Phenotypic and genotypic characterization of clinical Staphylococcus aureus isolates from Kenya

Staphylococcus aureus associated with surgical site infections in Western Kenya reveals genomic hotspots for pathogen evolution

Objectives. Staphylococcus aureus is one of the most common pathogens attributed to hospital infections. Although S. aureus infections have been well studied in developed countries, far less is known about the biology of the pathogen in sub-Saharan Africa. Methods. Here, we report on the isolation, antibiotic resistance profiling, whole genome sequencing, and genome comparison of six multi-drug resistant isolates of S. aureus obtained from a referral hospital in Kakamega, Western Kenya. Results. Five of the six isolates contained a 20.7 kb circular plasmid carrying blaZ (associated with resistance to β-lactam antibiotics). These five strains all belonged to the same sequence type, ST152. Despite the similarity of the plasmid in these isolates, whole genome sequencing revealed that the strains differed, depending on whether they were associated with hospital-acquired or community-acquired infections. Conclusion. The intriguing finding is that the hospital-acquired and the community-acquired isolates of S. aureus belonging to the same genotype, ST152, formed two separate sub-clusters in the phylogenetic tree and differed by the repertoire of accessory virulence genes. These data suggest ongoing adaptive evolution and significant genomic plasticity.

Displacement of Hospital-Acquired, Methicillin-Resistant Staphylococcus aureus Clones by Heterogeneous Community Strains in Kenya over a 13-Year Period

We determined antibiotic susceptibility and employed Oxford Nanopore whole-genome sequencing to explore strain diversity, resistance, and virulence gene carriage among methicillin-resistant Staphylococcus aureus (MRSA) strains from different infection sites and timepoints in a tertiary Kenyan hospital. Ninety-six nonduplicate clinical isolates recovered between 2010 and 2023, identified and tested for antibiotic susceptibility on the VITEK ID/AST platform, were sequenced. Molecular typing, antibiotic resistance, and virulence determinant screening were performed using the relevant bioinformatics tools. The strains, alongside those from previous studies, were stratified into two periods covering 2010-2017 and 2018-2023 and comparisons were made. Mirroring phenotypic profiles, aac(6')-aph(2″) [aminoglycosides]; gyrA (S84L) and grlA (S80Y) [fluoroquinolones]; dfrG [anti-folates]; and tet(K) [tetracycline] resistance determinants dominated the collection. While the proportion of ST239/241-t037-SCCmec III among MRSA reduced from 37.7% to 0% over the investigated period, ST4803-t1476-SCCmec IV and ST152-t355-SCCmec IV were pre-eminent. The prevalence of Panton-Valentine leucocidin (PVL) and arginine catabolic mobile element (ACME) genes was 38% (33/87) and 6.8% (6/87), respectively. We observed the displacement of HA-MRSA ST239/241-t037-SCCmec III with the emergence of ST152-t355-SCCmec IV and a greater clonal heterogeneity. The occurrence of PVL+/ACME+ CA-MRSA in recent years warrants further investigations into their role in the CA-MRSA virulence landscape, in a setting of high PVL prevalence.

Comparative genomics reveals the correlations of stress response genes and bacteriophages in developing antibiotic resistance of Staphylococcus saprophyticus

IMPORTANCE

Staphylococcus saprophyticus is the second most common bacteria associated with urinary tract infections (UTIs) in women. The antimicrobial treatment regimen for uncomplicated UTI is normally nitrofurantoin, trimethoprim-sulfamethoxazole (TMP-SMX), or a fluoroquinolone without routine susceptibility testing of S. saprophyticus recovered from urine specimens. However, TMP-SMX-resistant S. saprophyticus has been detected recently in UTI patients, as well as in our cohort. Herein, we investigated the understudied resistance patterns of this pathogenic species by linking genomic antibiotic resistance gene (ARG) content to susceptibility phenotypes. We describe ARG associations with known and novel SCCmec configurations as well as phage elements in S. saprophyticus, which may serve as intervention or diagnostic targets to limit resistance transmission. Our analyses yielded a comprehensive database of phenotypic data associated with the ARG sequence in clinical S. saprophyticus isolates, which will be crucial for resistance surveillance and prediction to enable precise diagnosis and effective treatment of S. saprophyticus UTIs.

