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The impact of antibiotics on growth, cocoon production was assessed in addition to isolation and characterization of bacteria associated with silkworm gut of infected larvae. Larval rearing was maintained at recommended conditions of temperature and humidity. Silkworm larvae showing abnormal symptoms were collected from the control group and dissected for gut collection. Bacteria were isolated from the gut content by spreading on agar plates and incubated at 37 °C for 48 hrs. Bacterial identification and phylogenetic analysis were carried out by 16S rRNA gene sequencing. The isolated bacteria were subjected to antimicrobial susceptibility test (disc diffusion methods) by using Penicillin (10 µg/mL), Tetracycline (30 µg/mL), Amoxicillin (25 µg/mL), Ampicillin (10 µg/mL), and Erythromycin (15 µg/mL). All isolated strains showed positive results for the catalase test. We isolated and identified bacterial strains (n = 06) from the gut of healthy and diseased silkworm larvae. Based on the 16S rRNA gene sequence, isolated bacteria showed close relation with Serratia, Bacillus, and Pseudomonas spp. Notably, 83.3% of strains were resistant to Penicillin, Tetracycline, Amoxicillin, Ampicillin, and Erythromycin but 16.6% showed antibiotic susceptibility to the above-mentioned commonly used antibiotics. Silkworm larvae fed on penicillin-treated leaves showed significant improvement in larval weight, larval length, and cocoon production. Significantly higher larval weight (6.88g), larval length (5.84cm), and cocoon weight (1.33g) were recorded for larvae fed on leaves treated with penicillin as compared to other antibiotics. Isolated bacterial strains showed close relation with Serratia spp., Bacillus spp. and Pseudomonas spp.

Routine blood culture is used for the detection of bloodstream infections by aerobic and anaerobic bacteria and by common pathogenic yeasts. A retrospective study was conducted in a public hospital in Maceió-AL, by collecting data of all medical records with positive blood cultures. Out of the 2,107 blood cultures performed, 17% were positive with Staphylococcus coagulase negative (51.14%), followed by Staphylococcus aureus (11.21%) and Klebsiella pneumoniae (6.32%). Gram-positive bacteria predominated among positive blood cultures, highlighting the group of Staphylococcus coagulase-negative. While Gram-negative bacteria had a higher number of species among positive blood cultures. Resumo A cultura sanguínea de rotina é usada para a detecção de infecções na corrente sanguínea por bactérias aeróbias e anaeróbias e por leveduras patogênicas comuns. Estudo retrospectivo realizado em hospital público de Maceió-AL, por meio da coleta de dados de todos os prontuários com culturas sanguíneas positivas. Das 2.107 culturas sanguíneas realizadas, 17% foram positivas com Staphylococcus coagulase negativo (51,14%), seguido por Staphylococcus aureus (11,21%) e Klebsiella pneumoniae (6,32%). As bactérias Gram-positiva predominaram entre as culturas de sangue positivas, destacando-se o grupo das Staphylococcus coagulase-negativo. Enquanto as bactérias Gram-negativas apresentaram um número maior de espécies entre as culturas de sangue positivas.

Background Carbapenemase producing gram-negative bacteria (GNB) has become a huge problem in majority of tertiary care centers worldwide. They are associated with very high morbidity and mortality rates, especially when they cause invasive infections. Therefore, rapid detection of these organisms is very important for prompt and adequate antibiotic therapy as well as infection control. The aim of this study was rapid detection of carbapenemase genes and thereby likely carbapenem resistance, 24–48 hours in advance, directly from the positive-flagged blood culture bottles using CHROMagar and Xpert® Carba-R. Methods Aspirate from positively flagged blood culture bottles was subjected to differential centrifuge. All gram-negative bacilli on gram stain from the deposit were processed in Xpert® Carba-R and inoculated on CHROMagar. The presence of genes and growth on CHROMagar was compared with carbapenem resistance on VITEK-2 Compact. Results A total of 119 GNB isolates were processed. One or more of the carbapenemase genes were detected in 80 isolates. On comparison with VITEK-2 result, 92 samples showed concordance for carbapenem resistance 48 hours in advance. There was discordance in 21 isolates with 12 major errors and 09 minor errors. The sensitivity of direct Xpert® Carba-R test for rapid detection of carbapenem resistance, 48 hours in advance, was 81.42%. The sensitivity of direct CHROMagar test for accurate detection of carbapenem resistance, 24 hours in advance, was 92.06%. Conclusion The ability to detect carbapenem resistance with very high accuracy, 48 hours in advance, helps in appropriate antibiotic therapy and implementation of effective infection control practices.

Під час розвитку маститу у корів формування біоплівки збудником захворювання є ефективним способом його збереження в мікрооточенні молочної залози. Біоплівкові інфекції важко піддаються лікуванню антимікробними засобами, порівняно з тим, що спостерігається при вирощуванні в планктонних умовах. Мета роботи – визначити та порівняти вплив антимікробних препаратів та бактеріофагу Phage SAvB14 при знищенні біоплівок сформованих S. aureus var. bovis. За результатами дослідження встановлено, що антибіотики згубно впливали на кількість бактерій у складі біоплівки, проте знищували її, в середньому, на 60%. 100% ефективність проявляв лише один антибіотик фторхінолонового ряду – енрофлоксацин - ймовірно, через його низьку молекулярну масу. При дослідженні впливу бактеріофагу Phage SAvB14 на життєздатність S. aureus var. bovis у складі біоплівки встановлено, що фаг впродовж 24 годин повністю руйнував сформовану біоплвку. Отже, отримані результати вказують на перспективність ефективного використання стафілококового бактеріофагу Phage SAvB14 для руйнування біоплівки, сформованої S. aureus var. bovis – при маститі корів.

The catfishes are a group of economically important freshwater fish in China, which in recent years have suffered heavy losses as a result of bacterial outbreaks. In this study, we examined the diversity of the microbiome of infected skin mucus of yellow catfish (Pelteobagrus fulvidraco) and channel catfish (Ictalurus punctatus) and analyzed the bacterial pathogens. We found several common pathogenic bacteria, such as Aeromonas spp., Vibrio spp., Moraxella spp. and Proteus spp. present in both fish species, but with significantly different bacterial community structures. We isolated and cultured Aeromonas veronii and Proteus mirabilis and validated their infectivity in zebrafish (Danio rerio) and yellow catfish. Intraperitoneal injection of either bacteria into zebrafish, but not immersion, caused 100% mortality and ovary fragmentation. Yellow catfish was more sensitive than zebrafish with 100% mortality in the immersion challenges with A. veronii or P. mirabilis, and with a higher abundance of A. veronii in the P. mirabilis-challenged group compared to control. To our knowledge, this is the first study on the pathogenicity of P. mirabilis in yellow catfish, and the results will help to develop effective strategies for the disease prevention and control in catfish farming.

