Loads contaminant organisms from common_commensals.csv and filters by syndrome and/or specimen type.
Arguments
- syndrome
Character. Optional syndrome name to filter by (e.g., "Bloodstream infections", "Urinary tract infections").
- specimen_type
Character. Optional specimen type to filter by (e.g., "Blood culture", "Urine culture").
- return_all
Logical. If TRUE, returns all contaminants from all syndromes. Default FALSE.
Examples
# Get all blood culture contaminants
get_contaminant_list(syndrome = "Bloodstream infections")
#> $names
#> [1] "Coagulase-negative Staphylococcus" "Staphylococcus epidermidis"
#> [3] "Staphylococcus hominis" "Staphylococcus haemolyticus"
#> [5] "Staphylococcus capitis" "Staphylococcus warneri"
#> [7] "Corynebacterium species" "Corynebacterium striatum"
#> [9] "Corynebacterium jeikeium" "Cutibacterium"
#> [11] "Cutibacterium acnes" "Micrococcus species"
#> [13] "Micrococcus luteus" "Bacillus (non-anthracis)"
#> [15] "Bacillus subtilis" "Bacillus cereus"
#> [17] "Viridans streptococci" "Aerococcus spp."
#> [19] "Kocuria spp." "Dermacoccus spp."
#> [21] "Rothia spp."
#>
#> $patterns
#> $patterns[[1]]
#> $patterns[[1]]$original
#> [1] "Coagulase-negative Staphylococcus"
#>
#> $patterns[[1]]$patterns
#> [1] "coagulase-negative staphylococcus" "^c\\.\\s"
#> [3] "^c\\.\\s*staphylococcus"
#>
#>
#> $patterns[[2]]
#> $patterns[[2]]$original
#> [1] "Staphylococcus epidermidis"
#>
#> $patterns[[2]]$patterns
#> [1] "staphylococcus epidermidis" "^s\\.\\s"
#> [3] "epidermidis" "^s\\.\\s*epidermidis"
#> [5] "staph.*epidermidis" "coag.*neg"
#> [7] "coagulase.*negative"
#>
#>
#> $patterns[[3]]
#> $patterns[[3]]$original
#> [1] "Staphylococcus hominis"
#>
#> $patterns[[3]]$patterns
#> [1] "staphylococcus hominis" "^s\\.\\s" "hominis"
#> [4] "^s\\.\\s*hominis" "staph.*hominis" "coag.*neg"
#> [7] "coagulase.*negative"
#>
#>
#> $patterns[[4]]
#> $patterns[[4]]$original
#> [1] "Staphylococcus haemolyticus"
#>
#> $patterns[[4]]$patterns
#> [1] "staphylococcus haemolyticus" "^s\\.\\s"
#> [3] "haemolyticus" "^s\\.\\s*haemolyticus"
#> [5] "staph.*haemolyticus" "coag.*neg"
#> [7] "coagulase.*negative"
#>
#>
#> $patterns[[5]]
#> $patterns[[5]]$original
#> [1] "Staphylococcus capitis"
#>
#> $patterns[[5]]$patterns
#> [1] "staphylococcus capitis" "^s\\.\\s" "capitis"
#> [4] "^s\\.\\s*capitis" "staph.*capitis" "coag.*neg"
#> [7] "coagulase.*negative"
#>
#>
#> $patterns[[6]]
#> $patterns[[6]]$original
#> [1] "Staphylococcus warneri"
#>
#> $patterns[[6]]$patterns
#> [1] "staphylococcus warneri" "^s\\.\\s" "warneri"
#> [4] "^s\\.\\s*warneri" "staph.*warneri" "coag.*neg"
#> [7] "coagulase.*negative"
#>
#>
#> $patterns[[7]]
#> $patterns[[7]]$original
#> [1] "Corynebacterium species"
#>
#> $patterns[[7]]$patterns
#> [1] "corynebacterium species" "corynebacterium"
#> [3] "^c\\.\\s" "^c\\.\\s*species"
#> [5] "coryno" "diphtheroids?"
#>
#>
#> $patterns[[8]]
#> $patterns[[8]]$original
#> [1] "Corynebacterium striatum"
#>
#> $patterns[[8]]$patterns
#> [1] "corynebacterium striatum" "^c\\.\\s"
#> [3] "striatum" "^c\\.\\s*striatum"
#> [5] "coryno" "diphtheroids?"
