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Microbiology Spectrum May 2024Lovebugs appeared in large numbers across a wide area in Seoul, South Korea, in June 2023. The sudden appearance of exotic insects not only discomforts people but also...
Lovebugs appeared in large numbers across a wide area in Seoul, South Korea, in June 2023. The sudden appearance of exotic insects not only discomforts people but also fosters anxiety, as their potential for pathogen transmission would be unknown. In this study, targeted next-generation sequencing (NGS) of the 16S rRNA gene V4 region was performed using iSeq 100 to screen for bacteria in lovebugs. Forty-one lovebugs (20 females and 21 males) collected in Seoul, Korea, were identified as based on mitochondrial cytochrome oxidase subunit 1 sequencing data using PCR. We analyzed the microbiome of the lovebugs and detected 453 species of bacteria. Among all bacteria screened based on NGS, was detected in all samples with an average relative abundance of 80.40%, followed by and . Diversity (alpha and beta) between females and males did not differ; however, only showed a higher relative abundance in females. Sequencing analysis of using a gene-specific primer by PCR showed that it had higher sequence similarity to the symbiont of arthropods than to the spotted fever group rickettsiae. Eleven samples in which was detected by iSeq 100 were confirmed by PCR and exhibited 100% sequence identity to strain DSM 23570. Consequently, the likelihood of pathogen transmission to humans is low. The applied method may play a crucial role in swiftly identifying bacterial species in the event of future outbreaks of exotic insects that may be harmful to humans.IMPORTANCELovebugs have recently emerged in large numbers in Seoul, causing major concern regarding potential health risks. By performing the next-generation sequencing of the 16S rRNA gene V4 region, we comprehensively examined the microbiome of these insects. We identified the presence of numerous bacteria, including and . Reassuringly, subsequent tests confirmed that these detected bacteria were not pathogenic. The present study addresses health concerns related to lovebugs and shows the accuracy and efficiency of our detection technique. Such methods prove invaluable for rapidly identifying bacterial species during potential outbreaks of unfamiliar insects, thereby ensuring public safety.
PubMed: 38809007
DOI: 10.1128/spectrum.03809-23 -
Frontiers in Microbiology 2024The fungus (=) is commonly saprotrophic, exhibiting a nature of decomposing organic matter. Additionally, it serves as a crucial starter in food fermentation and can...
The fungus (=) is commonly saprotrophic, exhibiting a nature of decomposing organic matter. Additionally, it serves as a crucial starter in food fermentation and can act as a pathogen causing mucormycosis in humans and animals. In this study, two distinct endofungal bacteria (EFBs), associated with individual strains of , were identified using live/dead staining, fluorescence hybridization, transmission electron microscopy, and 16S rDNA sequencing. The roles of these bacteria were elucidated through antibiotic treatment, pure cultivation, and comparative genomics. The bacterial endosymbionts, EFB03792 and EFB03829, were purified from the host fungal strains XY03792 and XY03829, respectively. Notably, this study marks the first report of as an EFB genus. Compared to its free-living counterparts, EFB03792 exhibited 28 specific virulence factor-related genes, six specific CE10 family genes, and 74 genes associated with type III secretion system (T3SS), emphasizing its pivotal role in invasion and colonization. Furthermore, this study introduces as a new host for EFB , with EFB contributing to host sporulation. Despite a visibly reduced genome, EFB03829 displayed a substantial number of virulence factor-related genes, CE10 family genes, T3SS genes, mobile elements, and significant gene rearrangement. While EFBs have been previously identified in , their toxin-producing potential in food fermentation has not been explored until this study. The discovery of these two new EFBs highlights their potential for toxin production within , laying the groundwork for identifying suitable strains for fermentation processes.
PubMed: 38486702
DOI: 10.3389/fmicb.2024.1346252 -
Microbiology Resource Announcements Apr 2024is a pathogenic bacterium naturally resistant to various antimicrobials, including colistin. Here, we report the whole-genome sequence of , which exhibits high-level...
is a pathogenic bacterium naturally resistant to various antimicrobials, including colistin. Here, we report the whole-genome sequence of , which exhibits high-level multidrug resistance, isolated from a hospitalized patient in Japan.
PubMed: 38470265
DOI: 10.1128/mra.01166-23 -
Journal of Global Antimicrobial... Mar 2024Gram-negative pathogens causing respiratory infection in people with cystic fibrosis and bronchiectasis are becoming progressively more resistant to conventional...
OBJECTIVES
Gram-negative pathogens causing respiratory infection in people with cystic fibrosis and bronchiectasis are becoming progressively more resistant to conventional antibiotics. Although cefiderocol is licenced for the treatment of infections due to Gram-negative organisms, there are limited data on the activity of cefiderocol against pathogens associated with chronic respiratory diseases. The aim of this study was to determine the susceptibility of Gram-negative pathogens from cystic fibrosis and bronchiectasis to cefiderocol and comparator antibiotics.
