Molecular detection of antimicrobial resistance genes in multidrug-resistant Gram-negative bacteria isolated from clinical samples in two hospitals in Niger

Background: According to the World Health Organization (WHO), bacterial resistance to antibiotics is a global public health challenge, which is also developing in Niger. The aim of this study was to determine the prevalence of antibiotic resistance genes in Gram-negative bacilli isolated from clinical samples in the biological laboratories of two selected health facilities in Niger. Methodology: Clinical bacterial isolates were randomly collected from two biological laboratories of Zinder National Hospital and Niamey General Reference Hospital. These were multi-resistant Gram-negative bacteria that have been routinely isolated from pathological samples of patients. Molecular detection of resistance genes was carried out by polymerase chain reaction (PCR) amplification using specific primers. These include plasmid-mediated AmpC beta lactamase genes (blaCITM, blaDHAM, blaFOXM), 'Cefotaxime-Munich' type beta lactamase genes (blaCTX-M-1, blaCTX-M-2, blaCTX-M-9), KPC-type beta lactamase gene (blaKPC), Oxa-type beta lactamase gene (blaOXA-48), SHV-type beta lactamase gene (blaSHV), TEM-type beta lactamase gene (blaTEM), quinolone resistance genes (qnrA, qnrB, qnrS), and sulfonamide resistance genes (sul1, sul2, sul3). Results: A total of 24 strains of multidrug-resistant Gram-negative bacteria isolated from different clinical samples were analysed. The distribution of the resistance genes detected is as follows; AmpC blaCITM (n=6; 25.0%), AmpC blaDHAM (n=4; 17.0%), AmpC blaFOXM (n=0), blaCTX-M-1 (n=11; 46.0%), blaCTX-M-2 (n=0), blaCTX-M-9 (n=0), blaKPC (n=0), blaOXA-48 (n=2; 8..0%), blaSHV (n=5; 21.0%), blaTEM (n=0), qnrA (n=0), qnrB (n=5; 21.0%), qnrS (n=17; 71.0%), sul1 (n=22; 92.0%), sul2 (n=12; 50.0%), and sul3 (n=0). All isolates tested had at least two resistance genes. Conclusion: The results of this study provide a better understanding of the resistance situation of clinical isolates in Niger. Therefore, it is more than necessary to intensify the detection on a larger number of samples and on a national scale. This will make it possible to assess the true extent of the phenomenon and consequently guide control strategies through a national multisectoral plan.

Profile of multidrug-resistant clinical bacterial isolates at the National Hospital of Zinder (NHZ), Niger Republic in 2021

Background: Today, bacterial resistance is a public health challenge throughout the world, and infections caused by resistant bacteria are associated with increased morbidity, mortality and health care costs. The objective of this descriptive study is to determine the prevalence and distribution of multi-drug resistant (MDR) clinical bacteria isolates at the National Hospital of Zinder, Niger Republic in 2021. Methodology: We conducted a descriptive cross-sectional study of in- and out-patients from whose clinical samples' bacteria were isolated at the bacteriology unit of the laboratory. Bacteria were isolated from the clinical samples following standard aerobic cultures and identified using conventional biochemical test schemes. Antibiotic susceptibility testing (AST) was performed by the agar disk diffusion technique, and categorization of the isolates into sensitive, intermediate or resistant was done according to the recommendations of the Antibiogram Committee of the French Society of Microbiology (CA-SFM) 2020 version 1.2. MDR was defined as resistance to at least one antibiotic in three or more categories, while selected MDR bacteria such as ESBL was identified using double disk synergy test, and MRSA by cefoxitin disk diffusion test. Results: Seventy-seven (6.7%) bacterial species were isolated from 1153 clinical samples processed at the bacteriology unit of the hospital laboratory between June and December 2021, of which 65.0% (50/77) were members of the order Enterobacteriales. Escherichia coli represented 40.3% (40/77) of the isolated bacteria, Staphylococcus aureus 13.0% (10/77) and Pseudomonas aeruginosa 11.7% (9/77). The overall prevalence of MDR was 44.2% (34/77), including 61.8% (21/34) ESBL-producing Enterobacteriales (ESBL-E), 26.5% (9/34) multi-resistant P. aeruginosa and 11.7% (4/34) MRSA, with 67.6% (23/34) of the MDR isolates from outpatients. Resistance rates of the Enterobacteriales to ciprofloxacin, gentamicin, amikacin and imipenem were 62.0%, 52.0%, 38.0% and 8.0% respectively. Resistance rates of P. aeruginosa were 100.0%, 88.9%, 77.8%, 33.3%, 22.2%, and 22.2% respectively to ceftazidime, ticarcillin, imipenem, ciprofloxacin, levofloxacin, and amikacin. Resistance rates of S. aureus were 100.0%, 50.0%, 40.0%, 10.0%, 0% and 0% to penicillin G,erythromycin, cefoxitin, tetracycline, fusidic acid, and chloramphenicol respectively. ESBL-E were 47.6%,85.7% and 0% resistant to amikacin, ciprofloxacin and imipenem, and MRSA resistance rates were 75.0%, 75.0%, 50.0% and 0% to erythromycin, tetracycline, gentamicin, and chloramphenicol respectively. Conclusion: This study reports high prevalence of MDR bacteria, mainly ESBL-E, with concerning high resistance to carbapenem. Rational use of antibiotics and implementation of surveillance system for MDR bacteria must be implemented in order to limit the emergence and spread of MDR bacteria in Niger Republic.

