Browsing by Subject "Staphylococcus aureus"
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- ItemOpen AccessBacteriome interactions in pediatric atopic dermatitis in a rural and urban South African cohort(2023) Ndhlovu, Gillian Ophelya Nondumiso; Dube, Sizwe; Shittu, AdebayoSkin and nasal bacterial dysbiosis is common in children with atopic dermatitis (AD). However, there is limited data of these bacterial changes in sub-Saharan children with AD. Therefore, this study investigated the bacterial alterations in skin and nasal bacterial communities in AD compared to healthy children in rural and urban South African settings. Staphylococcus aureus was more common in children with AD (cases) than healthy children (controls). S. aureus carriage was also associated with increased disease severity. Using spa typing, we also showed that cases and controls were colonised by distinct spa types. This led us to comprehensively explore genomic differences of S. aureus in cases and controls using whole-genome sequencing. Here, we showed that S. aureus strains from cases and controls had distinct genomic features, with cases harbouring genes associated with antibiotic resistance, DNA damage repair and virulence while controls had genes associated with adhesion. Recent reports indicate the potential role of coagulase-negative Staphylococcus (CoNS) in AD pathology. This study found that CoNS and S. aureus were commonly co-carried on nonlesional skin among cases (regardless of location) and anterior nares among urban cases than the control group. The carriage of S. capitis on nonlesional skin and anterior nares was positively associated with more severe disease in both rural and urban cases. 16S rDNA amplicon sequencing analysis revealed that bacterial diversity was higher on the nonlesional skin and anterior nares of controls. Bacterial community structure differed on lesional skin, nonlesional skin and anterior nares based on AD disease status. The relative abundance of Streptococcus, Granulicatela, Veillonella and Prevotella was high in lesional skin specimens, Anoxybacillus and Cutibacterium on nonlesional skin, and Staphylococcus, Veillonella and Sphingomonas in the anterior nares among cases Overall, the findings presented in this thesis indicate that S. aureus and other CoNS, particularly S. capitis, may predominate among cases and are associated with increased disease severity. However, the increased relative abundance of genera such as Streptococcus, especially among skin samples, indicates that other bacterial genera may be contributing to disease activity on lesional skin in AD than the traditionally reported Staphylococcus.
- ItemOpen AccessCharacterization of methicillin-susceptible and -resistant staphylococci in the clinical setting: a multicentre study in Nigeria(BioMed Central Ltd, 2012) Shittu, Adebayo; Oyedara, Omotayo; Abegunrin, Fadekemi; Okon, Kenneth; Raji, Adeola; Taiwo, Samuel; Ogunsola, Folasade; Onyedibe, Kenneth; Elisha, GayBACKGROUND: The staphylococci are implicated in a variety of human infections; however, many clinical microbiology laboratories in Nigeria do not identify staphylococci (in particular coagulase negative staphylococci - CNS) to the species level. Moreover, data from multi-centre assessment on antibiotic resistance and epidemiology of the staphylococci are not available in Nigeria. This study investigated 91 non-duplicate staphylococcal isolates obtained from the microbiology laboratories of eight hospitals in Nigeria during the period January to April 2010. METHODS: Identification and antibiotic susceptibility testing was performed using the VITEK 2 system, detection of resistance genes by PCR, and molecular characterization was determined by SCCmec typing, spa and multilocus sequence typing (MLST). RESULTS: All the isolates were susceptible to mupirocin, tigecycline, vancomycin and linezolid, but 72.5% of CNS and 82.3% of Staphylococcus aureus were resistant to cotrimoxazole, while multiresistance was observed in 37 of the 40 CNS isolates. Untypeable SCCmec types (ccrC/Class A mec and ccr-negative/Class C2 mec gene complex) in two methicillin-resistant S. aureus (MRSA) were identified. Additionally, ccr-negative/Class A mec and ccr type 4/Class C2 mec gene complex was detected in one isolate each of S. sciuri and S. haemolyticus, respectively. The S. aureus isolates were classified into 21 spa types including two new types (t8987, t9008) among the methicillin-susceptible S. aureus (MSSA) isolates. Two (CC8-SCCmecnon-typeable and CC88-SCCmec IV) and four (CC8-SCCmec III/IV/V; CC30-SCCmec II/III; CC88-SCCmec