TABLE 1.
Characteristics of the 60 isolates sequenced in this study
| Location HHa | Sample | Source | Phylogroupb | STc | Intestinal marker(s)d | AMR phenotypee | Acquired gene(s)f or chromosomal mutation(s)g associated with AMR | Plasmid replicon(s) |
|---|---|---|---|---|---|---|---|---|
| Sreehori Para, Mirzapur | HH03C | Cattle | B1 | 8369 | astA | ColpVC | ||
| HH03CH | Chicken | B1 | 2165 | aatA, astA | SXTr | aadA5, dfrA17, sul2 | IncY | |
| HH03H | Human | B1 | 180 | TETr | tet(A) | |||
| HH03S | Soil | B1 | 392 | IncFIA(HI1), IncFIB(AP001918), IncFIC(FII) | ||||
| Sarishadair, Mirzapur | HH08C | Cattle | B1 | 223 | ATMi | IncFIB(AP001918), IncB/O/K/Z | ||
| HH08CH | Chicken | A | 226 | aatA | AMPr, CFMr, CTXr, CROr, CAZi, ATMr | blaCTX-M-15, qnrS1, mdf(A) | ||
| HH08H | Human | B1 | 7130 | astA | IncFIB(AP001918), IncFII(pRSB107) | |||
| Andhora, Mirzapur | HH13C | Cattle | B1 | 155 | IncFIA(AP001918), IncFIB(AP001918) | |||
| HH13CH | Chicken | B1 | 162 | TETr, AMPr, SXTr NALr, CIPr | tet(B), blaTEM-1, aadA5, aph(3′')-Ib, aph(6)-Id, dfrA17, sul2, gyrA(S83L), gyrA(D87N), parC(pS80I) | IncFIB(AP001918), IncFIC(FII), IncFII(pSFO), IncQ1, ColpVC | ||
| HH13H | Human | B1 | 641 | eltA, eltB | AMPr, CFMr, SXTi, AZMr | blaDHA-1, dfrA17, sul1, qnrB4, mph(A) | IncFII(pSFO) | |
| HH13S | Soil | B1 | 2073 | IncI1(Alpha), Col(BS512) | ||||
| Dulla Begum, Bhatgram | HH14C | Cattle | B1 | IncFIA(AP001918), IncFIB(AP001918) | ||||
| HH14CH | Chicken | B1 | 1326 | aatA | TETr, SXTr | tet(A), aadA5, dfrA17, sul2 | IncFIB(AP001918), IncFII(pRSB107), IncY | |
| HH14H | Human | A | aatA | |||||
| HH14S | Soil | B1 | 1656 | astA | ||||
| Dulla Begum, Bhatgram | HH15C | Cattle | E | 3233 | IncFIB(AP001918), IncFIC(FII), IncFII(pSFO), IncI1(alpha) | |||
| HH15CH | Chicken | A | 752 | eae, aatA | AMPr | aph(3′′)-Ib, aph(6)-Id | IncFIB(AP001918), IncFIC(FII), IncFII(pSFO), p0111 | |
| HH15H | Human | B2 | 1193 | NALr, CIPr, AZMr | erm(B), gyrA(S83L), gyrA(D87N), parC(S80I), parE(L416F) | IncFIA(AP001918), IncFIB(AP001918), Col(BS512), Col156 | ||
| Dulla Begum, Bhatgram | HH16C | Cattle | B1 | 2522 | TETr | tet(B) | ||
| HH16CH | Chicken | B1 | 180 | |||||
| HH16H | Human | B1 | 224 | TETr, AMPr, SXTr, NALr, CIPr, CHLi | tet(A), aadA2, cmlA1, dfrA12, sul3, gyrA(S83L), gyrA(D87N), parC(S80I), parE(S458A) | IncFIB(AP001918), IncFII(pSE11), Col(BS512), ColpVC | ||
| HH16S | Soil | B1 | 40 | astA | AMPr | IncFIA(AP001918), IncFIB(AP001918), IncFIC(FII), IncFII(pSFO), Col(BS512), Col156 | ||
| K. Deohata, Gorai | HH17C | Cattle | A | 2207 | aatA, astA | catB4 | IncFIB(AP001918), IncFII(pHN7A8), IncFII(pRSB107) | |
