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SARS-CoV-2

Respiratory

Genitourinary

Hospital Acquired Infections

Respiratory

VIRUSES
SARS-CoV-2 (COVID-19)	Sarbecovirus (SARS, SARS like, SARS-CoV-2)	Influenza A
Coronavirus 229E/NL63	Adenovirus A/B/C/D/E	Influenza B
Coronavirus OC43/HKUI	Enterovirus A/B/C	Rhinovirus A/B
Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

VIRUSES
SARS-CoV-2 (COVID-19)

VIRUSES
SARS-CoV-2 (COVID-19)

VIRUSES
Influenza A	Coronavirus OC43/HKUI	Parainfluenza virus 3
Influenza B	Enterovirus A/B/C	Parainfluenza virus 4
Adenovirus A/B/C/D/E	Metapneumovirus	Respiratory syncytial virus A/B
Bocavirus 1/2/3	Parainfluenza virus 1	Rhinovirus A/B/C
Coronavirus 229E/NL63	Parainfluenza virus 2
BACTERIA
Bordetella parapertussis	Haemophilus influenzae	Mycoplasma pneumoniae
Bordetella pertussis	Legionella pneumophila	Streptococcus pneumoniae
Chlamydophila pneumoniae	Moraxella catarrhalis

VIRUSES
Influenza A	Influenza B	Respiratory Syncytial Virus (RSV)

VIRUSES
Adenovirus	Respiratory syncytial virus B	Influenza B
Metapneumovirus	Rhinovirus A/B/C
Respiratory syncytial virus A	Influenza virus A
BACTERIA
Achromobacter xylosoxidans	Moraxella catarrhalis	Pseudomonas aeruginosa
Bordetella pertussis	Mycoplasma pneumoniae	Staphylococcus aureus
Burkholderia cepacia complex (21 spp)	Non-tuberculous mycobacterium (15 spp	Stenotrophomonas maltophila
Burkholderia Cenocepacia	Mycobacterium abscessus subgroup (4 spp)	Streptococcus pneumoniae (21spp)
Burkholderia multivorans	Mycobacterium avium complex (4 spp)	Streptococcus species (19 spp)
Chlamydia pneumoniae	Pandoraea species (5spp)	Veillonella species (3 spp)
Haemophilus influenza	Prevotella species (16 spp)
FUNGI
Aspergillus fumigatus	Candida albicans	Exophialia dermatitidis
Scedosporium species (7 spp)
ANTIBIOTIC RESISTANCE MARKERS
mecA (incl MRSA)

Genitourinary

VIRUSES
Neisseria Gonorrhoeae (NG)	Haemophilus Ducreyi (HD)
Mycoplasma Genitalium (MG)	Mycoplasma Hominis (MH)
Ureaplasma Urealyticum (UU)	Treponema Pallidum (TP)
Chlamydia Trachomatis (CT)	Herpes Simplex virus 1(HSV-1)
Trichomonas Vaginalis (TV)	Herpes Simplex virus 2(HSV-2)

BACTERIA
Citrobacter freundii	Klebsiella oxytoca	Serratia marcescens
Citrobacter koseri	Klebsiella pneumoniae	Staphylococcus aureus
Klebsiella aerogenes	Morganella morganii	Staphylococcus epidermidis
Enterobacter cloacae	Proteus spp.	Staphylococcus saprophyticus
Enterococcus faecalis	Pseudomonas aeruginosa	Streptococcus agalactiae (GBS)
Enterococcus faecium	Providencia rettgeri
FUNGUS
Candida albicans
ANTIOBIOTIC RESISTANCE MARKERS
mecA (incl MRSA)	Trimethoprim Resistance 3	Van A (Vancomycin Resistance A)
Trimethoprim Resistance 1	Trimethoprim Resistance 4	Van B (Vancomycin Resistance B)
Trimethoprim Resistance 2	Trimethoprim Resistance 5

Hospital Acquired Infections

BACTERIA
Methicillin-resistant Staphylococcus aureus (MRSA)	Methicillin-sensitive Staphylococcus aureus (MSSA)	Methicillin-resistant coagulase-negative Staphylococci (MRCoNS)

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