Hasil untuk "Microbiology"

S. Debast, M. Bauer, E. Kuijper

M. Inouye, Harriet Dashnow, Lesley-Ann Raven et al.

Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significant challenges. Here we present SRST2, a read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data. Using >900 genomes from common pathogens, we show SRST2 is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment. We include validation of SRST2 within a public health laboratory, and demonstrate its use for microbial genome surveillance in the hospital setting. In the face of rising threats of antimicrobial resistance and emerging virulence among bacterial pathogens, SRST2 represents a powerful tool for rapidly extracting clinically useful information from raw WGS data.Source code is available from http://katholt.github.io/srst2/.

K. Timmis

E. Paul

M. Gerardi

J. V. Van Hamme, A. Singh, O. Ward

J. Lagier, Perrine Hugon, S. Khelaifia et al.

S. Mehler

隋明爽, 黄亚明

B. Gonçalves, C. Ferreira, C. Alves et al.

S. Khalajian, N. Mooraki, M. Honarvar et al.

This research investigates the lactic fermentation process of sugar beet (Beta vulgaris L.) puree with the aim of creating a functional probiotic product. The focus is on optimizing fermentation conditions to enhance health benefits, thereby serving as a functional ingredient for various applications within the food industry. The lactic fermentation process utilized two strains, Lactobacillus plantarum and Lactobacillus casei, which were evaluated at different concentrations in both single (phase A) and mixed (phase B) applications. Critical parameters analyzed included fermentation duration, corn steep liquor (CSL), whey and glucose syrup, with a focus on their impacts on betaine levels, probiotic viability, antioxidant capacity, pectin content, sugar, lactic acid, and acetic acid. Through response surface methodology, optimal conditions were determined: For the A - L. casei sample, the optimal conditions included 4.78 % inoculation, 9.64 % syrup, and 1 % whey, with a fermentation period of 39.96 h. Under these conditions, the process yielded 1.833 mg/mL betaine and exhibited an antioxidant activity of 491.5 µm. The A - L. plantarum sample exhibited 5 % inoculation under similar conditions, yielding 1.863 mg/mL of betaine and an antioxidant activity of 475.71 µm. In the mixed B sample, the optimal conditions were identified as 5 % inoculation with a combination of 34.76 % L. plantarum and 25 % L. casei. Under these conditions, 1.38 mg/mL of betaine was produced after 67.76 h. These optimized samples hold significant potential as ingredients for the development of functional food products.

J. Gilbert, Brent E. Stephens

Fatema S. Mohamed, Rim Hamdy, Essam M. Abd-Elkhader

Liliane Nkengurutse, John O. Otshudiema, Godefroid Kamwenubusa et al.

(1) Objectives: Studies on mpox patterns, severity predictors, and public health impacts in Burundi remain limited. Therefore, we aimed to identify the clinical predictors and determinants of mpox complications among hospitalized patients in Bujumbura, Burundi, during an active outbreak. (2) Methods: We conducted a prospective cohort study of laboratory-confirmed mpox cases across three treatment centers (July–October 2024). Clinical characteristics and outcomes were assessed through a systematic review of medical and laboratory records supplemented by structured interviews with patients or caregivers. Risk factors for disease complications were evaluated using multivariate Firth penalized logistic regression. (3) Results: Complications developed in 3.1% of 850 patients (54.4% male; median age, 20.3 years). Conjunctivitis (odds ratio [OR]: 27.30; 95% confidence interval [CI], 7.67–122.23) and sore throat (OR: 12.63; 95% CI, 5.78–30.21) were significant predictors of severe disease progression. Conversely, generalized rash (OR, 0.10; 95% CI, 0.04–0.24) and lymphadenopathy (OR, 0.24; 95% CI, 0.08–0.62) were associated with a mild disease course. Sexual transmission was the predominant route of infection (58.6%). (4) Conclusions: Noncutaneous manifestations, particularly conjunctivitis and sore throat, are early indicators of mpox severity. These findings inform clinical risk stratification in resource-limited settings and highlight the need for further investigation of pathophysiological mechanisms.

P. Ramanan, A. Bryson, M. Binnicker et al.

Chizoba M. Enemchukwu, Christiana Nwabueze, Oluchi J. Osuala et al.

Background: The adult human vagina hosts a complex biota containing diverse communities of microorganisms. The occurrence of multi-drug-resistant strains of these microorganisms has persistently increased due to poor hygiene and misuse or abuse of antibiotics. The vaginal microflora may exhibit patterns of growth, biochemical expression, or response to the standard drugs which consequently lead to answer the complex questions of antimicrobial resistance. Aim: The study aimed to quantify the susceptibility profile of microorganisms isolated from vaginal discharge and evaluate the minimum inhibitory concentration of diverse antimicrobial drugs. Methods: Fifty vaginal swabs were collected from female students of Madonna University, Nigeria while two samples were collected each from a pregnant and a non-pregnant woman at the university’s tertiary care teaching hospital. The isolates were grown in selective media and identified through Gram-staining and biochemical physiology for identification. The Kirby-Bauer disc diffusion method was used for microbial susceptibility testing, and the agar dilution method was used to determine the minimum inhibitory concentration of commonly prescribed antibiotics at the teaching hospital. Results: Sixty-eight microorganisms comprising 17 Gram-positive (Staphylococcus sp.) and 31 Gram-negative (Escherichia coli and others) bacteria and 20 fungi (Candida sp.) were isolated. The bacteria showed a high resistance (>80%) to amoxicillin, cefuroxime, and cefixime but were relatively susceptible (35–100%) to levofloxacin and ofloxacin. Cefepime showed high activity with a minimum inhibitory concentration range of 25–50 µg/mL against the studied bacteria. The isolated fungi were susceptible to amphotericin B (35–40%) but resistant (>85%) to other antifungal drugs tested. Conclusion: The study suggests that bacterial vaginosis prevalence at the university could best be treated with ofloxacin (second generation- fluoroquinlone), levofloxacin (third generation- fluoroquinolone), and cefepime (fourth generation- cephalosporin) due to their greater sensitivity, while candidiasis could best be treated with amphotericin B (a pyolene).