Evaluation of the antimicrobial susceptibility testing process in clinical microbiology laboratories at Niamey, Niger

Background: Risk assessment is the means of identifying and evaluating potential errors or problems that may occur in testing process. The aim of this study was to perform risk assessment of antimicrobial susceptibility testing (AST) process in clinical microbiology laboratories of Niamey, Niger Republic. Methodology: We conducted a descriptive cross-sectional study from October 1 to December 31, 2019, to evaluate AST performance in seven clinical microbiology laboratories at Niamey, the capital city of Niger republic. The evaluation focused on the determination of the criticality index (CI) of each critical point (frequency of occurrence of anomalies, severity of the process anomaly, and detectability of the anomaly during the process) in the AST process and the performance of the AST through an observation sheet using two reference strains; Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 29213. Results: The criticality index (CI) was greater than 6 for most of the critical points related to material, medium, equipment, method and labour for the AST process in all the laboratories. A range of 18-100% errors on the inhibition zone diameters of the reference strains were observed. Major and/or minor categorization (Sensitive S, Intermediate I and Resistance R) discrepancies were found at all the laboratories for either one or both reference strains. The antibiotics most affected by the S/I/R discrepancies were trimethoprim (100%), vancomycin (100%), amoxicillin (80%) and amoxicillin + clavulanic acid (70%). Conclusion: This study showed a deficiency in the control of critical control points that impacts the performance of the AST reported by the laboratories in Niger. Corrective actions are needed to improve the performance of AST in clinical microbiology laboratories in Niger

Evaluating Deep Learning Algorithms in Pulmonary Nodule Detection.

Lung cancer is considered the deadliest cancer worldwide. In order to detect it, radiologists need to inspect multiple Computed Tomography (CT) scans. This task is tedious and time consuming. In recent years, promising methods based on deep learning object detection algorithms were proposed for the automatic nodule detection and classification. With those techniques, Computed Aided Detection (CAD) software can be developed to alleviate radiologist's burden and help speed-up the screening process. However, among available object detection frameworks, there are just a limited number that have been used for this purpose. Moreover, it can be challenging to know which one to choose as a baseline for the development of a new application for this task. Hence, in this work we propose a benchmark of recent state-of-the-art deep learning detectors such as Faster-RCNN, YOLO, SSD, RetinaNet and EfficientDet in the challenging task of pulmonary nodule detection. Evaluation is done using automatically segmented 2D images extracted from volumetric chest CT scans.

[Clinical and Therapeutic Profile and Outcomes of Patients with Tuberculosis at the Regional Hospital of Tahoua, Republic of the Niger]. / Profil clinique, thérapeutique et évolutif de la tuberculose au centre hospitalier régional (CHR) de Tahoua, république du Niger.

This study aims to describe the epidemiological, clinical, therapeutic characteristics of patients followed for tuberculosis at the Regional Hospital Center of Tahoua (Niger) as well as their outcomes.We conducted a retrospective and descriptive study from the medical records of patients followed for tuberculosis between January 1, 2017 and December 31, 2019. A total of 465 patients were included in the present study (304 men and 161 women; mean age: 30 years). Patients coming from urban areas represented 51% of the cases. Bacteriologically confirmed pulmonary tuberculosis represented 63% of the cases, 15% of clinically diagnosed pulmonary tuberculosis and 22% of extrapulmonary tuberculosis including Pott's disease. The HIV testing rate was 97.8%. Tuberculosis-HIV association represented 13% of the cases. The therapeutic success was 90.5%. The lethality rate was 5.2% (24/465). Among 24 patients who died, three had tuberculosis-HIV association.

