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1. Genome sequencing of Plasmodium malariae identifies continental segregation and mutations associated with reduced pyrimethamine susceptibility

Author

Ibrahim, Amy, Mohring, Franziska, Manko, Emilia, van Schalkwyk, Donelly A., Phelan, Jody E., Nolder, Debbie, Borrmann, Steffen, Adegnika, Ayola A., Di Santi, Silvia Maria, Alam, Mohammad Shafiul, Mondal, Dinesh, Nosten, Francois, Sutherland, Colin J., Moon, Robert W., Clark, Taane G., and Campino, Susana

Published
2024
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5. Whole genome sequence analysis of population structure and insecticide resistance markers in Anopheles melas from the Bijagós Archipelago, Guinea-Bissau

Author

Moss, Sophie, Pretorius, Elizabeth, Ceesay, Sainey, da Silva, Eunice Teixeira, Hutchins, Harry, Ndiath, Mamadou Ousmane, Acford-Palmer, Holly, Collins, Emma L., Higgins, Matthew, Phelan, Jody, Jones, Robert T., Vasileva, Hristina, Rodrigues, Amabelia, Krishna, Sanjeev, Clark, Taane G., Last, Anna, and Campino, Susana

Published
2024
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6. A Pan Plasmodium lateral flow recombinase polymerase amplification assay for monitoring malaria parasites in vectors and human populations

Author

Higgins, Matthew, Kristan, Mojca, Collins, Emma L., Messenger, Louisa A., Dombrowski, Jamille G., Vanheer, Leen N., Nolder, Debbie, Drakeley, Christopher J., Stone, William, Mahamar, Almahamoudou, Bousema, Teun, Delves, Michael, Bandibabone, Janvier, N’Do, Sévérin, Bantuzeko, Chimanuka, Zawadi, Bertin, Walker, Thomas, Sutherland, Colin J., Marinho, Claudio R. F., Cameron, Mary M., Clark, Taane G., and Campino, Susana

Published
2024
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7. Whole genome sequencing analysis of Mycobacterium tuberculosis reveals circulating strain types and drug-resistance mutations in the Philippines

Author

Wang, Linfeng, Lim, Dodge R., Phelan, Jody E., Reyes, Lorenzo T., Palparan, Alma G., Sanchez, Maria Guileane C., Asuncion, Louella Abigail A., Tujan, Ma. Angelica A., Medado, Inez Andrea P., Daga, Chona Mae A., Llames, Jo-Hannah S., Mitarai, Satoshi, Murase, Yoshiro, Morishige, Yuta, Ang, Concepcion F., Malabad, John Carlo M., Montoya, Jaime C., Hafalla, Julius C., Campino, Susana, Hibberd, Martin L., Ama, Cecilia G., Basilio, Ramon P., La Paz, Eva Maria Cutiongoco-De, and Clark, Taane G.

Published
2024
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14. Genomic surveillance of Anopheles mosquitoes on the Bijagós Archipelago using custom targeted amplicon sequencing identifies mutations associated with insecticide resistance

Author

Moss, Sophie, Pretorius, Elizabeth, Ceesay, Sainey, Hutchins, Harry, da Silva, Eunice Teixeira, Ndiath, Mamadou Ousmane, Jones, Robert T., Vasileva, Hristina, Phelan, Jody, Acford-Palmer, Holly, Collins, Emma, Rodrigues, Amabelia, Krishna, Sanjeev, Clark, Taane G., Last, Anna, and Campino, Susana

Published
2024
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15. Newly Identified Mycobacterium africanum Lineage 10, Central Africa

Author

Guyeux, Christophe, Senelle, Gaetan, Le Meur, Adrien, Supply, Philip, Gaudin, Cyril, Phelan, Jody E., Clark, Taane G., Rigouts, Leen, de Jong, Bouke, Sola, Christophe, and Refregier, Guislaine