IV; and ST152-SCCmecnon-typeable) MRSA clones were identified in Maiduguri (North-East Nigeria) and South-West Nigeria, respectively. The proportion of Panton-Valentine leukocidin (PVL)-positive MSSA was high (44.4%) and 56.3% of these strains were associated with sequence type (ST) 152. CONCLUSIONS: The identification of multiresistant mecA positive S. haemolyticus and S. sciuri from clinical samples indicates that characterization of CNS is important in providing information on their diversity and importance in Nigeria. There is the need to develop new SCCmec classification methods for non-typeable methicillin-resistant staphylococci, and to curtail the spread and establishment of the S. aureus ST152 clone in Nigeria. The study presents the first report of a PVL-positive ST152-SCCmecnontypeable MRSA and SCCmec typing of methicillin-resistant CNS in Nigeria.
- ItemOpen AccessChronic otorrhoea: Spectrum of microorganisms and antibiotic sensitivity in a South African cohort(2013) Meyer, E; Whitelaw, A; Edkins, O; Fagan, J JBACKGROUND: Chronic otorrhoea is difficult to treat, with treatment in South Africa (SA) being protocol driven and generally initiated at the primary healthcare level. There is a lack of local studies that focus on the bacteriology and antimicrobial sensitivities of chronic otorrhoea, which underpins the management advice offered. AIMS: To determine the microbiological profile and antimicrobial susceptibility of patients with chronic otorrhoea and the validity of the Department of Health's (DoH) current guideline. METHODS: We conducted a prospective study at Groote Schuur Hospital from 2005 to 2009. We included patients with chronic otorrhoea classified as either otitis media or otitis externa, according to our definitions. Pus swabs were taken, from which microorganisms were cultured and tested for antimicrobial susceptibility. RESULTS: Of 79 patients with otorrhoea, 50 had otitis media, 21 had otitis externa and the condition was not determined in 8 patients. The most common organism isolated with otitis media was Proteus mirabilis (18/50; 36%) and with otitis externa, Pseudomonas aeruginosa (7/21; 33%). Otorrhoea had a different microbial spectrum compared with international reports, with methicillin-resistant Staphylococcus aureus infection in a single patient. The organisms isolated were susceptible mainly to fluoroquinolones (96%) and aminoglycosides (81%). CONCLUSION: Amoxicillin is a poor choice of antibiotic due to its low sensitivity, which calls into question the current DoH guideline for otorrhoea. Antimicrobial treatment protocols should be based on local data and be revisited from time to time. This study suggests that, should first-line treatment fail, an antibiotic with Gram-negative cover, e.g. a topical fluoroquinolone, should be considered.
- ItemOpen AccessEpidemiology of Staphylococcus aureus bacteraemia at a tertiary children's hospital in Cape Town, South Africa(Public Library of Science, 2013) Naidoo, Reené; Nuttall, James; Whitelaw, Andrew; Eley, BrianBACKGROUND: Staphylococcus aureus is an important pathogen in paediatric patients with bloodstream infections. The epidemiology of S. aureus bacteraemia, however, has not been well documented in children in South Africa. METHODS: A retrospective study was conducted at a children's hospital in Cape Town, South Africa, to investigate the epidemiology of S. aureus bacteraemia from 2007-2011. The incidence, clinical presentation, risk factors, management and outcomes of methicillin sensitive S. aureus (MSSA) and methicillin resistant S. aureus (MRSA) bacteraemia were compared. RESULTS: Over the five year study period, 365 episodes of S. aureus bacteraemia were identified. The annual incidence was 3.28 cases per 1000 hospital admissions. MRSA was responsible for 26% of S. aureus bacteraemia and 72% of nosocomial infections. Only six possible cases of community-acquired MRSA infections were described. MSSA bacteraemia was more likely to present as pulmonary and bone or joint infections, while bacteraemia without a source was the most common presentation with MRSA. Infants, children with malnutrition, and residents of long-term care facilities were at highest risk for MRSA bacteraemia. The overall case fatality rate for S. aureus bacteraemia was 8.8% over five years, with MRSA being the only significant risk factor for mortality. CONCLUSION: The incidence of S. aureus bacteraemia and MRSA bacteraemia in children has remained stable over the past five years. MRSA is a predominantly nosocomial pathogen in children with S. aureus bacteraemia in Cape Town, South Africa.
