Use of light-emitting diode fluorescence microscopy to detect acid-fast bacilli in sputum as proficient alternative tool in the diagnosis of pulmonary tuberculosis in countries with limited resource settings.

Background: Despite recent advances in the development of more sensitive technologies for the diagnosis of tuberculosis (TB), in resource-limited settings, the diagnosis continues to rely on sputum smear microscopy. This is because smear microscopy is simple, cost-efficient and the most accessible tool for the diagnosis of TB. Our study evaluated the performance of light-emitting diode fluorescence microscopy (LED-FM) using auramine/rhodamine (auramine) and the fluorescein di-acetate (FDA) vital stain in the diagnostic of pulmonary TB in Bamako, Mali. Methods: Sputum smear microscopy was conducted using the FDA and auramine/rhodamine staining procedures on fresh samples using LED-FM to evaluate the Mycobacterium TB (MTB) metabolic activity and to predict contagiousness. Mycobacterial culture assay was utilized as a gold standard method. Results: Out of 1401 TB suspected patients, 1354 (96.65%) were retrieved from database, which were MTB complex culture positive, and 47 (3.40%) were culture negative (no mycobacterial growth observed). Out of the 1354 included patients, 1343 (95.86%), were acid-fast bacillus (AFB) positive after direct FDA staining, 1352 (96.50%) AFB positive after direct Auramine, and 1354 (96.65%) AFB positive with indirect auramine after digestion and centrifugation. Overall, the FDA staining method has a sensitivity of 98.82%, while the sensitivity of Auramine with direct observation was 99.48%, and 99.56% with the indirect examination. Conclusion: This study showed that, using fresh sputum both auramine/rhodamine and FDA are highly sensitive methods in diagnosing pulmonary TB and could be easily used in countries with limited resource settings.

Multidrug resistant bacteria isolated from nosocomial infections at University Teaching Hospital of Point-G, Bamako, Mali.

An infection is said to be nosocomial or hospital if it is absent when the patient enters the hospital and it appears and develops at least 48 h late. The objective of this study was to determine the resistance phenotypes of bacteria isolated from nosocomial infections at the University Teaching Hospital of Point G. Urine, blood, pus, skin and bronchoalveolar fluid samples were taken in different units, and bacteria isolations were performed on usual selective media such as Drigalski Colombia agar supplemented with nalidixic acid and colistin and 5% sheep blood and chocolate agar. Identifications of bacteria such as Enterobacteriaceae, Pseudomonas and acinetobacter, and Staphylococci were done using API20E gallery, API20NE gallery and catalase/oxidase tests, and the Pastorex Staph kit respectively. The antimicrobial susceptibility testing was performed on Mueller-Hinton agar using the diffusion method. A total of 463 patients were inpatients for at least 48 h in the different units, and a nosocomial infection was notified in at least 57 patients (12.3%). A total of 65 episodes of nosocomial infections were observed in these 57 patients. Of the bacteria isolated, multidrug-resistant bacteria (MDR) represented 63.7% (n=36). These were extended-spectrum beta-lactamase (ESBL)-secreting Enterobacteriaceae (n=21), high-level cephalosporinase (n=13) and methicillin-resistant coagulase-negative Staphylococci (n=2). Despite this high number of multi-resistant bacteria isolated in this study; colistin and amikacin had very good activity on enterobacteriaceae. The results show the need to strengthen hygiene in the intensive care units in order to fight against nosocomial infections at the UTH of Point G.

First description of IncX3 NDM-5-producing plasmid within Escherichia coli ST448 in Mali.

Carbapenem resistance in Enterobacteriaceae has become an increasingly worrying threat. So far, no epidemiological data regarding NDM-producing enterobacterial isolates has been available on these strains in West Africa. The aim of this study was to seek for carbapenemase-producing Enterobacteriaceae clinical strains isolated in Bamako Teaching Hospital in Mali. Of 50 strains isolated between May 2016 and September 2016, we found a ST448 E. coli harbouring an IncX3 plasmid with bla NDM-5 embedded in the ΔISAba125-ble MBL structure. This study reports the first description of NDM-5 in Mali isolated in an undescribed ST E. coli in West Africa.