#>
#>
#> $patterns[[9]]
#> $patterns[[9]]$original
#> [1] "Corynebacterium jeikeium"
#>
#> $patterns[[9]]$patterns
#> [1] "corynebacterium jeikeium" "^c\\.\\s"
#> [3] "jeikeium" "^c\\.\\s*jeikeium"
#> [5] "coryno" "diphtheroids?"
#>
#>
#> $patterns[[10]]
#> $patterns[[10]]$original
#> [1] "Cutibacterium"
#>
#> $patterns[[10]]$patterns
#> [1] "cutibacterium" "^c\\.\\s" "propioni" "cuti"
#> [5] "p\\.?\\s*acnes"
#>
#>
#> $patterns[[11]]
#> $patterns[[11]]$original
#> [1] "Cutibacterium acnes"
#>
#> $patterns[[11]]$patterns
#> [1] "cutibacterium acnes" "^c\\.\\s" "acnes"
#> [4] "^c\\.\\s*acnes" "propioni" "cuti"
#> [7] "p\\.?\\s*acnes"
#>
#>
#> $patterns[[12]]
#> $patterns[[12]]$original
#> [1] "Micrococcus species"
#>
#> $patterns[[12]]$patterns
#> [1] "micrococcus species" "micrococcus" "^m\\.\\s"
#> [4] "^m\\.\\s*species" "micro"
#>
#>
#> $patterns[[13]]
#> $patterns[[13]]$original
#> [1] "Micrococcus luteus"
#>
#> $patterns[[13]]$patterns
#> [1] "micrococcus luteus" "^m\\.\\s" "luteus"
#> [4] "^m\\.\\s*luteus" "micro"
#>
#>
#> $patterns[[14]]
#> $patterns[[14]]$original
#> [1] "Bacillus (non-anthracis)"
#>
#> $patterns[[14]]$patterns
#> [1] "bacillus (non-anthracis)" "^b\\.\\s"
#> [3] "(non-anthracis)" "^b\\.\\s*(non-anthracis)"
#> [5] "bacil"
#>
#>
#> $patterns[[15]]
#> $patterns[[15]]$original
#> [1] "Bacillus subtilis"
#>
#> $patterns[[15]]$patterns
#> [1] "bacillus subtilis" "^b\\.\\s" "subtilis"
#> [4] "^b\\.\\s*subtilis" "bacil"
#>
#>
#> $patterns[[16]]
#> $patterns[[16]]$original
#> [1] "Bacillus cereus"
#>
#> $patterns[[16]]$patterns
#> [1] "bacillus cereus" "^b\\.\\s" "cereus" "^b\\.\\s*cereus"
#> [5] "bacil"
#>
#>
#> $patterns[[17]]
#> $patterns[[17]]$original
#> [1] "Viridans streptococci"
#>
#> $patterns[[17]]$patterns
#> [1] "viridans streptococci" "^v\\.\\s" "streptococci"
#> [4] "^v\\.\\s*streptococci"
#>
#>
#> $patterns[[18]]
#> $patterns[[18]]$original
#> [1] "Aerococcus spp."
#>
#> $patterns[[18]]$patterns
#> [1] "aerococcus spp." "aerococcus" "^a\\.\\s" "^a\\.\\s*spp."
#>
#>
#> $patterns[[19]]
#> $patterns[[19]]$original
#> [1] "Kocuria spp."
#>
#> $patterns[[19]]$patterns
#> [1] "kocuria spp." "kocuria" "^k\\.\\s" "^k\\.\\s*spp."
#>
#>
#> $patterns[[20]]
#> $patterns[[20]]$original
#> [1] "Dermacoccus spp."
#>
#> $patterns[[20]]$patterns
#> [1] "dermacoccus spp." "dermacoccus" "^d\\.\\s" "^d\\.\\s*spp."
#>
#>
#> $patterns[[21]]
#> $patterns[[21]]$original
#> [1] "Rothia spp."
#>
#> $patterns[[21]]$patterns
#> [1] "rothia spp." "rothia" "^r\\.\\s" "^r\\.\\s*spp."
