Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin

Accession ARO:3004480
CARD Short NameBado_rpoB_RIF
DefinitionBifidobacterium are antibiotic resistant probiotics are prescribed to upkeep the population beneficial bacteria in the gut microbiome. However, horizontal gene transfer among gut microbes could create harmful antibiotic-resistant pathogenic bacteria, such as Mycobacterium tuberculosis. Lokesh et al. analyzed Bifidobacterium antitubercular drug resistance and mutations in rpoB. They found that B. animalis, B. longum and B. adolescentis showed considerable resistance to pyrazinamide, isoniazid, and streptomycin, while B. adolescentis had mutations both in the rifampicin (RIF) pocket and in regions outside the pockets, and also showed considerable resistance to RIF.
AMR Gene Familyrifamycin-resistant beta-subunit of RNA polymerase (rpoB)
Drug Classrifamycin antibiotic
Resistance Mechanismantibiotic target alteration, antibiotic target replacement
Resistomes with Sequence VariantsBifidobacterium animalisg+wgs, Bifidobacterium bifidumg+wgs, Bifidobacterium breveg+wgs, Bifidobacterium dentiumg+wgs, Bifidobacterium longumg+wgs, Bifidobacterium thermophilumg+wgs, Gardnerella vaginalisg+wgs, Parascardovia denticolenswgs
Classification11 ontology terms | Show
Parent Term(s)2 ontology terms | Show
+ rifamycin-resistant beta-subunit of RNA polymerase (rpoB) [AMR Gene Family]
+ confers_resistance_to_antibiotic rifampin [Antibiotic]
Publications

Lokesh D, et al. 2018. Sci Rep 8(1):11897 Bifidobacterium adolescentis is intrinsically resistant to antitubercular drugs. (PMID 30093677)

Resistomes

Prevalence of Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 413 important pathogens (see methodological details and complete list of analyzed pathogens). Values reflect percentage of genomes, plasmids, genome islands, or whole-genome shotgun assemblies that have at least one hit to the AMR detection model. Default view includes percentages calculated based on Perfect plus Strict RGI hits. Select the checkbox to view percentages based on only Perfect matches to AMR reference sequences curated in CARD (note: this excludes resistance via mutation as references in protein variant models are often wild-type, sensitive sequences).

Prevalence: protein homolog model (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
Bifidobacterium animalis100%0%65.81%0%
Bifidobacterium bifidum100%0%63.18%0%
Bifidobacterium breve98.04%0%49.4%0%
Bifidobacterium dentium100%0%61.36%0%
Bifidobacterium longum98.95%0%78.13%0%
Bifidobacterium thermophilum100%0%100%0%
Gardnerella vaginalis100%0%68.93%0%
Parascardovia denticolens0%0%33.33%0%
Show Perfect Only


Detection Models

Model Type: protein homolog model

Model Definition: Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.

Bit-score Cut-off (blastP): 2000


>gb|WP_041777404.1|-|Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin [Bifidobacterium adolescentis]
MAEATTNTTTIIARADQHDIDLHKASDRVNFGSIREPIDVPYLLGVQTDSFDWLIGNERWQKRVQEDLENGTNTVPHTSGLDEVFQEISP
IENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGDTGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGV
YFDRSQDRTSDKEVFGAKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTKDEIADAFKDYPLVMDALAKETVQTQDEALT
DLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVGRYKINRKLGLEKDVNDRSLSREDIIATIKYLVTLHAGETKFPGKRDGQDVDLR
VDVDDIDHFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDPEAITPQSLINIRPVNATIKEFFGTSQLSQFMDQNNPLAGVTNKRR
LSALGPGGLSRDRASMEVRDVHPSHFGRMCPIESPEGPNIGLIGSLATFGRINPFGFIETPYRKVVNGHVTDEVEYMTADRDAEHVIAQA
NQELDENGNFVKKQALARVGEEEAVDVPVSSVDYMDVSPRQMVSVGASLIPFLEHDEGHRALMGTNMQRQAVPLIESERPLVGTGAEWRA
AVDSGDVILAEKPGVVTYVSADIIRTMNDDGTTSSYKLAKFQRSNQTTCYNQVPLIHDGERVEAGTVLADGPATQKGEMALGKNLLIAFM
PWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAVANLDERGIIRIGAEVEAGDILVGKVTPKGETEL
TPEERLLRAIFGEKSREVRDTSLRVPHGETGTVIAVKEITREDAEEDGDELPNGVNQMIRVYIAQHRKITQGDKLSGRHGNKGVISRILP
EEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIAHAGWDISLDPDAEAAWKKYVPQGAEKGAPGTPVATPVFDGVRPETIKGLL
SCTLPDRDGNKLVGPDGKATLFDGRTGEPFPKPISVGYMYMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAY
GAAYTLHEMMTTKSDDVDGRVRVYGAIVKGENLPPAGIPESFKVLLKEMQSLSLNVEVLNADGVAIDMKEEDDDPSTSSDDLGFNIGARP
DAAAKEDQVAEEPEFQ


