Diagnostic stewardship in infectious diseases:a continuum of antimicrobial stewardship in the fight against antimicrobial resistance

Antimicrobial resistance (AMR) has been exacerbated by the inappropriate use of diagnostics, leading to excessive prescription of antimicrobials, and is an imminent threat to global health. Diagnostic stewardship (DS) is an auxiliary to antimicrobial stewardship (AMS) and comprises ordering the right tests, for the right patient, at the right time. It also promotes the judicious use of rapid and novel molecular diagnostic tools to enable the initiation of proper antibiotic therapy, while avoiding excessive use of broad-spectrum antibiotics. Proper interpretation of test results is crucial to avoid overdiagnosis and excessive healthcare costs. Although many rapid diagnostic tools have been developed with a high diagnostic yield, they are often limited by accessibility, cost, and lack of knowledge regarding their use. Careful consideration of clinical signs and symptoms with knowledge of the local epidemiology are essential for DS. This enables appropriate interpretation of microbiological results. Multidisciplinary teams that include well trained professionals should cooperate to promote DS. Challenges and barriers to the implementation of DS are mostly caused by scarcity of resources and lack of trained personnel and, most importantly, lack of knowledge. The lack of resources is often due to absence of awareness of the impact that good medical microbiology diagnostic facilities and expertise can have on the proper use of antibiotics.</p

Infections Du Site Opératoire À l’Hôpital National De Zinder, Niger: Aspects Épidémiologiques Et Bactériologiques

Objectif : Rapporter les caractéristiques épidémiologiques et bactériologiques des infections du site opératoire (ISO) dans les services de chirurgie de l'hôpital national de Zinder, Niger. Patients et méthodes : Il s’agissait d’une étude transversale qui s’est déroulée sur une période de 5 mois (Mai à Aout 2016) aux services de chirurgie et de laboratoire de l’Hôpital National de Zinder (HNZ) au Niger incluant tous les patients opérés et ayant&nbsp;développé une ISO. Résultats : Durant l’étude, 485 patients avaient été opérés et 38 cas d’ISO étaient enregistrés soit une incidence de 7,83 %. L’âge médian était de 31,5 ans (8-78 ans). Le sexe masculin était majoritaire avec un sexratio de 6,6 (33/5). Les urgences chirurgicales représentaient 57,9% des cas (n=22). Selon la classification d’Alte Meier, 13 cas (34,2%) étaient considérés comme une chirurgie contaminée et 21 cas (55,3%) une chirurgie sale. Les ISO étaient superficielles dans 36,8% (n=14), profondes dans 42,1% (n=16). Sur les 38 prélèvements analysés, 33 cultures étaient positives soit 86,8%. Les entérobactéries représentaient 69,7% (n=23), les Cocci à Gram positif 24,2% (n=8). Escherichia coli était l’espèce prédominante avec 45,5% (n=15), suivie de Staphylococcus aureus avec 18,2% (n=6). La majeure partie des cultures positives provenait du service de chirurgie viscérale 15 cas (45,5%) puis de l’urologie et de traumatologie-orthopédie avec respectivement 10 cas (30,3%) et 8 cas (24,2%). La quasi-totalité des entérobactéries était résistante aux antibiotiques usuels (amoxicilline, amoxicilline-acide clavulanique) et plus de 84% étaient résistantes à la ceftriaxone. En général les bacilles Gram négatifs étaient sensibles à l’imipenème (100%), la colistine (93,8%), l’aztréonam (68,7%) et le chloramphénicol (47,8%). Les cocci-Gram positifs étaient sensibles à la vancomycine, au chloramphénicol et à l’érythromycine dans respectivement 100% ; 62,5% et 57,1%. Conclusion : Les infections du site opératoires représentent un problème majeur. La fréquence des ISO rend indispensable la mise en place d'une équipe multidisciplinaire pour la surveillance de celles-ci. Le fort taux de résistance aux antibiotiques usuels doit susciter des actions préventives et systématiser l’examen bactériologique en cas de suppurations postopératoires. Objective: To report the epidemiological and bacteriological characteristics of surgical site infections (SSI) in the surgical departments of Zinder National Hospital. Patients and methods: This was a cross-sectional study that took place over a period of 5 months (May to August 2016) at the Zinder National Hospital (HNZ) Surgical and Laboratory Services in Niger including all patients operated on and having developed an SSI. Results: During the study, 485 patients had been operated on and 38 cases of ISO were recorded with an incidence of 7.83%. The median age was 31.5 years (8-78 years). The male sex was in the majoritywith a sex ratio of 6.6 (33/5). Surgical&nbsp;emergencies accounted for 57.9% of cases (n = 22). According to Altemeier's classification, 13 cases (34.2%) were considered as contaminated surgery and 21 cases (55.3%) were dirty surgery. Surgical site infections were superficial in 36.8% (n = 14), deep in 42.1% (n = 16). Of the 38 samplings analyzed, 33 cultures were positive, i.e. 86.8%. The enterobacteria accounted for 69.7% (n = 23), Gram-positive Cocci 24.2% (n = 8). Escherichia coli was the predominant species with 45.5% (n = 15), followed by Staphylococcus aureus with 18.2% (n = 6). The majority of positive cultures came from the visceral surgery department 15 cases (45.5%) followed by urology and orthopedic trauma with respectively 10 cases (30.3%) and 8 cases (24.2%). Virtually all enterobacteria were resistant to the usual antibiotics (amoxicillin, amoxicillinclavulanic acid) and more than 84% were resistant to ceftriaxone. In general Gram-negative bacilli were sensitive to imipenem (100%), colistin (93.8%), aztreonam (68.7%) and chloramphenicol (47.8%). Gram-positive cocci were sensitive to vancomycin, chloramphenicol and erythromycin in 100%, respectively; 62.5% and 57.1%. Conclusion: Surgical site infections represent a major problem. The frequency of SSI makes it essential to set up a multidisciplinary team to monitor them. The high rate of resistance to the usual antibiotics must provoke preventive actions and systematize the bacteriological examination in case of postoperative suppuration