Subjects
Central Africa -- Health aspects, Central Africa -- Environmental aspects, Identification and classification, Genetic aspects, Risk factors, Natural history, Causes of, Health aspects, Environmental aspects, Tuberculosis -- Causes of -- Risk factors, Mycobacteria -- Identification and classification -- Genetic aspects -- Natural history, Mycobacterium -- Identification and classification -- Genetic aspects -- Natural history
Abstract

The traditional view of restricted diversity among bacterial agents causing human and animal tuberculosis is being revised thanks to wide use of wholegenome sequencing (WGS). Besides Mycobacterium canettii, representative of [...]

Published
2024
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23. Genome-wide genetic variation and molecular surveillance of drug resistance in Plasmodium falciparum isolates from asymptomatic individuals in Ouélessébougou, Mali

Author

Vanheer, Leen N., Mahamar, Almahamoudou, Manko, Emilia, Niambele, Sidi M., Sanogo, Koualy, Youssouf, Ahamadou, Dembele, Adama, Diallo, Makonon, Maguiraga, Seydina O., Phelan, Jody, Osborne, Ashley, Spadar, Anton, Smit, Merel J., Bousema, Teun, Drakeley, Chris, Clark, Taane G., Stone, William, Dicko, Alassane, and Campino, Susana

Published
2023
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27. Genome-wide host-pathogen analyses reveal genetic interaction points in tuberculosis disease

Author

Phelan, Jody, Gomez-Gonzalez, Paula Josefina, Andreu, Nuria, Omae, Yosuke, Toyo-Oka, Licht, Yanai, Hideki, Miyahara, Reiko, Nedsuwan, Supalert, de Sessions, Paola Florez, Campino, Susana, Sallah, Neneh, Parkhill, Julian, Smittipat, Nat, Palittapongarnpim, Prasit, Mushiroda, Taisei, Kubo, Michiaki, Tokunaga, Katsushi, Mahasirimongkol, Surakameth, Hibberd, Martin L., and Clark, Taane G.

Published
2023
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31. IFNγ, TNFα polymorphisms and IFNγ serum levels are associated with the clearance of drug-resistant P. falciparum in Malian children

Author

Kouriba, Bourema, Arama, Charles, Ouologuem, Dinkorma T., Cissoko, Yacouba, Diakite, Mahamadou, Beavogui, Abdoul Habib, Wele, Mamadou, Tekete, Mamadou, Fofana, Bakary, Dama, Souleymane, Maiga, Hamma, Kone, Aminatou, Niangaly, Amadou, Diarra, Issa, Daou, Modibo, Guindo, Ando, Traore, Karim, Coulibaly, Drissa, Kone, Abdoulaye K., Dicko, Alassane, Clark, Taane G., Doumbo, Ogobara K., and Djimde, Abdoulaye

Published
2023
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32. Risk factors for SARS-CoV-2 infection in primary and secondary school students and staff in England in the 2020/2021 school year: a longitudinal study

Author

Nguipdop-Djomo, Patrick, Oswald, William E, Halliday, Katherine E, Cook, Sarah, Sturgess, Joanna, Sundaram, Neisha, Warren-Gash, Charlotte, Fine, Paul EM, Glynn, Judith, Allen, Elizabeth, Clark, Taane G., Ford, Benjamin, Judd, Alison, Ireland, Georgina, Poh, John, Bonell, Chris, Dawe, Fiona, Rourke, Emma, Diamond, Ian, Ladhani, Shamez N, Langan, Sinéad M, Hargreaves, James, and Mangtani, Punam

Published
2023
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33. Population-based genomic study of Plasmodium vivax malaria in seven Brazilian states and across South America

