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1. Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape

Author

Muloi, Dishon M., Wee, Bryan A., McClean, Deirdre M. H., Ward, Melissa J., Pankhurst, Louise, Phan, Hang, Ivens, Alasdair C., Kivali, Velma, Kiyong’a, Alice, Ndinda, Christine, Gitahi, Nduhiu, Ouko, Tom, Hassell, James M., Imboma, Titus, Akoko, James, Murungi, Maurice K., Njoroge, Samuel M., Muinde, Patrick, Nakamura, Yukiko, Alumasa, Lorren, Furmaga, Erin, Kaitho, Titus, Öhgren, Elin M., Amanya, Fredrick, Ogendo, Allan, Wilson, Daniel J., Bettridge, Judy M., Kiiru, John, Kyobutungi, Catherine, Tacoli, Cecila, Kang’ethe, Erastus K., Davila, Julio D., Kariuki, Samuel, Robinson, Timothy P., Rushton, Jonathan, Woolhouse, Mark E. J., and Fèvre, Eric M.

Published
2022
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2. Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya

Author

Muloi, Dishon M., Hassell, James M., Wee, Bryan A., Ward, Melissa J., Bettridge, Judy M., Kivali, Velma, Kiyong’a, Alice, Ndinda, Christine, Gitahi, Nduhiu, Ouko, Tom, Imboma, Titus, Akoko, James, Murungi, Maurice K., Njoroge, Samuel M., Muinde, Patrick, Alumasa, Lorren, Kaitho, Titus, Amanya, Fredrick, Ogendo, Allan, van Bunnik, Bram A. D., Kiiru, John, Robinson, Timothy P., Kang’ethe, Erastus K., Kariuki, Samuel, Pedersen, Amy B., Fèvre, Eric M., and Woolhouse, Mark E. J.

Published
2022
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5. HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations.

Author

Faria, Nuno R, Rambaut, Andrew, Suchard, Marc A, Baele, Guy, Bedford, Trevor, Ward, Melissa J, Tatem, Andrew J, Sousa, João D, Arinaminpathy, Nimalan, Pépin, Jacques, Posada, David, Peeters, Martine, Pybus, Oliver G, and Lemey, Philippe

Subjects
Humans, HIV-1, Communicable Diseases, Emerging, Acquired Immunodeficiency Syndrome, Population Dynamics, Evolution, Molecular, Phylogeny, Recombination, Genetic, Urbanization, History, 20th Century, History, 21st Century, Democratic Republic of the Congo, Pandemics, Communicable Diseases, Emerging, Evolution, Molecular, Recombination, Genetic, History, 20th Century, 21st Century, General Science & Technology
Abstract

Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa (in what is now the Democratic Republic of Congo) was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and nonpandemic group O were similar until ~1960, after which group M underwent an epidemiological transition and outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and emphasize the role of social changes and transport networks in the establishment of this virus in human populations.

Published
2014

7. Epidemiological connectivity between humans and animals across an urban landscape

Author

Hassell, James M., primary, Muloi, Dishon M., additional, VanderWaal, Kimberly L., additional, Ward, Melissa J., additional, Bettridge, Judy, additional, Gitahi, Nduhiu, additional, Ouko, Tom, additional, Imboma, Titus, additional, Akoko, James, additional, Karani, Maurice, additional, Muinde, Patrick, additional, Nakamura, Yukiko, additional, Alumasa, Lorren, additional, Furmaga, Erin, additional, Kaitho, Titus, additional, Amanya, Fredrick, additional, Ogendo, Allan, additional, Fava, Francesco, additional, Wee, Bryan A., additional, Phan, Hang, additional, Kiiru, John, additional, Kang’ethe, Erastus, additional, Kariuki, Sam, additional, Robinson, Timothy, additional, Begon, Michael, additional, Woolhouse, Mark E. J., additional, and Fèvre, Eric M., additional

Published
2023
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8. Epidemiological connectivity between humans and animals across an urban landscape

Author

Hassell, James M, Muloi, Dishon, VanderWaal, Kimberly L, Ward, Melissa J., Bettridge, Judy, Gitahi, Nduhiu, Ouko, Tom, Imboma, Titus, Akoko, James, Karani, Maurice, Muinde, Patrick, Nakamura, Yukiko, Alumasa, Lorren, Furmaga, Erin, Kaitho, Titus, Amanya, Fredrick, Ogendo, Allan, Fava, Francesco, Wee, Bryan A, Phan, Hang, Kiiru, John, Kang’ethe, Erastus, Kariuki, Sam, Robinson, Timothy, Begon, Michael, Woolhouse, Mark E. J., and Fevre, Eric M.

