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Microbiology Spectrum Apr 2024A landmark study by Poore et al. showed intratumor bacteria (ITBs) playing a critical role in most cancers by reproduction of The Cancer Genome Atlas (TCGA)...
UNLABELLED
A landmark study by Poore et al. showed intratumor bacteria (ITBs) playing a critical role in most cancers by reproduction of The Cancer Genome Atlas (TCGA) transcriptome data. A recent study by Salzberg et al. argued that ITBs, being overstated as a methodology by Poore et al., were problematic. We previously reported that ITBs were prognostic in adrenocortical carcinoma (ACC), a highly aggressive rare disease using data by Poore et al., and here, we aimed to answer whether ITBs truly existed and were prognostic in ACC. ACC samples from our institutes underwent 16S rRNA sequencing [adrenocortical carcinoma blocks from Huashan Hospital and China Medical University (HS) cohort]. The ITB profile was compared to TCGA data processed by Poore et al. (TCGA-P) and TCGA data processed by Salzberg et al. (TCGA-S), respectively. The primary outcome was overall survival (OS). A total of 26 ACC cases (HS cohort) and 10 paraffin controls were sequenced. The TCGA cohort encompassed 77 cases. Two and four amid the top 10 abundant genera in HS cohort were not detected in TCGA-P and TCGA-S, respectively. Neither was alpha or beta diversity associated with survival nor could ACC be subtyped by ITB signature in the HS cohort. Notably, a five-genera ITB risk score (, , , , and ) for OS trained in the HS cohort was validated in both TCGA-P and TCGA-S cohorts and was independently prognostic. Whereas ITB signature on the whole may not be associated with ACC subtypes, certain ITB features are associated with prognosis, and a risk score could be generated and validated externally.
IMPORTANCE
In this report, we looked at the role of ITBs in ACC in patients with different race and sequencing platforms. We found a five-genera ITB risk score consistently predicted overall survival in all cohorts. We conclude that certain ITB features are universally pathogenic to ACC.
Topics: Humans; Adrenocortical Carcinoma; Prognosis; Adrenal Cortex Neoplasms; RNA, Ribosomal, 16S; Risk Factors; Bacteria
PubMed: 38421176
DOI: 10.1128/spectrum.03727-23 -
Antimicrobial Stewardship & Healthcare... 2024and are emerging nosocomial, non-glucose fermenting, Gram-negative pathogens. In this nested case-control trial, independent predictors for infections were...
and are emerging nosocomial, non-glucose fermenting, Gram-negative pathogens. In this nested case-control trial, independent predictors for infections were hemodialysis and recent antibiotic usage (overall), while recent usage of fluoroquinolones, was independently associated with infections. Infections were independently associated with multiple worse outcomes.
PubMed: 38415099
DOI: 10.1017/ash.2024.11 -
The Journal of Hospital Infection Apr 2024Nosocomial outbreaks of urinary tract infections caused by Achromobacter spp. have been rare in recent decades.
BACKGROUND
Nosocomial outbreaks of urinary tract infections caused by Achromobacter spp. have been rare in recent decades.
AIM
To identify the origin of an Achromobacter sp. outbreak, conduct multi-modal infection control measures, and finally to stop the outbreak. To this end, an epidemiological outbreak investigation and risk factor analysis were performed.
METHODS
Achromobacter sp. was detected in 22 patients in our urology wards and six environmental cultures of specimens obtained from the operating rooms. Strains isolated were submitted for antimicrobial susceptibility testing. An on-site epidemiological investigation, evaluation of patient medical records, and environmental sampling were performed to identify the source of the outbreak, and implementation of infection control intervention. A case-control study was performed to analyse the potential risk factors.
FINDINGS
Environmental sampling showed that the source of the infection for 22 patients was an ISA-IIIA-type medical pressurizer containing contaminated water. A case-control analysis showed that the risk factors for infection were: diagnosis of kidney/ureteral stones, surgery, placement of a double-J stent, and history of hospitalization in the past three months.
CONCLUSION
It was concluded that the outbreak occurred in patients who underwent internal lithotripsy and double-J stent placement, due to contact transmission with the contaminated sensor and connecting tubes of the ISA-IIIA-type medical pressurizer.
