bluuebunny/crossref_metadata_2025 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

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 >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

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 < 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

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 < 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

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

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

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

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

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

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

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

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

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

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

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.
Lyophilized cell-free supernatants of the oral probiotics Streptococcus salivarius M18 and Streptococcus salivarius K12 show promises for milk safety
Authors: Karaçam Sevinç , Tunçer Sinem
Published: April 2024

The functional food ingredients market has been growing due to the preferences for healthier, nutritional, environment-friendly, and convenience foods. Here, we evaluated the antimicrobial potential of the lyophilized cell-free supernatants of the two most promising oral probiotic strains Streptococcus salivarius M18 and S. salivarius K12 on Pseudomonas aeruginosa to be applied for safety purposes in the milk. We showed that the lyophilized culture supernatant of the strain M18 inhibited the pathogen growth in milk by about 75%, 70%, and 60% when incubated at 37°C, room temperature, and +4°C, respectively. The inhibition levels were about 50%, 30%, and 45% for the lyophilized K12 cell-free supernatant. Besides, the lyophilized culture supernatants of the oral probiotics, especially of S. salivarius M18, exhibited anti-cancer activities on colon cancer cells in vitro. Thus, the results of this manuscript suggest that the cell-free supernatants of the M18 and K12 strains are potential candidates, which merit more investigation for their applications, as biopreservatives in foods and beverages and as anti-cancer biotics for human health.
Isolation and characterization of the 2,5-pyridinedicarboxylic acid-degrading bacterium Agrobacterium sp. strain YJ-5
Authors: Jiang Yinhu , Zhang Yueyue , Wang Xiao , Zhang Fuyin , Xu Siqiong , Chen Qing , Hong Qing , He Jian , Qiu Jiguo
Published: April 2024

2,5-Pyridinedicarboxylic acid (2,5-PDA), a natural N-heterocyclic compound and a substitute for production in plastics, was widely distributed in industrial wastewater. However, the biodegradation of 2,5-PDA has been rarely reported. In this study, strain YJ-5, which could utilize 2,5-PDA as the sole carbon source for growth was isolated from pesticide-contaminated soil. Based on the comparative analysis of the 16S rRNA gene sequence, strain YJ-5 was identified as Agrobacterium sp. 2,5-PDA was completely degraded within 7 d and the optimal growth conditions of temperature, pH, and substrate concentration were 30°C, 7.0, and 0.6 mmol−1, respectively. A new intermediate 6-hydroxy-2,5-PDA was determined by UV/VIS spectroscopy and liquid chromatograph coupled time of flight mass spectrometry. When the electron acceptor (2,6-dichlorophenolindophenol) was employed, the 2,5-PDA could be converted by cell extracts of strain YJ-5 cells into 6-hydroxy-2,5-PDA. These results provided new insights for biodegradation on pyridine dicarboxylate.
Prevalence of antimicrobial-resistant bacteria in conventional vs. organic livestock farms in Egypt: a cross-sectional comparative study
Authors: ElSayed Nada , El-Attar Laila , Amine Amira
Published: April 2024

The silent pandemic of antimicrobial resistance (AR) has been on the rise for the past decades. It is essential to determine the burden of AR in animal farms that spreads leading to human exposure. A total of 100 samples including soil, litter, animal excreta, and wastewater were collected from seven conventional and one organic farm in Egypt. The prevalence of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-producing E. coli), fluoroquinolone-resistant E. coli, fluoroquinolone-resistant Salmonella, and vancomycin-resistant enterococci (VRE) was determined in studied farms. Conventional farms had a higher prevalence of antimicrobial-resistant bacteria than the organic farm (73.81% vs. 18.75%, P < .001). In conventional farms 21.43% of samples yielded mixed isolates; however, in the organic farm, only single isolates of ESBL-producing E. coli were detected. The most prevalent ESBL-production gene was blaTEM (82.14%), followed by blaCTX-M (48.22%), and blaSHV (19.64%), either alone or in combination with another gene. The most prevalent fluoroquinolone-resistance genes were qnrS (82.69%) and qnrB (42.30%), either alone or in combination with another gene(s). A total of five VRE isolates harbored vanA gene (83.33%), none carried vanB gene, and one isolate was negative for both genes. The studied conventional livestock farms had significantly higher rates of serious AR threats than the organic farm.
Evaluation of CHROMagar Acinetobacter and MacConkey media for the recovery of Acinetobacter baumannii from soil samples
Authors: Yusuf I , Skiebe E , Wilharm G
Published: April 2024

