Draft Genome Sequence of Methicillin-Resistant Clinical Staphylococcus aureus Isolate 51S (Sequence Type 291)

et al. 2019

Preprint

Background: Staphylococcus aureus carriage is a known risk factor for staphylococcal disease. However, the carriage rates vary by country, demographic group and profession. This study aimed to determine the S. aureus carriage rate in children in Eastern Uganda, and identify S. aureus lineages that cause infection in Uganda. Methods: Nasopharyngeal samples from 742 healthy children less than 5 years residing in the Iganga/Mayuge Health & Demographic Surveillance Site in Eastern Uganda were processed for isolation of S. aureus. Antibiotic susceptibility testing based on minimum inhibitory concentrations (MICs) was determined by the BD PhoenixTM system. Genotyping was performed by spa typing. Results: The processed samples yielded 144 S. aureus isolates (one per child) therefore, the S. aureus carriage rate in children was 19.4% (144/742). Thirty one percent (45/144) of the isolates were methicillin resistant (MRSA) yielding a carriage rate of 6.1% (45/742). All isolates were susceptible to rifampicin, vancomycin and linezolid. Moreover, all MRSA were susceptible to vancomycin, linezolid and clindamycin. Compared to methicillin susceptible S. aureus (MSSA) isolates (68.8%, 99/144), MRSA isolates were more resistant to non-beta-lactam antimicrobials –trimethoprim/sulfamethoxazole 73.3% (33/45) vs. 27.3% (27/99) [P<0.0001]; erythromycin 75.6% (34/45) vs. 24.2% (24/99) [P<0.0001]; chloramphenicol 60% (27/45) vs. 19.2% (19/99) [P<0.0001]; gentamicin 55.6% (25/45) vs. 25.3% (25/99) [P=0.0004]; and ciprofloxacin 35.6% (16/45) vs. 2% (2/99) [P<0.0001]. Furthermore, 42 MRSA (93.3%) were multidrug resistant (MDR) and one exhibited high-level resistance to mupirocin. Overall, 61 MSSA (61.6%) were MDR, including three mupirocin and clindamycin resistant isolates. Seven spa types were detected in MRSA, of which t037 & t064 were predominant and associated with SCCmec types I & IV, respectively. Fourteen spa types were detected in MSSA, of which t645 & t4353 were predominant. Conclusions: S. aureus carriage rate in healthy children in Eastern Uganda is high and comparable to rates for hospitalized patients in Kampala. The detection of mupirocin resistance is worrying as it could rapidly increase if mupirocin is administered in a low-income setting. S. aureus strains of spa types t064, t037 (MRSA) and t645, t4353 (MSSA) are prevalent and could be responsible for majority of staphylococcal infections in Uganda.

Section: Discussionmentioning

confidence: 99%

Nasopharyngeal carriage, spa types and antibiotic susceptibility profiles of Staphylococcus aureus from healthy children less than 5 years in Eastern Uganda

et al. 2019

Preprint

“…First, we used the http://spatyper.fortinbras.us/ server for identification of spa types as it is freely accessible but it is not the official database for determining spa types (this perhaps resulted in a number of unidentified spa types in this study). However, several investigators worldwide [48][49][50][51] have used the http://spatyper.fortinbras.us/ server to accurately determine spa types. Generally, PCR genotyping approaches are prone to errors in interpretation and the molecular marker itself can yield results that may depict homoplasy events and/or convergent evolution.…”

Section: Discussionmentioning

confidence: 99%

Nasopharyngeal carriage, spa types and drug susceptibility profiles of Staphylococcus aureus from healthy children under 5 years in eastern Uganda

