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1. Global and regional epidemiology of HIV-1 recombinants in 1990–2015: a systematic review and global survey

Author

Abimiku, Alash'le G, Agwale, Simon, Archibald, Chris, Avidor, Boaz, Barbás, María Gabriela, Barre-Sinoussi, Francoise, Barugahare, Banson, Belabbes, El Hadj, Bertagnolio, Silvia, Birx, Deborah, Bobkov, Aleksei F, Brandful, James, Bredell, Helba, Brennan, Catherine A, Brooks, James, Bruckova, Marie, Buonaguro, Luigi, Buonaguro, Franco, Buttò, Stefano, Buvé, Anne, Campbell, Mary, Carr, Jean, Carrera, Alex, Carrillo, Manuel Gómez, Celum, Connie, Chaplin, Beth, Charles, Macarthur, Chatzidimitriou, Dimitrios, Chen, Zhiwei, Chijiwa, Katsumi, Cooper, David, Cunningham, Philip, Dagnra, Anoumou, de Gascun, Cillian F, Del Amo, Julia, Delgado, Elena, Dietrich, Ursula, Dwyer, Dominic, Ellenberger, Dennis, Ensoli, Barbara, Essex, Max, Gao, Feng, Fleury, Hervé, Fonjungo, Peter N, Foulongne, Vincent, Gadkari, Deepak A, García, Federico, Garsia, Roger, Gershy-Damet, Guy Michel, Glynn, Judith R, Goodall, Ruth, Grossman, Zehava, Lindenmeyer-Guimarães, Monick, Hahn, Beatrice, Hamers, Raph L, Hamouda, Osamah, Handema, Ray, He, Xiang, Herbeck, Joshua, Ho, David D, Holguin, Africa, Hosseinipour, Mina, Hunt, Gillian, Ito, Masahiko, Bel Hadj Kacem, Mohamed Ali, Kahle, Erin, Kaleebu, Pontiano, Kalish, Marcia, Kamarulzaman, Adeeba, Kang, Chun, Kanki, Phyllis, Karamov, Edward, Karasi, Jean-Claude, Kayitenkore, Kayitesi, Kelleher, Tony, Kitayaporn, Dwip, Kostrikis, Leondios G, Kucherer, Claudia, Lara, Claudia, Leitner, Thomas, Liitsola, Kirsi, Lingappa, Jai, Linka, Marek, Lorenzana de Rivera, Ivette, Lukashov, Vladimir, Maayan, Shlomo, Mayr, Luzia, McCutchan, Francine, Meda, Nicolas, Menu, Elisabeth, Mhalu, Fred, Mloka, Doreen, Mokili, John L, Montes, Brigitte, Mor, Orna, Morgado, Mariza, Mosha, Fausta, Moussi, Awatef, Mullins, James, Najera, Rafael, Nasr, Mejda, Ndembi, Nicaise, Neilson, Joel R, Nerurkar, Vivek R, Neuhann, Florian, Nolte, Claudine, Novitsky, Vlad, Nyambi, Philippe, Ofner, Marianna, Paladin, Fem J, Papa, Anna, Pape, Jean, Parkin, Neil, Parry, Chris, Peeters, Martine, Pelletier, Alexandra, Pérez-Álvarez, Lucía, Pillay, Deenan, Pinto, Angie, Quang, Trinh Duy, Rademeyer, Cecilia, Raikanikoda, Filimone, Rayfield, Mark A, Reynes, Jean-Marc, Rinke de Wit, Tobias, Robbins, Kenneth E, Rolland, Morgane, Rousseau, Christine, Salazar-Gonzales, Jesus, Salem, Hanan, Salminen, Mika, Salomon, Horacio, Sandstrom, Paul, Santiago, Mario L, Sarr, Abdoulaye D, Schroeder, Bryan, Segondy, Michel, Selhorst, Philippe, Sempala, Sylvester, Servais, Jean, Shaik, Ansari, Shao, Yiming, Slim, Amine, Soares, Marcelo A, Songok, Elijah, Stewart, Debbie, Stokes, Julie, Subbarao, Shambavi, Sutthent, Ruengpung, Takehisa, Jun, Tanuri, Amilcar, Tee, Kok Keng, Thapa, Kiran, Thomson, Michael, Tran, Tyna, Urassa, Willy, Ushijima, Hiroshi, van de Perre, Philippe, van der Groen, Guido, van Laethem, Kristel, van Oosterhout, Joep, van Sighem, Ard, van Wijngaerden, Eric, Vandamme, Anne-Mieke, Vercauteren, Jurgen, Vidal, Nicole, Wallace, Lesley, Williamson, Carolyn, Wolday, Dawit, Xu, Jianqing, Yang, Chunfu, Zhang, Linqi, Zhang, Rong, Hemelaar, Joris, Elangovan, Ramyiadarsini, Yun, Jason, Dickson-Tetteh, Leslie, Kirtley, Shona, Gouws-Williams, Eleanor, and Ghys, Peter D

Published
2020
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2. Global and regional molecular epidemiology of HIV-1, 1990–2015: a systematic review, global survey, and trend analysis

Author

Abimiku, Alash'le G, Agwale, Simon, Archibald, Chris, Avidor, Boaz, Barbás, María Gabriela, Barre-Sinoussi, Francoise, Barugahare, Banson, Belabbes, El Hadj, Bertagnolio, Silvia, Birx, Deborah, Bobkov, Aleksei F, Brandful, James, Bredell, Helba, Brennan, Catherine A, Brooks, James, Bruckova, Marie, Buonaguro, Luigi, Buonaguro, Franco, Buttò, Stefano, Buve, Anne, Campbell, Mary, Carr, Jean, Carrera, Alex, Carrillo, Manuel Gómez, Celum, Connie, Chaplin, Beth, Charles, Macarthur, Chatzidimitriou, Dimitrios, Chen, Zhiwei, Chijiwa, Katsumi, Cooper, David, Cunningham, Philip, Dagnra, Anoumou, de Gascun, Cillian F, Del Amo, Julia, Delgado, Elena, Dietrich, Ursula, Dwyer, Dominic, Ellenberger, Dennis, Ensoli, Barbara, Essex, Max, Gao, Feng, Fleury, Herve, Fonjungo, Peter N, Foulongne, Vincent, Gadkari, Deepak A, García, Federico, Garsia, Roger, Gershy-Damet, Guy Michel, Glynn, Judith R, Goodall, Ruth, Grossman, Zehava, Lindenmeyer-Guimarães, Monick, Hahn, Beatrice, Hamers, Raph L, Hamouda, Osamah, Handema, Ray, He, Xiang, Herbeck, Joshua, Ho, David D, Holguin, Africa, Hosseinipour, Mina, Hunt, Gillian, Ito, Masahiko, Bel Hadj Kacem, Mohamed Ali, Kahle, Erin, Kaleebu, Pontiano Kaleebu, Kalish, Marcia, Kamarulzaman, Adeeba, Kang, Chun, Kanki, Phyllis, Karamov, Edward, Karasi, Jean-Claude, Kayitenkore, Kayitesi, Kelleher, Tony, Kitayaporn, Dwip, Kostrikis, Leondios G, Kucherer, Claudia, Lara, Claudia, Leitner, Thomas, Liitsola, Kirsi, Lingappa, Jai, Linka, Marek, Lorenzana de Rivera, Ivette, Lukashov, Vladimir, Maayan, Shlomo, Mayr, Luzia, McCutchan, Francine, Meda, Nicolas, Menu, Elisabeth, Mhalu, Fred, Mloka, Doreen, Mokili, John L, Montes, Brigitte, Mor, Orna, Morgado, Mariza, Mosha, Fausta, Moussi, Awatef, Mullins, James, Najera, Rafael, Nasr, Mejda, Ndembi, Nicaise, Neilson, Joel R, Nerurkar, Vivek R, Neuhann, Florian, Nolte, Claudine, Novitsky, Vlad, Nyambi, Philippe, Ofner, Marianna, Paladin, Fem J, Papa, Anna, Pape, Jean, Parkin, Neil, Parry, Chris, Peeters, Martine, Pelletier, Alexandra, Pérez-Álvarez, Lucía, Pillay, Deenan, Pinto, Angie, Quang, Trinh Duy, Rademeyer, Cecilia, Raikanikoda, Filimone, Rayfield, Mark A, Reynes, Jean-Marc, Rinke de Wit, Tobias, Robbins, Kenneth E, Rolland, Morgane, Rousseau, Christine, Salazar-Gonzales, Jesus, Salem, Hanan, Salminen, Mika, Salomon, Horacio, Sandstrom, Paul, Santiago, Mario L, Sarr, Abdoulaye D, Schroeder, Bryan, Segondy, Michel, Selhorst, Philippe, Sempala, Sylvester, Servais, Jean, Shaik, Ansari, Shao, Yiming, Slim, Amine, Soares, Marcelo A, Songok, Elijah, Stewart, Debbie, Stokes, Julie, Subbarao, Shambavi, Sutthent, Ruengpung, Takehisa, Jun, Tanuri, Amilcar, Tee, Kok Keng, Thapa, Kiran, Thomson, Michael, Tran, Tyna, Urassa, Willy, Ushijima, Hiroshi, van de Perre, Philippe, van der Groen, Guido, van Laethem, Kristel, van Oosterhout, Joep, van Sighem, Ard, van Wijngaerden, Eric, Vandamme, Anne-Mieke, Vercauteren, Jurgen, Vidal, Nicole, Wallace, Lesley, Williamson, Carolyn, Wolday, Dawit, Xu, Jianqing, Yang, Chunfu, Zhang, Linqi, Zhang, Rong, Hemelaar, Joris, Elangovan, Ramyiadarsini, Yun, Jason, Dickson-Tetteh, Leslie, Fleminger, Isabella, Kirtley, Shona, Williams, Brian, Gouws-Williams, Eleanor, and Ghys, Peter D