- ItemOpen AccessHost adapted intramammary infections in pregnant heifers which were co-housed and reared on fresh milk as calves(BioMed Central Ltd, 2013) Petzer, Inge-Marie; Karzis, Joanne; Lesosky, Maia; Watermeyer, Johanna; Badenhorst, RenetteBACKGROUND:Heifers can calve down with intramammary infections (IMI) and udder damage. This will have a negative impact on their longevity, future milk yield and financial return. Co-housed pre-weaned calves that are fed fresh milk have the opportunity to suckle each other's teats and may infect udders of fellow heifer calves with pathogens present in milk. The prevalence of IMI in pregnant heifers in South Africa (SA) which were co-housed and reared on fresh milk as calves, is not known. Quarter secretion samples from both pregnant heifers (n=2065) and dry cows (n=5365) were collected for microbiological analysis from eight SA dairy herds. All heifers tested in this study were co-housed pre-weaning and were fed fresh milk as calves. RESULTS: The prevalence of coagulase negative staphylococci, Staphylococcus aureus, Streptococcus agalactiae, environmental streptococci, coliforms and samples with no bacterial growth in heifers was 26%, 0.9%, 0.08%, 1.4%, 0.4% and 66%, respectively. The overall prevalence ratio between heifers and cows for Staphylococcus aureus IMI was 0.76 (95% CI: 0.59, 0.98). Four of the individual herds had prevalence ratios of less than one (p<0.05), one herd had a prevalence ratio of 3.15 (95% CI: 1.52, 6.32), and the remaining 3 herds had a prevalence ratio not significantly different from 1.0. Marginally significant differences were found between Staphylococcus aureus IMI in pregnant heifers compared to cows in their second and later lactations (p=0.06, p=0.05, respectively) but no significant differences between heifers and cows in their first lactation. CONCLUSIONS: The presence of Streptococcus agalactiae IMI in heifers came as a surprise, especially as herd infection rates were low. The high prevalence ratio of Staphylococcus aureus between heifers and cows in one herd warrants further investigation due to the potential danger of udder damage in a young cow at the start of her productive life. The IMI in heifers with host adapted pathogens can also act as a source of new IMI for lactating dairy cows.
- ItemOpen AccessMolecular characterization of Staphylococcus aureus isolates from various healthcare institutions in Nairobi, Kenya: a cross sectional study(2016) Omuse, Geoffrey; Van Zyl, Kristien Nel; Hoek, Kim; Abdulgader, Shima; Kariuki, Samuel; Whitelaw, Andrew; Revathi, GunturuAbstract 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.