Topics: Humans; Achromobacter; Case-Control Studies; Disease Outbreaks; Equipment and Supplies, Hospital; Risk Factors; Water; Cross Infection
PubMed: 38403082
DOI: 10.1016/j.jhin.2024.02.002 -
Microorganisms Feb 2024This study aimed to explore the phenotype and relationship of drug resistance genes in livestock and poultry farm wastewater and drinking water reservoirs to provide...
This study aimed to explore the phenotype and relationship of drug resistance genes in livestock and poultry farm wastewater and drinking water reservoirs to provide evidence for the transmission mechanisms of drug resistance genes, in order to reveal the spread of drug resistance genes in wastewater from intensive farms in Central China to urban reservoirs that serve as drinking water sources and provide preliminary data for the treatment of wastewater from animal farms to reduce the threat to human beings. DNA extraction and metagenomic sequencing were performed on eight groups of samples collected from four water reservoirs and four related wastewaters from animal farms in Central China. Metagenomic sequencing showed that the top 20 AROs with the highest abundance were _gene, _gene, , , , _gene_, _gene, , _gene, _gene, , , , , _gene, , _gene, , , and . The resistance genes mentioned above belong to the following categories of drug resistance mechanisms: antibiotic target replacement, antibiotic target protection, antibiotic inactivation, and antibiotic efflux. The resistomes that match the top 20 genes are and ; ; ; and . ; ; and ; and ; , , , , , , , , , and ; and ; , , , , , and ; and ; and ; , , and ; , , , , , , and . Unreported drug resistance genes and drug-resistant bacteria in Central China were identified in 2023. In the transmission path of drug resistance genes, the transmission path from aquaculture wastewater to human drinking water sources cannot be ignored. For the sake of human health and ecological balance, the treatment of aquaculture wastewater needs to be further strengthened, and the effective blocking of drug resistance gene transmission needs to be considered.
PubMed: 38399800
DOI: 10.3390/microorganisms12020396 -
Environmental Science and Pollution... Mar 2024Chloroxylenol is a commonly used antimicrobial agent in antibacterial and disinfection products, which has been detected in various environments, such as wastewater...
Chloroxylenol is a commonly used antimicrobial agent in antibacterial and disinfection products, which has been detected in various environments, such as wastewater treatment plants, rivers, seawater, and even drinking water, with concentrations ranging from ng/L to mg/L. However, the biodegradation of chloroxylenol received limited attention with only sporadic reports available so far. In this study, an efficient chloroxylenol-degrading consortium, which could degrade 20 mg/L chloroxylenol within two days, was obtained after five months of enrichment. Amplicon sequencing analysis revealed a decrease in the α-diversity (e.g., Shannon index and Inv_Simpson index) of the community during the domestication process. Microbial community dynamics were uncovered, with sequences affiliated to Achromobacter, Pseudomonas, and Rhodococcus identified as the most abundant taxonomic groups. From the consortium, five pure isolates were obtained; however, it was found that only one strain of Rhodococcus could degrade chloroxylenol. Strain Rhodococcus sp. DMU2021 could degrade chloroxylenol efficiently under the conditions of temperature 30-40 °C, and neutral/alkaline conditions. Chloroxylenol was toxic to strain DMU2021 and triggered both enzymatic and non-enzymatic antioxidant systems in response. This study provides novel insights into the biodegradation process of chloroxylenol, as well as valuable bioresources for bioremediation.
Topics: Biodegradation, Environmental; Achromobacter; Anti-Bacterial Agents; Rhodococcus; Xylenes
PubMed: 38393562
DOI: 10.1007/s11356-024-32365-3 -
Pathogens (Basel, Switzerland) Jan 2024spp. are intrinsically resistant to multiple antibiotics and can also acquire resistance to those commonly used for the treatment of respiratory infections, especially...