Diversity of staphylococcal cassette chromosome mec structures in methicillin-resistant Staphylococcus epidermidis and Staphylococcus haemolyticus strains among outpatients from four countries.

In staphylococci, methicillin (meticillin) resistance (MR) is mediated by the acquisition of the mecA gene, which is carried on the size and composition variable staphylococcal cassette chromosome mec (SCCmec). MR has been extensively studied in Staphylococcus aureus, but little is known about MR coagulase-negative staphylococci (MR-CoNS). Here, we describe the diversity of SCCmec structures in MR-CoNS from outpatients living in countries with contrasting environments: Algeria, Mali, Moldova, and Cambodia. Their MR-CoNS nasal carriage rates were 29, 17, 11, and 31%, respectively. Ninety-six MR-CoNS strains, comprising 75 (78%) Staphylococcus epidermidis strains, 19 (20%) Staphylococcus haemolyticus strains, 1 (1%) Staphylococcus hominis strain, and 1 (1%) Staphylococcus cohnii strain, were analyzed. Eighteen different SCCmec types were observed, with 28 identified as type IV (29%), 25 as type V (26%), and 1 as type III (1%). Fifteen strains (44%) were untypeable for their SCCmec. Thirty-four percent of MR-CoNS strains contained multiple ccr copies. Type IV and V SCCmec were preferentially associated with S. epidermidis and S. haemolyticus, respectively. MR-CoNS constitute a widespread and highly diversified MR reservoir in the community.

[The movement of wild poliovirus in West Africa: the Malian case]. / Circulation des poliovirus sauvages en Afrique de l'Ouest: l'exemple du Mali.

The objective of this study was to examine the evolution of the movement patterns and trends of the wild poliovirus in Mali through surveillance of acute flaccid paralysis. A retrospective descriptive study was conducted between 1 January 1998 and 31 December 2005 on 1,002 cases of acute flaccid paralysis (AFP) investigated across the country. Reports made to the National Center for Immunization (CNI) of children under 15 years suffering from AFP were included as part of the epidemiological surveillance. The isolation of the poliovirus was done with stool examinations carried out at the Pasteur Institute in Abidjan. Among 1,002 cases of AFP, 156 stool samples were positive for enteroviruses including 59 cases of poliovirus (31 cases of polio vaccine and 28 cases of wild poliovirus), a frequency of 2.3%. Children 0 to 5 years of age were most affected by AFP (59.78%). Paralysis of the legs represented the most frequently affected zone (69.56%). The Mopti region was most heavily affected are with 11 cases of the 28 cases of wild poliovirus, of which boys were most affected (71.43%). Despite the efforts made so far in the fight against polio, wild poliovirus continues to circulate and spread in Mall and the West African sub-region. All countries in West Africa and on the African continent must reach a sufficient level of vaccination coverage in order to eradicate the wild strain like industrialized countries have.

[Cholera epidemics in Mali between 1995 and 2004]. / Les epidémies de choléra au Mali de 1995 & 2004.

INTRODUCTION: Cholera represents a public health problem in developing countries like Mali. AIM: This work aims to describe the characteristics of the cholera epidemics which occurred in Mali between 1995 and 2004. METHOD: A retrospective survey was conducted within the Division of the fight against the diseases of epidemic potential and the Institute of Public Health and Research of the Ministry of Health of Mali. Individual medical records tracking the follow-up of patients as well as the registers of these structures were used as sources to collect data for the study. RESULTS: There were 12,176 cases of cholera recorded, including 1,406 deaths, from 1995 to 2004. Cholera outbreaks in Mali have been a regular occurrence every year since 2001. The regions of Mopti and Segou seem to be the most impacted by these epidemics. The lethal rates were higher than 1% at the time of each of these epidemics during this period. Vibrio cholerae O: 1, biotype El Tor were responsible for the epidemics, and the serotype Ogawa was prevalent. CONCLUSION: Cholera epidemics have been constant in Mali since the beginning of the 21st century in spite of the efforts which have been made to prevent and control them. A rigorous analysis of the factors which support this persistence and appropriate measures are essential to reverse cholera in this country.

The carriage population of Staphylococcus aureus from Mali is composed of a combination of pandemic clones and the divergent Panton-Valentine leukocidin-positive genotype ST152.

