Neutralization of the Staphylococcus aureus Panton-Valentine leukocidin by African and Caucasian sera.

BACKGROUND: The prevalence of Staphylococcus aureus isolates carrying the Panton-Valentine leukocidin (PVL) gene is higher in Africa (≈50%) compared to Europe (< 5%). The study aimed to measure anti-PVL-antibodies in Africans and Germans in a multi-center study and to test whether detected antibodies can neutralize the cytotoxic effect of PVL on polymorphonuclear leukocytes (PMNs). METHODS: Sera from asymptomatic Africans (n = 22, Nigeria, Gabon) and Caucasians (n = 22, Germany) were used to quantify antibody titers against PVL and α-hemolysin (in arbitrary units [AU]) by ELISA. PMNs from one African and German donor were exposed to 5 nM recombinant PVL to measure the neutralizing effect of serial dilutions of pooled sera from African and Caucasian participants, or donor sera at 0.625 and 2.5% (v/v). RESULTS: Anti-PVL-antibodies were significantly higher in Africans than in Germans (1.9 vs. 0.7 AU, p < 0.0001). The pooled sera from the study participants neutralized the cytotoxic effect of PVL on African and German PMNs in a dose dependent manner. Also, neutralization of PVL on PMNs from the African and German donors had a stronger effect with African sera (half-maximal inhibitory concentration (IC50) = 0.27 and 0.47%, respectively) compared to Caucasian sera (IC50 = 3.51 and 3.59% respectively). CONCLUSION: Africans have higher levels of neutralizing anti-PVL-antibodies. It remains unclear if or at what level these antibodies protect against PVL-related diseases.

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.

Tropical pyomyositis: an update.

Tropical pyomyositis (TP) is a life-threatening bacterial infection of the skeletal muscle that occurs particularly among children, young adults and those with immunocompromised conditions. The appropriate diagnosis and treatment are often delayed due to its non-specific signs, leading to fatal consequences. Staphylococcus aureus, especially methicillin-susceptible S. aureus, is responsible for most TP cases. However, other bacteria (i.e. streptococci, Pseudomonas aeruginosa, Escherichia coli, Klebsiella spp., Candida spp., Mycobacterium spp.) have been reported. This narrative review provides an update on the epidemiology and clinical course of TP. A special focus is laid on the role of toxins (i.e. Panton-Valentine Leucocidin and α-toxin) in the pathogenesis of TP and their implication for the clinical management of infection.

La pyomyosite tropicale (TP) est une infection bactérienne potentiellement mortelle du muscle squelettique qui survient particulièrement chez les enfants, les jeunes adultes et les personnes immunodéprimées. Le diagnostic et le traitement appropriés sont souvent retardés en raison de ses signes non spécifiques, entraînant des conséquences fatales. Staphylococcus aureus, en particulier S. aureus sensible à la méthicilline, est responsable de la plupart des cas de TP. Cependant, d'autres bactéries (ex: streptocoques, Pseudomonas aeruginosa, Escherichia coli, Klebsiella spp., Candida spp., Mycobacterium spp.) ont été rapportées. Cette revue narrative fournit une mise à jour sur l'épidémiologie et l'évolution clinique du TP. Un accent particulier est mis sur le rôle des toxines (la Leukocidine de Panton-Valentine et l'α-toxine) dans la pathogenèse du TP et leur implication pour la prise en charge clinique de l'infection.

Antibiotic-resistant staphylococci from the wastewater treatment plant and grey-water samples in Obafemi Awolowo University, Ile-Ife, Nigeria.

This study examined the occurrence and molecular basis for antibiotic-resistant staphylococci from the wastewater treatment plant and grey-water samples in Obafemi Awolowo University, Nigeria. Standard microbiological techniques and molecular methods were utilized. The species identified (MALDI score >1.7) comprised S. saprophyticus (19), S. cohnii (8), S. sciuri (7), S. aureus (4), S. epidermidis (3), S. warneri (2), S. equorum (1), S. haemolyticus (1), S. nepalensis (1), S. condimenti (1), and S. pasteuri (1). Resistance to trimethoprim, tetracycline and cefoxitin were observed in 78.3% (47/60), 36.7% (22/60) and 25% (15/60) of the isolates, respectively. The rate of multidrug resistance was 53.3% (32/60) and observed in eight species from different sampling sites. Seven (S. sciuri; n = 5; S. aureus; n = 1; S. warneri; n = 1) of the 20 selected (representing the various staphylococcal species and antibiotypes) isolates were mecA-positive. Furthermore, the tetK gene was detected in nine isolates, six with dfrA, and four were positive for the dfrG gene. One S. aureus was mecA, tetK and dfrG gene positive. The study provides insights on antibiotic-resistant staphylococci from a non-clinical setting and highlights the need for active surveillance to understand the burden of antimicrobial resistance in Nigeria. This is key to improve synergy across the human, animal and environmental health sectors in Nigeria.

