Last data update: May 06, 2024. (Total: 46732 publications since 2009)
Records 1-30 (of 63 Records) |
Query Trace: Neil K[original query] |
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Multistate outbreak of Salmonella Oranienburg infections linked to bulb onions imported from Mexico – United States, 2021
Mitchell MR , Kirchner M , Schneider B , McClure M , Neil KP , Madad A , Jemaneh T , Tijerina M , Nolte K , Wellman A , Neises D , Pightling A , Swinford A , Piontkowski A , Sexton R , McKenna C , Cornell J , Sandoval AL , Wang H , Bell RL , Stager C , Zamora Nava MC , Lara de la Cruz JL , Sánchez Córdova LI , Galván PR , Ortiz JA , Flowers S , Grisamore A , Gieraltowski L , Bazaco M , Viazis S . Food Control 2024 160 In 2021, the U.S. Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), and state and local health and regulatory partners investigated an outbreak of Salmonella enterica serovar Oranienburg infections linked to bulb onions from Mexico, resulting in 1040 illnesses and 260 hospitalizations across 39 states, the District of Columbia, and Puerto Rico. The Kansas Department of Agriculture recovered the outbreak strain of Salmonella Oranienburg from a sample of condiment collected from an ill person's home. The condiment was made with cilantro, lime, and onions, but, at the time of collection, there were no onions remaining in it. FDA conducted traceback investigations for white, yellow, and red bulb onions, cilantro, limes, tomatoes, and jalapeño peppers. Growers in the state of Chihuahua, Mexico, were identified as supplying the implicated onions that could account for exposure to onions for all illnesses included in the traceback investigation, but investigators could not determine a single source or route of contamination. FDA collected product and environmental samples across the domestic supply chain but did not recover the outbreak strain of Salmonella. Binational collaboration and information sharing supported Mexican authorities in collecting environmental samples from two packing plants and onion, water, and environmental samples from 15 farms and firms in Chihuahua, Mexico identified through FDA's traceback investigation, but did not recover the outbreak strain. Distributors of the implicated onions issued voluntary recalls of red, yellow, and white whole, fresh onions imported from the state of Chihuahua, Mexico. This outbreak showcased how investigators overcame significant traceback and epidemiologic challenges, the need for strengthening the ongoing collaboration between U.S. and Mexican authorities and highlighted the need for identifying practices across the supply chain that can help improve the safety of onions. © 2024 |
Of Those We Have Lost and Those Who Have Saved So Many Others
Chorba T . Emerg Infect Dis 2022 28 (7) 1537-9 Modernism is a term ascribed to styles and transformative movements in multiple cultural spheres—philosophy, music, art, architecture, and literature. In its essence, modernism has at its core experimentation, as a term usually applied to efforts and creations of the late 19th or early 20th century, but sometimes later, characterized by intentional departures from traditional forms. | | There are many well-known examples of modernist efforts in their respective spheres and periods. In biology, Charles Darwin questioned the concept of human uniqueness with the theory of evolution. In literature, the term modernist has been applied to European and American writers who created substantive departures from tradition, as was seen in the works of Fyodor Dostoyevsky, Gustave Flaubert, James Joyce, and William Carlos Williams. In music, modernism is a term ascribed to the period 1890–1930, and postmodernism is a term sometimes accorded to phenomena with modernist qualities but occurring after 1930; however, some critics use modernism to describe a movement of rebellion that continues, dependent on the musician’s attitude rather than the musician’s moment in time. Certainly, Ella Fitzgerald, Miles Davis, Bob Dylan, John Lennon, Charles Mingus, the Rolling Stones, and Neil Young created musical forms that featured modernist iconoclasm, stepping well beyond the early 20th century. In art, modernism is used as a broader categorization of several novel stylistic departures including realism, postimpressionism, fauvism, cubism, dadaism, surrealism, abstract expressionism, and minimalism, each with elements of deliberate experimentation and innovation. |
Cohort Profile: a Prospective Household cohort study of Influenza, Respiratory Syncytial virus, and other respiratory pathogens community burden and Transmission dynamics in South Africa (PHIRST), 2016-2018 (preprint)
Cohen C , McMorrow ML , Martinson NA , Kahn K , Treurnicht FK , Moyes J , Mkhencele T , Hellferscee O , Lebina L , Moroe M , Motlhaoleng K , Gómez-Olivé FX , Wagner R , Tollman S , Wafawanaka F , Ngobeni S , Kleynhans J , Mathunjwa A , Buys A , Maake L , Wolter N , Carrim M , Piketh S , Language B , Mathee A , von Gottberg A , Tempia S . medRxiv 2021 2021.01.06.21249313 Purpose The PHIRST study (Prospective Household cohort study of Influenza, Respiratory Syncytial virus, and other respiratory pathogens community burden and Transmission dynamics in South Africa) aimed to estimate the community burden of influenza and respiratory syncytial virus (RSV) including the incidence of infection, symptomatic fraction, and disease severity, and to assess household transmission. We further aimed to estimate the impact of HIV infection and age on disease burden and transmission, and to assess the burden of Bordetella pertussis and Streptococcus pneumoniae.Participants We enrolled 1684 individuals in 327 randomly selected households in two sites (rural Agincourt subdistrict, Mpumalanga Province and urban Jouberton Township, North West Province) over 3 consecutive influenza and RSV seasons. A new cohort of households was enrolled each year. Eligible households included those with >2 household members where ≥80% of household members provided consent (and assent for children aged 7-17 years). Enrolled household members were sampled with nasopharyngeal swabs twice weekly during the RSV and influenza seasons of the year of enrolment. Serology samples were collected at enrolment and before and after the influenza season annually.Findings to date There were 122,113 potential individual follow-up visits over the 3 years, and participants were interviewed for 105,783 (87%) of these. Out of 105,683 nasopharyngeal swabs from follow-up visits, 1,258 (1%), 1,026 (1%), 273 (<1%), 38,829 (37%) tested positive on PCR for influenza viruses, respiratory syncytial virus, pertussis and pneumococcus respectively.Future plans Future planned analyses include analysis of influenza serology results and RSV burden and transmission. Households enrolled in the PHIRST study during 2016-2018 were eligible for inclusion in a study of SARS-CoV-2 transmission initiated in July 2020. This study uses similar testing frequency and household selection methods to assess the community burden of SARS-CoV-2 infection and the role of asymptomatic infection in virus transmission.Registration Clinical trials.gov NCT02519803Strengths and limitations of this studyPHIRST was conducted in urban and rural African settings with high HIV prevalence, allowing assessment of the effect of HIV on community burden and transmission dynamics of respiratory pathogens.Households were selected randomly to provide a representative sample of the community. Twice weekly sampling from each cohort of individuals for 6-10 months irrespective of symptoms allows estimation of community burden, household secondary infection risk, and serial interval including asymptomatic or paucisymptomatic episodes.Polymerase chain reaction testing of >100,000 nasopharyngeal swab samples for multiple pathogens (influenza, respiratory syncytial virus, pertussis and Streptoccocus pneumonia) allows detailed examination of disease burden and transmission and pathogen interactionsPHIRST was not powered to assess severe outcomes (i.e. hospitalisation and death).We only examined four pathogens, but other micro-organisms may be important. Samples have been stored which could allow us to implement broader multi-pathogen testing in the future.Competing Interest StatementCheryl Cohen has received research grants awarded to her institution from Sanofi Pasteur, US Centers for Disease Control and Prevention. Cheryl Cohen has had costs for travel to a meeting supported by Parexel. Maimuna Carrim was awarded the Robert Austrian Research Award in Pneumococcal Vaccinology sponsored by Pfizer. Neil Martinson has a research grant awarded to his institution by Pfizer South Africa. Anne von Gottberg has received research grants awarded to her institution from Sanofi Pasteur, Pfizer and US Centers for Disease Control and Prevention.Clinical TrialNCT02519803Funding StatementThe study was funded through a cooperative agreement with the United States Centers for Disease Control and Prevention (CDC) (grant number 1U01IP001048). Testing for RSV and pneumococcus was supported by the Bill and Melin a Gates Foundation (Grant number: OPP1164778). Testing for B. pertussis was supported by Sanofi Pasteur (Grant number: PER00059). The Agincourt Health and Socio-Demographic Surveillance System is a node of the South African Population Research Infrastructure Network (SAPRIN) and is supported by the National Department of Science and Innovation, the Medical Research Council and the University of the Witwatersrand, South Africa, and the Wellcome Trust, UK (grants 058893/Z/99/A; 069683/Z/02/Z; 085477/Z/08/Z; 085477/B/08/Z).Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:University of the Witwatersrand Human Research Ethics CommitteeAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesPrimary study results for influenza as well as a description of the quality of housing at the two sites have been prepared and submitted to international peer-reviewed journals. Analysis of the data for other pathogens is planned to be completed by December 2021. Additional modelling and serologic studies will be concluded within 3 years and primary de-identified data should be publicly available no later than November 2023. The investigators welcome enquiries about possible collaborations and access to the data set. Investigators interested in more details about this study, or in accessing these resources, should contact the principle investigator, Prof Cheryl Cohen, at NICD (cherylc{at}nicd.ac.za). |