>gb|NC_008618.1|-|1667064-1670624|Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin [Bifidobacterium adolescentis]
TTGGCTGAGGCTACGACGAACACCACCACCATCATCGCACGCGCCGACCAGCATGATATTGATCTGCACAAGGCGTCGGACCGTGTGAAT
TTCGGCTCCATCCGCGAGCCCATTGATGTACCCTACCTGTTGGGTGTACAGACTGACAGCTTTGACTGGCTCATCGGCAACGAGCGCTGG
CAGAAGCGAGTCCAGGAGGATCTGGAGAACGGCACCAACACCGTGCCCCACACCTCCGGTCTTGACGAGGTCTTCCAGGAGATCTCCCCG
ATCGAGAACTTCGCTCAGACCATGAGCCTGACCTTCTCCGATCCGTACTTCGAAGAACCGCGCCACACCGTGCAGGAATGCAAGGAGAAG
GATTACACCTACTCCGCGCCGCTGTACGTGAACGCCGAATTCGAGAACGGCGACACCGGCGAAATCAAGTCCCAGACCGTGTTCATGGGC
GATTTCCCGCTGCAGACCCCGCACGGCACCTTCATCATCGGTGGTACCGAGCGAGTGATCGTGTCCCAGCTCGTGCGTTCCCCGGGCGTG
TACTTCGACCGTTCCCAGGACCGTACCTCCGATAAGGAAGTCTTCGGCGCGAAGATCATCCCGAGCCGTGGCGCATGGCTCGAGTTCGAG
ATCGACAAGCGCGACGTCCTCGGCGTGCGCGTGGACCGTAAGCGCAAGCAGTCCGCCATCGTGTTCCTCATGGCCATCGGCATGACCAAG
GATGAAATTGCCGACGCCTTCAAGGACTACCCGCTGGTCATGGACGCTCTCGCCAAGGAGACCGTGCAGACCCAGGACGAGGCCCTGACC
GACCTGTACCGCAAGATCCGTCCGGCCGACACCCCGACTCCGGAAGCCGGCAAGAACCTGCTGGACTCCTTCTACTTCAACACCAAGCGT
TACGATCTGGCCCGCGTCGGCCGTTACAAGATCAACCGCAAGCTTGGTCTGGAAAAGGACGTCAACGACCGCAGCCTGTCCCGCGAGGAC
ATCATCGCCACCATCAAGTACTTGGTCACCCTGCATGCGGGCGAGACCAAGTTCCCGGGCAAGCGCGACGGCCAGGACGTTGACCTGCGC
GTGGACGTCGACGATATCGACCACTTCGGCAACCGTCGTATCCGCCAGGTCGGCGAGCTGATCCAGAACCAGCTGCGCACCGGTCTGAGC
CGTATGGAGCGTGTGGTCCGCGAACGTATGACCACCCAGGATCCCGAGGCCATCACCCCGCAGTCCCTGATCAACATCCGTCCGGTGAAC
GCCACCATCAAGGAGTTCTTCGGAACCTCCCAGCTGTCCCAGTTCATGGATCAGAACAACCCGCTGGCTGGCGTGACCAACAAGCGTCGT
CTGTCCGCTCTGGGCCCCGGTGGCCTGTCCCGCGACCGCGCCTCCATGGAAGTGCGAGACGTGCACCCGTCCCATTTCGGCCGTATGTGC
CCGATCGAGTCTCCTGAAGGCCCGAACATCGGTCTGATCGGCTCCCTGGCAACCTTCGGTCGCATCAACCCGTTCGGTTTCATCGAGACC
CCGTACCGCAAGGTCGTCAACGGCCACGTCACCGATGAAGTCGAGTACATGACCGCTGACCGCGATGCCGAGCACGTCATCGCCCAGGCC
AACCAGGAGCTCGACGAGAACGGCAACTTCGTCAAGAAGCAGGCTCTTGCCCGAGTCGGCGAAGAGGAAGCGGTCGATGTGCCGGTCAGC
