The characteristics of children sampled were described previously [13, 31]. Briefly, about half of the children were less than 2 years old and 50% were female with a mean age of 30 months. Majority (82%) of the children lived in rural areas and their primary source of water was spring water (74%) and well water (26%); only 1% of the children had access to piped water. The median number of children per household was 2 while the median number of household members per bedroom (as a measure of crowding) was 4. Based on reports of mothers 90% of the children had been sick in the previous 2 weeks and the most common symptoms were fever, running nose and cough. Of the children who had been sick around 30% were reported to have been given antibiotics, mostly cotrimoxazole and ampicillin.
MSSA and MRSA carriage rates
The processed samples yielded 600 Gram positive and catalase positive isolates (one isolate per sample/child), of which 144 were confirmed to be S. aureus (one isolate per sample/child), Figure 1 & Additional file 1: Table S1. Thus, the nasopharyngeal carriage rate of S. aureus in the children was 19.4% (144/742). Furthermore, 45 (31.3%, 45/144) of the isolates were confirmed to be MRSA yielding a carriage rate of 6.1% (45/742) in the children.
Spa Types and antibiotic resistance patterns of MRSA isolates
All MRSA isolates were susceptible to vancomycin, linezolid and generally clindamycin though two exhibited intermediate resistance to this drug, Table 1 & Additional file 1: Table S1. Compared to MSSA, MRSA isolates were generally more resistant to non-β-lactam antimicrobial agents i.e. tetracycline (91.1%, 41/45), SXT (73.3%, 33/45), erythromycin (75.6%, 34/99), chloramphenicol (60%, 19/99), gentamicin (55.6%, 25/45) and ciprofloxacin (35.6%, 16/45). One MRSA isolate (K2283) exhibited high-level mupirocin resistance (HLMupr) while 42 (93.3%, 42/45) were multidrug resistant (MDR –resistance to three or more classes of antimicrobials) including the mupirocin resistant isolate, Table 1 & Additional file 1: Table S1. Again, compared to MSSA, slightly more MRSA isolates (13.2%, 19/45) carried PVL genes but the difference was not statistically significant (P=0.4562). All PVL-positive MRSA isolates were MDR and generally the presence of PVL genes was associated with the MDR phenotype (P=0.0332).
Seven spa types (t064, t4353, t002, t037, t355, t3092 and t12939) were detected in MRSA isolates, of which t064 (20%, 9/45) and t037 (15.6%, 7/45) were predominant, Table 1 & Additional file 1: Table S1. Spa types t037 and t064 were significantly associated with MRSA and SCCmec types I & IV respectively, with t037 exclusively occurring in MRSA isolates, Table 2. On PFGE analysis isolates of spa types t064 and t037 clustered together, Additional file 2: Figure S1.
Spa Types and antibiotic resistance patterns of MSSA isolates
Ninety nine (68.8%, 99/144) isolates were MSSA as they were cefoxtin susceptible and mecA gene negative, Table 1 & Additional file 1: Table S1. Nevertheless, MSSA isolates were highly resistant to penicillin (78.8%, 78/99), tetracycline (79.8%, 79/99), SXT (27.3%, 27/99), erythromycin (24.2%, 24/99), gentamicin (25.3%, 25/99) and chloramphenicol (19.2%, 19/99) but compared to MRSA, they were not as resistant to ciprofloxacin (2%, 2/99). Three (3%, 3/99) MSSA isolates (K277-1, K251 & K1064) exhibited high-level mupirocin resistance and were also clindamycin resistant, Table 1 & Additional file 1: Table S1. A total of 61 (61.6%, 61/99) MSSA were MDR including the three mupirocin resistant isolates, Table 1 & Additional file 1: Table S1. Only two isolates (R16 & R180, both MSSA) were pan-susceptible to the tested antibiotics, Additional file 1: Table S1. Generally all isolates, MSSA and MRSA, were susceptible to rifampicin, vancomycin and linezolid. Fourteen spa types were detected in MSSA, of which t645 (11.1%, 11/99), t4353 (9.1%, 9/99), t064 (6.1%, 6/99) and t002 (6.1%, 6/99) were predominant, Table 1 & Additional file 1: Table S1. Spa type t645 exclusively occurred in MSSA isolates, Table 2.
When we compared the genotypes of isolates from IMHDSS to genotypes of previously characterized isolates in Uganda, we found that the spa types we detected at the IMHDSS were previously reported for S. aureus from Mulago Hospital in Kampala, but they were slightly different from spa types for isolates from rural western Uganda, Additional file 4: Figure S2. The predominant lineages in each of the three settings from where isolates were obtained were t064, t645, t4353, t002 & t037 (IMHDSS); t645, t4353, t064, t084, t355, t3772 & t4609 (Mulago Hospital); and t318, t064, t645, t186, t11656, t127, t786 & t2771 (rural western Uganda), Additional file 4: Figure S2. Overall, 40 spa types account for clinical and colonizing MSSA/MRSA clones circulating in Uganda, of which t645, t064, t4353, t002, t318, t037, t355, t084, t3772, t127 and t186 are predominant, Figure 2 & Additional file 3: Table S2. Note, spa type t037 was detected only at Mulago Hospital & IMHDS but not western Uganda, and again, it exclusively occurred in MRSA. Spa types t645 and t4353 were detected in all the three sites and they were significantly associated with MSSA, Figure 2 & Additional file 3: Table S2. When we analyzed isolates from the three sites together, spa types t4353, t002 and t355 were neither associated with MRSA nor MSSA; Note, spa type t064 that was significantly associated with MRSA at IMHDSS was no longer associated with MRSA, Table 2 & Additional file 3: Table S2.