Sarah E. Schmedes

Florida Department of Health

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Bruce Budowle

University of Helsinki

Jason Blanton

Florida Department of Health

Eldin Talundzic

Division of Parasitic Diseases and Malaria

Dhruviben Patel

Division of Parasitic Diseases and Malaria

Jonathan L. King

University of North Texas Health Science Center

Omer Tekin

Florida Department of Health

August E. Woerner

University of North Texas Health Science Center

Naomi W. Lucchi

Division of Parasitic Diseases and Malaria

Mateusz M. Pluciński

U.S. President's Malaria Initiative

Julia Kelley

Centers for Disease Control and Prevention

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Centers for Disease Control and Prevention

106

Florida Department of Health

National Center for Immunization and Respiratory Diseases

Center for Global Health

National Center for Emerging and Zoonotic Infectious Diseases

Division of Parasitic Diseases and Malaria

Yale University

University of California, Irvine

Centers for Disease Control and Prevention

Johns Hopkins University

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Validation of high throughput sequencing and microbial forensics applications

Investigative Genetics (2014)

Bruce Budowle Nancy Connell Anna Bielecka-Oder Rita R. Colwell Cindi R. Corbett

High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security.

Instrumentation

10.1186/2041-2223-5-9

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Citations (67)

Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid ofYersinia pestisfrom victims of the Black Death

Proceedings of the National Academy of Sciences (2011)

Verena J. Schuenemann Kirsten I. Bos Sharon N. DeWitte Sarah E. Schmedes Joslyn Jamieson

Although investigations of medieval plague victims have identified Yersinia pestis as the putative etiologic agent of the pandemic, methodological limitations have prevented large-scale genomic investigations to evaluate changes in the pathogen's virulence over time. We screened over 100 skeletal remains from Black Death victims of the East Smithfield mass burial site (1348-1350, London, England). Recent methods of DNA enrichment coupled with high-throughput DNA sequencing subsequently permitted reconstruction of ten full human mitochondrial genomes (16 kb each) and the full pPCP1 (9.6 kb) virulence-associated plasmid at high coverage. Comparisons of molecular damage profiles between endogenous human and Y. pestis DNA confirmed its authenticity as an ancient pathogen, thus representing the longest contiguous genomic sequence for an ancient pathogen to date. Comparison of our reconstructed plasmid against modern Y. pestis shows identity with several isolates matching the Medievalis biovar; however, our chromosomal sequences indicate the victims were infected with a Y. pestis variant that has not been previously reported. Our data reveal that the Black Death in medieval Europe was caused by a variant of Y. pestis that may no longer exist, and genetic data carried on its pPCP1 plasmid were not responsible for the purported epidemiological differences between ancient and modern forms of Y. pestis infections.

Yersinia pestis

plague

10.1073/pnas.1105107108

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Citations (250)

Forensic human identification with targeted microbiome markers using nearest neighbor classification

Forensic Science International Genetics (2018)

August E. Woerner Nicole M.M. Novroski Frank R. Wendt Angie Ambers Rachel Wiley

Identification

10.1016/j.fsigen.2018.10.003

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Citations (57)

Targeted deep amplicon sequencing of kelch 13 and cytochrome b in Plasmodium falciparum isolates from an endemic African country using the Malaria Resistance Surveillance (MaRS) protocol

Parasites & Vectors (2020)

Mariangela L’Episcopia Julia Kelley Dhruviben Patel Sarah E. Schmedes Shashidahar Ravishankar

Abstract Background Routine molecular surveillance for imported drug-resistant malaria parasites to the USA and European Union is an important public health activity. The obtained molecular data are used to help keep chemoprophylaxis and treatment guidelines up to date for persons traveling to malaria endemic countries. Recent advances in next-generation sequencing (NGS) technologies provide a new and effective way of tracking malaria drug-resistant parasites. Methods As part of a technology transfer arrangement between the CDC Malaria Branch and the Istituto Superiore di Sanità (ISS), Rome, Italy, the recently described Malaria Resistance Surveillance (MaRS) protocol was used to genotype 148 Plasmodium falciparum isolates from Eritrea for kelch 13 ( k13 ) and cytochrome b ( cytb ) genes, molecular markers associated with resistance to artemisinin (ART) and atovaquone/proguanil (AP), respectively. Results Spanning the full-length k13 gene, seven non-synonymous single nucleotide polymorphisms (SNPs) were found (K189N, K189T, E208K, D281V, E401Q, R622I and T535M), of which none have been associated with artemisinin resistance. No mutations were found in cytochrome b . Conclusion All patients successfully genotyped carried parasites susceptible to ART and AP treatment. Future studies between CDC Malaria Branch and ISS are planned to expand the MaRS system, including data sharing, in an effort to maintain up to date treatment guidelines for travelers to malaria endemic countries.

