TABLE 3.

Molecular and virulence characteristics of PAI of bacterial pathogens causing disease in humans, animals, and plantsa

Species (pathogroup)Strainc or serovarPAI nameSize (bp)Insertion siteStability% G+CdCharacteristic and virulence determinants encoded on PAI
Gram-negative bacteria
    E. coli
        (UPEC)536PAI I53676,843tRNA selCLow46.0Alpha-hemolysin, fimbriae, adhesins
        (UPEC)536PAI II536102,200tRNA leuXLow46.0Alpha-hemolysin, P-fimbriae, Hek-adhesin, hemagglutinin-like adhesins
        (UPEC)536PAI III53668,124tRNA thrWLow47.0S-fimbriae, iro siderophore system, Sap adhesin, TSH-like hemoglobin protease, HmuR-like heme receptor
        (UPEC)536PAI IV53630,200tRNA asnTLow57.0Siderophore synthesis, iron uptake, see HPI
        (UPEC)J96PAI IJ96>170,000tRNA pheVNPlNPAlpha-hemolysin, P-pilus
        (UPEC)J96PAI IIJ96>110,000tRNA pheUNPNPAlpha-hemolysin, Prs, (CNF1), heat-resistant hemagglutinin
        (UPEC)CFT073PAI ICFT07357,988tRNA pheVNP42.9Alpha-hemolysin, P-fimbriae, aerobactin
        (UPEC)CFT073PAI IICFT073>71,684tRNA pheUNP48.8eP-fimbriae, iron-regulated genes
        (MNEC)C5PAI IC5NPtRNA leuXMidNPAlpha-hemolysin, Prs, CNF1, heat-resistant hemagglutinin
        (MNEC)RS218GimA∼20,300yjiD/yiiENP46.2eIbeRAT, GcxKRCI (glyoxylate pathway), CglDTEC (glycerol metabolism), PtnIPKC (PTS system)
        (SEPEC)AL863PAI IAL862∼61,000tRNA pheRNP46.4eAfaE-III adhesin, ribose metabolism, PTS system
PAI IIAL863NPtRNA pheVNPNPAfaE-III adhesin (similar to PAIAL862)
        (EHEC)EDL933LEE43,590tRNA selCHigh40.91Translocation of Tir, T3SS
68-24TAI>8,040NPNPNPIha (IrgA homologue adhesin), TlpA-D (telluriteR)
EDL933OI#735,140tRNA aspVNPNPMacrophage toxin, ClpB-like chaperone
OI#2825,164ybaTNPNPRTX-like exotoxin, transport system
OI#4387,620clpNPNPUrease gene cluster
OI#4731,726ycdTNPNPAdhesin, polyketide biosynthesis system
OI#4887,547ycdUNPNPUrease gene cluster
OI#11516,947Z4179NPNPspa-inv invasion determinants
OI#12223,454pheVNPNPPagC-like factor
OI#14843,417tRNA selCNPNPLEE
        (EHEC)RIMD-0509952SPLE186,249tRNA serXNPNPContains TAI
SPLE213,459yeeXNPNPNP
SPLE323,454tRNA pheINPNP
SPLE443,450tRNA selCNPLEE
SPLE510,235tRNA leuXNPNP
SPLE634,148tRNA leuXfNPNP
        (EPEC)E2348/69LEE35,624tRNA selCHigh38.36Eae, translocation of Tir, T3SS
E2348/69EspC15,195ssrANP40.5EspC, ORF3
        (EPEC)jRDEC-1LEE∼34,000lifANPNPEae, translocation of Tir, T3SS
        (EPEC)kRW1372LEE∼80,000tRNA pheVNPNPEae, translocation of Tir, T3SS
        (ETEC)HT10407Tia-PAI∼46,000tRNA selCNP∼43.7eTia, Leo
        (ETEC)VariousHPINPtRNA asnTNPNPFyuA, Irp1, 2, Ybt
        (STEC)4794/97LPA33,014tRNA selCNP47.4EspI, BtuB, Iha
        (EAEC)VariousHPINPtRNA asnTNPNPFyuA, Irp1, Irp2, Ybt