A novel bacterial strain, designated GeG2T, was isolated from soils of native Cerrado, a highly biodiverse savanna-like Brazilian biome. 16S rRNA gene sequence analysis of strain GeG2T revealed high sequence identity (100%) to the alphaproteobacterium Novosphingobium rosa, however, comparisons with N. rosa DSM7285T showed several distinctive features, prompting a full characterization of the new strain in terms of growth, morphology, biochemistry and, ultimately, its genome. GeG2T cells were Gram-stain negative bacilli, facultatively anaerobic, motile, positive for catalase and oxidase activities and for starch hydrolysis. Strain GeG2T presented planktonic-sessile dimorphism and cell aggregates surrounded by extracellular matrix and nanometric spherical structures were observed in liquid cultures, suggesting the production of exopolysaccharides (EPS) and outer membrane vesicles (OMVs). Whole genome assembly revealed four circular replicons: a 4.1 Mb chromosome, a 2.7 Mb extrachromosomal megareplicon and two plasmids (212.7 and 68.6 kb). The megareplicon contains few core genes and plasmid-type replication/maintenance systems, consistent with its classification as a chromid. Genome annotation shows a vast repertoire of carbohydrate active enzymes and genes involved in the degradation of aromatic compounds, highlighting the biotechnological potential of the new isolate obtained from Cerrado soils, especially regarding EPS production and biodegradation of recalcitrant compounds. Chemotaxonomic features, including polar lipid and fatty acid profiles, as well as physiological, molecular and whole genome comparisons showed significant differences between strain GeG2T and a N. rosa, clearly indicating that it represents a novel species, for which the name Novosphingobium terrae is proposed. The type strain is GeG2T (=CBMAI 2313T =CBAS 753T).IMPORTANCENovosphingobium is an alphaproteobacterial genus presenting diverse physiological profiles and broad biotechnological applications. However, many aspects regarding the biology of this important bacterial group remain elusive. A novel Novosphingobium strain was isolated from soils of Cerrado, an important Brazilian biome. Despite 100% 16S rRNA gene identity with Novosphingobium rosa, polyphasic characterizations, including physiological, chemotaxonomic, and whole genome- based analyses revealed significant differences between GeG2T and N. rosa DSM7285T, reinforcing resolution limitations in phylogenetic analysis based solely on 16S RNA and highlighting the importance of employing different approaches for the description of bacterial species. Using short and long read sequencing approaches, a high-quality fully resolved genome assembly was generated and one of the largest chromids reported to date was identified. A comprehensive characterization of environmental isolates allows us to better elucidate the diversity and biology of members of this bacterial group with potential biotechnological importance, guiding future bioprospecting efforts and genomic studies.

This research was directed to understand the bactericidal effect of epidermal mucus of two Asian cat fish species viz. Clarias batrachus and Heteropneustes fossilis. Epidermal mucus extracts (raw and diluted) of both cat fish species were tested against several Gram negative (Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumonia, A. hydrophila) and Gram positive bacterial strains (Bacillius cereus, Staphylococcus aureus, S. epidermidis) and antibacterial results were also compared with two standard antibiotics viz. amikacin and chloramphenicol used as positive control. An A. hydrophila challenge experiment was also performed on all selected test fish species to examine the change in the amount of mucus production and its bactericidal impact.. Both epidermal mucus extracts (raw and diluted) of all selected normal and bacterial challenged test objects showed potent bactericidal effect against all pathogenic bacterial strains taken under study. However, former was more effective than later. Also raw epidermal mucus extracts of both normal and bacterial challenged cat fish species exhibited significantly higher ZOI values against all selected microbial strains than diluted mucus extracts and antibiotic chloramphenicol. Hence, these outcomes have clearly revealed that this cost effective natural product acquired from fishes is the key component of their defensive system. Therefore, it could be utilized as a novel ‘antimicrobial’ in human as well as veterinary sector for combating against several bacterial diseases.

Antibiotic resistance is an emerging problem in both developed and developing countries. It has been responsible for 700,000 deaths worldwide. Some genotypes of bacteria are sensitive to certain antibiotics than others. Hence by conducting phylogenetic analysis of bacteria and detecting the presence of resistance genes in each genotype, we can select the antibiotic that would be most effective for the bacteria in that certain genotype. A total of fortyfive Salmonella species were investigated for the presence of antibiotic resistance genes through in silico PCR (polymerase chain reaction) amplification and PFGE (pulsed-field gel electrophoresis) analysis was conducted to assess the phylogenetic relationship. Total twenty-eight antibiotic resistance genes were selected for screening the isolates and seventeen antibiotic resistance genes among the Salmonella strains were found. Almost all the isolates (n=43) exhibited PCR amplification product for gyrA genes while fluoroquinolone resistance gyrB (66.67%), parC (68.89%) and parE (15.56%) genes were also present. About 15.56% and 11.11% isolates were found to harbor adenylyltransferase gene, aadA1 and aadA2, respectively while phosphotransferase gene was detected in only one isolate. Two isolates expressed both chloramphenicol acetyltransferase genes, cat1 and cat2. Three isolates (6.67%) harbored chloramphenicol resistance gene cmlA gene while two isolates (4.44%) expressed florfenicol resistance gene, floR. Tetracycline resistance gene, tetA was more prevalent (8.89%) than tetG genes (2.22%). Salmonella harbored all three sulfonamide resistance genes while sulII was more prevalent (17.78%). Genotype 2 contained fifteen antibiotic resistance genes while genotype 3 contained only one antibiotic resistance genes. These investigations used a computer aided approach to genotype isolates and assess the difference in antibiotic resistance profile of Salmonella species based on genotype. This data helps to predict antibiotic resistance genes that might be present for an isolate of known genotype and select antibiotic for the treatment of Salmonella infections based on their phylogenetic group.

Background Protection against Plasmodium falciparum is observed in a population deficient in glucose-6-phosphate dehydrogenase (G6PD), particularly in African and Mediterranean regions. However, such protection remains unknown among G6PD-deficient individuals in Southeast Asia. Methods In this study, we assessed the invasion and maturation of P falciparum K1 in a culture of erythrocytes isolated from Thai subjects carrying Viangchan (871G > A) and Mahidol (487G > A). Results We found that the parasites lost their ability to invade hemizygous and homozygous G6PD-deficient erythrocytes of Viangchan and Mahidol variants in the second and third cycles of intraerythrocytic development. It is interesting to note that P falciparum parasites selectively grew in erythrocytes from hemi- and homozygous genotypes with normal G6PD activity. Moreover, externalization of phosphatidylserine upon P falciparum infection was significantly increased only in Viangchan hemizygous variant cells. Conclusions This study is the first to show that blockage of invasion in long-term culture and potentially enhanced removal of parasitized erythrocytes were observed for the first time in erythrocytes from Viangchan and Mahidol G6PD-deficient individuals.

Acinetobacter baumannii causes healthcare-associated infections worldwide. Capsular polysaccharide (CPS) is shown an important virulence factor of A. baumannii both in vitro and in vivo. Capsule locus 2 (KL2) for CPS is the most common KL type and is associated with carbapenem resistance. It is unclear whether KL2 is related to the clinical outcome of invasive A. baumannii infection. Here we had followed patients with A. baumannii bacteraemia prospectively between 2009 and 2014. One-third of the unduplicated blood isolates were randomly selected each year for microbiological and clinical studies. The KL2 gene cluster was identified using polymerase chain reaction. A total of 148 patients were enrolled randomly. Eighteen isolates (12.2%) carried KL2, and 130 isolates (87.8%) didn't. Compared with non-KL2 isolates, KL2 isolates had significantly higher resistance to imipenem, sulbactam, and tigecycline. Compared with the non-KL group, in the KL2 group, the hospital stay before development of bacteraemia was longer (P

Background Klebsiella pneumoniae is a gram-negative opportunistic pathogen that causes diseases mostly in immunocompromised individuals. Recently, hypervirulent K. pneumoniae strains also cause severe disease in healthy individuals. Capsular polysaccharide (CPS) is the major virulence determinant in hypervirulent K. pneumoniae and protects the cell against the bactericidal activity of the immune system. Gallic acid (GA), a natural phenolic compound, is known to exhibit wide spectrum antibacterial activity; however, its effect on hypervirulent K. pneumoniae remains largely unresolved. We aimed to identify the effects of GA on CPS biosynthesis in hypervirulent K. pneumoniae. Methods Antibacterial activity of GA was evaluated by counting colonies. CPS amount was determined by glucuronic acid content. The transcriptions of cps gene cluster were measured by quantitative real time PCR (qRT-PCR) and the β-galactosidase activity. The effect of GA on the resistance of K. pneumoniae to streptonigrin (SNG), an iron-activated antibiotic, was evaluated. The effect of GA on the resistance of K. pneumoniae to serum killing and phagocytosis by macrophages was observed. Results GA inhibited the growth and CPS biosynthesis in K. pneumoniae. GA may affect the iron availability in K. pneumoniae, thus possibly repressing the cps transcription. In addition, GA reduced the resistance of K. pneumoniae to serum killing and enhanced its susceptibility to phagocytosis. Conclusion GA possesses bactericidal activity and inhibits the CPS biosynthesis in hypervirulent K. pneumoniae, thereby facilitating pathogen clearance by the host immune system. Therefore, GA may represent a promising strategy for the prevention or treatment of patients with hypervirulent K. pneumoniae infections.

