Journal of Applied Microbiology最新文献

Aims: The aim of this prospective study was to evaluate the diagnostic value of targeted next-generation sequencing (tNGS) in identifying pathogens from bronchoalveolar lavage fluid (BALF) in thoracic surgery ICU patients, offering additional diagnostic methods for clinical practice.

Methods and results: We collected clinical data from patients with suspected pulmonary infections in the thoracic surgery ICU of the Second Affiliated Hospital of Air Force Medical University. A total of 50 patients were enrolled in this study. Traditional pathogen detection (TPD), involving culture and loop-mediated isothermal amplification assays for 12 pathogens, along with tNGS, was employed for pathogen identification in BALF samples. Our findings demonstrated that the positive rate of tNGS was significantly greater than that of TPD (96% vs. 68%). Among the 50 samples analyzed, tNGS identified a total of 165 pathogens, whereas TPD detected only 48 pathogens. The TPD method primarily detected bacteria and fungi, whereas tNGS exhibited broader capabilities, identifying 104 cases with bacteria, 19 with fungi, 34 with DNA viruses, and 8 with RNA viruses. Notably, tNGS displayed enhanced efficiency in detecting atypical pathogens such as fungi, DNA viruses and RNA viruses. Furthermore, compared with TPD, tNGS demonstrated superior sensitivity (95.83% vs. 68.75%).

Conclusions: tNGS technology, characterized by its high sensitivity, specificity, and cost-effectiveness, holds great promise as a reliable diagnostic tool for assessing pulmonary infections in the thoracic surgery ICU patients.

Aims: The aim of this study was to evaluate the antioxidant and anti-inflammatory effects of marine fungal cerebroside flavuside B (FlaB) on Staphylococcus aureus-infected keratinocytes in in vitro skin wounds and to identify FlaB targets in bacterial and human cells.

Methods and results: A combination of enzyme-linked immunosorbent assay (ELISA), plate spectrofluorimetry, and flow cytometry with fluorescence dye staining, scratch assay, and real-time cell imaging techniques was used to investigate the effects of FlaB on S. aureus-infected HaCaT keratinocytes. FlaB decreased reactive oxygen species levels, nitrite oxide levels, and TNF-α and IL-18 release in S. aureus-infected HaCaT cells. FlaB reversed the inhibition of HaCaT cell proliferation caused by S. aureus infection. FlaB significantly increased keratinocyte migration and wound healing in an in vitro S. aureus-infected wound skin model. Using real-time qPCR, we found that FlaB caused a 1.7-fold reduction in agrA expression, which controls quorum sensing system in S. aureus. Bioinformatics analysis and molecular docking, together with experimental data, suggest that FlaB targets the pro/antioxidant defense system in human cells.

Conclusions: Thus, FlaB can play a dual role as an antibacterial and pro/antioxidant machinery modulator, providing an observable positive effect in S. aureus-infected in vitro skin wounds. Staphylococcal sortase A enzyme and Arg systems are the targets of FlaB in bacterial cells. Nrf2/Bach1 dependent pro/antioxidant defense system is a target of FlaB in human cells. Some suggestions have also been made regarding the biological role of this marine fungal metabolite and its therapeutic possibilities.

Aims: Myxobacteria are non-pathogenic, saprophytic, soil-dwelling predatory bacteria known for their antimicrobial potential. Many pathogenic bacteria form biofilms to protect themselves from antimicrobial agents and the immune system. This study has investigated the predatory activities of myxobacteria against pathogenic bacteria in biofilms.

Methods and results: A total of 50 soil samples were collected in and around Cardiff, South Wales (UK). Using a baiting method with 6 prey organisms, 32 myxobacteria were isolated and identified by 16S rRNA sequencing, of which 18 were Myxococcus spp. and 14 were Corallococcus spp. Predation assays, biofilm inhibition and disruption assays, and a dynamic, polymicrobial wound biofilm model were used with live myxobacteria to assess efficacy of predation. Good activity in predation assays was observed against Escherichia coli, while Enterococcus faecalis was more recalcitrant to myxobacteria. Staphylococcus aureus and Citrobacter freundii were significantly (P < 0.05) reduced in both biofilm inhibition and disruption assays compared to other pathogens. Considerable reductions (>3 log10 CFU) in the wound infection model were seen after 96 h of incubation, particularly for C. freundii and E. coli.

Conclusion: Using live predatory bacteria as an alternative therapeutic agent has received attention in the recent past to combat the problem of antimicrobial resistance. Myxobacteria isolated from soil using multiple prey organisms yielded diverse isolates, including strains which exhibited therapeutically promising activities in a variety of infection/biofilm assays.

Aim: The aim of this study is to increase the diversity of culturable halophilic archaea by comparing various isolation conditions and to explore the application of halophilic archaea for enzyme-producing activities and antimicrobial properties.

