Pub Date : 2024-10-04DOI: 10.1017/S0950268824001298
Sachin Phakey, Patricia T Campbell, Katherine B Gibney
In the last 10-15 years, there has been a global resurgence of scarlet fever, an infection historically associated with significant morbidity and mortality. It is unknown whether scarlet fever incidence has increased in Australia. We aimed to examine the incidence, predictors and severity of scarlet fever in the state of Victoria, Australia from 2007 to 2017, analyzing scarlet fever emergency department (ED) presentations, hospitalizations and deaths. Of the 1 578 scarlet fever cases during the study period, most occurred in children aged <10 years (1 344, 85%), in males (882, 56%), and during winter and spring months (918, 57%). There were no deaths with scarlet fever, however, 374 cases (24%) were admitted to hospital. The annual incidence of scarlet fever was stable during the study period (mean, 2.5; range, 1.9-3.1 cases per 100 000). Annual incidence was highest in children aged <5 years (19.3 per 100 000), and was 21% higher in males than females, adjusting for age and year (incidence rate ratio, 1.21, 95%CI 1.09-1.34). Whilst scarlet fever ED presentations and hospitalizations were stable in Victoria from 2007 to 2017, the recent identification of a Streptococcus pyogenes variant in Australia associated with epidemic scarlet fever overseas highlights the risk of future outbreaks.
{"title":"Epidemiology of scarlet fever in Victoria, Australia, 2007-2017.","authors":"Sachin Phakey, Patricia T Campbell, Katherine B Gibney","doi":"10.1017/S0950268824001298","DOIUrl":"10.1017/S0950268824001298","url":null,"abstract":"<p><p>In the last 10-15 years, there has been a global resurgence of scarlet fever, an infection historically associated with significant morbidity and mortality. It is unknown whether scarlet fever incidence has increased in Australia. We aimed to examine the incidence, predictors and severity of scarlet fever in the state of Victoria, Australia from 2007 to 2017, analyzing scarlet fever emergency department (ED) presentations, hospitalizations and deaths. Of the 1 578 scarlet fever cases during the study period, most occurred in children aged <10 years (1 344, 85%), in males (882, 56%), and during winter and spring months (918, 57%). There were no deaths with scarlet fever, however, 374 cases (24%) were admitted to hospital. The annual incidence of scarlet fever was stable during the study period (mean, 2.5; range, 1.9-3.1 cases per 100 000). Annual incidence was highest in children aged <5 years (19.3 per 100 000), and was 21% higher in males than females, adjusting for age and year (incidence rate ratio, 1.21, 95%CI 1.09-1.34). Whilst scarlet fever ED presentations and hospitalizations were stable in Victoria from 2007 to 2017, the recent identification of a <i>Streptococcus pyogenes</i> variant in Australia associated with epidemic scarlet fever overseas highlights the risk of future outbreaks.</p>","PeriodicalId":11721,"journal":{"name":"Epidemiology and Infection","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11450502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-04DOI: 10.1017/S0950268824001006
Hannah Charles, Katy Sinka, Ian Simms, Kate S Baker, Gauri Godbole, Claire Jenkins
We reviewed all diagnoses of Shigella species notified to the UK Health Security Agency from January 2016 to March 2023. An overall increase in notifications of shigellosis was seen between 2016 (n = 415/quarter) and 2023 (n = 1 029/quarter). However, notifications dramatically declined between March 2020 and September 2021 during the COVID-19 pandemic (n = 208/quarter) highlighting the impact of travel and social distancing restrictions on transmission. S. sonnei diagnoses were more affected by lockdown restrictions than S. flexneri, most likely due to a combination of species-specific characteristics and host attributes. Azithromycin resistance continued to be associated with epidemics of sexually transmissible S. flexneri (adult males = 45.6% vs. adult females = 8.7%) and S. sonnei (adult males = 59.5% vs. adult females = 14.6%). We detected resistance to ciprofloxacin in S. sonnei from adult male cases not reporting travel at a higher frequency (79.4%) than in travel-associated cases (61.7%). Extensively drug-resistant Shigella species associated with sexual transmission among men almost exclusively had ESBL encoded by blaCTX-M-27, whereas those associated with returning travellers had blaCTX-M-15. Given the increasing incidence of infections and AMR, we recommend that enhanced surveillance is used to better understand the impact of travel and sexual transmission on the acquisition and spread of MDR and XDR Shigella species.
