MALDI-TOF MS Research Articles

Investigation of different methods in rapid microbial identification directly from positive blood culture bottles by MALDI-TOF MS.

Sepsis is a life-threatening condition, and rapid and accurate identification of the causative microorganisms from blood cultures is crucial for timely and effective treatment. Although there are many studies on direct identification from blood cultures with MALDI-TOF MS, further standardization is still needed. In our study, we analyzed the performance of three different preparation methods and compared by using two analysis modules of the Bruker Biotyper MALDI-TOF MS for direct identification of bacteria from numerous positive blood culture bottles. The literature reports a limited number of studies that compare different preparation methods for direct blood culture identification, processing a large number of blood samples concurrently and evaluating the same samples as in our study. Moreover, although SDS is used very frequently in medical laboratories, there are few studies on direct identification from blood culture bottles. In our study, the highest correct identification rate was observed with the SDS method.

Pseudocin 196, a novel lantibiotic produced by Bifidobacterium pseudocatenulatum elicits antimicrobial activity against clinically relevant pathogens

ABSTRACT Bacteriocins are broad or narrow-spectrum antimicrobial compounds that have received significant scientific attention due to their potential to treat infections caused by antibiotic-resistant pathogenic bacteria. The genome of Bifidobacterium pseudocatenulatum MM0196, an antimicrobial-producing, fecal isolate from a healthy pregnant woman, was shown to contain a gene cluster predicted to encode Pseudocin 196, a novel lantibiotic, in addition to proteins involved in its processing, transport and immunity. Following antimicrobial assessment against various indicator strains, protease-sensitive Pseudocin 196 was purified to homogeneity from cell-free supernatant. MALDI TOF mass spectrometry confirmed that the purified antimicrobial compound corresponds to a molecular mass of 2679 Da, which is consistent with that deduced from its genetic origin. Pseudocin 196 is classified as a lantibiotic based on its similarity to lacticin 481, a lanthionine ring-containing lantibiotic produced by Lactococcus lactis. Pseudocin 196, the first reported bacteriocin produced by a B. pseudocatenulatum species of human origin, was shown to inhibit clinically relevant pathogens, such as Clostridium spp. and Streptococcus spp. thereby highlighting the potential application of this strain as a probiotic to treat and prevent bacterial infections.

Diversity and Antibiotic Susceptibility of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae from the Urine of Human Population Using Bacteria-Contaminated Water in Butembo Urban Area (DR Congo, Central Africa)

Aims: This study aims to investigate the extended-spectrum beta-lactamases (ESBLs)-producing Enterobacteriaceae in the human urine samples and to understand the potential influence of the contaminated water the urine donors use. Study Design and Methodology: One hundred urine samples from females and the same number from males were collected from donors of different age groups and analysed. One hundred urine samples from females and the same number from males were collected from donors of different age groups. The enterobacterial isolation was done on CLED agar medium. Their identification was carried out first by the enzymatic technic, then using MALDI–TOF MS method. ESBLs-producing enterobacteria were identified by searching the synergy between Clavulanic acid and 3rd generation Cephalosporins. The antimicrobial susceptibility tests were carried out using the disk diffusion method. Results: In male urine samples, the identified ESBLs-producing strains belong to E. coli, E. agglomerans and K. pneumoniae. They were in 11 samples: 3 from donors aged 20 years or less, 3 also from those aged 21 to 40 years as well as in those aged 41 to 60 years, and 2 in samples from donors aged over than 60 years. In female urine samples, the identified ESBLs-producing strains belong to Escherichia coli, Enterobacter agglomerans, Yersinia frederiksenii, Salmonella typhi and Klebsiella pneumoniae. They were in 27 samples: 3 from donors aged 20 years or less, 9 from those aged 21 to 40 years, 12 from those aged 41 to 60 years, and 3 from donors aged over than 60 years. All the strains were sensitive to Imipenem and resistant to Cefotaxim, Ceftazidin, Amoxicillin+Clavulanic acid and Nitrofurantoin. The Multi-Antibiotic Resistance (MAR) index varied from 0.416 (E. coli strains, youngest male donors) to 0.916 (E. coli strains, old female donors). Most of strains react differently from one antibiotic to another (P<0.05), with the exception of E. coli strains from most samples. Most of the identified ESBLs-producing species have been reported in surface and groundwater the population use. These water resources could play a role in the human urinary tract infections. Conclusion: There is a serious health problem with great MAR indices for all bacterial species identified. Treating water before use could reduce the viability and spreading of ESBLs-producing bacteria and genes into the population.

