Pathogen |
qPCR test (qPCR instrument) |
Target gene (protein) |
Probe type |
Refs. |
Staphylococcus aureus/methicillin-resistant S. aureus |
In-house (LightCycler) |
sa442, nuc (nuclease), mecA (PLP2a) |
Dual-Hyb |
[23] |
Roche Light Cycler MRSA (LightCycler) |
mecA |
Dual-Hyb |
[24] |
In-house (LightCycler 2.0) |
mecA, nuc |
Dual-Hyb |
[21] |
Methicillin-resistant S. aureus carriage |
BD GeneOhm™ MRSA ACP (SmartCycler® II) |
mecA |
Beacon |
[16] |
BD GeneOhm MRSA/Xpert® MRSA (SmartCycler II/GeneXpert®) |
mecA and chromosomal gene/SPA, SCCmec and mecA |
Beacon |
[17] |
Xpert MRSA (GeneXpert) |
SPA, SCCmec, mecA |
Beacon |
[18] |
LightCycler MRSA/BD GeneOhm MRSA |
mecA |
Dual-Hyb |
[19] |
BD GeneOhm MRSA |
SPA, SCCmec, mecA |
Beacon |
[20] |
Streptococcus pneumoniae |
In-house (ABI Prism® 7000) |
lytA (autolysine) |
TaqMan |
[26] |
In-house (ABI Prism 7300) |
ply (pneumolysin) |
TaqMan |
[27] |
In-house (Rotor-Gene 3000 and LightCycler) |
ply, lytA, Spn9802 intergenic region |
TaqMan and Dual-Hyb |
[29] |
In-house (LightCycler) |
Ply, lytA |
Dual-Hyb |
[30] |
In-house (Stratagene M×3000P™, ABI Prism 7500) |
lytA, ply, psaA (Mn ABC transporter substrate-binding lipoprotein) |
TaqMan |
[31] |
Streptococcus agalactiae |
Cepheid, Xpert GBS (GeneXpert) |
cfb (diffusible extracellular protein) |
Beacon |
[33,37] |
BD Max™ GBS (BD Max) |
Cfb |
Scorpion |
[34] |
Somagen®, IDI StrepB™ (SmartCycler) |
Cfb |
NS |
[35] |
In-house (SmartCycler) |
ssrA (tmRNA) |
Dual-Hyb |
[36] |
Streptococcus pyogenes |
In-house (Mx3005P™, Stratagene) |
NS |
TaqMan |
[40] |
Roche Applied Science (LightCycler) |
pts1 (phosphotransferase) |
Dual-Hyb |
[39] |
Neisseria meningitidis |
In-house LAMP (ABI Prism 7000) |
ctrA (outer membrane protein regulating capsule transport) |
SYBR Green |
[43] |
In-house (NS) |
ctrA |
TaqMan |
[47] |
In-house (LightCycler 480) |
ctrA |
Taqman |
[48] |
In-house (ABI Prism 7000) |
ctrA, siadD (sialic acids of the polysaccharide capsule) |
TaqMan |
[44,45] |
Haemophilus influenzae |
In-house (NS) |
hpd (protein D) |
TaqMan |
[50] |
In-house (Rotor-Gene® 3000) |
ompP6, rnpB (RNase P RNA), bexA (capsule) |
TaqMan |
[51] |
In-house (ABI Prism 7500) |
bexA, cap locus (capsular types a to f) |
TaqMan |
[52] |
Shiga toxin-producing Escherichia coli |
In-house (ABI Prism 7000 or 7500) |
stx1 and stx2 (shiga-like toxins) |
TaqMan, SYBR Green |
[55,56] |
In-house (LightCycler) |
stx1 and stx2 |
Dual-Hyb |
[58] |
In-house (Rotor-Gene 6000) |
stx1 and stx2 |
SYBR Green |
[59] |
In-house (PTC200 and Chromo 4™ optical detector) |
stx1 and stx2 |
SYBR Green |
[60] |
Mycobacterium tuberculosis complex |
Xpert MTB/RIF (GeneXpert) |
rpoB (RNA polymerase subunit B) |
Beacon |
[67,68] |
M. tuberculosis complex |
Xpert MTB RIF/Roche Cobas® TaqMan MTB |
rpoB/16S rRNA gene |
