Complete Genome Sequence of the Complex Carbohydrate-Degrading Marine Bacterium, Saccharophagus degradans Strain 2-40T

The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40) is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment

Assessment of protein silver nanoparticles toxicity against pathogenic Alternaria solani

Mycogenic synthesis of silver nanoparticles (AgNPs) was carried out in the present investigation using an aqueous extract of endophytic non-pathogenic Alternaria solani F10 (KT721914). The mycosynthesized AgNPs were characterized by means of spectroscopic and microscopic techniques. The surface plasmon resonance found at 430 nm confirmed the formation of stable AgNPs for several weeks at room temperature. Also, the results revealed the formation of spherical and monodispersed AgNPs with an average size of 14.8 +/- 1.2 nm. The FT-IR spectrum suggested that the fungal extracellular proteins and secondary metabolites had the role in Ag reduction and AgNPs capping of which protein Ag nanoconjugates were formed. Furthermore, the mycosynthesized AgNPs exhibited potent antifungal activity against different pathogenic isolates of the same Alternaria solani fungus, the causal pathogen of tomato early blight disease. The antifungal efficiency of the AgNPs at 1, 5 and 10 ppm were evaluated for 8 days after incubation by measuring the inhibition rate of fungal radial growth. The results were further supported by investigating fungal hyphae morphology alteration by scanning and transmission electron microscopy. Treated fungal hyphae showed formation of pits and pores. Also, the mycosynthesized AgNPs were able to pass and distribute throughout the fungal cell area and interact with the cell components.A financial support from European Commission by Erasmus Mundus Scholarship-ACTION 2 WELCOME program is gratefully acknowledged. Work in JAD laboratory was supported by grant BIO2014-54269-R from the Ministerio de Economia y Competividad (Spain).Abdel-Hafez, SII.; Nafady, NA.; Abdel-Rahim, IR.; Shaltout, AM.; Daros Arnau, JA.; Mohamed, MA. (2016). Assessment of protein silver nanoparticles toxicity against pathogenic Alternaria solani. 3 Biotech. 6(199):1-12. https://doi.org/10.1007/s13205-016-0515-6S1126199Abd-Alla MH, Nafady NA, Khalaf DM (2016) Assessment of silver nanoparticles contamination on faba bean-Rhizobium leguminosarum bv. viciae-Glomus aggregatum symbiosis: implications for induction of autophagy process in root nodule. Agric Ecosyst Environ 15(218):163–177Abdel-Hafez SI, Nafady NA, Abdel-Rahim IR, Shaltout AM, Mohamed MA (2016) Biogenesis and optimisation of silver nanoparticles by the endophytic fungus cladosporium sphaerospermum. Int J Nano Chem 2(1):11–19Agrios GN (1997) Plant pathology, 4th edn. Academic Press, LondonAzizi S, Namvar F, Mahdavi M, Ahmad MB, Mohamad R (2013) Biosynthesis of silver nanoparticles using brown marine macroalga, Sargassum muticum aqueous extract. Materials 6(12):5942–5950Birla S, Tiwari V, Gade A, Ingle A, Yadav A, Rai M (2009) Fabrication of silver nanoparticles by Phoma glomerala and its combined effect against Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus. Lett Appl Microbiol 48(2):173–179Chohan S, Perveen R, Mehmood MA, Naz S, Akram N (2015) Morpho-physiological studies, management and screening of tomato germplasm against alternaria solani, the causal agent of tomato early blight. Int J Agric Biol 17(1):111–118Das VL, Thomas R, Varghese RT, Soniya EV, Mathew J, Radhakrishnan EK (2014) Extracellular synthesis of silver nanoparticles by the Bacillus strain CS 11 isolated from industrialized area. 3 Biotech 4(2):121–126Datar VV, Mayee CD (1981) Assessment of losses in tomato yield due to early blight. Indian phytopathol 34:191–195Elyasi M, Khalilzadeh MA, Karimi-Maleh H (2013) High sensitive voltammetric sensor based on Pt/CNTs nanocomposite modified ionic liquid carbon paste