Chrispin Chaguza, PhD

• Akiko Iwasaki
• Albert Ko
• Andreas Coppi
• Bony De Kumar
• Carolina Lucas
• Chantal Vogels
• Chikondi Peno
• David Ferguson
• Kien Pham
• Marie-Louise Landry
• Miyu Moriyama
• Nathan Grubaugh
• Scott Roberts
• Sten H. Vermund
• Wade Schulz

Bacteria; Carrier State; Disease Outbreaks; Drug Resistance, Microbial; Opportunistic Infections; Phylogeny; Pneumococcal Infections; Pneumonia, Pneumococcal; Respiratory Tract Infections; Statistics as Topic; Streptococcal Infections; Virulence; Viruses; Molecular Epidemiology; Disease Transmission, Infectious; Evolution, Molecular; Computational Biology; Drug Resistance, Bacterial; Public Health Informatics; Genome-Wide Association Study; Microbiota; Data Science; Vaccine-Preventable Diseases

Antimicrobial Resistance; Disease Transmission; Global Health; Infectious Diseases; Respiratory Disease/Infections; Vaccines

• Population genomics of Group B Streptococcus reveals the genetics of neonatal disease onset and meningeal invasionChaguza C, Jamrozy D, Bijlsma M, Kuijpers T, van de Beek D, van der Ende A, Bentley S. Population genomics of Group B Streptococcus reveals the genetics of neonatal disease onset and meningeal invasion. Nature Communications 2022, 13: 4215. PMID: 35864107, PMCID: PMC9304382, DOI: 10.1038/s41467-022-31858-4.
• Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide CapsuleChaguza C, Andam CP, Harris SR, Cornick JE, Yang M, Bricio-Moreno L, Kamng’ona A, Parkhill J, French N, Heyderman RS, Kadioglu A, Everett DB, Bentley SD, Hanage WP. Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule. MBio 2016, 7: e01053-16. PMID: 27677790, PMCID: PMC5040112, DOI: 10.1128/mbio.01053-16.
• Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisationChaguza C, Senghore M, Bojang E, Gladstone RA, Lo SW, Tientcheu PE, Bancroft RE, Worwui A, Foster-Nyarko E, Ceesay F, Okoi C, McGee L, Klugman KP, Breiman RF, Barer MR, Adegbola RA, Antonio M, Bentley SD, Kwambana-Adams BA. Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation. Nature Communications 2020, 11: 3442. PMID: 32651390, PMCID: PMC7351774, DOI: 10.1038/s41467-020-17327-w.
• Development of an amplicon-based sequencing approach in response to the global emergence of mpoxChen N, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, Hall J, Ash S, Harrington R, Cofsky S, Clancy S, Kapsak C, Sevinsky J, Libuit K, Park D, Hemarajata P, Garrigues J, Green N, Sierra-Patev S, Carpenter-Azevedo K, Huard R, Pearson C, Incekara K, Nishimura C, Huang J, Gagnon E, Reever E, Razeq J, Muyombwe A, Borges V, Ferreira R, Sobral D, Duarte S, Santos D, Vieira L, Gomes J, Aquino C, Savino I, Felton K, Bajwa M, Hayward N, Miller H, Naumann A, Allman R, Greer N, Fall A, Mostafa H, McHugh M, Maloney D, Dewar R, Kenicer J, Parker A, Mathers K, Wild J, Cotton S, Templeton K, Churchwell G, Lee P, Pedrosa M, McGruder B, Schmedes S, Plumb M, Wang X, Barcellos R, Godinho F, Salvato R, Ceniseros A, Breban M, Grubaugh N, Gallagher G, Vogels C. Development of an amplicon-based sequencing approach in response to the global emergence of mpox. PLOS Biology 2023, 21: e3002151. PMID: 37310918, PMCID: PMC10263305, DOI: 10.1371/journal.pbio.3002151.