Staphylococcus aureus is an important human pathogen, but it appears more commonly in asymptomatic colonization of the nasopharynx than in cases of invasive disease. Evidence concerning the global population structure of S. aureus is limited by the overrepresentation in the multilocus sequence testing database of disease isolates recovered from Western Europe, the Americas, Australia, and Japan. We address this by presenting data from the S. aureus carriage population in Mali, the first detailed characterization of asymptomatic carriage from an African population. These data confirm the pandemic spread of many of the common S. aureus clones in the carriage population. We also note the high frequency (approximately 24%) of a single divergent genotype, sequence type 152 (ST152), which has not previously been recovered from nasal carriage isolates but corresponds to a sporadic Panton-Valentine leukocidin (PVL)-positive, community-acquired methicillin-resistant S. aureus clone noted mostly in Central Europe. We show that 100% of the ST152 isolates recovered from nasal carriage samples in Mali are PVL positive and discuss implications relating to the emergence and spread of this virulent genotype.

[The Hospital Wastewater Antibiotic Residues In Bamako (Mali)]. / Les Residus D'Antibiotiques Dans Les Effluents Hospitaliers De Bamako (Mali).

The aim of this study was to determine the wastewaters antibiotic residues concentration in two hospitals (CHU Point G and CHU Luxembourg) in Bamako. METHODS: The samples of wastewater were collected three times consecutively on three days every week at 9 a.m., 3 p.m. and 9 p.m. in 2016. The samples were stored at 4°C and transferred to the veterinary central laboratory (LCV). The antibiotic residues were detected by High Performance Liquid Chromatography and the antibiotic concentrations were determined by a spectrophotometer UV-Visible Hewlett Packard. RESULTS: The detected and measured antibiotic residues were amoxicillin ((0.066 ± 0.08 µg/l), erythromycin (0.04 ± 0.0 µg/l), co-trimoxazole (sulfamethoxazole 0.06 ± 0.21 µg/l + trimethoprime 0.08 ± 0.006 µg/l) and metronidazole (0.02 ± 0.0 µg/l in the hospital wastewater and in the sewer systems. Amoxicillin and sulfamethoxazole were detected before and after the Point G wastewater treatment. No antibiotic residue was detected in the "Chikoroni" sewer system which discharged the Point G wastewater. Amoxicillin and sulfamethoxazole were also detected in the wastewater of the hospital "le Luxembourg" which doesn't have a wastewater treatment plant and in the "Djafranako" sewer system which discharged the wastewater of this hospital. Erythromycin and metronidazole were detected only in the Point G wastewater. Chloramphenicol, ciprofloxacin and tetracyclin were not detected in the two hospital wastewater. The antibiotic residues concentrations at the different moments show the same high level in the different sites. CONCLUSION: Hospitals play a role in the antibiotic dissemination into the environment. In Bamako, the wastewater quality is not alarming, but every hospital must get a sewer system.

L'objectif de ce travail était de déterminer la concentration des résidus d'antibiotiques dans les effluents de deux hôpitaux de Bamako. MÉTHODES: La collecte des échantillons des effluents hospitaliers a été réalisée trois fois par jour à des heures précises : 9 heures, 15 heures et 21 heures conformément au moment des rejets de la station d'épuration, trois jours consécutifs par semaine et pendant un mois. L'analyse des échantillons a été faite par chromatographie phase liquide (HPLC), Agilent 1100 sur colonne C18. La concentration des antibiotiques a été mesurée à l'aide d'un spectrophotomètre UV-Visible Hewlett Packard. RÉSULTATS: Quatre antibiotiques ont été détectés et quantifiés dont trois régulièrement dans les effluents hospitaliers. Il s'agit de l'amoxicilline (0,066 ± 0,08 µg/l), l'érythromycine (0,04 ± 0,0 µg/l), sulfaméthoxazole + triméthoprime (0,06 ± 0,21 / 0,08 ± 0,006 µg/l) et du métronidazole (0,02 ± 0,0 µg/l). L'amoxicilline et le sulfaméthoxazole ont été détectés et quantifiés sur les deux points, l'érythromycine et le métronidazole seulement au CHU du Point « G ¼. Le sulfaméthoxazole a été dosé aux différentes heures dans les effluents des deux hôpitaux, il n'est pas détecté dans les eaux du canal de « Chikoroni ¼. Le chloramphénicol, la ciprofloxacine et la tétracycline n'ont été détectés à aucun point de prélèvement. Les concentrations d'antibiotiques observées aux différentes heures de prélèvements montrent des pics en général semblables au niveau des différents sites. CONCLUSION: La qualité de nos effluents n'est pas aussi alarmante. Des mesures doivent être prises en vue de l'évaluation du risque sanitaire et du développement des méthodes nécessaires pour limiter les rejets de résidus médicamenteux dans l'environnement.