Published
2019
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3. Evaluation of the influenza-like illness surveillance system in Tunisia, 2012–2015

Author

Rihab Yazidi, Wafa Aissi, Hind Bouguerra, Mariem Nouira, Ghassen Kharroubi, Latifa Maazaoui, Mokhtar Zorraga, Naima Abdeddaiem, Sadok Chlif, Awatef El Moussi, Mohamed Ali Ben Hadj Kacem, Mohamed Ali Snoussi, Wissem Ghawar, Makram Koubaa, Lauren Polansky, Margaret McCarron, Mohamed Boussarsar, Khaled Menif, Slim Amine, Jalila Ben Khelil, Mounir Ben Jemaa, Jihene Bettaieb, Nissaf Bouafif Ben Alaya, and Afif Ben Salah

Subjects
Surveillance, Health system, Influenza, ILI, Evaluation, Tunisia, Public aspects of medicine, RA1-1270
Abstract

Abstract Background This study was initiated to evaluate, for the first time, the performance and quality of the influenza-like illness (ILI) surveillance system in Tunisia. Methods The evaluation covered the period of 2012–2015 and used different data sources to measure indicators related to data quality and completeness, representativeness, timeliness, simplicity, acceptability, flexibility, stability and utility. Results During the evaluation period, 485.221 ILI cases were reported among 6.386.621 outpatients at 268 ILI sentinel sites. To conserve resources, cases were only enrolled and tested for influenza during times when the number of patients meeting the ILI case definition exceeded 7% (10% after 2014) of the total number of outpatients for the week. When this benchmark was met, five to 10 patients were enrolled and sampled by nasopharyngeal swabs the following week. In total, The National Influenza Center (NIC) received 2476 samples, of which 683 (27.6%) were positive for influenza. The greatest strength of the system was its representativeness and flexibility. The timeliness of the data and the acceptability of the surveillance system performed moderately well; however, the utility of the data and the stability and simplicity of the surveillance system need improvement. Overall, the performance of the Tunisian influenza surveillance system was evaluated as performing moderately well for situational awareness in the country and for collecting representative influenza virologic samples. Conclusions The influenza surveillance system in Tunisia provided pertinent evidence for public health interventions related to influenza situational awareness. To better monitor influenza, we propose that ILI surveillance should be limited to sites that are currently performing well and the quality of data collected should be closely monitored and improved.

Published
2019
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8. Applying the moving epidemic method to determine influenza epidemic and intensity thresholds using influenza‐like illness surveillance data 2009‐2018 in Tunisia

Author

Nissaf Ben Alaya, M.K. Chahed, Afif Ben Salah, Souha Bougatef, Slim Amine, H Bouguerra, L Maazaoui, Salma Abid, Amal Cherif, N Abdeddaiem, Rihab Yazidi, Awatef ElMoussi, Elyes Boutouria, Jihene Bettaieb, Mokhtar Zorraga, and Leila Bouabid

Subjects
Pulmonary and Respiratory Medicine, Average duration, R language, Tunisia, Surveillance data, Adolescent, Epidemiology, Influenza season, 030312 virology, ILI surveillance, 03 medical and health sciences, Influenza, Human, Pandemic, Influenza prevention, epidemic threshold, Humans, Medicine, Child, Pandemics, 0303 health sciences, Influenza-like illness, business.industry, Infant, Newborn, Public Health, Environmental and Occupational Health, Infant, Mathematical Concepts, Original Articles, Intensity (physics), Infectious Diseases, Research Design, Child, Preschool, moving epidemic method, Epidemiological Monitoring, Original Article, Seasons, influenza, business, Sentinel Surveillance, Demography
Abstract

Background Defining the start and assessing the intensity of influenza seasons are essential to ensure timely preventive and control measures and to contribute to the pandemic preparedness. The present study aimed to determine the epidemic and intensity thresholds of influenza season in Tunisia using the moving epidemic method. Methods We applied the moving epidemic method (MEM) using the R Language implementation (package “mem”). We have calculated the epidemic and the different intensity thresholds from historical data of the past nine influenza seasons (2009‐2010 to 2017‐2018) and assessed the impact of the 2009‐2010 pandemic year. Data used were the weekly influenza‐like illness (ILI) proportions compared with all outpatient acute consultations. The goodness of the model was assessed using a cross validation procedure. Results The average duration of influenza epidemic during a typical season was 20 weeks and ranged from 11 weeks (2009‐2010 season) to 23 weeks (2015‐2016 season). The epidemic threshold with the exclusion of the pandemic season was 6.25%. It had a very high sensitivity of 85% and a high specificity of 69%. The different levels of intensity were established as follows: low, if ILI proportion is below 9.74%, medium below 12.05%; high below 13.27%; and very high above this last rate. Conclusions This is the first mathematically based study of seasonal threshold of influenza in Tunisia. As in other studies in different countries, the model has shown both good specificity and sensitivity, which allows timely and accurate detection of the start of influenza seasons. The findings will contribute to the development of more efficient measures for influenza prevention and control.

Published
2020
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9. Family cluster of Middle East respiratory syndrome coronavirus infections, Tunisia, 2013

Author

Abroug, Fekri, Slim, Amine, Ouanes-Besbes, Lamia, Kacem, Mohamed-Ali Hadj, Dachraoui, Fahmi, Ouanes, Islem, Lu, Xiaoyan, Tao, Ying, Paden, Clinton, Caidi, Hayat, Miao, Congrong, Al-Hajri, Mohammed Mohammed, Zorraga, Mokhtar, Ghaouar, Wissem, BenSalah, Afif, and Gerber, Susan I.

Subjects
United States. Centers for Disease Control and Prevention, Severe acute respiratory syndrome -- Health aspects, Health, World Health Organization
Abstract

As of May 23, 2014, a total of 635 laboratory-confirmed human cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infections had been reported to the World Health Organization; the epidemic [...]