Dental and microbiological status of COVID-19 convalescent patients with simple marginal gingivitis

The pattern of dental morbidity in the population of the Russian Federation evidences about a high incidence of inflammatory periodontal diseases, which varies based on patient age and comorbidity. The negative age-related dynamics of dental health emphasizes the problem of concomitant pathology and requires constant monitoring of risk factors for inflammatory periodontal diseases. Insufficient attention is paid to endogenous risk factors, such as neurodystrophic disorders, diseases of the cardiovascular system, leukemia, anemia, gastrointestinal tract diseases, infections, etc. At the same time, the growth of “new” infections (HIV-infection, HCV-infection, Ebola fever, new coronavirus infection) is recorded with elevating level of other infectious diseases. The aim of the study is to assess dental and microbiological status of COVID-19 convalescent patients. A survey of 100 patients diagnosed with simple marginal gingivitis (ICD-10 code: K 05.10) was carried out consisting of the following groups: main group — 75 COVID-19 convalescent patients, control group — 25 COVID-19-negative subjects. All individuals underwent microbiological diagnostics for gingival groove contents and an assessed dental status. The index assessment was performed using the simplified Green-Vermillion Oral Hygiene Index (OHI-S), the PMA index (Parma) and the gingival papilla blood flow index (PBI). In the laboratory, the collected material was seeded onto expanded list of dense nutrient media. The identification of isolated microorganisms was carried out using MALDI-ToF mass spectrometry. Our analysis of the index assessment in both groups showed that the average values of the indices 1 month after the diagnosis of new coronavirus infection (ICD-10 code: U07.1) in main group are higher than in control group. Based on the results of a microbiological study, significant differences in the frequency of microbial species isolation were identified for 12 species. Thus, it is important to develop approaches to predicting development of chronic gingivitis and its exacerbation in COVID-19 patients.

Genomic analysis of <i>Klebsiella pneumoniae</i> strains virulence and antibiotic resistance

Recently, Klebsiella pneumoniae strains have become widespread both in community-acquired infectious processes and in nosocomial infections. There are two pathotypes of K. pneumoniae: classical (cKp) and hypervirulent (hvKp). Representatives of any pathotype are prone to acquire and further transmit genetic factors of antibiotic resistance and virulence. This combination accounts for severity of the infectious process. Therefore, information about whether the strain belongs to either pathotype can help in prescribing proper therapy. Since there is no consensus upon hypervirulence marker, we attempted to find the most significant combinations of genetic markers of virulence and antibiotic resistance in K. pneumoniae strains. The study was aimed to conduct a genomic analysis of virulence and antibiotic resistance of K. pneumoniae clinical isolates. Materials and methods. There were examined 85 strains of K. pneumoniae isolated from diverse clinical material samples from patients in large St. Petersburg hospitals. In our work, we used classical bacteriological methods, including determination of the hypermucoviscous type using the “string test”, the mass spectrometric method (MALDI-ToF MS) for identifying bacteria, molecular methods for studying markers of virulence and antibiotic resistance (multilocus sequence typing, genome sequencing of K. pneumoniae strains). Results. Among the studied K. pneumoniae strains, the most common carbapenemase genes were OXA-48 (18.7%) and NDM-1 genes — 17.3% of strains; in 6.7% of strains, NDM-1 and OXA-48 genes were found simultaneously. The percentage of strains with β-lactamase genes CTX-M-15 was 54.7%, OXA-1 — 17.3%, TEM-1D — 13.3%, and in 17.3% of cases the OXA-1 and TEM-1D genes were simultaneously present in bacterial strains. Quinolone resistance genes were found in 68.4% of strains. The most common genes were qnrS1 (40% of strains) and qnrB1 (22.7%). Phenotypic antimicrobial susceptibility testing showed that 23.5% and 64.7% strains were resistant to colistin and carbapenems, respectively. 32.9% K. pneumoniae strains, isolated in patients with phlegmon, pneumonia, sepsis, and peritonitis, had a hypermucoid phenotype. The most common sequence types were: ST395 (24.3%), ST23 (17.6%) and ST512 (9.5%). 8% and 25.3% of strains belonged to capsule types K1 and K2, respectively. The polyketide synthesis locus ybt, which characterizes virulent strains, was detected in 69.3% isolates, and the clb locus was present in 10.7% of strains. In 73.3% and 14.7% strains, the plasmid-associated virulence loci iuc and iro were identified, which encode the biosynthesis of the siderophores aerobactin and salmochelin. We described 44 cases (58.7% of strains) of genotypic convergence of virulence and antibiotic resistance, as shown by simultaneously detected the aerobactin (iuc) locus and β-lactamase or carbapenemase genes. Thus, identification of hypervirulence may provide valuable information for the clinical management of patients with hvKp infections. Therefore, it is is obviously necessary to develop comprehensive diagnostic test for simultaneous screening of multidrug-resistant hypervirulent K. pneumoniae strains.

