Get 20M+ Full-Text Papers For Less Than $1.50/day. Subscribe now for You or Your Team.

Learn More →

Carriage of Staphylococcus aureus in Thika Level 5 Hospital, Kenya: a cross-sectional study

Carriage of Staphylococcus aureus in Thika Level 5 Hospital, Kenya: a cross-sectional study Background: Methicillin-resistant Staphylococcus aureus (MRSA) is an important nosocomial pathogen but little is known about its circulation in hospitals in developing countries. We aimed to describe carriage of S.aureus amongst inpatients in a mid-sized Kenyan government hospital. Methods: We determined the frequency of S.aureus and MRSA carriage amongst inpatients in Thika Hospital, Kenya by means of repeated cross-sectional ward surveys. For all S.aureus isolates, we performed antibiotic susceptibility tests, genomic profiling using a DNA microarray and spa typing and MLST. Results: In this typical mid-sized Kenyan Government hospital, we performed 950 screens for current carriage of S. aureus amongst inpatients over a four month period. We detected S.aureus carriage (either MSSA or MRSA) in 8.9% (85/950; 95%CI 7.1-10.8) of inpatient screens, but patients with multiple screens were more likely have detection of carriage. MRSA carriage was rare amongst S.aureus strains carried by hospital inpatients – only 7.0% (6/86; 95%CI 1.5-12.5%) of all isolates were MRSA. Most MRSA (5/6) were obtained from burns patients with prolonged admissions, who only represented a small proportion of the inpatient population. All MRSA strains were of the same clone (MLST ST239; spa type t037) with concurrent resistance to multiple antibiotic classes. MSSA isolates were diverse and rarely expressed antibiotic resistance except against benzyl-penicillin and co-trimoxazole. Conclusions: Although carriage rates for S.aureus and the MRSA prevalence in this Kenyan hospital were both low, burns patient were identified as a high risk group for carriage. The high frequency of genetically indistinguishable isolates suggests that there was local transmission of both MRSA and MSSA. Keywords: Staphylococcus aureus, MRSA, Kenya, Hospitals, Carriage prevalence Background control [3] - these could represent near-ideal conditions Staphylococcus aureus is both a human commensal and for nosocomial circulation of drug-resistant bacteria. In an important pathogen [1]. Methicillin-resistant S.aureus sub-Saharan Africa, screening for MRSA carriage during (MRSA) is a common cause of healthcare-associated in- hospital admission is rarely considered a healthcare pri- fections in both developed and developing countries, ority and is infrequently performed, so patients carrying though limited information is available from the latter MRSA in hospitals in this region are unlikely to be iden- [2]. In hospital wards in developing countries, the risk of tified or isolated. nosocomial transmission is likely to be high due to close Carriage of S.aureus is most commonly detected in the physical proximity of patients, inadequate staffing, unre- anterior nares (nostrils), though other sites on the body liable water-supply for handwashing, lack of alcohol are frequently colonised, most commonly the groin and hand-rub, isolation facilities or expertise for infection the axillae [1]. Isolates from the nares are normally in- distinguishable by molecular typing from those found on other body sites [4]. Most S.aureus infections originate * Correspondence: alexander.aiken@lshtm.ac.uk from self-carried strains, although disease only develops London School of Hygiene and Tropical Medicine, Keppel Street, London, UK 2 in a small minority of carriers [4,5]. Cross-sectional Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, studies in adult populations have typically found nasal Kenya Full list of author information is available at the end of the article © 2014 Aiken et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Aiken et al. Antimicrobial Resistance and Infection Control 2014, 3:22 Page 2 of 7 http://www.aricjournal.com/content/3/1/22 carriage rates of around 25%, although much of this the types of MRSA circulating in East Africa are largely work has been conducted in high-income settings [1]. unknown. Carriage of S.aureus (either MRSA or methicillin-sensitive We aimed to describe the prevalence and diversity of S.aureus (MSSA)) often lasts from months to years, and MSSA and MRSA carriage amongst inpatients in a typ- tends to be longer amongst individuals with chronic skin ical mid-sized public-service hospital in Kenya. disease [6]. MRSA expresses resistance to all β-lactam antibiotics Methods (penicillins, cephalosporins, carbapenems) by producing Study setting and patient procedures a penicillin-binding protein (PBP2a) from the mecA gene Thika Level 5 Hospital is a 300-bed Government Hospital in the staphylococcal cassette chromosome (SCCmec). in the town of Thika, approximately 50 km north-east of MRSA was first described in 1961 in the UK, very soon Nairobi, in Central Province, Kenya. It provides medical, after the introduction of anti-staphylococcal penicillins surgical, gynaecological, obstetric and paediatric services to [7]. Some of the earliest reports of MRSA in sub-Saharan a mixed urban and rural population and has a total of African came from various Kenyan Hospitals (including seven inpatient wards. Throughout this study there was no Thika Hospital) in the early 1990’s, where it was princi- full-time infection control nurse in Thika Hospital, though pally found amongst burns patients [8]. The prevalence a Hospital Infection Prevention and Control Committee of MRSA is the percentage of a collection of S.aureus iso- met monthly. Daily bed occupancy rates in adult wards in lates expressing resistance to methicillin – a marker for 2011 were typically between 120 and 140% and all patients the presence of mecA. This has been estimated in a small were nursed in communal bays. th th number of studies in sub-Saharan Africa over the past Between the 11 July and 7 November 2011, each 25 years, mostly based on clinical (disease-causing) iso- week all current inpatients in two out of the five adult lates obtained at university teaching hospitals in major inpatient wards (rotating between male and female med- cities [9-12]. However, there are relatively few studies ical, male and female surgical and gynaecological) were examining the prevalence of S.aureus carriage and of screened for carriage of S.aureus. Any patients who MRSA amongst these carriage isolates from patient pop- stayed in the ward overnight prior to screening were eli- ulations in sub-Saharan Africa [13-18] – see Table 1. gible for inclusion, provided that they (or a family member) These studies show considerable variation in MRSA car- were able to give consent. The surgical wards included riage prevalence amongst inpatient groups: from as high some paediatric patients receiving treatment for surgical as 21% amongst TB inpatients in Tulega Ferry, South conditions, who were also included in screening. Patients Africa to as low as 1.3% amongst a population compris- who were MRSA-negative were repeatedly screened ing paediatric and surgical inpatients in Accra, Ghana - it throughout their entire period of hospitalisation, resulting is unclear what gives rise to this diversity. in some patients being screened multiple times. Initial re- Most MRSA strains in Africa appear to derive from sults regarding MRSA carriage were relayed to patients a small number of common ancestors: a recent study and clinicians as soon as these became available. Patients examining 86 MRSA isolates from clinical isolates at found to have carriage of MRSA were subsequently treated five hospitals in West Africa and Madagascar found with vancomycinifaninfection with S.aureus was sus- that 88% of these isolates were from one of three clonal pected. Patient data were collected from patient notes or strains [12]. By contrast, there was wide diversity amongst by direct interview during screening and single-entered MSSA clones from the same institutions [11]. No simi- into a local database. Statistical analysis was carried out lar studies have been reported from East Africa and using STATA v12. Table 1 Estimates of carriage of S.aureus and MRSA in patient populations in sub-Saharan Africa Study location Carriage isolates from Proportion with S.aureus Proportion of MRSA Overall MRSA S.aureus carriage carriage rate MRSA/S.aureus carriage rate Mogadishu, Somalia [13] Paediatric inpatients 21/46 46% 1/21 5% 2.2% Tulega Ferry, South Africa [14] Inpatients with TB 13/52 25% 11/13 85% 21% Lagos, Nigeria [15] HIV + patients (outpatients) 124/374 33% 20/124 16% 5.3% Lambaréné, Gabon [16] Sickle-cell disease paediatric 34/73 47% 1/34 2.9% 1.4% outpatients Ife-Ife, Nigeria [17] Patients on admission to 61/192 32% 7/61 11% 3.6% surgical wards Accra, Ghana [18] Inpatients (Paediatric and 63/452 