Prevalence of tigecycline resistance in methicillin-resistant Staphylococcus aureus: a systematic review and meta-analysis

Tigecycline (TG) is one of the newest antimicrobial drugs used in the treatment of methicillin-resistant Staphylococcus aureus (MRSA) infections. The TG Resistance Evaluation and Monitoring Test (T.E.S.T.) is a global surveillance study aimed at monitoring bacterial resistance to TG in MRSA. This study will provide comprehensive data on the activity of TG against MRSA strains across the world by 2022. An electronic search was conducted for articles published during 1997 to 2022 in Pubmed/Medline (n = 361), Scopus (n = 1735) and Web of science (n = 439) for the following keywords: ((Tygacil [Title/Abstract]) OR (Tigecycline [Title/Abstract])) AND (((Staphylococcus aureus [Title/Abstract]) OR (Methicillin resistant Staphylococcus aureus [Title/Abstract])) OR (MRSA [Title/Abstract])). The titles and abstracts of 2535 articles were screened and 48 publications that fulfilled the inclusion criteria were included. From all studies, 35 studies had a cross-sectional design, 11 studies were cohort and 2 studies were case control. Blood and respiratory tract were the main specimen source in MRSA. Meta-analysis showed the proportion of TG resistance is more than 0.004. The region (countries, continent), study type and detection method were examined as the contributing factors of heterogeneity among the studies. Microbial resistance to this antibiotic has been reported to be low, but this does not mean that it can be used widely and without supervision, but the resistance caused by it in MRSA and other pathogens should be carefully and regularly evaluated.

Enhancing capacity for national genomics surveillance of antimicrobial resistance in public health laboratories in Kenya

Genomic surveillance is vital for detecting outbreaks and understanding the epidemiology and transmission of bacterial strains, yet it is not integrated into many national antimicrobial resistance (AMR) surveillance programmes. Key factors are that few scientists in the public health sector are trained in bacterial genomics, and the diverse sequencing platforms and bioinformatic tools make it challenging to generate reproducible outputs. In Kenya, these gaps were addressed by training public health scientists to conduct genomic surveillance on isolates from the national AMR surveillance repository and produce harmonized reports. The 2-week training combined theory and laboratory and bioinformatic experiences with Klebsiella pneumoniae isolates from the surveillance repository. Whole-genome sequences generated on Illumina and Nanopore sequencers were analysed using publicly available bioinformatic tools, and a harmonized report was generated using the HAMRonization tool. Pre- and post-training tests and self-assessments were used to assess the effectiveness of the training. Thirteen scientists were trained and generated data on the K. pneumoniae isolates, summarizing the AMR genes present consistently with the reported phenotypes and identifying the plasmid replicons that could transmit antibiotic resistance. Ninety per cent of the participants demonstrated an overall improvement in their post-training test scores, with an average increase of 14 %. Critical challenges were experienced in delayed delivery of equipment and supplies, power fluctuations and internet connections that were inadequate for bioinformatic analysis. Despite this, the training built the knowledge and skills to implement bacterial genomic surveillance. More advanced and immersive training experiences and building supporting infrastructure would solidify these gains to produce tangible public health outcomes.

Antimicrobial resistance and clonality of Staphylococcus aureus causing bacteraemia in children admitted to the Manhiça District Hospital, Mozambique, over two decades

BACKGROUND

Staphylococcus aureus is one of the main causes of bacteraemia, associated with high mortality, mainly due to the occurrence of multidrug resistant (MDR) strains. Data on antibiotic susceptibility and genetic lineages of bacteraemic S. aureus are still scarce in Mozambique. The study aims to describe the antibiotic susceptibility and clonality of S. aureus isolated from blood cultures of children admitted to the Manhiça District Hospital over two decades (2001-2019).