Bacterial spot (BS) is a severe bacterial disease induced by Xanthomonas campestris pv. vesicatoria (Xcv), a pathogen that causes serious damage to pepper growth and yield. It is therefore important to study the mechanisms of pepper resistance to Xcv and to breed and promote Xcv-resistant pepper varieties. However, studies of the responses to Xcv infection in peppers at the protein level are limited. Here, we examined Xcv-induced proteomic changes in leaves of the BS susceptible bell pepper ECW and the resistant bell pepper VI037601 using the isobaric tags for relative and absolute quantitation (iTRAQ)-based protein labeling technology. A total of 6 120 distinct proteins were identified, and there were 1 289 significantly differentially accumulated proteins (DAPs) in ECW and VI037601 leaves after Xcv inoculation. Among these, 339 (250 up- and 89 down-regulated) and 479 (300 up- and 179 down-regulated) DAPs were specifically identified in ECW and VI037601, respectively, with 459 (364 up- and 95 down-regulated) similarly expressed DAPs being shared by ECW and VI037601. Based on bioinformatics analysis, many defense-associated proteins were identified as up-regulated in ECW and VI037601, especially the proteins involved in plant-pathogen interaction, phenylpropanoid biosynthesis, protein processing in the endoplasmic reticulum, and MAPK signaling pathway - plant. Moreover, we evaluated transcript levels of six differentially expressed genes from the iTRAQ results by qRT-PCR. The analysis revealed transcriptional changes that were consistent with the changes at the protein level. This study will provide a valuable resource for understanding the molecular basis of pepper resistance to Xcv infection and for improving the disease resistance of pepper cultivars.

Emerging evidence shows that some Lactobacillus fermentum strains can contribute to the prevention and treatment of ulcerative colitis (UC). In this study, 105 isolates of L. fermentum strains were separated from fecal samples of populations in different regions in China and their draft genomes were sequenced. Pan-genomic and phylogenetic characterizations of these strains and four model strains (L. fermentum 3872, CECT5716, IFO3956 and VRI003) were performed. Phylogenetic analysis indicated that there was no significant adaptive evolution between the genomes of L. fermentum strains and the geographical location, sex, ethnicity and age of the hosts. Three L. fermentum strains (FWXBH115, FGDLZR121, and FXJCJ61) from different branches of the phylogenetic tree and strain type L. fermentum CECT5716 were selected and their anti-inflammatory and immune modulatory activities in a dextran sulphate sodium (DSS)-induced colitis mouse model were further investigated. Both L. fermentum FXJCJ61 and CECT5716 significantly alleviated UC by reducing all colitis-associated histological indices, maintaining mucosal integrity, and stimulating replenishment of short-chain fatty acids (SCFAs), while the other two strains failed to offer similar protection. The anti-inflammatory mechanisms of L. fermentum FXJCJ61 and CECT5716 were related to the inhibition of nuclear factor kappa-B (NF-κB) signaling pathway activation and enhancement of interleukin 10 (IL-10) production. Comparative genomic analysis of these strains identified candidate genes that may contribute to the anti-inflammatory effects of specific L. fermentum strains.

Many microorganisms have mechanisms that protect cells against attack from viruses. The fermentation components of Streptomyces sp. 1647 exhibit potent anti-influenza A virus (IAV) activity. This strain was isolated from soil in southern China in the 1970s, but the chemical nature of its antiviral substance(s) has remained unknown until now. We used an integrated multi-omics strategy to identify the antiviral agents from this streptomycete. The antibiotics and Secondary Metabolite Analysis Shell (antiSMASH) analysis of its genome sequence revealed 38 biosynthetic gene clusters (BGCs) for secondary metabolites, and the target BGCs possibly responsible for the production of antiviral components were narrowed down to three BGCs by bioactivity-guided comparative transcriptomics analysis. Through bioinformatics analysis and genetic manipulation of the regulators and a biosynthetic gene, cluster 36 was identified as the BGC responsible for the biosynthesis of the antiviral compounds. Bioactivity-based molecular networking analysis of mass spectrometric data from different recombinant strains illustrated that the antiviral compounds were a class of structural analogues. Finally, 18 pseudo-tetrapeptides with an internal ureido linkage, omicsynins A1–A6, B1–B6, and C1–C6, were identified and/or isolated from fermentation broth. Among them, 11 compounds (omicsynins A1, A2, A6, B1–B3, B5, B6, C1, C2, and C6) are new compounds. Omicsynins B1–B4 exhibited potent antiviral activity against IAV with the 50% inhibitory concentration (IC50) of approximately 1 µmol∙L–1 and a selectivity index (SI) ranging from 100 to 300. Omicsynins B1–B4 also showed significant antiviral activity against human coronavirus HCoV-229E. By integrating multi-omics data, we discovered a number of novel antiviral pseudo-tetrapeptides produced by Streptomyces sp. 1647, indicating that the secondary metabolites of microorganisms are a valuable source of novel antivirals.

To determinate the antimicrobial effect of chloramphenicol and aqueous extract against multidrug-resistant enterohemorrhagic Escherichia coli (EHEC) and Salmonella enterica serovar Typhimurium in C...

Methicillin-resistant Staphylococcus aureus (MRSA), biofilms, and persisters are three major factors leading to recurrent and recalcitrant implant infections. Although antibiotics are still the primary treatment for chronic implant infections in clinical, only few drugs are effective in clearing persisters and formed biofilms. Here, felodipine, a dihydropyridine calcium channel blocker, was reported for the first time to have antibacterial effects against MRSA, biofilm, and persisters. Even after continuous exposure to sub-lethal concentrations of felodipine, bacteria are less likely to develop resistance. Besides, low doses of felodipine enhances the antibacterial activity of gentamicin by inhibiting the expression of protein associated with aminoglycoside resistance (aacA-aphD). Next, biofilm eradication test and persisters killing assay suggested felodipine has an excellent bactericidal effect against formed biofilms and persisters. Furthermore, the result of protein profiling, and quantitative metabonomics analysis indicated felodipine reduce MRSA virulence (agrABC), biofilm formation and TCA cycle. Then, molecular docking showed felodipine inhibit the growth of persisters by binding to the H pocket of ClpP protease, which could lead to substantial protein degradation. Furthermore, murine infection models suggested felodipine in combination with gentamicin alleviate bacterial burden and inflammatory response. In conclusion, low dose of felodipine might be a promising agent for biomaterial delivery to enhance aminoglycosides efficacy against implant infections caused by MRSA, biofilm, and persisters.

Due to the worldwide epidemic of allergic disease and a cure nowhere in sight, there is a crucial need to explore its pathophysiological mechanisms. As allergic disease has been associated with gut dysbiosis, we searched for a possible mechanism from the perspective of the molecular interface between host and microbiota with concurrent metabolomics and microbiome composition analysis. Sprague-Dawley rats were injected with Artemisia pollen extract to stimulate a hyper reaction to pollen. This hyper reaction decreased the circulation of valine, isoleucine, aspartate, glutamate, glutamine, indole-propionate (IPA), and myo-inositol, and reduced short-chain fatty acids (SCFAs) in feces. Several beneficial genera belonging to Ruminococcaceae, Lachnospiraceae, and Clostridiales declined in the model group, whereas Helicobacter and Akkermansia were only expressed in the model group. Furthermore, the expression of intestinal claudin-3 and liver fatty acid binding protein was downregulated in the model group and associated with metabolic changes and bacteria. Our results suggest that alterations in amino acids as well as their derivatives (especially valine, and IPA which is the reductive product of tryptophan) , SCFAs, and the gut microbiome (specifically Akkermansia and Helicobacter) may disrupt the intestinal barrier function by inhibiting the expression of claudin proteins and affecting the mucus layer, which further results in hay fever.