14% 6/63 10% 1.3% Surgical Departments) Aiken et al. Antimicrobial Resistance and Infection Control 2014, 3:22 Page 3 of 7 http://www.aricjournal.com/content/3/1/22 Ethics statement (Ridom GmbH, Würzburg, Germany) and the Ridom This study was approved by the Kenya Medical Research SpaServer (http://www.spaserver.ridom.de) [21] after Institute National Ethical Review Committee. All pa- adhering to the SeqNet.org quality procedure [22]. A sin- tients (or their relatives) gave written informed consent gle representative of each spa type was analyzed by to nasal and skin swab collection. MLST. Sequences of each MLST locus were compared to the data in the S.aureus MLST database (http://saureus. Swab processing mlst.net/), and resulting allelic profiles were assigned to Paired nasal and axillary skin swabs were collected from particular sequence types (STs) for each isolate. eBURST each patient and were immediately transferred to Man- software (v3, http://eburst.mlst.net) was used to classify nitol Salt broth (HiMedia Laboratories, Mumbai, India) related Sequence Types (STs) into clonal complexes for overnight selective enrichment. The following day, (CCs) A singleton was defined as a sequence type that aliquots were plated onto Blood Agar (BA) media. Single did not group with any clonal complex. The diagnostic colonies from plates which showed suspected S.aureus DNA microarrays (StaphyType; Alere Technologies, Jena, colony growth, were further processed by Gram stain, Germany) and StaphyType DNA microarray kit were catalase and coagulase test, and checked for the ability used for study of the presence of genes encoding spe- to hydrolyse DNA. Disc diffusion tests with cefoxitin cies markers, agr types and virulence factors as described (10 μg) were used to identify suspected MRSA according previously [23]. to British Society for Antimicrobial Chemotherapy guide- lines. All media were locally prepared and batch controlled Results using appropriate internal quality control strains (S.aureus Carriage of S.aureus ATCC 25923, S.epidermidis ATCC 12228, E.coli ATCC A total of 950 screening swabs were obtained from 733 25922). These initial screening tests were performed in inpatients in the medical, surgical and gynaecological Thika Hospital, Kenya. Isolates were initially kept at −20°C wards of Thika Hospital. Patients ranged in age between and then transferred to −80°C for storage. Isolates were 1 and 90 years and 52% of screens were performed in later shipped to the University Medical Centre Groningen, male patients (see Table 2). We found no association be- the Netherlands for further investigations. tween carriage of S.aureus and either age-group or sex (χ test; p > 0.1). As a result of the repeated rounds of Antimicrobial susceptibility testing cross-sectional inpatient screening, an average of 1.4 Susceptibility to a standard panel of antibiotics plus chlor- screens were performed per patient over the study period amphenicol was performed using the automated Vitek 2 (range 1–8 screens; see Table 3). system (bioMerieux, Marcy l’Etoile,France).The results A total of 85 inpatient screenings (85/950; 8.9%; 95% were interpreted in accordance with the 2012 guidelines of CI 7.1-10.8) detected carriage of S.aureus. One patient the Clinical and Laboratory Standards Institute. Isolates had two distinct S.aureus strains simultaneously (one positive for inducible clindamycin resistance were assumed MRSA and one MSSA). Thus, a total of 86 S.aureus to be resistant to lincosamines and macrolides. isolates were collected. Species identification was con- firmed by the presence of the S.aureus-specific genes Extraction of genomic DNA (spa, coA, nuc1)and mecA for MRSA. Among the S.aureus Total DNA was prepared from a loop of S.aureus cells isolates obtained, six (6/86; 7.0%; 95%CI 1.5-12.5%) were lifted from blood agar plates and transferred to 2-ml tubes containing 500 μl of water and zirconia/silica beads. Table 2 Patient characteristics in screening tests The tubes were fixed in a TissueLyser homogenizer Characteristic Screening Any S.aureus MRSA negative (%) detected (%) detected (%) (Qiagen, Venlo, Netherlands) and the cells were disrupted by vortexing for 5 min at 30 Hz. The suspensions were Median age, years (range) 34 (1–90) 40 (2–80) 27 (2–57) clarified by centrifugation (14,000 rpm for 10 min), and Age < 14 yrs 103 (12) 4 (5) 4 (67) the supernatant was used for DNA extraction with the Male sex 450 (52) 48 (56) 4 (67) DNeasy Blood & Tissue kit (Qiagen) according to the man- Ward location ufacturer’s protocol. The DNA concentration was quanti- Surgical - Male 298 (52) 44 (34) 4 (67) fied using a NanoDrop spectrophotometer (NanoDrop Surgical - Female 215 (25) 22 (26) 2 (33) Technologies, Wilmington, DE) at 260 nm. Medical - Male 127 (15) 7 (8) 0 (0) Genotyping Medical - Female 141 (16) 8 (9) 0 (0) Spa typing [19] and Multi Locus Sequence Typing (MLST) Gynaecology 84 (10) 4 (5) 0 (0) [20] were performed as described previously. Spa types Total 865 (100) 85 (100) 6 (100) were assigned by Ridom StaphType software version 1.4.6 Aiken et al. Antimicrobial Resistance and Infection Control 2014, 3:22 Page 4 of 7 http://www.aricjournal.com/content/3/1/22 Table 3 Rounds of S.aureus screening amongst inpatients Number of screens Number of Total number S.aureus not Screens with Screens with S.aureus ever detected performed patients of screens detected on screen MSSA detected MRSA detected in patient (%) 1 609 609 566 39 4 43/609 (7.1%) 2 72 144 125 18 1 14/72 (19.4%) 3 27 81 74 7 0 5/27 (18.5%) 4 15 60 50 10 0 7/15 (46.7%) 5 7 35 33 2 0 2/7 (28.6%) 6 1 6 5 1 0 1/1 (100%) 7 1 7 4 3 0 1/1 (100%) 8 1 8 7 0 1 1/1 (100%) Total 733 950 865 79 6 74/733 (10.1%) MRSA. All of these were obtained from surgical pa- by four or less MSSA isolates. Isolates obtained from ini- tients, comprising three adult men and one male child tial patient-screens were less likely to have spa types with (male surgical ward) and one woman and one female multiple (≥3) occurrences (39/57, 68%) than those isolates child (female surgical ward). All of these patients had obtained from subsequent rounds of screening (24/29, been hospitalised for a prolonged period, five with ex- 83%), though this difference did not reach statistical signifi- tensive burns and one with a fractured femur. The cance (χ test; p = 0.16). median admission length prior to MRSA detection was Using MLST, twenty STs were identified. Five new 27 days (range 25–172 days). When comparing pa- MLST allelic profiles and three new STs were found; the tients with single versus multiple rounds of screening latter were assigned as ST2429, ST2430, and ST2431. performed, there was evidence that having multiple All six MRSA isolates belonged to international clone screens was associated with higher likelihood of S.aureus ST239. The correspondence between MLST and spa typ- being detected (χ test; p < 0.001 – see Table 3). Out of all ing is shown in Table 5. patients in the study, a total of 74 were found to have car- Using eBURSTv3, all MLST STs obtained in the study riage of S.aureus in at least one screen (74/733; 10.1%; were assigned to CCs. This method identified ST2430 as 95%CI 7.2-12.3). a single locus variant of CC121; the remaining 18 STs were unrelated. Subsequently, MLST data obtained in Antibiotic resistance this study were compared to the S.aureus MLST data- All six MRSA isolates were co-resistant to gentamicin, base. Of the 68 isolates which were grouped into 14 ciprofloxacin, tetracycline and co-trimoxazole and five CCs, the majority of these (64/68, 94%) had a founder were also resistant to lincosamine and macrolide antibi- sequence type – see Table 5. otics. All MRSA isolates were susceptible to chloram- phenicol, vancomycin and mupirocin. Amongst the MSSA Table 4 Sensitivity patterns of MRSA and MSSA carriage isolates obtained, resistance to penicillin, tetracycline and isolates from Thika Hospital, Kenya SXT was common, but not to any other antibiotics – see Antibiotic Proportion susceptible (%) Table 4. MSSA (n = 80) MRSA (n = 6) Cefoxitin 100 0 Diversity of isolates established by spa typing and MLST analyses Benzylpenicillin 26 0 The 86 S.aureus isolates were assigned to 28 spa types, Co-trimoxazole 60 0 ranging in length between four (t10499) and 12 (t005) Tetracycline 85 0 repeats. Two new repeats, r558 and r559, and five new Gentamicin 99 0 spa types, t10496, t10497, t10498, t10499 and t10960, Ciprofloxacin 100 0 were found and assigned over the course of this study. Erythromicin/Clindamycin 99 17 Sixteen spa types were represented by 2 or more isolates (73 isolates in total), while 13 spa types contained a sin- Rifampicin 99 83 gle isolate. All six MRSA isolates identified were of spa Chloramphenicol 100 100 type t037. Among the MSSA isolates, t223 (n = 15) was Vancomycin 100 100 the most frequent spa type, followed