Published
2014
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13. Escherichia coli colonizing healthy children in Tunisia: High prevalence of extra-intestinal pathovar and occurrence of non-extended-spectrum-β-lactamase-producing ST131 clone

Author

Sana Ferjani, Mabrouka Saidani, Zeineb Hamzaoui, Houda Hosni, Ilhem Boutiba-Ben Boubaker, Faouzi Slim Amine, Sarra Harbaoui, and Elaa Maamar

Subjects
Male, 0301 basic medicine, Microbiology (medical), Tunisia, Adolescent, Genotype, Virulence Factors, 030106 microbiology, Virulence, Microbial Sensitivity Tests, Drug resistance, Biology, beta-Lactamases, Microbiology, Feces, 03 medical and health sciences, Antibiotic resistance, Plasmid, Escherichia coli, Prevalence, medicine, Animals, Humans, Pharmacology (medical), Child, Escherichia coli Infections, Phylogeny, Antiinfective agent, General Medicine, biology.organism_classification, Healthy Volunteers, Anti-Bacterial Agents, Molecular Typing, Infectious Diseases, Genes, Bacterial, Pathovar, Ticarcillin, Colistin, Female, Plasmids, medicine.drug
Abstract

This study was performed to investigate the distribution of antimicrobial resistance genes and extra-intestinal virulence determinants in a collection of 98 Escherichia coli strains isolated from rectal swabs of healthy children. Forty-six isolated strains were resistant to at least one of the tested antibiotics (usually active against enterobacteria). They were mainly resistant to ampicillin and ticarcillin (42.97%), tetracyclin (26.5%), and trimethoprim/sulfamethoxazole (18.4%). No resistance to the third generation of cephalosporins, carbapenems, aminoglycosides and colistin was found. Resistance to penicillins was encoded by blaTEM-1 (n=34) and blaSHV-1 genes (n=4). Tetracyclin resistance was encoded by tetB (n=12), tetA (n= 5), and tetC (n=1) genes. Amongst resistant quinolones isolated (n=5), chromosomal mutations in gyrA and parC genes were detected in four isolates and qnrS1 gene in two strains. Nine plasmid replicon types were detected; IncFIB (n=36) and IncI1 (n=7) were the most frequent ones. Isolates frequently belonged to phylogenetic groups A (51.1%) and D (27.5%). Extra-intestinal pathovar (n=38) occurred mainly in B2 phylogroup (P=0.0002). Amongst them, two isolates (non-extended-spectrum-β-lactamase (ESBL)-producers) belonged to the pandemic clone ST131. A significant distribution of virulence determinants and pathogenicity island marker was observed within strains belonging to B2 and D phylogroups. Interestingly, our results showed that ExPEC strains, including ST131 pandemic clone, are present within fecal isolates in healthy children. These findings highlight the importance of intestinal microbiota as a reservoir for virulent and resistant strains. Thus, reinforcing hand hygiene and antibiotic rational use is imperative to avoid the diffusion of these pathogens in the community.

Published
2018
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17. Global and regional epidemiology of HIV-1 recombinants in 1990–2015: a systematic review and global survey

Author

Hemelaar, Joris, primary, Elangovan, Ramyiadarsini, additional, Yun, Jason, additional, Dickson-Tetteh, Leslie, additional, Kirtley, Shona, additional, Gouws-Williams, Eleanor, additional, Ghys, Peter D, additional, Abimiku, Alash'le G, additional, Agwale, Simon, additional, Archibald, Chris, additional, Avidor, Boaz, additional, Barbás, María Gabriela, additional, Barre-Sinoussi, Francoise, additional, Barugahare, Banson, additional, Belabbes, El Hadj, additional, Bertagnolio, Silvia, additional, Birx, Deborah, additional, Bobkov, Aleksei F, additional, Brandful, James, additional, Bredell, Helba, additional, Brennan, Catherine A, additional, Brooks, James, additional, Bruckova, Marie, additional, Buonaguro, Luigi, additional, Buonaguro, Franco, additional, Buttò, Stefano, additional, Buvé, Anne, additional, Campbell, Mary, additional, Carr, Jean, additional, Carrera, Alex, additional, Carrillo, Manuel Gómez, additional, Celum, Connie, additional, Chaplin, Beth, additional, Charles, Macarthur, additional, Chatzidimitriou, Dimitrios, additional, Chen, Zhiwei, additional, Chijiwa, Katsumi, additional, Cooper, David, additional, Cunningham, Philip, additional, Dagnra, Anoumou, additional, de Gascun, Cillian F, additional, Del Amo, Julia, additional, Delgado, Elena, additional, Dietrich, Ursula, additional, Dwyer, Dominic, additional, Ellenberger, Dennis, additional, Ensoli, Barbara, additional, Essex, Max, additional, Gao, Feng, additional, Fleury, Hervé, additional, Fonjungo, Peter N, additional, Foulongne, Vincent, additional, Gadkari, Deepak A, additional, García, Federico, additional, Garsia, Roger, additional, Gershy-Damet, Guy Michel, additional, Glynn, Judith R, additional, Goodall, Ruth, additional, Grossman, Zehava, additional, Lindenmeyer-Guimarães, Monick, additional, Hahn, Beatrice, additional, Hamers, Raph L, additional, Hamouda, Osamah, additional, Handema, Ray, additional, He, Xiang, additional, Herbeck, Joshua, additional, Ho, David D, additional, Holguin, Africa, additional, Hosseinipour, Mina, additional, Hunt, Gillian, additional, Ito, Masahiko, additional, Bel Hadj Kacem, Mohamed Ali, additional, Kahle, Erin, additional, Kaleebu, Pontiano, additional, Kalish, Marcia, additional, Kamarulzaman, Adeeba, additional, Kang, Chun, additional, Kanki, Phyllis, additional, Karamov, Edward, additional, Karasi, Jean-Claude, additional, Kayitenkore, Kayitesi, additional, Kelleher, Tony, additional, Kitayaporn, Dwip, additional, Kostrikis, Leondios G, additional, Kucherer, Claudia, additional, Lara, Claudia, additional, Leitner, Thomas, additional, Liitsola, Kirsi, additional, Lingappa, Jai, additional, Linka, Marek, additional, Lorenzana de Rivera, Ivette, additional, Lukashov, Vladimir, additional, Maayan, Shlomo, additional, Mayr, Luzia, additional, McCutchan, Francine, additional, Meda, Nicolas, additional, Menu, Elisabeth, additional, Mhalu, Fred, additional, Mloka, Doreen, additional, Mokili, John L, additional, Montes, Brigitte, additional, Mor, Orna, additional, Morgado, Mariza, additional, Mosha, Fausta, additional, Moussi, Awatef, additional, Mullins, James, additional, Najera, Rafael, additional, Nasr, Mejda, additional, Ndembi, Nicaise, additional, Neilson, Joel R, additional, Nerurkar, Vivek R, additional, Neuhann, Florian, additional, Nolte, Claudine, additional, Novitsky, Vlad, additional, Nyambi, Philippe, additional, Ofner, Marianna, additional, Paladin, Fem J, additional, Papa, Anna, additional, Pape, Jean, additional, Parkin, Neil, additional, Parry, Chris, additional, Peeters, Martine, additional, Pelletier, Alexandra, additional, Pérez-Álvarez, Lucía, additional, Pillay, Deenan, additional, Pinto, Angie, additional, Quang, Trinh Duy, additional, Rademeyer, Cecilia, additional, Raikanikoda, Filimone, additional, Rayfield, Mark A, additional, Reynes, Jean-Marc, additional, Rinke de Wit, Tobias, additional, Robbins, Kenneth E, additional, Rolland, Morgane, additional, Rousseau, Christine, additional, Salazar-Gonzales, Jesus, additional, Salem, Hanan, additional, Salminen, Mika, additional, Salomon, Horacio, additional, Sandstrom, Paul, additional, Santiago, Mario L, additional, Sarr, Abdoulaye D, additional, Schroeder, Bryan, additional, Segondy, Michel, additional, Selhorst, Philippe, additional, Sempala, Sylvester, additional, Servais, Jean, additional, Shaik, Ansari, additional, Shao, Yiming, additional, Slim, Amine, additional, Soares, Marcelo A, additional, Songok, Elijah, additional, Stewart, Debbie, additional, Stokes, Julie, additional, Subbarao, Shambavi, additional, Sutthent, Ruengpung, additional, Takehisa, Jun, additional, Tanuri, Amilcar, additional, Tee, Kok Keng, additional, Thapa, Kiran, additional, Thomson, Michael, additional, Tran, Tyna, additional, Urassa, Willy, additional, Ushijima, Hiroshi, additional, van de Perre, Philippe, additional, van der Groen, Guido, additional, van Laethem, Kristel, additional, van Oosterhout, Joep, additional, van Sighem, Ard, additional, van Wijngaerden, Eric, additional, Vandamme, Anne-Mieke, additional, Vercauteren, Jurgen, additional, Vidal, Nicole, additional, Wallace, Lesley, additional, Williamson, Carolyn, additional, Wolday, Dawit, additional, Xu, Jianqing, additional, Yang, Chunfu, additional, Zhang, Linqi, additional, and Zhang, Rong, additional