The efficacious delivery of antimicrobial drugs to intractable oral biofilms remains a challenge due to inadequate biofilm penetration and lack of pathogen targeting. Herein, we have developed a microenvironment-activated poly(ethylene glycol) (PEG)-sheddable nanoplatform to mediate targeted delivery of drugs into oral biofilms for the efficient prevention of dental caries. The PEGylated nanoplatform with enhanced biofilm penetration is capable of deshielding the PEG layer under slightly acidic conditions in a PEG chain length-dependent manner to re-expose the bacteria-targeting ligands, thereby facilitating targeted codelivery of ciprofloxacin (CIP) and IR780 to the bacteria after accumulation within biofilms. The nanoplatform tends to induce bacterial agglomeration and suffers from degradation in the acidic oral biofilm microenvironment, triggering rapid drug release on demand around bacterial cells. The self-modulating nanoplatform under near-infrared (NIR) irradiation accordingly displays greatly augmented potency in oral biofilm penetration and disruption compared with drugs alone. Topical oral treatment with nanoplatforms involving synergetic pharmacological and photothermal/photodynamic trinary therapy results in robust biofilm dispersion and efficacious suppression of severe tooth decay in rats. This versatile nanoplatform can promote local accumulation and specific drug transport into biofilms and represents a new paradigm for targeted drug delivery for the management of oral biofilm-associated infections.

Background Since the last two decades, substantial increase in fungal infections has been observed in immunocompromised hosts. Virulence factors of Candida albicans play a role in adherence, haemolytic activity, phenotypic switching and production of hydrolytic enzymes. The secreted aspartyl proteinases (SAP family) contribute to adhesion, tissue damage and invasion, while phospholipase (PLB) supports the hydrolysis of phospholipids. Very few studies showed the correlation of phenotypic activity and detection of genes contributing to the similar enzyme activity. Therefore, our study aimed at demonstrating correlation between in vitro phenotypic production of phospholipase and proteinase enzymes with genetic level detection of SAP and PLB genes. Methods The present study was carried out on a total of 799 samples over a period of one year. Culturing was carried out on Sabouraud's dextrose agar. Confirmation and speciation of Candida spp. was carried out using cornmeal agar and CHROMagar and by the germ tube test, urease test and automated identification system Vitek-2, and antifungal susceptibility testing was performed on Candida isolates. Phenotypic phospholipase and proteinase activity was analysed, and molecular detection of SAP4 and PLB genes was carried out. Results In our study, we have screened 799 samples for mycological protocol; of which, 269 (33.6%) were Candida species, 44% (119) of which were C. albicans. Proteinase activity was exhibited by 77 (64.7%) and phospholipase activity was exhibited by 73 (61.34%) isolates, while 46.2% exhibited both activities among the C. albicans species. The PLB gene was detected in 97.3% isolates, while SAP4 was detected in 94.7% of C. albicans isolates. Conclusion The study of in vitro expression of virulence factors and gene detection of C. albicans will help to improve the prognosis despite the nature of the sample.

Vibrio parahaemolyticus carrying a plasmid encoding the PirAvp and PirBvp toxins is the causative agent of acute hepatopancreatic necrosis disease (AHPND) in penaeid shrimps. In the Pacific white shrimp farming industry, one possible strategy to reduce economic loss due to AHPND is the development of a shrimp line resistant to the disease. In this study, we identified single nucleotide polymorphisms (SNPs) in the Litopenaeus vannamei anti-lipopolysaccharide factor 1 (nLvALF1) and penaeidin 2-1 (PEN2-1) genes, and we analyzed the associations between these SNPs and resistance/susceptibility to V. parahaemolyticus infection in the Pacific white shrimp. Postlarvae (PL20) shrimp from a local hatchery in Prachuap Khiri Khan Province were challenged with an isolate of VPAHPND and mortality was observed for 14 days. DNA was extracted from susceptible (died within 6 days) and resistant (survived the challenge) shrimp (45 individuals/group) and used for PCR amplifications of nLvALF1 (397 bp) and PEN2-1 (637 bp) gene fragments. PCR products were sequenced by direct sequencing and SNPs were identified from sequencing chromatograms. Nine and seven SNPs were identified in nLvALF1 and PEN2-1 gene fragments, respectively. Analyses of allele frequencies in susceptible and resistant samples using Chi-square tests revealed that four and six SNPs in nLvALF1 and PEN2-1, respectively, were associated with resistance/susceptibility to V. parahaemolyticus infection (P

A total of 11 bacterial strains capable of completely degrading 2-butoxyethanol (2-BE) were isolated from forest soil, a biotrickling filter, a bioscrubber, and activated sludge, and identified by 16S rRNA gene sequence analysis. Eight of these strains belong to the genus Pseudomonas; the remaining three strains are Hydrogenophaga pseudoflava BOE3, Gordonia terrae BOE5, and Cupriavidus oxalaticus BOE300. In addition to 2-BE, all isolated strains were able to grow on 2-ethoxyethanol and 2-propoxyethanol, ethanol, n-hexanol, ethyl acetate, 2-butoxyacetic acid (2-BAA), glyoxylic acid, and n-butanol. Apart from the only gram-positive strain isolated, BOE5, none of the strains were able to grow on the nonpolar ethers diethyl ether, di-n-butyl ether, n-butyl vinyl ether, and dibenzyl ether, as well as on 1-butoxy-2-propanol. Strains H. pseudoflava BOE3 and two of the isolated pseudomonads, Pseudomonas putida BOE100 and P. vancouverensis BOE200, were studied in more detail. The maximum growth rates of strains BOE3, BOE100, and BOE200 at 30 °C were 0.204 h-1 at 4 mM, 0.645 h-1 at 5 mM, and 0.395 h-1 at 6 mM 2-BE, respectively. 2-BAA, n-butanol, and butanoic acid were detected as potential metabolites during the degradation of 2-BE. These findings indicate that the degradation of 2-BE by the isolated gram-negative strains proceeds via oxidation to 2-BAA with subsequent cleavage of the ether bond yielding glyoxylate and n-butanol. Since Gordonia terrae BOE5 was the only strain able to degrade nonpolar ethers like diethyl ether, the degradation pathway of 2-BE may be different for this strain., Projekt DEAL, Landesgraduiertenförderung der Universität Stuttgart

It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a metagenome-based VMR estimate (mVRM) that accounts for DNA viruses across all stages of their replication cycles (virion, intracellular lytic and lysogenic) by using normalised RPKM (reads per kilobase of gene sequence per million of mapped metagenome reads) counts of the major capsid protein (MCP) genes and cellular universal single-copy genes (USCGs) as proxies for virus and cell counts, respectively. After benchmarking this strategy using mock metagenomes with increasing VMR, we inferred mVMR across different biomes. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa-200 µm size-range) in freshwater, seawater and solar saltern ponds (10 metagenomes, 2 control metaviromes). Viruses outnumbered cells in freshwater by ∼13 fold and in plankton from marine and saline waters by ∼2-4 fold. However, across an additional set of 121 diverse non-aquatic metagenomes including microbial mats, microbialites, soils, freshwater and marine sediments and metazoan-associated microbiomes, viruses, on average, outnumbered cells by barely two-fold. Although viruses likely are the most diverse biological entities on Earth, their global numbers might be closer to those of cells than previously estimated.