by t064 (n = 10) and Mupirocin 100 100 t131 (n = 10). Other spa types (n = 25) were represented Aiken et al. Antimicrobial Resistance and Infection Control 2014, 3:22 Page 5 of 7 http://www.aricjournal.com/content/3/1/22 Table 5 MLST and spa types from 86 S.aureus isolates might be better estimated by the proportion of patients in obtained at Thika Hospital, Kenya the study who were ever detected to have S.aureus carriage MLST CC* ST within CC spa types (number of isolates, (74/733; 10.1%; 95%CI 7.2-12.3) – though some of these (number of isolates) if >1 spa type) patients probably acquired carriage during admission. CC22 ST22 (17) t223 (15), t005 (1), t10498 (1) MRSA constituted only 6.9% (95%CI 1.5-12.5%) of all S. CC8 ST8 (14) t064 (10), t121 (3), t10497 (1) aureus isolates obtained. Both the overall carriage rate and the proportion of MRSA were surprisingly low, given that ST2430 (4) t645 CC121 nasal carriage of S.aureus in European populations is typic- ST121 (3) t314 ally around 25% [1,25] and the crowded conditions in CC239 ST239 (6) t037† Thika Hospital should have led to frequent transmission CC97 ST97 (5) t359 (2), t1965 (2), t267 (1) of MRSA. The small number of MRSA isolates obtained CC5 ST5 (3) t002 leaves us with a wide confidence interval for the true CC30 ST30 (3) t318 microbiological prevalence. Almost all MRSA carriage was confined to patients CC7 ST7 (3) t091 with burns who constituted approximately 10% of adult CC6 ST6 (2) t701 inpatients admitted to the surgical wards and approxi- CC15 ST15 (2) t084 (1), t491 (1) mately 5% of inpatients overall. In sub-Saharan Africa, CC25 ST25 (2) t3772 prolonged hospital admission after burns injuries are CC72 ST72 (2) t148 (1), t4353 (1) common [26], and as specialist burns units are rarely CC1 ST1 (1) t127 available, these patients often make up a sizeable propor- tion of the general inpatient population. Burns patients CC45 ST45 (1) t015 are at increased risk of invasive bacterial disease [27] and ST1290 (10) t131 hence colonisation of these patients with a multi-drug re- ST152 (4) t355 sistance organism is of particular concern. Chlorampheni- Singletons ST2431 (2) t10496 col is a widely used 2nd line antibiotic in sub-Saharan ST2019 (1) t10499 Africa and as all isolates in Thika Hospital were found to ST2429 (1) t10960 be susceptible to this drug, this might be a suitable empir- ical alternative to vancomycin for suspected MRSA infec- * = Clonal Complex nomenclature derived from MLST database. † = all 6 isolates of t037 were MRSA, all other isolates were MSSA. tions in this setting. These Thika MRSA isolates belong to the wide- Microarrays spread ST239 strain, formerly known as the Hungarian/ The distribution of genes of the core variable genome Brazilian epidemic strain which is typically associated with and the identification of the allelic variants of genes of hospital-acquisition. This has been documented to occur the core genome varied between MLST sequence type. in sub-Saharan Africa in Senegal, Niger [12], South Africa Amongst the 6 MRSA isolates, all carried the SCCmec [28] and was noted to be common amongst hospitalised III element, but none carried the lukF/lukS (PVL) genes. burns patients in Nigeria [10]. The pattern of multi-class Amongst the 80 MSSA isolates, the frequency of car- antibiotic resistance that we found in Thika Hospital is typ- riage of the following genetic elements was as follows: ical of this strain in African settings [12]. lukF-PV/lukS-PV (PVL; n = 15; 19%), toxic shock syn- When designing this study, we expected S.aureus and drome toxin 1 (tst1; n = 18; 23%), staphylococcal entero- MRSA to occur considerably more frequently than we toxin a (sea, n = 17; 21%) and exfoliative toxin a (eta; actually found. We used a repeated cross-sectional ap- n = 6; 8%). Full details of the microarray results including proach for detecting carriage but this may have missed descriptions of profiles for all isolates are given as supple- some cases of nosocomial acquisition occurring late in mentary material in Additional file 1. admission, which could have been detected by additional screening on discharge. Discussion Thereasonfor thesurprisinglylow overallrateof In this typical mid-sized Kenyan government hospital, S.aureus carriage(8.9%)inour studyisunclear.We carriage of S.aureus amongst inpatients was found to be feel that is it unlikely that procedural errors with swab relatively infrequent (8.9%; 95%CI 7.1-10.8) in individual collection could account for this – all swab collection screens. Due to the repeating cross-sectional sampling was supervised in person and regularly quality-controlled design, this result may underestimate the actual in- by one investigator (AA) and an experienced researcher (HG) made an on-site review of the collection and pro- patient prevalence due to a time-dependant bias [24] intro- duced by only performing multiple rounds of screening cessing methods in the first month of the study. The an- in patients with longer admissions. The actual prevalence terior nares and axillae are widely accepted to be reliable Aiken et al. Antimicrobial Resistance and Infection Control 2014, 3:22 Page 6 of 7 http://www.aricjournal.com/content/3/1/22 sites for S.aureus detection [1] and we used an enrich- challenges that are typical of those encountered in African ment culture intermediate step to assist with detection of healthcare facilities. Much work is needed in Kenya and small numbers of organisms. However, we accept that throughout the region to formulate appropriate national swabs from the skin surface have inherently limited sen- and local policies to tackle issues such as MRSA and, more sitivity to detect carriage organisms and we note that in importantly, to put these into effective practice. our study, patients who had multiple screenings per- formed were more likely to ever have had S.aureus car- Additional file riage detected. It is therefore possible that a single round of screening is not sufficient to exclude carriage in this Additional file 1: Full S.aureus microarray results from Thika Hospital. setting. Alternatively, progressive acquisition of carriage during hospital admission, as evidenced by our molecular Competing interest All authors declare that they have no competing interest. studies, could provide some explanation for this finding of increasing carriage with repeated screening. Genetic Authors’ contributions differences might also provide an explanation for a low AA, JAGS and HG designed the study. AA, JM and HG supervised collection of carriage rate – human genetic factors are thought to be samples from patients. IMM, SCM, AJS, VA and AWF conducted and supervised laboratory analysis of samples in Thika Hospital and UMCG. AA drafted the important determinants for persistent colonisation with manuscript and all authors read and approved the final manuscript. S.aureus [29]. There were some intriguing findings revealed by the Acknowledgments molecular analyses. In particular, we note that in com- The authors wish to thank patients and staff in Thika Hospital, KEMRI-Wellcome Trust Research Programme and University Medical Centre Groeningen for their parison to isolate collections from other settings, there assistance. were high proportions of isolates with genes for the Panton-Valentine Leukocidin (PVL, 15/86, 19%) and toxic Funding shocksyndrome toxin1(tst1, 18/86, 23%). From the per- This study was funded as part of a Training Fellowship for AA (grant number 085042) from the Wellcome Trust of Great Britain. spective of staphylococcal classification systems, many of the spa types (18%; 5/28) and MLST profiles (15%, 3/20) Author details identified in this population were novel. This is reflective London School of Hygiene and Tropical Medicine, Keppel Street, London, UK. Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, of the limited contribution of African sites to the relevant Kenya. Department of Medical Microbiology, University of Groningen, University typing databases. The lack of diversity amongst the MRSA 4 Medical Center Groningen, Groningen, The Netherlands. Thika Level 5 Hospital, and MSSA isolates obtained in our institution over a four Thika, Kenya. month period suggests that these were probably being Received: 4 December 2013 Accepted: 23 June 2014 transmitted by local (within-hospital) routes rather than Published: 15 July 2014 repeated introduction from external sources, though with- out greater knowledge of the diversity of strains circulating References 1. Wertheim HF, Melles DC, Vos MC, van Leeuwen W, van Belkum A, Verbrugh HA, in Kenya or East Africa as a whole, we cannot be cer- Nouwen JL: The role of nasal carriage in Staphylococcus aureus infections. tain of this. Due to overcrowding and lack of isolation Lancet Infect Dis 2005, 5(12):751–762. facilities, eliminating nosocomial transmission of organ- 2. Allegranzi B, Bagheri Nejad S, Combescure C, Graafmans W, Attar H, Donaldson L, Pittet D: Burden of endemic health-care-associated infection isms such as MRSA in institutions like Thika Hospital will in developing countries: systematic review and meta-analysis. Lancet be challenging. 