Comparison of qPCR and metagenomic sequencing methods for quantifying antibiotic resistance genes in wastewater

Surveillance methods of circulating antibiotic resistance genes (ARGs) are of utmost importance in order to tackle what has been described as one of the greatest threats to humanity in the 21st century. In order to be effective, these methods have to be accurate, quickly deployable, and scalable. In this study, we compare metagenomic shotgun sequencing (TruSeq DNA sequencing) of wastewater samples with a state-of-the-art PCR-based method (Resistomap HT-qPCR) on four wastewater samples that were taken from hospital, industrial, urban and rural areas. ARGs that confer resistance to 11 antibiotic classes have been identified in these wastewater samples using both methods, with the most abundant observed classes of ARGs conferring resistance to aminoglycoside, multidrug-resistance (MDR), macrolide-lincosamide-streptogramin B (MLSB), tetracycline and beta-lactams. In comparing the methods, we observed a strong correlation of relative abundance of ARGs obtained by the two tested methods for the majority of antibiotic classes. Finally, we investigated the source of discrepancies in the results obtained by the two methods. This analysis revealed that false negatives were more likely to occur in qPCR due to mutated primer target sites, whereas ARGs with incomplete or low coverage were not detected by the sequencing method due to the parameters set in the bioinformatics pipeline. Indeed, despite the good correlation between the methods, each has its advantages and disadvantages which are also discussed here. By using both methods together, a more robust ARG surveillance program can be established. Overall, the work described here can aid wastewater treatment plants that plan on implementing an ARG surveillance program.

Long-term study on wastewater SARS-CoV-2 surveillance across United Arab Emirates

Wastewater-based epidemiology (WBE) demonstrates an efficient tool to monitor and predict SARS-CoV-2 community distribution. Many countries across the world have adopted the technique, however, most of these studies were conducted for a short duration with a limited sampling size. In this study, long-term reliability and quantification of wastewater SARS-CoV-2 surveillance is reported via analyzing 16,858 samples collected from 453 different locations across the United Arab Emirates (UAE) from May 2020 to June 2022. The collected composite samples were first incubated at 60 °C followed by filtration, concentration, and then RNA extraction using commercially available kits. The extracted RNA was then analyzed by one-step RT-qPCR and RT-ddPCR, and the data was compared to the reported clinical cases. The average positivity rate in the wastewater samples was found to be 60.61 % (8.41-96.77 %), however, the positivity rate obtained from the RT-ddPCR was significantly higher than the RT-qPCR suggesting higher sensitivity of RT-ddPCR. Time-lagged correlation analysis indicated an increase in positive cases in the wastewater samples when the clinical positive cases declined suggesting that wastewater data are highly affected by the unreported asymptomatic, pre-symptomatic and recovering individuals. The weekly SARS-CoV-2 viral count in the wastewater samples are positively correlated with the diagnosed new clinical cases throughout the studied period and the studied locations. Viral count in wastewater peaked approximately one to two weeks prior to the peaks appearing in active clinical cases indicating that wastewater viral concentrations are effective in predicting clinical cases. Overall, this study further confirms the long-term sensitivity and robust approach of WBE to detect trends in SARS-CoV-2 spread and helps contribute to pandemic management.

Analysis of SARS-CoV-2 viral loads in stool samples and nasopharyngeal swabs from COVID-19 patients in the United Arab Emirates

Coronavirus disease 2019 (COVID-19) was first identified in respiratory samples and was found to commonly cause cough and pneumonia. However, non-respiratory symptoms including gastrointestinal disorders are also present and a big proportion of patients test positive for the virus in stools for a prolonged period. In this cross-sectional study, we investigated viral load trends in stools and nasopharyngeal swabs and their correlation with multiple demographic and clinical factors. The study included 211 laboratory-confirmed cases suffering from a mild form of the disease and completing their isolation period at a non-hospital center in the United Arab Emirates. Demographic and clinical information was collected by standardized questionnaire and from the medical records of the patient. Of the 211 participants, 25% tested negative in both sample types at the time of this study and 53% of the remaining patients had detectable viral RNA in their stools. A positive fecal viral test was associated with male gender, diarrhea as a symptom, and hospitalization during infection. A positive correlation was also observed between a delayed onset of symptoms and a positive stool test. Viral load in stools positively correlated with, being overweight, exercising, taking antibiotics in the last 3 months and blood type O. The viral load in nasopharyngeal swabs, on the other hand, was higher for blood type A, and rhesus positive (Rh factor). Regression analysis showed no correlation between the viral loads measured in stool and nasopharyngeal samples in any given patient. The results of this work highlight the factors associated with a higher viral count in each sample. It also shows the importance of stool sample analysis for the follow-up and diagnosis of recovering COVID-19 patients.