Characterization of a novel thermostable nuclease homolog (NucM) in a highly divergent Staphylococcus aureus clade.

A thermostable nuclease homologue (NucM) in an animal-associated divergent clade of Staphylococcus aureus in sub-Saharan Africa has a highly divergent nucleotide sequence compared to those of the classical nuc1 and nuc2 genes of S. aureus. Its deduced amino acid sequences, tertiary structures, and nuclease activities, however, are similar.

Emergence of trimethoprim resistance gene dfrG in Staphylococcus aureus causing human infection and colonization in sub-Saharan Africa and its import to Europe.

OBJECTIVES: Co-trimoxazole (trimethoprim/sulfamethoxazole) is clinically valuable in treating skin and soft tissue infections (SSTIs) caused by community-associated methicillin-resistant Staphylococcus aureus (MRSA). The genetic basis of emerging trimethoprim/sulfamethoxazole resistance in S. aureus from Africa is unknown. Such knowledge is essential to anticipate its further spread. We investigated the molecular epidemiology of trimethoprim resistance in S. aureus collected in and imported from Africa. METHODS: Five hundred and ninety-eight human S. aureus isolates collected at five locations across sub-Saharan Africa [Gabon, Namibia, Nigeria (two) and Tanzania] and 47 isolates from travellers treated at six clinics in Europe because of SSTIs on return from Africa were tested for susceptibility to trimethoprim, sulfamethoxazole and trimethoprim/sulfamethoxazole, screened for genes mediating trimethoprim resistance in staphylococci [dfrA (dfrS1), dfrB, dfrG and dfrK] and assigned to spa genotypes and clonal complexes. RESULTS: In 313 clinical and 285 colonizing S. aureus from Africa, 54% of isolates were resistant to trimethoprim, 21% to sulfamethoxazole and 19% to trimethoprim/sulfamethoxazole. We found that 94% of trimethoprim resistance was mediated by the dfrG gene. Of the 47 S. aureus isolates from travellers with SSTIs, 27 (57%) were trimethoprim resistant and carried dfrG. Markers of trimethoprim resistance other than dfrG were rare. The presence of dfrG genes in S. aureus was neither geographically nor clonally restricted. CONCLUSIONS: dfrG, previously perceived to be an uncommon cause of trimethoprim resistance in human S. aureus, is widespread in Africa and abundant in imported S. aureus from ill returning travellers. These findings may foreshadow the loss of trimethoprim/sulfamethoxazole for the empirical treatment of SSTIs caused by community-associated MRSA.

Molecular characterization of non-aureus staphylococci and Mammaliicoccus from Hipposideros bats in Southwest Nigeria.

Bats are not only ecologically valuable mammals but also reservoirs of zoonotic pathogens. Their vast population, ability to fly, and inhabit diverse ecological niches could play some role in the spread of antibiotic resistance. This study investigated non-aureus staphylococci and Mammaliicoccus colonization in the Hipposideros bats at Obafemi Awolowo University, Ile-Ife, Nigeria. Pharyngeal samples (n = 23) of the insectivorous bats were analyzed, and the presumptive non-aureus staphylococcal and Mammaliicoccus isolates were confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The isolates were characterized based on antibiotic susceptibility testing and whole-genome sequencing (WGS). Six bacterial genomes were assembled, and three species were identified, including Mammaliicoccus sciuri (n = 4), Staphylococcus gallinarum (n = 1), and Staphylococcus nepalensis (n = 1). All the isolates were resistant to clindamycin, while the M. sciuri and S. gallinarum isolates were also resistant to fusidic acid. WGS analysis revealed that the M. sciuri and S. gallinarum isolates were mecA-positive. In addition, the M. sciuri isolates possessed some virulence (icaA, icaB, icaC, and sspA) genes. Multi-locus sequence typing identified two new M. sciuri sequence types (STs) 233 and ST234. The identification of these new STs in a migratory mammal deserves close monitoring because previously known ST57, ST60, and ST65 sharing ack (8), ftsZ (13), glpK (14), gmk (6), and tpiA (10) alleles with ST233 and ST234 have been linked to mastitis in animals. Moreover, the broad host range of M. sciuri could facilitate the dispersal of antibiotic resistance genes. This study provides evidence of the importance of including migratory animals in monitoring the development and spread of antibiotic resistance.

