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Article ; Online: Impact of Growth Rate on the Protein-mRNA Ratio in Pseudomonas aeruginosa.

Zhang, Mengshi / Michie, Kelly L / Cornforth, Daniel M / Dolan, Stephen K / Wang, Yifei / Whiteley, Marvin

2022 Volume 14, Issue 1, Page(s) e0306722

Abstract: Our understanding of how bacterial pathogens colonize and persist during human infection has been hampered by the limited characterization of bacterial physiology during infection and a research bias ... ...

Abstract	Our understanding of how bacterial pathogens colonize and persist during human infection has been hampered by the limited characterization of bacterial physiology during infection and a research bias toward
MeSH term(s)	Humans ; Pseudomonas aeruginosa/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Cystic Fibrosis/microbiology ; Gene Expression Profiling ; Transcriptome ; Pseudomonas Infections/microbiology
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2022-12-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.03067-22
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak.

Park, Sang Woo / Cornforth, Daniel M / Dushoff, Jonathan / Weitz, Joshua S

Epidemics

2020 Volume 31, Page(s) 100392

Abstract: The role of asymptomatic carriers in transmission poses challenges for control of the COVID-19 pandemic. Study of asymptomatic transmission and implications for surveillance and disease burden are ongoing, but there has been little study of the ... ...

Abstract	The role of asymptomatic carriers in transmission poses challenges for control of the COVID-19 pandemic. Study of asymptomatic transmission and implications for surveillance and disease burden are ongoing, but there has been little study of the implications of asymptomatic transmission on dynamics of disease. We use a mathematical framework to evaluate expected effects of asymptomatic transmission on the basic reproduction number R
MeSH term(s)	Asymptomatic Diseases ; Basic Reproduction Number ; COVID-19 ; Coronavirus Infections/epidemiology ; Coronavirus Infections/transmission ; Disease Outbreaks ; Epidemics ; Humans ; Pandemics ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/transmission
Keywords	covid19
Language	English
Publishing date	2020-05-11
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2467993-8
ISSN	1878-0067 ; 1755-4365
ISSN (online)	1878-0067
ISSN	1755-4365
DOI	10.1016/j.epidem.2020.100392
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak.

Park, Sang Woo / Cornforth, Daniel M / Dushoff, Jonathan / Weitz, Joshua S

medRxiv : the preprint server for health sciences

2020

Abstract	The role of asymptomatic carriers in transmission poses challenges for control of the COVID-19 pandemic. Study of asymptomatic transmission and implications for surveillance and disease burden are ongoing, but there has been little study of the implications of asymptomatic transmission on dynamics of disease. We use a mathematical framework to evaluate expected effects of asymptomatic transmission on the basic reproduction number
Keywords	covid19
Language	English
Publishing date	2020-04-14
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.03.09.20033514
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Antibiotics and the art of bacterial war.

Cornforth, Daniel M / Foster, Kevin R

Proceedings of the National Academy of Sciences of the United States of America

2015 Volume 112, Issue 35, Page(s) 10827–10828

MeSH term(s)	Anti-Bacterial Agents/biosynthesis ; Streptomyces/physiology
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2015-09-01
Publishing country	United States
Document type	Comment ; Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1513608112
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Quantitative Framework for Model Evaluation in Microbiology Research Using

Cornforth, Daniel M / Diggle, Frances L / Melvin, Jeffrey A / Bomberger, Jennifer M / Whiteley, Marvin

mBio

2020 Volume 11, Issue 1

Abstract: Laboratory models are a cornerstone of modern microbiology, but the accuracy of these models has not been systematically evaluated. As a result, researchers often choose models based on intuition or incomplete data. We propose a general quantitative ... ...

Abstract	Laboratory models are a cornerstone of modern microbiology, but the accuracy of these models has not been systematically evaluated. As a result, researchers often choose models based on intuition or incomplete data. We propose a general quantitative framework to assess model accuracy from RNA sequencing data and use this framework to evaluate models of
MeSH term(s)	Computational Biology ; Cystic Fibrosis/microbiology ; Epithelial Cells/microbiology ; Humans ; In Vitro Techniques ; Lung/microbiology ; Microbiological Techniques ; Models, Biological ; Pseudomonas aeruginosa/genetics ; Pseudomonas aeruginosa/physiology ; RNA-Seq ; Sputum/microbiology
Language	English
Publishing date	2020-01-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.03042-19
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Application of a quantitative framework to improve the accuracy of a bacterial infection model.

