Lyndsay Bottichio

National Center for Emerging and Zoonotic Infectious Diseases

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Matthew E. Wise

Centers for Disease Control and Prevention

Colin Basler

Centers for Disease Control and Prevention

Jeffrey Higa

California Department of Public Health

Beth Tolar

National Center for Emerging and Zoonotic Infectious Diseases

Stephen Soroka

Centers for Disease Control and Prevention

Natasha Dowell

Centers for Disease Control and Prevention

Laura Whitlock

Centers for Disease Control and Prevention

Laura Gieraltowski

National Center for Emerging and Zoonotic Infectious Diseases

Carlota Medus

Minnesota Department of Health

Morgan N. Schroeder

National Center for Emerging and Zoonotic Infectious Diseases

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National Center for Emerging and Zoonotic Infectious Diseases

Waterborne Environmental (United States)

United States Food and Drug Administration

Epidemic Intelligence Service

Center for Surveillance, Epidemiology, and Laboratory Services

Minnesota Department of Health

Center for Food Safety and Applied Nutrition

California Department of Public Health

National Center for Immunization and Respiratory Diseases

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Multistate outbreak of Salmonella Poona infections associated with imported cucumbers, 2015–2016

Epidemiology and Infection (2019)

Mark E. Laughlin Lyndsay Bottichio Joli Weiss Jeffrey Higa Eric McDonald

We investigated a large multistate outbreak that occurred in the United States in 2015-2016. Epidemiologic, laboratory, and traceback studies were conducted to determine the source of the infections. We identified 907 case-patients from 40 states with illness onset dates ranging from July 3, 2015 to March 2, 2016. Sixty-three percent of case-patients reported consuming cucumbers in the week before illness onset. Ten illness sub-clusters linked to events or purchase locations were identified. All sub-clusters investigated received cucumbers from a single distributor which were sourced from a single grower in Mexico. Seventy-five cucumber samples were collected, 19 of which yielded the outbreak strain. Whole genome sequencing performed on 154 clinical isolates and 19 cucumber samples indicated that the sequenced isolates were closely related genetically to one another. This was the largest US foodborne disease outbreak in the last ten years and the third largest in the past 20 years. This was at least the fifth multistate outbreak caused by contaminated cucumbers since 2010. The outbreak is noteworthy because a recall was issued only 17 days after the outbreak was identified, which allowed for the removal of the contaminated cucumbers still available in commerce, unlike previous cucumber associated outbreaks. The rapid identification and response of multiple public health agencies resulted in preventing this from becoming an even larger outbreak.

10.1017/s0950268819001596

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Citations (38)

Multistate Outbreak of HumanSalmonellaPoona Infections Associated with Pet Turtle Exposure — United States, 2014

MMWR Morbidity and Mortality Weekly Report (2015)

Colin Basler Lyndsay Bottichio Jeffrey Higa Belinda Prado Michael Wong

In May 2014, a cluster of human Salmonella Poona infections was identified through PulseNet, the national molecular subtyping network for foodborne disease surveillance. Historically, this rare serotype has been identified in multiple Salmonella outbreaks associated with pet turtle exposure and has posed a particular risk to small children. Although the sale and distribution of small turtles (those with carapace [upper shell] lengths <4 inches [<10.2 cm]) is prohibited by federal law, they are still available for legal purchase online for "bona-fide" scientific, educational, or exhibition purposes, other than use as pets. In addition, small turtles are still available for illegal purchase through transient street vendors, at flea markets, and at fairs.

