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3. Genomic insights into the 2022–2023Vibrio cholerae outbreak in Malawi

Author

Chaguza, Chrispin, Chibwe, Innocent, Chaima, David, Musicha, Patrick, Ndeketa, Latif, Kasambara, Watipaso, Mhango, Chimwemwe, Mseka, Upendo L., Bitilinyu-Bangoh, Joseph, Mvula, Bernard, Kipandula, Wakisa, Bonongwe, Patrick, Munthali, Richard J., Ngwira, Selemani, Mwendera, Chikondi A., Kalizang’oma, Akuzike, Jambo, Kondwani C., Kambalame, Dzinkambani, Kamng’ona, Arox W., Steele, A. Duncan, Chauma-Mwale, Annie, Hungerford, Daniel, Kagoli, Matthew, Nyaga, Martin M., Dube, Queen, French, Neil, Msefula, Chisomo L., Cunliffe, Nigel A., and Jere, Khuzwayo C.

Published
2024
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4. Longitudinal analysis within one hospital in sub-Saharan Africa over 20 years reveals repeated replacements of dominant clones of Klebsiella pneumoniae and stresses the importance to include temporal patterns for vaccine design considerations

Author

Heinz, Eva, Pearse, Oliver, Zuza, Allan, Bilima, Sithembile, Msefula, Chisomo, Musicha, Patrick, Siyabu, Patriciah, Tewesa, Edith, Graf, Fabrice E., Lester, Rebecca, Lissauer, Samantha, Cornick, Jennifer, Lewis, Joseph M., Kawaza, Kondwani, Thomson, Nicholas R., and Feasey, Nicholas A.

Published
2024
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6. Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050

