Emerging Pathogens Institute

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Emerging Pathogens Institute

Laboratory, United States
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News Article | October 28, 2016
Site: www.eurekalert.org

A non-virulent variant of the deadly Vibrio cholerae O1 strain has likely been present in Haitian aquatic environments for several hundred years, with the potential to become virulent through gene transfer with the toxigenic strain introduced by UN peacekeepers, according to research published today by scientists at the University of Florida's Emerging Pathogens Institute. "Since the 2010 earthquake and cholera epidemic in Haiti, researchers have debated whether toxigenic Vibrio cholerae was already present in Haiti's aquatic environments," said Dr. J. Glenn Morris, MD, a professor in the University of Florida's College of Medicine and the director of the Emerging Pathogens Institute. Morris is a senior author of the study, published online October 27, 2016 in Scientific Reports. "While the strain responsible for the 2010 cholera epidemic was almost certainly introduced from outside of Haiti by U.N. Peacekeeping troops, this study suggests that cholera was present in Haiti at some point in the past, possibly as early as the time of Columbus. These 'ancient' strains are now non-toxigenic, and consequently cannot cause cholera. However, their identification raises questions about whether these older strains might interact with the toxigenic V. cholerae O1 introduced by UN peacekeepers, becoming virulent in the process," Morris said. Although the V. cholerae species of bacteria are common throughout the world, the toxic strains V. cholerae O1 and V. cholerae O139 are primarily found in Asia and Africa. Investigators isolated two non-toxic V. cholerae O1 strains from estuaries in Port-au-Prince Bay, initially thinking that the isolates were foreign toxigenic strains that had lost their virulence genes. However, on closer examination, they discovered that these isolates were more similar to strains that caused the first cholera pandemics than they were to modern pandemic strains of the bacteria. "When we used the genomic data to trace the history of these isolates, we found that they shared a common ancestor with the 'modern' cholera strains around 1548," said Taj Azarian, a postdoctoral fellow at the Harvard School of Public Health and a former doctoral student in the University of Florida's College of Public Health and Health Professions. "This was well before any records of cholera in Hispaniola," said Azarian, one of the main authors of the publication. Although the researchers suggest that these cholera strains may have been in Haiti's aquatic environments since the 1500s, they admit that it is also possible that the strains were introduced at some time after that - becoming endemic, though not pathogenic, well before the 2010 cholera outbreak. Similarly, the researchers have not yet established the likelihood of modern, toxigenic cholera strains trading genetic information with these older strains, rendering the older strains harmful through the process. The isolates analyzed in the study shed new light on the history of the pathogen, however. "These non-toxigenic strains are believed to be the progenitor of known toxigenic V. cholerae strains, including both the Classical and El Tor biotypes," said Afsar Ali, a research associate professor in the College of Public Health and Health Profession's department of environmental and global health and a faculty member at the Emerging Pathogens Institute. Ali is the co-first author of the paper, along with Azarian. The researchers relied on phylogenetic analysis to determine the last common ancestor of toxigenic V. cholerae O1 and the non-toxigenic V. cholerae O1 isolates found in Port-au-Prince Bay. "To analyze the isolates we used a computational technique called molecular clock analysis, which allows us to date the origin of strains isolated from the environment," said Marco Salemi, an associate professor in the UF College of Medicine's department of pathology, immunology and laboratory medicine and a member of the Emerging Pathogens Institute. Salemi is a senior author of the study and oversaw the phylogenetic analysis. Underscoring the significance of these findings, he said the study shows that non-pathogenic cholera strains with the potential to acquire pathogenic genes have been circulating in this region for a significant amount of time, and that such bacterial reservoirs can potentially give rise to new epidemic strains. Azarian emphasized the need for increased surveillance. "As cliché as it sounds, if you don't look, you won't find," he said. "Prior to the 2010 epidemic, no one was looking for cholera in Haitian waterways. It was only when we started surveillance for the epidemic strain that we discovered these isolates that provided insight into the evolutionary history of pandemic cholera. The same could be said about other pathogens like Ebola and Zika viruses prior to the recent epidemics. There was little effort in surveillance, which we now know was a mistake. More resources should be put into identifying emerging pathogens and assessing their epidemic potential. In the end, you never know what you may find."