Beacon/TaqMan |
[70] |
Xpert MTB RIF/in-house IS6110 qPCR |
rpoB/IS6110 |
Beacon/TaqMan |
[69] |
Roche Cobas TaqMan MTB (TaqMan 48) |
16S rRNA gene |
TaqMan |
[71] |
In-house (Stratagene M×3005P) |
IS6110 |
TaqMan |
[73] |
In-house (SmartCycler II) |
IS6110 |
SYBR Green |
[74] |
Non-tuberculous mycobacteria |
In-house, Mycobacterium avium subsp. paratuberculosis (ABI 7500) |
IS900, F57 |
TaqMan |
[63] |
In-house, M. avium subsp. paratuberculosis |
MAP2765c, MAP0865, IS900, |
TaqMan |
[64] |
In-house, M. avium subsp. hominissuis (LightCycler 480) |
IS901, IS1245 |
TaqMan |
[65] |
In-house, six species |
hsp65 (heat shock protein 65) |
Dual-Hyb |
[66] |
Chlamydia trachomatis and Neisseria gonorrhoeae |
Siemens VERSANT® CT/GC (kPCR system) |
Cryptic plasmid and pivNG |
NS |
[77] |
Abbott RealTime™ CT/NG (m2000) |
Cryptic plasmid and Opa gene |
TaqMan |
[78,80,81] |
Cobas 4800 CT/NG (Cobas 4800) |
Cryptic plasmid, chromosomal gene and DR9 |
NS |
[79] |
Chlamydophila pneumoniae |
In-house LUX-PCR or TaqMan-PCR (NS) |
pm4 (polymorphic membrane protein 4), ompA (major outer membrane protein A) |
LUX or TaqMan |
[93] |
In-house (ABI Prism 7700) |
ompB (major outer membrane protein B) |
TaqMan |
[90] |
In-house (SmartCycler) |
ompA (major outer membrane protein A), 16S rRNA gene |
TaqMan |
[88] |
In-house (ABI Prism 7700) |
53-kDa protein gene |
TaqMan |
[95] |
Nuclisens®, bioMérieux (real-time NASBA) |
16S rRNA gene |
Beacon |
[86] |
Chlamydophila psittaci |
Takara Bio Dice™ Real-Time System TP800 |
envB (cysteine-rich protein) |
SYBR Green |
[92] |
In-house (Corbett 3000) |
16S rRNA gene, 16–23S rRNA interspacer |
SYBR Green |
[87] |
In-house (LightCycler) |
ompA (outer membrane protein A) |
TaqMan |
[89] |
In-house (ABI Prism 7000) |
incA (inclusion membrane protein) |
TaqMan |
[91] |
Rickettsia |
In-house (ABI Prism 7900) |
16S rRNA gene, gltA (citrate synthase) |
TaqMan |
[96] |
In-house (LightCycler) |
RC0338, RP278, RAF-pORF1267, RC0743, 23S rRNA gene, intergenic sequence |
TaqMan |
[97] |
In-house (SmartCycler II) |
17-kDa antigen gene, ompB |
TaqMan |
[99] |
In-house (Bio-Rad™ iQ5) |
ompA, 17-kDa lipoprotein precursor gene, 56-kDa major outer membrane protein gene |
TaqMan |
[98] |
Coxiella burnetii |
In-house (MX-4000) |
IS1111 |
NS |
[101] |
In-house (ABI Prism 7500) |
IS1111 |
TaqMan |
[102] |
In-house (LightCycler) |
IS1111, IS30a |
TaqMan |
[100] |
Anaplasma phagocytophilum |
In-house LAMP (Teramecs LA200) |
msp2 (major surface protein 2) |
TaqMan |
[105] |
In-house (iCycler™) |
msp2 |
TaqMan |
[106] |
Ehrlichia chaffeensis |
In-house (iCycler) |
Dsb (disulfide bond formation protein) |
SYBR Green |
[107] |
Bartonella |
In-house (NS) |
NADH dehydrogenase g-subunit gene |
None |
[110] |
In-house (ABI Prism 7900 HT) |
