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Table 3 Genetic diversity of Methicillin Resistance S. aureus (MRSA) 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

Pathogens

Source

Genotyping tools

Proportion of MRSA genes,

n (%)

Phylogroups/sequence types

Lineages/spa type

Country

Reference

Time period for collection of isolates

MRSA

human

WGS, MLST

mecA (10/30;33.3%)

13 sequence types (ST-8, ST-1, ST-152, ST-15, ST-1847, ST-188, ST-22, ST-239, ST-30, ST-5, ST-580, ST-6

 

Tanzania

[71]

August 2013 to August 2015

MRSA

human

Multiplex PCR

SCCmec I (1/69;1.4%), SCCmec II (52/69; 75.4%), SCCmec IV (2/69; 2.9%)

–

 

Kenya

[72]

2005–2007

MRSA

human, environment

Multiplex PCR

SCCmec I (22/41;54%), SCCmec V (6/41;15%), SCCmec IV (3/41;7%)

–

 

Uganda

[73]

November, 2009 and February, 2010

MRSA

human

PCR, MLST

SCCmecA (24/24:100%)

ST88, ST 1797, ST1820

t064, t104, t1855, t186, t667, t690, t7237, t7231,

Tanzania

[74]

Between January and December 2008

MRSA

human

PCR, MLST

SCCmec type V (3/30;10%), SCCmec type IV (12/30;40%), SCCmec type III (13/30;43.3%), SCCmec type I (1/30;3.3%), SCCmec type II (1/30;3.3%)

ST22, ST88, ST789, ST5, ST8, ST241, ST30,

t037, t13149, t005, t022, t1339, t648, t345, t318, t293, t2029, t852, t689, t104, t1476, t13150, t091, t3202, t9622

Kenya

[75]

Between January 2010 and July 2013

MRSA

human

PCR, Multiplex PCR

SCCmec V (33.3%, 8/24), SCCmec IV (4.2% (1/24) SCCmec II (8.3% (2/24), SCCmec type 1 (16.7%, 4/24)

–

t645, t4353, t064, t355, t4609, t10277

Uganda

[76]

September 2011 to April 2012

MRSA

human

PCR, Multiplex PCR, WGS

SCCmec type I (56.4%), SCCmec type IV (17.9%)

–

–

Rwanda

[97]

 

MRSA

human

WGS

SCCmec III (6/6; 100%)

ST239

t037

Kenya

[77]

Between the 11th July and 7th November 2011,

MRSA

cattle

PCR, Multiplex PCR, PFGE

SCCmec type V (21/23; 91.3%)

–

t7753, t1398, t2112, t3992, t127

Uganda

[78]

July to August 2013

MRSA

human

PCR, WGS

SCCmecA

ST612

t690

Tanzania

[66]

Between December 2014 and September 2015

MRSA

human

PCR, WGS

SCCmec type IV (40.5%, 17/42), SCCmec type I (38.1%, 16/42), SCCmec types I, II and III (50%,21/42)

–

t064 (19%, 8/42), t037 (12%, 5/42).

t002, t037, t064, t4353 and t12939

Uganda

[16]

Between February and October 2011