Subtyping

10.15585/mmwr.mm6429a7

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Citations (19)

Multistate nontyphoidal Salmonella and Shiga toxin-producing Escherichia coli outbreaks linked to international travel — United States, 2017–2020

Epidemiology and Infection (2024)

Caroline Habrun Meseret G. Birhane Louise Francois Watkins Katharine M. Benedict Lyndsay Bottichio

Abstract Enteric bacterial infections are common among people who travel internationally. During 2017–2020, the Centers for Disease Control and Prevention investigated 41 multistate outbreaks of nontyphoidal Salmonella and Shiga toxin-producing Escherichia coli linked to international travel. Resistance to one or more antimicrobial agents was detected in at least 10% of isolates in 16 of 30 (53%) nontyphoidal Salmonella outbreaks and 8 of 11 (73%) Shiga toxin-producing E. coli outbreaks evaluated by the National Antimicrobial Resistance Monitoring System. At least 10% of the isolates in 14 nontyphoidal Salmonella outbreaks conferred resistance to one or more of the clinically significant antimicrobials used in human medicine. This report describes the epidemiology and antimicrobial resistance patterns of these travel-associated multistate outbreaks. Investigating illnesses among returned travellers and collaboration with international partners could result in the implementation of public health interventions to improve hygiene practices and food safety standards and to prevent illness and spread of multidrug-resistant organisms domestically and internationally.

10.1017/s0950268823002017

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Notes from the Field: Multistate Outbreak of Salmonella Agbeni Associated with Consumption of Raw Cake Mix — Five States, 2018

MMWR Morbidity and Mortality Weekly Report (2019)

Stephen Ladd-Wilson Karim Morey Sarah E Koske Bailey Burkhalter Lyndsay Bottichio

Consumption

10.15585/mmwr.mm6834a5

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Improving efficiency of COVID-19 aggregate case and death surveillance data transmission for jurisdictions: current and future role of application programming interfaces (APIs)

Journal of the American Medical Informatics Association (2022)

Diba Khan Meeyoung Park Samuel Lerma Stephen Soroka Denise M. Gaughan

Abstract During the coronavirus disease-2019 (COVID-19) pandemic, the Centers for Disease Control and Prevention (CDC) supplemented traditional COVID-19 case and death reporting with COVID-19 aggregate case and death surveillance (ACS) to track daily cumulative numbers. Later, as public health jurisdictions (PHJs) revised the historical COVID-19 case and death data due to data reconciliation and updates, CDC devised a manual process to update these records in the ACS dataset for improving the accuracy of COVID-19 case and death data. Automatic data transfer via an application programming interface (API), an intermediary that enables software applications to communicate, reduces the time and effort in transferring data from PHJs to CDC. However, APIs must meet specific content requirements for use by CDC. As of March 2022, CDC has integrated APIs from 3 jurisdictions for COVID-19 ACS. Expanded use of APIs may provide efficiencies for COVID-19 and other emergency response planning efforts as evidenced by this proof-of-concept. In this article, we share the utility of APIs in COVID-19 ACS.

2019-20 coronavirus outbreak

Pandemic

10.1093/jamia/ocac090

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Citations (2)

Multidrug-Resistant Salmonella I 4,[5],12:i:− and Salmonella Infantis Infections Linked to Whole Roasted Pigs from a Single Slaughter and Processing Facility

Journal of Food Protection (2019)

Vance Kawakami Lyndsay Bottichio Jennifer K. Lloyd Heather A. Carleton Molly Leeper

Food microbiology

10.4315/0362-028x.jfp-19-048

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Citations (16)

Utility of Combining Whole Genome Sequencing with Traditional Investigational Methods To Solve Foodborne Outbreaks of Salmonella Infections Associated with Chicken: A New Tool for Tackling This Challenging Food Vehicle

Journal of Food Protection (2017)

Samuel J. Crowe Alice Green Kimberly Hernandez Vi Peralta Lyndsay Bottichio

High consumption rates and a multitude of brands make multistate foodborne outbreaks of Salmonella infections associated with chicken challenging to investigate, but whole genome sequencing is a powerful tool that can be used to assist investigators. Whole genome sequencing of pathogens isolated from clinical, environmental, and food samples is increasingly being used in multistate foodborne outbreak investigations to determine with unprecedented resolution how closely related these isolates are to one another genetically. In 2014, federal and state health officials investigated an outbreak of 146 Salmonella Heidelberg infections in 24 states. A follow-up analysis was conducted after the conclusion of the investigation in which 27 clinical and 24 food isolates from the outbreak underwent whole genome sequencing. These isolates formed seven clades, the largest of which contained clinical isolates from a subcluster of case patients who attended a catered party. One isolate from a chicken processed by a large producer was closely related genetically (zero to three single-nucleotide polymorphism differences) to the clinical isolates from these subcluster case patients. Chicken from this large producer was also present in the kitchen of the caterer on the day before the event, thus providing additional evidence that the chicken from this producer was the outbreak source. This investigation highlights how whole genome sequencing can be used with epidemiologic and traceback evidence to identify chicken sources of foodborne outbreaks.

