Salmonella Genomics and Evolution Quiz
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Questions and Answers

What are pathogenicity islands and what role do they play in microbes?

  • They facilitate horizontal gene transfer between different species.
  • They are plasmids that carry antibiotic resistance genes.
  • They are regions that contribute to the virulence of certain microbes. (correct)
  • They are stable regions in bacterial chromosomes.

    • Which process was highlighted as a mechanism for Salmonella's evolution?

  • Chromosomal inversion
  • Point mutations
  • Lateral gene transfer (correct)
  • Gene duplication

    • What evidence did comparative genomics of Salmonella enterica indicate?

  • Simplification of bacterial genomes over time.
  • Increased mutation rates in host cells.
  • CRISPR-mediated adaptive sublineage evolution. (correct)
  • Resistance to all known antibiotics.

    • Which study aspect is addressed by the reference collection of strains in Salmonella research?

    <p>Tracking genetic variations across different strains.</p> Signup and view all the answers

    What potential threat do integrons and antibiotic resistance genes pose?

    <p>They can contribute to the spread of resistance among pathogens.</p> Signup and view all the answers

    What phenomenon is associated with selection and recombination in type I restriction-modification systems?

    <p>Evolution of bacterial defense mechanisms.</p> Signup and view all the answers

    How do Salmonella genomic islands function in relation to antibiotic resistance?

    <p>They are segments of DNA that can provide resistance traits.</p> Signup and view all the answers

    What major issue is raised concerning extended-spectrum cephalosporin-resistant Gram-negative organisms?

    <p>They pose an emerging problem for human health.</p> Signup and view all the answers

    What is the primary difference between vertical and horizontal evolution?

    <p>Vertical evolution focuses on inherited genetic changes.</p> Signup and view all the answers

    How can horizontal gene transfer (HGT) affect the interpretation of phylogenetic trees?

    <p>HGT can create the illusion of close relationships despite distant relatedness.</p> Signup and view all the answers

    What methods are mentioned that help filter out the effects of horizontal elements when building phylogenetic trees?

    <p>Whole-genome sequencing and multilocus sequence typing.</p> Signup and view all the answers

    What percentage of the Salmonella genome is estimated to have been influenced by horizontal gene transfer?

    <p>25%</p> Signup and view all the answers

    Which of the following: plasmids and phages, are relevant to horizontal gene transfer?

    <p>They contribute to the exchange of genetic material between organisms.</p> Signup and view all the answers

    What is the main purpose of whole-genome sequencing (WGS) in food safety as mentioned in the content?

    <p>To identify the most closely related isolates.</p> Signup and view all the answers

    What aspect of genetic diversification do studies support regarding Salmonella?

    <p>HGT has played a crucial role in its evolutionary diversification.</p> Signup and view all the answers

    What term is used to describe the evolutionary process impacted by gene transfer from one organism to another?

    <p>Horizontal gene transfer (HGT).</p> Signup and view all the answers

    What is a significant public health concern associated with AMR S.enterica strains?

    <p>Enteric foodborne illness</p> Signup and view all the answers

    Which of the following is NOT associated with AMR genes in Salmonella?

    <p>Vitamin K deficiency</p> Signup and view all the answers

    What percentage of AMR genes is found in Salmonella associated with produce?

    <p>72%</p> Signup and view all the answers

    What is the primary focus of the research conducted by Allard et al. in 2018?

    <p>Salmonella serotype determination using genomic data</p> Signup and view all the answers

    What does the AMRFinderPlus database predict in addition to AMR genes?

    <p>Genes related to stress and virulence</p> Signup and view all the answers

    Which method was highlighted by Cox et al. in 2019 for detecting Salmonella serovars?

    <p>Preenrichment method and selective enrichment media</p> Signup and view all the answers

    What was the outcome of the 2014 outbreak linked to cucumbers in the United States?

    <p>Documented cases of Salmonella Newport infections</p> Signup and view all the answers

    How does recombination affect the evolution of AMR genes in Salmonella?

    <p>It continues to introduce advantageous traits.</p> Signup and view all the answers

    What technology did Alikhan et al. mention as useful for identifying multiple Salmonella serovars?

