Last data update: Nov 04, 2024. (Total: 48056 publications since 2009)
Records 1-30 (of 64 Records) |
Query Trace: Basler C[original query] |
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Outbreak of highly pathogenic avian influenza A(H5N1) viruses in U.S. dairy cattle and detection of two human cases - United States, 2024
Garg S , Reed C , Davis CT , Uyeki TM , Behravesh CB , Kniss K , Budd A , Biggerstaff M , Adjemian J , Barnes JR , Kirby MK , Basler C , Szablewski CM , Richmond-Crum M , Burns E , Limbago B , Daskalakis DC , Armstrong K , Boucher D , Shimabukuro TT , Jhung MA , Olsen SJ , Dugan V . MMWR Morb Mortal Wkly Rep 2024 73 (21) 501-505 |
Multistate outbreaks of salmonellosis linked to contact with backyard poultry-United States, 2015-2022
Stapleton GS , Habrun C , Nemechek K , Gollarza L , Ellison Z , Tolar B , Koski L , Brandenburg JM , Salah Z , Palacios A , Basler C , Varela K , Nichols M , Benedict K . Zoonoses Public Health 2024 AIMS: Contact with backyard poultry (i.e., privately-owned, non-commercial poultry) was first associated with a multistate outbreak of salmonellosis in 1955. In recent years, backyard poultry-associated salmonellosis outbreaks have caused more illnesses in the United States than salmonellosis outbreaks linked to any other type of animal. Here, we describe the epidemiology of outbreaks from 2015-2022 to inform prevention efforts. METHODS AND RESULTS: During 2015-2022, there were 88 multistate backyard poultry-associated salmonellosis outbreaks and 7866 outbreak-associated illnesses caused by 21 different Salmonella serotypes. Salmonella Enteritidis accounted for the most outbreaks (n = 21) and illnesses (n = 2400) of any serotype. Twenty-four percent (1840/7727) of patients with available information were <5 years of age. In total, 30% (1710/5644) of patients were hospitalized, and nine deaths were attributed to Salmonella infection. Throughout this period, patients reported behaviours that have a higher risk of Salmonella transmission, including kissing or snuggling poultry or allowing poultry inside their home. CONCLUSIONS: Despite ongoing efforts to reduce the burden of salmonellosis associated with backyard poultry, outbreak-associated illnesses have nearly tripled and hospitalizations more than quadrupled compared with those in 1990-2014. Because this public health problem is largely preventable, government officials, human and veterinary healthcare providers, hatcheries, and retailers might improve the prevention of illnesses by widely disseminating health and safety recommendations to the public and by continuing to develop and implement prevention measures to reduce zoonotic transmission of Salmonella by backyard poultry. |
Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets
Haas KM , McGregor MJ , Bouhaddou M , Polacco BJ , Kim EY , Nguyen TT , Newton BW , Urbanowski M , Kim H , Williams MAP , Rezelj VV , Hardy A , Fossati A , Stevenson EJ , Sukerman E , Kim T , Penugonda S , Moreno E , Braberg H , Zhou Y , Metreveli G , Harjai B , Tummino TA , Melnyk JE , Soucheray M , Batra J , Pache L , Martin-Sancho L , Carlson-Stevermer J , Jureka AS , Basler CF , Shokat KM , Shoichet BK , Shriver LP , Johnson JR , Shaw ML , Chanda SK , Roden DM , Carter TC , Kottyan LC , Chisholm RL , Pacheco JA , Smith ME , Schrodi SJ , Albrecht RA , Vignuzzi M , Zuliani-Alvarez L , Swaney DL , Eckhardt M , Wolinsky SM , White KM , Hultquist JF , Kaake RM , García-Sastre A , Krogan NJ . Nat Commun 2023 14 (1) 6030 Influenza A Virus (IAV) is a recurring respiratory virus with limited availability of antiviral therapies. Understanding host proteins essential for IAV infection can identify targets for alternative host-directed therapies (HDTs). Using affinity purification-mass spectrometry and global phosphoproteomic and protein abundance analyses using three IAV strains (pH1N1, H3N2, H5N1) in three human cell types (A549, NHBE, THP-1), we map 332 IAV-human protein-protein interactions and identify 13 IAV-modulated kinases. Whole exome sequencing of patients who experienced severe influenza reveals several genes, including scaffold protein AHNAK, with predicted loss-of-function variants that are also identified in our proteomic analyses. Of our identified host factors, 54 significantly alter IAV infection upon siRNA knockdown, and two factors, AHNAK and coatomer subunit COPB1, are also essential for productive infection by SARS-CoV-2. Finally, 16 compounds targeting our identified host factors suppress IAV replication, with two targeting CDK2 and FLT3 showing pan-antiviral activity across influenza and coronavirus families. This study provides a comprehensive network model of IAV infection in human cells, identifying functional host targets for pan-viral HDT. |
Investigation of a multistate outbreak of Listeria monocytogenes infections linked to frozen vegetables produced at individually quick-frozen vegetable manufacturing facilities
Madad A , Heiman Marshall K , Blessington T , Hardy C , Salter M , Basler C , Conrad A , Stroika S , Luo Y , Dwarka A , Gerhardt T , Rosa Y , Cibulskas K , Rosen HE , Adcock B , Kiang D , Hutton S , Parish M , Podoski B , Patel B , Viazis S . J Food Prot 2023 86 (8) 100117 In 2016, the U.S. Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), and state partners investigated nine Listeria monocytogenes infections linked to frozen vegetables. The investigation began with two environmental L. monocytogenes isolates recovered from Manufacturer A, primarily a processor of frozen onions, that were a match by whole genome sequencing (WGS) to eight clinical isolates and historical onion isolates with limited collection details. Epidemiologic information, product distribution, and laboratory evidence linked suspect food items, including products sourced from Manufacturer B, also a manufacturer of frozen vegetable/fruit products, with an additional illness. The environmental isolates were obtained during investigations at Manufacturers A and B. State and federal partners interviewed ill people, analyzed shopper card data, and collected household and retail samples. Nine ill persons between 2013 and 2016 were reported in four states. Of four ill people with information available, frozen vegetable consumption was reported by three, with shopper cards confirming purchases of Manufacturer B brands. Two identified outbreak strains of L. monocytogenes (Outbreak Strain 1 and Outbreak Strain 2) were a match to environmental isolates from Manufacturer A and/or isolates from frozen vegetables recovered from open and unopened product samples sourced from Manufacturer B; the investigation resulted in extensive voluntary recalls. The close genetic relationship between isolates helped investigators determine the source of the outbreak and take steps to protect public health. This is the first known multistate outbreak of listeriosis in the United States linked to frozen vegetables and highlights the significance of sampling and WGS analyses when there is limited epidemiologic information. Additionally, this investigation emphasizes the need for further research regarding food safety risks associated with frozen foods. |
Detecting national human enteric disease outbreaks linked to animal contact in the United States of America.
