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Molecular Epidemiology: Subtyping Bacteria and its Applications, Exams of Molecular biology

Johnson University Florida (JUFL)Molecular biology

A comprehensive overview of molecular epidemiology, focusing on the importance of subtyping bacteria for public health, animal health, and food production. It delves into the concepts of isolates, strains, clones, and taxa, explaining their significance in bacterial identification and subtyping. The document also explores various molecular techniques used in molecular epidemiology, including their advantages and limitations. It highlights the importance of discriminatory power in molecular typing methods and provides a detailed explanation of its calculation and interpretation. Finally, it discusses the different types of bacterial identification and subtyping methods, including phenotypic and genotypic techniques.

Typology: Exams

2023/2024

Available from 10/31/2024

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VBSC 444- Molecular Epidemiology Set #22
Questions And Answers 2023
why do we need to subtype bacteria? in order to safeguard _______ health, _______
health, ______ production - ANS-human, animal, food
what is the study of the distribution and determinants of infectious diseases that utilizes
molecular biology methods? - ANS-molecular epidemiology
molecular epidemiology the study of the _________ and _______ of infectious diseases
that utilizes _________ methods - ANS-distribution, determinants, molecular biology
_________ is the term for A population of microbial cells in pure culture derived from a
single colony on an isolation plate and identified to the species level - ANS-isolate
isolate is the term for A population of microbial cells in __________ derived from a
______________ on an isolation plate and identified to the species level - ANS-pure
culture, single colony
a ________ is An isolate or group of isolates exhibiting phenotypic and/or genotypic
traits belonging to the same lineage, distinct from those of other isolates of the same
species - ANS-strain
a strain is An isolate or group of isolates exhibiting _______ and/or _______ traits
belonging to the same _______, distinct from those of other isolates of the _________ -
ANS-phenotypic, genotypic, same lineage, same species
a ______ is an An isolate or a group of isolates descending from a common precursor
strain by nonsexual reproduction exhibiting phenotypic or genotypic traits characterized
by a strain-typing method to belong to the same group. - ANS-clone
a clone is an isolate or a group of isolates descending from a common ______ strain by
nonsexual reproduction exhibiting phenotypic or genotypic traits characterized by a
______________ to belong to the same group. - ANS-precursor, strain-typing method
_______ is a general taxonomic unit defined by a set of characteristics common to each
member of that unit (e.g., family, genus, species, subspecies, and infraspecies) - ANS-
taxon
taxon is a general taxonomic unit defined by a set of ________ common to each
________ of that unit (e.g., family, genus, species, subspecies, and infraspecies) -
ANS-characteristics, member
family, genus, species, subspecies, and infraspecies are examples of a _______ - ANS-
taxon
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VBSC 444- Molecular Epidemiology Set

Questions And Answers 2023

why do we need to subtype bacteria? in order to safeguard _______ health, _______ health, ______ production - ANS-human, animal, food what is the study of the distribution and determinants of infectious diseases that utilizes molecular biology methods? - ANS-molecular epidemiology molecular epidemiology the study of the _________ and _______ of infectious diseases that utilizes _________ methods - ANS-distribution, determinants, molecular biology _________ is the term for A population of microbial cells in pure culture derived from a single colony on an isolation plate and identified to the species level - ANS-isolate isolate is the term for A population of microbial cells in __________ derived from a ______________ on an isolation plate and identified to the species level - ANS-pure culture, single colony a ________ is An isolate or group of isolates exhibiting phenotypic and/or genotypic traits belonging to the same lineage, distinct from those of other isolates of the same species - ANS-strain a strain is An isolate or group of isolates exhibiting _______ and/or _______ traits belonging to the same _______, distinct from those of other isolates of the _________ - ANS-phenotypic, genotypic, same lineage, same species a ______ is an An isolate or a group of isolates descending from a common precursor strain by nonsexual reproduction exhibiting phenotypic or genotypic traits characterized by a strain-typing method to belong to the same group. - ANS-clone a clone is an isolate or a group of isolates descending from a common ______ strain by nonsexual reproduction exhibiting phenotypic or genotypic traits characterized by a ______________ to belong to the same group. - ANS-precursor, strain-typing method _______ is a general taxonomic unit defined by a set of characteristics common to each member of that unit (e.g., family, genus, species, subspecies, and infraspecies) - ANS- taxon taxon is a general taxonomic unit defined by a set of ________ common to each ________ of that unit (e.g., family, genus, species, subspecies, and infraspecies) - ANS-characteristics, member family, genus, species, subspecies, and infraspecies are examples of a _______ - ANS- taxon

