[Multi-Resistant Bacteria in Patients in Hospitals and Medical Practices as well as in Residents of Nursing Homes in Saxony - Results of a Prevalence Study 2017/2018]. / Multiresistente Bakterien bei Patienten in Krankenhäusern und Arztpraxen sowie bei Bewohnern von Altenpflegeheimen in Sachsen ­ Ergebnisse einer Prävalenzstudie 2017/2018.

OBJECTIVE: The aim of this study was to determine the prevalence of methicillin-resistant Staphylococcus aureus (MRSA), multi-resistant gram-negative bacteria (MRGN) and vancomycin-resistant enterococci (VRE) in three study groups (hospital patients, residents in nursing homes for the elderly and patients in GP practices) and additionally, risk factors for carriage of multidrug-resistant organisms (MDRO). METHODS: Screening for MDRO was performed as a point prevalence study by obtaining nasal, pharyngeal and rectal swabs or stool samples from voluntary participants in 25 hospitals, 14 nursing homes for the elderly as well as 33 medical practices in 12 of 13 districts of Saxony. Suspicious isolates were further examined phenotypically and partially by molecular methods. The participants completed a questionnaire on possible risk factors for MDRO colonisation; the data were statistically evaluated by correlation analyses. RESULTS: In total, 1,718 persons, 629 from hospitals, 498 from nursing homes and 591 from medical practices, were examined. MDRO was detected in 8.4% of all participants; 1.3% persons tested positive for MRSA, 5.2% for 3MRGN, 0.1% for 4MRGN and 2.3% for VRE. Nine persons were colonized with more than one MDRO. The following independent risk factors could be significantly associated with the detection of MDRO: presence of a degree of care (MDRO), male sex (MDRO/VRE), current antibiosis (MDRO/VRE), antibiosis within the last 6 months (MDRO/MRSA/MRGN/VRE), current tumour disease (MDRO/3MRGN), peripheral artery disease (PAD) (MRSA) as well as urinary incontinence (3MRGN). CONCLUSIONS: To our knowledge, this study represents the first survey of prevalence of different multiresistant pathogen groups in 3 study groups including outpatients in Germany. 3MRGN were the pathogens most frequently detected and were also found in patients of younger age groups. VRE were found almost exclusively in specific clinics. In addition to current and past antibiotic therapy, in particular the presence of PAD for MRSA detection, urinary incontinence for 3MRGN detection and a current tumour disease for MDRO and 3MRGN detection were determined as independent risk factors.

Clinical infection in house rats (Rattus rattus) caused by Streptobacillus notomytis.

Rat bite fever is an under-reported, under-diagnosed emerging zoonosis with worldwide distribution. Besides Spirillum minus, Streptobacillus moniliformis is the major causative microorganism although it usually colonises rats without any clinical signs. A group of house rats (Rattus rattus) kept in a zoo exhibition for educational purposes suffered from neurological signs including disorientation, torticollis, stall walking, ataxia and death. Gross pathological and histo-pathological examinations of the investigated rats revealed high-grade otitis interna et media, from which Streptobacillus notomytis was isolated in pure culture or as the predominant microorganism. This case series underlines a previously expressed hypothesis that R. rattus might be naturally colonised with S. notomytis, whereas the traditional rat bite fever organism, S. moniliformis, might be restricted to the Norway rat (Rattus norvegicus). However, the general paucity of Streptobacillus isolates, especially from their respective animal hosts, precludes definitive proof of these host tropisms. This is the first report of S. notomytis detection outside Asia and Australia and the first evidence for its role as a facultative pathogen in house rats.

Tateyamaria pelophila sp. nov., a facultatively anaerobic alphaproteobacterium isolated from tidal-flat sediment, and emended descriptions of the genus Tateyamaria and of Tateyamaria omphalii.

A Gram-negative motile rod, strain SAM4T, was isolated from the highest positive dilution of a most probable number series inoculated with tidal-flat sediments from the German North Sea coast. The isolate grew at 4-35 degrees C and showed constant growth yields throughout almost the whole temperature range. Growth was observed between pH 6 and 9 and at salinities of 0.3-10.2%. Strain SAM4T required Na+ for growth, contained bacteriochlorophyll a and was catalase- and oxidase-positive. It was nutritionally versatile growing on a variety of carbon compounds including carbohydrates, amino acids and organic acids like lactate or succinate. It grew anaerobically on complex media such as marine broth, indicating fermentation, and by reducing trimethylammonium oxide. The dominant phospholipids were phosphatidylethanolamine and phosphatidylglycerol, whereas only traces of phosphatidylcholine and an unidentified lipid were found. The major fatty acid was n-C18:1omega7c. The DNA G+C content was 56.4 mol%. The isolate was identified as a member of the Roseobacter clade within the class Alphaproteobacteria. However, based on phylogenetic, phenotypic and physiological data, it clearly differs from its closest relative Tateyamaria omphalii. Therefore, a novel species is proposed: Tateyamaria pelophila sp. nov., with strain SAM4T (=DSM 17270T=LMG 23018T) as the type strain. Emended descriptions of the genus Tateyamaria and of Tateyamaria omphalii are also presented.

Methane and sulfate profiles within the subsurface of a tidal flat are reflected by the distribution of sulfate-reducing bacteria and methanogenic archaea.