Late blight caused by the oomycete Phytophthora infestans is considered to be one of the most severe diseases of potato and tomato worldwide. Whilst current synthetic fungicides are efficient at controlling this disease, they are an environmental and economic burden. In line with EU directives to reduce the use of synthetic pesticides and increase the use of sustainable alternative disease control strategies that can form part of integrated pest management systems, practical biological control solutions are urgently needed. Despite the fact that there has been a large body of scientific research into microorganisms with potential for the biological control of late blight disease, relatively few commercial biocontrol agents, licensed to control late blight, exist. Furthermore, the practical uptake of those in Europe is lower than might be expected, suggesting that such solutions are not yet feasible, or effective. Here we review the scientific literature, focusing on the most recent developments in the hunt for efficient and sustainable biological control of late blight disease. We discuss the progress in our mechanistic understanding of mycoparasite–prey interactions, in the context of late blight and the challenges and limitations to the use of such knowledge in practical disease control within a European context.

Root rot of Panax notoginseng, a precious Chinese medicinal plant, seriously impacts its sustainable production. However, the molecular regulatory mechanisms employed by P. notoginseng against root rot pathogens, including Fusarium solani, are still unclear. In this study, the PnMYB2 gene was isolated, and its expression was affected by independent treatments with four signaling molecules (methyl jasmonate, ethephon, salicylic acid, and hydrogen peroxide) as assessed by quantitative real-time PCR. Moreover, the PnMYB2 expression level was induced by F. solani infection. The PnMYB2 protein localized to the nucleus and may function as a transcription factor. When overexpressed in transgenic tobacco, the PnMYB2 gene conferred resistance to F. solani. Jasmonic acid (JA) metabolism and disease resistance-related genes were induced in the transgenic tobacco, and the JA content significantly increased compared with in the wild type. Additionally, transcriptome sequencing, Kyoto Encyclopedia of Genes and Genomes annotation enrichment, and metabolic pathway analyses of the differentially expressed genes in the transgenic tobacco revealed that JA metabolic, photosynthetic, and defense response-related pathways were activated. In summary, PnMYB2 is an important transcription factor in the defense responses of P. notoginseng against root rot pathogens that acts by regulating JA signaling, photosynthesis, and disease-resistance genes.

Carboxysomes are a family of bacterial microcompartments (BMCs), present in all cyanobacteria and some proteobacteria, which encapsulate the primary CO2-fixing enzyme, Rubisco, within a virus-like polyhedral protein shell. Carboxysomes provide significantly elevated levels of CO2 around Rubisco to maximize carboxylation and reduce wasteful photorespiration, thus functioning as the central CO2-fixation organelles of bacterial CO2-concentration mechanisms. Their intriguing architectural features allow carboxysomes to make a vast contribution to carbon assimilation on a global scale. In this review, we discuss recent research progress that provides new insights into the mechanisms of how carboxysomes are assembled and functionally maintained in bacteria and recent advances in synthetic biology to repurpose the metabolic module in diverse applications.

Sheath blight is a serious rice disease worldwide, and genes involved in resistance remain unclear. In the present study, a virulent field isolate of Rhizoctonia solani was used to inoculate detached leaves of a sheath blight-resistant rice cultivar, Jasmine 85; a suppression subtractive cDNA library was constructed using RNA isolated 16 h postinoculation (hpi); and differentially expressed genes were identified from the cDNA library. A total of 159 uniquely expressed sequence tags were identified, including 105 from rice with enrichment in categories related to cellular response, molecular signaling, and host defense. Coupled with gene expression studies by DNA microarray, 27 highly induced genes involved in signal transduction and defense responses were identified within 16 hpi. Three members of the ATP-binding cassette (ABC) transporter gene family ( OsABC1, OsABC9, and OsABC12) encoding pleiotropic drug resistance-like ABC transporters were mapped to different sheath blight resistance quantitative trait loci (QTLs), and their differential expressions were validated. Three high-resolution melting (HRM) markers were developed from these ABC gene family members to distinguish alleles between sheath blight-susceptible cultivar Lemont and resistant cultivar Jasmine 85. Association of sheath blight resistance to these HRM markers was examined in 77 recombinant inbred lines derived from the cross between Jasmine 85 and Lemont. The OsABC9 gene located in a major sheath blight resistance QTL qShB9-2 showed a major contribution to sheath blight resistance. These results are useful for marker-assisted selection and functional validation of the ABC genes in sheath blight disease resistance. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.

Objectives To explore the in vitro antimicrobial susceptibility among clinically important Gram-negative bacteria (GNB) in Taiwan. Methods From 2016 through 2018, a total of 5458 GNB isolates, including Escherichia coli (n = 1545), Klebsiella pneumoniae (n = 1255), Enterobacter species (n = 259), Pseudomonas aeruginosa (n = 1127), Acinetobacter baumannii complex (n = 368), and Stenotrophomonas maltophilia (n = 179), were collected. The susceptibility results were summarized by the breakpoints of minimum inhibitory concentration (MIC) of CLSI 2020, EUCAST 2020 (for colistin), or published articles (for ceftolozane/tazobactam). The resistance genes among multidrug-resistant (MDR) or extensively drug-resistant (XDR)-GNB were investigated by multiplex PCR. Results Significantly higher rates of non-susceptibility (NS) to ertapenem and carbapenemase production, predominantly KPC and OXA-48-like beta-lactamase, were observed in Enterobacterales isolates causing respiratory tract infection than those causing complicated urinary tract or intra-abdominal infection (12.7%/3.44% vs. 5.7%/0.76% or 7.7%/0.97%, respectively). Isolates of Enterobacter species showed higher rates of phenotypic extended-spectrum β-lactamase and NS to ertapenem than E. coli or K. pneumoniae isolates. Although moderate activity (54–83%) was observed against most potential AmpC-producing Enterobacterales isolates, ceftolozane/tazobactam exhibited poor in vitro (44.7–47.4%) activity against phenotypic AmpC Enterobacter cloacae isolates. Additionally, 251 (22.3%) P. aeruginosa isolates exhibited the carbapenem-NS phenotype, and their MDR and XDR rate was 63.3% and 33.5%, respectively. Fifteen (75%) of twenty Burkholderia cenocepacia complex isolates were inhibited by ceftolozane/tazobactam at MICs of ≤4 μg/mL. Conclusions With the increase in antibiotic resistance in Taiwan, it is imperative to periodically monitor the susceptibility profiles of clinically important GNB.

Objectives Despite excessive resistance of Helicobacter pylori to clarithromycin among Iranian population, unfortunately, clarithromycin-based therapy is still prescribed in Iran. Recent studies have shown high rates of H. pylori eradication in patients treated with levofloxacin. The main purpose of this study was to compare the effect of levofloxacin with clarithromycin on the eradication of H. pylori infection in Iranian population. Methods A comprehensive meta-analysis was done for the relevant cohort studies and clinical trials to compare the therapeutic effects of levofloxacin with clarithromycin in Iranian population. We pooled the data using odds ratio corresponding to 95% confidence intervals to find the clinical efficacy of levofloxacin versus clarithromycin to treat H. pylori infection. The heterogeneity and publication bias were also measured for the included studies. Results A total of 13 studies were included in the quantitative synthesis. Eradication rate in patients receiving levofloxacin and clarithromycin were 75% and 66.3%, respectively (OR: 1.76; 95% CI: 1.40-2.20). In addition, in the subgroup analysis, it was confirmed that cure rate is relatively higher in levofloxacin-treated cases. However, there is significant heterogeneity as well as publication bias, thus, the results need to be interpreted with caution. Conclusions We found that the success of levofloxacin treatment was significantly higher than that of clarithromycin. Therefore, it is suggested that clarithromycin-based triple therapy be replaced by levofloxacin-based triple therapy in countries with high resistance rate to clarithromycin such as Iran. Nevertheless, findings of the present study need to be approved with larger investigation on Iranian population.

