Virulence factors and genotypes of Staphylococcus aureus from infection and carriage in Gabon

Temporal trends of skin and soft tissue infections caused by methicillin-resistant Staphylococcus aureus in Gabon

BACKGROUND

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the leading causes of mortality due to bacterial antimicrobial resistance. While S. aureus is common in skin and soft tissue infections (SSTI) in Africa, data on MRSA rates are scarce and reports vary widely across the continent (5%-80%). In this study, we describe the proportion of MRSA causing SSTI in Lambaréné, Gabon, over an 11-year period.

METHODS

We retrospectively analyzed data from 953 bacterial specimens collected from inpatients and outpatients with SSTI at the Albert Schweitzer Hospital, Lambaréné, Gabon, between 2009 and 2019. We determined temporal changes in the prevalence of MRSA and identified risk factors for SSTI with MRSA.

RESULTS

68% of all specimens with bacterial growth yielded S. aureus (n = 499/731), of which 7% (36/497) with antimicrobial susceptibility testing were identified as MRSA. Age above 18 years, admission to the surgical ward, and deep-seated infections were significantly associated with MRSA as the causative agent. After an initial decline from 7% in 2009, there was a marked increase in the proportion of MRSA among all S. aureus from SSTI from 3 to 20% between 2012 and 2019. The resistance rate to erythromycin was significantly higher in MRSA than in methicillin-susceptible S. aureus (73% vs. 10%), and clindamycin resistance was detected exclusively in MRSA isolates (8%).

CONCLUSION

The increasing proportion of MRSA causing SSTI over the 11-year period contrasts with many European countries where MRSA is on decline. Continuous surveillance of MRSA lineages in the hospital and community along with antibiotic stewardship programs could address the increasing trend of MRSA.

Microbial keratitis in Southern Malawi: a microbiological pilot study

OBJECTIVE

Microbial keratitis (MK) is a significant cause of blindness in sub-Saharan Africa. We investigated the feasibility of using a novel corneal impression membrane (CIM) for obtaining and processing samples by culture, PCR and whole-genome sequencing (WGS) in patients presenting with suspected MK in Malawi.

METHODS AND ANALYSIS

Samples were collected from patients presenting with suspected MK using a 12 mm diameter polytetrafluoroethylene CIM disc. Samples were processed using culture and PCR for Acanthamoeba, herpes simplex virus type 1 (HSV-1) and the bacterial 16S rRNA gene. Minimum inhibitory concentrations of isolates to eight antimicrobials were measured using susceptibility strips. WGS was used to characterise Staphylococcus aureus isolates.

RESULTS

71 eyes of 71 patients were included. The overall CIM isolation rate was 81.7% (58 positive samples from 71 participants). 69 (81.2%) of isolates were Gram-positive cocci. Coagulase-negative Staphylococcus 31.8% and Streptococcus species 14.1% were the most isolated bacteria. Seven (9.9%) participants were positive for HSV-1. Fungi and Acanthamoeba were not detected. Moxifloxacin and chloramphenicol offered the best coverage for both Gram-positive and Gram-negative isolates when susceptibility was determined using known antimicrobial first quartile concentrations and European Committee on Antimicrobial Susceptibility Testing breakpoints, respectively. WGS identified known virulence genes associated with S. aureus keratitis.

CONCLUSIONS

In a resource-poor setting, a CIM can be used to safely sample the cornea in patients presenting with suspected MK, enabling identification of causative microorganisms by culture and PCR. Although the microbiological spectrum found was limited to the dry season, these preliminary results could be used to guide empirical treatment.

The Occurrence and Characteristics of Methicillin-Resistant Staphylococcal Isolates from Foods and Containers

Antimicrobial resistance (AMR) has emerged as an urgent global public health issue that requires immediate attention. Methicillin-resistant staphylococci (MRS) is a major problem, as it may cause serious human and animal infections, eventually resulting in death. This study determined the proportional distribution, genetic characteristics, and antimicrobial susceptibility of mecA- or mecC-carrying staphylococci isolated from food chain products. A total of 230 samples were taken from meat, food, fermented food, and food containers. Overall, 13.9% (32/230) of the samples were identified to have Staphylococcus aureus isolates; of those, 3.9% (9/230) were MRS, with eight mecA-positive and one mecC-positive samples, and 1.3% (3/230) methicillin-resistant Staphylococcus aureus (MRSA). MRSA strains belonging to three sequence types (ST9, ST22, and a newly identified ST), three different spa types (T005, t526, and a newly identified type), and three different SCCmec types (IV, V, and an unidentified SCCmec) were detected. Additionally, eight mecA-positive staphylococcal isolates were identified as S. haemolyticus, S. sciuri, S. simulans, and S. warneri, while the mecC-harboring isolate was S. xylosus. The enterotoxin gene, SEm, was detected at 1.56% in S. aureus, whereas SEq was detected at 0.31%, and SEi was also found in MRSA. Our study emphasizes the importance of enhanced hygiene standards in reducing the risk of occupational and foodborne MRSA infections associated with the handling or consumption of meat, food, and preserved food products.

Molecular Characterization of Staphylococcus aureus Isolated from Raw Milk and Humans in Eastern Tanzania: Genetic Diversity and Inter-Host Transmission

Staphylococcus aureus is a common cause of infection in humans and animals, including bovine mastitis, globally. The objective of this study was to genetically characterize a collection of S. aureus isolates recovered from milk and nasal swabs from humans with and without animal contact (bovine = 43, human = 12). Using whole genome sequencing (NextSeq550), isolates were sequence typed, screened for antimicrobial resistance and virulence genes and examined for possible inter-species host transmission. Multi locus sequence typing (MLST) and single nucleotide polymorphism (SNP)-based phylogeny revealed 14 different sequence types, including the following six novel sequence types: ST7840, 7841, 7845, 7846, 7847, and 7848. The SNP tree confirmed that MLST clustering occurred most commonly within CC97, CC5477, and CC152. ResFinder analysis revealed five common antibiotic resistance genes, namely tet(K), blaZ, dfrG, erm©, and str, encoding for different antibiotics. mecA was discovered in one human isolate only. Multidrug resistance was observed in 25% of the isolates, predominantly in CC152 (7/8) and CC121 (3/4). Known bovine S. aureus (CC97) were collected in humans and known human S. aureus lineages (CC152) were collected in cattle; additionally, when these were compared to bovine-isolated CC97 and human-isolated CC152, respectively, no genetic distinction could be observed. This is suggestive of inter-host transmission and supports the need for surveillance of the human-animal interface.

Virulence Determinants and Methicillin Resistance in Biofilm-Forming Staphylococcus aureus from Various Food Sources in Bangladesh

The eradication of staphylococcal infections has become more difficult due to the development of antibiotic resistance and virulence in biofilm-forming Staphylococcus aureus. The presence of the life-threatening zoonotic pathogen, methicillin-resistant S. aureus (MRSA), in foods indicates a public health issue. This study, therefore, aimed to determine virulence factors and methicillin resistance in biofilm-forming S. aureus isolates from different foods and food handlers. A total of 100 PCR-positive S. aureus isolates (97 biofilm formers and three non-biofilm formers) were screened using the disk diffusion method and PCR assay. By PCR, genes encoding virulence factors, e.g., enterotoxin (sea, 30%, 95% CI: 21.90−39.59%), toxic shock syndrome toxin (tst, 20%, 95% CI: 13.34−28.88%), and Panton−Valentine leukocidin toxin (PVL, 15%, 95% CI: 9.31−23.28%), were detected in the S. aureus isolates. By the disk diffusion method, 100% (95% CI: 96.30−100.00%) of S. aureus isolates were phenotypically MRSA in nature, showing 100% resistance to oxacillin and cefoxitin. Moreover, the methicillin-resistant gene mecA was found in 61 (61%, 95% CI: 51.20−69.98%) MRSA isolates. Furthermore, all the S. aureus isolates were phenotypically resistant to ampicillin and penicillin, 30% to erythromycin, and 11% to gentamycin. Among them, 51% (95% CI: 41.35−60.58%) of S. aureus isolates were phenotypically multidrug-resistant in nature, and the multiple antibiotic resistance index varied from 0.33 to 0.55. Genes encoding resistance to beta-lactams (blaZ, 100%, 95% CI: 96.30−100.00%) and tetracyclines (tetA and tetC, 3%, 95% CI: 0.82−8.45%) were found positive in the S. aureus isolates. Genes encoding virulence determinants and MRSA were significantly (p < 0.05) higher in strong biofilm-forming S. aureus than in moderate and non-biofilm-forming isolates. To our knowledge, this is the first study in Bangladesh to incorporate preliminary data on the occurrence of virulence determinants and methicillin resistance, including resistance to clinically important antibiotics, in biofilm-forming S. aureus isolates from different foods and food handlers in Bangladesh, emphasizing a potential threat to human health.