The anoxic layers of marine sediments are dominated by sulfate reduction and methanogenesis as the main terminal oxidation processes. The aim of this study was to analyze the vertical succession of microbial populations involved in these processes along the first 4.5 m of a tidal-flat sediment. Therefore, a quantitative PCR approach was applied using primers targeting the domains of Bacteria and Archaea, and key functional genes for sulfate reduction (dsrA) and methanogenesis (mcrA). The sampling site was characterized by an unusual sulfate peak at 250 cm depth resulting in separate sulfate-methane transition zones. Methane and sulfate profiles were diametrically opposed, with a methane maximum in the sulfate-depleted zone showing high numbers of archaea and methanogens. The methane-sulfate interfaces harbored elevated numbers of sulfate reducers, and revealed a slight increase in mcrA and archaeal 16S rRNA genes, suggesting sulfate-dependent anaerobic oxidation of methane. A diversity analysis of both functional genes by PCR-denaturing gradient gel electrophoresis revealed a vertical succession of subpopulations that were governed by geochemical and sedimentologic conditions. Along the upper 200 cm, sulfate-reducing populations appeared quite uniform and were dominated by the Deltaproteobacteria. In the layers beneath, an apparent increase in diversity and a shift to the Firmicutes as the predominant group was observed.

Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters.

The subsurface of a tidal-flat sediment was analyzed down to 360 cm in depth by molecular and geochemical methods. A community structure analysis of all three domains of life was performed using domain-specific PCR followed by denaturing gradient gel electrophoresis analysis and sequencing of characteristic bands. The sediment column comprised horizons easily distinguishable by lithology that were deposited in intertidal and salt marsh environments. The pore water profile was characterized by a subsurface sulfate peak at a depth of about 250 cm. Methane and sulfate profiles were opposed, showing increased methane concentrations in the sulfate-free layers. The availability of organic carbon appeared to have the most pronounced effect on the bacterial community composition in deeper sediment layers. In general, the bacterial community was dominated by fermenters and syntrophic bacteria. The depth distribution of methanogenic archaea correlated with the sulfate profile and could be explained by electron donor competition with sulfate-reducing bacteria. Sequences affiliated with the typically hydrogenotrophic Methanomicrobiales were present in sulfate-free layers. Archaea belonging to the Methanosarcinales that utilize noncompetitive substrates were found along the entire anoxic-sediment column. Primers targeting the eukaryotic 18S rRNA gene revealed the presence of a subset of archaeal sequences in the deeper part of the sediment cores. The phylogenetic distance to other archaeal sequences indicates that these organisms represent a new phylogenetic group, proposed as "tidal-flat cluster 1." Eukarya were still detectable at 360 cm, even though their diversity decreased with depth. Most of the eukaryotic sequences were distantly related to those of grazers and deposit feeders.

Deep biosphere-related bacteria within the subsurface of tidal flat sediments.

Biogeochemical and microbiological processes in the upper sediment layers of tidal flats were analysed in many investigations, while deeper zones remained largely unexplored. Therefore, denaturant gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments along the depth profile of up to 5.5 m-long sediment cores was performed in comparison with lithological and geochemical parameters. The investigation revealed that different compartments of the sediment columns were characterized by specific microbial communities. These compartments were analysed by sequencing of 113 DGGE bands. The upper layers down to 160-200 cm were dominated by gamma- and delta-Proteobacteria representing more than 60% of the total number of phylotypes. Underneath, a striking shift in community composition was observed, as the Proteobacteria were replaced by Chloroflexi with more than 60% of all sequences. As sulfate was still available as an electron acceptor in these layers, the abundance of Chloroflexi might be promoted by the electron donor or the quality of the carbon source. The dominance of this group, previously known as green non-sulfur bacteria, indicates the presence of a typical deep-biosphere microbial community in relatively young subsurface sediments. Thus, tidal flats might offer a convenient possibility to study and understand certain aspects of the deep biosphere in general.

Microbial diversity in coastal subsurface sediments: a cultivation approach using various electron acceptors and substrate gradients.

Microbial communities in coastal subsurface sediments are scarcely investigated and have escaped attention so far. But since they are likely to play an important role in biogeochemical cycles, knowledge of their composition and ecological adaptations is important. Microbial communities in tidal sediments were investigated along the geochemical gradients from the surface down to a depth of 5.5 m. Most-probable-number (MPN) series were prepared with a variety of different carbon substrates, each at a low concentration, in combination with different electron acceptors such as iron and manganese oxides. These achieved remarkably high cultivation efficiencies (up to 23% of the total cell counts) along the upper 200 cm. In the deeper sediment layers, MPN counts dropped significantly. Parallel to the liquid enrichment cultures in the MPN series, gradient cultures with embedded sediment subcores were prepared as an additional enrichment approach. In total, 112 pure cultures were isolated; they could be grouped into 53 different operational taxonomic units (OTU). The isolates belonged to the Proteobacteria, "Bacteroidetes," "Fusobacteria," Actinobacteria, and "Firmicutes." Each cultivation approach yielded a specific set of isolates that in general were restricted to this single isolation procedure. Analysis of the enrichment cultures by PCR and denaturing gradient gel electrophoresis revealed an even higher diversity in the primary enrichments that was only partially reflected by the culture collection. The majority of the isolates grew well under anoxic conditions, by fermentation, or by anaerobic respiration with nitrate, sulfate, ferrihydrite, or manganese oxides as electron acceptors.