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