Author

Naghavi, Mohsen, Vollset, Stein Emil, Ikuta, Kevin S, Swetschinski, Lucien R, Gray, Authia P, Wool, Eve E, Robles Aguilar, Gisela, Mestrovic, Tomislav, Smith, Georgia, Han, Chieh, Hsu, Rebecca L, Chalek, Julian, Araki, Daniel T, Chung, Erin, Raggi, Catalina, Gershberg Hayoon, Anna, Davis Weaver, Nicole, Lindstedt, Paulina A, Smith, Amanda E, Altay, Umut, Bhattacharjee, Natalia V, Giannakis, Konstantinos, Fell, Frederick, McManigal, Barney, Ekapirat, Nattwut, Mendes, Jessica Andretta, Runghien, Tilleye, Srimokla, Oraya, Abdelkader, Atef, Abd-Elsalam, Sherief, Aboagye, Richard Gyan, Abolhassani, Hassan, Abualruz, Hasan, Abubakar, Usman, Abukhadijah, Hana J, Aburuz, Salahdein, Abu-Zaid, Ahmed, Achalapong, Sureerak, Addo, Isaac Yeboah, Adekanmbi, Victor, Adeyeoluwa, Temitayo Esther, Adnani, Qorinah Estiningtyas Sakilah, Adzigbli, Leticia Akua, Afzal, Muhammad Sohail, Afzal, Saira, Agodi, Antonella, Ahlstrom, Austin J, Ahmad, Aqeel, Ahmad, Sajjad, Ahmad, Tauseef, Ahmadi, Ali, Ahmed, Ayman, Ahmed, Haroon, Ahmed, Ibrar, Ahmed, Mohammed, Ahmed, Saeed, Ahmed, Syed Anees, Akkaif, Mohammed Ahmed, Al Awaidy, Salah, Al Thaher, Yazan, Alalalmeh, Samer O, AlBataineh, Mohammad T, Aldhaleei, Wafa A, Al-Gheethi, Adel Ali Saeed, Alhaji, Nma Bida, Ali, Abid, Ali, Liaqat, Ali, Syed Shujait, Ali, Waad, Allel, Kasim, Al-Marwani, Sabah, Alrawashdeh, Ahmad, Altaf, Awais, Al-Tammemi, Alaa B., Al-Tawfiq, Jaffar A, Alzoubi, Karem H, Al-Zyoud, Walid Adnan, Amos, Ben, Amuasi, John H, Ancuceanu, Robert, Andrews, Jason R, Anil, Abhishek, Anuoluwa, Iyadunni Adesola, Anvari, Saeid, Anyasodor, Anayochukwu Edward, Apostol, Geminn Louis Carace, Arabloo, Jalal, Arafat, Mosab, Aravkin, Aleksandr Y, Areda, Demelash, Aremu, Abdulfatai, Artamonov, Anton A, Ashley, Elizabeth A, Asika, Marvellous O, Athari, Seyyed Shamsadin, Atout, Maha Moh'd Wahbi, Awoke, Tewachew, Azadnajafabad, Sina, Azam, James Mba, Aziz, Shahkaar, Azzam, Ahmed Y., Babaei, Mahsa, Babin, Francois-Xavier, Badar, Muhammad, Baig, Atif Amin, Bajcetic, Milica, Baker, Stephen, Bardhan, Mainak, Barqawi, Hiba Jawdat, Basharat, Zarrin, Basiru, Afisu, Bastard, Mathieu, Basu, Saurav, Bayleyegn, Nebiyou Simegnew, Belete, Melaku Ashagrie, Bello, Olorunjuwon Omolaja, Beloukas, Apostolos, Berkley, James A, Bhagavathula, Akshaya Srikanth, Bhaskar, Sonu, Bhuyan, Soumitra S, Bielicki, Julia A, Briko, Nikolay Ivanovich, Brown, Colin Stewart, Browne, Annie J, Buonsenso, Danilo, Bustanji, Yasser, Carvalheiro, Cristina G, Castañeda-Orjuela, Carlos A, Cenderadewi, Muthia, Chadwick, Joshua, Chakraborty, Sandip, Chandika, Rama Mohan, Chandy, Sara, Chansamouth, Vilada, Chattu, Vijay Kumar, Chaudhary, Anis Ahmad, Ching, Patrick R, Chopra, Hitesh, Chowdhury, Fazle Rabbi, Chu, Dinh-Toi, Chutiyami, Muhammad, Cruz-Martins, Natalia, da Silva, Alanna Gomes, Dadras, Omid, Dai, Xiaochen, Darcho, Samuel D, Das, Saswati, De la Hoz, Fernando Pio, Dekker, Denise Myriam, Dhama, Kuldeep, Diaz, Daniel, Dickson, Benjamin Felix Rothschild, Djorie, Serge Ghislain, Dodangeh, Milad, Dohare, Sushil, Dokova, Klara Georgieva, Doshi, Ojas Prakashbhai, Dowou, Robert Kokou, Dsouza, Haneil Larson, Dunachie, Susanna J, Dziedzic, Arkadiusz Marian, Eckmanns, Tim, Ed-Dra, Abdelaziz, Eftekharimehrabad, Aziz, Ekundayo, Temitope Cyrus, El Sayed, Iman, Elhadi, Muhammed, El-Huneidi, Waseem, Elias, Christelle, Ellis, Sally J, Elsheikh, Randa, Elsohaby, Ibrahim, Eltaha, Chadi, Eshrati, Babak, Eslami, Majid, Eyre, David William, Fadaka, Adewale Oluwaseun, Fagbamigbe, Adeniyi Francis, Fahim, Ayesha, Fakhri-Demeshghieh, Aliasghar, Fasina, Folorunso Oludayo, Fasina, Modupe Margaret, Fatehizadeh, Ali, Feasey, Nicholas A, Feizkhah, Alireza, Fekadu, Ginenus, Fischer, Florian, Fitriana, Ida, Forrest, Karen M, Fortuna Rodrigues, Celia, Fuller, John E, Gadanya, Muktar A, Gajdács, Márió, Gandhi, Aravind P, Garcia-Gallo, Esteban E, Garrett, Denise O, Gautam, Rupesh K, Gebregergis, Miglas Welay, Gebrehiwot, Mesfin, Gebremeskel, Teferi Gebru, Geffers, Christine, Georgalis, Leonidas, Ghazy, Ramy Mohamed, Golechha, Mahaveer, Golinelli, Davide, Gordon, Melita, Gulati, Snigdha, Gupta, Rajat Das, Gupta, Sapna, Gupta, Vijai Kumar, Habteyohannes, Awoke Derbie, Haller, Sebastian, Harapan, Harapan, Harrison, Michelle L, Hasaballah, Ahmed I, Hasan, Ikramul, Hasan, Rumina Syeda, Hasani, Hamidreza, Haselbeck, Andrea Haekyung, Hasnain, Md Saquib, Hassan, Ikrama Ibrahim, Hassan, Shoaib, Hassan Zadeh Tabatabaei, Mahgol Sadat, Hayat, Khezar, He, Jiawei, Hegazi, Omar E, Heidari, Mohammad, Hezam, Kamal, Holla, Ramesh, Holm, Marianne, Hopkins, Heidi, Hossain, Md Mahbub, Hosseinzadeh, Mehdi, Hostiuc, Sorin, Hussein, Nawfal R, Huy, Le Duc, Ibáñez-Prada, Elsa D, Ikiroma, Adalia, Ilic, Irena M, Islam, Sheikh Mohammed Shariful, Ismail, Faisal, Ismail, Nahlah Elkudssiah, Iwu, Chidozie Declan, Iwu-Jaja, Chinwe Juliana, Jafarzadeh, Abdollah, Jaiteh, Fatoumatta, Jalilzadeh Yengejeh, Reza, Jamora, Roland Dominic G, Javidnia, Javad, Jawaid, Talha, Jenney, Adam W J, Jeon, Hyon Jin, Jokar, Mohammad, Jomehzadeh, Nabi, Joo, Tamas, Joseph, Nitin, Kamal, Zul, Kanmodi, Kehinde Kazeem, Kantar, Rami S, Kapisi, James Apollo, Karaye, Ibraheem M, Khader, Yousef Saleh, Khajuria, Himanshu, Khalid, Nauman, Khamesipour, Faham, Khan, Ajmal, Khan, Mohammad Jobair, Khan, Muhammad Tariq, Khanal, Vishnu, Khidri, Feriha Fatima, Khubchandani, Jagdish, Khusuwan, Suwimon, Kim, Min Seo, Kisa, Adnan, Korshunov, Vladimir Andreevich, Krapp, Fiorella, Krumkamp, Ralf, Kuddus, Mohammed, Kulimbet, Mukhtar, Kumar, Dewesh, Kumaran, Emmanuelle A P, Kuttikkattu, Ambily, Kyu, Hmwe Hmwe, Landires, Iván, Lawal, Basira Kankia, Le, Thao Thi Thu, Lederer, Ingeborg Maria, Lee, Munjae, Lee, Seung Won, Lepape, Alain, Lerango, Temesgen Leka, Ligade, Virendra S, Lim, Cherry, Lim, Stephen S, Limenh, Liknaw Workie, Liu, Chaojie, Liu, Xiaofeng, Liu, Xuefeng, Loftus, Michael J, M Amin, Hawraz Ibrahim, Maass, Kelsey Lynn, Maharaj, Sandeep B, Mahmoud, Mansour Adam, Maikanti-Charalampous, Panagiota, Makram, Omar M, Malhotra, Kashish, Malik, Ahmad Azam, Mandilara, Georgia D, Marks, Florian, Martinez-Guerra, Bernardo Alfonso, Martorell, Miquel, Masoumi-Asl, Hossein, Mathioudakis, Alexander G, May, Juergen, McHugh, Theresa A, Meiring, James, Meles, Hadush Negash, Melese, Addisu, Melese, Endalkachew Belayneh, Minervini, Giuseppe, Mohamed, Nouh Saad, Mohammed, Shafiu, Mohan, Syam, Mokdad, Ali H, Monasta, Lorenzo, Moodi Ghalibaf, AmirAli, Moore, Catrin E, Moradi, Yousef, Mossialos, Elias, Mougin, Vincent, Mukoro, George Duke, Mulita, Francesk, Muller-Pebody, Berit, Murillo-Zamora, Efren, Musa, Sani, Musicha, Patrick, Musila, Lillian A, Muthupandian, Saravanan, Nagarajan, Ahamarshan Jayaraman, Naghavi, Pirouz, Nainu, Firzan, Nair, Tapas Sadasivan, Najmuldeen, Hastyar Hama Rashid, Natto, Zuhair S, Nauman, Javaid, Nayak, Biswa Prakash, Nchanji, G Takop, Ndishimye, Pacifique, Negoi, Ionut, Negoi, Ruxandra Irina, Nejadghaderi, Seyed Aria, Nguyen, QuynhAnh P, Noman, Efaq Ali, Nwakanma, Davis C, O'Brien, Seamus, Ochoa, Theresa J, Odetokun, Ismail A, Ogundijo, Oluwaseun Adeolu, Ojo-Akosile, Tolulope R, Okeke, Sylvester Reuben, Okonji, Osaretin Christabel, Olagunju, Andrew T, Olivas-Martinez, Antonio, Olorukooba, Abdulhakeem Abayomi, Olwoch, Peter, Onyedibe, Kenneth Ikenna, Ortiz-Brizuela, Edgar, Osuolale, Olayinka, Ounchanum, Pradthana, Oyeyemi, Oyetunde T, P A, Mahesh Padukudru, Paredes, Jose L, Parikh, Romil R, Patel, Jay, Patil, Shankargouda, Pawar, Shrikant, Peleg, Anton Y, Peprah, Prince, Perdigão, João, Perrone, Carlo, Petcu, Ionela-Roxana, Phommasone, Koukeo, Piracha, Zahra Zahid, Poddighe, Dimitri, Pollard, Andrew J, Poluru, Ramesh, Ponce-De-Leon, Alfredo, Puvvula, Jagadeesh, Qamar, Farah Naz, Qasim, Nameer Hashim, Rafai, Clotaire Donatien, Raghav, Pankaja, Rahbarnia, Leila, Rahim, Fakher, Rahimi-Movaghar, Vafa, Rahman, Mosiur, Rahman, Muhammad Aziz, Ramadan, Hazem, Ramasamy, Shakthi Kumaran, Ramesh, Pushkal Sinduvadi, Ramteke, Pramod W, Rana, Rishabh Kumar, Rani, Usha, Rashidi, Mohammad-Mahdi, Rathish, Devarajan, Rattanavong, Sayaphet, Rawaf, Salman, Redwan, Elrashdy Moustafa Mohamed, Reyes, Luis Felipe, Roberts, Tamalee, Robotham, Julie V, Rosenthal, Victor Daniel, Ross, Allen Guy, Roy, Nitai, Rudd, Kristina E, Sabet, Cameron John, Saddik, Basema Ahmad, Saeb, Mohammad Reza, Saeed, Umar, Saeedi Moghaddam, Sahar, Saengchan, Weeravoot, Safaei, Mohsen, Saghazadeh, Amene, Saheb Sharif-Askari, Narjes, Sahebkar, Amirhossein, Sahoo, Soumya Swaroop, Sahu, Maitreyi, Saki, Morteza, Salam, Nasir, Saleem, Zikria, Saleh, Mohamed A, Samodra, Yoseph Leonardo, Samy, Abdallah M, Saravanan, Aswini, Satpathy, Maheswar, Schumacher, Austin E, Sedighi, Mansour, Seekaew, Samroeng, Shafie, Mahan, Shah, Pritik A, Shahid, Samiah, Shahwan, Moyad Jamal, Shakoor, Sadia, Shalev, Noga, Shamim, Muhammad Aaqib, Shamshirgaran, Mohammad Ali, Shamsi, Anas, Sharifan, Amin, Shastry, Rajesh P, Shetty, Mahabalesh, Shittu, Aminu, Shrestha, Sunil, Siddig, Emmanuel Edwar, Sideroglou, Theologia, Sifuentes-Osornio, Jose, Silva, Luís Manuel Lopes Rodrigues, Simões, Eric A F, Simpson, Andrew J H, Singh, Amit, Singh, Surjit, Sinto, Robert, Soliman, Sameh S M, Soraneh, Soroush, Stoesser, Nicole, Stoeva, Temenuga Zhekova, Swain, Chandan Kumar, Szarpak, Lukasz, T Y, Sree Sudha, Tabatabai, Shima, Tabche, Celine, Taha, Zanan Mohammed-Ameen, Tan, Ker-Kan, Tasak, Nidanuch, Tat, Nathan Y, Thaiprakong, Areerat, Thangaraju, Pugazhenthan, Tigoi, Caroline Chepngeno, Tiwari, Krishna, Tovani-Palone, Marcos Roberto, Tran, Thang Huu, Tumurkhuu, Munkhtuya, Turner, Paul, Udoakang, Aniefiok John, Udoh, Arit, Ullah, Noor, Ullah, Saeed, Vaithinathan, Asokan Govindaraj, Valenti, Mario, Vos, Theo, Vu, Huong T L, Waheed, Yasir, Walker, Ann Sarah, Walson, Judd L, Wangrangsimakul, Tri, Weerakoon, Kosala Gayan, Wertheim, Heiman F L, Williams, Phoebe C M, Wolde, Asrat Arja, Wozniak, Teresa M, Wu, Felicia, Wu, Zenghong, Yadav, Mukesh Kumar Kumar, Yaghoubi, Sajad, Yahaya, Zwanden Sule, Yarahmadi, Amir, Yezli, Saber, Yismaw, Yazachew Engida, Yon, Dong Keon, Yuan, Chun-Wei, Yusuf, Hadiza, Zakham, Fathiah, Zamagni, Giulia, Zhang, Haijun, Zhang, Zhi-Jiang, Zielińska, Magdalena, Zumla, Alimuddin, Zyoud, Sa'ed H. H, Zyoud, Samer H, Hay, Simon I, Stergachis, Andy, Sartorius, Benn, Cooper, Ben S, Dolecek, Christiane, and Murray, Christopher J L

Published
2024
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7. The burden of bacterial antimicrobial resistance in the WHO African region in 2019: a cross-country systematic analysis