groEL (heat shock protein) |
Taqman |
[111] |
In-house (LightCycler) |
pap31 (extracellular matrix adhesion) |
SYBR Green |
[112] |
In-house (LightCycler) |
gltA (citrate synthase) |
Dual-Hyb |
[113] |
In-house (LightCycler) |
ribC (riboflavin synthase) |
SYBR Green |
[114] |
Mycoplasma pneumoniae |
In-house (LightCycler) |
RepMP2 (repetitive element of the P1 cytadhesin gene) |
Dual-Hyb |
[116] |
In-house (Microfluidic) |
Mp181 (toxin) |
Taqman |
[117] |
In-house HRM-qPCR (Rotor-Gene 6000) |
RepMP2/3 regions within the P1 gene |
SYBR Green |
[122] |
Five commercial kits |
P1 cytadhesin gene |
TaqMan |
[118] |
In-house (ABI 7500) |
Mp3 and Mp7 (ATPases), Mp181 (CARDS toxin) |
TaqMan |
[119, 120] |
In-house (LightCycler) |
repMp1 (repetitive element of the P1 cytadhesin gene) |
TaqMan |
[121] |
Mycoplasma hominis |
In-house (LightCycler 480) |
yidC (membrane protein translocase) |
TaqMan |
[124] |
In-house (ABI Prism 7900) |
16S rRNA gene |
TaqMan |
[125] |
Mycoplasma genitalium |
In-house (Rotor-Gene 6000) |
pdhD (dihydrolipoamide dehydrogenase) |
TaqMan |
[129] |
In-house (LightCycler 480) |
MgPa (adhesion protein), 16S rRNA gene |
TaqMan |
[126] |
In-house (Rotor-Gene 6000) |
mg219 |
TaqMan |
[130] |
Ureaplasma urealyticum and Ureaplasma parvum |
In-house (Bio-Rad iQ5) |
urease B gene |
TaqMan |
[127] |
In-house (LightCycler 2.0) |
UUR10_0680 and UP063 |
Dual-Hyb |
[128] |
Helicobacter pylori |
In-house (Rotor-Gene 6000) |
16S rRNA and 23S rRNA genes |
TaqMan |
[134] |
In-house (Light Cycler)/Seeplex® ClaR-H. pylori ACE |
23S rRNA gene |
Dual-Hyb/none |
[135] |
Ingenetix ClariRes (LightCycler) |
23S rRNA gene |
SYBR Green |
[136] |
In-house(Rotor-Gene 6000) |
ureC (urease α subunit) |
TaqMan |
[133] |
Clostridium difficile |
Xpert CD/Epi (GeneXpert)/Meridian Illumigene™ CD (LAMP) |
tcdB, cdt, tcdC deletion of 027 strains/tcdA |
Beacon |
[138] |
In-house (ABI Prism 7300) |
tcdB, tcdC deletion of 027 strains |
TaqMan |
[139] |
In-house (LightCycler 2.0) |
tcdA, tcdB |
TaqMan |
[140] |
In-house (ABI Prism 7500)/BD GeneOhm CD (SmartCycler) |
tcdA, tcdB, tcdC deletion of 027 strains/tcdB |
TaqMan |
[141] |
In-house (ABI Prism 7500) |
tcdA, tcdB |
TaqMan |
[142] |
BD GeneOhm CD (SmartCycler) |
tcdB |
TaqMan |
[143] |
Legionella |
In-house, Sg1-qPCR (Bio-Rad Chromo4 system) |
wzm and wzt (lipopolysaccharide biosynthesis proteins) |
TaqMan |
[146] |
In-house (LightCycler) |
16S rRNA gene, MIP |
Dual-Hyb |
[147] |
In-house (ABI Prism 7900) |
23S-5S rRNA intergenic spacer region |
TaqMan |
[148] |
In-house (ABI Prism 7900) |
16S rRNA gene, MIP |
TaqMan |
[149] |
Bordetella pertussis and Bordetella parapertussis |
In-house (ABI 7500) |
IS481, IS1001, ptxS1 (pertussis toxin subunit S1) |
TaqMan |
[152] |
In-house (SmartCycler) and four commercial tests |
IS481 |
