Molecular characterization of Staphylococcus aureus isolates from various healthcare institutions in Nairobi, Kenya: a cross sectional study

Background: Staphylococcus aureus (S. aureus) has established itself over the years as a major cause of morbidity and mortality both within the community and in healthcare settings. Methicillin resistant S. aureus (MRSA) in particular has been a major cause of nosocomial infections resulting in significant increase in healthcare costs. In Africa, the MRSA prevalence has been shown to vary across different countries. In order to better understand the epidemiology of MRSA in a setting, it is important to define its population structure using molecular tools as different clones have been found to predominate in certain geographical locations. Methods: We carried out PFGE, MLST, SCCmec and spa typing of selected S. aureus isolates from a private and public referral hospital in Nairobi, Kenya. Results: A total of 93 S. aureus isolates were grouped into 19 PFGE clonal complexes (A–S) and 12 singletons. From these, 55 (32 MRSA and 23 MSSA) representative isolates from each PFGE clonal complex and all singletons were spa typed. There were 18 different MRSA spa types and 22 MSSA spa types. The predominant MRSA spa type was t037 comprising 40.6 % (13/32) of all MRSA. In contrast, the MSSA were quite heterogeneous, only 2 out of 23 MSSA shared the same spa type. Two new MRSA spa types (t13149 and t13150) and 3 new MSSA spa types (t13182, t13193 and t13194) were identified. The predominant clonal complex was CC 5 which included multi-locus sequence types 1, 8 and 241. Conclusion: In contrast to previous studies published from Kenya, there’s marked genetic diversity amongst clinical MRSA isolates in Nairobi including the presence of well-known epidemic MRSA clones. Given that these clones are resident within our referral hospitals, adherence to strict infection control measures needs to be ensured to reduce morbidity and mortality associated with hospital acquired MRSA infections

Longitudinal Population Dynamics of Staphylococcus aureus in the Nasopharynx During the First Year of Life

Background:Staphylococcus aureus colonization is a risk factor for invasive disease. Few studies have used strain genotype data to study S. aureus acquisition and carriage patterns. We investigated S. aureus nasopharyngeal carriage in infants in an intensively sampled South African birth cohort.Methods: Nasopharyngeal swabs were collected at birth and fortnightly from 137 infants through their first year of life. S. aureus was characterized by spa-typing. The incidence of S. aureus acquisition, and median carriage duration for each genotype was determined. S. aureus carriage patterns were defined by combining the carrier index (proportion of samples testing positive for S. aureus) with genotype diversity measures. Persistent or prolonged carriage were defined by a carrier index ≥0.8 or ≥0.5, respectively. Risk factors for time to acquisition of S. aureus were determined.Results: Eighty eight percent (121/137) of infants acquired S. aureus at least once. The incidence of acquisition at the species and genotype level was 1.83 and 2.8 episodes per child-year, respectively. No children had persistent carriage (defined as carrier index of >0.8). At the species level 6% had prolonged carriage, while only 2% had prolonged carriage with the same genotype. Carrier index correlated with the absolute number of spa-CCs carried by each infant (r = 0.5; 95% CI 0.35–0.62). Time to first acquisition of S. aureus was shorter in children from households with ≥5 individuals (HR 1.06, 95% CI 1.07–1.43), with S. aureus carrier mothers (HR; 1.5, 95% CI 1.2–2.47), or with a positive tuberculin skin test during the first year of life (HR; 1.81, 95% CI 0.97–3.3).Conclusion: Using measures of genotype diversity, we showed that S. aureus NP carriage is highly dynamic in infants. Prolonged carriage with a single strain occurred rarely; persistent carriage was not observed. A correlation was observed between carrier index and genotype diversity

Carbapenem resistance expressed by Gram-negative bacilli isolated from a cohort of Libyan patients

