Molecular biodiversity of microbial communities in polluted soils and their role in soil phytoremediation

Les métaux lourds (ML) s’accumulent de plus en plus dans les sols à l’échelle mondiale, d’une part à cause des engrais minéraux et divers produits chimiques utilisés en agriculture intensive, et d’autre part à cause des activités industrielles. Toutes ces activités génèrent des déchets toxiques qui s’accumulent dans l’environnement. Les ML ne sont pas biodégradables et leur accumulation cause donc des problèmes de toxicité des sols et affecte la biodiversité des microorganismes qui y vivent. La fertilisation en azote (N) est une pratique courante en agriculture à grande échelle qui permet d’augmenter la fertilité des sols et la productivité des cultures. Cependant, son utilisation à long terme cause plusieurs effets néfastes pour l'environnement. Par exemple, elle augmente la quantité des ML dans les sols, les nappes phréatiques et les plantes. En outre, ces effets néfastes réduisent et changent considérablement la biodiversité des écosystèmes terrestres. La structure des communautés des champignons mycorhiziens à arbuscules (CMA) a été étudiée dans des sols contaminés par des ML issus de la fertilisation à long terme en N. Le rôle des différentes espèces de CMA dans l'absorption et la séquestration des ML a été aussi investigué. Dans une première expérience, la structure des communautés de CMA a été analysée à partir d’échantillons de sols de sites contaminés par des ML et de sites témoins non-contaminés. Nous avons constaté que la diversité des CMA indigènes a été plus faible dans les sols et les racines des plantes récoltées à partir de sites contaminés par rapport aux sites noncontaminés. Nous avons également constaté que la structure de la communauté d'AMF a été modifiée par la présence des ML dans les sols. Certains ribotypes des CMA ont été plus souvent associés aux sites contaminés, alors que d’autres ribotypes ont été associés aux sites non-contaminés. Cependant, certains ribotypes ont été observés aussi bien dans les sols pollués que non-pollués. Dans une deuxième expérience, les effets de la fertilisation organique et minérale (N) sur les différentes structures des communautés des CMA ont été étudiés. La variation de la structure de la communauté de CMA colonisant les racines a été analysée en fonction du type de fertilisation. Certains ribotypes de CMA étaient associés à la fertilisation organique et d'autres à la fertilisation minérale. En revanche, la fertilisation minérale a réduit le nombre de ribotypes de CMA alors que la fertilisation organique l’a augmenté. Dans cette expérience, j’ai démontré que le changement de structure des communautés de CMA colonisant des racines a eu un effet significatif sur la productivité des plantes. Dans une troisième expérience, le rôle de deux espèces de CMA (Glomus irregulare et G. mosseae) dans l'absorption du cadmium (Cd) par des plants de tournesol cultivés dans des sols amendés avec trois niveaux différents de Cd a été évalué. J’ai démontré que les deux espèces de CMA affectent différemment l’absorption ou la séquestration de ce ML par les plants de tournesol. Cette expérience a permis de mieux comprendre le rôle potentiel des CMA dans l'absorption des ML selon la concentration de cadmium dans le sol et les espèces de CMA. Mes recherches de doctorat démontrent donc que la fertilisation en N affecte la structure des communautés des CMA dans les racines et le sol. Le changement de structure de la communauté de CMA colonisant les racines affecte de manière significative la productivité des plantes. J’ai aussi démontré que, sous nos conditions expériemntales, l’espèce de CMA G. irregulare a été observée dans tous les sites (pollués et non-pollués), tandis que le G. mosseae n’a été observé en abondance que dans les sites contaminés. Par conséquent, j’ai étudié le rôle de ces deux espèces (G. irregulare et G. mosseae) dans l'absorption du Cd par le tournesol cultivé dans des sols amendés avec trois différents