TCCGTCGATTACATGGACGTCTCCCCGCGTCAGATGGTTTCCGTCGGCGCCTCCCTGATTCCGTTCCTGGAGCACGATGAGGGCCACCGA
GCGCTGATGGGCACCAACATGCAGCGTCAGGCCGTGCCGCTGATCGAATCCGAGCGTCCGCTCGTGGGCACCGGCGCCGAATGGCGCGCC
GCCGTCGATTCCGGCGACGTCATCCTGGCCGAGAAGCCGGGCGTGGTGACCTACGTGTCCGCCGACATCATCCGTACCATGAACGACGAT
GGCACCACCAGCTCCTACAAGCTGGCCAAATTCCAGCGTTCCAACCAGACCACCTGCTACAACCAGGTCCCGCTCATCCACGACGGTGAA
CGCGTGGAAGCCGGCACCGTGCTGGCCGATGGTCCGGCAACCCAGAAGGGCGAGATGGCACTGGGCAAGAACCTGCTCATCGCCTTCATG
CCGTGGAACGGCTACAACTACGAGGATGCTGTGATCATCTCCCAGCGCCTTGTGCAGGACGACACCCTGAGCTCCATCCACATCGAGGAG
TACGAGATCGATGCCCGTGAAACCAAGCTGGGCGCCGAAGAGATCACCCGCGACCTGCCGAACGTCGGCGAGGACGCGGTGGCCAACCTC
GACGAGCGTGGCATCATCCGCATCGGCGCCGAAGTCGAAGCCGGCGACATCCTGGTCGGCAAGGTCACCCCGAAGGGCGAGACCGAGCTG
ACTCCGGAAGAGCGCCTGCTGCGCGCCATCTTCGGTGAGAAGAGCCGCGAAGTGCGTGACACCTCGCTGCGCGTGCCTCACGGCGAGACC
GGCACCGTCATCGCGGTCAAGGAAATCACCCGCGAGGACGCCGAGGAAGACGGCGACGAACTGCCGAACGGCGTGAACCAGATGATTCGC
GTCTACATCGCACAGCACCGTAAGATCACCCAGGGCGACAAGCTCTCCGGCCGTCACGGCAACAAGGGCGTCATCTCCCGCATCCTGCCG
GAAGAGGACATGCCGTTCCTCGCCGACGGTACTCCGGTGGACATCATGCTGAACCCGCTGGGCGTGCCTTCTCGAATGAACCTTGGCCAG
GTGCTGGAACTGCACCTCGGCTGGATCGCGCACGCTGGCTGGGACATCTCCCTGGATCCGGATGCCGAGGCCGCTTGGAAGAAGTACGTG
CCGCAGGGCGCCGAAAAGGGCGCTCCGGGCACTCCGGTGGCCACCCCGGTGTTCGACGGCGTCCGTCCGGAAACCATCAAGGGCCTGCTC
AGCTGCACCCTTCCGGACCGCGACGGCAACAAGCTCGTCGGCCCCGACGGCAAGGCGACCCTGTTCGACGGCCGTACCGGCGAACCGTTC
CCGAAGCCGATCTCCGTGGGCTACATGTACATGCTGAAGCTGCACCACCTGGTCGACGACAAGATCCACGCCCGCTCCACCGGCCCGTAC
TCCATGATCACCCAGCAGCCGCTGGGCGGCAAGGCTCAGTTCGGTGGCCAGCGCTTCGGCGAGATGGAAGTGTGGGCCCTCGAGGCCTAC
GGTGCCGCCTACACGCTGCACGAAATGATGACCACCAAGTCCGATGACGTCGACGGCCGCGTGCGCGTCTACGGCGCCATCGTGAAGGGC
GAGAACCTGCCGCCGGCAGGCATCCCGGAGTCCTTCAAGGTGCTGCTTAAGGAAATGCAGTCCCTGTCCCTGAATGTCGAAGTGCTCAAC
GCCGACGGCGTGGCTATCGACATGAAGGAAGAGGACGACGATCCGTCCACATCCTCCGATGATCTGGGCTTCAACATTGGTGCGCGTCCT
GACGCTGCCGCCAAGGAAGATCAGGTTGCCGAGGAACCCGAATTCCAGTGA