Characterization of carbapenem resistant Acinetobacter baumannii isolated from intensive care units in two teaching hospitals from Algeria and Tunisia

Introduction: This study was conducted to identify the enzymatic mechanism of carbapenem resistance in A. baumannii isolated from intensive care units of 2 teaching hospitals (Charles Nicolle hospital of Tunis and University hospital of Annaba). Methods: Twenty seven non repetitive carbapenem-resistant A. baumannii were collected (7 strains in Algeria and 20 in Tunisia). Antibiotic susceptibility was performed by disk diffusion method. MICs were determined by agar dilution method. EDTA-disk synergy test was performed for metallo-β-lactamases (MBL) phenotypicdetection. Detection of blaOXA-23-like, blaOXA-24-like, blaOXA-51-like and blaOXA-58-like families was performed by PCR followed by sequencing. Geneticrelatedness between strains was investigated by pulsed-field gel electrophoresis (PFGE). Results: Strains were recovered especially from respiratory tract specimens (n=12) and blood (n=11). All strains were co-resistant to all β-lactams, gentamicin, amikacin and ciprofloxacin, but remainded susceptible to colistin. MBL production was negative for all isolates. blaOXA-51-like was detected in all strains and blaOXA-23-like in 23 strains. However, blaOXA-58-like and blaOXA-24-like were not found in any isolate. Six major PFGE patterns were found in the Tunisian isolates. However, the Algerian strains were clustered in one clone.Conclusion: This study shows a high distribution of blaOXA-23 in imipenem-resistant A. baumannii isolated in Tunisia and Algeria. It demonstrated the epidemic diffusion of this multidrug resistant pathogen. Thus, strengthening of prevention measures are required to control further spread of carbapenemases in the two countries.Key words: A. baumannii, Carbapenem resistance, OXA-23-like, Pulsed-field gel electrophoresi

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Impact of intersection type and a vehicular fleet's hybridization level on energy consumption and emissions

A vehicle's energy consumption and emissions are two major constraints in sustainable development. Both of them have proportionally raised in recent decades with the exponential growth of world traffic demands. The reduction of road traffic-generated energy consumption and emissions have thus become unprecedentedly challenging and worth examining. This paper investigates energy consumption and environmental problems present at roundabout and signalized intersection to analyze the impact of the hybridization level's fleet and intersection type on vehicle consumption and pollution. Instantaneous fuel consumption and emission models coupled with simulation of urban mobility (SUMO) are in this study. The authors started with modeling energy consumption. Then, an emission model emissions from traffic (EMIT) was implemented to quantify vehicle emissions of CO2, CO and NOx. These models help investigate the influence of intersection type on energy consumption and environmental conditions. The authors implemented a signalized intersection and roundabout using SUMO. The input data are collected from the roundabout of Sousse (Tunisia) using video data collection. Since there is a lack of econometric models that emulate hybridized stream behavior near intersections, two energy consumption models for the roundabout and crossroad are developed using traffic flow and hybridization level as the input variables. Compared to crossroads, a roundabout can obtain more environmental improvements and substantial reductions in energy consumption and road traffic emissions

Acute kidney injury with granulomatous interstitial nephritis and vasculitis revealing sarcoidosis

Sarcoidosis is an inflammatory disease that affects mostly the lungs and lymph glands. Renal involvement is rare and especially vasculitis. We report a case who presented an acute kidney failure and had sarcoidosis with vasculitis and nodular splenic involvement. A 35-year-old woman presenting a Lofgren syndrome was hospitalized for acute renal failure with cervical lymphadenopathy without other clinical findings. Laboratory data disclosed elevated angiotensin converting enzyme serum level. Abdominal ultrasound showed a multinodular spleen. Renal histology revealed granulomatous interstitial nephritis with necrotizing vasculitis. Outcome was favorable after the institution of high dose corticosteroids along with cyclophosphamide. Renal involvement is rare in sarcoidosis. However, the diagnostic delay should be avoided to improve the outcome

High prevalence of gut microbiota colonization with broad-spectrum cephalosporin resistant Enterobacteriaceae in a Tunisian intensive care unit

Healthcare-associated infections due to cefotaxime-resistant Enterobacteriaceae (CRE) have become a major public health threat, especially in intensive care units (ICUs). Often acquired nosocomially, CRE can be introduced initially by patients at admission. This study aimed to determine the prevalence and genetic characteristics of CRE-intestinal carriage in ICU patients, to evaluate the rate of acquisition of these organisms during hospitalization, and to explore some of the associated risk factors for both carriage and acquisition.Between December 2014 and February 2015, the 63 patients admitted in the ICU of Charles Nicolle hospital were screened for rectal CRE colonization at admission and once weekly thereafter to identify acquisition. CRE fecal carriage rate was 20.63% (13/63) at admission and the acquisition rate was 42.85% (15/35). Overall, 35 CRE isolates were collected from 28 patients (25 Klebsiella pneumoniae, 7 Escherichia coli and 3 Enterobacter cloacae strains). Seven patients were simultaneously colonized with 2 CRE isolates. CTX-M-15 was detected in most of the CRE isolates (30/35, 88.23%).Three strains co-produced CMY-4 and 22 strains were carbapenem-resistant and co-produced a carbapenemase OXA-48 (n=13) or NDM-1 (n=6). All isolates were multidrug resistant. Molecular typing of K. pneumoniae strains, revealed 8 Pulsed field gel electrophoresis (PFGE) patterns and 4 sequence types (ST) ST101, ST147, ST429 and ST336. However, E. coli isolates were genetically unrelated and belonged to A (n=2), B1 (n=2) and B2 (n=3) phylogenetic groups and to ST131 (2 strains), ST572 (2 strains), ST615 (one strain) and ST617 (one strain). Five colonized patients were infected by CRE (4 with the same strain identified from their rectal swab and 1 with a different strain). Whether imported or acquired during the stay in the ICU, colonization by CRE is a major risk factor for the occurrence of serious nosocomial infections. Their systematic screening in fecal carriage is mandatory to prevent the spread of these multidrug resistant bacteria

A regionally based precision medicine implementation initiative in North Africa:The PerMediNA consortium

International audiencePrecision Medicine is being increasingly used in the developed world to improve health care. While several Precision Medicine (PM) initiatives have been launched worldwide, their implementations have proven to be more challenging particularly in low- and middle-income countries. To address this issue, the “Personalized Medicine in North Africa” initiative (PerMediNA) was launched in three North African countries namely Tunisia, Algeria and Morocco. PerMediNA is coordinated by Institut Pasteur de Tunis together with the French Ministry for Europe and Foreign Affairs, with the support of Institut Pasteur in France. The project is carried out along with Institut Pasteur d’Algérie and Institut Pasteur du Maroc in collaboration with national and international leading institutions in the field of PM including Institut Gustave Roussy in Paris. PerMediNA aims to assess the readiness level of PM implementation in North Africa, to strengthen PM infrastructure, to provide workforce training, to generate genomic data on North African populations, to implement cost effective, affordable and sustainable genetic testing for cancer patients and to inform policy makers on how to translate research knowledge into health products and services. Gender equity and involvement of young scientists in this implementation process are other key goals of the PerMediNA project.In this paper, we are describing PerMediNA as the first PM implementation initiative in North Africa. Such initiatives contribute significantly in shortening existing health disparities and inequities between developed and developing countries and accelerate access to innovative treatments for global health