First Genome-Based Characterisation and Staphylococcal Enterotoxin Production Ability of Methicillin-Susceptible and Methicillin-Resistant Staphylococcus aureus Strains Isolated from Ready-to-Eat Foods in Algiers (Algeria)

Staphylococcus aureus is a pathogenic microorganism of humans and animals, able to cause foodborne intoxication due to the production of staphylococcal enterotoxins (SEs) and to resist antibiotic treatment as in the case of methicillin-resistant S. aureus (MRSA). In this study, we performed a genomic characterisation of 12 genetically diverse S. aureus strains isolated from ready-to-eat foods in Algiers (Algeria). Moreover, their ability to produce some classical and new staphylococcal enterotoxins (SEs) was investigated. The 12 S. aureus strains resulted to belong to nine known sequence types (STs) and to the novel ST7199 and ST7200. Furthermore, S. aureus SA46 was assigned to the European clone MRSA-ST80-SCCmec-IV. The 12 strains showed a wide endowment of se and sel (staphylococcal enterotoxin-like toxin) genes (sea, seb, sed, seg, seh, sei, selj, sek, sem, sen, seo, seq, ser, selu2, selw, selx, sey, sel30; ψent1-ψent2), including variants and pseudogenes, and harboured the enterotoxin gene cluster (egc) types 1 and 5. Additionally, they produced various amounts of SEA (64.54-345.02 ng/mL), SEB (2871.28-14739.17 ng/mL), SED (322.70-398.94 ng/mL), SEH (not detectable-239.48 ng/mL), and SER (36,720.10-63,176.06 ng/mL) depending on their genotypes. The genetic determinants related to their phenotypic resistance to β-lactams (blaZ, mecA), ofloxacin (gyrA-S84L), erythromycin (ermB), lincomycin (lmrS), kanamycin (aph(3')-III, ant(6)-I), and tetracyclin (tet(L), tet(38)) were also detected. A plethora of virulence-related genes, including major virulence genes such as the tst gene, determinant for the toxic shock syndrome toxin-1, and the lukF-PV and lukS-PV genes, encoding the panton-valentine leukocidin (PVL), were present in the S. aureus strains, highlighting their pathogenic potential. Furthermore, a phylogenomic reconstruction including worldwide foodborne S. aureus showed a clear clustering based on ST and geographical origin rather than the source of isolation.

Antimicrobial Resistance, Multilocus Sequence, and spa Typing of Staphylococcus aureus Isolated from Retail Raw Meat Products

With a high capacity to acquire antimicrobial resistance, Staphylococcus aureus is an important pathogen causing severe infections in animals and humans. A total of 50 Staphylococcus aureus isolates from retail ground beef, chicken meat, and fish were characterized by antimicrobial resistance profiling, staphylococcal protein A gene (spa) typing, and multilocus sequence typing (MLST). The broth microdilution test results showed that all isolates were resistant to penicillin and sulphamethoxazole but had varying resistance rates to tetracycline (24%), erythromycin (4%), gentamicin (2%), ciprofloxacin (2%), trimethoprim (2%), and chloramphenicol (0%). The blaZ and sulI genes were detected in 100% of the isolates followed by grlA (94%), norA (92%), tetK (80%), chlA (60%), tetM (26%), aacA-aphD (2%), ermA (2%), fexA (0%), and dfrA (0%). Moreover, 26% of the isolates were multidrug-resistant, with five or more resistance genes. The spa typing analysis revealed 22 spa types, with t091 (16%), t1677 (8%), and t14538 (8%) being the most common, and one new spa type, t19851, was uncovered. MLST identified seven sequence types (STs), with ST7 (40%), ST15 (20%), and ST199 (13%) being the most common, and two STs (ST7435 and ST7436) were newly identified. In this study, S. aureus isolated from raw meat showed multidrug resistance and different clones associated with human infections. As a result, foods of animal origin may act as potential vehicles for transmission of multidrug-resistant S. aureus isolates, and the dissemination of potentially pathogenic clonal types, posing a health risk to humans.

Staphylococcus schweitzeri—An Emerging One Health Pathogen?

The Staphylococcus aureus-related complex is formed by the Staphylococcus aureus, Staphylococcus schweitzeri, Staphylococcus argenteus, Staphylococcus roterodami and Staphylococcus singaporensis. Within this complex, S. schweitzeri is the only species mainly found in African wildlife, but it is rarely detected as a colonizer in humans or as a contaminant of fomites. The few detections in humans are most likely spillover events after contact with wildlife. However, since S. schweitzeri can be misidentified as S. aureus using culture-based routine techniques, it is likely that S. schweitzeri is under-reported in humans. The low number of isolates in humans, though, is consistent with the fact that the pathogen has typical animal adaptation characteristics (e.g., growth kinetics, lack of immune evasion cluster and antimicrobial resistance); however, evidence from selected in vitro assays (e.g., host cell invasion, cell activation, cytotoxicity) indicate that S. schweitzeri might be as virulent as S. aureus. In this case, contact with animals colonized with S. schweitzeri could constitute a risk for zoonotic infections. With respect to antimicrobial resistance, all described isolates were found to be susceptible to all antibiotics tested, and so far no data on the development of spontaneous resistance or the acquisition of resistance genes such the mecA/mecC cassette are available. In summary, general knowledge about this pathogen, specifically on the potential threat it may incur to human and animal health, is still very poor. In this review article, we compile the present state of scientific research, and identify the knowledge gaps that need to be filled in order to reliably assess S. schweitzeri as an organism with global One Health implications.

Paediatric osteoarticular infections caused by staphylococcus aureus producing panton-valentine leucocidin in morocco: Risk factors and clinical features

OBJECTIVE

We aimed to estimate the prevalence of Staphylococcus aureus producing Panton-Valentine leucocidin (PVL) isolated from children diagnosed with osteoarticular infections (OAIs), and to examine risk factors and clinical features.

METHODS

This prospective study was conducted from January 2017 to December 2018. All hospitalised children diagnosed with S. aureus OAI are included. Blood cultures, articular fluids, synovial tissues and/or bone fragments were collected for bacteriological culture. Antimicrobial susceptibility tests were determined by disk diffusion method. Genes encoding methicillin resistance (mecA) and PVL virulence factors (luk-S-PV and luk-F-PV) were detected by multiplex polymerase chain reaction. The demographic, clinical, laboratory, radiographic and clinical features were reviewed prospectively from medical records.

RESULTS

A total of 37 children with S. aureus OAIs were included, 46% of them have PVL-positive infection and 70.6% were male. The mean age was 8.12 years (±4.57), and almost were from rural settings (76.5%). Children with Staphylococcus aureus producing Panton-Valentine leucocidin (SA-PVL) were significantly associated with type of infection (P = 0.005), location of infection (P = 0.037) and abnormal X-ray (P = 0.029). All strains SA-PVL+ are sensitive to methicillin, but one strain SA-PVL negative was methicillin-resistant S. aureus, confirmed by gene mecA positive.

CONCLUSION

The prevalence of S. aureus infections producing PVL toxin was high in OAIs amongst Moroccan children, mainly due to methicillin-susceptible S. aureus. Type and location of infections and abnormal X-ray were significantly associated with SA-PVL. Routine diagnostic testing of PVL-SA, continuous epidemiological surveillance and multidisciplinary management of OAI is essential to prevent serious complications.

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

Background

Staphylococcus aureus has been associated with the exacerbation and severity of atopic dermatitis (AD). Studies have not investigated the colonisation dynamics of S. aureus lineages in African toddlers with AD. We determined the prevalence and population structure of S. aureus in toddlers with and without AD from rural and urban South African settings.

Methods

We conducted a study of AD-affected and non-atopic AmaXhosa toddlers from rural Umtata and urban Cape Town, South Africa. S. aureus was screened from skin and nasal specimens using established microbiological methods and clonal lineages were determined by spa typing. Logistic regression analyses were employed to assess risk factors associated with S. aureus colonisation.

Results

S. aureus colonisation was higher in cases compared to controls independent of geographic location (54% vs. 13%, p < 0.001 and 70% vs. 35%, p = 0.005 in Umtata [rural] and Cape Town [urban], respectively). Severe AD was associated with higher colonisation compared with moderate AD (86% vs. 52%, p = 0.015) among urban cases. Having AD was associated with colonisation in both rural (odds ratio [OR] 7.54, 95% CI 2.92–19.47) and urban (OR 4.2, 95% CI 1.57–11.2) toddlers. In rural toddlers, living in an electrified house that uses gas (OR 4.08, 95% CI 1.59–10.44) or utilises kerosene and paraffin (OR 2.88, 95% CI 1.22–6.77) for heating and cooking were associated with increased S. aureus colonisation. However, exposure to farm animals (OR 0.3, 95% CI 0.11–0.83) as well as living in a house that uses wood and coal (OR 0.14, 95% CI 0.04–0.49) or outdoor fire (OR 0.31, 95% CI 0.13–0.73) were protective. Spa types t174 and t1476, and t272 and t1476 were dominant among urban and rural cases, respectively, but no main spa type was observed among controls, independent of geographic location. In urban cases, spa type t002 and t442 isolates were only identified in severe AD, t174 was more frequent in moderate AD, and t1476 in severe AD.

Conclusion

The strain genotype of S. aureus differed by AD phenotypes and rural-urban settings. Continued surveillance of colonising S. aureus lineages is key in understanding alterations in skin microbial composition associated with AD pathogenesis and exacerbation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06044-4.