• Comparative whole genome analysis reveals re-emergence of human Wa-like and DS-1-like G3 rotaviruses after Rotarix vaccine introduction in MalawiMhango C, Banda A, Chinyama E, Mandolo J, Kumwenda O, Malamba-Banda C, Barnes K, Kumwenda B, Jambo K, Donato C, Esona M, Mwangi P, Steele A, Iturriza-Gomara M, Cunliffe N, Ndze V, Kamng'ona A, Dennis F, Nyaga M, Chaguza C, Jere K. Comparative whole genome analysis reveals re-emergence of human Wa-like and DS-1-like G3 rotaviruses after Rotarix vaccine introduction in Malawi. Virus Evolution 2023, 9: vead030. PMID: 37305707, PMCID: PMC10256189, DOI: 10.1093/ve/vead030.
• Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariantsMoriyama M, Lucas C, Monteiro V, Initiative Y, Iwasaki A, Chen N, Breban M, Hahn A, Pham K, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W, Vogels C, Grubaugh N. Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2221652120. PMID: 37036977, PMCID: PMC10120007, DOI: 10.1073/pnas.2221652120.
• Toward a global virus genomic surveillance networkHill V, Githinji G, Vogels C, Bento A, Chaguza C, Carrington C, Grubaugh N. Toward a global virus genomic surveillance network. Cell Host & Microbe 2023, 31: 861-873. PMID: 36921604, PMCID: PMC9986120, DOI: 10.1016/j.chom.2023.03.003.
• Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster doseFilardi B, Monteiro V, Schwartzmann P, do Prado Martins V, Zucca L, Baiocchi G, Malik A, Silva J, Hahn A, Chen N, Pham K, Pérez-Then E, Miric M, Brache V, Cochon L, Larocca R, Della Rosa Mendez R, Silveira D, Pinto A, Croda J, Yildirim I, Omer S, Ko A, Vermund S, Grubaugh N, Iwasaki A, Lucas C, Initiative Y, Vogels C, Breban M, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W. Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose. Science Translational Medicine 2023, 15: eade6023. PMID: 36791210, DOI: 10.1126/scitranslmed.ade6023.
• Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infectionChaguza C, Hahn A, Petrone M, Zhou S, Ferguson D, Breban M, Pham K, Peña-Hernández M, Castaldi C, Hill V, Initiative Y, Billig K, Earnest R, Fauver J, Kalinch C, Kerantzas N, Koch T, De Kumar B, Landry M, Ott I, Peaper D, Tikhonova I, Vogels C, Schulz W, Swanstrom R, Roberts S, Grubaugh N. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Reports Medicine 2023, 4: 100943. PMID: 36791724, PMCID: PMC9906997, DOI: 10.1016/j.xcrm.2023.100943.
• Novel Multilocus Sequence Typing and Global Sequence Clustering Schemes for Characterizing the Population Diversity of Streptococcus mitisKalizang’oma A, Kwambana-Adams B, Chan J, Viswanath A, Gori A, Richard D, Jolley K, Lees J, Goldblatt D, Beleza S, Bentley S, Heyderman R, Chaguza C. Novel Multilocus Sequence Typing and Global Sequence Clustering Schemes for Characterizing the Population Diversity of Streptococcus mitis. Journal Of Clinical Microbiology 2022, 61: e00802-22. PMID: 36515506, PMCID: PMC9879099, DOI: 10.1128/jcm.00802-22.
• Daily Rapid Antigen Exit Testing to Tailor University COVID-19 Isolation Policy - Volume 28, Number 12—December 2022 - Emerging Infectious Diseases journal - CDCEarnest R, Chen C, Chaguza C, Hahn A, Grubaugh N, Wilson M, . Daily Rapid Antigen Exit Testing to Tailor University COVID-19 Isolation Policy - Volume 28, Number 12—December 2022 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2022, 28: 2455-2462. PMID: 36417936, PMCID: PMC9707582, DOI: 10.3201/eid2812.220969.
