kodjovi Mlaga - Academia.edu (original) (raw)

Papers by kodjovi Mlaga

Frontiers in Microbiology, May 5, 2021

Introduction: The fungi ITS sequence length dissimilarity, non-specific amplicons, including chim... more Introduction: The fungi ITS sequence length dissimilarity, non-specific amplicons, including chimaera formed during Polymerase Chain Reaction (PCR), added to sequencing errors, create bias during similarity clustering and abundance estimation in the downstream analysis. To overcome these challenges, we present a novel approach, Hierarchical Clustering with Kraken (HCK), to classify ITS1 amplicons and Abundance-Base Alternative Approach (ABAA) pipeline to detect and filter non-specific amplicons in fungi metabarcoding sequencing datasets. Materials and Methods: We compared the performances of both pipelines against QIIME, KRAKEN, and DADA2 using publicly available fungi ITS mock community datasets and using BLASTn as a reference. We calculated the Precision, Recall, F-score using the True-Positive, False-positive, and False-negative estimation. Alpha diversity (Chao1 and Shannon metrics) was also used to evaluate the diversity estimation of our method. Results: The analysis shows that ABAA reduced the number of false-positive with all metabarcoding methods tested, and HCK increases precision and recall. HCK, coupled with ABAA, improves the F-score and bring alpha diversity metric value close to that of the BLASTn alpha diversity values when compared to QIIME, KRAKEN, and DADA2. Conclusion: The developed HCK-ABAA approach allows better identification of the fungi community structures while avoiding use of a reference database for non-specific amplicons filtration. It results in a more robust and stable methodology over time. The software can be downloaded on the following link: https://bitbucket.org/GottySG36/ hck/src/master/.

The development of cost-effective next-generation sequencing technology (NGS), recent advances in... more The development of cost-effective next-generation sequencing technology (NGS), recent advances in whole genome sequencing (WGS), and decreasing costs have had a significant impact on our knowledge of the behaviour of the bacteria which cause infectious diseases. Bacterial genome recombinations through point mutations and gene exchanges, including horizontal gene transfer and gene loss have contributed significantly to the adaptation and evolution of bacteria and have become the driving force of bacterial survival in the host niches. In this paper, we propose a review of publicly available computational biology tools, frequently used for real-time genomics in clinical microbiology over the past decade and highlight the impact of bacterial genome recombinations in clinical microbiology. Article II Using MALDI-TOF MS typing method to decipher outbreak: the case of Staphylococcus saprophyticus causing urinary tract infections (UTIs) in Marseille, France.

Journal of global antimicrobial resistance, Sep 1, 2019

OBJECTIVES Carbapenem resistance in Klebsiella pneumoniae (CRKP) is an increasing problem worldwi... more OBJECTIVES Carbapenem resistance in Klebsiella pneumoniae (CRKP) is an increasing problem worldwide and infections caused by this bacterium can be difficult to treat. Here we reported the case of a patient from Romania hospitalized in Bulgaria after an accident trauma that came in France for the treatment of an osteitis caused by a K. pneumoniae carrying both blaNDM-1 and blaOXA-48. METHOD The resistome of this extremely-drug-resistant bacterium was analyzed both with phenotypic (large antibiotic susceptibility testing) and genomic method (genome sequencing). The genetic environment of the two carbapenemases was studied. RESULTS K. pneumoniae ST307 carrying both a blaNDM-1 gene and a blaOXA-48 gene located on two different plasmids, an Inc L/M and an IncFII. Patient was successfully treated by a combination of intravenous colistin (9 MUI, then 4.5 MUI 2 times/day), intravenous fosfomycin (4 g 3 times/day) and oral doxycycline (100 mg 2 times/day) for 3 months. Fecal microbiota transplantation was successfully conducted for a stool carriage. CONCLUSION The ST307 type is becoming endemic in hospital environment and is frequently associated with carbapenem resistance. Treatment of infection caused by multi-drug resistant bacteria are a clinical challenge and the use of old antibiotics associated with a screening and decolonization of the reservoirs can be an efficient therapeutic alternative.

European Journal of Clinical Microbiology & Infectious Diseases, Aug 22, 2017

Staphylococcus saprophyticus is one of the leading causes of urinary tract infections (UTI). In D... more Staphylococcus saprophyticus is one of the leading causes of urinary tract infections (UTI). In December 2014, our surveillance system identified an abnormal increase in S. saprophyticus causing UTIs in four university hospitals in Marseille, indicating a suspected community S. saprophyticus UTI outbreak. This was detected by our surveillance system BALYSES (Bacterial real-time Laboratory-based Surveillance System). S. saprophyticus/ Escherichia coli UTI ratio increased threefold from 0.0084 in 2002 to 0.025 in December 2015 in Marseille with an abnormal peak in December 2014, and with an annual estimated ratio trend of 5.10 −6 (p-value < 10 −3). Matrix-Assisted Laser Desorption Ionisation-Time of Flight Mass Spectrometry (MALDI-TOF MS) spectral analysis of strains was used to analyse strains cluster expansion, comparing strains from Marseille to those from Nice during the same period. MALDI-TOF MS spectral analysis revealed a geographical restricted clonal expansion of the strains clusters in Marseille as compared to Nice. Our finding suggests (i) a geographically restricted expansion of a specific S. saprophyticus strain clusters circulating in Marseille, and (ii) MALDI-TOF MS can be used as a costeffective tool to investigate an outbreak.

