Information

Antibiotic Responses
Submitted by: danr October 29, 2022

Tables for how gut bacteria respond to antibiotics.

 CAUTION - This database can be used as a guide but should not be used to make medical decisions or to determine a course of antibiotics that should be taken for a particular medical condition.

Antibiotic classifications have been constructed from the following sources: Wikipedia, TOKU-E

All Antibiotics

Penicillins and Penems

Shorthand Longhand/ Other names Gen. (Xth) Susceptible (widespread colonisers) Resistant (widespread colonisers) Significance
amoxicillin     Veillonella parvula, Bifidobacterium longum subsp. longum, Escherichia coli, Bifidobacterium adolescentis, Roseburia hominis + 16 others Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides xylanisolvens, Phocaeicola vulgatus  
Augmentin amoxicillin-clavulanic acid, amox-clav   Anaerostipes caccae, Bacteroides ovatus, Bifidobacterium adolescentis, Blautia massiliensis, Collinsella aerofaciens, + 9 others Moderate colonisers: Enterobacter cloacae, Enterococcus faecium; Minor colonisers: Alistipes obesi, Bacillus cereus, Morganella morganii  
ampicillin     Blautia producta, Bifidobacterium adolescentis, Clostridium leptum, Odoribacter splanchnicus, Roseburia hominis + 16 others Bacteroides caccae, Bacteroides pectinophilus, Bacteroides thetaiotaomicron, Bacteroides uniformis. Phocaeicola vulgatus  
amp-sulb ampicillin-sulbactam   Bacteroides fragilis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides xylanisolvens Bacteroides caccae, Phocaeicola vulgatus, Enterobacter cloacae (moderate coloniser), Citrobacter koseri (minor coloniser), Hafnia alvei (minor coloniser)  
azlocillin     Bacteroides ovatus, Bifidobacterium adolescentis, Blautia obeum, Dorea formicigenerans, Ruminococcus bromii + 14 others Bacteroides caccae, Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides xylanisolvens, Escherichia coli  
aztreonam     Dorea formicigenerans, Odoribacter splanchnicus, Veillonella parvula, Escherichia coli, Prevotella copri (moderate coloniser) Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Roseburia hominis, Ruminococcus gnavus + 15 others  
bacamplicill bacampicillin   Bifidobacterium adolescentis, Blautia obeum, Coprococcus comes, Phocaeicola vulgatus, Roseburia hominis + 11 others Bacteroides caccae, Bacteroides fragilis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides xylanisolvens, Escherichia coli, Parabacteroides distasonis  
bn-penicill benzylpenicillin   Bifidobacterium adolescentis, Blautia obeum, Eubacterium rectale, Phocaeicola vulgatus, Bacteroides fragilis + 18 others Bacteroides thetaiotaomicron, Enterocloster bolteae (moderate coloniser); Minor colonisers: Acinetobacter radioresistens, Bacillus cereus, Dysgonomonas gadei  
carbenicill carbenicillin   Campylobacter concisus (moderate coloniser); Minor colonisers: Campylobacter showae, Haemophilus influenzae, Cedecea davisae, Sphingomonas paucimobilis Klebsiella pneumoniae (moderate coloniser); Minor colonisers: Aliarcobacter cryaerophilus, Campylobacter coli, Kluyvera ascorbata, Raoultella ornithinolytica  
cloxacillin     Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Phocaeicola vulgatus, Roseburia hominis + 13 others Bacteroides fragilis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides xylanisolvens, Escherichia coli, Parabacteroides distasonis, Veillonella parvula  
dicloxacill dicloxacillin   Bacteroides caccae, Bifidobacterium longum subsp. longum, Blautia obeum, Dorea formicigenerans, Phocaeicola vulgatus + 14 others Bacteroides fragilis, Bacteroides thetaiotaomicron, Escherichia coli, Parabacteroides distasonis, Veillonella parvula  