electrode for determination of Sudan I in food samples. Food Chem 141(4):4311–4317Ensafi AA, Karimi-Maleh H (2010) Modified multiwall carbon nanotubes paste electrode as a sensor for simultaneous determination of 6-thioguanine and folic acid using ferrocenedicarboxylic acid as a mediator. J Electroanal Chem 640(1):75–83Fayaz M, Tiwary CS, Kalaichelvan PT, Venkatesan R (2010) Blue orange light emission from biogenic synthesized silver nanoparticles using Trichoderma viride. Colloids Surf B Biointerfaces 75(1):175–178Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol Ecol 2(2):113–118Gurunathan S, Lee KJ, Kalishwaralal K, Sheikpranbabu S, Vaidyanathan R, Eom SH (2009) Antiangiogenic properties of silver nanoparticles. Biomaterials 30(31):6341–6350Kagithoju S, Godishala V, Nanna RS (2015) Eco-friendly and green synthesis of silver nanoparticles using leaf extract of Strychnos potatorum Linn. F. and their bactericidal activities. 3 Biotech 5(5):709–714Kanmani P, Lim ST (2013) Synthesis and structural characterization of silver nanoparticles using bacterial exopolysaccharide and its antimicrobial activity against food and multidrug resistant pathogens. Process Biochem 48(7):1099–1106Khan MR, Rizvi TF (2014) Nanotechnology: scope and application in plant disease management. Plant Pathol J 13:214–231Khan M, Rizwani GH, Shareef H, Cavar S, Zia-Ul-Haq M (2013) Assessment of total phenolic content and antioxidant potential of methanol extract of Peltophorum pterocarpum (DC.) Backer ex K. Heyne. Pak J Pharm Sci 26(5):967–972Kim KJ, Sung WS, Suh BK, Moon SK, Choi JS, Kim JG, Lee DG (2009a) Antifungal activity and mode of action of silver nano-particles on Candida albicans. Biometals 22(2):235–242Kim SW, Kim KS, Lamsal K, Kim YJ, Kim SB, Jung M, Sim SJ, Kim HS, Chang SJ, Kim JK, Lee YS (2009b) An in vitro study of the antifungal effect of silver nanoparticles on oak wilt pathogen Raffaelea sp. J Microbiol Biotechnol 19(8):760–764Kim SW, Jung JH, Lamsal K, Kim YS, Min JS, Lee YS (2012) Antifungal effects of silver nanoparticles (AgNPs) against various plant pathogenic fungi. Mycobiology 40(1):53–58Kirk AB, Martinelango PK, Tian K, Dutta A, Smith EE, Dasgupta PK (2005) Perchlorate and iodide in dairy and breast milk. Environ Sci Technol 39(7):2011–2017Kumar CG, Sujitha P (2014) Green synthesis of Kocuran-functionalized silver glyconanoparticles for use as antibiofilm coatings on silicone urethral catheters. Nanotechnology 25(32):325101Liu L, Yang J, Xie J, Luo Z, Jiang J, Yang YY, Liu S (2013) The potent antimicrobial properties of cell penetrating peptide-conjugated silver nanoparticles with excellent selectivity for Gram-positive bacteria over erythrocytes. Nanoscale 5(9):3834–3840Loza K, Diendorf J, Sengstock C, Ruiz-Gonzalez L, Gonzalez-Calbet J, Vallet- Regi M, Köller M, Epple M (2014) The dissolution and biological effects of silver nanoparticles in biological media. J Mater Chem B 2:1634–1643Malik P, Shankar R, Malik V, Sharma N, Mukherjee TK (2014) Green chemistry based benign routes for nanoparticle synthesis. J Nanopart 24:1–14McDonnell G, Russell AD (2001) Antiseptics and disinfectants: activity, action, and resistance. Clin Microbiol Rev 14(1):227Metuku RP, Pabba S, Burra S, Gudikandula K, Charya MS (2014) Biosynthesis of silver nanoparticles from Schizophyllum radiatum HE 863742.1: their characterization and antimicrobial activity. 