Variation in Interleukin-4, -6, and -10 in Mastitis Milk: Associations with Infections, Pathogens, Somatic Cell Counts, and Oxidative Stress.

Poor mastitis control favors intramammary infection (IMI), which always involves CNS. This study aimed to determine the relationships of IL-4, IL-6, and IL-10 in mastitis milk with concurrent infection, bacterial pathogens, SCC, and MDA, an oxidative stress marker. All mastitis quarters from five smallholder dairy farms were sampled aseptically before morning milking and again before afternoon milking for bacteriological identification using MALDI-TOF mass spectrometry. The samples with the concomitant infection between streptococci and CNS and their pairs of another sample from the quarters were selected. In addition, samples were randomly chosen to have a controlled single infection. IL-4, IL-6, and IL-10 were measured with ELISA kits. MDA was measured using HPLC, while SCC was measured using Fossomatic™ FC. The results from a repeated measure analysis showed that IL-4 positively correlated with SCC, while IL-6 showed a negative trend. IL-4 levels were highest in CNS infections and significantly higher than in non-infected or mixed infections (p < 0.05). The IL-6 level of the mixed bacteria was highest and showed a different trend from non-infection, and the quarter was infected with streptococcal bacteria. In conclusion, from a single infection, the streptococci and CNS quarter showed varied immune responses, including trendily higher IL-6 and IL-4.

Determination of metformin from micro-liter plasma and blood glucose test strip using eco-friendly micro-extraction procedures for point-of-care diagnostics

Metformin is commonly used in the treatment of type 2 diabetes and polycystic ovary syndrome. Beyond these common applications, it also holds promise in treating chronic pain, and as an antiaging and anticancer agent. In addition, it has cardiovascular protective and neuroprotective effects. However, elevated concentrations of metformin in the plasma, such as in patients with renal impairment or with conditions that can disrupt lactate clearance, could cause metformin-associated lactic acidosis. Moreover, metformin can cause a deficiency of vitamin-B12 and folic acid and impact one-carbon metabolism negatively. This study employs micro-extraction procedures to extract metformin from the human plasma and blood glucose test strips followed by detection using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Under the optimized micro-extraction procedures and by using an eco-friendly base and solvent, the proposed method required only 10 µL of the human plasma and a small piece of the blood glucose test strip for metformin analysis. The method exhibits a linear range of 0.05–5 μg mL−1 with a coefficient of determination (r2) of 0.999 and a limit of detection of 0.01 μg mL−1. The relative standard deviation (RSD) and relative error (RE) were both below 6.7 %. The test strip is a disposable product; its reuse before disposal could increase its additional applicability. Furthermore, major blood proteins and their modifications could be identified using this tiny volume of blood by mass spectrometry after protein digestion. The proposed technique could be invaluable in point-of-care diagnostics, enabling rapid monitoring of metformin plasma concentration and major plasma proteins to help patients mitigate the risk of metformin-associated lactic acidosis. To reduce organic waste in clinical applications, micro-extraction is a simple and efficient protocol for sample preparation using minute volumes of blood samples.

Genomic oropharyngeal Neisseria surveillance detects MALDI-TOF MS species misidentifications and reveals a novel Neisseria cinerea clade.