methicillin     Bacillus subtilis (minor coloniser) Bacillus cereus (minor coloniser), Stenotrophomonas maltophilia (minor coloniser)  
mezlocillin     Minor colonisers: Bacillus cereus, Bacillus circulans, Butyricicoccus pullicaecorum, Dermabacter hominis, Oribacterium sinus, Providencia alcalifaciens Anaerobiospirillum succiniciproducens (minor coloniser)  
oxacillin     Bacteroides ovatus, Bifidobacterium adolescentis, Blautia obeum, Intestinimonas butyriciproducens, Ruminococcus bromii + 14 others Bacteroides caccae, Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides xylanisolvens, Escherichia coli, Parabacteroides distasonis, Phocaeicola vulgatus, Veillonella parvula  
penicillin     Ruminococcus gnavus; Moderate colonisers:  Enterocloster aldenensis, Faecalicatena contorta, Ligilactobacillus salivarius, Finegoldia magna, Erysipelatoclostridium ramosum Bacteroides thetaiotaomicron, Bacteroides uniformis, Phocaeicola vulgatus, Parabacteroides distasonis, Anaerostipes caccae  
penicillin G     Bifidobacterium adolescentis, Bifidobacterium angulatum, Bifidobacterium longum subsp. infantis, Bifidobacterium longum subsp. longum, Clostridium leptum, Streptococcus parasanguinis, Collinsella aerofaciens, Ruminococcus gnavus Bacteroides caccae, Bacteroides fragilis, Bacteroides pectinophilus, Bacteroides stercoris  
pipercillin     Bifidobacterium adolescentis, Ruminococcus gnavus, Blautia obeum, Lachnospira eligens, Roseburia intestinalis + 14 others Bacteroides caccae, Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides uniformis, Parabacteroides distasonis, Phocaeicola vulgatus, Veillonella parvula  
piper-taz piperacillin-tazobactam   Anaerostipes caccae, Bifidobacterium adolescentis, Bifidobacterium longum subsp. longum, Bacteroides fragilis, Bacteroides xylanisolvens, Clostridium leptum, Collinsella aerofaciens Bacteroides caccae, Bacteroides thetaiotaomicron, Phocaeicola vulgatus, Veillonella parvula  
ticarcillin   4 Bifidobacterium adolescentis, Collinsella aerofaciens, Streptococcus parasanguinis, Blautia obeum, Eubacterium rectale + 14 others Bacteroides caccae, Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides uniformis, Escherichia coli, Phocaeicola vulgatus, Veillonella parvula  
tica-clav ticarcillin-clavulanic acid   Bacteroides fragilis, Blautia massiliensis; Moderate colonisers: Bacteroides eggerthii, Brevundimonas diminuta, Clostridium perfringens, Sutterella wadsworthensis Parabacteroides distasonis, Veillonella parvula; Enterobacter cloacae (moderate coloniser); Minor colonisers: Bacillus cereus, Christensenella hongkongensis, Ralstonia pickettii Biovar Va-1&2  
daripenem     Bacteroides fragilis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Parabacteroides distasonis, Phocaeicola vulgatus    
ertapenem     Anaerostipes caccae, Bacteroides fragilis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Parabacteroides distasonis, Phocaeicola vulgatus, Ruminococcus gnavus Moderate colonisers: Enterococcus avium, Enterococcus casseliflavus, Enterococcus durans, Enterococcus faecalis, Enterococcus faecium, Enterococcus gallinarum  
imipenem     Bacteroides stercoris, Bifidobacterium adolescentis, Clostridium leptum, Phocaeicola vulgatus, Roseburia intestinalis + 23 others Moderate colonisers: Enterococcus durans, Enterococcus faecium, Enterococcus gallinarum  
meropenem     Bacteroides stercoris, Bifidobacterium adolescentis, Blautia obeum, Collinsella aerofaciens, Eubacterium rectale + 20 others Moderate colonisers: Enterococcus faecium, Enterococcus faecalis; Minor colonisers: Stenotrophomonas maltophilia, Ralstonia pickettii Biovar Va-1&2  

