Daniel Jonas

A field guide to pandemic, epidemic and sporadic clones of methicillin-resistant Staphylococcus aureus

In recent years, methicillin-resistant Staphylococcus aureus (MRSA) have become a truly global challenge. In addition to the long-known healthcare-associated clones, novel strains have also emerged outside of the hospital settings, in the community as well as in livestock. The emergence and spread of virulent clones expressing Panton-Valentine leukocidin (PVL) is an additional cause for concern. In order to provide an overview of pandemic, epidemic and sporadic strains, more than 3,000 clinical and veterinary isolates of MRSA mainly from Germany, the United Kingdom, Ireland, France, Malta, Abu Dhabi, Hong Kong, Australia, Trinidad & Tobago as well as some reference strains from the United States have been genotyped by DNA microarray analysis. This technique allowed the assignment of the MRSA isolates to 34 distinct lineages which can be clearly defined based on non-mobile genes. The results were in accordance with data from multilocus sequence typing. More than 100 different strains were distinguished based on affiliation to these lineages, SCCmec type and the presence or absence of PVL. These strains are described here mainly with regard to clinically relevant antimicrobial resistance- and virulence-associated markers, but also in relation to epidemiology and geographic distribution. The findings of the study show a high level of biodiversity among MRSA, especially among strains harbouring SCCmec IV and V elements. The data also indicate a high rate of genetic recombination in MRSA involving SCC elements, bacteriophages or other mobile genetic elements and large-scale chromosomal replacements.

Plasmid-Mediated Quinolone Resistance in Isolates Obtained in German Intensive Care Units

ABSTRACT Screening of 703 isolates of Enterobacteriaceae, obtained from 34 German intensive care units (ICUs), revealed qnr-positive, integron-containing isolates of Enterobacter sp. and Citrobacter freundii from four patients in 2 German ICUs. This is one of the first reports of qnr-positive strains obtained from patients in Europe.

A Stenotrophomonas maltophilia Multilocus Sequence Typing Scheme for Inferring Population Structure

Stenotrophomonas maltophilia is an opportunistic, highly resistant, and ubiquitous pathogen. Strains have been assigned to genogroups using amplified fragment length polymorphism. Hence, isolates of environmental and clinical origin predominate in different groups. A multilocus sequence typing (MLST) scheme was developed using a highly diverse selection of 70 strains of various ecological origins from seven countries on all continents including strains of the 10 previously defined genogroups. Sequence data were assigned to 54 sequence types (ST) based on seven loci. Indices of association for all isolates and clinical isolates of 2.498 and 2.562 indicated a significant linkage disequilibrium, as well as high congruence of tree topologies from different loci. Potential recombination events were detected in one-sixth of all ST. Calculation of the mean divergence between and within predicted clusters confirmed previously defined groups and revealed five additional groups. Consideration of the different ecological origins showed that 18 out of 31 respiratory tract isolates, including 12 out of 19 isolates from cystic fibrosis (CF) patients, belonged to genogroup 6. In contrast, 16 invasive strains isolated from blood cultures were distributed among nine different genogroups. Three genogroups contained isolates of strictly environmental origin that also featured high sequence distances to other genogroups, including the S. maltophilia type strain. On the basis of this MLST scheme, isolates can be assigned to the genogroups of this species in order to further scrutinize the population structure of this species and to unravel the uneven distribution of environmental and clinical isolates obtained from infected, colonized, or CF patients.

Characteristics of mixed microbial culture at different sludge ages: Effect on variable kinetics for substrate utilization

The study focused on variable kinetics for substrate utilization, primarily addressing the following issue: Is variable process kinetics observed under different operating conditions and culture history (sludge ages), the result of changes inflicted on the metabolic machinery of the same microbial culture? Or, is this the result of a different microbial population selected under different operating conditions? For this purpose, the study mainly emphasized to assess the microbial population composition sustained at different sludge ages. It explored the relationship between observed process kinetics and microbial population structure using respirometric modeling and high-throughput sequencing of 16S rRNA gene. Experimental results indicated a significant change in the composition of the microbial community fed with the same organic substrate, when the culture history was changed, lower sludge age selecting a different and faster growing microbial community.