Nichols M , Stevenson L , Koski L , Basler C , Wise M , Whitlock L , Francois Watkins L , Friedman CR , Chen J , Tagg K , Joseph L , Caidi H , Patel K , Tolar B , Hise K , Classon A , Ceric O , Reimschuessel R , Williams IT . Rev Sci Tech 2020 39 (2) 471-480 Enteric pathogens, such as non-typhoidal Salmonella, Campylobacter and Escherichia coli, can reside in the intestinal tract of many animals, including livestock, companion animals, small mammals and reptiles. Often, these animals can appear healthy; nonetheless, humans can become infected after direct or indirect contact, resulting in a substantial illness burden. An estimated 14% of the 3.2 million illnesses that occur in the United States of America (USA) each year from such enteric pathogens are attributable to animal contact. Surveillance for enteric pathogens in the USA includes the compilation and interpretation of both laboratory and epidemiologic data. However, the authors feel that a collaborative, multisectoral and transdisciplinary - or One Health - approach is needed for data collection and analysis, at every level. In addition, they suggest that the future of enteric illness surveillance lies in the development of improved technologies for pathogen detection and characterisation, such as genomic sequencing and metagenomics. In particular, using whole-genome sequencing to compare genetic sequences of enteric pathogens from humans, food, animals and the environment, can help to predict antimicrobial resistance among these pathogens, determine their genetic relatedness and identify outbreaks linked to a common source. In this paper, the authors describe three recent, multi-state human enteric illness outbreaks linked to animal contact in the USA and discuss how integrated disease surveillance was essential to outbreak detection and response. Additional datasharing between public health and animal health laboratories and epidemiologists at the local, national, regional and international level may help to improve surveillance for emerging animal and human health threats and lead to new opportunities for prevention. |
Multistate reptile- and amphibian-associated salmonellosis outbreaks in humans, United States, 20092018
Waltenburg MA , Perez A , Salah Z , Karp BE , Whichard J , Tolar B , Gollarza L , Koski L , Blackstock A , Basler C , Nichols M . Zoonoses Public Health 2022 69 (8) 925-937 Non-typhoidal Salmonella cause an estimated 1.4 million human illnesses, 26,000 hospitalizations and 400 deaths annually in the United States. Approximately 11% of these infections are attributed to animal contact. Reptiles and amphibians are known sources of salmonellosis; young children (aged <5 years) are disproportionately affected by reptile- and amphibian-associated salmonellosis (RAAS) outbreaks. We describe multistate RAAS outbreaks to characterize illnesses and inform prevention efforts. RAAS outbreaks were defined as ≥2 culture-confirmed human Salmonella infections with similar pulsed-field gel electrophoresis patterns and epidemiologic, laboratory or traceback evidence linking them to a common reptile/amphibian exposure. Data sources included the Animal Contact Outbreak Surveillance System; CDC Outbreak Response and Prevention Branch's outbreak management database; PulseNet, the national molecular subtyping network for foodborne disease surveillance in the United States; and the National Antimicrobial Resistance Monitoring System. Twenty-six RAAS outbreaks were reported during 2009–2018, resulting in 1465 illnesses and 306 hospitalizations. The outbreaks were associated with turtles (19), lizards (5), snakes (1) and frogs (1). Sixteen (61.5%) outbreaks were linked to small turtles (<4 inches), resulting in 914 illnesses. Forty-nine percent of outbreak-associated patients were aged <5 years. Of 362 patients/caregivers interviewed, 111 (30.7%) were aware that reptiles/amphibians can carry Salmonella. Among 267 patient isolates with antimicrobial susceptibility information, 20 (7.5%) were non-susceptible to ≥1 antibiotic used to treat human salmonellosis. RAAS outbreaks result in considerable morbidity, particularly among young children. Illnesses linked to small turtles are preventable through education, targeted outreach to caregivers and paediatricians, and when appropriate, enforcement. Historically, individual states and jurisdictions have enforced existing or promulgated new authorities to address outbreaks. Preventing future RAAS outbreaks requires addressing challenges related to the illegal sale/distribution of small turtles; and for legal reptile sales, providing information on RAAS risk to consumers at point of sale to support informed pet ownership decisions. Published 2022. This article is a U.S. Government work and is in the public domain in the USA. Zoonoses and Public Health published by Wiley-VCH GmbH. |
A 2019 Outbreak Investigation of Hepatitis A Virus Infections in the United States Linked to Imported Fresh Blackberries.
McClure M , Nsubuga J , Montgomery MP , Jenkins E , Crosby A , Schoelen D , Basler C , Ramachandran S , Lin Y , Xia GL , Khudaykov Y , Suktankar V , Wagley A , Thomas V , Woods J , Hintz L , Oliveira J , Sandoval AL , Frederick J , Hendrickson B , Gieraltowski L , Viazis S . Food Environ Virol 2022 14 (3) 236-245 Globally, hepatitis A virus (HAV) is one of the most common agents of acute viral hepatitis and causes approximately 1.4 million cases and 90,000 deaths annually despite the existence of an effective vaccine. In 2019, federal, state, and local partners investigated a multi-state outbreak of HAV infections linked to fresh blackberries sourced from multiple suppliers in Michoacn, Mexico. A total of 20 individuals with outbreak-related HAV infection were reported in seven states, including 11 hospitalizations, and no deaths. The Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), and Nebraska State and Douglas County Health Departments conducted a traceback investigation for fresh blackberries reportedly purchased by 16 ill persons. These individuals reported purchasing fresh blackberries from 11 points of service from September 16 through 29, 2019 and their clinical isolates assessed through next-generation sequencing and phylogenetic analysis were genetically similar. The traceback investigation did not reveal convergence on a common grower or packing house within Mexico, but all of the blackberries were harvested from growers in Michoacn, Mexico. FDA did not detect the pathogen after analyzing fresh blackberry samples from four distributors, one consumer, and from nine importers at the port of entry as a result of increased screening. Challenges included gaps in traceability practices and the inability to recover the pathogen from sample testing, which prohibited investigators from determining the source of the implicated blackberries. This multi-state outbreak illustrated the importance of food safety practices for fresh produce that may contribute to foodborne illness outbreaks. |
Propagation and Quantification of SARS-CoV-2.
Jureka AS , Basler CF . Methods Mol Biol 2022 2452 111-129 In late 2019, the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China. Since its emergence, SARS-CoV-2 has been responsible for a world-wide pandemic resulting in over 80 million infections and over 1.8 million deaths. The severity of the pandemic has prompted widespread research efforts to more fully understand SARS-CoV-2 and the disease it causes, COVID-19. Research into this novel virus will be facilitated by the availability of clearly described and effective protocols that enable the propagation and quantification of infectious virus. Here, we describe protocols for the propagation of SARS-CoV-2 in Vero E6 cells as well as two human cells lines, the intestinal epithelial Caco-2 cell line and the respiratory epithelial Calu-3 cell line. Additionally, we provide protocols for the quantification of SARS-CoV-2 by plaque assays and immunofocus forming assays in Vero E6 cells utilizing liquid overlays. These protocols provide a foundation for laboratories acquiring the ability to study SARS-CoV-2 to address this ongoing pandemic. |
Multistate outbreak of Salmonella Typhimurium linked to pet hedgehogs, United States, 2018-2019.