METHODS

A total of 336 S. aureus isolates detected in blood cultures of children aged <5 years were analyzed for antibiotic susceptibility by disk diffusion or minimal inhibitory concentration, and for the presence of resistance determinants by PCR. The clonality was evaluated by SmaI-PFGE, spa typing, and MLST. The SCCmec element was characterized by SCCmec typing.

RESULTS

Most S. aureus (94%, 317/336) were resistant to at least one class of antibiotics, and one quarter (25%) showed a MDR phenotype. High rates of resistance were detected to penicillin (90%) and tetracycline (48%); followed by erythromycin/clindamycin (25%/23%), and co-trimoxazole (11%), while resistance to methicillin (MRSA strains) or gentamicin was less frequent (≤5%). The phenotypic resistance to distinct antibiotics correlated well with the corresponding resistance determinants (Cohen's κ test: 0.7-1.0). Molecular typing revealed highly diverse clones with predominance of CC5 (17%, 58/336) and CC8 (16%), followed by CC15 (11%) and CC1 (11%). The CC152, initially detected in 2001, re-emerged in 2010 and became predominant throughout the remaining surveillance period, while other CCs (CC1, CC5, CC8, CC15, CC25, CC80, and CC88) decreased over time. The 16 MRSA strains detected belonged to clones t064-ST612/CC8-SCCmecIVd (69%, 11/16), t008-ST8/CC8-SCCmecNT (25%, 4/16) and t5351-ST88/CC88-SCCmecIVa (6%, 1/16). Specific clonal lineages were associated with extended length of stay and high in-hospital mortality.

CONCLUSION

We document the circulation of diverse MDR S. aureus causing paediatric bacteraemia in Manhiça district, Mozambique, requiring a prompt recognition of S. aureus bacteraemia by drug resistant clones to allow more targeted clinical management of patients.

Clonal diversity of Staphylococcus aureus isolates in clinical specimens from selected health facilities in Ethiopia

Staphylococcus aureus is among the top three causative agents of nosocomial infection in Ethiopia. The majority of studies in Ethiopia have focused on the epidemiology of S. aureus in hospital settings, with limited molecular genotyping results. Molecular characterization of S. aureus is essential for identification of strains, and contributes to the control and prevention of S. aureus infection. The aim of the current study was to determine the molecular epidemiology of methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) isolates recovered from clinical specimens in Ethiopia. A total of 161 MSSA and 9 MRSA isolates were characterized using pulsed-field gel electrophoresis (PFGE) and staphylococcal protein A (spa) typing. Based on the PFGE analysis, MSSA isolates were grouped into eight pulso-types groups (from A to I), while MRSA isolates clustered into three (A, B and C) pulso-types with more than 80% similarity. The spa typing analysis showed diversity of S. aureus with 56 distinct spa types. Spa type t355 was most prevalent (56/170, 32.9%), while eleven new spa types were detected including t20038, t20039, and t20042. The identified spa types were clustered into 15 spa-clonal complexes (spa-CCs) using BURP analysis; novel/unknown spa types were further subjected to MLST analysis. The majority of isolates belonged to spa-CC 152 (62/170, 36.4%), followed by spa-CC 121 (19/170, 11.2%), and spa-CC 005 (18 /170, 10.6%). Of the nine MRSA isolates, 2 (22.2%) were spa-CC 239 with staphylococcal cassette chromosome (SCC)mec III. These findings highlight the diversity of S. aureus strains in Ethiopia, as well as the presence of potentially epidemic strains circulating in the country necessitating further characterization of S. aureus for antimicrobial resistance detection and infection prevention purposes.