Author

Ibrahim, Amy, Manko, Emilia, Dombrowski, Jamille G., Campos, Mónica, Benavente, Ernest Diez, Nolder, Debbie, Sutherland, Colin J., Nosten, Francois, Fernandez, Diana, Vélez-Tobón, Gabriel, Castaño, Alberto Tobón, Aguiar, Anna Caroline C., Pereira, Dhelio Batista, da Silva Santos, Simone, Suarez-Mutis, Martha, Di Santi, Silvia Maria, Regina de Souza Baptista, Andrea, Dantas Machado, Ricardo Luiz, Marinho, Claudio R.F., Clark, Taane G., and Campino, Susana

Published
2023
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35. List of contributors

Author

Aggarwal, Suruchi, primary, Ahmed, Faizan, additional, Akkina, Rajani Chowdary, additional, Arora, Gunjan, additional, Asadulghani, Md., additional, Bahl, Aayush, additional, Banerjee, Aniruddha, additional, Banerjee, Chaitali, additional, Banerjee, Shukla, additional, Banerjee, Somok, additional, Chaitanya, Kolluru Viswanatha, additional, Clark, Taane G., additional, Dhawan, Gagan, additional, Dhawan, Uma, additional, Ghosh, Soumyadip, additional, Gupta, Anil Kumar, additional, Gupta, Kuldeepkumar Ramnaresh, additional, Gupta, Payal, additional, Hussain, Arif, additional, Ismaeel, Sana, additional, Katiyar, Arti Singh, additional, Kumar, Ashutosh, additional, Laskar, Mani Kankana, additional, Mahajan, Pallavi, additional, Mamillapalli, Anitha, additional, Mazumder, Razib, additional, Mondal, Dinesh, additional, Nandanwar, Nishant, additional, Pandey, Monika, additional, Pandey, Saurabh, additional, Pati, Swatilekha, additional, Peddireddy, Vidyullatha, additional, Prakash, Palkar Omkar, additional, Rakshit, Roopshali, additional, Rayasam, Keerthi, additional, Sajid, Andaleeb, additional, Sarma, Jayshree, additional, Sengupta, Aveepsa, additional, Sengupta, Shatabdi, additional, Shaheen, Shakila, additional, Sharma, Bipin Kumar, additional, Sharma, Divakar, additional, Singh, Amit, additional, Sulakshana, Palla Mary, additional, Tenguria, Shivendra, additional, Tripathi, Deeksha, additional, Yadav, Alka, additional, and Yadav, Amit Kumar, additional

Published
2023
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37. Epidemiology of SARS-CoV-2 infection among staff and students in a cohort of English primary and secondary schools during 2020–2021

Author

Abramsky, Tanya, Ahmad, Shazaad, Aiano, Felicity, Baawuah, Frances, Bankiewicz, Urszula, Batt, Sarah, Beckmann, Joanne, Bhavsar, Ami, Brent, Bernadette, Brent, Andrew, Brouwer, Simon, Brown, Kevin, Browne, Richard, Childs, Kevin, Cook, Sarah, Cousens, Simon, Day, Ieuan, Felton, Antonio, Fine, Paul, Foster, David, Garstang, Joanna, Gates, David, Grant, Claire, Griffiths-Tong, Bethany, Hele, Claire, Hemsi, Rowan, Jones, Pete, Jordan, Helena, Kucharski, Adam, Lacey, Andrea, Leeson, Rebecca, Lelii, Ffion, Lovely, Philip, Lunskey, Madeleine, McLanachan, Chris, Munday, James, Okike, Ifeanyichukwu, O'Reilly, Kathleen, Parker, Penelope, Powell, Annabel, Proud, Sarah, Ramsay, Mary, Rudd, Lee, Russell, Timothy, Shute, Justin, Tilouche, Nerissa, Virgin, Charmaine, Wyatt, Sian-Elin, YEO, KELLY, Hargreaves, James R., Langan, Sinéad M., Oswald, William E., Halliday, Katherine E., Sturgess, Joanna, Phelan, Jody, Nguipdop-Djomo, Patrick, Ford, Benjamin, Allen, Elizabeth, Sundaram, Neisha, Ireland, Georgina, Poh, John, Ijaz, Samreen, Diamond, Ian, Rourke, Emma, Dawe, Fiona, Judd, Alison, Warren-Gash, Charlotte, Clark, Taane G., Glynn, Judith R., Edmunds, W. John, Bonell, Chris, Mangtani, Punam, and Ladhani, Shamez N.

