The role of vaccine status homophily in the COVID-19 pandemic: a cross-sectional survey with modelling.

BACKGROUND: Vaccine homophily describes non-heterogeneous vaccine uptake within contact networks. This study was performed to determine observable patterns of vaccine homophily, as well as the impact of vaccine homophily on disease transmission within and between vaccination groups under conditions of high and low vaccine efficacy. METHODS: Residents of British Columbia, Canada, aged ≥ 16 years, were recruited via online advertisements between February and March 2022, and provided information about vaccination status, perceived vaccination status of household and non-household contacts, compliance with COVID-19 prevention guidelines, and history of COVID-19. A deterministic mathematical model was used to assess transmission dynamics between vaccine status groups under conditions of high and low vaccine efficacy. RESULTS: Vaccine homophily was observed among those with 0, 2, or 3 doses of the vaccine. Greater homophily was observed among those who had more doses of the vaccine (p < 0.0001). Those with fewer vaccine doses had larger contact networks (p < 0.0001), were more likely to report prior COVID-19 (p < 0.0001), and reported lower compliance with COVID-19 prevention guidelines (p < 0.0001). Mathematical modelling showed that vaccine homophily plays a considerable role in epidemic growth under conditions of high and low vaccine efficacy. Furthermore, vaccine homophily contributes to a high force of infection among unvaccinated individuals under conditions of high vaccine efficacy, as well as to an elevated force of infection from unvaccinated to suboptimally vaccinated individuals under conditions of low vaccine efficacy. INTERPRETATION: The uneven uptake of COVID-19 vaccines and the nature of the contact network in the population play important roles in shaping COVID-19 transmission dynamics.

COVID-19 endgame: From pandemic to endemic? Vaccination, reopening and evolution in low- and high-vaccinated populations.

COVID-19 remains a major public health concern, with large resurgences even where there has been widespread uptake of vaccines. Waning immunity and the emergence of new variants will shape the long-term burden and dynamics of COVID-19. We explore the transition to the endemic state, and the endemic incidence in British Columbia (BC), Canada and South Africa (SA), to compare low and high vaccination coverage settings with differing public health policies, using a combination of modelling approaches. We compare reopening (relaxation of public health measures) gradually and rapidly as well as at different vaccination levels. We examine how the eventual endemic state depends on the duration of immunity, the rate of importations, the efficacy of vaccines and the transmissibility. These depend on the evolution of the virus, which continues to undergo selection. Slower reopening leads to a lower peak level of incidence and fewer overall infections in the wave following reopening: as much as a 60% lower peak and a 10% lower total in some illustrative simulations; under realistic parameters, reopening when 70% of the population is vaccinated leads to a large resurgence in cases. The long-term endemic behaviour may stabilize as late as January 2023, with further waves of high incidence occurring depending on the transmissibility of the prevalent variant, duration of immunity, and antigenic drift. We find that long term endemic levels are not necessarily lower than current pandemic levels: in a population of 100,000 with representative parameter settings (Reproduction number 5, 1-year duration of immunity, vaccine efficacy at 80% and importations at 3 cases per 100K per day) there are over 100 daily incident cases in the model. Predicted prevalence at endemicity has increased more than twofold after the emergence and spread of Omicron. The consequent burden on health care systems depends on the severity of infection in immunized or previously infected individuals.

Does Counting Different Life Stages Impact Estimates for Extinction Probabilities for Tsetse (Glossina spp)?

As insect populations decline, due to climate change and other environmental disruptions, there has been an increased interest in understanding extinction probabilities. Generally, the life cycle of insects occurs in well-defined stages: when counting insects, questions naturally arise about which life stage to count. Using tsetse flies (vectors of trypanosomiasis) as a case study, we develop a model that works when different life stages are counted. Previous branching process models for tsetse populations only explicitly represent newly emerged adult female tsetse and use that subpopulation to keep track of population growth/decline. Here, we directly model other life stages. We analyse reproduction numbers and extinction probabilities and show that several previous models used for estimating extinction probabilities for tsetse populations are special cases of the current model. We confirm that the reproduction number is the same regardless of which life stage is counted, and show how the extinction probability depends on which life stage we start from. We demonstrate, and provide a biological explanation for, a simple relationship between extinction probabilities for the different life stages, based on the probability of recruitment between stages. These results offer insights into insect population dynamics and provide tools that will help with more detailed models of tsetse populations. Population dynamics studies of insects should be clear about life stages and counting points.