Characterization of Staphylococcus aureus isolates from faecal samples of the Straw-Coloured Fruit Bat (Eidolon helvum) in Obafemi Awolowo University (OAU), Nigeria.

BACKGROUND: Bats (Chiroptera) are one of the most diverse groups of mammals which carry out important ecological and agricultural functions that are beneficial to humans. However, they are increasingly recognized as natural vectors for a number of zoonotic pathogens and favourable hosts for zoonotic infections. Large populations of the Straw-Coloured Fruit Bat (Eidolon helvum) colonize the main campus of the Obafemi Awolowo University (OAU), Ile-Ife, Nigeria, but the public health implications of faecal contamination and pollution by these flying mammals is unknown. This study characterized S. aureus obtained from faecal samples of these migratory mammals with a view to determining the clonal types of the isolates, and to investigate the possibility of these flying animals as potential reservoir for zoonotic S. aureus infections. RESULTS: One hundred and seven (107) S. aureus isolates were recovered from 560 faecal samples in eleven roosting sites from January 2008 to February 2010. A large proportion of the isolates were susceptible to antibiotics, and molecular characterization of 70 isolates showed that 65 (92.9%) were assigned in coagulase type VI, while accessory gene typing classified 69 isolates into the following: type I (12; 17.1%), type II (3; 4.3%), type III (1; 1.4%) and type IV (53; 75.7%). On the whole, the isolates were grouped in five (A-E) main genotypes. Of the ten representative isolates selected for multilocus sequence typing (MLST), nine isolates were assigned with new sequence types: ST1725, ST1726, ST1727, ST2463-ST2467 and ST2470. Phylogenetic analysis provided evidence that S. aureus isolates in group C were closely related with ST1822 and associated clones identified in African monkeys, and group D isolates with ST75, ST883 and ST1223. The two groups exhibited remarkable genetic diversity compared to the major S. aureus clade. CONCLUSIONS: Antibiotic resistance in faecal S. aureus isolates of E. helvum is low and multiple unique S. aureus lineages co-existed with E. helvum. The Straw-Coloured Fruit Bat in Ile-Ife, Nigeria is colonized predominantly by ST1725, ST1726, ST2463 and ST2470 with distinct genotypic characteristics that are rarely found in humans. This study has demonstrated on the possible existence of a reservoir of indigenous and anciently-divergent S. aureus clones among mammals in Africa.

Characterization of methicillin-susceptible and -resistant staphylococci in the clinical setting: a multicentre study in Nigeria.

BACKGROUND: The staphylococci are implicated in a variety of human infections; however, many clinical microbiology laboratories in Nigeria do not identify staphylococci (in particular coagulase negative staphylococci - CNS) to the species level. Moreover, data from multi-centre assessment on antibiotic resistance and epidemiology of the staphylococci are not available in Nigeria. This study investigated 91 non-duplicate staphylococcal isolates obtained from the microbiology laboratories of eight hospitals in Nigeria during the period January to April 2010. METHODS: Identification and antibiotic susceptibility testing was performed using the VITEK 2 system, detection of resistance genes by PCR, and molecular characterization was determined by SCCmec typing, spa and multilocus sequence typing (MLST). RESULTS: All the isolates were susceptible to mupirocin, tigecycline, vancomycin and linezolid, but 72.5% of CNS and 82.3% of Staphylococcus aureus were resistant to cotrimoxazole, while multiresistance was observed in 37 of the 40 CNS isolates. Untypeable SCCmec types (ccrC/Class A mec and ccr-negative/Class C2 mec gene complex) in two methicillin-resistant S. aureus (MRSA) were identified. Additionally, ccr-negative/Class A mec and ccr type 4/Class C2 mec gene complex was detected in one isolate each of S. sciuri and S. haemolyticus, respectively. The S. aureus isolates were classified into 21 spa types including two new types (t8987, t9008) among the methicillin-susceptible S. aureus (MSSA) isolates. Two (CC8-SCCmecnon-typeable and CC88-SCCmec IV) and four (CC8-SCCmec III/IV/V; CC30-SCCmec II/III; CC88-SCCmec IV; and ST152-SCCmecnon-typeable) MRSA clones were identified in Maiduguri (North-East Nigeria) and South-West Nigeria, respectively. The proportion of Panton-Valentine leukocidin (PVL)-positive MSSA was high (44.4%) and 56.3% of these strains were associated with sequence type (ST) 152. CONCLUSIONS: The identification of multiresistant mecA positive S. haemolyticus and S. sciuri from clinical samples indicates that characterization of CNS is important in providing information on their diversity and importance in Nigeria. There is the need to develop new SCCmec classification methods for non-typeable methicillin-resistant staphylococci, and to curtail the spread and establishment of the S. aureus ST152 clone in Nigeria. The study presents the first report of a PVL-positive ST152-SCCmecnontypeable MRSA and SCCmec typing of methicillin-resistant CNS in Nigeria.