    <p>CRISPR-SeroSeq</p> Signup and view all the answers

    Which of the following AMR genes is most elevated in food isolates?

    <p>Amino-glycoside resistance genes</p> Signup and view all the answers

    The 2016 study by Hoffmann et al. focused on tracing origins of which specific Salmonella strain?

    <p>Salmonella Bareilly</p> Signup and view all the answers

    What does HGT stand for in the context of AMR genes in Salmonella?

    <p>Horizontal gene transfer</p> Signup and view all the answers

    Which of the following was NOT a focus of Stevens et al. in their 2018 study?

    <p>Effects of environmental conditions on Salmonella survival</p> Signup and view all the answers

    Which of the following is a characteristic of the automated AMR typing approach developed for Salmonella?

    <p>It relies on genomic data.</p> Signup and view all the answers

    What type of research publication was the work of Williams et al. associated with?

    <p>Journal of Clinical Microbiology</p> Signup and view all the answers

    According to the research, which geographic locations were studied concerning the hypermutable Salmonella enterica strains?

    <p>Russia, Belarus, and Kazakhstan</p> Signup and view all the answers

    What is the primary characteristic of Salmonella enterica?

    <p>It comprises over 2,600 serovars.</p> Signup and view all the answers

    In which environments can Salmonella persist?

    <p>Water, soil, and various plants</p> Signup and view all the answers

    What has contributed to the understanding of non-typhoidal Salmonella serovars in the environment?

    <p>The rise of the genomics era</p> Signup and view all the answers

    How many Salmonella genomes are currently available in public databases?

    <p>Over 340,000</p> Signup and view all the answers

    Which technique has transformed the characterization of Salmonella strains?

    <p>Whole-genome sequencing (WGS)</p> Signup and view all the answers

    What is one of the implications of widespread whole-genome sequencing availability?

    <p>It allows for rapid differentiation of Salmonella strains.</p> Signup and view all the answers

    Which of the following animals is NOT mentioned as a host for Salmonella?

    <p>Insects</p> Signup and view all the answers

    Why is Salmonella considered a highly adapted environmental microbe?

    <p>It can persist in a variety of environmental niches.</p> Signup and view all the answers

    What is a characteristic feature of host-adaptive (HA) and host-restricted (HR) Salmonella serovars compared to unrestricted-host-range serovars?

    <p>They have a reduced allelic variation.</p> Signup and view all the answers

    What is the effect of the loss of genes in HA and HR serovars on their virulence?

    <p>It diminishes their pathogenicity.</p> Signup and view all the answers

    Which of the following factors is primarily associated with the evolutionary adaptation of Salmonella serovars?

    <p>Host-specific infection capacity.</p> Signup and view all the answers

    During the adaptation process, which structures tend to be lost in HA and HR serovars?

    <p>Adhesins and fimbriae.</p> Signup and view all the answers

    Which key difference underlines the emergence of host-adaptive serovars in salmonellae?

    <p>Their predominant infection in a single natural host.</p> Signup and view all the answers

    How do HA and HR salmonella serovars generally differ from unrestricted-host-range serovars in terms of gene content?

    <p>They possess more pseudogenes.</p> Signup and view all the answers

    What does the adaptation of certain Salmonella serovars to specific hosts indicate about their evolutionary trajectory?

    <p>They have reduced genetic diversity due to specialization.</p> Signup and view all the answers

    What key concept explains the limited duration of infection caused by Salmonella in its host?

    <p>The action of the host's immune response.</p> Signup and view all the answers

    Which statement accurately describes the role of type III secretion systems in Salmonella evolution?

    <p>They played a significant role early in Salmonella evolution.</p> Signup and view all the answers

    What does the term 'allelic shuffling' refer to in the context of Salmonella

    <p>The exchange of gene variants among different strains.</p> Signup and view all the answers

    Which types of genes retain unusually low GC content in Salmonella?

    <p>Pilin genes encoding fimbrial adhesins.</p> Signup and view all the answers

    How does horizontal gene transfer (HGT) influence the genetic structure of Salmonella?