Published
2020
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19. Mutation analysis of the neuraminidase gene of influenza A(H1N1)pdm09 in Tunisia between 2009 and 2017 seasons

Author

Moussi, Awatef El, primary, Abid, Salma, additional, Charaa, Latifa, additional, Nasr, Mejda, additional, Jarroudi, Najoua, additional, Ennigrou, Dorra Arab, additional, Landolssi, Ichak, additional, Pozo, Francisco, additional, Casas, Inmaculada, additional, Daniels, Rod, additional, Ermetal, Burcu, additional, McCauley, John, additional, and Slim, Amine, additional

Published
2020
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24. HIV-1 drug resistance genotyping from antiretroviral therapy (ART) naïve and first-line treatment failures in Djiboutian patients

Author

Elmi Abar Aden, Jlizi Asma, Darar Houssein, Kacem MohamedAliBenHadj, and Slim Amine

Subjects
HIV-1 drug resistance, First-line antiretroviral therapy failure, Antiretroviral naive, Djibouti, Virological failure, Pathology, RB1-214
Abstract

Abstract In this study we report the prevalence of antiretroviral drug resistant HIV-1 genotypes of virus isolated from Djiboutian patients who failed first-line antiretroviral therapy (ART) and from ART naïve patients. Patients and methods A total of 35 blood samples from 16 patients who showed first-line ART failure (>1000 viral genome copies/ml) and 19 ART-naïve patients were collected in Djibouti from October 2009 to December 2009. Both the protease (PR) and reverse transcriptase (RT) genes were amplified and sequenced using National Agency for AIDS Research (ANRS) protocols. The Stanford HIV database algorithm was used for interpretation of resistance data and genotyping. Results Among the 16 patients with first-line ART failure, nine (56.2%) showed reverse transcriptase inhibitor-resistant HIV-1 strains: two (12.5%) were resistant to nucleoside (NRTI), one (6.25%) to non-nucleoside (NNRTI) reverse transcriptase inhibitors, and six (37.5%) to both. Analysis of the DNA sequencing data indicated that the most common mutations conferring drug resistance were M184V (38%) for NRTI and K103N (25%) for NNRTI. Only NRTI primary mutations K101Q, K103N and the PI minor mutation L10V were found in ART naïve individuals. No protease inhibitor resistant strains were detected. In our study, we found no detectable resistance in ∼ 44% of all patients who experienced therapeutic failure which was explained by low compliance, co-infection with tuberculosis and malnutrition. Genotyping revealed that 65.7% of samples were infected with subtype C, 20% with CRF02_AG, 8.5% with B, 2.9% with CRF02_AG/C and 2.9% with K/C. Conclusion The results of this first study about drug resistance mutations in first-line ART failures show the importance of performing drug resistance mutation test which guides the choice of a second-line regimen. This will improve the management of HIV-infected Djiboutian patients. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/2051206212753973

Published
2012
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25. Global and regional molecular epidemiology of HIV-1, 1990–2015: a systematic review, global survey, and trend analysis