Dynamics of germs responsible for acute bacterial meningitis in Burkina Faso in the last ten years (2005-2014)

The aim of this study was to analyze ten (10) years of epidemiological surveillance data of meningitis in Burkina Faso for high risk germs patterns identification in order to contribute to the strengthening of prevention strategies.A retrospective study of the past decade (2005- 2014) of cases of acute bacterial meningitis occurred in the thirteen health regions, collected through epidemiological surveillance data meningitis in Burkina Faso. From a total of 88 057 suspected cases of acute bacterial meningitis, we recorded 9134 deaths. From the laboratory confirmed cases, the identified germs were as follows: 56.79% of Neisseria meningitidis, 41.09% of Streptococcus pneumoniae and 2.13% of Haemophilus influenzae. Among the meningococcus isolated, we observed the following distribution: 23.11% of NmA, 58.84% of NmW and 18% of NmX.Mortality associated with acute bacterial meningitis remains still high in Burkina Faso despite the complete disappearance of NmA since 2012, after the conjugate vaccine A (MenAfriVac) has been introduced in this country. However the emergence of NmX, the reemergence of NmW and the persistence of high prevalence of Streptococcus pneumoniae are a major concern in the fight against meningitis in Burkina Faso. So, it is necessary, in addition to the strengthening of surveillance, diagnosis and case management to develop and make available and accessible a conjugate trivalent vaccine against NmA the NmX and NmW serogroups.Keywords: meningococcal meningitis, W and X serogroups, Streptococcus pneumoniae, MenAfriVa

Genomic Epidemiology of SARS-CoV-2 in Western Burkina Faso, West Africa.

BACKGROUND: After its initial detection in Wuhan, China, in December 2019, SARS-CoV-2 has spread rapidly, causing successive epidemic waves worldwide. This study aims to provide a genomic epidemiology of SARS-CoV-2 in Burkina Faso. METHODS: Three hundred and seventy-seven SARS-CoV-2 genomes obtained from PCR-positive nasopharyngeal samples (PCR cycle threshold score &lt; 35) collected between 5 May 2020, and 31 January 2022 were analyzed. Genomic sequences were assigned to phylogenetic clades using NextClade and to Pango lineages using pangolin. Phylogenetic and phylogeographic analyses were performed to determine the geographical sources and time of virus introduction in Burkina Faso. RESULTS: The analyzed SARS-CoV-2 genomes can be assigned to 10 phylogenetic clades and 27 Pango lineages already described worldwide. Our analyses revealed the important role of cross-border human mobility in the successive SARS-CoV-2 introductions in Burkina Faso from neighboring countries. CONCLUSIONS: This study provides additional insights into the genomic epidemiology of SARS-CoV-2 in West Africa. It highlights the importance of land travel in the spread of the virus and the need to rapidly implement preventive policies. Regional cross-border collaborations and the adherence of the general population to government policies are key to prevent new epidemic waves