    <p>It leads to a homogenization of allele structures within related populations.</p> Signup and view all the answers

    What role do restriction-modification (R-M) complexes play in Salmonella genetics?

    <p>They are involved in the open exchange of R-M alleles.</p> Signup and view all the answers

    Which phenomenon is observed regarding housekeeping genes in Salmonella enterica?

    <p>Their evolutionary paths are decoupled from specific strains.</p> Signup and view all the answers

    What can be inferred about the evolutionary history of genes within Salmonella?

    <p>Different genes evolve independently from their host.</p> Signup and view all the answers

    What is the significance of R-M genes in the context of Salmonella populations?

    <p>They demonstrate compatibility for gene exchange in genetic panmixia.</p> Signup and view all the answers

    What is the primary goal of establishing global genomic standards for foodborne bacteria?

    <p>To provide consistency in whole-genome sequencing (WGS) approaches</p> Signup and view all the answers

    Which of the following components is NOT included in the three parts of the standard for WGS?

    <p>Storage of bacterial cultures</p> Signup and view all the answers

    What kind of changes can nonsynonymous nucleotide changes lead to in bacteria?

    <p>Modifications of the protein structure and phenotype</p> Signup and view all the answers

    How does combining cladistics, character optimization, and WGS benefit scientists studying foodborne pathogens?

    <p>It allows identification of genotype-to-phenotype changes.</p> Signup and view all the answers

    What aspect of bacterial culture handling is addressed by the genomic characterization methods?

    <p>Genomic DNA isolation and handling</p> Signup and view all the answers

    Which of the following is a primary outcome of utilizing whole-genome sequencing in foodborne microorganism research?

    <p>Predicting correlations between genomic changes and known virulence</p> Signup and view all the answers

    What kind of sequence repository deposition is included in the standard's parameters?

    <p>End-to-end WGS workflow validation</p> Signup and view all the answers

    Which of the following is a significant benefit of harmonizing test protocols across different organizations?

    <p>Facilitates direct comparisons of WGS results globally</p> Signup and view all the answers

    What is the role of high-resolution SNP analysis in relation to isolates in an outbreak?

    <p>It resolves isolates down to very tips of the phylogenetic tree.</p> Signup and view all the answers

    How does whole-genome sequencing (WGS) aid in identifying foodborne outbreaks?

    <p>By providing genetic support for phylogenetic connections.</p> Signup and view all the answers

    What impact do false inclusions have in ecological and epidemiological models?

    <p>They complicate the investigation process.</p> Signup and view all the answers

    Which method is used to separate outbreak signals from background noise in contamination investigations?

    <p>Whole-genome sequencing.</p> Signup and view all the answers

    In the context of identifying common contaminants, what role does exposure data play?

    <p>It helps define case scopes on the phylogenetic tree.</p> Signup and view all the answers

    What is a significant challenge posed by polyclonal outbreaks as suggested in the content?

    <p>They are difficult to trace due to multiple pathogen lineages.</p> Signup and view all the answers

    What is meant by monophyletic isolates in the context of WGS?

    <p>Isolates that share a common ancestor.</p> Signup and view all the answers

    What is the effect of using reduced resolution methods during contamination investigations?

    <p>They often lead to false positives in cluster formation.</p> Signup and view all the answers

    What significant outcome was linked to the outbreak of Salmonella Newport infections in the United States?

    <p>Contamination of cucumbers.</p> Signup and view all the answers

    Which method was identified as influential in Salmonella serovar detection on broiler carcasses?

    <p>Selective enrichment media.</p> Signup and view all the answers

    What is the primary focus of genomic studies related to Salmonella conducted by researchers?

    <p>Identifying serovar populations.</p> Signup and view all the answers

    Which technological advancement is utilized for identifying multiple Salmonella serovars in a single sample?

    <p>CRISPR-SeroSeq.</p> Signup and view all the answers

    Which study highlighted the long-term dissemination of a specific Salmonella strain in multiple countries?

    <p>Hoffmann et al. (2014).</p> Signup and view all the answers

    Which of the following options is associated with advancements in microbial food safety regarding Salmonella?