In vitro α-glucosidase inhibitory activity of Tamarix nilotica shoot extracts and fractions

α-glucosidase inhibitors represent an important class of type 2 antidiabetic drugs and they act by lowering postprandial hyperglycemia. Today, only three synthetic inhibitors exist on the market, and there is a need for novel, natural and more efficient molecules exhibiting this activity. In this study, we investigated the ability of Tamarix nilotica ethanolic and aqueous shoot extracts, as well as methanolic fractions prepared from aqueous crude extracts to inhibit α-glucosidase. Both, 50% ethanol and aqueous extracts inhibited α-glucosidase in a concentration-dependent manner, with IC₅₀ values of 12.5 μg/mL and 24.8 μg/mL, respectively. Importantly, α-glucosidase inhibitory activity observed in the T. nilotica crude extracts was considerably higher than pure acarbose (IC₅₀ = 151.1 μg/mL), the most highly prescribed α-glucosidase inhibitor on the market. When T. nilotica crude extracts were fractionated using methanol, enhanced α-glucosidase inhibitory activity was observed in general, with the highest observed α-glucosidase inhibitory activity in the 30% methanol fraction (IC₅₀ = 5.21 μg/mL). Kinetic studies further revealed a competitive reversible mechanism of inhibition by the plant extract. The phytochemical profiles of 50% ethanol extracts, aqueous extracts, and the methanolic fractions were investigated and compared using a metabolomics approach. Statistical analysis revealed significant differences in the contents of the crude extracts and fractions and potentially identified the molecules that were most responsible for these observed variations. Higher α-glucosidase inhibitory activity was associated with an enrichment of terpenoids, fatty acids, and flavonoids. Among the identified molecules, active compounds with known α-glucosidase inhibitory activity were detected, including unsaturated fatty acids, triterpenoids, and flavonoid glycosides. These results put forward T. nilotica as a therapeutic plant for type 2 diabetes and a source of α-glucosidase inhibitors.

A Putative Lignin Copper Oxidase from Trichoderma reesei

The ability of Trichoderma reesei, a fungus widely used for the commercial production of hemicellulases and cellulases, to grow and modify technical soda lignin was investigated. By quantifying fungal genomic DNA, T. reesei showed growth and sporulation in solid and liquid cultures containing lignin alone. The analysis of released soluble lignin and residual insoluble lignin was indicative of enzymatic oxidative conversion of phenolic lignin side chains and the modification of lignin structure by cleaving the β-O-4 linkages. The results also showed that polymerization reactions were taking place. A proteomic analysis conducted to investigate secreted proteins at days 3, 7, and 14 of growth revealed the presence of five auxiliary activity (AA) enzymes in the secretome: AA6, AA9, two AA3 enzymes), and the only copper radical oxidase encoded in the genome of T. reesei. This enzyme was heterologously produced and characterized, and its activity on lignin-derived molecules was investigated. Phylogenetic characterization demonstrated that this enzyme belonged to the AA5_1 family, which includes characterized glyoxal oxidases. However, the enzyme displayed overlapping physicochemical and catalytic properties across the AA5 family. The enzyme was remarkably stable at high pH and oxidized both, alcohols and aldehydes with preference to the alcohol group. It was also active on lignin-derived phenolic molecules as well as simple carbohydrates. HPSEC and LC-MS analyses on the reactions of the produced protein on lignin dimers (SS ββ, SS βO4 and GG β5) uncovered the polymerizing activity of this enzyme, which was accordingly named lignin copper oxidase (TrLOx). Polymers of up 10 units were formed by hydroxy group oxidation and radical formation. The activations of lignin molecules by TrLOx along with the co-secretion of this enzyme with reductases and FAD flavoproteins oxidoreductases during growth on lignin suggest a synergistic mechanism for lignin breakdown.

