Analyzing multiclonality of Staphylococcus aureus in clinical diagnostics using spa-based denaturing gradient gel electrophoresis

Chlorhexidine sensitivity in staphylococci isolated from patients with central line-associated bloodstream infection

Since 2011, 2% chlorhexidine in 70% isopropyl alcohol (2% chlorhexidine tincture) has been widely used in Korea. To investigate changes in chlorhexidine sensitivity of staphylococci causing central line-associated bloodstream infections, 264 blood culture isolates from adult patients treated in intensive care units of five university hospitals between 2008 and 2016 were analysed. We observed no significant changes in chlorhexidine minimum inhibitory and bactericidal concentrations, or in the prevalence of resistance-associated genes before and after introduction of 2% chlorhexidine tincture. Thus, there was no evidence of increased resistance to chlorhexidine in staphylococci causing central line-associated bloodstream infections.

Effects of Physico-Chemical Parameters on Actinomycetes Communities during Composting of Agricultural Waste

The objective of this study was to investigate the influence of physico-chemical parameters on Actinomycetes communities and to prioritize those parameters that contributed to Actinomycetes community composition during the composting of agricultural waste. Denaturing gradient gel electrophoresis of polymerase chain reaction (PCR-DGGE) and redundancy analysis (RDA) were used to determine the relationships between those parameters and Actinomycetes community composition. Quantitative PCR (qPCR) and regression analysis were used to monitor the 16S rDNA copy numbers of Actinomycetes and to analyse the correlations between physico-chemical parameters and Actinomyces 16S rDNA gene abundance, respectively. The RDA results showed that moisture content, water soluble carbon (WSC) and pH (p < 0.05) made the main contributions to the temporal variations of Actinomycetes community composition. The output of the regression analysis indicated that moisture content (R2 = 0.407, p < 0.01) showed a negative linear relationship with the Actinomyces 16S rDNA gene abundance.

Differences in molecular epidemiology of Staphylococcus aureus and Escherichia coli in nursing home residents and people in unassisted living situations

BACKGROUND

The usefulness of colonization pressure as a working model and proxy for infection transmission is limited due to the inability to grade or quantify the specific risk within environments that are subject to change.

AIM

To elaborate on the colonization pressure model by comparing the molecular epidemiology of two bacteria, Staphylococcus aureus and Escherichia coli, among residents in a nursing home and people in unassisted living situations.

METHODS

A cross-sectional study of 73 elderly residents from a village in south-central Sweden was conducted. Of these, 35 were residents of a nursing home, and 34 lived in an own place of residence in the same geographical area. Samples of two representative bacterial species were collected from multiple body sites and analysed for molecular diversity.

FINDINGS

Combining all body sites, 47% of the participants were colonized with S. aureus and 93% with E. coli. The nursing home group, the group in unassisted living situations, and both units combined, held 16, 17, and 29 different S. aureus spa types, respectively. The corresponding numbers of different E. coli serogenotypes were 34, 28, and 48. Diabetes mellitus was associated with more frequent colonization with S. aureus.

CONCLUSION

The molecular diversity of bacteria found within different forms of accommodation was within the same range. Hospital quality hygiene might have contributed to the absence of homogenization of the molecular diversity within the nursing home group. Diabetes mellitus might have played a role in a patient selection characterized by advanced age.

Large and finite sample properties of a maximum-likelihood estimator for multiplicity of infection

