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Extended Respiratory Viral / Acute Rhinosinusitis

Specimen Types:

Nasopharyngeal/Nares, Oropharynx/Throat/Oral, Cough Sputum

Common Signs + Symptoms:

Acute upper respiratory tract infection, high-grade fever, acute cough, runny nose, pain in throat, wheezing, or nasal congestion.

Viral:

• Adenovirus
• Coronaviruses (229E, HKU1, NL63, & OC43)
• COVID-19 Coronavirus (SARS-CoV-2)
• Enterovirus D68
• Human metapneumovirus
• Influenza virus A, B
• Parainfluenza virus (types 1, 2, 3, 4)
• Respiratory syncytial virus
• Rhinovirus/Enterovirus

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Treatable Respiratory Viruses

Specimen Types:

Nasopharyngeal/Nares, Oropharynx/Throat/Oral, Cough Sputum

Common Signs + Symptoms:

Acute upper respiratory tract Infection, high-grade fever, cough, runny nose, pain in throat, wheezing, nasal congestion, shortness of breath, malaise.

Viral:

• COVID-19 Coronavirus (SARS-CoV-2)
• Influenza virus A, B
• Respiratory syncytial virus

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Pharyngitis / Laryngitis

Specimen Types:

Oropharynx/Throat/Oral

Common Signs + Symptoms:

Pain in throat, fever, pharyngeal edema, patchy tonsillar exudates, and tender/swollen anterior cervical lymph nodes.

Bacterial:

• Chlamydia pneumoniae
• Fusobacterium nucleatum, necrophorum
• Mycoplasma pneumoniae
• Streptococcus dysgalactiae (Group C & G Strep)
• Streptococcus pyogenes (Group A Strep)

Viral:

• Adenovirus
• Coronaviruses (229E, HKU1, NL63, & OC43)
• COVID-19 Coronavirus (SARS-CoV-2)
• Enterovirus D68
• Human metapneumovirus
• Influenza virus A, B
• Parainfluenza virus (types 1, 2, 3, 4)
• Respiratory syncytial virus
• Rhinovirus/Enterovirus

Resistance:

• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• tet B, tet M

ADD-ON:

Epstein-Barr Virus (Human Herpesvirus 4, EBV), Herpes simplex virus 1, Herpes simplex virus 2

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Bronchitis

Specimen Types:

Nasopharyngeal/Nares, Oropharynx/Throat/Oral, Cough Sputum

Common Signs + Symptoms:

Upper or lower respiratory tract infection, including cough, moderate temperature elevation, and mucopurulent sputum.

Bacterial:

• Haemophilus influenzae
• Moraxella catarrhalis
• Streptococcus pneumoniae

Atypical Bacteria:

• Bordetella pertussis, parapertussis, bronchiseptica
• Chlamydia pneumoniae
• Mycoplasma pneumoniae

Viral:

• Adenovirus
• Coronaviruses (229E, HKU1, NL63, & OC43)
• COVID-19 Coronavirus (SARS-CoV-2)
• Enterovirus D68
• Human metapneumovirus
• Influenza virus A, B
• Parainfluenza virus (types 1, 2, 3, 4)
• Respiratory syncytial virus
• Rhinovirus/Enterovirus

Resistance:

• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• tet B, tet M

ADD-ON:

Epstein-Barr Virus (Human Herpesvirus 4, EBV)

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Pneumonia

Specimen Types:

Cough Sputum, Oropharynx/Throat/Oral, Nasopharyngeal/Nares

Common Signs + Symptoms:

Lower respiratory tract infection, high-grade fever, dyspnea, cough, sputum production, or hypoxia & chest x-ray opacity.