The African Network for Improved Diagnostics, Epidemiology and Management of common infectious Agents

In sub-Saharan Africa, acute respiratory infections (ARI), acute gastrointestinal infections (GI) and acute febrile disease of unknown cause (AFDUC) have a large disease burden, especially among children, while respective aetiologies often remain unresolved. The need for robust infectious disease surveillance to detect emerging pathogens along with common human pathogens has been highlighted by the ongoing novel coronavirus disease2019 (COVID-19) pandemic. The African Network for Improved Diagnostics, Epidemiology and Management of Common Infectious Agents (ANDEMIA) is a sentinel surveillance study on the aetiology and clinical characteristics of ARI, GI and AFDUC in sub-Saharan Africa.Peer Reviewe

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants

Ten golden rules for optimal antibiotic use in hospital settings: the WARNING call to action

Antibiotics are recognized widely for their benefits when used appropriately. However, they are often used inappropriately despite the importance of responsible use within good clinical practice. Effective antibiotic treatment is an essential component of universal healthcare, and it is a global responsibility to ensure appropriate use. Currently, pharmaceutical companies have little incentive to develop new antibiotics due to scientific, regulatory, and financial barriers, further emphasizing the importance of appropriate antibiotic use. To address this issue, the Global Alliance for Infections in Surgery established an international multidisciplinary task force of 295 experts from 115 countries with different backgrounds. The task force developed a position statement called WARNING (Worldwide Antimicrobial Resistance National/International Network Group) aimed at raising awareness of antimicrobial resistance and improving antibiotic prescribing practices worldwide. The statement outlined is 10 axioms, or “golden rules,” for the appropriate use of antibiotics that all healthcare workers should consistently adhere in clinical practice

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

Prévalence, circulation et caractérisation des bactéries multirésistantes au Burkina Faso

