Epidemic Events Research Articles

Supervised Learning for Automated Infectious-Disease-Outbreak Detection

ObjectiveBy systematically scoring algorithms and integrating outbreak data through statistical learning, evaluate and improve the performance of automated infectious-disease-outbreak detection. The improvements should be directly relevant to the epidemiological practice. A broader objective is to explore the usefulness of machine-learning approaches in epidemiology.IntroductionWithin the traditional surveillance of notifiable infectious diseases in Germany, not only are individual cases reported to the Robert Koch Institute, but also outbreaks themselves are recorded: A label is assigned by epidemiologists to each case, indicating whether it is part of an outbreak and of which. This expert knowledge represents, in the language of machine leaning, a "ground truth" for the algorithmic task of detecting outbreaks from a stream of surveillance data. The integration of this kind of information in the design and evaluation of algorithms is called supervised learning.MethodsReported cases were aggregated weekly and divided into two count time series, one for endemic (not part of an outbreak) and one for epidemic cases. Two new algorithms were developed for the analysis of such time series: farringtonOutbreak is an adaptation of the standard method farringtonFlexible as implemented in the surveillance R package: It trains on endemic case counts but detects anomalies on total case counts. The second algorithm is hmmOutbreak, which is based on a hidden Markov model (HMM): A binary hidden state indicates whether an outbreak was reported in a given week, the transition matrix for this state is learned from the outbreak data and this state is integrated as factor in a generalised linear model of the total case count. An explicit probability of being in a state of outbreak is then computed for each week (one-week ahead) and a signal is generated if it is higher than a user-defined threshold.To evaluate performance, we framed outbreak detection as a simple binary classification problem: Is there an outbreak in a given week, yes or no? Was a signal generated for this week, yes or no? One can thus count, for each time series, the true positives (outbreak data and signals agree), false positives, true negatives and false negatives. From those, classical performance scores can be computed, such as sensitivity, specificity, precision, F-score or area under the ROC curve (AUC).For the evaluation with real-word data we used time series of reported cases of salmonellosis and campylobacteriosis for each of the 412 German counties over 9 years. We also ran simple simulations with different parameter sets, generating count time series and outbreaks with the sim.pointSource function of the surveillance R package.ResultsWe have developed a supervised-learning framework for outbreak detection based on reported infections and outbreaks, proposing two algorithms and an evaluation method. hmmOutbreak performs overall much better than the standard farringtonFlexible, with e.g. a 60% improvement in sensitivity (0.5 compared to 0.3) at a fixed specificity of 0.9. The results were confirmed by simulations. Furthermore, the computation of explicit outbreak probabilities allows a better and clearer interpretation of detection results than the usual testing of the null hypothesis "is endemic".ConclusionsMethods of machine learning can be usefully applied in the context of infectious-disease surveillance. Already a simple HMM shows large improvements and better interpretability: More refined methods, in particular semi-supervised approaches, look thus very promising. The systematic integration of available expert knowledge, in this case the recording of outbreaks, allows an evaluation of algorithmic performance that is of direct relevance for the epidemiological practice, in contrast to the usual intrinsic statistical metrics. Beyond that, this knowledge can be readily used to improve that performance and, in the future, gain insights in outbreak dynamics. Moreover, other types of labels will be similarly integrated in automated surveillance analyses, e.g. user feedback on whether a signal was relevant (reinforcement learning) or messages on specialised internet platforms that were found to be useful warnings of international epidemic events.

Forest structure and climate mediate drought-induced tree mortality in forests of the Sierra Nevada, USA.

