenem-non-susceptible and metronidazole-resistant, respectively. Significant numbers of false-susceptibility and/or false-resistance results were observed at the CA-SFM breakpoint but not the EUCAST breakpoint. Higher rates of imipenem and/or metronidazole resistance were detected in B. fragilis division II, B. caccae, B. ovatus, B. salyersiae, B. stercoris and Parabacteroides. Co-resistance to imipenem and metronidazole was detected in 3 B. fragilis division II isolates.

CONCLUSIONS

The data demonstrated emerging BFG resistance to several important anti-anaerobic antibiotics and highlights the importance of anaerobic susceptibility testing in clinical laboratories to guide therapy.

Phenotypic and genotypic identification of carbapenem resistance in Bacteroides fragilis clinical strains

Bacteroides fragilis is an important etiological agent of serious infections in humans. Rapid methods, readily adaptable to use in medical laboratories, are needed to detect antibiotic resistance and decrease the likelihood of therapy failure. The aim of this study was to determine the prevalence of B. fragilis cfiA-positive isolates. The second purpose was to investigate the carbapenemase activity in B. fragilis strains by Carba NP test. In the study, 5.2% of B. fragilis isolates are phenotypically resistant to meropenem. The cfiA gene was identified in 6.1% of B. fragilis isolates. The MICs of meropenem were significantly higher in cfiA-positive strains. The presence of the cfiA gene along with the IS1186 was detected in one B. fragilis strain which was resistant to meropenem (MIC 1.5 mg/L). The Carba NP test results were positive for all the cfiA-positive strains, including those susceptible to carbapenems based on their MIC values. A review of the literature revealed that the rate of B. fragilis with the cfiA gene varies from 7.6 to 38.9% worldwide. Presented results are in line with the other European studies. Phenotypic testing with the Carba NP test, it seems to be a viable alternative for the cfiA gene detection in B. fragilis isolates. The positive result obtained is of greater clinical importance than the detection of the gene cfiA.

Characterization of a Bacteriophage GEC_vB_Bfr_UZM3 Active against Bacteroides fragilis

Bacteroides fragilis is a commensal gut bacterium that is associated with a number of blood and tissue infections. It has not yet been recognized as one of the drug-resistant human pathogens, but cases of the refractory infections, caused by strains that are not susceptible to the common antibiotic regimes established for B. fragilis, have been more frequently reported. Bacteriophages (phages) were found to be a successful antibacterial alternative to antibiotic therapy in many cases of multidrug-resistant (MDR) bacterial infections. We have characterized the bacteriophage GEC_vB_Bfr_UZM3 (UZM3), which was used for the treatment of a patient with a chronic osteomyelitis caused by a B. fragilis mixed infection. Studied biological and morphological properties of UZM3 showed that it seems to represent a strictly lytic phage belonging to a siphovirus morphotype. It is characterized by high stability at body temperature and in pH environments for about 6 h. Whole genome sequencing analysis of the phage UZM3 showed that it does not harbor any known virulence genes and can be considered as a potential therapeutic phage to be used against B. fragilis infections.

High prevalence of cfiA positive Bacteroides fragilis isolates collected at a teaching hospital in Hohhot, China

OBJECTIVES

Carbapenem-resistant Bacteroides fragilis has emerged globally and cfiA is the key underlying factor. However, the prevalence of cfiA-positive carbapenem-resistant B. fragilis varies among countries. Therefore, we investigated the prevalence of cfiA-positive B. fragilis clinical isolates in a tertiary hospital in China.

METHODS

Carbapenem-resistant cfiA-positive B. fragilis isolates were identified using polymerase chain reaction. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to identify the characteristic mass spectra of cfiA-positive B. fragilis.

RESULTS

The prevalence of cfiA among 153 B. fragilis isolates was 22.2% (34/153), when 20.6% (7/34) cfiA-positive B. fragilis strains were isolated from pediatric patients. Twenty-one carbapenem-resistant B. fragilis isolates were identified and were all positive with cfiA gene. Two characteristic peaks (4825 and 9642 Da) were identified using MALDI-TOF MS, and the sensitivity, specificity, and both the positive and negative predictive values of these two peaks were 100%. A new peak shift from 9627 Da for cfiA-negative isolates to 9642 Da for cfiA-positive isolates was observed.

CONCLUSIONS

A high prevalence of cfiA was observed among B.fragilis isolates in this study, especially those isolated from pediatric patients. Characteristic MS spectra can accurately discriminate cfiA-positive and -negative B. fragilis isolates and can contribute to the rapid screening of cfiA-positive B. fragilis isolates in clinical laboratories.