ELIXIR and Toxicology: a community in development

Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics and computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology has strong links with other fields such as biology, chemistry, pharmacology and medicine. With the rise of synthetic and new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment for existing chemicals, early predictive evaluations are becoming of utmost importance to both scientific and regulatory purposes. ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. To coordinate the linkage of various life science efforts around modern predictive toxicology, the establishment of a new ELIXIR Community is seen as instrumental. In the past few years, joint efforts, building on incidental overlap, have been piloted in the context of ELIXIR. For example, the EU-ToxRisk, diXa, HeCaToS, transQST, and the nanotoxicology community have worked with the ELIXIR TeSS, Bioschemas, and Compute Platforms and activities. In 2018, a core group of interested parties wrote a proposal, outlining a sketch of what this new ELIXIR Toxicology Community would look like. A recent workshop (held September 30th to October 1st, 2020) extended this into an ELIXIR Toxicology roadmap and a shortlist of limited investment-high gain collaborations to give body to this new community. This Whitepaper outlines the results of these efforts and defines our vision of the ELIXIR Toxicology Community and how it complements other ELIXIR activities.

Performance of Mali's biosafety level 3 laboratory in the external quality assessment in preparedness of laboratory accreditation and support to clinical trials

Background:

The external quality assessment (EQA) or external quality control is an evaluation conducted by a certified external organization to inquire about the quality of the results provided by a laboratory. The primary role of EQA is to verify the accuracy of laboratory results. This is essential in research because research data should be published in international peer-reviewed journals, and laboratory results must be repeatable. In 2007, the University Clinical Research Center (UCRC’s) biosafety level 3 (BSL-3) laboratory joined the EQA program with the College of American Pathologists in acid-fast staining and culture and identification of mycobacteria as per laboratory accreditation preparedness. Thus, after 11 years of participation, the goal of our study was to evaluate the performance of our laboratory during the different interlaboratory surveys.

Methods:

We conducted a descriptive retrospective study to evaluate the results of UCRC mycobacteriology laboratory from surveys conducted during 2007 and 2017.

Results:

Of the 22 evaluations, the laboratory had satisfactory (100% of concordance results) in 18 (81.8%) and good (80% of concordance results) in 4 (18.2%). Overall, the laboratory was above the commended/accepted limits of 75%.

Conclusion:

So far, UCRC’s BSL-3 performed well during the first 11 years of survey participation, and efforts should be deployed to maintain this high quality in the preparedness for laboratory accreditation and support to clinical trials.

Diabetes Mellitus among new tuberculosis patients in Bamako, Mali

Introduction

Diabetes Mellitus (DM) increases worldwide, mostly in low- and middle-income countries. In Mali, the prevalence in the adult population is estimated at 1.8%, but tuberculosis (TB) patients are not systematically screened. The goal of our study was to determine the prevalence of DM among newly diagnosed TB patients.

Methods

We conducted a cross sectional study and a pilot prospective cohort study in four health centers in Bamako. All patients underwent fasting capillary-blood glucose (FCBG) test at Day 0, and repeated after one-week of TB treatment. Venous FBG test was performed for discrepancies between the two FCBG results. Thereafter, FCBG was performed for pilot study at month-2 (M2) and M5 of TB treatment.

Results

Two hundred and one patients were enrolled in this study. Impaired fasting blood glucose was identified in 17 (8.5%), of whom 11 (5.5%) had DM (VFBG >7 mmol/L). Among patients with DM, seven (63.6%) had successful TB treatment outcome, versus 142 (74.7%) of those without DM (p = 0.64), and (OR: 1.69, 95%CI 0.47–6.02).

Conclusion

The prevalence of DM among TB patients in Bamako exceeds that of the general population and screening at TB diagnosis suffices to identify those with DM. Systematic screening of both diseases will allow better treatment.

Establishing Reference Ranges of Hematological Parameters from Malian Healthy Adults

INTRODUCTION

Measurement of immuno-hematological parameters has been historically helpful in the diagnosis and treatment monitoring of many infectious diseases and cancers. However, these parameters have not yet been established in many developing countries where patient care strongly relies on such low-cost tests. This study describes the immuno-hematological parameter ranges for Malian healthy adults.

