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Article: Exploiting the microbiota of organic and inorganic acid-treated raw poultry products to improve shelf-life.

Dittoe, Dana K / Feye, Kristina M / Ovall, Christina / Thompson, Hayley A / Ricke, Steven C

2024 Volume 15, Page(s) 1348159

Abstract: Introduction: Targeted amplicon sequencing of the 16S rRNA delineates the complex microbial interactions that occur during food spoilage, providing a tool to intensively screen microbiota response to antimicrobial processing aids and interventions. The ... ...

Abstract	Introduction: Targeted amplicon sequencing of the 16S rRNA delineates the complex microbial interactions that occur during food spoilage, providing a tool to intensively screen microbiota response to antimicrobial processing aids and interventions. The current research determines the microbiota and spoilage indicator (total aerobes and lactic acid bacteria; LAB) response to inorganic and organic antimicrobial intervention use on the shelf-life of fresh, never-frozen, skin-on, bone-in chicken wings. Methods: Wings ( Results: Spoilage was indicated for all products by day 21 according to APC counts (>7 Log Discussion: Therefore, there are differential effects on the microbial community depending on the chemical intervention used with organic and inorganic acids, impacting the microbial ecology differently.
Language	English
Publishing date	2024-02-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2024.1348159
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Article ; Online: Seasonal use case for the RTS,S/AS01 malaria vaccine: a mathematical modelling study.

Thompson, Hayley A / Hogan, Alexandra B / Walker, Patrick G T / Winskill, Peter / Zongo, Issaka / Sagara, Issaka / Tinto, Halidou / Ouedraogo, Jean-Bosco / Dicko, Alassane / Chandramohan, Daniel / Greenwood, Brian / Cairns, Matt / Ghani, Azra C

The Lancet. Global health

2022 Volume 10, Issue 12, Page(s) e1782–e1792

Abstract: Background: A 2021 clinical trial of seasonal RTS,S/AS01: Methods: We used a mathematical, individual-based model of malaria transmission that was fitted to data on the relationship between entomological inoculation rate and parasite prevalence, ... ...

Abstract	Background: A 2021 clinical trial of seasonal RTS,S/AS01 Methods: We used a mathematical, individual-based model of malaria transmission that was fitted to data on the relationship between entomological inoculation rate and parasite prevalence, clinical disease, severe disease, and deaths from multiple sites across Africa. The model was validated with results from a phase 3b trial assessing the effect of SV-RTS,S in Mali and Burkina Faso. We developed three intervention efficacy models with varying degrees and durations of protection for our population-level modelling analysis to assess the potential effect of an RTS,S vaccination schedule based on age (doses were delivered to children aged 6 months, 7·5 months, and 9 months for the first three doses, and at 27 months of age for the fourth dose) or season (children aged 5-17 months at the time of first vaccination received the first three doses in the 3 months preceding the transmission season, with any subsequent doses up to five doses delivered annually) in seasonal transmission settings both in the absence and presence of SMC with sulfadoxine-pyrimethamine plus amodiaquine. This is modelled as a full therapeutic course delivered every month for four or five months of the peak in transmission season. Estimates of cases and deaths averted in a population of 100 000 children aged 0-5 years were calculated over a 15-year time period for a range of levels of malaria transmission intensity (Plasmodium falciparum parasite prevalence in children aged 2-10 years between 10% and 65%) and over two west Africa seasonality archetypes. Findings: Seasonally targeting RTS,S resulted in greater absolute reductions in malaria cases and deaths compared with an age-based strategy, averting an additional 14 000-47 000 cases per 100 000 children aged 5 years and younger over 15 years, dependent on seasonality and transmission intensity. We predicted that adding seasonally targeted RTS,S to SMC would reduce clinical incidence by up to an additional 42 000-67 000 cases per 100 000 children aged 5 years and younger over 15 years compared with SMC alone. Transmission season duration was a key determinant of intervention effect, with the advantage of adding RTS,S to SMC predicted to be smaller with shorter transmission seasons. Interpretation: RTS,S vaccination in seasonal settings could be a valuable additional tool to existing interventions, with seasonal delivery maximising the effect relative to an age-based approach. Decisions surrounding deployment strategies of RTS,S in such settings will need to consider the local and regional variations in seasonality, current rates of other interventions, and potential achievable RTS,S coverage. Funding: UK Medical Research Council, UK Foreign Commonwealth & Development Office, The Wellcome Trust, and The Royal society.
MeSH term(s)	Child ; Humans ; Malaria Vaccines/therapeutic use ; Seasons ; Malaria/epidemiology ; Malaria/prevention & control ; Plasmodium falciparum ; Burkina Faso/epidemiology
Chemical Substances	Malaria Vaccines
Language	English
Publishing date	2022-09-01
Publishing country	England
Document type	Clinical Trial, Phase III ; Journal Article
ZDB-ID	2723488-5
ISSN	2214-109X ; 2214-109X
ISSN (online)	2214-109X
ISSN	2214-109X
DOI	10.1016/S2214-109X(22)00416-8
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Article ; Online: Modelling the roles of antibody titre and avidity in protection from Plasmodium falciparum malaria infection following RTS,S/AS01 vaccination.

