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Diouf FS, Tidjani Alou M, Bassene H, Cortaredona S, Diatta G, Raoult D, Sokhna C, Lagier JC. Seasonal variation of asymptomatic viral and bacterial nasopharyngeal carriage in rural Senegal. J Infect Public Health 2024; 17:922-928. [PMID: 38579539 DOI: 10.1016/j.jiph.2024.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/26/2024] [Accepted: 03/17/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND The surveillance of respiratory pathogens in rural areas of West Africa has, to date, largely been focussed on symptoms. In this prospective study conducted prior to the COVID-19 pandemic, we aimed to assess the asymptomatic prevalence of respiratory pathogen carriage in a group of individuals living in a rural area of Senegalese. METHODS Longitudinal follow up was performed through monthly nasopharyngeal swabbing during the dry season and weekly swabbing during the rainy season. We enrolled 15 individuals from the village of Ndiop. A total of 368 nasopharyngeal swabs were collected over a one-year period. We investigated the prevalence of 18 respiratory viruses and eight respiratory bacteria in different age groups using singleplex and multiplex PCR. RESULTS In total, 19.56% of the samples (72/368) were positive for respiratory viruses and 13.60% of the samples (50/368) were positive for respiratory bacteria. Coronaviruses (19/72, 26.39%), adenoviruses (17/72, 23.61%), rhinoviruses (14/72, 19.44%), Streptococcus pneumoniae (17/50, 34%), and Moraxella catarrhalis (15/50, 30%) were the most frequently detected viruses. Interestingly, the carriage of respiratory pathogens was shown to be more frequent during the rainy season, as pluviometry was shown to be positively associated with the occurrence of respiratory viruses such as influenza (P = .0078, r2 =.523) and RSV (P = .0055, r2 =.554). CONCLUSIONS Our results show a non-negligible circulation of respiratory pathogens in a rural area in Senegal (West Africa) with an underestimated proportion of asymptomatic individuals. This study highlights the fact that the circulation of viruses and bacteria in the community has been overlooked.
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Affiliation(s)
- Fatou Samba Diouf
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal; IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Maryam Tidjani Alou
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Hubert Bassene
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal
| | - Sebastien Cortaredona
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal; IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Georges Diatta
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal
| | - Didier Raoult
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal; IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Cheikh Sokhna
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal; IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France.
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Goumballa N, Diouf FS, Beye M, Sambou M, Bassène H, Dieng M, Aïdara A, Targa LLE, Colson P, Gautret P, Sokhna C. Influenza at the 2021 Grand Magal of Touba and possible spread to rural villages in South Senegal - a genomic epidemiological study. Int J Infect Dis 2024; 141:106952. [PMID: 38336005 DOI: 10.1016/j.ijid.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
OBJECTIVES Influenza is frequent among pilgrims participating in the Grand Magal de Touba (GMT), in Senegal, with a potential to spread to contacts when they return home. METHODS Ill pilgrims consulting at a health care center in Mbacké city close to Touba during the 2021 GMT, pilgrims returning to Dielmo and Ndiop villages, and patients who did not travel to Touba and consulted at health care centers in these two villages in 2021 were tested for the influenza virus by polymerase chain reaction on nasopharyngeal samples. Next-generation sequencing and comparative and phylogenetic analyses of influenza A virus genomes were performed. RESULTS A total of 62 of 685 patients tested positive for influenza A virus, including 34 of 53 who were consulted in Mbacké in late September, six of 129 pilgrims who returned home in early October, and 20 of 42 villagers from October 3 to 29. A total of 27 genomes were obtained. Four clusters were observed based on the phylogenetic analyses, suggesting that Mbacké patients and returned pilgrims may have shared closely related viral strains with patients inhabiting the villages who did not participate in the GMT. CONCLUSIONS Villagers in Ndiop and Dielmo may have been infected with viral strains originating from the GMT and possibly imported by pilgrims who returned from the GMT.
