Coronavirus disease 2019 (COVID-19) pandemic triggered an unprecedented global effort in developing rapid and inexpensive diagnostic and prognostic tools. Since the genome of SARS-CoV-2 was uncovered, detection of viral RNA by RT-qPCR has played the most significant role in preventing the spread of the virus through early detection and tracing of suspected COVID-19 cases and through screening of at-risk population. However, a large number of alternative test methods based on SARS-CoV-2 RNA or proteins or host factors associated with SARS-CoV-2 infection have been developed and evaluated. The application of metabolomics in infectious disease diagnostics is an evolving area of science that was boosted by the urgency of COVID-19 pandemic. Metabolomics approaches that rely on the analysis of volatile organic compounds exhaled by COVID-19 patients hold promise for applications in a large-scale screening of population in point-of-care (POC) setting. On the other hand, successful application of mass-spectrometry to detect specific spectral signatures associated with COVID-19 in nasopharyngeal swab specimens may significantly save the cost and turnaround time of COVID-19 testing in the diagnostic microbiology and virology laboratories. Active research is also ongoing on the discovery of potential metabolomics-based prognostic markers for the disease that can be applied to serum or plasma specimens. Several metabolic pathways related to amino acid, lipid and energy metabolism were found to be affected by severe disease with COVID-19. In particular, tryptophan metabolism via the kynurenine pathway were persistently dysregulated in several independent studies, suggesting the roles of several metabolites of this pathway such as tryptophan, kynurenine and 3-hydroxykynurenine as potential prognostic markers of the disease. However, standardization of the test methods and large-scale clinical validation are necessary before these tests can be applied in a clinical setting. With rapidly expanding data on the metabolic profiles of COVID-19 patients with varying degrees of severity, it is likely that metabolomics will play an important role in near future in predicting the outcome of the disease with a greater degree of certainty.

Nosocomial carbapenem-non-susceptible Enterobacteriaceae are moderately spread in Lebanon and the predominant mechanism is OXA-48 production.

This survey established baseline evidence of OXA-23 and GES-11-producing A. baumannii in Lebanon, indicating the need for further surveillance.

Introduction Although extended-spectrum β-lactamase (ESBL)–producing Enterobacterales are a public health problem in the Arabian Peninsula, data on the molecular characteristic of their antimicrobial resistance determinants in children is limited. Aim To determine the molecular characteristics of ESBL-producing Escherichia coli and Klebsiella pneumoniae in the pediatric population of Qatar. Methods Whole-genome sequencing was performed on ESBL-producing E. coli and K. pneumoniae isolates recovered from screening and clinical specimens from pediatric patients at Sidra Medicine in Doha from January to December 2018. Results A total of 327 ESBL producers were sequenced: 254 E. coli and 73 K. pneumoniae . Non-susceptibility rates to non-β-lactam antibiotics for both species were 18.1 and 30.1% for gentamicin, 0.8 and 4.1% for amikacin, 41.3 and 41.1% for ciprofloxacin, and 65.8 and 76.1% for cotrimoxazole. The most common sequence types (STs) were ST131 (16.9%), ST38 and ST10 (8.2% each) in E. coli and ST307 (9.7%), and ST45 and ST268 (6.9% each) in K. pneumoniae . CTX-M type ESBLs were found in all but one isolate, with CTX-M-15 accounting for 87.8%. Among other β-lactamases, TEM-1B and OXA-1 were coproduced in 41 and 19.6% of isolates. The most common plasmid-mediated quinolone resistance genes cocarried were qnr A/B/E/S (45.3%). Ninety percent of gentamicin non-susceptible isolates harbored genes encoding AAC(3) enzymes, mainly aac(3)-IIa . Only two of 57 isolates harboring aac(6′)-Ib-cr were non-susceptible to amikacin. Chromosomal mutations in genes encoding DNA gyrase and topoisomerase IV enzymes were detected in 96.2% fluoroquinolone-non-susceptible E. coli and 26.7% fluoroquinolone-non-susceptible K. pneumoniae . Conclusion Our data show that CTX-M enzymes are largely the most prevalent ESBLs in children in Qatar with a predominance of CTX-M-15. Carbapenem-sparing options to treat ESBL infections are limited, given the frequent coproduction of OXA-1 and TEM-1B enzymes and coresistance to antibiotic classes other than β-lactams.