Thompson, Hayley A / Hogan, Alexandra B / Walker, Patrick G T / White, Michael T / Cunnington, Aubrey J / Ockenhouse, Christian F / Ghani, Azra C

Vaccine

2020 Volume 38, Issue 47, Page(s) 7498–7507

Abstract: Anti-circumsporozoite antibody titres have been established as an essential indicator for evaluating the immunogenicity and protective capacity of the RTS,S/AS01 malaria vaccine. However, a new delayed-fractional dose regime of the vaccine was recently ... ...

Abstract	Anti-circumsporozoite antibody titres have been established as an essential indicator for evaluating the immunogenicity and protective capacity of the RTS,S/AS01 malaria vaccine. However, a new delayed-fractional dose regime of the vaccine was recently shown to increase vaccine efficacy, from 62.5% (95% CI 29.4-80.1%) under the original dosing schedule to 86.7% (95% CI, 66.8-94.6%) without a corresponding increase in antibody titres. Here we reanalyse the antibody data from this challenge trial to determine whether IgG avidity may help to explain efficacy better than IgG titre alone by adapting a within-host mathematical model of sporozoite inoculation. We demonstrate that a model incorporating titre and avidity provides a substantially better fit to the data than titre alone. These results also suggest that in individuals with a high antibody titre response that also show high avidity (both metrics in the top tercile of observed values) delayed-fractional vaccination provided near perfect protection upon first challenge (98.2% [95% Credible Interval 91.6-99.7%]). This finding suggests that the quality of the vaccine induced antibody response is likely to be an important determinant in the development of highly efficacious pre-erythrocytic vaccines against malaria.
MeSH term(s)	Antibodies, Protozoan ; Antibody Formation ; Humans ; Malaria ; Malaria Vaccines ; Malaria, Falciparum/prevention & control ; Plasmodium falciparum ; Vaccination
Chemical Substances	Antibodies, Protozoan ; Malaria Vaccines
Language	English
Publishing date	2020-10-09
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2020.09.069
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Article: Modelling the roles of antibody titre and avidity in protection from Plasmodium falciparum malaria infection following RTS,S/AS01 vaccination

Thompson, Hayley A / Hogan, Alexandra B / Walker, Patrick G.T / White, Michael T / Cunnington, Aubrey J / Ockenhouse, Christian F / Ghani, Azra C

Vaccine. 2020 Nov. 03, v. 38, no. 47

2020

Abstract	Anti-circumsporozoite antibody titres have been established as an essential indicator for evaluating the immunogenicity and protective capacity of the RTS,S/AS01 malaria vaccine. However, a new delayed-fractional dose regime of the vaccine was recently shown to increase vaccine efficacy, from 62.5% (95% CI 29.4–80.1%) under the original dosing schedule to 86.7% (95% CI, 66.8–94.6%) without a corresponding increase in antibody titres. Here we reanalyse the antibody data from this challenge trial to determine whether IgG avidity may help to explain efficacy better than IgG titre alone by adapting a within-host mathematical model of sporozoite inoculation. We demonstrate that a model incorporating titre and avidity provides a substantially better fit to the data than titre alone. These results also suggest that in individuals with a high antibody titre response that also show high avidity (both metrics in the top tercile of observed values) delayed-fractional vaccination provided near perfect protection upon first challenge (98.2% [95% Credible Interval 91.6–99.7%]). This finding suggests that the quality of the vaccine induced antibody response is likely to be an important determinant in the development of highly efficacious pre-erythrocytic vaccines against malaria.
Keywords	Plasmodium falciparum ; antibodies ; antibody formation ; falciparum malaria ; immunogenicity ; malaria vaccines ; mathematical models ; sporozoites ; vaccination
Language	English
Dates of publication	2020-1103
Size	p. 7498-7507.
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2020.09.069
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Article ; Online: Leveraging community mortality indicators to infer COVID-19 mortality and transmission dynamics in Damascus, Syria.