Xu Rongchang

lumbodorsal myofasciitis is a common injury in badminton and a common disease in clinical practice. Clinically, acupuncture, cupping, massage, extracorporeal shock wave and other methods are usually used. This paper summarizes and classifies the commonly used treatment methods in the clinic, which are mainly divided into traditional Chinese medicine (TCM) combined treatment methods, Chinese medicine treatment combined physical therapy methods and physical combined therapy. In the clinic, TCM combined treatment methods and TCM combined physical therapy methods are mainly used, and TCM combined physical therapy methods should be the main research direction in the future. There are many therapeutic methods, but the efficacy of combining multiple therapeutic methods is better than that of single method. This study can provide a theoretical basis and reference for subsequent research and clinical treatment.

Kun He, Jiayu Lin, Yulei Liang et al.

ABSTRACT The interaction between coexisting plasmids can affect plasmid-carried resistance gene persistence and spread. However, whether the persistence of the blaCTX-M gene in clinical Enterobacteriaceae is related to the interaction of coresident nonresistance-conferring plasmids has not been reported. This study was initiated to elucidate how a nonresistance-conferring IncI1 plasmid affected the blaCTX-M-bearing IncFII plasmid colocated on the same cell. Herein, we constructed three isogenic derivatives of E. coli C600, designated as C600FII, C600I1, and C600FII+I1, which harbored the blaCTX-M-IncFII plasmid and/or the nonresistance-IncI1 one. We discovered that strain C600FII+I1 conferred higher fitness advantages than strain C600FII; also, the stability of the blaCTX-M-IncFII plasmid was noticeably improved in an antibiotic-free environment when it coexisted with the IncI1 plasmid. To further explore why the IncI1 plasmid enhanced the persistence of the blaCTX-M-IncFII plasmid, we assessed the blaCTX-M-IncFII plasmid's copy numbers, conjugation frequencies, and rep gene expressions in strains C600FII and C600FII+I1. The results demonstrated that the rep expressions of the blaCTX-M-IncFII plasmid in strain C600FII+I1 was greatly decreased, along with the plasmid’s copy numbers and mating efficiencies, compared to those in strain C600FII. Moreover, further study revealed that the intracellular ATP levels of strain C600FII+I1 were far lower than those of strain C600FII. Our findings confirmed that coexistence of the nonresistance-IncI1 plasmid can keep the blaCTX-M-IncFII plasmid more stable by increasing the fitness advantages of the host bacteria, which will pose a threat to preventing the long-term presence of the plasmid-carried blaCTX-M gene in clinical Enterobacteriaceae.IMPORTANCESo far, plasmid-carried blaCTX-M is still the most common extended-spectrum beta-lactamase (ESBL) genotype in clinical settings worldwide. Except for the widespread use of third-generation cephalosporins, the interaction between coexisting plasmids can also affect the long-term stable existence of the blaCTX-M gene; however, the study on that is still sparse. In the present study, we assess the interaction of coinhabitant plasmids blaCTX-M-IncFII and nonresistance-IncI1. Our results confirmed that the increased fitness advantages of strain C600FII+I1 were attributable to the cohabitant nonresistance-IncI1 plasmid, which largely reduced the intracellular ATP levels of host bacteria, thus decreasing the rep gene expression of the blaCTX-M-IncFII plasmid, its copy numbers, and mating efficiencies, while the higher fitness advantages of strain C600FII+I1 enhanced the persistence of the blaCTX-M-IncFII plasmid. The results indicate that the nonresistance-IncI1 plasmid contributes to the long-term existence of the blaCTX-M-IncFII plasmid, implying a potentially new strategy for controlling the spread of resistance plasmids in clinical settings by targeting nonresistance plasmids.

D. Hutchins, J. Jansson, J. Remais et al.

Kaiyang Qu, Fei Guo, Xiangrong Liu et al.

Microorganisms are ubiquitous and closely related to people’s daily lives. Since they were first discovered in the 19th century, researchers have shown great interest in microorganisms. People studied microorganisms through cultivation, but this method is expensive and time consuming. However, the cultivation method cannot keep a pace with the development of high-throughput sequencing technology. To deal with this problem, machine learning (ML) methods have been widely applied to the field of microbiology. Literature reviews have shown that ML can be used in many aspects of microbiology research, especially classification problems, and for exploring the interaction between microorganisms and the surrounding environment. In this study, we summarize the application of ML in microbiology.