Parasitology

Atovaquone

Sanger sequencing

10.1186/s13071-020-4005-7

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Citations (18)

Introduction and community transmission of SARS-CoV-2 lineage A.2.5 in Florida with novel spike INDELS

medRxiv (Cold Spring Harbor Laboratory) (2021)

Sarah E. Schmedes Taj Azarian Eleonora Cella Jessy Motes Omer Tekin

Abstract SARS-CoV-2 (SC2) variants of concern (VOC) continue to emerge and spread globally, threatening the use of monoclonal antibody therapies and vaccine effectiveness. Several mutations in the SC2 spike glycoprotein have been associated with reduction in antibody neutralization. Genomic surveillance of SC2 variants has been imperative to inform the public health response regarding the use of clinical therapies in specific jurisdictions based on the proportion of particular variants (e.g., Gamma (P.1)) in a region. Florida Department of Health Bureau of Public Health Laboratories (BPHL) performs tiled-amplicon whole genome sequencing for baseline and targeted surveillance of SC2 isolates in Florida from clinical specimens collected from county health departments and hospitals throughout the state. Here, we describe the introduction of SC2 lineage A.2.5 in Florida, which contains S:L452R (a substitution of therapeutic concern) and two novel Spike INDELS, the deletion of 141-143 and ins215AGY, with unknown implications on immune response. The A.2.5 lineage was first detected in Florida among an outbreak at a healthcare facility in January 2021, and subsequent A.2.5 isolates were detected across all geographical regions throughout the state. A time-scaled maximum clade credibility phylogeny determined there were at least eight separate introductions of A.2.5 in the state. The time of introduction of a monophyletic Florida clade was established to be December 2020. The Spike INDELS were determined to reside in the N-terminal domain, a region associated with antibody neutralization. As community transmission of SARS-CoV-2 in Florida continues, genomic surveillance of circulating variants in Florida and the detection of emerging variants are critical for informing public health response to COVID-19.

Indel

Lineage (genetic)

Concordance

Herd Immunity

10.1101/2021.12.03.21266538

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Citations (2)

COVID-19 on the Nile: a cross-sectional investigation of COVID-19 among Nile River cruise travellers returning to the United States, February–March 2020

Journal of Travel Medicine (2022)

Sarah Anne J. Guagliardo Laura A.S. Quilter Anna Uehara Stefanie White Sarah Talarico

Abstract Background Early in the pandemic, cruise travel exacerbated the global spread of SARS-CoV-2. We report epidemiologic and molecular findings from an investigation of a cluster of travellers with confirmed COVID-19 returning to the USA from Nile River cruises in Egypt. Methods State health departments reported data on real-time reverse transcription-polymerase chain reaction-confirmed COVID-19 cases with a history of Nile River cruise travel during February–March 2020 to the Centers for Disease Control and Prevention (CDC). Demographic and epidemiologic data were collected through routine surveillance channels. Sequences were obtained either from state health departments or from the Global Initiative on Sharing Avian Flu Data (GISAID). We conducted descriptive analyses of epidemiologic data and explored phylogenetic relationships between sequences. Results We identified 149 Nile River cruise travellers with confirmed COVID-19 who returned to 67 different US counties in 27 states: among those with complete data, 4.7% (6/128) died and 28.1% (38/135) were hospitalized. These individuals travelled on 20 different Nile River cruise voyages (12 unique vessels). Fifteen community transmission events were identified in four states, with 73.3% (11/15) of these occurring in Wisconsin (as the result of a more detailed contact investigation in that state). Phylogenetic analyses supported the hypothesis that travellers were most likely infected in Egypt, with most sequences in Nextstrain clade 20A 93% (87/94). We observed genetic clustering by Nile River cruise voyage and vessel. Conclusions Nile River cruise travellers with COVID-19 introduced SARS-CoV-2 over a very large geographic range, facilitating transmission across the USA early in the pandemic. Travellers who participate in cruises, even on small river vessels as investigated in this study, are at increased risk of SARS-CoV-2 exposure. Therefore, history of river cruise travel should be considered in contact tracing and outbreak investigations.