Comparative genomics of the major parasitic worms (preprint)
International Helminth Genomes Consortium , Coghlan Avril , Tyagi Rahul , Cotton James A , Holroyd Nancy , Rosa Bruce A , Tsai Isheng Jason , Laetsch Dominik R , Beech Robin N , Day Tim A , Hallsworth-Pepin Kymberlie , Ke Huei-Mien , Kuo Tzu-Hao , Lee Tracy J , Martin John , Maizels Rick M , Mutowo Prudence , Ozersky Philip , Parkinson John , Reid Adam J , Rawlings Neil D , Ribeiro Diogo M , Seshadri Swapna Lakshmipuram , Stanley Eleanor , Taylor David W , Wheeler Nicolas J , Zamanian Mostafa , Zhang Xu , Allan Fiona , Allen Judith E , Asano Kazuhito , Babayan Simon A , Bah Germanus , Beasley Helen , Bennett Hayley M , Bisset Stewart A , Castillo Estela , Cook Joseph , Cooper Philip J , Cruz-Bustos Teresa , Cuéllar Carmen , Devaney Eileen , Doyle Stephen R , Eberhard Mark L , Emery Aidan , Eom Keeseon S , Gilleard John S , Gordon Daria , Harcus Yvonne , Harsha Bhavana , Hawdon John M , Hill Dolores E , Hodgkinson Jane , Horák Petr , Howe Kevin L , Huckvale Thomas , Kalbe Martin , Kaur Gaganjot , Kikuchi Taisei , Koutsovoulos Georgios , Kumar Sujai , Leach Andrew R , Lomax Jane , Makepeace Benjamin , Matthews Jacqueline B , Muro Antonio , O’Boyle Noel Michael , Olson Peter D , Osuna Antonio , Partono Felix , Pfarr Kenneth , Rinaldi Gabriel , Foronda Pilar , Rollinson David , Gomez Samblas Mercedes , Sato Hiroshi , Schnyder Manuela , Scholz Tomáš , Shafie Myriam , Tanya Vincent N , Toledo Rafael , Tracey Alan , Urban Joseph F , Wang Lian-Chen , Zarlenga Dante , Blaxter Mark L , Mitreva Makedonka , Berriman Matthew . bioRxiv 2017 236539 Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating chronic infections of humans and animals, decimate crop production and are a major impediment to socioeconomic development. Here we compare the genomes of 81 nematode and platyhelminth species, including those of 76 parasites. From 1.4 million genes, we identify gene family births and hundreds of large expanded gene families at key nodes in the phylogeny that are relevant to parasitism. Examples include gene families that modulate host immune responses, enable parasite migration though host tissues or allow the parasite to feed. We use a wide-ranging in silico screen to identify and prioritise new potential drug targets and compounds for testing. We also uncover lineage-specific differences in core metabolism and in protein families historically targeted for drug development. This is the broadest comparative study to date of the genomes of parasitic and non-parasitic worms. It provides a transformative new resource for the research community to understand and combat the diseases that parasitic worms cause. |
Searching for evidence in public health emergencies: a white paper of best practices
Brody S , Loree S , Sampson M , Mensinkai S , Coffman J , Mueller MH , Askin N , Hamill C , Wilson E , McAteer MB , Staines H , Hamill C , Dobbins M , Claussen AM , Kothari KU , De Brún C , Young S , Neil-Sztramko SE , Wilson E , Featherstone RM , Sampson M , Staines H , Knuth M . J Med Libr Assoc 2023 111 566-578 Objectives: Information professionals have supported medical providers, administrators and decision-makers, and guideline creators in the COVID-19 response. Searching COVID-19 literature presented new challenges, including the volume and heterogeneity of literature and the proliferation of new information sources, and exposed existing issues in metadata and publishing. An expert panel developed best practices, including recommendations, elaborations, and examples, for searching during public health emergencies. Methods: Project directors and advisors developed core elements from experience and literature. Experts, identified by affiliation with evidence synthesis groups, COVID-19 search experience, and nomination, responded to an online survey to reach consensus on core elements. Expert participants provided written responses to guiding questions. A synthesis of responses provided the foundation for focus group discussions. A writing group then drafted the best practices into a statement. Experts reviewed the statement prior to dissemination. Results: Twelve information professionals contributed to best practice recommendations on six elements: core resources, search strategies, publication types, transparency and reproducibility, collaboration, and conducting research. Underlying principles across recommendations include timeliness, openness, balance, preparedness, and responsiveness. Conclusions: The authors and experts anticipate the recommendations for searching for evidence during public health emergencies will help information specialists, librarians, evidence synthesis groups, researchers, and decision-makers respond to future public health emergencies, including but not limited to disease outbreaks. The recommendations complement existing guidance by addressing concerns specific to emergency response. The statement is intended as a living document. Future revisions should solicit input from a broader community and reflect conclusions of meta-research on COVID-19 and health emergencies. © 2023, Medical Library Association. All rights reserved. |
Preliminary Estimate of Excess Mortality During the COVID-19 Outbreak - New York City, March 11-May 2, 2020.
New York City Department of Health and Mental Hygiene (DOHMH) COVID-19 Response Team , Olson Donald R , Huynh Mary , Fine Annie , Baumgartner Jennifer , Castro Alejandro , Chan Hiu Tai , Daskalakis Demetre , Devinney Katelynn , Guerra Kevin , Harper Scott , Kennedy Joseph , Konty Kevin , Li Wenhui , McGibbon Emily , Shaff Jaimie , Thompson Corinne , Vora Neil M , Van Wye Gretchen . MMWR Morb Mortal Wkly Rep 2020 69 (19) 603-605 SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), was first identified in December 2019 in Wuhan, China, and has since spread worldwide. On March 11, 2020, the World Health Organization declared COVID-19 a pandemic (1). That same day, the first confirmed COVID-19-associated fatality occurred in New York City (NYC). To identify confirmed COVID-19-associated deaths, defined as those occurring in persons with laboratory-confirmed SARS-CoV-2 infection, on March 13, 2020, the New York City Department of Health and Mental Hygiene (DOHMH) initiated a daily match between all deaths reported to the DOHMH electronic vital registry system (eVital) (2) and laboratory-confirmed cases of COVID-19. Deaths for which COVID-19, SARS-CoV-2, or an equivalent term is listed on the death certificate as an immediate, underlying, or contributing cause of death, but that do not have laboratory-confirmation of COVID-19 are classified as probable COVID-19-associated deaths. As of May 2, a total of 13,831 laboratory-confirmed COVID-19-associated deaths, and 5,048 probable COVID-19-associated deaths were recorded in NYC (3). Counting only confirmed or probable COVID-19-associated deaths, however, likely underestimates the number of deaths attributable to the pandemic. The counting of confirmed and probable COVID-19-associated deaths might not include deaths among persons with SARS-CoV-2 infection who did not access diagnostic testing, tested falsely negative, or became infected after testing negative, died outside of a health care setting, or for whom COVID-19 was not suspected by a health care provider as a cause of death. The counting of confirmed and probable COVID-19-associated deaths also does not include deaths that are not directly associated with SARS-CoV-2 infection. The objective of this report is to provide an estimate of all-cause excess deaths that have occurred in NYC in the setting of widespread community transmission of SARS-CoV-2. Excess deaths refer to the number of deaths above expected seasonal baseline levels, regardless of the reported cause of death. Estimation of all-cause excess deaths is used as a nonspecific measure of the severity or impact of pandemics (4) and public health emergencies (5). Reporting of excess deaths might provide a more accurate measure of the impact of the pandemic. |
A Public Health Research Agenda for Managing Infodemics: Methods and Results of the First WHO Infodemiology Conference.
