bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Seegene AnyPlexTM II STI-7e with standard-of-care diagnostic methods for the detection of Mycoplasma genitalium, Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis
Authors: Bodiybadu Kaveesha , Danielewski Jennifer , Plummer Erica , Bradshaw Catriona S , Machalek Dorothy A , Garland Suzanne M , Vodstrcil Lenka A , Murray Gerald L 
Published: April 2024

Abstract
The AnyPlexTM II STI-7e panel assay (Seegene) detects seven sexually transmitted organisms (Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, M. hominis, Ureaplasma urealyticum, U. parvum, and Trichomonas vaginalis). This study compared the performance of AnyPlexTM II STI-7e with standard-of-care diagnostic methods. Samples (cervical or vaginal swabs, or urine) from 1330 women were tested on standard-of-care assays; 83/1318 (6.3%) tested positive for M. genitalium (ResistancePlus® MG), 99/1317 (7.5%) positive for C. trachomatis and 11/1316 (0.8%) positive for N. gonorrhoeae (Hologic® Aptima Combo 2®), and 6/689 (0.9%) positive for T. vaginalis (wet mount microscopy). AnyPlexTM II STI-7e had good agreement for the detection of M. genitalium [Cohen’s kappa of 0.80, 95% confidence intervals (CI) 0.74–0.87] and C. trachomatis (kappa of 0.87, 95% CI 0.82–0.92), with positive and negative % agreement &gt;96% for both infections. There was lower agreement for the detection of N. gonorrhoeae (kappa of 0.37, 95%CI 0.19–0.55) and T. vaginalis (kappa of 0.521, 95%CI 0.25–0.80). In summary, the test performed well in this comparison for M. genitalium and C. trachomatis detection, but results were less conclusive for N. gonorrhoeae and T. vaginalis due to low prevalence in the population.
Urban wastewater contributes to the emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) in an urban receiving river in eastern India
Authors: Sahoo Saubhagini , Sahoo Rajesh Kumar , Gaur Mahendra , Behera Dibyajyoti Uttameswar , Sahu Anshuman , Das Aradhana , Dey Suchanda , Dixit Sangita , Subudhi Enketeswara 
Published: April 2024

Abstract
The present study revealed the emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) and the associated driving factors in an urban river system surrounding Cuttack city, Odisha. The high contamination factor and contamination degree indicate poor water quality. The CRKP isolates showed 100% resistance against piperacillin, amoxicillin-clavulanic acid, piperacillin-tazobactam, ceftriaxone, ceftazidime, meropenem, and imipenem but less resistance to colistin (12.85%). Among the CRKP isolates, carbapenemase genes blaNDM, blaOXA-48-like, and blaKPC were detected in 94.28%, 35%, and 10% of isolates, respectively. The resistance genes (blaNDM, blaTEM, and blaCTX-M) were found to be significantly correlated with toxic metals (As, Cd, Co, Cu, Fe, Mn, Pb) (P &lt; 0.05). Detection of virulence factors (yersiniabactin and aerobactin) and capsular serotypes (K1, K2, and K54 types) explain the pathogenicity of CRKP isolates. Enterobacterial repetitive intergenic consensus-PCR based molecular typing separated the CRKP strains into 13 clusters, of which VI and XI clusters showed similar resistance and virulence determinants, indicating the dissemination of clones from wastewater to the river system. Our results provide first-hand information on assessing risks to public health posed by the CRKP isolates and toxic metals in the Kathajodi River. Molecular surveillance of nearby hospitals for the prevalence of CRKP will help trace their transmission route.
Effect of Lactobacillus spp. cell-free supernatant against planktonic growth and biofilm formation of foodborne Escherichia coli isolates
Authors: Fernandes Mariane Silveira Magalhães , Rios Juliana Carla , Vasconcelos Brendda Miranda , Lourenço Maria Leilah Monte Coelho , Matos Maria Nágila Carneiro , Cavalcante Rafaela Mesquita Bastos , de Almeida Marilia Viana Albuquerque , Costa Renata Albuquerque , Carneiro Victor Alves 
Published: April 2024