niveaux de Cd en serre. Les résultats indiquent que les espèces de CMA ont un potentiel différent pour atténuer la toxicité des ML dans les plantes hôtes, selon le niveau de concentration en Cd. En conclusion, mes travaux suggèrent que le G. irregulare est une espèce potentiellement importante pour la phytoextration du Cd, alors que le G. mosseae pourrait être une espèce appropriée pour phytostabilisation du Cd et du Zn.Trace metals (TM) are continually world-wide added to soils through the intensive use of mineral fertilizers and agriculture chemicals, together with industrial and other activities generating toxic wastes. Problems associated with metal-contaminated soil exists because TM are not biodegradable. TM that accumulate in soils affect the biodiversity of soil microorganisms. Nitrogen (N) fertilization is a widespread practice to increase soil fertility and crop production. However, the long-term use of N fertilization causes many detrimental effects in the environment. The intensive use of N fertilization increase TM input in soils, and in extreme cases, N fertilization result in TM pollution of the surrounding soil and water and increase TM concentration in plant tissues. In addition, the long-term use of N fertilizers changes and declines the biodiversity of above and underground ecosystems. The community structure of arbuscular mycorrhizal fungi (AMF) was investigated in TM contaminated and long-term N fertilized soils. In addition, the role of different AMF species in TM uptake or sequestration was investigated. In the first experiment, AMF community structure was analyzed from non-contaminated and TM contaminated sites. We found the diversity of native AMF was lower in soils and plant roots harvested from TM polluted soils than from unpolluted soils. We also found that the community structure of AMF was modified by TM contamination. Some AMF ribotypes were more often associated with TM contaminated sites, other ribotypes with uncontaminated sites, while still other ribotypes were found both in polluted and unpolluted soils. In the second experiment, the effect of different organic and mineral N fertilization on AMF community structure was investigated. Variation in root-colonizing AMF community structure was observed in both organic and mineral fertilization. Some AMF ribotypes were more affiliated to organic fertilization and other to mineral fertilization. In addition, mineral fertilization reduced AMF ribotypes number while organic fertilization increased AMF ribotypes number. In this experiment, it was demonstrated that change in root-colonizing AMF community structure had a significant effect on plant productivity. In the third experiment, the role of different AMF species (G. irregulare and G. mosseae) in TM uptake by sunflower plants grown in soil amended with three different Cd levels was evaluated. It was demonstrated that AMF species differentially affected TM uptake or sequestration by sunflower plants. This experiment supported a different effect of AMF in TM uptake based on Cd concentration in soil and the AMF species involved. Our research demonstrated that TM and N fertilization affected and shifted AMF community structure within roots and soils. It was shown that change in root-colonizing AMF community structure significantly affected plant productivity. In this study, it was showed that the AMF species G. irregulare was recorded in all uncontaminated sites while G. mosseae was the most abundant AMF species in TM contaminated sites. Therefore, the role of G. irregulare and G. mosseae in Cd uptake by sunflower plants grown in soils amended with three different Cd levels was investigated. The results indicated that AMF species mediate different mechanisms to alleviate TM toxicity in host plants, depending on AMF species and soil Cd level involved. We hypothesize that G. irregulare is a potentially important species for Cd phytoextration processes, while G. mosseae might be a suitable candidate for Cd and Zn phytostabilization processes