Prevalence and Potential Risk Factors for the Acquisition of Antibiotic-Resistant Staphylococcus spp. Bacteria Among Pastoralist Farmers in Kajiado Central Subcounty, Kenya

Antimicrobial resistance (AMR) is a growing health problem globally. To address this challenge, there is a need to generate baseline data on the prevalence and AMR profile of the main disease-causing bacteria. Here, we interrogated the prevalence of bacteria in the nasal cavity of healthy pastoralists in Kajiado Central Subcounty, Kenya, and the occurrence of AMR in Staphylococcus isolates among the study subjects. Nasal swabs from 176 pastoralists were cultured, and the bacteria isolates identified using standard phenotypic and biochemical bacteriological methods. Among the obtained 195 isolates, the most prevalent isolates were coagulase-negative Staphylococcus (CoNS) (44.9%), followed by Enterococci spp. (43.2%) while Staphylococcus aureus prevalence was 8%. Antimicrobial sensitivity of the Staphylococcus spp. isolates to 14 antibiotics representing six antibiotic groups was undertaken using the Kirby-Bauer disk diffusion method. Among the CoNS, the highest resistance was reported in amoxicillin (78.7%) and ceftazidime (76%), while the most resistance for S. aureus was reported in ceftazidime (100%), amoxicillin (71.4%), and streptomycin (71.4%). From an administered questionnaire looking at gender, animal contact frequency, history of hospital visitation and antibiotic usage, and habitual intake of raw milk, the study showed that male participants had a higher risk of carrying multiple drug resistant (MDR) bacteria than females (p = 0.02, OR = 1.3). Likewise, habitual intake of raw milk was significantly associated MDR acquisition (p = 0.02, OR = 1.82). This study reveals a high prevalence of AMR Staphylococcus isolates in the study area laying a foundation for further analysis of molecular characterization of the observed resistance as well as the development of interventions that can reduce the occurrence of AMR in the study area.

Characteristics of Staphylococcus aureus Isolated from Patients in Busia County Referral Hospital, Kenya

Staphylococcus aureus is an important pathogen associated with hospital, community, and livestock-acquired infections, with the ability to develop resistance to antibiotics. Nasal carriage by hospital inpatients is a risk for opportunistic infections. Antibiotic susceptibility patterns, virulence genes and genetic population structure of S. aureus nasal isolates, from inpatients at Busia County Referral Hospital (BCRH) were analyzed. A total of 263 inpatients were randomly sampled, from May to July 2015. The majority of inpatients (85.9%) were treated empirically with antimicrobials, including ceftriaxone (65.8%) and metronidazole (49.8%). Thirty S. aureus isolates were cultured from 29 inpatients with a prevalence of 11% (10.3% methicillin-susceptible S. aureus (MSSA), 0.8% methicillin resistant S. aureus (MRSA)). Phenotypic and genotypic resistance was highest to penicillin-G (96.8%), trimethoprim (73.3%), and tetracycline (13.3%) with 20% of isolates classified as multidrug resistant. Virulence genes, Panton-Valentine leukocidin (pvl), toxic shock syndrome toxin-1 (tsst-1), and sasX gene were detected in 16.7%, 23.3% and 3.3% of isolates. Phylogenetic analysis showed 4 predominant clonal complexes CC152, CC8, CC80, and CC508. This study has identified that inpatients of BCRH were carriers of S. aureus harbouring virulence genes and resistance to a range of antibiotics. This may indicate a public health risk to other patients and the community.