Introduction. Commensal Neisseria spp. are highly prevalent in the oropharynx as part of the healthy microbiome. N. meningitidis can colonise the oropharynx too from where it can cause invasive meningococcal disease. To identify N. meningitidis, clinical microbiology laboratories often rely on Matrix Assisted Laser Desorption/Ionisation Time of Flight Mass Spectrometry (MALDI-TOF MS).Hypothesis/Gap statement. N. meningitidis may be misidentified by MALDI-TOF MS.Aim. To conduct genomic surveillance of oropharyngeal Neisseria spp. in order to: (i) verify MALDI-TOF MS species identification, and (ii) characterize commensal Neisseria spp. genomes.Methodology. We analysed whole genome sequence (WGS) data from 119 Neisseria spp. isolates from a surveillance programme for oropharyngeal Neisseria spp. in Belgium. Different species identification methods were compared: (i) MALDI-TOF MS, (ii) Ribosomal Multilocus Sequence Typing (rMLST) and (iii) rplF gene species identification. WGS data were used to further characterize Neisseria species found with supplementary analyses of Neisseria cinerea genomes.Results. Based on genomic species identification, isolates from the oropharyngeal Neisseria surveilence study were composed of the following species: N. meningitidis (n=23), N. subflava (n=61), N. mucosa (n=15), N. oralis (n=8), N. cinerea (n=5), N. elongata (n=3), N. lactamica (n=2), N. bacilliformis (n=1) and N. polysaccharea (n=1). Of these 119 isolates, four isolates identified as N. meningitidis (n=3) and N. subflava (n=1) by MALDI-TOF MS, were determined to be N. polysaccharea (n=1), N. cinerea (n=2) and N. mucosa (n=1) by rMLST. Phylogenetic analyses revealed that N. cinerea isolates from the general population (n=3, cluster one) were distinct from those obtained from men who have sex with men (MSM, n=2, cluster two). The latter contained genomes misidentified as N. meningitidis using MALDI-TOF MS. These two N. cinerea clusters persisted after the inclusion of published N. cinerea WGS (n=42). Both N. cinerea clusters were further defined through pangenome and Average Nucleotide Identity (ANI) analyses.Conclusion. This study provides insights into the importance of genomic genus-wide Neisseria surveillance studies to improve the characterization and identification of the Neisseria genus.

Specification of Rhizospheric Characteristics of Some Bacteria Identified by MALDI TOF MS from Agricultural Soils in Kirsehir Province (Akçakent and Çiçekdağı) Districts

The rhizosphere are site of plant-microorganism interaction, and have critical impotance in events like nutrient supply, the production of compounds that support plant growth and phytopathogen protection. This study reports 52 bacteria isolated from 5 different plant rhizospheres (Hordeum vulgare, Avena sativa, Cicer arietinum, Helianthus annuus, and Phaseolus vulgaris) of two agricultural districts of Kırşehir (Akçakent and Çicekdağı regions) in Türkiye. Morphological, biochemical, plant growth-promoting characteristics (including production of indole-3-acetic acid, siderophore, nitrogen fixation, and phosphate solubilization) using MALDI-TOF-MS techniques were used to identify the isolates. Among all isolates, 33 isolate were Gram positive and 19 were Gram negative. Furthermore 40% of them were classified as Bacillus species, 10% belonged to Pseudomonas species, 7% were Acinetobacter species, 4% were Pantoeae species, and 39% other species (Blastomonas, Lysinibacillus, Comamonas, Alcaligenes, Bifidobacterium, Aromatoleum). It was seen that 12 isolates fixed nitrogen, 8 isolates produced dissolved inorganic phosphate, 12 isolates produced siderophores, 9 isolates were produced by IAA, and 14 isolates produced HCN during the screening of plant growth promoting properties. It is concluded that the culture of bacteria living in the rhizosphere are essential to promote soil fertility and sustainable agriculture. Therefore, there is a need to identify and use these strains with plant growth promoting properties in agriculture.

New Structure of Aeromonas salmonicida O-Polysaccharide Isolated from Ill Farmed Fish.