Author

Sartorius, Benn, Gray, Authia P, Davis Weaver, Nicole, Robles Aguilar, Gisela, Swetschinski, Lucien R, Ikuta, Kevin S, Mestrovic, Tomislav, Chung, Erin, Wool, Eve E, Han, Chieh, Gershberg Hayoon, Anna, Araki, Daniel T, Abd-Elsalam, Sherief, Aboagye, Richard Gyan, Adamu, Lawan Hassan, Adepoju, Abiola Victor, Ahmed, Ayman, Akalu, Gizachew Taddesse, Akande-Sholabi, Wuraola, Amuasi, John H, Amusa, Ganiyu Adeniyi, Argaw, Ayele Mamo, Aruleba, Raphael Taiwo, Awoke, Tewachew, Ayalew, Melese Kitu, Azzam, Ahmed Y, Babin, Francois-Xavier, Banerjee, Indrajit, Basiru, Afisu, Bayileyegn, Nebiyou Simegnew, Belete, Melaku Ashagrie, Berkley, James A, Bielicki, Julia A, Dekker, Denise, Demeke, Dessalegn, Demsie, Desalegn Getnet, Dessie, Anteneh Mengist, Dunachie, Susanna J, Ed-Dra, Abdelaziz, Ekholuenetale, Michael, Ekundayo, Temitope Cyrus, El Sayed, Iman, Elhadi, Muhammed, Elsohaby, Ibrahim, Eyre, David, Fagbamigbe, Adeniyi Francis, Feasey, Nicholas A, Fekadu, Ginenus, Fell, Frederick, Forrest, Karen M, Gebrehiwot, Mesfin, Gezae, Kebede Embaye, Ghazy, Ramy Mohamed, Hailegiyorgis, Tewodros Tesfa, Haines-Woodhouse, Georgina, Hasaballah, Ahmed I, Haselbeck, Andrea Haekyung, Hsia, Yingfen, Iradukunda, Arnaud, Iregbu, Kenneth Chukwuemeka, Iwu, Chidozie C D, Iwu-Jaja, Chinwe Juliana, Iyasu, Assefa N, Jaiteh, Fatoumatta, Jeon, Hyonjin, Joshua, Charity Ehimwenma, Kassa, Gebrehiwot G, Katoto, Patrick DMC, Krumkamp, Ralf, Kumaran, Emmanuelle A P, Kyu, Hmwe Hmwe, Manilal, Aseer, Marks, Florian, May, Jürgen, McLaughlin, Susan A, McManigal, Barney, Melese, Addisu, Misgina, Kebede Haile, Mohamed, Nouh Saad, Mohammed, Mustapha, Mohammed, Shafiu, Mohammed, Shikur, Mokdad, Ali H, Moore, Catrin E, Mougin, Vincent, Mturi, Neema, Mulugeta, Temesgen, Musaigwa, Fungai, Musicha, Patrick, Musila, Lillian A, Muthupandian, Saravanan, Naghavi, Pirouz, Negash, Hadush, Nuckchady, Dooshanveer C, Obiero, Christina W, Odetokun, Ismail A, Ogundijo, Oluwaseun Adeolu, Okidi, Lawrence, Okonji, Osaretin Christabel, Olagunju, Andrew T, Olufadewa, Isaac Iyinoluwa, Pak, Gi Deok, Perovic, Olga, Pollard, Andrew, Raad, Mathieu, Rafaï, Clotaire, Ramadan, Hazem, Redwan, Elrashdy Moustafa Mohamed, Roca, Anna, Rosenthal, Victor Daniel, Saleh, Mohamed A, Samy, Abdallah M, Sharland, M, Shittu, Aminu, Siddig, Emmanuel Edwar, Sisay, Eskinder Ayalew, Stergachis, Andy, Tesfamariam, Wegen Beyene, Tigoi, Caroline, Tincho, Marius Belmondo, Tiruye, Tenaw Yimer, Umeokonkwo, Chukwuma David, Walsh, Timothy, Walson, Judd L, Yusuf, Hadiza, Zeru, Naod Gebrekrstos, Hay, Simon I, Dolecek, Christiane, Murray, Christopher J L, and Naghavi, Mohsen

Published
2024
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8. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis

Author

Murray, Christopher J L, Ikuta, Kevin Shunji, Sharara, Fablina, Swetschinski, Lucien, Robles Aguilar, Gisela, Gray, Authia, Han, Chieh, Bisignano, Catherine, Rao, Puja, Wool, Eve, Johnson, Sarah C, Browne, Annie J, Chipeta, Michael Give, Fell, Frederick, Hackett, Sean, Haines-Woodhouse, Georgina, Kashef Hamadani, Bahar H, Kumaran, Emmanuelle A P, McManigal, Barney, Achalapong, Sureeruk, Agarwal, Ramesh, Akech, Samuel, Albertson, Samuel, Amuasi, John, Andrews, Jason, Aravkin, Aleskandr, Ashley, Elizabeth, Babin, François-Xavier, Bailey, Freddie, Baker, Stephen, Basnyat, Buddha, Bekker, Adrie, Bender, Rose, Berkley, James A, Bethou, Adhisivam, Bielicki, Julia, Boonkasidecha, Suppawat, Bukosia, James, Carvalheiro, Cristina, Castañeda-Orjuela, Carlos, Chansamouth, Vilada, Chaurasia, Suman, Chiurchiù, Sara, Chowdhury, Fazle, Clotaire Donatien, Rafai, Cook, Aislinn J, Cooper, Ben, Cressey, Tim R, Criollo-Mora, Elia, Cunningham, Matthew, Darboe, Saffiatou, Day, Nicholas P J, De Luca, Maia, Dokova, Klara, Dramowski, Angela, Dunachie, Susanna J, Duong Bich, Thuy, Eckmanns, Tim, Eibach, Daniel, Emami, Amir, Feasey, Nicholas, Fisher-Pearson, Natasha, Forrest, Karen, Garcia, Coralith, Garrett, Denise, Gastmeier, Petra, Giref, Ababi Zergaw, Greer, Rachel Claire, Gupta, Vikas, Haller, Sebastian, Haselbeck, Andrea, Hay, Simon I, Holm, Marianne, Hopkins, Susan, Hsia, Yingfen, Iregbu, Kenneth C, Jacobs, Jan, Jarovsky, Daniel, Javanmardi, Fatemeh, Jenney, Adam W J, Khorana, Meera, Khusuwan, Suwimon, Kissoon, Niranjan, Kobeissi, Elsa, Kostyanev, Tomislav, Krapp, Fiorella, Krumkamp, Ralf, Kumar, Ajay, Kyu, Hmwe Hmwe, Lim, Cherry, Lim, Kruy, Limmathurotsakul, Direk, Loftus, Michael James, Lunn, Miles, Ma, Jianing, Manoharan, Anand, Marks, Florian, May, Jürgen, Mayxay, Mayfong, Mturi, Neema, Munera-Huertas, Tatiana, Musicha, Patrick, Musila, Lilian A, Mussi-Pinhata, Marisa Marcia, Naidu, Ravi Narayan, Nakamura, Tomoka, Nanavati, Ruchi, Nangia, Sushma, Newton, Paul, Ngoun, Chanpheaktra, Novotney, Amanda, Nwakanma, Davis, Obiero, Christina W, Ochoa, Theresa J, Olivas-Martinez, Antonio, Olliaro, Piero, Ooko, Ednah, Ortiz-Brizuela, Edgar, Ounchanum, Pradthana, Pak, Gideok D, Paredes, Jose Luis, Peleg, Anton Yariv, Perrone, Carlo, Phe, Thong, Phommasone, Koukeo, Plakkal, Nishad, Ponce-de-Leon, Alfredo, Raad, Mathieu, Ramdin, Tanusha, Rattanavong, Sayaphet, Riddell, Amy, Roberts, Tamalee, Robotham, Julie Victoria, Roca, Anna, Rosenthal, Victor Daniel, Rudd, Kristina E, Russell, Neal, Sader, Helio S, Saengchan, Weerawut, Schnall, Jesse, Scott, John Anthony Gerard, Seekaew, Samroeng, Sharland, Mike, Shivamallappa, Madhusudhan, Sifuentes-Osornio, Jose, Simpson, Andrew J, Steenkeste, Nicolas, Stewardson, Andrew James, Stoeva, Temenuga, Tasak, Nidanuch, Thaiprakong, Areerat, Thwaites, Guy, Tigoi, Caroline, Turner, Claudia, Turner, Paul, van Doorn, H Rogier, Velaphi, Sithembiso, Vongpradith, Avina, Vongsouvath, Manivanh, Vu, Huong, Walsh, Timothy, Walson, Judd L, Waner, Seymour, Wangrangsimakul, Tri, Wannapinij, Prapass, Wozniak, Teresa, Young Sharma, Tracey E M W, Yu, Kalvin C, Zheng, Peng, Sartorius, Benn, Lopez, Alan D, Stergachis, Andy, Moore, Catrin, Dolecek, Christiane, and Naghavi, Mohsen

Published
2022
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10. Household acquisition and transmission of extended-spectrum β-lactamase (ESBL) -producing Enterobacteriaceae after hospital discharge of ESBL-positive index patients

