The soil microbiome can produce, resist, or degrade antibiotics and even catabolize them. Resistance genes are widely distributed in the soil and may act as a reservoir for pathogen antibiotic resistance. Work done in the Dantas lab has identified high diversity of genes encoding antibiotic resistance across all antibiotic classes, but generally these genes are not at great risk of mobilization to pathogens. However, the sub-group of resistant, culturable Proteobacteria show both resistance to high concentrations of antibiotics and resistance across many antibiotic classes. These highly resistant Proteobacteria are related to human pathogens, and show evidence of increased horizontal gene transfer of resistance genes. Interestingly, many of these Proteobacteria are not only antibiotic resistant, they have also been found to be capable of antibiotic catabolism. Little is known about the enzymes, mechanisms, and pathways involved in antibiotic catabolism. We describe a pathway for penicillin catabolism in four strains of Proteobacteria. Genomic and transcriptomic sequencing revealed β -lactamase, amidase, and phenylacetic acid catabolon upregulation. Knocking out part of the phenylacetic acid catabolon or an apparent penicillin utilization operon (put) resulted in loss of penicillin catabolism in one isolate. A hydrolase from the put operon was found to degrade in vitro benzylpenicilloic acid, the β -lactamase penicillin product. To test the generality of this strategy, an Escherichia coli strain was engineered to co-express a β -lactamase and a penicillin amidase or the put operon, enabling it to grow using penicillin or benzylpenicilloic acid, respectively. Elucidation of additional pathways may allow bioremediation of antibiotic-contaminated soils and discovery of antibiotic-remodeling enzymes with industrial utility.

Learning Objectives: 

1. Antibiotics and pharmaceuticals are not privileged molecules, they can be modified or catabolized by microbes. 
2. Metabolism of these molecules in unexpected ways can impact human health.

PacBio Sequencing has been recognized as the gold standard in microbial sequencing due to simultaneously providing long sequence reads (genome contiguity), high consensus accuracy (genome accuracy), minimal sequence bias (genome completeness), and methylation detection (bacterial epigenome). I will highlight new advances and updates on applying PacBio sequencing in microbiology, including multiplexed microbial sequencing on the Sequel System and full-length bacterial RNA sequencing. In the second part of my talk, I will highlight how the generation of high-accuracy single-molecule consensus reads (through a process called circular consensus sequencing (CCS)), a capability unique to PacBio sequencing technology, can be leveraged for high-resolution insights into immune repertoires and other immunology relevant studies. 
 

Learning Objectives: 

1. Understand the differences of high-quality PacBio long-read sequencing to traditional short-read sequencing
2. Get familiar with applications in microbiology for close microbial genomes, full-length transcript sequencing, and direct methylation detection
3. Understand new methods for directly sequencing, at full-length and high accuracy, RNA & DNA from regions relevant in immunology

Sexually transmitted diseases remain a major global public health burden despite the availability of effective prevention strategies to diagnose and treat bacterial STDs.  Concerning trends include increases in syphilis among men having sex with men as well as among women of reproductive age and congenital syphilis, decreased susceptibility and resistance among gonorrhea strains as well as emerging STD such as Mycoplasma genitalium, all of which present major challenges for local public health programs serving populations at risk.  While some of these increases are associated with technological advances such as geospatial apps for seeking partners,  it is important to recognize that technology in multiple forms can also be developed and used as an effective prevention measure for increasing access to screening, partner services, and health promotion.  This webinar will provide an overview of global STD and local trends with focus on US and recent California data as well as how advances in technology that link people to STD services should be a priority for research and development.
 