Trends in Number and Distribution of COVID-19 Hotspot Counties - United States, March 8-July 15, 2020.

The geographic areas in the United States most affected by the coronavirus disease 2019 (COVID-19) pandemic have changed over time. On May 7, 2020, CDC, with other federal agencies, began identifying counties with increasing COVID-19 incidence (hotspots) to better understand transmission dynamics and offer targeted support to health departments in affected communities. Data for January 22-July 15, 2020, were analyzed retrospectively (January 22-May 6) and prospectively (May 7-July 15) to detect hotspot counties. No counties met hotspot criteria during January 22-March 7, 2020. During March 8-July 15, 2020, 818 counties met hotspot criteria for ≥1 day; these counties included 80% of the U.S. population. The daily number of counties meeting hotspot criteria peaked in early April, decreased and stabilized during mid-April-early June, then increased again during late June-early July. The percentage of counties in the South and West Census regions* meeting hotspot criteria increased from 10% and 13%, respectively, during March-April to 28% and 22%, respectively, during June-July. Identification of community transmission as a contributing factor increased over time, whereas identification of outbreaks in long-term care facilities, food processing facilities, correctional facilities, or other workplaces as contributing factors decreased. Identification of hotspot counties and understanding how they change over time can help prioritize and target implementation of U.S. public health response activities.

Body Composition and Epicardial Fat in Type 2 Diabetes Patients Following Insulin Detemir Versus Insulin Glargine Initiation.

The aim of the study was to compare body composition and epicardial fat thickness changes in insulin-naïve inadequately controlled patients with type 2 diabetes following basal insulin initiation with detemir vs. glargine. Six-month, open-label, interventional randomized pilot study was conducted. Dual-energy X-ray absorptiometry and echocardiography were used to estimate the body composition and epicardial fat thickness respectively. Thirty-six patients in the detemir group and 20 in the glargine group completed the study. Study groups baseline characteristics were comparable. At 6 months, for similar glycemic control, those on detemir significantly gained less total weight (0.6±2.5 vs. 4.2±4.1 kg, p=0.004), total fat mass (0.9±2.2 vs. 2.9±2.4 kg, p=0.02), and truncal fat mass (0.8±1.5 vs. 2.1±1.7 kg, p=0.02), with a loss in truncal lean mass (- 0.8±1.9 kg vs. 0.3±1.7 kg; p=0.02). EFT significantly decreased from baseline in both group (detemir - 1.7±0.52-mm, glargine - 1.1±1.6-mm; p<0.05, without significant difference inter-groups). Within the detemir group, epicardial fat thickness change correlated with truncal fat and total fat mass changes (r=0.65, p=0.06 and r=0.60, p=0.07). In conclusion, detemir resulted in less fat mass gain, a trend for a more pronounced epicardial fat thickness reduction when compared with glargine.

Spatial distribution and determinants of HIV high burden in the Southern African sub-region.

BACKGROUND: Spatial analysis at different levels can help understand spatial variation of human immunodeficiency virus (HIV) infection, disease drivers, and targeted interventions. Combining spatial analysis and the evaluation of the determinants of the HIV burden in Southern African countries is essential for a better understanding of the disease dynamics in high-burden settings. METHODS: The study countries were selected based on the availability of demographic and health surveys (DHS) and corresponding geographic coordinates. We used multivariable regression to evaluate the determinants of HIV burden and assessed the presence and nature of HIV spatial autocorrelation in six Southern African countries. RESULTS: The overall prevalence of HIV for each country varied between 11.3% in Zambia and 22.4% in South Africa. The HIV prevalence rate was higher among female respondents in all six countries. There were reductions in prevalence estimates in most countries yearly from 2011 to 2020. The hotspot cluster findings show that the major cities in each country are the key sites of high HIV burden. Compared with female respondents, the odds of being HIV positive were lesser among the male respondents. The probability of HIV infection was higher among those who had sexually transmitted infections (STI) in the last 12 months, divorced and widowed individuals, and women aged 25 years and older. CONCLUSIONS: Our research findings show that analysis of survey data could provide reasonable estimates of the wide-ranging spatial structure of the HIV epidemic in Southern African countries. Key determinants such as individuals who are divorced, middle-aged women, and people who recently treated STIs, should be the focus of HIV prevention and control interventions. The spatial distribution of high-burden areas for HIV in the selected countries was more pronounced in the major cities. Interventions should also be focused on locations identified as hotspot clusters.