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.

First Report of a Methicillin-Resistant, High-Level Mupirocin-Resistant Staphylococcus argenteus.

We describe the identification of a methicillin-resistant, high-level mupirocin-resistant Staphylococcus argenteus. The isolate (1801221) was characterized as t6675-ST2250-SCCmecIVc, and whole-genome sequencing revealed that the isolate possessed two plasmids. One plasmid (34,870 bp), designated p1_1801221 with rep23, harboured the mupirocin resistance (mupA) gene. The second plasmid (20,644 bp), assigned as p2_1801221 with rep5a and rep16, carried the resistance determinants for penicillin (blaZ) and cadmium (cadD). Phylogenetic analysis revealed that the isolate clustered with the European ST2250 lineage. The overall high similarity of both plasmids in S. argenteus with published DNA sequences of Staphylococcus aureus plasmids strongly suggests an interspecies transfer. The pathogenic potential, community and nosocomial spread, and acquisition of antibiotic resistance gene determinants, including the mupA gene by S. argenteus, highlight its clinical significance and the need for its correct identification.

Description of Staphylococcal Strains from Straw-Coloured Fruit Bat (Eidolon helvum) and Diamond Firetail (Stagonopleura guttata) and a Review of their Phylogenetic Relationships to Other Staphylococci.

The phylogenetic tree of the Staphylococcus aureus complex consists of several distinct clades and the majority of human and veterinary S. aureus isolates form one large clade. In addition, two divergent clades have recently been described as separate species. One was named Staphylococcus argenteus, due to the lack of the "golden" pigment staphyloxanthin. The second one is S. schweitzeri, found in humans and animals from Central and West Africa. In late 2021, two additional species, S. roterodami and S. singaporensis, have been described from clinical samples from Southeast Asia. In the present study, isolates and their genome sequences from wild Straw-coloured fruit bats (Eidolon helvum) and a Diamond firetail (Stagonopleura guttata, an estrildid finch) kept in a German aviary are described. The isolates possessed staphyloxanthin genes and were closer related to S. argenteus and S. schweitzeri than to S. aureus. Phylogenetic analysis revealed that they were nearly identical to both, S. roterodami and S. singaporensis. We propose considering the study isolates, the recently described S. roterodami and S. singaporensis as well as some Chinese strains with MLST profiles stored in the PubMLST database as different clonal complexes within one new species. According to the principle of priority we propose it should be named S. roterodami. This species is more widespread than previously believed, being observed in West Africa, Southeast Asia and Southern China. It has a zoonotic connection to bats and has been shown to be capable of causing skin and soft tissue infections in humans. It is positive for staphyloxanthin, and it could be mis-identified as S. aureus (or S. argenteus) using routine procedures. However, it can be identified based on distinct MLST alleles, and "S. aureus" sequence types ST2470, ST3135, ST3952, ST3960, ST3961, ST3963, ST3965, ST3980, ST4014, ST4075, ST4076, ST4185, ST4326, ST4569, ST6105, ST6106, ST6107, ST6108, ST6109, ST6999 and ST7342 belong to this species.

Skin and nasal colonization of coagulase-negative staphylococci are associated with atopic dermatitis among South African toddlers.