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Affiliation(s)
- Ndiaw Goumballa
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; VITROME, Campus International IRD-UCAD de l'IRD, Dakar, Senegal; IHU-Méditerranée Infection, Marseille, France
| | - Fatou Samba Diouf
- VITROME, Campus International IRD-UCAD de l'IRD, Dakar, Senegal; IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, SSA, MEPHI, Marseille, France
| | | | - Masse Sambou
- VITROME, Campus International IRD-UCAD de l'IRD, Dakar, Senegal
| | - Hubert Bassène
- VITROME, Campus International IRD-UCAD de l'IRD, Dakar, Senegal
| | | | | | - Lorlane L E Targa
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, SSA, MEPHI, Marseille, France
| | - Philippe Colson
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, SSA, MEPHI, Marseille, France
| | - Philippe Gautret
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Cheikh Sokhna
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; VITROME, Campus International IRD-UCAD de l'IRD, Dakar, Senegal; IHU-Méditerranée Infection, Marseille, France.
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Diouf FS, Tidjani Alou M, Million M, Diatta G, Goumballa N, Ndiaye D, Bassene H, Dubourg G, Raoult D, Sokhna C, Lagier JC. Influence of Microbiota on Clinical Expressions of Respiratory Viral Infections. Am J Trop Med Hyg 2024; 110:391-398. [PMID: 38109763 PMCID: PMC10859809 DOI: 10.4269/ajtmh.23-0244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/12/2023] [Indexed: 12/20/2023] Open
Abstract
Respiratory infections, mainly due to viruses, are among the leading causes of worldwide morbidity and mortality. We investigated the prevalence of viruses and bacteria in a cross-sectional survey conducted in Dielmo, a village in rural Senegal with a population of 481 inhabitants. Nasopharyngeal sampling was performed in 50 symptomatic subjects and 101 asymptomatic subjects. Symptomatic subjects were defined as individuals presenting with clinical signs of respiratory infection, whereas asymptomatic subjects were recruited in the same households. The identification of pathogens was performed by polymerase chain reaction for 18 respiratory viruses and eight respiratory bacteria. The prevalence results for respiratory viruses detected in each study group demonstrated that 83.6% of symptomatic samples were positive for at least one respiratory virus, and 21.8% were detected in asymptomatic samples. Influenza A (P = 0.0001), metapneumovirus (P = 0.04), and enterovirus (P = 0.001) were significantly more prevalent in symptomatic patients. Overall, 82.0% of symptomatic subjects and 26.9% of asymptomatic subjects were positive for at least one respiratory bacterium. The most frequent pathogenic bacteria detected were Moraxella catarrhalis (56%) and Streptococcus pneumoniae (48.0%) among symptomatic individuals, whereas in asymptomatic subjects Corynebacterium propinquum was more prevalent (18%). A principal component analysis showed that parainfluenzas 2 and 4 were associated with asymptomatic subjects, whereas influenza A was associated with the presence of symptoms. Considering these results, a large epidemiological surveillance of the circulation of these respiratory pathogens in the general population should be conducted to provide a better understanding of their carriage and to potentially prevent epidemics.