Nature communications

2021 Volume 12, Issue 1, Page(s) 2394

Abstract: The COVID-19 pandemic has resulted in substantial mortality worldwide. However, to date, countries in the Middle East and Africa have reported considerably lower mortality rates than in Europe and the Americas. Motivated by reports of an overwhelmed ... ...

Abstract	The COVID-19 pandemic has resulted in substantial mortality worldwide. However, to date, countries in the Middle East and Africa have reported considerably lower mortality rates than in Europe and the Americas. Motivated by reports of an overwhelmed health system, we estimate the likely under-ascertainment of COVID-19 mortality in Damascus, Syria. Using all-cause mortality data, we fit a mathematical model of COVID-19 transmission to reported mortality, estimating that 1.25% of COVID-19 deaths (sensitivity range 1.00% - 3.00%) have been reported as of 2 September 2020. By 2 September, we estimate that 4,380 (95% CI: 3,250 - 5,550) COVID-19 deaths in Damascus may have been missed, with 39.0% (95% CI: 32.5% - 45.0%) of the population in Damascus estimated to have been infected. Accounting for under-ascertainment corroborates reports of exceeded hospital bed capacity and is validated by community-uploaded obituary notifications, which confirm extensive unreported mortality in Damascus.
MeSH term(s)	COVID-19/epidemiology ; COVID-19/mortality ; COVID-19/virology ; Humans ; Mortality/trends ; Pandemics ; Population Surveillance/methods ; SARS-CoV-2/isolation & purification ; SARS-CoV-2/physiology ; Survival Rate ; Syria/epidemiology
Language	English
Publishing date	2021-04-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-22474-9
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Article ; Online: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Setting-specific Transmission Rates: A Systematic Review and Meta-analysis.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2021 Volume 73, Issue 3, Page(s) e754–e764

Abstract: Background: Understanding the drivers of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission is crucial for control policies, but evidence of transmission rates in different settings remains limited.: Methods: We conducted a ... ...

Abstract	Background: Understanding the drivers of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission is crucial for control policies, but evidence of transmission rates in different settings remains limited. Methods: We conducted a systematic review to estimate secondary attack rates (SARs) and observed reproduction numbers (Robs) in different settings exploring differences by age, symptom status, and duration of exposure. To account for additional study heterogeneity, we employed a beta-binomial model to pool SARs across studies and a negative-binomial model to estimate Robs. Results: Households showed the highest transmission rates, with a pooled SAR of 21.1% (95% confidence interval [CI]:17.4-24.8). SARs were significantly higher where the duration of household exposure exceeded 5 days compared with exposure of ≤5 days. SARs related to contacts at social events with family and friends were higher than those for low-risk casual contacts (5.9% vs 1.2%). Estimates of SARs and Robs for asymptomatic index cases were approximately one-seventh, and for presymptomatic two-thirds of those for symptomatic index cases. We found some evidence for reduced transmission potential both from and to individuals younger than 20 years of age in the household context, which is more limited when examining all settings. Conclusions: Our results suggest that exposure in settings with familiar contacts increases SARS-CoV-2 transmission potential. Additionally, the differences observed in transmissibility by index case symptom status and duration of exposure have important implications for control strategies, such as contact tracing, testing, and rapid isolation of cases. There were limited data to explore transmission patterns in workplaces, schools, and care homes, highlighting the need for further research in such settings.
MeSH term(s)	COVID-19 ; Contact Tracing ; Family Characteristics ; Humans ; Incidence ; SARS-CoV-2
Language	English
Publishing date	2021-02-07
Publishing country	United States
Document type	Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't ; Systematic Review
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/ciab100
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Article ; Online: The projected impact of mitigation and suppression strategies on the COVID-19 epidemic in Senegal: A modelling study

Thompson, Hayley A / Mboup, Aminata / Cisse, Badara / Nayagam, Shevanthi / Watson, Oliver J / Whittaker, Charles / Walker, Patrick G T / Ghani, Azra C / Mboup, Souleymane

medRxiv

Abstract: Background: Physical distancing measures that reduce social contacts have formed a key part of national COVID-19 containment and mitigation strategies. Many Sub-Saharan African nations are now facing increasing numbers of cases of COVID-19 and there is a ...

