TABLE 1.
Mechanisms of bacterial tolerance to chlorhexidine in strain Ab-2_clon_2010-CHLX, revealed by transcriptomic studiesa
| GenBankb protein accession no. | Gene expression fold change determined by: |
Functional description | Defense mechanism (reference no.) | Tolerome type (reference no.) | |
|---|---|---|---|---|---|
| DESeq2 | EdgeR | ||||
| ODA53993.1 | 6.933753475 | 6.982635042 | AdeA protein | AdeABC system (RND-type) (10) | Transporter/efflux pump (5) |
| ODA53994.1 | 6.149907892 | 6.175526694 | AdeB protein | ||
| ODA53995.1 | 4.257153566 | 4.270842036 | AdeC protein | ||
| ODA55718.1 | 6.119321647 | 6.133494454 | Tetracycline resistance protein | MFS system | |
| ODA54617.1 | 5.377292457 | 7.227172031 | Arsenite efflux pump | ACR3 system (13) | |
| ODA56577.1 | 3.498098186 | 3.528728206 | Aminoglycoside phosphotransferase | APT family | |
| ODA54814.1 | 3.605781331 | 3.649808635 | Chlorexidine efflux pump | AceI system (16) | |
| ODA56167.1 | 5.265550668 | 7.054151044 | MFS transporter | MFS system | |
| ODA53764.1 | 12.16763575 | 14.92175121 | OXA 24/40 β-lactamase | AbATCC329p/pMMCU3 | Plasmid (5) |
| ODA53763.1 | 8.975633873 | 11.30715263 | DNA replication protein A | ||
| ODA53762.1 | 5.273985066 | 5.329333593 | RepB family plasmid replication initiator | ||
| ODA54084.1 | 3.511019975 | 3.547062538 | CsuA protein | CsuABCDE (17, 18) | Biofilm (14) |
| ODA54083.1 | 3.199749378 | 3.259685195 | CsuB protein | ||
| ODA54082.1 | 2.575094974 | 2.584527435 | CsuC protein | ||
| ODA54081.1 | 2.810613341 | 2.819199271 | CsuD protein | ||
| ODA54080.1 | 2.782552791 | 2.791313686 | CsuE protein | ||
| ODA53940.1 | 2.037734523 | 2.053934504 | Cytochrome b | Cytochrome operon (19–21) | Stress oxidative (ROS) (21) |
| ODA57053.1 | 2.173049691 | 2.184371809 | Cytochrome bd biosynthesis protein | ||
| ODA56663.1 | 2.405101873 | 2.428897655 | Sodium/proline symporter | ||
| ODA56171.1 | 10.75708444 | 13.32903693 | Cytochrome bd biosynthesis protein | ||
| ODA56172.1 | 10.35093438 | 12.86380541 | Cytochrome d ubiquinol oxidase subunit | ||
| ODA54604.1 | 10.07652823 | 12.56398102 | Taurine ABC transporter substrate-binding | Taurine transporter (22, 23) | Electron transport |
| ODA54605.1 | 9.758316312 | 12.21616998 | Taurine transporter-binding subunit (TauB) | ||
| ODA54606.1 | 8.966908008 | 11.30350134 | Taurine ABC transporter permease (TauC) | ||
| ODA54607.1 | 10.85324686 | 13.44475271 | Taurine dioxygenase (TauD) | ||
| ODA55153.1 | −6.486154998 | −6.530626555 | Hypothetical protein | Replication | ppGpp network (28)c |
| ODA54592.1 | 0.932475218 | 0.929842277 | DNA polymerase I | ||
| ODA54625.1 | 0.931688577 | 0.929428817 | DNA polymerase III subunit alpha | ||
| ODA54730.1 | −1.77207536 | −1.816317901 | Response regulator | ||
| ODA55878.1 | 0.500078184 | 0.506140675 | 50S ribosomal protein L17 | ||
| ODA55763.1 | 0.438241011 | 0.436148678 | RNA polymerase subunit omega | ||
| ODA55654.1 | 0.582523178 | 0.580921263 | 50S ribosomal protein L7/L12 | ||
| ODA55933.1 | −0.523115918 | −0.531876133 | ATP synthase subunit beta | ATP metabolism | Energy production (31, 32)c |
| ODA55935.1 | −0.570647356 | −0.579254835 | ATP synthase subunit alpha | ||
| ODA54585.1 | 0.422390483 | 0.418615357 | Transcription termination factor rho | ||
a
The relative expression (expressed as fold change [FC]) of abaI (3.05) and abaR (2.88) genes, determined by RT-PCR, indicated activation of the quorum-sensing system.
b
Sanger sequencing of these genes from the Ab-2_clon_2010-CHLX strain, as well as of the regulatory genes adeR and adeS, did not show mutations with respect to the sequence of strain Ab-2_clon_2010.
c
Genes that belonged to the ppGpp network and energy production categories showed downregulation (FC, <1).