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Affiliation(s)
- Fatou Samba Diouf
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal
- Aix Marseille Université, Institut de recherche pour le développement, Assistance Publique - Hôpitaux de Marseille, Microbes, Évolution, Phylogénie et Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Maryam Tidjani Alou
- Aix Marseille Université, Institut de recherche pour le développement, Assistance Publique - Hôpitaux de Marseille, Microbes, Évolution, Phylogénie et Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Mathieu Million
- Aix Marseille Université, Institut de recherche pour le développement, Assistance Publique - Hôpitaux de Marseille, Microbes, Évolution, Phylogénie et Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Georges Diatta
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal
| | - Ndiaw Goumballa
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal
- Aix-Marseille Université, Institut de recherche pour le développement, Assistance Publique-Hôpitaux de Marseille, Service de santé des armées, Vecteurs – Infections Tropicales et Méditerranéennes, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Dame Ndiaye
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal
| | - Hubert Bassene
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal
| | - Gregory Dubourg
- Aix Marseille Université, Institut de recherche pour le développement, Assistance Publique - Hôpitaux de Marseille, Microbes, Évolution, Phylogénie et Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Université, Institut de recherche pour le développement, Assistance Publique - Hôpitaux de Marseille, Microbes, Évolution, Phylogénie et Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Cheikh Sokhna
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal
- Aix Marseille Université, Institut de recherche pour le développement, Assistance Publique - Hôpitaux de Marseille, Microbes, Évolution, Phylogénie et Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille Université, Institut de recherche pour le développement, Assistance Publique - Hôpitaux de Marseille, Microbes, Évolution, Phylogénie et Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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Sarr M, Alou MT, Padane A, Diouf FS, Beye M, Sokhna C, Fenollar F, Mboup S, Raoult D, Million M. A review of the literature of Listeria monocytogenes in Africa highlights breast milk as an overlooked human source. Front Microbiol 2023; 14:1213953. [PMID: 38173673 PMCID: PMC10761537 DOI: 10.3389/fmicb.2023.1213953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
According to the latest WHO estimates (2015) of the global burden of foodborne diseases, Listeria monocytogenes is responsible for one of the most serious foodborne infections and commonly results in severe clinical outcomes. The 2013 French MONALISA prospective cohort identified that women born in Africa has a 3-fold increase in the risk of maternal neonatal listeriosis. One of the largest L. monocytogenes outbreaks occurred in South Africa in 2017-2018 with over 1,000 cases. Moreover, recent findings identified L. monocytogenes in human breast milk in Mali and Senegal with its relative abundance positively correlated with severe acute malnutrition. These observations suggest that the carriage of L. monocytogenes in Africa should be further explored, starting with the existing literature. For that purpose, we searched the peer-reviewed and grey literature published dating back to 1926 to date using six databases. Ultimately, 225 articles were included in this review. We highlighted that L. monocytogenes is detected in various sample types including environmental samples, food samples as well as animal and human samples. These studies were mostly conducted in five east African countries, four west African countries, four north African countries, and two Southern African countries. Moreover, only ≈ 0.2% of the Listeria monocytogenes genomes available on NCBI were obtained from African samples, contracted with its detection. The pangenome resulting from the African Listeria monocytogenes samples revealed three clusters including two from South-African strains as well as one consisting of the strains isolated from breast milk in Mali and Senegal and, a vaginal post-miscarriage sample. This suggests there was a clonal complex circulating in Mali and Senegal. As this clone has not been associated to infections, further studies should be conducted to confirm its circulation in the region and explore its association with foodborne infections. Moreover, it is apparent that more resources should be allocated to the detection of L. monocytogenes as only 15/54 countries have reported its detection in the literature. It seems paramount to map the presence and carriage of L. monocytogenes in all African countries to prevent listeriosis outbreaks and the related miscarriages and confirm its association with severe acute malnutrition.
