Microbiology

Retraction Note to: Ecological Significance of Microdiversity: Coexistence Among Casing Soil Bacterial Strains Through Allocation of Nutritional Resource The Editor-in-Chief has retracted this article [1] because of significant overlap with a previously published article by Jaspers and Overmann [2]. All authors agree to this retraction.

Detection of Wolbachia Phage (WO) in Indian Lac Insect [ Kerria lacca (Kerr.)] and Its Implications Abstract Wolbachia, a maternally inherited bacterium induces reproductive alterations in its hosts such as feminization of males, male killing and parthenogenesis. It is the most diverse endosymbiont infecting more than 70% of the insects ranging from pests to pollinators. Kerria lacca—a hemipteran is a sedentary, oriental insect known to produce lac—the only resin of animal origin. The present study was conducted to screen the presence of Wolbachia and its associated phages in the two infrasubspecific forms (four insect lines) of K. lacca viz. kusmi and rengeeni differing from each other on the basis of host preference. Wolbachia and its associated phage were found to be prevalent in all the insect lines analyzed. We, hereby, report the presence of WO-phage (Wolbachia phage) for the first time in K. lacca. Further, phylogenetic data differentiated the kusmi and rengeeni infrasubspecific forms into two different groups on the basis of WO-phage sequences.

Importance of the 3′-Terminal Nucleotide of the Forward Primer for Nucleoprotein Gene Detection of Viral Hemorrhagic Septicemia Virus by Conventional Reverse-Transcription PCR Abstract Viral hemorrhagic septicemia virus (VHSV), causing severe diseases in farmed fish, is detected and genotyped using conventional reverse-transcription PCR (cRT-PCR) targeting the nucleoprotein gene with corresponding VN F (forward) and VN R (reverse) primers. However, these primers have low sensitivity to VHSV subtype IVa; I investigated the cause for the poor cRT-PCR performance using various primer combinations. The results demonstrated that a 3′-end mismatch in the VN F primer reduced sensitivity and plays a critical role in VHSV detection by cRT-PCR.

Spoilage Bacteria Identification and Food Safety Risk Assessment of Whole Soybean Curd Abstract As a highly hydrated gel-type food, soybean curd is perishable and the development of spoilage bacteria has been described. Whole soybean curd (WSC), an innovative soy product retains the most nutrients in raw ingredients and exhibits more nutritive value compared with conventional soybean curd (CSC). However, the risk assessment of WSC is not well evaluated up to now. In this study, the same species of spoilage microorganism were separated from WSC and CSC. Two main spoilage strains were separated and identified as B. subtilis and B. cereus. The risk ranking scores of WSC was higher than that of CSC but still within medium risk range. In summary, we reported the presence of B. subtilis and B. cereus in WSC for the first time. Further, application of the risk ranger tool confirmed that the risk profile of WSC was medium and acceptable.

Putative Role of Bacterial Biosorbent in Metal Sequestration Revealed by SEM–EDX and FTIR Abstract Bacterial exopolysaccharides (EPS) play a critical role in sequestration of metals from contaminated environment. Considering these, this study was aimed at extracting EPS from metal tolerant Pseudomonas aeruginosaCPSB1 and Azotobacter chroococcum CAZ3 and to ascertain its role in metal removal. P. aeruginosa CPSB1 and A. chroococcum CAZ3 secreted 1306.7 and 1660 µg mL−1 EPS, respectively in the presence of 200 and 100 µg mL−1 Pb, respectively with glucose as C source. The binding of metal ions to bacterial EPS was validated by SEM and EDX. The functional group involved in metal chelation was revealed by FT-IR. The metal ions were adsorbed onto EPS and hence, EPS could play a crucial role in metal detoxification. Due to this novel trait, P. aeruginosa CPSB1 and A. chroococcum CAZ3 could be developed as bioinoculant to cleanup metal contaminated sites.