Mycobacterium africanum (Lineage 6) shows slower sputum smear conversion on tuberculosis treatment than Mycobacterium tuberculosis (Lineage 4) in Bamako, Mali.

OBJECTIVE: Ancestral M. tuberculosis complex lineages such as M. africanum are underrepresented among retreatment patients and those with drug resistance. To test the hypothesis that they respond faster to TB treatment, we determined the rate of smear conversion of new pulmonary tuberculosis patients in Bamako, Mali by the main MTBc lineages. METHODS: Between 2015 and 2017, we conducted a prospective cohort study of new smear positive pulmonary tuberculosis patients in Bamako. Confirmed MTBc isolates underwent genotyping by spoligotyping for lineage classification. Patients were followed at 1 month (M), 2M and 5M to measure smear conversion in auramine (AR) and Fluorescein DiAcetate (FDA) vital stain microscopy. RESULT: All the first six human MTBc lineages were represented in the population, plus M. bovis in 0.8% of the patients. The most widely represented lineage was the modern Euro-American lineage (L) 4, 57%, predominantly the T family, followed by L6 (M. africanum type 2) in 22.9%. Ancestral lineages 1, 5, 6 and M. bovis combined amounted to 28.8%. Excluding 25 patients with rifampicin resistance, smear conversion, both by AR and FDA, occurred later in L6 compared to L4 (HR 0.80 (95% CI 0.66-0.97) for AR, and HR 0.81 (95%CI 0.68-0.97) for FDA). In addition we found that HIV negative status, higher BMI at day 0, and patients with smear grade at baseline ≤ 1+ were associated with earlier smear conversion. CONCLUSION: The six major human lineages of the MTBc all circulate in Bamako. Counter to our hypothesis, we found that patients diseased with modern M. tuberculosis complex L4 respond faster to TB treatment than those with M. africanum L6.

Very high prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae in bacteriemic patients hospitalized in teaching hospitals in Bamako, Mali.

The worldwide dissemination of extended-spectrum beta-lactamase producing Enterobacteriaceae, (ESBL-E) and their subset producing carbapenemases (CPE), is alarming. Limited data on the prevalence of such strains in infections from patients from Sub-Saharan Africa are currently available. We determined, here, the prevalence of ESBL-E/CPE in bacteriemic patients in two teaching hospitals from Bamako (Mali), which are at the top of the health care pyramid in the country. During one year, all Enterobacteriaceae isolated from bloodstream infections (E-BSI), were collected from patients hospitalized at the Point G University Teaching Hospital and the pediatric units of Gabriel Touré University Teaching Hospital. Antibiotic susceptibility testing, enzyme characterization and strain relatedness were determined. A total of 77 patients had an E-BSI and as many as 48 (62.3%) were infected with an ESBL-E. ESBL-E BSI were associated with a previous hospitalization (OR 3.97 95% IC [1.32; 13.21]) and were more frequent in hospital-acquired episodes (OR 3.66 95% IC [1.07; 13.38]). Among the 82 isolated Enterobacteriaceae, 58.5% were ESBL-E (20/31 Escherichia coli, 20/26 Klebsiella pneumoniae and 8/15 Enterobacter cloacae). The remaining (5 Salmonella Enteritidis, 3 Morganella morganii 1 Proteus mirabilis and 1 Leclercia adecarboxylata) were ESBL negative. CTX-M-1 group enzymes were highly prevalent (89.6%) among ESBLs; the remaining ones being SHV. One E. coli produced an OXA-181 carbapenemase, which is the first CPE described in Mali. The analysis of ESBL-E relatedness suggested a high rate of cross transmission between patients. In conclusion, even if CPE are still rare for the moment, the high rate of ESBL-BSI and frequent cross transmission probably impose a high medical and economic burden to Malian hospitals.