{"title":"Trends in shigellosis notifications in England, January 2016 to March 2023.","authors":"Hannah Charles, Katy Sinka, Ian Simms, Kate S Baker, Gauri Godbole, Claire Jenkins","doi":"10.1017/S0950268824001006","DOIUrl":"10.1017/S0950268824001006","url":null,"abstract":"<p><p>We reviewed all diagnoses of <i>Shigella</i> species notified to the UK Health Security Agency from January 2016 to March 2023. An overall increase in notifications of shigellosis was seen between 2016 (<i>n</i> = 415/quarter) and 2023 (<i>n</i> = 1 029/quarter). However, notifications dramatically declined between March 2020 and September 2021 during the COVID-19 pandemic (<i>n</i> = 208/quarter) highlighting the impact of travel and social distancing restrictions on transmission. <i>S. sonnei</i> diagnoses were more affected by lockdown restrictions than <i>S. flexneri</i>, most likely due to a combination of species-specific characteristics and host attributes. Azithromycin resistance continued to be associated with epidemics of sexually transmissible S. <i>flexneri</i> (adult males = 45.6% vs. adult females = 8.7%) and <i>S. sonnei</i> (adult males = 59.5% vs. adult females = 14.6%). We detected resistance to ciprofloxacin in <i>S. sonnei</i> from adult male cases not reporting travel at a higher frequency (79.4%) than in travel-associated cases (61.7%). Extensively drug-resistant <i>Shigella</i> species associated with sexual transmission among men almost exclusively had ESBL encoded by <i>bla</i><sub>CTX-M-27</sub>, whereas those associated with returning travellers had <i>bla</i><sub>CTX-M-15</sub>. Given the increasing incidence of infections and AMR, we recommend that enhanced surveillance is used to better understand the impact of travel and sexual transmission on the acquisition and spread of MDR and XDR Shigella species.</p>","PeriodicalId":11721,"journal":{"name":"Epidemiology and Infection","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11450503/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-02DOI: 10.1017/S0950268824000864
Simon Packer, Piotr Patrzylas, Rachel Merrick, Clare Sawyer, Andrew McAuley, William Crowe, Gillian Armstrong, Leonardo Green, Lucy Findlater, Charlie Turner, Obaghe Edeghere, Charlotte Anderson
We aimed to estimate the secondary attack rate of mpox among UK household contacts and determine factors associated with transmission to inform public health management of contacts, during the global outbreak in 2022. Information was collected via NHS and public health services and included age, gender, place of residence, setting, and type of contact. Aggregate information was summarized for the UK. Record level data was combined for England, Wales and Northern Ireland, and multivariable logistic regression was used to determine factors associated with transmission. The secondary attack rate among UK household mpox contacts was 4% (60/1 526). Sexual contact with the index case was associated with a 11-fold increase in adjusted odds of becoming a case in England, Wales, and Northern Ireland (95% CI 5.5-22, p < 0.001). Household contacts outside of London had increased odds compared to London residents (adjusted OR 2.9, 95%CI 1.6-5.4, p < 0.001), while female contacts had reduced odds of becoming a case (aOR: 0.41, 95% CI: 0.15-0.95). We found a low overall secondary attack rate among household mpox contacts with strong evidence of increased transmission risk associated with sexual contact. This evidence will inform the risk assessment of contacts and support prioritization of those with close intimate contact for follow up.