Lewin, Gina R / Kapur, Ananya / Cornforth, Daniel M / Duncan, Rebecca P / Diggle, Frances L / Moustafa, Dina A / Harrison, Simone A / Skaar, Eric P / Chazin, Walter J / Goldberg, Joanna B / Bomberger, Jennifer M / Whiteley, Marvin

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 19, Page(s) e2221542120

Abstract: Laboratory models are critical to basic and translational microbiology research. Models serve multiple purposes, from providing tractable systems to study cell biology to allowing the investigation of inaccessible clinical and environmental ecosystems. ... ...

Abstract	Laboratory models are critical to basic and translational microbiology research. Models serve multiple purposes, from providing tractable systems to study cell biology to allowing the investigation of inaccessible clinical and environmental ecosystems. Although there is a recognized need for improved model systems, there is a gap in rational approaches to accomplish this goal. We recently developed a framework for assessing the accuracy of microbial models by quantifying how closely each gene is expressed in the natural environment and in various models. The accuracy of the model is defined as the percentage of genes that are similarly expressed in the natural environment and the model. Here, we leverage this framework to develop and validate two generalizable approaches for improving model accuracy, and as proof of concept, we apply these approaches to improve models of
MeSH term(s)	Humans ; Ecosystem ; Bacterial Infections ; Pseudomonas Infections/microbiology ; Transcriptome ; Epithelial Cells/microbiology ; Culture Media/metabolism ; Cystic Fibrosis/microbiology ; Pseudomonas aeruginosa/genetics ; Sputum/microbiology
Chemical Substances	Culture Media
Language	English
Publishing date	2023-05-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2221542120
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Article ; Online: Competition sensing: the social side of bacterial stress responses.

Cornforth, Daniel M / Foster, Kevin R

Nature reviews. Microbiology

2013 Volume 11, Issue 4, Page(s) 285–293

Abstract: The field of ecology has long recognized two types of competition: exploitative competition, which occurs indirectly through resource consumption, and interference competition, whereby one individual directly harms another. Here, we argue that these two ... ...

Abstract	The field of ecology has long recognized two types of competition: exploitative competition, which occurs indirectly through resource consumption, and interference competition, whereby one individual directly harms another. Here, we argue that these two forms of competition have played a dominant role in the evolution of bacterial regulatory networks. In particular, we argue that several of the major bacterial stress responses detect ecological competition by sensing nutrient limitation (exploitative competition) or direct cell damage (interference competition). We call this competition sensing: a physiological response that detects harm caused by other cells and that evolved, at least in part, for that purpose. A key prediction of our hypothesis is that bacteria will counter-attack when they sense ecological competition but not when they sense abiotic stress. In support of this hypothesis, we show that bacteriocins and antibiotics are frequently upregulated by stress responses to nutrient limitation and cell damage but very rarely upregulated by stress responses to heat or osmotic stress, which typically are not competition related. We argue that stress responses, in combination with the various mechanisms that sense secretions, enable bacteria to infer the presence of ecological competition and navigate the 'microbe-kill-microbe' world in which they live.
MeSH term(s)	Anti-Bacterial Agents/metabolism ; Bacteria/genetics ; Bacteria/growth & development ; Bacterial Physiological Phenomena ; Bacteriocins/metabolism ; Biological Evolution ; Gene Expression Regulation, Bacterial ; Gene Regulatory Networks ; Microbial Interactions ; Models, Biological ; Quorum Sensing ; Stress, Physiological
Chemical Substances	Anti-Bacterial Agents ; Bacteriocins
Language	English
Publishing date	2013-03-04
Publishing country	England
Document type	Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2139054-X
ISSN	1740-1534 ; 1740-1526
ISSN (online)	1740-1534
ISSN	1740-1526
DOI	10.1038/nrmicro2977
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Article ; Online: Bacterial tweets and podcasts #signaling#eavesdropping#microbialfightclub.