2011, 377(9761):228–241. Antibiotic resistance is a growing concern in develop- 3. Okeke IN, Laxminarayan R, Bhutta ZA, Duse AG, Jenkins P, O'Brien TF, Pablos-Mendez A, Klugman KP: Antimicrobial resistance in developing ing countries [30] and local studies are needed to under- countries. Part I: recent trends and current status. Lancet Infect Dis 2005, stand the transmission of drug-resistant organisms and 5(8):481–493. guide strategies for containment. MRSA is an important 4. Reighard A, Diekema D, Wibbenmeyer L, Ward M, Herwaldt L: Staphylococcus aureus nasal colonization and colonization or infection at other body sites nosocomial pathogen in developed countries but is little- in patients on a burn trauma unit. Infect Control Hosp Epidemiol 2009, known in sub-Saharan Africa. This is the largest study 30(8):721–726. examining inpatient carriage of S.aureus in sub-Saharan 5. Nouwen JL, van Belkum A, Verbrugh HA: Determinants of Staphylococcus aureus nasal carriage. Neth J Med 2001, 59(3):126–133. Africa and it was conducted in a typical mid-sized Kenyan 6. Hoeger PH, Lenz W, Boutonnier A, Fournier JM: Staphylococcal skin Government Hospital. We found inpatient carriage of colonization in children with atopic dermatitis: prevalence, persistence, MRSA to be relatively infrequent and was mainly confined and transmission of toxigenic and nontoxigenic strains. J Infect Dis 1992, 165(6):1064–1068. to patients with burns. The lack of genetic diversity 7. Cookson B: Five decades of MRSA: controversy and uncertainty amongst the isolates obtained suggests “within-hospital” continues. Lancet 2011, 378(9799):1291–1292. transmission. The multiple drug resistance of MRSA 8. Muthotho JN, Waiyaki PG, Mbalu M, Wairugu A, Mwanthi B, Odongo B: Control of spread of Methicillin Resistant Staphylococcus aureus (MRSA) found in Thika hospital coupled with the vulnerability of in Burns Units. Afr J Health Sci 1995, 2(1):232–235. burns patients to invasive bacterial infection is a cause 9. Kesah C, Ben Redjeb S, Odugbemi TO, Boye CS, Dosso M, Ndinya Achola JO, for concern. Thika Hospital faces many infection control Koulla-Shiro S, Benbachir M, Rahal K, Borg M: Prevalence of methicillin-resistant Aiken et al. Antimicrobial Resistance and Infection Control 2014, 3:22 Page 7 of 7 http://www.aricjournal.com/content/3/1/22 Staphylococcus aureus in eight African hospitals and Malta. Clin Microbiol 26. Albertyn R, Bickler SW, Rode H: Paediatric burn injuries in Sub Saharan Infect 2003, 9(2):153–156. Africa–an overview. Burns 2006, 32(5):605–612. 10. Ghebremedhin B, Olugbosi MO, Raji AM, Layer F, Bakare RA, Konig B, Konig W: 27. Cook N: Methicillin-resistant Staphylococcus aureus versus the burn Emergence of a community-associated methicillin-resistant Staphylococcus patient. Burns 1998, 24(2):91–98. aureus strain with a unique resistance profile in Southwest Nigeria. JClin 28. Moodley A, Oosthuysen WF, Duse AG, Marais E: Molecular characterization Microbiol 2009, 47(9):2975–2980. of clinical methicillin-resistant Staphylococcus aureus isolates in South 11. BreurecS,Fall C,Pouillot R,Boisier P, Brisse S, Diene-Sarr F, DjiboS,Etienne J, Africa. J Clin Microbiol 2010, 48(12):4608–4611. Fonkoua MC, Perrier-Gros-Claude JD, Ramarokoto CE, Randrianirina F, 29. van Belkum A, Melles DC, Nouwen J, van Leeuwen WB, van Wamel W, Thiberge JM, Zriouil SB, Garin B, Laurent F: Epidemiology of methicillin- Vos MC, Wertheim HF, Verbrugh HA: Co-evolutionary aspects of human susceptible Staphylococcus aureus lineages in five major African towns: high colonisation and infection by Staphylococcus aureus. Infect Genet Evol prevalence of Panton-Valentine leukocidin genes. Clin Microbiol Infect 2011, 2009, 9(1):32–47. 17(4):633–639. 30. Laxminarayan R, Heymann DL: Challenges of drug resistance in the 12. Breurec S, Zriouil SB, Fall C, Boisier P, Brisse S, Djibo S, Etienne J, Fonkoua MC, developing world. BMJ 2012, 344:e1567. Perrier-Gros-Claude JD, Pouillot R, Ramarokoto CE, Randrianirina F, Tall A, Thiberge JM, Laurent F, Garin B: Epidemiology of methicillin-resistant doi:10.1186/2047-2994-3-22 Staphylococcus aureus lineages in five major African towns: emergence Cite this article as: Aiken et al.: Carriage of Staphylococcus aureus in Thika and spread of atypical clones. Clin Microbiol Infect 2011, 17(2):160–165. Level 5 Hospital, Kenya: a cross-sectional study. Antimicrobial Resistance and Infection Control 2014 3:22. 13. Nur YA, VandenBergh MF, Yusuf MA, Van Belkum A, Verbrugh H: Nasal Carriage of Multiresistant Staphylococcus aureus among Health Care Workers and Pediatric Patients in two Hospitals in Mogadishu, Somalia. Int J Infect Dis 1997, 1:186–191. 14. Heysell SK, Shenoi SV, Catterick K, Thomas TA, Friedland G: Prevalence of methicillin-resistant Staphylococcus aureus nasal carriage among hospitalised patients with tuberculosis in rural Kwazulu-Natal. S Afr Med J 2011, 101(5):332–334. 15. Olalekan AO, Schaumburg F, Nurjadi D, Dike AE, Ojurongbe O, Kolawole DO, Kun JF, Zanger P: Clonal expansion accounts for an excess of antimicrobial resistance in Staphylococcus aureus colonising HIV-positive individuals in Lagos, Nigeria. Int J Antimicrob Agents 2012, 40(3):268–272. 16. Schaumburg F, Biallas B, Alabi AS, Grobusch MP, Feugap EN, Lell B, Mellmann A, Peters G, Kremsner PG, Becker K, Adegnika AA: Clonal structure of Staphylococcus aureus colonizing children with sickle cell anaemia and healthy controls. Epidemiol Infect 2013, 141(8):1717–1720. 17. Kolawole DO, Adeyanju A, Schaumburg F, Akinyoola AL, Lawal OO, Amusa YB, Kock R, Becker K: Characterization of colonizing Staphylococcus aureus isolated from surgical wards’ patients in a Nigerian university hospital. PLoS One 2013, 8(7):e68721. 18. Egyir B, Guardabassi L, Nielsen SS, Larsen J, Addo KK, Newman MJ, Larsen AR: Prevalence of nasal carriage and diversity of Staphylococcus aureus among inpatients and hospital staff at Korle Bu Teaching Hospital, Ghana. J Global Antimicrob Resist 2013, 1(4):189–193. 19. Aires-de-Sousa M, Boye K, de Lencastre H, Deplano A, Enright MC, Etienne J, Friedrich A, Harmsen D, Holmes A, Huijsdens XW, Kearns AM, Mellmann A, Meugnier H, Rasheed JK, Spalburg E, Strommenger B, Struelens MJ, Tenover FC, Thomas J, Vogel U, Westh H, Xu J, Witte W: High interlaboratory reproducibility of DNA sequence-based typing of bacteria in a multicenter study. J Clin Microbiol 2006, 44(2):619–621. 20. Enright MC, Day NP, Davies CE, Peacock SJ, Spratt BG: Multilocus sequence typing for characterization of methicillin-resistant and methicillin- susceptible clones of Staphylococcus aureus. J Clin Microbiol 2000, 38(3):1008–1015. 21. Harmsen D, Claus H, Witte W, Rothganger J, Turnwald D, Vogel U: Typing of methicillin-resistant Staphylococcus aureus in a university hospital setting by using novel software for spa repeat determination and database management. J Clin Microbiol 2003, 41(12):5442–5448. 22. Friedrich AW, Witte W, de Lencastre H, Hryniewicz W, Scheres J, Westh H, SeqNet.org p: A European laboratory network for sequence-based typing of methicillin-resistant Staphylococcus aureus (MRSA) as a communication Submit your next manuscript to BioMed Central platform between human and veterinary medicine–an update on SeqNet. and take full advantage of: org. Euro Surveill 2008, 13(19):18862. 23. Monecke S, Coombs G, Shore AC, Coleman DC, Akpaka P, Borg M, Chow H, • Convenient online submission Ip M, Jatzwauk L, Jonas D, Kadlec K, Kearns A, Laurent F, O’Brien FG, Pearson J, Ruppelt A, Schwarz S, Scicluna E, Slickers P, Tan HL, Weber S, Ehricht R: Afield • Thorough peer review guide to pandemic, epidemic and sporadic clones of methicillin-resistant • No space constraints or color figure charges Staphylococcus aureus. PLoS One 2011, 6(4):e17936. • Immediate publication on acceptance 24. Schumacher M, Allignol A, Beyersmann J, Binder N, Wolkewitz M: Hospital- acquired infections–appropriate statistical treatment is urgently needed! • Inclusion in PubMed, CAS, Scopus and Google Scholar Int J Epidemiol 2013, 42(5):1502–1508. • Research which is freely available for redistribution 25. Grundmann H, Tami A, Hori S, Halwani M, Slack R: Nottingham Staphylococcus aureus population study: prevalence of MRSA among elderly people in the Submit your manuscript at community. BMJ 2002, 324(7350):1365–1366. www.biomedcentral.com/submit http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Antimicrobial Resistance & Infection Control Springer Journals

Carriage of Staphylococcus aureus in Thika Level 5 Hospital, Kenya: a cross-sectional study

Loading next page...
