Molecular characterization of enterovirus detected in cerebrospinal fluid and wastewater samples in Monastir, Tunisia, 2014-2017.

BACKGROUND: Enteroviruses (EVs) are considered the main causative agents responsible for aseptic meningitis worldwide. This study was conducted in the Monastir region of Tunisia in order to know the prevalence of EV infections in children with meningitis symptoms. Detected EV types were compared to those identified in wastewater samples. METHODS: Two hundred CSF samples collected from hospitalized patients suspected of having aseptic meningitis for an EV infection between May 2014 and May 2017 and 80 wastewater samples collected in the same time-period were analyzed. EV detection and genotyping were performed using PCR methods followed by sequencing. Phylogenetic analyses in the 3'-VP1 region were also carried-out. RESULTS: EVs were detected in 12% (24/200) CSF and in 35% (28/80) wastewater samples. EV genotyping was reached in 50% (12/24) CSF-positive samples and in 64% (18/28) sewage. Most frequent types detected in CSF were CVB3, E-30 and E-9 (25% each). In wastewater samples, the same EVs were identified, but also other types non-detected in CSF samples, such as E-17,CVA9 and CVB1 from EV species B, and EV-A71 and CVA8 from EV-A, suggesting their likely lower pathogenicity. Phylogenetic analysis showed that within the same type, different strains circulate in Tunisia. For some of the EV types such as E-9, E-11 or CVB3, the same strains were detected in CSF and wastewater samples. CONCLUSIONS: Epidemiological studies are important for the surveillance of the EV infections and to better understand the emergence of certain types and variants.

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.

Phylogenetic analysis of the neuraminidase segment gene of Influenza A/H1N1 strains isolated from Monastir Region (Tunisia) during the 2017-2018 outbreak.

Influenza A/H1N1 is widely considered to be a very evolutionary virus causing major public health problems. Since the pandemic of 2009, there has been a rapid rise in human Influenza virus characterization. However, little data is available in Tunisia regarding its genetic evolution. In light of this fact, our paper aim is to genetically characterize the Neuraminidase, known as the target of antiviral inhibitors, in Tunisian isolates circulating in Monastir region during 2017-2018. In total of 31 positive Influenza A/H1N1 detected by multiplex real-time PCR, RT-PCR of neuraminidase was performed. Among the 31 positive samples, 7 samples representing fatal and most severe cases were conducted for sequencing and genetic analysis. The results thus obtained showed genetic evolution of the A/H1N1 neuraminidase between 2009 and 2010 and 2018-2019 outbreaks. All Tunisian isolates were genetically related to the recommended vaccine strain with a specific evolution. Moreover, the phylogenetic analysis demonstrated that France and especially Italian strains were the major related strains. Interestingly, our results revealed a specific cluster of Tunisian isolates where two intragroup were evolved in correlation with the severity and the fatalities cases. From the outcome of our investigation, this study confirms the genetic evolution of the Influenza A virus circulating in Tunisia and gives a preliminary analysis for a better comprehension of new emerging Tunisian strain's virulence and thus, a more appropriate monitoring of Influenza virus A/H1N1 during each round of outbreaks. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11756-021-00723-y.

Bacterial and Viral Infection in Patients Hospitalized for Acute Exacerbation of Chronic Obstructive Pulmonary Disease: Implication for Antimicrobial Management and Clinical Outcome.