METHODS

A cross sectional study was conducted from August 2004 to May 2013. We included 213 healthy volunteers (173 male and 40 female), aged between 18-59 years. Median, 2.5 and 97.5 percentile ranges for each immuno-hematological parameter are presented.

RESULTS

In our study population, the hematological parameters' ranges were mostly different to the universal established ranges. We found in our population a Median white blood cell (WBC) count of 5200 cells/μL [3237.5-11900], Red Blood Cell (RBC) count of 4.94 10^6 [3.56-6.17], hemoglobin (Hb) of 14.2 g/dL [12.2-17.38], platelet count (Plt) of 275 10^3/μL [145.4-614.4], lymphocytes 2050/μL [1200-3800], neutrophils 2200/μL [1040-6220]; monocytes 200/μL [100-660]; eosinophils 131/μL [0-1026]; CD4 902 cells/μL [444-1669] and CD8 485 cells/μL [0-1272]. We found significant gender differences in RBC, Hb level and MPV. However, RBC and Hb were higher in males median values compared to females (median values) (p<0.001), whereas the Mean platelet volume lower values (MPV) in males than females (P<0.047). The hemoglobin level for some West African countries (Mali, Burkina Faso, Togo, and Nigeria) ranged from 13.5 to 15.1 g/dL for males and 12 to 13 g/dL for females. However in East and Southern Africa, the values were anywhere from 14.1 to 16.1 for males and 11.2 to 14.4 for females.

CONCLUSION

Our data may help physicians to better define hematological abnormalities in patients. They may also be used to define new "normal hematological values" in Malian population or in the whole West African population.

Performance of microscopic observation drug susceptibility for the rapid diagnosis of tuberculosis and detection of drug resistance in Bamako, Mali

OBJECTIVES

In Mali early detection and treatment of multidrug-resistant tuberculosis (MDR-TB) are still challenging due to the cost, time and/or complexity associated with regular tests. Microscopic Observation Drug Susceptibility (MODS) is a low-cost assay validated by WHO in 2010. It is a liquid-culture-based assay to detect the 'cording' characteristic of Mycobacterium tuberculosis complex and to assess susceptibility to both isoniazid and rifampicin defining multidrug-resistant tuberculosis (MDR-TB). In this study we aimed to evaluate the performance of MODS as diagnostic tool compared with a validated method-Mycobacteria Growth Indicator Tube/Antimicrobial Susceptibility Testing/Streptomycin, Isoniazid, Rifampicin and Ethambutol (MGIT/AST/SIRE).

METHODS AND RESULTS

Between January 2010 and October 2015 we included 98 patients with suspected TB in an observational cohort study. The sensitivity and specificity of MODS assay for detecting TB were respectively 94.12% and 85.71% compared with the reference MGIT/7H11 culture, with a Cohen κ coefficient of 0.78 (95% CI 0.517-1.043). The median time to culture positivity for MODS assay and MGIT (plus interquartile range, IQR) was respectively 8 days (IQR 5-11) and 6 days (IQR 5-6). In detecting patients with MDR-TB, the sensitivity and specificity of MODS assay were respectively 100% and 95.92%. The positive predictive value and negative predictive value were, respectively, 66.7% and 100%. The median turnaround times for obtaining MDR-TB results using MODS assay and MGIT/AST/SIRE was respectively 9 days and 35 days. Hence, the MODS assay rapidly identifies MDR-TB in Mali compared with the MGIT/AST/SIRE.

CONCLUSION

As an easy, simple, fast and affordable method, the MODS assay could significantly improve the management of TB.

Tuberculosis drug resistance in Bamako, Mali, from 2006 to 2014

Background

Although Drug resistance tuberculosis is not a new phenomenon, Mali remains one of the “blank” countries without systematic data.

Methods

Between 2006 and 2014, we enrolled pulmonary TB patients from local TB diagnostics centers and a university referral hospital in several observational cohort studies. These consecutive patients had first line drug susceptibility testing (DST) performed on their isolates. A subset of MDR was subsequently tested for second line drug resistance.