The diversity of O-polysaccharides (O-antigens) among 28 Aeromonas salmonicida strains isolated from ill fish has been determined by using high-resolution magic angle spinning (HR MAS) NMR spectroscopy. The new O-polysaccharide has been identified in two isolates. This new structure was investigated by 1H and 13C NMR spectroscopy and matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The following structure of the linear hexasaccharide repeating unit of A. salmonicida O-antigen has been established: →3)-α-L-Rhap-(1→3)-α-D-ManpNAc-(1→2)-β-D-Glcp-(1→3)-α-L-Rhap2OAc4OAc-(1→3)-β-D-ManpNAc-(1→3)-α-D-Glcp-(1→. This new A. salmonicida O-polysaccharide was detected among two isolates collected from trout and turbot fish in 2010 and 2011, respectively. Further investigations should be conducted to evaluate the distribution of this new O-polysaccharide among a larger collection of isolates, depending on their geographic origin, the species of fish, and the health status of the fish.

Colistin Resistance Mechanisms and Molecular Epidemiology of Enterobacter cloacae Complex Isolated from a Tertiary Hospital in Shandong, China.

Enterobacter cloacae complex (ECC), which includes major nosocomial pathogens, causes urinary, respiratory, and bloodstream infections in humans, for which colistin is one of the last-line drugs. This study aimed to analyse the epidemiology and resistance mechanisms of colistin-resistant Enterobacter cloacae complex (ECC) strains isolated from Shandong, China. Two hundred non-repetitive ECC strains were collected from a tertiary hospital in Shandong Province, China, from June 2020 to June 2022. Whole-genome sequencing and bioinformatics analyses were performed to understand the molecular epidemiology of the colistin-resistant ECC strains. The nucleotide sequences of heat shock protein (hsp60) were analyzed by using BLAST search to classify ECC. The gene expression levels of ramA, soxS, acrA, acrB, phoP, and phoQ were assessed using RT-qPCR. MALDI-TOF MS was used to analyse the modification of lipid A. Twenty-three colistin-resistant strains were detected among the 200 ECC clinical strains (11.5%). The hsp60 cluster analysis revealed that 20 of the 23 ECC strains belonged to heterogeneous resistance clusters. Variants of mgrB, phoPQ, and pmrAB, particularly phoQ and pmrB, were detected in the 23 ECC strains. The soxS and acrA genes were significantly overexpressed in all 23 colistin-resistant ECC strains (P < 0.05). Additionally, all 23 ECC strains contained modified lipid A related to colistin resistance, which showed five ion peaks at m/z 1876, 1920, 1955, 2114, and 2158. Among the 23 ECC strains, 6 strains possessed a phosphoethanolamine (pETN) moiety, 16 strains possessed a 4-amino-4-deoxy-L-arabinose (-L-Ara4N) moiety, and one strain had both pETN and -L-Ara4N moieties. This study suggests that diverse colistin resistance existed in ECC, including unknown resistance mechanisms, exist in ECC. Mechanistic investigations of colistin resistance are warranted to optimise colistin use in clinical settings and minimise the emergence of resistance.

Early Candida colonisation impact on patients and healthcare professionals in an intensive care unit.

Candida spp. is an opportunistic pathogen that causes superficial and invasive infections with nosocomial outbreaks without strict hygiene protocols. Herein, we assessed oral colonisation by Candida spp. in 209 Intensive Care Unit (ICU) patients between July 2021 and April 2022, conducting clinical, epidemiological, and microbiological characterisation of those developing oral or invasive candidiasis. Initial oral swabs were collected within 24 h of admission in the ICU, followed by collections on Days 2, 4, 6 and 8. Swabs from denture-wearing patients, abiotic surfaces, healthcare professionals' hands, and retroauricular regions were also obtained. Recovered yeasts and filamentous fungi were identified using MALDI-TOF MS and morphological characteristics, respectively. Genetic similarity of Candida spp. isolates was evaluated using Amplified fragment length polymorphism (AFLP), and the antifungal susceptibility profile was determined by broth microdilution. In the study, 64.11% of patients were orally colonised by Candida spp. Of these, 80.59% were colonised within the first 24 h. Oral colonisation also occurred on subsequent days: 50%/Day 2, 26.92%/Day 4, and 11.53%/Days 6 and 8. Of the patients, 8.61% had oral candidiasis, mainly pseudomembranous. Among orally colonised patients, 2.23% developed invasive candidiasis. Besides, 89.47% of healthcare professionals evaluated were colonised. MALDI-TOF MS identified different yeast species, and C. albicans (45.34%), C. tropicalis (15.7%), and C. parapsilosis sensu stricto (9.88%) were the most prevalent. AFLP analysis indicated a high genetic correlation (≥97%) between C. parapsilosis sensu stricto isolates from patients and professionals. Three resistant C. albicans isolates were also found. This study reported a diversity of yeast and filamentous fungi species in ICU patients and highlighted early Candida spp. colonisation risks for invasive candidiasis, as well as the potential horizontal transmission in the nosocomial setting, emphasising the need for effective infection control measures.