Patients with chronic obstructive pulmonary disease (COPD) exhibit frequent acute exacerbations (AE). The objectives of this study were first to evaluate the prevalence of pathogens associated to these episodes by combining conventional bacteriology and multiplex viral and bacterial PCR assays in sputum specimens, and second to determine whether C-reactive protein (CRP) value and clinical outcome could be influenced by the type of microbial agent(s) recovered from these samples. A cohort of 84 Tunisian patients hospitalized at the emergency room for AECOPD was investigated prospectively for the semi-quantitative detection of bacteria by conventional culture (the threshold of positivity was of 107 CFU/ml) and for the detection of viral genome and DNA of atypical bacteria by quantitative PCR using two commercial multiplex respiratory kits (Seegene and Fast-track). The two kits exhibited very similar performances although the Seegene assay was a bit more sensitive. A large number and variety of pathogens were recovered from the sputum samples of these 84 patients, including 15 conventional bacteria, one Chlamydia pneumoniae and 63 respiratory viruses, the most prevalent being rhinoviruses (n = 33) and influenza viruses (n = 13). From complete results available for 74 patients, the presence of bacteria was significantly associated with risk of recurrence at 6 and 12 months post-infection. The combination of these different markers appears useful for delineating correctly the antimicrobial treatment and for initiating a long-term surveillance in those patients with high risk of recurrent exacerbation episodes. A prospective study is required for confirming the benefits of this strategy aimed at improving the stewardship of antibiotics.

Comparative study of virulence factors among methicillin resistant Staphylococcus aureus clinical isolates.

BACKGROUND: Methicillin resistant Staphylococcus aureus (MRSA) is recognized worldwide as a leading cause of hospital and community infections. Biofilm formation by MRSA is an extremely important virulence factor to be understood. Our aim was to establish phenotypic and genotypic characterization of virulence factors among 43 MRSA clinical isolates in a Tunisian hospital. METHODS: We investigated enzymatic profiles, biofilm production and prevalences of genes encoding intracellular adhesion molecules (icaA and icaD), Microbial Surface Components Recognizing Adhesive Matrix Molecules genes (fnbA, fnbB and cna) and exoenzymes genes (geh, sspA and sspB). RESULTS: Our findings revealed that caseinase, gelatinase, lipase and lecithinase activities were detected in 100%, 100%, 76.6% and 93.3% of cases respectively. This study showed that 23 strains (76.7%) were slime producers on Congo red medium. Furthermore, 46.5% and 53.5% of isolates were respectively highly and moderately biofilm-forming on polystyrene. Significant association was found between both biofilm tests. PCR detection showed that 74.4%, 18.6%, 69.8%, 65.1% and 74.4% of isolates harbored fnbA, fnbB, icaA, icaD and cna genes respectively. In addition, 34.9%, 18.6% and 30.2% of MRSA strains were found positive for sspA, sspB and geh genes respectively. Further, statistical data showed that the presence of the fnbA and fnbB genes was significantly associated with a high biofilm production on polystyrene. However, no statistical association was observed for the icaA, icaD and cna genes. CONCLUSIONS: This study indicates that the detection of fnbA and fnbB contributing to the first step of biofilm formation has been predictable of high biofilm production. As studied factors contribute to MRSA virulence, this research could be of value in orienting towards the development of new preventive and therapeutic measures.

Lessons about Causes and Management of an Ebola Outbreak.

Ebola virus disease (EVD) is one of the deadliest viral diseases. It is characterized by a high mortality rate due to the lack of effective and safe treatments or vaccines and its ability to spread at an unstoppable pace. The West Africa outbreak ended but the disease may strike again at any time. The latest epidemic was, by far, the deadliest to date. The most concern was why this outbreak was so different from the previous ones. We proposed in this review firstly to summarize the principal causes of its unprecedented spread and secondly to identify the steps for an effective management approach of a future Ebola outbreak. Attributes of the affected populations and insufficient control efforts were the main reasons of its amplification. This was complicated by a delayed international response. The health crisis was ignored for months until it got out of control. The management of Ebola presents a multitude of challenges in terms of preparedness and capacity to face an outbreak. In addition to the need for adequate health care facilities, ongoing surveillance tools, appropriate training of health workers and raising population awareness, readiness requires a large scale and coordinated international intervention to support affected and at-risk nations, to intensify their response activities and to strengthen their capacities. Constant interventions after the outbreak are still needed to ensure that vital health and related service institutions in these countries are fully prepared to respond to an eminent epidemic.