• Zooming into the structure of the microbiomeMurray G, Chaguza C. Zooming into the structure of the microbiome. Nature Reviews Microbiology 2022, 21: 5-5. PMID: 36451022, DOI: 10.1038/s41579-022-00834-6.
• Pneumococcal within-host diversity during colonization, transmission and treatmentTonkin-Hill G, Ling C, Chaguza C, Salter SJ, Hinfonthong P, Nikolaou E, Tate N, Pastusiak A, Turner C, Chewapreecha C, Frost SDW, Corander J, Croucher NJ, Turner P, Bentley SD. Pneumococcal within-host diversity during colonization, transmission and treatment. Nature Microbiology 2022, 7: 1791-1804. PMID: 36216891, PMCID: PMC9613479, DOI: 10.1038/s41564-022-01238-1.
• Evaluation of Dried Blood and Cerebrospinal Fluid Filter Paper Spots for Storing and Transporting Clinical Material for the Molecular Diagnosis of Invasive Meningococcal DiseaseKwambana-Adams B, Clark S, Tay N, Agbla S, Chaguza C, Kagucia E, Borrow R, Heyderman R. Evaluation of Dried Blood and Cerebrospinal Fluid Filter Paper Spots for Storing and Transporting Clinical Material for the Molecular Diagnosis of Invasive Meningococcal Disease. International Journal Of Molecular Sciences 2022, 23: 11879. PMID: 36233182, PMCID: PMC9569512, DOI: 10.3390/ijms231911879.
• Prophage-encoded immune evasion factors are critical for Staphylococcus aureus host infection, switching, and adaptationChaguza C, Smith J, Bruce S, Gibson R, Martin I, Andam C. Prophage-encoded immune evasion factors are critical for Staphylococcus aureus host infection, switching, and adaptation. Cell Genomics 2022, 2: 100194. PMID: 36465278, PMCID: PMC9718559, DOI: 10.1016/j.xgen.2022.100194.
• Comparative genomics of disease and carriage serotype 1 pneumococciChaguza C, Ebruke C, Senghore M, Lo S, Tientcheu P, Gladstone R, Tonkin-Hill G, Cornick J, Yang M, Worwui A, McGee L, Breiman R, Klugman K, Kadioglu A, Everett D, Mackenzie G, Croucher N, Roca A, Kwambana-Adams B, Antonio M, Bentley S. Comparative genomics of disease and carriage serotype 1 pneumococci. Genome Biology And Evolution 2022, 14: evac052-. PMID: 35439297, PMCID: PMC9048925, DOI: 10.1093/gbe/evac052.
• A Streptococcus pneumoniae lineage usually associated with pneumococcal conjugate vaccine (PCV) serotypes is the most common cause of serotype 35B invasive disease in South Africa, following routine use of PCVNdlangisa K, du Plessis M, Lo S, de Gouveia L, Chaguza C, Antonio M, Kwambana-Adams B, Cornick J, Everett D, Dagan R, Hawkins P, Beall B, Corso A, Grassi Almeida S, Ochoa T, Obaro S, Shakoor S, Donkor E, Gladstone R, Ho P, Paragi M, Doiphode S, Srifuengfung S, Ford R, Moïsi J, Saha S, Bigogo G, Sigauque B, Eser Ö, Elmdaghri N, Titov L, Turner P, Kumar K, Kandasamy R, Egorova E, Ip M, Breiman R, Klugman K, McGee L, Bentley S, von Gottberg A, The Global Pneumococcal Sequencing Consortium. A Streptococcus pneumoniae lineage usually associated with pneumococcal conjugate vaccine (PCV) serotypes is the most common cause of serotype 35B invasive disease in South Africa, following routine use of PCV. Microbial Genomics 2022, 8: 000746. PMID: 35384831, PMCID: PMC9453074, DOI: 10.1099/mgen.0.000746.
• Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated personsChaguza C, Coppi A, Earnest R, Ferguson D, Kerantzas N, Warner F, Young HP, Breban MI, Billig K, Koch RT, Pham K, Kalinich CC, Ott IM, Fauver JR, Hahn AM, Tikhonova IR, Castaldi C, De Kumar B, Pettker CM, Warren JL, Weinberger DM, Landry ML, Peaper DR, Schulz W, Vogels CBF, Grubaugh ND. Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons. Med 2022, 3: 325-334.e4. PMID: 35399324, PMCID: PMC8983481, DOI: 10.1016/j.medj.2022.03.010.
• Author Correction: Hypervirulent pneumococcal serotype 1 harbours two pneumolysin variants with differential haemolytic activityPanagiotou S, Chaguza C, Yahya R, Audshasai T, Baltazar M, Ressel L, Khandaker S, Alsahag M, Mitchell T, Prudhomme M, Kadioglu A, Yang M. Author Correction: Hypervirulent pneumococcal serotype 1 harbours two pneumolysin variants with differential haemolytic activity. Scientific Reports 2022, 12: 5099. PMID: 35332175, PMCID: PMC8948227, DOI: 10.1038/s41598-022-08813-w.
• A new perspective on ancient Mitis group streptococcal geneticsBelman S, Chaguza C, Kumar N, Lo S, Bentley SD. A new perspective on ancient Mitis group streptococcal genetics. Microbial Genomics 2022, 8: 000753. PMID: 35225216, PMCID: PMC8942026, DOI: 10.1099/mgen.0.000753.
• Widespread sharing of pneumococcal strains in a rural African setting: proximate villages are more likely to share similar strains that are carried at multiple timepointsSenghore M, Chaguza C, Bojang E, Tientcheu P, Bancroft R, Lo S, Gladstone R, McGee L, Worwui A, Foster-Nyarko E, Ceesay F, Okoi C, Klugman K, Breiman R, Bentley S, Adegbola R, Antonio M, Hanage W, Kwambana-Adams B. Widespread sharing of pneumococcal strains in a rural African setting: proximate villages are more likely to share similar strains that are carried at multiple timepoints. Microbial Genomics 2022, 8: 000732. PMID: 35119356, PMCID: PMC8942022, DOI: 10.1099/mgen.0.000732.
• Serotype 1 pneumococcus: epidemiology, genomics, and disease mechanismsChaguza C, Yang M, Jacques L, Bentley S, Kadioglu A. Serotype 1 pneumococcus: epidemiology, genomics, and disease mechanisms. Trends In Microbiology 2021, 30: 581-592. PMID: 34949516, PMCID: PMC7613904, DOI: 10.1016/j.tim.2021.11.007.
• RCandy: an R package for visualizing homologous recombinations in bacterial genomesChaguza C, Tonkin-Hill G, Lo S, Hadfield J, Croucher N, Harris S, Bentley S. RCandy: an R package for visualizing homologous recombinations in bacterial genomes. Bioinformatics 2021, 38: 1450-1451. PMID: 34864895, PMCID: PMC8826011, DOI: 10.1093/bioinformatics/btab814.
• Erratum for Betts et al., “Complete Genome Sequence of Streptococcus pneumoniae Strain BVJ1JL, a Serotype 1 Carriage Isolate from Malawi”Betts M, Jarvis S, Jeffries A, Gori A, Chaguza C, Msefula J, Weight CM, Kwambana-Adams B, French N, Swarthout TD, Brown JS, Heyderman RS. Erratum for Betts et al., “Complete Genome Sequence of Streptococcus pneumoniae Strain BVJ1JL, a Serotype 1 Carriage Isolate from Malawi”. Microbiology Resource Announcements 2021, 10: e00985-21. PMID: 34672715, PMCID: PMC8530034, DOI: 10.1128/mra.00985-21.