Hoff C , Nichols M , Gollarza L , Scheftel J , Adams J , Tagg KA , Francois Watkins L , Poissant T , Stapleton GS , Morningstar-Shaw B , Signs K , Bidol S , Donovan D , Basler C . Zoonoses Public Health 2022 69 (3) 167-174 In December 2018, PulseNet, the national laboratory network for enteric disease surveillance, identified an increase in Salmonella Typhimurium isolates with an uncommon pulsed-field gel electrophoresis pattern which was previously isolated from hedgehogs. CDC, state, and local health partners interviewed patients with a questionnaire that focused on hedgehog exposures, conducted traceback of patients' hedgehog purchases, and collected hedgehog faecal pellets and environmental samples. Isolates in this outbreak were analysed using core-genome multi-locus sequence typing (cgMLST) and compared to sequence data from historic clinical isolates from a 2011-2013 outbreak of Salmonella Typhimurium illnesses linked to pet hedgehogs. Fifty-four illnesses in 23 states were identified between October 2018 and September 2019. Patients ranged from <1 to 95 years, and 65% were female. Eight patients were hospitalized. Eighty-one per cent (29/36) of patients interviewed reported contact with a hedgehog before becoming ill; of these, 21 (72%) reported owning a hedgehog. Analysis of 53 clinical, 11 hedgehog, and two hedgehog bedding isolates from this outbreak, seven hedgehog isolates obtained prior to this outbreak, and two clinical isolates from the 2011-2013 outbreak fell into three distinct groupings (37 isolates in Clade 1 [0-10 alleles], 28 isolates in Clade 2 [0-7 alleles], and eight isolates in Clade 3 [0-12 alleles]) and were collectively related within 0-31 alleles by cgMLST. Purchase information available from 20 patients showed hedgehogs were purchased from multiple breeders across nine states, a pet store, and through an online social media website; a single source of hedgehogs was not identified. This outbreak highlights the ability of genetic sequencing analysis to link historic and ongoing Salmonella illness outbreaks and demonstrates the strain of Salmonella linked to hedgehogs might continue to be a health risk to hedgehog owners unless measures are taken to prevent transmission. |
A Series of Papaya-Associated Salmonella Illness Outbreak Investigations in 2017 and 2019: A Focus on Traceback, Laboratory, and Collaborative Efforts.
Whitney BM , McClure M , Hassan R , Pomeroy M , Seelman SL , Singleton LN , Blessington T , Hardy C , Blankenship J , Pereira E , Davidson CN , Luo Y , Pettengill J , Curry P , McConnell T , Gieraltowski L , Schwensohn C , Basler C , Fritz K , McKenna C , Nieves K , Oliveira J , Sandoval AL , Crosby A , Williams D , Crocker K , Thomas D , Fulton T , Muetter L , Li L , Omoregie E , Holloman K , Brennan C , Thomas N , Barnes A , Viazis S . J Food Prot 2021 84 (11) 2002-2019 In 2017 and 2019, five outbreaks of infections from multiple strains of Salmonella linked to the consumption of whole, fresh Maradol papayas were reported in the United States, resulting in 325 ill persons. Traceback, laboratory, and epidemiologic evidence indicated papayas as the likely vehicle for each of these outbreaks and identified the source of papayas. State and U.S. Food and Drug Administration (FDA) laboratories recovered Salmonella from papaya samples from various points of distribution, including at import entry, and conducted serotyping, pulsed-field gel electrophoresis, and phylogenetic analyses of whole genome sequencing data. Federal and state partners led traceback investigations to determine the source of papayas. Four different suppliers of papayas were linked by traceback and laboratory results to five separate outbreaks of Salmonella infections associated with papayas. In 2017, multiple states tested papaya samples collected at retail, and Maryland and Virginia investigators recovered strains of Salmonella associated with one outbreak. FDA collected 183 papaya samples in 2017, and 11 samples yielded 62 isolates of Salmonella. Eleven serotypes of Salmonella were recovered from FDA papaya samples, and nine serotypes were closely related genetically by pulsed-field gel electrophoresis and whole genome sequencing to clinical isolates of four outbreaks, including the outbreak associated with positive state sample results. Four farms in Mexico were identified, and their names were released to the general public, retailers, and foreign authorities. In 2019, FDA collected 119 papaya samples, three of which yielded Salmonella; none yielded the 2019 outbreak strain. Investigators determined that papayas of interest had been sourced from a single farm in Campeche, Mexico, through traceback. This information was used to protect public health through public guidance, recalls, and import alerts and helped FDA collaborate with Mexican regulatory partners to enhance the food safety requirements for papayas imported from Mexico. |
Salmonella Illness Outbreaks linked to Backyard Poultry Purchasing during the COVID-19 Pandemic - United States, 2020.
Nichols M , Gollarza L , Palacios A , Stapleton GS , Basler C , Hoff C , Low M , McFadden K , Koski L , Leeper M , Brandenburg J , Tolar B . Epidemiol Infect 2021 149 1-10 Poultry contact is a risk factor for zoonotic transmission of non-typhoidal Salmonella spp. Salmonella illness outbreaks in the United States are identified by PulseNet, the national laboratory network for enteric disease surveillance. During 2020, PulseNet observed a 25% decline in the number of Salmonella clinical isolates uploaded by state and local health departments. However, 1722 outbreak-associated Salmonella illnesses resulting from 12 Salmonella serotypes were linked to contact with privately owned poultry, an increase from all previous years. This report highlights the need for continued efforts to prevent backyard poultry-associated outbreaks of Salmonella as ownership increases in the United States. |
Ongoing Outbreak of Extensively Drug-Resistant Campylobacter jejuni Infections Associated With US Pet Store Puppies, 2016-2020.