Antibiotic Resistance Profiles of Escherichia coli and Salmonella spp. Isolated From Dairy Farms and Surroundings in a Rural Area of Western Anatolia, Turkey.

Background Antibiotic resistance is a significant public health issue worldwide. Antibiotic-resistant zoonotic bacteria such as Escherichia coli (E. coli), Campylobacter, Salmonella, Listeria, Coxiella, and Mycobacterium can be particularly isolated from biofertilizers. Epidemiological studies have shown that cases of foodborne infections and intoxications are significantly related to animal-derived foods. The presence of these species in aquatic environments indicates areas or organisms contaminated with animal or human feces. Especially, the presence of E. coli in aquatic environments has become a serious problem worldwide. Pathogenic strains of E. coli cause waterborne and foodborne diseases. Materials and methods This study included a total of 290 samples collected from five different dairy farms between April and September 2023 which comprised 20 samples of cow manure, 20 samples of milk, three samples of dairy workers' hand washing water, five samples ofsoil, five samples of water, and five samples of vegetables. The samples taken from the farms were homogenized with 0.1% peptone water at a ratio of 1/10. They were then cultured on xylose lysine deoxycholate (XLD), eosin methylene blue agar (EMB), and blood agar media, and gram-negative colonies were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and the VITEK2 automated system (BioMerieux Inc., Durham, NC). Amplification of the isolated DNA extracts was performed with A.B.T.™ 2X HS-PCR MasterMix (A.B.T Laboratory Industry, Arnavutköy, Turkey) in the SimpliAmp™ thermal cycler (Thermo Fischer Scientific Inc., Waltham, MA) and visualized by agarose gel electrophoresis. Results Among the 52E. coli strains isolated in our study, the highest antibiotic sensitivity rate was observed in meropenem, while the lowest sensitivity rates were determined in cefazolin and cefuroxime. While two of the Salmonella spp. (n = 2) isolates were found to be resistant to tetracycline, and one was found to be resistant to penicillin and ampicillin. No resistance to trimethoprim/sulfamethoxazole was detected in either isolate. Extended-spectrum beta-lactamases (ESBLs) were detected in only four (7.7%) E. coli strains. While tetA, tetB, and TEM genes were seen in almost all E. coli strains, they were not found in Salmonella spp. Conclusion In conclusion, our study revealed the presence of antimicrobial resistance genes in E. coli and Salmonella spp. isolates collected from various farms and environmental samples, which render the antimicrobials used for disease treatment ineffective. Consequently, research should be undertaken to prevent the development of new resistance genes in our country, as creating new medications and treatment strategies for these diseases is costly and time-intensive.

Matrix-assisted laser desorption/ionization mass spectrometry for the rapid and high throughput analysis of betaine and trigonelline in Lycium chinense Mill. and trigonelline in coffee

A rapid, simple, effective, and green method for the determination of betaine and trigonelline from Lycium chinense Mill. (LCM) and the quantification of the trigonelline in coffee was proposed and validated by matrix-assisted laser desorption ionization time-of-flight mass spectrometric (MALDI-TOF MS) detection. Due to without chromatographic separation, the method greatly shortened the detection time. The detection of betaine and trigonelline concentration showed good linearity in the range of 1–100 μg/mL and 0.01–100 μg/mL, with correlation coefficients r2 = 0.9962 and 0.9946, respectively. The good reproducibility and reliability of the method were demonstrated by excellent intraday and interday precisions with RSD <8.3%, and the recovery of betaine and trigonelline ranged from 92.2% to 116.0%. Analysis of LCM and coffee extracts (raw, light-roasted, and dark-roasted coffee beans) gave results in agreement with the literature. The method appeared as a fast and reliable alternative method for routine Lycium chinense and coffee analysis.