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Affiliation(s)
- Marièma Sarr
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
- Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation (IRESSEF), Dakar, Senegal
| | - Maryam Tidjani Alou
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Abdou Padane
- Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation (IRESSEF), Dakar, Senegal
| | - Fatou Samba Diouf
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - Mamadou Beye
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Cheikh Sokhna
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Souleymane Mboup
- Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation (IRESSEF), Dakar, Senegal
| | - Didier Raoult
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Matthieu Million
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
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Ndiaye EHI, Diarra AZ, Diouf FS, Bouganali C, Almeras L, Sokhna C, Diatta G, Parola P. Ornithodoros sonrai Soft Ticks and Associated Bacteria in Senegal. Pathogens 2023; 12:1078. [PMID: 37764886 PMCID: PMC10534570 DOI: 10.3390/pathogens12091078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/14/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
The soft ticks, Ornithodoros sonrai, are known as vectors of the tick-borne relapsing fever caused by Borrelia spp. and have also been reported to carry other micro-organisms. The objective of this study was to collect and to identify O. sonrai ticks and to investigate the micro-organisms associated with them. In 2019, an investigation of burrows within human dwellings was conducted in 17 villages in the Niakhar area and in 15 villages in the Sine-Saloum area in the Fatick region of Senegal. Ticks collected from the burrows were identified morphologically and by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Micro-organism screening was performed by bacteria-specific qPCR and some identifications were made by standard PCR and gene sequencing. O. sonrai ticks were found in 100% (17/17) of the villages surveyed in the Niakhar area and in 66% (10/15) of the villages in the Sine-Saloum area. A total of 1275 soft tick specimens were collected from small mammal burrows. The ticks collected were morphologically identified as O. sonrai. About 20% (259/1275) of the specimens were also submitted to MALDI-TOF MS for identification. Among the resulting MS profiles, 87% (139/159) and 95% (95/100) were considered good quality specimens, preserved in alcohol and silica gel, respectively. All spectra of good quality were tested against our MALDI-TOF MS arthropod spectra database and identified as O. sonrai species, corroborating the morphological classification. The carriage of four micro-organisms was detected in the ticks with a high prevalence of Bartonella spp., Anaplasmataceae, and Borrelia spp. of 35, 28, and 26%, respectively, and low carriage of Coxiella burnetii (2%). This study highlights the level of tick infestation in domestic burrows, the inventory of pathogens associated with the O. sonrai tick, and the concern about the potential risk of tick involvement in the transmission of these pathogens in Senegal.
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Affiliation(s)
- El Hadji Ibrahima Ndiaye
- Faculté des Sciences Médicales et Paramédicales, Aix Marseille Univ IRD, AP-HM, SSA, VITROME, 19–21 Boulevard Jean Moulin, 13005 Marseille, France; (E.H.I.N.); (A.Z.D.); (F.S.D.); (L.A.); (C.S.)
- IHU Méditerranée Infection, 13005 Marseille, France
- VITROME, Campus International IRD-UCAD Hann, Dakar 1386, Senegal; (C.B.); (G.D.)
| | - Adama Zan Diarra
- Faculté des Sciences Médicales et Paramédicales, Aix Marseille Univ IRD, AP-HM, SSA, VITROME, 19–21 Boulevard Jean Moulin, 13005 Marseille, France; (E.H.I.N.); (A.Z.D.); (F.S.D.); (L.A.); (C.S.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Fatou Samba Diouf
- Faculté des Sciences Médicales et Paramédicales, Aix Marseille Univ IRD, AP-HM, SSA, VITROME, 19–21 Boulevard Jean Moulin, 13005 Marseille, France; (E.H.I.N.); (A.Z.D.); (F.S.D.); (L.A.); (C.S.)
- IHU Méditerranée Infection, 13005 Marseille, France
- VITROME, Campus International IRD-UCAD Hann, Dakar 1386, Senegal; (C.B.); (G.D.)
| | - Charles Bouganali
- VITROME, Campus International IRD-UCAD Hann, Dakar 1386, Senegal; (C.B.); (G.D.)
| | - Lionel Almeras
- Faculté des Sciences Médicales et Paramédicales, Aix Marseille Univ IRD, AP-HM, SSA, VITROME, 19–21 Boulevard Jean Moulin, 13005 Marseille, France; (E.H.I.N.); (A.Z.D.); (F.S.D.); (L.A.); (C.S.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
| | - Cheikh Sokhna
- Faculté des Sciences Médicales et Paramédicales, Aix Marseille Univ IRD, AP-HM, SSA, VITROME, 19–21 Boulevard Jean Moulin, 13005 Marseille, France; (E.H.I.N.); (A.Z.D.); (F.S.D.); (L.A.); (C.S.)