Francois Watkins LK , Laughlin ME , Joseph LA , Chen JC , Nichols M , Basler C , Breazu R , Bennett C , Koski L , Montgomery MP , Hughes MJ , Robertson S , Lane CG , Singh AJ , Stanek D , Salehi E , Brandt E , McGillivary G , Mowery J , DeMent J , Aubert RD , Geissler AL , de Fijter S , Williams IT , Friedman CR . JAMA Netw Open 2021 4 (9) e2125203 IMPORTANCE: Extensively drug-resistant Campylobacter jejuni infections cannot be treated with any commonly recommended antibiotics and pose an increasing public health threat. OBJECTIVES: To investigate cases of extensively drug-resistant C jejuni associated with pet store puppies and describe the epidemiologic and laboratory characteristics of these infections. DESIGN, SETTING, AND PARTICIPANTS: In August 2017, health officials identified, via survey, patients with C jejuni infections who reported contact with puppies sold by pet stores. In conjunction with state and federal partners, the Centers for Disease Control and Prevention investigated cases of culture-confirmed C jejuni infections in US patients with an epidemiologic or molecular association with pet store puppies between January 1, 2016, and February 29, 2020. Available records from cases occurring before 2016 with genetically related isolates were also obtained. MAIN OUTCOMES AND MEASURES: Patients were interviewed about demographic characteristics, health outcomes, and dog exposure during the 7 days before illness onset. Core genome multilocus sequence typing was used to assess isolate relatedness, and genomes were screened for resistance determinants to predict antibiotic resistance. Isolates resistant to fluoroquinolones, macrolides, and 3 or more additional antibiotic classes were considered to be extensively drug resistant. Cases before 2016 were identified by screening all sequenced isolates submitted for surveillance using core genome multilocus sequence typing. RESULTS: A total of 168 patients (median [interquartile range] age, 37 [19.5-51.0] years; 105 of 163 female [64%]) with an epidemiologic or molecular association with pet store puppies were studied. A total of 137 cases occurred from January 1, 2016, to February 29, 2020, with 31 additional cases dating back to 2011. Overall, 117 of 121 patients (97%) reported contact with a dog in the week before symptom onset, of whom 69 of 78 (88%) with additional information reported contact with a pet store puppy; 168 isolates (88%) were extensively drug resistant. Traceback investigation did not implicate any particular breeder, transporter, distributer, store, or chain. CONCLUSIONS AND RELEVANCE: Strains of extensively drug-resistant C jejuni have been circulating since at least 2011 and are associated with illness among pet store customers, employees, and others who come into contact with pet store puppies. The results of this study suggest that practitioners should ask about puppy exposure when treating patients with Campylobacter infection, especially when they do not improve with routine antibiotics, and that the commercial dog industry should take action to help prevent the spread of extensively drug-resistant C jejuni from pet store puppies to people. |
2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
Kuhn JH , Adkins S , Agwanda BR , Al Kubrusli R , Alkhovsky Aльxoвcкий Cepгeй Bлaдимиpoвич SV , Amarasinghe GK , Avšič-Županc T , Ayllón MA , Bahl J , Balkema-Buschmann A , Ballinger MJ , Basler CF , Bavari S , Beer M , Bejerman N , Bennett AJ , Bente DA , Bergeron É , Bird BH , Blair CD , Blasdell KR , Blystad DR , Bojko J , Borth WB , Bradfute S , Breyta R , Briese T , Brown PA , Brown JK , Buchholz UJ , Buchmeier MJ , Bukreyev A , Burt F , Büttner C , Calisher CH , Cao 曹孟籍 M , Casas I , Chandran K , Charrel RN , Cheng Q , Chiaki 千秋祐也 Y , Chiapello M , Choi IR , Ciuffo M , Clegg JCS , Crozier I , Dal Bó E , de la Torre JC , de Lamballerie X , de Swart RL , Debat H , Dheilly NM , Di Cicco E , Di Paola N , Di Serio F , Dietzgen RG , Digiaro M , Dolnik O , Drebot MA , Drexler JF , Dundon WG , Duprex WP , Dürrwald R , Dye JM , Easton AJ , Ebihara 海老原秀喜 H , Elbeaino T , Ergünay K , Ferguson HW , Fooks AR , Forgia M , Formenty PBH , Fránová J , Freitas-Astúa J , Fu 付晶晶 J , Fürl S , Gago-Zachert S , Gāo 高福 GF , García ML , García-Sastre A , Garrison AR , Gaskin T , Gonzalez JJ , Griffiths A , Goldberg TL , Groschup MH , Günther S , Hall RA , Hammond J , Han 韩彤 T , Hepojoki J , Hewson R , Hong 洪健 J , Hong 洪霓 N , Hongo 本郷誠治 S , Horie 堀江真行 M , Hu JS , Hu T , Hughes HR , Hüttner F , Hyndman TH , Ilyas M , Jalkanen R , Jiāng 姜道宏 D , Jonson GB , Junglen S , Kadono 上遠野冨士夫 F , Kaukinen KH , Kawate M , Klempa B , Klingström J , Kobinger G , Koloniuk I , Kondō 近藤秀樹 H , Koonin EV , Krupovic M , Kubota 久保田健嗣 K , Kurath G , Laenen L , Lambert AJ , Langevin SL , Lee B , Lefkowitz EJ , Leroy EM , Li 李邵蓉 S , Li 李龙辉 L , Lǐ 李建荣 J , Liu 刘华珍 H , Lukashevich IS , Maes P , de Souza WM , Marklewitz M , Marshall SH , Marzano SL , Massart S , McCauley JW , Melzer M , Mielke-Ehret N , Miller KM , Ming TJ , Mirazimi A , Mordecai GJ , Mühlbach HP , Mühlberger E , Naidu R , Natsuaki 夏秋知英 T , Navarro JA , Netesov Heтёcoв Cepгeй Bиктopoвич SV , Neumann G , Nowotny N , Nunes MRT , Olmedo-Velarde A , Palacios G , Pallás V , Pályi B , Papa Άννα Παπά A , Paraskevopoulou Σοφία Παρασκευοπούλου S , Park AC , Parrish CR , Patterson DA , Pauvolid-Corrêa A , Pawęska JT , Payne S , Peracchio C , Pérez DR , Postler TS , Qi 亓立莹 L , Radoshitzky SR , Resende RO , Reyes CA , Rima BK , Luna GR , Romanowski V , Rota P , Rubbenstroth D , Rubino L , Runstadler JA , Sabanadzovic S , Sall AA , Salvato MS , Sang R , Sasaya 笹谷孝英 T , Schulze AD , Schwemmle M , Shi 施莽 M , Shí 石晓宏 X , Shí 石正丽 Z , Shimomoto 下元祥史 Y , Shirako Y , Siddell SG , Simmonds P , Sironi M , Smagghe G , Smither S , Song 송진원 JW , Spann K , Spengler JR , Stenglein MD , Stone DM , Sugano J , Suttle CA , Tabata A , Takada 高田礼人 A , Takeuchi 竹内繁治 S , Tchouassi DP , Teffer A , Tesh RB , Thornburg NJ , Tomitaka 冨高保弘 Y , Tomonaga 朝長啓造 K , Tordo N , Torto B , Towner JS , Tsuda 津田新哉 S , Tu 涂长春 C , Turina M , Tzanetakis IE , Uchida J , Usugi 宇杉富雄 T , Vaira AM , Vallino M , van den Hoogen B , Varsani A , Vasilakis Νίκος Βασιλάκης N , Verbeek M , von Bargen S , Wada 和田治郎 J , Wahl V , Walker PJ , Wang 王林发 LF , Wang 王国平 G , Wang 王雁翔 Y , Wang 王亚琴 Y , Waqas M , Wèi 魏太云 T , Wen 温少华 S , Whitfield AE , Williams JV , Wolf YI , Wu 吴建祥 J , Xu 徐雷 L , Yanagisawa 栁澤広宣 H , Yang 杨彩霞 C , Yang 杨作坤 Z , Zerbini FM , Zhai 翟立峰 L , Zhang 张永振 YZ , Zhang 张松 S , Zhang 张靖国 J , Zhang 张哲 Z , Zhou 周雪平 X . Arch Virol 2021 166 (12) 3513-3566 In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV. |
Notes from the Field: Recurrence of a Multistate Outbreak of Salmonella Typhimurium Infections Linked to Contact with Hedgehogs - United States and Canada, 2020.