METHODS
Minimal inhibitory concentrations (MICs) of cefiderocol and 15 comparator antibiotics were determined by broth microdilution against 300 respiratory isolates: Burkholderia spp., Stenotrophomonas spp., Achromobacter spp., Ralstonia spp. and Pandoraea spp., and used to calculate the MIC of each antibiotic required to inhibit 50% (MIC) and 90% (MIC) of isolates.
RESULTS
The MIC and MIC of cefiderocol for all 300 isolates tested was 0.25 and 32 mg/L, with 232 (77.3%) isolates having an MIC value ≤2 mg/L. In addition, cefiderocol demonstrated excellent activity against Stenotrophomonas spp. and Achromobacter spp. isolates, with 86.7% and 87.2%, respectively, exhibiting an MIC of 2 mg/L. Tigecycline also demonstrated good activity against all isolates with an MIC of <0.5 mg/L.
CONCLUSIONS
These in vitro data demonstrated that cefiderocol had greater activity than most comparator antibiotics and could be an alternative treatment option for respiratory infection caused by these pathogens that has not responded to first-line therapy.
Topics: Humans; Cefiderocol; Cephalosporins; Cystic Fibrosis; Gram-Negative Bacteria; Drug Resistance, Multiple, Bacterial; Anti-Bacterial Agents; Bronchiectasis; Respiratory Tract Infections
PubMed: 38336228
DOI: 10.1016/j.jgar.2024.01.023 -
Frontiers in Microbiology 2023Pathogenic invasion of profoundly altered microflora in the crop production system, impacting diversity and composition in both artificial bed-log and fruiting bodies....
Pathogenic invasion of profoundly altered microflora in the crop production system, impacting diversity and composition in both artificial bed-log and fruiting bodies. A more complex ecological network between the diseased and healthy bodies. Researchers still have poor knowledge about how the important agricultural relationship between the composition of the microbiome of the artificial bed-log and the fruiting bodies is infected by the pathogenic invasive microbes , but this knowledge is crucial if we want to use or improve it. Here, we investigated 8 groups (48 biological samples) across 5 growth stages of the production system using metagenomic technology. Diseased and healthy fruiting bodies exhibited distinct microbial compositions, while core members in artificial bed-logs remained stable. Core microbiota analysis highlighted and bacterial genera, as well as , , , and fungal genera as biomarker species after the bodies were treated with the pathogenic invasive microbes . In diseased bodies, these core members upregulated pathways including polymyxin resistance, L-arginine degradation II, superpathway of L-arginine and L-ornithine degradation, glucose degradation (oxidative), glucose and glucose-1-phosphate degradation, promoting fruit spoilage. Our data confirm that plays an important role in the early stages of disease development in the crop generation system. The exposed volatile core microbiome may play an important role in accelerating -induced decay of fruiting bodies.
PubMed: 38029184
DOI: 10.3389/fmicb.2023.1263982 -
Microbiology Resource Announcements Dec 2023We report here seven draft genomes of bacterial strains from two Danish wastewater facilities, two of which might be characterized as a new group within the and...
We report here seven draft genomes of bacterial strains from two Danish wastewater facilities, two of which might be characterized as a new group within the and genera, respectively. These genomes will provide useful references for understanding bacterial interactions and horizontal gene transfer within bacterial communities.
PubMed: 37966239
DOI: 10.1128/MRA.00529-23 -
Emerging Infectious Diseases Nov 2023Pandoraea spp. are gram-negative, nonfermenting rods mainly known to infect patients with cystic fibrosis (CF). Outbreaks have been reported from several CF centers. We... (Review)
Review
Pandoraea spp. are gram-negative, nonfermenting rods mainly known to infect patients with cystic fibrosis (CF). Outbreaks have been reported from several CF centers. We report a Pandoraea spp. outbreak comprising 24 non-CF patients at a large university hospital and a neighboring heart center in Germany during July 2019-December 2021. Common features in the patients were critical illness, invasive ventilation, antimicrobial pretreatment, and preceding surgery. Complicated and relapsing clinical courses were observed in cases with intraabdominal infections but not those with lower respiratory tract infections. Genomic analysis of 15 isolates identified Pandoraea commovens as the genetically most similar species and confirmed the clonality of the outbreak strain, designated P. commovens strain LB-19-202-79. The strain exhibited resistance to most antimicrobial drugs except ampicillin/sulbactam, imipenem, and trimethoprim/sulfamethoxazole. Our findings suggest Pandoraea spp. can spread among non-CF patients and underscore that clinicians and microbiologists should be vigilant in detecting and assessing unusual pathogens.
Topics: Humans; Cystic Fibrosis; Gram-Negative Bacteria; Anti-Infective Agents; Trimethoprim, Sulfamethoxazole Drug Combination; Burkholderiaceae; Germany
PubMed: 37877517
DOI: 10.3201/eid2911.230493 -
Cancer Research and Treatment Jan 2024Triple-negative breast cancer (TNBC) is a breast cancer subtype that has poor prognosis and exhibits a unique tumor microenvironment. Analysis of the tumor microbiome...
PURPOSE
Triple-negative breast cancer (TNBC) is a breast cancer subtype that has poor prognosis and exhibits a unique tumor microenvironment. Analysis of the tumor microbiome has indicated a relationship between the tumor microenvironment and treatment response. Therefore, we attempted to reveal the role of the tumor microbiome in patients with TNBC receiving neoadjuvant chemotherapy.