Jones M.K.,Emerging Pathogens Institute | Watanabe M.,Emerging Pathogens Institute | Zhu S.,Emerging Pathogens Institute | Graves C.L.,University of Florida | And 9 more authors.
Science | Year: 2014

The cell tropism of human noroviruses and the development of an in vitro infection model remain elusive. Although susceptibility to individual human norovirus strains correlates with an individual's histo-blood group antigen (HBGA) profile, the biological basis of this restriction is unknown. We demonstrate that human and mouse noroviruses infected B cells in vitro and likely in vivo. Human norovirus infection of B cells required the presence of HBGA-expressing enteric bacteria. Furthermore, mouse norovirus replication was reduced in vivo when the intestinal microbiota was depleted by means of oral antibiotic administration. Thus, we have identified B cells as a cellular target of noroviruses and enteric bacteria as a stimulatory factor for norovirus infection, leading to the development of an in vitro infection model for human noroviruses. © 2014, American Association for the Advancement of Science. All rights reserved.

News Article | February 22, 2017
Site: news.yahoo.com

ATLANTA — Infectious-disease specialists are concerned that climate change is contributing to the spread of certain diseases, including the germs that cause cholera and other diarrheal illnesses. Data now suggest that the locations where certain pathogens are found have changed, said Dr. Glenn Morris, the director of the Emerging Pathogens Institute at the University of Florida. Morris gave a talk here today (Feb. 16) at the Climate & Health Meeting, a gathering of experts from public health organizations, universities and advocacy groups that addressed the health impacts of climate change. Pathogens tend to live in places that have ideal sets of conditions, Morris said. For example, these bugs may have evolved to function best within certain temperature ranges, he said. And as climate change occurs and global average temperatures rise, researchers are beginning to see some indications that the areas where certain pathogens can live are shifting, he said. [5 Ways Climate Change Will Affect Your Health] "We are seeing the spread of pathogens to new ecological niches," Morris said. And the pathogens that live in water are among scientists' top concerns, Morris told Live Science. An increase in sea temperatures, of even just a degree or two, can have a large impact on an organism's ability to live and multiply, Morris said. In many cases, as waters warm, pathogens will be able to expand into new areas. On the other hand, if water temperatures in a region increase too much, the number of pathogens there may decrease, Morris added. One group of bacteria, called Vibrio species, are particularly well-studied, Morris said. Vibro bacteria are responsible for cholera and other diarrheal diseases. Although cholera can be treated by rehydration according to the World Health Organization, the disease can still be fatal if not treated quickly enough. Vibriobacteria live in seawater, and with sea temperatures rising, scientists have recently observed a northward shift in the bacteria's range, he said. In addition, diseases such as cholera often spread following events like flooding, which may become more common with climate change, Morris said. Other waterborne diseases can come from harmful algal blooms, which are caused by toxic forms of algae, Morris said. Algal blooms have been linked to illnesses such as ciguatera, which people get from eating fish that contain toxins produced by the algae Gambierdiscus toxicus, according to the Centers for Disease Control and Prevention. Another illness linked to harmful algal blooms is amnesic shellfish poisoning, which is caused by eating contaminated shellfish. These harmful algal blooms are showing up in places where they previously didn't occur, including the Pacific Northwest, Alaska and Maine, Morris said. But what about mosquitos? Morris noted that there have also been some concerns about mosquito-borne diseases, because of evidence suggesting that certain species of the insect are moving farther north than they used to. But it's unclear what impact this will have in the long term, Morris told Live Science. He noted that in developed countries, including U.S., many aspects of homes help protect people against mosquito bites, such as the use of window screens and air conditioning. [6 Unexpected Effects of Climate Change] While the illnesses Morris noted in his talk are all known diseases, they can still pose public health challenges when they move into parts of the world where they haven't occurred before, he said. "We've always thought about tropical areas as having particularly significant problems with infectious diseases," but "we're starting to see some greater indications that those diseases may be creeping up here" in the U.S., he said. Morris said that the U.S. can handle those diseases, but the bigger concern is that pathogens are always evolving. Mcroorganisms may be able to change over time, "and increasingly take advantage of conditions that may not have been present before," he said.