Waltenburg MA , Nichols M , Waechter H , Higa J , Cronquist L , Lowe AM , Adams JK , McFadden K , McConnell JA , Blank R , Basler C . MMWR Morb Mortal Wkly Rep 2021 70 (32) 1100-1102 In July 2020, PulseNet, the national molecular subtyping network for enteric disease surveillance, detected a cluster of 17 Salmonella Typhimurium infections. The isolates were closely related genetically to each other (four allele differences) by whole genome sequencing (WGS) analysis and related to isolates from two previous outbreaks of S. Typhimurium infections linked to pet hedgehogs (1,2). An investigation was initiated to characterize illnesses and identify the outbreak source. | | A case was defined as the isolation of S. Typhimurium closely related by WGS to the outbreak strain in a specimen from a patient with illness onset during April–November 2020. State and local officials interviewed patients about hedgehog exposures and purchase information. Animal and environmental sampling of hedgehog enclosures was conducted at some patient residences. Hedgehog purchase locations were contacted in an attempt to identify a possible common source or supplier of hedgehogs. This activity was reviewed by CDC and was conducted consistent with applicable federal law and CDC policy.* |
Veterinarians role in preventing zoonotic salmonellosis from hedgehogs
Waltenburg MA , Basler C , Nichols M , Scheftel J , Stobierski MG . J Am Vet Med Assoc 2021 258 (10) 1066-1067 A recent outbreak of human salmonellosis linked to contact with pet hedgehogs1 highlights the need to address Salmonella carriage in hedgehogs as an issue of public health importance. Three multistate outbreaks involving a single Salmonella strain linked to hedgehogs have caused 129 human illnesses in the United States since 2011; 17% (21/122) of these illnesses occurred in children < 5 years of age.1–3 The finding of a genetically nearly identical strain over multiple years indicates this strain might be persisting in the pet hedgehog population, including the breeding population, representing a continued health risk to hedgehog owners. Despite public health outreach and recommendations made during outbreak investigations, continued occurrence of this strain in human illness outbreaks indicates additional efforts are needed to engage with hedgehog breeders to reduce the burden of Salmonella spp in hedgehog populations, which may prevent disease transmission to people. |
Notes from the Field: Multistate Outbreak of Escherichia coli O26 Infections Linked to Raw Flour - United States, 2019
Vasser M , Barkley J , Miller A , Gee E , Purcell K , Schroeder MN , Basler C , Neil KP . MMWR Morb Mortal Wkly Rep 2021 70 (16) 600-601 On February 20, 2019, PulseNet, the molecular subtyping network for foodborne disease surveillance, identified six Shiga toxin–producing Escherichia coli (STEC) O26:H11 infections with the same pulsed-field gel electrophoresis (PFGE) pattern combination. This PFGE pattern combination matched that of infections from a July 2018 outbreak that was associated with ground beef. In response, CDC initiated an investigation with federal, state, and local partners to identify the outbreak source and implement prevention measures. | | CDC defined a case as STEC O26 infection with an isolate matching the outbreak strain by PFGE or related by core genome multilocus sequence typing scheme (cgMLST), with dates of illness onset during December 11, 2018–May 21, 2019. Investigators initially hypothesized that ground beef was the outbreak cause because of the PFGE match to the July 2018 outbreak and because in early interviews, patients commonly reported eating ground beef and leafy greens. Investigators used cgMLST to compare the genetic sequences of isolates from both outbreaks and determined that they fell into separate genetic clades (differing by 6–11 alleles), suggesting that something other than ground beef caused the illness in 2019. CDC noted that one patient consumed raw cookie dough and that most patients were young adult females, similar to demographic distributions of past flour-associated STEC outbreaks (1–3). Investigators developed a supplemental questionnaire focusing on beef, leafy greens, and flour exposures. |
Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States.
Washington NL , Gangavarapu K , Zeller M , Bolze A , Cirulli ET , Schiabor Barrett KM , Larsen BB , Anderson C , White S , Cassens T , Jacobs S , Levan G , Nguyen J , Ramirez JM3rd , Rivera-Garcia C , Sandoval E , Wang X , Wong D , Spencer E , Robles-Sikisaka R , Kurzban E , Hughes LD , Deng X , Wang C , Servellita V , Valentine H , De Hoff P , Seaver P , Sathe S , Gietzen K , Sickler B , Antico J , Hoon K , Liu J , Harding A , Bakhtar O , Basler T , Austin B , MacCannell D , Isaksson M , Febbo PG , Becker D , Laurent M , McDonald E , Yeo GW , Knight R , Laurent LC , de Feo E , Worobey M , Chiu CY , Suchard MA , Lu JT , Lee W , Andersen KG . Cell 2021 184 (10) 2587-2594 e7 The highly transmissible B.1.1.7 variant of SARS-CoV-2, first identified in the United Kingdom, has gained a foothold across the world. Using S gene target failure (SGTF) and SARS-CoV-2 genomic sequencing, we investigated the prevalence and dynamics of this variant in the United States (US), tracking it back to its early emergence. We found that, while the fraction of B.1.1.7 varied by state, the variant increased at a logistic rate with a roughly weekly doubling rate and an increased transmission of 40%-50%. We revealed several independent introductions of B.1.1.7 into the US as early as late November 2020, with community transmission spreading it to most states within months. We show that the US is on a similar trajectory as other countries where B.1.1.7 became dominant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality. |
Impact of community health promoters on awareness of a rural social marketing program, purchase and use of health products, and disease risk, Kenya, 20142016
Kim S , Laughlin M , Morris J , Otieno R , Odhiambo A , Oremo J , Graham J , Hirai M , Wells E , Basler C , Okello A , Matanock A , Eleveld A , Quick R . J Water Sanit Hyg Dev 2020 10 (4) 940-950 The Safe Water and AIDS Project (SWAP), a non-governmental organization in western Kenya, opened kiosks run as businesses by community health promoters (CHPs) to increase access to health products among poor rural families. We conducted a baseline survey in 2014 before kiosks opened, and a post-intervention follow-up in 2016, enrolling 1,517 households with children <18 months old. From baseline to follow-up, we observed increases in reported exposure to the SWAP program (311%, p = 0.01) and reported purchases of any SWAP product (310%, p < 0.01). The percent of households with confirmed water treatment (detectable free chlorine residual (FCR) >0.2 mg/ml) was similar from baseline to follow-up (7% vs. 8%, p = 0.57). The odds of reported diarrhea in children decreased from baseline to follow-up (odds ratios or OR: 0.77, 95% CI: 0.640.93) and households with detectable FCR had lower odds of diarrhea (OR: 0.53, 95% CI: 0.340.83). Focus group discussions with CHPs suggested that high product prices, lack of affordability, and expectations that products should be free contributed to low sales. In conclusion, modest reported increases in SWAP exposure and product sales in the target population were insufficient to impact health, but children in households confirmed to chlorinate their water had decreased diarrhea. |
2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
Kuhn JH , Adkins S , Alioto D , Alkhovsky SV , Amarasinghe GK , Anthony SJ , Avšič-Županc T , Ayllón MA , Bahl J , Balkema-Buschmann A , Ballinger MJ , Bartonička T , Basler C , Bavari S , Beer M , Bente DA , Bergeron É , Bird BH , Blair C , Blasdell KR , Bradfute SB , Breyta R , Briese T , Brown PA , Buchholz UJ , Buchmeier MJ , Bukreyev A , Burt F , Buzkan N , Calisher CH , Cao M , Casas I , Chamberlain J , Chandran K , Charrel RN , Chen B , Chiumenti M , Choi IR , Clegg JCS , Crozier I , da Graça JV , Dal Bó E , Dávila AMR , de la Torre JC , de Lamballerie X , de Swart RL , Di Bello PL , Di Paola N , Di Serio F , Dietzgen RG , Digiaro M , Dolja VV , Dolnik O , Drebot MA , Drexler JF , Dürrwald R , Dufkova L , Dundon WG , Duprex WP , Dye JM , Easton AJ , Ebihara H , Elbeaino T , Ergünay K , Fernandes J , Fooks AR , Formenty PBH , Forth LF , Fouchier RAM , Freitas-Astúa J , Gago-Zachert S , Gāo GF , García ML , García-Sastre A , Garrison AR , Gbakima A , Goldstein T , Gonzalez JJ , Griffiths A , Groschup MH , Günther S , Guterres A , Hall RA , Hammond J , Hassan M , Hepojoki J , Hepojoki S , Hetzel U , Hewson R , Hoffmann B , Hongo S , Höper D , Horie M , Hughes HR , Hyndman TH , Jambai A , Jardim R , Jiāng D , Jin Q , Jonson GB , Junglen S , Karadağ S , Keller KE , Klempa B , Klingström J , Kobinger G , Kondō H , Koonin EV , Krupovic M , Kurath G , Kuzmin IV , Laenen L , Lamb RA , Lambert AJ , Langevin SL , Lee B , Lemos ERS , Leroy EM , Li D , Lǐ J , Liang M , Liú W , Liú Y , Lukashevich IS , Maes P , Marciel de Souza W , Marklewitz M , Marshall SH , Martelli GP , Martin RR , Marzano SL , Massart S , McCauley JW , Mielke-Ehret N , Minafra A , Minutolo M , Mirazimi A , Mühlbach HP , Mühlberger E , Naidu R , Natsuaki T , Navarro B , Navarro JA , Netesov SV , Neumann G , Nowotny N , Nunes MRT , Nylund A , Økland AL , Oliveira RC , Palacios G , Pallas V , Pályi B , Papa A , Parrish CR , Pauvolid-Corrêa A , Pawęska JT , Payne S , Pérez DR , Pfaff F , Radoshitzky SR , Rahman AU , Ramos-González PL , Resende RO , Reyes CA , Rima BK , Romanowski V , Robles Luna G , Rota P , Rubbenstroth D , Runstadler JA , Ruzek D , Sabanadzovic S , Salát J , Sall AA , Salvato MS , Sarpkaya K , Sasaya T , Schwemmle M , Shabbir MZ , Shí X , Shí Z , Shirako Y , Simmonds P , Širmarová J , Sironi M , Smither S , Smura T , Song JW , Spann KM , Spengler JR , Stenglein MD , Stone DM , Straková P , Takada A , Tesh RB , Thornburg NJ , Tomonaga K , Tordo N , Towner JS , Turina M , Tzanetakis I , Ulrich RG , Vaira AM , van den Hoogen B , Varsani A , Vasilakis N , Verbeek M , Wahl V , Walker PJ , Wang H , Wang J , Wang X , Wang LF , Wèi T , Wells H , Whitfield AE , Williams JV , Wolf YI , Wú Z , Yang X , Yáng X , Yu X , Yutin N , Zerbini FM , Zhang T , Zhang YZ , Zhou G , Zhou X . Arch Virol 2020 165 (12) 3023-3072 In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV. |
COVID-19 Outbreak Among Employees at a Meat Processing Facility - South Dakota, March-April 2020.