spp. are intrinsically resistant to multiple antibiotics and can also acquire resistance to those commonly used for the treatment of respiratory infections, especially in patients with cystic fibrosis. The aim of this study was to perform the genetic and biochemical characterization of AXC-2 from and to analyze all available AXC variants. Steady-state kinetic parameters were determined on a purified AXC-2 enzyme. It exhibited higher catalytic efficiencies towards amino-penicillins and older cephalosporins, while carbapenems behaved as poor substrates. Phylogenetic analysis of all variants available in the NCBI was conducted. AXC was encoded in almost all genomes, whereas it was only found in 30% of . AXC-1 was prevalent among . AXC variants were clustered in two main groups, correlating with the species. No association could be established between the presence of variants and a specific lineage of ; however, a proportion of AXC-1-producing isolates corresponded to ST 182 and ST 447. In conclusion, this study provides valuable insights into the genetic context and kinetic properties of AXC-2, identified in . It also provides a thorough description of all AXC variants and their association with species and various lineages.
PubMed: 38392853
DOI: 10.3390/pathogens13020115 -
Applied Biochemistry and Biotechnology Feb 2024A novel gene encoding aspartate dehydrogenase (ASPDH) has been discovered in Achromobacter denitrificans. The product of this gene has a strict dependence on NADH and...
A novel gene encoding aspartate dehydrogenase (ASPDH) has been discovered in Achromobacter denitrificans. The product of this gene has a strict dependence on NADH and demonstrated significant reductive activity towards not only oxaloacetate (OAA) but also 2-ketobutyric acid. Further enzymatic characterization revealed the kinetic parameters of ASPDH for OAA and 2-ketobutyric acid were as follows: K values of 4.25 mM and 0.89 mM, V values of 10.67 U mg and 2.10 U mg, and K values of 3.70 s and 0.72 s, respectively. The enzyme also showed a dependency on metal ions, with EDTA and Cu exerting strong inhibitory effects, while Ca and Fe exhibited pronounced enhancing effects. By utilizing a whole-cell biocatalyst system comprising glucose dehydrogenase (GDH) and ASPDH as a coupled system to replenish cofactors by oxidizing glucose, enabling the effective conversion of 2-ketobutyric acid to L-2-aminobutyric acid (L-2-ABA) with 97.2% yield.
PubMed: 38386141
DOI: 10.1007/s12010-024-04867-w -
Food Chemistry: X Mar 2024The physicochemical indexes and microbial diversity were investigated to compare the altered quality properties of the abdomen and cheliped muscle in swimming crab ()...
The physicochemical indexes and microbial diversity were investigated to compare the altered quality properties of the abdomen and cheliped muscle in swimming crab () during 100 days of frozen storage at -20℃. Over the extended duration of frozen storage, the sensory evaluation, moisture content, water activity (Aw), and water-holding capacity (WHC) in the abdomen and cheliped muscles of swimming crab decreased, while the pH, total volatile basic nitrogen (TVB-N), and trimethylamine (TMA) increased. The increase and decrease rates of these indicators were smaller in the abdomen than those in the cheliped muscle. High-throughput sequencing results indicated a reduction in the microbial richness and diversity in the abdomen and cheliped muscles of the swimming crab as frozen storage time extended. , , and , , , and were the dominant phylum and genus in both muscle tissues, respectively. Furthermore, the correlation analysis between the composition of the microbiota and physiochemical properties revealed that the growths of , , and were closely related to the physiochemical factors. The study provides a theoretical reference for quality deterioration and develops new products of different parts in the swimming crab during frozen storage.
PubMed: 38379803
DOI: 10.1016/j.fochx.2024.101210 -
European Archives of... Apr 2024Achromobacter xylosoxidans is an emerging pathogen mainly associated with resistant nosocomial infections. This bacteria had been isolated in the ear together with other...
PURPOSE
Achromobacter xylosoxidans is an emerging pathogen mainly associated with resistant nosocomial infections. This bacteria had been isolated in the ear together with other pathogens in cultures from patients with chronic otitis media, but it had never been reported as a cause of osteomyelitis of the external auditory canal.