Author

Brossier, Caroline, von Dach, Elodie, Renzi, Gesuele, Schrenzel, Jacques, Bunk, Stefanie, Goepel, Siri, Hölzl, Florian, Eib, Michael, Autenrieth, Ingo B., Pascual, Álvaro, Bertrand, Xavier, Scharringa, Jelle, Musicha, Patrick, Riccio, Maria E., Verschuuren, Tess, Conzelmann, Nadine, Martak, Daniel, Meunier, Alexandre, Salamanca, Elena, Delgado, Mercedes, Guther, Julia, Peter, Silke, Paganini, Julian, Martischang, Romain, Sauser, Julien, de Kraker, Marlieke E.A., Cherkaoui, Abdessalam, Fluit, Ad C., Cooper, Ben S., Hocquet, Didier, Kluytmans, Jan A.J.W., Tacconelli, Evelina, Rodriguez-Baño, Jesús, and Harbarth, Stephan

Published
2021
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13. Duration of Carbapenemase-Producing Enterobacteriaceae Carriage in Hospital Patients

Author

Mo, Yin, Hernandez-Koutoucheva, Anastasia, Musicha, Patrick, Bertrand, Denis, Lye, David, Ng, Oon Tek, Fenlon, Shannon N., Chen, Swaine L., Ling, Moi Lin, Tang, Wen Ying, Barkham, Timothy, Nagarajan, Niranjan, Cooper, Ben S., and Marimuthu, Kalisvar

Subjects
Hospital patients -- Health aspects, Medical research -- Health aspects, Infection -- Risk factors, Infection control -- Health aspects, Methicillin -- Health aspects, Meropenem -- Health aspects, Health
Abstract

Rapid global dissemination of carbapenemase-producing Enterobacteriaceae (CPE) poses a public health threat (1). To prevent the spread of CPE in healthcare settings, international guidelines advocate for early identification, isolation, and [...]

Published
2020
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14. Salmonella carriage by geckos detected within households in Malawi

Author

Wilson, Catherine N., Musicha, Patrick, Beale, Mathew A., Diness, Yohane, Kanjerwa, Oscar, Salifu, Chifundo, Katuah, Zefaniah, Duncan, Patricia, Nyangu, John, Mungu, Andrew, Deleza, Muonaouza, Banda, Lawrence, Makhaza, Lumbani, Elviss, Nicola, Jewell, Christopher P., Pinchbeck, Gina, Thomson, Nicholas R., Feasey, Nicholas A., and Fèvre, Eric M.

Published
2024
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15. Longitudinal analysis within one hospital in sub-Saharan Africa over 20 years reveals repeated replacements of dominant clones of Klebsiella pneumoniae and stresses the importance to include temporal patterns for vaccine design considerations

Author

Heinz, Eva, primary, Pearse, Oliver, additional, Zuza, Allan, additional, Bilima, Sithembile, additional, Msefula, Chisomo, additional, Musicha, Patrick, additional, Siyabu, Patriciah, additional, Tewesa, Edith, additional, Graf, Fabrice E, additional, Lester, Rebecca, additional, Lissauer, Samantha, additional, Cornick, Jennifer, additional, Lewis, Joseph M, additional, Kawaza, Kondwani, additional, Thomson, Nicholas R, additional, and Feasey, Nicholas A, additional

Published
2023
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16. Household geckos as a potential vector for Salmonella transmission in Malawi

Author

Wilson, Catherine N., primary, Musicha, Patrick, additional, Beale, Mathew A., additional, Diness, Yohane, additional, Kanjerwa, Oscar, additional, Salifu, Chifundo, additional, Katuah, Zefaniah J., additional, Duncan, Patricia, additional, Nyangu, Johnson, additional, Mungu, Andrew, additional, Deleza, Muonaouza, additional, Banda, Lawrence, additional, Elviss, Nicola, additional, Jewell, Christopher, additional, Pinchbeck, Gina, additional, Thomson, Nicholas, additional, Feasey, Nicholas A., additional, and Fevre, Eric M., additional

Published
2023
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18. Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in Malawi

Author

Chaguza, Chrispin, Cornick, Jennifer E., Andam, Cheryl P., Gladstone, Rebecca A., Alaerts, Maaike, Musicha, Patrick, Peno, Chikondi, Bar-Zeev, Naor, Kamng'ona, Arox W., Kiran, Anmol M., Msefula, Chisomo L., McGee, Lesley, Breiman, Robert F., Kadioglu, Aras, French, Neil, Heyderman, Robert S., Hanage, William P., Bentley, Stephen D., and Everett, Dean B.

Published
2017
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19. Drivers of Resistance in Uganda and Malawi (DRUM): a protocol for the evaluation of One-Health drivers of Extended Spectrum Beta Lactamase (ESBL) resistance in Low-Middle Income Countries (LMICs)

Author

Cocker, Derek, primary, Sammarro, Melodie, additional, Chidziwisano, Kondwani, additional, Elviss, Nicola, additional, Jacob, Shevin T., additional, Kajumbula, Henry, additional, Mugisha, Lawrence, additional, Musoke, David, additional, Musicha, Patrick, additional, Roberts, Adam P., additional, Rowlingson, Barry, additional, Singer, Andrew C., additional, Byrne, Rachel L., additional, Edwards, Thomas, additional, Lester, Rebecca, additional, Wilson, Catherine N., additional, Hollihead, Beth, additional, Thomson, Nicholas, additional, Jewell, Christopher P., additional, Morse, Tracy, additional, and Feasey, Nicholas A., additional

Published
2023
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20. Evidence of widespread endemic populations of highly multidrug resistant Klebsiella pneumoniae in hospital settings in Hanoi, Vietnam: a prospective cohort study

Author

Pham, My H, primary, Hoi, Le Thi, additional, Beale, Mathew A, additional, Khokhar, Fahad A, additional, Hoa, Nguyen Thi, additional, Musicha, Patrick, additional, Blackwell, Grace A, additional, Long, Hoang Bao, additional, Huong, Dang Thi, additional, Binh, Nguyen Gia, additional, Co, Dao Xuan, additional, Giang, Tran, additional, Bui, Cuong, additional, Tran, Hai Ninh, additional, Bryan, James, additional, Herrick, Archie, additional, Feltwell, Theresa, additional, Nadjm, Behzad, additional, Parkhill, Julian, additional, van Doorn, Hindrik Rogier, additional, Trung, Nguyen Vu, additional, Van Kinh, Nguyen, additional, Török, Mili Estée, additional, and Thomson, Nicholas R, additional

Published
2023
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21. Drivers of resistance in Uganda and Malawi (DRUM): a protocol for the evaluation of One-Health drivers of extended spectrum beta lactamase (ESBL) resistance in low-middle income countries (LMICs)

Author

Cocker, Derek, Sammarro, Melodie, Chidziwisano, Kondwani, Elviss, Nicola, Jacob, Shevin T., Kajumbula, Henry, Mugisha, Lawrence, Musoke, David, Musicha, Patrick, Roberts, Adam P., Rowlingson, Barry, Singer, Andrew C., Byrne, Rachel L., Edwards, Thomas, Lester, Rebecca, Wilson, Catherine N., Hollihead, Beth, Thomson, Nicholas R., Jewell, Christopher P., Morse, Tracy, Feasey, Nicholas A., Cocker, Derek, Sammarro, Melodie, Chidziwisano, Kondwani, Elviss, Nicola, Jacob, Shevin T., Kajumbula, Henry, Mugisha, Lawrence, Musoke, David, Musicha, Patrick, Roberts, Adam P., Rowlingson, Barry, Singer, Andrew C., Byrne, Rachel L., Edwards, Thomas, Lester, Rebecca, Wilson, Catherine N., Hollihead, Beth, Thomson, Nicholas R., Jewell, Christopher P., Morse, Tracy, and Feasey, Nicholas A.

Abstract

In sub-Saharan Africa (sSA), there is high morbidity and mortality from severe bacterial infection and this is compounded by antimicrobial resistance, in particular, resistance to 3rd-generation cephalosporins. This resistance is typically mediated by extended-spectrum beta lactamases (ESBLs). To interrupt ESBL transmission it will be important to investigate how human behaviour, water, sanitation, and hygiene (WASH) practices, environmental contamination, and antibiotic usage in both urban and rural settings interact to contribute to transmission of ESBL E. coli and ESBL K. pneumoniae between humans, animals, and the environment. Here we present the protocol for the Drivers of Resistance in Uganda and Malawi (DRUM) Consortium, in which we will collect demographic, geospatial, clinical, animal husbandry and WASH data from a total of 400 households in Uganda and Malawi. Longitudinal human, animal and environmental sampling at each household will be used to isolate ESBL E. coli and ESBL K. pneumoniae. This will be complimented by a Risks, Attitudes, Norms, Abilities and Self-Regulation (RANAS) survey and structured observations to understand the contextual and psychosocial drivers of regional WASH practices. Bacterial isolates and plate sweeps will be further characterised using a mixture of short-,long-read and metagenomic whole-genome sequencing. These datasets will be integrated into agent-based models to describe the transmission of EBSL resistance in Uganda and Malawi and allow us to inform the design of interventions for interrupting transmission of ESBL-bacteria.