Salmonella Food Poisoning

10.4315/0362-028x.jfp-16-364

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Protecting Privacy and Transforming COVID-19 Case Surveillance Datasets for Public Use

Public Health Reports (2021)

Brian Lee Brandi Dupervil Nicholas P. Deputy Wil Duck Stephen Soroka

Objectives Federal open-data initiatives that promote increased sharing of federally collected data are important for transparency, data quality, trust, and relationships with the public and state, tribal, local, and territorial partners. These initiatives advance understanding of health conditions and diseases by providing data to researchers, scientists, and policymakers for analysis, collaboration, and use outside the Centers for Disease Control and Prevention (CDC), particularly for emerging conditions such as COVID-19, for which data needs are constantly evolving. Since the beginning of the pandemic, CDC has collected person-level, de-identified data from jurisdictions and currently has more than 8 million records. We describe how CDC designed and produces 2 de-identified public datasets from these collected data. Methods We included data elements based on usefulness, public request, and privacy implications; we suppressed some field values to reduce the risk of re-identification and exposure of confidential information. We created datasets and verified them for privacy and confidentiality by using data management platform analytic tools and R scripts. Results Unrestricted data are available to the public through Data.CDC.gov, and restricted data, with additional fields, are available with a data-use agreement through a private repository on GitHub.com. Practice Implications Enriched understanding of the available public data, the methods used to create these data, and the algorithms used to protect the privacy of de-identified people allow for improved data use. Automating data-generation procedures improves the volume and timeliness of sharing data.

Data Sharing

Public health surveillance

10.1177/00333549211026817

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Citations (5)

Outbreak of Salmonella Oslo Infections Linked to Persian Cucumbers — United States, 2016

MMWR Morbidity and Mortality Weekly Report (2016)

Lyndsay Bottichio Carlota Medus Alida Sorenson Danielle Donovan R.N. SHARMA

In April 2016, PulseNet, the national molecular subtyping network for foodborne disease surveillance, detected a multistate cluster of Salmonella enterica serotype Oslo infections with an indistinguishable pulsed-field gel electrophoresis (PFGE) pattern (XbaI PFGE pattern OSLX01.0090).* This PFGE pattern was new in the database; no previous infections or outbreaks have been identified. CDC, state and local health and agriculture departments and laboratories, and the Food and Drug Administration (FDA) conducted epidemiologic, traceback, and laboratory investigations to identify the source of this outbreak. A total of 14 patients in eight states were identified, with illness onsets occurring during March 21-April 9, 2016. Whole genome sequencing, a highly discriminating subtyping method, was used to further characterize PFGE pattern OSLX01.0090 isolates. Epidemiologic evidence indicates Persian cucumbers as the source of Salmonella Oslo infections in this outbreak. This is the fourth identified multistate outbreak of salmonellosis associated with cucumbers since 2013. Further research is needed to understand the mechanism and factors that contribute to contamination of cucumbers during growth, harvesting, and processing to prevent future outbreaks.

Subtyping

Salmonella enterica

Salmonella Food Poisoning

Disease Surveillance

10.15585/mmwr.mm655051a3

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Citations (22)

Outbreak of human infections with uncommon Salmonella serotypes linked to pet bearded dragons, 2012–2014

Zoonoses and Public Health (2020)

Craig Kiebler Lyndsay Bottichio Latoya Simmons Colin Basler Rachel Klos

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.

10.1111/zph.12701

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Citations (24)