Results

A total of 1186 mycobacterial cultures were performed on samples from 522 patients, including 1105 sputa and 81 blood samples, yielding one or more Mycobacterium tuberculosis complex (Mtbc) positive cultures for 343 patients. Phenotypic DST was performed on 337 (98.3%) unique Mtbc isolates, of which 127 (37.7%) were resistant to at least one drug, including 75 (22.3%) with multidrug resistance (MDR). The overall prevalence of MDR-TB was 3.4% among new patients and 66.3% among retreatment patients. Second line DST was available for 38 (50.7%) of MDR patients and seven (18.4%) had resistance to either fluoroquinolones or second-line injectable drugs.

Conclusion

The drug resistance levels, including MDR, found in this study are relatively high, likely related to the selected referral population. While worrisome, the numbers remained stable over the study period. These findings prompt a nationwide drug resistance survey, as well as continuous surveillance of all retreatment patients, which will provide more accurate results on countrywide drug resistance rates and ensure that MDR patients access appropriate second line treatment.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-016-2060-7) contains supplementary material, which is available to authorized users.

Molecular strain typing of Mycobacterium tuberculosis complex in Bamako, Mali

OBJECTIVE

To identify strains of Mycobacterium tuberculosis complex (MTC) circulating in Bamako and to examine the relationship between the strains and their drug susceptibility profiles.

METHODS

Between 2006 and 2010, we conducted a cross-sectional study using spoligotyping to identify strains of MTC recovered from 126 tuberculosis (TB) patients under treatment in Bamako, Mali.

RESULT

Three members of the MTC were isolated: M. tuberculosis (71.4%), M. africanum (27.8%) and M. bovis (0.8%). Of these, three strains were found to be the most prevalent: M. tuberculosis T1 (MTB T1; 38.9%), M. africanum F2 (MAF2; 26.2%) and M. tuberculosis Latin American and Mediterranean 10 (MTB LAM 10; 10.3%). MAF2 and MTB LAM 10 strains have a lower risk of multidrug resistance (MDR) than MTB T1 (respectively OR 0.1, 95%CI 0.03-0.4 and OR 0.1, 95%CI 0.01-0.8). Age ≥ 32 years (OR 1.4, 95%CI 0.4-3.9), negative human immunodeficiency virus status (OR 0.4, 95%CI 0.1-2.5) and male sex (OR 4, 95%CI 0.9-16.5) were not associated with MDR. The prevalence of MDR among treatment and retreatment failure patients was respectively 25% and 81.8% compared to new patients (2.9%).

CONCLUSION

This study indicates a low level of primary drug resistance in Bamako, affirms the importance of using correct drug regimens, and suggests that the MTB T1 strain may be associated with the development of resistance.

[External genital excision sequelae at the Yalgado Ouedraogo national central hospital: epidemiology and surgical treatment]

By a prospective study in one year time, the authors noticed that female genital mutilation complications were 7.3 per cent of external gynecologic consultations and most complications were overdraft between 15 and 24 years old (36 cases out of 49). The main consultation motives were dyspareunia and difficult sexual relationship. Surgery under local anesthetic was very efficient (more than 90% success) and cheaper than surgery under general anesthetic.

[Abdominal pregnancy and tubal pregnancy. Apropos of 1 case. An exceptional clinical event]

A case of non-progressive and earlier abdominal pregnancy, associated with an evolutionary tubal pregnancy is reported by the authors. This clinical situation is very rare, indeed, exceptional, because it concerns two successive and ectopic pregnancies. The poor obstetrical cover and the ineffectual supervision of the pregnancy explain in part these situations in our countries.

[Fetal weight gain curve for a cohort of 126 pregnant women at Ouagadougou, Burkino Faso]

We carried out a prospective study at Ouagadougou, from March 1 1997 to April 30 1998, in which we plotted curves of fetal weight gain, estimated by ultrasound biometry, with the aim of comparing our results to those of other authors and establishing a local chart. We established a growth curve from 936 fetal weights estimated during the follow up of 126 pregnant women. The mean age of the women included was 26 +/- 0,8 years and 52.4% were of the mean socioeconomic level. We identified significant differences between our weight gain curve and those of other authors. The factors involved in this difference are unclear but may be nutritive, ecological and ethnic in nature. Further work is required to produce local charts, to optimize the estimation of fetal weight.