Predominance of PVL-negative community-associated methicillin-resistant Staphylococcus aureus sequence type 8 in newly diagnosed HIV-infected adults, Tanzania

Difficult-to-treat infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are of concern in people living with HIV infection as they are more vulnerable to infection. We aimed to identify molecular characteristics of MRSA colonizing newly diagnosed HIV-infected adults in Tanzania. Individuals newly diagnosed with HIV infection were recruited in Dar es Salaam, Tanzania, from April 2017 to May 2018, as part of the randomized clinical trial CoTrimResist (ClinicalTrials.gov identifier: NCT03087890). Nasal/nasopharyngeal isolates of Staphylococcus aureus were susceptibility tested by disk diffusion method, and cefoxitin-resistant isolates were characterized by short-reads whole genome sequencing. Four percent (22/537) of patients carried MRSA in the nose/nasopharynx. MRSA isolates were frequently resistant towards gentamicin (95%), ciprofloxacin (91%), and erythromycin (82%) but less often towards trimethoprim-sulfamethoxazole (9%). Seventy-three percent had inducible clindamycin resistance. Erythromycin-resistant isolates harbored ermC (15/18) and LmrS (3/18) resistance genes. Ciprofloxacin resistance was mediated by mutations of the quinolone resistance-determining region (QRDR) sequence in the gyrA (S84L) and parC (S80Y) genes. All isolates belonged to the CC8 and ST8-SCCmecIV MRSA clone. Ninety-five percent of the MRSA isolates were spa-type t1476, and one exhibited spa-type t064. All isolates were negative for Panton-Valentine leucocidin (PVL) and arginine catabolic mobile element (ACME) type 1. All ST8-SCCmecIV-spa-t1476 MRSA clones from Tanzania were unrelated to the globally successful USA300 clone. Carriage of ST8 MRSA (non-USA300) was common among newly diagnosed HIV-infected adults in Tanzania. Frequent co-resistance to non-beta lactam antibiotics limits therapeutic options when infection occurs.

Development of sustainable research excellence with a global perspective on infectious diseases: Centre de Recherches Médicales de Lambaréné (CERMEL), Gabon

Medical research in sub-Saharan Africa is of high priority for societies to respond adequately to local health needs. Often enough it remains a challenge to build up capacity in infrastructure and human resources to highest international standards and to sustain this over mid-term to long-term periods due to difficulties in obtaining long-term institutional core funding, attracting highly qualified scientists for medical research and coping with ever changing structural and political environments. The Centre de Recherches Médicales de Lambaréné (CERMEL) serves as model for how to overcome such challenges and to continuously increase its impact on medical care in Central Africa and beyond. Starting off as a research annex to the Albert Schweitzer Hospital in Lambaréné, Gabon, it has since then expanded its activities to academic and regulatory clinical trials for drugs, vaccines and diagnostics in the field of malaria, tuberculosis, and a wide range of poverty related and neglected tropical infectious diseases. Advancing bioethics in medical research in Africa and steadily improving its global networks and infrastructures, CERMEL serves as a reference centre for several international consortia. In close collaboration with national authorities, CERMEL has become one of the main training hubs for medical research in Central Africa. It is hoped that CERMEL and its leitmotiv “to improve medical care for local populations” will serve as an inspiration to other institutions in sub-Saharan Africa to further increase African capacity to advance medicine.

Links between airborne microbiome, meteorology, and chemical composition in northwestern Turkey

The composition of atmospheric aerosols is dynamic and influenced by their emission sources, organic and inorganic composition, transport pathways, chemical and physical processes, microorganisms' content and more. Characterization of such factors can improve the ability to evaluate air quality and health risks under different atmospheric scenarios. Here we investigate the microbial composition of the atmospheric particulate matter (<10 μm; PM₁₀), sampled in Bolu, Turkey, and the linkage to the chemical composition changes, and different environmental factors. We show distinct differences between aerosol composition of different sources and air-mass transport patterns, sampled in July-August 2017 and in February 2018. The summer samples had a typical northern component air mass trajectories and higher local wind speed. They were characterized by high PM₁₀ levels, marine and mineral dust tracers and high relative abundance of Ascomycota, suggesting long-range transport of the particles from remote sources. In contrast, samples collected in February were characterized by a dominant contribution of southern air masses, and low wind speed. They had low PM₁₀ values, higher relative abundance of antibiotic resistance genes and anthropogenic ions related to local industries and farming, suggesting a dominance of local sources. With the microbiome analyses reported here for the first time for this region, we show good agreement between airborne microbial composition, aerosol mass load, chemistry, and meteorology. These results allow better air quality evaluation and prediction capabilities.

Prevalence of Staphylococcus aureus colonization in patients for total joint arthroplasty in South Africa

BACKGROUND

Periprosthetic joint infections (PJIs) are a major source of morbidity and mortality for patients undergoing total joint arthroplasty (TJA). Staphylococcus aureus (S. aureus) colonization is an independent, modifiable risk factor for periprosthetic joint infections. Post-operative infections are reported to be ten times greater in S. aureus carriers than in non-carriers in developed countries though recorded data is lacking for the developing world. This study aims to determine the prevalence of S. aureus colonization in patients awaiting TJA in South Africa.

METHODS

We prospectively assessed 119 patients awaiting total knee arthroplasty and total hip arthroplasty between May and October 2016. We screened three separate anatomical sites on each patient for S. aureus. Patients with positive cultures were treated with intranasal mupirocin ointment and chlorhexidine body wash. Univariate and comparative statistical analyses to determine risk factors for colonization was conducted using t tests, Fisher's exact tests, and chi-square analyses.

RESULTS

The overall prevalence of methicillin-sensitive S. aureus colonization was 31.9% (n = 38). There were no patients colonized with methicillin-resistant S. aureus. Nasal swabs returned a yield of 81.6% (n = 31), with groin swabs and axillary swabs at 39.5% (n = 15) and 28.9% (n = 11), respectively. Eradication was successful in 94.74% (n = 36) after 5 days treatment. All patients (100%) were decolonized after counseling and repeat eradication treatment. The overall complication rate was 7.6% (n = 9). The 30-day readmission rate in the S. aureus-colonized group was 7.9% (n = 3) as opposed to 7.4% (n = 6) in the non-colonized cohort. There were no 60- and 90-day readmissions and no cases were revised at a mean follow-up of 2.26 years.

CONCLUSIONS

The rate of S. aureus colonization in patients undergoing elective TJA in a developing country was 31.9% and is equivalent to reported rates in developed countries. Eradication treatment with combined intranasal mupirocin ointment and chlorhexidine body wash is a successful treatment modality. A larger cohort of patients is recommended to determine risk factors and post-operative septic sequelae in this population group.

Characterization of Antibiotic and Biocide Resistance Genes and Virulence Factors of Staphylococcus Species Associated with Bovine Mastitis in Rwanda

The present study was conducted from July to August 2018 on milk samples taken at dairy farms in the Northern Province and Kigali District of Rwanda in order to identify Staphylococcus spp. associated with bovine intramammary infection. A total of 161 staphylococcal isolates originating from quarter milk samples of 112 crossbred dairy cattle were included in the study. Antimicrobial susceptibility testing was performed and isolates were examined for the presence of various resistance genes. Staphylococcus aureus isolates were also analyzed for the presence of virulence factors, genotyped by spa typing and further phenotypically subtyped for capsule expression using Fourier Transform Infrared (FTIR) spectroscopy. Selected S. aureus were characterized using DNA microarray technology, multi-locus sequence typing (MLST) and whole-genome sequencing. All mecA-positive staphylococci were further genotyped using dru typing. In total, 14 different staphylococcal species were detected, with S. aureus being most prevalent (26.7%), followed by S. xylosus (22.4%) and S. haemolyticus (14.9%). A high number of isolates was resistant to penicillin and tetracycline. Various antimicrobial and biocide resistance genes were detected. Among S. aureus, the Panton-Valentine leukocidin (PVL) genes, as well as bovine leukocidin (LukM/LukF-P83) genes, were detected in two and three isolates, respectively, of which two also carried the toxic shock syndrome toxin gene tsst-1 bovine variant. t1236 was the predominant spa type. FTIR-based capsule serotyping revealed a high prevalence of non-encapsulated S. aureus isolates (89.5%). The majority of the selected S. aureus isolates belonged to clonal complex (CC) 97 which was determined using DNA microarray based assignment. Three new MLST sequence types were detected.