Steinberg J , Kennedy ED , Basler C , Grant MP , Jacobs JR , Ortbahn D , Osburn J , Saydah S , Tomasi S , Clayton JL . MMWR Morb Mortal Wkly Rep 2020 69 (31) 1015-1019 On March 24, 2020, the South Dakota Department of Health (SDDOH) was notified of a case of coronavirus disease 2019 (COVID-19) in an employee at a meat processing facility (facility A) and initiated an investigation to isolate the employee and identify and quarantine contacts. On April 2, when 19 cases had been confirmed among facility A employees, enhanced testing for SARS-CoV-2, the virus that causes COVID-19, was implemented, so that any employee with a COVID-19-compatible sign or symptom (e.g., fever, cough, or shortness of breath) could receive a test from a local health care facility. By April 11, 369 COVID-19 cases had been confirmed among facility A employees; on April 12, facility A began a phased closure* and did not reopen during the period of investigation (March 16-April 25, 2020). At the request of SDDOH, a CDC team arrived on April 15 to assist with the investigation. During March 16-April 25, a total of 929 (25.6%) laboratory-confirmed COVID-19 cases were diagnosed among 3,635 facility A employees. At the outbreak's peak, an average of 67 cases per day occurred. An additional 210 (8.7%) cases were identified among 2,403 contacts of employees with diagnosed COVID-19. Overall, 48 COVID-19 patients were hospitalized, including 39 employees and nine contacts. Two employees died; no contacts died. Attack rates were highest among department-groups where employees tended to work in proximity (i.e., <6 feet [2 meters]) to one another on the production line. Cases among employees and their contacts declined to approximately 10 per day within 7 days of facility closure. SARS-CoV-2 can spread rapidly in meat processing facilities because of the close proximity of workstations and prolonged contact between employees (1,2). Facilities can reduce this risk by implementing a robust mitigation program, including engineering and administrative controls, consistent with published guidelines (1). |
Comparison of Molecular Subtyping and Antimicrobial Resistance Detection Methods Used in a Large Multi-State Outbreak of Extensively Drug-Resistant Campylobacter jejuni Infections Linked to Pet Store Puppies.
Joseph LA , Francois Watkins LK , Chen J , Tagg KA , Bennett C , Caidi H , Folster JP , Laughlin ME , Koski L , Silver R , Stevenson L , Robertson S , Pruckler J , Nichols M , Pouseele H , Carleton HA , Basler C , Friedman CR , Geissler A , Hise KB , Aubert RD . J Clin Microbiol 2020 58 (10) Campylobacter jejuni is a leading cause of enteric bacterial illness in the United States. Traditional molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE) and 7-gene multilocus sequencing typing (MLST), provided limited resolution to adequately identify C. jejuni outbreaks and separate out sporadic isolates during outbreak investigations. Whole genome sequencing (WGS) has emerged as a powerful tool for C. jejuni outbreak detection. In this investigation, 45 human and 11 puppy isolates obtained during a 2016-2018 outbreak linked to pet store puppies were sequenced. Core genome multilocus sequence typing (cgMLST) and high-quality single nucleotide polymorphism (hqSNP) analysis of the sequence data separated the isolates into the same two clades containing minor within clade differences; however, cgMLST analysis does not require selection of an appropriate reference genome making this method preferable to hqSNP analysis for Campylobacter surveillance and cluster detection. The isolates were classified as ST2109-a rarely seen MLST sequence type. PFGE was performed on 38 human and 10 puppy isolates; PFGE patterns did not reliably predict clustering by cgMLST analysis. Genetic detection of antimicrobial resistance determinants predicted that all outbreak-associated isolates would be resistant to six drug classes. Traditional antimicrobial susceptibility testing (AST) confirmed a high correlation between genotypic and phenotypic antimicrobial resistance determinations. WGS analysis linked C. jejuni isolates in humans and pet store puppies even when canine exposure information was unknown, aiding the epidemiological investigation during this outbreak. WGS data were also used to quickly identify the highly drug-resistant profile of these outbreak-associated C. jejuni isolates. |
COVID-19 Among Workers in Meat and Poultry Processing Facilities - 19 States, April 2020.