[Maternal mortality in adolescents at the university hospital of Ouagadougu]

This retrospective study evaluates the adolescent mortality rate at the University Hospital of Ouagadougou in the year 1995. Twenty lethal cases were collected amongst 646 deliveries giving birth to 490 children. The in-hospital adolescent maternal mortality rate come to be 4081 for 100,000 living births (4.08%) and represented 16.3% of all maternal deaths occurring during the study period. The most frequent causes of death were related to clandestine abortion (30%) and chronic anemia due to malnutrition (30%). Pregnancy in an adolescent girl is a high-risk event that requires special care due to a precarious global health status.

[Intrapartum hemorrhages in the maternity ward of the Yalgado Ouédraogo University Hospital Center of Ouagadougou, Burkina Faso]

On 12,175 childbirth registered in 4 years, 200 cases of delivery haemorrhage have been observed giving a rate of 1.6% of these accumulated childbirth. 60 patients (30.5%) have been evacuated from region of the country. The main etiology were: placental retention (54.5%), uterine inertia (24.5%) and coagulation disorders (21%). Blood was not available for emergency transfusion of 72 patients (54.1%) 26 deplorable cases of death raised the rate of lethality by 13%. Instant research of risk factors on all parturients, recycling of all personal on elementary first aid and life saving, also an improvement of sanitary references will enable to lower incidences related to haemorrhage by delivery.

[Evaluation of the pre-introduction of contraception by means of subcutaneous levonorgestrel implants in Burkina Faso]

It is a prospective study based on the pre introduction evaluation of Norplant implants conducted from September 92 to September 93 in the city of Ouagadougou. 197 women were selected for the study. Based on unemployed women with an average age of 31 years old. The average parity was of 5.47% of patients were multiparas. A gain of weight of an average of 2.43 kg was observed. The main side effects observed was cycle disorders and headache. The continuing rate after 12 months was 96.5%. Conclusion from this study is that Norplant Implants are well tolerated and accepted by women.

[Adnexal torsion during pregnancy. Diagnostic and therapeutic problems in Burkina Faso]

The authors report a case of adnexal torsion during early pregnancy. Because of a late diagnosis they had to practise an unilateral adnexectomy with a conservative medical treatment of the pregnancy. They recommend an early surgical treatment, that will save the adnexa and permit a normal evolution of the pregnancy. In a young patient, the loss of an ovary may be a tragic event.

[The financial costs of health care: a follow-up survey of women having a high-risk delivery]

Our aim was to analyze the financial costs of health care for women in labor transferred to primary referral maternity units in childbirth at risk. Another aim was to consider the willingness of women and their husbands to financially save and support the increasing costs of health care. For 15 consecutive days, medical students interviewed all women transferred for a risky delivery in 12 of the 17 primary referral maternity units in Burkina Faso. The median cost for transferring the women and their necessary health care was approximately 30,500 CFA. The median cost for the kit of surgical supplies was 15,000 CFA; the costs of medicine and transportation fare for the woman and her husband were 14,000 CFA and 9,800 CFA, respectively. The median cost for the health care of the newborn was 2,400 CFA. When the decision for the transfer was made, the necessary money to pay for the expenses was available for only 40 out of 79 women. Women and their husbands were willing to save for health care either through existing community institutions such as groups of villagers and popular savings developments (69 women and men); or through annuity schemes to be created (33 women and men); or through banks (4 women and men). Four women and 6 men refused to contribute because of previous experiences of poor management of collective funds. The average savings were low and insufficient to cover the expected expenses for the transfer and care of the women. The savings were reserved for payment of the transportation fare for the women and their husbands to the referral units (21 women and 20 men), prescriptions (9 women and 5 men), the medical consultation (1 woman), and to provide for both (37 women and 39 men). The costs of health care are expensive. The poverty of the couple facing an urgent problem of life or death made them discover new options for investing in their available community associations such as groups of villagers and popular savings developments and other options such as annuity schemes. A policy directed towards the involvement of these populations could facilitate the transfer and treatment of women during their pregnancy.