BACKGROUND: Skin colonization with coagulase-negative staphylococci (CoNS) is generally beneficial, but recent investigations suggest its association with flares and atopic dermatitis (AD) severity. However, this relationship remains unclear. OBJECTIVE: To assess patterns of staphylococcal colonization and biofilm formation in toddlers with and without AD from rural and urban South African settings. METHODS: We conducted a cross-sectional study of AD-affected and non-atopic AmaXhosa toddlers from rural Umtata and urban Cape Town, South Africa. CoNS isolates were recovered from lesional, nonlesional skin samples and the anterior nares of participants. Identification of the staphylococci was achieved by MALDI-TOF mass spectrometry. The microtiter plate assay assessed in-vitro biofilm formation. RESULTS: CoNS and S. aureus commonly co-colonized nonlesional skin among cases (urban: 24% vs. 3%, p = 0.037 and rural 21% vs. 6%, p<0.001), and anterior nares in urban cases (24% vs. 0%, p = 0.002) than the control group. S. capitis colonization on nonlesional skin and anterior nares was positively associated with more severe disease in rural (48.3±10.8 vs. 39.7±11.5, P = 0.045) and urban cases (74.9±10.3 vs. 38.4±13, P = 0.004), respectively. Biofilm formation was similar between cases and controls, independent of rural-urban living. CONCLUSION: CoNS colonization is associated with AD and disease severity and may be implicated in AD exacerbations. Studies are needed to understand their underlying pathological contribution in AD pathogenesis.

Epidemiology and antimicrobial resistance of staphylococci other than Staphylococcus aureus from domestic animals and livestock in Africa: a systematic review.

Introduction: Staphylococci other than Staphylococcus aureus (SOSA) in animals are becoming more pathogenic and antibiotic resistant and can potentially disseminate to humans. However, there is little synthesized information regarding SOSA from animals in Africa. This systematic review provides a comprehensive overview of the epidemiology and antimicrobial resistance of SOSA in companion animals (pets) and livestock in Africa. Method: This systematic review (PROSPERO-CRD42021252303) was conducted according to the PRISMA guidelines, and 75 eligible studies from 13 countries were identified until August 2022. Three electronic databases (Pubmed, Scopus and Web of Science) were employed. Results: The frequently isolated SOSA were S. epidermidis, S. intermedius, S. pseudintermedius, S. xylosus, S. chromogenes, S. hyicus, M. sciuri, S. hominis, and S. haemolyticus. Thirty (40%) studies performed antibiotic susceptibility testing (AST). Penicillin (58%) and tetracycline (28%) resistance were most common across all SOSA with high rates of resistance to aminoglycosides, fluoroquinolones, and macrolides in some species. Resistance to last-resort antibiotics such as linezolid and fusidic acid were also reported. Limited data on strain typing and molecular resistance mechanisms precluded analysis of the clonal diversity of SOSA on the continent. Conclusion: The findings of this review indicate that research on livestock-associated SOSA in Africa is lacking in some regions such as Central and Western Africa, furthermore, research on companion animals and more advanced methods for identification and strain typing of SOSA need to be encouraged. Systematic review registration: https://www.crd.york.ac.uk/prospero/, identifier: CRD42021252303.

Antibiotic resistance and molecular epidemiology of Staphylococcus aureus in Nigeria.

BACKGROUND: Staphylococcus aureus is an important pathogen causing a wide range of infections in the hospital and community setting. In order to have adequate information for treatment of S. aureus infections, it is crucial to understand the trends in the antibiotic-resistance patterns. In addition, the occurrence and changes in types of S. aureus, clonal identities, and their geographic spread is essential for the establishment of adequate infection control programmes. In this study, 68 S. aureus isolates obtained from clinical and non-clinical sources in Nigeria between January and April 2009 were characterized using phenotypic and molecular methods. RESULTS: All the S. aureus isolates were susceptible to teicoplanin, vancomycin, phosphomycin, fusidic acid, rifampicin, daptomycin, mupirocin, linezolid and tigecycline. Sixteen percent of the isolates were resistant to oxacillin, while 55% and 72% of isolates were resistant to tetracycline and trimethoprim/sulphamethoxazole (cotrimoxazole), respectively (Table 1). There was excellent correlation between the broth microdilution assay and detection of antibiotic resistance genes by the multiplex PCR, in the determination of S. aureus resistance to erythromycin, gentamicin, methicillin and tetracycline. A total of 28 spa types were identified in the study, and the predominant spa type among the methicillin-susceptible S. aureus (MSSA) isolates was t084 (13 isolates). The t037-ST241-SCCmecIII type was the only clone identified in Maiduguri (North-East Nigeria) while in South-West Nigeria, diversity among the MRSA isolates (t451-ST8-SCCmecV; t008-ST94-SCCmecIV; t002-ST5-SCCmecV; t064-ST8-SCCmecV) was observed. The toxin genes seh and etd were detected in isolates affiliated with clonal complexes CC1, CC80 and sequence type ST25, respectively. The proportion of PVL-positive isolates among MSSA was high (40%). Most of the PVL-positive MSSA isolates were obtained from wound infections and associated with clonal complexes CC1, CC30, CC121 and with sequence type ST152. CONCLUSIONS: The use of phenotypic and molecular methods provided useful information on antibiotic resistance and molecular diversity of S. aureus in Nigeria. The high proportion of PVL-positive MSSA isolates affiliated to various clonal complexes and detected in all the health institutions is a major concern, both as a source of severe infections and as a potential reservoir that could lead to the emergence of PVL-positive MRSA. This study presents the first baseline information on the nature of the antibiotic resistance genes from S. aureus isolates in Nigeria. There is the need to curtail the spread and establishment of MRSA and PVL-positive MSSA clones in Nigerian health care institutions.