Evaluation of five susceptibility test methods for detection of tobramycin resistance in a cluster of epidemiologically related Acinetobacter baumannii isolates.

Acinetobacter baumannii is a major nosocomial pathogen causing infections in critically ill patients. This organism has acquired the propensity to rapidly develop resistance to most antibiotics. At several hospitals within Cape Town, South Africa, tobramycin and colistin are frequently the only therapeutic options. Vitek2 automated susceptibility testing (AST) is used in the clinical laboratory to determine selected susceptibility profiles. The suspicion of a possible AST-related technical error when testing for susceptibility to tobramycin in A. baumannii precipitated this study. Thirty-nine A. baumannii strains isolated from clinical specimens (June to December 2006) were included in this prospective study. Tobramycin susceptibility testing results obtained by AST, disc diffusion, the epsilometer test (Etest), and agar dilution were compared to those for broth microdilution (BMD), the reference method. The tobramycin susceptibility results revealed errors in 25/39 (64%) isolates (10 very major and 15 minor errors) when AST was compared to BMD, 12/39 (31%) (2 very major and 10 minor errors) when Etest was compared to BMD, 16/39 (41%) (3 very major and 13 minor errors) when disc diffusion was compared to BMD, and 21/39 (54%) (10 very major and 11 minor errors) when agar dilution was compared to BMD. Using PCR, we detected aac(3)-IIa, which is associated with tobramycin resistance, in 21/25 of the discrepant isolates. Molecular typing (using pulsed-field gel electrophoresis and repetitive sequence-based PCR [rep-PCR]) showed that these isolates were genetically related. Clinical laboratories that routinely use the Vitek2 system should consider an alternative testing method for determining susceptibility to tobramycin.

Modelling outbreak response impact in human vaccine-preventable diseases: A systematic review of differences in practices between collaboration types before COVID-19.

BACKGROUND: Outbreak response modelling often involves collaboration among academics, and experts from governmental and non-governmental organizations. We conducted a systematic review of modelling studies on human vaccine-preventable disease (VPD) outbreaks to identify patterns in modelling practices between two collaboration types. We complemented this with a mini comparison of foot-and-mouth disease (FMD), a veterinary disease that is controllable by vaccination. METHODS: We searched three databases for modelling studies that assessed the impact of an outbreak response. We extracted data on author affiliation type (academic institution, governmental, and non-governmental organizations), location studied, and whether at least one author was affiliated to the studied location. We also extracted the outcomes and interventions studied, and model characteristics. Included studies were grouped into two collaboration types: purely academic (papers with only academic affiliations), and mixed (all other combinations) to help investigate differences in modelling patterns between collaboration types in the human disease literature and overall differences with FMD collaboration practices. RESULTS: Human VPDs formed 227 of 252 included studies. Purely academic collaborations dominated the human disease studies (56%). Notably, mixed collaborations increased in the last seven years (2013-2019). Most studies had an author affiliated to an institution in the country studied (75.2%) but this was more likely among the mixed collaborations. Contrasted to the human VPDs, mixed collaborations dominated the FMD literature (56%). Furthermore, FMD studies more often had an author with an affiliation to the country studied (92%) and used complex model design, including stochasticity, and model parametrization and validation. CONCLUSION: The increase in mixed collaboration studies over the past seven years could suggest an increase in the uptake of modelling for outbreak response decision-making. We encourage more mixed collaborations between academic and non-academic institutions and the involvement of locally affiliated authors to help ensure that the studies suit local contexts.

Similar associations of total adiponectin and high molecular weight adiponectin with cardio-metabolic risk factors in a population of overweight and obese postmenopausal women: a MONET study.