    <p>Genomic surveillance.</p> Signup and view all the answers

    Which of the following describes a method to improve the understanding of serovar variation in Salmonella?

    <p>Application of MLST (multilocus sequence typing).</p> Signup and view all the answers

    Which ecological role does Salmonella primarily serve that contributes to its persistence in various environments?

    <p>Highly adapted environmental microbe.</p> Signup and view all the answers

    Study Notes

    Pathogenicity Islands and Microbial Roles

    • Pathogenicity islands are genomic regions contributing to a microbe's virulence.

    Salmonella Evolution

    • Horizontal gene transfer is a key mechanism in Salmonella evolution.

    Comparative Genomics of Salmonella enterica

    • Comparative genomics reveals the extensive impact of horizontal gene transfer on Salmonella enterica's genome.

    Reference Collection of Salmonella Strains

    • A reference collection of Salmonella strains aids in studying genetic diversity and evolution.

    Integrons and Antibiotic Resistance

    • Integrons carrying antibiotic resistance genes pose a significant threat to public health.

    Type I Restriction-Modification Systems

    • Selection and recombination in type I restriction-modification systems lead to genome diversification.

    Salmonella Genomic Islands and Antibiotic Resistance

    • Salmonella genomic islands play a crucial role in antibiotic resistance.

    Extended-Spectrum Cephalosporin Resistance

    • Extended-spectrum cephalosporin resistance in Gram-negative organisms is a major clinical concern.

    Vertical vs. Horizontal Evolution

    • Vertical evolution involves inheritance from parent to offspring, while horizontal gene transfer involves acquisition of genes from other organisms.

    Horizontal Gene Transfer and Phylogenetic Trees

    • Horizontal gene transfer can complicate phylogenetic tree interpretation.

    Filtering Horizontal Gene Transfer in Phylogenetic Analyses

    • Methods exist to minimize the effects of horizontal gene transfer when constructing phylogenetic trees.

    Horizontal Gene Transfer in Salmonella Genome

    • A significant portion (estimated percentage not specified) of the Salmonella genome is believed to have originated through horizontal gene transfer.

    Horizontal Gene Transfer Agents

    • Plasmids and phages are key vectors for horizontal gene transfer.

    Whole-Genome Sequencing (WGS) in Food Safety

    • WGS is crucial for rapid identification and tracking of bacterial pathogens in food.

    Salmonella Genetic Diversification

    • Studies support the role of both mutation and horizontal gene transfer in Salmonella's genetic diversification.

    Horizontal Gene Transfer Terminology

    • Horizontal gene transfer is the process by which genes are transferred between organisms.

    Public Health Concern: AMR S. enterica

    • Antibiotic resistance in S. enterica strains is a major public health concern.

    Factors NOT Associated with AMR in Salmonella (Not specified in the prompt)

    • Information on factors NOT associated with AMR genes in Salmonella is missing.

    Allard et al. (2018) Research Focus

    • Allard et al. (2018) focused on (specific research focus not provided).

    Percentage of AMR Genes in Produce-Associated Salmonella

    • The percentage of AMR genes in produce-associated Salmonella (Specific percentage data not provided).

    Cox et al. (2019) Salmonella Detection Method

    • Cox et al. (2019) highlighted a method for detecting Salmonella serovars (method not specified).

    AMRFinderPlus Database Predictions

    • The AMRFinderPlus database predicts not only AMR genes but also (additional prediction not specified).

    2014 Cucumber Outbreak

    • The 2014 U.S. cucumber outbreak (specific details on the outcome not provided).

    Recombination and AMR Gene Evolution

    • Recombination influences the evolution of AMR genes.

    Alikhan et al. Technology for Salmonella Serovar Identification

    • Alikhan et al. mentioned a technology useful for identifying multiple Salmonella serovars (technology not specified).

    Most Elevated AMR Gene in Food Isolates (Not specified in the prompt)

    • Information on the most elevated AMR gene in food isolates is missing.

    Hoffmann et al. (2016) Study Focus

    • Hoffmann et al. (2016) traced the origins of a specific Salmonella strain (strain not specified).

    HGT Acronym

    • HGT stands for horizontal gene transfer.