#>
#>
#>
# Get all contaminants for a specific specimen type
get_contaminant_list(specimen_type = "Blood culture")
#> $names
#> [1] "Coagulase-negative Staphylococcus" "Staphylococcus epidermidis"
#> [3] "Staphylococcus hominis" "Staphylococcus haemolyticus"
#> [5] "Staphylococcus capitis" "Staphylococcus warneri"
#> [7] "Corynebacterium species" "Corynebacterium striatum"
#> [9] "Corynebacterium jeikeium" "Cutibacterium"
#> [11] "Cutibacterium acnes" "Micrococcus species"
#> [13] "Micrococcus luteus" "Bacillus (non-anthracis)"
#> [15] "Bacillus subtilis" "Bacillus cereus"
#> [17] "Viridans streptococci" "Aerococcus spp."
#> [19] "Kocuria spp." "Dermacoccus spp."
#> [21] "Rothia spp."
#>
#> $patterns
#> $patterns[[1]]
#> $patterns[[1]]$original
#> [1] "Coagulase-negative Staphylococcus"
#>
#> $patterns[[1]]$patterns
#> [1] "coagulase-negative staphylococcus" "^c\\.\\s"
#> [3] "^c\\.\\s*staphylococcus"
#>
#>
#> $patterns[[2]]
#> $patterns[[2]]$original
#> [1] "Staphylococcus epidermidis"
#>
#> $patterns[[2]]$patterns
#> [1] "staphylococcus epidermidis" "^s\\.\\s"
#> [3] "epidermidis" "^s\\.\\s*epidermidis"
#> [5] "staph.*epidermidis" "coag.*neg"
#> [7] "coagulase.*negative"
#>
#>
#> $patterns[[3]]
#> $patterns[[3]]$original
#> [1] "Staphylococcus hominis"
#>
#> $patterns[[3]]$patterns
#> [1] "staphylococcus hominis" "^s\\.\\s" "hominis"
#> [4] "^s\\.\\s*hominis" "staph.*hominis" "coag.*neg"
#> [7] "coagulase.*negative"
#>
#>
#> $patterns[[4]]
#> $patterns[[4]]$original
#> [1] "Staphylococcus haemolyticus"
#>
#> $patterns[[4]]$patterns
#> [1] "staphylococcus haemolyticus" "^s\\.\\s"
#> [3] "haemolyticus" "^s\\.\\s*haemolyticus"
#> [5] "staph.*haemolyticus" "coag.*neg"
#> [7] "coagulase.*negative"
#>
#>
#> $patterns[[5]]
#> $patterns[[5]]$original
#> [1] "Staphylococcus capitis"
#>
#> $patterns[[5]]$patterns
#> [1] "staphylococcus capitis" "^s\\.\\s" "capitis"
#> [4] "^s\\.\\s*capitis" "staph.*capitis" "coag.*neg"
#> [7] "coagulase.*negative"
#>
#>
#> $patterns[[6]]
#> $patterns[[6]]$original
#> [1] "Staphylococcus warneri"
#>
#> $patterns[[6]]$patterns
#> [1] "staphylococcus warneri" "^s\\.\\s" "warneri"
#> [4] "^s\\.\\s*warneri" "staph.*warneri" "coag.*neg"
#> [7] "coagulase.*negative"
#>
#>
#> $patterns[[7]]
#> $patterns[[7]]$original
#> [1] "Corynebacterium species"
#>
#> $patterns[[7]]$patterns
#> [1] "corynebacterium species" "corynebacterium"
#> [3] "^c\\.\\s" "^c\\.\\s*species"
#> [5] "coryno" "diphtheroids?"
#>
#>
#> $patterns[[8]]
#> $patterns[[8]]$original
#> [1] "Corynebacterium striatum"
#>
#> $patterns[[8]]$patterns
#> [1] "corynebacterium striatum" "^c\\.\\s"
#> [3] "striatum" "^c\\.\\s*striatum"
#> [5] "coryno" "diphtheroids?"