 

Cephems (Cephalosporins)

Shorthand Longhand/ Other names Gen. (Xth) Susceptible (widespread colonisers) Resistant (widespread colonisers) Significance
cefaclor   2 Bifidobacterium adolescentis, Blautia obeum, Collinsella aerofaciens, Coprococcus comes, Dorea formicigenerans, Eubacterium rectale, Odoribacter splanchnicus, Roseburia hominis, Roseburia intestinalis, Ruminococcus bromii, Ruminococcus gnavus, Streptococcus parasanguinis, Veillonella parvula Phocaeicola vulgatus, Bacteroides thetaiotaomicron, Bacteroides fragilis, Bacteroides caccae, Bacteroides uniformis, Bacteroides xylanisolvens, Bifidobacterium longum subsp. longum, Escherichia coli, Lachnospira eligens infections of the ear, lung, skin, throat, and urinary tract
cefadroxil cefadroxyl 1 Blautia obeum, Roseburia hominis Bifidobacterium adolescentis, Coprococcus comes, Roseburia intestinalis, Ruminococcus gnavus, Bacteroides fragilis +17 others  
cefalexin cephalexin 1 Collinsella aerofaciens (vr), Veillonella parvula (vr), Bifidobacterium longum subsp. longum (vr) Phocaeicola vulgatus  
cefamandole   2   Bacteroides thetaiotaomicron, Parabacteroides distasonis, Phocaeicola vulgatus, Bacteroides fragilis, Bacteroides uniformis, Bacteroides ovatus  
cefazolin cephazolin 1 Parabacteroides distasonis, Bacteroides uniformis, Collinsella aerofaciens, Roseburia hominis + 17 others Bacteroides fragilis, Bacteroides thetaiotaomicron  
cefdinir   3 Bifidobacterium adolescentis, Coprococcus comes, Roseburia intestinalis, Lachnospira eligens + 16 others Bacteroides fragilis, Bacteroides ovatus, Bacteroides xylanisolvens, Bacteroides thetaiotaomicron  
cefepime   4 Blautia massiliensis, Escherichia coli, Ruminococcus bromii, Bifidobacterium adolescentis + 16 others Bifidobacterium longum subsp. longum, Bacteroides caccae, Bacteroides ovatus, Bacteroides xylanisolvens, Bacteroides thetaiotaomicron  
cefixime   3 Bacteroides uniformis, Veillonella parvula, Blautia obeum, Roseburia hominis + 10 others Bacteroides fragilis, Bacteroides ovatus, Coprococcus comes, Ruminococcus gnavus, Bifidobacterium longum subsp. longum, Bacteroides caccae, Bacteroides xylanisolvens  
cefmetazole   3 Collinsella aerofaciens, Dorea formicigenerans, Eubacterium rectale, Lachnospira eligens +11 others Bacteroides fragilis, Parabacteroides distasonis, Bacteroides thetaiotaomicron, Bacteroides caccae, Phocaeicola vulgatus, Bacteroides ovatus, Bifidobacterium longum subsp. longum, Bacteroides xylanisolvens  
cefoperazone   3 Roseburia hominis, Bifidobacterium adolescentis, Roseburia intestinalis, Ruminococcus bromii + 11 others Bacteroides fragilis, Parabacteroides distasonis, Bacteroides thetaiotaomicron, Bacteroides caccae, Phocaeicola vulgatus, Bacteroides ovatus, Bacteroides uniformis, Bacteroides xylanisolvens, Veillonella parvula  
cefotaxime   3 Intestinimonas butyriciproducens, Eubacterium rectale, Streptococcus parasanguinis, Escherichia coli, + 19 others Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides xylanisolvens  
cefotetan   2 Bifidobacterium adolescentis, Roseburia hominis, Blautia obeum, Bifidobacterium angulatum, Bifidobacterium longum subsp. infantis + 11 others Bacteroides fragilis, Bacteroides thetaiotaomicron, Ruminococcus gnavus, Bacteroides uniformis, Parabacteroides distasonis, Bacteroides ovatus, Bifidobacterium longum subsp. longum, Bacteroides caccae, Bacteroides xylanisolvens  
cefotiam   2 Blautia obeum, Roseburia hominis, Bifidobacterium adolescentis, Eubacterium rectale, Roseburia intestinalis + 14 others Phocaeicola vulgatus, Bacteroides uniformis, Bacteroides fragilis, Parabacteroides distasonis, Bacteroides thetaiotaomicron, Bacteroides ovatus, Bacteroides xylanisolvens  
cefoxitin   3 Alistipes putredinis, Bifidobacterium angulatum, Bifidobacterium longum subsp. infantis, Clostridium leptum, Roseburia hominis + 12 others Bacteroides fragilis, Parabacteroides distasonis, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides ovatus, Bacteroides stercoris, Bacteroides caccae, Phocaeicola vulgatus, Veillonella parvula  
cefpirom cefpirome 4 Minor colonisers: Haemophilus influenzae, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Serratia marcescens, Shigella sonnei, Streptococcus pneumoniae, Streptococcus pyogenes Enterococcus faecalis (moderate coloniser), Enterococcus faecium (moderate coloniser), Dysgonomonas gadei (minor coloniser)  
cefpodoxime   3 Escherichia coli, Haemophilus parainfluenzae (moderate coloniser) Moderate colonisers: Clostridioides difficile, Enterococcus faecalis, Enterococcus faecium  
cefprozil cefproxil 2 Minor gut colonisers: Staphylococcus warneri, Staphylococcus hominis subsp. hominis, Staphylococcus simulans, Bacillus clausii, Bacillus subtilis Bacteroides fragilis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Phocaeicola vulgatus. Moderate colonisers: Enterococcus faecalis, Clostridioides difficile, Enterobacter cloacae  
ceftazidime   3 Bacteroides fragilis, Bifidobacterium adolescentis, Phocaeicola vulgatus, Roseburia intestinalis + 12 others Bacteroides thetaiotaomicron, Ruminococcus gnavus, Bacteroides uniformis, Parabacteroides distasonis, Bacteroides ovatus, Bifidobacterium longum subsp. longum, Bacteroides caccae, Bacteroides xylanisolvens  
ceftizoxime   3 Veillonella parvula. Moderate colonisers: Cutibacterium acnes and Sutterella wadsworthensis Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides uniformis, Parabacteroides distasonis, Phocaeicola vulgatus  
cefuroxime   2 Dorea formicigenerans, Escherichia coli, Bifidobacterium longum subsp. longum, Bacteroides uniformis, Coprococcus comes + 12 others Bacteroides caccae, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides xylanisolvens, Parabacteroides distasonis  
cephalot cephalothin, cefalothin 1 Bacteroides pectinophilus, Flavonifractor plautii, Bacteroides fragilis, Bifidobacterium adolescentis, Bifidobacterium longum subsp. infantis + 20 others Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides xylanisolvens; Moderate colonisers: Akkermansia muciniphila, Clostridioides difficile, Enterocloster bolteae  
moxalactam   3 Bifidobacterium adolescentis, Collinsella aerofaciens, Eubacterium rectale, Roseburia intestinalis, Ruminococcus bromii + 11 others Bacteroides caccae, Bacteroides thetaiotaomicron, Parabacteroides distasonis, Bacteroides xylanisolvens; Moderate colonisers: Akkermansia muciniphila, Bilophila wadsworthia, Ruminococcus torques  