For instance, humans and whales are two _______ organisms from different perspectives; however, both are considered mammals and ________ related - ANS- unrelated, taxonomically The term "_____________" is frequently used to describe studies that should be more appropriately referred to as molecular taxonomy or phylogeny - ANS-molecular epidemiology The term "molecular epidemiology" is frequently used to describe studies that should be more appropriately referred to as molecular _________ or _________ - ANS-taxonomy, phylogeny ___________ is the Science of classification of organisms into naturally related grounds based on a factor common to each - ANS-taxonomy taxonomy is the Science of _________ of organisms into naturally related grounds based on a ___________ - ANS-classification, factor common to each _____ is the Study of lines of descent or evolutionary development of an organism - ANS-phylogeny phylogeny is study of ________ or evolutionary development of an organism - ANS- lines of descent In molecular epidemiology main target of analysis is the _________ itself and its interaction with the ______ and the _____ in which it resides - ANS-organism, hot, environment In taxonomy or phylogeny when applied to infectious agents, the data that are generated are used to describe ________ and ________ of organisms. The main target of analysis is the _______ and its relationship to other organisms - ANS-properties, characteristics, organism, relationship the decision to use a molecular technique over conventional methods should be based on what five things? - ANS-simplicity, high throughput, cost, appropriateness, and speed The decision to use molecular technique over conventional methods should be based on the following:

  • _________: PCR assay for diarrheagenic E. Coli in Brazil - ANS-simplicity The decision to use molecular technique over conventional methods should be based on the following:
  • ___________: pooling of samples; high volume analysis; ribotyping - ANS-high throughput

the genotype method of bacterial identification and subtyping methods is techniques that involve direct _________ analysis of chromosomal or extrachromosomal _______ elements - ANS-DNA-based, genetic four bacterial identification and subtyping systems? - ANS-phenotype, genotype, antibody, chemotaxonic which of the four bacterial identification and subtyping systems includes phenotype identification - ANS-phenotype which of the four bacterial identification and subtyping systems includes ribotyping, DNA amplification, tDNA-PCR, DNA-DNA hybridization, DNA sequencing, rRNA sequencing

  • ANS-genotype which of the four bacterial identification and subtyping systems includes serology - ANS- antibody which of the four bacterial identification and subtyping systems includes MALDI - ANS- chemotaxonic ___________________ is the ability of the test to generate distinct and discrete units of information from different isolates, usually at subspecies level - ANS-Discriminatory power Discriminatory power is the ability of the test to generate ______ and ______ units of information from different ________, usually at subspecies level - ANS-distinct, discrete, isolates in terms of discriminatory power:
  • ____ is the index of discriminatory power
  • _____ the number of unrelated strains tested
  • ____ the number of different types
  • ____ the number of strains belonging to the _____ type, assuming that strains will be classified into mutually exclusive categories - ANS-D, N, S, xj the ___________ is the average probability that the typing system will assign different type to two unrelated strains randomly sampled in the microbial population of a given taxon. - ANS-discriminatory power (D) the discriminatory power (D) is the average probability that the typing system will assign a different type to two _________ strains _______ sampled in the microbial population of a given taxon. - ANS-unrelated, randomly for discriminatory power, D value of an index of _____ would indicate that a typing method was able to distinguish each member of a strain population from all other members of that population - ANS-1.