Food-borne Enterococci Integrate Into Oral Biofilm: An In Vivo Study

INTRODUCTION Enterococci, particularly Enterococcus faecalis, are still a primary concern in endodontic infections. To date, enterococci have been considered to be only transiently present in the oral cavity. The aim of this study was to examine whether different enterococci from food are able to reside in oral biofilm. METHODS Six healthy volunteers wore dental splints loaded with enamel slabs. After 3 days, the volunteers consumed cheese containing enterococci. The fate of the enterococci was analyzed by culture technique and 16S rRNA gene sequencing. All isolates were characterized genotypically by macrorestriction analysis (SmaI) and pulsed-field gel electrophoresis. E. faecalis was also analyzed by using fluorescent in situ hybridization (FISH). RESULTS E. faecalis, E. faecium, E. avium, and E. durans were detected in the initial biofilm after 2 hours, as well as in the 5-day-old oral biofilm. E. faecalis, E. faecium, and E. avium isolated from the initial biofilm and from the 5-day-old biofilm, as well as those isolated from cheese, showed genetic homogeneity. E. faecium and E. avium had integrated into a pre-existing 3-day-old biofilm. No genetic similarity between E. durans strains isolated from cheese and those from the initial and 5-day-old oral biofilm was detected. E. faecalis was also detected in the oral biofilm by using FISH. CONCLUSIONS Food-borne enterococci, particularly E. faecalis, might not only be transient but could also survive in the oral biofilm and become a source for endodontic infections. Moreover, genotypic analysis is required to study the source of oral enterococci.

Comparison of the Bacterial Composition and Structure in Symptomatic and Asymptomatic Endodontic Infections Associated with Root-Filled Teeth Using Pyrosequencing

Residual microorganisms and/or re-infections are a major cause for root canal therapy failure. Understanding of the bacterial content could improve treatment protocols. Fifty samples from 25 symptomatic and 25 asymptomatic previously root-filled teeth were collected from Sudanese patients with periradicular lesions. Amplified 16S rRNA gene (V1-V2) variable regions were subjected to pyrosequencing (FLX 454) to determine the bacterial profile. Obtained quality-controlled sequences from forty samples were classified into 741 operational taxonomic units (OTUs) at 3% dissimilarity, 525 at 5% dissimilarity and 297 at 10% dissimilarity, approximately corresponding to species-, genus- and class levels. The most abundant phyla were: Firmicutes (29.9%), Proteobacteria (26.1%), Actinobacteria (22.72%), Bacteroidetes (13.31%) and Fusobacteria (4.55%). Symptomatic patients had more Firmicutes and Fusobacteria than asymptomatic patients, while asymptomatic patients showed more Proteobacteria and Actinobacteria. Interaction of disease status and age was observed by two-way ANOSIM. Canonical correspondence analysis for age, tooth restoration and disease status showed a correlation of disease status with the composition and prevalence of different members of the microbial community. The pyrosequencing analysis revealed a distinctly higher diversity of the microbiota compared to earlier reports. The comparison of symptomatic and asymptomatic patients showed a clear association of the composition of the bacterial community with the presence and absence of symptoms in conjunction with the patients’ age.

Effect of sludge age on population dynamics and acetate utilization kinetics under aerobic conditions.

The study addressed acetate utilization by an acclimated mixed microbial culture under different growth conditions. It explored changes in the composition of the microbial community and variable process kinetics induced by different culture history. Sequencing batch reactors were operated at steady-state at different sludge ages of two and ten days. Microbial population structure was determined using high-throughput sequencing of 16S rRNA genes. Parallel batch experiments were conducted with acclimated biomass for respirometric analyses. A lower sludge age sustained a different community, which also reflected as variable kinetics for microbial growth and biopolymer storage. The maximum growth rate was observed to change from 3.9/d to 8.5/d and the substrate storage rate from 3.5/d to 5.9/d when the sludge age was decreased from 10 d to 2.0 d. Results challenge the basic definition of heterotrophic biomass in activated sludge models, at least by means of variable kinetics under different growth conditions.

Enterococcus faecalis from Food, Clinical Specimens, and Oral Sites: Prevalence of Virulence Factors in Association with Biofilm Formation

Enterococci have gained significance as the cause of nosocomial infections; they occur as food contaminants and have also been linked to dental diseases. E. faecalis has a great potential to spread virulence as well as antibiotic resistance genes via horizontal gene transfer. The integration of food-borne enterococci into the oral biofilm in-vivo has been observed. Therefore, we investigated the virulence determinants and antibiotic resistance of 97 E. faecalis isolates from the oral cavity, food, and clinical specimens. In addition, phenotypic expression of gelatinase and cytolysin were tested, in-vitro biofilm formation was quantified and isolates were compared for strain relatedness via pulsed field gel electrophoresis (PFGE). Each isolate was found to possess two or more virulence genes, most frequently gelE, efaA, and asa1. Notably, plaque/saliva isolates possessed the highest abundance of virulence genes, the highest levels of phenotypic gelatinase and hemolysin activity and concurrently a high ability to form biofilm. The presence of asa1 was associated with biofilm formation. The biofilm formation capacity of clinical and plaque/saliva isolates was considerably higher than that of food isolates and they also showed similar antibiotic resistance patterns. These results indicate that the oral cavity can constitute a reservoir for virulent E. faecalis strains possessing antibiotic resistance traits and at the same time distinct biofilm formation capabilities facilitating exchange of genetic material.