• Complete Genome Sequence of Streptococcus pneumoniae Strain BVJ1JL, a Serotype 1 Carriage Isolate from MalawiBetts M, Jarvis S, Jeffries A, Gori A, Chaguza C, Msefula J, Weight CM, Kwambana-Adams B, French N, Swarthout TD, Brown JS, Heyderman RS. Complete Genome Sequence of Streptococcus pneumoniae Strain BVJ1JL, a Serotype 1 Carriage Isolate from Malawi. Microbiology Resource Announcements 2021, 10: e00715-21. PMID: 34591678, PMCID: PMC8483660, DOI: 10.1128/mra.00715-21.
• Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitisKalizang'oma A, Chaguza C, Gori A, Davison C, Beleza S, Antonio M, Beall B, Goldblatt D, Kwambana-Adams B, Bentley SD, Heyderman RS. Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis. Microbial Genomics 2021, 7: 000622. PMID: 34550067, PMCID: PMC8715442, DOI: 10.1099/mgen.0.000622.
• Author Correction: Hypervirulent pneumococcal serotype 1 harbours two pneumolysin variants with differential haemolytic activityPanagiotou S, Chaguza C, Yahya R, Audshasai T, Baltazar M, Ressel L, Khandaker S, Alsahag M, Mitchell T, Prudhomme M, Kadioglu A, Yang M. Author Correction: Hypervirulent pneumococcal serotype 1 harbours two pneumolysin variants with differential haemolytic activity. Scientific Reports 2021, 11: 6658. PMID: 33731755, PMCID: PMC7969593, DOI: 10.1038/s41598-021-86214-1.
• Metagenomics for surveillance of respiratory pathogensCarr VR, Chaguza C. Metagenomics for surveillance of respiratory pathogens. Nature Reviews Microbiology 2021, 19: 285-285. PMID: 33707741, PMCID: PMC7950416, DOI: 10.1038/s41579-021-00541-8.
• Pneumococcal colonisation and virulence factors identified via experimental evolution in infection modelsGreen AE, Howarth D, Chaguza C, Echlin H, Langendonk RF, Munro C, Barton TE, Hinton J, Bentley SD, Rosch JW, Neill DR. Pneumococcal colonisation and virulence factors identified via experimental evolution in infection models. Molecular Biology And Evolution 2021, 38: msab018-. PMID: 33502519, PMCID: PMC8136498, DOI: 10.1093/molbev/msab018.
• Carriage Dynamics of Pneumococcal Serotypes in Naturally Colonized Infants in a Rural African Setting During the First Year of LifeChaguza C, Senghore M, Bojang E, Lo SW, Ebruke C, Gladstone RA, Tientcheu PE, Bancroft RE, Worwui A, Foster-Nyarko E, Ceesay F, Okoi C, McGee L, Klugman KP, Breiman RF, Barer MR, Adegbola RA, Antonio M, Bentley SD, Kwambana-Adams BA. Carriage Dynamics of Pneumococcal Serotypes in Naturally Colonized Infants in a Rural African Setting During the First Year of Life. Frontiers In Pediatrics 2021, 8: 587730. PMID: 33489998, PMCID: PMC7820366, DOI: 10.3389/fped.2020.587730.
• Whole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, MoroccoNzoyikorera N, Diawara I, Fresia P, Maaloum F, Katfy K, Nayme K, Maaloum M, Cornick J, Chaguza C, Timinouni M, Belabess H, Zerouali K, Elmdaghri N. Whole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, Morocco. BMC Genomics 2021, 22: 39. PMID: 33413118, PMCID: PMC7792055, DOI: 10.1186/s12864-020-07316-0.
• Lower Density and Shorter Duration of Nasopharyngeal Carriage by Pneumococcal Serotype 1 (ST217) May Explain Its Increased Invasiveness over Other SerotypesBricio-Moreno L, Chaguza C, Yahya R, Shears RK, Cornick JE, Hokamp K, Yang M, Neill DR, French N, Hinton JCD, Everett DB, Kadioglu A. Lower Density and Shorter Duration of Nasopharyngeal Carriage by Pneumococcal Serotype 1 (ST217) May Explain Its Increased Invasiveness over Other Serotypes. MBio 2020, 11: e00814-20. PMID: 33293378, PMCID: PMC7733939, DOI: 10.1128/mbio.00814-20.