我们的目的是估计英国家庭接触者中天花的二次发病率,并确定与传播相关的因素,以便在 2022 年全球疫情爆发期间为接触者的公共卫生管理提供信息。我们通过国家医疗服务体系和公共卫生服务机构收集信息,包括年龄、性别、居住地、环境和接触者类型。对英国的信息进行了汇总。合并了英格兰、威尔士和北爱尔兰的记录级数据,并使用多变量逻辑回归法确定与传播相关的因素。英国家庭水痘接触者的二次发病率为 4%(60/1 526)。在英格兰、威尔士和北爱尔兰,与指数病例有性接触者成为病例的调整后几率增加了 11 倍(95% CI 5.5-22,p < 0.001)。与伦敦居民相比,伦敦以外的家庭接触者成为病例的几率增加(调整后 OR 2.9,95%CI 1.6-5.4,p < 0.001),而女性接触者成为病例的几率降低(aOR:0.41,95% CI:0.15-0.95)。我们发现,水痘家庭接触者的总体二次发病率较低,但有确凿证据表明性接触会增加传播风险。这些证据将为接触者的风险评估提供依据,并支持优先对有密切亲密接触者进行随访。
{"title":"Mpox in UK households: estimating secondary attack rates and factors associated with transmission, May-November 2022.","authors":"Simon Packer, Piotr Patrzylas, Rachel Merrick, Clare Sawyer, Andrew McAuley, William Crowe, Gillian Armstrong, Leonardo Green, Lucy Findlater, Charlie Turner, Obaghe Edeghere, Charlotte Anderson","doi":"10.1017/S0950268824000864","DOIUrl":"10.1017/S0950268824000864","url":null,"abstract":"<p><p>We aimed to estimate the secondary attack rate of mpox among UK household contacts and determine factors associated with transmission to inform public health management of contacts, during the global outbreak in 2022. Information was collected via NHS and public health services and included age, gender, place of residence, setting, and type of contact. Aggregate information was summarized for the UK. Record level data was combined for England, Wales and Northern Ireland, and multivariable logistic regression was used to determine factors associated with transmission. The secondary attack rate among UK household mpox contacts was 4% (60/1 526). Sexual contact with the index case was associated with a 11-fold increase in adjusted odds of becoming a case in England, Wales, and Northern Ireland (95% CI 5.5-22, <i>p</i> < 0.001). Household contacts outside of London had increased odds compared to London residents (adjusted OR 2.9, 95%CI 1.6-5.4, <i>p</i> < 0.001), while female contacts had reduced odds of becoming a case (aOR: 0.41, 95% CI: 0.15-0.95). We found a low overall secondary attack rate among household mpox contacts with strong evidence of increased transmission risk associated with sexual contact. This evidence will inform the risk assessment of contacts and support prioritization of those with close intimate contact for follow up.</p>","PeriodicalId":11721,"journal":{"name":"Epidemiology and Infection","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11450552/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-02DOI: 10.1017/S0950268824001043
Hannah L Moore, Charlie Turner, Chris Rawlinson, Cong Chen, Neville Q Verlander, Charlotte Anderson, Gareth J Hughes
Contact tracing for COVID-19 in England operated from May 2020 to February 2022. The clinical, demographic and exposure information collected on cases and their contacts offered a unique opportunity to study secondary transmission. We aimed to quantify the relative impact of host factors and exposure settings on secondary COVID-19 transmission risk using 550,000 sampled transmission links between cases and their contacts. Links, or 'contact episodes', were established where a contact subsequently became a case, using an algorithm accounting for incubation period, setting, and contact date. A mixed-effects logistic regression model was used to estimate adjusted odds of transmission. Of sampled episodes, 8.7% resulted in secondary cases. Living with a case (71% episodes) was the most significant risk factor (aOR = 2.6, CI = 1.9-3.6). Other risk factors included unvaccinated status (aOR = 1.2, CI = 1.2-1.3), symptoms, and older age (66-79 years; aOR = 1.4, CI = 1.4-1.5). Whilst global COVID-19 strategies emphasized protection outside the home, including education, travel, and gathering restrictions, this study evidences the relative importance of household transmission. There is a need to reconsider the contribution of household transmission to future control strategies and the requirement for effective infection control within households.