PLoS ONE, 2014

Background: Although tuberculosis is transmitted by the airborne route, direct information on the... more Background: Although tuberculosis is transmitted by the airborne route, direct information on the natural output of bacilli into air by source cases is very limited. We sought to address this through sampling of expelled aerosols in face masks that were subsequently analyzed for mycobacterial contamination. Methods: In series 1, 17 smear microscopy positive patients wore standard surgical face masks once or twice for periods between 10 minutes and 5 hours; mycobacterial contamination was detected using a bacteriophage assay. In series 2, 19 patients with suspected tuberculosis were studied in Leicester UK and 10 patients with at least one positive smear were studied in The Gambia. These subjects wore one FFP30 mask modified to contain a gelatin filter for one hour; this was subsequently analyzed by the Xpert MTB/RIF system. Results: In series 1, the bacteriophage assay detected live mycobacteria in 11/17 patients with wearing times between 10 and 120 minutes. Variation was seen in mask positivity and the level of contamination detected in multiple samples from the same patient. Two patients had non-tuberculous mycobacterial infections. In series 2, 13/20 patients with pulmonary tuberculosis produced positive masks and 0/9 patients with extrapulmonary or non-tuberculous diagnoses were mask positive. Overall, 65% of patients with confirmed pulmonary mycobacterial infection gave positive masks and this included 3/6 patients who received diagnostic bronchoalveolar lavages. Conclusion: Mask sampling provides a simple means of assessing mycobacterial output in non-sputum expectorant. The approach shows potential for application to the study of airborne transmission and to diagnosis.

L'objectif de notre thèse est d'appliquer la génomique en temps réel pour déchiffrer les ... more L'objectif de notre thèse est d'appliquer la génomique en temps réel pour déchiffrer les caractéristiques génomiques bactériennes et les événements de recombinaison du génome des bactéries atypiques ainsi que leur impact sur les maladies infectieuses. Au cours de ma thèse, nous avons effectué une revue sur les outils bioinformatiques les plus courants utilisés en microbiologie clinique et mis en évidence l’impact de la recombinaison sur le comportement des bacteries. Le deuxième projet de notre thèse est de déchiffrer une epidémis de Staphylococcus saprophyticus causant des infections urinaires en utilisant la technologie MALDI-TOF MS et une analyse comparative du génome de S. saprophyticus pour comprendre leur évolution génomique. Nous avons démontré qu'il existe un groupe de S. saprophyticus géographiquement restreint à Marseille comparé au souches de Nice. De plus, nous avons montré que S. saprophyticus qui était initialement considéré comme une bactérie saprophyte a ...

L'objectif de notre thèse est d'appliquer la génomique en temps réel pour déchiffrer les ... more L'objectif de notre thèse est d'appliquer la génomique en temps réel pour déchiffrer les caractéristiques génomiques bactériennes et les événements de recombinaison du génome des bactéries atypiques ainsi que leur impact sur les maladies infectieuses. Au cours de ma thèse, nous avons effectué une revue sur les outils bioinformatiques les plus courants utilisés en microbiologie clinique et mis en évidence l’impact de la recombinaison sur le comportement des bacteries. Le deuxième projet de notre thèse est de déchiffrer une epidémis de Staphylococcus saprophyticus causant des infections urinaires en utilisant la technologie MALDI-TOF MS et une analyse comparative du génome de S. saprophyticus pour comprendre leur évolution génomique. Nous avons démontré qu'il existe un groupe de S. saprophyticus géographiquement restreint à Marseille comparé au souches de Nice. De plus, nous avons montré que S. saprophyticus qui était initialement considéré comme une bactérie saprophyte a ...

L'objectif de notre these est d'appliquer la genomique en temps reel pour dechiffrer les ... more L'objectif de notre these est d'appliquer la genomique en temps reel pour dechiffrer les caracteristiques genomiques bacteriennes et les evenements de recombinaison du genome des bacteries atypiques ainsi que leur impact sur les maladies infectieuses. Au cours de ma these, nous avons effectue une revue sur les outils bioinformatiques les plus courants utilises en microbiologie clinique et mis en evidence l’impact de la recombinaison sur le comportement des bacteries. Le deuxieme projet de notre these est de dechiffrer une epidemis de Staphylococcus saprophyticus causant des infections urinaires en utilisant la technologie MALDI-TOF MS et une analyse comparative du genome de S. saprophyticus pour comprendre leur evolution genomique. Nous avons demontre qu'il existe un groupe de S. saprophyticus geographiquement restreint a Marseille compare au souches de Nice. De plus, nous avons montre que S. saprophyticus qui etait initialement considere comme une bacterie saprophyte a ...

Introduction The fungi ITS sequence length dissimilarity, non-specific amplicons, including chima... more Introduction The fungi ITS sequence length dissimilarity, non-specific amplicons, including chimaera formed during Polymerase Chain Reaction (PCR), added to sequencing errors, create bias during similarity clustering and abundance estimation in the downstream analysis. To overcome these challenges, we present a novel approach, Hierarchical Clustering with Kraken (HCK), to classify ITS1 amplicons and Abundance-Base Alternative Approach (ABAA) pipeline to detect and filter non-specific amplicons in fungi metabarcoding sequencing datasets. Materials and Methods We compared the performances of both pipelines against QIIME, KRAKEN, and DADA2 using publicly available fungi ITS mock community datasets and using BLASTn as a reference. We calculated the Precision, Recall, F-score using the True-Positive, False-positive, and False-negative estimation. Alpha diversity (Chao1 and Shannon metrics) was also used to evaluate the diversity estimation of our method. Results The analysis shows that A...