Humanity is facing an enormous and growing worldwide threat from the emergence of multi-drug-resistant Gram-negative bacteria such as Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii. Polymyxin B and E (colistin) constitute the last-line therapies for treating multi-drug-resistant Gram-negative bacteria. Polymyxin is a cationic antibacterial peptide that can destroy the outer membrane of Gram-negative bacteria. With the increasing clinical application of polymyxin, however, there have been many reports of the occurrence of polymyxin-resistant Gram-negative bacteria. This resistance is mainly mediated by the modification or complete loss of lipopolysaccharide (LPS). LPS is also a virulence factor of Gram-negative bacteria, and alterations of LPS may correlate with virulence. Although it is generally believed that the biological costs associated with drug resistance may enable benign susceptible bacteria to overcome resistant bacteria when antibiotic pressure is reduced, some studies have shown that polymyxin-resistant bacteria are associated with higher virulence and greater fitness compared with their susceptible counterparts. To predict the development of polymyxin resistance and evaluate interventions for its mitigation, it is important to understand the relative biological cost of polymyxin resistance compared with susceptibility. The impact of polymyxin resistance mechanisms on the virulence and fitness of these three Gram-negative bacteria are summarized in this review.

Peanut (Arachis hypogea L.) bacterial wilt (BW) is a devastating disease caused by Ralstonia solanacearum that results in severe yield and quality losses. Plant defensins are short cysteine-rich peptides with antimicrobial activity. The role of defensin genes (AhDef) in peanut is unclear. A genome-wide investigation of AhDef genes was undertaken, and 12 identified AhDef genes were classified into two groups containing the gamma-thionin domain formed by four disulfide pairs: Cys1-Cys8, Cys2-Cys5, Cys3-Cys6, and Cys4-Cys7. In silico analysis revealed that AhDef genes showed highly conserved architectural features and contained cis-elements associated with phytohormone signaling and defense responses. A highly resistant cultivar, H108 (R) and a susceptible accession, H107 (S) were tested by R. solanacearum inoculation. H108 (R) showed fewer symptoms than H107 (S) owing to inhibition of bacterial reproduction and spread in the vascular bundles of roots and stems. In a transcriptomic expression profile, AhDef genes, particularly AhDef1.6 and AhDef2.2, were up-regulated in H108 (R) compared with H107 (S) under R. solanacearum infection and phytohormone treatment. Subcellular localization showed that the AhDef1.6 and AhDef2.2 proteins were both expressed specifically on the plasma membrane. Overexpression of protein fusion AhDef2.2-YFP in Nicotiana benthamiana and peanut leaves increased resistance to R. solanacearum, suggesting its role in response to BW infection. AhDef2.2 may be valuable for peanut resistance breeding.

A 69-year-old woman who had undergone renal transplantation and was receiving sulfamethoxazole/trimethoprim (ST) developed pulmonary nocardiosis. To our knowledge, this is the first report of the identification of Nocardia elegans using nanopore sequencing, supported by 16S rDNA capillary sequencing findings. Chest computed tomography performed after ST initiation revealed significant improvement of the pulmonary shadows compared to previous findings. We herein report the value of nanopore sequencing for rapid identification of rare pathogens, such as Nocardia elegans. Furthermore, our findings suggest that Nocardia may infect even patients receiving ST, which is currently the most effective prophylactic drug.

BACKGROUNDNasopharyngeal carriage of pathogenic bacteria precedes invasive disease and higher rates are found in low socioeconomic-status (SES) settings. Local immune responses are important for controlling colonization, but whether SES affects these responses is currently unknown.OBJECTIVEExamining bacterial colonization and cytokine response in nasal mucosa of children from high and low SES.METHODSTwenty-five cytokines were measured in nasal fluid. qPCR was performed to determine carriage and density of Haemophilus influenzae (H. influenzae), Streptococcus pneumoniae (S. pneumoniae), Moraxella catarrhalis (M. catarrhalis) and Staphylococcus aureus (S. aureus).RESULTSThe densities of H. influenzae and S. pneumoniae were increased in low compared to the high SES (p=0.006, p=0.026), with respectively 6 and 67 times higher median densities. Densities of H. influenzae and S. pneumoniae were positively associated with levels of IL-1beta (p=0.002, p=0.008) and IL-6 (pp=0.006). After correcting for bacterial density, IL-6 levels were increased in colonized children from high compared to low SES for both H. influenzae and S. pneumoniae (both p=0.039).CONCLUSIONIncreased density of H. influenzae and S. pneumoniae was observed in low SES children, while IL-6 levels associated with colonization were reduced in these children, indicating that immune responses to bacterial colonization were altered by SES.

Introduction Fusarium graminearum is a most destructive fungal pathogen that causes Fusarium head blight (FHB) disease in cereal crops, resulting in severe yield loss and mycotoxin contamination in food and feed. Silver nanoparticles (AgNPs) are extensively applied in multiple fields due to their strong antimicrobial activity and are considered alternatives to fungicides. However, the antifungal mechanisms and the effects of AgNPs on mycotoxin production have not been well characterized. Objectives This study aimed to investigate the antifungal activity and mechanisms of AgNPs against both fungicide-resistant and fungicide-sensitive F. graminearum strains, determine their effects on mycotoxin deoxynivalenol (DON) production, and evaluate the potential of AgNPs for FHB management in the field. Methods Scanning electron microscopy (SEM), transmission electron microscopy (TEM), and fluorescence microscopy were used to examine the fungal morphological changes caused by AgNPs. In addition, RNA-Seq, qRT-PCR, and western blotting were conducted to detect gene transcription and DON levels. Results AgNPs with a diameter of 2 nm exhibited effective antifungal activity against both fungicide-sensitive and fungicide-resistant strains of F. graminearum. Further studies showed that AgNP application could impair the development, cell structure, cellular energy utilization, and metabolism pathways of this fungus. RNA-Seq analysis and sensitivity determination revealed that AgNP treatment significantly induced the expression of azole-related ATP-binding cassette (ABC) transporters without compromising the control efficacy of azoles in F. graminearum. AgNP treatment stimulated the generation of reactive oxygen species (ROS), subsequently induced transcription of DON biosynthesis genes, toxisome formation, and mycotoxin production. Conclusion This study revealed the underlying mechanisms of AgNPs against F. graminearum, determined their effects on DON production, and evaluated the potential of AgNPs for controlling fungicide-resistant F. graminearum strains. Together, our findings suggest that combinations of AgNPs with DON-reducing fungicides could be used for the management of FHB in the future.

Fungal corneal ulcers are an uncommon, yet challenging, cause of vision loss. In the United States, geographic location appears to dictate not only the incidence of fungal ulcers, but also the fungal genera most encountered. These patterns of infection can be linked to environmental factors and individual characteristics of fungal organisms. Successful management of fungal ulcers is dependent on an early diagnosis. New diagnostic modalities like confocal microscopy and polymerase chain reaction (PCR) are being increasingly used to detect and identify infectious organisms. Several novel therapies, including crosslinking and light therapy, are currently being tested as alternatives to conventional antifungal medications. We explore the biology of Candida, Fusarium, and Aspergillus, the three most common genera of fungi causing corneal ulcers in the United States and discuss current treatment regimens for the management of fungal keratitis.

Campylobacter rectus is a campylobacterium considered to be a primary periodontal pathogen. Thus, C. rectus has rarely been isolated from extraoral specimens, especially in the thoracic region. We herein report a case of thoracic empyema in which Campylobacter infection was suspected after Gram staining of the pleural effusion, and C. rectus was isolated using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Fusobacterium nucleatum was also detected. Molecular identification was performed using polymerase chain reaction amplification and a sequencing analysis of the 16S rRNA gene. Estimation of the causative bacteria using Gram staining led to the proper culture and identification of the causative bacteria.

