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The genomic epidemiology of shigellosis in South Africa
As a leading cause of diarrhoeal mortality and morbidity, authors examine the epidemiology and genome dynamics of shigellosis in South Africa, utilising whole genome sequence analysis.
- George E. Stenhouse
- , Karen H. Keddy
- & Kate S. Baker
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Distributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century
Core genome multilocus sequence typing (cgMLST) is used to classify bacterial strains for epidemiological applications. Here, the authors describe a distributed cgMLST scheme that does not require a central database of allelic sequences, and apply it to study evolutionary patterns of epidemic and endemic strains of the genus Neisseria.
- Ling Zhong
- , Menghan Zhang
- & Zhemin Zhou
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The evolution and international spread of extensively drug resistant Shigella sonnei
An increase in shigellosis cases among men who have sex with men in the United Kingdom has been linked to an extensively drug-resistant strain of Shigella sonnei. In this genomic epidemiology study, the authors investigate the genetic basis, evolutionary history, and international dissemination of the outbreak strain.
- Lewis C. E. Mason
- , David R. Greig
- & Kate S. Baker
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A Shigella sonnei clone with extensive drug resistance associated with waterborne outbreaks in China
Shigella sonnei is a major contributor to the global burden of dysenteric diarrhoea in developed countries. In this work, authors report a S. sonnei clone which has caused numerous waterborne shigellosis outbreaks in China from 2015 to 2020.
- Shaofu Qiu
- , Kangkang Liu
- & Hongbin Song
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Inflammation and immune activation are associated with risk of Mycobacterium tuberculosis infection in BCG-vaccinated infants
The identification of immune correlates of protection in humans would inform on the design and development of tuberculosis vaccine candidates. In this work, authors examine samples collected from South African infants, to determine whether the correlates of risk of tuberculosis disease, previously identified in this population, are also correlates of risk of M. tuberculosis infection.
- Iman Satti
- , Rachel E. Wittenberg
- & Helen McShane
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A Sarcina bacterium linked to lethal disease in sanctuary chimpanzees in Sierra Leone
Infections with bacteria of the genus Sarcina are associated with gastric diseases of unclear etiology. Here, Owens et al. show that infection with a distinct Sarcina species is strongly associated with a lethal disease that affects sanctuary chimpanzees in Sierra Leone.
- Leah A. Owens
- , Barbara Colitti
- & Tony L. Goldberg
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Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines
Whole-genome sequencing (WGS) can support drug resistance surveillance, but is rare in low- and middle-income countries. Here, the authors integrate WGS within the national antimicrobial resistance surveillance program in the Philippines and conduct a retrospective sequencing survey to characterize bacterial populations and dissect resistance phenotypes.
- Silvia Argimón
- , Melissa A. L. Masim
- & Celia C. Carlos
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High residual carriage of vaccine-serotype Streptococcus pneumoniae after introduction of pneumococcal conjugate vaccine in Malawi
Impact of pneumococcal conjugate vaccines (PCV) in controlling carriage needs to be evaluated to inform vaccine policy. Here, Swarthout et al. show in a prospective rolling cross-sectional study in Malawi a high residual prevalence of vaccine-serotype S. pneumoniae 7 years after PCV introduction.
- Todd D. Swarthout
- , Claudio Fronterre
- & Robert S. Heyderman
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Bridging of Neisseria gonorrhoeae lineages across sexual networks in the HIV pre-exposure prophylaxis era
Here, Williamson et al. combine epidemiological and genomic analysis of 2,186 Neisseria gonorrhoeae isolates from Australia and show that men who have sex with men and women are a possible ‘bridging’ population between men who have sex with men and heterosexuals.
- Deborah A. Williamson
- , Eric P. F. Chow
- & Benjamin P. Howden
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Genomic structure and diversity of Plasmodium falciparum in Southeast Asia reveal recent parasite migration patterns
Understanding genomic variation in Plasmodium falciparum parasites and inferring migration patterns can guide malaria elimination strategies. Using genome-wide data for 1722 parasites collected from 54 districts, the authors use identity-by-descent approaches to estimate regional parasite migration and spread of artemisinin drug resistance.
- Amol C. Shetty
- , Christopher G. Jacob
- & Marie A. Onyamboko
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Plasmodium falciparum sexual differentiation in malaria patients is associated with host factors and GDV1-dependent genes
Here, the authors quantify early gametocyte-committed ring (gc-ring) stage Plasmodium falciparum parasites in 260 malaria patients 10 days before maturation to transmissible stage V gametocytes, and show that the ratio of circulating gc-rings is positively correlated with parasitemia and negatively correlated with body temperature.
- Miho Usui
- , Surendra K. Prajapati
- & Kim C. Williamson
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Mathematical modelling of the impact of expanding levels of malaria control interventions on Plasmodium vivax
Plasmodium vivax poses a unique challenge for malaria elimination worldwide. Here, White et al. develop an individual-based mathematical model of P. vivax transmission and evaluate intervention strategies in Papua New Guinea.
- Michael T. White
- , Patrick Walker
- & Ivo Mueller
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Estimating spatiotemporally varying malaria reproduction numbers in a near elimination setting
Twenty one countries have been identified for malaria elimination by 2020 and their progress needs to be constantly evaluated. Here, the authors present a method that estimates individual reproduction numbers and their variation through time and space and use it to monitor elimination success in El Salvador between 2010 and 2016.
- Isobel Routledge
- , José Eduardo Romero Chevéz
- & Samir Bhatt
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Plasmepsin II–III copy number accounts for bimodal piperaquine resistance among Cambodian Plasmodium falciparum
Piperaquine (PPQ) resistance of Plasmodium is an increasing problem. Here, Bopp et al. find a bimodal dose−response curve of Cambodian isolates exposed to PPQ, with the area under the curve correlating with in vitro PPQ resistance, and show the importance of Plasmepsin II–III copy number to PPQ resistance.
- Selina Bopp
- , Pamela Magistrado
- & Sarah K. Volkman
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Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock
The role of wild elk in the spread and persistence of bovine brucellosis in the Great Yellowstone area is unclear. Here, Kamath et al. analyse the genomic sequences of 245 Brucella abortusisolates from elk, bison and cattle, supporting the idea that elk is an important reservoir and source of livestock infections.
- Pauline L. Kamath
- , Jeffrey T. Foster
- & Paul C. Cross
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Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe
Tuberculosis was once a major killer in Europe. Here the authors use metagenomics to obtain genomic sequences of Mycobacterium tuberculosisfrom human remains from eighteenth-century Hungary, revealing mixed infections within individuals as well as presence of the same strain in two individuals.
- Gemma L. Kay
- , Martin J. Sergeant
- & Mark J. Pallen
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Evolution and emergence of infectious diseases in theoretical and real-world networks
The continual evolution of pathogens makes infectious disease control very challenging. Here the authors examine how host population structure influences disease evolution, and show that heterogeneous contact networks lower the fixation probability of newly arising pathogen strains.
- Gabriel E. Leventhal
- , Alison L. Hill
- & Sebastian Bonhoeffer
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Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline
Group B streptococci (GBS) started causing serious infections in newborn babies in the 1960s. Here, the authors show that the emergence of GBS diseases was associated with worldwide dissemination of a few clones that were resistant to tetracycline, an antibiotic that became widely used in the 1950s.
- Violette Da Cunha
- , Mark R. Davies
- & Philippe Glaser
Global emergence of a hypervirulent carbapenem-resistant Escherichia coli ST410 clone