Microorganisms

Here, we performed a comparative genomic analysis of all available genomes of E. faecalis (n = 15... more Here, we performed a comparative genomic analysis of all available genomes of E. faecalis (n = 1591) and E. faecium (n = 1981) and investigated the association between the presence or absence of CRISPR-Cas systems, endonuclease/anti-endonuclease systems and the acquisition of antimicrobial resistance, especially vancomycin resistance genes. Most of the analysed Enterococci were isolated from humans and less than 14% of them were from foods and animals. We analysed and detected CRISPR–Cas systems in 75.36% of E. faecalis genomes and only 4.89% of E. faecium genomes with a significant difference (p-value < 10−5). We found a negative correlation between the number of CRISPR–Cas systems and genome size (r = −0.397, p-value < 10−5) and a positive correlation between the genome %GC content and the number of CRISPR–Cas systems (r = 0.215, p-value < 10−5). Our findings showed that the presence of the anti-endonuclease ardA gene may explain the decrease in the number of CRISPR–Cas s...

Journal of Global Antimicrobial Resistance

Journal of Advances in Microbiology

The aim of this study is to describe the antibiotic profile and identify the molecular type of be... more The aim of this study is to describe the antibiotic profile and identify the molecular type of betalactamase-producing Escherichia coli isolated from clinical specimens at Sylvanus Olympio teaching hospital in Lomé. The study span from 1 st March 2009 to 31 st December 2010. We collected fiftythree isolates of Escherichia coli, identified by api20E. Antibiotic susceptibility test was performed Original Research Article

New Microbes and New Infections, 2017

We propose the main characteristics of a new bacterium species named Nissabacter archeti strain 2... more We propose the main characteristics of a new bacterium species named Nissabacter archeti strain 2134 (CSURP3445 = LT631518), isolated from pustule scalp of a 29-year-old man at hospital Archet 2, Nice, south of France.

Bulletin of the World Health Organization, 2016

Study procedures Three teams-each consisting of a research clinician who led a team of 7 trained ... more Study procedures Three teams-each consisting of a research clinician who led a team of 7 trained fieldworkers and a radiographer-performed the fieldwork from December 2011 to January 2013. Data collection in each cluster was done over a seven-day period. The field Objective To estimate the population prevalence of active pulmonary tuberculosis in Gambia. Methods Between December 2011 and January 2013, people aged ≥ 15 years participating in a nationwide, multistage cluster survey were screened for active pulmonary tuberculosis with chest radiography and for tuberculosis symptoms. For diagnostic confirmation, sputum samples were collected from those whose screening were positive and subjected to fluorescence microscopy and liquid tuberculosis cultures. Multiple imputation and inverse probability weighting were used to estimate tuberculosis prevalence. Findings Of 100 678 people enumerated, 55 832 were eligible to participate and 43 100 (77.2%) of those participated. A majority of participants (42 942; 99.6%) were successfully screened for symptoms and by chest X-ray. Only 5948 (13.8%) were eligible for sputum examination, yielding 43 bacteriologically confirmed, 28 definite smear-positive and six probable smear-positive tuberculosis cases. Chest X-ray identified more tuberculosis cases (58/69) than did symptoms alone (43/71). The estimated prevalence of smear-positive and bacteriologically confirmed pulmonary tuberculosis were 90 (95% confidence interval, CI: 53-127) and 212 (95% CI: 152-272) per 100 000 population, respectively. Tuberculosis prevalence was higher in males (333; 95% CI: 233-433) and in the 35-54 year age group (355; 95% CI: 219-490). Conclusion The burden of tuberculosis remains high in Gambia but lower than earlier estimates of 490 per 100 000 population in 2010. Less than half of all cases would have been identified based on smear microscopy results alone. Successful control efforts will require interventions targeting men, increased access to radiography and more accurate, rapid diagnostic tests.

New Microbes and New Infections, 2015

Drug-resistant tuberculosis (TB) is emerging as an important health problem in Togo. From sputum ... more Drug-resistant tuberculosis (TB) is emerging as an important health problem in Togo. From sputum of previously treated TB patients, multidrug-resistant (MDR) TB was diagnosed in 24% (10/42) patients via GeneXpert MTB/RIF compared to 25% (6/24) patients via conventional drug susceptibility testing (BACTEC MGIT 960 system). The agreement between these two methods to detect MDR-TB is excellent. However, GeneXpert MTB/RIF offers the advantage of rapidly detecting Mycobacterium tuberculosis complex in sputum samples in instances where the cultures are negative (33%, 14/42) or contaminated (9.5%, 4/42). GeneXpert MTB/RIF permitted us to estimate the prevalence of MDR-TB in previously treated TB patients and to improve TB diagnostics among HIV-positive and-negative patients in Togo, where culturing M. tuberculosis complex from sputum samples is challenging.