Published
2022
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39. A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission.

Author

Sobkowiak, Benjamin, Cudahy, Patrick, Chitwood, Melanie H., Clark, Taane G., Colijn, Caroline, Grandjean, Louis, Walter, Katharine S., Crudu, Valeriu, and Cohen, Ted

Subjects
MIXED infections, WHOLE genome sequencing, MYCOBACTERIUM tuberculosis, GAUSSIAN mixture models, MYCOBACTERIAL diseases
Abstract

Background: Mixed infection with multiple strains of the same pathogen in a single host can present clinical and analytical challenges. Whole genome sequence (WGS) data can identify signals of multiple strains in samples, though the precision of previous methods can be improved. Here, we present MixInfect2, a new tool to accurately detect mixed samples from Mycobacterium tuberculosis short-read WGS data. We then evaluate three approaches for reconstructing the underlying mixed constituent strain sequences. This allows these samples to be included in downstream analysis to gain insights into the epidemiology and transmission of mixed infections. Methods: We employed a Gaussian mixture model to cluster allele frequencies at mixed sites (hSNPs) in each sample to identify signals of multiple strains. Building upon our previous tool, MixInfect, we increased the accuracy of classifying in vitro mixed samples through multiple improvements to the bioinformatic pipeline. Major and minor proportion constituent strains were reconstructed using three approaches and assessed by comparing the estimated sequence to the known constituent strain sequence. Lastly, mixed infections in a real-world Mycobacterium tuberculosis population from Moldova were detected with MixInfect2 and clusters of recent transmission that included major and minor constituent strains were built. Results: All 36/36 in vitro mixed and 12/12 non-mixed samples were correctly classified with MixInfect2, and major strain proportions were estimated with high accuracy (within 3% of the true strain proportion), outperforming previous tools. Reconstructed major strain sequences closely matched the true constituent sequence by taking the allele at the highest frequency at hSNPs, while the best-performing approach to reconstruct the minor proportion strain sequence was identifying the closest non-mixed isolate in the same population, though no approach was effective when the minor strain proportion was at 5%. Finally, fewer mixed infections were identified in Moldova than previous estimates (6.6% vs 17.4%) and we found multiple instances where the constituent strains of mixed samples were present in transmission clusters. Conclusions: MixInfect2 accurately detects samples with evidence of mixed infection from short-read WGS data and provides an excellent estimate of the mixture proportions. While there are limitations in reconstructing the constituent strain sequences of mixed samples, we present recommendations for the best approach to include these isolates in further analyses. [ABSTRACT FROM AUTHOR]

Published
2025
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40. Serological insights from SARS-CoV-2 heterologous prime and boost responses in Thailand.

Author

Ward, Daniel, Pattarapreeyakul, Lapasrada, Pitaksalee, Rujiraporn, Thawong, Naphatcha, Sawaengdee, Waritta, Tuntigumthon, Suthida, Patterson, Catriona, Tetteh, Kevin, Campino, Susana, Dhepakson, Panadda, Mahasirimongkol, Surakameth, and Clark, Taane G.