- ItemOpen AccessMupirocin-resistant Staphylococcus aureus in Africa: a systematic review and meta-analysis(BioMed Central, 2018-08-15) Shittu, Adebayo O; Kaba, Mamadou; Abdulgader, Shima M; Ajao, Yewande O; Abiola, Mujibat O; Olatimehin, Ayodele OBackground Mupirocin is widely used for nasal decolonization of Staphylococcus aureus to prevent subsequent staphylococcal infection in patients and healthcare personnel. However, the prolonged and unrestricted use has led to the emergence of mupirocin-resistant (mupR) S. aureus. The aim of this systematic review was to investigate the prevalence, phenotypic and molecular characteristics, and geographic spread of mupR S. aureus in Africa. Methods We examined five electronic databases (EBSCOhost, Google Scholar, ISI Web of Science, MEDLINE, and Scopus) for relevant English articles on screening for mupR S. aureus from various samples in Africa. In addition, we performed random effects meta-analysis of proportions to determine the pooled prevalence of mupR S. aureus in Africa. The search was conducted until 3 August 2016. Results We identified 43 eligible studies of which 11 (26%) were obtained only through Google Scholar. Most of the eligible studies (28/43; 65%) were conducted in Nigeria (10/43; 23%), Egypt (7/43; 16%), South Africa (6/43; 14%) and Tunisia (5/43; 12%). Overall, screening for mupR S. aureus was described in only 12 of 54 (22%) African countries. The disk diffusion method was the widely used technique (67%; 29/43) for the detection of mupR S. aureus in Africa. The mupA-positive S. aureus isolates were identified in five studies conducted in Egypt (n = 2), South Africa (n = 2), and Nigeria (n = 1). Low-level resistance (LmupR) and high-level resistance (HmupR) were both reported in six human studies from South Africa (n = 3), Egypt (n = 2) and Libya (n = 1). Data on mupR-MRSA was available in 11 studies from five countries, including Egypt, Ghana, Libya, Nigeria and South Africa. The pooled prevalence (based on 11 human studies) of mupR S. aureus in Africa was 14% (95% CI =6.8 to 23.2%). The proportion of mupA-positive S. aureus in Africa ranged between 0.5 and 8%. Furthermore, the frequency of S. aureus isolates that exhibited LmupR, HmupR and mupR-MRSA in Africa were 4 and 47%, 0.5 and 38%, 5 and 50%, respectively. Conclusions The prevalence of mupR S. aureus in Africa (14%) is worrisome and there is a need for data on administration and use of mupirocin. The disk diffusion method which is widely utilized in Africa could be an important method for the screening and identification of mupR S. aureus. Moreover, we advocate for surveillance studies with appropriate guidelines for screening mupR S. aureus in Africa.
- ItemOpen AccessPrevalence and antimicrobial resistance profiles of respiratory microbial flora in African children with HIV-associated chronic lung disease(2021-02-25) Abotsi, Regina E; Nicol, Mark P; McHugh, Grace; Simms, Victoria; Rehman, Andrea M; Barthus, Charmaine; Mbhele, Slindile; Moyo, Brewster W; Ngwira, Lucky G; Mujuru, Hilda; Makamure, Beauty; Mayini, Justin; Odland, Jon Ø; Ferrand, Rashida A; Dube, Felix SBackground HIV-associated chronic lung disease (CLD) is common among children living with HIV (CLWH) in sub-Saharan Africa, including those on antiretroviral therapy (ART). However, the pathogenesis of CLD and its possible association with microbial determinants remain poorly understood. We investigated the prevalence, and antibiotic susceptibility of Streptococcus pneumoniae (SP), Staphylococcus aureus (SA), Haemophilus influenzae (HI), and Moraxella catarrhalis (MC) among CLWH (established on ART) who had CLD (CLD+), or not (CLD-) in Zimbabwe and Malawi. Methods Nasopharyngeal swabs (NP) and sputa were collected from CLD+ CLWH (defined as forced-expiratory volume per second z-score < − 1 without reversibility post-bronchodilation with salbutamol), at enrolment as part of a randomised, placebo-controlled trial of azithromycin (BREATHE