| HH17CH | Chicken | B1 | 155 | aatA | TETr, AMPr, NALi | tet(A) | IncFIB(AP001918), IncFII(pCoo), p0111 | |
| HH17H | Human | A | 1823 | IncHI1A, IncHI1B(R27), ColpVC | ||||
| HH17S | Soil | A | 10 | aatA | Col(BS512) | |||
| K. Deohata, Gorai | HH18C | Cattle | A | 542 | aatA, astA | NALr | gyrA(S83L) | IncFIB(AP001918), IncFII(pSFO) |
| HH18CH | Chicken | A | 542 | aatA, astA | NALr | gyrA(S83L) | IncFIB(AP001918), IncFII(pHN7A8), IncFII(pRSB107) | |
| HH18H | Human | D | 106 | Col156, ColpVC | ||||
| HH18S | Soil | B1 | 5730 | astA | IncN, Col(BS512) | |||
| Baimhati, Mirzapur | HH19C | Cattle | B1 | 224 | ||||
| HH19CH | Chicken | B1 | 2160 | IncFIB(AP001918), IncFII(pRSB107) | ||||
| HH19H | Human | A | 10 | aatA, astA | AMPr, NALr, AZMr | blaTEM-1, mph(A), gyrA(S83L) | IncFII(pSFO), Col(BS512), Col(MG828), ColpVC | |
| HH19S | Soil | B1 | 2160 | IncFIB(AP001918), IncFII(pRSB107) | ||||
| Baimhati, Mirzapur | HH20C | Cattle | B1 | 101 | astA | IncFIA(AP001918), IncFIB(AP001918), IncFIC(FII), IncFII(pSFO), Col(MG828), Col156 | ||
| HH20CH | Chicken | B1 | 111 | aatA | IncFIB(AP001918), IncFIC(FII), IncFII(pSFO) | |||
| HH20H | Human | B1 | 224 | |||||
| HH20S | Soil | A | 10 | astA | TETr, AMPR, CFMr, CTXr, CROr, CAZR, ATMr, SXTr, NALr, CIPr AZMr, CHLr | catA1, tet(B), blaOXA-1, blaCTX-M-15, aadA5, aac(6')Ib-cr, dfrA17, sul1, mph(A), erm(B), gyrA(S83L), gyrA(D87N), parC(S80I), parE(S458A) | IncFIA(AP001918), IncFIB(AP001918), Col(BS512), ColRNAI | |
| Sinjuri, Bhatgram | HH24C | Cattle | B1 | 101 | IncFIA(AP001918), IncFIB(AP001918), IncFIC(FII), IncFII(pSFO) | |||
| HH24CH | Chicken | B1 | 40 | eae, nleA, nleC | AMPi | IncQ1 | ||
| HH24H | Human | B1 | 40 | eae, nleA, nleC | ||||
| Sinjuri, Bhatgram | HH25C | Cattle | A | 6622 | aatA | TETr, SXTr | tet(A), dfrA14, sul2, qnrS1 | IncFIB(AP001918), IncFII, IncX4 |
| HH25CH | Chicken | B1 | aatA | TETr, AMPi, SXTr | tet(A), dfrA14, sul2, qnrS1 | IncFIB(AP001918), IncFII(pSFO), p0111 | ||
| HH25H | Human | B1 | 162 | astA | TETr | tet(A) | IncFIB(AP001918), IncI1(alpha), ColpVC | |
| HH25S | Soil | A | aatA, astA | IncFII(pSFO), IncI2 | ||||
| Sinjuri, Bhatgram | HH26C | Cattle | Fh /B2 | IncFIB(AP001918), IncFIC(FII), IncFII, IncFII(pSFO) | ||||
| HH26CH | Chicken | Clade I | 5273 | aatA, astA | IncFIB(AP001918) | |||
| HH26H | Human | A | 206 | eae, perA, aatA, nleA, nleC | AMPr, CFMr, CTXr, CROr, ATMi | blaCTX-M-15, qnrS1 | IncFIA(HI1), IncFIB(AP001918), IncFII(pSFO), IncI2(delta), Col156 | |
| HH26S | Soil | A | 4 | aatA, astA | TETr | tet(A) | Col(BS512), p0111 | |
