TABLE 3.
Genomic characteristics of Escherichia coli and Klebsiella pneumoniae strains isolated from globally produced food.
| Resistance genes |
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| Isolatea | Product | Origin | Speciesb | MLSTc | Plasmid replicons | Phenotyped | Virulence genes | Aminoglycoside | Beta-lactam | Fluoroquinolone | Fosfomycin | Macrolide, Lincosamide, Streptogramin B | Phenicol | Rifampicin | Sulfonamide | Tetracycline | Trimethoprim |
| A35-1 | Chili pepper | Malaysia | K. pneumoniae | ST307 | IncFIB(K), IncFII(K) | ESBL | N/A | aac(3)-IIa, aac(6′)-Ib-cr, aph(3′′)-Ib, aph(6)-Id | blaCTX–M–15, blaOXA–1, blaSHV–28, blaTEM–1B | aac(6′)-Ib-cr, oqxA, oqxB, qnrB1 | fosA | catB3 | sul2 | tet(A) | dfrA14 | ||
| A35.2-2 | Chili pepper | Malaysia | K. pneumoniae | ST101 | IncFIB(K), IncFII(pK91) | AmpC | N/A | blaDHA–1, blaSHV–28 | oqxA, oqxB, qnrS1 | fosA | sul1 | tet(A) | dfrA1 | ||||
| A40.2-1 | Coriander | Malaysia | E. coli | ST155 | IncFIB, IncFIC(FII) | ESBL | cma, gad, IpfA | aph(3′)-Ia, aph(3′′)-Ib, aph(6)-Id | blaCTX–M–55, blaTEM–1B | mdf(A) | floR | ARR-2 | sul2 | tet(A) | dfrA14 | ||
| A41.2-1 | Coriander | Malaysia | E. coli | ST479* | IncFIB, p0111 | ESBL | gad, IpfA | aac(3)-IV, aadA5, aph(4)-Ia | blaCTX–M–65 | oqxA, oqxB | mdf(A) | floR | sul1, sul2 | tet(A) | dfrA17 | ||
| C32.1-2 | Frozen turkey ligament | Poland | K. pneumoniae | ST307 | IncFIB(K), IncFII(K) | ESBL | N/A | aac(3)-IIa, aac(6′)-Ib-cr, aph(6)-Id, aph(3′′)-Ib | blaCTX–M–15, blaOXA–1, blaSHV–28, blaTEM–1B | aac(6′)-Ib-cr, oqxA, oqxB, qnrB1 | fosA | catB3 | sul2 | tet(A) | dfrA14 | ||
| C51-1 | Raw broiler meat | Lithuania | E. coli | ST189 | IncI1-I(Gamma) | ESBL | astA, cif, eae, espA, espB, espF, espJ, gad, nleA, nleB, tir | aadA1, aadA2 | blaSHV–12 | mdf(A) | cmlA1 | sul3 | tet(A) | ||||
| C51.2-2 | Raw broiler meat | Lithuania | Escherichia fergusonii** | ST8330 | ColpVC, IncB/O/K/Z, IncFIB, IncFII, IncI2, IncX1 | ESBL + AmpC | cma, gad, mchF | aac(3)-IV, aadA1, ant(2′′)-Ia, aph(3′)-Ia, aph(3′′)-Ib, aph(4)-Ia, aph(6)-Id | blaCMY–2, blaTEM–1B | catA1, floR | sul1, sul2 | tet(B) | |||||
| C56.1-1 | Raw broiler meat | Lithuania | E. coli | ST4994 | Col156, Col8282, ColpVC, IncI1-I(Gamma), IncI2(Delta) | ESBL | air, astA, celb, eilA, gad, iha, iss | blaTEM–52C | mdf(A) | ||||||||
| C61-1 | Raw broiler meat | Lithuania | E. coli | ST1011 | IncFIB, IncFII, IncI1-I(Gamma) | ESBL + AmpC | cma, eilA, iroN, iss, mchF | aadA2, aph(3′′)-Ib, aph(6)-Id | blaCMY–2, blaTEM–1B | mdf(A) | sul2 | tet(A) | dfrA12 | ||||
| C66-1 | Raw broiler meat | Lithuania | E. coli | ST423 | IncFIB(pLF82), IncFII(pSE11), IncI1-I(Gamma) | ESBL | gad, IpfA | aadA1, aadA2 | blaCARB–2, blaSHV–12 | mdf(A) | cmlA1 | sul3 | tet(A) | dfrA16 | |||
| C71.1-1 | Raw broiler meat | Lithuania | E. coli | ST1485 | IncB/O/K/Z, IncFIA, IncFIB, IncFIC(FII), IncHI2, IncHI2A, p0111 | ESBL | air, eilA, gad, iha, iroN, IpfA, iss, mchF, mcmA, tsh | aadA1, aadA2, aph(3′′)-Ib, aph(6)-Id | blaCMY–2, blaTEM–1B | mdf(A) | cmlA1 | sul2, sul3 | tet(A) | dfrA14 | |||