 

Aminoglycosides and Macrolides
Shorthand Longhand/ Other names Susceptible (widespread colonisers) Resistant (widespread colonisers) Significance
amikacin   Bifidobacterium longum subsp. longum, Collinsella aerofaciens, Coprococcus comes, Eubacterium rectale, Roseburia intestinalis, Ruminococcus bromii, Ruminococcus gnavus, Streptococcus parasanguinis Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Roseburia hominis, Veillonella parvula + 12 others  
apramycin   Campylobacter jejuni subsp. jejuni (minor coloniser) Dermabacter hominis (minor coloniser)  
diHstrep dihydrostreptomycin Bifidobacterium longum subsp. longum, Roseburia intestinalis, Streptococcus parasanguinis; Ruminococcus torques (moderate coloniser); Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Eubacterium rectale, Roseburia hominis + 16 others  
framycetin   Phyllobacterium myrsinacearum (rare coloniser); Unlikely colonisers: Aureimonas altamirensis, Methylorubrum zatmanii    
gentamicin   Roseburia intestinalis; Moderate colonisers: Klebsiella pneumoniae, Enterococcus faecalis, Staphylococcus epidermidis Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Dorea formicigenerans, Phocaeicola vulgatus + 21 others  
gen500ug gentamicin (500 ug) Rare colonisers: Actinomyces ihuae, Butyricimonas phoceensis, Paenibacillus tuaregi, Kallipyga massiliensis, Peptoniphilus obesi    
kanamycin   Blautia wexlerae, Flavonifractor plautii; Moderate colonisers: Acidaminococcus intestini, Dialister succinatiphilus, Turicibacter sanguinis Alistipes finegoldii, Bacteroides caccae, Bifidobacterium adolescentis, Blautia producta, Roseburia hominis + 25 others  
neomycin   Blautia producta; Acidaminococcus fermentans (moderate coloniser); Minor colonisers: Bacillus subtilis, Campylobacter coli, Megamonas hypermegale Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia intestinalis + 21 others  
netilmycin   Minor colonisers: Corynebacterium mucifaciens, Hafnia alvei, Proteus penneri, Sphingomonas paucimobilis Minor colonisers: Dysgonomonas gadei, Achromobacter xylosoxidans, Atlantibacter hermannii  
sisomicin   Roseburia intestinalis; Ruminococcus torques (moderate coloniser); M Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 18 others  
spectinomycin   Bifidobacterium longum subsp. longum, Coprococcus comes, Eubacterium rectale, Roseburia intestinalis, Streptococcus parasanguinis Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 15 others  
streptomycin   Blautia producta; Moderate colonisers: Bacillus badius, Brevundimonas diminuta, Campylobacter concisus, Oxalobacter formigenes Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 20 others  
tobramycin   Collinsella aerofaciens, Eubacterium rectale, Roseburia intestinalis, Ruminococcus bromii, Streptococcus parasanguinis Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 16 others  
azithromycin   Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 18 others Moderate colonisers: Clostridioides difficile, Clostridium innocuum, Ruthenibacterium lactatiformans; Minor colonisers: Aliarcobacter butzleri, Fusobacterium mortiferum, Klebsiella oxytoca, Staphylococcus hominis subsp. hominis  
erythromycin   Alistipes putredinis, Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 21 others Escherichia coli  
clarithromycin   Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 18 others Moderate colonisers: Bilophila wadsworthia, Clostridium innocuum, Haemophilus parainfluenzae; Minor colonisers: Fusobacterium nucleatum, Edwardsiella tarda, Morganella morganii (+ 17 others)  
fidaxomicin   Moderate colonisers: Clostridium innocuum, Clostridium paraputrificum; Minor colonisers: Staphylococcus aureus subsp. aureus, Paeniclostridium sordellii Bacteroides fragilis; Moderate colonisers: Enterococcus faecalis, Enterococcus faecium, Bilophila wadsworthia  
josamycin   Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 18 others Escherichia coli; Clostridioides difficile (moderate coloniser); Corynebacterium amycolatum (minor coloniser)  
oleandomycin   Minor colonisers: Bacillus cereus, Bacillus circulans, Bacillus pumilus, Bacillus thuringiensis, Eubacterium barkeri, Gemella haemolysans, Rothia mucilaginosa Bacillus licheniformis (minor coloniser); Rare colonisers: Aestuariimicrobium kwangyangense, Amycolatopsis alba, Bacillus mycoides, Bhargavaea beijingensis, Fusobacterium perfoetens, Streptomyces thermoviolaceus  
pristinamycin   Bifidobacterium adolescentis, Bifidobacterium angulatum, Bifidobacterium longum subsp. infantis, Bifidobacterium longum subsp. longum; Bifidobacterium bifidum (moderate coloniser) Bacillus pakistanensis (rare coloniser)  
quin-dalf quinupristin-dalfopristin Bifidobacterium adolescentis, Clostridium leptum, Bifidobacterium longum subsp. longum; Moderate colonisers: Finegoldia magna, Eggerthella lenta, Bifidobacterium bifidum Bacteroides fragilis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Parabacteroides distasonis, Phocaeicola vulgatus  
roxithromycin   Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 18 others Escherichia coli; Moderate colonisers: Bilophila wadsworthia, Clostridium innocuum, Finegoldia magna  
spiramycin   Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 19 others Escherichia coli, Veillonella parvula; Moderate colonisers: Bilophila wadsworthia, Clostridioides difficile, Clostridium spiroforme, Parvimonas micra  
telithromycin   Bifidobacterium adolescentis, Bifidobacterium angulatum, Bifidobacterium longum subsp. infantis, Bifidobacterium longum subsp. longum; Moderate colonisers: Bilophila wadsworthia, Clostridioides difficile, Bifidobacterium breve Clostridium innocuum (moderate coloniser); Mycoplasma hominis (minor coloniser), Bacillus clausii (minor coloniser)  

