From Shadows to Spotlight: Enhancing Bacterial DNA Detection in Blood Samples through Cutting-Edge Molecular Pre-Amplification

One of the greatest challenges to the use of molecular methods for diagnostic purposes is the detection of target DNA that is present only in low concentrations. One major factor that negatively impacts accuracy, diagnostic sensitivity, and specificity is the sample matrix, which hinders the attainment of the required detection limit due to the presence of residual background DNA. To address this issue, various methods have been developed to enhance sensitivity through targeted pre-amplification of marker sequences. Diagnostic sensitivity to the single molecular level is critical, particularly when identifying bloodstream infections. In cases of clinically manifest sepsis, the concentration of bacteria in the blood may reach as low as one bacterial cell/CFU per mL of blood. Therefore, it is crucial to achieve the highest level of sensitivity for accurate detection. In the present study, we have established a method that fills the analytical gap between low concentrations of molecular markers and the minimum requirements for molecular testing. For this purpose, a sample preparation of whole blood samples with a directly downstream pre-amplification was developed, which amplifies specific species and resistance markers in a multiplex procedure. When applying pre-amplification techniques, the sensitivity of the pathogen detection in whole blood samples was up to 100 times higher than in non-pre-amplified samples. The method was tested with blood samples that were spiked with several Gram-positive and Gram-negative bacterial pathogens. By applying this method to artificial spiked blood samples, it was possible to demonstrate a sensitivity of 1 colony-forming unit (CFU) per millilitre of blood for S. aureus and E. faecium. A detection limit of 28 and 383 CFU per ml of blood was achieved for E. coli and K. pneumoniae, respectively. If the sensitivity is also confirmed for real clinical blood samples from septic patients, the novel technique can be used for pathogen detection without cultivation, which might help to accelerate diagnostics and, thus, to decrease sepsis mortality rates.

Molecular Characterization of Chimeric Staphylococcus aureus Strains from Waterfowl

Staphylococcus aureus is a versatile pathogen that does not only occur in humans but also in various wild and domestic animals, including several avian species. When characterizing S. aureus isolates from waterfowl, isolates were identified as atypical CC133 by DNA microarray analysis. They differed from previously sequenced CC133 strains in the presence of the collagen adhesin gene cna; some also showed a different capsule type and a deviant spa type. Thus, they were subjected to whole-genome sequencing. This revealed multiple insertions of large regions of DNA from other S. aureus lineages into a CC133-derived backbone genome. Three distinct strains were identified based on the size and extent of these inserts. One strain comprised two small inserts of foreign DNA up- and downstream of oriC; one of about 7000 nt or 0.25% originated from CC692 and the other, at ca. 38,000 nt or 1.3% slightly larger one was of CC522 provenance. The second strain carried a larger CC692 insert (nearly 257,000 nt or 10% of the strain's genome), and its CC522-derived insert was also larger, at about 53,500 nt or 2% of the genome). The third strain carried an identical CC692-derived region (in which the same mutations were observed as in the second strain), but it had a considerably larger CC522-like insertion of about 167,000 nt or 5.9% of the genome. Both isolates of the first, and two out of four isolates of the second strain also harbored a hemolysin-beta-integrating prophage carrying "bird-specific" virulence factors, ornithine cyclodeaminase D0K6J8 and a putative protease D0K6J9. Furthermore, isolates had two different variants of SCC elements that lacked mecA/mecC genes. These findings highlight the role of horizontal gene transfer in the evolution of S. aureus facilitated by SCC elements, by phages, and by a yet undescribed mechanism for large-scale exchange of core genomic DNA.

Clonal Complexes Distribution of Staphylococcus aureus Isolates from Clinical Samples from the Caribbean Islands

The aim of this study was to comprehensively characterise S. aureus from the Caribbean Islands of Trinidad and Tobago, and Jamaica. A total of 101 S. aureus/argenteus isolates were collected in 2020, mainly from patients with skin and soft tissue infections. They were characterised by DNA microarray allowing the detection of ca. 170 target genes and assignment to clonal complexes (CC)s and strains. In addition, the in vitro production of Panton-Valentine leukocidin (PVL) was examined by an experimental lateral flow assay. Two isolates were identified as S. argenteus, CC2596. The remaining S. aureus isolates were assigned to 21 CCs. The PVL rate among methicillin-susceptible S. aureus (MSSA) isolates was high (38/101), and 37 of the 38 genotypically positive isolates also yielded positive lateral flow results. The isolate that did not produce PVL was genome-sequenced, and it was shown to have a frameshift mutation in agrC. The high rate of PVL genes can be attributed to the presence of a known local CC8-MSSA clone in Trinidad and Tobago (n = 12) and to CC152-MSSA (n = 15). In contrast to earlier surveys, the USA300 clone was not found, although one MSSA isolate carried the ACME element, probably being a mecA-deficient derivative of this strain. Ten isolates, all from Trinidad and Tobago, were identified as MRSA. The pandemic ST239-MRSA-III strain was still common (n = 7), but five isolates showed a composite SCCmec element not observed elsewhere. Three isolates were sequenced. That showed a group of genes (among others, speG, crzC, and ccrA/B-4) to be linked to its SCC element, as previously found in some CC5- and CC8-MRSA, as well as in S. epidermidis. The other three MRSA belonged to CC22, CC72, and CC88, indicating epidemiological connections to Africa and the Middle East.