Apple Valsa canker is considered one of the most serious apple diseases. Dopamine is a catecholamine with key physiological functions in plants. Tyrosine decarboxylase (TYDC) is not only involved in the synthesis of dopamine in plants but may also play an important role in the resistance of plants to pathogen infection. In this study, we show that 100-μM exogenous dopamine application and Malus domestica TYDC (MdTYDC) overexpression (or overexpressing, OE) enhances the resistance of apple to Valsa mali infection, likely because the increased dopamine content reduces the accumulation of H2O2 and increases the accumulation of phenolic compounds and salicylic acid (SA) in dopamine-treated and OE apple plants. The activity of chitinase and β-1, 3-glucanase and the expression of SA-related genes were induced more strongly by V. mali in dopamine-treated and OE apples. The dopamine content was significantly higher in dopamine-treated and OE apples than in their respective controls under both normal and inoculated conditions (P < 0.05). Overall, these findings indicate that the application of exogenous dopamine and the OE of MdTYDC may enhance the resistance of apples to V. mali infection by altering the dopamine content, which improves antioxidant capacity, promotes the accumulation of phenolic compounds and SA, and enhances the activity of disease resistance-related proteins.

Broomcorn millet smut caused by the fungus Anthracocystis destruens is one of the most destructive diseases in broomcorn millet production. The life cycle of A. destruens and host defense responses against A. destruens remain elusive. Here we investigated the disease symptom development and the parasitic process of A. destruens as well as the ultrastructure of the host–pathogen interface. The results showed that there are four typical symptoms of broomcorn millet smut, which are blackfly, cluster leaves, hedgehog head, and incomplete fruiting. A. destruens colonizes all tissues of broomcorn millet but produces teliospores only in the inflorescence. After infection, A. destruens proliferates in the host, likely in a systemic manner. Ultrastructural study of the infected inflorescence showed that the pathogen grows intercellularly and intracellularly within the host. The host activates defense response to prevent pathogen infection, accumulation of callose analogs and highly electron-dense deposits to resist A. destruens infection.

Objective The toxin-producing Klebsiella oxytoca causes antibiotic-associated haemorrhagic colitis (AAHC). The disease-relevant cytotoxins tilivalline and tilimycine produced by certain K. oxytoca isolates are encoded by the non-ribosomal peptide synthetase genes A (npsA) and B (npsB). In this study, the new LightMix® Modular kit for detection of relevant K. oxytoca sensu lato (s.l.) toxin genes was evaluated. Methods DNA was extracted on the automated EMAG® platform. Amplification was done on the Light Cycler® 480 II instrument. A total of 130 residual faecal specimens that had been collected from patients with antibiotic-associated diarrhoea were studied to determine the clinical sensitivity and specificity. Toxigenic culture served as reference method. Results With the new kit, the limit of detection was 15 CFU/mL for all targets. For the K. oxytoca s.l. specific pehX target, 65 of 130 clinical specimens were positive while toxin specific targets (npsA/npsB) were positive in 47 of 130. The npsA/npsB PCR targets showed a clinical sensitivity of 100% (95% CI of 80.5% to 100%) and a specificity of 73.5% (95% CI of 64.3% to 81.3%) with a positive predictive value of 16.5% (95% CI of 12.7% to 21.2%) and a negative predictive value of 100%. Conclusion Compared with culture, additional K. oxytoca s.l.-positive clinical specimens were detected with real-time PCR. The specificity of the toxin targets appears moderate due to the inferior sensitivity of the culture-based reference method. Since the developed assay is highly sensitive, it may be used as first-line method to improve AAHC diagnosis.

Carbapenemase-producing Enterobacteriaceae (CPE) isolates are recognized as one of the most severe threats to public health. However, the population structure and genetic characteristics of CPE isolates among bloodstream infections (BSIs) are largely unknown. To address this knowledge gap, in this study, we included patients with clinically significant BSIs due to Enterobacterales isolates, recruited from 26 sentinel hospitals in China (2014–2015). CPE isolates were microbiologically and genomically characterized, including their susceptibility profiles, molecular typing, phylogenetic features, and genetic context analysis of carbapenemase-encoding genes. Of the 2569 BSI Enterobacterales isolates enrolled, 42 (1.6%) were carbapenemase-positive. Moreover, among the 2242 investigated isolates, 1111 (49.6%) extended-spectrum β-lactamase (ESBL)-producing isolates were identified in Escherichia (E.) coli, Klebsiella (K.) pneumoniae, Proteus (P.) mirabilis, and K. oxytoca. Whole genome sequencing analysis showed the clonal spread of K. pneumoniae carbapenemase (KPC)-2-producing K. pneumoniae sequence type 11 (ST11) and New Delhi metallo-β-lactamase (NDM)-5-producing E. coli ST167 in our collection. Plasmid analysis revealed that carbapenemase-encoding genes were located on multiple plasmids. A high prevalence of biofilm-encoding type 3 fimbriae clusters and yesiniabactin-associated genes was observed in K. pneumoniae isolates. This work demonstrates the high prevalence of ESBLs and the wide dissemination of CPE among BSI isolates in China, which represent real clinical threats. Moreover, our findings first illustrate a more comprehensive genome scenario of CPE isolates among BSIs. The clonal spread of KPC-2-producing K. pneumoniae ST11 and NDM-5-producing E. coli ST167 needs to be closely monitored.

A 61-year-old woman was transferred with a complaint of a fever and productive cough. She had tested positive for Mycobacterium avium and Nocardia cyriacigeorgica at least twice, and Streptococcus pneumonia (PISP) was isolated (3+) from her purulent sputum. As radiological findings, a lower lung field-dominant infiltration shadow and nodular shadow with cavity were recognized in the bilateral lung fields. We diagnosed her with pneumococcal pneumonia co-infection with M. avium and N. cyriacigeorgica. She was treated with MEPM for pneumococcal pneumonia, a standard regimen containing clarithromycin for pulmonary M. avium complex (MAC) disease, and sulfamethoxazole/trimethoprim for pulmonary nocardiosis. She improved with appropriate treatment.

Background: Mouse model is one of of the most widely used animal models for exploring the roles of human gut microbiota, a complex system involving in human immunity and metabolism. However, the structure of mouse gut bacterial community has not been explored at a large scale. To address this concern, the diversity and composition of the gut bacteria of 600 mice was characterized in this study. Results: The results showed that the bacteria belonging to 8 genera were found in the gut microbiota of all mouse individuals, indicating that the 8 bacteria were the core bacteria of mouse gut microbiota. The dominant genera of the mouse gut bacteria contained 15 bacterial genera. It was found that the bacteria in the gut microbiota were mainly involved in host’s metabolisms via the collaborations between the gut bacteria. The further analysis demonstrated that the composition of mouse gut microbiota was similar to that of human gut microbiota. Conclusion: Our study presented a bacterial atlas of mouse gut microbiota, providing a solid basis for investing the bacterial communities of mouse gut microbiota.

Biocontrol agents can control pathogens by reenforcing systemic plant resistance through systemic acquired resistance (SAR) or induced systemic resistance (ISR). Trichoderma spp. can activate the plant immune system through ISR, priming molecular mechanisms of defense against pathogens. Entomopathogenic fungi (EPF) can infect a wide range of arthropod pests and play an important role in reducing pests’ population. Here, we investigated the mechanisms by which EPF control plant diseases. We tested two well studied EPF, Metarhizium brunneum isolate Mb7 and Beauveria bassiana as the commercial product Velifer, for their ability to induce systemic immunity and disease resistance against several fungal and bacterial phytopathogens, and their ability to promote plant growth. We compared the activity of these EPF to an established biocontrol agent, Trichoderma harzianum T39, a known inducer of systemic plant immunity and broad disease resistance. The three fungal agents were effective against several fungal and bacterial plant pathogens and arthropod pests. Our results indicate that EPF induce systemic plant immunity and disease resistance by activating the plant host defense machinery, as evidenced by increases in reactive oxygen species production and defense gene expression, and that EPF promote plant growth. EPF should be considered as control means for Tuta absoluta. We demonstrate that, with some exceptions, biocontrol in tomato can be equally potent by the tested EPF and T. harzianum T39, against both insect pests and plant pathogens. Taken together, our findings suggest that EPF may find use in broad-spectrum pest and disease management and as plant growth promoting agents.