Bacterial:

• Acinetobacter baumannii
• Enterobacter cloacae complex, Klebsiella (Enterobacter) aerogenes
• Escherichia coli
• Haemophilus influenzae
• Klebsiella pneumoniae, oxytoca
• Moraxella catarrhalis
• Proteus mirabilis, vulgaris
• Pseudomonas aeruginosa
• Serratia marcescens
• Staphylococcus aureus
• Streptococcus agalactiae (Group B Strep)
• Streptococcus pneumoniae
• Streptococcus pyogenes (Group A Strep)

Atypical Bacteria:

• Bordetella pertussis, parapertussis, bronchiseptica
• Chlamydia pneumoniae
• Legionella pneumophila
• Mycoplasma pneumoniae

Viral:

• Adenovirus
• Coronaviruses (229E, HKU1, NL63, & OC43)
• COVID-19 Coronavirus (SARS-CoV-2)
• Enterovirus D68
• Human metapneumovirus
• Influenza virus A, B
• Parainfluenza virus (types 1, 2, 3, 4)
• Respiratory syncytial virus
• Rhinovirus/Enterovirus

Resistance:

• ACT, MIR, FOX, ACC Groups
• CTX-M1 (15), M2 (2), M9 (9), M8/25 Groups
• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• IMP, NDM, VIM Groups
• mecA
• OXA-48, OXA-51
• qnrA1, A2, B2
• SHV, KPC Groups
• tet B, tet M

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Acute Otitis Media / Mastoiditis

Specimen Types:

Ear, Nasopharyngeal/Nares

Common Signs + Symptoms:

Otitis media, ear pain, decreased or muffled hearing, bulging ear drum, drainage from ear, mastoiditis, redness or swelling behind ear lobe, fever, headache, or hearing loss.

Bacterial:

• Enterobacter cloacae complex, Klebsiella (Enterobacter) aerogenes
• Fusobacterium nucleatum, necrophorum
• Haemophilus influenzae
• Klebsiella pneumoniae, oxytoca
• Moraxella catarrhalis
• Mycoplasma pneumoniae
• Proteus mirabilis, vulgaris
• Pseudomonas aeruginosa
• Staphylococcus aureus
• Streptococcus pneumoniae
• Streptococcus pyogenes (Group A Strep)

Viral:

• Adenovirus
• Coronaviruses (229E, HKU1, NL63, & OC43)
• COVID-19 Coronavirus (SARS-CoV-2)
• Enterovirus D68
• Human metapneumovirus
• Influenza virus A, B
• Parainfluenza virus (types 1, 2, 3, 4)
• Respiratory syncytial virus
• Rhinovirus/Enterovirus

Resistance:

• ACT, MIR, FOX, ACC Groups
• CTX-M1 (15), M2 (2), M9 (9), M8/25 Groups
• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• IMP, NDM, VIM Groups
• mecA
• OXA-48, OXA-51
• qnrA1, A2, B2
• SHV, KPC Groups
• tet B, tet M

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Ophthalmology

Specimen Types:

Eye (external)

Common Signs + Symptoms:

Eye pain, eye redness, blurred vision, sensitivity to light, excessive tearing, and/or eye discharge.

Bacterial:

• Acinetobacter baumannii
• Chlamydia trachomatis
• Citrobacter freundii
• Cutibacterium (Propionibacterium) acnes
• Enterobacter cloacae complex, Klebsiella (Enterobacter) aerogenes
• Enterococcus faecalis, faecium
• Escherichia coli
• Fusarium oxysporum, Neocosmospora solani
• Haemophilus influenzae
• Klebsiella pneumoniae, oxytoca
• Moraxella catarrhalis
• Neisseria gonorrhoeae
• Proteus mirabilis, vulgaris
• Pseudomonas aeruginosa
• Staphylococcus aureus
• Streptococcus agalactiae (Group B Strep)
• Streptococcus pneumoniae
• Streptococcus pyogenes (Group A Strep)

Viral:

• Adenovirus
• Cytomegalovirus (Human Herpesvirus 5, CMV)
• Enterovirus (pan)
• Epstein-Barr virus (Human Herpesvirus 4, EBV)
• Herpes simplex virus 1, 2
• Varicella zoster virus (Human Herpesvirus 3, VZV)

Protozoal:

• Acanthamoeba castellani, polyphaga; Vermamoeba (Hartmannella) vermiformis
• Microsporidia (Encephalitozoon hellum, cuniculi, Nosema (Vittaforma) ocularum)

Fungal:

• Aspergillus flavus, fumigatus, niger, terreus
• Candida albicans, glabrata, parapsilosis, tropicalis
• Fusarium oxysporum, Neocosmospora solani

Resistance:

• ACT, MIR, FOX, ACC Groups
• CTX-M1 (15), M2 (2), M9 (9), M8/25 Groups
• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• IMP, NDM, VIM Groups
• mecA
• OXA-48, OXA-51
• qnrA1, A2, B2
• SHV, KPC Groups
• tet B, tet M
• VanA, VanB

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Otolaryngology

Specimen Types:

Nasopharyngeal/Nares, Oropharynx/Throat/Oral, Ear, Sino-Nasal

Common Signs + Symptoms:

Chronic or complicated ear, nose, or throat infection.