Subjects
one health, disease ecology, interface, urbanization, pathogen spillover
Abstract

Urbanization is predicted to be a key driver of disease emergence through human exposure to novel, animal-borne pathogens. However, while we suspect that urban landscapes are primed to expose people to novel animal-borne diseases, evidence for the mechanisms by which this occurs is lacking. To address this, we studied how bacterial genes are shared between wild animals, livestock, and humans (n = 1,428) across Nairobi, Kenya—one of the world’s most rapidly developing cities. Applying a multilayer network framework, we show that low biodiversity (of both natural habitat and vertebrate wildlife communities), coupled with livestock management practices and more densely populated urban environments, promotes sharing of Escherichia coli–borne bacterial mobile genetic elements between animals and humans. These results provide empirical support for hypotheses linking resource provision, the biological simplification of urban landscapes, and human and livestock demography to urban dynamics of cross-species pathogen transmission at a landscape scale. Urban areas where high densities of people and livestock live in close association with synanthropes (species such as rodents that are more competent reservoirs for zoonotic pathogens) should be prioritized for disease surveillance and control.

Published
2023
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9. Additional file 1 of Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya

Author

Muloi, Dishon M., Hassell, James M., Wee, Bryan A., Ward, Melissa J., Bettridge, Judy M., Kivali, Velma, Kiyong’a, Alice, Ndinda, Christine, Gitahi, Nduhiu, Ouko, Tom, Imboma, Titus, Akoko, James, Murungi, Maurice K., Njoroge, Samuel M., Muinde, Patrick, Alumasa, Lorren, Kaitho, Titus, Amanya, Fredrick, Ogendo, Allan, van Bunnik, Bram A. D., Kiiru, John, Robinson, Timothy P., Kang’ethe, Erastus K., Kariuki, Samuel, Pedersen, Amy B., Fèvre, Eric M., and Woolhouse, Mark E. J.

Abstract

Additional file 1.

Published
2023
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10. Draft Genome Sequence of an Enterotoxigenic Escherichia coli Strain Carrying Genes for Colonization Surface Antigen 13 and a Heat-Labile Toxin

Author

Njoroge, Samuel M., primary, Madé, Laure F., additional, von Mentzer, Astrid, additional, Kulohoma, Benard W., additional, Kamanu, Timothy K., additional, Ouko, Tom T., additional, Kiiru, John, additional, Ward, Melissa J., additional, Thomson, Nicholas R., additional, Fèvre, Eric M., additional, Woolhouse, Mark, additional, and Kariuki, Samuel, additional

Published
2022
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15. Phylodynamics of infectious disease epidemics

Author

Volz, Erik M., Pond, Sergei L. Kosakovsky, Ward, Melissa J., Brown, Andrew J. Leigh, and Frost, Simon D. W.

Subjects
Communicable diseases -- Diagnosis, Communicable diseases -- Causes of, DNA sequencing -- Research, Nucleotide sequencing -- Research, Phylogeny -- Analysis, Population genetics -- Research, Biological sciences
Published
2009

20. Are Food Animals Responsible for Transfer of Antimicrobial-Resistant Escherichia coli or Their Resistance Determinants to Human Populations?:A Systematic Review

Author

Muloi, Dishon, Ward, Melissa J, Pedersen, Amy B, Fèvre, Eric M, Woolhouse, Mark E J, and van Bunnik, Bram A D

Subjects
Journal Article
Abstract

The role of farm animals in the emergence and dissemination of both AMR bacteria and their resistance determinants to humans is poorly understood and controversial. Here, we systematically reviewed the current evidence that food animals are responsible for transfer of AMR to humans. We searched PubMed, Web of Science, and EMBASE for literature published between 1940 and 2016. Our results show that eight studies (18%) suggested evidence of transmission of AMR from food animals to humans, 25 studies (56%) suggested transmission between animals and humans with no direction specified and 12 studies (26%) did not support transmission. Quality of evidence was variable among the included studies; one study (2%) used high resolution typing tools, 36 (80%) used intermediate resolution typing tools, six (13%) relied on low resolution typing tools, and two (5%) based conclusions on co-occurrence of resistance. While some studies suggested to provide evidence that transmission of AMR from food animals to humans may occur, robust conclusions on the directionality of transmission cannot be drawn due to limitations in study methodologies. Our findings highlight the need to combine high resolution genomic data analysis with systematically collected epidemiological evidence to reconstruct patterns of AMR transmission between food animals and humans.

