MOLECULAR EPIDEMIOLOGY: PRINCIPLES AND PRACTICES

By CHARLOTTE RODRIGUEZ

PRINCIPLES AND APPROACHES INTRODUCTION DE?NITIONS DIFFERENTIATING MOLECULAR EPIDEMIOLOGY FROM TAXONOMY AND PHYLOGENY EPIDEMIOLOGIC PROBLEMS ADDRESSED BY MOLECULAR STRAIN-TYPING TECHNIQUES DETERMINING DYNAMICS OF DISEASE TRANSMISSION IN GEOGRAPHICALLY WIDESPREAD AREAS IDENTIFYING RISK AND QUANTITATING ATTRIBUTABLE RISK FRACTIONS IN SPORADIC OCCURRENCE OF INFECTIOUS DISEASES STRATIFYING DATA AND RE?NING EPIDEMIOLOGIC STUDY DESIGNS DISTINGUISHING PATHOVARS FROM NONPATHOVARS ADDRESSING HOSPITAL AND INSTITUTIONAL INFECTIOUS DISEASE PROBLEMS IDENTIFYING GENETIC DETERMINANTS OF DISEASE TRANSMISSION APPLICATION TO EPIDEMIOLOGY OF MOLECULAR STRAIN-TYPING METHODS WHEN TO USE MOLECULAR STRAIN-TYPING METHODS HOW TO SELECT MOLECULAR STRAIN-TYPING METHODS TO APPLY TO EPIDEMIOLOGIC INVESTIGATIONS VALIDATING NEW MOLECULAR STRAIN-TYPING METHODS CONCLUDING REMARKS REFERENCES CONTENTS LABORATORY METHODS USED FOR STRAIN TYPING OF PATHOGENS: CONVENTIONAL AND MOLECULAR TECHNIQUES PHENOTYPIC STRAIN-TYPING METHODS TYPING BY GROWTH AND MORPHOLOGIC CHARACTERISTICS TYPING BASED ON BIOCHEMICAL CHARACTERISTICS TYPING BY SEROLOGIC CHARACTERISTICS TYPING BY FUNCTIONAL OR PHYSIOLOGIC CHARACTERISTICS GENOTYPIC STRAIN-TYPING METHODS NUCLEIC ACID EXTRACTION: OVERVIEW ANALYSIS OF EXTRACHROMOSOMAL DNA ELEMENTS GENOME-BASED TYPING METHODS LABORATORY METHODS USED FOR STRAIN TYPING OF PATHOGENS: PCR-BASED STRAIN TYPING METHODS OVERVIEW OF PCR PROCEDURE EPIDEMIOLOGIC APPLICATION OF PCR-BASED STRAIN-TYPING METHODS SIMPLICITY HIGH THROUGHPUT COST APPROPRIATENESS LIMITATIONS OF PCR TESTS STRAIN-TYPING METHODS BASED ON PCR ASSAYS PCR STRAIN-TYPING METHODS BASED ON RANDOM SEQUENCES PCR STRAIN-TYPING METHODS BASED ON HETEROGENEITY WITHIN RESTRICTION ENDONUCLEASE SITES PCR STRAIN-TYPING METHODS BASED ON INTERSPERSED DNA REPETITIVE ELEMENTS ANALYSIS OF SIMILARITY AND RELATEDNESS IN MOLECULAR EPIDEMIOLOGY METHODS OF CLASSI?CATION CLADISTIC MODELS TO INFER RELATIONSHIPS PHENETIC METHODS TO INFER RELATIONSHIPS ASSESSING VALIDITY AND RELIABILITY OF RELATIONSHIP MEASURES COMPUTER-ASSISTED ANALYSES OF PATHOGEN RELATIONSHIPS DISTINGUISHING EPIDEMIC AND ENDEMIC OCCURRENCE OF INFECTIOUS DISEASES ENDEMIC VERSUS EPIDEMIC OCCURRENCES OF INFECTIOUS DISEASE EPIDEMIOLOGY