Background and objectives: Carbapenem-resistant Enterobacteriaceae (CRE) and other Gram-negative bacteria are among the most common pathogens responsible for both community and hospital acquired infection. The global spread of cephalosporinases in Enterobacteriaceae has led to the increased use of carbapenems resulting in the emergence and rapid spread of CRE. This has become an alarming public health concern, yet the condition in Libya remains unclear. The aim of this study was to obtain a better understanding of CRE strains prevalent in Libyan patients by investigating their phenotypic characteristics and antibiograms. Methods: Gram-negative bacterial species were collected from Misrata Central Hospital, Misrata Cancer Centre and Privet Pathology Laboratories. Clinical samples and swabs were obtained from hospitalised and non-hospitalised patients and from mechanical ventilation and suction machines. Patients who had received antibiotic therapy for at least three days prior to the study were excluded. The identification and characterization of the isolated species were achieved using the growth characteristics on MacConkey and blood agar, spot tests and API 20E or API 20NE biochemical testing systems. Screening for carbapenem resistance was performed using the disk diffusion method with carbapenem 10 μg and cephalosporin 30 μg disks and minimum inhibitory concentrations (MIC) determined using the Sensititre Gram-negative Xtra plate format (GNX2F). All strains demonstrating resistance or reduced susceptibility to one of the four carbapenems were subjected to carbapenememase activity detection using the RAPIDEC CARBA NP test, Modified Hodge test and carbapenem inactivation methods. Results: A total of one hundred and forty isolates representing fourteen bacterial species were isolated from 140 non-duplicated specimens. Clinical specimens included urine samples (96/140, 68.57%), sputum (15/140, 10.71%), surgical wound swabs (18/140, 12.85%), foot swabs from diabetes mellitus (DM) patients (6/140, 4.29%), ear swabs (3/140, 2.14%) and wound swabs (2/140, 1.43%). Thirty-four (24.29%) isolates demonstrated resistance to at least one of the four carbapenems with Klebsiella pneumoniae representing 73.53% (25 isolates) of all carbapenem resistant species, followed by 8.82% for Pseudomonas aeruginosa (3 isolates), 5.88% for both Proteus mirabilis (2 isolates) and Escherichia coli (2 isolates) and 2.94% for both Citrobacter koseri (1 isolate) and Rahnella aquatilis (1 isolate). The other isolates were either susceptible or cephalosporinase producers. Conclusion: This study has revealed the high rate of carbapenem resistance amongst Libyan patients and emphasizes the crucial need for accurate screening, identification and susceptibility testing to prevent further spread of nosocomial and community acquired resistance. This may be achieved through the establishment of antibiotic stewardship programmes along with firm infection control practices.National Research Foundation of South Africa; Libyan GovernmentWeb of Scienc

The prevalence and molecular mechanisms of mupirocin resistance in Staphylococcus aureus isolates from a Hospital in Cape Town, South Africa

CITATION: Abdulgader, S. M., et al. 2020. The prevalence and molecular mechanisms of mupirocin resistance in Staphylococcus aureus isolates from a Hospital in Cape Town, South Africa. Antimicrobial Resistance and Infection Control, 9:47, doi:10.1186/s13756-020-00707-8.The original publication is available at https://aricjournal.biomedcentral.comPublication of this article was funded by the Stellenbosch University Open Access FundAbstract Background: Antimicrobial resistance is an increasingly serious problem in public health globally. Monitoring resistance levels within healthcare and community settings is critical to combat its ongoing increase. This study aimed to describe the rates and molecular mechanisms of mupirocin resistance in clinical Staphylococcus aureus isolates from Tygerberg Hospital, and to describe its association with strain types. Methods: We retrospectively selected 212 S. aureus isolates which were identified from blood samples and pus swabs during the years 2009–2011 and 2015–2017. The isolates were identified using conventional microbiological methods and genotyping was done using spa typing. Cefoxitin (30 μg) disc diffusion and the two disc strategy (5 μg and 200 μg) were used to determine susceptibility to methicillin and mupirocin, respectively. Isolates with high-level resistance were screened for the plasmid mediated genes mupA and mupB by PCR, and sequencing of the ileS gene was done for all isolates exhibiting low-level resistance to describe the mutations associated with this phenotype. Chi-square test was used to assess the associations between mupirocin resistance and S. aureus genotypes. Results: Of 212 S. aureus isolates, 12% (n = 25) were resistant to mupirocin, and 44% (n = 93) were methicillin resistant. Strain typing identified 73 spa types with spa t045 being the most predominant constituting 11% of the isolates. High-level mupirocin resistance was observed in 2% (n = 5), and low-level resistance in 9% (n = 20) of the isolates. The prevalence of high-level mupirocin resistance amongst MRSA and MSSA was 4 and 1% respectively, while the prevalence of low-level mupirocin resistance was significantly higher in MRSA (18%) compared to MSSA (3%), (p = 0.032). mupA was the only resistance determinant for high-level resistance, and the IleS mutation V588F was identified in 95% of the isolates which showed low-level resistance. A significant association was observed between spa type t032 and high-level mupirocin resistance, and types t037 and t012 and low-level resistance (p < 0.0001). Conclusion: The study reported higher rates of low-level mupirocin resistance compared to high-level resistance, and in our setting, mupirocin resistance was driven by certain genotypes. Our study advocates for the continuous screening for mupirocin resistance in S. aureus in clinical settings to better guide treatment and prescribing practices. Background Antimicrobial resistance is an increasingly serious problem in public health globally. Monitoring resistance levels within healthcare and community settings is critical to combat its ongoing increase. This study aimed to describe the rates and molecular mechanisms of mupirocin resistance in clinical Staphylococcus aureus isolates from Tygerberg Hospital, and to describe its association with strain types. Methods We retrospectively selected 212 S. aureus isolates which were identified from blood samples and pus swabs during the years 2009–2011 and 2015–2017. The isolates were identified using conventional microbiological methods and genotyping was done using spa typing. Cefoxitin (30 μg) disc diffusion and the two disc strategy (5 μg and 200 μg) were used to determine susceptibility to methicillin and mupirocin, respectively. Isolates with high-level resistance were screened for the plasmid mediated genes mupA and mupB by PCR, and sequencing of the ileS gene was done for all isolates exhibiting low-level resistance to describe the mutations associated with this phenotype. Chi-square test was used to assess the associations between mupirocin resistance and S. aureus genotypes. Results Of 212 S. aureus isolates, 12% (n = 25) were resistant to mupirocin, and 44% (n = 93) were methicillin resistant. Strain typing identified 73 spa types with spa t045 being the most predominant constituting 11% of the isolates. High-level mupirocin resistance was observed in 2% (n = 5), and low-level resistance in 9% (n = 20) of the isolates. The prevalence of high-level mupirocin resistance amongst MRSA and MSSA was 4 and 1% respectively, while the prevalence of low-level mupirocin resistance was significantly higher in MRSA (18%) compared to MSSA (3%), (p = 0.032). mupA was the only resistance determinant for high-level resistance, and the IleS mutation V588F was identified in 95% of the isolates which showed low-level resistance. A significant association was observed between spa type t032 and high-level mupirocin resistance, and types t037 and t012 and low-level resistance (p <  0.0001). Conclusion The study reported higher rates of low-level mupirocin resistance compared to high-level resistance, and in our setting, mupirocin resistance was driven by certain genotypes. Our study advocates for the continuous screening for mupirocin resistance in S. aureus in clinical settings to better guide treatment and prescribing practices.https://aricjournal.biomedcentral.com/articles/10.1186/s13756-020-00707-8Publisher's versio