Author

Hemelaar, Joris, Elangovan, Ramyiadarsini, Yun, Jason, Dickson-Tetteh, Leslie, Fleminger, Isabella, Kirtley, Shona, Williams, Brian, Gouws-Williams, Eleanor, Ghys, Peter D, Abimiku, Alash'le G, Agwale, Simon, Archibald, Chris, Avidor, Boaz, Barbás, María Gabriela, Barre-Sinoussi, Francoise, Barugahare, Banson, Belabbes, El Hadj, Bertagnolio, Silvia, Birx, Deborah, Bobkov, Aleksei F, Brandful, James, Bredell, Helba, Brennan, Catherine A, Brooks, James, Bruckova, Marie, Buonaguro, Luigi, Buonaguro, Franco, Buttò, Stefano, Buve, Anne, Campbell, Mary, Carr, Jean, Carrera, Alex, Carrillo, Manuel Gómez, Celum, Connie, Chaplin, Beth, Charles, Macarthur, Chatzidimitriou, Dimitrios, Chen, Zhiwei, Chijiwa, Katsumi, Cooper, David, Cunningham, Philip, Dagnra, Anoumou, de Gascun, Cillian F, Del Amo, Julia, Delgado, Elena, Dietrich, Ursula, Dwyer, Dominic, Ellenberger, Dennis, Ensoli, Barbara, Essex, Max, Gao, Feng, Fleury, Herve, Fonjungo, Peter N, Foulongne, Vincent, Gadkari, Deepak A, García, Federico, Garsia, Roger, Gershy-Damet, Guy Michel, Glynn, Judith R, Goodall, Ruth, Grossman, Zehava, Lindenmeyer-Guimarães, Monick, Hahn, Beatrice, Hamers, Raph L, Hamouda, Osamah, Handema, Ray, He, Xiang, Herbeck, Joshua, Ho, David D, Holguin, Africa, Hosseinipour, Mina, Hunt, Gillian, Ito, Masahiko, Bel Hadj Kacem, Mohamed Ali, Kahle, Erin, Kaleebu, Pontiano Kaleebu, Kalish, Marcia, Kamarulzaman, Adeeba, Kang, Chun, Kanki, Phyllis, Karamov, Edward, Karasi, Jean-Claude, Kayitenkore, Kayitesi, Kelleher, Tony, Kitayaporn, Dwip, Kostrikis, Leondios G, Kucherer, Claudia, Lara, Claudia, Leitner, Thomas, Liitsola, Kirsi, Lingappa, Jai, Linka, Marek, Lorenzana de Rivera, Ivette, Lukashov, Vladimir, Maayan, Shlomo, Mayr, Luzia, McCutchan, Francine, Meda, Nicolas, Menu, Elisabeth, Mhalu, Fred, Mloka, Doreen, Mokili, John L, Montes, Brigitte, Mor, Orna, Morgado, Mariza, Mosha, Fausta, Moussi, Awatef, Mullins, James, Najera, Rafael, Nasr, Mejda, Ndembi, Nicaise, Neilson, Joel R, Nerurkar, Vivek R, Neuhann, Florian, Nolte, Claudine, Novitsky, Vlad, Nyambi, Philippe, Ofner, Marianna, Paladin, Fem J, Papa, Anna, Pape, Jean, Parkin, Neil, Parry, Chris, Peeters, Martine, Pelletier, Alexandra, Pérez-Álvarez, Lucía, Pillay, Deenan, Pinto, Angie, Quang, Trinh Duy, Rademeyer, Cecilia, Raikanikoda, Filimone, Rayfield, Mark A, Reynes, Jean-Marc, Rinke de Wit, Tobias, Robbins, Kenneth E, Rolland, Morgane, Rousseau, Christine, Salazar-Gonzales, Jesus, Salem, Hanan, Salminen, Mika, Salomon, Horacio, Sandstrom, Paul, Santiago, Mario L, Sarr, Abdoulaye D, Schroeder, Bryan, Segondy, Michel, Selhorst, Philippe, Sempala, Sylvester, Servais, Jean, Shaik, Ansari, Shao, Yiming, Slim, Amine, Soares, Marcelo A, Songok, Elijah, Stewart, Debbie, Stokes, Julie, Subbarao, Shambavi, Sutthent, Ruengpung, Takehisa, Jun, Tanuri, Amilcar, Tee, Kok Keng, Thapa, Kiran, Thomson, Michael, Tran, Tyna, Urassa, Willy, Ushijima, Hiroshi, van de Perre, Philippe, van der Groen, Guido, van Laethem, Kristel, van Oosterhout, Joep, van Sighem, Ard, van Wijngaerden, Eric, Vandamme, Anne-Mieke, Vercauteren, Jurgen, Vidal, Nicole, Wallace, Lesley, Williamson, Carolyn, Wolday, Dawit, Xu, Jianqing, Yang, Chunfu, Zhang, Linqi, Zhang, Rong, John Radcliffe Hospital [Oxford University Hospital], Centre for Statistics in Medicine, University of Oxford [Oxford], Stellenbosch University, UNAIDS [Genève, Suisse] (ONUSIDA), Institut Pasteur [Paris], Noguchi Memorial Institute for Medical Research [Accra, Ghana] (NMIMR), University of Ghana, Institute of Tropical Medicine [Antwerp] (ITM), State Key Laboratory of Silkworm Genome Biology, Southwest University, Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Georg-Speyer-Haus, The University of Sydney, National AIDS Centre, Istituto Superiore di Sanita [Rome], Harvard School of Public Health, Digital Enterprise Research Institute (DERI-NUIG), National University of Ireland [Galway] (NUI Galway), Microbiologie cellulaire et moléculaire et pathogénicité (MCMP), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Virologie, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Pathogénèse et contrôle des infections chroniques (PCCI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre Hospitalier Universitaire de Montpellier (CHU Montpellier ), Departments of Medicine and Microbiology, University of Alabama at Birmingham [ Birmingham] (UAB), Robert Koch Institute [Berlin] (RKI), Beihang University (BUAA), Statens Serum Institut [Copenhagen], Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), SANTE/SIDA [Bobo-Dioulasso, Burkina Faso], Institut de Recherche en Sciences de la Santé (IRSS) / Centre Muraz, Department of Microbiology, University of Washington School of Medicine, Department of Microbiology, Medical School, University of Thessaly [Volos] (UTH), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Africa Centre for Health and Population Studies, University of KwaZulu-Natal (UKZN)-Medical Research Council of South Africa, Lab-STICC_UBO_CID_IHSEV, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Laboratory of Virology, CHU Rouen, Normandie Université (NU)-Normandie Université (NU), Universidade Federal do Rio de Janeiro (UFRJ), Departements of Medicine and Microbiology, University of Alabama [Tuscaloosa] (UA), Stichting HIV Monitoring [Amsterdam], Universiteit van Amsterdam (UvA), Département Génétique Internal Médecine, Hôpital Universitaire Leuven, Department of Chemical and Biomolecular Engineering [Baltimore], Johns Hopkins University (JHU), Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, China Academy of Chinese Medical Sciences, Chatzidimitriou, Dimitrios [0000-0001-9656-5898], University of Oxford, Institut Pasteur [Paris] (IP), Istituto Superiore di Sanità (ISS), Microbiologie Fondamentale et Pathogénicité (MFP), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), University of KwaZulu-Natal [Durban, Afrique du Sud] (UKZN)-Medical Research Council of South Africa, Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), UNAIDS, Noguchi Memorial Institute for Medical Research, University of Ghana, Laboratoire d'Electronique et des Technologies de l'Information (CEA-LETI), Université Grenoble Alpes (UGA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Beihang University, Recherches Translationnelles sur le VIH et les maladies infectieuses (TransVIHMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 1 (UM1)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Universtié Yaoundé 1 [Cameroun]-Université de Montpellier (UM), Universidade Federal do Rio de Janeiro [Rio de Janeiro] (UFRJ), Nuffield Department of Women's and Reproductive Health (NDWRH), University of Oxford- John Radcliffe Hospital [Oxford University Hospital], South African Centre for Epidemiological Modelling and Analysis, JH is supported by the Oxford University Clinical Academic Graduate School (Oxford, UK) and Linacre College, Oxford University (Oxford, UK)., WHO–UNAIDS Network for HIV Isolation Characterisation : Alash'le G Abimiku, Simon Agwale, Chris Archibald, Boaz Avidor, María Gabriela Barbás, Francoise Barre-Sinoussi, Banson Barugahare, El Hadj Belabbes, Silvia Bertagnolio, Deborah Birx, Aleksei F Bobkov, James Brandful, Helba Bredell, Catherine A Brennan, James Brooks, Marie Bruckova, Luigi Buonaguro, Franco Buonaguro, Stefano Buttò, Anne Buve, Mary Campbell, Jean Carr, Alex Carrera, Manuel Gómez Carrillo, Connie Celum, Beth Chaplin, Macarthur Charles, Dimitrios Chatzidimitriou, Zhiwei Chen, Katsumi Chijiwa, David Cooper, Philip Cunningham, Anoumou Dagnra, Cillian F de Gascun, Julia Del Amo, Elena Delgado, Ursula Dietrich, Dominic Dwyer, Dennis Ellenberger, Barbara Ensoli, Max Essex, Feng Gao, Herve Fleury, Peter N Fonjungo, Vincent Foulongne, Deepak A Gadkari, Federico García, Roger Garsia, Guy Michel Gershy-Damet, Judith R Glynn, Ruth Goodall, Zehava Grossman, Monick Lindenmeyer-Guimarães, Beatrice Hahn, Raph L Hamers, Osamah Hamouda, Ray Handema, Xiang He, Joshua Herbeck, David D Ho, Africa Holguin, Mina Hosseinipour, Gillian Hunt, Masahiko Ito, Mohamed Ali Bel Hadj Kacem, Erin Kahle, Pontiano Kaleebu Kaleebu, Marcia Kalish, Adeeba Kamarulzaman, Chun Kang, Phyllis Kanki, Edward Karamov, Jean-Claude Karasi, Kayitesi Kayitenkore, Tony Kelleher, Dwip Kitayaporn, Leondios G Kostrikis, Claudia Kucherer, Claudia Lara, Thomas Leitner, Kirsi Liitsola, Jai Lingappa, Marek Linka, Ivette Lorenzana de Rivera, Vladimir Lukashov, Shlomo Maayan, Luzia Mayr, Francine McCutchan, Nicolas Meda, Elisabeth Menu, Fred Mhalu, Doreen Mloka, John L Mokili, Brigitte Montes, Orna Mor, Mariza Morgado, Fausta Mosha, Awatef Moussi, James Mullins, Rafael Najera, Mejda Nasr, Nicaise Ndembi, Joel R Neilson, Vivek R Nerurkar, Florian Neuhann, Claudine Nolte, Vlad Novitsky, Philippe Nyambi, Marianna Ofner, Fem J Paladin, Anna Papa, Jean Pape, Neil Parkin, Chris Parry, Martine Peeters, Alexandra Pelletier, Lucía Pérez-Álvarez, Deenan Pillay, Angie Pinto, Trinh Duy Quang, Cecilia Rademeyer, Filimone Raikanikoda, Mark A Rayfield, Jean-Marc Reynes, Tobias Rinke de Wit, Kenneth E Robbins, Morgane Rolland, Christine Rousseau, Jesus Salazar-Gonzales, Hanan Salem, Mika Salminen, Horacio Salomon, Paul Sandstrom, Mario L Santiago, Abdoulaye D Sarr, Bryan Schroeder, Michel Segondy, Philippe Selhorst, Sylvester Sempala, Jean Servais, Ansari Shaik, Yiming Shao, Amine Slim, Marcelo A Soares, Elijah Songok, Debbie Stewart, Julie Stokes, Shambavi Subbarao, Ruengpung Sutthent, Jun Takehisa, Amilcar Tanuri, Kok Keng Tee, Kiran Thapa, Michael Thomson, Tyna Tran, Willy Urassa, Hiroshi Ushijima, Philippevan de Perre, Guidovan der Groen, Kristel van Laethem, Joep van Oosterhout, Ard van Sighem, Eric van Wijngaerden, Anne-Mieke Vandamme, Jurgen Vercauteren, Nicole Vidal, Lesley Wallace, Carolyn Williamson, Dawit Wolday, Jianqing Xu, Chunfu Yang, Linqi Zhang, and Rong Zhang