Rand K.H.,University of Florida | Turner B.,University of Florida | Seifert H.,University of Florida | Hansen C.,University of Florida | And 2 more authors.
American Journal of Clinical Pathology | Year: 2011

Plasmid-mediated AmpC-producing Escherichia coli and Klebsiella pneumoniae have been associated with poor clinical outcomes, but they are not readily identified in hospital microbiology laboratories. We tested 753 gram-negative bloodstream isolates for AmpC by using the EDTA disk test and the modified Hodge test (n = 172) and the modified Hodge test alone (n = 581). The 30-day mortality for the AmpC group was 9% (2/23) and was 6% (3/51) for the control group. The clinical response was similar: Afebrile on day 2 (AmpC group, 16/23 [70%]; control group, 32/45 [71%]) and on day 4 (AmpC group, 19/22 [86%]; control group, 37/44 [84%]). Patients with isolates in the AmpC group were more likely to be in an intensive care unit at the time of the positive blood culture (P = 01) and more likely to be intubated (P = 05) than patients with isolates in the control group. Effective antibiotic treatment within the first 48 hours was given to 47 (92%) of 51 patients with isolates in the control group but to only 14 (61%) of 23 patients with isolates in the AmpC group (P = 001).The modified Hodge test and the EDTA disk test did not identify patients at risk for a poor outcome from AmpC-producing bacterial infections. © American Society for Clinical Pathology.

Prosperi M.C.F.,University of Manchester | Prosperi M.C.F.,University of Florida | Yin L.,University of Florida | Yin L.,Florida Center for Research | And 8 more authors.
Scientific Reports | Year: 2013

Next generation sequencing (NGS) is superseding Sanger technology for analysing intra-host viral populations, in terms of genome length and resolution. We introduce two new empirical validation data sets and test the available viral population assembly software. Two intra-host viral population 'quasispecies' samples (type-1 human immunodeficiency and hepatitis C virus) were Sanger-sequenced, and plasmid clone mixtures at controlled proportions were shotgun-sequenced using Roche's 454 sequencing platform. The performance of different assemblers was compared in terms of phylogenetic clustering and recombination with the Sanger clones. Phylogenetic clustering showed that all assemblers captured a proportion of the most divergent lineages, but none were able to provide a high precision/recall tradeoff. Estimated variant frequencies mildly correlated with the original. Given the limitations of currently available algorithms identified by our empirical validation, the development and exploitation of additional data sets is needed, in order to establish an efficient framework for viral population reconstruction using NGS.

Sun Y.,University of Florida | Cai Y.,University of Florida | Huse S.M.,Josephine Bay Paul Center for Comparative Molecular Biology and Evolution | Knight R.,University of Colorado at Boulder | And 3 more authors.
Briefings in Bioinformatics | Year: 2012

Recent advances in massively parallel sequencing technology have created new opportunities to probe the hidden world of microbes. Taxonomy-independent clustering of the 16S rRNA gene is usually the first step in analyzing microbial communities. Dozens of algorithms have been developed in the last decade, but a comprehensive benchmark study is lacking. Here, we survey algorithms currently used by microbiologists, and compare seven representative methods in a large-scale benchmark study that addresses several issues of concern. A new experimental protocol was developed that allows different algorithms to be compared using the same platform, and several criteria were introduced to facilitate a quantitative evaluation of the clustering performance of each algorithm. We found that existing methods vary widely in their outputs, and that inappropriate use of distance levels for taxonomic assignments likely resulted in substantial overestimates of biodiversity inmany studies.The benchmark study identified our recently developed ESPRIT-Tree, a fast implementation of the average linkage-based hierarchical clustering algorithm, as one of the best algorithms available in terms of computational efficiency and clustering accuracy. © The Author 2011. Published by Oxford University Press.