3 Biotech 4(3):227–234Mohamed AM (2015) One-step functionalization of silver Nanoparticles using the orsellinic acid compound isolated from the endophytic fungus Epicoccum Nigrum: characterization and antifungal activity. Int J Nano Chem. 1(3):103–110Moradi R, Sebt SA, Karimi-Maleh H, Sadeghi R, Karimi F, Bahari A, Arabi H (2013) Synthesis and application of FePt/CNTs nanocomposite as a sensor and novel amide ligand as a mediator for simultaneous determination of glutathione, nicotinamide adenine dinucleotide and tryptophan. Phys Chem Chem Phys 15(16):5888–5897Nadworny PL, Wang J, Tredget EE, Burrell RE (2008) Anti-inflammatory activity of nanocrystalline silver in a porcine contact dermatitis model. Nanomedicine 4(3):241–251Namanda S, Olanya OM, Adipala E, Hakiza JJ, El-Bedewy R, Baghsari AS, Ewell P (2004) Fungicide application and host-resistance for potato late blight management: benefits assessment from on-farm studies in SW Uganda. Crop Prot 23(11):1075–1083Narayanan KB, Sakthivel N (2010) Biological synthesis of metal nanoparticles by microbes. Adv Colloid Interface Sci 156(1):1–3Netala VR, Kotakadi VS, Bobbu P, Gaddam SA, Tartte V (2016) Endophytic fungal isolate mediated biosynthesis of silver nanoparticles and their free radical scavenging activity and anti microbial studies. 3 Biotech 6(2):1–9Petrini O, Fisher PJ (1988) A comparative study of fungal endophytes in xylem and whole stems of Pinus sylvestris and Fagus sylvatica. Trans Br Mycol Soc 91(2):233–238Qin Y, Ji X, Jing J, Liu H, Wu H, Yang W (2010) Size control over spherical silver nanoparticles by ascorbic acid reduction. Colloids Surf A Physicochem Eng Asp 372(1):172–176Ramamurthy CH, Padma M, Mareeswaran R, Suyavaran A, Kumar MS, Premkumar K, Thirunavukkarasu C (2013) The extra cellular synthesis of gold and silver nanoparticles and their free radical scavenging and antibacterial properties. Colloids Surf B Biointerfaces 102:808–815Rogers JV, Parkinson CV, Choi YW, Speshock JL, Hussain SM (2008) A preliminary assessment of silver nanoparticle inhibition of monkeypox virus plaque formation. Nanoscale Res Lett 3(4):129–133Sadeghi R, Karimi-Maleh H, Khalilzadeh MA, Beitollahi H, Ranjbarha Z, Zanousi MB (2013) A new strategy for determination of hydroxylamine and phenol in water and waste water samples using modified nanosensor. Environ Sci Pollut Res Int 20(9):6584–6593Saharan V, Sharma G, Yadav M, Choudhary MK, Sharma SS, Pal A, Biswas P (2015) Synthesis and in vitro antifungal efficacy of Cu–chitosan nanoparticles against pathogenic fungi of tomato. Int J Biol Macromolec 75:346–353Satyavani K, Ramanathan T, Gurudeeban S (2011) Plant mediated synthesis of biomedical silver nanoparticles by using leaf extract of Citrullus colocynthis. R J Nanosci Nanotech 1(2):95–101Siddique YH, Fatima A, Jyoti S, Naz F, Khan W, Singh BR, Naqvi AH (2013) Evaluation of the toxic potential of graphene copper nanocomposite (GCNC) in the third instar larvae of transgenic Drosophila melanogaster (hsp70-lacZ) Bg 9. PloS one 8(12):e80944Stoimenov PK, Klinger RL, Marchin GL, Klabunde KJ (2002) Metal oxide nanoparticles as bactericidal agents. Langmuir 18(17):6679–6686Tanvir S, Oudet F, Pulvin S, Anderson WA (2012) Coenzyme based synthesis of silver nanocrystals. Enzyme Microb Technol 51(4):231–236Thakkar KN, Mhatre SS, Parikh RY (2010) Biological synthesis of metallic nanoparticles. Nanomedicine 6(2):257–262Vahdati AR, Sadeghi B (2013) A study on the assessment of DNA strand-breaking activity by silver and silica nanoparticles. J Nanostruct Chem 1:1–3Wu D, Fan W, Kishen A, Gutmann JL, Fan B (2014) Evaluation of the antibacterial efficacy of silver nanoparticles against Enterococcus faecalis biofilm. J Endod 40:285–290Zachariadis PC, Hadjikakou SK, Hadjiliadis N, Skoulika S, Michaelides A, Balzarini J, De Clercq E (2004) Synthesis, characterization and in vitro study of the cytostatic and antiviral activity of new polymeric silver (I) complexes with ribbon structures derived from the conjugated heterocyclic thioamide 2-mercapto-3, 4, 5, 6-tetra-hydropyrimidine. Eur J Inorg Chem 7:1420–1426Zhang W, Qiao X, Chen J (2007) Synthesis of silver nanoparticles—effects of concerned parameters in water/oil microemulsion. Mater Sci Eng, B 142(1):1–5Zhao N, Gao J, Enns CA, Knutson MD (2010) ZRT/IRT-like protein 14 (ZIP14) promotes the cellular assimilation of iron from transferrin. J Biol Chem 285(42):32141–3215