Learning Objectives: 

1. Describe global and local trends in bacterial STDs and priority populations at risk
2. Discuss gaps in access to effective STD prevention strategies  
3. Describe innovative technologies and policies that can improve access to STD screening and diagnosis

While rapid identification of pathogens, novel therapeutic interventions, and passive immunization have critical roles in disease control, none can substitute for pre-existing protective immunity. Mucosally delivered bacterial live vector vaccines represent a practical and effective strategy for immunization.  In live vector vaccines, genes that encode protective antigens of unrelated pathogens are expressed in an attenuated vaccine strain and delivered mucosally to generate relevant local and systemic immune responses. We hypothesize that by appropriate manipulation of novel Salmonella enterica serovar Typhi live vector platform technologies, we can construct a mucosally administered bivalent vaccine against potentially lethal infections caused by Acinetobacter baumannii.  Our unique research strategy is designed to remodel the outer membrane of an attenuated S. Typhi-based live vector vaccine into an antigen presentation platform in which protective outer membrane antigens from A. baumannii are mucosally delivered to immune inductive sites via a novel inducible outer membrane vesicle delivery system. Mucosal delivery of recombinant outer membrane vesicles (rOMVs) via live vector vaccines offers significant advantages over conventional acellular OMV-based vaccination strategies including: 1] sustained in vivo delivery to mucosal inductive sites, and 2] delivery of rOMVs enriched in properly folded protective antigens. To enhance delivery of these protective antigens to immune effector cells, thereby improving the protective efficacy of this mucosal vaccine, we enhance delivery of rOMVs through inducible over-expression of the hypervesiculating protein PagL. If successful, our novel and highly innovative approach could result in a mucosal live carrier vaccine, effective against potentially lethal systemic and pulmonary infections with A. baumannii, which could prove highly valuable in both civilian and military settings.

Learning Objectives: 

1. What is a carrier vaccine?    
2. How can carrier vaccines be used to combat the antibiotic resistance crisis in public health?

The greatest need in agriculture this century is to mitigate impacts of abiotic (drought, temperature, salinity) and biotic (pathogens, pests) stresses on crop plants.  Efforts over the last 40 years to generate stress tolerant crops via breeding or genetic modification have not been very fruitful because the underlying strategies assumed plants adapt themselves to stress.  However, plants in high-stress habitats are adapted to environmental stresses only through symbiosis with fungal endophytes. Without the fungal partners, plants are no more adapted to stress than agricultural crops.  Although several biochemical processes have been correlated to plant stress tolerance, few processes correlate with symbiotically conferred stress tolerance.  Symbiotically conferred stress tolerance involves altered plant gene regulation, increased metabolic efficiency, and an increased ability to manage reactive oxygen species. Based on >25 years of research studying how plants in nature adapt to stress, Adaptive Symbiotic Technologies (AST) developed the product line BioEnsure®, a novel seed treatment comprising fungal endophytes that form symbiotic associations with a diverse group of crop plants and confer significant levels of abiotic stress tolerance. Field tests have demonstrated that during periods of high drought, temperature and salinity stress, BioEnsure® increases crop yield as much as 300%.  During growing seasons with little to no stress, BioEnsure® increases yields an average of 3%.   The seminar will cover the science and development of Symbiotic technologies to mitigate the impacts of climate change in agriculture.


Learning Objectives: 

1. To learn that all plants in natural ecosystems are symbiotic with microscopic fungi that live entirely within plant tissues.
2. To understand that plants do not adapt themselves to high stress habitats.  Instead, they establish symbiotic associations with fungal endophytes that confer stress tolerance for optimal fitness and survival.

The bacterium Pantoea stewartii subsp. stewartii causes Stewart’s wilt disease in corn and serves as a model for other xylem-dwelling phytopathogens. P. stewartii is transmitted to plants via corn flea beetles where it first colonizes the apoplast causing water-soaked lesions, then migrates to the xylem and forms a biofilm that blocks water transport. P. stewartii uses quorum sensing to insure the exopolysaccharide production necessary for biofilm formation occurs only at high cell density during growth in the xylem. To gain broader insights into what genes are important for plant pathogens like P. stewartii during in planta growth, the bacteria were grown inside the xylem followed by genomic-level analyses in vitro.  RNA purified from in planta grown P. stewartii was used to determine the most highly expressed genes via RNA-Seq through Next-generation Illumina sequencing of cDNA. Analysis of the transcriptome data via gene ontology revealed that bacterial transporters and systems important for oxidation-reduction processes are highly expressed in response to the environment inside the plant.  A subsequent genomic-level Tn-Seq analysis was performed to identify bacterial genes essential for survival in planta. A mariner transposon library of approximately 40,000 mutants was constructed and used to inoculate corn seedlings through a xylem infection model. The Tn-Seq analysis suggested that over 400 genes are important for xylem survival. In planta competition assays and virulence assays have so far revealed important roles for outer membrane proteins and Lon protease in bacterial colonization, growth and/or virulence in the corn plant. These studies are giving us new insights into the lifestyle of a pathogenic plant bacterium when living inside its plant host.
 