Methods and results: We systematically compared the isolation performance of various archaeal and bacterial media by isolating halophilic archaea from the Da Qaidam Salt Lake, a magnesium sulfate subtype hypersaline lake on the Qinghai-Tibet Plateau, China, using multiple enrichment culture and gradient dilution conditions. A total of 490 strains of halophilic archaea were isolated, which belonged to five families and 11 genera within the order Halobacteriales of the class Halobacteria of the phylum Euryarchaeota. The 11 genera consisted of nine known genera and two potentially new genera, the former including Halorubrum, Natranaeroarchaeum, Haloplanus, Haloarcula, Halorhabdus, Halomicrobium, Halobacterium, Natrinema, and Haloterrigene. Halorubrum was the dominant genus with a relative abundance of 78.98%. By comparing different culture conditions, we found that bacterial media 2216E and R2A showed much better isolation performance than all archaeal media, and enrichment culture after 60 d and dilution gradients of 10-1 and 10-2 were best fitted for halophilic archaea cultivation. The screening of 40 halophilic archaeal strains of different species indicated that these halophilic archaea had great extracellular enzyme activities, including amylase (62.5%), esterase (50.0%), protease (27.5%), and cellulase (15.0%), and possessed great antimicrobial activities against human pathogens. A total of 34 strains exhibited antimicrobial activity against four or more pathogens, and 19 strains exhibited antimicrobial activity against all six pathogens.

Conclusions: The diversity of culturable halophilic archaea was significantly increased by enrichment culture and selection of bacterial media, and screening of representative strains showed that halophilic archaea have multiple extracellular enzyme activities and broad-spectrum antimicrobial activity against human pathogens.

Aims: To characterize Escherichia coli O25 ST131 (O25-ST131) isolated from Georgia poultry-a "global high-risk" clonal strain.

Methods and results: Using multiplex PCR to detect target genes in 98 isolates of avian pathogenic E. coli (APEC) O25 recovered from avians diagnosed with colibacillosis (n = 87) and healthy chicks (n = 11) in Georgia, USA. Eighty-eight isolates were classified as sequence type ST131 clade b and 56% (n = 49) belong to the phylogenetic group B2. Overall, 17% were identified as uropathogenic E. coli (UPEC)-like and 94% of the isolates formed strong to moderate biofilms. The extended-spectrum β-lactamases encoding genes, blaCTX M-15 (24%), carbapenemases encoding genes, and blaOXA48 (16%) were also detected. The isolates harbored FIB (88%), FIC (28%), A/C (14%), and FIIA (6%) plasmid replicons. Interestingly, 78% of the isolates were found to be resistant to chicken serum and 92% showed capabilities for growth in human urine. The isolates showed phenotypic resistance to several antibiotics including chloramphenicol (63%), ciprofloxacin (57%), trimethoprim-sulfamethoxazole (28%), streptomycin (17%), and cefoxitin and meropenem (14%) using the national antimicrobial resistance monitoring system panel.

Conclusions: Overall, our study provides evidence of the virulence of these global "high-risk" clones in Georgia poultry with some isolates showing genotypic overlap between APEC and UPEC. Also, this clone harbored several virulence genes, antimicrobial-resistant genes, and plasmids. Interestingly, the majority of APEC O25-ST131 isolates can survive and grow in both chicken serum and human urine and warrant further investigation of their potential pathogenicity for both chickens and humans.

This is a timely and important review that focuses on the appropriateness of established cleaning, disinfection, and sterilization methods to safely and effectively address infectious fungal drug-resistant pathogens that can potentially contaminate reusable medical devices used in healthcare environment in order to mitigate the risk of patient infection. The release of the World Health Organization (WHO) fungal priority pathogen list (FPPL) in 2022 highlighted the public health crisis of antimicrobial resistance (AMR) in clinically relevant fungal species. Contamination of medical devices with drug-resistant fungal pathogens (including those on the FPPL) in healthcare is a rare event that is more likely to occur due to cross-transmission arising from lapses in hand hygiene practices. Established disinfection and sterilization methods decontaminate fungal pathogens on single-use and reusable medical devices; however, there are assumptions that reusable devices destined for semi-critical use are appropriately cleaned and do not harbour biofilms that may undermine the ability to effectively decontamination these type devices in healthcare. International standards dictate that manufacturer's instructions for use must provide appropriate guidance to healthcare facilities to meet safe reprocessing expectations that include addressing drug-resistant fungal pathogens. Increased environmental monitoring and vigilance surrounding fungal pathogens in healthcare is advised, including adherence to hand hygiene/aseptic practices and appropriate cleaning encompassing the simplification of reusable device features for 'ease-of-reach'. There are emereging opportunities to promote a more integrated multiactor hub approach to addressing these sophisticated challenges, including future use of artificial intelligence and machine learning for improved diagnostics, monitoring/surveillance (such as healthcare and wastewater-based epidemiology), sterility assurance, and device design. There is a knowledge gap surrounding the occurrence and potential persistence of drug-resistant fungal pathogens harboured in biofilms, particularly for ascertaining efficacy of high-level disinfection for semi-critical use devices.