Abstract	Background: Physical distancing measures that reduce social contacts have formed a key part of national COVID-19 containment and mitigation strategies. Many Sub-Saharan African nations are now facing increasing numbers of cases of COVID-19 and there is a need to understand what levels of measures may be required to successfully reduce transmission. Methods: We collated epidemiological data along with information on key COVID-19 specific response policies and health system capacity estimates for services needed to treat COVID-19 patients in Senegal. We calibrated an age-structured SEIR model to these data to capture transmission dynamics accounting for demography, contact patterns, hospital capacity and disease severity. We simulated the impact of mitigation and suppression strategies focussed on reducing social contact rates. Results: Senegal acted promptly to contain the spread of SARS-CoV-2 and as a result has reduced the reproduction number from 1.9 (95% CI 1.7-2.2) to 1.3 (95% CI 1.2-1.5), which has slowed but not fully interrupted transmission. We estimate that continued spread is likely to peak in October, and to overwhelm the healthcare system with an estimated 77,400 deaths(95% CI 55,270-100,700). Further reductions in contact rates to suppress transmission (Rt<1) could significantly reduce this burden on healthcare services and improve overall health outcomes. Conclusions: Our results demonstrate that Senegal has already significantly reduced transmission. Enhanced physical distancing measures and rapid scale up of hospital capacity is likely to be needed to reduce mortality and protect healthcare infrastructure from high levels of demand.
Keywords	covid19
Language	English
Publishing date	2020-07-04
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.07.03.20144949
Database	COVID19

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Article ; Online: COVID-19 epidemic severity is associated with timing of non-pharmaceutical interventions

Ragonnet-Cronin, Manon / Boyd, Olivia / Geidelberg, Lily / Jorgensen, David / Nascimento, Fabricia F / Siveroni, Igor / Johnson, Robert / Baguelin, Marc / Cucunuba, Zulma M / Jauneikaite, Elita / Mishra, Swapnil / Thompson, Hayley A / Watson, Oliver J / Ferguson, Neil / Donnelly, Christl A / Volz, Erik

medRxiv

Abstract: Background: Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non-pharmaceutical interventions is still debated. International ... ...

Abstract	Background: Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non-pharmaceutical interventions is still debated. International comparisons are hampered by highly variable conditions under which epidemics spread and differences in the timing and scale of interventions. Cumulative COVID-19 morbidity and mortality are functions of both the rate of epidemic growth and the duration of uninhibited growth before interventions were implemented. Incomplete and sporadic testing during the early COVID-19 epidemic makes it difficult to identify how long SARS-CoV-2 was circulating in different places. SARS-CoV-2 genetic sequences can be analyzed to provide an estimate of both the time of epidemic origin and the rate of early epidemic growth in different settings. Methods: We carried out a phylogenetic analysis of more than 29,000 publicly available whole genome SARS-CoV-2 sequences from 57 locations to estimate the time that the epidemic originated in different places. These estimates were cross-referenced with dates of the most stringent interventions in each location as well as the number of cumulative COVID-19 deaths following maximum intervention. Phylodynamic methods were used to estimate the rate of early epidemic growth and proxy estimates of epidemic size. Findings: The time elapsed between epidemic origin and maximum intervention is strongly associated with different measures of epidemic severity and explains 46% of variance in numbers infected at time of maximum intervention. The reproduction number is independently associated with epidemic severity. In multivariable regression models, epidemic severity was not associated with census population size. The time elapsed between detection of initial COVID-19 cases to interventions was not associated with epidemic severity, indicating that many locations experienced long periods of cryptic transmission. Interpretation: Locations where strong non-pharmaceutical interventions were implemented earlier experienced much less severe COVID-19 morbidity and mortality during the period of study.
Keywords	covid19
Language	English
Publishing date	2020-09-18
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.09.15.20194258
Database	COVID19

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Article ; Online: Understanding the Potential Impact of Different Drug Properties on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission and Disease Burden: A Modelling Analysis.