Dyal JW , Grant MP , Broadwater K , Bjork A , Waltenburg MA , Gibbins JD , Hale C , Silver M , Fischer M , Steinberg J , Basler CA , Jacobs JR , Kennedy ED , Tomasi S , Trout D , Hornsby-Myers J , Oussayef NL , Delaney LJ , Patel K , Shetty V , Kline KE , Schroeder B , Herlihy RK , House J , Jervis R , Clayton JL , Ortbahn D , Austin C , Berl E , Moore Z , Buss BF , Stover D , Westergaard R , Pray I , DeBolt M , Person A , Gabel J , Kittle TS , Hendren P , Rhea C , Holsinger C , Dunn J , Turabelidze G , Ahmed FS , deFijter S , Pedati CS , Rattay K , Smith EE , Luna-Pinto C , Cooley LA , Saydah S , Preacely ND , Maddox RA , Lundeen E , Goodwin B , Karpathy SE , Griffing S , Jenkins MM , Lowry G , Schwarz RD , Yoder J , Peacock G , Walke HT , Rose DA , Honein MA . MMWR Morb Mortal Wkly Rep 2020 69 (18) Congregate work and residential locations are at increased risk for infectious disease transmission including respiratory illness outbreaks. SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is primarily spread person to person through respiratory droplets. Nationwide, the meat and poultry processing industry, an essential component of the U.S. food infrastructure, employs approximately 500,000 persons, many of whom work in proximity to other workers (1). Because of reports of initial cases of COVID-19, in some meat processing facilities, states were asked to provide aggregated data concerning the number of meat and poultry processing facilities affected by COVID-19 and the number of workers with COVID-19 in these facilities, including COVID-19-related deaths. Qualitative data gathered by CDC during on-site and remote assessments were analyzed and summarized. During April 9-27, aggregate data on COVID-19 cases among 115 meat or poultry processing facilities in 19 states were reported to CDC. Among these facilities, COVID-19 was diagnosed in 4,913 (approximately 3%) workers, and 20 COVID-19-related deaths were reported. Facility barriers to effective prevention and control of COVID-19 included difficulty distancing workers at least 6 feet (2 meters) from one another (2) and in implementing COVID-19-specific disinfection guidelines.* Among workers, socioeconomic challenges might contribute to working while feeling ill, particularly if there are management practices such as bonuses that incentivize attendance. Methods to decrease transmission within the facility include worker symptom screening programs, policies to discourage working while experiencing symptoms compatible with COVID-19, and social distancing by workers. Source control measures (e.g., the use of cloth face covers) as well as increased disinfection of high-touch surfaces are also important means of preventing SARS-CoV-2 exposure. Mitigation efforts to reduce transmission in the community should also be considered. Many of these measures might also reduce asymptomatic and presymptomatic transmission (3). Implementation of these public health strategies will help protect workers from COVID-19 in this industry and assist in preserving the critical meat and poultry production infrastructure (4). |
Outbreak of human infections with uncommon Salmonella serotypes linked to pet bearded dragons, 2012-2014
Kiebler CA , Bottichio L , Simmons L , Basler C , Klos R , Gurfield N , Roberts E , Kimura A , Lewis LS , Bird K , Stiles F , Schlater LK , Lantz K , Edling T , Barton Behravesh C . Zoonoses Public Health 2020 67 (4) 425-434 Reptiles are one of the fastest growing sectors in the United States pet industry. Reptile-associated salmonellosis (RAS) continues to be an important public health problem, especially among children. We investigated an outbreak of human Salmonella infections resulting from serotypes Cotham and Kisarawe, predominately occurring among children. An outbreak of illnesses was identified in persons with exposure to pet bearded dragon lizards. Human and animal health officials, in cooperation with the pet industry, conducted epidemiologic, traceback and laboratory investigations. Onsite sampling was conducted at two US breeding facilities, one foreign breeding facility, and a large pet retail chain. A total of 166 patients in 36 states were identified with illness onset dates from 02/2012-06/2014. The median patient age was 3 years (range, <1-79 years), 57% were aged </=5 years, and 37% were aged </=1 year. Forty-four patients (37%) were hospitalized, predominantly children. Sampling at breeding facilities and a national pet store chain resulted in isolation of outbreak serotypes at each facility; isolation proportions ranged from 2%-24% of samples collected at each facility.Epidemiologic, microbiologic and traceback evidence linked an outbreak of uncommon Salmonella serotypes to contact with pet bearded dragons. The high proportion of infants involved in this outbreak highlights the need to educate owners about the risk of RAS in children and the potential for household contamination by pet reptiles or their habitats. Strategies should be developed to improve breeding practices, biosecurity and monitoring protocols to reduce Salmonella in the pet reptile trade. |
Shiga Toxin-Producing E. coli Infections Associated with Romaine Lettuce - United States, 2018.
Bottichio L , Keaton A , Thomas D , Fulton T , Tiffany A , Frick A , Mattioli M , Kahler A , Murphy J , Otto M , Tesfai A , Fields A , Kline K , Fiddner J , Higa J , Barnes A , Arroyo F , Salvatierra A , Holland A , Taylor W , Nash J , Morawski BM , Correll S , Hinnenkamp R , Havens J , Patel K , Schroeder MN , Gladney L , Martin H , Whitlock L , Dowell N , Newhart C , Watkins LF , Hill V , Lance S , Harris S , Wise M , Williams I , Basler C , Gieraltowski L . Clin Infect Dis 2019 71 (8) e323-e330 BACKGROUND: Produce-associated outbreaks of Shiga toxin-producing Escherichia coli (STEC) were first identified in 1991. In April 2018, New Jersey and Pennsylvania officials reported a cluster of STEC O157 infections associated with multiple locations of a restaurant chain. CDC queried PulseNet, the national laboratory network for foodborne disease surveillance, for additional cases and began a national investigation. METHODS: A case was defined as an infection between March 13 and August 22, 2018 with one of the 22 identified outbreak-associated E. coli O157:H7 or E. coli O61 pulsed-field gel electrophoresis pattern combinations, or with a strain STEC O157 that was closely related to the main outbreak strain by whole genome sequencing. We conducted epidemiologic and traceback investigations to identify illness sub-clusters and common sources. An FDA-led environmental assessment, which tested water, soil, manure, compost, and scat samples, was conducted to evaluate potential sources of STEC contamination. RESULTS: We identified 240 case-patients from 37 states; 104 were hospitalized, 28 developed hemolytic uremic syndrome, and five died. Of 179 people who were interviewed, 152 (85%) reported consuming romaine lettuce in the week before illness onset. Twenty sub-clusters were identified. Product traceback from sub-cluster restaurants identified numerous romaine lettuce distributors and growers; all lettuce originated from the Yuma growing region. Water samples collected from an irrigation canal in the region yielded the outbreak strain of STEC O157. CONCLUSION: We report on the largest multistate leafy green-linked STEC O157 outbreak in several decades. The investigation highlights the complexities associated with investigating outbreaks involving widespread environmental contamination. |
Multistate outbreak of Salmonella infections linked to raw turkey products - United States, 2017-2019
Hassan R , Buuck S , Noveroske D , Medus C , Sorenson A , Laurent J , Rotstein D , Schlater L , Freiman J , Douris A , Simmons M , Donovan D , Henderson J , Tewell M , Snyder K , Oni O , Von Stein D , Dassie K , Leeper M , Adediran A , Dowell N , Gieraltowski L , Basler C . MMWR Morb Mortal Wkly Rep 2019 68 (46) 1045-1049 During 2018–2019, CDC, local and state public health partners, the U.S. Department of Agriculture (USDA), and the Food and Drug Administration (FDA) investigated a multistate outbreak of 356 Salmonella Reading infections from 42 states and the District of Columbia (DC) linked to turkey. The outbreak strain was isolated from raw turkey products, raw turkey pet food, and live turkeys. In July 2018, CDC and USDA’s Food Safety and Inspection Service (FSIS) shared outbreak investigation results with representatives from the U.S. turkey industry, engaging with an industry group rather than a specific company for the first time during an outbreak, and CDC issued a public investigation notice. During the investigation, four recalls of turkey products were issued. Evidence suggested that the outbreak strain of Salmonella was widespread in the turkey industry, and therefore, interventions should target all parts of the supply chain, including slaughter and processing facilities and upstream farm sources. |
Onsite investigation at a mail-order hatchery following a multistate Salmonella illness outbreak linked to live poultry-United States, 2018.