DNA microarray analysis of Staphylococcus aureus from Nigeria and South Africa.

Staphylococcus aureus is an important human pathogen with an arsenal of virulence factors and a propensity to acquire antibiotic resistance genes. The understanding of the global epidemiology of S. aureus through the use of various typing methods is important in the detection and tracking of novel and epidemic clones in countries and regions. However, detailed information on antibiotic resistance and virulence genes of S. aureus, and its population structure is still limited in Africa. In this study, S. aureus isolates collected in South Africa (n = 38) and Nigeria (n = 2) from 2001-2004 were characterized by spa typing and DNA microarray. The combination of these two methods classified the isolates into seven spa types and three clonal complexes (CCs) i.e. t064-CC8 (n = 17), t037-CC8 (n = 8), t1257-CC8 (n = 6), t045-CC5 (n = 5), t951-CC8 (n = 1), t2723-CC88 (n = 1), t6238-CC8 (n = 1), and untypeable-CC8 (n = 1). A high percentage agreement (>95%) and kappa coefficient (>0.60) was largely observed with antibiotic susceptibility testing and DNA microarray, indicating substantial agreement. Some antibiotic and virulence gene markers were associated with specific clones. The detection of the collagen-binding adhesion (cna) gene was unique for t037-CC8-MRSA while the enterotoxin gene cluster (egc) and staphylococcal complement inhibitor (scn) gene were identified with t045-CC5-MRSA. Moreover, the combination of genes encoding enterotoxins (entA, entB, entK, entQ) was noted with most of the CC8 isolates. The t045-CC5-MRSA clone was positive for the mercury resistance (mer) operon. DNA microarray provides information on antibiotic resistance and virulence gene determinants and can be a useful tool to identify gene markers for specific S. aureus clones in Africa.

Survey data on land tenure and food security among farming households in northern Nigeria.

This dataset presents data collected from the households' survey in Northern Nigeria to examine land tenure and property rights among smallholder rice farmers and the influence it has on household food security. Data collection was by personal interviews of adult members of the farmers' households, focusing on the households' socio-economics, United States Department of Agriculture'- 18 Household Food Security questions for households with children, land titling status and land tenure type on farmland cultivated during the 2016/17 farming season. The data were collected from 475 rice farmers selected by multistage sampling across 84 rice-growing communities, seven States and the three geopolitical zones in northern Nigeria. Household food security was assessed within the framework of the United States Department of Agriculture' HFS Survey Module. Land Tenure and Property Rights (LTPRs) assessment was in terms of the type (source) and registration of titles to farmlands. The hypothesis that guided the cross-sectional survey conducted to generate these data is that insecure land tenure and property rights are important drivers of food insecurity.

Genomic analysis of Staphylococcus aureus from the West African Dwarf (WAD) goat in Nigeria.