 

Glycopeptides (Vancomycins) and Polyketides
Shorthand Longhand/ Other names Susceptible (widespread colonisers) Resistant (widespread colonisers) Significance
bacitracin   Bifidobacterium adolescentis, Bacteroides uniformis, Blautia obeum, Roseburia hominis, Ruminococcus bromii + 11 others Bacteroides caccae, Bacteroides thetaiotaomicron, Clostridium leptum, Escherichia coli, Phocaeicola vulgatus + 4 others  
gramicidin   Bacillus badius (moderate coloniser); Staphylococcus aureus subsp. aureus (minor coloniser), Bacillus circulans (minor coloniser) Minor colonisers: Bacillus licheniformis, Bacillus pumilus, Bacillus subtilis  
nisin A   Bifidobacterium longum subsp. infantis, Bifidobacterium longum subsp. longum; Moderate colonisers: Bifidobacterium animalis, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium dentium Catenulispora acidiphila (unlikely coloniser)  
rifabutin   Bacteroides caccae, Bifidobacterium longum subsp. longum, Blautia obeum, Dorea formicigenerans, Ruminococcus gnavus + 19 others    
rifalazil   Bacteroides fragilis, Clostridioides difficile (moderate coloniser), Mycobacterium florentinum (rare coloniser), Enterococcus saccharolyticus (rare coloniser)    
rifampicin   Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 23 others Flavonifractor plautii; Moderate colonisers: Campylobacter concisus, Erysipelatoclostridium saccharogumia, Mitsuokella multacida, Enterococcus faecium, Bifidobacterium animalis, Erysipelatoclostridium ramosum  
rifapentine   Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 19 others Erysipelatoclostridium ramosum (moderate coloniser), Corynebacterium striatum (rare coloniser)  
dalbavancin   Moderate colonisers: Clostridioides difficile, Clostridium innocuum, Faecalicatena contorta, Paraclostridium bifermentans, Terrisporobacter glycolicus + 4 others Enterococcus faecium (moderate coloniser)  
teicoplanin   Bifidobacterium adolescentis, Clostridium leptum, Eubacterium rectale, Intestinimonas butyriciproducens, Roseburia intestinalis + 4 others Bacteroides caccae, Bacteroides fragilis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Escherichia coli, Parabacteroides distasonis, Phocaeicola vulgatus  
vancomycin   Bifidobacterium adolescentis, Blautia obeum, Intestinimonas butyriciproducens, Roseburia hominis, Ruminococcus bromii + 14 others Alistipes finegoldii, Bacteroides caccae, Blautia producta, Escherichia coli, Phocaeicola vulgatus + 10 others  

 