Multi-Drug Resistant Staphylococcus aureus Carriage in Abattoir Workers in Busia, Kenya

Abattoir workers have been identified as high-risk for livestock-associated Staphylococcus aureus carriage. This study investigated S. aureus carriage in abattoir workers in Western Kenya. Nasal swabs were collected once from participants between February-November 2012. S. aureus was isolated using bacterial culture and antibiotic susceptibility testing performed using the VITEK 2 instrument and disc diffusion methods. Isolates underwent whole genome sequencing and Multi Locus Sequence Types were derived from these data. S. aureus (n = 126) was isolated from 118/737 (16.0%) participants. Carriage was higher in HIV-positive (24/89, 27.0%) than HIV−negative participants (94/648, 14.5%; p = 0.003). There were 23 sequence types (STs) identified, and half of the isolates were ST152 (34.1%) or ST8 (15.1%). Many isolates carried the Panton-Valentine leucocidin toxin gene (42.9%). Only three isolates were methicillin resistant S. aureus (MRSA) (3/126, 2.4%) and the prevalence of MRSA carriage was 0.4% (3/737). All MRSA were ST88. Isolates from HIV-positive participants (37.0%) were more frequently resistant to sulfamethoxazole/trimethoprim compared to isolates from HIV-negative participants (6.1%; p < 0.001). Similarly, trimethoprim resistance genes were more frequently detected in isolates from HIV-positive (81.5%) compared to HIV-negative participants (60.6%; p = 0.044). S. aureus in abattoir workers were representative of major sequence types in Africa, with a high proportion being toxigenic isolates. HIV-positive individuals were more frequently colonized by antimicrobial resistant S. aureus which may be explained by prophylactic antimicrobial use.

Molecular Characteristics and Antibiotic Resistance of Staphylococcus aureus Isolated from Patient and Food Samples in Shijiazhuang, China

Staphylococcus aureus (S. aureus) is a common opportunistic and zoonotic pathogen in the world and could easily cause human infections and food contaminations. This study investigated the sequence typing and resistance profiles of S. aureus isolates from patient and food samples in Shijiazhuang, China. A total of 101 S. aureus isolates were distributed into six clonal complexes (CCs) and 16 singletons. A total of 86 patient isolates were distributed into six clonal CCs and 12 singletons, including a new ST. CC59, CC5, CC22, and CC398 were the predominant CCs of patient isolates. A total of 15 foodborne S. aureus isolates were distributed into 3 CCs and 4 STs, and CC1 was the most prevalent CC. Moreover, 101 S. aureus isolates had high resistance to penicillin and low resistance to chloramphenicol and rifampicin. A total of 39 strains of methicillin-resistant Staphylococcus aureus (MRSA) were detected in this study, including thirty-eight strains of patient isolates (44.2%, 38/86) and one strain of food isolates (6.7%, 1/15). MRSA-ST5, MRSA-ST59, and MRSA-ST239 were the predominant MRSA isolates in hospitals. The present study explained the relationship between S. aureus isolated from patient and food samples and indicated the risks of S. aureus in infectious diseases.

Phenotypic and genotypic profiling reveals a high prevalence of methicillin-resistant Staphylococcus aureus isolated from hospitals, houseflies and adjacent informal food retailers in Botswana

The increasing occurrence of methicillin-resistant Staphylococcus aureus (MRSA) in the environment, food and healthcare systems is a global public health concern. MRSA is reported to cause food poisoning, osteomyelitis and pyogenic infections of the skin, and consequently has been categorized as a high-priority pathogen by the World Health Organization. Here, we determined the presence of MRSA in clinical (n=56), food (n=150) and housefly samples (n=970) collected from two hospitals in Botswana. Characterization based on phenotypic (antimicrobial resistance, biofilm production) and genotypic (antimicrobial resistance genes and integrons) profiles were performed on all isolates. Of the total samples tested, 64 were positive for MRSA following conventional culture methods and PCR amplification of the mecA and mecC genes for confirmation of presumptive MRSA isolates. The confirmed isolates included 71 % (95 % CI 83.2-59.6) from clinical, 9 % (95 % CI 14--4.8) from food, and 1 % (95 % CI 1.6-0.4) collected from housefly samples. In total 89 % (n=57) isolates in the current study showed a multidrug resistance phenotype, among these, resistance to β-lactams and glycoside antibiotic classes were predominant. Genotypic characterization showed the domination of the blatem gene (95 %) followed by fox (63 %) and tetO (19 %) whilst vanA was only reported in 13 % of the isolates. Integrons were detected in 50 % (32/64) of the total MRSA isolates, and we report a high prevalence of etd gene, detected in 67 % (43/64) of the isolates followed by eta 38 % (24/64) whilst tsst-1 (3%) was the least detected genetic determinant. The genes etb and PVL were not detected in a ll the tested MRSA isolates. We provide the first report on the prevalence of MRSA isolated from the clinical-food-vector nexus harbouring biofilm and blatem genes, and antibiotic resistance profiles in Botswana. These results are significant for risk-assessment analysis and the development of improved MRSA infection prevention and control strategies.