Molecular Characterization of Methicillin- Resistant Staphylococcus aureus in a Tertiary Care hospital in Kuwait

Methicillin-resistant Staphylococcus aureus (MRSA) are a major cause of healthcare and community- associated infections due to their ability to express a variety of virulence factors. We investigated 209 MRSA isolates obtained from 1 January to 31 December 2016 using a combination of phenotypic and genotypic methods to understand the genetic backgrounds of MRSA strains obtained in a General hospital in Kuwait. Antibiotics susceptibility was performed with disk diffusion, and MIC was measured with Etest strips. Molecular typing was performed using SCCmec typing, spa typing, and DNA microarray for antibiotic resistance and virulence genes. The isolates were susceptible to vancomycin, teicoplanin, rifampicin, ceftaroline, and linezolid but were resistant to gentamicin, tetracycline, erythromycin, fusidic acid, chloramphenicol and ciprofloxacin. Molecular typing revealed six SCCmec types, 56 spa types and 16 clonal complexes (CC). The common SCCmec types were type IV (39.5%), type III (34.4%), type V (25.8%) and type VI (3.8%). The dominant spa types were t860 (23.9%), t945 (8.6%), t127 (6.7%), t688 (6.7%), t304 (6.2) and t044 (5.7%). The other spa types occurred sporadically. Genes for PVL was detected in 59 (28.2%) of the isolates. CC8-ST239-MRSA-III + SCCmer (23.3%) was the most prevalent clone, followed by CC6-MRSA-IV (8.3%), CC80-MRSA-IV [PVL+] (5.8%), CC5-MRSA-VI + SCCfus (5.0%), CC30-MRSA-IV[PVL+] (4.1%), CC1-MRSA-V + SCCfus [PVL+] (4.1%), CC5-MRSA-V + SCCfus (4.1%) and CC22-MRSA-IV[PVL+] (4.1%). The study revealed that despite the emergence of MRSA with diverse genetic backgrounds over the years, ST239-MRSA-III remained the dominant clone in the hospital. This warrants reassessment of infection prevention and control procedures at this hospital.

Adhesion and biofilm formation by Staphylococcus aureus clinical isolates under conditions relevant to the host: relationship with macrolide resistance and clonal lineages

PURPOSE

Staphylococcus aureus isolates, collected from various clinical samples, were analysed to evaluate the contribution of the genetic background of both erythromycin-resistant (ERSA) and -susceptible (ESSA) S. aureus strains to biofilm formation.

METHODS

A total of 66 ESSA and 43 ERSA clinical isolates were studied for adhesiveness and biofilm formation under different atmospheres. All isolates were evaluated for phenotypic and genotypic macrolide resistance, and for clonal relatedness by pulsed-field gel electrophoresis (PFGE), and by spa typing on representative isolates.

RESULTS

A high genetic heterogeneity was encountered, although 10 major PFGE types accounted for 86 % with a few small spatially and temporally related clusters. Overall, biofilm formation under anoxia was significantly lower than under oxic and micro-aerophilic atmospheres. Biofilm formation by ESSA was significantly higher compared to ERSA under oxic and micro-aerophilic conditions. Adhesiveness to plastic was significantly higher among respiratory tract infection isolates under micro-aerophilic conditions, while surgical site infection isolates formed significantly higher biomass of biofilm under oxic and micro-aerophilic atmospheres compared to anoxia. Pulsotype 2 and 4 strains formed significantly higher biofilm biomass than pulsotype 1, with strains belonging to CC8 forming significantly more compared to those belonging to CC5, under both oxic and micro-aerophilic atmospheres.

CONCLUSIONS

S. aureus biofilm formation appears to be more efficient in ESSA than ERSA, associated with specific S. aureus lineages, mainly CC8 and CC15, and affected by atmosphere. Further studies investigating the relationship between antibiotic resistance and biofilm formation could prove useful in the development of new strategies for the management of S. aureus infections.

A genomic infection control study for Staphylococcus aureus in two Ghanaian hospitals

Background

Whole genome sequencing analysis (WGSA) provides the best resolution for typing of bacterial isolates and has the potential for identification of transmission pathways. The aim of the study was to apply WGSA to elucidate the possible transmission events involved in two suspected Staphylococcus aureus hospital outbreaks in Ghana and describe genomic features of the S. aureus isolates sampled in the outbreaks.

Methods

The study was carried out at Korle-Bu Teaching Hospital and Lekma Hospital where the suspected outbreaks occurred in 2012 and 2015, respectively. The S. aureus isolates collected from the two hospitals were from three sources including carriage, invasive disease, and the environment. Whole genome sequencing of the S. aureus isolates was performed and the sequence reads were mapped to the S. aureus reference genome of strain USA300_FPR3757. A maximum-likelihood phylogenetic tree was reconstructed. Multilocus sequence typing together with the analysis of antimicrobial resistance and virulence genes were performed by short read mapping using the SRST2.

Results

The S. aureus isolates belonged to diverse sequence types (STs) with ST15 and ST152 most common. All isolates carried the blaZ gene, with low prevalence of tetK and dfrG genes also observed. All isolates were mecA negative. The pvl genes were common and observed in distinct lineages that revealed diverse Sa2int phages. At Korle-Bu Teaching Hospital, the genomics data indicated several transmission events of S. aureus ST15 involving contamination of various surfaces in the pediatric emergency ward where the outbreak occurred.

Conclusion

The pattern of dissemination of the ST15 clone in the emergency ward of Korle-Bu Teaching Hospital highlights a basic problem with disinfection of environmental surfaces at the hospital. Diverse phage population rather than a single highly transmissible phage type likely mediates the high prevalence of pvl genes among the S. aureus isolates.

Methicillin-Resistant Staphylococcus aureus: Molecular Characterization, Evolution, and Epidemiology

Staphylococcus aureus, a major human pathogen, has a collection of virulence factors and the ability to acquire resistance to most antibiotics. This ability is further augmented by constant emergence of new clones, making S. aureus a "superbug." Clinical use of methicillin has led to the appearance of methicillin-resistant S. aureus (MRSA). The past few decades have witnessed the existence of new MRSA clones. Unlike traditional MRSA residing in hospitals, the new clones can invade community settings and infect people without predisposing risk factors. This evolution continues with the buildup of the MRSA reservoir in companion and food animals. This review focuses on imparting a better understanding of MRSA evolution and its molecular characterization and epidemiology. We first describe the origin of MRSA, with emphasis on the diverse nature of staphylococcal cassette chromosome mec (SCCmec). mecA and its new homologues (mecB, mecC, and mecD), SCCmec types (13 SCCmec types have been discovered to date), and their classification criteria are discussed. The review then describes various typing methods applied to study the molecular epidemiology and evolutionary nature of MRSA. Starting with the historical methods and continuing to the advanced whole-genome approaches, typing of collections of MRSA has shed light on the origin, spread, and evolutionary pathways of MRSA clones.

Intra-Hospital, Inter-Hospital and Intercontinental Spread of ST78 MRSA From Two Neonatal Intensive Care Unit Outbreaks Established Using Whole-Genome Sequencing

From 2009 to 2011 [transmission period (TP) 1] and 2014 to 2017 (TP2), two outbreaks involving community-associated clonal complex (CC) 88-MRSA spa types t186 and t786, respectively, occurred in the Neonatal Intensive Care Unit (NICU) of an Irish hospital (H1). This study investigated the relatedness of these isolates, their relationship to other CC88 MRSA from Ireland and their likely geographic origin, using whole-genome sequencing (WGS). All 28 CC88-MRSA isolates identified at the Irish National MRSA Reference Laboratory between 2009 and 2017 were investigated including 20 H1 patient isolates, two H1 isolates recovered from a single healthcare worker (HCW) 2 years apart, three patient isolates from a second hospital (H2) and one patient isolate from each of three different hospitals (H3, H4, and H5). All isolates underwent DNA microarray profiling. Thirteen international isolates with similar microarray profiles to at least one Irish isolate were selected from an extensive global database. All isolates underwent Illumina MiSeq WGS. The majority of Irish isolates (25/28; all H1 isolates, two H2 isolates and the H3 isolate) were identified as ST78-MRSA-IVa and formed a large cluster, exhibiting 1–71 pairwise allelic differences, in a whole-genome MLST-based minimum spanning tree (MST) involving all Irish isolates. A H1/H2, H1/H3, and H1 HCW/patient isolate pair each exhibited one allelic difference. The TP2 isolates were characterised by a different spa type and the loss of hsdS. The three remaining Irish isolates (from H2, H4, and H5) were identified as ST88-MRSA-IVa and dispersed at the opposite end of the MST, exhibiting 81–211 pairwise allelic differences. Core-genome MLST and sequence-based plasmid analysis revealed the recent shared ancestry of Irish and Australian ST78-MRSA-IVa, and of Irish and French/Egyptian ST88-MRSA-IVa. This study revealed the homogeneity of isolates recovered during two NICU outbreaks (despite spa type and hsdS carriage variances), HCW involvement in the outbreak transmission chain and the strain's spread to two other Irish hospitals. The outbreak strain, CC88/ST78-MRSA-IVa, was likely imported from Australia, where it is prevalent. CC88/ST88-MRSA-IVa was also identified in Irish hospitals and was likely imported from Africa, where it is predominant, and/or a country with a large population of African descent.