TaqMan |
[153] |
In-house (variable) |
IS481 |
Dual-Hyb, TaqMan, Beacon |
[154] |
In-house (LightCycler) |
ptxA-pr (pertussis toxin S1 promoter), IS481 |
Dual-Hyb |
[155] |
In-house (LightCycler) |
BP283 and BO485 DNA regions |
TaqMan |
[156] |
In-house (ABI 7900, ABI 7500, SmartCycler II, Rotor-Gene 3000) |
IS481, IS1001 |
TaqMan |
[157] |
Corynebacterium diphtheria and Corynebacterium ulcerans |
In-house (LightCycler) |
tox (diphtheria toxin) |
Dual-Hyb |
[160] |
In-house (Stratagene Mx3000P) |
tox (diphtheria toxin) |
TaqMan |
[162] |
Brucella |
In-house (LightCycler) |
IS711 |
TaqMan |
[165] |
In-house (LightCycler) |
BCSP31 gene |
TaqMan |
[166] |
In-house (LightCycler) |
BCSP31 gene |
TaqMan |
[167] |
In-house (LightCycler 2.0) |
BCSP31 gene |
Dual-Hyb |
[168] |
Francisella tularensis |
In-house (LightCycler 2.0) |
ISFtu2, Tul4 (surface protein gene) |
TaqMan |
[169,170] |
In-house (SmartCycler II) |
FTT0376, FTT0523 |
TaqMan |
[170] |
In-house (LightCycler 1.2) |
pdpD (pathogenicity determinant protein D), AY06 (junction ISFtu2 and flanking 3′ DNA) |
Taq Man |
[171] |
Leptospira |
In-house (Bio-Rad CFX96) |
secY (preprotein translocase), lfb1 (protein of unknown function), lipL32 (lipoprotein) |
SYBR Green and TaqMan |
[173] |
In-house (Rotor-Gene 3000) |
rrs (16SrRNA gene), lipL32 (outer membrane lipoprotein) |
TaqMan |
[174] |
In-house (Bio-Rad iQ5) |
secY (preprotein translocase) |
SYBR Green |
[175] |
In-house (ABI 7500) |
lipL32 (outer membrane lipoprotein) |
TaqMan |
[176] |
In-house LAMP (MJ Opticon 2) |
lipL41 (outer membrane protein) |
SYBR Green |
[177] |
Treponema pallidum |
In-house (LightCycler 2.0) |
tpp47 (47-kDa membrane lipoprotein) |
SYBR Green |
[178] |
In-house (Rotor-Gene 3000) |
polA (DNA polymerase) |
TaqMan |
[180] |
Borrelia (Lyme disease) |
In-house (LightCycler) |
hbb (histone-like protein) |
Dual-Hyb |
[185] |
In-house (LightCycler 2.0) |
borrelial plasminogen binding protein gene |
Dual-Hyb |
[184] |
In-house (LightCycler 2.0) |
ospA (outer surface protein A) |
TaqMan |
[183] |
Bacillus anthracis |
In-house (ABI 7900) |
capA, capB, capC (capsule), lef and pag (toxins) |
Beacon |
[187] |
In-house (ABI 7000 SDS or 7700 SDS) |
pXO1 (protective antigen) |
TaqMan |
[188] |
Yersinia pestis |
In-house (Rotor-Gene 3000) |
pla (plasminogen activator), caf1 (F1 antigen), ymt (phospholipase D) |
TaqMan |
[190] |
In-house (Rotor-Gene 2000) |
ypo2088 (putative methyltransferase), pla (plasminogen activator) |
TaqMan |
[191] |
Enterococcus (VRE) |
BD GeneOhmVanR (SmartCycler II) |
vanA, vanB |
TaqMan |
[227] |
Xpert VanA/vanB, Cepheid (GeneXpert) |
vanA, vanB |
Beacon |
[228] |
Roche Light Cycler VRE (LightCycler) |
vanA, vanB |
Dual-Hyb |
[229] |
BD GeneOhm VanR (SmartCycler II) |
vanA, vanB |
TaqMan |
[230] |
Comments