Abstract
The aim of this work was to evaluate the anti-Escherichia coli effect of cell-free supernatant (CFS) of Lactobacillus spp. against planktonic and biofilm forms of foodborne isolates. Escherichiacoli strains (P12, P25, P35 and P36), previously isolated from fresh filets of fish, were subjected to antimicrobial susceptibility determination by the disc-diffusion agar method. Subsequently, the antagonistic effect between probiotic and pathogenic strains was determined by spot overlay assay. Finally, the CFS activity against pre-established (12 h) biofilms was demonstrated through biomass quantification by crystal violet staining and scanning electron microscopy (SEM). All isolates presented some pattern of resistance, primarily to ampicillin and tetracycline. Probiotic strains presented high antagonistic effects against all E. coli strains, presenting inhibition zones (R) ranging from 15.60 to 20.67 mm. Additionally, the residual biomass of pre-established (12 h) biofilm was drastically reduced about 50% after CFS treatment (P &lt; 0.01). What can be noted by SEM images, which show less surface-attached cells of CFS-treated biofilms of E. coli (P12). Thus, cell-free preparations produced from Lactobacillus spp. may represent a tool in the battle against planktonic cells and biofilm forms of antibiotic-resistant E. coli.
Biocontrol of sheath blight of rice (Oryza sativa L.) through alteration in expression dynamics of candidate effector genes of Rhizoctonia solani AG1-IA during pathogenesis
Authors: Dauda Wadzani Palnam , Shanmugam Veerubommu , Tyagi Aditya 
Published: April 2024

Abstract
In genome analyses of Rhizoctonia solani AG1–IA causing sheath blight (ShB) of rice, many genes were identified to have a hypothetical role in pathogenesis. To understand their roles in pathogenesis, their expressions during fungal infection were studied. An aggressive R. solani strain, RIRS-K, was first identified among six isolates, RIRS-K, RIRS-17, RIRS-S, RIRS-T, RIRS-MU and RIRS-FD, for inducing a maximum relative lesion height (RLH) of 32.7% on a ShB susceptible cultivar, Pusa Basmati-1. Hypothetical pathogenicity genes (52 nos) identified by in silico analyses of the publicly available genomic database of the pathogen strain were evaluated in Pathogen–Host Interaction (PHI) blast and RIRS-K. Though PHI blast identified 26 genes as potential ones, only 8 were constitutively expressive in RIRS-K cultured in a minimal broth. Among them, only expressions of AG1IA_06195, AG02692, AG04508, and AG05730 were induced in the rice plant inoculated with RIRS-K and, hence, were identified as the candidate ones. The candidate genes were highly expressed in the aggressive strain (RIRS-K) in comparison to the less aggressive one (RIRS-17). In further testing of their expressions in the highly aggressive fungal strain, RIRS-K infecting PB-1 pre-colonized by a potent biocontrol consortium comprising of Bacillus subtilis (S17TH), Pseudomonas putida (TEPF-Sungal-1), and Trichoderma harzianum (S17TH), the disease scoring and gene expression studies indicated that the candidate genes were downregulated. The studies, therefore, speculated that these genes might play a role in pathogen aggressiveness and ShB development.
Investigation of the nitrogen removal performance and microbial community structure in a full-scale A/O1/H/O2 coking wastewater treatment system
Authors: Zhang Baoshan , Deng Jinsi , Xie Junting , Tan Zhijie , Wei Chaohai , Zhu Shuang 
Published: April 2024

Abstract
Biological treatment processes are an effective method for removing the nitrogen-containing contaminants that exist in coking wastewater. However, little is known about microbial composition and keystone taxa involved in biological nitrogen removal processes. In order to improve the removal efficiency of nitrogen-containing contaminants in anaerobic-aerobic-hydrolytic-aerobic (A/O1/H/O2) system, the microbial composition and interactions of keystone taxa should be clarified. The present work clarifies the removal performance of nitrogen-containing contaminants in the A/O1/H/O2 system, identifies the microbial community involved in various bioreactors, and reveals the keystone taxa within the microbial communities. Combined the processes of ammoniation, denitrification, and nitrification, total nitrogen decreased from 248 to 31 mg L−1 and achieved a removal efficiency of 87.5% in the full-scale A/O1/H/O2 system. High-throughput MiSeq sequencing revealed that Proteobacteria was the most abundant phylum in the A/O1/H/O2 system with relative abundances of 24%–50%. Thiobacillus dominated in bioreactors A and O1 with relative abundances of 2.90% and 4.44%, respectively, while Nitrospira was identified as the most dominant genus in bioreactors H and O2, accounting for 13.33% and 18.38%, respectively. The microbial community composition and co-occurrence network analysis showed that the keystone taxa belonged to Thiobacillus, Nitrospira, Bdellovibrio, Planctomyces, Desulfotomaculum, and Sphingobium, which are related to nitrogen degradation.
Racemization rate and biomolecular characterization of D-serine synthesizing bacteria Bacillus tequilensis A1C1
Authors: Kapil Shikha , Bhattu Monika , Sharma Vipasha , Kumar Tarun 
Published: April 2024