et al. 2019

Preprint

Background: Staphylococcus aureus carriage is a known risk factor for staphylococcal disease. However, the carriage rates vary by country, demographic group and profession. This study aimed to determine the S. aureus carriage rate in children in Eastern Uganda, and track Staphylococcus strains that can cause infection in Uganda. Methods: Nasopharyngeal samples from 742 healthy children under 5 years residing in the Iganga/Mayuge Health & Demographic Surveillance Site in Eastern Uganda were processed for isolation of S. aureus. Antibiotic resistance based on minimum inhibitory concentrations (MICs) was determined by the BD Phoenix™ automated identification & susceptibility testing system. Genotyping was performed by spa typing. Results: The processed samples yielded 144 S. aureus isolates (one per child) therefore, the S. aureus carriage rate in children was 19.4% (144/742). Thirty one percent (45/144) of the isolates were methicillin resistant (MRSA) yielding a carriage rate of 6.1% (45/742). All MRSA isolates were susceptible to vancomycin, linezolid and clindamycin however, compared to methicillin susceptible S. aureus (MSSA) (68.8%, 99/144), MRSA isolates were more resistant to non-beta-lactam antimicrobials –tetracycline (91.1%, 41/45), trimethoprim/sulfamethoxazole (73.3%, 33/45), erythromycin (75.6%, 34/45), chloramphenicol (60%, 27/45), gentamicin (55.6%, 25/45) and ciprofloxacin (35.6%, 16/45). Furthermore, one MRSA isolate was mupirocin resistant and 42 (93.3%, 42/45) were multidrug resistant (MDR); three (3%, 3/99) MSSA isolates were mupirocin and clindamycin resistant, while 61 (61.6%, 61/99) were MDR. All MSSA/MRSA isolates were susceptible to rifampicin, vancomycin and linezolid but only three MSSA were pan-susceptible to antibiotics. Seven spa types were detected in MRSA, of which t037 & t064 were predominant and associated with SCCmec types I & IV, respectively. Fourteen spa types were detected in MSSA, of which t645 & t4353 were predominant. Conclusions: S. aureus (MSSA/MRSA) carriage rate in children in Eastern Uganda is high and comparable to rates for hospitalized patients in Kampala city. The detection of mupirocin resistance is worrying as it could rapidly increase if mupirocin is administered in a low-income setting. S. aureus strains of spa types t064, t037 (MRSA) and t645, t4353 (MSSA) are prevalent and could be responsible for majority of staphylococcal infections in Uganda.

“…First, we used the http://spatyper.fortinbras.us/ server for identification of spa types as it is freely accessible but it is not the official database for determining 13 spa types. However, several investigators[48][49][50][51] have used the http://spatyper.fortinbras.us/ server to accurately determine spa types. Generally, PCR genotyping approaches are prone to errors in interpretation and the molecular marker itself can yield results that may depict homoplasy events and/or convergent evolution.…”

mentioning

confidence: 99%

Nasopharyngeal carriage, spa types and antibiotic susceptibility profiles of Staphylococcus aureus from healthy children less than 5 years in Eastern Uganda

et al. 2019

Preprint

Background: Staphylococcus aureus carriage is a known risk factor for staphylococcal disease. However, the carriage rates vary by country, demographic group and profession. This study aimed to determine the S. aureus carriage rate in children in Eastern Uganda, and identify S. aureus lineages that cause infection in Uganda. Methods: Nasopharyngeal samples from 742 healthy children less than 5 years residing in the Iganga/Mayuge Health and Demographic Surveillance Site in Eastern Uganda were processed for isolation of S. aureus. Antibiotic susceptibility testing based on minimum inhibitory concentrations (MICs) was determined by the BD PhoenixTM system. Genotyping was performed by spa and SCCmec typing. Results: The processed samples yielded 144 S. aureus isolates (one per child) therefore, the S. aureus carriage rate in children was 19.4% (144/742). Thirty one percent (45/144) of the isolates were methicillin resistant (MRSA) yielding a carriage rate of 6.1% (45/742). All isolates were susceptible to rifampicin, vancomycin and linezolid. Moreover, all MRSA were susceptible to vancomycin, linezolid and clindamycin. Compared to methicillin susceptible S. aureus (MSSA) isolates (68.8%, 99/144), MRSA isolates were more resistant to non-beta-lactam antimicrobials –trimethoprim/sulfamethoxazole 73.3% (33/45) vs. 27.3% (27/99) [p<0.0001]; erythromycin 75.6% (34/45) vs. 24.2% (24/99) [p<0.0001]; chloramphenicol 60% (27/45) vs. 19.2% (19/99) [p<0.0001]; gentamicin 55.6% (25/45) vs. 25.3% (25/99) [p=0.0004]; and ciprofloxacin 35.6% (16/45) vs. 2% (2/99) [p<0.0001]. Furthermore, 42 MRSA (93.3%) were multidrug resistant (MDR) and one exhibited high-level resistance to mupirocin. Overall, 61 MSSA (61.6%) were MDR, including three mupirocin and clindamycin resistant isolates. Seven spa types were detected among MRSA, of which t037 and t064 were predominant and associated with SCCmec types I and IV, respectively. Fourteen spa types were detected in MSSA which consisted mainly of t645 and t4353. Conclusions: S. aureus carriage rate in healthy children in Eastern Uganda is high and comparable to rates for hospitalized patients in Kampala. The detection of mupirocin resistance is worrying as it could rapidly increase if mupirocin is administered in a low-income setting. S. aureus strains of spa types t064, t037 (MRSA) and t645, t4353 (MSSA) are prevalent and could be responsible for majority of staphylococcal infections in Uganda.