Aims: In the Amazon region, pastures are the main land use subsequent to deforestation and this change can result in soil acidification and degradation. Liming is a management practice to increase soil pH, important to recover degraded lands and increase soil fertility, but its impacts on soil methane cycling in tropical soils are unknown. Here we investigate the role of soil pH on methane uptake under high concentrations of the gas, manipulating pasture and forest soils pH by liming and evaluating the active methane cycling microbial community.

Methods and results: Top layer of forest and pasture soils were subjected to liming treatment and incubated with ∼10 000 ppm of 13CH4. Soil DNA was evaluated with Stable Isotopic Probing (SIP-DNA), methanotrophic abundance was quantified (pmoA gene), and high throughput sequencing of 16S rRNA was performed. Liming increased the methane uptake in both forest (∼10%) and pasture (∼25%) soils. Methanotrophs Methylocaldum spp. (type I) and potential methanotrophs in Beijerinckiaceae (type II) were identified to actively incorporate carbon from methane in limed pasture soils. In limed forest soils, Nitrososphaeraceae were identified as 13C-enriched taxa, indicating that ammonia oxidizers can oxidize methane in these soils.

Conclusions: Liming Amazonian pasture soils not only contributes to the fertility and recovery of degraded areas but also has the potential to improve the oxidation of methane at high concentrations of this gas.

Aims: This study evaluated the phenotypic and genotypic traits of mcr-1.1-harboring Escherichia coli isolates from chickens, pigs, humans, and farm environments. The resistome and the mobile genetic elements associated with the spread of mcr-1.1 in Southern Brazil were also characterized.

Methods and results: The 22 mcr-1.1-harboring E. coli isolates from different origins were selected for antimicrobial susceptibility testing and whole genome sequencing for characterization of the resistome, plasmids, and sequence types. All isolates presented several resistance genes and harbored the mcr-1.1 gene in a highly similar IncX4 plasmid. Furthermore, the mcr-1.1 gene co-occurred with the mcr-3.12 gene in a multidrug-resistant isolate from the farm environment.

Conclusions: These findings demonstrate that the mcr-1.1 gene in E. coli isolates from Brazil is spreading mainly by horizontal transfer of the IncX4 plasmid. The co-occurrence of mcr-1.1 and mcr-3.12 highlights pig farming as an important reservoir of colistin resistance.

Aims: Bacterial resistance and systemic risks associated with periodontitis underscore the need for novel antimicrobial agents. Cannabis sativa is a promising source of antimicrobial molecules, and cannabidiol (CBD) attracts significant interest. This study evaluated the antibacterial and antibiofilm activity of CBD against periodontopathogens, and assessed its toxicity in vivo model.

Methods and results: Antibacterial activity was determined by the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). Biofilm inhibition was determined the minimum inhibitory concentration of biofilm (MICB50). Toxicity was assessed using Caeonorhabditis elegans. The periodontopathogens tested were Actinomyces naeslundii (ATCC 19039), Peptostreptococcus anaerobius (ATCC 27337), Veillonella parvula (ATCC 17745), Fusobacterium nucleatum (ATCC 10953), and Aggregatibacter actinomycetemcomitans (ATCC 43717). CBD exhibited antibacterial effects with MICs of 0.39 to 3.12 µg ml-1 and MICB50 of 0.39 µg ml-1 to 1.56 µg ml-1 against biofilms, without toxicity below 375 µg ml-1.

Conclusion: The results suggest that CBD is a non-toxic product with antibacterial and antibiofilm potential, exhibiting promise as a therapeutic alternative for oral diseases.

Enteroviruses (EVs) are a highly diverse group of viruses multiplying primarily in the gastrointestinal tract and/or the upper respiratory tract, initially distributed in two separate genera: Enterovirus and Rhinovirus, respectively. According to the similarities in genome organization and particle structure, rhinovirus species were later reclassified as also belonging to genus Enterovirus. Human EV infections are usually asymptomatic or causing mild clinical manifestations. Nevertheless, some EV infections may derive in severe neural complications, including acute flaccid paralysis (AFP) such as poliomyelitis, whose etiological agent is poliovirus, a member of the Enterovirus C species. The inactivated polio vaccine (IPV) and particularly the oral attenuated polio vaccine (OPV) have contributed to the virtual eradication of the disease. However, sustained global circulation of vaccine-derived poliovirus 2 (cVDPV2), originated from the genetic instability of OPV strain 2 and intertypic recombination between Sabin OPV strains and members of the Enterovirus C species, still causes outbreaks of AFP worldwide. In addition, humanitarian crises, in particular armed conflicts, hamper polio vaccination campaigns and facilitate the occurrence of cases. Additionally, besides poliovirus, other EV may also cause AFP, among them EV A71 or EV D68, and it is highly advisable to implement wastewater surveillance to elucidate the occurrence of not only polioviruses, but also of other EV susceptible to derive in serious neural complications, since the screening of viral RNA in cerebrospinal fluid samples in patients suffering from AFP is not a reliable diagnostic tool.