| C76.1-1 | Raw broiler meat | Lithuania | E. coli | ST201 | IncFIB, IncFII(pCoo), IncI1-I(Gamma) | ESBL + AmpC | cma, gad, iroN, IpfA, iss | aadA1 | blaCMY–2, blaTEM–1B | qnrS1 | mdf(A) | cmlA1 | sul3 | tet(A) | dfrA15 | ||
| C76.1-2 | Raw broiler meat | Lithuania | E. coli | ST83* | IncFIA, IncFIB, IncI1-I(Gamma) | ESBL | astA, gad, iroN, iss, mchF, tsh | aadA1, aadA2 | blaSHV–12 | mdf(A) | cmlA1 | sul3 | tet(A) | ||||
| C81.1-1 | Raw broiler meat | Lithuania | E. coli | ST38 | Col156, IncFII(29), IncI1-I(Gamma) | ESBL | air, eilA, gad | aadA5 | blaCTX–M–1 | mdf(A) | sul2 | dfrA17 | |||||
| C81.3-1 | Raw broiler meat | Lithuania | E. coli | ST1638 | IncFIB, IncFIC(FII), IncFII(pHN7A8), IncI1-I(Gamma), IncX1, Col(pHAD28) | AmpC | gad, iss | aadA1, aadA2, aph(3′′)-Ib, aph(6)-Id | blaCMY–2, blaTEM–1B | qnrB19 | mdf(A) | cmlA1 | sul3 | tet(B) | dfrA8 | ||
| C81.1-2 | Raw broiler meat | Lithuania | E. coli | ST641 | IncFIB, IncFIB(pLF82), IncFII(pSE11), IncX1 | ESBL + AmpC | etpD, gad, IpfA, iss | aadA1, aadA2 | blaCARB–2, blaCMY–2, blaTEM–1B | qnrS1 | mdf(A) | cmlA1 | sul3 | tet(A) | dfrA16 | ||
| C86.1-1 | Raw broiler meat | Lithuania | E. coli | ST641 | IncFIB, IncFIB(pLF82), IncFII(29), IncFII(pSE11), IncX1 | ESBL + AmpC | etpD, gad, iss, IpfA | aadA1, aadA3 | blaCARB–2, blaCMY–2, blaTEM–1B | qnrS1 | mdf(A) | cmlA1 | sul3 | tet(A) | dfrA16 | ||
| C86.1-2 | Raw broiler meat | Lithuania | E. coli | ST38 | Col156, IncFII(29), IncI1-I(Gamma) | ESBL | air, eilA, gad, ireA | aadA1, aadA5, aph(3′′)-Ib, aph(6)-Id | blaCTX–M–1 | mdf(A) | floR | sul1, sul2 | tet(A) | dfrA17 | |||
| C86.3-1 | Raw broiler meat | Lithuania | K. pneumoniae | ST37 | IncFIA(HI1), IncR | ESBL | N/A | aac(3)-IId, aph(3′′)-Ib, aph(6)-Id | blaCTX–M–15, blaSHV–81, blaTEM–1B | oqxA, oqxB | fosA | sul2 | dfrA14 | ||||
| C91-2 | Raw broiler meat | Lithuania | E. coli | ST117 | ColpVC, IncB/O/K/Z, IncFIB, IncFIC(FII), IncFII(29) | AmpC | celb, gad, ireA, iroN, IpfA, iss, mchB, mchC, mchF, pic | aadA1, aph(3′′)-Ib, aph(6)-Id | blaCMY–2, blaTEM–1B | mdf(A) | sul1, sul2 | tet(A) | dfrA8 | ||||
| C96-1 | Raw broiler meat | Lithuania | E. coli | ST88 | IncFII(29), IncI1-I(Gamma) | AmpC | gad, iss, IpfA | aadA1, aph(3′′)-Ib, aph(6)-Id | blaCMY–2, blaTEM–1B | mdf(A), mph(B) | catA1 | sul1, sul2 | dfrA1, dfrA8 | ||||
aSuffix −1 indicates first incubation temperature of 44°C and −2 of 37 °C. bAnalysis tools by Center for Genomic Epidemiology: SPAdes 3.9 for assembly, KmerFinder 3.1 for species determination (** identified as E. coli with SpeciesFinder 1.2), MLST 2.0 for multilocus sequence typing [* scheme Escherichia coli #1 used first, if sequence type (ST) unidentified then #2 (Jaureguy et al., 2008) used], PlasmidFinder 2.0 for plasmid replicons, VirulenceFinder 2.0 for E. coli virulence genes (N/A, not applicable for K. pneumoniae), ResFinder 3.1 for acquired resistance genes. cMLST, multilocus sequence typing. dBased on phenotypic tests; ESBL, extended-spectrum beta-lactamase.