Identification and characterization of two novel superantigens among Staphylococcus aureus complex

Staphylococcal enterotoxins (SEs), also known as superantigens, play a very important role in infections and food poisoning caused by Staphylococcus aureus. Recently, S. argenteus and S. schweitzeri were recognized as novel species closely related to S. aureus. In this study of these three species, it was found that two putative SE genes were located upstream of some vSaβ pathogenicity islands and the deduced amino acid sequences showed < 65.3% identity with those of known SEs. The related proteins, designated staphylococcal enterotoxin-like toxin 26 (SEl26) and 27 (SEl27), were identified and characterized among the three species. The mRNAs encoding SEl26 and SEl27 were expressed during all the growth phases. Recombinant SEl26 and SEl27 exhibited superantigenic activity in human peripheral blood mononuclear cells and mouse splenocytes by examining cell proliferation and cytokine production. Interestingly, these two genes were present universally in S. argenteus sequence type 2250 with clinical importance. Meanwhile, SEl27 variants from different species showed differential sensitivity to human peripheral blood mononuclear cells, which corresponded to the primary bacterial species hosts. It was demonstrated from these results that SEl26 and SEl27 were characterized to be two novel SE toxins and some SEs evolved along with the bacteria when the organisms adapted the hosts' immune systems.

Staphylococcus aureus in two municipal abattoirs in Nigeria: Risk perception, spread and public health implications

Staphylococcus aureus is a zoonotic pathogen of significant public health concern. Information on the prevalence and risk factors facilitating bacterial colonization and spread under abattoir settings in Nigeria are scarce. This cross-sectional study was designed to determine prevalence of S. aureus as well as risk factors on knowledge and practices facilitating pathogen carriage among workers and slaughter animals in two municipal abattoirs of Ilorin and Ibadan, Nigeria. Swab samples (n = 1671) from nostrils of cattle, goats, pigs and abattoir workers, and from meat tables and abattoir walls were collected for detection of S. aureus. A questionnaire was administered to 275 workers to elucidate risk factors of pathogen carriage applying a logistic regression model. S. aureus prevalence was 6.5%. In total, MSSA and MRSA were detected at a frequency of 5.4% and 1.1%. Molecular analysis of the isolates revealed 19 different spa types, including a novel spa type (t16751). Gender, marital status, occupation and abattoir location were factors influencing worker's practices in relation to pathogen carriage and spread in the abattoir setting. This present study detected not only low MSSA and MRSA prevalence, in both abattoirs but also low risk perception and hygiene practices employed by abattoir workers. Good practices among workers at Nigerian abattoirs are needed to mitigate S. aureus carriage. Further studies expounding the antibiotic resistance and relationships of MSSA and MRSA strains detected in this study are needed to complement understanding of the spread of S. aureus in the abattoir food chain.

Staphylococcus aureus and Methicillin-Resistant Staphylococcus aureus in Workers in the Food Industry

Staphylococcus aureus is part of the common flora on the skin and mucous membranes of mammals and approximately 20–30% of humans are persistently colonized, mainly by mostly susceptible human-adapted isolates. In contrast, colonization with methicillin-resistant S. aureus is rare (approximately 1%), predominantly transient and associated with prior contact to the health care system. Additionally, in recent years livestock-associated S. aureus clones contributed to colonization in humans, especially in those working in close contact to farm animals. A considerable percentage of colonizing S. aureus isolates is equipped with enterotoxin genes. Humans carrying enterotoxigenic isolates represent a contamination source when handling food, thus generating a continuous risk of S. aureus food intoxication. Molecular characterization of isolates colonizing humans and obtained from food, respectively, enables the tracing of food-related outbreaks back to the source of food intoxication. We will summarize current knowledge about the S. aureus population colonizing humans, including those in close contact to animals and food, respectively. Additionally, we will review data on the molecular characterization of S. aureus isolates related to staphylococcal foodborne disease and the elucidation of staphylococcal foodborne outbreaks. Staphylococcal food poisoning is a common foodborne disease, mediated by the ingestion of enterotoxins produced by enterotoxigenic strains of S. aureus. For several outbreaks of foodborne S. aureus disease, colonized personnel could be identified as the source of food contamination. However, because of the widespread occurrence of enterotoxigenic strains as human colonizers and the often transient nature of colonization, the source of contamination cannot always be identified unambiguously. Therefore, compliance with hygiene measures is the most important requirement to prevent food contamination by both human colonization and environmental S. aureus reservoirs.

Genetics of bi-component leukocidin and drug resistance in nasal and clinical Staphylococcus aureus in Lagos, Nigeria

BACKGROUND

Resistant and virulent Staphylococcus aureus is a global public health challenge. Staphylococcal Bi-component leukotoxins are cytolytic to immune cells and evolve to disarm the innate immunity during infections, hence the severity of the disease.

OBJECTIVE

We studied drug resistance profile and the occurrence of bi-component leukocidin in clinical and nasal S. aureus in Lagos, Nigeria.

METHOD

Ninety-two S. aureus (70 clinical and 22 nasal) strains were characterized by conventional and molecular methods.

RESULT

Of the resistance profiles generated, no isolate was resistant to fosfomycin, fusidic acid, teicoplanin, vancomycin, linezolid, mupirocin, nitrofurantoin and tigecycline. Twelve MRSA carrying staphylococcal cassette chromosome mecA gene types I, III, and IV elements were identified only in the clinical samples and type I dominated. High rates of lukE/D (100% among MRSA) and lukPV (dominated MSSA) were recorded among the nasal and clinical isolates. Staphylococcus aureus harboring only lukE/D (from clinical & colonizing MSSA) and combined lukE/D and lukPV (mostly from clinical MSSA, colonizing MSSA and clinical MRSA) toxins were found.

CONCLUSION

Although, mecA resistant genes were found only among clinical MRSA, the occurrence of other bi-component leukocidin genes in a large proportion among the isolates from both community and clinical settings is a major concern. The need for effective resistance and virulence factor surveillance, re-enforcement of antibiotic stewardship and good infection control policy, to prevent dissemination of epidemic strains is highlighted.

Origin, evolution, and global transmission of community-acquired Staphylococcus aureus ST8

USA300 is a hypervirulent, community-acquired, multidrug-resistant Staphylococcus aureus clone that started to spread in the United States around 17 years ago. Many studies detected it also in South America, Europe, and the Asia-Pacific region. In this study, we show that USA300 is also circulating in sub-Saharan Africa. Locating the temporal and spatial origin of clonal lineages is important with respect to epidemiology and molecular evolution of pathogens. We show that USA300 evolved from a less virulent and less resistant ancestor circulating in Central Europe around 160 years ago. Constant surveillance of pathogen transmission routes is vital to prevent and control potential outbreaks. Whole genome sequencing proved to be a useful tool for epidemiological surveillance.

USA300 is a pandemic clonal lineage of hypervirulent, community-acquired, methicillin-resistant Staphylococcus aureus (CA-MRSA) with specific molecular characteristics. Despite its high clinical relevance, the evolutionary origin of USA300 remained unclear. We used comparative genomics of 224 temporal and spatial diverse S. aureus isolates of multilocus sequence type (ST) 8 to reconstruct the molecular evolution and global dissemination of ST8, including USA300. Analyses of core SNP diversity and accessory genome variations showed that the ancestor of all ST8 S. aureus most likely emerged in Central Europe in the mid-19th century. From here, ST8 was exported to North America in the early 20th century and progressively acquired the USA300 characteristics Panton–Valentine leukocidin (PVL), SCCmec IVa, the arginine catabolic mobile element (ACME), and a specific mutation in capsular polysaccharide gene cap5E. Although the PVL-encoding phage ϕSa2USA was introduced into the ST8 background only once, various SCCmec types were introduced to ST8 at different times and places. Starting from North America, USA300 spread globally, including Africa. African USA300 isolates have aberrant spa-types (t112, t121) and form a monophyletic group within the clade of North American USA300. Large parts of ST8 methicillin-susceptible S. aureus (MSSA) isolated in Africa represent a symplesiomorphic group of ST8 (i.e., a group representing the characteristics of the ancestor), which are rarely found in other world regions. Isolates previously discussed as USA300 ancestors, including USA500 and a “historic” CA-MRSA from Western Australia, were shown to be only distantly related to recent USA300 clones.

The Impact of the Staphylococcus aureus Virulome on Infection in a Developing Country: A Cohort Study

We performed a cohort study to analyze the virulome of Staphylococcus aureus from the Democratic Republic of the Congo using whole genome sequencing and to assess its impact on the course of S. aureus infections. Community-associated S. aureus from nasal colonization (n = 100) and infection (n = 86) were prospectively collected. Phenotypic susceptibility testing and WGS was done for each isolate. WGS data were used to screen for 79 different virulence factors and for genotyping purposes (spa typing, multilocus sequence typing). The majority of the 79 virulence factors were equally distributed among isolates from colonization and infection. Panton-Valentine leukocidin (PVL) and the non-truncated hemolysin β were associated with skin and soft tissue infection (SSTI) and recurrence of disease but did not influence the course of infection (i.e., mortality, surgical intervention). For the first time, we show that not only PVL but also hemolysin β could contribute to the development of SSTI in PVL-endemic areas such as Africa.