Genomic characterization of two community-acquired methicillin-resistant Staphylococcus aureus with novel sequence types in Kenya

Staphylococcus aureus is a clinically important bacteria with high antimicrobial resistance (AMR) challenge globally. The emergence of methicillin-resistant Staphylococcus aureus (MRSA) clones with unique sequence types have been identified in the community showing evidence that the epidemiology of MRSA globally is changing and requires continual surveillance. We utilized whole genome sequencing to characterize two community acquired-MRSA (CA-MRSA) strains isolated from wound swabs from community-onset infections in two health facilities in Kenya. The two strains belonged to multilocus sequence type (MLST) sequence type (ST) 7460, and ST 7635. The resistance genes detected showed that the novel STs are carriers of clinically relevant resistance genes. Linezolid and mupirocin resistance was observed, yet mupirocin is not commonly used in the country. Mutations within resistance genes were also detected and the pathogenicity toward the human host matched various pathogenic global S. aureus families, e.g., S. aureus subsp. aureus USA300. Multidrug efflux transporters, important in antimicrobial resistance including restriction enzymes type I and type IV were detected. Plasmids identified showed similarities with the plasmids in other clinically significant non-staphylococcal species, such as Pseudomonas aeruginosa, Escherichia coli, Morganella morganii, and Enterococcus faecium. Both STs belong to clonal complex 8 (CC8) which is the most successful MRSA clone in Kenya. Spa type t30 to which ST 7635 belongs has not been reported in the country. The results of this study further highlight the need for epidemiological studies to reveal circulating strains and antimicrobial resistance spread between hospitals and the community. The genomic research highlights resistance to anti-staphylococcal broad-spectrum antimicrobials not used frequently in the country, jeopardizing successful MRSA treatment since most health facilities do not perform genotypic resistance tests for routine patient management. Preliminary insights into unidentified STs of CA-MRSA in Kenya show the need for molecular epidemiological surveillance studies to further understand the diversity of S. aureus in Africa.

Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore

Staphylococcus aureus infection is considered to be a neglected tropical disease with huge impact on human and animal health alike. Dairy production in sub-Saharan Africa (SSA) relies heavily on various animals such as cows, goats, and camels, depending on the region. S. aureus causes mastitis and exhibits high prevalence in raw milk. The population structure including genotypic and phenotypic traits of dairy S. aureus in relation to animal and human isolates is, however, unknown for SSA. In this work, 20 S. aureus dairy isolates from East and West Africa were selected for comparative genomics and phenotypic analysis. Comparing their population structure revealed a large diversity of different origins suggesting milk to be a reservoir for human and animal strains alike. Furthermore, a novel putative siderophore was detected in multiple strains in a distinct animal-clade with strains of global origin. This putative siderophore shares a high genetic identity with that from Streptococcus equi suggesting possible horizontal gene transfer. These findings combined with the virulence genes harbored by these dairy-derived strains such as pvl, human evasion factor scn, various enterotoxin, leucocidin and antibiotic resistance genes, stresses the need for an integrative One Health approach to tackle the problem of S. aureus infections in animals and humans in sub-Saharan Africa.