Michie, Kelly L / Cornforth, Daniel M / Whiteley, Marvin

Molecular and biochemical parasitology

2016 Volume 208, Issue 1, Page(s) 41–48

Abstract: Once thought to live independently, bacteria are now known to be highly social organisms. Their behaviors ranges from cooperatively forming complex multispecies communities to fiercely competing for resources. Work over the past fifty years has shown ... ...

Abstract	Once thought to live independently, bacteria are now known to be highly social organisms. Their behaviors ranges from cooperatively forming complex multispecies communities to fiercely competing for resources. Work over the past fifty years has shown that bacteria communicate through diverse mechanisms, such as exchanging diffusible molecules, exporting molecules in membrane vesicles, and interacting through direct cell-cell contact. These methods allow bacteria to sense and respond to other cells around them and coordinate group behavior. In this review, we share the discoveries and lessons learned in the field of bacterial communication with the aim of providing insights to parasitologists and other researchers working on related questions.
Language	English
Publishing date	2016-07
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	756166-0
ISSN	1872-9428 ; 0166-6851
ISSN (online)	1872-9428
ISSN	0166-6851
DOI	10.1016/j.molbiopara.2016.05.005
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Article: The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak

Park, Sang Woo / Cornforth, Daniel M / Dushoff, Jonathan / Weitz, Joshua S

Epidemics

Abstract	The role of asymptomatic carriers in transmission poses challenges for control of the COVID-19 pandemic. Study of asymptomatic transmission and implications for surveillance and disease burden are ongoing, but there has been little study of the implications of asymptomatic transmission on dynamics of disease. We use a mathematical framework to evaluate expected effects of asymptomatic transmission on the basic reproduction number R0 (i.e., the expected number of secondary cases generated by an average primary case in a fully susceptible population) and the fraction of new secondary cases attributable to asymptomatic individuals. If the generation-interval distribution of asymptomatic transmission differs from that of symptomatic transmission, then estimates of the basic reproduction number which do not explicitly account for asymptomatic cases may be systematically biased. Specifically, if asymptomatic cases have a shorter generation interval than symptomatic cases, R0 will be over-estimated, and if they have a longer generation interval, R0 will be under-estimated. Estimates of the realized proportion of asymptomatic transmission during the exponential phase also depend on asymptomatic generation intervals. Our analysis shows that understanding the temporal course of asymptomatic transmission can be important for assessing the importance of this route of transmission, and for disease dynamics. This provides an additional motivation for investigating both the importance and relative duration of asymptomatic transmission.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #349772
Database	COVID19

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Article ; Online: The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak

Park, Sang Woo / Cornforth, Daniel M / Dushoff, Jonathan / Weitz, Joshua S

medRxiv

Abstract: We assess the impact of asymptomatic transmission on epidemic potential of novel respiratory pathogens (like COVID-19) -- as measured both by the basic reproduction number (i.e., the expected number of secondary cases generated by an average primary case ...

Abstract	We assess the impact of asymptomatic transmission on epidemic potential of novel respiratory pathogens (like COVID-19) -- as measured both by the basic reproduction number (i.e., the expected number of secondary cases generated by an average primary case in a fully susceptible population) and the fraction of new secondary cases attributable to asymptomatic individuals. We show that the impact of asymptomatic transmission depends on generation intervals (i.e., time between when an individual is infected and when that individual infects another person). If the generation-interval distribution of asymptomatic transmission differs from that of symptomatic transmission, then estimates of the basic reproduction number which do not explicitly account for asymptomatic cases may be systematically biased. Specifically, if asymptomatic cases have a shorter generation interval than symptomatic cases, R_0 will be over-estimated, and if they have a longer generation interval, R_0 will be under-estimated. We also show that as the length of asymptomatic generation intervals increase, estimates of the realized proportion of asymptomatic transmission during the exponential phase of the epidemic decrease. Our analysis provides a rationale for assessing the duration of asymptomatic cases of COVID-19 in addition to their prevalence in the population.
Keywords	covid19
Language	English
Publishing date	2020-03-13
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.03.09.20033514
Database	COVID19

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