Published
2018
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21. A cross-sectional survey of practices and knowledge among antibiotic retailers in Nairobi, Kenya

Author

Muloi, Dishon, primary, Fèvre, Eric M, additional, Bettridge, Judy, additional, Rono, Robert, additional, Ong'are, Daniel, additional, Hassell, James M, additional, Karani, Maurice K, additional, Muinde, Patrick, additional, van Bunnik, Bram, additional, Street, Alice, additional, Chase-Topping, Margo, additional, Pedersen, Amy B, additional, Ward, Melissa J, additional, and Woolhouse, Mark, additional

Published
2019
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23. Clinically relevant antimicrobial resistance at the wildlife-livestock-human interface in Nairobi : an epidemiological study

Author

Hassell, James M., Ward, Melissa J., Muloi, Dishon, Bettridge, Judy M., Robinson, Timothy P., Kariuki, Sam, Ogendo, Allan, Kiiru, John, Imboma, Titus, Kang'ethe, Erastus K., Öghren, Elin M., Williams, Nicola J., Begon, Michael, Woolhouse, Mark E. J., Fevre, Eric M., Hassell, James M., Ward, Melissa J., Muloi, Dishon, Bettridge, Judy M., Robinson, Timothy P., Kariuki, Sam, Ogendo, Allan, Kiiru, John, Imboma, Titus, Kang'ethe, Erastus K., Öghren, Elin M., Williams, Nicola J., Begon, Michael, Woolhouse, Mark E. J., and Fevre, Eric M.

Abstract

Background: Antimicrobial resistance is one of the great challenges facing global health security in the modern era. Wildlife, particularly those that use urban environments, are an important but understudied component of epidemiology of antimicrobial resistance. We investigated antimicrobial resistance overlap between sympatric wildlife, humans, livestock, and their shared environment across the developing city of Nairobi, Kenya. We use these data to examine the role of urban wildlife in the spread of clinically relevant antimicrobial resistance. Methods: 99 households across Nairobi were randomly selected on the basis of socioeconomic stratification. A detailed survey was administered to household occupants, and samples (n=2102) were collected from the faeces of 75 wildlife species inhabiting household compounds (ie, the household and its perimeter; n=849), 13 livestock species (n=656), and humans (n=333), and from the external environment (n=288). Escherichia coli, our sentinel organism, was cultured and a single isolate from each sample tested for sensitivity to 13 antibiotics. Diversity of antimicrobial resistant phenotypes was compared between urban wildlife, humans, livestock, and the environment, to investigate whether wildlife are a net source for antimicrobial resistance in Nairobi. Generalised linear mixed models were used to determine whether the prevalence of antimicrobial resistant phenotypes and multidrug-resistant E coli carriage in urban wildlife is linked to variation in ecological traits, such as foraging behaviour, and to determine household-level risk factors for sharing of antimicrobial resistance between humans, wildlife, and livestock. Findings: E coli were isolated from 485 samples collected from wildlife between Sept 6,2015, and Sept 28, 2016. Wildlife carried a low prevalence of E coli isolates susceptible to all antibiotics tested (45 [9%] of 485 samples) and a high prevalence of clinically relevant multidrug resistance (252 [52%] of 485

Published
2019
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24. Socio‐ecological drivers of vertebrate biodiversity and human‐animal interfaces across an urban landscape.

Author

Hassell, James M., Bettridge, Judy M., Ward, Melissa J., Ogendo, Allan, Imboma, Titus, Muloi, Dishon, Fava, Francesco, Robinson, Timothy P., Begon, Michael, and Fèvre, Eric M.