- IHU Méditerranée Infection, 13005 Marseille, France
- VITROME, Campus International IRD-UCAD Hann, Dakar 1386, Senegal; (C.B.); (G.D.)
| | - Georges Diatta
- VITROME, Campus International IRD-UCAD Hann, Dakar 1386, Senegal; (C.B.); (G.D.)
| | - Philippe Parola
- Faculté des Sciences Médicales et Paramédicales, Aix Marseille Univ IRD, AP-HM, SSA, VITROME, 19–21 Boulevard Jean Moulin, 13005 Marseille, France; (E.H.I.N.); (A.Z.D.); (F.S.D.); (L.A.); (C.S.)
- IHU Méditerranée Infection, 13005 Marseille, France
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Diouf FS, Beye M, Gaye M, Mbaye B, Alibar S, Sarr M, Dubourg G, Lagier JC, Sokhna C, Fenollar F, Fournier PE, Lo CI. Description of Streptococcus thalassemiae sp. nov., a Bacterium Isolated from Human Blood. Int J Microbiol 2023; 2023:3802590. [PMID: 37559874 PMCID: PMC10409578 DOI: 10.1155/2023/3802590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/13/2023] [Accepted: 05/04/2023] [Indexed: 08/11/2023] Open
Abstract
Blood is a precious biological liquid that is normally sterile. Therefore, bacteria in the bloodstream are shown a priori anomaly. A blood culture is systematically performed to diagnose the cause of the bacteremia. Indeed, a patient received in our service had a thalassemia major and underwent a genoidentical transplant. Then, a blood test was performed to diagnose a four-day fever. In this context, we have isolated strain Marseille-Q2617 from the blood sample. It revealed a new bacterial strain that belongs to the genus Streptococcus. It is a Gram-positive coccus, nonmotile, and nonspore forming. The major fatty acid found is hexadecanoic acid, with 49.5%. A taxonomic method was used to characterize the strain by studying their phenotypic, phylogenetic, and genomic characteristics. In addition, sequence analysis of the 16S rRNA gene shows that the strain Marseille-Q2617 has 99.94% sequence similarity to Streptococcus mitis. Average nucleotide identity (ANI) analysis for strain Marseille-Q2617T showed the highest similarity of 92.9% with S. mitis. The DNA-DNA hybridization value obtained (50.2%) between strain Marseille-Q2607 and S. mitis, its closest related species, was below the recommended threshold (<70%). Strain Marseille-Q2617T has a genome size of 2.02 Mbp with 40.5 mol% of G + C content. Based on these results, we propose a new species of the genus Streptococcus, for which the name Streptococcus thalassemiae sp. nov., Marseille-Q2617T (=CSUR Q2617 = CECT 30109) was proposed.