Extreme drought stress and associated bark beetle population growth contributed to an extensive tree mortality event in California, USA, resulting in more than 129million trees dying between 2012 and 2016. Although drought is an important driver of this mortality event, past and ongoing fire suppression and the consequent densification of forests may have contributed. In some areas, land management agencies have worked to reduce stand density through mechanical treatments and prescribed fire to restore forests to less dense, more open conditions that are presumably more resilient to disturbance and changing climate. Here, we evaluate if stand structural conditions associated with treated (e.g., thinned and prescribed burned) forests in the Sierra Nevada of California conferred more resistance to the bark beetle epidemic and drought event of 2012-2016. We found that, compared to untreated units, treated units had lower stand densities, larger average tree diameters, and greater dominance of pines (Pinus), the historically dominant trees. For all tree species studied, mortality was substantially greater in climatically drier areas (i.e., lower elevations and latitudes). Both pine species studied (ponderosa pine [Pinus ponderosa] and sugar pine [Pinus lambertiana]) had greater mortality in areas where their diameters were larger, suggesting a size preference for their insect mortality agents. For ponderosa pine, the tree species experiencing greatest mortality, individual-tree mortality probability (for a given tree diameter) was significantly lower in treated stands. Ponderosa pine mortality was also positively related to density of medium- to large-sized conspecific trees, especially in areas with lower precipitation, suggesting that abundance of nearby host trees for insect mortality agents was an important determinant of pine mortality. Mortality of incense cedar (Calocedrus decurrens) and white fir (Abies concolor) was positively associated with basal area, suggesting sensitivity to competition during drought, but overall mortality was lower, likely because the most prevalent and effective mortality agents (the bark beetles Dendroctonus brevicomis and D.ponderosae) are associated specifically with pine species within our study region. Our findings suggest that forest thinning treatments are effective in reducing drought-related tree mortality in forests, and they underscore the important interaction between water and forest density in mediating bark beetle-caused mortality.

Thunderstorm-triggered asthma: what we know so far.

Thunderstorm-triggered asthma (TA) is the occurrence of acute asthma attacks immediately following a thunderstorm. Epidemics have occurred across the world during pollen season and have the capacity to rapidly inundate a health care service, resulting in potentially catastrophic outcomes for patients. TA occurs when specific meteorological and aerobiological factors combine to affect predisposed patients. Thunderstorm outflows can concentrate aeroallergens, most commonly grass pollen in TA, at ground level to release respirable allergenic particles after rupture by osmotic shock related to humidity and rainfall. Inhalation of high concentrations of these aeroallergens by sensitized individuals can induce early asthmatic responses which are followed by a late inflammatory phase. Other environmental factors such as rapid temperature change and agricultural practices contribute to the causation of TA. The most lethal TA event occurred in Melbourne, Australia, in 2016. Studies on the affected individuals found TA to be associated with allergic rhinitis, ryegrass pollen sensitization, pre-existing asthma, poor adherence to inhaled corticosteroid preventer therapy, hospital admission for asthma in the previous year and outdoor location at the time of the storm. Patients without a prior history of asthma were also affected. These factors are important in extending our understanding of the etiology of TA and associated clinical indicators as well as possible biomarkers which may aid in predicting those at risk and thus those who should be targeted in prevention campaigns. Education on the importance of recognizing asthma symptoms, adherence to asthma treatment and controlling seasonal allergic rhinitis is vital in preventing TA. Consideration of allergen immunotherapy in selected patients may also mitigate risk of future TA. Epidemic TA events are predicted to increase in frequency and severity with climate change, and identifying susceptible patients and preventing poor outcomes is a key research and public health policy priority.

Epidemic Thunderstorm Asthma

Introduction:On November 21 and 22 of 2016, Victoria witnessed an unprecedented epidemic thunderstorm asthma emergency event in size acuity and impact. This scenario was never exercised nor contemplated. The event resulted in a 73% increase in calls to the Emergency Services Telecommunications Authority and 814 ambulance cases in the six hours from 6 pm on November 21, 2016. A 58% increase in people presented to public hospital emergency departments in Melbourne and Geelong on November 21 and 22, 2016 (based on the three-year average). 313 calls were made to the nurse on call from people with breathing, respiratory, and allergy problems (compared to an average of 63 calls for the previous month). Tragically, ten deaths are linked to this event.Methods:A substantial amount of work has been completed, much of which goes towards addressing the Inspector-General for Emergency Management recommendations following a review of the event, including: Release of an epidemic thunderstorm asthma campaign and education programs which were rolled out across Victoria for the community and health professionals from September through November 2017;Development of a new epidemic thunderstorm asthma forecasting system on 1 October 2017 and updated warning protocols during the 2017 grass pollen season;Implementation of a Real-time Health Emergency Monitoring System to alert the department of demands on public hospital emergency departments on the system; andIntroduction of a new State Health Emergency Response Plan in October 2017 to improve coordination and communications before and during a health emergency.Discussion:The presentation will concentrate on the lessons learned more than two years down the track from the event in November 2016.