Abramowitz S.A.,University of Florida | McLean K.E.,Yale University | McKune S.L.,University of Florida | Bardosh K.L.,University of Edinburgh | And 5 more authors.
PLoS Neglected Tropical Diseases | Year: 2015

The West African Ebola epidemic has demonstrated that the existing range of medical and epidemiological responses to emerging disease outbreaks is insufficient, especially in post-conflict contexts with exceedingly poor healthcare infrastructures. In this context, community-based responses have proven vital for containing Ebola virus disease (EVD) and shifting the epidemic curve. Despite a surge in interest in local innovations that effectively contained the epidemic, the mechanisms for community-based response remain unclear. This study provides baseline information on community-based epidemic control priorities and identifies innovative local strategies for containing EVD in Liberia. This study was conducted in September 2014 in 15 communities in Monrovia and Montserrado County, Liberia – one of the epicenters of the Ebola outbreak. Findings from 15 focus group discussions with 386 community leaders identified strategies being undertaken and recommendations for what a community-based response to Ebola should look like under then-existing conditions. Data were collected on the following topics: prevention, surveillance, care-giving, community-based treatment and support, networks and hotlines, response teams, Ebola treatment units (ETUs) and hospitals, the management of corpses, quarantine and isolation, orphans, memorialization, and the need for community-based training and education. Findings have been presented as community-based strategies and recommendations for (1) prevention, (2) treatment and response, and (3) community sequelae and recovery. Several models for community-based management of the current Ebola outbreak were proposed. Additional findings indicate positive attitudes towards early Ebola survivors, and the need for community-based psychosocial support. Local communities’ strategies and recommendations give insight into how urban Liberian communities contained the EVD outbreak while navigating the systemic failures of the initial state and international response. Communities in urban Liberia adapted to the epidemic using multiple coping strategies. In the absence of health, infrastructural and material supports, local people engaged in self-reliance in order to contain the epidemic at the micro-social level. These innovations were regarded as necessary, but as less desirable than a well-supported health-systems based response; and were seen as involving considerable individual, social, and public health costs, including heightened vulnerability to infection. © 2015 Abramowitz et al.

News Article | November 2, 2016
Site: www.techtimes.com

A recent study from researchers at University of Florida's Emerging Pathogens Institute has it that a non-virulent Vibrio cholerae O1 strain could be present in Haitian aquatic environments for centuries, long before cholera epidemic emerged in Haiti. It noted that the non-pathogenic V. cholerae O1 strain could have become virulent through the transfer of genetic material from virulent strains from U.N. peacekeepers. Dr. J. Glenn Morris, the senior author of the study, said that it has been a question of debate since the cholera outbreak in Haiti following the 2010 earthquake, whether virulent V. cholerae strain already existed in Haiti's water environment. Morris added that though it is certain that  V. cholerae strain that caused cholera back in 2010 was introduced by U.N. peacekeepers, the study suggests a possibility that non-pathogenic V. cholerae strain was present in Haiti as early as Columbus' period. Though the ancient strains are non-toxigenic to cause infection, the findings pave way for a speculation whether the non-virulent strains became pathogenic after interacting with the virulent strains from the U.N. peacemaking troops. While several strains of V. cholerae are found worldwide, the strains that have the potential to cause infection are found mostly in Africa and Asia. V. cholerae O139 and V. cholerae O1 are the two common strains that cause cholera in humans. When the non-virulent V. cholerae O1 strain was isolated from estuaries in Port-au-Prince Bay, the researchers thought that it was toxigenic strain from Asia or Africa that lost its virulence eventually. It was later identified that the strains were more related to the ones that caused the first cholera pandemic in the world than the modern pandemic strains. Meanwhile, Taj Azarian, from the Harvard School of Public Health, said the genomic data analysis suggests that the newly found strain has the common ancestors as that of the 1548 modern cholera strain, which was way before the emergence of cholera in Hispaniola. According to Afsar Ali, the study's co-first author, the non-toxigenic V. cholerae is the progenitor for toxigenic El Tor and Classical biotypes. "To analyze the isolates we used a computational technique called molecular clock analysis, which allows us to date the origin of strains isolated from the environment," said Marco Salemi, the senior author of the study, in a press release. According to Salemi, it is sensible to think that the non-virulent strains of V. cholerae were present in Haitian aquatic environment with the potential to become pathogenic on interaction with toxigenic strains, which could pave way for the emergence of new epidemic strains over time. © 2017 Tech Times, All rights reserved. Do not reproduce without permission.