    Stevens et al. (2018) Study Focus (Missing Information)

    • Information on what was NOT a focus of Stevens et al. (2018) is missing.

    Automated AMR Typing Approach for Salmonella

    • An automated AMR typing approach for Salmonella (Characteristics not specified).

    Williams et al. Publication Type (Missing Information)

    • Information on the publication type of Williams et al.'s work is missing.

    Geographic Locations Studied (Missing Information)

    • Information on the geographic locations studied regarding hypermutable Salmonella enterica strains is missing.

    Salmonella enterica Characteristics

    • Salmonella enterica is a (characteristics not specified).

    Salmonella Persistence Environments

    • Salmonella can persist in various environments (environments not specified).

    Understanding Non-Typhoidal Salmonella

    • (Factors contributing to understanding non-typhoidal Salmonella serovars in the environment are not specified).

    Available Salmonella Genomes

    • The number of Salmonella genomes in public databases is (number not specified).

    Transformation in Salmonella Characterization

    • Whole-genome sequencing has transformed the characterization of Salmonella strains.

    Implications of Widespread WGS Availability

    • Widespread WGS availability has several implications (implications not specified).

    Salmonella Hosts (Missing Information)

    • Information on animals that are NOT hosts for Salmonella is missing.

    Salmonella Adaptation

    • Salmonella is a highly adapted environmental microbe (reasons not specified).

    Salmonella Genomics and Evolution

    • Salmonella pathogenicity islands (SPIs), such as SPI-1 (encoding a type III secretion system), were likely acquired through horizontal gene transfer (HGT).
    • The inv-spa gene cluster shows extensive allelic shuffling among Salmonella enterica groups.
    • Type 1 pilin genes exhibit unusually low GC content and obscured phylogenies compared to other fimbrial genes.
    • Evolutionary histories of housekeeping genes in Salmonella are often decoupled from S. enterica strain history.
    • HGT and recombination play a significant role in homogenizing allele structure within closely related Salmonella populations.
    • R-M (restriction-modification) genes show a panmictic structure among group I Salmonella, indicating open exchange of alleles and compatibility of R-M complexes.
    • Successful HGT of entire gene sequences among closely related strains is facilitated by shared or recently shared common R-M alleles.

    Host Adaptation in Salmonella

    • Some Salmonella serovars have adapted to cause invasive disseminated disease, losing the ability to infect a broad range of hosts.
    • Host-adaptive (HA) serovars infect one or two main animal hosts but can infect others.
    • Host-restricted (HR) serovars predominantly infect one host and rarely infect others.
    • HA and HR serovars often exhibit auxotrophy for specific amino acids and vitamins.
    • HA and HR serovars have lost genes in anaerobic metabolic pathways and show reduced numbers of virulence factors compared to broad-host-range serovars.
    • HA and HR serovars have a large number of pseudogenes.
    • Many genes degraded in HA and HR serovars are involved in motility, chemotaxis, type III secretion, or attachment to host cells.
    • Allelic variation within the HA and HR group is reduced compared to host generalist serovars.

    Whole Genome Sequencing (WGS) in Salmonella Epidemiology

    • WGS provides genetic support for phylogenetic clusters linking food, environmental, and clinical isolates.
    • WGS helps separate outbreak signals from background noise in foodborne contaminations.
    • High-resolution SNP analysis resolves isolates down to the tips of phylogenetic trees.
    • WGS helps break down polyclonal outbreaks into smaller, solvable parts, treating each lineage as an independent pathogen.
    • Combining cladistics, character optimization, and WGS helps identify genotype-to-phenotype changes allowing foodborne pathogens to survive.
    • WGS aids in predicting genomic changes correlating with outbreaks and uncovering pathogenicity and virulence gene variants.

    Global Genomic Standards for Salmonella

    • Harmonization of test protocols is important for generating comparable WGS data globally.
    • Standards address laboratory operations, validation, and metadata for WGS of foodborne microorganisms.
    • Standards cover bacterial culture handling, genomic DNA isolation, sequencing, bioinformatics analysis, and metadata capture.
    • Minimum parameters for generating and analyzing WGS data from foodborne bacteria are defined.

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