Geographic Distribution of Epizootic haematopoietic necrosis virus (EHNV) in Freshwater Fish in South Eastern Australia: Lost Opportunity for a Notifiable Pathogen to Expand Its Geographic Range.

Epizootic haematopoietic necrosis virus (EHNV) was originally detected in Victoria, Australia in 1984. It spread rapidly over two decades with epidemic mortality events in wild redfin perch (Perca fluviatilis) and mild disease in farmed rainbow trout (Oncorhynchus mykiss) being documented across southeastern Australia in New South Wales (NSW), the Australian Capital Territory (ACT), Victoria, and South Australia. We conducted a survey for EHNV between July 2007 and June 2011. The disease occurred in juvenile redfin perch in ACT in December 2008, and in NSW in December 2009 and December 2010. Based on testing 3622 tissue and 492 blood samples collected from fish across southeastern Australia, it was concluded that EHNV was most likely absent from redfin perch outside the endemic area in the upper Murrumbidgee River catchment in the Murray–Darling Basin (MDB), and it was not detected in other fish species. The frequency of outbreaks in redfin perch has diminished over time, and there have been no reports since 2012. As the disease is notifiable and a range of fish species are known to be susceptible to EHNV, existing policies to reduce the likelihood of spreading out of the endemic area are justified.

Phylogenetic analysis of porcine circovirus type 2 in Sardinia, Italy, shows genotype 2d circulation among domestic pigs and wild boars

Porcine circovirus type 2 (PCV2) is associated with multi-factorial syndromes, commonly known as porcine-circovirus–associated diseases, which cause severe economic losses in the swine industry worldwide. Four genotypes (PCV2a, PCV2b, PCV2c, and PCV2d) have been identified. Lately, the prevalence of PCV2d has been increasing in many countries, thereby prefiguring a global replacement of PCV2b. Wild boars are also susceptible to PCV2 infection, with virus prevalence similar to that of domestic pigs. This work was aimed at expanding the knowledge about the molecular epidemiology of PCV2 in Italy. For this purpose, we analysed 40 complete ORF-2 sequences from PCV2 strains isolated from domestic pigs and wild boars in Sardinia (Italy) over a period of 5 years (2009–2013). Phylogenetic and Bayesian analyses were performed on three data sets compiled from DNA sequences over a large geographical area. PCV2b was found to be dominant in Sardinia, whereas no PCV2a and PCV2c were found. This study indicates the presence of genotype PCV2d-2 infecting both domestic and wild pigs, thus confirming its circulation in Italy. Sardinian sequences clustered mostly with Italian isolates and with strains from China, Belgium, Croatia, Taiwan, Korea, and Portugal. Genetic variability of PCV2 in Sardinia appears to be a result of both local viral evolution and different epidemic introduction events.

Serratia marcescens Infections in Neonatal Intensive Care Units (NICUs).

Serratia marcescens belongs to the family Enterobacteriaceae, which is commonly found in water, soil, animals, insects, plants. Although S. marcescens displays relatively low virulence, it causes nosocomial infections and outbreaks in severely immunocompromised or critically ill patients, particularly in settings such as intensive care units (ICUs), especially neonatal units (NICUs). This microorganism gives rise to a wide range of clinical manifestations in newborns: from asymptomatic colonization to keratitis, conjunctivitis, urinary tract infections, pneumonia, surgical wound infections, sepsis, bloodstream infection and meningitis. The most frequent site of infection is the bloodstream, followed by the respiratory apparatus and the gastrointestinal tract. Strains of S. marcescens involved in epidemic events have frequently proved to be multi-resistant. Indeed, this species displays intrinsic resistance to several classes of antibiotics. Often, the specific source of the infection cannot be identified. However, the contaminated hands of healthcare workers are believed to be a major vehicle of its transmission. In neonatal intensive care units, colonized or infected newborns are the main potential source of S. marcescens, particularly in the respiratory apparatus, but also in the gastrointestinal tract. The early identification of colonized or infected patients and the prompt implementation of infection control measures, particularly rigorous hand hygiene and contact precautions, are essential in order to curb the spread of infection.

Control of Acute Arboviral Infection by Natural Killer Cells.