Abstract
D-amino acids, the important components of the bacterial cell walls, are valuable molecular and genetic markers of bacterial-derived organic material in the environment. D-serine, a racemization product of L-serine is one such amino acid present in various prokaryotes and eukaryotes. It is a well-recognized regulator of various activities in the human nervous system. In plants, it has a role in the nitrogen cycle regulation and pollen tube growth. Serine enantiomers are present in different concentrations and few bacterial strains are reported to contribute to D-serine in the environment. During the present study, soil samples from different places in North India were collected and processed to isolate and screen the bacteria on M9 minimal media (Himedia) for D-serine synthesis. Thin-layer chromatography (TLC Silica gel 60 F 254 (20 × 20 cm, Merck, Darmstadt, Germany) and Mass spectroscopic analysis (Bruker MICROTOF II spectrometer) studies, etc were performed. D-serine-producing isolates were characterized as per standard procedures. Bacterial isolate A1C1 with maximum D-serine (0.919 ± 0.02 nM) synthesis under optimal growth conditions (37°C ± 0.5, 150 ± 0.5 RPM, and 7 ± 0.5 pH) was identified as Bacillus tequilensis based on 16sRNA sequencing. The isolate could be a valuable serine racemization tool for various industrial and environmental applications.
Changes in fungal community during different phases in conventional and bioreactor composting systems according to metatranscriptomics analysis
Authors: Ding Jianli , Wei Dan , An Zhizhuang , Jin Liang , Wu Fengxi , Suo Linna , Wang Lei , Li Yan , Cai Shanshan 
Published: April 2024

Abstract
We determined the changes that occurred in fungal community structures and their functions in conventional and bioreactor composting systems. The Illumina MiSeq platform was employed to sequence cDNA by reverse transcription to conduct metatranscriptomics analysis of RNA, and the FUNGuild tool was applied. The α-diversity of fungi in the bioreactor composter increased throughout composting, especially in the initial three phases, but decreased in the conventional composting system. The three dominant phyla in the bioreactor system were Ascomycota (30.27%–68.50%), Mortierellomycota (3.81%–39.51%), and Basidiomycota (9.17%–30.86%). Ascomycota (76.96%–97.18%) was the main phylum in the conventional composting system. Mortierella, Guehomyces, Plectosphaerella, Chaetomium, Millerozyma, and Coprinopsis were the main genera in the bioreactor composter. In the same phase, significant differences in the fungal functions were found between the two composting methods. Available phosphorus was the main factor that affected the community structures and functions of fungi in the bioreactor composter.
Anti-Pythium insidiosum activity of bioactive compounds from medicinal plants
Authors: Silveira Júlia de Souza , Braga Caroline Quintana , Bermann Carolina dos Santos , Ianiski Lara Baccarin , Bruhn Fábio Raphael Pascoti , Botton Sônia de Avila , Pereira Daniela Isabel Brayer 
Published: April 2024

Abstract
Pythiosis is a serious disease caused by the aquatic oomycete Pythium insidiosum that mainly affects mammals. Unlike fungal and bacterial resistance induced by the indiscriminate use of drugs, P. insidiosum has low susceptibility to antifungal drugs. In this sense, essential oils and their major components emerge as a promising treatment line for this disease. Given the above, this study sought to verify P. insidiosum (n = 34) susceptibility to the bioactive compounds eugenol, α-terpineol, menthol, and carvacrol and correlate them with the respective essential oils of Eugenia caryophyllata, Melaleuca alternifolia, Mentha piperita, and Origanum vulgare. The essential oils and bioactive compounds were purchased commercially and tested according to the Clinical and Laboratory Standards Institute protocol M38-A2. Our findings showed that eugenol, α-terpineol, and carvacrol had superior anti-P. insidiosum action than their respective essential oils, suggesting that they may be responsible for inhibitory activity against P. insidiosum. Notably, the major compound with the best anti-P. insidiosum activity was α-terpineol; nonetheless, menthol showed less activity than its essential oil. The results imply that essential oils and their major compounds may be important allies in treating pythiosis, expanding the perspectives of developing new drugs with anti-P. insidiosum activity.
Oomicidal activity of polypyrrole nanoparticles against Pythium insidiosum
Authors: Ianiski Lara Baccarin , Maciel Aline Fontanella , Weiblen Carla , Stibbe Paula Cristina , de Oliveira Helinando Pequeno , da Costa Mateus Matiuzzi , Sangioni Luis Antônio , Pereira Daniela Isabel Brayer , Santurio Janio Morais , Botton Sônia de Avila 
Published: April 2024