Published
2023

24. Effect of resistance to third-generation cephalosporins on morbidity and mortality from bloodstream infections in Blantyre, Malawi: a prospective cohort study

Author

Lester, Rebecca, primary, Musicha, Patrick, additional, Kawaza, Kondwani, additional, Langton, Josephine, additional, Mango, James, additional, Mangochi, Helen, additional, Bakali, Winnie, additional, Pearse, Oliver, additional, Mallewa, Jane, additional, Denis, Brigitte, additional, Bilima, Sithembile, additional, Gordon, Stephen B, additional, Lalloo, David G, additional, Jewell, Christopher P, additional, and Feasey, Nicholas A, additional

Published
2022
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25. Drivers of resistance in Uganda and Malawi (DRUM): a protocol for the evaluation of One-Health drivers of extended spectrum beta lactamase (ESBL) resistance in low-middle income countries (LMICs)

Author

Cocker, Derek, Sammarro, Melodie, Chidziwisano, Kondwani, Elviss, Nicola, Jacob, Shevin T., Kajumbula, Henry, Mugisha, Lawrence, Musoke, David, Musicha, Patrick, Roberts, Adam P., Rowlingson, Barry, Singer, Andrew C., Byrne, Rachel L., Edwards, Thomas, Lester, Rebecca, Wilson, Catherine N., Hollihead, Beth, Thomson, Nicholas, Jewell, Christopher P., Morse, Tracy, Feasey, Nicholas, Cocker, Derek, Sammarro, Melodie, Chidziwisano, Kondwani, Elviss, Nicola, Jacob, Shevin T., Kajumbula, Henry, Mugisha, Lawrence, Musoke, David, Musicha, Patrick, Roberts, Adam P., Rowlingson, Barry, Singer, Andrew C., Byrne, Rachel L., Edwards, Thomas, Lester, Rebecca, Wilson, Catherine N., Hollihead, Beth, Thomson, Nicholas, Jewell, Christopher P., Morse, Tracy, and Feasey, Nicholas

Abstract

In sub-Saharan Africa (sSA), there is high morbidity and mortality from severe bacterial infection and this is compounded by antimicrobial resistance, in particular, resistance to 3rd-generation cephalosporins. This resistance is typically mediated by extended-spectrum beta lactamases (ESBLs). To interrupt ESBL transmission it will be important to investigate how human behaviour, water, sanitation, and hygiene (WASH) practices, environmental contamination, and antibiotic usage in both urban and rural settings interact to contribute to transmission of ESBL E. coli and ESBL K. pneumoniae between humans, animals, and the environment. Here we present the protocol for the Drivers of Resistance in Uganda and Malawi (DRUM) Consortium, in which we will collect demographic, geospatial, clinical, animal husbandry and WASH data from a total of 400 households in Uganda and Malawi. Longitudinal human, animal and environmental sampling at each household will be used to isolate ESBL E. coli and ESBL K. pneumoniae. This will be complimented by a Risks, Attitudes, Norms, Abilities and Self-Regulation (RANAS) survey and structured observations to understand the contextual and psychosocial drivers of regional WASH practices. Bacterial isolates and plate sweeps will be further characterised using a mixture of short-,long-read and metagenomic whole-genome sequencing. These datasets will be integrated into agent-based models to describe the transmission of EBSL resistance in Uganda and Malawi and allow us to inform the design of interventions for interrupting transmission of ESBL-bacteria.

Published
2022

26. Drivers of Resistance in Uganda and Malawi (DRUM):a protocol for the evaluation of One-Health drivers of Extended Spectrum Beta Lactamase (ESBL) resistance in Low-Middle Income Countries (LMICs)

Author

Cocker, Derek, Sammarro, Melodie, Chidziwisano, Kondwani, Elviss, Nicola, Jacob, Shevin T., Kajumbula, Henry, Mugisha, Lawrence, Musoke, David, Musicha, Patrick, Roberts, Adam P., Rowlingson, Barry, Singer, Andrew C., Byrne, Rachel L., Edwards, Thomas, Lester, Rebecca, Wilson, Catherine, Hollihead, Beth, Thomson, Nicholas, Jewell, Christopher P., Morse, Tracy, Feasey, Nicholas, Cocker, Derek, Sammarro, Melodie, Chidziwisano, Kondwani, Elviss, Nicola, Jacob, Shevin T., Kajumbula, Henry, Mugisha, Lawrence, Musoke, David, Musicha, Patrick, Roberts, Adam P., Rowlingson, Barry, Singer, Andrew C., Byrne, Rachel L., Edwards, Thomas, Lester, Rebecca, Wilson, Catherine, Hollihead, Beth, Thomson, Nicholas, Jewell, Christopher P., Morse, Tracy, and Feasey, Nicholas

Abstract

In sub-Saharan Africa (sSA), there is high morbidity and mortality from severe bacterial infection and this is compounded by antimicrobial resistance, in particular, resistance to 3rd-generation cephalosporins. This resistance is typically mediated by extended-spectrum beta lactamases (ESBLs). To interrupt ESBL transmission it will be important to investigate how human behaviour, water, sanitation, and hygiene (WASH) practices, environmental contamination, and antibiotic usage in both urban and rural settings interact to contribute to transmission of ESBL E. coli and ESBL K. pneumoniae between humans, animals, and the environment. Here we present the protocol for the Drivers of Resistance in Uganda and Malawi (DRUM) Consortium, in which we will collect demographic, geospatial, clinical, animal husbandry and WASH data from a total of 400 households in Uganda and Malawi. Longitudinal human, animal and environmental sampling at each household will be used to isolate ESBL E. coli and ESBL K. pneumoniae. This will be complimented by a Risks, Attitudes, Norms, Abilities and Self-Regulation (RANAS) survey and structured observations to understand the contextual and psychosocial drivers of regional WASH practices. Bacterial isolates and plate sweeps will be further characterised using a mixture of short-,long-read and metagenomic whole-genome sequencing. These datasets will be integrated into agent-based models to describe the transmission of EBSL resistance in Uganda and Malawi and allow us to inform the design of interventions for interrupting transmission of ESBL-bacteria.

Published
2022

27. Effect of resistance to third-generation cephalosporins on morbidity and mortality from bloodstream infections in Blantyre, Malawi:a prospective cohort study

Author

Lester, Rebecca, Musicha, Patrick, Kawaza, Kondwani, Langton, Josephine, Mango, James, Mangochi, Helen, Bakali, Winnie, Pearse, Oliver, Mallewa, Jane, Denis, Brigitte, Bilima, Sithembile, Gordon, Stephen B, Lalloo, David G, Jewell, Christopher P, Feasey, Nicholas A, Lester, Rebecca, Musicha, Patrick, Kawaza, Kondwani, Langton, Josephine, Mango, James, Mangochi, Helen, Bakali, Winnie, Pearse, Oliver, Mallewa, Jane, Denis, Brigitte, Bilima, Sithembile, Gordon, Stephen B, Lalloo, David G, Jewell, Christopher P, and Feasey, Nicholas A

Abstract

Background: The burden of antimicrobial resistance is a major threat to global health; however, prospective clinical outcome data from Africa are scarce. In Malawi, third-generation cephalosporins are the antibiotics of choice in patients admitted to hospital despite a rapid proliferation of resistance to these drugs. We aimed to quantify the effect of resistance to third-generation cephalosporins on mortality and length of hospital stay among patients with bloodstream infections. Methods: We did a prospective cohort study of patients admitted to Queen Elizabeth Central Hospital in Blantyre, Malawi. Patients of all ages who had positive blood cultures for Enterobacterales were included, with the exception of those from the genus Salmonella, and were followed up for 180 days. We characterised blood culture isolates using whole-genome sequencing and used Cox regression models to estimate the effect of resistance to third-generation cephalosporins on length of hospital stay, in-hospital mortality, and survival. Findings: Between Jan 31, 2018, and Jan 13, 2020, we recruited 326 patients, from whom 220 (68%) of 326 isolates were resistant to third-generation cephalosporins. The case fatality proportion was 45% (99 of 220) in patients with bloodstream infections that were resistant to third-generation cephalosporins, and 34% (36 of 106) in patients with bloodstream infections that were sensitive to third-generation cephalosporins. Resistance to third-generation cephalosporins was associated with an increased probability of in-hospital mortality (hazard ratio [HR] 1·44, 95% CI 1·02–2·04), longer hospital stays (1·5 days, 1·0–2·0) and decreased probability of discharge alive (HR 0·31, 0·22–0·45). Whole-genome sequencing showed a high diversity of sequence types of both Escherichia coli and Klebsiella pneumoniae. Although isolates associated with death were distributed across clades, we identified three E coli clades (ST410, ST617, and ST648) that were isolated from 14 patie

Published
2022

28. Drivers of Resistance in Uganda and Malawi (DRUM): a protocol for the evaluation of One-Health drivers of Extended Spectrum Beta Lactamase (ESBL) resistance in Low-Middle Income Countries (LMICs)

Author

Cocker, Derek, primary, Sammarro, Melodie, additional, Chidziwisano, Kondwani, additional, Elviss, Nicola, additional, Jacob, Shevin T., additional, Kajumbula, Henry, additional, Mugisha, Lawrence, additional, Musoke, David, additional, Musicha, Patrick, additional, Roberts, Adam P., additional, Rowlingson, Barry, additional, Singer, Andrew C., additional, Byrne, Rachel L., additional, Edwards, Thomas, additional, Lester, Rebecca, additional, Wilson, Catherine N., additional, Hollihead, Beth, additional, Thomson, Nicholas, additional, Jewell, Christopher P., additional, Morse, Tracy, additional, and Feasey, Nicholas A., additional