The opportunistic pathogen Acinetobacter baumannii occupies niches in human and veterinary clinics and other environments. This comparative study was designed to assess the recovery rate of Ac. baumannii from 20 soil samples collected in Germany (from which Ac. baumannii had been previously isolated) on selective CHROMagar Acinetobacter (CMA) and MacConkey Agar (MCA). Suspected Ac. baumannii were confirmed by detection and sequencing of blaOXA-51-like genes. Overall, the recovery rate of Ac. baumannii from both media was similar. Out of the 20 soil samples enriched in mineral salt medium (MM) plus 0.2% acetate for 5 h, Ac. baumannii was recovered from 12 (60%) on CMA and 11 (55%) on MCA, and from 14 (70%) with both selective media after enrichment for 24 h. Typical and distinct colonies of Ac. baumannii were more often observed on CMA with soil enriched in MM for 5 h, while on MCA distinct colonies were more obvious after 24 h. In five soil samples (25%), strains harbouring different OXA-51-like variants were recovered on MCA. Late lactose fermentation (48 h) was observed on MCA. The study suggests that no single growth medium would efficiently recover Ac. baumannii from all soil samples.
Modulation of quorum sensing activity by copper sulfate, potassium dichromate, and cadmium chloride in biosensor strains
Authors: Torres Mariela Analía , Palacios Eva Aida Rebeca , Lacosegliaz Mariano José , de Figueroa Lucía Inés Castellanos , Nieto-Peñalver Carlos Gabriel
Published: April 2024

Beyond their biological roles, metals have a strong impact on the environment. It has been reported that metals are also inhibitory of Quorum Sensing (QS) mechanisms, ones of the best characterized signaling systems in bacteria and fungi. We analyzed the effect of CuSO4, CdCl2, and K2Cr2O7, on QS systems sharing or differing in the bacterial host or the QS signal. The results in this study show that CuSO4 can not only be inhibitory, but also stimulatory of QS activity: at 0.2 mM increased six fold the activity in Chromobacterium subtsugae CV026. This behavior is related to the concentration of the metal and the particular QS system: E. coli MT102 (pJBA132) was no affected, but CuSO4 decreased the QS activity of Pseudomonas putida F117 (pKR-C12) to half its control values. K2Cr2O7 increased four and three folds the QS activities of E. coli MT102 (pJBA132) and P. putida F117 (pAS-C8), respectively, but without effect when combined with CuSO4 or CdCl2. CdCl2 only showed a positive effect in CV026 when combined with CuSO4. Results suggest that factors related with the culture conditions impact on the influence of the metals, and reinforce the importance of the environment in the modulation of QS activity.
Evaluating iQ-CheckTM real-time PCR to detect Salmonella from poultry environmental samples in Fraser Valley, British Columbia, Canada
Authors: Kenmuir Ethan , Knowles Daniel , Hughes Giselle , Battle Jaime , Ghosh Kazal
Published: April 2024