#>
#>
#> $patterns[[9]]
#> $patterns[[9]]$original
#> [1] "Corynebacterium jeikeium"
#>
#> $patterns[[9]]$patterns
#> [1] "corynebacterium jeikeium" "^c\\.\\s"
#> [3] "jeikeium" "^c\\.\\s*jeikeium"
#> [5] "coryno" "diphtheroids?"
#>
#>
#> $patterns[[10]]
#> $patterns[[10]]$original
#> [1] "Cutibacterium"
#>
#> $patterns[[10]]$patterns
#> [1] "cutibacterium" "^c\\.\\s" "propioni" "cuti"
#> [5] "p\\.?\\s*acnes"
#>
#>
#> $patterns[[11]]
#> $patterns[[11]]$original
#> [1] "Cutibacterium acnes"
#>
#> $patterns[[11]]$patterns
#> [1] "cutibacterium acnes" "^c\\.\\s" "acnes"
#> [4] "^c\\.\\s*acnes" "propioni" "cuti"
#> [7] "p\\.?\\s*acnes"
#>
#>
#> $patterns[[12]]
#> $patterns[[12]]$original
#> [1] "Micrococcus species"
#>
#> $patterns[[12]]$patterns
#> [1] "micrococcus species" "micrococcus" "^m\\.\\s"
#> [4] "^m\\.\\s*species" "micro"
#>
#>
#> $patterns[[13]]
#> $patterns[[13]]$original
#> [1] "Micrococcus luteus"
#>
#> $patterns[[13]]$patterns
#> [1] "micrococcus luteus" "^m\\.\\s" "luteus"
#> [4] "^m\\.\\s*luteus" "micro"
#>
#>
#> $patterns[[14]]
#> $patterns[[14]]$original
#> [1] "Bacillus (non-anthracis)"
#>
#> $patterns[[14]]$patterns
#> [1] "bacillus (non-anthracis)" "^b\\.\\s"
#> [3] "(non-anthracis)" "^b\\.\\s*(non-anthracis)"
#> [5] "bacil"
#>
#>
#> $patterns[[15]]
#> $patterns[[15]]$original
#> [1] "Bacillus subtilis"
#>
#> $patterns[[15]]$patterns
#> [1] "bacillus subtilis" "^b\\.\\s" "subtilis"
#> [4] "^b\\.\\s*subtilis" "bacil"
#>
#>
#> $patterns[[16]]
#> $patterns[[16]]$original
#> [1] "Bacillus cereus"
#>
#> $patterns[[16]]$patterns
#> [1] "bacillus cereus" "^b\\.\\s" "cereus" "^b\\.\\s*cereus"
#> [5] "bacil"
#>
#>
#> $patterns[[17]]
#> $patterns[[17]]$original
#> [1] "Viridans streptococci"
#>
#> $patterns[[17]]$patterns
#> [1] "viridans streptococci" "^v\\.\\s" "streptococci"
#> [4] "^v\\.\\s*streptococci"
#>
#>
#> $patterns[[18]]
#> $patterns[[18]]$original
#> [1] "Aerococcus spp."
#>
#> $patterns[[18]]$patterns
#> [1] "aerococcus spp." "aerococcus" "^a\\.\\s" "^a\\.\\s*spp."
#>
#>
#> $patterns[[19]]
#> $patterns[[19]]$original
#> [1] "Kocuria spp."
#>
#> $patterns[[19]]$patterns
#> [1] "kocuria spp." "kocuria" "^k\\.\\s" "^k\\.\\s*spp."
#>
#>
#> $patterns[[20]]
#> $patterns[[20]]$original
#> [1] "Dermacoccus spp."
#>
#> $patterns[[20]]$patterns
#> [1] "dermacoccus spp." "dermacoccus" "^d\\.\\s" "^d\\.\\s*spp."
#>
#>
#> $patterns[[21]]
#> $patterns[[21]]$original
#> [1] "Rothia spp."
#>
#> $patterns[[21]]$patterns
#> [1] "rothia spp." "rothia" "^r\\.\\s" "^r\\.\\s*spp."