    C. rodentiumDBS100LEE36,126IS679/ABCgNP38.05Eae, translocation of Tir, T3SS
    S. entericasv. TyphimuriumSPI-1∼40,000fhlAmid42.0InvA, OrgA, SptP, SipA, SipB, SipC, SopE (T3SS, invasion and enteropathogenesis)
sv. TyphimuriumSPI-2∼40,000tRNA valVHigh44.3-55.5nSsaJ, SseABC, SpiC (intracellular proliferation; T3SS)
sv. TyphimuriumSPI-3∼17,000tRNA selCNP47.5MgtC, B, MarT, MisL (intracellular proliferation, Mg2+ uptake)
sv. TyphimuriumSPI-4∼25,000ssb/soxSRNP37-54nT1SS, toxin secretion?, apoptosis
sv. TyphimuriumSPI-5∼7,000tRNA serTNP43.6SopB (SigD), PipB (effector proteins for SPI-1 and SPI-2)
sv. TyphiMajor PAI/    SPI-7134,000-146,900tRNA pheUNPNPVi antigen, SopE, type IV pili
sv. Typhi CT18SPI-6∼59,000tRNA aspNPNPsafA-D, tcsA-R usher-fimbrial operons
sv. Typhi CT18SPI-8∼6,800tRNA pheNPNPBacteriocin pseudogenes
sv. Typhi CT18SPI-9∼16,000ssrANPNPT1SS, RTX-like protein
sv. Typhi CT18SPI-10∼33,000tRNA leuNPNPsefA-R chaperone-usher fimbrial operon
(DT104)SGI152,415thdFNP41-58nMultidrug-resistance, ampicillinR (Pse-1), chloramphenicolR (FloR, Cat), streptomycinR (AadA2), sulfonamidesR (Sul I), and tetracyclineR (TetR, TetG)
ssp. III, IVHPINPtRNA asnTNPNPFyuA, Irp1, 2, Ybt, YchF (siderophore synthesis and uptake)
    Y. enterocoliticaYE8081HPI∼43,000tRNA asnTLow60.0FyuA, Irp1, 2, Ybt
    Y. pestis6/69MHPI/pgm119,443tRNA asnTLow59FyuA, Irp1, 2, Ybt, pigmentation locus (siderophore synthesis and uptake)
    Y. pseudotuberculosisIP32637HPI∼36,000tRNA asnT, asnU, asnWMid60FyuA, Irp1, 2, Ybt (siderophore synthesis and uptake)
    P. aeruginosaPAO1PAGI-I48,890PAO2217NP54.9-63.7nDehydrogenases, paraquat-inducible proteins, detoxification of reactive oxygen
CPAGI-2(C)104,996tRNA glyNP64.8Transport of heavy metals and ions, cytochrome c biogenesis, mercuryR
SG17MPAGI-3(SG)103,304tRNA gluNP59.8Transport of amino acids, coenzymes, porphyrins, putative enzyme
PAKGlycosylation∼16,000flgL/fliCNP63.3Flagellin glycosylation, biosynthetic island pathways
    P. syringaeHRP∼21,000tRNA leuNP46-59Hop, Avr, hypersensitive response
    D. nodosusvap∼11,900tRNA serVNPNPVap antigens
vrl∼27,000NPNPNPVrl antigens
    H. pyloricag∼37,000-40,000glrLow35.0Translocation of CagA, T4SS, stimulation of IL-8 synthesis
    S. flexneriYSH6000TSHI-146,603tRNA pheVLow49.0SigA, Pic (She), Shet1A and Shet1B, Sap (enterotoxin, proteases)
SA100/M90TSHI-223,800tRNA selCNP48.6IucA, IucB, IucC, IucD, IutA aerobactin, immunity to colicin V
    S. boydiiO1392SHI-3∼21,000tRNA pheUNP51.0Aerobactin operon (iron uptake)
    S. flexneriY53SHI-O10,600tRNA thrWNP40.0GtrA, GtrB, Gtr (LPS biosynthesis)
YSH6000SRL66,257tRNA serXLow49.8streptomycinR, ampicillinR, tetracyclineR, ferric dicitrate uptake
    V. choleraeEl Tor O1VPI-1∼40,000ssrANP∼35.0TcpA-adhesin, Mop, ToxT regulator