Published
2022
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29. Household acquisition and transmission of extended-spectrum β-lactamase (ESBL) -producing Enterobacteriaceae after hospital discharge of ESBL-positive index patients

Author

Riccio, Maria, Verschuuren, Tess, Conzelmann, Nadine, Martak, Daniel, Meunier, Alexandre, Salamanca, Elena, Delgado, Mercedes, Guther, Julia, Peter, Silke, Paganini, Julian, Martischang, Romain, Sauser, Julien, de Kraker, Marlieke, Cherkaoui, Abdessalam, Fluit, Ad, Cooper, Ben, Hocquet, Didier, Kluytmans, Jan, Tacconelli, Evelina, Rodriguez-Baño, Jesús, Harbarth, Stephan, de Kraker, Marlieke E.A., Kluytmans, Jan A.J.W., Brossier, Caroline, Von Dach, Elodie, Renzi, Gesuele, Schrenzel, Jacques, Bunk, Stefanie, Goepel, Siri, Hölzl, Florian, Eib, Michael, Autenrieth, Ingo, Pascual, Álvaro, Bertrand, Xavier, Scharringa, Jelle, Musicha, Patrick, Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Instituto de Salud Carlos III, Netherlands Organisation for Health Research and Development, Swiss National Science Foundation, Federal Ministry of Education and Research (Germany), Agence Nationale de la Recherche (France), Innovative Medicines Initiative, European Commission, European Federation of Pharmaceutical Industries and Associations, Ministerio de Ciencia, Innovación y Universidades (España), Red Española de Investigación en Patología Infecciosa, Brossier, Caroline, Von Dach-Saouter, Elodie, Renzi, Gesuele, Centre Hospitalier Régional Universitaire [Besançon] (CHRU Besançon), and Laboratoire Chrono-environnement - CNRS - UFC (UMR 6249) (LCE)

Subjects
0301 basic medicine, Index (economics), Klebsiella pneumoniae, law.invention, 0302 clinical medicine, Hygiene, law, Risk Factors, polycyclic compounds, 030212 general & internal medicine, Prospective Studies, Prospective cohort study, Index case, Household, media_common, ddc:616, Family Characteristics, biology, Incidence (epidemiology), Enterobacteriaceae Infections, General Medicine, Hospitals, Patient Discharge, 3. Good health, Infectious Diseases, Transmission (mechanics), [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Microbiology (medical), medicine.medical_specialty, media_common.quotation_subject, 030106 microbiology, beta-Lactamases, 03 medical and health sciences, Extended-spectrum β-lactamase, Internal medicine, medicine, Escherichia coli, Humans, Transmission, business.industry, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, bacterial infections and mycoses, Clinical trial, Acquisition, bacteria, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

MODERN WP2 study group: Caroline Brossier, Elodie von Dach, Gesuele Renzi, Jacques Schrenzel, Stefanie Bunk, Siri Goepel, Florian Hölzl, Michael Eib, Ingo B.Autenrieth, Álvaro Pascual, Xavier Bertrand, Jelle Scharringa, Patrick Musicha., [Objectives] This study aimed to determine rates and risk factors of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) acquisition and transmission within households after hospital discharge of an ESBL-PE-positive index patient., [Methods] Two-year prospective cohort study in five European cities. Patients colonized with ESBL-producing Escherichia coli (ESBL-Ec) or Klebsiella pneumoniae (ESBL-Kp), and their household contacts were followed up for 4 months after hospital discharge of the index case. At each follow up, participants provided a faecal sample and personal information. ESBL-PE whole-genome sequences were compared using pairwise single nucleotide polymorphism-based analysis., [Results] We enrolled 71 index patients carrying ESBL-Ec (n = 45), ESBL-Kp (n = 20) or both (n = 6), and 102 household contacts. The incidence of any ESBL-PE acquisition among household members initially free of ESBL-PE was 1.9/100 participant-weeks at risk. Nineteen clonally related household transmissions occurred (case to contact: 13; contact to case: 6), with an overall rate of 1.18 transmissions/100 participant-weeks at risk. Most of the acquisition and transmission events occurred within the first 2 months after discharge. The rate of ESBL-Kp household transmission (1.16/100 participant-weeks) was higher than of ESBL-Ec (0.93/100 participant-weeks), whereas more acquisitions were noted for ESBL-Ec (1.06/100 participant-weeks) compared with ESBL-Kp (0.65/100 participant-weeks). Providing assistance for urinary and faecal excretion to the index case by household members increased the risk of ESBL-PE transmission (adjusted prevalence ratio 4.3; 95% CI 1.3–14.1)., [Conclusions] ESBL-PE cases discharged from the hospital are an important source of ESBL-PE transmission within households. Most acquisition and transmission events occurred during the first 2 months after hospital discharge and were causally related to care activities at home, highlighting the importance of hygiene measures in community settings., [Clinical study registration] German Clinical Trials Register, DRKS-ID: DRKS00013250., This study was part of a Joint Programming Initiative on Antimicrobial Resistance collaborative research project, under the 2016 Joint Call framework (Transnational Research Projects on the Transmission Dynamics of Antibacterial Resistance). It received funding from the following national research agencies: Instituto de Salud Carlos III (grant no. AC16/00076), Netherlands Organization for Health Research and Development (grant no. AC681055), Swiss National Science Foundation (grant no. 40AR40-173608), German Federal Ministry of Education and Research (grant no. 01KI1830) and Agence Nationale de la Recherche (grant no. ANR-16-JPEC-0007-03). As part of a separate research project, Marlieke de Kraker has received support from the Innovative Medicines Initiative Joint Undertaking under grant agreement nos 115523, 115620 and 115737 (Combatting Bacterial Resistance in Europe projects (COMBACTE)), resources of which are composed of financial contribution from the European Union's 7th Framework Programme (FP7/2007±2013) and the European Federation of Pharmaceutical Industries and associations companies' in-kind contribution. Also, Elena Salamanca, Mercedes Delgado and Jesús Rodríguez-Baño received support for research from by the Plan Nacional de I+D+i 2013-2016 and Instituto de Salud Carlos III, Subdirección General de Redes y Centros de Investigación Cooperativa, Ministerio de Ciencia, Innovación y Universidades, Spanish Network for Research in Infectious Diseases (REIPI RD16/0016/0001), co-financed by the European Development Regional Fund ‘A way to achieve Europe’, Operative Programme Intelligence Growth 2014-2020.

Published
2021
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31. ChloS-HRM, a novel assay to identify chloramphenicol-susceptible Escherichia coli and Klebsiella pneumoniae in Malawi

Author

Williams, Christopher T, Musicha, Patrick, Feasey, Nicholas A, Adams, Emily R, and Edwards, Thomas

Subjects
Klebsiella pneumoniae, Malawi, Chloramphenicol, Genes, Bacterial, Escherichia coli, Humans, Public Health Surveillance, Microbial Sensitivity Tests, Sensitivity and Specificity, Escherichia coli Infections, Original Research, Klebsiella Infections
Abstract

Objectives:Chloramphenicol is a broad-spectrum antimicrobial widely available in sub-Saharan Africa. With susceptibility re-emerging among Enterobacteriaceae in Blantyre, Malawi, we designed and evaluated a new high-resolution melt (HRM) RT-PCR assay, ChloS-HRM, to identify chloramphenicol-susceptible infections in a hospital setting. Methods:Seventy-two previously whole-genome sequenced isolates of Escherichia coli and Klebsiella pneumoniae from the Queen Elizabeth Central Hospital, Malawi, were subjected to determination of chloramphenicol MICs. Primers were designed to detect 18 chloramphenicol resistance genes that produce seven distinct peaks correlating with different gene groups (catA1, catA2, catA3, catB2, catB group 3, cmlA and floR) following HRM analysis. ChloS-HRM results were compared with MIC and WGS results. Results:ChloS-HRM correctly identified 15 of 17 phenotypically susceptible isolates and 54 of 55 resistant isolates, giving an accuracy of 88% in identifying susceptibility and 98% in identifying resistance. WGS identified 16 of 17 susceptible and 54 of 55 resistant isolates, giving an accuracy of 94% in identifying susceptibility and 98% in identifying resistance. The single false-susceptible result had no detectable gene by ChloS-HRM or WGS. Compared with WGS, ChloS-HRM had 100% sensitivity and specificity for catA (catA1-3), cmlA and floR, and 96% specificity for catB; sensitivity could not be estimated due to the lack of catB in the clinical sample collection. The overall agreement between MIC and HRM was 96% and between MIC and WGS it was 97%. Conclusions:ChloS-HRM could support antimicrobial stewardship in enabling de-escalation from third-generation cephalosporins by identifying chloramphenicol-susceptible infections. This would be valuable in areas with chloramphenicol-susceptible MDR and XDR Enterobacteriaceae.

