Prevalence of SARS-CoV-2 and co-occurrence/co-infection with malaria during the first wave of the pandemic (the Burkina Faso case)

Africa accounts for 1.5% of the global coronavirus disease 2019 (COVID-19) cases and 2.7% of deaths, but this low incidence has been partly attributed to the limited testing capacity in most countries. In addition, the population in many African countries is at high risk of infection with endemic infectious diseases such as malaria. Our aim is to determine the prevalence and circulation of SARS-CoV-2 variants, and the frequency of co-infection with the malaria parasite. We conducted serological tests and microscopy examinations on 998 volunteers of different ages and sexes in a random and stratified population sample in Burkina-Faso. In addition, nasopharyngeal samples were taken for RT-qPCR of SARS-COV-2 and for whole viral genome sequencing. Our results show a 3.2% and a 2.5% of SARS-CoV-2 seroprevalence and PCR positivity; and 22% of malaria incidence, over the sampling period, with marked differences linked to age. Importantly, we found 2 cases of confirmed co-infection and 8 cases of suspected co-infection mostly in children and teenagers. Finally, we report the genome sequences of 13 SARS-CoV-2 isolates circulating in Burkina Faso at the time of analysis, assigned to lineages: A.19, A.21, B.1.1.404, B.1.1.118, B.1 and grouped into clades; 19B, 20A and 20B. This is the first population-based study about SARS-CoV-2 and malaria in Burkina Faso during the first wave of the pandemic, providing a relevant estimation of the real prevalence of SARS-CoV-2 and variants circulating in this Sub-Saharan African country. Besides, it highlights the low frequency of co-infection with malaria in African communities.This research work received funding from by the European Commission NextGenerationEU (Regulation EU 2020/2094) and grant 202020E159 through CSIC Global Health Platform (PTI Salud Global).N

Fréquence et profils microbiologiques des infections urinaires chez les patients porteurs de sonde à demeure au Laboratoire de Bactériologie du Centre Muraz

Titre court : Fréquence et microbiologie des infections urinaires sur sonde L’infection du tractus urinaire représente un risque majeur chez les personnes porteuses de sonde urinaire. Le risque et le profil des microorganismes en cause peuvent être influencé par l’hygiène précaire dans les structures de soins ainsi qu’au domicile du patient. La présente étude avait pour but de déterminer la fréquence et le profil des agents étiologiques des infections du tractus urinaire chez les patients porteurs de sonde à demeure, reçus pour Examen Cytobactériologique des Urines au Laboratoire de Bactériologie du Centre Muraz. Au total 47 patients ont été inclus dans cette étude entre le 01 Juin 2020 et le 16 Septembre 2021. Parmi ces derniers, le sex-ratio était égal à 14,67 soit 44 patients de sexe masculin, et la moyenne d’âge était de 66,91 avec des extrêmes 25 ans et 98 ans. Cette étude a mis en évidence le fait que les entérobactéries (en particulier E. coli et K. pneumoniae) représentent les agents étiologiques majeurs des infections du tractus urinaire chez les patients porteurs de sondes à demeure avec des cas de résistance importants à la Ceftriaxone, à l’Amoxicilline-Clavulanate et à la Norfloxacine. Ces résultats mettent en lumière le risque élevé d’infection du tractus urinaire chez les porteurs de sondes à demeure, en particulier chez les patients âgés de sexe masculin. Ce risque semble aussi associé à une résistance aux antibiotiques et nécessite un renforcement de l’hygiène pour sa diminution mais également pour un diagnostic de qualité.   Frequency and microbiological profile of urinary tract infections in patients with indwelling catheters at Bacteriology Laboratory of Centre Muraz Short title : Frequency and microbiology of urinary catheter infections   Urinary tract infection is a major risk for people with urinary catheters. The risk and profile of the microorganisms involved can be influenced by poor hygiene in healthcare facilities as well as in the patient's home. The purpose of the present study was to determine the frequency and the profile of urinary tract infections etiological agents in patients with indwelling catheters, requesting Cytobacteriological Examination of the Urine at the Bacteriology Laboratory of Centre Muraz. A total of 47 patients were enrolled in this study between June 01, 2020 and September 16, 2021. Among these, the sex-ratio was equal to 14.67 or 44 male and the average age was 66.91 with extremes of 25 years and 98 years. This study highlighted the fact that enterobacteria (in particular E. coli and K. pneumoniae) represent the major etiological agents of urinary tract infections in patients with indwelling catheters, with significant drug resistance cases associated to Ceftriaxone, Amoxicillin-Clavulanate and Norfloxacin.These results highlight the high risk of urinary tract infection in indwelling tube carriers, especially in elderly male patients. This risk also seems to be associated with antibiotic resistance and requires a strengthening of hygiene for its reduction but also for a quality diagnosis