El Tor O1VPI-257,300tRNA serNP42.0Neuraminidase, utilization of amino sugars
El Tor O1VSP-1∼16,000VC0174/VC0186NP∼40.0Deoxycytidylate deaminase-related protein, phospholipase A
El Tor O1VSP-2∼7,500NPNP∼41NP
    N. gonorrhoeaeVariousatlA∼8,900NPNP43AtlA (PG hydrolase), Cps, Sac-4
    N. meningitidisVariousexl1, hmbR exl21,900-6,000NPNPNPLipoproteins, HmbR (hemoglobin receptor)
    P. gingivalisW50rag∼9,500Orf3/IS 1126NP41.0Rag (receptor antigen A)
    B. fragilis86-5543-2-2BFPAI6,033bfmB/bfmCNP35.0BFET (enterotoxin)
Gram-positive bacteria
    L. monocytogenesVariousLIPI-1∼9,000NPHighNPPlcB (phosholipase C), LLO, ActA
    L. ivanoviiLIPI-2∼22,000NPLowNPSmlC (sphingomyelinase), Inl (internalin)
    S. aureusVariousSCC mec36,000-53,000bNPNPNPMethicillinR (mecA), erythromycinR (ermA), bleomycinR (bleo), kanamycinR (aadD)
SaPI115,233attc(tyrB)Midi35TSST-1, VapE homologue, enterotoxin?
SaPI2hNPNPMidiNPTSST-1
    SaPI315,900NPNP41.4Seb, Sek, Seq, VapE homologue
    SaPIbov15,891gmpsHighNPSec-bovine variant, Sel, TSST
    νSaα25,000-40,000NPHighNPSet (enterotoxins), LukDE (leukotoxin)
νSaβ30,000-40,000NPhighNPSuperantigens, enterotoxins; LukDE (leukotoxin)
etd9,054NPNPNPExfoliative toxins (Etd and Edin-B)
νSa3NPNPNPNPEnterotoxins (Sel, Sec)
νSa4NPNPNPNPEnterotoxins (Sel, Sec), TSST
    S. pneumonie0100993PPI-1∼27,200OrfBNP32.6Pit2ABCD
    E. faecalisMMH594NPm153,571H-RFLow32.2Cytolysin (Cyl), biofilm formation (EspP)
    C. difficileVPI 10463PaLoc∼19,600cdu1, cdu2-2, cdd/2-4HighNPToxin A (TcdA), toxin B (TcdB)
  • a Characteristic features of various PAI of bacterial pathogens are presented. tRNA indicates the presence of gene loci for tRNA that are adjacent to the PAI. Low, mid, and high stability indicate if the PAI is frequently deleted or stably inserted in the genome.

  • b Indicates variations between different strains.

  • c Strain that has been used for PAI identification and characterization.

  • d The G+C contents of the entire chromosomal background (core) genomes are as follows: E. coli, ∼50.5%; and S. enterica, 52 to 53%; V. cholerae E1 Tor, 47.7%; P. aeruginosa PAO1, ∼66 to 67.0% Y. enterocolitica, 42.3%; Y. pseudotuberculosis and Y. pestis, 46 to 48%; S. pneumoniae, 40%; D. nodosus, 45%; H. pylori, 39%; N. meningitidis, 51.8%; N. gonorrhoeae, 50%; P. gingivalis, 48 to 57%; B. fragilis, 42%; E. faecalis, 37.5%; C. difficile, 26%; S. aureus, 32.8 to 32.9%.

  • e G+C content in the sequenced region; may differ from the G+C content of the entire island.

  • f Integrated in tandem with SPLE5.

  • g Genes encoding an ABC transporter.

  • h Similar to SaPI1.

  • i Mobilizable by phage.

  • j Rabbit-pathogenic E. coli.

  • k Bovine isolate.

  • l NP, not published.

  • m NNP, no name published.

  • n Mosaic structure.