Molecular Mechanism of Antibiotic Resistance: The Untouched Area of Future Hope Abstract The treatment of bacterial infections is becoming increasingly ineffective due to rapid mutation which leads to antibiotic resistant and resistant bacteria become more prevalent. As a result the existing antibiotics are gradually obsolete and again new drugs are needed to be designed for the same threat. However, the prediction of evolutionary processes/antibiotic resistance is uncertain. Still, the understanding of mode of evolution of resistance in bacteria is a determining step in the preclinical development of new antibiotics, because drug developers assess the risk of resistance arising against a drug during preclinical development. Multidrug efflux pump systems play an important role for making multidrug resistance to a range of clinically important antibiotics in gram-negative bacteria like Pseudomonas aeruginosa, which lower the intracellular drug concentration by exporting incoming antibiotics across the membranes. We tried to show that the wild type susceptible bacteria P. aeruginosa modified its genetic makeup at mutational hotspots under stress. This strain may either become multidrug resistant or remain susceptible depending on position of amino acid changes in regulatory proteins of efflux pump. Multidrug resistant strain made significant changes at the amino acid positions, 103rd (G → A) and 126th (E → V) through the mutation on the nucleotide position of 308th (G → C); both 377th (A → T) and 378th (G → T), respectively in mexR, a repressor of mexAB-oprM efflux pump. This mutant protein showed low affinity with their operator. But the alteration at 103th position (G → A) in mexR may provide almost similar structural and functional stability as wild type. It was found that mutation was seemed to be well regulated within the limit and position specific under stress which might be back to its original form by supplying counter stress unless addition or deletion takes place.

Microbial Inoculants Assisted Growth of Chrysopogon zizanioides Promotes Phytoremediation of Salt Affected Soil Abstract Restoration of salt-affected soil through cultivation Chrysopogon zizanioides is a promising approach. The two way benefit of such an approach is that reclamation of salt-affected soil concomitant to improve plant growth and increased yield of essential oil produced in the plants roots. Earlier studies showed physiological changes and reduced growth of C. zizanioides under salinity. In the present study, plant growth promoting microorganisms viz. Pseudomonas monteilii, Bacillus megaterium, Azotobacter chroococcum and Rhizophagus intraradices were used as bio-inoculants for cultivation of C. zizanioides under salt-affected soil. Bio-inoculants in combination with vermicompost significantly increased the growth and productivity of C. zizanioides under salt-affected soil, and simultaneously improved soil health. When compared to control, the soil physico-chemical and biological properties of bio-inoculants treated plants was significantly improved. The reclamation of salt-affected soil was evident by the significant decrease in the level of soil pH (11.0%), electrical conductivity (23.5%), sodium adsorption ratio (15.3%), and exchangeable sodium percent (12.4%) of bio-inoculants treated plants. The improvement of soil cation exchange capacity indicated the decrease in soil salinity. Whereas increase in the microbial count (four-fold), AMF spores (447 spores), dehydrogenase (six-fold), acid (two-fold) and alkaline phosphatase (five-fold) activities in rhizosphere soil of bio-inoculant treated plants indicated the improved biological properties. A positive correlation of plant biomass production to soil organic carbon, total Kjeldahl nitrogen, available phosphorus and cation exchange capacity depicted improved nutrients content in rhizosphere soil of bio-inoculant treated plants. The findings of this study suggest that P. monteilii and R. intraradices with vermicompost can be effectively used as bio-inoculants for encouragement of phytoremediation in salt-affected soil.