Subjects
0301 basic medicine, Serotype, Genotype, Genotyping Techniques, 030106 microbiology, DIVERSITY, MULTICENTER, VACCINE, HIV Infections, Genome, Viral, Biology, Global Health, Serogroup, SUBTYPES, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Surveys and Questionnaires, INFECTION, Genetic variation, Global health, Humans, HIV vaccine, Serotyping, AIDS Vaccines, Science & Technology, Molecular epidemiology, Genetic Variation, Subtyping, 3. Good health, Trend analysis, 030104 developmental biology, Infectious Diseases, 13. Climate action, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, HIV-1, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Life Sciences & Biomedicine, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Demography
Abstract

BACKGROUND: Global genetic diversity of HIV-1 is a major challenge to the development of HIV vaccines. We aimed to estimate the regional and global distribution of HIV-1 subtypes and recombinants during 1990-2015. METHODS: We searched PubMed, EMBASE (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) for HIV-1 subtyping studies published between Jan 1, 1990, and Dec 31, 2015. We collected additional unpublished HIV-1 subtyping data through a global survey. We included prevalence studies with HIV-1 subtyping data collected during 1990-2015. We grouped countries into 14 regions and analysed data for four time periods (1990-99, 2000-04, 2005-09, and 2010-15). The distribution of HIV-1 subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs) in individual countries was weighted according to the UNAIDS estimates of the number of people living with HIV (PLHIV) in each country to generate regional and global estimates of HIV-1 diversity in each time period. The primary outcome was the number of samples designated as HIV-1 subtypes A, B, C, D, F, G, H, J, K, CRFs, and URFs. The systematic review is registered with PROSPERO, number CRD42017067164. FINDINGS: This systematic review and global survey yielded 2203 datasets with 383 519 samples from 116 countries in 1990-2015. Globally, subtype C accounted for 46·6% (16 280 897/34 921 639 of PLHIV) of all HIV-1 infections in 2010-15. Subtype B was responsible for 12·1% (4 235 299/34 921 639) of infections, followed by subtype A (10·3%; 3 587 003/34 921 639), CRF02_AG (7·7%; 2 705 110/34 921 639), CRF01_AE (5·3%; 1 840 982/34 921 639), subtype G (4·6%; 1 591 276/34 921 639), and subtype D (2·7%; 926 255/34 921 639). Subtypes F, H, J, and K combined accounted for 0·9% (311 332/34 921 639) of infections. Other CRFs accounted for 3·7% (1 309 082/34 921 639), bringing the proportion of all CRFs to 16·7% (5 844 113/34 921 639). URFs constituted 6·1% (2 134 405/34 921 639), resulting in recombinants accounting for 22·8% (7 978 517/34 921 639) of all global HIV-1 infections. The distribution of HIV-1 subtypes and recombinants changed over time in countries, regions, and globally. At a global level during 2005-15, subtype B increased, subtypes A and D were stable, and subtypes C and G and CRF02_AG decreased. CRF01_AE, other CRFs, and URFs increased, leading to a consistent increase in the global proportion of recombinants over time. INTERPRETATION: Global and regional HIV diversity is complex and evolving, and is a major challenge to HIV vaccine development. Surveillance of the global molecular epidemiology of HIV-1 remains crucial for the design, testing, and implementation of HIV vaccines. FUNDING: None. ispartof: LANCET INFECTIOUS DISEASES vol:19 issue:2 pages:143-155 ispartof: location:United States status: published

Published
2018
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27. Global and regional molecular epidemiology of HIV-1, 1990–2015: a systematic review, global survey, and trend analysis

Author

Hemelaar, Joris, primary, Elangovan, Ramyiadarsini, additional, Yun, Jason, additional, Dickson-Tetteh, Leslie, additional, Fleminger, Isabella, additional, Kirtley, Shona, additional, Williams, Brian, additional, Gouws-Williams, Eleanor, additional, Ghys, Peter D, additional, Abimiku, Alash'le G, additional, Agwale, Simon, additional, Archibald, Chris, additional, Avidor, Boaz, additional, Barbás, María Gabriela, additional, Barre-Sinoussi, Francoise, additional, Barugahare, Banson, additional, Belabbes, El Hadj, additional, Bertagnolio, Silvia, additional, Birx, Deborah, additional, Bobkov, Aleksei F, additional, Brandful, James, additional, Bredell, Helba, additional, Brennan, Catherine A, additional, Brooks, James, additional, Bruckova, Marie, additional, Buonaguro, Luigi, additional, Buonaguro, Franco, additional, Buttò, Stefano, additional, Buve, Anne, additional, Campbell, Mary, additional, Carr, Jean, additional, Carrera, Alex, additional, Carrillo, Manuel Gómez, additional, Celum, Connie, additional, Chaplin, Beth, additional, Charles, Macarthur, additional, Chatzidimitriou, Dimitrios, additional, Chen, Zhiwei, additional, Chijiwa, Katsumi, additional, Cooper, David, additional, Cunningham, Philip, additional, Dagnra, Anoumou, additional, de Gascun, Cillian F, additional, Del Amo, Julia, additional, Delgado, Elena, additional, Dietrich, Ursula, additional, Dwyer, Dominic, additional, Ellenberger, Dennis, additional, Ensoli, Barbara, additional, Essex, Max, additional, Gao, Feng, additional, Fleury, Herve, additional, Fonjungo, Peter N, additional, Foulongne, Vincent, additional, Gadkari, Deepak A, additional, García, Federico, additional, Garsia, Roger, additional, Gershy-Damet, Guy Michel, additional, Glynn, Judith R, additional, Goodall, Ruth, additional, Grossman, Zehava, additional, Lindenmeyer-Guimarães, Monick, additional, Hahn, Beatrice, additional, Hamers, Raph L, additional, Hamouda, Osamah, additional, Handema, Ray, additional, He, Xiang, additional, Herbeck, Joshua, additional, Ho, David D, additional, Holguin, Africa, additional, Hosseinipour, Mina, additional, Hunt, Gillian, additional, Ito, Masahiko, additional, Bel Hadj Kacem, Mohamed Ali, additional, Kahle, Erin, additional, Kaleebu, Pontiano Kaleebu, additional, Kalish, Marcia, additional, Kamarulzaman, Adeeba, additional, Kang, Chun, additional, Kanki, Phyllis, additional, Karamov, Edward, additional, Karasi, Jean-Claude, additional, Kayitenkore, Kayitesi, additional, Kelleher, Tony, additional, Kitayaporn, Dwip, additional, Kostrikis, Leondios G, additional, Kucherer, Claudia, additional, Lara, Claudia, additional, Leitner, Thomas, additional, Liitsola, Kirsi, additional, Lingappa, Jai, additional, Linka, Marek, additional, Lorenzana de Rivera, Ivette, additional, Lukashov, Vladimir, additional, Maayan, Shlomo, additional, Mayr, Luzia, additional, McCutchan, Francine, additional, Meda, Nicolas, additional, Menu, Elisabeth, additional, Mhalu, Fred, additional, Mloka, Doreen, additional, Mokili, John L, additional, Montes, Brigitte, additional, Mor, Orna, additional, Morgado, Mariza, additional, Mosha, Fausta, additional, Moussi, Awatef, additional, Mullins, James, additional, Najera, Rafael, additional, Nasr, Mejda, additional, Ndembi, Nicaise, additional, Neilson, Joel R, additional, Nerurkar, Vivek R, additional, Neuhann, Florian, additional, Nolte, Claudine, additional, Novitsky, Vlad, additional, Nyambi, Philippe, additional, Ofner, Marianna, additional, Paladin, Fem J, additional, Papa, Anna, additional, Pape, Jean, additional, Parkin, Neil, additional, Parry, Chris, additional, Peeters, Martine, additional, Pelletier, Alexandra, additional, Pérez-Álvarez, Lucía, additional, Pillay, Deenan, additional, Pinto, Angie, additional, Quang, Trinh Duy, additional, Rademeyer, Cecilia, additional, Raikanikoda, Filimone, additional, Rayfield, Mark A, additional, Reynes, Jean-Marc, additional, Rinke de Wit, Tobias, additional, Robbins, Kenneth E, additional, Rolland, Morgane, additional, Rousseau, Christine, additional, Salazar-Gonzales, Jesus, additional, Salem, Hanan, additional, Salminen, Mika, additional, Salomon, Horacio, additional, Sandstrom, Paul, additional, Santiago, Mario L, additional, Sarr, Abdoulaye D, additional, Schroeder, Bryan, additional, Segondy, Michel, additional, Selhorst, Philippe, additional, Sempala, Sylvester, additional, Servais, Jean, additional, Shaik, Ansari, additional, Shao, Yiming, additional, Slim, Amine, additional, Soares, Marcelo A, additional, Songok, Elijah, additional, Stewart, Debbie, additional, Stokes, Julie, additional, Subbarao, Shambavi, additional, Sutthent, Ruengpung, additional, Takehisa, Jun, additional, Tanuri, Amilcar, additional, Tee, Kok Keng, additional, Thapa, Kiran, additional, Thomson, Michael, additional, Tran, Tyna, additional, Urassa, Willy, additional, Ushijima, Hiroshi, additional, van de Perre, Philippe, additional, van der Groen, Guido, additional, van Laethem, Kristel, additional, van Oosterhout, Joep, additional, van Sighem, Ard, additional, van Wijngaerden, Eric, additional, Vandamme, Anne-Mieke, additional, Vercauteren, Jurgen, additional, Vidal, Nicole, additional, Wallace, Lesley, additional, Williamson, Carolyn, additional, Wolday, Dawit, additional, Xu, Jianqing, additional, Yang, Chunfu, additional, Zhang, Linqi, additional, and Zhang, Rong, additional