 
/lp/springer-journals/carriage-of-staphylococcus-aureus-in-thika-level-5-hospital-kenya-a-eDFxDm0WXr

References (30)

Publisher
Springer Journals
Copyright
Copyright © 2014 by Aiken et al.; licensee BioMed Central Ltd.
Subject
Biomedicine; Medical Microbiology; Drug Resistance; Infectious Diseases
eISSN
2047-2994
DOI
10.1186/2047-2994-3-22
pmid
25057351
Publisher site
See Article on Publisher Site

Abstract

Background: Methicillin-resistant Staphylococcus aureus (MRSA) is an important nosocomial pathogen but little is known about its circulation in hospitals in developing countries. We aimed to describe carriage of S.aureus amongst inpatients in a mid-sized Kenyan government hospital. Methods: We determined the frequency of S.aureus and MRSA carriage amongst inpatients in Thika Hospital, Kenya by means of repeated cross-sectional ward surveys. For all S.aureus isolates, we performed antibiotic susceptibility tests, genomic profiling using a DNA microarray and spa typing and MLST. Results: In this typical mid-sized Kenyan Government hospital, we performed 950 screens for current carriage of S. aureus amongst inpatients over a four month period. We detected S.aureus carriage (either MSSA or MRSA) in 8.9% (85/950; 95%CI 7.1-10.8) of inpatient screens, but patients with multiple screens were more likely have detection of carriage. MRSA carriage was rare amongst S.aureus strains carried by hospital inpatients – only 7.0% (6/86; 95%CI 1.5-12.5%) of all isolates were MRSA. Most MRSA (5/6) were obtained from burns patients with prolonged admissions, who only represented a small proportion of the inpatient population. All MRSA strains were of the same clone (MLST ST239; spa type t037) with concurrent resistance to multiple antibiotic classes. MSSA isolates were diverse and rarely expressed antibiotic resistance except against benzyl-penicillin and co-trimoxazole. Conclusions: Although carriage rates for S.aureus and the MRSA prevalence in this Kenyan hospital were both low, burns patient were identified as a high risk group for carriage. The high frequency of genetically indistinguishable isolates suggests that there was local transmission of both MRSA and MSSA. Keywords: Staphylococcus aureus, MRSA, Kenya, Hospitals, Carriage prevalence Background control [3] - these could represent near-ideal conditions Staphylococcus aureus is both a human commensal and for nosocomial circulation of drug-resistant bacteria. In an important pathogen [1]. Methicillin-resistant S.aureus sub-Saharan Africa, screening for MRSA carriage during (MRSA) is a common cause of healthcare-associated in- hospital admission is rarely considered a healthcare pri- fections in both developed and developing countries, ority and is infrequently performed, so patients carrying though limited information is available from the latter MRSA in hospitals in this region are unlikely to be iden- [2]. In hospital wards in developing countries, the risk of tified or isolated. nosocomial transmission is likely to be high due to close Carriage of S.aureus is most commonly detected in the physical proximity of patients, inadequate staffing, unre- anterior nares (nostrils), though other sites on the body liable water-supply for handwashing, lack of alcohol are frequently colonised, most commonly the groin and hand-rub, isolation facilities or expertise for infection the axillae [1]. Isolates from the nares are normally in- distinguishable by molecular typing from those found on other body sites [4]. Most S.aureus infections originate * Correspondence: alexander.aiken@lshtm.ac.uk from self-carried strains, although disease only develops London School of Hygiene and Tropical Medicine, Keppel Street, London, UK 2 in a small minority of carriers [4,5]. Cross-sectional Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, studies in adult populations have typically found nasal Kenya Full list of author information is available at the end of the article © 2014 Aiken et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Aiken et al. Antimicrobial Resistance and Infection Control 2014, 3:22 Page 2 of 7 http://www.aricjournal.com/content/3/1/22 carriage rates of around 25%, although much of this the types of MRSA circulating in East Africa are largely work has been conducted in high-income settings [1]. unknown. Carriage of S.aureus (either MRSA or methicillin-sensitive We aimed to describe the prevalence and diversity of S.aureus (MSSA)) often lasts from months to years, and MSSA and MRSA carriage amongst inpatients in a typ- tends to be longer amongst individuals with chronic skin ical mid-sized public-service hospital in Kenya. disease [6]. MRSA expresses resistance to all β-lactam antibiotics Methods (penicillins, cephalosporins, carbapenems) by producing Study setting and patient procedures a penicillin-binding protein (PBP2a) from the mecA gene Thika Level 5 Hospital is a 300-bed Government Hospital in the staphylococcal cassette chromosome (SCCmec). in the town of Thika, approximately 50 km north-east of MRSA was first described in 1961 in the UK, very soon Nairobi, in Central Province, Kenya. It provides medical, after the introduction of anti-staphylococcal penicillins surgical, gynaecological, obstetric and paediatric services to [7]. Some of the earliest reports of MRSA in sub-Saharan a mixed urban and rural population and has a total of African came from various Kenyan Hospitals (including seven inpatient wards. Throughout this study there was no Thika Hospital) in the early 1990’s, where it was princi- full-time infection control nurse in Thika Hospital, though pally found amongst burns patients [8]. The prevalence a Hospital Infection Prevention and Control Committee of MRSA is the percentage of a collection of S.aureus iso- met monthly. Daily bed occupancy rates in adult wards in lates expressing resistance to methicillin – a marker for 2011 were typically between 120 and 140% and all patients the presence of mecA. This has been estimated in a small were nursed in communal bays. th th number of studies in sub-Saharan Africa over the past Between the 11 July and 7 November 2011, each 25 years, mostly based on clinical (disease-causing) iso- week all current inpatients in two out of the five adult lates obtained at university teaching hospitals in major inpatient wards (rotating between male and female med- cities [9-12]. However, there are relatively few studies ical, male and female surgical and gynaecological) were examining the prevalence of S.aureus carriage and of screened for carriage of S.aureus. Any patients who MRSA amongst these carriage isolates from patient pop- stayed in the ward overnight prior to screening were eli- ulations in sub-Saharan Africa [13-18] – see Table 1. gible for inclusion, provided that they (or a family member) These studies show considerable variation in MRSA car- were able to give consent. The surgical wards included riage prevalence amongst inpatient groups: from as high some paediatric patients receiving treatment for surgical as 21% amongst TB inpatients in Tulega Ferry, South conditions, who were also included in screening. Patients Africa to as low as 1.3% amongst a population compris- who were MRSA-negative were repeatedly screened ing paediatric and surgical inpatients in Accra, Ghana - it throughout their entire period of hospitalisation, resulting is unclear what gives rise to this diversity. in some patients being screened multiple times. Initial re- Most MRSA strains in Africa appear to derive from sults regarding MRSA carriage were relayed to patients a small number of common ancestors: a recent study and clinicians as soon as these became available. Patients examining 86 MRSA isolates from clinical isolates at found to have carriage of MRSA were subsequently treated five hospitals in West Africa and Madagascar found with vancomycinifaninfection with S.aureus was sus- that 88% of these isolates were from one of three clonal pected. Patient data were collected from patient notes or strains [12]. By contrast, there was wide diversity amongst by direct interview during screening and single-entered MSSA clones from the same institutions [11]. No simi- into a local database. Statistical analysis was carried out lar studies have been reported from East Africa and using STATA v12. Table 1 Estimates of carriage of S.aureus and MRSA in patient populations in sub-Saharan Africa Study location Carriage isolates from Proportion with S.aureus Proportion of MRSA Overall MRSA S.aureus carriage carriage rate MRSA/S.aureus carriage rate Mogadishu, Somalia [13] Paediatric inpatients 21/46 46% 1/21 5% 2.2% Tulega Ferry, South Africa [14] Inpatients with TB 13/52 25% 11/13 85% 21% Lagos, Nigeria [15] HIV + patients (outpatients) 124/374 33% 20/124 16% 5.3% Lambaréné, Gabon [16] Sickle-cell disease paediatric 34/73 47% 1/34 2.9% 1.4% outpatients Ife-Ife, Nigeria [17] Patients on admission to 61/192 32% 7/61 11% 3.6% surgical wards Accra, Ghana [18] Inpatients (Paediatric and 63/452 14% 6/63 10% 1.3% Surgical Departments) Aiken et al. Antimicrobial Resistance and Infection Control 2014, 3:22 Page 3 of 7 http://www.aricjournal.com/content/3/1/22 Ethics statement (Ridom GmbH, Würzburg, Germany) and the Ridom This study was approved by the Kenya Medical Research SpaServer (http://www.spaserver.ridom.de) [21] after Institute National Ethical Review Committee. All pa- adhering to the SeqNet.org quality procedure [22]. A sin- tients (or their relatives) gave written informed consent gle representative of each spa type was analyzed by to nasal and skin swab collection. MLST. Sequences of each MLST locus were compared to the data in the S.aureus MLST database (http://saureus. Swab processing mlst.net/), and resulting allelic profiles were assigned to Paired nasal and axillary skin swabs were collected from particular sequence types (STs) for each isolate. eBURST each patient and were immediately transferred to Man- software (v3, http://eburst.mlst.net) was used to classify nitol Salt broth (HiMedia Laboratories, Mumbai, India) related Sequence Types (STs) into clonal complexes for overnight selective enrichment. The following day, (CCs) A singleton was defined as a sequence type that aliquots were plated onto Blood Agar (BA) media. Single did not group with any clonal complex. The diagnostic colonies from plates which showed suspected S.aureus DNA microarrays (StaphyType; Alere Technologies, Jena, colony growth, were further processed by Gram stain, Germany) and StaphyType DNA microarray kit were catalase and coagulase test, and checked for the ability used for study of the presence of genes encoding spe- to hydrolyse DNA. Disc diffusion tests with cefoxitin cies markers, agr types and virulence factors as described (10 μg) were used to identify suspected MRSA according previously [23]. to British Society for Antimicrobial Chemotherapy guide- lines. All media were locally prepared and batch controlled Results using appropriate internal quality control strains (S.aureus Carriage of S.aureus ATCC 25923, S.epidermidis ATCC 12228, E.coli ATCC A total of 950 screening swabs were obtained from 733 25922). These initial screening tests were performed in inpatients in the medical, surgical and gynaecological Thika Hospital, Kenya. Isolates were initially kept at −20°C wards of Thika Hospital. Patients ranged in age between and then transferred to −80°C for storage. Isolates were 1 and 90 years and 52% of screens were performed in later shipped to the University Medical Centre Groningen, male patients (see Table 2). We found no association be- the Netherlands for further investigations. tween carriage of S.aureus and either age-group or sex (χ test; p > 0.1). As a result of the repeated rounds of Antimicrobial susceptibility testing cross-sectional inpatient screening, an average of 1.4 Susceptibility to a standard panel of antibiotics plus chlor- screens were performed per patient over the study period amphenicol was performed using the automated Vitek 2 (range 1–8 screens; see Table 3). system (bioMerieux, Marcy l’Etoile,France).The results A total of 85 inpatient screenings (85/950; 8.9%; 95% were interpreted in accordance with the 2012 guidelines of CI 7.1-10.8) detected carriage of S.aureus. One patient the Clinical and Laboratory Standards Institute. Isolates had two distinct S.aureus strains simultaneously (one positive for inducible clindamycin resistance were assumed MRSA and one MSSA). Thus, a total of 86 S.aureus to be resistant to lincosamines and macrolides. isolates were collected. Species identification was con- firmed by the presence of the S.aureus-specific genes Extraction of genomic DNA (spa, coA, nuc1)and mecA for MRSA. Among the S.aureus Total DNA was prepared from a loop of S.aureus cells isolates obtained, six (6/86; 7.0%; 95%CI 1.5-12.5%) were lifted from blood agar plates and transferred to 2-ml tubes containing 500 μl of water and zirconia/silica beads. Table 2 Patient characteristics in screening tests The tubes were fixed in a TissueLyser homogenizer Characteristic Screening Any S.aureus MRSA negative (%) detected (%) detected (%) (Qiagen, Venlo, Netherlands) and the cells were disrupted by vortexing for 5 min at 30 Hz. The suspensions were Median age, years (range) 34 (1–90) 40 (2–80) 27 (2–57) clarified by centrifugation (14,000 rpm for 10 min), and Age < 14 yrs 103 (12) 4 (5) 4 (67) the supernatant was used for DNA extraction with the Male sex 450 (52) 48 (56) 4 (67) DNeasy Blood & Tissue kit (Qiagen) according to the man- Ward location ufacturer’s protocol. The DNA concentration was quanti- Surgical - Male 298 (52) 44 (34) 4 (67) fied using a NanoDrop spectrophotometer (NanoDrop Surgical - Female 215 (25) 22 (26) 2 (33) Technologies, Wilmington, DE) at 260 nm. Medical - Male 127 (15) 7 (8) 0 (0) Genotyping Medical - Female 141 (16) 8 (9) 0 (0) Spa typing [19] and Multi Locus Sequence Typing (MLST) Gynaecology 84 (10) 4 (5) 0 (0) [20] were performed as described previously. Spa types Total 865 (100) 85 (100) 6 (100) were assigned by Ridom StaphType software version 1.4.6 Aiken et al. Antimicrobial Resistance and Infection Control 2014, 3:22 Page 4 of 7 http://www.aricjournal.com/content/3/1/22 Table 3 Rounds of S.aureus screening amongst inpatients Number of screens Number of Total number S.aureus not Screens with Screens with S.aureus ever detected performed patients of screens detected on screen MSSA detected MRSA detected in patient (%) 1 609 609 566 39 4 43/609 (7.1%) 2 72 144 125 18 1 14/72 (19.4%) 3 27 81 74 7 0 5/27 (18.5%) 4 15 60 50 10 0 7/15 (46.7%) 5 7 35 33 2 0 2/7 (28.6%) 6 1 6 5 1 0 1/1 (100%) 7 1 7 4 3 0 1/1 (100%) 8 1 8 7 0 1 1/1 (100%) Total 733 950 865 79 6 74/733 (10.1%) MRSA. All of these were obtained from surgical pa- by four or less MSSA isolates. Isolates obtained from ini- tients, comprising three adult men and one male child tial patient-screens were less likely to have spa types with (male surgical ward) and one woman and one female multiple (≥3) occurrences (39/57, 68%) than those isolates child (female surgical ward). All of these patients had obtained from subsequent rounds of screening (24/29, been hospitalised for a prolonged period, five with ex- 83%), though this difference did not reach statistical signifi- tensive burns and one with a fractured femur. The cance (χ test; p = 0.16). median admission length prior to MRSA detection was Using MLST, twenty STs were identified. Five new 27 days (range 25–172 days). When comparing pa- MLST allelic profiles and three new STs were found; the tients with single versus multiple rounds of screening latter were assigned as ST2429, ST2430, and ST2431. performed, there was evidence that having multiple All six MRSA isolates belonged to international clone screens was associated with higher likelihood of S.aureus ST239. The correspondence between MLST and spa typ- being detected (χ test; p < 0.001 – see Table 3). Out of all ing is shown in Table 5. patients in the study, a total of 74 were found to have car- Using eBURSTv3, all MLST STs obtained in the study riage of S.aureus in at least one screen (74/733; 10.1%; were assigned to CCs. This method identified ST2430 as 95%CI 7.2-12.3). a single locus variant of CC121; the remaining 18 STs were unrelated. Subsequently, MLST data obtained in Antibiotic resistance this study were compared to the S.aureus MLST data- All six MRSA isolates were co-resistant to gentamicin, base. Of the 68 isolates which were grouped into 14 ciprofloxacin, tetracycline and co-trimoxazole and five CCs, the majority of these (64/68, 94%) had a founder were also resistant to lincosamine and macrolide antibi- sequence type – see Table 5. otics. All MRSA isolates were susceptible to chloram- phenicol, vancomycin and mupirocin. Amongst the MSSA Table 4 Sensitivity patterns of MRSA and MSSA carriage isolates obtained, resistance to penicillin, tetracycline and isolates from Thika Hospital, Kenya SXT was common, but not to any other antibiotics – see Antibiotic Proportion susceptible (%) Table 4. MSSA (n = 80) MRSA (n = 6) Cefoxitin 100 0 Diversity of isolates established by spa typing and MLST analyses Benzylpenicillin 26 0 The 86 S.aureus isolates were assigned to 28 spa types, Co-trimoxazole 60 0 ranging in length between four (t10499) and 12 (t005) Tetracycline 85 0 repeats. Two new repeats, r558 and r559, and five new Gentamicin 99 0 spa types, t10496, t10497, t10498, t10499 and t10960, Ciprofloxacin 100 0 were found and assigned over the course of this study. Erythromicin/Clindamycin 99 17 Sixteen spa types were represented by 2 or more isolates (73 isolates in total), while 13 spa types contained a sin- Rifampicin 99 83 gle isolate. All six MRSA isolates identified were of spa Chloramphenicol 100 