Whittaker, Charles / Watson, Oliver J / Alvarez-Moreno, Carlos / Angkasekwinai, Nasikarn / Boonyasiri, Adhiratha / Carlos Triana, Luis / Chanda, Duncan / Charoenpong, Lantharita / Chayakulkeeree, Methee / Cooke, Graham S / Croda, Julio / Cucunubá, Zulma M / Djaafara, Bimandra A / Estofolete, Cassia F / Grillet, Maria Eugenia / Faria, Nuno R / Figueiredo Costa, Silvia / Forero-Peña, David A / Gibb, Diana M /

Gordon, Anthony C / Hamers, Raph L / Hamlet, Arran / Irawany, Vera / Jitmuang, Anupop / Keurueangkul, Nukool / Kimani, Teresia Njoki / Lampo, Margarita / Levin, Anna S / Lopardo, Gustavo / Mustafa, Rima / Nayagam, Shevanthi / Ngamprasertchai, Thundon / Njeri, Ng'ang'a Irene Hannah / Nogueira, Mauricio L / Ortiz-Prado, Esteban / Perroud, Mauricio W / Phillips, Andrew N / Promsin, Panuwat / Qavi, Ambar / Rodger, Alison J / Sabino, Ester C / Sangkaew, Sorawat / Sari, Djayanti / Sirijatuphat, Rujipas / Sposito, Andrei C / Srisangthong, Pratthana / Thompson, Hayley A / Udwadia, Zarir / Valderrama-Beltrán, Sandra / Winskill, Peter / Ghani, Azra C / Walker, Patrick G T / Hallett, Timothy B

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2021 Volume 75, Issue 1, Page(s) e224–e233

Abstract: Background: The public health impact of the coronavirus disease 2019 (COVID-19) pandemic has motivated a rapid search for potential therapeutics, with some key successes. However, the potential impact of different treatments, and consequently research ... ...

Abstract	Background: The public health impact of the coronavirus disease 2019 (COVID-19) pandemic has motivated a rapid search for potential therapeutics, with some key successes. However, the potential impact of different treatments, and consequently research and procurement priorities, have not been clear. Methods: Using a mathematical model of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, COVID-19 disease and clinical care, we explore the public-health impact of different potential therapeutics, under a range of scenarios varying healthcare capacity, epidemic trajectories; and drug efficacy in the absence of supportive care. Results: The impact of drugs like dexamethasone (delivered to the most critically-ill in hospital and whose therapeutic benefit is expected to depend on the availability of supportive care such as oxygen and mechanical ventilation) is likely to be limited in settings where healthcare capacity is lowest or where uncontrolled epidemics result in hospitals being overwhelmed. As such, it may avert 22% of deaths in high-income countries but only 8% in low-income countries (assuming R = 1.35). Therapeutics for different patient populations (those not in hospital, early in the course of infection) and types of benefit (reducing disease severity or infectiousness, preventing hospitalization) could have much greater benefits, particularly in resource-poor settings facing large epidemics. Conclusions: Advances in the treatment of COVID-19 to date have been focused on hospitalized-patients and predicated on an assumption of adequate access to supportive care. Therapeutics delivered earlier in the course of infection that reduce the need for healthcare or reduce infectiousness could have significant impact, and research into their efficacy and means of delivery should be a priority.
MeSH term(s)	Cost of Illness ; Humans ; Pandemics/prevention & control ; Pharmaceutical Preparations ; SARS-CoV-2 ; COVID-19 Drug Treatment
Chemical Substances	Pharmaceutical Preparations
Language	English
Publishing date	2021-09-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/ciab837
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Article: Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment.

Ainslie, Kylie E C / Walters, Caroline E / Fu, Han / Bhatia, Sangeeta / Wang, Haowei / Xi, Xiaoyue / Baguelin, Marc / Bhatt, Samir / Boonyasiri, Adhiratha / Boyd, Olivia / Cattarino, Lorenzo / Ciavarella, Constanze / Cucunuba, Zulma / Cuomo-Dannenburg, Gina / Dighe, Amy / Dorigatti, Ilaria / van Elsland, Sabine L / FitzJohn, Rich / Gaythorpe, Katy /

Wellcome open research

2020 Volume 5, Page(s) 81

Abstract: ... ...

Abstract	Background
Keywords	covid19
Language	English
Publishing date	2020-10-01
Publishing country	England
Document type	Journal Article
ISSN	2398-502X
ISSN	2398-502X
DOI	10.12688/wellcomeopenres.15843.2
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