Journal: Emerging Infectious Diseases

Abbreviation

Emerg Infect Dis

Publisher

Centers for Disease Control and Prevention

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ISSN

1080-6059
1080-6040

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Publications 1 - 10 of 11
  • Genomic Epidemiology of Early SARS-CoV-2 Transmission Dynamics, Gujarat, India
    Item type: Journal Article
    Raghwani, Jayna; Du Plessis, Louis; McCrone, John T.; et al. (2022)
    Emerging Infectious Diseases
    Limited genomic sampling in many high-incidence countries has impeded studies of severe respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic epidemiology. Consequently, critical questions remain about the generation and global distribution of virus genetic diversity. We investigated SARS-CoV-2 transmission dynamics in Gujarat, India, during the state’s first epidemic wave to shed light on spread of the virus in one of the regions hardest hit by the pandemic. By integrating case data and 434 whole-genome sequences sampled across 20 districts, we reconstructed the epidemic dynamics and spatial spread of SARS-CoV-2 in Gujarat. Our findings indicate global and regional connectivity and population density were major drivers of the Gujarat outbreak. We detected >100 virus lineage introductions, most of which appear to be associated with international travel. Within Gujarat, virus dissemination occurred predominantly from densely populated regions to geographically proximate locations that had low population density, suggesting that urban centers contributed disproportionately to virus spread.
  • Multidisciplinary Tracking of Highly Pathogenic Avian Influenza A (H5N1) Outbreak in Griffon Vultures, Southern Europe, 2022
    Item type: Journal Article
    Hirschinger, Julien; Höfle, Ursula; Sánchez-Cano, Alberto; et al. (2025)
    Emerging Infectious Diseases
    Since 2021, highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b virus has affected wild bird populations globally. Griffon vultures (Gyps fulvus), a species hitherto considered unexposed, experienced an HPAI H5N1 outbreak in 2022 in southern Europe, leading to moderate mortality and reduced breeding success. The integration of virological, serologic, phylogenetic, and ecologic data revealed a short yet intense viral circulation and a probable common source of infection. The dissemination across Spain and France was likely caused by frequent interpopulation movements of birds. This integrated overview of the 2022 HPAI outbreak in vultures provides novel insights into the role of large-scale movements of wild birds in the spread of such disease. Understanding the epidemiologic dynamics of HPAI H5N1 in these scavenger species is crucial because the birds play vital roles in ecosystem functioning. Their susceptibility to this virus highlights potential broader ecologic effects of the ongoing outbreaks.
  • Genetic Cluster of Extended-Spectrum β-lactamase–Producing Klebsiella pneumoniae in Humans and Food, Switzerland, 2018–2019
    Item type: Journal Article
    Aguilar-Bultet, Lisandra; Gómez-Sanz, Elena; Vock, Isabelle; et al. (2025)
    Emerging Infectious Diseases
    We describe a cluster of genetically related extended-spectrum β-lactamase–producing Klebsiella pneumoniae sequence type 14 recovered from human clinical samples and an alfalfa-cress sample collected by systematic food sampling in Basel, Switzerland. Our findings suggest food could represent a reservoir contributing to spread of extended-spectrum β-lactamase–producing Enterobacterales.
  • Predictive Mapping of Antimicrobial Resistance for Escherichia coli, Salmonella, and Campylobacter in Food-Producing Animals, Europe, 2000-2021
    Item type: Journal Article
    Mulchandani, Ranya; Zhao, Cheng; Tiseo, Katie; et al. (2024)
    Emerging Infectious Diseases
    In Europe, systematic national surveillance of antimicrobial resistance (AMR) in food-producing animals has been conducted for decades; however, geographic distribution within countries remains unknown. To determine distribution within Europe, we combined 33,802 country-level AMR prevalence estimates with 2,849 local AMR prevalence estimates from 209 point prevalence surveys across 31 countries. We produced geospatial models of AMR prevalence in Escherichia coli, nontyphoidal Salmonella, and Campylobacter for cattle, pigs, and poultry. We summarized AMR trends by using the proportion of tested antimicrobial compounds with resistance >50% and generated predictive maps at 10 × 10 km resolution that disaggregated AMR prevalence. For E. coli, predicted prevalence rates were highest in southern Romania and southern/eastern Italy; for Salmonella, southern Hungary and central Poland; and for Campylobacter, throughout Spain. Our findings suggest that AMR distribution is heterogeneous within countries and that surveillance data from below the country level could help with prioritizing resources to reduce AMR.
  • Reduction in antimicrobial use and resistance to salmonella, campylobacter, and escherichia coli in broiler chickens, Canada, 2013–2019
    Item type: Review Article
    Huber, Laura; Agunos, Agnes; Gow, Sheryl P.; et al. (2021)
    Emerging Infectious Diseases