Anti-biofilm and Antibacterial Activity of Allium sativum Against Drug Resistant Shiga-Toxin Producing Escherichia coli (STEC) Isolates from Patient Samples and Food Sources Abstract Escherichia coli (E. coli) colonizes human intestinal tract and is usually harmless to the host. However, several strains of E. coli have acquired virulent genes and could cause enteric diseases, urinary tract and even brain infections. Shiga toxin producing Escherichia coli (STEC) is an enterohaemorrhagic E. coli (EHEC) which can result in bloody diarrhoea and could potentially lead to deadly heamolytic uremic syndrome (HUS). STEC is one of the important food borne pathogens that causes food poisoning leading to diarrhoea and number of STEC outbreaks have occurred across the world. The use of standard antibiotics to treat STEC infection is not recommended as it increases the production of shiga toxin which could lead to HUS. Therefore, use of alternative approaches which include use of plant products to treat STEC infections have been gaining attention. The objective of this study was to evaluate the antibacterial and anti-biofilm activity of garlic (Allium sativum) against STEC strains isolated from various patient and food samples using in vitro assays. The microbiological isolation of STEC from various patient and food samples resulted in eight STEC isolates of which seven strains were multidrug resistant. Antibacterial assay results indicated that all the strains exhibited dose dependent sensitivity towards garlic with zone of inhibition diameters ranging from 7 to 24 mm with 15 µl of fresh garlic extract (FGE). Minimum inhibitory  concentration (MIC) of FGE for isolates ranged from 30 to 140 µl/ml. Interestingly, the biofilm formation of all isolates in presence of 4% of FGE decreased by 35 to 59%. FTIR analysis indicated that treatment with 1% FGE results in compositional and content changes in the biofilm. In addition, the total carbohydrate content of biofilm was reduced by 40% upon 1% FGE treatment. The results of the present study report for the first time the antibacterial and anti-biofilm activity of garlic against STEC. The findings will enable development of novel garlic organosulfide based drugs for the prevention and treatment of STEC infections.

Pattern of Antimicrobial Sensitivity in Microbiologically Documented Infections in Neutropenic Patients with Haematological Malignancies: A single Center Study Abstract Febrile neutropenia is a medical emergency that complicates the clinical course and treatment of haematological malignancies, significantly enhancing the financial burden and worsening the overall outcome. This study was carried out to evaluate the efficacy of institution's current first-line antibiotic regimen for febrile neutropenia in view of recent spectrum of institution's local flora and its susceptibility pattern. 163 episodes of microbiologically documented infections in 110 adult patients were studied over a period of 1 year. Of 110 patients, 61 patients were male. The mean age of the patient population, mean absolute neutrophil count and temperature as documented were 30.1 years (SD ± 16.8), 450 cells/ul, and 101.9 °C respectively. Gram-negative and gram-positive organisms accounted for 79% and 21% of the febrile neutropenic infections respectively. E. coli and Staphylococcus aureus were the most common gram positive and gram negative pathogens respectively. A susceptibility pattern of > 60% was documented for all the gram negative pathogen's associated febrile neutropenic infections for the current first-line antibiotic combination of Piperacillin/Tazobactum and Amikacin. Comparative analysis of results with the institutional data of 2015 study revealed no statistically significant difference in the resistance pattern of the organisms hence, validating the persistent use of Piperacillin/Tazobacum and Amikacin combination as a potent and efficacious therapy for febrile neutropenia patients with haematological malignancies. However, continuous surveillance remains prudent for the emerging changes in the spectrum and resistance pattern of local flora so that timely revision of empirical antibiotic regimens can save the added financial burdens and associated high morbidity and mortality.

Agrobacterium-Mediated Transformation of Diaporthe schini Endophytes Associated with Vitis labrusca L. and Its Antagonistic Activity Against Grapevine Phytopathogens Abstract Fungus-caused diseases are among the greatest losses in grapevine culture. Biological control of pathogens by endophytes may be used to decrease fungicide application rates and environmental impacts. Previously, Diaporthe sp. B46-64 and C27-07 were highlighted as antagonists of grapevine phytopathogens. Herein, molecular multigene (ITS-TUB-TEF1) identification and phylogenetic analysis allowed the identification of these endophytes as belonging to Diaporthe schini species. Agrobacterium tumefaciens-mediated transformation was employed for obtaining 14 stable and traceable gfp- or DsRed-expressing transformants, with high transformation efficiency: 96% for the pFAT-GFP plasmid and 98% for pCAM-DsRed plasmid. Transformants were resistant to hygromycin B with gene hph confirmed by polymerase chain reaction and proved to be mitotically stable, expressing the fluorescent phenotype, with morphological differences in the colonies when compared with wild strains. In vitro antagonism tests revealed an increased antagonistic activity of some transformant strains. The current genetic transformation of D. schini mediated by A. tumefaciens proved to be an efficient technique within the randomized insertion of reporter genes for the monitoring of the strain in the environment.