Quinolones and Tetracyclines
Shorthand Longhand/ Other names Gen. (Xth) Susceptible (widespread colonisers) Resistant (widespread colonisers) Significance
linezold linezolid   Bacteroides xylanisolvens, Bifidobacterium longum subsp. longum, Blautia obeum, Dorea formicigenerans, Phocaeicola vulgatus + 13 others Erysipelatoclostridium ramosum (moderate coloniser), Ruthenibacterium lactatiformans (moderate coloniser), Aerococcus viridans (minor coloniser), Bordetella hinzii (unlikely coloniser), Moraxella catarrhalis (unlikely coloniser)  
besiflox besifloxicin   Moderate colonisers: Klebsiella pneumoniae, Clostridium perfringens, Cutibacterium acnes, Enterobacter cloacae, Streptococcus anginosus, Streptococcus mitis, Streptococcus salivarius    
ciproflox ciprofloxicin 2 Alistipes putredinis, Bacteroides caccae, Bifidobacterium adolescentis, Blautia producta, Roseburia intestinalis + 20 others Bacteroides ovatus, Bacteroides uniformis, Blautia massiliensis, Phocaeicola vulgatus; Moderate colonisers: Akkermansia muciniphila, Clostridioides difficile, Ligilactobacillus salivarius  
clavulan clavulanic acid   Odoribacter splanchnicus, Ruminococcus bromii, Streptococcus equi subsp. equi (rare coloniser), Helicobacter pylori (non-bowel coloniser) Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 17 others  
clinaflox clinafloxicin   Bacteroides caccae, Bifidobacterium longum subsp. longum, Blautia obeum, Lachnospira eligens, Ruminococcus bromii + 19 others Akkermansia muciniphila (moderate coloniser), Ruminococcus torques (moderate coloniser),  
enoxacin     Bacteroides caccae, Collinsella aerofaciens, Eubacterium rectale, Parabacteroides distasonis, Ruminococcus gnavus + 11 others Bifidobacterium adolescentis, Bifidobacterium longum subsp. longum, Blautia obeum, Coprococcus comes, Lachnospira eligens, Roseburia hominis, Ruminococcus bromii, Streptococcus parasanguinis  
garenox garenoxicin   Bacteroides caccae, Bacteroides fragilis, Bacteroides ovatus, Bacteroides stercoris, Bacteroides thetaiotaomicron, Parabacteroides distasonis, Phocaeicola vulgatus Alcaligenes faecalis (minor coloniser), Streptococcus pneumoniae (minor coloniser), Pseudocitrobacter faecalis (rare coloniser)  
gatiflox gatifloxicin 4 Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia intestinalis + 19 others Eubacterium rectale; Moderate colonisers: Akkermansia muciniphila, Enterococcus faecium, Ruminococcus torques  
gemiflox gemifloxicin   Minor colonisers: Bacillus clausii, Haemophilus influenzae, Mycoplasma hominis, Porphyromonas uenonis, Serratia marcescens Clostridioides difficile (moderate coloniser), Fusobacterium canifelinum (rare coloniser), Pseudocitrobacter faecalis (rare coloniser)  
levoflox levofloxicin 3 Bacteroides fragilis, Collinsella aerofaciens, Parabacteroides distasonis, Streptococcus parasanguinis, Veillonella parvula Bacteroides ovatus, Bacteroides uniformis, Ruminococcus gnavus; Moderate colonisers: Enterocloster aldenensis, Hungatella hathewayi, Ruthenibacterium lactatiformans  
moxiflox moxifloxicin 4 Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 17 others Akkermansia muciniphila (moderate coloniser), Ruminococcus torques (moderate coloniser); Minor colonisers: Anaerococcus vaginalis, Bacteroides fluxus, Providencia alcalifaciens, Streptococcus pneumoniae  
nalidixic nalidixic acid 1 Bacteroides xylanisolvens, Escherichia coli; Moderate colonisers: Bacillus badius, Clostridium perfringens, Klebsiella pneumoniae Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis, +20 others  
norflox norfloxicin 2 Bacteroides caccae, Bifidobacterium adolescentis, Escherichia coli, Ruminococcus gnavus, Veillonella parvula + 5 others Bacteroides thetaiotaomicron, Bifidobacterium longum subsp. longum, Blautia obeum, Roseburia hominis, Ruminococcus bromii + 8 others  
oflox ofloxicin 2 Bacteroides caccae, Bifidobacterium adolescentis, Escherichia coli, Phocaeicola vulgatus, Streptococcus parasanguinis + 9 others Blautia obeum, Coprococcus comes, Lachnospira eligens, Roseburia hominis, Ruminococcus gnavus + 5 others  
peflox perfloxicin 2 Bacteroides caccae, Collinsella aerofaciens, Escherichia coli, Odoribacter splanchnicus, Phocaeicola vulgatus + 5 others Bifidobacterium adolescentis, Blautia obeum, Parabacteroides distasonis, Roseburia intestinalis, Streptococcus parasanguinis + 9 others  
pipemidic pipemidic acid 1 Escherichia coli, Serratia marcescens (minor coloniser) Bacteroides caccae, Bifidobacterium longum subsp. longum, Blautia obeum, Lachnospira eligens, Roseburia hominis + 16 others  
saraflox sarafloxicin   Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 18 others Roseburia hominis, Akkermansia muciniphila (moderate coloniser), Ornithobacterium rhinotracheale (rare coloniser)  
sparflox sparfloxicin 3 Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 16 others Dorea formicigenerans, Roseburia hominis, Ruminococcus bromii, Akkermansia muciniphila (moderate coloniser), Ruminococcus torques (moderate coloniser)  
trovaflox trovafloxicin   Bacteroides fragilis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Parabacteroides distasonis, Phocaeicola vulgatus    
doxycycl doxycycline   Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 18 others Moderate colonisers: Clostridium spiroforme, Enterococcus avium, Finegoldia magna; Minor colonisers: Alistipes obesi, Anaerococcus vaginalis, Corynebacterium mucifaciens  
chlortetr chlortetracycline   Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 18 others Alcaligenes faecalis (minor coloniser), Streptococcus suis (minor coloniser); Corynebacterium cystitidis (rare coloniser)  
deoxycycl deoxycycline   Bacteroides togonis (rare coloniser), Phyllobacterium myrsinacearum (rare coloniser) Alistipes inops (rare coloniser)  
meclocycl meclocycline   Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 19 others    
methacycl methacycline   Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 19 others    
minocycl minocycline   Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 20 others Bacteroides fragilis; Moderate colonisers: Bifidobacterium bifidum, Bifidobacterium pseudocatenulatum, Enterococcus faecalis; Minor colonisers: Bifidobacterium pseudolongum, Proteus mirabilis, Staphylococcus warneri  
oxytetr oxytetracycline   Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 19 others Prevotella copri (moderate coloniser); Minor colonisers: Bacillus subtilis, Staphylococcus aureus subsp. aureus, Treponema succinifaciens  
tetracycl tetracycline   Bacteroides fragilis, Bacteroides pectinophilus, Blautia producta, Escherichia coli, Roseburia intestinalis + 20 others Moderate colonisers: Enterococcus avium, Enterococcus faecalis, Enterococcus faecium, Ligilactobacillus salivarius, Prevotella copri  
tigecycl tigecycline   Bacteroides caccae, Bacteroides ovatus, Bacteroides thetaiotaomicron, Blautia massiliensis, Escherichia coli, Eubacterium rectale, Phocaeicola vulgatus, Roseburia intestinalis, Ruminococcus gnavus Minor colonisers: Achromobacter xylosoxidans, Anaerococcus vaginalis, Morganella morganii, Proteus penneri  

