Table 2 The genetic diversity of extended–spectrum beta-lactamase (ESBL) genes

E. coli

chickens

PCR

^blaTEM (100%), ^blaOXA-1 (75.0%), blaCMY-2 (62.5%), ^blaCTX-M-8 (50%), ^blaCTX-M − 9 (37.5%, ^blaCTX-M − 1,15 (12.5%), ^blaSHV (12.5%)

–

–

Tanzania

[67]

2016

E. coli

pigs, cattle, sheep, goats, dogs, chicken

WGS, MLST

blaOXA-1 & ^blaTEM-1B (32%, 8/25), ^blaOXA-1 (2/25, 8%), ^blaTEM-1B 60% (15/25)

ST617, ST1303, ST2852, ST131,

IncFIA, IncFIB, IncFII, IncY,B/O/K/Z, IncX1, IncQ1, IncX3, IncX4, IncFIB(K), IncFIA

A, B1, B2, D

Tanzania

[12]

August and September 2014

K. pneumoniae

human

PCR, WGS, AFLP

^blaTEM-63 (4/9;44.4%), ^blaSHV-12 (0%), ^blaSHV-2a (0%), ^blaCTX-M-15 (5/9;55.6%),

–

–

Tanzania

[23]

August 2001 to August 2002,

E. coli

human

PCR, WGS, AFLP

^blaTEM-63 (4/25, 16%), ^blaSHV-2a (0/25, 0%), ^blaSHV-12 (0/25, 0%), ^blaCTX-M-15 (5/25, 20%)

–

–

Tanzania

[23]

August 2001 to August 2002,

Salmonellae

human

PCR, WGS, AFLP

^blaTEM-63 (3/17, 17.6%), ^blaSHV-2a (2/17, 11.8%), ^blaSHV-12 (2/17, 11.8%), ^blaCTX-M-15 (1/17, 5.9%)

–

Tanzania

[23]

August 2001 to August 2002,

K. pneumoniae

Human (blood, wounds, urine)

PCR, WGS, PFGE, MLST

^blaCTX-M-15 (70/92; 76%), ^blaTEM-1, ^blaTEM-104 (18%), ^blaSHV-11 (3.2%), ^blaTEM-176 (2%)

ST48, ST14, ST348, ST10,

IncFII, IncND, IncFIA

–

Tanzania

[22]

Between April 2009 and March 2010

E. coli

cattle

ERIC-PCR, WGS

^blaTEM-1B, ^blaOXA-1, ^blaTEM-1A

ST1139, ST617, ST3202, ST59, ST4741, ST181, ST69, ST5303, ST452, ST297, ST5307, ST101, ST602, ST1147, ST58

IncFIB (AP001918), ColRNAI, IncFIA, IncFII, IncFIC(FII),, InQ1, IncP, IncFII(pCoo), IncB/O/K/Z, Col156, IncFIB(pB171), IncFIA(HI1),, IncFII (pSE11),, IncX1, IncR, Incl1, Col(MG828),

A, B1, D

Tanzania

[13]

2014

E. coil

human

ERIC-PCR, WGS

^blaTEM-1B, ^blaOXA-1, ^blaTEM-1A

IncFIB (AP001918), ColRNAI, IncFIA, IncFII, ColBS512, IncFII(pCoo), IncFII(29), IncFIB(K),lnO2,IncX4, Col(MP18),Col8282,

–

Tanzania

[13]

2014

K. pneumonia

environment

PCR

^blaCTX-M-1

–

–

Tanzania

[15]

February 2014

E. coli

environment

PCR

^blaCTX-M-1 (100%), ^blaCTX-M-9(5.9), other than ^blaCTM-1 & ^blaCTM-9 (17.6%)

–

–

Tanzania

[15]

February 2014

K. pneumoniae

Human (blood)

WGS

^blaCTX-M-15, ^blaSHV-1, ^blaTEM-1B, ^blaSHV-11, blaSHV-33, ^blaSCO-1, ^blaOXA-1, ^blaSHV-28, ^blaSHV-83, ^blaSHV-27,