Published
2019

32. Evidence of widespread endemic populations of highly multidrug-resistant Klebsiella pneumoniae seen concurrently through the lens of two hospital intensive care units in Vietnam

Author

Pham, My H., primary, Hoi, Le Thi, additional, Beale, Mathew A., additional, Khokhar, Fahad, additional, Hoa, Nguyen Thi, additional, Musicha, Patrick, additional, Blackwell, Grace, additional, Long, Hoang Bao, additional, Huong, Dang Thi, additional, Binh, Nguyen Gia, additional, Co, Dao Xuan, additional, Giang, Tran, additional, Bui, Cuong, additional, Tran, Hai Ninh, additional, Bryan, James, additional, Herrick, Archie, additional, Feltwell, Theresa, additional, Nadjm, Behzad, additional, Parkhill, Julian, additional, van Doorn, H. Rogier, additional, Trung, Nguyen Vu, additional, Van Kinh, Nguyen, additional, Estée Török, M., additional, and Thomson, Nicholas R., additional

Published
2021
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33. Household acquisition and transmission of extended-spectrum β-lactamase (ESBL) -producing Enterobacteriaceae after hospital discharge of ESBL-positive index patients

Author

Riccio, Maria E., Verschuuren, Tess, Conzelmann, Nadine, Martak, Daniel, Meunier, Alexandre, Salamanca, Elena, Rodríguez-Baño, Jesús, Pascual Hernández, Álvaro, Musicha, Patrick, Universidad de Sevilla. Departamento de Medicina, and Universidad de Sevilla. Departamento de Microbiología

Subjects
Acquisition, Extended-spectrum b-lactamase, Prospective cohort study, Transmission, Household
Abstract

Objectives: This study aimed to determine rates and risk factors of extended-spectrum b-lactamaseproducing Enterobacteriaceae (ESBL-PE) acquisition and transmission within households after hospital discharge of an ESBL-PE-positive index patient. Methods: Two-year prospective cohort study in five European cities. Patients colonized with ESBLproducing Escherichia coli (ESBL-Ec) or Klebsiella pneumoniae (ESBL-Kp), and their household contacts were followed up for 4 months after hospital discharge of the index case. At each follow up, participants provided a faecal sample and personal information. ESBL-PE whole-genome sequences were compared using pairwise single nucleotide polymorphism-based analysis. Results: We enrolled 71 index patients carrying ESBL-Ec (n ¼ 45), ESBL-Kp (n ¼ 20) or both (n ¼ 6), and 102 household contacts. The incidence of any ESBL-PE acquisition among household members initially free of ESBL-PE was 1.9/100 participant-weeks at risk. Nineteen clonally related household transmissions occurred (case to contact: 13; contact to case: 6), with an overall rate of 1.18 transmissions/100 participant-weeks at risk. Most of the acquisition and transmission events occurred within the first 2 months after discharge. The rate of ESBL-Kp household transmission (1.16/100 participant-weeks) was higher than of ESBL-Ec (0.93/100 participant-weeks), whereas more acquisitions were noted for ESBL-Ec (1.06/100 participant-weeks) compared with ESBL-Kp (0.65/100 participant-weeks). Providing assistance for urinary and faecal excretion to the index case by household members increased the risk of ESBL-PE transmission (adjusted prevalence ratio 4.3; 95% CI 1.3e14.1). Instituto de Salud Carlos III

Published
2021

34. Household acquisition and transmission of ESBL-producing Enterobacteriaceae after hospital discharge of ESBL-positive index patients

Author

Riccio, M E, Verschuuren, T, Conzelmann, N, Martak, D, Meunier, A, Salamanca, E, Delgado, M, Guther, J, Peter, S, Paganini, J, Martischang, R, Sauser, J, de Kraker, M E A, Cherkaoui, A, Fluit, A C, Cooper, B S, Hocquet, D, Kluytmans, J A J W, Tacconelli, E, Rodriguez-Baño, J, Harbarth, S, Brossier, Caroline, von Dach, Elodie, Renzi, Gesuele, Schrenzel, Jacques, Bunk, Stefanie, Goepel, Siri, Hölzl, Florian, Eib, Michael, Autenrieth, Ingo B, Pascual, Álvaro, Bertrand, Xavier, Scharringa, Jelle, and Musicha, Patrick

Subjects
ESBL, Prospective cohort study, transmission, acquisition, household
Published
2021

35. Dissemination routes of the carbapenem resistance plasmid pOXA-48 in a hospital setting

Author

Leon-Sampedro, Ricardo, DelaFuente, Javier, Díaz-Agero, Cristina, Crellen, Thomas, Musicha, Patrick, Rodríguez-Beltrán, Jerónimo, de la Vega, Carmen, Hernández-García, Marta, R-GNOSIS WP5 Study Group, López-Fresneña, Nieves, Ruiz-Garbajosa, Patricia, Cantón, Rafael, Cooper, Ben S., and San Millan, Alvaro

Subjects
biochemical phenomena, metabolism, and nutrition
Abstract

Infections caused by carbapenemase-producing enterobacteria (CPE) are a major concern in clinical settings worldwide. Two fundamentally different processes shape the epidemiology of CPE in hospitals: the dissemination of CPE clones from patient to patient (between-patient transfer), and the transfer of carbapenemase-encoding plasmids between enterobacteria in the gut microbiota of individual patients (within-patient transfer). The relative contribution of each process to the overall dissemination of carbapenem resistance in hospitals remains poorly understood. Here, we used mechanistic models combining epidemiological data from more than 9,000 patients with whole genome sequence information from 250 enterobacteria clones to characterise the dissemination routes of the carbapenemase-encoding plasmid pOXA-48 in a hospital setting over a two-year period. Our results revealed frequent between-patient transmission of high-risk pOXA-48-carrying clones, mostly of Klebsiella pneumoniae and sporadically Escherichia coli. The results also identified pOXA-48 dissemination hotspots within the hospital, such as specific wards and individual rooms within wards. Using high-resolution plasmid sequence analysis, we uncovered the pervasive within-patient transfer of pOXA-48, suggesting that horizontal plasmid transfer occurs in the gut of virtually every colonised patient. The complex and multifaceted epidemiological scenario exposed by this study provides new insights for the development of intervention strategies to control the in-hospital spread of CPE., bioRxiv

Published
2020

36. A NOVEL AIR-DRIED MULTIPLEX HIGH RESOLUTION MELT ASSAY FOR THE DETECTION OF EXTENDED SPECTRUM BETA-LACTAMASE AND CARBAPENEMASE GENES

Author

Cubas-Atienzar, Ana I., primary, Williams, Christopher T., additional, Karkey, Abhilasha, additional, Dongol, Sabina, additional, Sulochana, Manandhar, additional, Rajendra, Shrestha, additional, Hobbs, Glyn, additional, Evans, Katie, additional, Musicha, Patrick, additional, Feasey, Nicholas, additional, Cuevas, Luis E., additional, Adams, Emily R., additional, and Edwards, Thomas, additional

Published
2021
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37. Acquisition and carriage dynamics of fluoroquinolone resistant Enterobacteriaceae at individual and household levels

Author

Musicha, Patrick, primary, Stewardson, Andrew J., additional, Mo, Yin, additional, Vervoort, Jascha, additional, Adriaenssens, Niels, additional, Coenen, Samuel, additional, Godycki-Cwirko, Maciek, additional, Kowalczyk, Anna, additional, Lammens, Christine, additional, Malhotra-Kumar, Surbhi, additional, Goossens, Herman, additional, Harbarth, Stephan, additional, and Cooper, Ben S., additional

Published
2020
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40. Carriage duration of carbapenemase-producing Enterobacteriaceae in a hospital cohort - implications for infection control measures

Author

Mo, Yin, primary, Hernandez-Koutoucheva, Anastasia, additional, Musicha, Patrick, additional, Bertrand, Denis, additional, Lye, David, additional, Tek, Ng Oon, additional, Fenlon, Shannon N., additional, Chen, Swaine L., additional, Lin, Ling Moi, additional, Tang, Wen Ying, additional, Barkham, Timothy, additional, Nagarajan, Niranjan, additional, Cooper, Ben S, additional, and Marimuthu, Kalisvar, additional

Published
2019
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42. Early Signals of Vaccine-driven Perturbation Seen in Pneumococcal Carriage Population Genomic Data

Author

Chaguza, Chrispin, primary, Heinsbroek, Ellen, additional, Gladstone, Rebecca A, additional, Tafatatha, Terence, additional, Alaerts, Maaike, additional, Peno, Chikondi, additional, Cornick, Jennifer E, additional, Musicha, Patrick, additional, Bar-Zeev, Naor, additional, Kamng’ona, Arox, additional, Kadioglu, Aras, additional, McGee, Lesley, additional, Hanage, William P, additional, Breiman, Robert F, additional, Heyderman, Robert S, additional, French, Neil, additional, Everett, Dean B, additional, and Bentley, Stephen D, additional

Published
2019
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43. Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages

Author

Musicha, Patrick, primary, Msefula, Chisomo L, additional, Mather, Alison E, additional, Chaguza, Chrispin, additional, Cain, Amy K, additional, Peno, Chikondi, additional, Kallonen, Teemu, additional, Khonga, Margaret, additional, Denis, Brigitte, additional, Gray, Katherine J, additional, Heyderman, Robert S, additional, Thomson, Nicholas R, additional, Everett, Dean B, additional, and Feasey, Nicholas A, additional

Published
2019
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45. Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting

Author

Musicha, Patrick, Feasey, Nicholas A., Cain, Amy K., Kallonen, Teemu, Chaguza, Chrispin, Peno, Chikondi, Khonga, Margaret, Thompson, Sarah, Gray, Katherine J., Mather, Alison E., Heyderman, Robert S., Everett, Dean B., Thomson, Nicholas R., and Msefula, Chisomo L.