Salmonella is a ubiquitous pathogen that accounts for foodborne and livestock illnesses worldwide. Robust surveillance programs must be implemented to maintain human and animal health and limit economic losses. The poultry industry in particular demands the implementation of rapid Salmonella detection methods that will facilitate the timely availability of results in a manner allowing actions to be taken for the associated poultry products. One such method, the iQ-CheckTM real-time PCR, has significantly reduced turnaround times compared to conventional culture methods. In this study, a total 733 poultry environmental samples was received from farms in the Fraser Valley of British Columbia, Canada and the real-time PCR method was assessed for its ability to detect Salmonella in comparison to the currently used culture protocol. The iQ-Check real-time PCR method was effective at accurately screening out the majority of negative samples, and demonstrated a very strong correlation with the culture method. This was especially true when selective enrichment was performed before PCR, with sensitivity, specificity, and accuracy values reaching 100.0%, 98.5%, and 98.9%, respectively. These results demonstrate that rapid detection methods could be effectively introduced into current Salmonella surveillance workflows dealing with environmental poultry samples to reduce turnaround times and minimize economic impacts on producers.
Evaluation of the health properties of lactobacilli isolated from an Iranian traditional dairy product
Authors: Shemshad Nina , Nasiraie Leila Roozbeh , Heravi Reza Majidzadeh
Published: April 2024

The different lactobacillus strains isolated from dairy resources may have unique functional properties on human health. Thus, the present study aimed to evaluate the health properties of the lactobacilli isolated from a traditional dairy product in vitro. A total of seven isolated lactobacilli abilities were evaluated for environmental pH reduction, antibacterial activity, cholesterol reduction, and antioxidant activity. Based on the results, the highest decrease in the environment pH was observed in Lactobacillusfermentum B166 with 57%. The antipathogen activity test showed the best results for inhibiting Salmonella typhimurium and Pseudomonas aeruginosa to be obtained by Lact. fermentum 10–18 and Lact. brevis SKB1021 strains, respectively. However, Lact. plantarum H1 and Lact. plantarum PS7319 represented the maximum activity in preventing Escherichia coli; also, Lact. fermentum APBSMLB166 inhibited Staphylococcus aureus more than other strains. Additionally, Lact. crustorum B481 and fermentum 10–18 strains significantly led to a higher reduction in the medium cholesterol than the other strains. The results of antioxidant tests demonstrated that Lact. brevis SKB1021 and Lact. fermentum B166 inhabited radical substrate significantly more than the other lactobacilli. Therefore, four lactobacilli isolated from a traditional dairy product improved some safety indexes positively; thus, they are suggested to be used in manufacturing probiotic supplements.
Simple template-based reverse transcription-recombinase polymerase amplification assay for routine diagnosis of citrus tristeza virus
Authors: Sharma Susheel Kumar , Pathaw Neeta , Wangkhem Baby , Jackson Kabrabam Suraj , Devi Konjengbam Sarda , Roy Subhra Saikat , Singh Akoijam Ratankumar , Singh Raghuveer , Banerjee Amrita , Kumar Sudhir , Ningombam Arati , Firake Dnyaneshwar Madhukar , Singh Thokchom Surjit
Published: April 2024

This study reports a simple template-based reverse transcription-polymerase amplification assay (ST-RT-RPA) for detection of citrus tristeza virus (CTV) from crude plant extract lysed in NaOH:EDTA (1:1) without the need of tedious RNA isolation. The developed assay showed versatility in its usage as amplification can be performed at wide temperature range (14°C to 42°C) and incubation time (4 to 32 min), although the best conditions were 38°C for 30 min. The developed ST-RT-RPA assay could detect the CTV up to 10−8 dilution of crude plant extract of NaOH:EDTA and up to 0.01 fg µl−1 of RNA of CTV-infected plant tissues and 0.001 ag µl−1 of plasmid DNA containing viral insert, thus exhibiting sufficient sensitivity. ST-RT-RPA assay showed high specificity without any cross-reaction with other citrus pathogens (Indian citrus ringspot virus, citrus yellow mosaic virus, citrus yellow vein clearing virus, and Candidatus Liberibacter asiaticus) and was more sensitive in detection of CTV infection in field samples as compared to standard reverse transcription-polymerase chain reaction (RT-PCR) with later showing false negative in 7.92% of samples tested after 1 week of sampling. The developed ST-RT-RPA assay used minimally processed crude plant extract as template, tolerant to sample degradation in transit and storage, while it can be easily performed at wide temperatures and could be adopted in resource-poor setup.
Gradually supply of isoamyl alcohol increases the isoamyl acetate production in solid-state fermentation
Authors: Sainz-Mellado Diana C , Méndez-Hernández Jazmín E , López-Miranda Javier , Páez-Lerma Jesús B , Aguilar Cristobal N , Soto-Cruz Nicolas O
Published: April 2024