{"title":"Risk factors for COVID-19 transmission in England: a multilevel modelling study using routine contact tracing data.","authors":"Hannah L Moore, Charlie Turner, Chris Rawlinson, Cong Chen, Neville Q Verlander, Charlotte Anderson, Gareth J Hughes","doi":"10.1017/S0950268824001043","DOIUrl":"10.1017/S0950268824001043","url":null,"abstract":"<p><p>Contact tracing for COVID-19 in England operated from May 2020 to February 2022. The clinical, demographic and exposure information collected on cases and their contacts offered a unique opportunity to study secondary transmission. We aimed to quantify the relative impact of host factors and exposure settings on secondary COVID-19 transmission risk using 550,000 sampled transmission links between cases and their contacts. Links, or 'contact episodes', were established where a contact subsequently became a case, using an algorithm accounting for incubation period, setting, and contact date. A mixed-effects logistic regression model was used to estimate adjusted odds of transmission. Of sampled episodes, 8.7% resulted in secondary cases. Living with a case (71% episodes) was the most significant risk factor (aOR = 2.6, CI = 1.9-3.6). Other risk factors included unvaccinated status (aOR = 1.2, CI = 1.2-1.3), symptoms, and older age (66-79 years; aOR = 1.4, CI = 1.4-1.5). Whilst global COVID-19 strategies emphasized protection outside the home, including education, travel, and gathering restrictions, this study evidences the relative importance of household transmission. There is a need to reconsider the contribution of household transmission to future control strategies and the requirement for effective infection control within households.</p>","PeriodicalId":11721,"journal":{"name":"Epidemiology and Infection","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11450508/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-01DOI: 10.1017/S095026882400092X
Lisa Glaser, Ross Harris, Tehreem Mohiyuddin, Jennifer A Davidson, Sharon Cox, Colin N J Campbell
Globally, there is seasonal variation in tuberculosis (TB) incidence, yet the biological and behavioural or social factors driving TB seasonality differ across countries. Understanding season-specific risk factors that may be specific to the UK could help shape future decision-making for TB control. We conducted a time-series analysis using data from 152,424 UK TB notifications between 2000 and 2018. Notifications were aggregated by year, month, and socio-demographic covariates, and negative binomial regression models fitted to the aggregate data. For each covariate, we calculated the size of the seasonal effect as the incidence risk ratio (IRR) for the peak versus the trough months within the year and the timing of the peak, whilst accounting for the overall trend. There was strong evidence for seasonality (p < 0.0001) with an IRR of 1.27 (95% CI 1.23-1.30). The peak was estimated to occur at the beginning of May. Significant differences in seasonal amplitude were identified across age groups, ethnicity, site of disease, latitude and, for those born abroad, time since entry to the UK. The smaller amplitude in older adults, and greater amplitude among South Asians and people who recently entered the UK may indicate the role of latent TB reactivation and vitamin D deficiency in driving seasonality.
在全球范围内,肺结核(TB)发病率存在季节性变化,但各国肺结核季节性的生物、行为或社会因素却不尽相同。了解英国特有的季节性风险因素有助于制定未来的结核病控制决策。我们利用 2000 年至 2018 年间 152,424 份英国结核病通知中的数据进行了时间序列分析。我们按年份、月份和社会人口协变量对通知进行了汇总,并对汇总数据拟合了负二项回归模型。对于每个协变量,我们计算了季节性效应的大小,即年内高峰月与低谷月的发病风险比(IRR)以及高峰的时间,同时考虑了总体趋势。有强有力的证据表明存在季节性(p < 0.0001),IRR 为 1.27(95% CI 1.23-1.30)。估计峰值出现在 5 月初。不同年龄组、种族、发病部位、纬度以及出生在国外的人进入英国后的时间在季节性振幅上存在显著差异。老年人的振幅较小,南亚人和新近进入英国的人的振幅较大,这可能表明潜伏肺结核再活化和维生素 D 缺乏在推动季节性方面发挥了作用。
{"title":"Analyzing the seasonality of tuberculosis case notifications in the UK, 2000-2018.","authors":"Lisa Glaser, Ross Harris, Tehreem Mohiyuddin, Jennifer A Davidson, Sharon Cox, Colin N J Campbell","doi":"10.1017/S095026882400092X","DOIUrl":"10.1017/S095026882400092X","url":null,"abstract":"<p><p>Globally, there is seasonal variation in tuberculosis (TB) incidence, yet the biological and behavioural or social factors driving TB seasonality differ across countries. Understanding season-specific risk factors that may be specific to the UK could help shape future decision-making for TB control. We conducted a time-series analysis using data from 152,424 UK TB notifications between 2000 and 2018. Notifications were aggregated by year, month, and socio-demographic covariates, and negative binomial regression models fitted to the aggregate data. For each covariate, we calculated the size of the seasonal effect as the incidence risk ratio (IRR) for the peak versus the trough months within the year and the timing of the peak, whilst accounting for the overall trend. There was strong evidence for seasonality (<i>p</i> < 0.0001) with an IRR of 1.27 (95% CI 1.23-1.30). The peak was estimated to occur at the beginning of May. Significant differences in seasonal amplitude were identified across age groups, ethnicity, site of disease, latitude and, for those born abroad, time since entry to the UK. The smaller amplitude in older adults, and greater amplitude among South Asians and people who recently entered the UK may indicate the role of latent TB reactivation and vitamin D deficiency in driving seasonality.