Chapter 11 Detection and Identification of Microorganisms
The goal of antiretroviral therapy in HIV-positive patients is to obtain a viral load of ____.
less than 50 copies/mL
Performance Comparison of Representative Molecular Epidemiology Methods
look at picture in phone, certification album
MRSA isolates in clinical specimens by direct detection of ___ is critical for effective patient management and prevention of infections occurring in hospitals due to MRSA
mecA
What does MRSA stand for?
methicillin-resistant staphylococcus aureus
the HPV β group and ultraviolet (UV) radiation exposure are associated with ____.
nonmelanoma squamous cell carcinomas
How many HPV types are there?
over 200
a_____ is a disease that sweeps across wide geographical areas
pandemic
Glycopeptide Antibiotic inhibit ___
peptidoglycan synthesis in the cell wall of susceptible organisms (principally gram-positive cocci)
HIV antigen tests tests for the ____ antigen
HIV p24
advantage of bDNA for HIV viral load
High throughput Broad dynamic range Applicable for group M subtypes A-G
What is the suffix for antimicrobial agents that inhibit microbial growth?
-static
Molecular Strain Typing Methods for Epidemiological Studies
1)Plasmid Analysis 2) Pulsed-Field Gel Electrophoresis 3)Restriction Fragment Length Polymorphism Analysis 4) Arbitrarily Primed PCR 5)Amplified Fragment Length Polymorphism (AFLP) Assay 6) Interspersed Repetitive Elements 7) Internal Transcribed Spacer Elements 8)spa Typing
Linearity during viral load measurement
A serial dilution of standard curve closely approximates a straight line
accuracy during viral load measurement
Closeness of measured value to a standard or known value
Sensitivity during viral load measurement
Lowest level detected at least 95% of the time
_____peptide profiles can discriminate resistant strains of organisms such as MRSA and VRE
MALDI-TOF mass spectrometry
What type of virus is HPV?
double stranded DNA virus
What type of virus is HCV?
enveloped, single stranded RNA virus
a ______ is a disease or condition that affects many unrelated individuals at the same time
epidemic
What are the 6 genotypes of HCV?
1a/1b, 2, 3, 4, 5, and 6
HIV dynamic Range/Sensitivity
400-750,000 copies/mL (standard)50-100,000 copies/mL (ultrasensitive)176,000-3,470,000 copies/mL75-500,000 copies/mL
HCV targeted regions
5′ untranslated region (UTR) 5′ UTR and core protein gene
HCV dynamic range/ sensitivity
600-800,000 IU/mL 3,200-40,000,000 copies/mL
What are the 5 HPV genotype groups?
(α, β, γ, μ) and ν)
What is the suffix for antimicrobial agents that kill organisms?
-cidal
Patients who are effectively treated with antiretroviral therapy will have a significant reduction in viral load after how long after the initiation of therapy?
1 week
6 types of Phenotypic typing
1) Biotyping, growth on selective media 2) Antimicrobial susceptibility 3) Serotyping, immunoblotting 4) Bacteriophage typing 5) Protein, enzyme typing by electrophoresis 6) MALDI-TOF mass spectrometry
8 types of genotypic typing
1) Plasmid analysis 2) Restriction endonuclease mapping 3) Pulsed-field gel electrophoresis 4) Ribotyping 5) Arbitrarily primed PCR, RAPD PCR 6) Melt-curve analysis 7) REP-PCR, ERIC PCR, ITS, spa typing 8) Mass parallel sequencing
What are the two major types of antimicrobial agents?
1) inhibit microbial growth and 2) kill organisms
What are the 4 resistance mechanisms?
1)Destruction/modification of agent 2)Elimination of agent 3)Altered cell wall structure 4)Alternate metabolic pathways
What are the 5 modes of action of antimicrobial agents?
1)Disrupts cell wall synthesis or integrity 2)Disrupts cell membrane structure or function 3)Inhibits protein synthesis 4)Inhibits nucleic acid synthesis or integrity 5)Inhibits metabolite synthesis
When should viral load be assessed in HIV?
1. before therapy is started 2. 2-8 weeks after therapy to observe initial response 3. 3-4 months to assess effectiveness
HIV Patients who maintain viral levels at fewer than _____in the early stages of the infection are at decreased risk of progression to ____
10,000 copies/mL ; AIDS
HPV dynamic range/sensitivity
105 copies/mL
Flexibility during viral load measurement
Accuracy of measurement of virus regardless of sequence variations
advantage of NASBA for HIV viral load
Broad dynamic range Performed on many specimen types and volumes
in HIV patients, the higher the viral load, the lower the ___ count.