Introduction : Les évaluations des tests de diagnos-tic Rapides/Simples (TDR) du VIH sont nécessa... more Introduction : Les évaluations des tests de diagnos-tic Rapides/Simples (TDR) du VIH sont nécessaires pour la détermination d'algorithmes de tests simples et rapides, utilisables au point de service pour le conseil et dépistage volontaire, la surveillance épidémiologi-que, la sécurité transfusionnelle et dans les services de consultations prénatales. Objectif : Evaluer la performance de trois (3) tests de diagnostic sérologique de l'infection à VIH dont un (1) test ELISA (EQUIPAR HIV 1/2 recombinant) et deux (2) tests rapides/simples (HEXAGON HIV et FIRSTRESPONSE). Méthodes : L'évaluation de la performance de trois tests pour le diagnostic de l'infection à VIH à Lomé (Togo) a été réalisée au centre national de référence pour les tests VIH/SIDA/IST sis au CHU de Lomé TOKOIN. Les tests évalués ont été EQUIPAR HIV ½ recombi-nant, HEXAGON HIV et FIRST RESPONSE Sang total HIV 1-2-0. Les sérums ont été collectés de Janvier à Juillet 2008 des malades hospitalisés au CHU Tok...

Bulletin of the World Health Organization, 2016

To estimate the population prevalence of active pulmonary tuberculosis in Gambia. Between Decembe... more To estimate the population prevalence of active pulmonary tuberculosis in Gambia. Between December 2011 and January 2013, people aged ≥ 15 years participating in a nationwide, multistage cluster survey were screened for active pulmonary tuberculosis with chest radiography and for tuberculosis symptoms. For diagnostic confirmation, sputum samples were collected from those whose screening were positive and subjected to fluorescence microscopy and liquid tuberculosis cultures. Multiple imputation and inverse probability weighting were used to estimate tuberculosis prevalence. Of 100 678 people enumerated, 55 832 were eligible to participate and 43 100 (77.2%) of those participated. A majority of participants (42 942; 99.6%) were successfully screened for symptoms and by chest X-ray. Only 5948 (13.8%) were eligible for sputum examination, yielding 43 bacteriologically confirmed, 28 definite smear-positive and six probable smear-positive tuberculosis cases. Chest X-ray identified more tu...

PLoS ONE, 2014

Background: Although tuberculosis is transmitted by the airborne route, direct information on the... more Background: Although tuberculosis is transmitted by the airborne route, direct information on the natural output of bacilli into air by source cases is very limited. We sought to address this through sampling of expelled aerosols in face masks that were subsequently analyzed for mycobacterial contamination. Methods: In series 1, 17 smear microscopy positive patients wore standard surgical face masks once or twice for periods between 10 minutes and 5 hours; mycobacterial contamination was detected using a bacteriophage assay. In series 2, 19 patients with suspected tuberculosis were studied in Leicester UK and 10 patients with at least one positive smear were studied in The Gambia. These subjects wore one FFP30 mask modified to contain a gelatin filter for one hour; this was subsequently analyzed by the Xpert MTB/RIF system. Results: In series 1, the bacteriophage assay detected live mycobacteria in 11/17 patients with wearing times between 10 and 120 minutes. Variation was seen in mask positivity and the level of contamination detected in multiple samples from the same patient. Two patients had non-tuberculous mycobacterial infections. In series 2, 13/20 patients with pulmonary tuberculosis produced positive masks and 0/9 patients with extrapulmonary or non-tuberculous diagnoses were mask positive. Overall, 65% of patients with confirmed pulmonary mycobacterial infection gave positive masks and this included 3/6 patients who received diagnostic bronchoalveolar lavages. Conclusion: Mask sampling provides a simple means of assessing mycobacterial output in non-sputum expectorant. The approach shows potential for application to the study of airborne transmission and to diagnosis.

PLoS ONE, 2014

Background: Although tuberculosis is transmitted by the airborne route, direct information on the... more Background: Although tuberculosis is transmitted by the airborne route, direct information on the natural output of bacilli into air by source cases is very limited. We sought to address this through sampling of expelled aerosols in face masks that were subsequently analyzed for mycobacterial contamination. Methods: In series 1, 17 smear microscopy positive patients wore standard surgical face masks once or twice for periods between 10 minutes and 5 hours; mycobacterial contamination was detected using a bacteriophage assay. In series 2, 19 patients with suspected tuberculosis were studied in Leicester UK and 10 patients with at least one positive smear were studied in The Gambia. These subjects wore one FFP30 mask modified to contain a gelatin filter for one hour; this was subsequently analyzed by the Xpert MTB/RIF system. Results: In series 1, the bacteriophage assay detected live mycobacteria in 11/17 patients with wearing times between 10 and 120 minutes. Variation was seen in mask positivity and the level of contamination detected in multiple samples from the same patient. Two patients had non-tuberculous mycobacterial infections. In series 2, 13/20 patients with pulmonary tuberculosis produced positive masks and 0/9 patients with extrapulmonary or non-tuberculous diagnoses were mask positive. Overall, 65% of patients with confirmed pulmonary mycobacterial infection gave positive masks and this included 3/6 patients who received diagnostic bronchoalveolar lavages. Conclusion: Mask sampling provides a simple means of assessing mycobacterial output in non-sputum expectorant. The approach shows potential for application to the study of airborne transmission and to diagnosis.