MATERIALS AND METHODS
We collected TNBC patient RNA-sequencing samples from the Gene Expression Omnibus and extracted microbiome count data. Differential and relative abundance were estimated with linear discriminant analysis effect size. We calculated the immune cell fraction with CIBERSORTx and conducted survival analysis using the Cancer Genome Atlas patient data. Correlations between the microbiome and immune cell compositions were analyzed and a prediction model was constructed to estimate drug response.
RESULTS
Among the pathological complete response group (pCR), the beta diversity varied considerably; consequently, 20 genera and 24 species were observed to express a significant differential and relative abundance. Pandoraea pulmonicola and Brucella melitensis were found to be important features in determining drug response. In correlation analysis, Geosporobacter ferrireducens, Streptococcus sanguinis, and resting natural killer cells were the most correlated factors in the pCR, whereas Nitrosospira briensis, Plantactinospora sp. BC1, and regulatory T cells were key features in the residual disease group.
CONCLUSION
Our study demonstrated that the microbiome analysis of tumor tissue can predict chemotherapy response of patients with TNBC. Further, the immunological tumor microenvironment may be impacted by the tumor microbiome, thereby affecting the corresponding survival and treatment response.
Topics: Humans; Triple Negative Breast Neoplasms; Neoadjuvant Therapy; Tumor Microenvironment; Antineoplastic Combined Chemotherapy Protocols; Prognosis
PubMed: 37499695
DOI: 10.4143/crt.2023.330 -
Microorganisms May 2023The respiratory tract of lung transplant recipients (LTR) is likely to be colonized with non-fermentative Gram-negative rods. As a consequence of the improvements in... (Review)
Review
The respiratory tract of lung transplant recipients (LTR) is likely to be colonized with non-fermentative Gram-negative rods. As a consequence of the improvements in molecular sequencing and taxonomy, an increasing number of bacterial species have been described. We performed a review of the literature of bacterial infections in LTR involving non-fermentative Gram-negative rods with exclusion of , , spp. and spp. Overall, non-fermenting GNR were recovered from 17 LTR involving the following genera: , , , , , and . We then discuss the issues raised by these bacteria, including detection and identification, antimicrobial resistance, pathogenesis, and cross-transmission.
PubMed: 37374970
DOI: 10.3390/microorganisms11061468 -
International Microbiology : the... Feb 2024Polymyxin B is considered a last-line therapeutic option against multidrug-resistant gram-negative bacteria, especially in COVID-19 coinfections or other serious...
BACKGROUND
Polymyxin B is considered a last-line therapeutic option against multidrug-resistant gram-negative bacteria, especially in COVID-19 coinfections or other serious infections. However, the risk of antimicrobial resistance and its spread to the environment should be brought to the forefront.
METHODS
Pandoraea pnomenusa M202 was isolated under selection with 8 mg/L polymyxin B from hospital sewage and then was sequenced by the PacBio RS II and Illumina HiSeq 4000 platforms. Mating experiments were performed to evaluate the transfer of the major facilitator superfamily (MFS) transporter in genomic islands (GIs) to Escherichia coli 25DN. The recombinant E. coli strain Mrc-3 harboring MFS transporter encoding gene FKQ53_RS21695 was also constructed. The influence of efflux pump inhibitors (EPIs) on MICs was determined. The mechanism of polymyxin B excretion mediated by FKQ53_RS21695 was investigated by Discovery Studio 2.0 based on homology modeling.
RESULTS
The MIC of polymyxin B for the multidrug-resistant bacterial strain P. pnomenusa M202, isolated from hospital sewage, was 96 mg/L. GI-M202a, harboring an MFS transporter-encoding gene and conjugative transfer protein-encoding genes of the type IV secretion system, was identified in P. pnomenusa M202. The mating experiment between M202 and E. coli 25DN reflected the transferability of polymyxin B resistance via GI-M202a. EPI and heterogeneous expression assays also suggested that the MFS transporter gene FKQ53_RS21695 in GI-M202a was responsible for polymyxin B resistance. Molecular docking revealed that the polymyxin B fatty acyl group inserts into the hydrophobic region of the transmembrane core with Pi-alkyl and unfavorable bump interactions, and then polymyxin B rotates around Tyr43 to externally display the peptide group during the efflux process, accompanied by an inward-to-outward conformational change in the MFS transporter. Additionally, verapamil and CCCP exhibited significant inhibition via competition for binding sites.
CONCLUSIONS
These findings demonstrated that GI-M202a along with the MFS transporter FKQ53_RS21695 in P. pnomenusa M202 could mediate the transmission of polymyxin B resistance.
Topics: Polymyxin B; Escherichia coli; Genomic Islands; Molecular Docking Simulation; Sewage; Membrane Transport Proteins; Anti-Bacterial Agents; Microbial Sensitivity Tests; Burkholderiaceae
PubMed: 37316617
DOI: 10.1007/s10123-023-00384-8