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Background: Antimicrobial resistance (AMR) is a major clinical challenge globally. It is mainly a consequence of inappropriate prescribing and use of antibiotics. Antimicrobial stewardship (AMS) ensures that antibiotics are prescribed and used appropriately. This study assessed AMS practice in selected Nigerian hospitals.Methodology: This was a cross sectional survey of 20 Federal, State and Private tertiary hospitals randomly selected from the six geopolitical zones of Nigeria. Using an adapted WHO tool on AMS, data were collected from each hospital as regard the existence of AMS committee, Accountability and Responsibility, AMS actions, Education and Training, Monitoring and Evaluation, Infection Prevention and Control (IPC) practice, facilities to support AMS, and challenges to AMS implementation. Gaps and challenges to the implementation of the AMS among the hospitals were identified.Results: Only 6 (30%) of the 20 hospitals had AMS committees while 2 (10%) had any evidence of leadership commitment to AMS. All the hospitals had laboratory facilities to support culture and sensitivity testing. There were no regular AMS-related education or training, monitoring, evaluation or reporting activities in the hospitals, except in 7 (25%) that had participated in the global point prevalence survey (Global-PPS) of antimicrobial use and resistance being hosted by the University of Antwerp, Belgium. Challenges impeding AMS activities included lack of human and financial resources, prescribers’ opposition, lack of awareness and absence of AMS committees. Most of the gaps and challenges bordered on seeming lack of knowledge and inadequate communication among prescribers and other stakeholders.Conclusion: There is need for intense education and training activities for prescribers and other stakeholders, including but not limited to hospital administrators. Keywords: Survey, Antimicrobial Stewardship, Antimicrobial Resistance; Nigeria   French title: Mise en œuvre de la gestion des antimicrobiens dans les hôpitaux Nigérians: lacunes et défis Contexte: La résistance aux antimicrobiens (RAM) est un défi clinique majeur à l'échelle mondiale. C'estprincipalement une conséquence d'une prescription et d'une utilisation inappropriées d'antibiotiques. La gestion des antimicrobiens (AMS) garantit que les antibiotiques sont prescrits et utilisés de manière appropriée. Cette étude a évalué la pratique de l'AMS dans certains hôpitaux Nigérians. Méthodologie: Il s'agissait d'une enquête transversale de 20 hôpitaux tertiaires fédéraux, d'État et privéssélectionnés au hasard dans les six zones géopolitiques du Nigéria. À l'aide d'un outil OMS adapté sur l'AMS, des données ont été collectées auprès de chaque hôpital en ce qui concerne l'existence d'un comité AMS, la responsabilité et la responsabilité, les actions AMS, l'éducation et la formation, le suivi et l'évaluation, la  pratique de prévention et de contrôle des infections (IPC), les installations pour soutenir l'AMS. et les défis de la mise en œuvre de l'AMS. Les lacunes et les défis liés à la mise en œuvre de l'AMS parmi les hôpitaux ont été identifiés. Résultats: Seuls 6 (30%) des 20 hôpitaux avaient des comités AMS tandis que 2 (10%) avaient des preuves d'engagement du leadership envers l'AMS. Tous les hôpitaux disposaient d'installations de laboratoire pour soutenir la culture et les tests de sensibilité. Il n'y avait pas d'activités régulières d'éducation ou de formation, de suivi, d'évaluation ou de rapportage liées à la MGS dans les hôpitaux, sauf dans 7 (25%) qui avaient participé à l'enquête mondiale sur la prévalence ponctuelle (Global-PPS) de l'utilisation et de la résistance aux  antimicrobiens organisée par l'Université d'Anvers, Belgique. Les défis entravant les activités de l'AMS  comprenaient le manque de ressources humaines et financières, l'opposition des prescripteurs, le manque de sensibilisation et l'absence de comités AMS. La plupart des lacunes et des défis se limitaient à un manque apparent de connaissances et à une communication inadéquate entre les prescripteurs et les autres intervenants.Conclusion: Des activités d'éducation et de formation intensives sont nécessaires pour les prescripteurs et autres intervenants, y compris, mais sans s'y limiter, les administrateurs d'hôpitaux. Mots clés: enquête, gestion des antimicrobiens, résistance aux antimicrobiens; Nigeria  

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