TABLE 1.
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 |
Location of the household: village, union.
Phylogenetic group based on the in-silico ClermonTyping.
Sequence type (ST) based on multilocus sequence typing Achtman scheme.
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.
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).
Acquired resistance genes with identity and coverage of >90% with the ResFinder database.
The gene and amino acid change and position are indicated.
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.