TABLE 1.
Probes included on the chip
| Target bacteria | Probe name | Probe sequence (5′ to 3′) | Accession no. (GenBank) or source |
|---|---|---|---|
| All bacteria | Uni_459 | CCGATAGTGAACCAGTACC | |
| Gram-positive bacteria | |||
| Nonspecific | GP_01 | YTTVTTYAGTTTTGAGAGGTY | |
| GP_02 | TGTATTCAGTTTTGAATGTTY | ||
| Enterococcus spp. | Enc | GAGTTTTTTAATAAGTTCAATTG | |
| E. faecalis | Enc_fs | GCTTATTTATTGATTAACC | AY351321 |
| E. faecium | Enc_fm | AGACTACACAATTTGTTTTT | AY351317 |
| E. avium | Enc_av | GGATACAGAAACAATTTTAA | AY116901 |
| Listeria spp. | Lis | CACAAGTAACCGAGAATCATCTG | |
| L. monocytogenes | Lis_mo | CATAGATAATTTATTATTTATGAC | AF514302 |
| L. ivanovii | Lis_iv | CTGTATAACCTATTTAAGGG | U57913 |
| L. grayi | Lis_gr | GAAACTTTCCGCTTTGGAAG | U57918 |
| L. welshimeri | Lis_we | AGAAAACAAAATATTATTTCC | U57917 |
| Staphylococcus spp. | Sta | AGATTTTACCAAGCAAAACCG | |
| S. aureus | Sta_au | AAACGCGTTATTAATCTTGTGA | U11787 |
| S. epidermidis | Sta_ep | TTGAATTCVTAAATAATCGC | U90018 |
| S. saprophyticus | Sta_sa | CTTACGAAGATGCAGGAAT | EU430992 |
| Streptococcus spp. | Str | CATTGAAAATTGAATAWCKA | |
| S. agalactiae | Str_ag | AGGAAACCTGCCATTTGCGTC | AF489592 |
| S. pneumoniae | Str_pn | ATCACCAAGTAATGCACATTG | AY347556 |
| S. pyogenes | Str_py | ACACGTTTATCGTCTTATTTAG | AY347560 |
| S. bovis | Str_bo | GTTTAAGGTCAACAGAACCAA | AY347547 |
| Gram-negative bacteria | |||
| Nonspecific | GN_01 | CTCAGTTGGTTAGAGCGCSMCM | |
| Bacteroides spp. | Bac | GTAGAGGTCGGCAGTTCAAC | |
| B. fragilis | Bac_fr | GAAAAGGAGATGAATCTGGC | AF172709 |
| B. thetaiotaomicron | Bac_th | GGTTAATACCTGATACTT | AF172710 |
| B. ovatus | Bac_ov | CCAGTATGAGAATAAAACGTT | AF176691 |
| Escherichia coli | Esc_co | AAAAAAGAAGCGTWCTTTGMAGTGCTC | AY684796 |
| Enterobacter/Klebsiella spp. | Kle/Enb | TAATGTGTGTTCGAGTCTCT | |
| E. cloacae | Enb_cl | CGAAGGGGACGTACAGTCTCA | AY116915 |
| E. aerogenes | Enb_ae | AAGTAGAGAAGCAAGGGGTC | AF047426 |
| E. agglomerans | Enb_ag | GATACCTTCCCGCGCAGTGTCC | AF041584 |
| K. pneumoniae | Kle_pn | GACGCGTGCCGATGTATC | AF047425 |
| K. oxytoca | Kle_ox | GCTGCGAAGTCGCGACACCT | AY116899 |
| Haemophilus spp. | Hae | CGAATCCCCGTGGGGACGCCA | |
| H. influenzae | Hae_in | GAGAGAAAGTCTGAGTAGGCA | Our laboratory |
| H. ducreyi | Hae_du | AAGTAGAAAGTCTGAGTAATC | Our laboratory |
| Pseudomonas spp. | Pse | ACAGTATAACCAGATTGCTT | |
| P. aeruginosa | Pse_ae | CCATCTAAAACAATCGTCG | AY684792 |
| P. stutzeri | Pse_st | CACGTTATAGACAGTAACC | AJ635307 |
| Serratia spp. | Ser | CCTCCTTACCTAASGATATT | |
| S. marcescens | Ser_ma | GCCACTCGAACTAATATCTT | Our laboratory |
| S. grimesii | Ser_gr | GATATTGATTGCGTGAAGTGC | Our laboratory |
| S. entomophila | Ser_en | CACTTCACTCGAATCAATATC | Our laboratory |