A 6-Year Update on the Diversity of Methicillin-Resistant Staphylococcus aureus Clones in Africa: A Systematic Review

Background

Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of hospital-associated (HA) and community-associated (CA) infections globally. The multi-drug resistant nature of this pathogen and its capacity to cause outbreaks in hospital and community settings highlight the need for effective interventions, including its surveillance for prevention and control. This study provides an update on the clonal distribution of MRSA in Africa.

Methods

A systematic review was conducted by screening for eligible English, French, and Arabic articles from November 2014 to December 2020, using six electronic databases (PubMed, EBSCOhost, Web of Science, Scopus, African Journals Online, and Google Scholar). Data were retrieved and analyzed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis guidelines (registered at PROSPERO: CRD42021277238). Genotyping data was based primarily on multilocus sequence types (STs) and Staphylococcal Cassette Chromosome mec (SCCmec) types. We utilized the Phyloviz algorithm in the cluster analysis and categorization of the MRSA STs into various clonal complexes (CCs).

Results

We identified 65 studies and 26 publications from 16 of 54 (30%) African countries that provided sufficient genotyping data. MRSA with diverse staphylococcal protein A (spa) and SCCmec types in CC5 and CC8 were reported across the continent. The ST5-IV [2B] and ST8-IV [2B] were dominant clones in Angola and the Democratic Republic of Congo (DRC), respectively. Also, ST88-IV [2B] was widely distributed across the continent, particularly in three Portuguese-speaking countries (Angola, Cape Verde, and São Tomé and Príncipe). The ST80-IV [2B] was described in Algeria and Egypt, while the HA-ST239/ST241-III [3A] was only identified in Egypt, Ghana, Kenya, and South Africa. ST152-MRSA was documented in the DRC, Kenya, Nigeria, and South Africa. Panton-Valentine leukocidin (PVL)-positive MRSA was observed in several CCs across the continent. The median prevalence of PVL-positive MRSA was 33% (ranged from 0 to 77%; n = 15).

Conclusion

We observed an increase in the distribution of ST1, ST22, and ST152, but a decline of ST239/241 in Africa. Data on MRSA clones in Africa is still limited. There is a need to strengthen genomic surveillance capacity based on a "One-Health" strategy to prevent and control MRSA in Africa.

Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda

Tackling antimicrobial resistance (AMR) is particularly challenging in low-resource settings such as Fort Portal Regional Referral Hospital (FPRRH) in Western Uganda. Specific knowledge of local AMR epidemiology is required to inform evidence-based improvement of antibiotic stewardship measures in the hospital. To address this, we combined existing antimicrobial susceptibility testing (AST) from FPRRH, with whole genome sequencing (WGS) of 41 Staphylococcus aureus isolates (2017-2019). AST revealed 73 % (30 of 41) of isolates were resistant to one or more antibiotics and 29 % (12 of 41) were multi-drug resistant (MDR). Resistance phenotypes were largely explained by the presence of antibiotic resistance genes in WGS data. Five isolates were methicillin-resistant S. aureus (MRSA) and MDR. Although all isolates were susceptible to clindamycin, a 24 % carriage of erm genes suggests potential for rapid development of resistance. We inferred a population structure for the S. aureus isolates by comparing their core genomes. Twenty isolates formed a tight cluster corresponding to multilocus sequence typing clonal complex (CC) 152, a CC found to be particularly prevalent in northern Africa. The frequency of genes associated with methicillin, chloramphenicol and ciprofloxacin resistance were significantly lower among CC152 strains than non-CC152 strains; thus, in keeping with previous work, we find that CC152 is almost exclusively methicillin-sensitive S. aureus (MSSA). Also, in agreement with other studies, we observed that the occurrence of Panton-Valentine leukocidin toxin-encoding genes was significantly higher among CC152 strains than non-CC152 strains. However, we also observed that the coagulase gene was over-represented in this CC, further defining the virulence strategy of this important pathogen. By generating detailed information about the epidemiology of circulating S. aureus and their antibiotic susceptibility, our study has provided, for the first time, data on which evidence-based infection and AMR interventions at FPRRH can be based.

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.