Nasopharyngeal carriage with Staphylococcus aureus in healthy children during the first year of life - The Drakenstein Child Health study

Background: Staphylococcus aureus carriage is a risk factor for subsequent infections. Data on the prevalence, determinants, population structure and molecular epidemiology of S. aureus nasal carriage among healthy African populations are scarce, especially during infancy. The different S. aureus nasal carriage patterns (intermittent and persistent) were defined in the adult population, however, were ill defined during infancy. A consensus definition for these patterns is still lacking since different approaches were used to define carriage patterns. In addition, few studies used strain genotype to support the intermittent and persistent carriage patterns. This thesis describes the prevalence, determinants, population structure and carriage patterns of S. aureus nasopharyngeal carriage among healthy South African infants and their mothers participating in an intensively sampled cohort. Methods: Nasopharyngeal swabs (NP) were collected on the day of birth from 137 mother-infant pairs and two-weekly thereafter from infants during the first year of life. S. aureus isolates were characterized by antibiotic susceptibility testing, PCR detection of the mecA and Panton-Valentine Leuckocidin (PVL) genes, and typed by targeting the Staphylococcal protein A locus. All genetically related spa types were clustered into spa-clonal complexes using the 'based upon repeat pattern clustering analysis. The Logistic regression model for binomial outcomes, Cox proportional hazards model, and Pearson's Chi-square and correlation coefficient tests were used to determine S. aureus NP carriage dynamics and determinants. Median permutation test was performed to determine the difference in the median carriage duration for each genotype. The NP carriage dynamics i.e. incidence, acquisition, and carriage patterns were analysed at the species and the genotype levels. Genotype diversity (number of spa-clonal complexes carried by the infant and the alpha diversity) were incorporated with the carrier index to define the carriage patterns. Results: S. aureus was identified in 21% (725/3292) of the NP swabs; 704 isolates from infants and 21 from mothers. S. aureus NP carriage occurred from birth, peaked by four weeks of age and declined over the following 11 months. Male gender, higher socioeconomic status, maternal carriage, large family size and hospitalization were risk factors for S. aureus NP carriage. The prevalence of methicillin-resistant S. aureus (MRSA) was 1.7% among infants and none of the mothers carried MRSA at birth. Genotyping of 725 S. aureus isolates by targeting the spa gene resulted in 85 spa types. BURP analysis clustered 71 spa types (n=578) into 11 spa-clonal complexes (spa-CCs). Eleven spa types (n=116) were singletons and three spa types (n=27) were excluded from the cluster analysis due to the small number of repeats. The PVL prevalence was 21% (155/725) consisted mainly on MSSA. Eighty three percent of S. aureus strains were resistant to penicillin, 9.1% to gentamicin, 3.4% to tetracycline, and 3.1% and 2.8% to cotrimoxazole and rifampicin, respectively. Constitutive erythromycin resistance was identified in 1.7% (n=12), whereas the inducible MLSB phenotype (ICR) was observed in 2% (n=18) of isolates. All isolates were susceptible to tigecycline, linezolid and mupirocin. A strong relationship between the spa-clonal complexes and antimicrobial resistance phenotypes was noted. We also documented shifts in the resistance patterns over time within the same genotype carried by the same infant. This study demonstrates the importance of strain genotyping to fully describe carriage dynamics; the incidence of acquisition was higher (0.65 episodes per 100 child days) at the genotype level compared to (0.24 episodes) the species level. During the first year of life, the acquisition rate was 1.8 acquisitions per 137 child-year at the species level compared to 2.4 acquisitions per 137 child-year. At the level of the individual child, a positive correlation (r=0.6; 95% CI 0.46 – 0.70, p < 0.0001) was observed between genotype diversity and the proportion of samples testing positive for S. aureus. Using the genotype diversity measure we found that true persistent carriage with a single strain is rare (2%) during infancy. Conclusion: This study provide baseline data on the prevalence, determinants, population structure and dynamics of S. aureus NP carriage among South African infants. A low prevalence of MRSA was observed in this cohort. A diverse MSSA population with relatively high PVL prevalence was observed. Persistent carriage with a single strain was uncommon during the first year of life. The detailed phenotypic and genotypic analysis of S. aureus in this intensively sampled birth cohort has extended our knowledge of the nature and determinants of NP carriage during infanc