Prevalence of ESBL-producing Enterobacteriaceae isolated from blood cultures in Mali.

INTRODUCTION: The increasing frequency of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae is becoming a serious public health concern. This study sought to determine ESBL frequency in Enterobacteriaceae isolated from patients' blood cultures in two university teaching hospitals of Bamako, Mali. METHODOLOGY: During a three-month period, the presence of Enterobacteriaceae from blood cultures of patients admitted to the university teaching hospitals of Bamako was evaluated. The microbial identifications were initially performed with an API 20E gallery and VITEK2 locally in Mali, and then confirmation in France was performed with a mass spectrometry MALDI-TOF in the bacteriology laboratory of the university teaching hospital of Bichat. Antibiotic susceptibility profiles were determined by the diffusion method as recommended by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). RESULTS: The isolated species were K. pneumoniae (14/40; 35.0%), E. coli (11/40; 27.5%), and E. cloacae (9/40; 22.5%). Of the strains isolated, 21/34 (61.8%) had an ESBL phenotype, including 10/14 (71.4%) K. pneumoniae, 8/11 (72.7%) E. coli, and 3/9 (33.3%) E. cloacae. Resistances associated with ESBL strains of K. pneumoniae, E. coli, and E. cloacae were as follows: gentamicin (10/10, 100%; 6/8, 75%; 2/3, 67%, respectively), amikacin (2/10, 20%; 0/8, 0%; 0/3, 0%, respectively), ofloxacin (8/10, 80%; 7/8, 87%; 3/3, 100%, respectively), and cotrimoxazole (10/10, 100%; 6/8, 75%; 3/3, 100%, respectively). CONCLUSION: Almost two-thirds (61.8%) of Enterobacteriaceae isolated from our blood cultures were ESBL producers. Only susceptibilities to carbapenems and to amikacin were fully conserved within the strains.

[Endoscopic contribution in the dilatation of caustic esophagus stenosis]. / Apport des moyens endoscopiques dans la dilatation des sténoses caustiques de l'œsophage.

INTRODUCTION: The aim of this work was to present the contribution of the endoscopy in the management of esophageal dilatation for caustic esophageal stenosis (CES). METHODS: This was a descriptive and prospective study in the thoracic surgery department at the Hospital of Mali. A total of 46 cases of CES is recorded and divided into 4 groups according to the topography of the esophageal lesions. For the different methods of dilatation the number of performed endoscopic support was determined to understand the contribution of endoscopic means in the success of dilatation for CES. The outcome, complications and mortality in the two methods were compared. RESULTS: Fibroscopy was used in 41.30% of patients with Savary Guillard dilators and in 47.82% of patients with Lerut dilators. Video laryngoscopy was used in 58.69% of patients who underwent dilatation with Lerut dilators. The passage of the guide wire was performed in 39.13% under video laryngoscopy and 58.68% under fibroscopy. In comparison of the two methods, there is a significant difference in the occurrence of complications (p=0.04075), general anesthesia (p=0.02287), accessibility (p=0.04805) and mortality (p=0.00402). CONCLUSION: The CES is a serious disease and under evaluated in Mali. The endoscopies contribute significantly to the success of esophageal dilatation for caustic stenosis in the different methods we used.

[Seroprevalence of the human cytomegalovirus among blood donors and AIDS patients in Bamako]. / La séroprévalence de l'infection par le cytomégalovirus humain chez les donneurs de sang et les malades atteints du sida à Bamako.

Our aim was to study the prevalence of the human cytomegalovirus (HCMV) among blood donors and AIDS patients and to examine a clinical correlation between AIDS and HCMV seroprevalence in Bamako (Mali, West Africa). We have used Elisa kits for detecting HIV and HCMV specific antibodies. The HCMV seroprevalence was 89% among AIDS patients, 71% among HIV-infected blood donors and 58% among HIV-uninfected blood donors. The HCMV seroprevalence rate was higher among AIDS patients than among HIV-uninfected blood donors (p=0.0000007) and than among HIV-infected blood donors (p=0.00146). There was no significant difference between the HCMV seroprevalence among HIV-infected blood donors and among HIV-uninfected blood donors (p=0.0547). There was no relationship between HCMV seroprevalence and sex or age among AIDS patients and blood donors. There was a significant difference on pneumonia among HCMV-infected AIDS patients and among HCMV-uninfected AIDS patients (40% versus 0%; p=0.005). Buccal and phaiyngal candidosis, dermatosis, Kaposi's sarcoma and nervous system diseases had the same frequency among HCMV-infected and HCMV-uninfected AIDS patients.