Subjects
MEDICAL personnel, COVID-19 pandemic, GAUSSIAN mixture models, MEDICAL sciences, COVID-19 vaccines
Abstract

During the COVID-19 pandemic, heterologous vaccination strategies were employed to alleviate the strain on vaccine supplies. The Thailand Ministry of Health adopted these strategies using vector, inactivated, and mRNA vaccines. However, this approach has introduced challenges for SARS-CoV-2 sero-epidemiology studies. Our study analysed 647 samples from healthcare workers who received CoronaVac, ChAdOx1 nCoV-19, and BNT162b2 vaccines. The serological profile encompassed responses to various SARS-CoV-2 variants and vectors, measuring IgG, IgM, and IgA isotypes, alongside IgG avidity assays. The results demonstrated that heterologous CoronaVac/ChAdOx1 nCoV-19 schedules elicited significantly stronger antibody responses compared to homologous schedules (IgG: 1.2-fold, IgM: 10.9-fold, IgA: 3.1-fold increase). Additionally, a heterologous BNT162b2 boost at 4-weeks post-initial vaccination showed greater antibody levels than a ChAdOx1 nCoV-19 boost (IgG: 1.1-fold, IgM: slight decrease, IgA: 1.5-fold increase). Using a combination of three analytes, IgG against wild-type Spike trimer, nucleoprotein and Omicron receptor binding domains, enabled the clustering of responses within a statistical Gaussian mixture model that successfully discriminates between breakthrough infections and vaccination types (F-score = 0.82). The development of statistical models to predict breakthrough infections can improve serological surveillance. Overall, our study underscores the necessity for vaccine (re-)development and the creation of serological tools to monitor vaccine performance. [ABSTRACT FROM AUTHOR]

Published
2025
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41. Dissemination of arr-2 and arr-3 is associated with class 1 integrons in Klebsiella pneumoniae clinical isolates from Portugal.

Author

Elias, Rita, Modesto, Ana, Machado, Diana, Pereira, Bruna, Phelan, Jody, Melo-Cristino, José, Lito, Luís, Gonçalves, Luísa, Portugal, Isabel, Viveiros, Miguel, Campino, Susana, Clark, Taane G., Duarte, Aida, and Perdigão, João

Subjects
RNA polymerases, WHOLE genome sequencing, INTEGRONS, KLEBSIELLA pneumoniae, RIFAMPIN
Abstract

\nKlebsiella pneumoniae is a common pathogen of healthcare-associated infections expressing a plethora of antimicrobial resistance loci, including ADP-ribosyltransferase coding genes (arr), able to mediate rifampicin resistance. The latter has activity against a broad range of microorganisms by inhibiting DNA-dependent RNA polymerases. This study aims to characterise the arr distribution and genetic context in 138 clinical isolates of K. pneumoniae and correlate these with rifampicin resistance. All isolates were subjected to whole-genome sequencing for species identification, typing and AMR genes identification, along with the determination of the minimum inhibitory concentration (MIC) of rifampicin. Molecular detection of arr genes and class 1 integrons was performed for rifampicin-resistant isolates. Efflux activity was investigated as a possible determinant of rifampicin resistance in isolates devoid of known genetic determinants. Twelve isolates exhibited high rifampicin MICs (≥ 64 mg/L), 124 showed intermediate MICs (16–32 mg/L) and two displayed low (8 mg/L) MICs. Two arr allelic variants, arr-2 and arr-3, were found across one and nine K. pneumoniae isolates, respectively, all within class 1 integrons, including a newly described integron, and all associated with high rifampicin MICs (≥ 64 mg/L). Elevated resistance levels were additionally linked to increased arr-2/3 expression and closer proximity to the promoter. No arr gene or rpoB mutations were found across the remaining two isolates and no correlation between efflux activity and high-level rifampicin resistance was found for both isolates. In conclusion, this study demonstrates that arr genes confer high levels of rifampicin resistance in K. pneumoniae highlighting its widespread dissemination within class 1 integrons. [ABSTRACT FROM AUTHOR]

Published
2025
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42. Antibiotic Susceptibility Patterns and Virulence Profiles of Classical and Hypervirulent Klebsiella pneumoniae Strains Isolated from Clinical Samples in Khyber Pakhtunkhwa, Pakistan.

