INCFinder

GenBank ID	CP031584.1
Plasmid name	pIncAC2-1502320
Classification	C1
Length	164 082 bp
GC content	52%
Organism	Klebsiella pneumoniae strain N4b
Curation	Manually annotated

Plasmid map

Notes

The 3' end of RHS1 is deleted from 3155 bp of the gene. The empty sites of I1 and I2 insertions are intact.

Characteristic genes

Gene name	Length	Location	Length of alignment	Identity (%)	Coverage (%)	E-value
repA	1057	1 - 1057 (+)	1057	99	96	0
ORF1832	5499	55240 - 60738 (+)	5499	100	100	0
RHS	3154	140167 - 143320 (+)	3154	100	86	0

Antimicrobial resistance genes

Type match	Model name	Model type	Location	E-value	Identity
Perfect	sul1	protein homolog model	107197 - 108036(+)	0	100 %
sulfonamide resistant sul AMR Gene Family The sul genes encode forms of dihydropteroate synthase that confer resistance to sulfonamide. sulfadiazine Antibiotic Sulfadiazine is a potent inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids. sulfadimidine Antibiotic Sulfadimidine is an alkaline sulfonamide antibiotic that inhibits dihydropteroate synthase, and enzyme in the tetrahydrofolic acid biosynthesis pathway. This interferes with the production of folate, which is a precursor to many amino acids and nucleotides. sulfadoxine Antibiotic Sulfadoxine is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids. sulfamethoxazole Antibiotic Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides. sulfisoxazole Antibiotic Sulfisoxazole is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids. sulfacetamide Antibiotic Sulfacetamide is a very soluable sulfonamide antibiotic previously used to treat urinary tract infections. Its relatively low activity and toxicity to those with Stevens-Johnson syndrome have reduced its use and availability. mafenide Antibiotic Mafenide is a sulfonamide used topically for treating burns. sulfasalazine Antibiotic Sulfasalazine is a derivative of the early sulfonamide sulfapyridine (salicylazosulfapyridine). It was developed to increase water solubility and is taken orally for ulcerative colitis. sulfamethizole Antibiotic Sulfamethizole is a short-acting sulfonamide that inhibits dihydropteroate synthetase. sulfonamide antibiotic Drug Class Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway. antibiotic target replacement Resistance Mechanism Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.
Perfect	QnrA1	protein homolog model	110315 - 110971(+)	3.68377e-163	100 %
quinolone resistance protein (qnr) AMR Gene Family Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics ciprofloxacin Antibiotic Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome. levofloxacin Antibiotic Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication. moxifloxacin Antibiotic Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases. gatifloxacin Antibiotic Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa. nalidixic acid Antibiotic Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments. norfloxacin Antibiotic Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes. sparfloxacin Antibiotic Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes. fluoroquinolone antibiotic Drug Class The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death. antibiotic target protection Resistance Mechanism Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.
Perfect	TEM-1	protein homolog model	120392 - 121252(+)	0	100 %
TEM beta-lactamase AMR Gene Family TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid. Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin/tazobactam, although resistance has been described. amoxicillin Antibiotic Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan. ampicillin Antibiotic Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin. cefalotin Antibiotic Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases. monobactam Drug Class Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. cephalosporin Drug Class Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. penam Drug Class Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. penem Drug Class Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur. antibiotic inactivation Resistance Mechanism Enzymatic inactivation of antibiotic to confer drug resistance.
Perfect	mphA	protein homolog model	123600 - 124505(-)	0	100 %
macrolide phosphotransferase (MPH) AMR Gene Family Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity. erythromycin Antibiotic Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited. roxithromycin Antibiotic Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited. telithromycin Antibiotic Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis. clarithromycin Antibiotic Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections. azithromycin Antibiotic Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation. dirithromycin Antibiotic Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis. oleandomycin Antibiotic Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis. macrolide antibiotic Drug Class Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins. antibiotic inactivation Resistance Mechanism Enzymatic inactivation of antibiotic to confer drug resistance.
Strict	ANT(3'')-IIa	protein homolog model	126161 - 126952(-)	0	99.62 %
ANT(3'') AMR Gene Family Nucleotidylylation of streptomycin at the hydroxyl group at position 3'' aminoglycoside antibiotic Drug Class Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth. antibiotic inactivation Resistance Mechanism Enzymatic inactivation of antibiotic to confer drug resistance.
Perfect	dfrA1	protein homolog model	127045 - 127518(-)	2.15234e-116	100 %
trimethoprim resistant dihydrofolate reductase dfr AMR Gene Family Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance. trimethoprim Antibiotic Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic. diaminopyrimidine antibiotic Drug Class Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups. They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis. antibiotic target replacement Resistance Mechanism Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.
Perfect	AAC(6')-Il	protein homolog model	127661 - 128119(-)	3.00218e-112	100 %
AAC(6') AMR Gene Family Acetylation of the aminoglycoside antibiotic on the amino group at position 6'. neomycin Antibiotic Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. dibekacin Antibiotic Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. amikacin Antibiotic Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. sisomicin Antibiotic Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. netilmicin Antibiotic Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin. kanamycin A Antibiotic Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. tobramycin Antibiotic Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. isepamicin Antibiotic A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae. arbekacin Antibiotic A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci. gentamicin B Antibiotic Gentamicin B is a semisynthetic aminoglycoside antibacterial. aminoglycoside antibiotic Drug Class Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth. antibiotic inactivation Resistance Mechanism Enzymatic inactivation of antibiotic to confer drug resistance.
Perfect	VIM-1	protein homolog model	128213 - 129013(-)	0	100 %
VIM beta-lactamase AMR Gene Family The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants. VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors. There is a strong incidence of these in East Asia. carbapenem Drug Class Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. cephalosporin Drug Class Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. cephamycin Drug Class Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases. penam Drug Class Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. penem Drug Class Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur. antibiotic inactivation Resistance Mechanism Enzymatic inactivation of antibiotic to confer drug resistance.