trial - NCT02426112 ), and from age- and sex-matched CLD- CLWH. Samples were cultured, and antibiotic susceptibility testing was conducted using disk diffusion. Risk factors for bacterial carriage were identified using questionnaires and analysed using multivariate logistic regression. Results A total of 410 participants (336 CLD+, 74 CLD-) were enrolled (median age, 15 years [IQR = 13–18]). SP and MC carriage in NP were higher in CLD+ than in CLD- children: 46% (154/336) vs. 26% (19/74), p = 0.008; and 14% (49/336) vs. 3% (2/74), p = 0.012, respectively. SP isolates from the NP of CLD+ children were more likely to be non-susceptible to penicillin than those from CLD- children (36% [53/144] vs 11% [2/18], p = 0.036). Methicillin-resistant SA was uncommon [4% (7/195)]. In multivariate analysis, key factors associated with NP bacterial carriage included having CLD (SP: adjusted odds ratio (aOR) 2 [95% CI 1.1–3.9]), younger age (SP: aOR 3.2 [1.8–5.8]), viral load suppression (SP: aOR 0.6 [0.4–1.0], SA: 0.5 [0.3–0.9]), stunting (SP: aOR 1.6 [1.1–2.6]) and male sex (SA: aOR 1.7 [1.0–2.9]). Sputum bacterial carriage was similar in both groups (50%) and was associated with Zimbabwean site (SP: aOR 3.1 [1.4–7.3], SA: 2.1 [1.1–4.2]), being on ART for a longer period (SP: aOR 0.3 [0.1–0.8]), and hot compared to rainy season (SP: aOR 2.3 [1.2–4.4]). Conclusions CLD+ CLWH were more likely to be colonised by MC and SP, including penicillin-non-susceptible SP strains, than CLD- CLWH. The role of these bacteria in CLD pathogenesis, including the risk of acute exacerbations, should be further studied.
- ItemOpen AccessPrevalence and trends of Staphylococcus aureus Bacteraemia in hospitalized patients in South Africa, 2010 to 2012: laboratory-based surveillance mapping of antimicrobial resistance and molecular epidemiology(Public Library of Science, 2015) Perovic, Olga; Iyaloo, Samantha; Kularatne, Ranmini; Lowman, Warren; Bosman, Noma; Wadula, Jeannette; Seetharam, Sharona; Duse, Adriano; Mbelle, Nontombi; Bamford, Colleen; Dawood, Halima; Mahabeer, Yesholata; Bhola, Prathna; Abrahams, Shareef; Singh-Moodley, AshikaIntroduction We aimed to obtain an in-depth understanding on recent antimicrobial resistance trends and molecular epidemiology trends of S . aureus bacteraemia (SAB). METHODS: Thirteen academic centres in South Africa were included from June 2010 until July 2012. S . aureus susceptibility testing was performed on the MicroScan Walkaway. Real-time PCR using the LightCycler 480 II was done for mec A and nuc . SCC mec and spa -typing were finalized with conventional PCR. We selected one isolate per common spa type per province for multilocus sequence typing (MLST). RESULTS: S . aureus from 2709 patients were included, and 1231 (46%) were resistant to methicillin, with a significant decline over the three-year period (p-value = 0.003). Geographical distribution of MRSA was significantly higher in Gauteng compared to the other provinces (P<0.001). Children <5 years were significantly associated with MRSA with higher rates compared to all other age groups (P = 0.01). The most prevalent SCC mec type was SCC mec type III (531 [41%]) followed by type IV (402 [31%]). Spa -typing discovered 47 different spa -types. The five (87%) most common spa- types were t037, t1257, t045, t064 and t012. Based on MLST, the commonest was ST612 clonal complex (CC8) (n = 7) followed by ST5 (CC5) (n = 4), ST36 (CC30) (n = 4) and ST239 (CC8) (n = 3). CONCLUSIONS: MRSA rate is high in South Africa. Majority of the isolates were classified as SCC mec type III (41%) and type IV (31%), which are typically associated with hospital and community- acquired infections, respectively. Overall, this study reveals the presence of a variety of hospital-acquired MRSA clones in South Africa dominance of few clones, spa 037 and 1257. Monitoring trends in resistance and molecular typing is recommended to detect changing epidemiological trends in AMR patterns of SAB.