Frontiers in Microbiology, May 5, 2021

Introduction: The fungi ITS sequence length dissimilarity, non-specific amplicons, including chim... more Introduction: The fungi ITS sequence length dissimilarity, non-specific amplicons, including chimaera formed during Polymerase Chain Reaction (PCR), added to sequencing errors, create bias during similarity clustering and abundance estimation in the downstream analysis. To overcome these challenges, we present a novel approach, Hierarchical Clustering with Kraken (HCK), to classify ITS1 amplicons and Abundance-Base Alternative Approach (ABAA) pipeline to detect and filter non-specific amplicons in fungi metabarcoding sequencing datasets. Materials and Methods: We compared the performances of both pipelines against QIIME, KRAKEN, and DADA2 using publicly available fungi ITS mock community datasets and using BLASTn as a reference. We calculated the Precision, Recall, F-score using the True-Positive, False-positive, and False-negative estimation. Alpha diversity (Chao1 and Shannon metrics) was also used to evaluate the diversity estimation of our method. Results: The analysis shows that ABAA reduced the number of false-positive with all metabarcoding methods tested, and HCK increases precision and recall. HCK, coupled with ABAA, improves the F-score and bring alpha diversity metric value close to that of the BLASTn alpha diversity values when compared to QIIME, KRAKEN, and DADA2. Conclusion: The developed HCK-ABAA approach allows better identification of the fungi community structures while avoiding use of a reference database for non-specific amplicons filtration. It results in a more robust and stable methodology over time. The software can be downloaded on the following link: https://bitbucket.org/GottySG36/ hck/src/master/.

The development of cost-effective next-generation sequencing technology (NGS), recent advances in... more The development of cost-effective next-generation sequencing technology (NGS), recent advances in whole genome sequencing (WGS), and decreasing costs have had a significant impact on our knowledge of the behaviour of the bacteria which cause infectious diseases. Bacterial genome recombinations through point mutations and gene exchanges, including horizontal gene transfer and gene loss have contributed significantly to the adaptation and evolution of bacteria and have become the driving force of bacterial survival in the host niches. In this paper, we propose a review of publicly available computational biology tools, frequently used for real-time genomics in clinical microbiology over the past decade and highlight the impact of bacterial genome recombinations in clinical microbiology. Article II Using MALDI-TOF MS typing method to decipher outbreak: the case of Staphylococcus saprophyticus causing urinary tract infections (UTIs) in Marseille, France.

Journal of global antimicrobial resistance, Sep 1, 2019

OBJECTIVES Carbapenem resistance in Klebsiella pneumoniae (CRKP) is an increasing problem worldwi... more OBJECTIVES Carbapenem resistance in Klebsiella pneumoniae (CRKP) is an increasing problem worldwide and infections caused by this bacterium can be difficult to treat. Here we reported the case of a patient from Romania hospitalized in Bulgaria after an accident trauma that came in France for the treatment of an osteitis caused by a K. pneumoniae carrying both blaNDM-1 and blaOXA-48. METHOD The resistome of this extremely-drug-resistant bacterium was analyzed both with phenotypic (large antibiotic susceptibility testing) and genomic method (genome sequencing). The genetic environment of the two carbapenemases was studied. RESULTS K. pneumoniae ST307 carrying both a blaNDM-1 gene and a blaOXA-48 gene located on two different plasmids, an Inc L/M and an IncFII. Patient was successfully treated by a combination of intravenous colistin (9 MUI, then 4.5 MUI 2 times/day), intravenous fosfomycin (4 g 3 times/day) and oral doxycycline (100 mg 2 times/day) for 3 months. Fecal microbiota transplantation was successfully conducted for a stool carriage. CONCLUSION The ST307 type is becoming endemic in hospital environment and is frequently associated with carbapenem resistance. Treatment of infection caused by multi-drug resistant bacteria are a clinical challenge and the use of old antibiotics associated with a screening and decolonization of the reservoirs can be an efficient therapeutic alternative.

European Journal of Clinical Microbiology & Infectious Diseases, Aug 22, 2017

Staphylococcus saprophyticus is one of the leading causes of urinary tract infections (UTI). In D... more Staphylococcus saprophyticus is one of the leading causes of urinary tract infections (UTI). In December 2014, our surveillance system identified an abnormal increase in S. saprophyticus causing UTIs in four university hospitals in Marseille, indicating a suspected community S. saprophyticus UTI outbreak. This was detected by our surveillance system BALYSES (Bacterial real-time Laboratory-based Surveillance System). S. saprophyticus/ Escherichia coli UTI ratio increased threefold from 0.0084 in 2002 to 0.025 in December 2015 in Marseille with an abnormal peak in December 2014, and with an annual estimated ratio trend of 5.10 −6 (p-value < 10 −3). Matrix-Assisted Laser Desorption Ionisation-Time of Flight Mass Spectrometry (MALDI-TOF MS) spectral analysis of strains was used to analyse strains cluster expansion, comparing strains from Marseille to those from Nice during the same period. MALDI-TOF MS spectral analysis revealed a geographical restricted clonal expansion of the strains clusters in Marseille as compared to Nice. Our finding suggests (i) a geographically restricted expansion of a specific S. saprophyticus strain clusters circulating in Marseille, and (ii) MALDI-TOF MS can be used as a costeffective tool to investigate an outbreak.