OF ANTIMICROBIAL DRUG-RESISTANT PATHOGENS SOURCES OF DRUG-RESISTANT STRAINS OF SALMONELLA SPATIAL TRANSMISSION PATTERNS OF DRUG-RESISTANT INFECTIOUS DISEASES EPIDEMIOLOGY OF DRUG-SUSCEPTIBLE INFECTIOUS DISEASES STRATI?CATION AND RE?NEMENT OF DATA IN EPIDEMIOLOGIC INVESTIGATIONS CHARACTERIZING DYNAMICS OF INFECTIOUS DISEASE TRANSMISSION IN COMMUNITY SETTINGS DRUG-RESISTANT SALMONELLOSIS IN BRAZIL MULTIDRUG-RESISTANT (MDR) TUBERCULOSIS IN NEW YORK CITY DETERMINING ATTRIBUTABLE RISKS IN COMMUNITY- OR INSTITUTION-ACQUIRED INFECTIONS SALMONELLOSIS TRACED TO PRECOOKED ROAST BEEF IN NEW JERSEY AND PENNSYLVANIA FOOD-BORNE DISEASE SURVEILLANCE IN MINNESOTA NOSOCOMIAL INFECTIONS WITH VANCOMYCIN-RESISTANT ENTEROCOCCUS FAECIUM RE?NING ANALYTICAL EPIDEMIOLOGIC STUDY DESIGNS DRUG-SUSCEPTIBLE TUBERCULOSIS IN NEW YORK CITY MAKING NEW INFERENCES FROM RARE EVENTS REVEALED BY STRAIN TYPING CREATING OPPORTUNITIES TO IDENTIFY NEW INTERVENTION STRATEGIES DISTINGUISHING PATHOVARS FROM NONPATHOVARS: ESCHERICHIA COLI E COLI CLASSI?CATIONS E COLI ASSOCIATED WITH INTESTINAL DISEASES CONVENTIONAL TECHNIQUES USED TO DIFFERENTIATE E COLI STRAINS THAT CAUSE DIARRHEA MOLECULAR BIOLOGY TECHNIQUES USED TO DIFFERENTIATE E COLI STRAINS THAT CAUSE DIARRHEA DIFFERENTIATION OF DIARRHEAGENIC E COLI PATHOTYPES IN EPIDEMIOLOGIC INVESTIGATIONS EXTRAINTESTINAL E COLI INFECTIONS CLINICAL SPECTRUM OF EXPEC INFECTIONS APPROACHES USED TO DIFFERENTIATE EXPEC MOLECULAR EPIDEMIOLOGIC APPROACH TO DISCRIMINATE EXPEC DISTINGUISHING PATHOVARS FROM NONPATHOVARS: STREPTOCOCCUS PNEUMONIAE S PNEUMONIAE (THE PNEUMOCOCCUS) CLINICAL SPECTRUM OF PNEUMOCOCCAL DISEASE CONVENTIONAL STRAIN-TYPING METHODS FOR PNEUMOCOCCI GENOTYPING METHODS FOR S PNEUMONIAE APPLICATION OF STRAIN-TYPING METHODS TO EPIDEMIOLOGIC INVESTIGATION OF PNEUMOCOCCAL INFECTIONS PENICILLIN-RESISTANT PNEUMOCOCCAL INFECTIONS PNEUMOCOCCAL COLONIZATION AND INFECTION COMPARISON OF STRAIN TYPES BETWEEN INVASIVE DISEASE AND NP ISOLATES COMPARISON OF STRAIN TYPES FROM OUTBREAKS COMPARISON OF PATHOGENICITY OF STRAIN TYPES IN THE MOUSE MODEL GENOTYPE-SPECI?C RISK FACTORS FOR SPORADIC PNEUMOCOCCAL INVASIVE DISEASES DISTINGUISHING PATHOVARS FROM NONPATHOVARS: HELICOBACTER PYLORI H PYLORI CLINICAL SPECTRUM OF H PYLORI DISEASES CONVENTIONAL STRAIN-TYPING METHODS FOR H PYLORI GENOTYPING