• Using genomics to improve preparedness and response of future epidemics or pandemics in AfricaChaguza C, Nyaga MM, Mwenda JM, Esona MD, Jere KC. Using genomics to improve preparedness and response of future epidemics or pandemics in Africa. The Lancet Microbe 2020, 1: e275-e276. PMID: 33345202, PMCID: PMC7729821, DOI: 10.1016/s2666-5247(20)30169-5.
• Hypervirulent pneumococcal serotype 1 harbours two pneumolysin variants with differential haemolytic activityPanagiotou S, Chaguza C, Yahya R, Audshasai T, Baltazar M, Ressel L, Khandaker S, Alsahag M, Mitchell TJ, Prudhomme M, Kadioglu A, Yang M. Hypervirulent pneumococcal serotype 1 harbours two pneumolysin variants with differential haemolytic activity. Scientific Reports 2020, 10: 17313. PMID: 33057054, PMCID: PMC7560715, DOI: 10.1038/s41598-020-73454-w.
• Rotavirus Genotypes in Hospitalized Children with Acute Gastroenteritis Before and After Rotavirus Vaccine Introduction in Blantyre, Malawi, 1997 – 2019Mhango C, Mandolo JJ, Chinyama E, Wachepa R, Kanjerwa O, Malamba-Banda C, Matambo PB, Barnes KG, Chaguza C, Shawa IT, Nyaga MM, Hungerford D, Parashar UD, Pitzer VE, Kamng’ona A, Iturriza-Gomara M, Cunliffe NA, Jere KC. Rotavirus Genotypes in Hospitalized Children with Acute Gastroenteritis Before and After Rotavirus Vaccine Introduction in Blantyre, Malawi, 1997 – 2019. The Journal Of Infectious Diseases 2020, 225: jiaa616-. PMID: 33033832, PMCID: PMC9200156, DOI: 10.1093/infdis/jiaa616.
• Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropismChaguza C, Yang M, Cornick JE, du Plessis M, Gladstone RA, Kwambana-Adams BA, Lo SW, Ebruke C, Tonkin-Hill G, Peno C, Senghore M, Obaro SK, Ousmane S, Pluschke G, Collard JM, Sigaùque B, French N, Klugman KP, Heyderman RS, McGee L, Antonio M, Breiman RF, von Gottberg A, Everett DB, Kadioglu A, Bentley SD. Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism. Communications Biology 2020, 3: 559. PMID: 33033372, PMCID: PMC7545184, DOI: 10.1038/s42003-020-01290-9.
• Bacterial survival: evolve and adapt or perishChaguza C. Bacterial survival: evolve and adapt or perish. Nature Reviews Microbiology 2019, 18: 5-5. PMID: 31748737, DOI: 10.1038/s41579-019-0303-5.
• Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic dataChaguza C, Heinsbroek E, Gladstone RA, Tafatatha T, Alaerts M, Peno C, Cornick JE, Musicha P, Bar-Zeev N, Kamng’ona A, Kadioglu A, McGee L, Hanage WP, Breiman RF, Heyderman RS, French N, Everett DB, Bentley SD. Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data. Clinical Infectious Diseases 2019, 70: 1294-1303. PMID: 31094423, PMCID: PMC7768739, DOI: 10.1093/cid/ciz404.
• Molecular epidemiology of G12 rotavirus strains during eight consecutive epidemic seasons in the Basque Country (North of Spain), 2010–2018Arana A, Jere KC, Chaguza C, Montes M, Alkorta M, Iturriza-Gomara M, Cilla G. Molecular epidemiology of G12 rotavirus strains during eight consecutive epidemic seasons in the Basque Country (North of Spain), 2010–2018. Infection Genetics And Evolution 2019, 71: 67-75. PMID: 30905774, DOI: 10.1016/j.meegid.2019.03.016.
• Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineagesMusicha P, Msefula CL, Mather AE, Chaguza C, Cain AK, Peno C, Kallonen T, Khonga M, Denis B, Gray KJ, Heyderman RS, Thomson NR, Everett DB, Feasey NA. Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages. Journal Of Antimicrobial Chemotherapy 2019, 74: 1223-1232. PMID: 30778540, PMCID: PMC6477993, DOI: 10.1093/jac/dkz032.
• Emergence of Double- and Triple-Gene Reassortant G1P[8] Rotaviruses Possessing a DS-1-Like Backbone after Rotavirus Vaccine Introduction in MalawiJere KC, Chaguza C, Bar-Zeev N, Lowe J, Peno C, Kumwenda B, Nakagomi O, Tate JE, Parashar UD, Heyderman RS, French N, Cunliffe NA, Iturriza-Gomara M. Emergence of Double- and Triple-Gene Reassortant G1P[8] Rotaviruses Possessing a DS-1-Like Backbone after Rotavirus Vaccine Introduction in Malawi. Journal Of Virology 2018, 92: e01246-17. PMID: 29142125, PMCID: PMC5774894, DOI: 10.1128/jvi.01246-17.
• Comparative Genomic Analysis and In Vivo Modeling of Streptococcus pneumoniae ST3081 and ST618 Isolates Reveal Key Genetic and Phenotypic Differences Contributing to Clonal Replacement of Serotype 1 in The GambiaBricio-Moreno L, Ebruke C, Chaguza C, Cornick J, Kwambana-Adams B, Yang M, Mackenzie G, Wren BW, Everett D, Antonio M, Kadioglu A. Comparative Genomic Analysis and In Vivo Modeling of Streptococcus pneumoniae ST3081 and ST618 Isolates Reveal Key Genetic and Phenotypic Differences Contributing to Clonal Replacement of Serotype 1 in The Gambia. The Journal Of Infectious Diseases 2017, 216: 1318-1327. PMID: 28968897, PMCID: PMC5853340, DOI: 10.1093/infdis/jix472.
• Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in MalawiChaguza C, Cornick JE, Andam CP, Gladstone RA, Alaerts M, Musicha P, Peno C, Bar-Zeev N, Kamng'ona AW, Kiran AM, Msefula CL, McGee L, Breiman RF, Kadioglu A, French N, Heyderman RS, Hanage WP, Bentley SD, Everett DB. Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in Malawi. Vaccine 2017, 35: 4594-4602. PMID: 28711389, PMCID: PMC5571440, DOI: 10.1016/j.vaccine.2017.07.009.
• Adaptation... that's what you need?Chaguza C, Bentley SD. Adaptation... that's what you need? Nature Reviews Microbiology 2017, 15: 452-452. PMID: 28690321, DOI: 10.1038/nrmicro.2017.78.
• Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African settingMusicha P, Feasey NA, Cain AK, Kallonen T, Chaguza C, Peno C, Khonga M, Thompson S, Gray KJ, Mather AE, Heyderman RS, Everett DB, Thomson NR, Msefula CL. Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting. Journal Of Antimicrobial Chemotherapy 2017, 72: 1602-1609. PMID: 28333330, PMCID: PMC5437524, DOI: 10.1093/jac/dkx058.
• Genomic Epidemiology of Penicillin-Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United StatesAndam CP, Mitchell PK, Callendrello A, Chang Q, Corander J, Chaguza C, McGee L, Beall BW, Hanage WP. Genomic Epidemiology of Penicillin-Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United States. Journal Of Clinical Microbiology 2017, 55: 1104-1115. PMID: 28100596, PMCID: PMC5377837, DOI: 10.1128/jcm.02453-16.