 

Heterocycles & Miscellaneous
Shorthand Longhand/ Other names Susceptible (widespread colonisers) Resistant (widespread colonisers) Significance
chloramph chloramphenicol Alistipes putredinis, Bacteroides pectinophilus, Bifidobacterium adolescentis, Roseburia intestinalis, Streptococcus parasanguinis + 18 others Blautia producta, Enterococcus faecalis (moderate coloniser), Enterococcus faecium (moderate coloniser), Desulfovibrio fairfieldensis (minor coloniser), Lysinibacillus fusiformis (minor coloniser)  
fosfomyc fosfomycin Escherichia coli, Roseburia intestinalis; Minor colonisers: Staphylococcus pasteuri, Citrobacter koseri, Fusobacterium nucleatum, Peptoniphilus grossensis Bacteroides caccae, Bacteroides fragilis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Eubacterium rectale, Phocaeicola vulgatus  
isoniazd isoniazid, isonicotinic acid hydrazide   Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis, +19 others  
metronid metronidazole Alistipes putredinis, Anaerostipes caccae, Blautia obeum, Intestinimonas butyriciproducens, Ruminococcus gnavus + 19 others Bifidobacterium adolescentis, Bifidobacterium angulatum, Bifidobacterium longum subsp. infantis, Bifidobacterium longum subsp. longum, Escherichia coli, Streptococcus parasanguinis  
nitrofur nitrofurantoin Bacteroides fragilis, Bifidobacterium angulatum, Blautia obeum, Parabacteroides distasonis, Ruminococcus bromii + 20 others Bacteroides caccae; Moderate colonisers: Akkermansia muciniphila, Bilophila wadsworthia, Clostridioides difficile, Parabacteroides merdae, Ruminococcus torques, Streptococcus salivarius  
ranbezold ranbezolid Bacteroides fragilis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Parabacteroides distasonis, Phocaeicola vulgatus    
sulfadiaz sulfadiazine  Minor colonisers: Kluyvera ascorbata, Atlantibacter hermannii, Cedecea davisae, Edwardsiella tarda, Raoultella ornithinolytica Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis, +19 others  
sulfadime sulfadimethoxine Staphylococcus hyicus (rare coloniser) Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis, +19 others  
sulfameth sulfamethoxazole Enterobacter cloacae (moderate coloniser); Minor colonisers: Enterobacter ludwigii, Helicobacter cinaedi, Pantoea agglomerans, Serratia marcescens, Staphylococcus kloosii Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis, +19 others  
sulfanil sulfanilamide Minor colonisers: 

Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis, +19 others; Fusobacterium nucleatum (minor coloniser)

  
trimetho trimethoprim Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Odoribacter splanchnicus, Ruminococcus gnavus + 8 others Bacteroides xylanisolvens, Blautia producta, Lachnospira eligens, Roseburia hominis, Veillonella parvula + 7 others  
SXT trimethoprim-sulfamethoxazole Bacteroides caccae, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Escherichia coli, Phocaeicola vulgatus Eubacterium rectale, Roseburia intestinalis; Moderate colonisers:  Clostridioides difficile, Intestinibacter bartlettii, Staphylococcus epidermidis  
SXT (cotrim) trimethoprim-sulfamethoxazole Moderate colonisers: Enterococcus durans, Enterococcus faecium, Staphylococcus epidermidis; Minor colonisers: Coprobacter fastidiosus, Streptococcus equinus, Staphylococcus haemolyticus Minor colonisers: Shigella flexneri, Cutibacterium granulosum, Cutibacterium avidum, Aeromonas caviae, Bacillus licheniformis, Dermabacter hominis, Peptoniphilus grossensis, Streptococcus pseudopneumoniae  
dalbavancin   Moderate colonisers: Erysipelatoclostridium ramosum, Faecalicatena contorta, Clostridioides difficile, Clostridium innocuum, Clostridium butyricum, Clostridium paraputrificum, Paraclostridium bifermentans, Terrisporobacter glycolicus, Clostridium perfringens Enterococcus faecium (moderate coloniser)  
teicoplanin   Bifidobacterium adolescentis, Bifidobacterium angulatum, Bifidobacterium longum subsp. infantis, Bifidobacterium longum subsp. longum, Clostridium leptum, Collinsella aerofaciens, Eubacterium rectale, Intestinimonas butyriciproducens, Roseburia intestinalis Bacteroides caccae, Bacteroides fragilis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Escherichia coli, Parabacteroides distasonis, Phocaeicola vulgatus  
vancomycin   Bacteroides xylanisolvens, Bifidobacterium adolescentis, Blautia obeum, Intestinimonas butyriciproducens, Ruminococcus bromii + 14 others Alistipes shahii, Bacteroides caccae, Blautia producta, Escherichia coli, Phocaeicola vulgatus, Veillonella parvula + 9 others  
clindamyc clindamycin Alistipes putredinis, Bacteroides pectinophilus, Bifidobacterium longum subsp. infantis, Blautia producta, Roseburia hominis + 16 others Anaerostipes caccae; Moderate colonisers: Enterococcus avium, Enterococcus casseliflavus, Enterococcus durans, Enterococcus gallinarum, Ruthenibacterium lactatiformans  
lincomyc lincomycin Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 20 others Escherichia coli; Clostridioides difficile (moderate coloniser), Clostridium spiroforme (moderate coloniser); Minor colonisers: Bacillus licheniformis, Bacillus pumilus, Dermabacter hominis  
daptomyc daptomycin Clostridium leptum, Bifidobacterium adolescentis, Bifidobacterium longum subsp. longum; Moderate colonisers: Clostridioides difficile, Enterococcus faecalis, Finegoldia magna Moderate colonisers: Erysipelatoclostridium ramosum, Clostridium paraputrificum; Minor colonisers: Anaerobiospirillum succiniciproducens, Clostridium tertium, Paeniclostridium sordellii  
monensin     Allisonella histaminiformans (minor coloniser)  
novobioc novobiocin Staphylococcus epidermidis (moderate coloniser), Minor colonisers: Bacillus sonorensis, Rothia mucilaginosa, Staphylococcus intermedius Bifidobacterium animalis (moderate coloniser); Minor colonisers: Alcaligenes faecalis, Bacillus subtilis, Bifidobacterium pseudolongum, Brachyspira pilosicoli, Staphylococcus kloosii  
colistin   Bacteroides caccae, Blautia obeum, Escherichia coli, Phocaeicola vulgatus, Roseburia intestinalis + 7 others Alistipes finegoldii, Bacteroides fragilis, Bifidobacterium adolescentis, Blautia wexlerae, Ruminococcus bromii + 12 others  
polymyx B polymyxin B Moderate colonisers: Mitsuokella multacida, Campylobacter concisus, Bacillus badius, Oxalobacter formigenes Bifidobacterium adolescentis, Bifidobacterium angulatum, Bifidobacterium longum subsp. longum, Bifidobacterium longum subsp. infantis  
fusidic fusidic acid Bacteroides caccae, Bifidobacterium adolescentis, Blautia obeum, Lachnospira eligens, Roseburia hominis + 18 others Escherichia coli; Moderate colonisers: Akkermansia muciniphila, Bilophila wadsworthia; Minor colonisers: Citrobacter braakii, Edwardsiella tarda, Streptococcus pyogenes  
bile   Acidaminococcus intestini (moderate coloniser), Acidaminococcus fermentans (moderate coloniser), Prevotella jejuni (minor coloniser), Christensenella hongkongensis (minor coloniser)    
vibrio129 vibriostatic agent O/129 Minor colonisers: Cedecea davisae, Edwardsiella tarda; Corynebacterium pyruviciproducens (rare coloniser) Minor colonisers: Bacillus subtilis, Staphylococcus pasteuri; Rare colonisers: Aeromonas dhakensis, Mammaliicoccus fleurettii, Staphylococcus nepalensis  

 

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