Abstract
This study evaluated in-vitro action of a new molecule, the polypyrrole nanoparticles (Ppy-NP), against Pythium insidiosum isolates using M38-A2/CLSI; the minimal inhibitory (MIC) and minimal oomicidal (MOC) concentrations were also determined. Additionally, changes in the hyphae wall of P. insidiosum CBS 575.85 treated with Ppy-NP were evaluated by scanning electron microscopy (SEM). The MIC100 and MOC for all isolates ranged from 8 to 32 μg mL−1, and the MIC90 and MIC50 were 16 μg mL−1. The SEM showed structural damage to the hyphae of P. insidisoum treated with Ppy-NP, as hyphae surfaces with less turgidity were found, thereby showing scaling and ruptures compared to the control (untreated hyphae). Our findings highlighted the anti-P. insidiosum properties of Ppy-NP proved to be a promising candidate for research using pythiosis experimental models.
Sediment-isolated Comamonas terrigena strain HJ-2: a novel nitrate-dependent ferrous-oxidizing bacterium with multifunction on pollutant transformation
Authors: Peng Rong , Shen Junhao , Li Shuang , Liu Hui 
Published: April 2024

Abstract
Microbially driven Fe(II) oxidation is vital for Fe-cycling processes. In the present study, a novel strain of nitrate-dependent Fe-oxidizing bacteria (FOB) was isolated from the riparian zone sediment of the Hanjiang River, China. It was identified as Comamonas terrigena strain HJ-2. The strain HJ-2 oxidized 2.80 mmol l−1 Fe(II) within 144 h to form Fe(III)/Fe(II) complex on the cell surface using 1.63 mmol l−1 nitrate as an electron acceptor. The formed nitrite from nitrate reduction chemically oxidized Fe(II). Surprisingly, this strain also reduced nitrilotriacetic iron to form 0.5 mmol l−1 Fe(II) in 120 h in anaerobic conditions primarily mediated by the NADH flavin oxidoreductase. Besides, the strain completely reduced 0.18 mmol l−1 nitrobenzene to aniline in 24 days and 15.6 μmol l−1 arsenate to arsenite in 7 days due to the existence of nitro and arsenate reductases. However, the Fe(II) inhibited the reduction of nitrate, nitrobenzene, and arsenate, possibly due to the impeding of transport of the solutes through the membrane or the synthesis of the related enzymes. These results provide new knowledge about the Fe(II)-cycling and the fate of some pollutants in the riparian zone. It also informed that some bacteria have universal functions on elements and contaminants transformation.
A panel of qPCR assays to detect and quantify soybean soil-borne pathogens
Authors: Rocha Leonardo F , Srour Ali Y , Pimentel Mirian , Subedi Arjun , Bond Jason P , Fakhoury Ahmad , Ammar Hala A 
Published: April 2024

Abstract
Fusarium oxysporum,F. graminearum,F. acuminatum,F. equiseti,F. proliferatum,F. solani, and Rhizoctonia solani are soil-borne fungal pathogens that cause substantial yield loss in a widespread list of crops worldwide. The objective of this study was to develop a panel of TaqMan assays for the detection and quantification of these six widespread soil-borne fungal species using real-time polymerase chain reaction (qPCR). The primers and probes were designed based on the intergenic spacer ribosomal RNA and translation elongation factor 1-alpha gene (tef1). These assays, although not multiplexed, can be performed simultaneously as they have similar reaction conditions, allowing more efficiency when targeting multiple pathogens in a sample. The assays presented high efficiency (94.3%–108.9%) and sensitivity, with a limit of detection of 0.05 picograms (50 femtograms) of target DNA. Results from an assay targeting 19 non-target and closely related species confirmed the specificity of the developed assays. The assays were also evaluated to detect the target species in different matrices, such as soil and plant material. This panel of qPCR assays is an additional tool that can be used by plant pathologists, microbiologists, plant breeders, diagnostic clinics, and other researchers interested in these fungal species.
Genome analysis of novel Apilactobacillus sp. isolate from butterfly (Pieris canidia) gut reveals occurrence of unique glucanogenic traits and probiotic potential
Authors: Jawad Iqra , Khaliq Shazia , Akhtar Nasrin , Saleem Muhammad , Akhtar Kalsoom , Ghauri Komal , Anwar Munir A 
Published: April 2024