#>
#>
#>
# Get all contaminants across all syndromes
get_contaminant_list(return_all = TRUE)
#> $names
#> [1] "Coagulase-negative Staphylococcus"
#> [2] "Staphylococcus epidermidis"
#> [3] "Staphylococcus hominis"
#> [4] "Staphylococcus haemolyticus"
#> [5] "Staphylococcus capitis"
#> [6] "Staphylococcus warneri"
#> [7] "Corynebacterium species"
#> [8] "Corynebacterium striatum"
#> [9] "Corynebacterium jeikeium"
#> [10] "Cutibacterium"
#> [11] "Cutibacterium acnes"
#> [12] "Micrococcus species"
#> [13] "Micrococcus luteus"
#> [14] "Bacillus (non-anthracis)"
#> [15] "Bacillus subtilis"
#> [16] "Bacillus cereus"
#> [17] "Viridans streptococci"
#> [18] "Aerococcus spp."
#> [19] "Kocuria spp."
#> [20] "Dermacoccus spp."
#> [21] "Rothia spp."
#> [22] "Same as blood (skin flora contamination during needle insertion)"
#> [23] "Viridans group streptococci"
#> [24] "Non-pathogenic Neisseria spp."
#> [25] "Haemophilus parainfluenzae"
#> [26] "Anaerobic oral flora (Prevotella, Porphyromonas, Fusobacterium)"
#> [27] "Actinomyces spp."
#> [28] "Same as blood"
#> [29] "Corynebacterium species (diphtheroids)"
#> [30] "Cutibacterium (Propionibacterium) acnes"
#> [31] "Bacillus species"
#> [32] "Bacteroides-Prevotella group"
#> [33] "Eubacterium"
#> [34] "Lactobacillus"
#> [35] "Faecalibacterium"
#> [36] "Lactobacillus species"
#> [37] "Coagulase-negative Staphylococcus (Staphylococcus epidermidis, Staphylococcus saprophyticus)"
#> [38] "Coagulase-negative Staphylococcus (Staphylococcus epidermidis, Staphylococcus hominis, Staphylococcus haemolyticus, Staphylococcus capitis)"
#> [39] "Neisseria spp. (non-pathogenic)"
#> [40] "Haemophilus spp."
#> [41] "Moraxella catarrhalis"
#> [42] "No typical commensals (growth usually clinically significant)"
#>
#> $patterns
#> $patterns[[1]]
#> $patterns[[1]]$original
#> [1] "Coagulase-negative Staphylococcus"
#>
#> $patterns[[1]]$patterns
#> [1] "coagulase-negative staphylococcus" "^c\\.\\s"
#> [3] "^c\\.\\s*staphylococcus"
#>
#>
#> $patterns[[2]]
#> $patterns[[2]]$original
#> [1] "Staphylococcus epidermidis"
#>
#> $patterns[[2]]$patterns
#> [1] "staphylococcus epidermidis" "^s\\.\\s"
#> [3] "epidermidis" "^s\\.\\s*epidermidis"
#> [5] "staph.*epidermidis" "coag.*neg"
#> [7] "coagulase.*negative"
#>
#>
#> $patterns[[3]]
#> $patterns[[3]]$original
#> [1] "Staphylococcus hominis"
#>
#> $patterns[[3]]$patterns
#> [1] "staphylococcus hominis" "^s\\.\\s" "hominis"
#> [4] "^s\\.\\s*hominis" "staph.*hominis" "coag.*neg"
#> [7] "coagulase.*negative"
#>
#>
#> $patterns[[4]]
#> $patterns[[4]]$original
#> [1] "Staphylococcus haemolyticus"
#>
#> $patterns[[4]]$patterns
#> [1] "staphylococcus haemolyticus" "^s\\.\\s"
#> [3] "haemolyticus" "^s\\.\\s*haemolyticus"
#> [5] "staph.*haemolyticus" "coag.*neg"
#> [7] "coagulase.*negative"
#>
#>
#> $patterns[[5]]
#> $patterns[[5]]$original
#> [1] "Staphylococcus capitis"
#>
#> $patterns[[5]]$patterns
#> [1] "staphylococcus capitis" "^s\\.\\s" "capitis"
#> [4] "^s\\.\\s*capitis" "staph.*capitis" "coag.*neg"
#> [7] "coagulase.*negative"
#>
#>
#> $patterns[[6]]
#> $patterns[[6]]$original
#> [1] "Staphylococcus warneri"
#>
#> $patterns[[6]]$patterns
#> [1] "staphylococcus warneri" "^s\\.\\s" "warneri"
#> [4] "^s\\.\\s*warneri" "staph.*warneri" "coag.*neg"
#> [7] "coagulase.*negative"
#>
#>
#> $patterns[[7]]
#> $patterns[[7]]$original
#> [1] "Corynebacterium species"
#>
#> $patterns[[7]]$patterns
#> [1] "corynebacterium species" "corynebacterium"
#> [3] "^c\\.\\s" "^c\\.\\s*species"
#> [5] "coryno" "diphtheroids?"