Bacterial:

• Cutibacterium (Propionibacterium) acnes
• Enterobacter cloacae complex, Klebsiella (Enterobacter) aerogenes
• Enterococcus faecalis, faecium
• Escherichia coli
• Fusobacterium nucleatum, necrophorum
• Haemophilus influenzae
• Klebsiella pneumoniae, oxytoca
• Moraxella catarrhalis
• Proteus mirabilis, vulgaris
• Pseudomonas aeruginosa
• Staphylococcus aureus
• Streptococcus agalactiae (Group B Strep)
• Streptococcus pneumoniae
• Streptococcus pyogenes (Group A Strep)

Viral:

• Adenovirus
• Cytomegalovirus (Human Herpesvirus 5, CMV)
• Enterovirus (pan)
• Epstein-Barr Virus (Human Herpesvirus 4, EBV)
• Herpes simplex virus 1, 2
• Varicella zoster virus (Human Herpesvirus 3, VZV)

Fungal:

• Aspergillus flavus, fumigatus, niger, terreus
• Candida albicans, glabrata, parapsilosis, tropicalis
• Fusarium oxysporum, Neocosmospora solani

Resistance:

• ACT, MIR, FOX, ACC Groups
• CTX-M1 (15), M2 (2), M9 (9), M8/25 Groups
• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• IMP, NDM, VIM Groups
• mecA
• OXA-48, OXA-51
• qnrA1, A2, B2
• SHV, KPC Groups
• tet B, tet M
• VanA, VanB

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Superficial Wound

Specimen Types:

Wound Swabs (all locations)

Common Signs + Symptoms:

Recent wound from trauma with erythema, edema, heat, purulent exudate, and/or pain

Bacterial:

• Acinetobacter baumannii
• Bacteroides fragilis, Phocaeicola vulgatus
• Citrobacter freundii
• Clostridium perfringens, novyi, septicum
• Enterobacter cloacae complex, Klebsiella (Enterobacter) aerogenes
• Enterococcus faecalis, faecium
• Escherichia coli
• Klebsiella pneumoniae, oxytoca
• Proteus mirabilis, vulgaris
• Pseudomonas aeruginosa
• Serratia marcescens
• Staphylococcus aureus
• Streptococcus agalactiae (Group B Strep)
• Streptococcus pyogenes (Group A Strep)
• Vibrio cholerae, parahaemolyticus, vulnificus

Resistance:

• ACT, MIR, FOX, ACC Groups
• CTX-M1 (15), M2 (2), M9 (9), M8/25 Groups
• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• IMP, NDM, VIM Groups
• mecA
• OXA-48, OXA-51
• qnrA1, A2, B2
• SHV, KPC Groups
• tet B, tet M
• VanA, VanB

ADD-ON:

Mpox (Monkeypox), Herpes simplex virus 1, Herpes simplex virus 2, Varicella zoster virus (Human Herpesvirus 3, VZV)

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Deep/Non-Healing Wound

Specimen Types:

Wound Swabs (all locations)

Common Signs + Symptoms:

Diabetic ulcer, tunneling wound, skin erythema, edema, warmth, abscess, or cellulitis

Bacterial:

• Acinetobacter baumannii
• Bacteroides fragilis, Phocaeicola vulgatus
• Citrobacter freundii
• Clostridium perfringens, novyi, septicum
• Corynebacterium jeikeium, striatum, tuberculostearicum
• Cutibacterium (Propionibacterium) acnes
• Enterobacter cloacae complex, Klebsiella (Enterobacter) aerogenes
• Enterococcus faecalis, faecium
• Escherichia coli
• Klebsiella pneumoniae, oxytoca
• Peptostreptococcus anaerobius, Peptoniphilus asaccharolyticus, Finegoldia magna, Anaerococcus prevotii
• Proteus mirabilis, vulgaris
• Pseudomonas aeruginosa
• Serratia marcescens
• Staphylococcus aureus
• Staphylococcus epidermidis, haemolyticus, lugdunensis, saprophyticus
• Streptococcus agalactiae (Group B Strep)
• Streptococcus pyogenes (Group A Strep)
• Vibrio cholerae, parahaemolyticus, vulnificus