Assembly of Na,K-ATPase alpha-subunit isoforms with Na,K-ATPase beta-subunit isoforms and H,K-ATPase beta-subunit

cDNA encoding an epitope tag was joined to cDNAs encoding the chicken Na,K-ATPase beta 1 and beta 2 and H,K-ATPase beta-subunits to allow recognition of these beta-subunits with the same monoclonal antibody during assembly assays. cDNAs encoding chicken Na,K-ATPase alpha 1, alpha 2, or alpha 3 and Na,K-ATPase beta 1 or beta 2 or H,K-ATPase beta-subunits were transiently coexpressed in mammalian cells. Subunit assembly was assayed by immune precipitation of alpha-isoforms with a monoclonal antibody to the epitope-tagged beta-subunits. Each of the chicken alpha-isoforms assembled with each of the Na,K-ATPase beta-subunits and the H,K-ATPase beta-subunit. Each of the epitope-tagged beta-subunits also assembled with a Na,K-ATPase/Ca-ATPase chimera that retained only 26 amino acids of the Na,K-ATPase alpha-subunit, demonstrating that all three beta-subunits recognize this same alpha-subunit assembly site.

[Semilunar dislocations. A report of 8 cases. (Orthopedic service-University Hospital Center of Treichville-Abidjan)]

The authors have underlined in a study made on 8 observations that the lunate dislocation is scar. All their patients were men under 40 years old. Industrial injury was the most dominant cause. Using WITVOET and ALLIEU's classification, they noticed a predominance of perilunar and posterior dislocations (7/8 cases). Perilunar anterior dislocations and isolated scaphoid carpal dislocation have not been encountered. The treatment which has been orthopaedic or surgical has given moderate results: Good results = 4; Average result = 1; Bad results = 2; Non seen to again = 1 The authors think that a precocious diagnosis and an orthopaedic treatment in the forms detected early and surgical treatment in ancient forms are the only guarantee of a good functional result avoiding dread diseases such as carpal instability, radiocarpal arthrosis.

Relation between the anion exchange protein in kidney medullary collecting duct cells and red cell band 3

A membrane protein that is immunochemically similar to the red cell anion exchange protein, band 3, has been identified on the basolateral face of the outer medullary collecting duct (MCD) cells in rabbit kidney. In freshly prepared separated rabbit MCD cells, M.L. Zeidel, P. Silva and J.L. Seifter (J. Clin. Invest. 77:1682-1688, 1986) found that C1-/HCO-3 exchange was inhibited by the stilbene anion exchange inhibitor, DIDS (4,4'-diisothiocyano-2,2'-disulfonic stilbene), with a K1 similar to that for the red cell. We have measured the binding affinities of a fluorescent stilbene inhibitor, DBDS (4,4'-dibenzamido-2,2'-disulfonic stilbene), to MCD cells in 28.5 mM citrate and have characterized both a high-affinity site (Ks1 = 93 +/- 24 nM) and a lower affinity site (Ks2 = 430 +/- 260 nM), which are closely similar to values for the red cell of 110 +/- 51 nM for the high-affinity site and 980 +/- 200 nM for the lower affinity site (A.S. Verkman, J.A. Dix & A.K. Solomon, J. Gen. Physiol. 81:421-449, 1983). When Cl- replaces citrate in the buffer, the two sites collapse into a single one with Ks1 = 1500 +/- 400 nM, similar to the single Ks1 = 1200 +/- 200 nM in the red cell (J.A. Dix, A.S. Verkman & A.K. Solomon, J. Membrane Biol. 89:211-223, 1986). The kinetics of DBDS binding to MCD cells at 0.25 microM-1 are characterized by a fast process, tau = 0.14 +/- 0.03 sec, similar to tau = 0.12 +/- 0.03 sec in the red cell. These similarities show that the physical chemical characteristics of stilbene inhibitor binding to MCD cell 'band 3' closely resemble those for red cell band 3, which suggests that the molecular structure is highly conserved.

Thiazide-induced hyponatremia

We have described a case of severe acute hyponatremia developing in a patient who had been taking thiazides for the previous eight months without having any electrolyte abnormalities. The onset of the electrolyte disturbance coincided with a physician-recommended hydration regimen, which we believe unmasked a drug-related impairment of water excretion. Withdrawal of thiazide therapy promptly resulted in water diuresis and rapid correction of the hyponatremia.