The recent explosive pandemic of chikungunya virus (CHIKV) followed by Zika (ZIKV) virus infections occurring throughout many countries represents the most unexpected arrival of arthropod-borne viral diseases in the past 20 years. Transmitted through the bite of Aedes mosquitoes, the clinical picture associated with these acute arbovirus infections, including Dengue (DENV), CHIKV and ZIKV, ranges from classical febrile illness to life-threatening disease. Whereas ZIKV and CHIKV-mediated infections have previously been recognized as relatively benign diseases, in contrast to Dengue fever, recent epidemic events have brought waves of increased morbidity and mortality leading to a serious public health problem. Although the host immune response plays a crucial role in controlling infections, it may also promote viral spread and immunopathology. Here, we review recent developments in our understanding of the immune response, with an emphasis on the early antiviral immune response mediated by natural killer cells and emphasize their Janus-faced effects in the control of arbovirus infection and pathogenesis. Improving our understanding knowledge on of the mechanisms that control viral infection is crucial in the current race against the globalization of arbovirus epidemics.

A qualitative descriptive study of the contextual factors influencing the practice of emergency nurses in managing emerging infectious diseases

ABSTRACT Purpose: Emergency nurses are engaged in the management of epidemic events that unfold along with the evolution of diseases. The goal of this study was to explore the contextual factors that inhibited the ability of emergency nurses to perform their duties in response to an outbreak. Methods: A qualitative descriptive design was used to explore the experiences and perceptions of emergency nurses. Participants were purposively recruited from 12 emergency departments in Hong Kong. Semi-structured face-to-face individual interviews were conducted with 26 emergency nurses. The audio-recorded interviews were transcribed verbatim and interpreted with a thematic analysis approach. Results: Four intertwined themes emerged from the analysis: resource constraints, threats of infection, ubiquitous changes and lingering uncertainties. These themes portrayed the constraints and challenges surrounding the work environment of emergency nurses. Conclusion: This study described the instabilities and vulnerabilities of the circumstances in which the emergency nurses were situated in during epidemic events. The findings shed light on the importance of hospitals and emergency departments in addressing both the technical problems and adaptive challenges that face emergency nurses during epidemic events.

Cuban Strategy and Medical Cooperation to Combat Ebola, 2014-2016.

The Ebola virus is a pathogen that causes high morbidity and mortality in epidemic events during which health personnel are frequently infected. Such an epidemic occurred in West Africa, prompting WHO to issue a call in 2014 for health personnel to be dispatched to affected countries. Cuba responded and signed an assistance agreement under which 265 Cuban health professionals, members of the Henry Reeve Emergency Medical Contingent, volunteered their services in the Republic of Guinea, Sierra Leone and Liberia. This article presents Cuba's strategy of medical aid and organization of the three medical teams formed; refers to the teams' contribution to epidemic control in treatment centers where they worked alongside other personnel; and describes measures taken in Cuba to prevent the virus from entering the country through returning volunteers or other means. In the centers where Cuban medical teams worked with other health professionals in West Africa, case fatality decreased from 80%-90% to 24%, contributing to control of the epidemic; no Ebola outbreaks occurred in Cuba. During the epidemic, two Cuban health professionals died of malaria and one physician fell ill with Ebola. This paper includes an overview of the treatment and evolution of the latter case, a doctor who contracted the disease in Sierra Leone and was treated in Geneva and Havana. KEYWORDS Ebola virus, treatment, strategy, followup, medical collaboration, Republic of Guinea, Sierra Leone, Liberia, Cuba.

Towards Personalized Vaccines—Tailoring Peptide Vaccines to Demographic Groups and Individuals

Traditional vaccines have seen spectacular successes in eradicating smallpox and have come close to eradicating poliomyelitis also. However, they have been short in combating viral epidemics which are now occurring with increasing frequency; the reasons are primarily due to rapid mutations in RNA viruses. Alternative procedures are to be found in the new science of vaccinomics where peptide vaccines have come to be recognized as a strong alternative strategy. While several issues still need to be resolved, and no license has yet been released for human use of peptide vaccines, such vaccines have found ready acceptance in cancer therapeutics where personalized vaccines are of necessity the de facto norm. This knowledge gives us the opportunity in the event of viral epidemics to tailor making vaccines for different communities for maximum efficiency and for immunocompromised individuals. We give a brief perspective on the current status and future prospects of new trends in vaccine research, specifically peptide vaccines development, in this paper.