Reliable measures of transmission intensities can be incorporated into metrics for monitoring disease-control interventions. Genetic (molecular) measures like multiplicity of infection (MOI) have several advantages compared with traditional measures, e.g., R0. Here, we investigate the properties of a maximum-likelihood approach to estimate MOI and pathogen-lineage frequencies. By verifying regulatory conditions, we prove asymptotical unbiasedness, consistency and efficiency of the estimator. Finite sample properties concerning bias and variance are evaluated over a comprehensive parameter range by a systematic simulation study. Moreover, the estimator's sensitivity to model violations is studied. The estimator performs well for realistic sample sizes and parameter ranges. In particular, the lineage-frequency estimates are almost unbiased independently of sample size. The MOI estimate's bias vanishes with increasing sample size, but might be substantial if sample size is too small. The estimator's variance matrix agrees well with the Cramér-Rao lower bound, even for small sample size. The numerical and analytical results of this study can be used for study design. This is exemplified by a malaria data set from Venezuela. It is shown how the results can be used to determine the necessary sample size to achieve certain performance goals. An implementation of the likelihood method and a simulation algorithm for study design, implemented as an R script, is available as S1 File alongside a documentation (S2 File) and example data (S3 File).

Bacterial Strain Diversity Within Wounds

Significance: Rare bacterial taxa (taxa of low relative frequency) are numerous and ubiquitous in virtually any sample-including wound samples. In addition, even the high-frequency genera and species contain multiple strains. These strains, individually, are each only a small fraction of the total bacterial population. Against the view that wounds contain relatively few kinds of bacteria, this newly recognized diversity implies a relatively high rate of migration into the wound and the potential for diversification during infection. Understanding the biological and medical importance of these numerous taxa is an important new element of wound microbiology. Recent Advances: Only recently have these numerous strains been discovered; the technology to detect, identify, and characterize them is still in its infancy. Multiple strains of both gram-negative and gram-positive bacteria have been found in a single wound. In the few cases studied, the distribution of the bacteria suggests microhabitats and biological interactions. Critical Issues: The distribution of the strains, their phenotypic diversity, and their interactions are still largely uncharacterized. The technologies to investigate this level of genomic detail are still developing and have not been largely deployed to investigate wounds. Future Directions: As advanced metagenomics, single-cell genomics, and advanced microscopy develop, the study of wound microbiology will better address the complex interplay of numerous individually rare strains with both the host and each other.

A likelihood approach to estimate the number of co-infections

The number of co-infections of a pathogen (multiplicity of infection or MOI) is a relevant parameter in epidemiology as it relates to transmission intensity. Notably, such quantities can be built into a metric in the context of disease control and prevention. Having applications to malaria in mind, we develop here a maximum-likelihood (ML) framework to estimate the quantities of interest at low computational and no additional costs to study designs or data collection. We show how the ML estimate for the quantities of interest and corresponding confidence-regions are obtained from multiple genetic loci. Assuming specifically that infections are rare and independent events, the number of infections per host follows a conditional Poisson distribution. Under this assumption, we show that a unique ML estimate for the parameter () describing MOI exists which is found by a simple recursion. Moreover, we provide explicit formulas for asymptotic confidence intervals, and show that profile-likelihood-based confidence intervals exist, which are found by a simple two-dimensional recursion. Based on the confidence intervals we provide alternative statistical tests for the MOI parameter. Finally, we illustrate the methods on three malaria data sets. The statistical framework however is not limited to malaria.

Prevalence and molecular epidemiology of Staphylococcus aureus in Swedish nursing homes - as revealed in the SHADES study

Knowledge of carriage and population dynamics of Staphylococcus aureus is crucial for infection risk assessment and to reveal transmission patterns of strains. We report the prevalence and molecular epidemiology of S. aureus in elderly people (n = 290) living in nursing homes in three cities in the south of Sweden. The overall carriage prevalence rate was 48% when results from nares (31%) and throat (34%) samples were combined. Common spa types were equally distributed but a frequent type, t160, was found only in one of the regions. Carriage of different spa types was detected in 23% of individuals and antimicrobial resistance rates were higher in S. aureus isolates from those carrying more than one spa type. Five of the 21 individuals who carried different spa types were colonized simultaneously with resistant and non-resistant strains. Seventeen per cent of the individuals carried S. aureus of the same spa type on all occasions. Methicillin resistance was not detected. In conclusion we found a high prevalence of S. aureus in this elderly population with a high rate of dual colonization with different spa types. We also found signs of institutional spread of one strain.