Subjects
SUSTAINABLE urban development, URBAN biodiversity, ANIMAL ecology, POPULATION, BIODIVERSITY, URBAN planning
Abstract

Urbanization can have profound impacts on the distributional ecology of wildlife and livestock, with implications for biodiversity conservation, ecosystem services and human health. A wealth of studies have assessed biotic responses to urbanization in North America and Europe, but there is little empirical evidence that directly links human activities to urban biodiversity in the tropics. Results from a large‐scale field study conducted in Nairobi, Kenya, are used to explore the impact of human activities on the biodiversity of wildlife and livestock with which humans co‐exist across the city. The structure of sympatric wildlife, livestock and human populations are characterized using unsupervised machine learning, and statistical modelling is used to relate compositional variation in these communities to socio‐ecological drivers occurring across the city. By characterizing landscape‐scale drivers acting on these interfaces, we demonstrate that socioeconomics, elevation and subsequent changes in habitat have measurable impacts upon the diversity, density and species assemblage of wildlife, livestock and humans. Restructuring of wildlife and livestock assemblages (both in terms of species diversity and composition) has important implications for the emergence of novel diseases at urban interfaces, and we therefore use our results to generate a set of testable hypotheses that explore the influence of urban change on microbial communities. These results provide novel insight into the impact of urbanization on biodiversity in the tropics. An understanding of associations between urban processes and the structure of human and animal populations is required to link urban development to conservation efforts and risks posed by disease emergence to human health, ultimately informing sustainable urban development policy. [ABSTRACT FROM AUTHOR]

Published
2021
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27. MCP-1 in pleural injury: CCR2 mediates haptotaxis of pleural mesothelial cells

Author

NASREEN, NAJMUNNISA, MOHAMMED, KAMAL A., GALFFY, GABRIELLA, WARD, MELISSA J., and ANTONY, VEENA B.

Subjects
Pleura -- Biopsy, Mesothelium -- Research, Interleukin-2 -- Physiological aspects, Endotoxins -- Physiological aspects, Biological sciences
Abstract

Nasreen, Najmunnisa, Kamal A. Mohammed, Gabriella Galffy, Melissa J. Ward, and Veena B. Antony. MCP-1 in pleural injury: CCR2 mediates haptotaxis of pleural mesothelial cells. Am. J. Physiol. Lung Cell. Mol. Physiol. 278: L591-L598, 2000.--Pleural injury results in the death of mesothelial cells and denudation of the mesothelial basement membrane. Repair of the mesothelium without fibrosis requires proliferation and migration of mesothelial cells into the injured area. We hypothesized that monocyte chemoattractant protein-1 (MCP-1) induces proliferative and haptotactic responses in pleural mesothelial cells (PMCs) and that the MCP-1 binding receptor CCR2 mediates the pleural repair process. We demonstrate that PMCs exhibited MCP-1-specific immunostaining on injury. MCP-1 induced proliferative and haptotactic responses in PMCs. PMCs express CCR2 in a time-dependent manner. Fluorescence-activated cell sorting analysis demonstrated that interleukin (IL)-2 upregulated CCR2 protein expression in PMCs, whereas lipopolysaccharide (LPS) downregulated the response at the initial period compared with that in resting PMCs. However, the inhibitory potential of LPS was lost after 12 h and showed a similar response at 24 and 48 h. Haptotactic migration was upregulated in PMCs that were cultured in the presence of IL-2. The increased haptotactic capacity of mesothelial cells in the presence of IL-2 correlated with increased CCR2 mRNA expression. PMCs cultured in the presence of LPS showed decreased haptotactic activity to MCP-1. Blocking the CCR2 with neutralizing antibodies decreased the haptotactic response of PMCs to MCP-1. These results suggest that the haptotactic migration of mesothelial cells in response to MCP-1 are mediated through CCR2, which may play a crucial role in reepithelialization of the denuded basement membrane at the site of pleural injury and may thus contribute to the regeneration of the mesothelium during the process of pleural repair. monocyte chemoattractant protein-1; interleukin-2; lipopolysaccharide

Published
2000

28. Identification of source and sink populations for the emergence and global spread of the East-Asia clone of community-associated MRSA

Author

Ward, Melissa J., primary, Goncheva, Mariya, additional, Richardson, Emily, additional, McAdam, Paul R., additional, Raftis, Emma, additional, Kearns, Angela, additional, Daum, Robert S., additional, David, Michael Z., additional, Lauderdale, Tsai Ling, additional, Edwards, Giles F., additional, Nimmo, Graeme R., additional, Coombs, Geoffrey W., additional, Huijsdens, Xander, additional, Woolhouse, Mark E. J., additional, and Fitzgerald, J. Ross, additional

Published
2016
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30. A single natural nucleotide mutation alters bacterial pathogen host tropism

Author

Viana, David, primary, Comos, María, additional, McAdam, Paul R, additional, Ward, Melissa J, additional, Selva, Laura, additional, Guinane, Caitriona M, additional, González-Muñoz, Beatriz M, additional, Tristan, Anne, additional, Foster, Simon J, additional, Fitzgerald, J Ross, additional, and Penadés, José R, additional