Prevalence and Genetic Characteristics of Staphylococcus aureus and Staphylococcus argenteus Isolates Harboring Panton-Valentine Leukocidin, Enterotoxins, and TSST-1 Genes from Food Handlers in Myanmar

Asymptomatic carriers of toxigenic Staphylococcus aureus are potential source of diseases, including food poisoning. Toxigenic potential and genetic traits of colonizing S. aureus were investigated for 563 healthy food handlers in Myanmar. Carriage of S. aureus was found in 110 individuals (19.5%), and a total of 144 S. aureus isolates were recovered from nasal cavities (110 isolates) and hands (34 isolates). Panton-Valentine leucocidin genes (pvl) were detected in 18 isolates (12.5%), among which 11 isolates were classified into coa-VIa, agr type III, and ST1930 (CC96) that had been also detected in pvl-positive clinical isolates in Myanmar. A pvl-positive, ST2250 nasal isolate was identified as S. argenteus, a novel coagulase-positive staphylococcus species. Toxic shock syndrome toxin-1 (TSST-1) gene was detected in five pvl-negative isolates. All of the 144 isolates harbored at least one of the 21 enterotoxin(-like) gene(s). The most prevalent enterotoxin(-like) gene was selw (98%), followed by selx (97%), sei (28%), sely (28%), sem (26%), sel (24%), and sea and sec (22% each). Considerable genetic diversity with five groups was detected for selw. The present study revealed the relatively high rate of pvl, as well as the wide distribution of enterotoxin(-like) genes among colonizing S. aureus in Myanmar.

Molecular Characterization of Community Acquired Staphylococcus aureus Bacteremia in Young Children in Southern Mozambique, 2001-2009

Background: The emergence of community-acquired Staphylococcus aureus infections is increasingly recognized as life threating problem worldwide. In Manhiça district, southern Mozambique, S. aureus is the leading cause of community-acquired bacteremia in neonates. Methods: Eighty-four S. aureus isolates from children less than 5 years admitted to Manhiça District Hospital from 2001 to 2009 were randomly selected and genetically characterized by DNA microarray and spa typing. Antimicrobial susceptibility was determined by VITEK 2. Results: Thirty-eight different spa types and 14 clonal complexes (CC) were identified. Spa-type t084 (n = 10; 12%) was the most predominant while CC8 (n = 18; 21%) and CC15 (n = 14; 16%) were the most frequent CCs. Mortality tended to be higher among children infected with CC45 (33.3%, 1/3) and CC8 (27.8%, 5/18). The majority of isolates possessed the accessory gene regulator I (45%) and belonged to either capsule type 8 (52%) or 5 (47%). Panton valentine leukocidin (PVL) encoding genes were detected in 30%. Antibiotic resistance was high for penicillin (89%), tetracycline (59%) and Trimethoprim Sulfamethoxazole (36%) while MRSA was uncommon (8%). Conclusions: Although MRSA were uncommon, we found high genetic diversity of methicillin susceptible S. aureus causing bacteremia in Mozambican children, associated with high resistance to the most available antibiotics in this community. Some CCs are likely to be more lethal indicating the need for prompt recognition and appropriate treatment.

Genomic analysis of ST88 community-acquired methicillin resistant Staphylococcus aureus in Ghana

Background

The emergence and evolution of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains in Africa is poorly understood. However, one particular MRSA lineage called ST88, appears to be rapidly establishing itself as an “African” CA-MRSA clone. In this study, we employed whole genome sequencing to provide more information on the genetic background of ST88 CA-MRSA isolates from Ghana and to describe in detail ST88 CA-MRSA isolates in comparison with other MRSA lineages worldwide.

Methods

We first established a complete ST88 reference genome (AUS0325) using PacBio SMRT sequencing. We then used comparative genomics to assess relatedness among 17 ST88 CA-MRSA isolates recovered from patients attending Buruli ulcer treatment centres in Ghana, three non-African ST88s and 15 other MRSA lineages.

Results

We show that Ghanaian ST88 forms a discrete MRSA lineage (harbouring SCCmec-IV [2B]). Gene content analysis identified five distinct genomic regions enriched among ST88 isolates compared with the other S. aureus lineages. The Ghanaian ST88 isolates had only 658 core genome SNPs and there was no correlation between phylogeny and geography, suggesting the recent spread of this clone. The lineage was also resistant to multiple classes of antibiotics including β-lactams, tetracycline and chloramphenicol.

Discussion

This study reveals that S. aureus ST88-IV is a recently emerging and rapidly spreading CA-MRSA clone in Ghana. The study highlights the capacity of small snapshot genomic studies to provide actionable public health information in resource limited settings. To our knowledge this is the first genomic assessment of the ST88 CA-MRSA clone.

Staphylococcus aureus nasal colonization among HIV-infected adults in Botswana: prevalence and risk factors

We sought to determine the clinical and epidemiologic determinants of Staphylococcus aureus nasal colonization in HIV-infected individuals at two outpatient centers in southern Botswana. Standard microbiologic techniques were used to identify S. aureus and methicillin-resistant S. aureus (MRSA). In a sample of 404 HIV-infected adults, prevalence of S. aureus nasal carriage was 36.9% (n = 152) and was associated with domestic overcrowding and lower CD4 cell count. MRSA prevalence was low (n = 13, 3.2%), but more common among individuals with asthma and eczema. The implications of these findings for HIV management are discussed.

Characterisation of Staphylococcus aureus isolates from bloodstream infections, Democratic Republic of the Congo

Staphylococcus aureus is known worldwide as an invasive pathogen, but information on S. aureus from bloodstream infections in Central Africa remains scarce. A collection of S. aureus blood culture isolates recovered from hospitals in four provinces in the Democratic Republic of the Congo (2009-2013) was assessed. A total of 27/108 isolates were methicillin-resistant S. aureus (MRSA), of which >70% were co-resistant to aminoglycosides, tetracyclines, macrolides and lincosamides. For MRSA and methicillin-susceptible S. aureus (MSSA) isolates, resistance to chloramphenicol and trimethoprim-sulphamethoxazole (TMP-SMX) was <10%. However, 66.7% (72/108) of all isolates harboured the trimethoprim resistance gene dfrG. More than three-quarters (84/108, 77.8%) of isolates belonged to CC5, CC8, CC121 or CC152. Genetic diversity was higher among MSSA (31 spa types) compared to MRSA (four spa types). Most MRSA (23/27, 85.2%) belonged to CC8-spa t1476-SCCmec V and 17/23 (73.9%) MRSA ST8 were oxacillin susceptible but cefoxitin resistant. Among MRSA and MSSA combined, 49.1% (53/108) and 19.4% (21/108) contained the genes encoding for Panton-Valentine leucocidin (lukS-lukF PV, PVL) and toxic shock syndrome toxin-1 (tst, TSST-1), respectively. PVL was mainly detected among MSSA (51/53 isolates harbouring PVL were MSSA, 96.2%) and associated with CC121, CC152, CC1 and CC5. TSST-1 was associated with CC8-spa t1476-SCCmec V. The immune evasion cluster (IEC) genes scn, sak and chp were detected in 81.5% of isolates (88/108, equally represented among MSSA and MRSA). The present study confirms the occurrence of MRSA with high levels of multidrug co-resistance and PVL-positive MSSA among invasive S. aureus isolates in Central Africa.

Molecular epidemiology of Staphylococcus aureus from Lambaréné, Gabon

While there is an abundance of data on the epidemiology and molecular typing of Staphylococcus aureus, especially those carrying Panton-Valentine leucocidin (PVL) genes or mecA from Western Europe, Northern America and Australia, comparably few studies target African strains. In this study, we characterised genes associated with virulence and resistance, as well the phylogenetic background of S. aureus from healthy carriers and outpatients in Gabon. In total, 103 isolates from 96 study participants were characterised. Seventy-nine isolates originated from throat swabs and 24 isolates from skin lesions. Three isolates carried mecA, although only one, belonging to CC8-MRSA-IV [PVL+] 'USA300', was found to be phenotypically oxacillin-resistant; two CC88-MRSA-IV isolates appeared to be oxacillin-susceptible. PVL genes were common, with a total of 44 isolates (43 %) found to be PVL-positive. CC15-MSSA [PVL+] (n = 29) and CC152-MSSA [PVL+] (n = 9) were the predominant clones among the PVL-positive isolates. Among PVL-negative isolates, CC5-MSSA (n = 12), CC101-MSSA (n = 10) and CC15 (n = 9) were the most frequent. A hitherto undescribed multilocus sequence type of S. schweitzeri was detected twice in unrelated patients. The data emphasise a need for further studies on the role of PVL in African populations and the clinical significance of S. schweitzeri.

Prevalence of nasal colonisation by methicillin-sensitive and methicillin-resistant Staphylococcus aureus among healthcare workers and students in Madagascar

BACKGROUND

Methicillin-resistant Staphylococcus aureus (MRSA) clones pose a significant threat to hospitalised patients because the bacteria can be transmitted by asymptomatic carriers within healthcare facilities. To date, nothing is known about the prevalence of S. aureus and MRSA among healthcare workers in Madagascar. The objective of our study was to examine the prevalence and clonal epidemiology of nasal S. aureus and MRSA among healthcare workers and non-medical University students in Antananarivo, Madagascar.