Laparoscopy in management of appendicitis in high-, middle-, and low-income countries: a multicenter, prospective, cohort study.

BACKGROUND: Appendicitis is the most common abdominal surgical emergency worldwide. Differences between high- and low-income settings in the availability of laparoscopic appendectomy, alternative management choices, and outcomes are poorly described. The aim was to identify variation in surgical management and outcomes of appendicitis within low-, middle-, and high-Human Development Index (HDI) countries worldwide. METHODS: This is a multicenter, international prospective cohort study. Consecutive sampling of patients undergoing emergency appendectomy over 6 months was conducted. Follow-up lasted 30 days. RESULTS: 4546 patients from 52 countries underwent appendectomy (2499 high-, 1540 middle-, and 507 low-HDI groups). Surgical site infection (SSI) rates were higher in low-HDI (OR 2.57, 95% CI 1.33-4.99, p = 0.005) but not middle-HDI countries (OR 1.38, 95% CI 0.76-2.52, p = 0.291), compared with high-HDI countries after adjustment. A laparoscopic approach was common in high-HDI countries (1693/2499, 67.7%), but infrequent in low-HDI (41/507, 8.1%) and middle-HDI (132/1540, 8.6%) groups. After accounting for case-mix, laparoscopy was still associated with fewer overall complications (OR 0.55, 95% CI 0.42-0.71, p < 0.001) and SSIs (OR 0.22, 95% CI 0.14-0.33, p < 0.001). In propensity-score matched groups within low-/middle-HDI countries, laparoscopy was still associated with fewer overall complications (OR 0.23 95% CI 0.11-0.44) and SSI (OR 0.21 95% CI 0.09-0.45). CONCLUSION: A laparoscopic approach is associated with better outcomes and availability appears to differ by country HDI. Despite the profound clinical, operational, and financial barriers to its widespread introduction, laparoscopy could significantly improve outcomes for patients in low-resource environments. TRIAL REGISTRATION: NCT02179112

Pooled analysis of WHO Surgical Safety Checklist use and mortality after emergency laparotomy

Background The World Health Organization (WHO) Surgical Safety Checklist has fostered safe practice for 10 years, yet its place in emergency surgery has not been assessed on a global scale. The aim of this study was to evaluate reported checklist use in emergency settings and examine the relationship with perioperative mortality in patients who had emergency laparotomy. Methods In two multinational cohort studies, adults undergoing emergency laparotomy were compared with those having elective gastrointestinal surgery. Relationships between reported checklist use and mortality were determined using multivariable logistic regression and bootstrapped simulation. Results Of 12 296 patients included from 76 countries, 4843 underwent emergency laparotomy. After adjusting for patient and disease factors, checklist use before emergency laparotomy was more common in countries with a high Human Development Index (HDI) (2455 of 2741, 89.6 per cent) compared with that in countries with a middle (753 of 1242, 60.6 per cent; odds ratio (OR) 0.17, 95 per cent c.i. 0.14 to 0.21, P <0001) or low (363 of 860, 422 per cent; OR 008, 007 to 010, P <0.001) HDI. Checklist use was less common in elective surgery than for emergency laparotomy in high-HDI countries (risk difference -94 (95 per cent c.i. -11.9 to -6.9) per cent; P <0001), but the relationship was reversed in low-HDI countries (+121 (+7.0 to +173) per cent; P <0001). In multivariable models, checklist use was associated with a lower 30-day perioperative mortality (OR 0.60, 0.50 to 073; P <0.001). The greatest absolute benefit was seen for emergency surgery in low- and middle-HDI countries. Conclusion Checklist use in emergency laparotomy was associated with a significantly lower perioperative mortality rate. Checklist use in low-HDI countries was half that in high-HDI countries.Peer reviewe

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Global variation in anastomosis and end colostomy formation following left-sided colorectal resection

Background End colostomy rates following colorectal resection vary across institutions in high-income settings, being influenced by patient, disease, surgeon and system factors. This study aimed to assess global variation in end colostomy rates after left-sided colorectal resection. Methods This study comprised an analysis of GlobalSurg-1 and -2 international, prospective, observational cohort studies (2014, 2016), including consecutive adult patients undergoing elective or emergency left-sided colorectal resection within discrete 2-week windows. Countries were grouped into high-, middle- and low-income tertiles according to the United Nations Human Development Index (HDI). Factors associated with colostomy formation versus primary anastomosis were explored using a multilevel, multivariable logistic regression model. Results In total, 1635 patients from 242 hospitals in 57 countries undergoing left-sided colorectal resection were included: 113 (6·9 per cent) from low-HDI, 254 (15·5 per cent) from middle-HDI and 1268 (77·6 per cent) from high-HDI countries. There was a higher proportion of patients with perforated disease (57·5, 40·9 and 35·4 per cent; P < 0·001) and subsequent use of end colostomy (52·2, 24·8 and 18·9 per cent; P < 0·001) in low- compared with middle- and high-HDI settings. The association with colostomy use in low-HDI settings persisted (odds ratio (OR) 3·20, 95 per cent c.i. 1·35 to 7·57; P = 0·008) after risk adjustment for malignant disease (OR 2·34, 1·65 to 3·32; P < 0·001), emergency surgery (OR 4·08, 2·73 to 6·10; P < 0·001), time to operation at least 48 h (OR 1·99, 1·28 to 3·09; P = 0·002) and disease perforation (OR 4·00, 2·81 to 5·69; P < 0·001). Conclusion Global differences existed in the proportion of patients receiving end stomas after left-sided colorectal resection based on income, which went beyond case mix alone