Screening New Xylanase Biocatalysts from the Mangrove Soil Diversity

Mangrove sediments from New Caledonia were screened for xylanase sequences. One enzyme was selected and characterized both biochemically and for its industrial potential. Using a specific cDNA amplification method coupled with a MiSeq sequencing approach, the diversity of expressed genes encoding GH11 xylanases was investigated beneath Avicenia marina and Rhizophora stylosa trees during the wet and dry seasons and at two different sediment depths. GH11 xylanase diversity varied more according to tree species and season, than with respect to depth. One complete cDNA was selected (OFU29) and expressed in Pichia pastoris. The corresponding enzyme (called Xyn11-29) was biochemically characterized, revealing an optimal activity at 40–50 °C and at a pH of 5.5. Xyn11-29 was stable for 48 h at 35 °C, with a half-life of 1 h at 40 °C and in the pH range of 5.5–6. Xyn11-29 exhibited a high hydrolysis capacity on destarched wheat bran, with 40% and 16% of xylose and arabinose released after 24 h hydrolysis. Its activity on wheat straw was lower, with a release of 2.8% and 6.9% of xylose and arabinose, respectively. As the protein was isolated from mangrove sediments, the effect of sea salt on its activity was studied and discussed.

[Attitude of psychiatrists and psychiatry residents in Lebanon towards restraint and informed consent]

OBJECTIVES

Psychiatry differs from the rest of medical specialties by the unique character of its pathologies, which makes ethical reflection difficult, including the collection of informed consent and the use of restraint and the seclusion-room. This reflection can be affected by subjectivity and a variety of influences, hence the interest of studying the attitude of psychiatrists and residents in psychiatry in Lebanon with regard to restraint and informed consent.

METHODS

We collected data using an anonymous questionnaire that we sent as a Google form to Lebanese psychiatrists and psychiatry residents by email and phone messages. The descriptive analysis was done using Microsoft Excel software, and the analytical analysis was done using the SPSS software and the following statistical tests: independent-sample test and the Mann Whitney U test.

RESULTS

Forty people responded, including 19 men and 21 women (16 psychiatric interns, 15 university psychiatrists and 9 non-university psychiatrists). Concerning the questions related to the use of restraint, 70% did not find that it is being commonly used in hospital practice. However, 92.5% would use it to counter the patient's dangerousness and 60% to help deliver treatment. 57.5% did not find the repeated usage of restraint as a dehumanization of care, but the majority (70%) agreed with the need for temporal limitation of any form of restraint. As for the ability to consent, 90% considered a patient in a psychotic state as unfit to consent.

CONCLUSIONS

Restraint is considered uncommon by psychiatrists and psychiatric residents in Lebanon and must remain an option of last resort with efforts being made upstream in order to avoid situations where the use of restraint becomes mandatory. Post critical thinking is paramount, and restraint should never respond to a lack of manpower or a security goal. Informed consent is one of the most important guarantors of the principle of autonomy, and must be sought in each patient, individually. Finally, no significant difference was found between the subgroups, which would therefore become a single population. Ethical reflection would therefore be directly linked to the population. Mental illnesses are becoming more common and an important source of morbidity worldwide. It is our role to ensure the dignity of the mentally ill. The introduction of the Psychiatric Nurse Diploma, an increase in the relational approach to the training of psychiatrists in Lebanon, and an increase in the number of health care teams may help to maximize the ability of capacity.

[Brachial Plexus: Dissection At The Laboratory Of Anatomy Of Bamako]

INTRODUCTION

The brachial plexus consists of the ventral twigs of the last four cervical nerves and the first thoracic nerve. It ensures the motor and sensitive innervations of the thoracic limb.

AIM

Our goal was to describe the brachial plexus of the cervical region to the middle third of the arm.

METHODOLOGY

We conducted a prospective study at the anatomy Laboratory of the Faculty of Medicine and Dentistry in Bamako from September 2016 to October 2017. We dissected the brachial plexus (PB) of 13 fresh adult corpses on both sides. The inclusion criteria were: Fresh adult corpses with cervical regions and brachial without scarring. The injected or scar-carrying corpses were not included in the cervical and brachial regions.

RESULTS

Twenty-six brachial plexus of which 18 bp in men and 8 bp in women were dissected. The average age of the subjects was 42 years (extreme: 18 and 70 years). We noted nerve block variations in 3.8%, fascicular in 3.8% and late terminal in 73.1%. The involvement of the anterior branch of the fourth spinal nerve (C4) was found in 46.2%.

CONCLUSION

The brachial plexus is the seat of many anatomical variations whose knowledge is indispensable to treat its lesions.