Calleja N , AbdAllah A , Abad N , Ahmed N , Albarracin D , Altieri E , Anoko JN , Arcos R , Azlan AA , Bayer J , Bechmann A , Bezbaruah S , Briand SC , Brooks I , Bucci LM , Burzo S , Czerniak C , De Domenico M , Dunn AG , Ecker UKH , Espinosa L , Francois C , Gradon K , Gruzd A , Gülgün BS , Haydarov R , Hurley C , Astuti SI , Ishizumi A , Johnson N , Johnson Restrepo D , Kajimoto M , Koyuncu A , Kulkarni S , Lamichhane J , Lewis R , Mahajan A , Mandil A , McAweeney E , Messer M , Moy W , Ndumbi Ngamala P , Nguyen T , Nunn M , Omer SB , Pagliari C , Patel P , Phuong L , Prybylski D , Rashidian A , Rempel E , Rubinelli S , Sacco P , Schneider A , Shu K , Smith M , Sufehmi H , Tangcharoensathien V , Terry R , Thacker N , Trewinnard T , Turner S , Tworek H , Uakkas S , Vraga E , Wardle C , Wasserman H , Wilhelm E , Würz A , Yau B , Zhou L , Purnat TD . JMIR Infodemiology 2021 1 (1) e30979 BACKGROUND: An infodemic is an overflow of information of varying quality that surges across digital and physical environments during an acute public health event. It leads to confusion, risk-taking, and behaviors that can harm health and lead to erosion of trust in health authorities and public health responses. Owing to the global scale and high stakes of the health emergency, responding to the infodemic related to the pandemic is particularly urgent. Building on diverse research disciplines and expanding the discipline of infodemiology, more evidence-based interventions are needed to design infodemic management interventions and tools and implement them by health emergency responders. OBJECTIVE: The World Health Organization organized the first global infodemiology conference, entirely online, during June and July 2020, with a follow-up process from August to October 2020, to review current multidisciplinary evidence, interventions, and practices that can be applied to the COVID-19 infodemic response. This resulted in the creation of a public health research agenda for managing infodemics. METHODS: As part of the conference, a structured expert judgment synthesis method was used to formulate a public health research agenda. A total of 110 participants represented diverse scientific disciplines from over 35 countries and global public health implementing partners. The conference used a laddered discussion sprint methodology by rotating participant teams, and a managed follow-up process was used to assemble a research agenda based on the discussion and structured expert feedback. This resulted in a five-workstream frame of the research agenda for infodemic management and 166 suggested research questions. The participants then ranked the questions for feasibility and expected public health impact. The expert consensus was summarized in a public health research agenda that included a list of priority research questions. RESULTS: The public health research agenda for infodemic management has five workstreams: (1) measuring and continuously monitoring the impact of infodemics during health emergencies; (2) detecting signals and understanding the spread and risk of infodemics; (3) responding and deploying interventions that mitigate and protect against infodemics and their harmful effects; (4) evaluating infodemic interventions and strengthening the resilience of individuals and communities to infodemics; and (5) promoting the development, adaptation, and application of interventions and toolkits for infodemic management. Each workstream identifies research questions and highlights 49 high priority research questions. CONCLUSIONS: Public health authorities need to develop, validate, implement, and adapt tools and interventions for managing infodemics in acute public health events in ways that are appropriate for their countries and contexts. Infodemiology provides a scientific foundation to make this possible. This research agenda proposes a structured framework for targeted investment for the scientific community, policy makers, implementing organizations, and other stakeholders to consider. |
Comparative genomics of the major parasitic worms
International Helminth Genomes Consortium , Coghlan Avril , Tyagi Rahul , Cotton James A , Holroyd Nancy , Rosa Bruce A , Tsai Isheng Jason , Laetsch Dominik R , Beech Robin N , Day Tim A , Hallsworth-Pepin Kymberlie , Ke Huei-Mien , Kuo Tzu-Hao , Lee Tracy J , Martin John , Maizels Rick M , Mutowo Prudence , Ozersky Philip , Parkinson John , Reid Adam J , Rawlings Neil D , Ribeiro Diogo M , Seshadri Swapna Lakshmipuram , Stanley Eleanor , Taylor David W , Wheeler Nicolas J , Zamanian Mostafa , Zhang Xu , Allan Fiona , Allen Judith E , Asano Kazuhito , Babayan Simon A , Bah Germanus , Beasley Helen , Bennett Hayley M , Bisset Stewart A , Castillo Estela , Cook Joseph , Cooper Philip J , Cruz-Bustos Teresa , Cuéllar Carmen , Devaney Eileen , Doyle Stephen R , Eberhard Mark L , Emery Aidan , Eom Keeseon S , Gilleard John S , Gordon Daria , Harcus Yvonne , Harsha Bhavana , Hawdon John M , Hill Dolores E , Hodgkinson Jane , Horák Petr , Howe Kevin L , Huckvale Thomas , Kalbe Martin , Kaur Gaganjot , Kikuchi Taisei , Koutsovoulos Georgios , Kumar Sujai , Leach Andrew R , Lomax Jane , Makepeace Benjamin , Matthews Jacqueline B , Muro Antonio , O’Boyle Noel Michael , Olson Peter D , Osuna Antonio , Partono Felix , Pfarr Kenneth , Rinaldi Gabriel , Foronda Pilar , Rollinson David , Gomez Samblas Mercedes , Sato Hiroshi , Schnyder Manuela , Scholz Tomáš , Shafie Myriam , Tanya Vincent N , Toledo Rafael , Tracey Alan , Urban Joseph F , Wang Lian-Chen , Zarlenga Dante , Blaxter Mark L , Mitreva Makedonka , Berriman Matthew . Nat Genet 2019 51 (1) 163-174 Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating chronic infections of humans and animals, decimate crop production and are a major impediment to socioeconomic development. Here we report a broad comparative study of 81 genomes of parasitic and non-parasitic worms. We have identified gene family births and hundreds of expanded gene families at key nodes in the phylogeny that are relevant to parasitism. Examples include gene families that modulate host immune responses, enable parasite migration though host tissues or allow the parasite to feed. We reveal extensive lineage-specific differences in core metabolism and protein families historically targeted for drug development. From an in silico screen, we have identified and prioritized new potential drug targets and compounds for testing. This comparative genomics resource provides a much-needed boost for the research community to understand and combat parasitic worms. |
Listeria monocytogenes Illness and Deaths Associated With Ongoing Contamination of a Multi-Regional Brand of Ice Cream Products, United States, 2010-2015.