Methicillin-resistant Staphylococcus aureus in German intensive care units during 2000-2003: data from Project SARI (Surveillance of Antimicrobial Use and Antimicrobial Resistance in Intensive Care Units).

OBJECTIVES The objective of this study was to analyze methicillin-resistant Staphylococcus aureus (MRSA) percentages (defined as the percentage of S. aureus isolates that are resistant to methicillin) and antimicrobial consumption in intensive care units (ICUs) participating in Project SARI (Surveillance of Antimicrobial Use and Antimicrobial Resistance in Intensive Care Units), to look for temporal changes in MRSA percentages and antimicrobial consumption in individual ICUs as an indicator of the impact of an active surveillance system, and to investigate the differences between ICUs with increased MRSA percentages versus those with decreased percentages during a period of 3 years (2001-2003). METHODS This was a prospective, ICU-based and laboratory-based surveillance study involving 38 German ICUs during 2000-2003. Antimicrobial use was reported in terms of defined daily doses (DDDs) per 1,000 patient-days. Temporal changes in the MRSA percentage and antimicrobial use in individual ICUs were calculated by means of the Wilcoxon signed rank test. The incidence density of nosocomial MRSA infection was defined as the number of nosocomial MRSA infections per 1,000 patient-days. RESULTS From February 2000 through December 2003, a total of 38 ICUs reported data on 499,694 patient-days and 9,552 S. aureus isolates, including 2,249 MRSA isolates and 660,029 DDDs of antimicrobials. Cumulative MRSA percentages ranged from 0% to 64.4%, with a mean of 23.6%. The MRSA incidence density ranged from 0 to 38.2 isolates per 1,000 patient-days, with a mean of 2.77 isolates per 1,000 patient-days. There was a positive correlation between MRSA percentage and imipenem and ciprofloxacin use (P<.05). Overall, comparison of data from 2001 with data from 2003 showed that MRSA percentages increased in 18 ICUs (median increase, 13.2% [range, 1.6%-38.4%]) and decreased in 14 ICUs (median decrease, 12% [range, 1.0%-48.4%]). Increased use of third-generation cephalosporins, glycopeptides, or aminoglycosides correlated significantly with an increase in the MRSA percentage (P<.05). The cumulative nosocomial MRSA infection incidence density for 141 ICUs that did not participate in SARI and, therefore, did not receive feedback increased from 0.26 to 0.35 infections per 1,000 patient-days during a 3-year period, whereas the rate in SARI ICUs decreased from 0.63 to 0.40 infections per 1,000 patient-days. CONCLUSION The MRSA situation in German ICUs is still heterogeneous. Because MRSA percentages range from 0% to 64.4%, further studies are required to confirm findings that no change in the MRSA percentage and a decrease in the nosocomial MRSA infection incidence density in SARI ICUs reflect the impact of an active surveillance system.

Microarray-Based Genotyping and Clinical Outcomes of Staphylococcus aureus Bloodstream Infection: An Exploratory Study

The clinical course of Staphylococcus aureus bacteremia varies extensively. We sought to determine the relationship between genetic characteristics of the infecting pathogen and clinical outcomes in an exploratory study. In two study centers, 317 blood culture isolates were analyzed by DNA microarray and spa genotyping. By uni- and multivariate regression analyses associations of genotype data with 30-day all-cause mortality, severe sepsis/septic shock, disseminated disease, endocarditis, and osteoarticular infection were investigated. Univariate analysis showed significant association between S. aureus genes/gene-clusters or clonal complexes and clinical endpoints. For example CC15 was associated with 30-day mortality and CC22 with osteoarticular infection. In multivariate analysis methicillin resistance (mecA, OR 4.8 [1.43–16.06]) and the beta-lactamase-gene (bla, OR 3.12 [1.17–8.30]) remained independently associated with 30-day mortality. The presence of genes for enterotoxins (sed/sej/ser) was associated with endocarditis (OR 5.11 [1.14–18.62]). Host factors such as McCabe classification (OR 4.52 [2.09–9.79] for mortality), age (OR 1.06 [1.03–1.10] per year), and community-acquisition (OR 3.40 [1.31–8.81]) had a major influence on disease severity, dissemination and mortality. Individual genotypes and clonal complexes of S. aureus can only partially explain clinical features and outcomes of S. aureus bacteremia. Genotype-phenotype association studies need to include adjustments for host factors like age, comorbidity and community-acquisition.