Molecular epidemiology of Methicillin-resistant Staphylococcus aureus in Africa: a systematic review

Methicillin-resistant Staphylococcus aureus (MRSA) infections are a serious global problem, with considerable impact on patients and substantial health care costs. This systematic review provides an overview on the clonal diversity of MRSA, as well as the prevalence of Panton-Valentine leukocidin (PVL)-positive MRSA in Africa. A search on the molecular characterization of MRSA in Africa was conducted by two authors using predefined terms. We screened for articles published in English and French through to October 2014 from five electronic databases. A total of 57 eligible studies were identified. Thirty-four reports from 15 countries provided adequate genotyping data. The hospital-associated MRSA ST239/ST241-III [3A] was identified in nine African countries. This clone was also described with SCCmec type IV [2B] in Algeria and Nigeria, and type V [5C] in Niger. In Africa, the European ST80-IV [2B] clone was limited to Algeria, Egypt and Tunisia. The clonal types ST22-IV [2B], ST36-II [2A] and ST612-IV [2B] were only reported in South Africa. No clear distinctions were observed between MRSA responsible for hospital and community infections. The community clones ST8-IV [2B] and ST88-IV [2B] were reported both in the hospital and community settings in Angola, Cameroon, Gabon, Ghana, Madagascar, Nigeria, and São Tomé and Príncipe. The proportion of PVL-positive MRSA carriage and/or infections ranged from 0.3% to 100% in humans. A number of pandemic clones were identified in Africa. Moreover, some MRSA clones are limited to specific countries or regions. We strongly advocate for more surveillance studies on MRSA in Africa

Epidemiology of Staphylococcus aureus Infections in Kenya: Current State, Gaps and Opportunities

Staphylococcus aureus has maintained its clinical relevance as a major cause of hospital and community acquired infections globally with a high burden of antimicrobial resistance (AMR). Though reported, the burden of infection, antimicrobial resistance and molecular epidemiology of S. aureus are not well defined in Kenya. This descriptive review evaluated reported data on the detection and characterization of S. aureus infections in Kenya. Published data between 2000 and 2020 were evaluated. S. aureus isolation frequencies varied from 1% in blood specimens to 52.6% among skin and soft tissues infections while MRSA rates ranged from 1% to 84.1%. While penicillin resistance has consistently been high, last line and recent antibiotics such as vancomycin, linezolid, teicoplanin and daptomycin have retained their efficacy. Data on MRSA carriage in the community, among HCWs and inpatients is limited. Global clones (CC1, CC5, CC8, CC22, CC30, CC45 and CC239) alongside a few novel MRSA strains have been reported with staphylococcal protein A (spa) sequence based clustering yielding four major clusters (spa CC359, spa CC005, spa CC121 and spa CC021) in circulation. MRSA strain ST239/241 (t037) seems predominant in the country. Despite a clear paucity of data, the present analysis points to a high infection and AMR burden in S. aureus with global MRSA clones in circulation. Standardized national surveillance and reporting incorporating molecular tools for identification and characterization will help fill existing gaps in the understanding of the evolving epidemiology of MRSA infections