Conrad AR , Tubach S , Cantu V , Webb LM , Stroika S , Moris S , Davis M , Hunt DC , Bradley KK , Kucerova Z , Strain E , Doyle M , Fields A , Neil KP , Gould LH , Jackson KA , Wise ME , Griffin PM , Jackson BR . Clin Infect Dis 2022 76 (1) 89-95 BACKGROUND: Frozen foods have rarely been linked to Listeria monocytogenes illness. We describe an outbreak investigation prompted both by hospital clustering of illnesses and product testing. METHODS: We identified outbreak-associated listeriosis cases using whole-genome sequencing (WGS), product testing results, and epidemiologic linkage to cases in the same Kansas hospital. We reviewed hospital medical and dietary records, product invoices, and molecular subtyping results. Federal and state officials tested product and environmental samples for L. monocytogenes. RESULTS: Kansas officials were investigating five cases of listeriosis at a single hospital when, simultaneously, unrelated sampling for a study in South Carolina identified L. monocytogenes in Company A ice cream products made in Texas. Isolates from four patients and Company A products were closely related by WGS, and the four patients with known exposures had consumed milkshakes made with Company A ice cream while hospitalized. Further testing identified L. monocytogenes in ice cream produced in a second Company A production facility in Oklahoma; these isolates were closely related by WGS to those from five patients in three other states. These ten illnesses, involving three deaths, occurred from 2010 through 2015. Company A ultimately recalled all products. CONCLUSION: In this U.S. outbreak of listeriosis linked to a widely distributed brand of ice cream, WGS and product sampling helped link cases spanning five years to two production facilities, indicating longstanding contamination. Comprehensive sanitation controls and environmental and product testing for L. monocytogenes, with regulatory oversight, should be implemented for ice cream production. |
Timing of first positive hepatitis c polymerase chain reaction test among pregnant women with hepatitis c infection Surveillance for Emerging Threats to Mothers and Babies Network
Woodworth Kate , Newton Suzanne , Sizemore Lindsey , Wingate Heather , Wills Aprielle , Thomas Nadia , Reynolds Bethany , Foster Monique , Gupta Neil , Wester Carolyn , Meaney-Delman Data , Gilboa Suzanne , Tong Van . Am J Obstet Gynecol 2022 226 (2) 305-306 Incidence of hepatitis C virus (HCV) infection in women of reproductive age is increasing, leading to rising numbers of women with HCV infection in pregnancy and concerns of perinatal transmission. In April 2020, the Centers for Disease Control and Prevention (CDC) began recommending HCV screening during each pregnancy. We describe maternal characteristics and timing of HCV testing among pregnant women identified with HCV infection. | |
Two multistate outbreaks of a reoccurring Shiga toxin-producing Escherichia coli strain associated with romaine lettuce - United States, 2018-2019
Waltenburg MA , Schwensohn C , Madad A , Seelman SL , Peralta V , Koske SE , Boyle MM , Arends K , Patel K , Mattioli M , Gieraltowski L , Neil KP . Epidemiol Infect 2021 150 e16 Leafy green vegetables are a common source of Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) foodborne illness outbreaks. Ruminant animals, primarily cattle, are the major reservoir of STEC O157. Epidemiological, traceback, and field investigations were conducted to identify potential outbreak sources. Product and environmental samples were tested for STEC. A reoccurring strain of STEC O157 caused two multistate outbreaks linked to romaine lettuce in 2018 and 2019, resulting in 234 illnesses in 33 states. Over 80% of patients interviewed consumed romaine lettuce before illness. The romaine lettuce was sourced from two California growing regions: Santa Maria and Salinas Valley in 2018 and Salinas Valley in 2019. The outbreak strain was isolated from environmental samples collected at sites >90 miles apart across growing regions, as well as from romaine-containing products in 2019. Although the definitive route of romaine contamination was undetermined, use of a contaminated agricultural water reservoir in 2018 and contamination from cattle grazing on adjacent land in 2019 were suspected as possible factors. Preventing lettuce contamination from growth to consumption is imperative to preventing illness. These outbreaks highlight the need to further understand mechanisms of romaine contamination, including the role of environmental or animal reservoirs for STEC O157. © 2021 Cambridge University Press. All rights reserved. |
Decreases in Hepatitis C Testing and Treatment During the COVID-19 Pandemic.
Kaufman HW , Bull-Otterson L , Meyer WA3rd , Huang X , Doshani M , Thompson WW , Osinubi A , Khan MA , Harris AM , Gupta N , Van Handel M , Wester C , Mermin J , Nelson NP . Am J Prev Med 2021 61 (3) 369-376 INTRODUCTION: The COVID-19 pandemic has disrupted healthcare services, reducing opportunities to conduct routine hepatitis C virus antibody screening, clinical care, and treatment. Therefore, people living with undiagnosed hepatitis C virus during the pandemic may later become identified at more advanced stages of the disease, leading to higher morbidity and mortality rates. Further, unidentified hepatitis C virus-infected individuals may continue to unknowingly transmit the virus to others. METHODS: To assess the impact of the COVID-19 pandemic, data were evaluated from a large national reference clinical laboratory and from national estimates of dispensed prescriptions for hepatitis C virus treatment. Investigators estimated the average number of hepatitis C virus antibody tests, hepatitis C virus antibody-positive test results, and hepatitis C virus RNA-positive test results by month in January-July for 2018 and 2019, compared with the same months in 2020. To assess the impact of hepatitis C virus treatment, dispensed hepatitis C virus direct-acting antiretroviral medications were examined for the same time periods. Statistical analyses of trends were performed using negative binomial models. RESULTS: Compared with the 2018 and 2019 months, hepatitis C virus antibody testing volume decreased 59% during April 2020 and rebounded to a 6% reduction in July 2020. The number of hepatitis C virus RNA-positive results fell by 62% in March 2020 and remained 39% below the baseline by July 2020. For hepatitis C virus treatment, prescriptions decreased 43% in May, 37% in June, and 38% in July relative to the corresponding months in 2018 and 2019. CONCLUSIONS: During the COVID-19 pandemic, continued public health messaging, interventions and outreach programs to restore hepatitis C virus testing and treatment to prepandemic levels, and maintenance of public health efforts to eliminate hepatitis C infections remain important. |
Incidence of Multisystem Inflammatory Syndrome in Children Among US Persons Infected With SARS-CoV-2.
Payne AB , Gilani Z , Godfred-Cato S , Belay ED , Feldstein LR , Patel MM , Randolph AG , Newhams M , Thomas D , Magleby R , Hsu K , Burns M , Dufort E , Maxted A , Pietrowski M , Longenberger A , Bidol S , Henderson J , Sosa L , Edmundson A , Tobin-D'Angelo M , Edison L , Heidemann S , Singh AR , Giuliano JSJr , Kleinman LC , Tarquinio KM , Walsh RF , Fitzgerald JC , Clouser KN , Gertz SJ , Carroll RW , Carroll CL , Hoots BE , Reed C , Dahlgren FS , Oster ME , Pierce TJ , Curns AT , Langley GE , Campbell AP , Balachandran N , Murray TS , Burkholder C , Brancard T , Lifshitz J , Leach D , Charpie I , Tice C , Coffin SE , Perella D , Jones K , Marohn KL , Yager PH , Fernandes ND , Flori HR , Koncicki ML , Walker KS , Di Pentima MC , Li S , Horwitz SM , Gaur S , Coffey DC , Harwayne-Gidansky I , Hymes SR , Thomas NJ , Ackerman KG , Cholette JM . JAMA Netw Open 2021 4 (6) e2116420 IMPORTANCE: Multisystem inflammatory syndrome in children (MIS-C) is associated with recent or current SARS-CoV-2 infection. Information on MIS-C incidence is limited. OBJECTIVE: To estimate population-based MIS-C incidence per 1 000 000 person-months and to estimate MIS-C incidence per 1 000 000 SARS-CoV-2 infections in persons younger than 21 years. DESIGN, SETTING, AND PARTICIPANTS: This cohort study used enhanced surveillance data to identify persons with MIS-C during April to June 2020, in 7 jurisdictions reporting to both the Centers for Disease Control and Prevention national surveillance and to Overcoming COVID-19, a multicenter MIS-C study. Denominators for population-based estimates were derived from census estimates; denominators for incidence per 1 000 000 SARS-CoV-2 infections were estimated by applying published age- and month-specific multipliers accounting for underdetection of reported COVID-19 case counts. Jurisdictions included Connecticut, Georgia, Massachusetts, Michigan, New Jersey, New York (excluding New York City), and Pennsylvania. Data analyses were conducted from August to December 2020. EXPOSURES: Race/ethnicity, sex, and age group (ie, ≤5, 6-10, 11-15, and 16-20 years). MAIN OUTCOMES AND MEASURES: Overall and stratum-specific adjusted estimated MIS-C incidence per 1 000 000 person-months and per 1 000 000 SARS-CoV-2 infections. RESULTS: In the 7 jurisdictions examined, 248 persons with MIS-C were reported (median [interquartile range] age, 8 [4-13] years; 133 [53.6%] male; 96 persons [38.7%] were Hispanic or Latino; 75 persons [30.2%] were Black). The incidence of MIS-C per 1 000 000 person-months was 5.1 (95% CI, 4.5-5.8) persons. Compared with White persons, incidence per 1 000 000 person-months was higher among Black persons (adjusted incidence rate ratio [aIRR], 9.26 [95% CI, 6.15-13.93]), Hispanic or Latino persons (aIRR, 8.92 [95% CI, 6.00-13.26]), and Asian or Pacific Islander (aIRR, 2.94 [95% CI, 1.49-5.82]) persons. MIS-C incidence per 1 000 000 SARS-CoV-2 infections was 316 (95% CI, 278-357) persons and was higher among Black (aIRR, 5.62 [95% CI, 3.68-8.60]), Hispanic or Latino (aIRR, 4.26 [95% CI, 2.85-6.38]), and Asian or Pacific Islander persons (aIRR, 2.88 [95% CI, 1.42-5.83]) compared with White persons. For both analyses, incidence was highest among children aged 5 years or younger (4.9 [95% CI, 3.7-6.6] children per 1 000 000 person-months) and children aged 6 to 10 years (6.3 [95% CI, 4.8-8.3] children per 1 000 000 person-months). CONCLUSIONS AND RELEVANCE: In this cohort study, MIS-C was a rare complication associated with SARS-CoV-2 infection. Estimates for population-based incidence and incidence among persons with infection were higher among Black, Hispanic or Latino, and Asian or Pacific Islander persons. Further study is needed to understand variability by race/ethnicity and age group. |
Disparities in COVID-19 Vaccination Coverage Between Urban and Rural Counties - United States, December 14, 2020-April 10, 2021.