Biotechnological applications of fungal endophytes associated with medicinal plant Asclepias sinaica (Bioss.)

AbstractFungal endophytes associated with medicinal plants have potential role to promote plant growth through different mechanisms. However, the biological and ecological roles of fungal endophytes still totally unexplored. In this study, three different fungal endophytes were isolated from the medicinal plant of Asclepias sinaica and identified as Penicillium chrysogenum Pc_25, Alternaria alternata Aa_27 and the third fungal strain was described as sterile hyphae Sh_26. It was recorded that, these endophytes had various ability to produce several extracellular enzymes including amylase, pectinase, cellulase, gelatinase, xylanase and tyrosinase. Their antimicrobial activities against different specific test organisms were investigated as well. In addition, both endophyte isolates i.e. Sh_26 and Aa_27 were found to promote root growth higher than Pc_25 and control treatments. These fungal isolates had a considerable impact on plant growth parameters including root elongation as a result of ammonia and IAA production

Clinical and Biochemical Assessment of Lycopene Gel Combined With Nanohydroxyapatite Graft in Treatment of Grade II Furcation Defects: A Randomized Controlled Clinical Study

Background: This study aimed to evaluate the effects of lycopene gel, as a natural antioxidant, mixed with a nanohydroxyapatite graft (NHG) covered by an occlusive resorbable collagen membrane (CM) in the surgical treatment of grade II furcation defects and on the gingival crevicular fluid (GCF) levels of 8-hydroxydeoxyguanosine (8-OHdG), as a marker of oxidative injury. Methods: In this randomized controlled clinical study a total of 24 patients with grade II furcation defects were randomly assigned into three equal groups. Furcation defects in group I were managed with lycopene gel mixed with NHG and CM, group II with NHG and CM, and group III with open flap debridement only. Site-specific changes in clinical parameters including probing depth (PD), vertical clinical attachment level (VCAL), horizontal clinical attachment level (HCAL), radiographic maximum vertical depth (MAX V), and maximum horizontal depth (MAX H) were measured at baseline and six months postoperatively. Gingival crevicular fluid levels of 8-OHdG were analyzed using enzyme-linked immunosorbent assay (ELISA) at baseline, one week, and three months. Results: Surgical management of grade II furcation defects resulted in a significant reduction in PD and 8-OHdG levels and a gain in CAL, MAX V, and MAX H in all groups. The differences between lycopene treated sites compared to NHG and CM alone were not significant at six months but demonstrated significantly superior clinical parameters compared to open flap debridement alone. Conclusion: Lycopene does not confer a benefit when combined with NHG in the surgical treatment of grade II furcation defects

Mitochondrial D-loop sequences and haplotypes diversity in Egyptian rabbit breeds

[EN] Rabbit breeds in Egypt are local and adapted foreign breeds that have been imported since the middle of the last century. Stressful environmental conditions including climatic changes, exposure to diseases and breeding selection have an influence on how gene flow has shaped the genetic diversity of the breeds. Mitochondrial DNA D-loop is a genetic marker used to trace the geographic distribution of genetic variation for the investigation of expansions, migrations and other gene flow patterns. The study aimed to determine the genetic diversity of the mitochondrial DNA D-loop (mtDNA D-loop) in Black Baladi, Red Baladi, Gabali, APRI line and New Zealand breeds to gather the scientific data required to create a proper conservation and sustainable management plan. Blood samples were taken from animals unrelated to each other. A 332-bp of mtDNA D-loop was successfully amplified and alignment sequences were deposited in the GenBank database. The results detected six haplotypes in the five breeds. Haplotype diversity within individual breeds varied from 0 (Red Baladi) to 0.551±0.114 (Gabali). The nucleotide diversity (π) value was relatively low (0.001-0.006), with greater values in APRI and New Zealand. Pairwise distances between breeds yielded varying values ranging from 0 to 0.254, and the values between the Red Baladi and other breeds were comparatively high, with pairwise distances from 0.172 to 0.254. The phylogenetic analysis involved 74 nucleotide sequences of the Egyptian rabbit and thirty-one sequences retrieved from GenBank of the reference samples of different haplogroups. The results of the phylogenetic analysis correlated to the reference mtDNA GenBank database showed that the five Egyptian rabbit breeds were grouped into haplotypes A, B and K. The results of the genetic diversity using mtDNA shed light on the importance of the local breed s genetic diversity information and revealed unique mtDNA haplotypes, which is an important finding for breeding strategies designed to conserve genetic variants and provide sustainable management.Ahmed, SSE.; Ali, NI.; Abdelhafez, MA.; Darwish, HR.; El-Keredy, A. (2022). Mitochondrial D-loop sequences and haplotypes diversity in Egyptian rabbit breeds. World Rabbit Science. 30(3):201-207. https://doi.org/10.4995/wrs.2022.1723520120730

Fluorescence microscope (Cyscope®) for malaria diagnosis in pregnant women in Medani Hospital, Sudan

<p>Abstract</p> <p>Background</p> <p>Accuracy of diagnosis is the core for malaria control. Although microscopy is the gold standard in malaria diagnosis, its reliability is largely dependent on user skill. We compared performance of Cyscope^®fluorescence microscope with the Giemsa stained light microscopy for the diagnosis of malaria among pregnant women at Medani Hospital in Central Sudan. The area is characterized by unstable malaria transmission.</p> <p>Methods</p> <p>Socio-demographic characteristics and obstetrics history were gathered using pre-tested questionnaires. Blood samples were collected from febrile pregnant women who were referred as malaria case following initial diagnosis by general microscopist.</p> <p>Results</p> <p>During the study period 128 febrile pregnant women presented at the hospital. Among them, <it>Plasmodium falciparum </it>malaria was detected in 82 (64.1%) and 80 (62.5%) by the Giemsa-stained light microscopy and the Cyscope^®fluorescence microscope, respectively. The sensitivity of the Cyscope^®fluorescence microscope was 97.6% (95% CI: 92.2%-99.6%). Out of 46 which were negative by Giemsa-stained light microscopy, 5 were positive by the Cyscope^®fluorescence microscope. This is translated in specificity of 89.1% (95% CI: 77.5%-95.9%). The positive and negative predictive value of Cyscope^®fluorescence microscope was 94.1% (95% CI: 87.4% -97.8%) and 95.3% (95% CI: 85.4% - 99.2%), respectively.</p> <p>Conclusion</p> <p>This study has shown that Cyscope^®fluorescence microscope is a reliable diagnostic, sensitive and specific in diagnosing <it>P. falciparum </it>malaria among pregnant women in this setting. Further studies are needed to determine effectiveness in diagnosing other <it>Plasmodium </it>species and to compare it with other diagnostic tools e.g. rapid diagnostic tests and PCR.</p