Learning Objectives: 

1. Explain the role of quorum sensing during plant disease caused by the phytopathogen Pantoea stewartii subsp. stewartii.
2. Design genome-levels experiments to study the expression and role in survival of bacterial genes during in planta growth.

Horizontal gene transfer (HGT) – or the non-genealogical transmission of DNA between organisms – is the dominant mode responsible for the spread of antibiotic resistance genes. Combined with antibiotic overuse and misuse, HGT (primarily via conjugation) has compromised the efficacy of nearly every single antimicrobial available. Traditionally, reducing overall antibiotic use has been the primary approach to reversing resistance. However, despite widespread antibiotic stewardship initiatives, resistance can persist for long periods of time.  In this webinar, we discuss the prevalence of plasmid-mediated antibiotic resistance, the role of HGT in maintaining antibiotic resistance even in the absence of antibiotic selection, and how we can use mathematical modeling to guide novel intervention strategies towards minimizing this risk.
 

Learning Objectives: 

1. What is horizontal gene transfer
2. How is HGT relevant to antibiotic resistance
3. Using mathematical modeling to understand HGT dynamics and guide useful therapeutic approaches

Viruses outnumber bacteria in soil by as much as 1000:1. However, there are few studies which examine the ways viral communities impact the soil microbiome, chemical cycles, and plants. Recent advances in viral ecology make it a discussion of soil viral ecology especially timely. Here, we discuss the burgeoning new field of soil virology, how DNA and RNA sequencing advances have allowed unprecedented insight into viral communities, and summarize recent discoveries. We then look to the future of soil virology, and discuss ongoing research in agricultural systems. 


Learning Objectives: 

1. Learn about the viruses found in soil
2. Learn about what these soil viruses are doing

In the US, the National Antimicrobial Resistance Monitoring System has been using WGS of Salmonella as a tool of routine surveillance since 2013. To date, NARMS has generated MIC and WGS data on over 10,000 Salmonella isolates from food animals, 9,000 from human clinical cases, 6,000 from retail meats, and 1,4OO from imported foods. Analysis of this dataset showed that the presence of known resistance determinants is very highly correlated with clinical resistance, indicating that WGS data can be used to predict resistance in Salmonella strains lacking traditional antimicrobial susceptibility data. To make these data accessible, the NARMS program has launched Resistome Tracker and other online tools that provide visually informative displays of antibiotic resistance genes. Resistome Tracker harvests resistance gene information on a weekly basis from genomic data deposited at NCBI. It presents the resistome data using interactive dashboards that allows users to customize visualizations by antibiotic drug class, compare resistance genes across different sources, identify new resistance genes, and map selected resistance genes to geographic region. The tool also provides alerts about new resistance traits as they emerge in a region or source to provide early warning on emergent trends. 

Learning Objectives: 

1. The technical aspects of integrated antimicrobial resistance monitoring 
2. The utility of whole genome sequence data in resistance surveillance
3. Visualization and reporting tools to foster global data sharing

Circular, Rep-encoding single-stranded (CRESS) DNA viruses were once thought to be a rare kind of viral genomic architecture.  While some significant agricultural diseases were caused by circoviruses and geminiviruses, they are not typically human pathogens, and it was only when metagenomic methods that were not biased towards double-stranded DNA were widely used did we identify single-stranded DNA viruses  ubiquitously.  Many of these sequence-only identified genomes don’t look like the characterized genera that scientists can grow in the lab, but the one commonality among most of these genomes is that they have a recognizable Replication-associated protein (Rep) that is homologous with all other eukaryote-infecting CRESS DNA viruses.  As we attempt to understand the evolution of this large and speciose group, we have identified idiosyncratic patterns in their nucleotide use, their protein evolution and have created a Rep genealogy that represents the evolution of their shared ORF.  Recently systematized groups of CRESS DNA viruses have not plumbed the depths of the uncharacterized viral diversity that has been sequenced, and the Rep tree suggests that existing families of CRESS DNA viruses may not be independently evolving — we suggest there is a common origin of the intron in the Rep of some geminiviriuses and all gemonoviruses. CRESS DNA viruses are a newly discovered component of microbiomes across eukaryotes and in environmental samples, and we are starting to understand how these pathogens have diversified over evolutionary time.