CD4
HPV clinical utility
Detection of HPV in endocervical swabs Differentiation of low-risk and high-risk types Monitoring women with abnormal Pap smears
Mode of action of Polymyxins (polymyxin B)Bacitracin
Disrupts cell membrane structure or function
Mode of action of Beta-lactams (penicillins and cephalosporins)Glycopeptides (vancomycin)
Disrupts cell wall synthesis or integrity
disadvantage of NASBA for HIV viral load
Does not detect all non-B subtypes
disadvantage of Amplicor RT-PCR for HIV viral load
Limited dynamic range
Mode of action of Sulfamethoxazole Trimethoprim
Inhibits metabolite synthesis
Mode of action of Quinolones (ciprofloxacin)Metronidazole
Inhibits nucleic acid synthesis or integrity
Mode of action of Aminoglycosides (gentamicin)Tetracyclines Macrolides (erythromycin)Lincosamides (clindamycin)
Inhibits protein synthesis
advantage of Amplicor RT-PCR for HIV viral load
Internal control has Good specificity
Mycobacterium tuberculosis can become resistant to ______ and the gene(s) conferring resistance is/are _____.
Isoniazid and Rifampin; katG, inhA and rpoB
HPV amplified target
L1 or E1 open reading frames
Specificity during viral load measurement
Negative samples are always negative, and positive results are true positives
disadvantage of bDNA for HIV viral load
No internal control False-positive results reported
Staphylococcus aureus can become resistant to ______ and the gene(s) conferring resistance is/are _____.
Oxacillin; mecA
What techniques are used to type mold?
PCR and sequencing of ITS regions or 28S rRNA
What methods are used for genotyping HCV?
PCR with restriction fragment length polymorphism (RFLP) analysis and reverse hybridization and direct DNA sequencing
HIV nucleic acid amplification methodology
PCR, RT-PCR, NASBA, bDNA
Streptococcus pneumoniae can become resistant to ______ and the gene(s) conferring resistance is/are _____.
Penicillin; pbp1a and pbp1b
Salmonella can become resistant to ______ and the gene(s) conferring resistance is/are _____.
Quinolones;gyrA, gyrB, parC, parE
HCV nucleic acid amplification methods
RT-PCR bDNA
precision during viral load measurement
Reproducibility of independently determined test results
_____ is one of the very few organisms that are still predictably susceptible to penicillin
Streptococcus pyogenes
Enterococcus can become resistant to ______ and the gene(s) conferring resistance is/are _____.
Vancomycin;vanA, vanB, vanC, vanD, vanE, vanG
HIV clinical utility
Viral quantitation Disease prognosis Treatment monitoring
What is an indicator that a person may be responding to HCV treatment?
a 2 log10 decrease in HCV RNA 12 weeks after treatment begins have a 65% chance of responding, defined by the lack of detection of HCV RNA in qualitative assays where the detection limit is 50 to 100 copies of virus/mL of plasma.
highly active antiretroviral therapy (HAART)
a very effective strategy for treating HIV-infected people with a combination of antiretroviral drugs, 2 RT inhibitors + protease inhibitor
HPVs 16, 18, 31, 33, 35, 39, 45, 51, 56, 58, 59, 68, 73, 82 are oncogenic and have been found to cause ____.
anogenital cancers
in addition to antigen and antibody testing, HIV in patient samples can also be detected by what 3 methods that detect integrated viral DNA?
bDNA, Amplicor RT-PCR, NASBA (nucleic acid sequencing based amplification)
What's an example of genetic factors being transferred from one bacterium to another by conjugation.
can gain vancomycin resistance from vancomycin-resistant enterococcus faecalis. lactic acid instead of alanine will be used for the cell wall generation- leading to drug resistance. via the Van genes.
The β HPV group infects the ______.
cutaneous epithelia
how do penicillin and other beta-lactam antimicrobials work?
inhibit bacteria by interfering with an enzyme that is involved in the synthesis of the bacterial cell wall
amplified targets of HIV
gag gene; 155 bp (HIV-1 group M [subtypes A-H], not HIV-2 or HIV-1 group O) gag (similar to Amplicor) HIV-1 groups M, O, and N pol; subtypes of group M (subtypes A-G, but not group O)
Which HCV genotypes respond better to treatment?
genotypes 2 and 3 will respond better to particular treatments than genotype 1
Viral load
how actively virus is replicating
HPV nucleic acid methodology
hybrid capture PCR qPCR
What part of the HCV genome is used to determine the genotype?
the core and/or 5′ untranslated regions of the genome
glycopeptide antibiotics include______.
vancomycin,teicoplanin, and ramoplanin
which is the largest HPV genotype group?
α
2nd HPV genotype group?
β
resistance to penicillin through the production of ________
β-lactamases
Gram-negatives can become resistant to ______ and the gene(s) conferring resistance is/are _____.
β-lactams;tem, shv, oxa, ctx-m
Which HPV groups normally only cause benign disease?
γ, μ and ν