ST101, ST348, ST35, ST45, ST14, ST17, ST20, ST2268, ST711, ST873

IncFIA, IncFIB, IncR, IncFII, IncHI1B, IncFR

–

Tanzania

[50]

Between July and December 2016

E. cloacae

human

WGS

^blaCTX-M-15, ^blaTEM-1B, ^blaOXA-1, ^blaACT, ^blaACT-7

ST93, ST116,

IncHI2A, IncHI2,

–

Tanzania

[50]

Between July and December 2016

A. baumanii

human

WGS

^blaADC-25, ^blaNDM-1, ^blaOXA-69, ^blaOXA-58, ^blaCARB-8,

ST405, ST1470

–

–

Tanzania

[50]

Between July and December 2016

E. coli

human

RT PCR, WGS

^blaCTX-M-15, ^blaCTX-M-14, ^blaCMY-2

–

–

–

Tanzania

[44]

From August 2010 to July 2011

K. pneumonia

human

RT PCR, WGS

^blaCTX-M-15,

–

–

–

Tanzania

[44]

From August 2010 to July 2011

K. oxytoca

human

RT PCR, WGS

^blaCTX-M-15,

–

–

–

Tanzania

[44]

From August 2010 to July 2011

E. cloacae complex

human

RT PCR, WGS

^blaCTX-M-15,

–

–

–

Tanzania

[44]

From August 2010 to July 2011

E. cloacae

inanimate surfaces and objects

PCR, DNA sequencing

–

ST84, ST513, ST109, ST825, ST827

–

–

[66]

Between December 2014 and September 2015,

Citrobacter spp

human

RT PCR, WGS

^blaCTX-M-15,

–

–

–

Tanzania

[6]

between 1992 and 2010

E. coli

human

PCR, WGS

^blaTEM-1, ^blaSHV-1, ^blaCTX-M-14, ^blaCTX-M-15, ^blaCTX-M-9, ^blaCTX-M, ^blaCTX-M-3, ^blaCTX-M-1, ^blaSHV-5, ^blaSHV-12, ^blaTEM-52, ^blaTEM-125, ^blaTEM-50, ^blaTEM-78, ^blaTEM-109, TEM − 152, ^blaTEM-158, ^blaTEM-103, ^blaCMY-2, ^blaCMY-1, ^blaOXA-1

–

–

Kenya

[68]

September and October 2009

E. coli

dogs, cats,

PCR, WGS, multiplex PCR

^blaCTX-M-15 (dogs,47/216;22%), ^blaCTX-M-15(cats, 2/50;4%), ^blaOXA-1(dogs,47/216;22%), ^blaOXA-1 (cats, 2/50;4%),

ST131

IncFIA, IncFIB, Incl1, IncFIA/FIB,

A, B1, B2

Kenya

[68]

September and October 2009

E. coli

human

PCR, multiplex PCR, WGS

^blaCTX-M-154 (4/23;17%), ^blaOXA-1(4/23;17%)

ST131

IncFIB

–

Kenya

[68]

September and October 2009

E. coli

human

PCR

^blaCTX-M, ^blaTEM

–

–

–

Kenya

[7]

March 2009 to February 2010

K. pneumoniae

human

PCR

^blaCTX-M, ^blaSHV, ^blaTEM

–

–

–

Kenya

[7]

March 2009 to February 2010

E. coli

human

PCR, WGS

^blaCTX-M-15, ^blaCMY-2

–

–

–

Uganda

[41]

May 2010 to July 2011

E. coli

human

PCR

^blaCTX-M, ^blaSHV, ^blaTEM

–

–

–

Uganda

[41]

May 2010 to July 2011

E. coli

human

PCR

^blaCTX-M, ^blaSHV, ^blaTEM

–

–

Uganda

[41]

May 2010 to July 2011

E. coli

Fish

PCR

^blaTEM (52%), ^blaSHV (36%), ^blaCTX 9.7%.