The aim of the study was to examine the association between total adiponectin and high molecular weight (HMW) adiponectin levels with cardio-metabolic risk factors in a population of sedentary, overweight, and obese postmenopausal women. Cross-sectional study was carried out on 55 nondiabetic sedentary overweight and obese postmenopausal women aged between 50 and 70 years. Insulin sensitivity was assessed by euglycemic-hyperinsulinemic clamp technique. Body composition and visceral fat were measured using dual X-ray absorptiometry and computed tomography, respectively. Other cardio-metabolic risk factors included: plasma lipids, hsC-reactive protein, energy expenditure (doubly labeled water), peak oxygen consumption, muscle strength (using weight training equipment) as well as total and HMW adiponectin. Correlations of total and HMW adiponectin with various cardio-metabolic risk factors were comparable. In addition, regression analysis results showed similar independent predictors of total and HMW adiponectin. Finally, the receiver operator characteristic (ROC) curves for total and HMW adiponectin to predict insulin sensitivity showed no difference between the areas under curve (AUC) (AUC total adiponectin=0.80 [95% CI: 0.66-0.95] versus AUC HMW adiponectin=0.76 [95% CI: 0.60-0.91], p=0.36). The present study indicates that HMW adiponectin does not seem to provide additional information than total adiponectin in relation to cardio-metabolic risk factors in overweight/obese postmenopausal women.

Extinction probabilities as a function of temperature for populations of tsetse (Glossina spp.).

Significant reductions in populations of tsetse (Glossina spp) in parts of Zimbabwe have been attributed to increases in temperature over recent decades. Sustained increases in temperature might lead to local extinctions of tsetse populations. Extinction probabilities for tsetse populations have not so far been estimated as a function of temperature. We develop a time-homogeneous branching process model for situations where tsetse live at different levels of fixed temperature. We derive a probability distribution pk(T) for the number of female offspring an adult female tsetse is expected to produce in her lifetime, as a function of the fixed temperature at which she is living. We show that pk(T) can be expressed as a geometric series: its generating function is therefore a fractional linear type. We obtain expressions for the extinction probability, reproduction number, time to extinction and growth rates. The results are valid for all tsetse, but detailed effects of temperature will vary between species. No G. m. morsitans population can escape extinction if subjected, for extended periods, to temperatures outside the range 16°C-32°C. Extinction probability increases more rapidly as temperatures approach and exceed the upper and lower limits. If the number of females is large enough, the population can still survive even at high temperatures (28°C-31°C). Small decreases or increases in constant temperature in the neighbourhoods of 16°C and 31°C, respectively, can drive tsetse populations to extinction. Further study is needed to estimate extinction probabilities for tsetse populations in field situations where temperatures vary continuously.

Uncertainty and sensitivity analyses of extinction probabilities suggest that adult female mortality is the weakest link for populations of tsetse (Glossina spp).

BACKGROUND: A relatively simple life history allows us to derive an expression for the extinction probability of populations of tsetse, vectors of African sleeping sickness. We present the uncertainty and sensitivity analysis of the extinction probability, to offer key insights into factors affecting the control or eradication of tsetse populations. METHODS: We represent tsetse population growth as a branching process, and derive closed form estimates of population extinction from that model. Statistical and mathematical techniques are used to analyse the uncertainties in estimating extinction probability, and the sensitivity of the extinction probability to changes in input parameters representing the natural life history and vital dynamics of tsetse populations. RESULTS: For fixed values of input parameters, the sensitivity of extinction probability depends on the baseline parameter values. Extinction probability is most sensitive to the probability that a female is inseminated by a fertile male when daily pupal mortality is low, whereas the extinction probability is most sensitive to daily mortality rate for adult females when daily pupal mortality, and extinction probabilities, are high. Global uncertainty and sensitivity analysis show that daily mortality rate for adult females has the highest impact on the extinction probability. CONCLUSIONS: The high correlation between extinction probability and daily female adult mortality gives a strong argument that control techniques which increase daily female adult mortality may be the single most effective means of ensuring eradication of tsetse population.

Outbreak response intervention models of vaccine-preventable diseases in humans and foot-and-mouth disease in livestock: a protocol for a systematic review.