BACKGROUND: Staphylococcus aureus can colonize various host species, and human-animal interaction is a significant factor for cross-species transmission. However, data on S. aureus colonization in animals, particularly on ruminants in close contact with humans, is limited. The West African Dwarf (WAD) goat is among the earliest domesticated ruminant associated with rural dwellers and small-holder farmers in sub-Saharan Africa. This study aimed to investigate the population structure, antibiotic resistance, and virulence gene determinants of S. aureus from the WAD goat in Nigeria. METHODS: Nasal samples were obtained from the WAD goat in five markets in Osun State, South-West Nigeria. S. aureus was characterized by antibiotic susceptibility testing, detection of virulence determinants, spa typing, and multilocus sequence typing (MLST). Representative isolates were selected for whole-genome sequencing, biofilm, and cytotoxicity assay. RESULTS: Of the 726 nasal samples obtained from the WAD goat, 90 S. aureus (12.4%) were recovered. Overall, 86 isolates were methicillin-susceptible, and four were mecA-positive (i.e., methicillin-resistant S. aureus [MRSA]). A diverse S. aureus clonal population was observed (20 sequence types [STs] and 37 spa types), while 35% (13/37) and 40% (8/20) were new spa types and STs, respectively. Eleven MLST clonal complexes (CC) were identified (CC1, CC5, CC8, CC15, CC30, CC45, CC97, CC121, CC133, CC152, CC522). The MRSA isolates were designated as t127-ST852-CC1-SCCmec type VII, t4690-ST152-CC152-SCCmec type Vc, and t8821-ST152-CC152-SCCmec type Vc. Phylogenetic analysis revealed that 60% (54/90) of all isolates were associated with ruminant lineages (i.e., CC133, CC522). Panton-Valentine Leukocidin (PVL)-positive S. aureus was identified in CC1, CC30, CC121, and CC152. For the CC522 isolates, we illustrate their pathogenic potential by the detection of the toxic shock syndrome gene and hemolysins, as well as their strong cytotoxicity and ability to form biofilms. CONCLUSIONS: This is the first detailed investigation on the genomic content of S. aureus from the WAD goat in Nigeria. The S. aureus population of the WAD goat consists mainly of ruminant-associated lineages (e.g., CC133, CC522), interspersed with human-associated clones, including PVL-positive MRSA CC1 and CC152.

Molecular characterization of Staphylococcus aureus complex from fomites in Nigeria.

Fomites serve as a potential route for the transmission of pathogens including community-acquired methicillin-resistant Staphylococcus aureus to humans. Phylogenetic and taxonomic analyses have established the Staphylococcus aureus complex (S. aureus, S. argenteus and S. schweitzeri), however, phenotypic characteristics are insufficient in the delineation of these species. In this study, we describe the S. aureus complex from inanimate surfaces in Nigeria. Fomite samples in Obafemi Awolowo University were initially screened for S. aureus and species differentiation was determined by MALDI-TOF, PCR of the S. aureus specific thermonuclease and the nonribosomal peptide synthetase genes. Characterization of the isolates was based on antimicrobial susceptibility, spa typing, multilocus sequence typing and virulence gene detection (lukS/lukF-PV, chp, sak, scn). Whole-genome sequencing was done for selected isolates. Of the 239 fomites samples, 14  S. aureus and two S. schweitzeri isolates were identified including three MRSA. Genotyping classified the S. aureus isolates into ST8/CC8, ST30/CC30, ST15/ST5875/CC15, ST508/ST5876/CC45, ST121/CC121, ST152/CC152 and ST3961. All the isolates in CC30, CC121, and CC152 were lukS/lukF-PV positive. The MRSA (PVL+) were assigned with CC152. Phylogenetic analysis revealed that the S. schweitzeri isolates were closely related with those from fruit bats (Eidolon helvum) in Nigeria. The differentiation of S. aureus from S. schweitzeri was clearly achieved through MALDI-TOF and PCR. Fomites are not only a reservoir for S. aureus but also for S. schweitzeri that was so far recovered primarily in African wildlife.

Cooccurrence of predominant Panton-Valentine leukocidin-positive sequence type (ST) 152 and multidrug-resistant ST 241 Staphylococcus aureus clones in Nigerian hospitals.

Ninety-six clinical isolates of Staphylococcus aureus from Nigeria were characterized phenotypically and genetically. Twelve multidrug-resistant methicillin (meticillin)-resistant S. aureus (MRSA) isolates carrying a new staphylococcal cassette chromosome mec element and a high proportion of Panton-Valentine leukocidin (PVL)-positive methicillin-susceptible S. aureus (MSSA) isolates were observed. The cooccurrence of multidrug-resistant MRSA and PVL-positive MSSA isolates entails the risk of emergence of a multidrug-resistant PVL-positive MRSA clone.