Banada P.P.,New Jersey Medical School | Sivasubramani S.K.,New Jersey Medical School | Sivasubramani S.K.,Tulane National Primate Research Center | Blakemore R.,New Jersey Medical School | And 6 more authors.
Journal of Clinical Microbiology | Year: 2010

The recently introduced Xpert MTB/RIF assay (Xpert) has point-of-care potential, but its capacity for biohazard containment remained to be studied. We compared the bioaerosols generated by the Xpert assay to acid-fast bacillus (AFB) microscope slide smear preparation. The Xpert assay sample treatment reagent (SR) was also studied for its sterilizing capacity, stability, and effect on assay sensitivity after prolonged treatment. During the preparation of AFB smears, sputum samples spiked with Mycobacterium bovis BCG at 5 × 10 8 CFU/ml produced 16 and 325 CFU/m 3 air measured with an Andersen impactor or BioSampler, respectively. In contrast, neither the sample preparation steps for the Xpert assay nor its automated processing produced any culturable bioaerosols. In testing of SR sterilizing capacity, clinical sputum samples from strongly smear-positive tuberculosis patients treated with SR at a 2:1 ratio eliminated Mycobacterium tuberculosis growth in all but 1/39 or 3/45 samples cultured on solid or liquid medium, respectively. These few unsterilized samples had a mean 13.1-day delay in the time to positive culture. SR treatment at a 3:1 ratio eliminated growth in all samples. SR retained a greater than 6-log-unit killing capacity despite storage at temperatures spanning 4 to 45°C for at least 3 months. The effect of prolonged SR sample treatment was also studied. Spiked sputum samples could be incubated in SR for up to 3 days without affecting Xpert sensitivity for M. tuberculosis detection and up to 8 h without affecting specificity for rifampin resistance detection. These results suggest that benchtop use of the Xpert MTB/RIF assay limits infection risk to the user. Copyright © 2010, American Society for Microbiology. All Rights Reserved.

Khan M.W.,Northwestern University | Zadeh M.,Emerging Pathogens Institute | Bere P.,Emerging Pathogens Institute | Gounaris E.,Northwestern University | And 3 more authors.
Immunotherapy | Year: 2012

Aim: To investigate the mechanism(s) by which the intestinal commensal microbe Lactobacillus acidophilus can affect host immunity, we studied the role of a component of the cell wall, lipoteichoic acid, in colitis. Materials & methods: Colitis was induced by the intraperitoneal injection of pathogenic CD4 +CD25 -CD45RB hi T cells into Rag1 -/- mice. The parental strain, NCK56, or the lipoteichoic acid-deficient strain, NCK2025, was then administered orally. Fluorescent microscopy was employed to examine resulting cell populations and their cytokine production in the colon. Results: NCK2025 enhanced IL-10 production by dendritic cells and macrophages. Increased numbers of regulatory dendritic cells coincided with the induction of activated FoxP3 + Tregs. Conclusion: These results suggest that the oral administration of the genetically modified strain NCK2025 may be an effective immunotherapeutic approach that reprograms the immune response in colonic inflammatory conditions. © 2012 Future Medicine Ltd.

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