100 type t037. Among the MSSA isolates, t223 (n = 15) was Vancomycin 100 100 the most frequent spa type, followed by t064 (n = 10) and Mupirocin 100 100 t131 (n = 10). Other spa types (n = 25) were represented Aiken et al. Antimicrobial Resistance and Infection Control 2014, 3:22 Page 5 of 7 http://www.aricjournal.com/content/3/1/22 Table 5 MLST and spa types from 86 S.aureus isolates might be better estimated by the proportion of patients in obtained at Thika Hospital, Kenya the study who were ever detected to have S.aureus carriage MLST CC* ST within CC spa types (number of isolates, (74/733; 10.1%; 95%CI 7.2-12.3) – though some of these (number of isolates) if >1 spa type) patients probably acquired carriage during admission. CC22 ST22 (17) t223 (15), t005 (1), t10498 (1) MRSA constituted only 6.9% (95%CI 1.5-12.5%) of all S. CC8 ST8 (14) t064 (10), t121 (3), t10497 (1) aureus isolates obtained. Both the overall carriage rate and the proportion of MRSA were surprisingly low, given that ST2430 (4) t645 CC121 nasal carriage of S.aureus in European populations is typic- ST121 (3) t314 ally around 25% [1,25] and the crowded conditions in CC239 ST239 (6) t037† Thika Hospital should have led to frequent transmission CC97 ST97 (5) t359 (2), t1965 (2), t267 (1) of MRSA. The small number of MRSA isolates obtained CC5 ST5 (3) t002 leaves us with a wide confidence interval for the true CC30 ST30 (3) t318 microbiological prevalence. Almost all MRSA carriage was confined to patients CC7 ST7 (3) t091 with burns who constituted approximately 10% of adult CC6 ST6 (2) t701 inpatients admitted to the surgical wards and approxi- CC15 ST15 (2) t084 (1), t491 (1) mately 5% of inpatients overall. In sub-Saharan Africa, CC25 ST25 (2) t3772 prolonged hospital admission after burns injuries are CC72 ST72 (2) t148 (1), t4353 (1) common [26], and as specialist burns units are rarely CC1 ST1 (1) t127 available, these patients often make up a sizeable propor- tion of the general inpatient population. Burns patients CC45 ST45 (1) t015 are at increased risk of invasive bacterial disease [27] and ST1290 (10) t131 hence colonisation of these patients with a multi-drug re- ST152 (4) t355 sistance organism is of particular concern. Chlorampheni- Singletons ST2431 (2) t10496 col is a widely used 2nd line antibiotic in sub-Saharan ST2019 (1) t10499 Africa and as all isolates in Thika Hospital were found to ST2429 (1) t10960 be susceptible to this drug, this might be a suitable empir- ical alternative to vancomycin for suspected MRSA infec- * = Clonal Complex nomenclature derived from MLST database. † = all 6 isolates of t037 were MRSA, all other isolates were MSSA. tions in this setting. These Thika MRSA isolates belong to the wide- Microarrays spread ST239 strain, formerly known as the Hungarian/ The distribution of genes of the core variable genome Brazilian epidemic strain which is typically associated with and the identification of the allelic variants of genes of hospital-acquisition. This has been documented to occur the core genome varied between MLST sequence type. in sub-Saharan Africa in Senegal, Niger [12], South Africa Amongst the 6 MRSA isolates, all carried the SCCmec [28] and was noted to be common amongst hospitalised III element, but none carried the lukF/lukS (PVL) genes. burns patients in Nigeria [10]. The pattern of multi-class Amongst the 80 MSSA isolates, the frequency of car- antibiotic resistance that we found in Thika Hospital is typ- riage of the following genetic elements was as follows: ical of this strain in African settings [12]. lukF-PV/lukS-PV (PVL; n = 15; 19%), toxic shock syn- When designing this study, we expected S.aureus and drome toxin 1 (tst1; n = 18; 23%), staphylococcal entero- MRSA to occur considerably more frequently than we toxin a (sea, n = 17; 21%) and exfoliative toxin a (eta; actually found. We used a repeated cross-sectional ap- n = 6; 8%). Full details of the microarray results including proach for detecting carriage but this may have missed descriptions of profiles for all isolates are given as supple- some cases of nosocomial acquisition occurring late in mentary material in Additional file 1. admission, which could have been detected by additional screening on discharge. Discussion Thereasonfor thesurprisinglylow overallrateof In this typical mid-sized Kenyan government hospital, S.aureus carriage(8.9%)inour studyisunclear.We carriage of S.aureus amongst inpatients was found to be feel that is it unlikely that procedural errors with swab relatively infrequent (8.9%; 95%CI 7.1-10.8) in individual collection could account for this – all swab collection screens. Due to the repeating cross-sectional sampling was supervised in person and regularly quality-controlled design, this result may underestimate the actual in- by one investigator (AA) and an experienced researcher (HG) made an on-site review of the collection and pro- patient prevalence due to a time-dependant bias [24] intro- duced by only performing multiple rounds of screening cessing methods in the first month of the study. The an- in patients with longer admissions. The actual prevalence terior nares and axillae are widely accepted to be reliable Aiken et al. Antimicrobial Resistance and Infection Control 2014, 3:22 Page 6 of 7 http://www.aricjournal.com/content/3/1/22 sites for S.aureus detection [1] and we used an enrich- challenges that are typical of those encountered in African ment culture intermediate step to assist with detection of healthcare facilities. Much work is needed in Kenya and small numbers of organisms. However, we accept that throughout the region to formulate appropriate national swabs from the skin surface have inherently limited sen- and local policies to tackle issues such as MRSA and, more sitivity to detect carriage organisms and we note that in importantly, to put these into effective practice. our study, patients who had multiple screenings per- formed were more likely to ever have had S.aureus car- Additional file riage detected. It is therefore possible that a single round of screening is not sufficient to exclude carriage in this Additional file 1: Full S.aureus microarray results from Thika Hospital. setting. Alternatively, progressive acquisition of carriage during hospital admission, as evidenced by our molecular Competing interest All authors declare that they have no competing interest. studies, could provide some explanation for this finding of increasing carriage with repeated screening. Genetic Authors’ contributions differences might also provide an explanation for a low AA, JAGS and HG designed the study. AA, JM and HG supervised collection of carriage rate – human genetic factors are thought to be samples from patients. IMM, SCM, AJS, VA and AWF conducted and supervised laboratory analysis of samples in Thika Hospital and UMCG. AA drafted the important determinants for persistent colonisation with manuscript and all authors read and approved the final manuscript. S.aureus [29]. There were some intriguing findings revealed by the Acknowledgments molecular analyses. In particular, we note that in com- The authors wish to thank patients and staff in Thika Hospital, KEMRI-Wellcome Trust Research Programme and University Medical Centre Groeningen for their parison to isolate collections from other settings, there assistance. were high proportions of isolates with genes for the Panton-Valentine Leukocidin (PVL, 15/86, 19%) and toxic Funding shocksyndrome toxin1(tst1, 18/86, 23%). From the per- This study was funded as part of a Training Fellowship for AA (grant number 085042) from the Wellcome Trust of Great Britain. spective of staphylococcal classification systems, many of the spa types (18%; 5/28) and MLST profiles (15%, 3/20) Author details identified in this population were novel. This is reflective London School of Hygiene and Tropical Medicine, Keppel Street, London, UK. Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, of the limited contribution of African sites to the relevant Kenya. Department of Medical Microbiology, University of Groningen, University typing databases. The lack of diversity amongst the MRSA 4 Medical Center Groningen, Groningen, The Netherlands. Thika Level 5 Hospital, and MSSA isolates obtained in our institution over a four Thika, Kenya. month period suggests that these were probably being Received: 4 December 2013 Accepted: 23 June 2014 transmitted by local (within-hospital) routes rather than Published: 15 July 2014 repeated introduction from external sources, though with- out greater knowledge of the diversity of strains circulating References 1. Wertheim HF, Melles DC, Vos MC, van Leeuwen W, van Belkum A, Verbrugh HA, in Kenya or East Africa as a whole, we cannot be cer- Nouwen JL: The role of nasal carriage in Staphylococcus aureus infections. tain of this. Due to overcrowding and lack of isolation Lancet Infect Dis 2005, 5(12):751–762. facilities, eliminating nosocomial transmission of organ- 2. Allegranzi B, Bagheri Nejad S, Combescure C, Graafmans W, Attar H, Donaldson L, Pittet D: Burden of endemic health-care-associated infection isms such as MRSA in institutions like Thika Hospital will in developing countries: systematic review and meta-analysis. Lancet be challenging. 