Antimicrobial resistance patterns among Acinetobacter baumannii isolated from burn intensive care unit in Tripoli, Libya

Background: Acinetobacter baumannii is a troublesome and increasingly problematic healthcare-associated pathogen, especially in critical care unit. These organisms have a capacity for long-term survival in the hospital environment. Aim: This study aimed to investigates the drug resistance patterns of Acinetobacter baumannii strains isolated from burn ICU (BICU). Method: The antibiotic susceptibility of 176 isolates to imipenem, meropenem, gentamicin, ciprofloxacin, fusidic acid, amikacin, trimethoprim, cefepime, ceftazidime, ceftriaxone, cefotaxime, and amoxicillin-calvulanic acid was determined by disk agar diffusion test. Findings: The overall proportion of A. baumannii isolates among all clinical isolates has increased slightly throughout the study from 3.5% to 4.2%. Carpabenem remained the antimicrobial most active antibiotic against A. braumannii isolates compared with other antibiotics, during the two years there was an increase in resistance from 50.6% to 71.3% to imipenem (P<0.01), and meropenem from 50.6% to 74.5% (P<0.01). ICU isolates exhibited significantly higher level of resistance to imipenem (71.6%) and meropenem (73.4%) compared with non-ICU strains (42.6% and 44.6% respectively) (P<0.01). Conclusion: In conclusion, the high prevalence of multidrug resistance A. baumannii (97.7%) and increased resistance to imipenem and meropenem in our unit might be due to long hospital stay, intubation, surgery and previous antibiotic prescription. It would seem that practices to prevent cross-transmission are more important in controlling resistance

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

Early detection of metallo-beta-lactamase NDM-1-and OXA-23 ă carbapenemase-producing Acinetobacter baumannii in Libyan hospitals

International audienceAcinetobacter baumannii is an opportunistic pathogen causing various ă nosocomial infections. The aim of this study was to characterise the ă molecular support of carbapenem-resistant A. baumannii clinical isolates ă recovered from two Libyan hospitals. Bacterial isolates were identified ă by matrix-assisted laser desorption/ionisation time-of-flight mass ă spectrometry (MALDI-TOF/MS). Antibiotic susceptibility testing was ă performed using disk diffusion and Etest methods, and carbapenem ă resistance determinants were studied by PCR amplification and ă sequencing. Multilocus sequence typing (MLST) was performed for typing ă of the isolates. All 36 imipenem-resistant isolates tested were ă identified as A. baumannii. The bla(OXA-23) gene was detected in 29 ă strains (80.6%). The metallo-beta-lactamase bla(NDM-1) gene was ă detected in eight isolates (22.2%), showing dissemination of ă multidrug-resistant (MDR) A. baumannii in Tripoli Medical Center and ă Burn and Plastic Surgery Hospital in Libya, including one isolate that ă co-expressed the bla(OXA-23) gene. MLST revealed several sequence types ă (STs). Imipenem-resistant A. baumannii ST2 was the predominant clone ă (16/36; 44.4%). This study shows that NDM-1 and OXA-23 contribute to ă antibiotic resistance in Libyan hospitals and represents the first ă incidence of the association of these two carbapenemases in an ă autochthonous MDR A. baumannii isolated from patients in Libya, ă indicating that there is a longstanding infection control problem in ă these hospitals. (C) 2016 Elsevier B.V. and International Society of ă Chemotherapy. All rights reserved

Genomic Characterization and Phylogenetic Analysis of SARS-CoV-2 in Libya

The COVID-19 epidemic started in Libya in March 2020 and rapidly spread. To shed some light on the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) strains circulating in Libya, viruses isolated from 10 patients in this country were sequenced, characterized at the genomic level, and compared to genomes isolated in other parts of the world. As nine genomes out of 10 belonged to the SS1 cluster and one to SS4, three datasets were built. One included only African strains and the other two contained internationally representative SS1 and SS4 genomes. Genomic analysis showed that the Libyan strains have some peculiar features in addition to those reported in other world regions. Considering the countries in which the strains are genetically more similar to the Libyan strains, SARS-CoV-2 could have entered Libya from a North African country (possibly Egypt), sub-Saharan Africa (e.g., Ghana, Mali, Nigeria), the Middle East (e.g., Saudi Arabia), or Asia (India, Bangladesh)

Influenza vaccination situation in Middle-East and North Africa countries: Report of the 7th MENA Influenza Stakeholders Network (MENA-ISN)

Background: The Middle East and North Africa (MENA) region faces a dual challenge with regard to influenza infection due to severe zoonotic influenza outbreaks episodes and the circulation of Northern Hemisphere human influenza viruses among pilgrims. Methods: The MENA Influenza Stakeholder Network (MENA-ISN) was set-up with the aim of increasing seasonal influenza vaccination coverage by (i) enhancing evidence-based exchanges, and (ii) increasing awareness on the safety and benefits of seasonal vaccination. During the 7th MENA-ISN meeting, representatives from 8 countries presented their influenza surveillance, vaccination coverage and actions achieved and provided a list of country objectives for the upcoming 3 years. Results: MENA-ISN countries share the goal to reduce influenza related morbidity and mortality. Participants admitted that lack of knowledge about influenza, its consequences in terms of morbidity, mortality and economy are the major barrier to attaining higher influenza vaccination coverage in their countries. The cost of the vaccine is another key barrier that could contribute to low vaccination coverage. Participants drew a list of strategic interventions to bridge gaps in the knowledge of influenza burden in this region. Conclusions: Participating countries concluded that despite an increase in vaccine uptake observed during the last few years, influenza vaccination coverage remains relatively low. Priority areas should be identified and action plans tailored to each country situation set-up to investigate the best way to move forward. Keywords: Influenza, Vaccination coverage, Surveillance, Middle East and North Afric

Influenza surveillance in Middle East, North, East and South Africa: Report of the 8th MENA Influenza Stakeholders Network

International audienc

Influenza vaccination situation in Middle-East and North Africa countries: Report of the 7th MENA Influenza Stakeholders Network (MENA-ISN)

Background: The Middle East and North Africa (MENA) region faces a dual challenge with regard to influenza infection due to severe zoonotic influenza outbreaks episodes and the circulation of Northern Hemisphere human influenza viruses among pilgrims. Methods: The MENA Influenza Stakeholder Network (MENA-ISN) was set-up with the aim of increasing seasonal influenza vaccination coverage by (i) enhancing evidence-based exchanges, and (ii) increasing awareness on the safety and benefits of seasonal vaccination. During the 7th MENA-ISN meeting, representatives from 8 countries presented their influenza surveillance, vaccination coverage and actions achieved and provided a list of country objectives for the upcoming 3 years. Results: MENA-ISN countries share the goal to reduce influenza related morbidity and mortality. Participants admitted that lack of knowledge about influenza, its consequences in terms of morbidity, mortality and economy are the major barrier to attaining higher influenza vaccination coverage in their countries. The cost of the vaccine is another key barrier that could contribute to low vaccination coverage. Participants drew a list of strategic interventions to bridge gaps in the knowledge of influenza burden in this region. Conclusions: Participating countries concluded that despite an increase in vaccine uptake observed during the last few years, influenza vaccination coverage remains relatively low. Priority areas should be identified and action plans tailored to each country situation set-up to investigate the best way to move forward. (C) 2018 The Authors. Published by Elsevier Limited on behalf of King Saud Bin Abdulaziz University for Health Sciences