Murthy BP , Sterrett N , Weller D , Zell E , Reynolds L , Toblin RL , Murthy N , Kriss J , Rose C , Cadwell B , Wang A , Ritchey MD , Gibbs-Scharf L , Qualters JR , Shaw L , Brookmeyer KA , Clayton H , Eke P , Adams L , Zajac J , Patel A , Fox K , Williams C , Stokley S , Flores S , Barbour KE , Harris LQ . MMWR Morb Mortal Wkly Rep 2021 70 (20) 759-764 Approximately 60 million persons in the United States live in rural counties, representing almost one fifth (19.3%) of the population.* In September 2020, COVID-19 incidence (cases per 100,000 population) in rural counties surpassed that in urban counties (1). Rural communities often have a higher proportion of residents who lack health insurance, live with comorbidities or disabilities, are aged ≥65 years, and have limited access to health care facilities with intensive care capabilities, which places these residents at increased risk for COVID-19-associated morbidity and mortality (2,3). To better understand COVID-19 vaccination disparities across the urban-rural continuum, CDC analyzed county-level vaccine administration data among adults aged ≥18 years who received their first dose of either the Pfizer-BioNTech or Moderna COVID-19 vaccine, or a single dose of the Janssen COVID-19 vaccine (Johnson & Johnson) during December 14, 2020-April 10, 2021 in 50 U.S. jurisdictions (49 states and the District of Columbia [DC]). Adult COVID-19 vaccination coverage was lower in rural counties (38.9%) than in urban counties (45.7%) overall and among adults aged 18-64 years (29.1% rural, 37.7% urban), those aged ≥65 years (67.6% rural, 76.1% urban), women (41.7% rural, 48.4% urban), and men (35.3% rural, 41.9% urban). Vaccination coverage varied among jurisdictions: 36 jurisdictions had higher coverage in urban counties, five had higher coverage in rural counties, and five had similar coverage (i.e., within 1%) in urban and rural counties; in four jurisdictions with no rural counties, the urban-rural comparison could not be assessed. A larger proportion of persons in the most rural counties (14.6%) traveled for vaccination to nonadjacent counties (i.e., farther from their county of residence) compared with persons in the most urban counties (10.3%). As availability of COVID-19 vaccines expands, public health practitioners should continue collaborating with health care providers, pharmacies, employers, faith leaders, and other community partners to identify and address barriers to COVID-19 vaccination in rural areas (2). |
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. |
Stable high-density and maternally inherited Wolbachia infections in Anopheles moucheti and Anopheles demeilloni mosquitoes.
Walker T , Quek S , Jeffries CL , Bandibabone J , Dhokiya V , Bamou R , Kristan M , Messenger LA , Gidley A , Hornett EA , Anderson ER , Cansado-Utrilla C , Hegde S , Bantuzeko C , Stevenson JC , Lobo NF , Wagstaff SC , Nkondjio CA , Irish SR , Heinz E , Hughes GL . Curr Biol 2021 31 (11) 2310-2320 e5 Wolbachia, a widespread bacterium that can reduce pathogen transmission in mosquitoes, has recently been reported to be present in Anopheles (An.) species. In wild populations of the An. gambiae complex, the primary vectors of Plasmodium malaria in Sub-Saharan Africa, Wolbachia DNA sequences at low density and infection frequencies have been detected. As the majority of studies have used highly sensitive nested PCR as the only method of detection, more robust evidence is required to determine whether Wolbachia strains are established as endosymbionts in Anopheles species. Here, we describe high-density Wolbachia infections in geographically diverse populations of An. moucheti and An. demeilloni. Fluorescent in situ hybridization localized a heavy infection in the ovaries of An.moucheti, and maternal transmission was observed. Genome sequencing of both Wolbachia strains obtained genome depths and coverages comparable to those of other known infections. Notably, homologs of cytoplasmic incompatibility factor (cif) genes were present, indicating that these strains possess the capacity to induce the cytoplasmic incompatibility phenotype, which allows Wolbachia to spread through host populations. These strains should be further investigated as candidates for use in Wolbachia biocontrol strategies in Anopheles aiming to reduce the transmission of malaria. |
Use of Stay-at-Home Orders and Mask Mandates to Control COVID-19 Transmission - Blackfeet Tribal Reservation, Montana, June-December 2020.
Pratt CQ , Chard AN , LaPine R , Galbreath KW , Crawford C , Plant A , Stiffarm G , Rhodes NS , Hannon L , Dinh TH . MMWR Morb Mortal Wkly Rep 2021 70 (14) 514-518 COVID-19 has disproportionately affected persons who identify as non-Hispanic American Indian or Alaska Native (AI/AN) (1). The Blackfeet Tribal Reservation, the northern Montana home of the sovereign Blackfeet Nation, with an estimated population of 10,629 (2), detected the first COVID-19 case in the community on June 16, 2020. Following CDC guidance,* and with free testing widely available, the Indian Health Service and Blackfeet Tribal Health Department began investigating all confirmed cases and their contacts on June 25. The relationship between three community mitigation resolutions passed and enforced by the Blackfeet Tribal Business Council and changes in the daily COVID-19 incidence and in the distributions of new cases was assessed. After the September 28 issuance of a strictly enforced stay-at-home order and adoption of a mask use resolution, COVID-19 incidence in the Blackfeet Tribal Reservation decreased by a factor of 33 from its peak of 6.40 cases per 1,000 residents per day on October 5 to 0.19 on November 7. Other mitigation measures the Blackfeet Tribal Reservation used included closing the east gate of Glacier National Park for the summer tourism season, instituting remote learning for public school students throughout the fall semester, and providing a Thanksgiving meal to every household to reduce trips to grocery stores. CDC has recommended use of routine public health interventions for infectious diseases, including case investigation with prompt isolation, contact tracing, and immediate quarantine after exposure to prevent and control transmission of SARS-CoV-2, the virus that causes COVID-19 (3). Stay-at-home orders, physical distancing, and mask wearing indoors, outdoors when physical distancing is not possible, or when in close contact with infected or exposed persons are also recommended as nonpharmaceutical community mitigation measures (3,4). Implementation and strict enforcement of stay-at-home orders and a mask use mandate likely helped reduce the spread of COVID-19 in the Blackfeet Tribal Reservation. |
Characteristics of Salmonella recovered from stools of children enrolled in the Global Enteric Multicenter Study.