Isolation and Characterization of a (Surfactin-Like Molecule) Produced by Bacillus subtilis: Antagonistic Impact on Root-Knot Nematodes

Plant-parasitic nematodes are severe soil-borne pathogens that cause significant damage to agricultural products each year, resulting in substantial financial losses globally. Thus, there is an urgent need to identify novel biological control agents or nematicides. The nematicidal potential of Bacillus subtilis-derived lipopeptides against Meloidogyne incognita was investigated at various concentrations (35 ppm, 25 ppm, 15 ppm, 5 ppm) under in vitro conditions. Egg hatching inhibition and mortality of second-stage juveniles (J2s) of M. incognita were analyzed after exposure for 6, 12, 24, 48, and 96 hours. Data showed that with the increase in concentration and exposure period, egg hatching inhibition and percent mortality increases. Maximum percent mortality of J2s was reported at 35ppm i.e., 45%, 55%, 67.75%, 77% and 85% at 6, 12, 24, 48 and 96 hrs, respectively. The maximum ovicidal activity was reported at 35ppm concentration, with 84.61% of eggs hatching inhibition on 96 hrs of the exposure period. The bacterial culture suspension of Bacillus subtilis and Pseudomonas putida at1.2x108cfu/ml, and the crude lipopeptide (35ppm) was also investigated as a biological control agent against M. incognita on tomato in a pot experiment under glasshouse condition. Combinational treatment of P. putida and B. subtilis culture, prior to inoculation of M. incognita on tomato plant caused a significant increase in plant growth attributes and in biochemical parameters over the inoculated control. In the same treatment, the maximum reduction in nematode population and root galling was recorded. However, in the crude lipopeptide experiment study, root dip and inoculation of crude lipopeptide in tomato after the introduction of M. incognita caused a major augment in all the parameters over the inoculated control. MALDI-TOF MS analysis of crude lipopeptide shows surfactin like molecules at m/z 1058 [M+Na]+. It is concluded that crude lipopeptide or combinational treatment of B. subtilis and P. putida culture suspension can be employed as a biocontrol agent against M. incognita and may act as a source of a novel nematicidal agent of bacterial origin.

Predictive modeling of mortality in carbapenem-resistant Acinetobacter baumannii bloodstream infections using machine learning.

Acinetobacter baumannii, a notable drug-resistant bacterium, often induces severe infections in healthcare settings, prompting a deeper exploration of treatment alternatives due to escalating carbapenem resistance. This study meticulously examined clinical, microbiological, and molecular aspects related to in-hospital mortality in patients with carbapenem-resistant A. baumannii (CRAB) bloodstream infections (BSIs). From 292 isolates, 153 cases were scrutinized, reidentified through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), and evaluated for antimicrobial susceptibility and carbapenemase genes via multiplex polymerase chain reaction (PCR). Utilizing supervised machine learning, the study constructed models to predict 14- and 30-day mortality rates, revealing the Naïve Bayes model's superior specificity (0.75) and area under the curve (0.822) for 14-day mortality, and the Random Forest model's impressive recall (0.85) for 30-day mortality. These models delineated eight and nine significant features for 14- and 30-day mortality predictions, respectively, with "septic shock" as a pivotal variable. Additional variables such as neutropenia with neutropenic days prior to sepsis, mechanical ventilator support, chronic kidney disease, and heart failure were also identified as ranking features. However, empirical antibiotic therapy appropriateness and specific microbiological data had minimal predictive efficacy. This research offers foundational data for assessing mortality risks associated with CRAB BSI and underscores the importance of stringent infection control practices in the wake of the scarcity of new effective antibiotics against resistant strains. The advanced models and insights generated in this study serve as significant resources for managing the repercussions of A. baumannii infections, contributing substantially to the clinical understanding and management of such infections in healthcare environments.