INTRODUCTION: Outbreaks of vaccine-preventable diseases continue to threaten public health, despite the proven effectiveness of vaccines. Interventions such as vaccination, social distancing and palliative care are usually implemented, either individually or in combination, to control these outbreaks. Mathematical models are often used to assess the impact of these interventions and for supporting outbreak response decision making. The objectives of this systematic review, which covers all human vaccine-preventable diseases, are to determine the relative impact of vaccination compared with other outbreak interventions, and to ascertain the temporal trends in the use of modelling in outbreak response decision making. We will also identify gaps and opportunities for future research through a comparison with the foot-and-mouth disease outbreak response modelling literature, which has good examples of the use of modelling to inform outbreak response intervention decision making. METHODS AND ANALYSIS: We searched on PubMed, Scopus, Web of Science, Google Scholar and some preprint servers from the start of indexing to 15 January 2020. Inclusion: modelling studies, published in English, that use a mechanistic approach to evaluate the impact of an outbreak intervention. Exclusion: reviews, and studies that do not describe or use mechanistic models or do not describe an outbreak. We will extract data from the included studies such as their objectives, model types and composition, and conclusions on the impact of the intervention. We will ascertain the impact of models on outbreak response decision making through visualisation of time trends in the use of the models. We will also present our results in narrative style. ETHICS AND DISSEMINATION: This systematic review will not require any ethics approval since it only involves scientific articles. The review will be disseminated in a peer-reviewed journal and at various conferences fitting its scope. PROSPERO REGISTRATION NUMBER: CRD42020160803.

Improved estimates for extinction probabilities and times to extinction for populations of tsetse (Glossina spp).

A published study used a stochastic branching process to derive equations for the mean and variance of the probability of, and time to, extinction in population of tsetse flies (Glossina spp) as a function of adult and pupal mortality, and the probabilities that a female is inseminated by a fertile male. The original derivation was partially heuristic and provided no proofs for inductive results. We provide these proofs, together with a more compact way of reaching the same results. We also show that, while the published equations hold good for the case where tsetse produce male and female offspring in equal proportion, a different solution is required for the more general case where the probability (ß) that an offspring is female lies anywhere in the interval (0, 1). We confirm previous results obtained for the special case where ß = 0.5 and show that extinction probability is at a minimum for ß > 0.5 by an amount that increases with increasing adult female mortality. Sensitivity analysis showed that the extinction probability was affected most by changes in adult female mortality, followed by the rate of production of pupae. Because females only produce a single offspring approximately every 10 days, imposing a death rate of greater than about 3.5% per day will ensure the eradication of any tsetse population. These mortality levels can be achieved for some species using insecticide-treated targets or cattle-providing thereby a simple, effective and cost-effective method of controlling and eradicating tsetse, and also human and animal trypanosomiasis. Our results are of further interest in the modern situation where increases in temperature are seeing the real possibility that tsetse will go extinct in some areas, without the need for intervention, but have an increased chance of surviving in other areas where they were previously unsustainable due to low temperatures.

Shiga toxin gene-containing Escherichia coli from cattle and diarrheic children in the pastoral systems of southwestern Uganda.

Shiga toxin-producing Escherichia coli (STEC) strains from cattle and diarrheic children in a pastoralist community in Uganda were investigated. The STEC strains belonged to a variety of different serogroups, and 70% of the strains were positive for the intimin gene, eae. STEC strains from two of the children were closely related to bovine strains.

Is IS(ABA-1) customized for Acinetobacter?

An insertion sequence (IS(ABA-1)) was identified in Acinetobacter spp., but not in Enterobacteriacea and Pseudomonas aeruginosa. Numerous copies of the IS were identified in Acinetobacter strains containing the element. In one of the Acinetobacter baumannii strains, IS(ABA-1) was identified adjacent to sulII and transcription of the resistance gene is presumed to be dependent on promoter sequences within the IS. Since the IS is adjacent to ampC and bla(OXA) in this A. baumannii strain, it may be that IS(ABA-1) plays an important role in the expression of antibiotic resistance genes in this genus.

Analysis of genes encoding D-alanine:D-alanine ligase-related enzymes in Leuconostoc mesenteroides and Lactobacillus spp.

Degenerate oligodeoxyribonucleotides complementary to sequences encoding conserved amino acid (aa) motifs in D-alanine:D-alanine ligases (Ddl) were used to amplify approx. 600-bp fragments from glycopeptide-resistant strains of Leuconostoc mesenteroides (Lm), Lactobacillus plantarum, La. salivarius and La. confusus, and from a susceptible strain of La. leichmannii. Comparison of the deduced aa sequences of the PCR products revealed that the Ddl-related enzymes of resistant Lm and Lactobacillus spp. are more akin to each other (47-63% aa identity) than to that of susceptible La. leichmannii (33-37% aa identity), indicating that the Ddl-related enzymes in these intrinsically resistant species of Gram+ bacteria exhibit structural differences with those in susceptible species. The Ddl-related enzymes, VanA and VanB, implicated in acquired resistance to glycopeptides in enterococci, were not closely related to their counterparts in Lm and Lactobacillus spp., as they displayed only 26-32% aa identity.