Viral:

• Herpes simplex virus 1
• Herpes simplex virus 2
• Varicella zoster virus (Human Herpesvirus 3, VZV)

Resistance:

• ACT, MIR, FOX, ACC Groups
• CTX-M1 (15), M2 (2), M9 (9), M8/25 Groups
• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• IMP, NDM, VIM Groups
• mecA
• OXA-48, OXA-51
• qnrA1, A2, B2
• SHV, KPC Groups
• tet B, tet M
• VanA, VanB

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Tinea

Specimen Types:

Wound Swabs (all locations)

Common Signs + Symptoms:

Scaly ring-shaped area, itchiness, scaly skin, or noninflamed dermatosis on the body or hair follicle (tinea capitis or tinea barbae)

Fungal:

• Candida albicans, glabrata, parapsilosis, tropicalis
• Epidermophyton floccosum
• Malassezia furfur, restricta, sympodialis, globosa
• Microsporum audouinii, canis; Nannizzia gypseum
• Trichophyton mentagrophytes/interdigitale, rubrum, tonsurans, violaceum

ADD-ON:

Candida auris

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Urinary Tract Infection

Specimen Types:

Urine (voided), Urine (catheter), Internal Urethra

Common Signs + Symptoms:

Dysuria, hematuria, urgency of urination, frequency of micturition, or pain of micturition

Bacterial:

• Acinetobacter baumannii
• Citrobacter freundii
• Enterobacter cloacae complex, Klebsiella (Enterobacter) aerogenes
• Enterococcus faecalis, faecium
• Escherichia coli
• Klebsiella pneumoniae, oxytoca
• Morganella morganii
• Proteus mirabilis, vulgaris
• Pseudomonas aeruginosa
• Serratia marcescens
• Staphylococcus aureus
• Staphylococcus epidermidis, haemolyticus, lugdunensis
• Staphylococcus saprophyticus
• Streptococcus agalactiae (Group B Strep)
• Streptococcus pyogenes (Group A Strep)

Fungal:

• Candida albicans, parapsilosis, tropicalis
• Candida glabrata (Nakaseomyces glabratus)
• Candida krusei (Pichia kudriavzevii)

Resistance:

• ACT, MIR, FOX, ACC Groups
• CTX-M1 (15), M2 (2), M9 (9), M8/25 Groups
• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• IMP, NDM, VIM Groups
• mecA
• OXA-48, OXA-51
• qnrA1, A2, B2
• SHV, KPC Groups
• tet B, tet M
• VanA, VanB

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Urinary Tract Infection + High Risk Sexual Behavior

Specimen Types:

Urine (voided), Urine (catheter), Internal Urethra

Common Signs + Symptoms:

Dysuria, hematuria, urgency of urination, frequency of micturition, pain of micturition, and high risk sexual behavior

Bacterial:

• Acinetobacter baumannii
• Chlamydia trachomatis
• Citrobacter freundii
• Enterobacter cloacae complex, Klebsiella (Enterobacter) aerogenes
• Enterococcus faecalis, faecium
• Escherichia coli
• Klebsiella pneumoniae, oxytoca
• Morganella morganii
• Mycoplasma genitalium
• Mycoplasma hominis
• Neisseria gonorrhoeae
• Proteus mirabilis, vulgaris
• Pseudomonas aeruginosa
• Serratia marcescens
• Staphylococcus aureus
• Staphylococcus epidermidis, haemolyticus, lugdunensis
• Staphylococcus saprophyticus
• Streptococcus agalactiae (Group B Strep)
• Streptococcus pyogenes (Group A Strep)
• Ureaplasma urealyticum
• Ureaplasma parvum

Protozoal:

• Trichomonas vaginalis

Fungal:

• Candida albicans, parapsilosis, tropicalis
• Candida glabrata (Nakaseomyces glabratus)
• Candida krusei (Pichia kudriavzevii)