CASE PRESENTATION
We present a unique case of a healthy 81-year-old woman who presented with left chronic otorrhea refractory to topical and oral antibiotic treatment. Otomicroscopy revealed an erythematous and exudative external auditory canal (EAC) with scant otorrhea. The tympanic membrane was intact, but an area of bone remodeling with a small cavity anterior and inferior to the bony tympanic frame was observed. Otic culture isolated multi-drug-resistant A. xylosoxidans, only sensitive to meropenem and cotrimoxazole. Temporal bone computed tomography showed an excavation of the floor of the EAC compatible with osteomyelitis. Targeted antibiotherapy for 12 weeks was conducted, with subsequent resolution of symptoms and no progression of the bone erosion.
CONCLUSIONS
Atypical pathogens such as A. xylosoxidans can be the cause of chronic otitis externa. Early diagnosis and specific antibiotherapy can prevent the development of further complications, such as osteomyelitis. In these cases, otic cultures play an essential role to identify the causal germ. This is the first case of EAC osteomyelitis due to A. xylosoxidans reported to date.
Topics: Female; Humans; Aged, 80 and over; Ear Canal; Achromobacter denitrificans; Otitis Externa; Osteomyelitis; Ear Diseases
PubMed: 38367073
DOI: 10.1007/s00405-024-08465-8 -
Poultry Science Apr 2024Artificial insemination (AI) technology has greatly promoted the development of the chicken industry. Recently, AI technology has also begun to be used in the duck...
Artificial insemination (AI) technology has greatly promoted the development of the chicken industry. Recently, AI technology has also begun to be used in the duck industry, but there are some problems. Numerous researchers have shown that microbes colonizing in semen can degrade semen quality, and AI can increase the harmful microbial load in hen's reproductive tract. Different from the degraded external genitalia of roosters, drakes have well-developed external genitalia, which may cause drake semen to be more susceptible to microbial contamination. However, information on the compositions, sources, and effects of semen microbes on semen quality remains unknown in drakes. In the current study, high-throughput sequencing technology was used to detect microbial communities in drake semen, environmental swabs, cloacal swabs, and the spermaduct after quantifying the semen quality of drakes to investigate the effects of microbes in the environment, cloaca, and spermaduct on semen microbiota and the relationships between semen microbes and semen quality. Taxonomic analysis showed that the microbes in the semen, environment, cloaca, and spermaduct samples were all classified into 4 phyla and 25 genera. Firmicutes and Proteobacteria were the dominant phyla. Phyllobacterium only existed in the environment, while Marinococcus did not exist in the cloaca. Of the 24 genera present in semen: Brachybacterium, Brochothrix, Chryseobacterium, Kocuria, Marinococcus, Micrococcus, Rothia, Salinicoccus, and Staphylococcus originated from the environment; Achromobacter, Aerococcus, Corynebacterium, Desemzia, Enterococcus, Jeotgalicoccus, Pseudomonas, Psychrobacter, and Turicibacter originated from the cloaca; and Agrobacterium, Carnobacterium, Chelativorans, Devosia, Halomonas, and Oceanicaulis originated from the spermaduct. In addition, K-means clustering analysis showed that semen samples could be divided into 2 clusters based on microbial compositions, and compared with cluster 1, the counts of Chelativorans (P < 0.05), Devosia (P < 0.01), Halomonas (P < 0.05), and Oceanicaulis (P < 0.05) were higher in cluster 2, while the sperm viability (P < 0.05), total sperm number (P < 0.01), and semen quality factor (SQF) (P < 0.01) were lower in cluster 2. Furthermore, functional prediction analysis of microbes showed that the activities of starch and sucrose metabolism, phosphotransferase system, ABC transporters, microbial metabolism in diverse environments, and quorum sensing pathways between cluster 1 and cluster 2 were significantly different (P < 0.05). Overall, environmental/cloacal microbes resulted in semen contamination, and microbes from the Chelativorans, Devosia, Halomonas, and Oceanicaulis genera may have negative effects on semen quality in drakes by affecting the activities of starch and sucrose metabolism, phosphotransferase system, ABC transporters, and quorum sensing pathways that are associated with carbohydrate metabolism. These data will provide a basis for developing strategies to prevent microbial contamination of drake semen.
Topics: Male; Animals; Female; Semen Analysis; Chickens; Seeds; ATP-Binding Cassette Transporters; Phosphotransferases; Starch; Sucrose
PubMed: 38359770
DOI: 10.1016/j.psj.2024.103533