Published
2019
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28. A comparative study of antimicrobial resistance rates and phylogenetic groups of community-acquired versus hospital-acquired invasive Escherichia coli

Author

Sana Ferjani, Faouzi Slim Amine, I. Boutiba Ben Boubaker, and M. Saidani

Subjects
Adult, Male, Tunisia, Cefotaxime, Adolescent, Hospital Departments, Bacteremia, Drug resistance, Peritonitis, Biology, Microbiology, Young Adult, Antibiotic resistance, Drug Resistance, Multiple, Bacterial, Escherichia coli, medicine, Humans, Child, Escherichia coli Infections, Phylogeny, Aged, Aged, 80 and over, Cross Infection, Sulfamethoxazole, Infant, Newborn, Infant, Hygiene, Middle Aged, medicine.disease, Trimethoprim, Anti-Bacterial Agents, Bacterial Typing Techniques, Community-Acquired Infections, Ciprofloxacin, Infectious Diseases, Amikacin, Child, Preschool, Female, medicine.drug
Abstract

Objectives Escherichia coli is the leading cause of various infections, both in community and nosocomial settings. Our objective was to determine the antibiotic resistance rates and the phylogenetic groups of invasive E. coli and to assess the relationship between these characteristics according to the community or nosocomial origin of the strains. Materials and methods One hundred non-redundant E. coli strains, causing invasive infections, were collected and investigated between 2010 and 2012. The phylogenetic groups were determined by triplex PCR. The statistical analysis was performed with Pearson χ 2 test and P -values below 0.05 were considered as statistically significant. Results Sixty-three strains were community-acquired (CA) and 37 were hospital-acquired (HA). The resistance rates among CA and HA strains were respectively: cefotaxime (11.1/37.8%), ciprofloxacin (19/43.2%), amikacin (3.2/27.2%), and cotrimoxazole (42.8/64.8%). E. coli strains caused bacteremia (CA = 34.9%; HA = 83.7%), peritonitis (CA = 58.7%; HA = 13.5%), appendicitis (CA = 3.2%; HA = 2.7%), and cholecystitis (CA = 3.2%; HA = 0%). The distribution of phylogenetic groups among CA and HA strains was: A (25.4/18.9%), B1 (9.5/16.2%), B2 (23.8/37.8%), and D group (41.3/27%). High resistance rates to cefotaxime ( P = 0.02), ciprofloxacin ( P = 0.01), amikacin ( P = 0.001), and cotrimoxazole ( P = 0.05) were statistically significantly associated with a nosocomial origin. Conclusion Our results prove the diversity of phylogroups among E. coli invasive strains whatever their origin, and a higher antibiotic resistance rate in nosocomial strains. An adequate use of antibiotics and applying strict hygiene measures would limit the transmission and selection of these bacteria in hospital as well as in community settings.

Published
2015
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29. Prevalence and Characterization of Plasmid-Mediated Quinolone Resistance Genes in Extended-Spectrum β-Lactamase-ProducingEnterobacteriaceaein a Tunisian Hospital

Author

Mabrouka Saidani, Sana Ferjani, Ilhem Boutiba-Ben Boubaker, and Faouzi Slim Amine

Subjects
Microbiology (medical), Tunisia, Klebsiella pneumoniae, medicine.drug_class, medicine.medical_treatment, Immunology, Drug resistance, Quinolones, medicine.disease_cause, Microbiology, beta-Lactamases, Plasmid, Enterobacteriaceae, Drug Resistance, Bacterial, Prevalence, medicine, Humans, Escherichia coli, Alleles, Pharmacology, biology, Enterobacteriaceae Infections, biology.organism_classification, Quinolone, Hospitals, Beta-lactamase, Enterobacter cloacae, Plasmids
Abstract

The objective of the study was to assess the prevalence of plasmid-mediated quinolone resistance (PMQR) genes (qnrA, qnrB, qnrC, qnrD, qnrS, aac(6')-Ib-cr, qepA, and oqxAB) in a collection of 120 extended-spectrum β-lactamases (ESBLs)-producing enterobacteria and to characterize them. Overall, PMQR determinants were detected in 72 (60%) isolates (20 Escherichia coli, 32 Klebsiella pneumoniae, and 20 Enterobacter cloacae). PMQR frequencies were as follows: qnr genes (25.8%), oqxAB (21.6%), and aac(6')-Ib-cr variant (19.2%). Four qnr alleles were identified as qnrB1 (83.8%), qnrB4 (6.4%), qnrB2 (3.2%), and qnrS1 (6.4%). qnr genes were mainly detected in E. cloacae (50%), aac(6')-Ib-cr in E. coli (47.5%), and oqxAB in K. pneumoniae (65%). Overall, blaCTX-M-15 (90.3%) was the most prevalent blaESBL type followed by blaSHV-12 (6.4%) and blaSHV-27 (2.7%). Rates of mutations in gyrA and parC genes were 75% for E. coli, 72.8% for K. pneumoniae, and 50% for E. cloacae. Isolates with mutations in their quinolone resistance-determining regions exhibited high fluoroquinolones resistance levels compared to those with wild ones. Genetic study of PMQR-harboring isolates revealed a great genomic diversity among each Enterobacteriaceae species. Our findings indicate the high prevalence of PMQR determinants among ESBL-producing Enterobacteriaceae isolates from our hospital and their diffusion in various unrelated CTX-M-15-producing clones.

Published
2015
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30. First molecular characterization of HIV-1 Tunisian strains

Author

Halima, Myriam Ben, Pasquier, Christophe, Slim, Amine, Chaabane, Taoufik Ben, Arrouji, Zakia, Puel, Jacqueline, Redjeb, Saida Ben, and Izopet, Jacques

Subjects
Biochemistry -- Research, Epidemiology -- Statistics, Epidemiology -- Research, HIV patients -- Demographic aspects, HIV patients -- Health aspects, HIV patients -- Care and treatment, HIV infection -- Prevention, HIV infection -- Demographic aspects, HIV infection -- Health aspects, AIDS (Disease) -- Research, Health
Abstract

The authors discuss their study on epidemiology of HIV-infection in Tunisia. They report that subtype B dominates in Tunisia, and suggest the probability that HIV-infection origin might have been imported and the importance of further investigation of potential diversification of HIV-1 isolates in Tunisia.