METHODS

This cross sectional study screened nasal swabs taken from students and healthcare workers for S. aureus. Multiplex PCR was performed to identify S. aureus-specific (nuc), MRSA-specific mecA and mecC genes, Panton-Valentine leukocidin (PVL) (lukF-PV), and toxic shock syndrome toxin-1 (TSST-1) specific genes in methicillin-sensitive S. aureus (MSSA) and MRSA isolates. Staphylococcus protein A gene (spa) typing was performed for all confirmed MRSA isolates. The frequency distribution of nasal S. aureus and MRSA of healthcare workers and non-medical students was compared using Pearson's χ(2) test.

RESULTS

Of 1548 nasal swabs tested, 171 (11 %) were positive for S. aureus; 20 (1.3 %) of these isolates were identified as MRSA. S. aureus was detected in 91 of 863 healthcare workers (10.4 %) and in 80 (11.8 %) of 685 students; however, 14 (1.5 %) healthcare workers carried MRSA compared with six (0.9 %) students. Nasal carriage of S. aureus and MRSA was more prevalent in women than in men, and 21 (11.7 %) S. aureus isolates were PVL-positive and 36 (21 %) were TSST-1 positive. The mecC gene was not detected in any isolates. Five different spa types were identified, with spa type t186 being the predominant MRSA clone (16/20).

CONCLUSION

The results of the present study reveal a low frequency of S. aureus and MRSA nasal carriage in both students and healthcare workers from Antananarivo, Madagascar. The predominant MRSA clone (t186) was previously described in hospitalised patients in Madagascar.

Possible healthcare-associated transmission as a cause of secondary infection and population structure of Staphylococcus aureus isolates from two wound treatment centres in Ghana

We have previously shown that secondary infections of Buruli ulcer wounds were frequently caused by Staphylococcus aureus. To gain understanding into possible routes of secondary infection, we characterized S. aureus isolates from patient lesions and surrounding environments across two Ghanaian health centres. One hundred and one S. aureus isolates were isolated from wounds (n = 93, 92.1%) and the hospital environment (n = 8, 7.9%) and characterized by the spa gene, mecA and the Panton–Valentine leucocidin toxin followed by spa sequencing and whole genome sequencing of a subset of 49 isolates. Spa typing and sequencing of the spa gene from 91 isolates identified 29 different spa types with t355 (ST152), t186 (ST88), and t346 dominating. Although many distinct strains were isolated from both health centres, genotype clustering was identified within centres. In addition, we identified a cluster consisting of isolates from a healthcare worker, patients dressed that same day and forceps used for dressing, pointing to possible healthcare-associated transmission. These clusters were confirmed by phylogenomic analysis. Twenty-four (22.8%) isolates were identified as methicillin-resistant S. aureus and lukFS genes encoding Panton–Valentine leucocidin were identified in 67 (63.8%) of the isolates. Phenotype screening showed widespread resistance to tetracycline, erythromycin, rifampicin, amikacin and streptomycin. Genomics confirmed the widespread presence of antibiotic resistance genes to β-lactams, chloramphenicol, trimethoprim, quinolone, streptomycin and tetracycline. Our findings indicate that the healthcare environment probably contributes to the superinfection of Buruli ulcer wounds and calls for improved training in wound management and infection control techniques.

The Recombinant Bacteriophage Endolysin HY-133 Exhibits In Vitro Activity against Different African Clonal Lineages of the Staphylococcus aureus Complex, Including Staphylococcus schweitzeri

HY-133 is a recombinant bacteriophage endolysin with bactericidal activity againstStaphylococcus aureus Here, HY-133 showedin vitroactivity against major African methicillin-susceptible and methicillin-resistantS. aureuslineages and ceftaroline/ceftobiprole- and borderline oxacillin-resistant isolates. HY-133 was also active againstStaphylococcus schweitzeri, a recently described species of theS. aureuscomplex. The activity of HY-133 on the tested isolates (MIC50, 0.25 μg/ml; MIC90, 0.5 μg/ml; range, 0.125 to 0.5 μg/ml) was independent of the species and strain background or antibiotic resistance.

Missense mutations of PBP2a are associated with reduced susceptibility to ceftaroline and ceftobiprole in African MRSA

OBJECTIVES

Ceftaroline and ceftobiprole are new cephalosporins, which are active against MRSA by inhibiting PBP2a. Recently, high rates of resistance to ceftaroline were reported from Ghana. The objective of this study was to assess rates of resistance to ceftaroline and ceftobiprole in MRSA from Africa and to describe potential missense mutations of PBP2a.

METHODS

MRSA isolates derived from Staphylococcus aureus colonization (n = 37) and infection (n = 23) and were collected in Côte d'Ivoire (n = 17), DR Congo (n = 6), Gabon (n = 21) and Nigeria (n = 16). The MICs were determined by the broth microdilution method. The mecA gene was sequenced and missense mutations were associated with the corresponding MLST ST.

RESULTS

In total, 16.7% (n = 10) and 15% (n = 9) of isolates were resistant to ceftaroline and ceftobiprole, respectively. The corresponding MICs of ceftaroline and ceftobiprole correlated significantly (r = 0.92). Isolates belonging to ST241 harboured a triple mutation of PBP2a (N146K-N204K-G246E), which was associated with high rates of resistance to ceftaroline (90.9%) and ceftobiprole (81.8%).

CONCLUSIONS

Resistances to ceftaroline and ceftobiprole were only detected in Nigeria and were associated with ST241 and a triple mutation of PBP2a.

Direct, Specific and Rapid Detection of Staphylococcal Proteins and Exotoxins Using a Multiplex Antibody Microarray

Background

S. aureus is a pathogen in humans and animals that harbors a wide variety of virulence factors and resistance genes. This bacterium can cause a wide range of mild to life-threatening diseases. In the latter case, fast diagnostic procedures are important. In routine diagnostic laboratories, several genotypic and phenotypic methods are available to identify S. aureus strains and determine their resistances. However, there is a demand for multiplex routine diagnostic tests to directly detect staphylococcal toxins and proteins.

Methods

In this study, an antibody microarray based assay was established and validated for the rapid detection of staphylococcal markers and exotoxins. The following targets were included: staphylococcal protein A, penicillin binding protein 2a, alpha- and beta-hemolysins, Panton Valentine leukocidin, toxic shock syndrome toxin, enterotoxins A and B as well as staphylokinase. All were detected simultaneously within a single experiment, starting from a clonal culture on standard media. The detection of bound proteins was performed using a new fluorescence reading device for microarrays.

Results

110 reference strains and clinical isolates were analyzed using this assay, with a DNA microarray for genotypic characterization performed in parallel. The results showed a general high concordance of genotypic and phenotypic data. However, genotypic analysis found the hla gene present in all S. aureus isolates but its expression under given conditions depended on the clonal complex affiliation of the actual isolate.

Conclusions

The multiplex antibody assay described herein allowed a rapid and reliable detection of clinically relevant staphylococcal toxins as well as resistance- and species-specific markers.

An assessment on DNA microarray and sequence-based methods for the characterization of methicillin-susceptible Staphylococcus aureus from Nigeria

Staphylococcus aureus is an important human pathogen causing nosocomial and community-acquired infections worldwide. In the characterization of this opportunistic pathogen, DNA microarray hybridization technique is used as an alternative to sequence based genotyping to obtain a comprehensive assessment on the virulence, resistance determinants, and population structure. The objective of this study was to characterize a defined collection of S. aureus isolates from Nigeria using the microarray technique, and to assess the extent that it correlates with sequence-based genotyping methods. The clonal diversity and genomic content of 52 methicillin-susceptible Staphylococcus aureus (MSSA) were investigated by spa typing, MLST and DNA microarray hybridization. More than half (55.8%) of these isolates were associated with clonal complexes (CCs) typically associated with methicillin-resistant S. aureus (MRSA) clones i.e., CC1, CC5, CC8, CC30, and CC45. Certain genes linked with virulence (hlgA and clfA) and adherence (ebpS, fnbA, sspA, sspB, and sspP) were detected in all isolates. A number of genes or gene clusters were associated with distinct clonal types. The enterotoxin gene cluster (egc) was linked with CC5, CC25, CC30, CC45, and CC121, enterotoxin H gene (seh) with CC1, exfoliative toxin D gene (etd) with CC25 and CC80, and the epidermal cell differentiation inhibitor B gene (edinB) with CC25, CC80, and CC152. The excellent agreement between data from DNA microarray and MLST in the delineation of Nigerian MSSA isolates indicates that the microarray technique is a useful tool to provide information on antibiotic resistance, clonal diversity and virulence factors associated with infection and disease.

