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Table 4 Genetic diversity of Carbapenem-resistant genes in the East Africa region

From: Genetic diversity and risk factors for the transmission of antimicrobial resistance across human, animals and environmental compartments in East Africa: a review

Pathogen

Source

Genotyping tools

Proportion of carbapenemase resistance genes

Phylogroups/sequence types

Lineages/cluster

Country

Reference

Time period for collection of isolates

P. aeruginosa

human, environment

PCR, WGS

blaIMP (36%, 9/25), blaVIM1 (32%, 8/25), blaSPM (16%, 4/25), blaNDM1 (4%, 1/25)

–

–

Uganda

[31]

Between February 2007 and September 2009

A. baumannii

human, environment

PCR, WGS

blaOXA-24 (7%, 1/15), blaVIM-1 (13%, 2/15), blaOXA-58 (13%, 2/15), blaOXA-23 (60%, 9/15)

–

–

Uganda

[31]

Between February 2007 and September 2009

P. aeruginosa

human

PCR, WGS, PFGE

blaVIM-2 (13.7%; 57/416), blaVIM-1 (13.7%; 57/416)

–

MBLA, MBLAR, MBLB,

Kenya

[32]

2006 and 2007

P. aeruginosa

human

PCR, WGS, PFGE

blaIMP (12/49;24.5%), blaVIM (9/28; 32.1%), blaOXA_48 (2/11;18.2%), blaKPC (1/8; 12.5%), blaNDM (1/8; 12.5%)

–

–

Tanzania

[9]

Between 2007 and 2012

P. aeruginosa

human

PCR, WGS

blaVIM-2

ST640, ST244

 

Tanzania

[41]

May 2010 to July 2011

K. pneumoniae

human

PCR, WGS, PFGE

blaIMP types (49/227; 21.6%), blaVIM types (28/227; 12.3%), blaOXA_48 11/227 (4.9%), blaKPC (8/227; 3.5%), blaNDM (7/227;3.1%), blaNDM-1, blaIMP, blaNDM-1,

ST14, ST15

–

Tanzania,

[9]

Between 2007 and 2012

K. pneumoniae

human

PCR, WGS, PFGE

blaNDM-1 (4/35; 11.4%), blaVIM (16/35;45.7%), blaIMP (5/35;8.16%), blaKPC (3/35;8.6%), blaOXA-48 (7/35;20%),

–

–

Uganda

[17]

between January, 2013 and March, 2014

K. pneumoniae

  

blaVIM (17/43;39.5%), blaOXA-48 (5/13;38.5%)

–

 

Uganda

[30]

January, 2013 and March, 2014

E. coli

human

PCR

blaIMP (19/32;59.4%), blaNDM (0/32;0%), blaVIM (4/32;12.5%), blaOXA_48 (3/32;9.4%), blaKPC (4/32; 12.5%), blaNDM (2/32;6.3%)

–

–

Tanzania,

[9]

Between 2007 and 2012

E. coli

human

PCR

blaNDM-1 (0/19; 0%), blaVIM (1/19;5.3%), blaIMP (6/19;31.6%), blaKPC (4/19;21.1%), blaOXA-48 (8/19;42.1%)

–

–

Uganda

[17]

between January, 2013 and March, 2014

E. coli

human

PCR

blaVIM (20/43;46.5%), blaOXA-48 (6/13;46.2%)

–

–

Uganda

[30]

January, 2013 and March, 2014

A. baumannii

human

PCR, PFGE, WGS

blaIMP types (3/3;100%),blaVIM (0/3; 0%)blaOXA_48 (0/3; 0%), blaKPC (0/3;0%), blaNDM (0/3;0%)

–

–

Tanzania,

[9]

Between 2007 and 2012

A. baumannii

human

PCR, PFGE, MLST

ISAba1-blaOXA-23, blaOXA-51-like, blaADC, blaNDM-1, ADC-57.

ST2, ST109, ST25, ST113

European clone II (ECII)

Kenya

[28]

January 2009 to August 2010

Salmonella spp

human

PCR

blaIMP types (1/2;50%),blaVIM(1/50; 50%)

–

–

Tanzania

[9]

Between 2007 and 2012

K. oxytoca

human

PCR

blaIMP types (3/5;60%),blaOXA481/5;20%),blaNDM1/5;20%)

–

–

Tanzania,

[9],

Between 2007 and 2012

K. oxytoca

human

PCR

blaNDM-1 (1/1; 100%), blaVIM (0/1;0%), blaIMP (0/1;0%),blaKPC (0/1;0%), blaOXA-48 (1/1;100%)

–

–

Uganda

[17]

between January, 2013 and March, 2014

C. freundii

human

PCR

blaIMP types (2/4;50%), blaVIM (1/4;25%), blaOXA_48 (1/4;25%),

–

–

Tanzania

[9]

Between 2007 and 2012

C. freundii

human

PCR

blaNDM-1 (1/1; 12.5%), blaVIM (0/1;0%), blaIMP (0/8;0%), blaKPC (0/1;0%), blaOXA-48 (0/1;0%),

–

–

Uganda

[17]

between January, 2013 and March, 2014

P. aeruginosa

human

PCR

blaIMP types (12/25;48%), blaVIM (9/25;36%), blaOXA_48 (2/25;8%),blaKPC (1/25;4%),blaNDM (1/25; 4%)

–

–

Tanzania

[9]

Between 2007 and 2012

Enterobacter spp.

human

PCR

blaNDM-1 (1/5; 20%), blaVIM (1/5;20%), blaIMP (0/1;0%), blaKPC (1/5;0%), blaOXA-48 (2/5;40%)

–

–

Uganda

[17]

between January, 2013 and March, 2014

Pantoea agglomerans

human

PCR

blaNDM-1 (0/1; 0%), blaVIM (0/1;0%), blaIMP (1/1;100%), blaKPC (0/1;0%), blaOXA-48 (0/1;0%)

–

–

Uganda

[17]

between January, 2013 and March, 2014

Proteus mirabilis

human

PCR

blaNDM-1 (0/2; 0%), blaVIM (0/2;0%), blaIMP (0/2;0%), blaKPC (1/2;50%), blaOXA-48 (1/2;100%)

–

–

Uganda

[17]

between January, 2013 and March, 2014

Proteus mirabilis

human

Multiplex PCR

blaVIM1/43;2.3%), blaOXA-48 (1/13;7.7),

–

–

Uganda

[30]

September 2013 to June 2014,

Serratia marcescens

human

PCR

blaNDM-1 (0/3; 0%), blaVIM (2/3;66.7%), blaIMP (0/3;0%), blaKPC (1/3;33.3%), blaOXA-48 (0/3;0%)

–

–

Uganda

[17]

between January, 2013 and March, 2014

Morganella morganii

human

Multiplex PCR

blaVIM1/43; %2.3), blaOXA-48 (0/13;0%),

–

–

Uganda

[30]

September 2013 to June 2014,

Enterobacter sakazaki

human

Multiplex PCR

blaVIM 0/13; 0%),blaOXA-48 (1/13; %7.7),

–

–

Uganda

[30]

September 2013 to June 2014,

Stenotrophomonas spp

human

Multiplex PCR

blaVIM (1/43;2.3%),blaOXA-48 (0/23;0%)

–

–

Uganda

[30]

September 2013 to June 2014,