Learning Objectives: 

1. Appreciate the ecological and molecular diversity of CRESS DNA viruses that infect eukaryotes.
2. Understand how the molecular evolution of unique groups of viruses differ from one another, and the value of accurate model choice in phylogenetics.

The Alkek Center for Metagenomics and Microbiome Research (CMMR) at Baylor College of Medicine is pursuing numerous research and development efforts in the study of how the microbiome impacts human disease and how this knowledge can be translated into novel therapeutics and diagnostics. Among these efforts is a new study involving the impact of major disasters, such as Hurricane Harvey, where associated flooding and other environmental exposures to chemicals or pathogens (e.g. mold), and their impact on human health, may be reflected in the microbiome of exposed individuals.  During Hurricane Harvey, Houston, Texas experienced 50 inches of rain and catastrophic flooding. This flooding caused uncontrolled releases into the environment from over a dozen Superfund sites and several chemical/petroleum facilities. In response to this disaster, we along with collaborators from Oregon State University, worked with affected communities to administer health questionnaires, deploy wristbands that detect chemical exposures, and collect biosamples for nasal, oral and gut microbiome analysis in the first 30 days after flooding, targeting 300 individuals. We are in the process of collecting a second set of data 12-months post-Hurricane Harvey from the same individuals to examine the long-term impact of this environmental disaster. These data will be integrated to identify potential exposures that adversely affect health, including in individuals with predisposition to certain diseases such as asthma. If environmental exposures and potential associated health risks are reflected in changes in the microbiome, then these microbiome associations can serve as targets or biomarkers for actionable, post-disaster responses or interventions.

Learning Objectives: 

1. How does one deploy a microbiome study during a time of crisis.
2. What fundamental information should be collected when sampling the human microbiome.

DiseaseLand is an integrated genomics database and visualization software that helps researchers explore 1000s of public and private datasets covering, but not limited to therapeutic areas such as Asthma/Respiratory Diseases, Arthritis, COPD, IBD, Psoriasis, Systemic Lupus Erythematosus, and immune oncology. In this virtual conference, Dr. Williams will present an overview of the DiseaseLand database and then explore how users can leverage its knowledge for biomarker discovery and target validation. 

Learning Objectives: 

1. What are OmicSoft Lands and how can I use them in my own research
2. Various methods used to process data

Reducing the impact of infectious diseases is becoming increasingly vital as the prevalence of antimicrobial resistance (AMR) continues to rise, threatening the effective prevention and treatment of an ever-increasing range of infections caused by bacteria, parasites, viruses and fungi. The evolution of “superbugs” that can evade one or multiple drugs is one of the biggest threats facing medicine today. 

At the beginning of the 20th century a forward-thinking UK microbiologist, Dr Sir John Ledingham, recognised a need for a trustworthy source of globally-available authentic bacteria for scientific studies and went on to establish the National Collection of Type Cultures (NCTC) in 1920. This collection of live clinically-significant bacteria, encompassing strains isolated during the 19th century alongside those from the present day, represents a history of bacterial pathogens that cannot be replicated in a modern post-antibiotic environment. 

By using long read whole genome sequencing technology, the team responsible for curating and operating NCTC collaborated with molecular scientists at the Wellcome Sanger Institute in decoding the DNA of more than 3000 reference strains of pathogenic bacteria, many of which cause deadly diseases such as plague, dysentery, cholera and tuberculosis. This project has provided genomic data that researchers will be able to use to better understand these diseases and how they become resistant to antibiotics. The publicly available genomic maps support the development of new diagnostic tests, vaccines and treatments.
 