Molecular Characterization and Antimicrobial Susceptibility of Staphylococcus aureus Isolates from Clinical Infection and Asymptomatic Carriers in Southwest Nigeria

Few reports from Africa suggest that resistance pattern, virulence factors and genotypes differ between Staphylococcus aureus from nasal carriage and clinical infection. We therefore compared antimicrobial resistance, selected virulence factors and genotypes of S. aureus from nasal carriage and clinical infection in Southwest Nigeria. Non-duplicate S. aureus isolates were obtained from infection (n = 217) and asymptomatic carriers (n = 73) during a cross sectional study in Lagos and Ogun States, Nigeria from 2010–2011. Susceptibility testing was performed using Vitek automated systems. Selected virulence factors were detected by PCR. The population structure was assessed using spa typing. The spa clonal complexes (spa-CC) were deduced using the Based Upon Repeat Pattern algorithm (BURP). Resistance was higher for aminoglycosides in clinical isolates while resistances to quinolones and tetracycline were more prevalent in carrier isolates. The Panton-Valentine leukocidin (PVL) was more frequently detected in isolates from infection compared to carriage (80.2 vs 53.4%; p<0.001, chi²-test). Seven methicillin resistant S. aureus isolates were associated with spa types t002, t008, t064, t194, t8439, t8440 and t8441. The predominant spa types among the methicillin-susceptible S. aureus isolates were t084 (65.5%), t2304 (4.4%) and t8435 (4.1%). spa-CC 084 was predominant among isolates from infection (80.3%, n = 167) and was significantly associated with PVL (OR = 7.1, 95%CI: 3.9–13.2, p<0.001, chi^2- test). In conclusion, PVL positive isolates were more frequently detected among isolates from infection compared to carriage and are associated with spa-CC 084.

Staphylococcus aureus nasal carriage among healthcare workers in Kisangani, the Democratic Republic of the Congo

Methicillin-resistant Staphylococcus aureus (MRSA) is a global health concern, but there are few data from Central Africa. The objective of our study was to characterise S. aureus colonisation isolates from healthcare-exposed professionals in the Democratic Republic of the Congo (DRC). Healthcare workers and medical students (n = 380) in Kisangani, DRC were screened for S. aureus nasal carriage in a single-centre cross-sectional study in the University Hospital of Kisangani. The isolates were identified and characterised using phenotypic and genotypic methods. The nasal carriage rate of S. aureus was 16.6 % and 10 out of 63 isolates (15.9 %) were MRSA. We found 28 different spa types. Most MRSA isolates belonged to ST8-spa t1476-SCCmec V. The majority of MRSA were multidrug-resistant to non-beta-lactam antibiotics. Overall, 28.5 % of S. aureus carried Panton-Valentine leucocidin (PVL)-encoding genes (all methicillin-sensitive) and 17.5 % carried toxic shock syndrome toxin-1 (TSST-1)-encoding genes. The finding of MRSA carriage among healthcare workers in a setting with limited access to diagnostic microbiology and appropriate therapy calls for improved education on infection control practices and supports the introduction of surveillance programmes.

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

Methicillin-resistant Staphylococcus aureus (MRSA) infections are a serious global problem, with considerable impact on patients and substantial health care costs. This systematic review provides an overview on the clonal diversity of MRSA, as well as the prevalence of Panton-Valentine leukocidin (PVL)-positive MRSA in Africa. A search on the molecular characterization of MRSA in Africa was conducted by two authors using predefined terms. We screened for articles published in English and French through to October 2014 from five electronic databases. A total of 57 eligible studies were identified. Thirty-four reports from 15 countries provided adequate genotyping data. CC5 is the predominant clonal complex in the healthcare setting in Africa. The hospital-associated MRSA ST239/ST241-III [3A] was identified in nine African countries. This clone was also described with SCCmec type IV [2B] in Algeria and Nigeria, and type V [5C] in Niger. In Africa, the European ST80-IV [2B] clone was limited to Algeria, Egypt and Tunisia. The clonal types ST22-IV [2B], ST36-II [2A], and ST612-IV [2B] were only reported in South Africa. No clear distinctions were observed between MRSA responsible for hospital and community infections. The community clones ST8-IV [2B] and ST88-IV [2B] were reported both in the hospital and community settings in Angola, Cameroon, Gabon, Ghana, Madagascar, Nigeria, and São Tomé and Príncipe. The proportion of PVL-positive MRSA carriage and/or infections ranged from 0.3 to 100% in humans. A number of pandemic clones were identified in Africa. Moreover, some MRSA clones are limited to specific countries or regions. We strongly advocate for more surveillance studies on MRSA in Africa.

Detection of Methicillin Resistance and Various Virulence Factors in Staphylococcus aureus Strains Isolated from Nasal Carriers

BACKGROUND

Staphylococus aureus can be found as a commensal on skin and nasal flora or it may cause local and invasive infections. S. aureus has a large number of virulence factors.

AIMS

To investigate the methicillin resistance and frequency of various virulence factors in S. aureus nasal isolates.

STUDY DESIGN

Descriptive study.

METHODS

Nasal samples collected from university students were cultured in media. S. aureus was identified by conventional methods and the Staphyloslide latex test (Becton Dickinson, Sparks, USA). Antibiotic susceptibility tests were conducted, and the methicillin resistance was determined. The mecA, nuc, pvl and staphylococcal toxin genes were examined by polymerase chain reaction (PCR).

RESULTS

S. aureus was isolated in 104 of 600 (17.3%) nasal samples. In total, 101 (97.1%) S. aureus isolates were methicillin-sensitive and the remaining 3 (2.9%) were methicillin-resistant. Furthermore, all but five isolates carried at least one staphylococcal enterotoxin gene, with seg being predominant. The tst and eta genes were determined in 29 (27.9%), and 3 (2.9%) isolates, respectively. None of the S. aureus isolates harbored see, etb, and pvl genes.

CONCLUSION

A moderate rate of S. aureus carriage and low frequency of MRSA were detected in healthy students. S. aureus isolates had a high prevalence of staphylococcal enterotoxin genes and the tst gene. In this study, a large number of virulence factors were examined in S. aureus nasal isolates, and the data obtained from this study can be used for monitoring the prevalence of virulence genes in S. aureus strains isolated from nasal carriers.

Persistent Staphylococcus aureus nasal colonization in ambulatory human immunodeficiency virus-infected patients in Nigeria: Risk factors and molecular features

This longitudinal study on Staphylococcus aureus colonization in Nigerian human immunodeficiency virus patients (n = 187) found a trend towards a higher proportion of persistent S. aureus carriage in patients with advanced human immunodeficiency virus infection, low CD4+ cell counts, and a predominance of isolates belonging to ST8/spa-CC064 in persistent carriers.

Prevalence of community-acquired bacteraemia in Guinea-Bissau: an observational study

Background

The burden of bloodstream infections is insufficiently studied in children in Africa and many healthcare facilities lack the capacity to identify invasive disease. Often studies have been limited to febrile patients or patients admitted to hospital.

Methods

Blood cultures and malaria diagnostics was performed on 372 consecutive children presenting with tachycardia and/or fever to a referral paediatric emergency department in Bissau, Guinea-Bissau. Bacterial species detection, antimicrobial susceptibility testing and molecular typing were performed. The capacity of clinical parameters to identify bacteraemia was evaluated.

Results

The prevalence of bloodstream infection was 12% (46/372) and in 46% (21/46) of the infections the child was non-febrile at presentation to the hospital. The predictive value for bacteraemia was poor for all assessed clinical parameters. Staphylococcus aureus accounted for 54% (26/48) of the isolates followed by non-typhoidal Salmonella, 10% (5/48), Streptococcus pneumoniae, 8% (4/48), and Salmonella Typhi, 6% (3/48). Among S. aureus there was a large diversity of spa types and 38% produced Pantone-Valentine leukocidin. Antibiotic resistance was low, however two out of three Klebsiella pneumoniae isolates produced extended-spectrum beta-lactamases. Malaria was laboratory confirmed in only 5% of the children but 64% (237/372) received a clinical malaria diagnosis.

Conclusions

Bacteraemia was common irrespective of the presence of fever among children presenting to the hospital. The high prevalence of Staphylococcus aureus may be due to contamination. There is an imminent need to improve microbiological diagnostic facilities and to identify algorithms that can identify children at risk of bloodstream infections in Africa.

Staphylococcus aureus complex from animals and humans in three remote African regions

Staphylococcus schweitzeri has been recently considered to be a highly divergent Staphylococcus aureus clade and usually colonises nonhuman primates and bats in sub-Saharan Africa. Its transmissibility to humans remains unclear. We therefore investigated the transmission of S. aureus and S. schweitzeri among humans, domestic animals, and wildlife in three remote African regions. A cross-sectional study on nasal and pharyngeal colonisation in humans (n = 1288) and animals (n = 698) was performed in Côte d'Ivoire, Gabon, and Democratic Republic of Congo (DR Congo). Isolates were subjected to spa typing and multilocus sequence typing. Antimicrobial susceptibility and selected virulence factors were tested. S. schweitzeri was found in monkeys from all study sites but no transmission to humans was evident, despite frequent contact of humans with wildlife. In contrast, human-associated S. aureus sequence types (ST1, ST6, ST15) were detected in domestic animals and nonhuman primates, pointing toward a human-to-monkey transmission in the wild. The proportion of methicillin-resistant S. aureus (MRSA) among all S. aureus was 0% (Gabon), 1.7% (DR Congo), and 5.3% (Côte d'Ivoire). The majority of MRSA isolates belonged to the African clone ST88. In conclusion, we did not find any evidence for a transmission of S. schweitzeri from animals to humans. However, such a transmission might remain possible due to the close phylogenetic relation of humans and nonhuman primates. The ST88-MRSA clone was widespread in Côte d'Ivoire but not in Gabon and DR Congo.