Grassland Phenology and Meteorology Co-Influence Grass Pollen Counts in Victoria, Australia

AIMThis study investigated the role of grassland phenology in driving daily and seasonal pollen counts in Melbourne, Victoria and characterized the ecological conditions leading up to Melbourne’s epidemic thunderstorm asthma event on 21/11/2016. Landscape ecological conditions have traditionally been overlooked as an environmental driver of pollen variability. An understanding of relationships of pollen counts with vegetation type and phenology is valuable to develop better tools to forecast the pollen season and the associated allergenic risks.METHODWe combined 2000-2016 Enhanced Vegetation Index (EVI) data from the Moderate Resolution Imaging Spectroradiometer (MODIS), gridded meteorology products and 1991-2016 grass pollen counts to assess spatial and temporal correspondences among phenology, meteorology and pollen counts in Victoria. Grassland and pollen phenological metrics were analysed for trends and anomalies, and comparisons made of correlations between pollen season metrics and meteorological variables and between pollen season metrics and phenology metrics.RESULTSSeasonal grass pollen highly correlated with the integrated EVI while daily grass pollen highly correlated with meteorology. We detected a broad hotspot area northwest of Melbourne which experienced both anomalously high EVI values and a significant delay of peak EVI date in 2016. > 20% of the landscape had not reached peak EVI by the start of the pollen season (05/10/2016), heightening exposure to local flowering and hence pollen emission.CONCLUSIONWe showed that grass phenology directly controls pollen production, including pollen hotspots, whereas meteorology determines where and when high pollen deposition will occur. Future forecasting of pollen season and the associated allergenic risks should take into account the timing and spatial variability of grassland phenology as well as the co-influences over pollen production, transport and deposition between vegetation and meteorology.

Melbourne epidemic thunderstorm asthma event 2016: Lessons learnt from the perfect storm.

Melbourne epidemic thunderstorm asthma event 2016: Lessons learnt from the perfect storm.

Naloxone Administration Frequency During Emergency Medical Service Events - United States, 2012-2016.

As the opioid epidemic in the United States has continued since the early 2000s (1,2), most descriptions have focused on misuse and deaths. Increased cooperation with state and local partners has enabled more rapid and comprehensive surveillance of nonfatal opioid overdoses (3).* Naloxone administrations obtained from emergency medical services (EMS) patient care records have served as a useful proxy for overdose surveillance in individual communities and might be a previously unused data source to describe the opioid epidemic, including fatal and nonfatal events, on a national level (4-6). Using data from the National Emergency Medical Services Information System (NEMSIS),† the trend in rate of EMS naloxone administration events from 2012 to 2016 was compared with opioid overdose mortality rates from National Vital Statistics System multiple cause-of-death mortality files. During 2012-2016, the rate of EMS naloxone administration events increased 75.1%, from 573.6 to 1004.4 administrations per 100,000 EMS events, mirroring the 79.7% increase in opioid overdose mortality from 7.4 deaths per 100,000 persons to 13.3. A bimodal age distribution of patients receiving naloxone from EMS parallels a similar age distribution of deaths, with persons aged 25-34 years and 45-54 years most affected. However, an accurate estimate of the complete injury burden of the opioid epidemic requires assessing nonfatal overdoses in addition to deaths. Evaluating and monitoring nonfatal overdose events via the novel approach of using EMS data might assist in the development of timely interventions to address the evolving opioid crisis.

Insights from outside BJOG

Insights from outside BJOG

Is autumn the key for dengue epidemics in non endemic regions? The case of Argentina.