METHODS FOR H PYLORI WHOLE-GENOME ANALYSIS OF H PYLORI APPLICATION OF STRAIN-TYPING METHODS TO EPIDEMIOLOGIC INVESTIGATION OF H PYLORI INFECTIONS GENOTYPIC DIFFERENCES IN H PYLORI STRAINS ISOLATED FROM STOMACHS WITH DISEASE VERSUS ASYMPTOMATIC COLONIZATION COLONIZATION AND POPULATION STRUCTURE OF H PYLORI STRAINS IN THE STOMACH DEMONSTRATING CLUSTERING OF DISEASE AND COLONIZATION HOSPITAL INFECTIONS: STAPHYLOCOCCUS AUREUS OVERVIEW OF CLINICAL AND EPIDEMIOLOGIC ISSUES RELATED TO BACTERIAL NOSOCOMIAL INFECTIONS STAPHYLOCOCCAL NOSOCOMIAL INFECTIONS CLINICAL SPECTRUM OF STAPHYLOCOCCAL DISEASES DRUG-RESISTANT INFECTIONS STRAIN-TYPING METHODS FOR S AUREUS CONVENTIONAL STRAIN-TYPING METHODS FOR S AUREUS GENOTYPING METHODS FOR S AUREUS APPLICATION OF STRAIN-TYPING METHODS TO EPIDEMIOLOGIC INVESTIGATION OF NOSOCOMIAL S AUREUS INFECTIONS S AUREUS COLONIZATION VERSUS INFECTION DETERMINING CLONAL DISTRIBUTION OF S AUREUS ISOLATES COMPARATIVE GENOMICS APPROACH TO DIFFERENTIATE S AUREUS STRAINS ENDEMIC VERSUS EPIDEMIC OCCURRENCE OF S AUREUS HOSPITAL INFECTIONS HOSPITAL INFECTIONS: GRAM-NEGATIVE BACTERIA CLINICAL SPECTRUM AND EPIDEMIOLOGY OF INFECTIONS CAUSED BY GRAM-NEGATIVE BACTERIA ANTIMICROBIAL DRUG RESISTANCE IN GRAM-NEGATIVE BACILLI STRAIN-TYPING METHODS FOR GRAM-NEGATIVE BACTERIAL ORGANISMS CONVENTIONAL STRAIN-TYPING METHODS FOR GRAM-NEGATIVE ORGANISMS GENOTYPING METHODS FOR GRAM-NEGATIVE ORGANISMS APPLICATION OF STRAIN-TYPING METHODS TO EPIDEMIOLOGIC INVESTIGATION OF NOSOCOMIAL INFECTIONS CAUSED BY GRAM-NEGATIVE BACTERIA MONOCLONAL VERSUS POLYCLONAL INFECTIONS REINFECTION VERSUS RELAPSE INFECTIONS COLONIZATION, ENVIRONMENTAL CONTAMINATION, AND INFECTION WITH GRAM-NEGATIVE BACTERIA ENDEMIC VERSUS EPIDEMIC OCCURRENCE OF NOSOCOMIAL INFECTIONS CAUSED BY GRAM-NEGATIVE BACTERIA IDENTIFYING A PATHOGEN’S BIOLOGIC DETERMINANTS OF DISEASE TRANSMISSION MODES OF DISEASE TRANSMISSION IDENTIFYING GENETIC DETERMINANTS OF DISEASE TRANSMISSION TUBERCULOSIS: IDENTIFYING PHENOTYPIC AND GENETIC FACTORS OF M TUBERCULOSIS ASSOCIATED WITH RAPID PROGRESSION TO DISEASE UTI CAUSED BY E COLI: THE COMPARATIVE GENOMICS APPROACH TO IDENTIFY NEW GENES ASSOCIATED WITH TRANSMISSION SALMONELLOSIS: IDENTIFYING BACTERIAL FACTORS THAT ALLOW THE ORGANISM TO ESTABLISH A RESERVOIR THAT BECOMES A RISK FACTOR FOR HUMAN TRANSMISSION