Work-Related musculoskeletal pain among lebanese dentists: An epidemiological study

INTRODUCTION

The aim of this study was to evaluate the prevalence of musculoskeletal disorders and identify their associated factors among a group of Lebanese dentists.

MATERIALS AND METHODS

A total of 314 Lebanese, dentists completed an anonymous questionnaire that focused on occupational health problems. This study was approved by the ethics committee of Saint-Joseph University of Beirut, Lebanon. The statistical analyses were performed using SPSS for windows. The alpha error was set to 0.05.

RESULTS

The mean age of the participants was 39.2 (±11.66) years. The results showed that 61.5% of the surveyed dentists complained of spinal pain: 31.6% of cervical pain, 22.3% of lumbar pain and 13.0% of dorsal pain. Moreover, the pain was continuous in 20.7% and, occasional in 65.8%. Our statistics showed that 7.6% had a problem with the carpal tunnel. A total of 22.3% suffered from tendinitis and 9.2% from arthritis of shoulder, elbow, wrist and hand. The frequency of headaches was 30.6%. Concerning sports activity, 49.7% practiced it occasionally and 3.6% did so frequently.

CONCLUSIONS

The occurrence of musculoskeletal pain in the upper extremities is a serious concern that affects Lebanese dentists. Most of them often complained of tendinitis and headaches because they do not practice sports; thus, encouraging them to practice sports may reduce or solve such health problems. Issuing brochures that include exercises to perform and hiring trained assistants could help reduce the risk of musculoskeletal disorders. Finally, these occupational health problems should be highlighted at all clinical and research symposia to increase awareness.

[Frequency of glucose-6-phosphate dehydrogenase deficiency (A-376/202) in three Malian ethnic groups]

Erythrocyte G6PD deficiency is the most common worldwide enzymopathy. The aim of this study was to determine erythrocyte G6PD deficiency in 3 ethnic groups of Mali and to investigate whether erythrocyte G6PD deficiency was associated to the observed protection against malaria seen in Fulani ethnic group. The study was conducted in two different areas of Mali: in the Sahel region of Mopti where Fulani and Dogon live as sympatric ethnic groups and in the Sudanese savannah area where lives mostly the Malinke ethnic group. The study was conducted in 2007 in Koro and in 2008 in Naguilabougou. It included a total 90 Dogon, 42 Fulani and 80 Malinke ethnic groups. Malaria was diagnosed using microscopic examination after Giemsa-staining of thick and thin blood smear. G6PD deficiency (A-(376/202)) samples were identified using RFLP (Restriction Fragment Length Polymorphism) assay and analysis of PCR-amplified DNA amplicon. G6PD deficiency (A-(376/202)) rate was 11.1%, 2.4%, and 13.3% in Dogon, Fulani, and Malinke ethnic group respectively. Heterozygous state for G6PD (A-(376/202)) was found in 7.8% in Dogon; 2.4% in Fulani and 9.3% in Malinke ethnic groups while hemizygous state was found at the frequency of 2.2% in Dogon and 4% in Malinke. No homozygous state was found in our study population.We conclude that G6PD deficiency is not differing significantly between the three ethnic groups, Fulani, Dogon and Malinke.

[Place of malaria among febrile illnesses in two ethnic tribes living in sympatry in Mali from 1998 to 2008]

In Africa, malaria is responsible for 25-40% of all outpatient visits and 20-50% of all hospitalizations. In malaria-endemic areas, individuals do not behave the same toward the outcome of clinical malaria. The aim of this study is to determine the prevalence of malaria in the locality among the different ethnic groups, evaluate the place of malaria among febrile illnesses, and assess the relationship between fever and parasite density of Plasmodium falciparum. Studies on susceptibility to malaria between the Fulani and Dogon groups in Mali were conducted in Mantéourou and the surrounding villages from 1998 to 2008. We carried out six cross-sectional studies during the malaria transmission and longitudinal surveys (July to December depending on the year) during the 10-year duration. In longitudinal studies, clinical data on malaria and other diseases frequently observed in the population were recorded. It appears from this work that malaria is the leading cause of febrile syndromes. We observed a significant reduction in malaria morbidity in the study population from 1998 to 2008. The pyrogenic threshold of parasitaemia was 1,000 parasites/mm(3) of blood in the Dogon and 5,000 parasites/mm(3) of blood in the Fulani.We have also found that high parasitical densities were not always associated with fever. Malaria morbidity was higher among the Dogon than in Fulani. The immunogenetic factors might account for this difference in susceptibility to malaria between Fulani and Dogon in the area under study. With regard to this study, it is important to take into account the ethnic origin of subjects when interpreting data of clinical and malarial vaccine trials.