Aims To evaluate the biological activity of extracts from cultures of marine bacteria against Toxoplasma gondii and Mycobacterium tuberculosis. Methods and Results Ethyl acetate extracts obtained from seven marine bacteria were tested against T. gondii GFP-RH and M. tuberculosis H37Rv. The cytotoxicity on HFF-1 cells was measured by a microplate resazurin fluorescent approach, and the haemolytic activity was determined photometrically. The extracts from Bacillus sp. (INV FIR35 and INV FIR48) affected the tachyzoite viability. The extracts from Bacillus, Pseudoalteromonas, Streptomyces and Micromonospora exhibited effects on infection and proliferation processes of parasite. Bacillus sp. INV FIR48 extract showed an minimum inhibitory concentration value of 50 µg ml−1 against M. tuberculosis H37Rv. All the extracts exhibited relatively low toxicity to HFF-1 cells and the primary culture of erythrocytes, except Bacillus sp. INV FIR35, which decreased cell viability under 20%. Liquid chromatography coupled to mass spectrometry analysis of the most active bacterial extract Bacillus sp. INV FIR48 showed the presence of peptide metabolites related to surfactin. Conclusions The extract from culture of deep-sea Bacillus sp. INV FIR48 showed anti-T. gondii and anti-tuberculosis (TB) biological activity with low cytotoxicity. In addition, peptide metabolites were detected in the extract. Significance and Impact of the Study Toxoplasmosis and TB are among the most prevalent diseases worldwide, and the current treatment drugs exhibit side effects. This study confirm that marine bacteria are on hand sources of anti-infective natural products.

Resumen Se estudió la actividad in vitro de delafloxacina, ciprofloxacina y levofloxacina por los métodos epsilométrico y de difusión por discos frente a 181 aislamientos clínicos de infecciones de piel y osteoarticulares. Se incluyeron 40 Staphylococcus aureus resistentes a meticilina (SARM), 44 S. aureus sensibles a meticilina (SASM), 46 estafilococos coagulasa negativos (ECN), 23 Klebsiella pneumoniae y 28 Pseudomonas aeruginosa. Las CIM50/CIM90 (mg/l) de delafloxacina, ciprofloxacina y levofloxacina respectivamente fueron 0,004/0,064, 0,25/16 y 0,125/4 frente a SARM; 0,002/0,004, 0,125/0,25 y 0,125/0,25 frente a SASM; 0,008/0,25, 0,125/>32 y 0,25/>32 frente a ECN; 4/>32,>32/>32 y 16/>32 frente a K. pneumoniae y 1/>32, 0,5/>32 y 4/>32 frente a P. aeruginosa. La proporción de aislamientos sensibles a delafloxacina, ciprofloxacina y levofloxacina fue la siguiente: SARM, 97,5%; 82,5% y 82,5%; SASM, 97,7%; 95,5% y 95,5%; ECN, 93,5%; 63,0% y 60,9%; K. pneumoniae, 21,7%; 26,1% y 43,5%; P. aeruginosa, 35,7%; 53,6% y 42,8%. La concordancia categórica del método de difusión por discos y el método epsilométrico para evaluar la actividad in vitro de la delafloxacina fue del 98,8% en S. aureus y del 91,3% en ECN. Abstract In vitro activities of delafloxacin, ciprofloxacin and levofloxacin were evaluated by epsilometric and disk diffusion methods against 181 bacterial isolates recovered from bone and skin infections. Isolates included were 84 Staphylococcus aureus (40 MRSA and 44 MSSA), 46 coagulase-negative staphylococci (CNS), 23 Klebsiella pneumoniae and 28 Pseudomonas aeruginosa. The MIC50/MIC90 (mg/l) for delafloxacin, ciprofloxacin and levofloxacin, respectively, were: MRSA, 0.004/0.064, 0.25/16 and 0.125/4; MSSA, 0.002/0.004, 0.125/0.25 and 0.125/0.25; CNS, 0.008/0.25, 0.125/>32 and 0.25/>32; K. pneumoniae, 4/>32,>32/>32 and 16/>32; P. aeruginosa, 1/>32, 0,5/>32 and 4/>32. Susceptibilities for delafloxacin, ciprofloxacin and levofloxacin, respectively, were: MRSA, 97.5%, 82.5% and 82.5%; MSSA, 97.7%, 95.5% and 95.5%; CNS, 93.5%, 63.0% and 60.9%; K. pneumoniae, 21.7%, 26.1% and 43.5%; P aeruginosa, 35.7%, 53.6% and 42.8%. The disk diffusion and epsilometric methods were concordant for evaluating in vitro susceptibility in staphylococci (categorical concordance of 98.8% for S. aureus and 91.3% for CNS).

BACKGROUND/PURPOSE Klebsiella pneumoniae bacteremia-induced sepsis is a clinically important condition with a high mortality rate and various known virulence factors. However, studies on the association of these virulence factors with the occurrence of K. pneumoniae bacteremia-induced sepsis are scarce. We aimed to investigate clinical variables and virulence factors in patients with K. pneumoniae bacteremia-induced sepsis. METHODS We retrospectively reviewed the medical records of 76 patients with K. pneumoniae bacteremia between January 2012 and July 2017. Patients were divided into sepsis (n = 25) and non-sepsis (n = 51) groups. Patient background characteristics, antimicrobial regimens, and prognosis were evaluated. We assessed the distribution of virulence factors related to K. pneumoniae, such as mucoviscosity, capsular polysaccharide, and siderophores. Siderophore production levels were determined by measuring the orange halo zone on chrome azurol S agar plate assay. RESULTS There were no intergroup differences in male-to-female ratio and age. Multivariable analysis revealed that siderophore production level (p

Pseudomonas syringae pv. syringae, which causes bacterial canker, is the most polyphagous bacterium in the P. syringae complex because of its broad host range. This pathogen is considered the major bacterial disease in cherry orchards. In this study, several samples were collected from infected sweet cherry (Prunus avium L.) trees in different locations of the Marmara region in Turkey between 2016 and 2018. Sixty-three isolates were identified as P. syringae pv. syringae by pathogenicity, LOPAT, GATTa, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry tests. Total genomic DNA was extracted to confirm identity, followed by PCR amplification of syrB and cfl genes. Out of 63 isolates, 12 were randomly selected for repetitive element sequence-based PCR and multilocus sequence typing analyses to gain insight into the relationships of those isolates. The cluster analysis of enterobacterial repetitive intergenic consensus-, repetitive extragenic palindromic-, and BOX-A1R-based repetitive extragenic-palindromic-PCR techniques could classify the isolates into two distinct clusters. Phylogenetic analysis was carried out to obtain the relation between isolates and the location. The multilocus sequencing typing analysis of gyrB, rpoDp, rpoDs, and gltA genes allowed a clear allocation of the isolates into two separate main clusters. The relationships among the isolates were also evaluated by constructing a genealogical median-joining network (MJN). The isolates from six locations produced 11 haplotypes that were illustrated in the MJN. The results of this study proved that location could not be an indicator for showing the genetic diversity of P. syringae pv. syringae from cherry orchards. As the genetic variability of Pseudomonads has been demonstrated, this study also showed high diversity among different isolates even within the populations. While more research is recommended, the results of this study contributed to a better understanding of the evolutionary progress of P. syringae pv. syringae and the genetic diversity of sweet cherry isolates.