Resistance:

• ACT, MIR, FOX, ACC Groups
• CTX-M1 (15), M2 (2), M9 (9), M8/25 Groups
• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• IMP, NDM, VIM Groups
• mecA
• OXA-48, OXA-51
• qnrA1, A2, B2
• SHV, KPC Groups
• tet B, tet M
• VanA, VanB

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Onychomycosis

Specimen Types:

Nail (toe), Nail (finger)

Common Signs + Symptoms:

Skin disorder presenting with nail discoloration (yellow, white, or brown), dystrophy (deformed), thickening, onycholysis (separation from nail bed)

Bacterial:

• Pseudomonas aeruginosa

Fungal:

• Aspergillus flavus, fumigatus, niger, terreus
• Candida albicans, glabrata, parapsilosis, tropicalis
• Cutaneotrichosporon mucoides, Trichosporon asahii
• Epidermophyton floccosum
• Fusarium oxysporum, Neocosmospora solani
• Malassezia furfur, restricta, sympodialis, globosa
• Microsporum audouinii, canis; Nannizzia gypseum
• Trichophyton mentagrophytes/interdigitale, rubrum, tonsurans, violaceum

Resistance:

• ACT, MIR, FOX, ACC Groups
• CTX-M1 (15), M2 (2), M9 (9), M8/25 Groups
• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• IMP, NDM, VIM Groups
• OXA-48, OXA-51
• qnrA1, A2, B2
• SHV, KPC Groups
• tet B, tet M

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Diarrheal Disease

Specimen Types:

Rectal (fecal), Stool

Common Signs + Symptoms:

Community-acquired diarrhea, pt has significant fever + bloody stools, <7 days of symptoms. Concern of parasitic infection if patient has symptoms >14 days.

Bacterial:

• Campylobacter coli, jejuni, upsaliensis
• Clostridioides difficile (toxins A, B)
• Clostridium perfringens
• Enteroinvasive E. coli (EIEC) / Shigella spp.
• Salmonella
• Shiga toxin producing E. coli (STEC)
• Shiga toxin producing E. coli O157 (STEC O157)
• Vibrio cholerae, parahaemolyticus, vulnificus
• Yersinia enterocolitica

Viral:

• Norovirus (Genogroup 1, 2)
• Rotavirus A, B, C

Resistance:

• ACT, MIR, FOX, ACC Groups
• CTX-M1 (15), M2 (2), M9 (9), M8/25 Groups
• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• IMP, NDM, VIM Groups
• OXA-48, OXA-51
• qnrA1, A2, B2
• SHV, KPC Groups
• tet B, tet M
• VanA, VanB

ADD-ON:

(ALL PARASITES: GSTROAO) Cryptosporidium, Cyclospora cayetanensis, Dientamoeba fragilis, Entamoeba histolytica, Giardia lamblia (intestinalis), Microsporidium (Enterocytozoon bienusi, Encephalitozoon intestinalis)

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Traveler's Diarrheal Disease

Specimen Types:

Rectal (fecal), Stool

Common Signs + Symptoms:

Traveler's diarrhea, pt has significant fever + bloody stools, <7 days of symptoms. Concern of parasitic infection if patient has symptoms >14 days.

Bacterial:

• Campylobacter coli, jejuni, upsaliensis
• Enteroaggregative E. coli (EAEC)
• Enteroinvasive E. coli (EIEC) / Shigella spp.
• Enteropathogenic E. coli (EPEC)
• Enterotoxigenic E. coli (ETEC)
• Salmonella
• Shiga toxin producing E. coli (STEC)
• Shiga toxin producing E. coli O157 (STEC O157)

Viral:

• Adenovirus F40/41
• Norovirus (Genogroup 1, 2)
• Rotavirus A, B, C

Resistance:

• ACT, MIR, FOX, ACC Groups
• CTX-M1 (15), M2 (2), M9 (9), M8/25 Groups
• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• IMP, NDM, VIM Groups
• OXA-48, OXA-51
• qnrA1, A2, B2
• SHV, KPC Groups
• tet B, tet M

ADD-ON:

(ALL PARASITES: GSTRPAO) Cryptosporidium, Cyclospora cayetanensis, Dientamoeba fragilis, Entamoeba histolytica, Giardia lamblia (intestinalis), Microsporidium (Enterocytozoon bienusi, Encephalitozoon intestinalis)

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Pediatric Diarrheal Disease

Specimen Types:

Rectal (fecal), Stool

Common Signs + Symptoms:

Community-acquired pediatric diarrhea, pt has significant fever + bloody stools, <7 days of symptoms. Concern of parasitic infection if patient has symptoms >14 days.