Pandemic

10.1093/jtm/taac153

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Citations (1)

Early Emergence Phase of SARS-CoV-2 Delta Variant in Florida, US

Viruses (2022)

Eleonora Cella Sobur Ali Sarah E. Schmedes Brittany Rife Magalis Simone Marini

SARS-CoV-2, the causative agent of COVID-19, emerged in late 2019. The highly contagious B.1.617.2 (Delta) variant of concern (VOC) was first identified in October 2020 in India and subsequently disseminated worldwide, later becoming the dominant lineage in the US. Understanding the local transmission dynamics of early SARS-CoV-2 introductions may inform actionable mitigation efforts during subsequent pandemic waves. Yet, despite considerable genomic analysis of SARS-CoV-2 in the US, several gaps remain. Here, we explore the early emergence of the Delta variant in Florida, US using phylogenetic analysis of representative Florida and globally sampled genomes. We find multiple independent introductions into Florida primarily from North America and Europe, with a minority originating from Asia. These introductions led to three distinct clades that demonstrated varying relative rates of transmission and possessed five distinct substitutions that were 3-21 times more prevalent in the Florida sample as compared to the global sample. Our results underscore the benefits of routine viral genomic surveillance to monitor epidemic spread and support the need for more comprehensive genomic epidemiology studies of emerging variants. In addition, we provide a model of epidemic spread of newly emerging VOCs that can inform future public health responses.

2019-20 coronavirus outbreak

Betacoronavirus

Coronavirus Infections

Pandemic

10.3390/v14040766

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Citations (5)

Heavy Rainfall, Sewer Overflows, and Salmonellosis in Black Skimmers (Rynchops niger)

EcoHealth (2022)

Lisa A. Shender Theresa Cody Mark G. Ruder Heather Fenton Kevin D. Niedringhaus

Animal ecology

Waterborne diseases

10.1007/s10393-022-01596-6

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Citations (1)

Concurrent Outbreaks of Hepatitis A, Invasive Meningococcal Disease, and Mpox, Florida, USA, 2021–2022

Emerging infectious diseases (2024)

Timothy J. Doyle Megan Gumke Danielle Stanek Joshua Moore B.E. Buck

Abstract In 2022, concurrent outbreaks of hepatitis A, invasive meningococcal disease (IMD), and mpox were identified in Florida, USA, primarily among men who have sex with men. The hepatitis A outbreak (153 cases) was associated with hepatitis A virus genotype IA. The IMD outbreak (44 cases) was associated with Neisseria meningitidis serogroup C, sequence type 11, clonal complex 11. The mpox outbreak in Florida (2,845 cases) was part of a global epidemic. The hepatitis A and IMD outbreaks were concentrated in Central Florida and peaked during March–June, whereas mpox cases were more heavily concentrated in South Florida and had peak incidence in August. HIV infection was more common (52%) among mpox cases than among hepatitis A (21%) or IMD (34%) cases. Where feasible, vaccination against hepatitis A, meningococcal disease, and mpox should be encouraged among at-risk groups and offered along with program services that target those groups.

10.3201/eid3004.231392

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Citations (5)

Next-generation Sequence-analysis Toolkit (NeST): A standardized bioinformatics framework for analyzing Single Nucleotide Polymorphisms in next-generation sequencing data

bioRxiv (Cold Spring Harbor Laboratory) (2018)

Shashidhar Ravishankar Sarah E. Schmedes Dhruviben Patel Mateusz M. Pluciński Venkatachalam Udhayakumar

Abstract Rapid advancements in next-generation sequencing (NGS) technologies have led to the development of numerous bioinformatics tools and pipelines. As these tools vary in their output function and complexity and some are not well-standardized, it is harder to choose a suitable pipeline to identify variants in NGS data. Here, we present NeST (NGS-analysis Toolkit), a modular consensus-based variant calling framework. NeST uses a combination of variant callers to overcome potential biases of an individual method used alone. NeST consists of four modules, that integrate open-source bioinformatics tools, a custom Variant Calling Format (VCF) parser and a summarization utility, that generate high-quality consensus variant calls. NeST was validated using targeted-amplicon deep sequencing data from 245 Plasmodium falciparum isolates to identify single-nucleotide polymorphisms conferring drug resistance. The results were verified using Sanger sequencing data for the same dataset in a supporting publication [28]. NeST offers a user-friendly pipeline for variant calling with standardized outputs and minimal computational demands for easy deployment for use with various organisms and applications.

Sanger sequencing

10.1101/323535

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Citations (0)