• The global distribution and diversity of protein vaccine candidate antigens in the highly virulent Streptococcus pnuemoniae serotype 1Cornick JE, Bishop Ö, Yalcin F, Kiran AM, Kumwenda B, Chaguza C, Govindpershad S, Ousmane S, Senghore M, du Plessis M, Pluschke G, Ebruke C, McGee L, Sigaùque B, Collard JM, Bentley SD, Kadioglu A, Antonio M, von Gottberg A, French N, Klugman KP, Heyderman RS, Alderson M, Everett DB, consortium F. The global distribution and diversity of protein vaccine candidate antigens in the highly virulent Streptococcus pnuemoniae serotype 1. Vaccine 2017, 35: 972-980. PMID: 28081968, PMCID: PMC5287219, DOI: 10.1016/j.vaccine.2016.12.037.
• Understanding pneumococcal serotype 1 biology through population genomic analysisChaguza C, Cornick JE, Harris SR, Andam CP, Bricio-Moreno L, Yang M, Yalcin F, Ousmane S, Govindpersad S, Senghore M, Ebruke C, Du Plessis M, Kiran AM, Pluschke G, Sigauque B, McGee L, Klugman KP, Turner P, Corander J, Parkhill J, Collard JM, Antonio M, von Gottberg A, Heyderman RS, French N, Kadioglu A, Hanage WP, Everett DB, Bentley SD, for the PAGe Consortium. Understanding pneumococcal serotype 1 biology through population genomic analysis. BMC Infectious Diseases 2016, 16: 649. PMID: 27821148, PMCID: PMC5100261, DOI: 10.1186/s12879-016-1987-z.
• Erratum for Kulohoma et al., Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core GenomeKulohoma B, Cornick J, Chaguza C, Yalcin F, Harris S, Gray K, Kiran A, Molyneux E, French N, Parkhill J, Faragher B, Everett D, Bentley S, Heyderman R. Erratum for Kulohoma et al., Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome. Infection And Immunity 2015, 83: 4896-4896. PMID: 26556879, PMCID: PMC4645377, DOI: 10.1128/iai.01156-15.
• Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core GenomeKulohoma BW, Cornick JE, Chaguza C, Yalcin F, Harris SR, Gray KJ, Kiran AM, Molyneux E, French N, Parkhill J, Faragher BE, Everett DB, Bentley SD, Heyderman RS. Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome. Infection And Immunity 2015, 83: 4165-4173. PMID: 26259813, PMCID: PMC4567637, DOI: 10.1128/iai.00814-15.
• Region-specific diversification of the highly virulent serotype 1 Streptococcus pneumoniaeCornick JE, Chaguza C, Harris SR, Yalcin F, Senghore M, Kiran AM, Govindpershad S, Ousmane S, Du Plessis M, Pluschke G, Ebruke C, McGee L, Sigaùque B, Collard JM, Antonio M, von Gottberg A, French N, Klugman KP, Heyderman RS, Bentley SD, Everett DB, Consortium F. Region-specific diversification of the highly virulent serotype 1 Streptococcus pneumoniae. Microbial Genomics 2015, 1: e000027. PMID: 28348812, PMCID: PMC5320570, DOI: 10.1099/mgen.0.000027.
• High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian childrenKamng’ona A, Hinds J, Bar-Zeev N, Gould KA, Chaguza C, Msefula C, Cornick JE, Kulohoma BW, Gray K, Bentley SD, French N, Heyderman RS, Everett DB. High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian children. BMC Infectious Diseases 2015, 15: 234. PMID: 26088623, PMCID: PMC4474563, DOI: 10.1186/s12879-015-0980-2.
• Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniaeChaguza C, Cornick JE, Everett DB. Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae. Computational And Structural Biotechnology Journal 2015, 13: 241-247. PMID: 25904996, PMCID: PMC4404416, DOI: 10.1016/j.csbj.2015.03.007.