Nowadays, isoamyl acetate production is carried out by chemical synthesis with a recent interest in developing biological producing processes, mainly based on microorganisms in submerged fermentation. This work assayed producing isoamyl acetate through solid-state fermentation (SSF), feeding the precursor in the gas phase. Polyurethane foam functioned as the inert support to contain 20 ml of a solution of molasses (10% w/v, pH 5.0). The yeast Pichia fermentans was inoculated at 3 × 107 cells per gram of initial dry weight. The airstream to supply oxygen also served to supply the precursor. Slow supply was obtained using an isoamyl alcohol solution of 5 g l−1 in the bubbling columns and an air stream of 50 ml min−1. For fast supply, fermentations were aerated using 10 g l−1 and 100 ml min−1 for isoamyl alcohol solution and air stream, respectively. It demonstrated the feasibility of isoamyl acetate production in SSF. Moreover, the slow supply of the precursor increased isoamyl acetate production up to 390 mg l−1, which is 12.5 times higher than that obtained without precursor (32 mg l−1). On the other hand, fast supply caused an evident inhibition of the growth and production capacity of the yeast.
Zinc solubilizing Bacillus sp (SS9) and Enterobacter sp (SS7) promote mung bean (Vigna radiata L.) growth, nutrient uptake and physiological profiles
Authors: Shreya Desai , Amaresan Natarajan , Supriya Naga Rathna
Published: April 2024

Zinc (Zn) is a crucial micronutrient required for optimum plant growth. Zn-solubilizing bacteria (ZSB) are potential alternatives for Zn supplementation and convert applied inorganic Zn to available forms. In this study, ZSB were isolated from the root nodules of wild legumes. From a set of 17 bacteria, the isolates SS9 and SS7 were found to be efficient in tolerating 1 g (w/v) Zn. The isolates were identified as Bacillus sp (SS9, MW642183) and Enterobacter sp (SS7, MW624528) based on morphology and 16S rRNA gene sequencing. The screening of PGP bacterial properties revealed that both isolates possessed production of indole acetic acid (50.9 and 70.8 µgmL–1), siderophore (40.2% and 28.0%), and solubilization of phosphate and potassium. The pot study experiment in the presence and absence of Zn revealed that the Bacillus sp and Enterobacter sp inoculated plants showed enhanced mung bean plant growth (45.0% to 61.0% increment in shoot length and 26.9 to 30.9% in root length) and biomass compared to the control. The isolates also enhanced photosynthetic pigments such as total chlorophyll (1.5 to 6.0-fold) and carotenoids (0.5 to 3.0-fold) and 1–2-fold increase in Zn, phosphorous (P), and nitrogen (N) uptake compared to the Zn-stressed control. The present results indicated that the inoculation of Bacillus sp (SS9) and Enterobacter sp(SS7) reduced the toxicity of Zn and, in turn, enhanced the plant growth and mobilization of Zn, N, and P to the plant parts.
Molecular characteristics and genetic analysis of the genes related to carbapenemase, efflux pump, and outer membrane proteins in carbapenem-resistant Klebsiella pneumoniae
Authors: Onishi Reo , Shigemura Katsumi , Osawa Kayo , Yang Young-Min , Maeda Koki , Tanimoto Hiroshi , Kado Mitsuki , Fang Shiuh-Bin , Fujisawa Masato
Published: April 2024