for discriminatory power, D value of an index of _______ would indicate that all members of a strain population were of an identical type - ANS-0. for discriminatory power, D value of an index of _______ would mean that if one strain was chosen at random from a strain population, then there would be a 50% probability that the next strain chosen at random would be indistinguishable from the first - ANS-

for discriminatory power, D value of an index of 1.0 would indicate that a typing method was able to _________ from all other ________ - ANS-distinguish each member of a strain population, members of that population for discriminatory power, D value of an index of 0.0 would indicate that all members of a _________ were of an __________ - ANS-strain population, identical type for discriminatory power, D value of an index of 0.50 would mean that if one strain was chosen at random from a strain population, then there would be a 50% probability that _______________ - ANS-the next strain chosen at random would be indistinguishable from the first limitations to phenotype-based methods

  • capacity of microorganisms to alter the _____________
  • _______ mutations can result in abnormal regulation or function responsible for a particular phenotype
  • requires ______ and pure cultures
  • _________ species cannot be phenotypically differentiated
  • corresponding databases are often ______, hampering accurate identification
  • typically takes ______ hrs (primary plating to ID) - ANS-expression of genes, point, culture, highly related, limited, 72- 96 biochemical to ________identification was the most significant advance in clinical microbiology (bacteriology) in 30 years - ANS-MALDI-TOF bacterial ______________ bacterial identification allows Rapid and cost effective identification of bacteria directly from isolated colonies based on protein biomarkers - ANS-MALDI-TOF MALDI-TOF bacterial identification allows _______ and _______ identification of bacteria directly from isolated colonies based on protein biomarkers - ANS-rapid, cost effective _____________ measured are highly expressed proteins responsible for housekeeping functions, suhc as ribosomal and transcription/translation factor proteins - ANS-protein biomarkers
  • commercially available and _____ approved - ANS-validation, FDA examples of genotype based bacterial sub-typing methods? - ANS-PCR, nested PCR, multiplex PCR, RT-PCR, microarrays, oligonucleotide probes PCR, nested PCR, multiplex PCR, RT-PCR, microarrays, oligonucleotide probes are examples of ___________ based bacterial subtyping methods - ANS-genotype Real-Time PCr is ______, _____ and a high dynamic _____ - ANS-sensitive, specific, range Real-Time PCr is simple, _____ and ______ (in terms of speed and reproductivity) - ANS-rapid, reproducible Real-Time PCr is has __________ and quantification of pathogen load - ANS-real time detection Real-Time PCr is useful for _________ data - ANS-qualitative end-point Real-Time PCr is is a _____ system with no need for post _______ processes - ANS- closed, amplification Real-Time PCr is low risk of _________, with automation, high throughput analysis - ANS-contamination Real-Time PCr has ______ instrumentation and appropriate chemistries - ANS-reliable Real-Time PCr has ___________ assays - ANS-pathogen detection DNA sequence analysis:
  • _______ sequence data are unequivocal - ANS-DNA/RNa DNA sequence analysis:
  • improved reliability and _______, and is easy to _______ with other labs - ANS- reproducibility, compare DNA sequence analysis:
  • culturables and ____________ - ANS-non-culturables DNA sequence analysis:
  • ______ databases such as GenBank - ANS-public DNA sequence analysis:
  • interpretation of results require some _______ (careful attention for sequence alignments and analysis) - ANS-skills

DNA sequence analysis:

  • __________ sequencing - new automatic, high throughput DNA
  • technologies remain rather complex successful adoption in the clinical microbiology lab will require expertise in both _______ and ________ - ANS-next generation, molecular biology, bioinformatics 16S rDNA sequencing:
  • DNA encoding 16S rRNA in present in _____________ - ANS-all bacterial species 16S rDNA sequencing:
  • 16S rDNA contains fully ______ and _______ regions - ANS-conserved, variable 16S rDNA sequencing:
  • __________ regions are used for design of primers that are compatible with 16S rDNa of all bacterial species and which allows for PCR amplification - ANS-conserved 16S rDNA sequencing:
  • conserved regions are used for design of _________ that are compatible with 16S rDNa of all bacterial species and which allows for __________ - ANS-primers, PCR amplification 16S rDNA sequencing:
  • _______ regions are unique for each bacterial species and allows for identification - ANS-variable 16S rDNA sequencing:
  • variable regions are _____ for each bacterial species and allows for ______ - ANS- unique, identification virus identification and sub-typing:
  • do not grow in ______ medium, rather _____ models, chicken embryos or cell cultures
  • ANS-artificial, animal virus identification and sub-typing:
  • identification is done by _______ methods such as ELISa, AGID, IFA - ANS- serological virus identification and sub-typing:
  • ______ methods are PCR - ANS-molecular virus identification and sub-typing:
  • ____typing and _____typing - ANS-sero, geno Whole-genome sequencing may still be _______ limiting for routine use in most clinical microbial laboratories - ANS-cost