Kasumba IN , Pulford CV , Perez-Sepulveda BM , Sen S , Sayed N , Permala-Booth J , Livio S , Heavens D , Low R , Hall N , Roose A , Powell H , Farag T , Panchalingham S , Berkeley L , Nasrin D , Blackwelder WC , Wu Y , Tamboura B , Sanogo D , Onwuchekwa U , Sow SO , Ochieng JB , Omore R , Oundo JO , Breiman RF , Mintz ED , O'Reilly CE , Antonio M , Saha D , Hossain MJ , Mandomando I , Bassat Q , Alonso PL , Ramamurthy T , Sur D , Qureshi S , Zaidi AKM , Hossain A , Faruque ASG , Nataro JP , Kotloff KL , Levine MM , Hinton JCD , Tennant SM . Clin Infect Dis 2021 73 (4) 631-641 BACKGROUND: The Global Enteric Multicenter Study (GEMS) determined the etiologic agents of moderate-to-severe diarrhea (MSD) in children under 5 years old in Africa and Asia. Here, we describe the prevalence and antimicrobial susceptibility of non-typhoidal Salmonella (NTS) serovars in GEMS and examine the phylogenetics of Salmonella Typhimurium ST313 isolates. METHODS: Salmonella isolated from children with MSD or diarrhea-free controls were identified by classical clinical microbiology and serotyped using antisera and/or whole genome sequence data. We evaluated antimicrobial susceptibility using the Kirby-Bauer disk diffusion method. Salmonella Typhimurium sequence types were determined using multi-locus sequence typing and whole genome sequencing was performed to assess the phylogeny of ST313. RESULTS: Out of 370 Salmonella-positive individuals, 190 (51.4%) were MSD cases and 180 (48.6%) were diarrhea-free controls. The most frequent Salmonella serovars identified were Salmonella Typhimurium, serogroup O:8 (C2-C3), serogroup O:6,7 (C1), Salmonella Paratyphi B Java and serogroup O:4 (B). The prevalence of NTS was low but similar across sites, regardless of age, and was similar amongst both cases and controls except in Kenya, where Salmonella Typhimurium was more commonly associated with cases than controls. Phylogenetic analysis showed that these Salmonella Typhimurium isolates, all ST313, were highly genetically related to isolates from controls. Generally, Salmonella isolates from Asia were resistant to ciprofloxacin and ceftriaxone but African isolates were susceptible to these antibiotics. CONCLUSION: Our data confirms that NTS is prevalent, albeit at low levels, in Africa and South Asia. Our findings provide further evidence that multi-drug resistant Salmonella Typhimurium ST313 can be carried asymptomatically by humans in sub-Saharan Africa. |
A Preparedness Model for Mother-Baby Linked Longitudinal Surveillance for Emerging Threats.
Woodworth KR , Reynolds MR , Burkel V , Gates C , Eckert V , McDermott C , Barton J , Wilburn A , Halai UA , Brown CM , Bocour A , Longcore N , Orkis L , Lopez CD , Sizemore L , Ellis EM , Schillie S , Gupta N , Bowen VB , Torrone E , Ellington SR , Delaney A , Olson SM , Roth NM , Whitehill F , Zambrano LD , Meaney-Delman D , Fehrenbach SN , Honein MA , Tong VT , Gilboa SM . Matern Child Health J 2021 25 (2) 1-9 INTRODUCTION: Public health responses often lack the infrastructure to capture the impact of public health emergencies on pregnant women and infants, with limited mechanisms for linking pregnant women with their infants nationally to monitor long-term effects. In 2019, the Centers for Disease Control and Prevention (CDC), in close collaboration with state, local, and territorial health departments, began a 5-year initiative to establish population-based mother-baby linked longitudinal surveillance, the Surveillance for Emerging Threats to Mothers and Babies Network (SET-NET). OBJECTIVES: The objective of this report is to describe an expanded surveillance approach that leverages and modernizes existing surveillance systems to address the impact of emerging health threats during pregnancy on pregnant women and their infants. METHODS: Mother-baby pairs are identified through prospective identification during pregnancy and/or identification of an infant with retrospective linking to maternal information. All data are obtained from existing data sources (e.g., electronic medical records, vital statistics, laboratory reports, and health department investigations and case reporting). RESULTS: Variables were selected for inclusion to address key surveillance questions proposed by CDC and health department subject matter experts. General variables include maternal demographics and health history, pregnancy and infant outcomes, maternal and infant laboratory results, and child health outcomes up to the second birthday. Exposure-specific modular variables are included for hepatitis C, syphilis, and Coronavirus Disease 2019 (COVID-19). The system is structured into four relational datasets (maternal, pregnancy outcomes and birth, infant/child follow-up, and laboratory testing). DISCUSSION: SET-NET provides a population-based mother-baby linked longitudinal surveillance approach and has already demonstrated rapid adaptation to COVID-19. This innovative approach leverages existing data sources and rapidly collects data and informs clinical guidance and practice. These data can help to reduce exposure risk and adverse outcomes among pregnant women and their infants, direct public health action, and strengthen public health systems. |
Early Insights from Statistical and Mathematical Modeling of Key Epidemiologic Parameters of COVID-19.
Biggerstaff M , Johansson MA , Kada S , Prasad PV , Quandelacy TM . Emerg Infect Dis 2020 26 (11) e1-e14 We report key epidemiologic parameter estimates for coronavirus disease identified in peer-reviewed publications, preprint articles, and online reports. Range estimates for incubation period were 1.8-6.9 days, serial interval 4.0-7.5 days, and doubling time 2.3-7.4 days. The effective reproductive number varied widely, with reductions attributable to interventions. Case burden and infection fatality ratios increased with patient age. Implementation of combined interventions could reduce cases and delay epidemic peak up to 1 month. These parameters for transmission, disease severity, and intervention effectiveness are critical for guiding policy decisions. Estimates will likely change as new information becomes available. |
Summary of Guidance for Public Health Strategies to Address High Levels of Community Transmission of SARS-CoV-2 and Related Deaths, December 2020.
Honein MA , Christie A , Rose DA , Brooks JT , Meaney-Delman D , Cohn A , Sauber-Schatz EK , Walker A , McDonald LC , Liburd LC , Hall JE , Fry AM , Hall AJ , Gupta N , Kuhnert WL , Yoon PW , Gundlapalli AV , Beach MJ , Walke HT . MMWR Morb Mortal Wkly Rep 2020 69 (49) 1860-1867 In the 10 months since the first confirmed case of coronavirus disease 2019 (COVID-19) was reported in the United States on January 20, 2020 (1), approximately 13.8 million cases and 272,525 deaths have been reported in the United States. On October 30, the number of new cases reported in the United States in a single day exceeded 100,000 for the first time, and by December 2 had reached a daily high of 196,227.* With colder weather, more time spent indoors, the ongoing U.S. holiday season, and silent spread of disease, with approximately 50% of transmission from asymptomatic persons (2), the United States has entered a phase of high-level transmission where a multipronged approach to implementing all evidence-based public health strategies at both the individual and community levels is essential. This summary guidance highlights critical evidence-based CDC recommendations and sustainable strategies to reduce COVID-19 transmission. These strategies include 1) universal face mask use, 2) maintaining physical distance from other persons and limiting in-person contacts, 3) avoiding nonessential indoor spaces and crowded outdoor spaces, 4) increasing testing to rapidly identify and isolate infected persons, 5) promptly identifying, quarantining, and testing close contacts of persons with known COVID-19, 6) safeguarding persons most at risk for severe illness or death from infection with SARS-CoV-2, the virus that causes COVID-19, 7) protecting essential workers with provision of adequate personal protective equipment and safe work practices, 8) postponing travel, 9) increasing room air ventilation and enhancing hand hygiene and environmental disinfection, and 10) achieving widespread availability and high community coverage with effective COVID-19 vaccines. In combination, these strategies can reduce SARS-CoV-2 transmission, long-term sequelae or disability, and death, and mitigate the pandemic's economic impact. Consistent implementation of these strategies improves health equity, preserves health care capacity, maintains the function of essential businesses, and supports the availability of in-person instruction for kindergarten through grade 12 schools and preschool. Individual persons, households, and communities should take these actions now to reduce SARS-CoV-2 transmission from its current high level. These actions will provide a bridge to a future with wide availability and high community coverage of effective vaccines, when safe return to more everyday activities in a range of settings will be possible. |
Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism.