[Case-control study of hepatitis C HBs Ag and antivirus antibodies in chronic hepatopathies]. / Etude de l'antigène HBs et des anticorps antivirus de l'hépatite C au cours des hépatopathies chroniques.

The aim of this study is to establish the prevalence of hepatitis C HBs Ag and of anti-virus antibodies in chronic hepatopathies. The prospective case-control study was carried out on 91 patients who needed to be treated for chronic hepatopathies and 92 occasional blood donors. The search for hepatitis C HBs Ag and anti-virus antibodies was done using third generation ELISA screening. At the end of the study, HBs Ag was found in 54% of the patients vs. 4.3% of the control (p=0.0006). The two markers were present more frequently in cirrhosis than in hepatocellular carcinoma (HCC) and their association was more frequent in the case of cirrhosis. In Mali, hepatitis B and C viruses play an important part in chronic hepatopathies.

Phylogenetic analysis of the precore/core gene of hepatitis B virus genotypes E and A in West Africa: new subtypes, mixed infections and recombinations.

One hundred and twenty-two new hepatitis B virus (HBV) preC/C sequences and three complete genomes from three major countries in West Africa were analysed. The majority of sequences were of genotype E and the only other genotype found was genotype A. Although for genotype E sequences, the genetic diversity of the preC/C gene was about two to three times higher than that of the preS/S gene, it was still considerably lower than that for genotype A sequences. The HBV/E preC/C gene was related most closely to subgenotype D1 and D2 sequences. Evidence of recombination was found in two strains that were of genotype A in the preS/S gene and of genotype E in the preC/C gene. The genotype A strains from Cameroon, Mali and Nigeria could be divided phylogenetically into three subtypes, A3 and two new subtypes, tentatively designated A4 and A5. Each subtype presented a genetic diversity of 2.19-3.85 % and intersubtype distances of 4.47-5.97 %. Interestingly, one sample from Nigeria showed evidence of a triple recombination of genotypes E/D and A, separated by a genotype G-specific insert of 36 bp. Of 110 patients, 19 (17.3 %) showed a coinfection of genotypes A and E, mostly in human immunodeficiency virus-positive children from Cameroon. Thus, in Cameroon, where both genotypes coexist, 37 % of all individuals tested had mixed infections. The low genetic variability in the preC/C gene of genotype E supports our previous speculation about a relatively short evolutionary history of this genotype, in contrast to the subtype-rich African genotype A strains.

Low genetic diversity despite hyperendemicity of hepatitis B virus genotype E throughout West Africa.

Sub-Saharan Africa suffers from an excessively high endemicity of hepatitis B virus (HBV), but little is known about the prevalent genotypes. In this study, we investigated the PreS1/PreS2/S genes of 127 viruses obtained from 12 locations in Mali, Burkina Faso, Togo, Benin, Nigeria, Cameroon, and the Democratic Republic of Congo. Except for those obtained from the Cameroon HIV cohort (18/22 HBV genotype A), 96 of 105 sequences belonged to HBV genotype E (HBV/E), and viral DNA was very similar (1.67% diversity) throughout this vast HBV/E crescent, which spans 6000 km across Africa. The low diversity suggests that HBV/E may have a short evolutionary history. Considering a typical mutation rate of DNA viruses, it would take only 200 years for the strain diversity of HBV/E viruses to develop from a single introductory event. The relatively recent introduction of HBV/E into humans would also explain its conspicuous absence in the Americas, despite the forced immigration of slaves from west Africa, until the early 19th century. Infection during infancy is mostly associated with chronic carrier status, and this combination can account for the explosive spread of virtually identical viruses within a community, but whether other routes of long-range transmissions must be considered becomes an important question.