what type of bacterial sub-typing/identification method has public databases and can be done with culturables and non-culturables - ANS-DNA sequence analysis what type of bacterial sub-typing/identification method does interpretation require some skills (careful attention for sequence alignments and analysis) - ANS-DNa sequence analysis what type of bacterial sub-typing/identification method is next generation sequencing = new automatic, high throughput dna - ANS-dna sequence analysis what type of bacterial sequencing method is DNA encoding something present in all bacterial species, with a fully conserved and variable regions? - ANS-16S rDNA sequencing what type of bacterial sequencing method is used to find out important metabolic and virulence pathways in microbes, and provides information about coding and non coding part of an organism? - ANS-whole genome sequencing what type of bacterial sequencing method is for evolutionary study and species comparison, important for more effective personalized medicine? - ANS-whole genome sequencing what type of bacterial sequencing method has identification of important secondary metabolite pathways? - ANS-whole genome sequencing what type of bacterial sequencing method has disease susceptibility prediction based on gene sequence varation - ANS-Whole genome sequencing endogenous _______ are like genetic fossils; remnants of ancient infections caught by sheep and their ancestors thousands of years ago whose dna has been integrated into the _______ of the animal and then passed on to subsequent _______ - ANS- retroviruses, genetic code, generations _______ Typing:

  • strains can be characterized by their pattern of resistance or susceptibility to a standard set of bacteriophages
  • This relies on the presence/absence of particular receptors on the bacterial surface that are used by the virus to bind to the bacterial wall
  • this method is used to isolate types of Staphylococcus aureus and Salmonella spp. and such stains are referred as _____ types - ANS-Phage Phage Typing:
  • strains can be characterized by their pattern of _____ or _______ to a standard set of bacteriophages - ANS-resistance, susceptibility, bacteriophages

Phage Typing:

  • relies on the presence/absence of particular ______ on the _____________ that are used by the virus to _____ to the bacterial wall - ANS-receptors, bacterial surface, bind Phage Typing:
  • this method is used to isolate types of Staphylococcus aureus and Salmonella spp. and such stains are referred as _____ - ANS-Phage Types Advantages of Phage Typing:
  • fair amount of _______, discriminatory power and ease of __________ - ANS- reproducibility, interpretation Disadvantages of Phage Typing:
  • this technique requires maintenance of biologically active phages and hence is available only at _______ centers.
  • Even for the _______ worker, the technique is ________.
  • Many strains are _______ - ANS-reference, experienced, demanding, non-typeable in terms of phage typing, different bacterial strains within a species show different _______ susceptibilities - ANS-bacteriophage what is serotyping - ANS-subtyping test based on differences in microbial (e.g., viral or bacterial) surfaces, specifically refers to the antibodies that form because of a viral or bacterial infection ______ is a subtyping test based on differences in microbial (e.g., viral or bacterial) surfaces, specifically refers to the antibodies that form because of a viral or bacterial infection - ANS-serotyping Advances in bacterial identification and subtyping (phenotype-based): Conventional methods were
  • ______ intensive
  • waste of _____ and ____
  • preparation of _______
  • difficult _______ So we switched over to _________ methods which fixed all the above issues - ANS- labor, space, time, media, interpretation, rapid identification over the years, advances in genotype-based bacterial identification and subtyping went from the _________ method, to unique DNA signatures, to now usage of _______ for years to come - ANS-16S rRNA, whole genome advances in ______ based bacterial identification and sub-typing
  • morphology to cultural characteristics to biochemical tests to enzymatic tests and susceptibility patterns to usage of virulence factors - ANS-phenotype