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Affiliation(s)
- Fatou Samba Diouf
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Mamadou Beye
- IHU-Mediterranean Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Mapenda Gaye
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Babacar Mbaye
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Stephane Alibar
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Mariema Sarr
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Gregory Dubourg
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Cheikh Sokhna
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - Florence Fenollar
- IHU-Mediterranean Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Pierre-Edouard Fournier
- IHU-Mediterranean Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Cheikh Ibrahima Lo
- IHU-Mediterranean Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
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Ben Khedher M, Diouf FS, Lo CI, Alibar S, Durand G, Raoult D, Fournier PE, Fenollar F. Collinsella ihumii sp. nov., a new anaerobic bacterium isolated from human stool. Arch Microbiol 2021; 203:6315-6322. [DOI: 10.1007/s00203-021-02562-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
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Diouf FS, Ndiaye EHI, Hammoud A, Diamanka A, Bassene H, Ndiaye M, Mediannikov O, Parola P, Raoult D, Sokhna C, Diatta G. Detection of Coxiella burnetii and Borrelia spp. DNA in Cutaneous Samples and in Household Dust in Rural Areas, Senegal. Vector Borne Zoonotic Dis 2021; 21:659-666. [PMID: 34534024 DOI: 10.1089/vbz.2020.2723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Q fever and tick-borne borreliosis are two zoonotic diseases rarely diagnosed in Senegalese health facilities, particularly in rural areas. Our study aims to better understand the circulation of Coxiella burnetii and Borrelia spp. DNA on human skin and the domestic environment in rural areas. Cutaneous swabs were taken from febrile patients being treated for borreliosis and/or Q fever, the members of patients' households and control households in the Niakhar area. Dust samples were also collected from 90 households where 54 cases of borreliosis and Q fever were reported as well as from the households of members of control populations in Dielmo, Ndiop, and Niakhar. C. burnetii and Borrelia spp. DNA were detected by quantitative PCR in cutaneous swabs and dust samples targeting spacers IS1111_IS30A and Bor 16S gene. Of 1365 persons tested, 76 were shown to carry C. burnetii, 13 Borrelia spp., and 6 were identified as carrying both C. burnetii and Borrelia spp. The prevalence of Borrelia spp. DNA in households was 16.7% in Dielmo, 6.7% in Ndiop, and 23.3% in all other villages in the Niakhar area, and the presence of C. burnetii in the same localities was 10%, 13.3% and 66.7%, respectively. Furthermore, C. burnetii genotyping identified the presence of Multispacer Sequence Typing group 6. These results revealed for the first time the carriage on the skin of C. burnetii and Borrelia spp. DNA in humans and its wide distribution across households. Our findings suggest that many populations are exposed to these diseases, with frequent contaminating cases of infectious origin arising from the domestic environment.
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Affiliation(s)
- Fatou Samba Diouf
- Unité Mixe de Recherche Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD), Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal
| | - El Hadji Ibrahima Ndiaye
- Unité Mixe de Recherche Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD), Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal
| | - Alissa Hammoud
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Arfang Diamanka
- Laboratoire de Parasitologie Générale, Département de Biologie Animale, Faculté des Sciences et Techniques (FST), Université Cheikh Anta Diop (UCAD) de Dakar, Dakar, Senegal
| | - Hubert Bassene
- Unité Mixe de Recherche Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD), Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal
| | - Mady Ndiaye
- Laboratoire d'Entomologie, Bactériologie, Rickettsiologie, Virologie, Département de Biologie Animale, FST, UCAD de Dakar, Dakar, Senegal
| | - Oleg Mediannikov
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Philippe Parola
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille Université, IRD, APHM, SSA, VITROME, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Cheikh Sokhna
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille Université, IRD, APHM, SSA, VITROME, Marseille, France
| | - Georges Diatta
- Unité Mixe de Recherche Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD), Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal.,Aix-Marseille Université, IRD, APHM, SSA, VITROME, Marseille, France
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Sarr M, Diouf FS, Lo CI, Tidjani Alou M, Alibar S, Million M, Sokhna C, Fenollar F. Taxonogenomics description of Bacillus marasmi sp. nov., a new species isolated from the stool sample. New Microbes New Infect 2021; 42:100906. [PMID: 34188938 PMCID: PMC8220230 DOI: 10.1016/j.nmni.2021.100906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/05/2022] Open
Abstract
Using the culturomics method, two strains were isolated, identified, and characterised following the taxonogenomics concept. Bacillus marasmi sp. nov. strain Marseille-P3556 (= CSURP3556) is isolated from a 13-month-old girl living in Niger. The phylogenetic tree, phenotypic criteria, and genomic analysis described here clearly show that this bacterium is different from previously known bacterial species withstanding in nomenclature and new members of Bacillus genus.