</p>","PeriodicalId":11721,"journal":{"name":"Epidemiology and Infection","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11450509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142343930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-30DOI: 10.1017/S0950268824001055
Leann Denich, Joyce M Cheng, Courtney R Smith, Marsha Taylor, Robin Atkinson, Eva Boyd, Linda Chui, Lance Honish, Leah Isaac, Ashley Kearney, Jennifer J Liang, Victor Mah, Anna J W Manore, Zachary D McCormic, Cynthia Misfeldt, Celine Nadon, Kane Patel, Davendra Sharma, Alexander Todd, April Hexemer
An investigation into an outbreak of Salmonella Newport infections in Canada was initiated in July 2020. Cases were identified across several provinces through whole-genome sequencing (WGS). Exposure data were gathered through case interviews. Traceback investigations were conducted using receipts, invoices, import documentation, and menus. A total of 515 cases were identified in seven provinces, related by 0-6 whole-genome multi-locus sequence typing (wgMLST) allele differences. The median age of cases was 40 (range 1-100), 54% were female, 19% were hospitalized, and three deaths were reported. Forty-eight location-specific case sub-clusters were identified in restaurants, grocery stores, and congregate living facilities. Of the 414 cases with exposure information available, 71% (295) had reported eating onions the week prior to becoming ill, and 80% of those cases who reported eating onions, reported red onion specifically. The traceback investigation identified red onions from Grower A in California, USA, as the likely source of the outbreak, and the first of many food recall warnings was issued on 30 July 2020. Salmonella was not detected in any tested food or environmental samples. This paper summarizes the collaborative efforts undertaken to investigate and control the largest Salmonella outbreak in Canada in over 20 years.
{"title":"A multi-provincial outbreak of <i>Salmonella</i> Newport infections associated with red onions: A report of the largest <i>Salmonella</i> outbreak in Canada in over 20 years.","authors":"Leann Denich, Joyce M Cheng, Courtney R Smith, Marsha Taylor, Robin Atkinson, Eva Boyd, Linda Chui, Lance Honish, Leah Isaac, Ashley Kearney, Jennifer J Liang, Victor Mah, Anna J W Manore, Zachary D McCormic, Cynthia Misfeldt, Celine Nadon, Kane Patel, Davendra Sharma, Alexander Todd, April Hexemer","doi":"10.1017/S0950268824001055","DOIUrl":"10.1017/S0950268824001055","url":null,"abstract":"<p><p>An investigation into an outbreak of <i>Salmonella</i> Newport infections in Canada was initiated in July 2020. Cases were identified across several provinces through whole-genome sequencing (WGS). Exposure data were gathered through case interviews. Traceback investigations were conducted using receipts, invoices, import documentation, and menus. A total of 515 cases were identified in seven provinces, related by 0-6 whole-genome multi-locus sequence typing (wgMLST) allele differences. The median age of cases was 40 (range 1-100), 54% were female, 19% were hospitalized, and three deaths were reported. Forty-eight location-specific case sub-clusters were identified in restaurants, grocery stores, and congregate living facilities. Of the 414 cases with exposure information available, 71% (295) had reported eating onions the week prior to becoming ill, and 80% of those cases who reported eating onions, reported red onion specifically. The traceback investigation identified red onions from Grower A in California, USA, as the likely source of the outbreak, and the first of many food recall warnings was issued on 30 July 2020. <i>Salmonella</i> was not detected in any tested food or environmental samples. This paper summarizes the collaborative efforts undertaken to investigate and control the largest <i>Salmonella</i> outbreak in Canada in over 20 years.</p>","PeriodicalId":11721,"journal":{"name":"Epidemiology and Infection","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11450499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142343929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-30DOI: 10.1017/S0950268824001092
