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Appendix C Acronyms AEEC attaching and effacing Escherichia coli AFMIC Armed Forces Medical Intelligence Center ANSI American National Standards Institute ATCC American Type Culture Collection Bd Batrachochytrium dendrobatidis BFP bundle-forming pili BLAST basic local alignment search tool CDC Centers for Disease Control and Prevention CLIA clinical laboratory improvement amendment COG cluster of orthologous groups of proteins DEC diarrheagenic Escherichia coli DHS Department of Homeland Security DNA deoxyribonucleic acid DOD Department of Defense DOJ Department of Justice DRISEE duplicate read inferred sequencing error estimation DTRA Defense Threat Reduction Agency EAEC enteroaggregative Escherichia coli EHEC enterohemorrhagic Escherichia coli EID emerging infectious disease EIEC enteroinvasive Escherichia coli 383

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384 THE SCIENCE AND APPLICATIONS OF MICROBIAL GENOMICS EPEC enteropathogenic Escherichia coli ESS Environmental Shotgun Sequencing ETEC enterotoxigenic Escherichia coli FBI Federal Bureau of Investigation FDA U.S. Food and Drug Administration GEBA Genomic Encyclopedia of Bacteria and Archaea GBS Group B streptococcus HAART highly active antiretroviral therapy HAI hospital-acquired infection HGT horizontal gene transfer HHS Department of Health and Human Services HIV human immunodeficiency virus IOM Institute of Medicine ISO International Organization for Standardization KEGG Kyoto Encyclopedia of Genes and Genomes LEE locus of enterocyte effacement MIRU mycobacterial interspersed repetitive unit MLST multi-locus sequence typing MRSA methicillin-resistant Staphylococcus aureus NGS next-generation sequencing ORF open reading frame OTU operational taxonomic unit PAUP phylogenetic analysis using parsimony PCoA principal coordinates analysis PCR polymerase chain reaction RNA ribonucleic acid rRNA ribosomal RNA SNP single nucleotide polymorphisms STEC shiga toxin-producing Escherichia coli

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APPENDIX C 385 TB tuberculosis TIGR The Institute for Genomic Research USAMRIID U.S. Army Medical Research Institute of Infectious Diseases USDA U.S. Department of Agriculture VNTR variable number tandem repeat

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