#>
#>
#> $patterns[[8]]
#> $patterns[[8]]$original
#> [1] "Corynebacterium striatum"
#>
#> $patterns[[8]]$patterns
#> [1] "corynebacterium striatum" "^c\\.\\s"
#> [3] "striatum" "^c\\.\\s*striatum"
#> [5] "coryno" "diphtheroids?"
#>
#>
#> $patterns[[9]]
#> $patterns[[9]]$original
#> [1] "Corynebacterium jeikeium"
#>
#> $patterns[[9]]$patterns
#> [1] "corynebacterium jeikeium" "^c\\.\\s"
#> [3] "jeikeium" "^c\\.\\s*jeikeium"
#> [5] "coryno" "diphtheroids?"
#>
#>
#> $patterns[[10]]
#> $patterns[[10]]$original
#> [1] "Cutibacterium"
#>
#> $patterns[[10]]$patterns
#> [1] "cutibacterium" "^c\\.\\s" "propioni" "cuti"
#> [5] "p\\.?\\s*acnes"
#>
#>
#> $patterns[[11]]
#> $patterns[[11]]$original
#> [1] "Cutibacterium acnes"
#>
#> $patterns[[11]]$patterns
#> [1] "cutibacterium acnes" "^c\\.\\s" "acnes"
#> [4] "^c\\.\\s*acnes" "propioni" "cuti"
#> [7] "p\\.?\\s*acnes"
#>
#>
#> $patterns[[12]]
#> $patterns[[12]]$original
#> [1] "Micrococcus species"
#>
#> $patterns[[12]]$patterns
#> [1] "micrococcus species" "micrococcus" "^m\\.\\s"
#> [4] "^m\\.\\s*species" "micro"
#>
#>
#> $patterns[[13]]
#> $patterns[[13]]$original
#> [1] "Micrococcus luteus"
#>
#> $patterns[[13]]$patterns
#> [1] "micrococcus luteus" "^m\\.\\s" "luteus"
#> [4] "^m\\.\\s*luteus" "micro"
#>
#>
#> $patterns[[14]]
#> $patterns[[14]]$original
#> [1] "Bacillus (non-anthracis)"
#>
#> $patterns[[14]]$patterns
#> [1] "bacillus (non-anthracis)" "^b\\.\\s"
#> [3] "(non-anthracis)" "^b\\.\\s*(non-anthracis)"
#> [5] "bacil"
#>
#>
#> $patterns[[15]]
#> $patterns[[15]]$original
#> [1] "Bacillus subtilis"
#>
#> $patterns[[15]]$patterns
#> [1] "bacillus subtilis" "^b\\.\\s" "subtilis"
#> [4] "^b\\.\\s*subtilis" "bacil"
#>
#>
#> $patterns[[16]]
#> $patterns[[16]]$original
#> [1] "Bacillus cereus"
#>
#> $patterns[[16]]$patterns
#> [1] "bacillus cereus" "^b\\.\\s" "cereus" "^b\\.\\s*cereus"
#> [5] "bacil"
#>
#>
#> $patterns[[17]]
#> $patterns[[17]]$original
#> [1] "Viridans streptococci"
#>
#> $patterns[[17]]$patterns
#> [1] "viridans streptococci" "^v\\.\\s" "streptococci"
#> [4] "^v\\.\\s*streptococci"
#>
#>
#> $patterns[[18]]
#> $patterns[[18]]$original
#> [1] "Aerococcus spp."
#>
#> $patterns[[18]]$patterns
#> [1] "aerococcus spp." "aerococcus" "^a\\.\\s" "^a\\.\\s*spp."
#>
#>
#> $patterns[[19]]
#> $patterns[[19]]$original
#> [1] "Kocuria spp."