Published
2015
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33. The early spread and epidemic ignition of HIV-1 in human populations

Author

Faria, Nuno R., primary, Rambaut, Andrew, additional, Suchard, Marc A., additional, Baele, Guy, additional, Bedford, Trevor, additional, Ward, Melissa J., additional, Tatem, Andrew J., additional, Sousa, João D., additional, Arinaminpathy, Nimalan, additional, Pépin, Jacques, additional, Posada, David, additional, Peeters, Martine, additional, Pybus, Oliver G., additional, and Lemey, Philippe, additional

Published
2014
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35. Are Food Animals Responsible for Transfer of Antimicrobial-Resistant Escherichia colior Their Resistance Determinants to Human Populations? A Systematic Review

Author

Muloi, Dishon, Ward, Melissa J., Pedersen, Amy B., Fèvre, Eric M., Woolhouse, Mark E.J., and van Bunnik, Bram A.D.

Abstract

AbstractThe role of farm animals in the emergence and dissemination of both AMR bacteria and their resistance determinants to humans is poorly understood and controversial. Here, we systematically reviewed the current evidence that food animals are responsible for transfer of AMR to humans. We searched PubMed, Web of Science, and EMBASE for literature published between 1940 and 2016. Our results show that eight studies (18%) suggested evidence of transmission of AMR from food animals to humans, 25 studies (56%) suggested transmission between animals and humans with no direction specified and 12 studies (26%) did not support transmission. Quality of evidence was variable among the included studies; one study (2%) used high resolution typing tools, 36 (80%) used intermediate resolution typing tools, six (13%) relied on low resolution typing tools, and two (5%) based conclusions on co-occurrence of resistance. While some studies suggested to provide evidence that transmission of AMR from food animals to humans may occur, robust conclusions on the directionality of transmission cannot be drawn due to limitations in study methodologies. Our findings highlight the need to combine high resolution genomic data analysis with systematically collected epidemiological evidence to reconstruct patterns of AMR transmission between food animals and humans.

Published
2018
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42. Identification of source and sink populations for the emergence and global spread of the East-Asia clone of community-associated MRSA

Author

Ward, Melissa J., Goncheva, Mariya, Richardson, Emily, McAdam, Paul R., Raftis, Emma, Kearns, Angela, Daum, Robert S., David, Michael Z., Lauderdale, Tsai Ling, Edwards, Giles F., Nimmo, Graeme R., Coombs, Geoffrey W., Huijsdens, Xander, Woolhouse, Mark E. J., and Fitzgerald, J. Ross

Subjects
Methicillin-Resistant Staphylococcus aureus, Asia, Genotype, Research, Staphylococcal Infections, Global Health, United States, Anti-Bacterial Agents, Community-Acquired Infections, Phylogeography, Genes, Bacterial, Drug Resistance, Bacterial, Humans, Public Health Surveillance, Phylogeny
Abstract

Background Our understanding of the factors influencing the emergence, dissemination and global distribution of epidemic clones of bacteria is limited. ST59 is a major epidemic clone of community-associated MRSA in East Asia, responsible for extensive morbidity and mortality, but has a much lower prevalence in other parts of the world. The geographic origin of ST59 and its international routes of dissemination are unclear and disputed in the literature. Results To investigate the origin and spread of the ST59 clone, we obtained whole genome sequences of isolates from four continents, sampled over more than a decade, and carried out a time-scaled phylogeographic analysis. We discover that two distinct ST59 clades emerged concurrently, in East Asia and the USA, but underwent clonal expansion at different times. The East Asia clade was strongly enriched for gene determinants associated with antibiotic resistance, consistent with regional differences in antibiotic usage. Both clones spread independently to Australia and Europe, and we found evidence of the persistence of multi-drug resistance following export from East Asia. Direct transfer of strains between Taiwan and the USA was not observed in either direction, consistent with geographic niche exclusion. Conclusions Our results resolve a longstanding controversy regarding the origin of the ST59 clone, revealing the major global source and sink populations and routes for the spread of multi-drug resistant clones. Additionally, our findings indicate that diversification of the accessory genome of epidemic clones partly reflects region-specific patterns of antibiotic usage, which may influence bacterial fitness after transmission to different geographic locations. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1022-0) contains supplementary material, which is available to authorized users.

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