PLoS ONE, 2014

Background: Although tuberculosis is transmitted by the airborne route, direct information on the... more Background: Although tuberculosis is transmitted by the airborne route, direct information on the natural output of bacilli into air by source cases is very limited. We sought to address this through sampling of expelled aerosols in face masks that were subsequently analyzed for mycobacterial contamination. Methods: In series 1, 17 smear microscopy positive patients wore standard surgical face masks once or twice for periods between 10 minutes and 5 hours; mycobacterial contamination was detected using a bacteriophage assay. In series 2, 19 patients with suspected tuberculosis were studied in Leicester UK and 10 patients with at least one positive smear were studied in The Gambia. These subjects wore one FFP30 mask modified to contain a gelatin filter for one hour; this was subsequently analyzed by the Xpert MTB/RIF system. Results: In series 1, the bacteriophage assay detected live mycobacteria in 11/17 patients with wearing times between 10 and 120 minutes. Variation was seen in mask positivity and the level of contamination detected in multiple samples from the same patient. Two patients had non-tuberculous mycobacterial infections. In series 2, 13/20 patients with pulmonary tuberculosis produced positive masks and 0/9 patients with extrapulmonary or non-tuberculous diagnoses were mask positive. Overall, 65% of patients with confirmed pulmonary mycobacterial infection gave positive masks and this included 3/6 patients who received diagnostic bronchoalveolar lavages. Conclusion: Mask sampling provides a simple means of assessing mycobacterial output in non-sputum expectorant. The approach shows potential for application to the study of airborne transmission and to diagnosis.

L'objectif de notre thèse est d'appliquer la génomique en temps réel pour déchiffrer les ... more L'objectif de notre thèse est d'appliquer la génomique en temps réel pour déchiffrer les caractéristiques génomiques bactériennes et les événements de recombinaison du génome des bactéries atypiques ainsi que leur impact sur les maladies infectieuses. Au cours de ma thèse, nous avons effectué une revue sur les outils bioinformatiques les plus courants utilisés en microbiologie clinique et mis en évidence l’impact de la recombinaison sur le comportement des bacteries. Le deuxième projet de notre thèse est de déchiffrer une epidémis de Staphylococcus saprophyticus causant des infections urinaires en utilisant la technologie MALDI-TOF MS et une analyse comparative du génome de S. saprophyticus pour comprendre leur évolution génomique. Nous avons démontré qu'il existe un groupe de S. saprophyticus géographiquement restreint à Marseille comparé au souches de Nice. De plus, nous avons montré que S. saprophyticus qui était initialement considéré comme une bactérie saprophyte a ...

L'objectif de notre thèse est d'appliquer la génomique en temps réel pour déchiffrer les ... more L'objectif de notre thèse est d'appliquer la génomique en temps réel pour déchiffrer les caractéristiques génomiques bactériennes et les événements de recombinaison du génome des bactéries atypiques ainsi que leur impact sur les maladies infectieuses. Au cours de ma thèse, nous avons effectué une revue sur les outils bioinformatiques les plus courants utilisés en microbiologie clinique et mis en évidence l’impact de la recombinaison sur le comportement des bacteries. Le deuxième projet de notre thèse est de déchiffrer une epidémis de Staphylococcus saprophyticus causant des infections urinaires en utilisant la technologie MALDI-TOF MS et une analyse comparative du génome de S. saprophyticus pour comprendre leur évolution génomique. Nous avons démontré qu'il existe un groupe de S. saprophyticus géographiquement restreint à Marseille comparé au souches de Nice. De plus, nous avons montré que S. saprophyticus qui était initialement considéré comme une bactérie saprophyte a ...

L'objectif de notre these est d'appliquer la genomique en temps reel pour dechiffrer les ... more L'objectif de notre these est d'appliquer la genomique en temps reel pour dechiffrer les caracteristiques genomiques bacteriennes et les evenements de recombinaison du genome des bacteries atypiques ainsi que leur impact sur les maladies infectieuses. Au cours de ma these, nous avons effectue une revue sur les outils bioinformatiques les plus courants utilises en microbiologie clinique et mis en evidence l’impact de la recombinaison sur le comportement des bacteries. Le deuxieme projet de notre these est de dechiffrer une epidemis de Staphylococcus saprophyticus causant des infections urinaires en utilisant la technologie MALDI-TOF MS et une analyse comparative du genome de S. saprophyticus pour comprendre leur evolution genomique. Nous avons demontre qu'il existe un groupe de S. saprophyticus geographiquement restreint a Marseille compare au souches de Nice. De plus, nous avons montre que S. saprophyticus qui etait initialement considere comme une bacterie saprophyte a ...

Introduction The fungi ITS sequence length dissimilarity, non-specific amplicons, including chima... more Introduction The fungi ITS sequence length dissimilarity, non-specific amplicons, including chimaera formed during Polymerase Chain Reaction (PCR), added to sequencing errors, create bias during similarity clustering and abundance estimation in the downstream analysis. To overcome these challenges, we present a novel approach, Hierarchical Clustering with Kraken (HCK), to classify ITS1 amplicons and Abundance-Base Alternative Approach (ABAA) pipeline to detect and filter non-specific amplicons in fungi metabarcoding sequencing datasets. Materials and Methods We compared the performances of both pipelines against QIIME, KRAKEN, and DADA2 using publicly available fungi ITS mock community datasets and using BLASTn as a reference. We calculated the Precision, Recall, F-score using the True-Positive, False-positive, and False-negative estimation. Alpha diversity (Chao1 and Shannon metrics) was also used to evaluate the diversity estimation of our method. Results The analysis shows that A...