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Affiliation(s)
- M Sarr
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - F S Diouf
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - C I Lo
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - M Tidjani Alou
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - S Alibar
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - M Million
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - C Sokhna
- IHU-Méditerranée Infection, Marseille, France.,Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - F Fenollar
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
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Ndiaye EHI, Diouf FS, Ndiaye M, Bassene H, Raoult D, Sokhna C, Parola P, Diatta G. Tick-borne relapsing fever Borreliosis, a major public health problem overlooked in Senegal. PLoS Negl Trop Dis 2021; 15:e0009184. [PMID: 33886571 PMCID: PMC8096072 DOI: 10.1371/journal.pntd.0009184] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 05/04/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Tick-borne relapsing fever (TBRF) is the most common vector-borne bacterial disease in humans in West Africa. It is frequently clinically confused with malaria. Our study aims to determine, on a micro-geographic scale, the conditions for the maintenance and spread of TBRF in the Niakhar district of Senegal. METHODOLOGY/PRINCIPAL FINDINGS We conducted clinical, entomological and animal reservoir investigations. Field surveys were carried out in order to investigate the presence of Ornithodoros sonrai vector ticks and to detect Borrelia spp. by qPCR using the 16S rRNA and glpQ genes, respectively. Micromammal trapping series were carried out inside homes and Borrelia infection was detected using brain tissue qPCR. Capillary blood samples from febrile patients were also tested for Borrelia using qPCR. More than 97% (40/41) of the villages surveyed were infested with O. sonrai ticks. The prevalence of Borrelia spp. infections in ticks was 13% (116/910), and over 73% (85/116) were positively confirmed as being Borrelia crocidurae. Borreliosis cases accounted for 12% (94/800) of episodes of fever and all age groups were infected, with children and young people between the ages of 8-14 and 22-28 being the most infected by the disease (16% and 18.4%). TBRF cases occurred in all seasons, with a peak in August. In two species of small rodents that were found to be infected (Arvicanthis niloticus, Mus musculus), the proportion of Borrelia infection was 17.5% (10/57), and the highest prevalence of infection (40.9%, 9/22) was observed in A. niloticus. CONCLUSION/SIGNIFICANCE Our study indicates that TBRF is an endemic disease in the Niakhar district, where children and young people are the most infected. Arvicanthis niloticus and O. sonrai ticks are massively present and appear to be the main epidemiological reservoirs causing its extensive spread to humans.
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Affiliation(s)
- El Hadji Ibrahima Ndiaye
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | | | - Mady Ndiaye
- Laboratoire d’Entomologie, Bactériologie, Rickettsiologie, Virologie, Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | - Hubert Bassene
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, Marseille, France
- VITROME, Campus International IRD-UCAD Hann, Dakar, Senegal
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - Cheikh Sokhna
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, Marseille, France
- VITROME, Campus International IRD-UCAD Hann, Dakar, Senegal
| | - Philippe Parola
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Georges Diatta
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, Marseille, France
- VITROME, Campus International IRD-UCAD Hann, Dakar, Senegal
- * E-mail:
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Ndiaye M, Diop AG, Dieng Y, Seydi M, Diouf FS, Diop BM, Ndiaye IP. [A case of meningoencephalitis caused by Acanthamoeba sp. in Dakar]. Med Trop (Mars) 2005; 65:67-8. [PMID: 15903081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Primary meningoencephalitis caused by free-living soil ameba is rare. We report the first diagnosed case of meningoencephalitis due to Acanthamoeba sp. in Senegal. The patient was a 24-year-old Senegalese woman hospitalized in the neurology department of Fann Hospital. Diagnosis was made 6 months after the onset of symptoms based mainly on headache with fever usually occurring in the evening, chills, and lumbar puncture demonstrating turbid fluid. Parasitological examination of cool cerebrospinal fluid sediment revealed the presence of free-living ameba trophozoites of the Acanthamoeba genus. Species determination by culture on 1.5% agar-agar enriched with Escherichia coli failed. The patient died one month following initiation of treatment using amphotericine B.
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Affiliation(s)
- M Ndiaye
- Service de Neurologie, du CHU Fann- Dakar, Sénégal.
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