Learning Objectives: 

1. Understand the value of a culture collection in biomedical research
2. Recognise the significance of historical strains in understanding microbial evolution
3. Recognise some of the benefits of long read sequencing techniques for delivering reference genomes for pathogenic bacteria 

Whole genome sequencing of bacterial isolates via next-generation sequencing is becoming a standard approach for clinical microbiology and bio-surveillance labs seeking to conduct outbreak investigations and genomic characterization of isolates. Knowing the identity of a pathogen, subtype, and potential antimicrobial resistance markers it may carry is essential for monitoring pathogens. 

CLC Genomics Workbench, along with the CLC Microbial Genomics Module, provides functionalities for molecular subtyping and epidemiological analyses of bacterial isolates in an easy to use, graphical user interface. In this webinar, we will demonstrate how to carry out taxonomic identification, multi locus sequence typing (MLST), identification of antimicrobial resistance (AMR) markers, and investigation suspect pathogens via SNP based phylogenetic analyses with associated sample metadata. We will also show how such analyses can be streamlined into a preconfigured workflow that ensures ease-of-use, reproducibility, and scalability to any sample throughput.

Learning Objectives: 

1. Assign sequence type and taxonomy
2. Detect antimicrobial resistance genes
3. Perform outbreak analyses

Every year, approximately 800,000 critically ill patients are hospitals in the USA with undiagnosed infections. The only option is to treat these patients with broad-spectrum antimicrobial therapy and hope for the best outcome. The inability to obtain specific actionable information in a clinically relevant time-frame, combined with ineffective treatment, contributes to increased disease burden, mortality, hospitalizations, and drug resistance. The consequence is direct hospitalization costs of more than $27 billion, with another $26 billion lost due to antimicrobial resistance. What is urgently needed is precise and comprehensive targeted pathogen identification, including the capacity to detect drug-resistant mutations, for routine diagnosis to support effective treatment and control measures.
Fusion Genomics Corp.’s mission is to address this need and enable precision medicine for infectious diseases by developing a pan-pathogen test - the ONETest™ PathoGenome - that identifies all human pathogens (~1,400) and provides the genomic information necessary to guide treatment, including drug resistance and human genetic susceptibility markers in a timely fashion. The assay uses next-generation DNA sequencing (NGS) along with Fusion’s novel DNA hybridization technology, QuantumProbes, to enrich bacterial/viral/fungal genomes prior to sequencing. The assay will be functionally equivalent, yet clinically superior, to whole metagenome sequencing, but at 1/10th the cost, 1/3rd the time, and several times the sensitivity.

Learning Objectives: 

1. learn how NGS will impact undiagnosed infections  
2. learn about the advantages of using targeted sequencing versus whole metagenome sequencing

Horizontal gene transfer (HGT) has long been recognized as an important source of genetic diversity. In the clinical setting, HGT plays an important role in the spread of antibiotic resistance genes and has the ability to turn easily treatable infections by common organisms like E. coli into untreatable, life-threatening conditions. Carbapenem-resistance, often mediated by plasmids carrying the blaKPC gene, is a worldwide threat. Although evidence-based guidelines to prevent transmission of carbapenemase-producing organisms (CPO) exist, they don't explicitly take into account HGT; which may complicate tracking nosocomial transmission. Here I'll present clinical investigations that underscore the consequences of HGT.

First, I'll present a study that tracked the long-term colonization of patients from a 2011 K. pneumoniae outbreak have remained consistently colonized with CPOs. Analysis of isolates collected from these patients revealed a complex network of plasmids, plasmid rearrangements and evidence of strain succession and re-emergence. Then I'll describe a study conducted at our hospital, where broad-range environmental sampling was conducted, including housekeeping closets, wastewater from hospital internal pipes, and external manholes. Whole-genome sequencing and analysis of 108 carbapenem-resistant isolates was compared to five years of patient isolates. We identified a vast, underappreciated reservoir of CPOs and identified a number of putative transmission links between patients and the environment. 