Subjects
Adult, Male, Malawi, Adolescent, Urban Population, Microbial Sensitivity Tests, beta-Lactam Resistance, beta-Lactamases, qw_45, Young Adult, Drug Resistance, Multiple, Bacterial, Escherichia coli, Journal Article, Humans, wc_290, qu_460, Child, Escherichia coli Infections, Phylogeny, Original Research, qu_500, Research Support, Non-U.S. Gov't, Genetic Variation, Genomics, Chloramphenicol, Genes, Bacterial, Child, Preschool, Female, Multilocus Sequence Typing
Abstract

Objectives: Efforts to treat Escherichia coli infections are increasingly being compromised by the rapid, global spread of antimicrobial resistance (AMR). Whilst AMR in E. coli has been extensively investigated in resource-rich settings, in sub-Saharan Africa molecular patterns of AMR are not well described. In this study, we have begun to explore the population structure and molecular determinants of AMR amongst E. coli isolates from Malawi.Methods: Ninety-four E. coli isolates from patients admitted to Queen's Hospital, Malawi, were whole-genome sequenced. The isolates were selected on the basis of diversity of phenotypic resistance profiles and clinical source of isolation (blood, CSF and rectal swab). Sequence data were analysed using comparative genomics and phylogenetics.Results: Our results revealed the presence of five clades, which were strongly associated with E. coli phylogroups A, B1, B2, D and F. We identified 43 multilocus STs, of which ST131 (14.9%) and ST12 (9.6%) were the most common. We identified 25 AMR genes. The most common ESBL gene was bla CTX-M-15 and it was present in all five phylogroups and 11 STs, and most commonly detected in ST391 (4/4 isolates), ST648 (3/3 isolates) and ST131 [3/14 (21.4%) isolates].Conclusions: This study has revealed a high diversity of lineages associated with AMR, including ESBL and fluoroquinolone resistance, in Malawi. The data highlight the value of longitudinal bacteraemia surveillance coupled with detailed molecular epidemiology in all settings, including low-income settings, in describing the global epidemiology of ESBL resistance.

Published
2017
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46. Duration of Carbapenemase-Producing Enterobacteriaceae Carriage in Hospital Patients.

Author

Yin Mo, Hernandez-Koutoucheva, Anastasia, Musicha, Patrick, Bertrand, Denis, Lye, David, Oon Tek Ng, Fenlon, Shannon N., Chen, Swaine L., Moi Lin Ling, Wen Ying Tang, Barkham, Timothy, Nagarajan, Niranjan, Cooper, Ben S., Marimuthu, Kalisvar, Mo, Yin, Ng, Oon Tek, Ling, Moi Lin, and Tang, Wen Ying

Subjects
HOSPITAL patients, ENTEROBACTERIACEAE, ANTI-infective agents, DRUG abuse, DECOLONIZATION
Abstract

To determine the duration of carbapenemase-producing Enterobacteriaceae (CPE) carriage, we studied 21 CPE carriers for »1 year. Mean carriage duration was 86 days; probability of decolonization in 1 year was 98.5%, suggesting that CPE-carriers' status can be reviewed yearly. Prolonged carriage was associated with use of antimicrobial drugs. [ABSTRACT FROM AUTHOR]

Published
2020
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47. Early Signals of Vaccine-driven Perturbation Seen in Pneumococcal Carriage Population Genomic Data.

Author

Chaguza, Chrispin, Heinsbroek, Ellen, Gladstone, Rebecca A, Tafatatha, Terence, Alaerts, Maaike, Peno, Chikondi, Cornick, Jennifer E, Musicha, Patrick, Bar-Zeev, Naor, Kamng'ona, Arox, Kadioglu, Aras, McGee, Lesley, Hanage, William P, Breiman, Robert F, Heyderman, Robert S, French, Neil, Everett, Dean B, and Bentley, Stephen D

Subjects
DRUG resistance in microorganisms, GENES, GENOMES, PNEUMOCOCCAL vaccines, SEROLOGY, STREPTOCOCCUS, SURVEYS, POPULATION health, SEQUENCE analysis
Abstract

Background Pneumococcal conjugate vaccines (PCVs) have reduced pneumococcal diseases globally. Pneumococcal genomic surveys elucidate PCV effects on population structure but are rarely conducted in low-income settings despite the high disease burden. Methods We undertook whole-genome sequencing (WGS) of 660 pneumococcal isolates collected through surveys from healthy carriers 2 years from 13-valent PCV (PCV13) introduction and 1 year after rollout in northern Malawi. We investigated changes in population structure, within-lineage serotype dynamics, serotype diversity, and frequency of antibiotic resistance (ABR) and accessory genes. Results In children <5 years of age, frequency and diversity of vaccine serotypes (VTs) decreased significantly post-PCV, but no significant changes occurred in persons ≥5 years of age. Clearance of VT serotypes was consistent across different genetic backgrounds (lineages). There was an increase of nonvaccine serotypes (NVTs)—namely 7C, 15B/C, and 23A—in children <5 years of age, but 28F increased in both age groups. While carriage rates have been recently shown to remain stable post-PCV due to replacement serotypes, there was no change in diversity of NVTs. Additionally, frequency of intermediate-penicillin-resistant lineages decreased post-PCV. Although frequency of ABR genes remained stable, other accessory genes, especially those associated with mobile genetic element and bacteriocins, showed changes in frequency post-PCV. Conclusions We demonstrate evidence of significant population restructuring post-PCV driven by decreasing frequency of vaccine serotypes and increasing frequency of few NVTs mainly in children under 5. Continued surveillance with WGS remains crucial to fully understand dynamics of the residual VTs and replacement NVT serotypes post-PCV. [ABSTRACT FROM AUTHOR]

Published
2020
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48. Prevalence and outcome of bloodstream infections due to third-generation cephalosporin-resistant Enterobacteriaceae in sub-Saharan Africa: a systematic review.

Author

Lester, Rebecca, Musicha, Patrick, Ginneken, Nadja van, Dramowski, Angela, Hamer, Davidson H, Garner, Paul, Feasey, Nicholas A, and van Ginneken, Nadja

Subjects
*CEPHALOSPORINS, *ENTEROBACTERIACEAE, *META-analysis, *DRUG resistance in microorganisms, *HOSPITAL mortality, *KLEBSIELLA, *ESCHERICHIA coli, *SYSTEMATIC reviews, *ENTEROBACTERIACEAE diseases, *SEPSIS, *DISEASE prevalence, *ANTIBIOTICS, *PHARMACODYNAMICS
Abstract

Background: The prevalence of bacterial bloodstream infections (BSIs) in sub-Saharan Africa (sSA) is high and antimicrobial resistance is likely to increase mortality from these infections. Third-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae are of particular concern, given the widespread reliance on ceftriaxone for management of sepsis in Africa.Objectives: Reviewing studies from sSA, we aimed to describe the prevalence of 3GC resistance in Escherichia coli, Klebsiella and Salmonella BSIs and the in-hospital mortality from 3GC-R BSIs.Methods: We systematically reviewed studies reporting 3GC susceptibility testing of E. coli, Klebsiella and Salmonella BSI. We searched PubMed and Scopus from January 1990 to September 2019 for primary data reporting 3GC susceptibility testing of Enterobacteriaceae associated with BSI in sSA and studies reporting mortality from 3GC-R BSI. 3GC-R was defined as phenotypic resistance to ceftriaxone, cefotaxime or ceftazidime. Outcomes were reported as median prevalence of 3GC resistance for each pathogen.Results: We identified 40 articles, including 7 reporting mortality. Median prevalence of 3GC resistance in E. coli was 18.4% (IQR 10.5 to 35.2) from 20 studies and in Klebsiella spp. was 54.4% (IQR 24.3 to 81.2) from 28 studies. Amongst non-typhoidal salmonellae, 3GC resistance was 1.9% (IQR 0 to 6.1) from 12 studies. A pooled mortality estimate was prohibited by heterogeneity.Conclusions: Levels of 3GC resistance amongst bloodstream Enterobacteriaceae in sSA are high, yet the mortality burden is unknown. The lack of clinical outcome data from drug-resistant infections in Africa represents a major knowledge gap and future work must link laboratory surveillance to clinical data. [ABSTRACT FROM AUTHOR]

Published
2020
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49. Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data

Author

Chaguza, Chrispin, primary, Heinsbroek, Ellen, additional, Gladstone, Rebecca A., additional, Tafatatha, Terence, additional, Alaerts, Maaike, additional, Peno, Chikondi, additional, Cornick, Jennifer E., additional, Musicha, Patrick, additional, Bar-Zeev, Naor, additional, Kamng’ona, Arox, additional, Kadioglu, Aras, additional, Mcgee, Lesley, additional, Hanage, William P., additional, Breiman, Robert F., additional, Heyderman, Robert S., additional, French, Neil, additional, Everett, Dean B., additional, and Bentley, Stephen D., additional

Published
2018
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