Chaguza C , Yang M , Cornick JE , du Plessis M , Gladstone RA , Kwambana-Adams BA , Lo SW , Ebruke C , Tonkin-Hill G , Peno C , Senghore M , Obaro SK , Ousmane S , Pluschke G , Collard JM , Sigaùque B , French N , Klugman KP , Heyderman RS , McGee L , Antonio M , Breiman RF , von Gottberg A , Everett DB , Kadioglu A , Bentley SD . Commun Biol 2020 3 (1) 559 Hyper-virulent Streptococcus pneumoniae serotype 1 strains are endemic in Sub-Saharan Africa and frequently cause lethal meningitis outbreaks. It remains unknown whether genetic variation in serotype 1 strains modulates tropism into cerebrospinal fluid to cause central nervous system (CNS) infections, particularly meningitis. Here, we address this question through a large-scale linear mixed model genome-wide association study of 909 African pneumococcal serotype 1 isolates collected from CNS and non-CNS human samples. By controlling for host age, geography, and strain population structure, we identify genome-wide statistically significant genotype-phenotype associations in surface-exposed choline-binding (P = 5.00 × 10(-08)) and helicase proteins (P = 1.32 × 10(-06)) important for invasion, immune evasion and pneumococcal tropism to CNS. The small effect sizes and negligible heritability indicated that causation of CNS infection requires multiple genetic and other factors reflecting a complex and polygenic aetiology. Our findings suggest that certain pathogen genetic variation modulate pneumococcal survival and tropism to CNS tissue, and therefore, virulence for meningitis. |
High levels of HIV drug resistance among adults failing second-line antiretroviral therapy in Namibia.
Jordan MR , Hamunime N , Bikinesi L , Sawadogo S , Agolory S , Shiningavamwe AN , Negussie T , Fisher-Walker CL , Raizes EG , Mutenda N , Hunter CJ , Dean N , Steegen K , Kana V , Carmona S , Yang C , Tang AM , Parkin N , Hong SY . Medicine (Baltimore) 2020 99 (37) e21661 To support optimal third-line antiretroviral therapy (ART) selection in Namibia, we investigated the prevalence of HIV drug resistance (HIVDR) at time of failure of second-line ART. A cross-sectional study was conducted between August 2016 and February 2017. HIV-infected people ≥15 years of age with confirmed virological failure while receiving ritonavir-boosted protease inhibitor (PI/r)-based second-line ART were identified at 15 high-volume ART clinics representing over >70% of the total population receiving second-line ART. HIVDR genotyping of dried blood spots obtained from these individuals was performed using standard population sequencing methods. The Stanford HIVDR algorithm was used to identify sequences with predicted resistance; genotypic susceptibility scores for potential third-line regimens were calculated. Two hundred thirty-eight individuals were enrolled; 57.6% were female. The median age and duration on PI/r-based ART at time of enrolment were 37 years and 3.46 years, respectively. 97.5% received lopinavir/ritonavir-based regimens. The prevalence of nucleoside reverse transcriptase inhibitor (NRTI), non-nucleoside reverse transcriptase inhibitor (NNRTI), and PI/r resistance was 50.6%, 63.1%, and 13.1%, respectively. No significant association was observed between HIVDR prevalence and age or sex. This study demonstrates high levels of NRTI and NNRTI resistance and moderate levels of PI resistance in people receiving PI/r-based second-line ART in Namibia. Findings underscore the need for objective and inexpensive measures of adherence to identify those in need of intensive adherence counselling, routine viral load monitoring to promptly detect virological failure, and HIVDR genotyping to optimize selection of third-line drugs in Namibia. |
The Global Meningitis Genome Partnership.
Rodgers E , Bentley SD , Borrow R , Bratcher HB , Brisse S , Brueggemann AB , Caugant DA , Findlow J , Fox L , Glennie L , Harrison LH , Harrison OB , Heyderman RS , van Rensburg MJ , Jolley KA , Kwambana-Adams B , Ladhani S , LaForce M , Levin M , Lucidarme J , MacAlasdair N , Maclennan J , Maiden MCJ , Maynard-Smith L , Muzzi A , Oster P , Rodrigues CMC , Serino ORL , Smith V , van der Ende A , Vazquez J , Wang X , Yezli S , Stuart JM . J Infect 2020 81 (4) 510-520 Genomic surveillance of bacterial meningitis pathogens is essential for effective disease control globally, enabling identification of emerging and expanding strains and consequent public health interventions. While there has been a rise in the use of whole genome sequencing, this has been driven predominately by a subset of countries with adequate capacity and resources. Global capacity to participate in surveillance needs to be expanded, particularly in low and middle-income countries with high disease burdens. In light of this, the WHO-led collaboration, Defeating Meningitis by 2030 Global Roadmap, has called for the establishment of a Global Meningitis Genome Partnership that links resources for: N. meningitidis (Nm), S. pneumoniae (Sp), H. influenzae (Hi) and S. agalactiae (Sa) to improve worldwide co-ordination of strain identification and tracking. Existing platforms containing relevant genomes include: PubMLST: Nm (31,622), Sp (15,132), Hi (1,935), Sa (9,026); The Wellcome Sanger Institute: Nm (13,711), Sp (>24,000), Sa (6,200), Hi (1738); and BMGAP: Nm (8,785), Hi (2,030). A steering group is being established to coordinate the initiative and encourage high-quality data curation. Next steps include: developing guidelines on open-access sharing of genomic data; defining a core set of metadata; and facilitating development of user-friendly interfaces that represent publicly available data. |
Strategies for Optimizing the Supply of N95 Filtering Facepiece Respirators During the Coronavirus Disease 2019 (COVID-19) Pandemic.
de Perio MA , Dowell CH , Delaney LJ , Radonovich LJ , Kuhar D , Gupta N , Patel A , Pillai SK , D'Alessandro M . Disaster Med Public Health Prep 2020 14 (5) 1-23 N95 respirators are the personal protective equipment most often used to control exposures to infections transmitted via the airborne route. Supplies of N95 respirators can become depleted during pandemics or when otherwise in high demand. In this paper, we offer strategies for optimizing supplies of N95 respirators in healthcare settings while maximizing the level of protection offered to healthcare personnel when there is limited supply in the United States during the Coronavirus Disease 2019 (COVID-19) pandemic. The strategies are intended for use by professionals who manage respiratory protection programs, occupational health services, and infection prevention programs in healthcare facilities to protect healthcare personnel from job-related risks of exposure to infectious respiratory illnesses. Consultation with federal, state, and local public health officials is also important. We use the framework of surge capacity and the occupational health and safety hierarchy of controls approach to discuss specific engineering control, administrative control, and personal protective equipment measures that may help in optimizing N95 respirator supplies. |
Multiple importations and transmission of colistin-resistant Klebsiella pneumoniae in a hospital in northern India.