Carl J E Suster, Anne E Watt, Qinning Wang, Sharon C-A Chen, Jen Kok, Vitali Sintchenko
In epidemiological investigations, pathogen genomics can provide insights and test epidemiological hypotheses that would not have been possible through traditional epidemiology. Tools to synthesize genomic analysis with other types of data are a key requirement of genomic epidemiology. We propose a new 'phylepic' visualization that combines a phylogenomic tree with an epidemic curve. The combination visually links the molecular time represented in the tree to the calendar time in the epidemic curve, a correspondence that is not easily represented by existing tools. Using an example derived from a foodborne bacterial outbreak, we demonstrated that the phylepic chart communicates that what appeared to be a point-source outbreak was in fact composed of cases associated with two genetically distinct clades of bacteria. We provide an R package implementing the chart. We expect that visualizations that place genomic analyses within the epidemiological context will become increasingly important for outbreak investigations and public health surveillance of infectious diseases.
在流行病学调查中,病原体基因组学可以提供传统流行病学无法提供的见解并检验流行病学假设。将基因组分析与其他类型的数据综合起来的工具是基因组流行病学的关键要求。我们提出了一种新的 "phylepic "可视化方法,将系统发生树与流行病曲线相结合。这种组合能将系统树中的分子时间与流行病曲线中的日历时间直观地联系起来,而现有的工具并不容易体现这种对应关系。我们以食源性细菌疫情为例,证明了系统树图能说明看似点源疫情实际上是由两个基因不同的细菌支系相关的病例组成的。我们提供了一个实现该图表的 R 软件包。我们预计,将基因组分析置于流行病学背景下的可视化方法对于传染病的爆发调查和公共卫生监测将变得越来越重要。
{"title":"Combined visualization of genomic and epidemiological data for outbreaks.","authors":"Carl J E Suster, Anne E Watt, Qinning Wang, Sharon C-A Chen, Jen Kok, Vitali Sintchenko","doi":"10.1017/S0950268824001092","DOIUrl":"10.1017/S0950268824001092","url":null,"abstract":"<p><p>In epidemiological investigations, pathogen genomics can provide insights and test epidemiological hypotheses that would not have been possible through traditional epidemiology. Tools to synthesize genomic analysis with other types of data are a key requirement of genomic epidemiology. We propose a new 'phylepic' visualization that combines a phylogenomic tree with an epidemic curve. The combination visually links the molecular time represented in the tree to the calendar time in the epidemic curve, a correspondence that is not easily represented by existing tools. Using an example derived from a foodborne bacterial outbreak, we demonstrated that the phylepic chart communicates that what appeared to be a point-source outbreak was in fact composed of cases associated with two genetically distinct clades of bacteria. We provide an R package implementing the chart. We expect that visualizations that place genomic analyses within the epidemiological context will become increasingly important for outbreak investigations and public health surveillance of infectious diseases.</p>","PeriodicalId":11721,"journal":{"name":"Epidemiology and Infection","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11450504/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142343931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-30DOI: 10.1017/S095026882400102X
Shixin Xiu, Zhuping Xu, Xuwen Wang, Li Zhang, Qiang Wang, Min Yang, Yuan Shen
Varicella is a vaccine-preventable infectious disease. Since 1 December 2018, the varicella vaccine has been included in the local Expanded Programme on Immunization (EPI) in Wuxi, China, and children born after 1 December 2014 are eligible for free vaccination. To evaluate the effect of varicella vaccination in Wuxi city, we selected 382 397 children born from 2012 to 2016 as subjects. Their disease data were obtained from the Chinese Disease Prevention and Control Information System, and their vaccination data were obtained from the Jiangsu Province Vaccination Integrated Service Management Information System. The incidence of breakthrough varicella cases increased in the first 4 years and reached the peak in the fifth year. With the increase of vaccination rate, the incidence of varicella decreased significantly. The vaccine effectiveness (VE) was found to be 88.17%-95.78% for one dose and 98.65%-99.93% for two doses. Although the VE per dose decreased from 99.57% in the first year to 93.04% in the eighth year, it remained high. These findings confirmed the effectiveness of varicella vaccination in children, supported the use of a two-dose varicella vaccination strategy to achieve better protection, and provided important insights into the optimal vaccination strategy for varicella prevention in children.