#>
#> $patterns[[19]]$patterns
#> [1] "kocuria spp." "kocuria" "^k\\.\\s" "^k\\.\\s*spp."
#>
#>
#> $patterns[[20]]
#> $patterns[[20]]$original
#> [1] "Dermacoccus spp."
#>
#> $patterns[[20]]$patterns
#> [1] "dermacoccus spp." "dermacoccus" "^d\\.\\s" "^d\\.\\s*spp."
#>
#>
#> $patterns[[21]]
#> $patterns[[21]]$original
#> [1] "Rothia spp."
#>
#> $patterns[[21]]$patterns
#> [1] "rothia spp." "rothia" "^r\\.\\s" "^r\\.\\s*spp."
#>
#>
#> $patterns[[22]]
#> $patterns[[22]]$original
#> [1] "Same as blood (skin flora contamination during needle insertion)"
#>
#> $patterns[[22]]$patterns
#> [1] "same as blood (skin flora contamination during needle insertion)"
#> [2] "^s\\.\\s"
#> [3] "as"
#> [4] "^s\\.\\s*as"
#> [5] "same as"
#>
#>
#> $patterns[[23]]
#> $patterns[[23]]$original
#> [1] "Viridans group streptococci"
#>
#> $patterns[[23]]$patterns
#> [1] "viridans group streptococci" "^v\\.\\s"
#> [3] "group" "^v\\.\\s*group"
#> [5] "viridans group"
#>
#>
#> $patterns[[24]]
#> $patterns[[24]]$original
#> [1] "Non-pathogenic Neisseria spp."
#>
#> $patterns[[24]]$patterns
#> [1] "non-pathogenic neisseria spp." "^n\\.\\s"
#> [3] "^n\\.\\s*neisseria" "non-pathogenic neisseria"
#>
#>
#> $patterns[[25]]
#> $patterns[[25]]$original
#> [1] "Haemophilus parainfluenzae"
#>
#> $patterns[[25]]$patterns
#> [1] "haemophilus parainfluenzae" "^h\\.\\s"
#> [3] "parainfluenzae" "^h\\.\\s*parainfluenzae"
#>
#>
#> $patterns[[26]]
#> $patterns[[26]]$original
#> [1] "Anaerobic oral flora (Prevotella, Porphyromonas, Fusobacterium)"
#>
#> $patterns[[26]]$patterns
#> [1] "anaerobic oral flora (prevotella, porphyromonas, fusobacterium)"
#> [2] "^a\\.\\s"
#> [3] "oral"
#> [4] "^a\\.\\s*oral"
#> [5] "anaerobic oral"
#>
#>
#> $patterns[[27]]
#> $patterns[[27]]$original
#> [1] "Actinomyces spp."
#>
#> $patterns[[27]]$patterns
#> [1] "actinomyces spp." "actinomyces" "^a\\.\\s" "^a\\.\\s*spp."
#>
#>
#> $patterns[[28]]
#> $patterns[[28]]$original
#> [1] "Same as blood"
#>
#> $patterns[[28]]$patterns
#> [1] "same as blood" "^s\\.\\s" "as" "^s\\.\\s*as"
#> [5] "same as"
#>
#>
#> $patterns[[29]]
#> $patterns[[29]]$original
#> [1] "Corynebacterium species (diphtheroids)"
#>
#> $patterns[[29]]$patterns
#> [1] "corynebacterium species (diphtheroids)"
#> [2] "corynebacterium"
#> [3] "^c\\.\\s"
#> [4] "^c\\.\\s*species"
#> [5] "corynebacterium species"
#> [6] "coryno"
#> [7] "diphtheroids?"