High prevalence of extended-spectrum ß-lactamase producing enterobacteriaceae among clinical isolates in Burkina Faso

International audienceBACKGROUND:Nothing is known about the epidemiology and resistance mechanisms of extended-spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-PE) in Burkina Faso. The objective of this study was to determine ESBL-PE prevalence and to characterize ESBL genes in Burkina Faso.METHODS:During 2 months (June-July 2014), 1602 clinical samples were sent for bacteriologic investigations to the microbiology laboratories of the tree main hospitals of Burkina Faso. Isolates were identified by mass spectrometry using a matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) BioTyper. Antibiotic susceptibility was tested using the disk diffusion method on Müller-Hinton agar. The different ESBL genes in potential ESBL-producing isolates were detected by PCR and double stranded DNA sequencing. Escherichia coli phylogenetic groups were determined using a PCR-based method.RESULTS:ESBL-PE frequency was 58 % (179 strains among the 308 Enterobacteriaceae isolates identified in the collected samples; 45 % in outpatients and 70 % in hospitalized patients). The CTX-M-1 group was dominant (94 %, CTX-M-15 enzyme), followed by the CTX-M-9 group (4 %). ESBL producers were more often found in E. coli (67.5 %) and Klebsiella pneumoniae (26 %) isolates. E. coli isolates (n = 202; 60 % of all Enterobacteriaceae samples) were distributed in eight phylogenetic groups (A = 49, B1 = 15, B2 = 43, C = 22, Clade I = 7, D = 37, F = 13 and 16 unknown); 22 strains belonged to the sequence type ST131. No association between a specific strain and ESBL production was detected.CONCLUSIONS:This report shows the alarming spread of ESBL genes in Burkina Faso. Public health efforts should focus on education (population and healthcare professionals), surveillance and promotion of correct and restricted antibiotic use to limit their dissemination

Prevalence of Group B Streptococcus among Pregnant Women in Bobo-Dioulasso (Burkina Faso)

info:eu-repo/semantics/publishe

Fecal carriage of extended-spectrum β-lactamase-producing Enterobacteriaceae in hospital and community settings in Chad

International audienceBackground : Fecal carriage of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) remains poorly documented in Africa. The objective of this study was to determine the prevalence of ESBL-PE fecal carriage in Chad.Methods : In total, 200 fresh stool samples were collected from 100 healthy community volunteers and 100 hospitalized patients from January to March 2017. After screening using ESBL-selective agar plates and species identification by MALDI-TOF mass spectrometry, antibiotic susceptibility was tested using the disk diffusion method, and ESBL production confirmed with the double-disc synergy test. The different ESBL genes in potential ESBL-producing isolates were detected by PCR and double stranded DNA sequencing. Escherichia coli phylogenetic groups were determined using a PCR-based method.Results : ESBL-PE fecal carriage prevalence was 44.5% (51% among hospitalized patients vs 38% among healthy volunteers; p < 0.05). ESBL-producing isolates were mostly Escherichia coli (64/89) and Klebsiella pneumoniae (16/89). PCR and sequencing showed that 98.8% (87/89) of ESBL-PE harbored bla CTX-M genes: bla CTX-M-15 in 94.25% (82/87) and bla CTX-M-14 in 5.75% (5/87). Phylogroup determination by quadruplex PCR indicated that ESBL-producing E. coli isolates belonged to group A (n = 17; 27%), C (n = 17; 27%), B2 (n = 9; 14%), B1 (n = 8; 13%), D (n = 8; 13%), E (n = 1; 1.6%), and F (n = 1; 1.6%). The ST131 clone was identified in 100% (9/9) of E. coli B2 strains.Conclusions : The high fecal carriage rate of ESBL-PE associated with CTX-M-15 in hospital and community settings of Chad highlights the risk for resistance transmission between non-pathogenic and pathogenic bacteria