| Sreehori Para, Mirzapur | HH29CH | Chicken | A | 752 | eae, aatA, nleA | TETr | tet(A), aph(3′′)-Ib, aph(6)-Id | IncFIB(AP001918), IncFIC(FII), IncFII(pSFO), Col(BS512), ColpVC, p0111 |
| HH29H | Human | A | 48 | aatA | TETr | tet(A) | IncHI2, IncHI2A, IncQ1, p0111 | |
| HH29S | Soil | B1 | 7130 | IncFIB(AP001918), IncFII(pRSB107) | ||||
| Dulla Begum, Bhatgram | HH34S | Soil | B1 | 155 | aatA | IncHI1B(CIT)_1_pNDM-CIT, IncY | ||
| Baimhati, Mirzapur | HH36S | Soil | A | 1585 | aatA | TETr, AMPr, CFMr, SXTr, NALr, CIPr, AZMr | tet(A), blaDHA-1, blaTEM-1, aadA5, aph(3′)-Ia, dfrA1, dfrA17, sul1, sul2, qnrB4, qnrS1, mph(A), gyrA(S83L), parC(S80I) | IncFIB(pB171), IncFII, IncI1(alpha), IncX1, Col(BS512), ColRNAI |
| Sinjuri, Bhatgram | HH41S | Soil | Clade I | TETr, AMPr | tet(A), blaTEM-1 | IncFII, IncHI1A, IncHI1B(CIT) | ||
| Satiachara, Jamurki | HH45S | Soil | D | 2914 | IncFIB(AP001918), IncI1(alpha), Col(BS512) | |||
| Sinjuri, Bhatgram | HH46S | Soil | B1 | 58 | AMPr, CTXr, CROr, CFMr, CAZi, ATMr | blaCTX-M-15, qnrS1 | ||
| Kanthalia, Mirzapur | HH49S | Soil | B1 | 3580 | ||||
| Kanthalia, Mirzapur | HH50S | Soil | B1 | 75 | TETr, AMPr | tet(B), blaTEM-1, qnrS1, mph(A) | IncFIA(HI1), IncFIB(AP001918), IncHI1A, IncHI1B(R27), ColpVC | |
| Kanthalia, Mirzapur | HH51S | Soil | B1 | 1079 | aatA, astA | IncY |
a
Location of the household: village, union.
b
Phylogenetic group based on the in-silico ClermonTyping.
c
Sequence type (ST) based on multilocus sequence typing Achtman scheme.
d
EPEC: eae, bfp, and perA; EAEC: aatA; EIEC: ipaH and ial; ETEC: eltA, eltB, and lt; EHEC: espK, espN, nleA, nlec, and nleG; STEC: astA, aaic, stx1a, stx1b, stx2a, and stx2db.
e
Antimicrobial resistance (AMR) phenotype by disk diffusion test for tetracycline (TET), the penicillin ampicillin (AMP), the third-generation cephalosporins cefixime (CFM), cefotaxime (CTX), ceftriaxone (CRO), and ceftazidime (CAZ), the monobactam aztreonam (ATM), the inhibitor of the folate pathway trimethoprim-sulfamethoxazole (SXT), the quinolones nalidixic acid (NAL) and ciprofloxacin (CIP), the macrolide azithromycin (AZM), and the pnenicol chloramphenicol (CHL) (only intermediate or resistance phenotypes are reported).
f
Acquired resistance genes with identity and coverage of >90% with the ResFinder database.
g
The gene and amino acid change and position are indicated.
h
Isolate HH26C is assigned to the Clermont phylogroup B2 based on the results of the in silico PCR (− + + −), but the Mash genome distance method classifies this strain as phylogroup F.