Microorganisms

Here, we performed a comparative genomic analysis of all available genomes of E. faecalis (n = 15... more Here, we performed a comparative genomic analysis of all available genomes of E. faecalis (n = 1591) and E. faecium (n = 1981) and investigated the association between the presence or absence of CRISPR-Cas systems, endonuclease/anti-endonuclease systems and the acquisition of antimicrobial resistance, especially vancomycin resistance genes. Most of the analysed Enterococci were isolated from humans and less than 14% of them were from foods and animals. We analysed and detected CRISPR–Cas systems in 75.36% of E. faecalis genomes and only 4.89% of E. faecium genomes with a significant difference (p-value < 10−5). We found a negative correlation between the number of CRISPR–Cas systems and genome size (r = −0.397, p-value < 10−5) and a positive correlation between the genome %GC content and the number of CRISPR–Cas systems (r = 0.215, p-value < 10−5). Our findings showed that the presence of the anti-endonuclease ardA gene may explain the decrease in the number of CRISPR–Cas s...

Journal of Global Antimicrobial Resistance

Journal of Advances in Microbiology

The aim of this study is to describe the antibiotic profile and identify the molecular type of be... more The aim of this study is to describe the antibiotic profile and identify the molecular type of betalactamase-producing Escherichia coli isolated from clinical specimens at Sylvanus Olympio teaching hospital in Lomé. The study span from 1 st March 2009 to 31 st December 2010. We collected fiftythree isolates of Escherichia coli, identified by api20E. Antibiotic susceptibility test was performed Original Research Article

New Microbes and New Infections, 2017

We propose the main characteristics of a new bacterium species named Nissabacter archeti strain 2... more We propose the main characteristics of a new bacterium species named Nissabacter archeti strain 2134 (CSURP3445 = LT631518), isolated from pustule scalp of a 29-year-old man at hospital Archet 2, Nice, south of France.

Bulletin of the World Health Organization, 2016

Study procedures Three teams-each consisting of a research clinician who led a team of 7 trained ... more Study procedures Three teams-each consisting of a research clinician who led a team of 7 trained fieldworkers and a radiographer-performed the fieldwork from December 2011 to January 2013. Data collection in each cluster was done over a seven-day period. The field Objective To estimate the population prevalence of active pulmonary tuberculosis in Gambia. Methods Between December 2011 and January 2013, people aged ≥ 15 years participating in a nationwide, multistage cluster survey were screened for active pulmonary tuberculosis with chest radiography and for tuberculosis symptoms. For diagnostic confirmation, sputum samples were collected from those whose screening were positive and subjected to fluorescence microscopy and liquid tuberculosis cultures. Multiple imputation and inverse probability weighting were used to estimate tuberculosis prevalence. Findings Of 100 678 people enumerated, 55 832 were eligible to participate and 43 100 (77.2%) of those participated. A majority of participants (42 942; 99.6%) were successfully screened for symptoms and by chest X-ray. Only 5948 (13.8%) were eligible for sputum examination, yielding 43 bacteriologically confirmed, 28 definite smear-positive and six probable smear-positive tuberculosis cases. Chest X-ray identified more tuberculosis cases (58/69) than did symptoms alone (43/71). The estimated prevalence of smear-positive and bacteriologically confirmed pulmonary tuberculosis were 90 (95% confidence interval, CI: 53-127) and 212 (95% CI: 152-272) per 100 000 population, respectively. Tuberculosis prevalence was higher in males (333; 95% CI: 233-433) and in the 35-54 year age group (355; 95% CI: 219-490). Conclusion The burden of tuberculosis remains high in Gambia but lower than earlier estimates of 490 per 100 000 population in 2010. Less than half of all cases would have been identified based on smear microscopy results alone. Successful control efforts will require interventions targeting men, increased access to radiography and more accurate, rapid diagnostic tests.

New Microbes and New Infections, 2015

Drug-resistant tuberculosis (TB) is emerging as an important health problem in Togo. From sputum ... more Drug-resistant tuberculosis (TB) is emerging as an important health problem in Togo. From sputum of previously treated TB patients, multidrug-resistant (MDR) TB was diagnosed in 24% (10/42) patients via GeneXpert MTB/RIF compared to 25% (6/24) patients via conventional drug susceptibility testing (BACTEC MGIT 960 system). The agreement between these two methods to detect MDR-TB is excellent. However, GeneXpert MTB/RIF offers the advantage of rapidly detecting Mycobacterium tuberculosis complex in sputum samples in instances where the cultures are negative (33%, 14/42) or contaminated (9.5%, 4/42). GeneXpert MTB/RIF permitted us to estimate the prevalence of MDR-TB in previously treated TB patients and to improve TB diagnostics among HIV-positive and-negative patients in Togo, where culturing M. tuberculosis complex from sputum samples is challenging.