Identification and Antibioresistance Characterisation of Culturable Bacteria in the Intestinal Microbiota of Mosquitoes

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Fecal Carriage of Enterobacteriaceae Producing Extended-Spectrum Beta-Lactamases in Hospitalized Patients and Healthy Community Volunteers in Burkina Faso

International audienceExtended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) have been described worldwide, but few reports focused on Burkina Faso. To assess the prevalence of digestive carriage of such bacteria in the community and in the hospital, 214 fecal samples, 101 from healthy volunteers and 113 from hospitalized patients without digestive pathology, were collected in Bobo Dioulasso, Burkina Faso economic capital, during July and August 2014. Stool samples were screened using ESBL agar plates. Strains were identified by mass spectrometry using the Biotyper MALDI-TOF. ESBL production was confirmed with the double-disc synergy test. Susceptibility was tested using the disk diffusion method on Müller-Hinton agar. The main ESBL genes were detected using multiplex PCR and bidirectional gene sequencing. Escherichia coli phylogenetic groups were identified using a PCR-based method. During the study period, prevalence of subjects with fecal ESBL-PE was 32% (69/214), 22% among healthy volunteers and 42% among inpatients. All but two ESBL, CTX-M-15 and ESBL-PE, were mostly E. coli (78%). Among the 60 ESBL-producing E. coli strains, 26% belonged to phylogenetic group D, 23.3% to group A, 20% to group B1, 6.6% to group B2, and 3.3% to the ST131 clone. Univariate analysis showed that history of hospitalization and previous antibiotic use were risk factors associated with ESBL-PE fecal carriage. In Burkina Faso, the prevalence of both healthy subjects from the community and hospitalized patients with fecal ESBL-PE is alarmingly high. This feature should be taken into consideration by both general practitioners and hospital doctors with regard to empirical treatments of infections, notably urinary tract infections

Prevalence of SARS-CoV-2 and co-infection with malaria during the first wave of the pandemic (the Burkina Faso case)

Peer reviewed: TrueAcknowledgements: We would like to thank all volunteers who participated in this study, as well as the local authorities and communities in Burkina Faso for their support. We also thank the IPBLN, IRSS and IBV core facilities for their support to project activities.Africa accounts for 1.5% of the global coronavirus disease 2019 (COVID-19) cases and 2.7% of deaths, but this low incidence has been partly attributed to the limited testing capacity in most countries. In addition, the population in many African countries is at high risk of infection with endemic infectious diseases such as malaria. Our aim is to determine the prevalence and circulation of SARS-CoV-2 variants, and the frequency of co-infection with the malaria parasite. We conducted serological tests and microscopy examinations on 998 volunteers of different ages and sexes in a random and stratified population sample in Burkina-Faso. In addition, nasopharyngeal samples were taken for RT-qPCR of SARS-CoV-2 and for whole viral genome sequencing. Our results show a 3.2 and a 2.5% of SARS-CoV-2 seroprevalence and PCR positivity; and 22% of malaria incidence, over the sampling period, with marked differences linked to age. Importantly, we found 8 cases of confirmed co-infection and 11 cases of suspected co-infection mostly in children and teenagers. Finally, we report the genome sequences of 13 SARS-CoV-2 isolates circulating in Burkina Faso at the time of analysis, assigned to lineages A.19, A.21, B.1.1.404, B.1.1.118, B.1 and grouped into clades; 19B, 20A, and 20B. This is the first population-based study about SARS-CoV-2 and malaria in Burkina Faso during the first wave of the pandemic, providing a relevant estimation of the real prevalence of SARS-CoV-2 and variants circulating in this Western African country. Besides, it highlights the non-negligible frequency of co-infection with malaria in African communities