Robertson SA , Sidge JL , Koski L , Hardy MC , Stevenson L , Signs K , Stobierski MG , Bidol S , Donovan D , Soehnlen M , Jones K , Robeson S , Hambley A , Stefanovsky L , Brandenburg J , Hise K , Tolar B , Nichols MC , Basler C . Poult Sci 2019 98 (12) 6964-6972 Centers for Disease Control and Prevention (CDC), health departments, and other state and federal partners have linked contact with live poultry to 70 human Salmonella outbreaks in the United States from 2000 to 2017, which resulted in a total of 4,794 illnesses, 894 hospitalizations, and 7 deaths. During human salmonellosis outbreaks environmental sampling is rarely conducted as part of the outbreak investigation. CDC was contacted by state health officials on June 12, 2018, to provide support during an investigation of risk factors for Salmonella infections linked to live poultry originating at a mail-order hatchery. From January 1, 2018, to June 15, 2018, 13 human Salmonella infections in multiple states were attributed to exposure to live poultry from a single hatchery. Two serotypes of Salmonella were associated with these infections, Salmonella Enteritidis and Salmonella Litchfield. Molecular subtyping of the S. Enteritidis clinical isolates revealed they were closely related genetically (within 0 to 9 alleles) by core genome multi-locus sequence typing (cgMLST) to isolates obtained from environmental samples taken from hatchery shipping containers received at retail outlets. Environmental sampling and onsite investigation of practices was conducted at the mail-order hatchery during an investigation on June 19, 2018. A total of 45 environmental samples were collected, and 4 (9%) grew Salmonella. A chick box liner from a box in the pre-shipping area yielded an isolate closely related to the S. Enteritidis outbreak strain (within 1 to 9 alleles by cgMLST). The onsite investigation revealed lapses in biosecurity, sanitation, quality assurance, and education of consumers. Review of Salmonella serotype testing performed by the hatchery revealed that the number of samples and type of samples collected monthly varied. Also, S. Enteritidis was identified at the hatchery every year since testing began in 2016. Recommendations to the hatchery for biosecurity, testing, and sanitation measures were made to help reduce burden of Salmonella in the hatchery and breeding flocks, thereby reducing the occurrence of human illness. |
Multidrug-Resistant Salmonella I 4,[5],12:i:- and Salmonella Infantis Infections Linked to Whole Roasted Pigs from a Single Slaughter and Processing Facility.
Kawakami V , Bottichio L , Lloyd J , Carleton H , Leeper M , Olson G , Li Z , Kissler B , Angelo KM , Whitlock L , Sinatra J , Defibaugh-Chavez S , Bicknese A , Kay M , Wise ME , Basler C , Duchin J . J Food Prot 2019 82 (9) 1615-1624 We describe two outbreaks of multidrug-resistant (MDR) Salmonella I 4,[5],12:i:- infection, occurring in 2015 to 2016, linked to pork products, including whole roaster pigs sold raw from a single Washington slaughter and processing facility (establishment A). Food histories from 80 ill persons were compared with food histories reported in the FoodNet 2006 to 2007 survey of healthy persons from all 10 U.S. FoodNet sites who reported these exposures in the week before interview. Antimicrobial susceptibility testing and whole genome sequencing were conducted on selected clinical, food, and environmental isolates. During 2015, a total of 192 ill persons were identified from five states; among ill persons with available information, 30 (17%) of 180 were hospitalized, and none died. More ill persons than healthy survey respondents consumed pork (74 versus 43%, P < 0.001). Seventeen (23%) of 73 ill persons for which a response was available reported attending an event where whole roaster pig was served in the 7 days before illness onset. All 25 clinical isolates tested from the 2015 outbreak and a subsequent 2016 smaller outbreak (n = 15) linked to establishment A demonstrated MDR. Whole genome sequencing of clinical, environmental, and food isolates (n = 69) collected in both investigations revealed one clade of highly related isolates, supporting epidemiologic and traceback data that establishment A as the source of both outbreaks. These investigations highlight that whole roaster pigs, an uncommon food vehicle for MDR Salmonella I 4,[5],12:i:- outbreaks, will need further attention from food safety researchers and educators for developing science-based consumer guidelines, specifically with a focus on the preparation process. |
Multistate Outbreak of Listeriosis Associated with Packaged Leafy Green Salads, United States and Canada, 2015-2016.
Self JL , Conrad A , Stroika S , Jackson A , Whitlock L , Jackson KA , Beal J , Wellman A , Fatica MK , Bidol S , Huth PP , Hamel M , Franklin K , Tschetter L , Kopko C , Kirsch P , Wise ME , Basler C . Emerg Infect Dis 2019 25 (8) 1461-1468 We investigated an outbreak of listeriosis detected by whole-genome multilocus sequence typing and associated with packaged leafy green salads. Nineteen cases were identified in the United States during July 5, 2015-January 31, 2016; isolates from case-patients were closely related (median difference 3 alleles, range 0-16 alleles). Of 16 case-patients interviewed, all reported salad consumption. Of 9 case-patients who recalled brand information, all reported brands processed at a common US facility. The Public Health Agency of Canada simultaneously investigated 14 cases of listeriosis associated with this outbreak. Isolates from the processing facility, packaged leafy green salads, and 9 case-patients from Canada were closely related to US clinical isolates (median difference 3 alleles, range 0-16 alleles). This investigation led to a recall of packaged leafy green salads made at the processing facility. Additional research is needed to identify best practices and effective policies to reduce the likelihood of Listeria monocytogenes contamination of fresh produce. |
Taxonomy of the order Mononegavirales: update 2019.
Amarasinghe GK , Ayllon MA , Bao Y , Basler CF , Bavari S , Blasdell KR , Briese T , Brown PA , Bukreyev A , Balkema-Buschmann A , Buchholz UJ , Chabi-Jesus C , Chandran K , Chiapponi C , Crozier I , de Swart RL , Dietzgen RG , Dolnik O , Drexler JF , Durrwald R , Dundon WG , Duprex WP , Dye JM , Easton AJ , Fooks AR , Formenty PBH , Fouchier RAM , Freitas-Astua J , Griffiths A , Hewson R , Horie M , Hyndman TH , Jiang D , Kitajima EW , Kobinger GP , Kondo H , Kurath G , Kuzmin IV , Lamb RA , Lavazza A , Lee B , Lelli D , Leroy EM , Li J , Maes P , Marzano SL , Moreno A , Muhlberger E , Netesov SV , Nowotny N , Nylund A , Okland AL , Palacios G , Palyi B , Paweska JT , Payne SL , Prosperi A , Ramos-Gonzalez PL , Rima BK , Rota P , Rubbenstroth D , Shi M , Simmonds P , Smither SJ , Sozzi E , Spann K , Stenglein MD , Stone DM , Takada A , Tesh RB , Tomonaga K , Tordo N , Towner JS , van den Hoogen B , Vasilakis N , Wahl V , Walker PJ , Wang LF , Whitfield AE , Williams JV , Zerbini FM , Zhang T , Zhang YZ , Kuhn JH . Arch Virol 2019 164 (7) 1967-1980 In February 2019, following the annual taxon ratification vote, the order Mononegavirales was amended by the addition of four new subfamilies and 12 new genera and the creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV). |
ICTV virus taxonomy profile: Filoviridae
Kuhn JH , Amarasinghe GK , Basler CF , Bavari S , Bukreyev A , Chandran K , Crozier I , Dolnik O , Dye JM , Formenty PBH , Griffiths A , Hewson R , Kobinger GP , Leroy EM , Muhlberger E , Netesov SV , Palacios G , Palyi B , Paweska JT , Smither SJ , Takada A , Towner JS , Wahl V . J Gen Virol 2019 100 (6) 911-912 Members of the family Filoviridae produce variously shaped, often filamentous, enveloped virions containing linear non-segmented, negative-sense RNA genomes of 15-19 kb. Several filoviruses (e.g., Ebola virus) are pathogenic for humans and are highly virulent. Several filoviruses infect bats (e.g., Marburg virus), whereas the hosts of most other filoviruses are unknown. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on Filoviridae, which is available at www.ictv.global/report/filoviridae. |
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