Antibiotic resistance is a major public health issue, particularly in developing countries where health conditions are still inadequate and antibiotic use is often unjustified and not properly regulated. The main objective of this thesis was to study the prevalence, spread and genetic features of multi-resistant bacteria (MRB) in Burkina Faso, a developing country. This work allows better understanding MRB spread in this country and gives essential information for the development of public health policies. This is the first study in this region and this thesis is therefore an original and informative work. Starting from a review of the literature data on the issue of MRB emergence in West Africa, the specific objectives are: i) to study the prevalence and to characterize phenotypically and genotypically the extended-spectrum beta lactamases (ESBL) in enterobacterial samples isolated from healthy carriers and during the clinical phase of infection; ii) to assess the sensitivity of such enterobacterial samples to carbapenem drugs; iii) to document the prevalence of nasal carriage of methicillin-resistant Staphylococcus aureus (MRSA) and to molecularly characterize all S. aureus isolates. Samples were collected by the public health services of three Burkina Faso University Hospital Centers (UHC) and were then cultured at the Laboratory of Bacteriology of Montpellier UHC [total n= 594 isolates of which 522 were Enterobacteriaceae isolates (214 from healthy carriers and 308 from patients with clinical infection) and 72 S. aureus isolates]. Bacterial species were identified by MALDI-TOF mass spectrometry. Antibiotic sensitivity was tested using the agar diffusion method. ESBL and carbapenemases in enterobacterial isolates were identified using molecular methods (PCR amplification and sequencing). S. aureus isolates were genetically characterized by using DNA arrays. This work shows that in Burkina Faso, ESBL-producing enterobacterial strains are frequent both in healthy carriers and hospitalized patients and that previous antibiotic use or hospitalizations are risk factors for colonization. Among the ESBL-producing enterobacterial strains, Escherichia coli was the predominant species and most ESBL-producing isolates were CTX-M-15, followed by CTX-M-14, 27 and SHV-12. The analysis of the E. coli phylogenetic groups suggests a plasmid-mediated spread of CTX-M-15 genes and not linked to an epidemic clone. Moreover, E. coli strains that produce the carbapenemase OXA-181 and with an IncX3-type plasmid have been identified. Concerning S. aureus, the rate of nasal carriage was classical with a low prevalence of MRSA. Among the S. aureus nasal samples, a high proportion of virulence genes (Panton Valentin leukocidin and EDIN) was detected. This constitutes an important risk of severe disease during clinical infection. The genetic analysis of the S. aureus isolates showed great clone diversity. These data are essential for understanding MRB epidemiology in Burkina Faso and represent a base for fighting and controlling resistant pathogens. In conclusion, these first studies carried out in Burkina Faso allow defining the future research perspectives and strategies to be developed for controlling the emergence and spread of these MRB.La résistance aux antibiotiques demeure un problème majeur de santé publique particulièrement dans les pays en voie de développement (PVD) où les conditions d’hygiène sont encore précaires et où l’utilisation des antibiotiques est souvent abusive et très peu contrôlée. Cette thèse a pour objectif principal d’étudier la prévalence, la circulation et la caractérisation génétique des bactéries multirésistantes (BMR) dans un PVD, le Burkina Faso. Ce travail permet de mieux comprendre la propagation de ces BMR dans ce pays et de donner des informations indispensables pour les services de santé publique. Dans cette région, c’est la première étude du genre et cette thèse représente donc un travail original et informatif. A partir d’une revue de la littérature réalisée sur la problématique de l’émergence des BMR en Afrique de l’ouest, les objectifs spécifiques sont : i) d’étudier la prévalence et la caractérisation phénotypique et génotypique des bêta-lactamases à spectre élargi (BLSE) chez les entérobactéries isolées en portage et dans les processus infectieux ; ii) d’évaluer la sensibilité des entérobactéries aux carbapénèmes ; iii) de documenter la prévalence du portage nasal de Staphylococcus aureus (SAUR) résistant à la méticilline (SARM) ainsi que d’effectuer la caractérisation moléculaire les isolats de SAUR. Les isolats ont été prélevés par les services de santé publique au sein des 3 CHU du Burkina et ont été remis en culture au laboratoire de bactériologie du CHU de Montpellier [un total de 594 souches, 522 entérobactéries (214 en portage et 308 dans les processus infectieux) et 72 SAUR]. L’identification des espèces bactériennes repose sur la spectrométrie de masse MALDI-TOF. L’évaluation de la sensibilité aux antibiotiques s’appuie sur la méthode de diffusion en milieu gélosé. Les BLSE et les carbapénémases chez les entérobactéries sont identifiées par méthodes moléculaires (PCR et séquençage) et la caractérisation génétique des isolats de SAUR par une technique de puce à ADN. Au Burkina Faso, les points importants sont : des taux très élevés en portage et dans les infections d’entérobactéries sécrétrices de BLSE en hospitalier et en communautaire; les antécédents de consommation d’antibiotiques ou d’hospitalisation sont des facteurs de risque de portage ; par les isolats BLSE, Escherichia coli est l’espèce prédominante ; la majorité des BLSE sont des CTX-M-15, suivi de CTX-M-14, 27 et SHV-12 ; l’étude des phylogroupes d’E. coli suggère une expansion des gènes CTX-M-15 d’origine plasmidique et non liée à une épidémie de clone ; des isolats d’E. coli producteurs de carbapénémase OXA-181 avec un support génétique plasmidique de type IncX3 sont identifiés. On observe un taux de portage nasal de SAUR classique avec une très faible prévalence de SARM ; on note dans une forte proportion des gènes de virulence (Leucocidine de Panton Valentin et du facteur EDIN) parmi les SAUR en portage constituant des facteurs de risques de gravité lors des infections ; l’analyse génétique des isolats de SAUR montre une grande diversité de clones. Les études de prévalence et de génétiques apportent des informations fondamentales pour l’épidémiologie des BMR, base indispensable pour appréhender la lutte et le contrôle de ces organismes pathogènes résistants. En conclusion, ces premières études réalisées au Burkina permettent de définir les perspectives de recherche et les stratégies à développer pour le contrôle l’émergence et la diffusion de ces BMR