Learning Objectives: 

1. Understand the importance of horizontal gene transfer for the spread of antibiotic resistance
2. Appreciate the diversity of antibiotic resistance plasmids in environmental reserviors

Some bacteria can use an electrode as an electron donor for respiration, generating an electrical current in the process. We are trying to understand a bacterial community that uses electricity as an energy source to fix CO2 to make biomass.  However, we are not able to grow some of the key organisms in pure cultures, so we need to use culture independent approaches. Metagenomics revealed 16 genome bins that were over 85% complete, each representing a different species. One of these species is a previously uncharacterized member of the Gammaproteobacteria that we described as “Candidatus Tenderia electrophaga.” At the genomic level, “Tenderia” has several genes also found in iron oxidizing bacteria that may allow it to make the proteins needed to transport electrons from the electrode into the cell.  It can then use them to generate the ATP and reducing equivalents necessary for CO2 fixation. We then used metatranscriptomics and metabolic inhibitors to ground truth the model developed from the “Tenderia” genome sequence. One of our lab’s goals is to develop synthetic biology systems that will help meet the needs of the US Navy. We are in the process of developing isolates from this community as chassis organisms that will be more robust in the environment that the typical lab strains used for most genetic engineering. 

Learning Objectives: 

1. Identify the ways culture independent methods are used to study difficult to culture microbes
2. Understand concept of extracellular electron transport (EET)
3. Describe the importance of reverse electron transport to some lithoautotrophic organisms

Understanding the microbial ecosystem dynamics of our planet is central to our role as custodians of the planet. The Earth Microbiome Project aimed to characterize the microbial diversity of the diverse ecosystems across our world, which we have used to model the ecosystem dynamics of these environments. Integrating these models with agricultural policy provides a framework on which to determine how climate change and shifting policy will influence the microbial metabolic dynamics, which will affect our ability to modulate system scale outcomes. In concert with this global perspective we are also characterizing the human microbiome, which has become a key part of patient care, provide new avenues to diagnose and treat human disease. The immune system controls our interaction with the microbial world, and yet the microbial communities in our bodies are central to modulating the immune response. Changes in the human microbiome have substantial influence on atopy, neurological disorders, metabolic disorders, and a range of complex conditions and disease states. We will discuss evidence of these mechanisms of interaction and how we have started to disturb the delicate balance of the immune-microbe equilibrium, impacting the development and function of our immune systems. Central to this disturbance is the distance we have placed between our children and the microbial world, which has been demonstrated to have a substantial influence on their physiological, immunological, neurological and even endocrinological development. Applying new strategies to identify how the microbial ecosystem correlates with diseases states and treatment efficacy through Microbiome-Wide Association Studies (MWAS) is altering the trajectory of precision medicine, and providing a new framework for facilitating patient care. 

Learning Objectives: 

1. Understand the microbial ecosystem dynamics of our planet
2. Learn how characterizing the human microbiome has become a key part of patient care
3. Discover new strategies to identify how the microbial ecosystem correlates with diseases states and treatment efficacy

The ongoing research and scientific debate on pathophysiology, classification, nomenclature and diagnosis of antiphospholipid syndrome illustrates the complexity of cellular membranes, their dynamic interplay with various components in circulating blood, and often tenuous balance between normal hemostasis and thrombosis. This main objective of this lecture is to succinctly identify the features of normal vs. pathological coagulation, and to familiarize the audience with the inextricable, and ever-evolving role of laboratory in diagnostic process of antiphospholipid syndrome.       
 

Learning Objectives: 

1. Understand the physiological role of phospholipids in normal hemostasis.
2. Identify a few proposed pathophysiological mechanisms for thrombosis in the presence of antiphospholipid antibodies.
3. Be familiar with the current diagnostic criteria for antiphospholipid syndrome ( APS).
4. Laboratory detection of antiphospholipid antibodies and future directions.

Antibiotic resistance is a national and global public health crisis.  Each year in the United States (US), at least 2 million people become infected with antibiotic-resistant bacteria and at least 23,000 people die as a direct result of these infections. An estimated 14,000 deaths each year occur due to C. difficile infection.  The driving force that selects for antibiotic-resistant bacteria and promotes Clostridium difficile (C. difficile) infection is antibiotic use. Since at least 50% of antibiotic use is inappropriate in the US regardless of healthcare setting, antibiotic stewardship activities are extremely important in managing antibiotic resistance.  