Author

Azra, Khan, Taj Ali, Ul Haq, Ihtisham, Hinthong, Woranich, Campino, Susana, Gohar, Aisha, Khan, Noman, Kashif, Muhammad, Ullah, Ihsan, and Clark, Taane G.

Subjects
CARBAPENEM-resistant bacteria, MICROBIAL sensitivity tests, DRUG resistance in bacteria, DRUG resistance in microorganisms, KLEBSIELLA pneumoniae
Abstract

The emergence of hypervirulent and carbapenem-resistant hypermucoviscous Klebsiella pneumoniae strains presents a significant public health challenge due to their increased virulence and resistance to multiple antibiotics. This study evaluates the antibiotic susceptibility patterns and virulence profiles of classical and hypervirulent K. pneumoniae strains isolated from various clinical samples. A total of 500 clinical samples were collected from patients at the Mardan Medical Complex and Ayub Medical Complex in KPK between July 2022 and June 2024. Among these, 64 K. pneumoniae strains were isolated and subsequently subjected to antimicrobial susceptibility testing (AST) and phenotypic virulence detection. Among the 64 isolates, 21 (32.8%) exhibited hypermucoviscosity, a characteristic associated with increased pathogenicity. Hemagglutination was observed in 35 (54.1%) of the isolates, indicating the presence of surface adhesins that facilitate bacterial adherence to host tissues. A high prevalence of biofilm formation was noted, with 54 (84%) isolates capable of forming biofilms, which are known to protect bacteria from antibiotics and the host immune response. Most isolates (59/64, 92.1%) were resistant against ampicillin, highlighting its limited efficacy against these strains. Conversely, the lowest resistance was observed for tigecycline, with only 15% (10/64) of the isolates showing resistance, indicating its potential utility as a treatment option. The study also found that 38 (59.3%) of the isolates were extended-spectrum beta-lactamase (ESBL) producers, 42 (65.6%) were multidrug-resistant (MDR), 32 (50%) were extensively drug-resistant (XDR), and 13 (20.3%) were resistant to carbapenems. The genetic study revealed biofilm producer and enhancer genes (mrkD, pgaABCD, fimH, treC, wzc, pilQ, and luxS) mainly in the hypervirulent strains. These hypervirulent strains also show a high number of resistance genes. The findings of this study underscore the critical need for the active surveillance of antimicrobial resistance and virulence determinants in K. pneumoniae. The coexistence of high levels of antibiotic resistance and virulence factors in these isolates poses a severe threat to public health, as it can lead to difficult-to-treat infections and increased morbidity and mortality. [ABSTRACT FROM AUTHOR]

Published
2025
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48. High-throughput barcoding method for the genetic surveillance of insecticide resistance and species identification in Anopheles gambiae complex malaria vectors

Author

Campos, Monica, Phelan, Jody, Spadar, Anton, Collins, Emma, Gonçalves, Adéritow, Pelloquin, Bethanie, Vaselli, Natasha Marcella, Meiwald, Anne, Clark, Emma, Stica, Caleb, Orsborne, James, Sylla, Moussa, Edi, Constant, Camara, Denka, Mohammed, Abdul Rahim, Afrane, Yaw Asare, Kristan, Mojca, Walker, Thomas, Gomez, Lara Ferrero, Messenger, Louisa A., Clark, Taane G., and Campino, Susana

Published
2022
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49. Genomic epidemiological analysis of Klebsiella pneumoniae from Portuguese hospitals reveals insights into circulating antimicrobial resistance

Author

Spadar, Anton, Phelan, Jody, Elias, Rita, Modesto, Ana, Caneiras, Cátia, Marques, Cátia, Lito, Luís, Pinto, Margarida, Cavaco-Silva, Patrícia, Ferreira, Helena, Pomba, Constança, Da Silva, Gabriela J., Saavedra, Maria José, Melo-Cristino, José, Duarte, Aida, Campino, Susana, Perdigão, João, and Clark, Taane G.

Published
2022
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