{"title":"Varicella vaccine effectiveness evaluation in Wuxi, China: A retrospective cohort study.","authors":"Shixin Xiu, Zhuping Xu, Xuwen Wang, Li Zhang, Qiang Wang, Min Yang, Yuan Shen","doi":"10.1017/S095026882400102X","DOIUrl":"10.1017/S095026882400102X","url":null,"abstract":"<p><p>Varicella is a vaccine-preventable infectious disease. Since 1 December 2018, the varicella vaccine has been included in the local Expanded Programme on Immunization (EPI) in Wuxi, China, and children born after 1 December 2014 are eligible for free vaccination. To evaluate the effect of varicella vaccination in Wuxi city, we selected 382 397 children born from 2012 to 2016 as subjects. Their disease data were obtained from the Chinese Disease Prevention and Control Information System, and their vaccination data were obtained from the Jiangsu Province Vaccination Integrated Service Management Information System. The incidence of breakthrough varicella cases increased in the first 4 years and reached the peak in the fifth year. With the increase of vaccination rate, the incidence of varicella decreased significantly. The vaccine effectiveness (VE) was found to be 88.17%-95.78% for one dose and 98.65%-99.93% for two doses. Although the VE per dose decreased from 99.57% in the first year to 93.04% in the eighth year, it remained high. These findings confirmed the effectiveness of varicella vaccination in children, supported the use of a two-dose varicella vaccination strategy to achieve better protection, and provided important insights into the optimal vaccination strategy for varicella prevention in children.</p>","PeriodicalId":11721,"journal":{"name":"Epidemiology and Infection","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11450501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142343944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-30DOI: 10.1017/S0950268824001067
Courtney R Smith, Marsha Taylor, Anna J W Manore, April Hexemer, Bijay Adhikari, David Alexander, Robin Atkinson, Linda Chui, Eleni Galanis, Colette Gaulin, Meghan Griffin, Lance Honish, Ashley Kearney, Victor Mah, Rachel McCormick, Michelle Murti
In December 2018, an outbreak of Salmonella Enteritidis infections was identified in Canada by whole-genome sequencing (WGS). An investigation was initiated to identify the source of the illnesses, which proved challenging and complex. Microbiological hypothesis generation methods included comparisons of Salmonella isolate sequence data to historical domestic outbreaks and international repositories. Epidemiological hypothesis generation methods included routine case interviews, open-ended centralized re-interviewing, thematic analysis of open-ended interview data, collection of purchase records, a grocery store site visit, analytic comparison to healthy control groups, and case-case analyses. Food safety hypothesis testing methods included food sample collection and analysis, and traceback investigations. Overall, 83 cases were identified across seven provinces, with onset dates from 6 November 2018 to 7 May 2019. Case ages ranged from 1 to 88 years; 60% (50/83) were female; 39% (22/56) were hospitalized; and three deaths were reported. Brand X profiteroles and eclairs imported from Thailand were identified as the source of the outbreak, and eggs from an unregistered facility were hypothesized as the likely cause of contamination. This study aims to describe the outbreak investigation and highlight the multiple hypothesis generation methods that were employed to identify the source.