Mathur P , Khurana S , de Man TJB , Rastogi N , Katoch O , Veeraraghavan B , Neeravi AR , Venkatesan M , Kumar S , Sagar S , Gupta A , Aggarwal R , Soni KD , Malhotra R , Velayudhan A , Siromany V , Malpiedi P , Lutgring J , Laserson K , Gupta N , Srikantiah P , Sharma A . Infect Control Hosp Epidemiol 2019 40 (12) 1-7 OBJECTIVE: Resistance to colistin, a last resort antibiotic, has emerged in India. We investigated colistin-resistant Klebsiella pneumoniae(ColR-KP) in a hospital in India to describe infections, characterize resistance of isolates, compare concordance of detection methods, and identify transmission events. DESIGN: Retrospective observational study. METHODS: Case-patients were defined as individuals from whom ColR-KP was isolated from a clinical specimen between January 2016 and October 2017. Isolates resistant to colistin by Vitek 2 were confirmed by broth microdilution (BMD). Isolates underwent colistin susceptibility testing by disk diffusion and whole-genome sequencing. Medical records were reviewed. RESULTS: Of 846 K. pneumoniae isolates, 34 (4%) were colistin resistant. In total, 22 case-patients were identified. Most (90%) were male; their median age was 33 years. Half were transferred from another hospital; 45% died. Case-patients were admitted for a median of 14 days before detection of ColR-KP. Also, 7 case-patients (32%) received colistin before detection of ColR-KP. All isolates were resistant to carbapenems and susceptible to tigecycline. Isolates resistant to colistin by Vitek 2 were also resistant by BMD; 2 ColR-KP isolates were resistant by disk diffusion. Moreover, 8 multilocus sequence types were identified. Isolates were negative for mobile colistin resistance (mcr) genes. Based on sequencing analysis, in-hospital transmission may have occurred with 8 case-patients (38%). CONCLUSIONS: Multiple infections caused by highly resistant, mcr-negative ColR-KP with substantial mortality were identified. Disk diffusion correlated poorly with Vitek 2 and BMD for detection of ColR-KP. Sequencing indicated multiple importation and in-hospital transmission events. Enhanced detection for ColR-KP may be warranted in India. |
A multistate outbreak of E Coli O157:H7 infections linked to soy nut butter
Hassan R , Seelman S , Peralta V , Booth H , Tewell M , Melius B , Whitney B , Sexton R , Dwarka A , Vugia D , Vidanes J , Kiang D , Gonzales E , Dowell N , Olson SM , Gladney LM , Jhung MA , Neil KP . Pediatrics 2019 144 (4) BACKGROUND: In 2017, we conducted a multistate investigation to determine the source of an outbreak of Shiga toxin-producing Escherichia coli (STEC) O157:H7 infections, which occurred primarily in children. METHODS: We defined a case as infection with an outbreak strain of STEC O157:H7 with illness onset between January 1, 2017, and April 30, 2017. Case patients were interviewed to identify common exposures. Traceback and facility investigations were conducted; food samples were tested for STEC. RESULTS: We identified 32 cases from 12 states. Twenty-six (81%) cases occurred in children <18 years old; 8 children developed hemolytic uremic syndrome. Twenty-five (78%) case patients ate the same brand of soy nut butter or attended facilities that served it. We identified 3 illness subclusters, including a child care center where person-to-person transmission may have occurred. Testing isolated an outbreak strain from 11 soy nut butter samples. Investigations identified violations of good manufacturing practices at the soy nut butter manufacturing facility with opportunities for product contamination, although the specific route of contamination was undetermined. CONCLUSIONS: This investigation identified soy nut butter as the source of a multistate outbreak of STEC infections affecting mainly children. The ensuing recall of all soy nut butter products the facility manufactured, totaling >1.2 million lb, likely prevented additional illnesses. Prompt diagnosis of STEC infections and appropriate specimen collection aids in outbreak detection. Child care providers should follow appropriate hygiene practices to prevent secondary spread of enteric illness in child care settings. Firms should manufacture ready-to-eat foods in a manner that minimizes the risk of contamination. |
Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data.
Chaguza C , Heinsbroek E , Gladstone RA , Tafatatha T , Alaerts M , Peno C , Cornick JE , Musicha P , Bar-Zeev N , Kamng'ona A , Kadioglu A , McGee L , Hanage WP , Breiman RF , Heyderman RS , French N , Everett DB , Bentley SD . Clin Infect Dis 2019 70 (7) 1294-1303 BACKGROUND: Pneumococcal conjugate vaccines (PCV) have reduced pneumococcal diseases globally. Pneumococcal genomic surveys elucidate PCV effects on population structure but are rarely conducted in low-income settings despite the high disease burden. METHODS: We undertook whole genome sequencing of 660 pneumococcal isolates collected through surveys from healthy carriers two years from PCV14 introduction and one-year post-rollout in northern Malawi. We investigated changes in population structure, within-lineage serotype dynamics, serotype diversity, and frequency of antibiotic resistance (ABR) and accessory genes. RESULTS: In the under-fives, frequency and diversity of vaccine serotypes (VT) decreased significantly post-PCV but no significant changes occurred in over-fives. Clearance of VT serotypes was consistent across different genetic backgrounds (lineages). There was an increase of non-vaccine serotypes (NVT) namely 7C, 15B/C, 23A in under-fives but 28F increased in both age groups. While carriage rates have been recently shown to remain stable post-PCV due replacement serotypes, there was no change in diversity of NVTs. Additionally, frequency of intermediate-penicillin-resistant lineages decreased post-PCV. While frequency of ABR genes remained stable, other accessory genes especially those associated with MGEs and bacteriocins showed changes in frequency post-PCV. CONCLUSIONS: We demonstrate evidence of significant population restructuring post-PCV driven by decreasing frequency of vaccine serotypes and increasing frequency of few NVTs mainly in under-fives. Continued surveillance with WGS remains crucial to fully understand dynamics of the residual VTs and replacement NVT serotypes post-PCV. |
Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents.
Cheleuitte-Nieves C , Gulvik CA , McQuiston JR , Humrighouse BW , Bell ME , Villarma A , Fischetti VA , Westblade LF , Lipman NS . PLoS One 2018 13 (12) e0209231 Corynebacterium bovis is an opportunistic bacterial pathogen shown to cause eye and prosthetic joint infections as well as abscesses in humans, mastitis in dairy cattle, and skin disease in laboratory mice and rats. Little is known about the genetic characteristics and genomic diversity of C. bovis because only a single draft genome is available for the species. The overall aim of this study was to sequence and compare the genome of C. bovis isolates obtained from different species, locations, and time points. Whole-genome sequencing was conducted on 20 C. bovis isolates (six human, four bovine, nine mouse and one rat) using the Illumina MiSeq platform and submitted to various comparative analysis tools. Sequencing generated high-quality contigs (over 2.53 Mbp) that were comparable to the only reported assembly using C. bovis DSM 20582T (97.8 +/- 0.36% completeness). The number of protein-coding DNA sequences (2,174 +/- 12.4) was similar among all isolates. A Corynebacterium genus neighbor-joining tree was created, which revealed Corynebacterium falsenii as the nearest neighbor to C. bovis (95.87% similarity), although the reciprocal comparison shows Corynebacterium jeikeium as closest neighbor to C. falsenii. Interestingly, the average nucleotide identity demonstrated that the C. bovis isolates clustered by host, with human and bovine isolates clustering together, and the mouse and rat isolates forming a separate group. The average number of genomic islands and putative virulence factors were significantly higher (p<0.001) in the mouse and rat isolates as compared to human/bovine isolates. Corynebacterium bovis' pan-genome contained a total of 3,067 genes of which 1,354 represented core genes. The known core genes of all isolates were primarily related to ''metabolism" and ''information storage/processing." However, most genes were classified as ''function unknown" or "unclassified". Surprisingly, no intact prophages were found in any isolate; however, almost all isolates had at least one complete CRISPR-Cas system. |
New product, old problem(s): multistate outbreak of Salmonella Paratyphi B variant L(+) tartrate(+) infections linked to raw sprouted nut butters, October 2015
Heiman Marshall KE , Booth H , Harrang J , Lamba K , Folley A , Ching-Lee M , Hannapel E , Greene V , Classon A , Whitlock L , Shade L , Viazis S , Nguyen T , Neil KP . Epidemiol Infect 2018 147 1-6 A cluster of Salmonella Paratyphi B variant L(+) tartrate(+) infections with indistinguishable pulsed-field gel electrophoresis patterns was detected in October 2015. Interviews initially identified nut butters, kale, kombucha, chia seeds and nutrition bars as common exposures. Epidemiologic, environmental and traceback investigations were conducted. Thirteen ill people infected with the outbreak strain were identified in 10 states with illness onset during 18 July-22 November 2015. Eight of 10 (80%) ill people reported eating Brand A raw sprouted nut butters. Brand A conducted a voluntary recall. Raw sprouted nut butters are a novel outbreak vehicle, though contaminated raw nuts, nut butters and sprouted seeds have all caused outbreaks previously. Firms producing raw sprouted products, including nut butters, should consider a kill step to reduce the risk of contamination. People at greater risk for foodborne illness may wish to consider avoiding raw products containing raw sprouted ingredients. |
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