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a life-threatening pathogen that has not been fully investigated on a molecular basis. Therefore, the molecular mechanisms of carbapenem resistance in CRKP collected from medical institutions in Hyogo Prefecture has been analyzed. Antimicrobial susceptibilities and the presence of carbapenemase along with epidemiological analyzes using multilocus sequence typing (MLST) have been investigated. The relative expression of efflux pump genes and mutations of ompK35 and ompK36, encoding the outer membrane porin, were also assessed for their relationship with carbapenem resistance. Most of the collected 22 CRKP isolates were non-susceptible to imipenem (68.2%), meropenem (90.9%), and ertapenem (81.8%), but all 22 strains were susceptible to colistin. Twelve strains (54.5%) were detected for carbapenemase genes such as blaIMP-6. Sequence type 37 was detected by MLST in 10 strains (45.5%). Non-carbapenemase-producing strains had high resistance rates for three carbapenems, and the main cause of resistance was ompK35 mutation. In conclusion, the main cause of resistance was imipenemase metallo-β-lactamase (IMP-6) production in carbapenemase-producing strains, and ompK35 mutation in non-carbapenemase-producing strains. Susceptibility to carbapenem did not differ in CRKP regardless of carbapenemase production, except for imipenem susceptibility. This result contributes to a more insightful understanding of the mechanisms of CRKP in Japan.
A nanobiocatalytic system based on the self-assembly of ferrous phosphate with a high regioselectivity nitrile hydratase
Authors: Wang Li , Huang Jiao , Cui Baocheng , Mu Er , Liang Changhai
Published: April 2024

Our previous study identified a novel nitrile hydratase (NHase) with remarkable biotransformation activity toward adipamide during the production of 5-cyanovaleramide (5-CVAM), an important intermediate of herbicide and chemical raw material. Nevertheless, free NHase will face harsh conditions if they are applied directly in industrial processes. In this study, we, therefore, prepared Fe3(PO4)2 hybrid nanoflowers for NHase immobilization based on the protein–inorganic hybrid self-assembly by establishing a novel and facile method. The results showed that the NHase@Fe3(PO4)2 nanoflowers had significantly enhanced tolerance to the temperature ranging from 40°C to 60°C when compared with free NHase. The catalytic activity of NHase@Fe3(PO4)2 nanoflowers remained high in extreme pH environments such as weak acid (pH 5) and strong alkali (pH 10) environments. In addition, the storage stability and reusability of encapsulated NHase were also superior to that of free NHase. NHase@Fe3(PO4)2 nanoflowers had a notable feature of high substrate tolerance. We found NHase@Fe3(PO4)2 nanoflowers still had 65% activity as the adiponitrile concentration increased up to 200 mmol L−1, whereas free NHase almost lost their catalytic activity when the adiponitrile concentration was just 100 mmol L−1. All of these results clearly demonstrated that ferrous phosphate nanocrystals might offer a novel strategy for 5-CVAM production with nanobiocatalytic systems.
Maize treatment with yeast cells induces resistance against Fusarium rot
Authors: Colombini Fernanda de Sousa , Ceccato-Antonini Sandra Regina , Rosa-Magri Márcia Maria
Published: April 2024

Maize is one of the most cultivated species and requires agrochOPemicals for nutrition and pathogen control. Fusarium verticillioides is responsible for damaging plants and stored grains. Plants naturally exposed to stresses have defense mechanisms that are triggered by chemical or biological agents, known as induced systemic resistance. In this study, the yeast Torulaspora globosa (strain CCA6S01) was evaluated as an immune response promoter in maize against F. verticillioides. The treatments started 4 days after maize emergence and consisted of control (saline solution), acetylsalicylic acid (ASA, 100 mg/L), yeast cells (1 × 105 cells/mL), or yeast metabolites (cell-free filtrates). After running the treatments, the plants were inoculated with 1 mL of a F. verticillioides suspension at a concentration of 1 × 106  spores/mL. The application of yeast cells provided similar results to ASA treatment, a known inducer of plant resistance. Yeast cells provided maize plants with fewer rot symptoms and higher activities of enzymes related to plant resistance. Thus, we concluded that T. globosa (strain CCA6S01) might be used in agriculture practice as a plant protection agent. It can help to decrease the application of fungicides in the field and maintain plant productivity under stress.
Enhanced production and immobilization of phytase from Aspergillus oryzae: a safe and ideal food supplement for improving nutrition
Authors: Pragya  , Sharma Krishna Kant , Kumar Sandeep , Manisha  , Singh Davender , Kumar Vijay , Singh Bijender
Published: April 2024