Published
2001

31. Prevalence and characterization of uropathogenic Escherichia coli harboring plasmid-mediated quinolone resistance in a Tunisian university hospital

Author

Ferjani Sana, Quentin Claudine, Slim Amine Faouzi, Saidani Mabrouka, Boutiba Ben Boubaker Ilhem, and Dubois Véronique

Subjects
Adult, Male, Microbiology (medical), clone (Java method), Tunisia, Adolescent, Virulence Factors, Virulence, Quinolones, Biology, medicine.disease_cause, Microbiology, Hospitals, University, Young Adult, Quinolone resistance, Plasmid, Drug Resistance, Bacterial, Prevalence, medicine, Cluster Analysis, Humans, Uropathogenic Escherichia coli, Child, Gene, Escherichia coli, Escherichia coli Infections, Aged, Aged, 80 and over, Molecular Epidemiology, Infant, General Medicine, Middle Aged, biochemical phenomena, metabolism, and nutrition, University hospital, Virology, Anti-Bacterial Agents, Molecular Typing, Infectious Diseases, Genes, Bacterial, Child, Preschool, Horizontal gene transfer, Female, Plasmids
Abstract

The prevalence of plasmid-mediated quinolone resistance (PMQR) determinants was investigated in a Tunisian collection of 300 uropathogenic Escherichia coli. PMQR genes were detected in 68 isolates (22.7%) as follows: aac(6')-Ib-cr (n=66), qnrB1 (n=3), qnrA6 (n=1), and qnrS1 (n=1). Three isolates carried the 2 determinants aac(6')-Ib-cr and qnrB1. aac(6')-Ib-cr was usually carried on IncF-type plasmids (n=47/60) and frequently associated with blaCTX-M-15 (n=60). Substitutions in gyrA and parC genes were detected in 57.5% of strains. A major cluster including 29 isolates was individualized, 28 of them belonged to the virulent ST131 clone. In our hospital, the high prevalence of PMQR in E. coli isolates was due to horizontal transfer but also to the spread of ST131 clone.

Published
2014
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32. An Outbreak of NDM-1-ProducingKlebsiella pneumoniae, Associated with OmpK35 and OmpK36 Porin Loss in Tunisia

Author

Hamzaoui, Zaineb, primary, Ocampo-Sosa, Alain, additional, Maamar, Elaa, additional, Fernandez Martinez, Marta, additional, Ferjani, Sana, additional, Hammami, Samia, additional, Harbaoui, Sarra, additional, Genel, Nathalie, additional, Arlet, Guillaume, additional, Saidani, Mabrouka, additional, Slim, Amine, additional, Boutiba-Ben Boubaker, Ilhem, additional, and Martinez-Martinez, Luis, additional

Published
2018
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34. Influenza activity in Tunisia: 2014-2015 season

Author

Aissi, Wafa, primary, Bettaieb, Jihène, additional, Kharroubi, Ghassen, additional, Nouira, Marien, additional, Moussi, Abir El, additional, Zorraga, Mokhtar, additional, Slim, Amine, additional, and Salah, Afif Ben, additional

Published
2018
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35. Genetic diversity of HIV-1 in Tunisia

Author

Moussi, Abir El, primary, Thomson, Michael, additional, Delgado, Elena, additional, Cuevas, Maria Teresa, additional, Nasr, Majda, additional, Abid, Salma, additional, Boutiba, Ilhem, additional, and Slim, Amine, additional

Published
2018
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37. Genetic Diversity of HIV-1 in Tunisia

Author

El Moussi, Awatef, primary, Thomson, Michael M., additional, Delgado, Elena, additional, Cuevas, María Teresa, additional, Nasr, Majda, additional, Abid, Salma, additional, Ben Hadj Kacem, Mohamed Ali, additional, Benaissa Tiouiri, Hanene, additional, Letaief, Amel, additional, Chakroun, Mohamed, additional, Ben Jemaa, Mounir, additional, Hamdouni, Hayet, additional, Tej Dellagi, Rafla, additional, Kheireddine, Khaled, additional, Boutiba, Ilhem, additional, Pérez-Álvarez, Lucía, additional, and Slim, Amine, additional

Published
2017
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38. High Prevalence of Gut Microbiota Colonization with Broad-Spectrum Cephalosporin Resistant Enterobacteriaceae in a Tunisian Intensive Care Unit

Author

Maamar, Elaa, primary, Ferjani, Sana, additional, Jendoubi, Ali, additional, Hammami, Samia, additional, Hamzaoui, Zaineb, additional, Mayonnove-Coulange, Laure, additional, Saidani, Mabrouka, additional, Kammoun, Aouatef, additional, Rehaiem, Amel, additional, Ghedira, Salma, additional, Houissa, Mohamed, additional, Boutiba-Ben Boubaker, Ilhem, additional, Slim, Amine, additional, and Dubois, Veronique, additional

Published
2016
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40. Time of onset, viral load, relapse, and duration of active cytomegalovirus infection in bone marrow transplant outcomes

Author

Ksouri, Habib, Torjman, Lamia, Lakhal, Amel, Abdelkefi, Abdelrahmen, Ladeb, Saloua, Eljed, Hana, Slim, Amine, Zouari, Bechir, Ben Othmen, Tarek, and Ben Hassen, Assia

Subjects
Adult, Male, Time Factors, Adolescent, Age Factors, Graft vs Host Disease, Middle Aged, Viral Load, Prognosis, Hematologic Diseases, Treatment Outcome, Child, Preschool, Cytomegalovirus Infections, Humans, Transplantation, Homologous, Female, Child, Bone Marrow Transplantation, Retrospective Studies
Abstract

Active cytomegalovirus infection remains a major problem for bone marrow transplant recipients. If not quickly diagnosed and treated, it can evolve into cytomegalovirus disease, which represents a life-threatening complication. In this work, we sought to evaluate the interactions between clinical complications after bone marrow transplant and factors associated with active cytomegalovirus infection.We evaluated 91 allogeneic bone marrow transplant recipients (35 female, 56 male; median age, 20 years; age range, 3-47 years) for malignant and nonmalignant hematologic diseases. Active cytomegalovirus infection was monitored using pp65 cytomegalovirus antigenemia and a semiquantitative cytomegalovirus polymerase chain reaction. Cytomegalovirus end-organ disease was defined as an association between compatible signs and symptoms (dyspnea, hypoxia, and diarrhea) and detection of cytomegalovirus (or= 2,000 cytomegalovirus genome copies/mL) by hybrid capture assay in tissue biopsy. Variables were compared using the chi-square and Fisher exact tests. Time of death after bone marrow transplant was plotted using the Kaplan-Meier method. A Cox regression model was used for multivariate survival analysis with 95% confidence limits.Sixty-four patients experienced active cytomegalovirus infection, 26 had acute graft-versus-host disease, and 11 had cytomegalovirus diseases. The overall survival rate at 4 years was 83.52%. On multivariate analyses, cytomegalovirus disease (hazard ratio = 15.9, P = .001) and age older than 18 years (hazard ratio = 8, P = .18) were the only independent negative prognostic factors for overall survival. Occurrence of acute graft-versus-host disease was increased by early active cytomegalovirus infection (P = .03) and represents a significant factor for active cytomegalovirus infection recurrence (P = .01). Viral load as quantified by antigenemia and cytomegalovirus DNA in the patients' peripheral blood leukocytes was significantly associated with clinical complications.Active cytomegalovirus infection interacts significantly in several ways with graft-versus-host disease and others infections. Acute graft-versus-host disease increases the chances of a poor outcome, especially of acquiring cytomegalovirus disease. Cytomegalovirus disease constitutes a significant independent risk factor for death after bone marrow transplant.

Published
2008

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