    Antimicrobial use contributes to the global rise of antimicrobial resistance (AMR). In 2014, the poultry industry in Canada initiated its Antimicrobial Use Reduction Strategy to mitigate AMR in the poultry sector. We monitored trends in antimicrobial use and AMR of foodborne bacteria (Salmonella, Escherichia coli, and Campylobacter) in broiler chickens during 2013 and 2019. We quantified the effect of antimicrobial use and management factors on AMR by using LASSO regression and generalized mixed-effect models. AMR in broiler chickens declined by 6%-38% after the decrease in prophylactic antimicrobial use. However, the withdrawal of individual compounds, such as cephalosporins and fluoroquinolones, prompted an increase in use of and resistance levels for other drug classes, such as aminoglycosides. Canada's experience with antimicrobial use reduction illustrates the potential for progressive transitions from conventional antimicrobial-dependent broiler production to more sustainable production with respect to antimicrobial use.
  • Role of Live-Duck Movement Networks in Transmission of Avian Influenza, France, 2016–2017
    Item type: Journal Article
    Guinat, Claire; Durand, Benoit; Vergne, Timothée; et al. (2020)
    Emerging Infectious Diseases
    The relative roles that movement and proximity networks play in the spread of highly pathogenic avian influenza (HPAI) viruses are often unknown during an epidemic, preventing effective control. We used network analysis to explore the devastating epidemic of HPAI A(H5N8) among poultry, in particular ducks, in France during 2016-2017 and to estimate the likely contribution of live-duck movements. Approximately 0.2% of live-duck movements could have been responsible for between-farm transmission events, mostly early during the epidemic. Results also suggest a transmission risk of 35.5% when an infected holding moves flocks to another holding within 14 days before detection. Finally, we found that densely connected groups of holdings with sparse connections between groups overlapped farmer organizations, which represents important knowledge for surveillance design. This study highlights the importance of movement bans in zones affected by HPAI and of understanding transmission routes to develop appropriate HPAI control strategies. © 2020 Centers for Disease Control and Prevention (CDC)
  • Mapping Global Bushmeat Activities to Improve Zoonotic Spillover Surveillance by Using Geospatial Modeling
    Item type: Journal Article
    Jagadesh, Soushieta; Zhao, Cheng; Mulchandani, Ranya; et al. (2023)
    Emerging Infectious Diseases
    Human populations that hunt, butcher, and sell bushmeat (bushmeat activities) are at increased risk for zoonotic pathogen spillover. Despite associations with global epidemics of severe illnesses, such as Ebola and mpox, quantitative assessments of bushmeat activities are lacking. However, such assessments could help prioritize pandemic prevention and preparedness efforts. We used geospatial models that combined published data on bushmeat activities and ecologic and demographic drivers to map the distribution of bushmeat activities in rural regions globally. The resulting map had high predictive capacity for bushmeat activities (true skill statistic = 0.94). The model showed that mammal species richness and deforestation were principal drivers of the geographic distribution of bushmeat activities and that countries in West and Central Africa had the highest proportion of land area associated with bushmeat activities. These findings could help prioritize future surveillance of bushmeat activities and forecast emerging zoonoses at a global scale.
  • Role of Backyard Flocks in Transmission Dynamics of Highly Pathogenic Avian Influenza A(H5N8) Clade 2.3.4.4, France, 2016–2017
    Item type: Journal Article
    Souvestre, Marie; Guinat, Claire; Niqueux, Eric; et al. (2019)
    Emerging Infectious Diseases
    Highly pathogenic avian influenza A(H5N8) clade 2.3.4.4 spread in France during 2016–2017. We assessed the biosecurity and avian influenza virus infection status of 70 backyard flocks near H5N8-infected commercial farms. One flock was seropositive for clade 2.3.4.4. Backyard flocks linked to commercial farms had elevated risk for H5 infection.
  • Undetected Circulation of African Swine Fever in Wild Boar, Asia
    Item type: Journal Article
    Vergne, Timothée; Guinat, Claire; Pfeiffer, Dirk U. (2020)
    Emerging Infectious Diseases
    African swine fever is a growing threat to the livestock industry. We examined data indicating that in most countries in Asia, most notified events were related to farm outbreaks; meanwhile, only a few wild boar cases were reported. We hypothesize the virus circulates unnoticed in wild boar populations in Asia.
  • Co-infections of adenovirus species in previously vaccinated patients
    Item type: Journal Article
    Vora, Gary J.; Lin, Baochuan; Gratwick, Kevin; et al. (2006)
    Emerging Infectious Diseases
    Despite the success of the adenovirus vaccine administered to US military trainees, acute respiratory disease (ARD) surveillance still detected breakthrough infections (respiratory illnesses associated with the adenovirus serotypes specifically targeted by the vaccine). To explore the role of adenoviral co-infection (simultaneous infection by multiple pathogenic adenovirus species) in breakthrough disease, we examined specimens from patients with ARD by using 3 methods to detect multiple adenoviral species: a DNA microarray, a polymerase chain reaction (PCR)–enzyme-linked immunosorbent assay, and a multiplex PCR assay. Analysis of 52 samples (21 vaccinated, 31 unvaccinated) collected from 1996 to 2000 showed that all vaccinated samples had co-infections. Most of these co-infections were community-acquired serotypes of species B1 and E. Unvaccinated samples primarily contained only 1 species (species E) associated with adult respiratory illness. This study highlights the rarely reported phenomenon of adenoviral co-infections in a clinically relevant environment suitable for the generation of new recombinational variants.
Publications 1 - 10 of 11