#>
#>
#> $patterns[[30]]
#> $patterns[[30]]$original
#> [1] "Cutibacterium (Propionibacterium) acnes"
#>
#> $patterns[[30]]$patterns
#> [1] "cutibacterium (propionibacterium) acnes"
#> [2] "^c\\.\\s"
#> [3] "(propionibacterium)"
#> [4] "^c\\.\\s*(propionibacterium)"
#> [5] "cutibacterium (propionibacterium)"
#> [6] "propioni"
#> [7] "cuti"
#> [8] "p\\.?\\s*acnes"
#>
#>
#> $patterns[[31]]
#> $patterns[[31]]$original
#> [1] "Bacillus species"
#>
#> $patterns[[31]]$patterns
#> [1] "bacillus species" "bacillus" "^b\\.\\s" "^b\\.\\s*species"
#> [5] "bacil"
#>
#>
#> $patterns[[32]]
#> $patterns[[32]]$original
#> [1] "Bacteroides-Prevotella group"
#>
#> $patterns[[32]]$patterns
#> [1] "bacteroides-prevotella group" "^b\\.\\s"
#> [3] "^b\\.\\s*group"
#>
#>
#> $patterns[[33]]
#> $patterns[[33]]$original
#> [1] "Eubacterium"
#>
#> $patterns[[33]]$patterns
#> [1] "eubacterium" "^e\\.\\s"
#>
#>
#> $patterns[[34]]
#> $patterns[[34]]$original
#> [1] "Lactobacillus"
#>
#> $patterns[[34]]$patterns
#> [1] "lactobacillus" "^l\\.\\s" "bacil" "lacto"
#>
#>
#> $patterns[[35]]
#> $patterns[[35]]$original
#> [1] "Faecalibacterium"
#>
#> $patterns[[35]]$patterns
#> [1] "faecalibacterium" "^f\\.\\s"
#>
#>
#> $patterns[[36]]
#> $patterns[[36]]$original
#> [1] "Lactobacillus species"
#>
#> $patterns[[36]]$patterns
#> [1] "lactobacillus species" "lactobacillus" "^l\\.\\s"
#> [4] "^l\\.\\s*species" "bacil" "lacto"
#>
#>
#> $patterns[[37]]
#> $patterns[[37]]$original
#> [1] "Coagulase-negative Staphylococcus (Staphylococcus epidermidis, Staphylococcus saprophyticus)"
#>
#> $patterns[[37]]$patterns
#> [1] "coagulase-negative staphylococcus (staphylococcus epidermidis, staphylococcus saprophyticus)"
#> [2] "^c\\.\\s"
#> [3] "^c\\.\\s*staphylococcus"
#> [4] "coagulase-negative staphylococcus"
#>
#>
#> $patterns[[38]]
#> $patterns[[38]]$original
#> [1] "Coagulase-negative Staphylococcus (Staphylococcus epidermidis, Staphylococcus hominis, Staphylococcus haemolyticus, Staphylococcus capitis)"
#>
#> $patterns[[38]]$patterns
#> [1] "coagulase-negative staphylococcus (staphylococcus epidermidis, staphylococcus hominis, staphylococcus haemolyticus, staphylococcus capitis)"
#> [2] "^c\\.\\s"
#> [3] "^c\\.\\s*staphylococcus"
#> [4] "coagulase-negative staphylococcus"
#>
#>
#> $patterns[[39]]
#> $patterns[[39]]$original
#> [1] "Neisseria spp. (non-pathogenic)"
#>
#> $patterns[[39]]$patterns
#> [1] "neisseria spp. (non-pathogenic)" "neisseria"
#> [3] "^n\\.\\s" "^n\\.\\s*spp."
#> [5] "neisseria spp."
#>
#>
#> $patterns[[40]]
#> $patterns[[40]]$original
#> [1] "Haemophilus spp."
#>
#> $patterns[[40]]$patterns
#> [1] "haemophilus spp." "haemophilus" "^h\\.\\s" "^h\\.\\s*spp."
#>
#>
#> $patterns[[41]]
#> $patterns[[41]]$original
#> [1] "Moraxella catarrhalis"
#>
#> $patterns[[41]]$patterns
#> [1] "moraxella catarrhalis" "^m\\.\\s" "catarrhalis"
#> [4] "^m\\.\\s*catarrhalis"
#>
#>
#> $patterns[[42]]
#> $patterns[[42]]$original
#> [1] "No typical commensals (growth usually clinically significant)"
#>
#> $patterns[[42]]$patterns
#> [1] "no typical commensals (growth usually clinically significant)"
#> [2] "^n\\.\\s"
#> [3] "typical"
#> [4] "^n\\.\\s*typical"
#> [5] "no typical"
#>
#>
#>