Testing the sensitivity and specificity of the fluorescence microscope (Cyscope®) for malaria diagnosis

<p>Abstract</p> <p>Background</p> <p>Early diagnosis and treatment of malaria are necessary components in the control of malaria. The gold standard light microscopy technique has high sensitivity, but is a relatively time-consuming procedure especially during epidemics and in areas of high endemicity. This study attempted to test the sensitivity and specificity of a new diagnostic tool - the Cyscope^®fluorescence microscope, which is based on the use of Plasmodium nucleic acid-specific fluorescent dyes to facilitate detection of the parasites even in low parasitaemia conditions due to the contrast with the background.</p> <p>Methods</p> <p>In this study, 293 febrile patients above the age of 18 years attending the malaria treatment centre in Sinnar State (Sudan) were interviewed using a structured questionnaire. Finger-prick blood samples were also collected from the participants to be tested for malaria using the hospital's microscope, the reference laboratory microscope, as well as the Cyscope^®microscope. The results of the investigations were then used to calculate the sensitivity, specificity, and positive and negative predictive values of the Cyscope^®microscope in reference to gold standard light microscopy.</p> <p>Results</p> <p>The sensitivity was found to be 98.2% (95% CI: 90.6%-100%); specificity = 98.3% (95% CI: 95.7% - 99.5%); positive predictive value = 93.3% (95% CI: 83.8% - 98.2%); and negative predictive value = 99.6% (95% CI: 97.6% - 100%).</p> <p>Conclusions</p> <p>In conclusion, the Cyscope^®microscope was found to be sensitive, specific and provide rapid, reliable results in a matter of less than 10 minutes. The Cyscope^®microscope should be considered as a viable, cheaper and time-saving option for malaria diagnosis, especially in areas where <it>Plasmodium falciparum </it>is the predominant parasite.</p

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

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

Burnout among surgeons before and during the SARS-CoV-2 pandemic: an international survey

Background: SARS-CoV-2 pandemic has had many significant impacts within the surgical realm, and surgeons have been obligated to reconsider almost every aspect of daily clinical practice. Methods: This is a cross-sectional study reported in compliance with the CHERRIES guidelines and conducted through an online platform from June 14th to July 15th, 2020. The primary outcome was the burden of burnout during the pandemic indicated by the validated Shirom-Melamed Burnout Measure. Results: Nine hundred fifty-four surgeons completed the survey. The median length of practice was 10&nbsp;years; 78.2% included were male with a median age of 37&nbsp;years old, 39.5% were consultants, 68.9% were general surgeons, and 55.7% were affiliated with an academic institution. Overall, there was a significant increase in the mean burnout score during the pandemic; longer years of practice and older age were significantly associated with less burnout. There were significant reductions in the median number of outpatient visits, operated cases, on-call hours, emergency visits, and research work, so, 48.2% of respondents felt that the training resources were insufficient. The majority (81.3%) of respondents reported that their hospitals were included in the management of COVID-19, 66.5% felt their roles had been minimized; 41% were asked to assist in non-surgical medical practices, and 37.6% of respondents were included in COVID-19 management. Conclusions: There was a significant burnout among trainees. Almost all aspects of clinical and research activities were affected with a significant reduction in the volume of research, outpatient clinic visits, surgical procedures, on-call hours, and emergency cases hindering the training. Trial registration: The study was registered on clicaltrials.gov "NCT04433286" on 16/06/2020