–

Tanzania

[47]

2017

E. coli

Fish

WGS

^blaCTX-M-15 (9/11;81.8%), ^blaOXA-1 (6/11;54.5%),

ST-38, ST-5173

IncI1, IncY,

E, B1

Tanzania

[69]

between July and September 2015

E. coli

Environment

WGS

^blaCTX-M-15 (12/13;92.3%), ^blaOXA-1 (1/13;7.7%)

ST38, ST-2852, ST-1049, ST-1421, ST-131, ST-10, ST-394, ST-1177, ST-58, ST-167, ST-48, ST-5173

IncY, IncI1, IncP, IncFII, IncFIA, IncFIB, IncQ1

B1, A, B2, E,

Tanzania

[69]

between July and September 2015

E. coli

inanimate surfaces and objects

PCR, DNA sequencing

^blaCTX-M-15

ST607, ST405

–

–

Tanzania

[66]

December 2014 and September 2015,

K. pneumoniae

inanimate surfaces and objects

PCR, DNA sequencing

^blaCTX-M-15

ST1962, ST280, ST403

–

–

Tanzania

[66]

December 2014 and September 2015,

E. cloacae

Fish

WGS

^blaCTX-M-15, ^blaTEM-1B, ^blaACT-15, ^blaOXA-1, ^blaMIR-3,

ST91, ST422, ST500

IncFII,IncFIB, IncFIB(K), IncFII, IncR

–

Tanzania

[69]

between July and September 2015

K. pneumoniae

Fish

WGS

^blaCTX-M-15, ^blaOXA-1, ^blaSHV-11, ^blaTEM-1B,

–

IncFII,IncFIB(K),IncHI1B,

–

Tanzania

[69]

between July and September 2015

E. coli

Animals

WGS

ST256, ST1303, ST1421, ST617,

ST38, ST131,

ST44,

ST1598, ST1642, ST2852, ST5455, ST746, ST410, ST4977

IncFIA, IncFIB, IncFII, IncY,B/O/K/Z,IncX1, IncQ1, IncX3,IncIFIA, X4, IncFIB(K),

B1, A, D, B2,

Tanzania

[12]

between August/September 2014

E. coli

human

WGS

^blaCTX-M-15, ^blaOXA-1, ^blaTEM-1B,

ST131, ST405, ST617, ST648

IncFIA, IncFIB, IncFII, IncI2, IncI1, Col156, IncQ1, IncY, IncQ, Col (BS512)

–

Tanzania

[50]

Between July and December 2016

A. baumanii

human

WGS

^blaADC-25, ^blaOXA-69, ^blaNDM-1, ^blaOXA-58

ST405, ST1470,

–

–

Tanzania

[50]

Between July and December 2016

E. cloacae

human

WGS

blaCTX-M-15, ^blaTEM-1B, ^blaOXA-1, ^blaACT, ^blaACT-7

ST116, ST93

IncHI2A, IncHI2

–

Tanzania

[50]

Between July and December 2016

K. pneumoniae

human

WGS

^blaCTX-M-15, ^blaSHV-1, ^blaTEM-1B, ^blaSHV-11, blaSHV-33, ^blaSCO-1, ^blaOXA-1, ^blaSHV-28, ^blaSHV-83, ^blaSHV-27,

ST101, ST348, ST35, ST45, ST48, ST14, ST17, ST20, ST2268, ST711, ST873

ncFIA, IncFIB, IncR, IncFII, IncHI1B,

Tanzania

[50]

Between July and December 2016

E. coli

human

PCR, DNA sequencing

^blaCTX-M-15, ^blaTEM-1

ST131, ST405, ST638, ST38, ST827, ST224, ST648, ST46, ST1845, ST1848

ncFIA, ncFIB, ncFII, ncFrepB, ncFIA- FIB

B2, D

Tanzania

[70]

2011

K. pneumoniae

human

WGS

^blaSHV, ^blaLEN, ^blaOKP, ^blaTEM, ^blaCTX-M-15, ^blaOXA, ^blaSCO, ^blaDHA1, ^blaCARB, ^blaNDM-1

ST15, ST54,

–

–

Kenya

[27]

1994–2002