Longitudinal population dynamics of staphylococcus aureus in the nasopharynx during the first year of life

The original publication is available at https://www.frontiersin.orgBackground: Staphylococcus aureus colonization is a risk factor for invasive disease. Few studies have used strain genotype data to study S. aureus acquisition and carriage patterns. We investigated S. aureus nasopharyngeal carriage in infants in an intensively sampled South African birth cohort. Methods: Nasopharyngeal swabs were collected at birth and fortnightly from 137 infants through their first year of life. S. aureus was characterized by spa-typing. The incidence of S. aureus acquisition, and median carriage duration for each genotype was determined. S. aureus carriage patterns were defined by combining the carrier index (proportion of samples testing positive for S. aureus) with genotype diversity measures. Persistent or prolonged carriage were defined by a carrier index ≥0.8 or ≥0.5, respectively. Risk factors for time to acquisition of S. aureus were determined. Results: Eighty eight percent (121/137) of infants acquired S. aureus at least once. The incidence of acquisition at the species and genotype level was 1.83 and 2.8 episodes per child-year, respectively. No children had persistent carriage (defined as carrier index of >0.8). At the species level 6% had prolonged carriage, while only 2% had prolonged carriage with the same genotype. Carrier index correlated with the absolute number of spa-CCs carried by each infant (r = 0.5; 95% CI 0.35–0.62). Time to first acquisition of S. aureus was shorter in children from households with ≥5 individuals (HR 1.06, 95% CI 1.07–1.43), with S. aureus carrier mothers (HR; 1.5, 95% CI 1.2–2.47), or with a positive tuberculin skin test during the first year of life (HR; 1.81, 95% CI 0.97–3.3). Conclusion: Using measures of genotype diversity, we showed that S. aureus NP carriage is highly dynamic in infants. Prolonged carriage with a single strain occurred rarely; persistent carriage was not observed. A correlation was observed between carrier index and genotype diversity.https://www.frontiersin.org/articles/10.3389/fgene.2019.00198/fullPublisher's versio

Molecular epidemiology of Staphylococcus aureus in African children from rural and urban communities with atopic dermatitis

Abstract Background Staphylococcus aureus has been associated with the exacerbation and severity of atopic dermatitis (AD). Studies have not investigated the colonisation dynamics of S. aureus lineages in African toddlers with AD. We determined the prevalence and population structure of S. aureus in toddlers with and without AD from rural and urban South African settings. Methods We conducted a study of AD-affected and non-atopic AmaXhosa toddlers from rural Umtata and urban Cape Town, South Africa. S. aureus was screened from skin and nasal specimens using established microbiological methods and clonal lineages were determined by spa typing. Logistic regression analyses were employed to assess risk factors associated with S. aureus colonisation. Results S. aureus colonisation was higher in cases compared to controls independent of geographic location (54% vs. 13%, p < 0.001 and 70% vs. 35%, p = 0.005 in Umtata [rural] and Cape Town [urban], respectively). Severe AD was associated with higher colonisation compared with moderate AD (86% vs. 52%, p = 0.015) among urban cases. Having AD was associated with colonisation in both rural (odds ratio [OR] 7.54, 95% CI 2.92–19.47) and urban (OR 4.2, 95% CI 1.57–11.2) toddlers. In rural toddlers, living in an electrified house that uses gas (OR 4.08, 95% CI 1.59–10.44) or utilises kerosene and paraffin (OR 2.88, 95% CI 1.22–6.77) for heating and cooking were associated with increased S. aureus colonisation. However, exposure to farm animals (OR 0.3, 95% CI 0.11–0.83) as well as living in a house that uses wood and coal (OR 0.14, 95% CI 0.04–0.49) or outdoor fire (OR 0.31, 95% CI 0.13–0.73) were protective. Spa types t174 and t1476, and t272 and t1476 were dominant among urban and rural cases, respectively, but no main spa type was observed among controls, independent of geographic location. In urban cases, spa type t002 and t442 isolates were only identified in severe AD, t174 was more frequent in moderate AD, and t1476 in severe AD. Conclusion The strain genotype of S. aureus differed by AD phenotypes and rural-urban settings. Continued surveillance of colonising S. aureus lineages is key in understanding alterations in skin microbial composition associated with AD pathogenesis and exacerbation