L'objectif de cette étude était de décrire le profil clinique, thérapeutique et évolutif des patients suivis pour tuberculose (TB) au centre hospitalier régional de Tahoua (Niger). Nous avons mené une étude rétrospective, descriptive à partir des dossiers des patients suivis pour TB entre le 1er janvier 2017 et le 31 décembre 2019. Au total, 465 patients ont été inclus dans la présente étude (304 hommes et 161 femmes, âge moyen : 30 ans). Les patients provenant du milieu urbain représentaient 51 % des cas. La TB pulmonaire confirmée bactériologiquement représentait 63 % des cas, la TB pulmonaire cliniquement diagnostiquée 15 %, la TB extrapulmonaire, notamment le mal de Pott, 22 %. L'association TB­VIH représentait 13 % des cas. Le succès thérapeutique était de 90,5 %. Le taux de létalité était de 5,2 % (24/465). Parmi les 24 patients décédés, trois présentaient l'association TB­VIH.

Persistence of Coxiella burnetii, the agent of Q fever, in murine adipose tissue.

Coxiella burnetii, the agent of Q fever, is known to persist in humans and rodents but its cellular reservoir in hosts remains undetermined. We hypothesized that adipose tissue serves as a C. burnetii reservoir during bacterial latency. BALB/c and C57BL/6 mice were infected with C. burnetii by the intraperitoneal route or the intracheal route. Adipose tissue was tested for the presence of C. burnetii several months after infection. C. burnetii was detected in abdominal, inguinal and dorsal adipose tissue 4 months post-infection, when no bacteria were detected in blood, liver, lungs and spleen, regardless of the inoculation route and independently of mouse strain. The transfer of abdominal adipose tissue from convalescent BALB/c mice to naïve immunodeficient mice resulted in the infection of the recipient animals. It is likely that C. burnetii infects adipocytes in vivo because bacteria were found in adipocytes within adipose tissue and replicated within in vitro-differentiated adipocytes. In addition, C. burnetii induced a specific transcriptional program in in-vivo and in vitro-differentiated adipocytes, which was enriched in categories associated with inflammatory response, hormone response and cytoskeleton. These changes may account for bacterial replication in in-vitro and chronic infection in-vivo. Adipose tissue may be the reservoir in which C. burnetii persists for prolonged periods after apparent clinical cure. The mouse model of C. burnetii infection may be used to understand the relapses of Q fever and provide new perspectives to the follow-up of patients.

Antibiotic susceptibility and intracellular localization of Diplorickettsia massiliensis.

Diplorickettsia massiliensis is an obligate intracellular bacterium from the Coxiellaceae family recently isolated from Ixodes ricinus ticks. The inhibitory effects of antimicrobial agents were assessed by two different methods, immunofluorescence and Gimenez staining assay. Different markers (EEA1, Lamp-1, Cathepsin D, and LysoTracker Red DND99) were used to reveal the nature of the vacuole containing the bacterium. Ciprofloxacin, levofloxacin, and rifampin had MIC values of 2 lg mL(-1). We found that 4 lg mL(-1) of Doxycycline inhibited the growth of D. massiliensis strain. Surprisingly, D. massiliensis was resistant to chloramphenicol up to the concentration of 64 lg mL(-1). We found that penicillin G, ammonium chloride, gentamycin, omeprazole, bafilomycin A1, and chloroquine were not active against D. massiliensis. Studies performed with markers EEA1, Lamp-1, Cathepsin D, and LysoTracker Red DND99 showed that D. massiliensis is localized within an acidic compartment that is not an early phagosome, but a late phagosome or a phagolysosome. Gimenez staining stays a good method that will work with a very low number of bacteria and can be used to determine the MICs of new therapeutic antibiotics precisely. The resistance profile of D. massiliensis was found to be quite unusual for intracellular Gram-negative bacterium with marked resistance to chloramphenicol. Despite of localization in acidic compartment, pH-neutralizing agents do not significantly inhibit intracellular growth of bacterium. The results of these studies prove that antibiotic resistance does not depend on pH of vacuole. This pH-related mechanism seems not to play a contributing role in the overall resistance of D. massiliensis.