Identification and characterization of an aadB gene cassette at a secondary site in a plasmid from Acinetobacter.

Transformation studies showed that an aminoglycoside resistance gene, aadB, is carried on a 6.0-kb plasmid (pRAY) in a clinical isolate of Acinetobacter (strain SUN). The gene was cloned and sequenced. An analysis of the DNA sequencing data showed that although the aadB gene is part of cassette, it is not associated with an integron. Rather, the aadB cassette has recombined at a secondary site downstream of putative promoters on pRAY.

Genetic heterogeneity of Campylobacter concisus determined by pulsed field gel electrophoresis-based macrorestriction profiling.

In order to investigate the genetic diversity of Campylobacter concisus to assist molecular typing studies, the use of macrorestriction profiling was examined. A suitable protocol was developed that included the use of formaldehyde pretreatment to prevent DNA degradation, and restriction enzyme NotI for pulsed field gel electrophoresis-based genotyping. Subsequently, 53 strains of C. concisus, principally from cases of diarrhoea in children, were examined. Fifty-one distinct patterns were obtained, indicating the high discriminatory potential of the method. Patterns comprised between one and 14 restriction fragments, with type and reference strains of two well-defined genomospecies of oral and faecal origin containing six and 12 fragments respectively. Our results show that C. concisus is genetically diverse and suggest the species as currently defined to be a taxonomic continuum comprised of several genomospecies. The pulsed field gel electrophoresis typing method described here has considerable potential for molecular epidemiological studies of C. concisus and may be a useful adjunctive method for helping to resolve key taxonomic issues for this species.

Marker entry into vestibular perilymph via the stapes following applications to the round window niche of guinea pigs.

It has been widely believed that drug entry from the middle ear into perilymph occurs primarily via the round window (RW) membrane. Entry into scala vestibuli (SV) was thought to be dominated by local, inter-scala communication between scala tympani (ST) and SV through permeable tissues such as the spiral ligament. In the present study, the distribution of the ionic marker trimethylphenylammonium (TMPA) was compared following intracochlear injections or applications to the RW niche, with or without occlusion of the RW membrane or stapes area. Perilymph TMPA concentrations were monitored either in real time with TMPA-selective microelectrodes sealed into ST and SV, or by the collection of sequential perilymph samples from the lateral semi-circular canal. Local inter-scala communication of TMPA was confirmed by measuring SV and ST concentrations following direct injections into perilymph of ST. Application of TMPA to the RW niche also showed a predominant entry into ST, with distribution to SV presumed to occur secondarily. When the RW membrane was occluded by a silicone plug, RW niche irrigation produced higher concentrations in SV compared to ST, confirming direct TMPA entry into the vestibule in the region of the stapes. The proportion of TMPA entering by the two routes was quantified by perilymph sampling from the lateral semi-circular canal. The TMPA levels of initial samples (originating from the vestibule) were markedly lower when the stapes area was occluded with silicone. These data were interpreted using a simulation program that incorporates all the major fluid and tissue compartments of the cochlea and vestibular systems. From this analysis it was estimated that 65% of total TMPA entered through the RW membrane and 35% entered the vestibule directly in the vicinity of the stapes. Direct entry of drugs into the vestibule is relevant to inner ear fluid pharmacokinetics and to the growing field of intratympanic drug delivery.

The dominant methicillin-resistant Staphylococcus aureus clone from hospitals in Cape Town has an unusual genotype: ST612.

There is currently limited information available on the molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in South Africa. A molecular characterization of 100 MRSA from five hospitals in Cape Town was carried out in this study. The strains were separated into six clusters by pulsed-field gel electrophoresis, indicating transmission of MRSA between local hospitals. None of the strains carried the Panton-Valentine Leukocidin gene. SCCmec typing, multilocus sequence typing and spa typing were used to further characterize the MRSA. Three clones corresponded to frequently described pandemic clones: ST239-MRSA-III, ST36-MRSA-II and ST5-MRSA-I. ST239-MRSA-III and ST36-MRSA-II were minor clones and collectively accounted for 16% of the isolates. ST5-MRSA-I was the second-most prevalent clone and accounted for 37% of the isolates. The dominant local clone was the infrequently described ST612-MRSA-IV (44% of isolates), which has only been described in South Africa and Australia.