Microbial phytases are potentially excellent candidates for eliminating anti-nutrient i.e. phytic acid, due to hydrolysis of phospho-monoester linkages present in the phytic acid. An average 2.29-fold increase in phytase production was obtained after statistical optimization in solid-state fermentation. Aspergillus oryzae SBS50 phytase was immobilized on a Ca-alginate matrix with an effectiveness of 53%. Immobilized-phytase retained > 50% activity after recycling for five cycles and also displayed more stability in the presence of organic solvents, metal ions, and detergents as compared to free enzyme. Values of Km and Vmax of immobilized phytase were recorded as 0.66 mM and 666.6 nmol/sec, respectively. Immobilized phytase efficiently hydrolyzed the phytate contents in wheat and pearl millet flours, exhibiting > 70% catalytic activity even after three cycles. Phytase supplementation resulted in the improved nutritional quality of these flours. Furthermore, the safety assessment of the treated and untreated samples reveals the absence of any aflatoxin in the phytase produced by the mould. The results revealed the improved stability of phytase after immobilization and as a safe and significant additive for application in the food industry.
Comparison of Candida colonization in intensive care unit patients with and without COVID-19: First prospective cohort study from Turkey
Authors: Çaklovica Küçükkaya Ilvana , Orhun Günseli , Çağatay Arif Atahan , Kalaycı Sadık , Esen Figen , Şahin Fikrettin , Ağaçfidan Ali , Erturan Zayre
Published: April 2024

Candida species are the primary cause of fungal infections in intensive care units (ICUs). Despite the increasing prevalence of Candida-related infections, monitoring the progression of these infections from colonization in COVID-19 ICU patients lacks sufficient information. This study aims prospectively to compare 62 COVID-19 and 60 non-COVID-19 ICU patients from admission to discharge in terms of colonization development, rates, isolated Candida species, risk factors, and Candida infections during hospitalization. A total of 1464 samples were collected at specific time intervals from various body sites [mouth, skin (axilla), rectal, and urine]. All samples were inoculated onto CHROMagar Candida and CHROMagar Candida Plus media, and isolates identified using MALDI-TOF MS. COVID-19 patients exhibited significantly higher colonization rates in oral, rectal, and urine samples compared to non-COVID-19 patients, (p < 0.05). Among the Candida species, non-albicans Candida was more frequently detected in COVID-19 patients, particularly in oral (75.8%–25%; p < 0.001) and rectal regions (74.19% – 46.66%; p < 0.05). Colonization with mixed Candida species was also more prevalent in the oropharyngeal region (p < 0.05). Mechanical ventilation and corticosteroid use emerged as elevated risk factors among COVID-19 patients (p < 0.05). Despite the colonization prevalence, both COVID-19-positive and negative patients exhibited low incidences of Candida infections, with rates of 9.67% (n = 6/62) and 6.67% (n = 3/60), respectively. Consequently, although Candida colonization rates were higher in COVID-19 ICU patients, there was no significant difference in Candida infection development compared to the non-COVID-19 group. However, the elevated rate of non-albicans Candida isolates highlights potential future infections, particularly given their intrinsic resistance in prophylactic or empirical treatments if needed. Additionally, the high rate of mixed colonization emphasizes the importance of using chromogenic media for routine evaluation.