CD36 c.1264 T>G null mutation impairs acquisition of IgG antibodies to Plasmodium falciparum MSP1₁₉ antigen and is associated with higher malaria incidences in Tanzanian children

Polymorphisms in genes that encode crucial signalling molecules have been proposed as factors that influence susceptibility to, and outcome of malaria. We studied the role of a mutation, c.1264 T>G, that causes CD36 deficiency on IgG responses to MSP-1₁₉ antigen and malaria incidence. Children were genotyped for the c.1264 T>G mutation at the beginning of the study using PCR-RFLP. IgG levels [optical density (OD) readings] and per cent seropositivity to MSP-1₁₉ were determined at baseline by ELISA. Children were followed for 12 months for acquisition of anti-MSP-1₁₉ IgG antibody and malaria incidence. We observed a significant increase in the production of anti-MSP-1₁₉ IgG antibody in normal and heterozygous children during the 12 months of follow-up, but not in homozygous mutants. Normal children had a significantly lower malaria incidence rate compared to other genotypes (χ² = 115.59; P < 0.01). We conclude that the presence of the c.1264 T>G mutation that leads to CD36 deficiency is closely associated with reduced IgG production and higher malaria incidence. It is most likely that deficiency of CD36 which is known to modulate dendritic cell function suppresses the production of protective IgG antibodies directed to Plasmodium falciparum MSP-1₁₉ antigen, which predisposes to the acquisition of clinical malaria in children.

[Ortner's syndrome and giant-cell vasculitis]

INTRODUCTION

Ortner's syndrome was first described as a left laryngeal nerve palsy caused by a dilated left atrium in mitral stenosis. Aortic aneurysm is another well-documented etiology.

CASE RECORD

We report the case of a 90 year-old woman with temporal arteritis with recent onset hoarseness, and simultaneous discovery of aortic arch aneurysm and left vocal cord palsy.

DISCUSSION

The occurrence of hoarseness and aortic aneurysm in Giant-cell vasculitis is discussed. We suggest to consider Horton's disease (GCA) as a possible etiology of Ortner's cardio-vocal syndrome.

Spleen enlargement and genetic diversity of Plasmodium falciparum infection in two ethnic groups with different malaria susceptibility in Mali, West Africa

The high resistance to malaria in the nomadic Fulani population needs further understanding. The ability to cope with multiclonal Plasmodium falciparum infections was assessed in a cross-sectional survey in the Fulani and the Dogon, their sympatric ethnic group in Mali. The Fulani had lower parasite prevalence and densities and more prominent spleen enlargement. Spleen rates in children aged 2-9 years were 75% in the Fulani and 44% in the Dogon (P<0.001). There was no difference in number of P. falciparum genotypes, defined by merozoite surface protein 2 polymorphism, with mean values of 2.25 and 2.11 (P=0.503) in the Dogon and Fulani, respectively. Spleen rate increased with parasite prevalence, density and number of co-infecting clones in asymptomatic Dogon. Moreover, splenomegaly was increased in individuals with clinical malaria in the Dogon, odds ratio 3.67 (95% CI 1.65-8.15, P=0.003), but not found in the Fulani, 1.36 (95% CI 0.53-3.48, P=0.633). The more susceptible Dogon population thus appear to respond with pronounced spleen enlargement to asymptomatic multiclonal infections and acute disease whereas the Fulani have generally enlarged spleens already functional for protection. The results emphasize the importance of spleen function in protective immunity to the polymorphic malaria parasite.

Immunotherapy of tumors with autologous tumor-derived heat shock protein preparations

Immunotherapy of mice with preexisting cancers with heat shock protein preparations derived from autologous cancer resulted in retarded progression of the primary cancer, a reduced metastatic load, and prolongation of life-span. Treatment with heat shock protein preparations derived from cancers other than the autologous cancer did not provide significant protection. Spontaneous cancers (lung cancer and melanoma), chemically induced cancers (fibrosarcoma and colon carcinoma), and an ultraviolet radiation-induced spindle cell carcinoma were tested, and the results support the efficacy of autologous cancer-derived heat shock protein-peptide complexes in immunotherapy of cancers without the need to identify specific tumor antigenic epitopes.