{"title":"Everything but the kitchen sink: The use of multiple hypothesis generation methods to investigate an outbreak of <i>Salmonella</i> Enteritidis associated with frozen profiteroles and eclairs.","authors":"Courtney R Smith, Marsha Taylor, Anna J W Manore, April Hexemer, Bijay Adhikari, David Alexander, Robin Atkinson, Linda Chui, Eleni Galanis, Colette Gaulin, Meghan Griffin, Lance Honish, Ashley Kearney, Victor Mah, Rachel McCormick, Michelle Murti","doi":"10.1017/S0950268824001067","DOIUrl":"10.1017/S0950268824001067","url":null,"abstract":"<p><p>In December 2018, an outbreak of <i>Salmonella</i> Enteritidis infections was identified in Canada by whole-genome sequencing (WGS). An investigation was initiated to identify the source of the illnesses, which proved challenging and complex. Microbiological hypothesis generation methods included comparisons of <i>Salmonella</i> isolate sequence data to historical domestic outbreaks and international repositories. Epidemiological hypothesis generation methods included routine case interviews, open-ended centralized re-interviewing, thematic analysis of open-ended interview data, collection of purchase records, a grocery store site visit, analytic comparison to healthy control groups, and case-case analyses. Food safety hypothesis testing methods included food sample collection and analysis, and traceback investigations. Overall, 83 cases were identified across seven provinces, with onset dates from 6 November 2018 to 7 May 2019. Case ages ranged from 1 to 88 years; 60% (50/83) were female; 39% (22/56) were hospitalized; and three deaths were reported. Brand X profiteroles and eclairs imported from Thailand were identified as the source of the outbreak, and eggs from an unregistered facility were hypothesized as the likely cause of contamination. This study aims to describe the outbreak investigation and highlight the multiple hypothesis generation methods that were employed to identify the source.</p>","PeriodicalId":11721,"journal":{"name":"Epidemiology and Infection","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11450506/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142343932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Influenza and other acute respiratory viral infections (ARVIs) are among the most common human diseases. In recent decades, the discovery of cytokines and their significance in the pathogenesis of diseases has led to extensive research on these compounds in various pathologies including ARVIs. The aim of the research was to study the cytokine profile in patients with ARVIs. The cases of 30 patients were investigated. Etiological diagnosis was performed by polymerase chain reaction. Different classes of cytokines in the serum were defined by the enzyme-linked immunosorbent assay (ELISA). The level of cytokines depended on the number of pathogens. The highest levels of pro-inflammatory interleukins and the lowest levels of anti-inflammatory IL-4 were observed in patients with a combination of five or more viruses compared to those with a monoinfection. Analysis of the data showed that in the acute phase, the levels of all studied pro-inflammatory cytokines - IL-2, IL-6, and TNF-α - increased by 8, 39, and 9 times, respectively, compared to those in healthy individuals. In the acute phase of ARVI, the levels of pro-inflammatory cytokines were significantly higher and depended on the severity of the disease. The imbalance of cytokines in the serum has been established in cases of ARVIs, depending on the severity of the disease.
{"title":"Interleukins in the pathogenesis of influenza and other acute respiratory viral infections.","authors":"Mykchaylo Andreychyn, Larysa Melnyk, Nataliia Zavidniiuk, Natalya Nychyk, Iaryna Iosyk","doi":"10.1017/S0950268824001109","DOIUrl":"10.1017/S0950268824001109","url":null,"abstract":"<p><p>Influenza and other acute respiratory viral infections (ARVIs) are among the most common human diseases. In recent decades, the discovery of cytokines and their significance in the pathogenesis of diseases has led to extensive research on these compounds in various pathologies including ARVIs. The aim of the research was to study the cytokine profile in patients with ARVIs. The cases of 30 patients were investigated. Etiological diagnosis was performed by polymerase chain reaction. Different classes of cytokines in the serum were defined by the enzyme-linked immunosorbent assay (ELISA). The level of cytokines depended on the number of pathogens. The highest levels of pro-inflammatory interleukins and the lowest levels of anti-inflammatory IL-4 were observed in patients with a combination of five or more viruses compared to those with a monoinfection. Analysis of the data showed that in the acute phase, the levels of all studied pro-inflammatory cytokines - IL-2, IL-6, and TNF-α - increased by 8, 39, and 9 times, respectively, compared to those in healthy individuals. In the acute phase of ARVI, the levels of pro-inflammatory cytokines were significantly higher and depended on the severity of the disease. The imbalance of cytokines in the serum has been established in cases of ARVIs, depending on the severity of the disease.</p>","PeriodicalId":11721,"journal":{"name":"Epidemiology and Infection","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11450507/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142343933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}