Modelling the rapid detection of Carbapenemase-resistant Klebsiella pneumoniae based on machine learning and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

In this study, 80 carbapenem-resistant Klebsiella pneumoniae (CR-KP) and 160 carbapenem-susceptible Klebsiella pneumoniae (CS-KP) strains detected in the clinic were selected and their matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) peaks were collected. K-means clustering was performed on the MS peak data to obtain the best "feature peaks", and four different machine learning models were built to compare the area under the ROC curve, specificity, sensitivity, test set score, and ten-fold cross-validation score of the models. By adjusting the model parameters, the test efficacy of the model is increased on the basis of reducing model overfitting. The area under the ROC curve of the Random Forest, Support Vector Machine, Logistic Regression, and Xgboost models used in this study are 0.99, 0.97, 0.96, and 0.97, respectively; the model scores on the test set are 0.94, 0.91, 0.90, and 0.93, respectively; and the results of the ten-fold cross-validation are 0.84, 0.81, 0.81, and 0.85, respectively. Based on the machine learning algorithms and MALDI-TOF MS assay data can realize rapid detection of CR-KP, shorten the in-laboratory reporting time, and provide fast and reliable identification results of CR-KP and CS-KP.

Extracting Structural Data from MALDI-ToF Mass Spectrometry Analysis of Alternating Conjugated Polymers – A Case Study on PBTTT Derivatives

Extracting Structural Data from MALDI-ToF Mass Spectrometry Analysis of Alternating Conjugated Polymers – A Case Study on PBTTT Derivatives

Thiazole-based metalloligands and their heteroleptic MOFs: Chromogenic and fluorometric detection of tryptophan and Z-l-phenylalanine using Cu(II)-complex and Cu(II)-Zn(II) MOF

Two thiazole-containing metalloligands based on the Cu(II) (P1) and Zn(II) (P2) comprising 2-(2-Pyridyl)-4-methylthiazole-5-carboxylic acid (HL1) and their extended heteroleptic metal-organic frameworks (MOFs) (CP1-CP2) have been prepared and further explored toward sensing. These compounds have been characterized through various spectro-analytical techniques, including elemental analysis, FT-IR, ESI-MS, SEM with EDX, PXRD, TGA, DSC/DTG, UV/vis and fluorescence spectroscopy. Structure of P1 has been confirmed by X-ray single crystal analysis. These compounds have been examined as chromogenic and fluorescent probes toward a series of amino acids wherein, P1 and CP1 showed highly selective chromogenic changes and fluorescence enhancement with Z-l-phenylalanine, respectively in aqueous-DMSO media. Notably, the association constant and detection limit were determined to be 2.25 × 105 M−1, 7.0 × 105 M−1 and 5.88 ppb, 0.39 ppb, respectively. Job's plot analysis, MALDI-TOF mass spectrometry and HRMS studies suggested the plausible interaction/ binding of Z-l-phenylalanine with P1 and CP1.

Comparison of the Direct Identification and Short-Term Incubation Methods for Positive Blood Cultures via MALDI-TOF Mass Spectrometry.

Timely pathogen identification in bloodstream infections is crucial for patient care. A comparison is made between positive blood culture (BC) pellets from serum separator tubes using a direct identification (DI) method and colonies on agar plates from a short-term incubation (STI) method with a matrix-assisted laser desorption/ionization Biotyper for the evaluation of 354 monomicrobial BCs. Both the DI and STI methods exhibited similar identification rates for different types of bacteria, except for Gram-positive and anaerobic bacteria. The DI method's results aligned closely with the STI method's results for Enterobacterales, glucose-non-fermenting Gram-negative bacilli (GNB), and carbapenem-resistant Enterobacterales. The DI method exhibited high concordance with the conventional method for GNB identification, achieving 88.2 and 87.5% accuracy at the genus and species levels, respectively. Compared with the STI method, the DI method showed a less successful performance for Gram-positive bacterial identification (50.5 vs. 71.3%; p < 0.01). The DI method was useful for anaerobic bacterial identification of slow-growing microorganisms without any need for colony growth, unlike in the STI method (46.7 vs. 13.3%; p = 0.04). However, both methods could not identify yeast in positive BCs. Overall, the DI method provided reliable results for GNB identification, offering many advantages over the STI method by significantly reducing the turnaround time and enabling quicker pathogen identification in positive BCs.