Hepatitis C Genotype Prevalence in Monastir Region, Tunisia: Correlation between 5' Untranslated Region (5'UTR), Non-structural 5B (NS5B), and Core Sequences in HCV Subtyping.

Hepatitis C virus (HCV) is a causative agent of chronic liver disease, cirrhosis, and hepatocellular carcinoma. It constitutes a major public health around the world. There is no vaccine available against HCV, and current therapies are effective in only small percentage of patients. HCV has wide population-specific genotype variability. Genotype knowledge and viral load assessment are equally important for designing therapeutic strategies. Taking into account that the molecular epidemiology of HCV variants circulating in Tunisia is not yet well elucidated, and that, at present, little is known about the distribution pattern of HCV in Monastir region (Tunisia), we aimed, herein, to evaluate the prevalence of HCV genotypes in Monastir and to identify risk-related factors. For this purpose, 50 anti-HCV antibody-positive cases were diagnosed and subjected to viral RNA extraction, amplification, genotyping, and viral load quantification. Molecular epidemiology was studied by 5' untranslated region (5' UTR) sequencing as compared with the non-structural 5B (NS5B) and core region sequences. Overall concordance between 5' UTR, core, and NS5B sequencing was 100 %. The highest prevalent genotype was 1b (50 %) followed by genotypes 1a (16 %), 4a (12 %), 2a (10 %), 2c (8 %), and 3a (4 %). Interestingly, the subtype 1b had a statistically significant higher viral load than the other genotypes followed by subtype 1a. Based on these data, this study revealed a high prevalence of HCV genotype 1 (subtypes 1b and 1a) compared to other genotypes. A continued monitoring of HCV and knowledge of circulating genotypes could impact on future vaccine formulations.

Enterovirus meningitis in Tunisia (Monastir, Mahdia, 2011-2013): identification of virus variants cocirculating in France.

Acute enterovirus (EV) meningitis is a frequent cause of hospitalisation, and over 100 EV serotypes may be involved. A total of 215 patients of all ages with meningitis signs were investigated in 2 Tunisian hospitals. Their cerebrospinal fluid (CSF) was analysed retrospectively for EVs with a TaqMan real-time RT-qPCR. The virus strains were typed, and their evolutionary relationships were determined by Bayesian phylogenetic methods. An EV genome was detected in 21/215 patients (9.8%). The CSF viral loads ranged from 3.27 to 5.63 log10 genome copies/mL. The strains were identified in 13/21 patients and assigned to EV-B types. Viruses identified in Tunisian patients were genetically related to variants detected in France. The viral loads were similar in Tunisian and French patients for most EV types. The phylogenetic data and viral loads determined in Tunisian and French patients suggest that close EV variants were involved in aseptic meningitis in the 2 countries over a same period.

[Management of the preanalytical phase: experience of the microbiology laboratory of "Fattouma Bourguiba" hospital of Monastir]. / Management de la phase pré-analytique: expérience pratique au laboratoire de microbiologie de l'hôpital Fattouma Bourguiba de Monastir.

UNLABELLED: We propose in this work to study the details of the preanalytical phase (PAP) in microbiology, in order to determinate gaps with the requirement of good laboratory practice guideline (GLPG), causes of dysfunction and actions to improve its quality in our establishment. METHODS: This study was carried out in the microbiology laboratory of the University Hospital of Monastir. We conducted a self-assessment grid and a satisfaction survey phlebotomist staff. A literature review was conducted in accordance with the requirements of normative and regulatory documents (ISO 15189 standard and GLPG). The analysis of non-conformities was performed by the method of 5M and the risk analysis by the preliminary risk analysis (PRA). RESULTS: The results show that the fault lies primarily in the management of human resources. The cause analysis puts the focus on a lack of awareness and training of the responsible staff. Risk analysis reveals another failure in the communication between laboratory and clinicians, and in the formulation of methods (procedures, instructions…). CONCLUSION: The Study of the PPA in details shows that all steps are critical. Indeed, the management of this phase requires the application of the requirements of the GLPG and awareness of a total quality management.