BackgroundDengue is a major and rapidly increasing public health problem. In Argentina, the southern extreme of its distribution in the Americas, epidemic transmission takes place during the warm season. Since its re-emergence in 1998 two major outbreaks have occurred, the biggest during 2016. To identify the environmental factors that trigger epidemic events, we analyzed the occurrence and magnitude of dengue outbreaks in time and space at different scales in association with climatic, geographic and demographic variables and number of cases in endemic neighboring countries.MethodsInformation on dengue cases was obtained from dengue notifications reported in the National Health Surveillance System. The resulting database was analyzed by Generalized Linear Mixed Models (GLMM) under three methodological approaches to: identify in which years the most important outbreaks occurred in association with environmental variables and propose a risk estimation for future epidemics (temporal approach); characterize which variables explain the occurrence of local outbreaks through time (spatio-temporal approach); and select the environmental drivers of the geographical distribution of dengue positive districts during 2016 (spatial approach).ResultsWithin the temporal approach, the number of dengue cases country-wide between 2009 and 2016 was positively associated with the number of dengue cases in bordering endemic countries and negatively with the days necessary for transmission (DNT) during the previous autumn in the central region of the country. Annual epidemic intensity in the period between 1999–2016 was associated with DNT during previous autumn and winter. Regarding the spatio-temporal approach, dengue cases within a district were also associated with mild conditions in the previous autumn along with the number of dengue cases in neighboring countries. As for the spatial approach, the best model for the occurrence of two or more dengue cases per district included autumn minimum temperature and human population as fixed factors, and the province as a grouping variable. Explanatory power of all models was high, in the range 57–95%.DiscussionGiven the epidemic nature of dengue in Argentina, virus pressure from endemic neighboring countries along with climatic conditions are crucial to explain disease dynamics. In the three methodological approaches, temperature conditions during autumn were best associated with dengue patterns. We propose that mild autumns represent an advantage for mosquito vector populations and that, in temperate regions, this advantage manifests as a larger egg bank from which the adult population will re-emerge in spring. This may constitute a valuable anticipating tool for high transmission risk events.

Post-Zika Guillain-Barre Syndrom: Description of clinical, biological, functional and electrophysiological characteristics observed during the Zika epidemic in Martinique

The objective is to carry out a descriptive study listing the clinical, biological, functional and electrophysiological characteristics observed in patients with post-ZIKA Guillain-Barre syndromes (SGB) during the ZIKA epidemic in Martinique, and hospitalized in a rehabilitation service. A retrospective study of subjects with post-ZIKA SGB from December 2015 to September 2016 in Martinique diagnosed according to Brighton criteria associated with molecular biology techniques, serology, and electrophysiology. Collection of data at nadir and discharge from hospitalization. Twenty-five subjects were included with a sex ratio of 1.27 and a median age of 65 years. In total, 13 patients were hospitalized in intensive care unit. At nadir, 21 patients (84%) were tetraparetic, 10 (40%) had facial diplegia, 15 (60%) had severe swallowing disorders, 12 (48%) were dysuric, 6 (24%) had acute urinary retention. Twenty-four patients (96%) had paresthesias, 11 (44%) had severe constipation requiring repeated enemas, 8 (32%) had infectious pneumonia with 7 (28%) pneumopathies with mechanical ventilation, 2 (8%) had a cardiorespiratory arrest. The median for the duration of the extension phase was 8 days versus 4 days for the plateau phase. The median for the delay between the first signs of ZIKA infection and the first neurological signs was 2.5 days. Sixteen urine PCR returned positive for ZIKA and serum neutralization was required for 9 subjects, Twenty-one acute inflammatory demyelinating polyradiculoneuritis were objectified. In total, 13 patients (52%) required a nasogastric tube, 4 (16%) required percutaneous gastrostomy, 9 (36%) had orotracheal intubation, and 6 (24%) had tracheotomy. All the patients returned home with a quasi-complete autonomy. The large number of disorders of swallowing and dysautonomia haemodynamic and vesicospincterian will be important elements to be favored in the acute management in the event of new epidemics due to their therapeutic urgency and residual incapacities. Despite severe clinical forms, patients presented good functional recovery.

The Melbourne epidemic thunderstorm asthma event 2016: an investigation of environmental triggers, effect on health services, and patient risk factors