2011, 377(9761):228–241. Antibiotic resistance is a growing concern in develop- 3. Okeke IN, Laxminarayan R, Bhutta ZA, Duse AG, Jenkins P, O'Brien TF, Pablos-Mendez A, Klugman KP: Antimicrobial resistance in developing ing countries [30] and local studies are needed to under- countries. Part I: recent trends and current status. Lancet Infect Dis 2005, stand the transmission of drug-resistant organisms and 5(8):481–493. guide strategies for containment. MRSA is an important 4. Reighard A, Diekema D, Wibbenmeyer L, Ward M, Herwaldt L: Staphylococcus aureus nasal colonization and colonization or infection at other body sites nosocomial pathogen in developed countries but is little- in patients on a burn trauma unit. Infect Control Hosp Epidemiol 2009, known in sub-Saharan Africa. This is the largest study 30(8):721–726. examining inpatient carriage of S.aureus in sub-Saharan 5. Nouwen JL, van Belkum A, Verbrugh HA: Determinants of Staphylococcus aureus nasal carriage. Neth J Med 2001, 59(3):126–133. Africa and it was conducted in a typical mid-sized Kenyan 6. Hoeger PH, Lenz W, Boutonnier A, Fournier JM: Staphylococcal skin Government Hospital. We found inpatient carriage of colonization in children with atopic dermatitis: prevalence, persistence, MRSA to be relatively infrequent and was mainly confined and transmission of toxigenic and nontoxigenic strains. J Infect Dis 1992, 165(6):1064–1068. to patients with burns. The lack of genetic diversity 7. Cookson B: Five decades of MRSA: controversy and uncertainty amongst the isolates obtained suggests “within-hospital” continues. Lancet 2011, 378(9799):1291–1292. transmission. The multiple drug resistance of MRSA 8. Muthotho JN, Waiyaki PG, Mbalu M, Wairugu A, Mwanthi B, Odongo B: Control of spread of Methicillin Resistant Staphylococcus aureus (MRSA) found in Thika hospital coupled with the vulnerability of in Burns Units. Afr J Health Sci 1995, 2(1):232–235. burns patients to invasive bacterial infection is a cause 9. Kesah C, Ben Redjeb S, Odugbemi TO, Boye CS, Dosso M, Ndinya Achola JO, for concern. Thika Hospital faces many infection control Koulla-Shiro S, Benbachir M, Rahal K, Borg M: Prevalence of methicillin-resistant Aiken et al. Antimicrobial Resistance and Infection Control 2014, 3:22 Page 7 of 7 http://www.aricjournal.com/content/3/1/22 Staphylococcus aureus in eight African hospitals and Malta. Clin Microbiol 26. Albertyn R, Bickler SW, Rode H: Paediatric burn injuries in Sub Saharan Infect 2003, 9(2):153–156. Africa–an overview. Burns 2006, 32(5):605–612. 10. Ghebremedhin B, Olugbosi MO, Raji AM, Layer F, Bakare RA, Konig B, Konig W: 27. Cook N: Methicillin-resistant Staphylococcus aureus versus the burn Emergence of a community-associated methicillin-resistant Staphylococcus patient. Burns 1998, 24(2):91–98. aureus strain with a unique resistance profile in Southwest Nigeria. JClin 28. Moodley A, Oosthuysen WF, Duse AG, Marais E: Molecular characterization Microbiol 2009, 47(9):2975–2980. of clinical methicillin-resistant Staphylococcus aureus isolates in South 11. BreurecS,Fall C,Pouillot R,Boisier P, Brisse S, Diene-Sarr F, DjiboS,Etienne J, Africa. J Clin Microbiol 2010, 48(12):4608–4611. Fonkoua MC, Perrier-Gros-Claude JD, Ramarokoto CE, Randrianirina F, 29. van Belkum A, Melles DC, Nouwen J, van Leeuwen WB, van Wamel W, Thiberge JM, Zriouil SB, Garin B, Laurent F: Epidemiology of methicillin- Vos MC, Wertheim HF, Verbrugh HA: Co-evolutionary aspects of human susceptible Staphylococcus aureus lineages in five major African towns: high colonisation and infection by Staphylococcus aureus. Infect Genet Evol prevalence of Panton-Valentine leukocidin genes. Clin Microbiol Infect 2011, 2009, 9(1):32–47. 17(4):633–639. 30. Laxminarayan R, Heymann DL: Challenges of drug resistance in the 12. Breurec S, Zriouil SB, Fall C, Boisier P, Brisse S, Djibo S, Etienne J, Fonkoua MC, developing world. BMJ 2012, 344:e1567. Perrier-Gros-Claude JD, Pouillot R, Ramarokoto CE, Randrianirina F, Tall A, Thiberge JM, Laurent F, Garin B: Epidemiology of methicillin-resistant doi:10.1186/2047-2994-3-22 Staphylococcus aureus lineages in five major African towns: emergence Cite this article as: Aiken et al.: Carriage of Staphylococcus aureus in Thika and spread of atypical clones. Clin Microbiol Infect 2011, 17(2):160–165. Level 5 Hospital, Kenya: a cross-sectional study. Antimicrobial Resistance and Infection Control 2014 3:22. 13. Nur YA, VandenBergh MF, Yusuf MA, Van Belkum A, Verbrugh H: Nasal Carriage of Multiresistant Staphylococcus aureus among Health Care Workers and Pediatric Patients in two Hospitals in Mogadishu, Somalia. Int J Infect Dis 1997, 1:186–191. 14. Heysell SK, Shenoi SV, Catterick K, Thomas TA, Friedland G: Prevalence of methicillin-resistant Staphylococcus aureus nasal carriage among hospitalised patients with tuberculosis in rural Kwazulu-Natal. S Afr Med J 2011, 101(5):332–334. 15. Olalekan AO, Schaumburg F, Nurjadi D, Dike AE, Ojurongbe O, Kolawole DO, Kun JF, Zanger P: Clonal expansion accounts for an excess of antimicrobial resistance in Staphylococcus aureus colonising HIV-positive individuals in Lagos, Nigeria. Int J Antimicrob Agents 2012, 40(3):268–272. 16. Schaumburg F, Biallas B, Alabi AS, Grobusch MP, Feugap EN, Lell B, Mellmann A, Peters G, Kremsner PG, Becker K, Adegnika AA: Clonal structure of Staphylococcus aureus colonizing children with sickle cell anaemia and healthy controls. Epidemiol Infect 2013, 141(8):1717–1720. 17. Kolawole DO, Adeyanju A, Schaumburg F, Akinyoola AL, Lawal OO, Amusa YB, Kock R, Becker K: Characterization of colonizing Staphylococcus aureus isolated from surgical wards’ patients in a Nigerian university hospital. PLoS One 2013, 8(7):e68721. 18. Egyir B, Guardabassi L, Nielsen SS, Larsen J, Addo KK, Newman MJ, Larsen AR: Prevalence of nasal carriage and diversity of Staphylococcus aureus among inpatients and hospital staff at Korle Bu Teaching Hospital, Ghana. J Global Antimicrob Resist 2013, 1(4):189–193. 19. Aires-de-Sousa M, Boye K, de Lencastre H, Deplano A, Enright MC, Etienne J, Friedrich A, Harmsen D, Holmes A, Huijsdens XW, Kearns AM, Mellmann A, Meugnier H, Rasheed JK, Spalburg E, Strommenger B, Struelens MJ, Tenover FC, Thomas J, Vogel U, Westh H, Xu J, Witte W: High interlaboratory reproducibility of DNA sequence-based typing of bacteria in a multicenter study. J Clin Microbiol 2006, 44(2):619–621. 20. Enright MC, Day NP, Davies CE, Peacock SJ, Spratt BG: Multilocus sequence typing for characterization of methicillin-resistant and methicillin- susceptible clones of Staphylococcus aureus. J Clin Microbiol 2000, 38(3):1008–1015. 21. Harmsen D, Claus H, Witte W, Rothganger J, Turnwald D, Vogel U: Typing of methicillin-resistant Staphylococcus aureus in a university hospital setting by using novel software for spa repeat determination and database management. J Clin Microbiol 2003, 41(12):5442–5448. 22. Friedrich AW, Witte W, de Lencastre H, Hryniewicz W, Scheres J, Westh H, SeqNet.org p: A European laboratory network for sequence-based typing of methicillin-resistant Staphylococcus aureus (MRSA) as a communication Submit your next manuscript to BioMed Central platform between human and veterinary medicine–an update on SeqNet. and take full advantage of: org. Euro Surveill 2008, 13(19):18862. 23. Monecke S, Coombs G, Shore AC, Coleman DC, Akpaka P, Borg M, Chow H, • Convenient online submission Ip M, Jatzwauk L, Jonas D, Kadlec K, Kearns A, Laurent F, O’Brien FG, Pearson J, Ruppelt A, Schwarz S, Scicluna E, Slickers P, Tan HL, Weber S, Ehricht R: Afield • Thorough peer review guide to pandemic, epidemic and sporadic clones of methicillin-resistant • No space constraints or color figure charges Staphylococcus aureus. PLoS One 2011, 6(4):e17936. • Immediate publication on acceptance 24. Schumacher M, Allignol A, Beyersmann J, Binder N, Wolkewitz M: Hospital- acquired infections–appropriate statistical treatment is urgently needed! • Inclusion in PubMed, CAS, Scopus and Google Scholar Int J Epidemiol 2013, 42(5):1502–1508. • Research which is freely available for redistribution 25. Grundmann H, Tami A, Hori S, Halwani M, Slack R: Nottingham Staphylococcus aureus population study: prevalence of MRSA among elderly people in the Submit your manuscript at community. BMJ 2002, 324(7350):1365–1366. www.biomedcentral.com/submit

Journal

Antimicrobial Resistance & Infection ControlSpringer Journals

Published: Jul 15, 2014

There are no references for this article.