Learning Objectives: 

1. Describe the importance and need for antibiotic stewardship 
2. Identify key areas of concern regarding antibiotic resistance 
3. Describe current and emerging antibiotic stewardship strategies to target antibiotic resistance
4. Assess the evidence for antibiotic stewardship in managing antibiotic resistance 

Whooping cough caused by Bordetella infection has resurged in recent years.  Dr. Karissa Culbreath will discuss the clinical presentation of Bordetella infection and its public health impact.  The prognostic value of B. pertussis and B. parapertussis detection for Bordetella diagnosis will be reexamined.

Learning Objectives: 

1. Humans are the only host of B. pertussis
2. Multicopy genes help to support diagnostic sensitivity
3. Diasorin Molecular B. pertussis/B. parapertussis reagents can be used to detect B. pertussis and parapertussis with or without extraction

There are new generations of comprehensive multiplex molecular panels available for infectious diseases syndromic diagnostics. They are able to rapidly detect and identify the most common pathogens in blood, cerebrospinal fluid, stool and respiratory specimens. Use of multiplex molecular panels is associated with quicker turnaround time, reduction of other unnecessary laboratory tests, faster diagnosis and targeted treatment. Although with initial increase in supply laboratory costs some studies showed improvements in infection control and cost savings with reduced cost of care.

Learning Objectives: 

1. Explain diagnostics by multiplex molecular panels
2. Asses impact, advantages and limitations 
3. Identify the opportunities to improve testing 

The WHO has set ambitious targets for eliminating TB in low-incidence countries such as the US and Canada. While it’s true that the majority of TB cases in these settings arise from reactivation of latent TB infection in persons born outside North America, person-to-person transmission of active TB within the US and Canada also contributes to the burden of disease; thus, reducing TB transmission is an integral part of regional and national TB elimination programs. Recently, whole genome sequencing (WGS) has emerged as a new paradigm for both rapid TB diagnosis and phenotyping, as well as for better identifying clusters of cases representing local transmission and even identifying specific transmission events, giving us an unique perspective on understanding TB transmission. In this talk, I’ll describe how the province of British Columbia, Canada has implemented WGS to better understand our local TB epidemiology and to change TB policy and practice in our setting. Topics to be covered include the role of WGS in the modern reference TB laboratory, methods for inferring transmission from TB genomic data alone, the key role for communication and knowledge translation when implementing WGS in a public health system, and insights gained from our sequencing of over 2000 TB isolates, representing cases diagnosed in BC dating back over a decade.

Learning Objectives: 

1. TB is the leading infectious disease killer in the world, despite being treatable.
2. Drug resistance is an emerging issue in TB, with resistance driven by point mutations. 

Next-generation DNA sequencing has opened new possibilities for microbial water quality monitoring, particularly for addressing emerging concerns like antibiotic resistance and opportunistic pathogens.   Here we will demonstrate how the approach is being applied to survey antibiotic resistance genes and pathogen gene markers in various water and environmental systems, including drinking water, wastewater, reclaimed water, and agricultural manure management systems.  Current efforts are focused on deriving various metrics from metagenomic data for assessing presence of these targets and potential to spread undesirable traits, such as antibiotic resistance and virulence genes.  As DNA sequencing and bioinformatic technologies are rapidly developing, development and validation of various approaches is needed, along with adoption of standardized methods by relevant stakeholders.

Learning Objectives: 

1. Describe what shotgun metagenomic sequencing is and benefits for water analysis
2. Describe current limitations to shotgun metagenomic approaches for pathogen and resistance monitoring
3. Describe new developments and approaches for advancing metagenomic tools for water monitoring

Viruses, and particularly phage that infect bacteria, are the most abundance and diversity life forms on the planet. Given their success throughout the biosphere, it is expected that phage are essential members of the animal and plant holobionts. We have shown that phage form a bacterial selective, adaptive immune system that helps protect the mucosal surfaces of animals and establish the microbiome. Additionally, phage are actively transported across epithelial layers and may provide a systemic protection against bacteria. These two findings strongly suggest that phage formed the first acquired immune system and they remain important in extant animal immunology. The biggest knowledge gap in my field is the overly cell-centric nature of most researchers, editors and funders.

Learning Objectives: 

1. How do phage protect mucosal surfaces
2. How do phage protect the inside of animals