Introduction : Les évaluations des tests de diagnos-tic Rapides/Simples (TDR) du VIH sont nécessa... more Introduction : Les évaluations des tests de diagnos-tic Rapides/Simples (TDR) du VIH sont nécessaires pour la détermination d'algorithmes de tests simples et rapides, utilisables au point de service pour le conseil et dépistage volontaire, la surveillance épidémiologi-que, la sécurité transfusionnelle et dans les services de consultations prénatales. Objectif : Evaluer la performance de trois (3) tests de diagnostic sérologique de l'infection à VIH dont un (1) test ELISA (EQUIPAR HIV 1/2 recombinant) et deux (2) tests rapides/simples (HEXAGON HIV et FIRSTRESPONSE). Méthodes : L'évaluation de la performance de trois tests pour le diagnostic de l'infection à VIH à Lomé (Togo) a été réalisée au centre national de référence pour les tests VIH/SIDA/IST sis au CHU de Lomé TOKOIN. Les tests évalués ont été EQUIPAR HIV ½ recombi-nant, HEXAGON HIV et FIRST RESPONSE Sang total HIV 1-2-0. Les sérums ont été collectés de Janvier à Juillet 2008 des malades hospitalisés au CHU Tok...

Bulletin of the World Health Organization, 2016

To estimate the population prevalence of active pulmonary tuberculosis in Gambia. Between Decembe... more To estimate the population prevalence of active pulmonary tuberculosis in Gambia. Between December 2011 and January 2013, people aged ≥ 15 years participating in a nationwide, multistage cluster survey were screened for active pulmonary tuberculosis with chest radiography and for tuberculosis symptoms. For diagnostic confirmation, sputum samples were collected from those whose screening were positive and subjected to fluorescence microscopy and liquid tuberculosis cultures. Multiple imputation and inverse probability weighting were used to estimate tuberculosis prevalence. Of 100 678 people enumerated, 55 832 were eligible to participate and 43 100 (77.2%) of those participated. A majority of participants (42 942; 99.6%) were successfully screened for symptoms and by chest X-ray. Only 5948 (13.8%) were eligible for sputum examination, yielding 43 bacteriologically confirmed, 28 definite smear-positive and six probable smear-positive tuberculosis cases. Chest X-ray identified more tu...

PLoS ONE, 2014

Background: Although tuberculosis is transmitted by the airborne route, direct information on the... more Background: Although tuberculosis is transmitted by the airborne route, direct information on the natural output of bacilli into air by source cases is very limited. We sought to address this through sampling of expelled aerosols in face masks that were subsequently analyzed for mycobacterial contamination. Methods: In series 1, 17 smear microscopy positive patients wore standard surgical face masks once or twice for periods between 10 minutes and 5 hours; mycobacterial contamination was detected using a bacteriophage assay. In series 2, 19 patients with suspected tuberculosis were studied in Leicester UK and 10 patients with at least one positive smear were studied in The Gambia. These subjects wore one FFP30 mask modified to contain a gelatin filter for one hour; this was subsequently analyzed by the Xpert MTB/RIF system. Results: In series 1, the bacteriophage assay detected live mycobacteria in 11/17 patients with wearing times between 10 and 120 minutes. Variation was seen in mask positivity and the level of contamination detected in multiple samples from the same patient. Two patients had non-tuberculous mycobacterial infections. In series 2, 13/20 patients with pulmonary tuberculosis produced positive masks and 0/9 patients with extrapulmonary or non-tuberculous diagnoses were mask positive. Overall, 65% of patients with confirmed pulmonary mycobacterial infection gave positive masks and this included 3/6 patients who received diagnostic bronchoalveolar lavages. Conclusion: Mask sampling provides a simple means of assessing mycobacterial output in non-sputum expectorant. The approach shows potential for application to the study of airborne transmission and to diagnosis.

PLoS ONE, 2014

Background: Although tuberculosis is transmitted by the airborne route, direct information on the... more Background: Although tuberculosis is transmitted by the airborne route, direct information on the natural output of bacilli into air by source cases is very limited. We sought to address this through sampling of expelled aerosols in face masks that were subsequently analyzed for mycobacterial contamination. Methods: In series 1, 17 smear microscopy positive patients wore standard surgical face masks once or twice for periods between 10 minutes and 5 hours; mycobacterial contamination was detected using a bacteriophage assay. In series 2, 19 patients with suspected tuberculosis were studied in Leicester UK and 10 patients with at least one positive smear were studied in The Gambia. These subjects wore one FFP30 mask modified to contain a gelatin filter for one hour; this was subsequently analyzed by the Xpert MTB/RIF system. Results: In series 1, the bacteriophage assay detected live mycobacteria in 11/17 patients with wearing times between 10 and 120 minutes. Variation was seen in mask positivity and the level of contamination detected in multiple samples from the same patient. Two patients had non-tuberculous mycobacterial infections. In series 2, 13/20 patients with pulmonary tuberculosis produced positive masks and 0/9 patients with extrapulmonary or non-tuberculous diagnoses were mask positive. Overall, 65% of patients with confirmed pulmonary mycobacterial infection gave positive masks and this included 3/6 patients who received diagnostic bronchoalveolar lavages. Conclusion: Mask sampling provides a simple means of assessing mycobacterial output in non-sputum expectorant. The approach shows potential for application to the study of airborne transmission and to diagnosis.