A multidisciplinary collaboration investigated the world's largest, most catastrophic epidemic thunderstorm asthma event that took place in Melbourne, Australia, on Nov 21, 2016, to inform mechanisms and preventive strategies. Meteorological and airborne pollen data, satellite-derived vegetation index, ambulance callouts, emergency department presentations, and data on hospital admissions for Nov 21, 2016, as well as leading up to and following the event were collected between Nov 21, 2016, and March 31, 2017, and analysed. We contacted patients who presented during the epidemic thunderstorm asthma event at eight metropolitan health services (each including up to three hospitals) via telephone questionnaire to determine patient characteristics, and investigated outcomes of intensive care unit (ICU) admissions. Grass pollen concentrations on Nov 21, 2016, were extremely high (>100 grains/m3). At 1800 AEDT, a gust front crossed Melbourne, plunging temperatures 10°C, raising humidity above 70%, and concentrating particulate matter. Within 30 h, there were 3365 (672%) excess respiratory-related presentations to emergency departments, and 476 (992%) excess asthma-related admissions to hospital, especially individuals of Indian or Sri Lankan birth (10% vs 1%, p<0·0001) and south-east Asian birth (8% vs 1%, p<0·0001) compared with previous 3 years. Questionnaire data from 1435 (64%) of 2248 emergency department presentations showed a mean age of 32·0 years (SD 18·6), 56% of whom were male. Only 28% had current doctor-diagnosed asthma. 39% of the presentations were of Asian or Indian ethnicity (25% of the Melbourne population were of this ethnicity according to the 2016 census, relative risk [RR] 1·93, 95% CI 1·74-2·15, p <0·0001). Of ten individuals who died, six were Asian or Indian (RR 4·54, 95% CI 1·28-16·09; p=0·01). 35 individuals were admitted to an intensive care unit, all had asthma, 12 took inhaled preventers, and five died. Convergent environmental factors triggered a thunderstorm asthma epidemic of unprecedented magnitude, tempo, and geographical range and severity on Nov 21, 2016, creating a new benchmark for emergency and health service escalation. Asian or Indian ethnicity and current doctor-diagnosed asthma portended life-threatening exacerbations such as those requiring admission to an ICU. Overall, the findings provide important public health lessons applicable to future event forecasting, health care response coordination, protection of at-risk populations, and medical management of epidemic thunderstorm asthma. None.

The intrinsic vulnerability of networks to epidemics

Contact networks are convenient models to investigate epidemics, with nodes and links representing potential hosts and infection pathways, respectively. The outcomes of outbreak simulations on networks are driven both by the underlying epidemic model, and by the networks’ structural properties, so that the same pathogen can generate different epidemic dynamics on different networks. Here we ask whether there are general properties that make a contact network intrinsically vulnerable to epidemics (that is, regardless of specific epidemiological parameters). By conducting simulations on a large set of modelled networks, we show that, when a broad range of network topologies is taken into account, the effect of specific network properties on outbreak magnitude is stronger than that of fundamental pathogen features such as transmission rate, infection duration, and immunization ability. Then, by focusing on a large set of real world networks of the same type (potential contacts between field voles, Microtus agrestis), we showed how network structure can be used to accurately assess the relative, intrinsic vulnerability of networks towards a specific pathogen, even when those have limited topological variability. These results have profound implications for how we prevent disease outbreaks; in many real world situations, the topology of host contact networks can be described and used to infer intrinsic vulnerability. Such an approach can increase preparedness and inform preventive measures against emerging diseases for which limited epidemiological information is available, enabling the identification of priority targets before an epidemic event.

Risk for interspecies transmission of zoonotic pathogens during poultry processing and pork production in Peru: A qualitative study.

Interspecies transmission of pathogens is an unfrequent but naturally occurring event and human activities may favour opportunities not previously reported. Reassortment of zoonotic pathogens like influenza A virus can result from these activities. Recently, swine and birds have played a central role as "mixing vessels" for epidemic and pandemic events related to strains like H1N1 and H5N1. Unsafe practices in poultry markets and swine farms can lead to interspecies transmission, favouring the emergence of novel strains. Thus, understanding practices that lead to interspecies interactions is crucial. This qualitative study aimed to evaluate poultry processing practices in formal and informal markets and the use of leftovers by swine farmers in three Peruvian cities: Lima (capital), Tumbes (coastal) and Tarapoto (jungle). We conducted 80 direct observations at formal and informal markets and interviewed 15 swine farmers. Processors slaughter and pluck chickens and vendors and/or processors eviscerate chickens. Food safety and hygiene practices were suboptimal or absent, although some heterogeneity was observed between cities and chicken vendors versus processors. Both vendors (76%) and processors (100%) sold the chicken viscera leftovers to swine farmers, representing the main source of chicken viscera for swine farms (53%). Swine farmers fed the chicken viscera to their swine. Chicken viscera cooking times varied widely and were insufficient in some cases. Non-abattoired poultry leads to the sale of poultry leftovers to small-scale swine farms, resulting in indirect but frequent interspecies contacts that can lead to interspecies transmission of bacterial pathogens or the reassortment of influenza A viruses. These interactions are exacerbated by suboptimal safety and hygiene conditions. People involved in these activities constitute an at-risk population who could play a central role in preventing the transmission of pathogens between species. Educational interventions on hygiene and food safety practices will be important for reducing the risk of interspecies influenza transmission.