Abstract
This study was conducted with a perception that fructose-rich niches may inhabit novel species of lactic acid bacteria that are gaining importance as probiotics and for the production of exopolysaccharides that have applications in food and pharmaceuticals. Recently, some Lactobacillus species have been reclassified as fructophilic lactic acid bacteria due to their preference for fructose over glucose as a carbon source. These bacteria are likely to be found in fructose rich niches such as flower nectar and insects that feed on it. We explored the butterfly gut and acquired a new isolate, designated as F1, of fructophilic lactic acid bacteria, which produces a glucan-type exopolysaccharide. Whole genome sequencing and in silico analysis revealed that F1 has significantly lower average nucleotide identity and DNA-DNA hybridization values as compared to its closest Apilactobacillus neighbors in phylogenetic analysis. Therefore, we declare the isolate F1 as a novel Apilactobacillus species with the proposed name of Apilactobacillus iqraium F1. Genome mining further revealed that F1 harbors genes for exopolysaccharide synthesis and health-promoting attributes. To this end, F1 is the only Apilactobacillus species harboring three diverse α-glucan-synthesis genes that cluster with different types of dextransucrases in the dendrogram. Moreover, many nutritional marker genes, as well as genes for epithelial cell adhesion and antimicrobial synthesis, were also detected suggesting the probiotic attributes of F1. Overall analysis suggests A. iqraium sp. F1 be a potential candidate for various health beneficial and pharmaceutical applications.
Bacillus velezensis (strains A6 & P42) as a potential biocontrol agent against Klebsiella variicola, a new causal agent of soft rot disease in carrot
Authors: Chandrashekar B S , Prasannakumar M K , Venkateshbabu Gopal , Mahesh H B , Puneeth M E , Narayan Karthik S , Parivallal P Buela , Pramesh D , Banakar Sahana N , Patil Swati S 
Published: April 2024

Abstract
Bacterial soft rot is one of the most devastating diseases and a major constraint encountered during carrot farming. Biological agents are the best eco-friendly alternatives to agrochemicals to manage soft rot disease to ensure environmental sustainability. In this study, about eight isolates of bacterial pathogen causing soft rot in carrots were collected from Karnataka, India. Based on the 16S rRNA sequencing the pathogen isolates causing soft rot of carrot were identified as Klebsiella variicola. The morphological characteristics of K. variicola was investigated under scanning electron microscopy. The pathogenicity assay showed that all eight isolates were pathogenic to the carrot. An in vitro and in planta assay of two novel strains of Bacillus velezensis (A6 and P42) against K. variicola indicated that both strains had strong antagonistic activity against all the pathogen strains. Furthermore, the volatile bioactive compounds produced by A6 and P42 strains were analyzed in GC-MS, which revealed the presence of 10 and 6 bioactive compounds in their culture filtrate, respectively, with antibacterial and antifungal properties. The present study suggests that both A6 and P42 strains of B. velezensis were antagonistic to K. variicola and can be used as biocontrol agents to manage soft rot diseases of carrot under field conditions.
Silver nanoparticles (AgNPs) in the control of Staphylococcus spp
Authors: da Cunha Kamila Furtado , Albernaz Déborah Trota Farias , Garcia Marcelle de Oliveira , Allend Suzane Olachea , Hartwig Daiane Drawanz 
Published: April 2024

Abstract
The Staphylococcus bacteria cause several infections, S. aureus is the major species, expressing different virulence factors. Therefore, coagulase-negative Staphylococcus (CoNS) are nosocomial pathogens, mainly associated with biofilm formation in invasive medical devices. Methicillin-resistant S. aureus (MRSA) and multidrug resistant (MDR) CoNS are widely distributed in the hospital environment, leading to infections that are difficult to treat. Thus, nanoparticles (NPs) are studied as an alternative in the control of these pathogens. Silver nanoparticles (AgNPs) stand out due to their different biological properties, broad-spectrum antibacterial activity, low toxicity, and use in combination with other drugs. Several studies with AgNPs evaluated in-vitro against S. aureus and MRSA validated the spectrum of action of the NPs. However, few studies attempted to explore the response of the CoNS, mainly in vivo studies. Research that explored the in vivo application of AgNPs against these bacteria helped to understand and better elucidate their activity on the skin through different biological models. Furthermore, the application of NPs is a viable alternative for controlling these bacteria, including MDR bacteria, in cases of skin infections by avoiding worsening the clinical condition and favoring tissue regeneration of the injured area.