Bacterial:

• Campylobacter coli, jejuni, upsaliensis
• Enteroaggregative E. coli (EAEC)
• Salmonella
• Shiga toxin producing E. coli (STEC)
• Shiga toxin producing E. coli O157 (STEC O157)
• Vibrio cholerae, parahaemolyticus, vulnificus

Viral:

• Adenovirus F40/41
• Astrovirus
• Norovirus (Genogroup 1, 2)
• Rotavirus A, B, C
• Sapovirus

Resistance:

• ACT, MIR, FOX, ACC Groups
• CTX-M1 (15), M2 (2), M9 (9), M8/25 Groups
• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• IMP, NDM, VIM Groups
• OXA-48, OXA-51
• qnrA1, A2, B2
• SHV, KPC Groups
• tet B, tet M

ADD-ON:

(ALL PARASITES: PEDGIAO) Cryptosporidium, Cyclospora cayetanensis, Dientamoeba fragilis, Entamoeba histolytica, Giardia lamblia (intestinalis), Microsporidium (Enterocytozoon bienusi, Encephalitozoon intestinalis)

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Urethritis / Discharge

Specimen Types:

Urine (voided), Internal Urethra

Common Signs + Symptoms:

Pain with urination, itching, burning, and discharge

Bacterial:

• Chlamydia trachomatis
• Mycoplasma genitalium
• Mycoplasma hominis
• Neisseria gonorrhoeae
• Ureaplasma urealyticum
• Ureaplasma parvum

Viral:

• Herpes simplex virus 1
• Herpes simplex virus 2

Protozoal:

• Trichomonas vaginalis

Resistance:

• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• tet B, tet M

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Vaginitis

Specimen Types:

Vaginal, Cervical/Endometrial, Vulva/Labia/Vestibule/Perineal, Urine (voided)

Common Signs + Symptoms:

Vaginal discharge, odor, itching, irritation, bacterial vaginosis, vulvovaginal candidiasis

Bacterial:

• Atopobium vaginae
• BVAB2, 3 (Bacterial vaginosis-associated bacteria 2, 3); Mobiluncus spp.
• Chlamydia trachomatis
• Gardnerella vaginalis
• Megasphaera (types 1, 2)
• Neisseria gonorrhoeae

Viral:

• Herpes simplex virus 1
• Herpes simplex virus 2

Protozoal:

• Trichomonas vaginalis

Fungal:

• Candida albicans, parapsilosis, tropicalis
• Candida glabrata (Nakaseomyces glabratus)
• Candida krusei (Pichia kudriavzevii)

Resistance:

• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• tet B, tet M

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Recurrent Vaginitis

Specimen Types:

Vaginal, Cervical/Endometrial, Vulva/Labia/Vestibule/Perineal, Urine (voided)

Common Signs + Symptoms:

Pain with urination, burning, urethral discharge, vaginal discharge, odor, itching, irritation, or recurrent vaginitis

Bacterial:

• Atopobium vaginae
• BVAB2, 3 (Bacterial vaginosis-associated bacteria 2, 3); Mobiluncus spp.
• Chlamydia trachomatis
• Gardnerella vaginalis
• Megasphaera (types 1, 2)
• Mycoplasma genitalium
• Mycoplasma hominis
• Neisseria gonorrhoeae
• Ureaplasma urealyticum
• Ureaplasma parvum

Viral:

• Herpes simplex virus 1
• Herpes simplex virus 2

Protozoal:

• Trichomonas vaginalis

Fungal:

• Candida albicans, parapsilosis, tropicalis
• Candida glabrata (Nakaseomyces glabratus)
• Candida krusei (Pichia kudriavzevii)

Resistance:

• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• tet B, tet M

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Genital Lesion

Specimen Types:

Genital Ulcer/Lesion, Vaginal, Cervical/Endometrial, Rectal/Anal/Peri-Anal, Oropharynx/Throat/Oral, Ulcer/lesion

Common Signs + Symptoms:

Genital ulcer or lesion

Bacterial:

• Chlamydia trachomatis
• Haemophilus ducreyi
• Treponema pallidum (Syphilis)

Viral:

• Herpes simplex virus 1
• Herpes simplex virus 2
• Mpox (Monkeypox)
• Varicella zoster virus (Human Herpesvirus 3, VZV)

Resistance:

• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• tet B, tet M

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Pelvic Inflammatory Disease

Specimen Types:

Vaginal, Cervical/Endometrial

Common Signs + Symptoms:

Lower abdominal pain, abnormal vaginal bleeding, urinary frequency, and vaginal discharge

Bacterial:

• Actinomyces israelii
• Chlamydia trachomatis
• Mycoplasma genitalium
• Mycoplasma hominis
• Neisseria gonorrhoeae
• Treponema pallidum (Syphilis)

Resistance:

• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• tet B, tet M

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Proctitis

Specimen Types:

Rectal/Anal

Common Signs + Symptoms:

Rectal pain, rectal bleeding, and purulent rectal discharge

Bacterial:

• Chlamydia trachomatis
• Neisseria gonorrhoeae
• Treponema pallidum (Syphilis)

Viral:

• Herpes simplex virus 1
• Herpes simplex virus 2
• Mpox (Monkeypox)

Resistance:

• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• tet B, tet M

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Complicated Genitourinary Infection

Specimen Types:

Urine (voided), Urine (catheter), Internal Urethra, Vaginal, Cervical/Endometrial, Vulva/Labia/Vestibule/Perineal, Rectal/Anal, Penile Meatus, Genital Skin, Oropharynx/Throat/Oral

Common Signs + Symptoms:

Dysuria, hematuria, urgency of urination, frequency of micturition, fever, abdominal pain, and aerobic vaginitis

Bacterial:

• Acinetobacter baumannii
• Atopobium vaginae
• BVAB2, 3 (Bacterial vaginosis-associated bacteria 2, 3); Mobiluncus spp.
• Chlamydia trachomatis
• Citrobacter freundii
• Enterobacter cloacae complex, Klebsiella (Enterobacter) aerogenes
• Enterococcus faecalis, faecium
• Escherichia coli
• Gardnerella vaginalis
• Klebsiella pneumoniae, oxytoca
• Megasphaera (types 1, 2)
• Mycoplasma genitalium
• Mycoplasma hominis
• Morganella morganii
• Neisseria gonorrhoeae
• Proteus mirabilis, vulgaris
• Pseudomonas aeruginosa
• Serratia marcescens
• Staphylococcus aureus
• Staphylococcus epidermidis, haemolyticus, lugdunensis
• Staphylococcus saprophyticus
• Streptococcus agalactiae (Group B Strep)
• Streptococcus pyogenes (Group A Strep)
• Ureaplasma parvum
• Ureaplasma urealyticum

Protozoal:

• Trichomonas vaginalis

Fungal:

• Candida albicans, parapsilosis, tropicalis
• Candida glabrata (Nakaseomyces glabratus)
• Candida krusei (Pichia kudriavzevii)

Resistance:

• ACT, MIR, FOX, ACC Groups
• CTX-M1 (15), M2 (2), M9 (9), M8/25 Groups
• dfr (A1, A5), sul (1, 2)
• ermB, C; mefA
• IMP, NDM, VIM Groups
• mecA
• OXA-48, OXA-51
• qnrA1, A2, B2
• SHV, KPC Groups
• tet B, tet M
• VanA, VanB

x close

CGT (Asymptomatic)

Specimen Types:

Urine (voided), Urine (catheter), Internal Urethra, Vaginal, Cervical/Endometrial, Vulva/Labia/Vestibule/Perineal, Rectal/Anal, Penile Meatus, Genital skin, Oropharynx/Throat/Oral

Common Signs + Symptoms:

High risk heterosexual behavior, high risk homosexual behavior, or suspected exposure to a sexually transmitted infection

Bacterial:

• Chlamydia trachomatis
• Neisseria gonorrhoeae

Protozoal:

• Trichomonas vaginalis