Characterisation of a Staphylococcus aureus Isolate Carrying Phage-Borne Enterotoxin E from a European Badger (Meles meles)

Staphylococcus (S.) aureus colonizes up to 30% of all humans and can occasionally cause serious infections. It is not restricted to humans as it can also often be found in livestock and wildlife. Recent studies have shown that wildlife strains of S. aureus usually belong to other clonal complexes than human strains and that they might differ significantly with regard to the prevalence of genes encoding antimicrobial resistance properties and virulence factors. Here, we describe a strain of S. aureus isolated from a European badger (Meles meles). For molecular characterisation, DNA microarray-based technology was combined with various next-generation sequencing (NGS) methods. Bacteriophages from this isolate were induced with Mitomycin C and characterized in detail by transmission electron microscopy (TEM) and NGS. The S. aureus isolate belonged to ST425 and had a novel spa repeat sequence (t20845). It did not carry any resistance genes. The uncommon enterotoxin gene see was detected in one of its three temperate bacteriophages. It was possible to demonstrate the induction of all three prophages, although only one of them was expected to be capable of excision based on its carriage of the excisionase gene xis. All three bacteriophages belonged to the family Siphoviridae. Minor differences in size and shape of their heads were noted in TEM images. The results highlight the ability of S. aureus to colonize or infect different host species successfully, which can be attributed to a variety of virulence factors on mobile genetic elements, such as bacteriophages. As shown in the strain described herein, temperate bacteriophages not only contribute to the fitness of their staphylococcal host by transferring virulence factors, but also increase mobility among themselves by sharing genes for excision and mobilization with other prophages.

Characterisation of Methicillin-Resistant Staphylococcus aureus from Alexandria, Egypt

The present study aims to characterise clinical MRSA isolates from a tertiary care centre in Egypt's second-largest city, Alexandria. Thirty isolates collected in 2020 were genotypically characterised by microarray to detect their resistance and virulence genes and assign them to clonal complexes (CC) and strains. Isolates belonged to 11 different CCs and 14 different strains. CC15-MRSA-[V+fus] (n = 6), CC1-MRSA-[V+fus+tir+ccrA/B-1] (PVL+) (n = 5) as well as CC1-MRSA-[V+fus+tir+ccrA/B-1] and CC1153-MRSA-[V+fus] (PVL+) (both with n = 3) were the most common strains. Most isolates (83%) harboured variant or composite SCCmec V or VI elements that included the fusidic acid resistance gene fusC. The SCCmec [V+fus+tir+ccrA/B-1] element of one of the CC1 isolates was sequenced, revealing a presence not only of fusC but also of blaZ, aacA-aphD and other resistance genes. PVL genes were also common (40%). The hospital-acquired MRSA CC239-III strain was only found twice. A comparison to data from a study on strains collected in 2015 (Montelongo et al., 2022) showed an increase in fusC and PVL carriage and a decreasing prevalence of the CC239 strain. These observations indicate a diffusion of community-acquired strains into hospital settings. The beta-lactam use in hospitals and the widespread fusidic acid consumption in the community might pose a selective pressure that favours MRSA strains with composite SCCmec elements comprising mecA and fusC. This is an unsettling trend, but more MRSA typing data from Egypt are required.

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.

Antimicrobial Resistance Genes in ESBL-Producing Escherichia coli Isolates from Animals in Greece

The prevalence of multidrug resistant, extended spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is increasing worldwide. The present study aimed to provide an overview of the multidrug resistance phenotype and genotype of ESBL-producing Escherichia coli (E. coli) isolates of livestock and wild bird origin in Greece. Nineteen phenotypically confirmed ESBL-producing E. coli strains isolated from fecal samples of cattle (n = 7), pigs (n = 11) and a Eurasian magpie that presented resistance to at least one class of non β-lactam antibiotics, were selected and genotypically characterized. A DNA-microarray based assay was used, which allows the detection of various genes associated with antimicrobial resistance. All isolates harbored blaCTX-M-1/15, while blaTEM was co-detected in 13 of them. The AmpC gene blaMIR was additionally detected in one strain. Resistance genes were also reported for aminoglycosides in all 19 isolates, for quinolones in 6, for sulfonamides in 17, for trimethoprim in 14, and for macrolides in 8. The intI1 and/or tnpISEcp1 genes, associated with mobile genetic elements, were identified in all but two isolates. This report describes the first detection of multidrug resistance genes among ESBL-producing E. coli strains retrieved from feces of cattle, pigs, and a wild bird in Greece, underlining their dissemination in diverse ecosystems and emphasizing the need for a One-Health approach when addressing the issue of antimicrobial resistance.

Constraints of propylene glycol degradation at low temperatures and saturated flow conditions

During snowmelt, the infiltration of large amounts of propylene glycol (PG), the major compound of many aircraft deicing fluids, affects redox processes and poses a contamination risk for the groundwater. To gain a better understanding about the degradation of PG and the associated biogeochemical processes under these conditions, we conducted saturated soil column experiments at 4 °C. During two successive PG pulses, we monitored the effect of the runway deicer formate (FO) and changing redox conditions on PG degradation. Furthermore, we applied first-order and simplified Monod kinetics to describe PG and FO transport. The transport of 50 mg l(-1) PG showed three stages of microbial degradation, which were defined as lag phase, aerobic phase, and anaerobic phase. During the second pulse, lag effects diminished due to the already accomplished microbial adaption, and the initial degradation rate of PG increased. Degradation of PG was most efficient during aerobic conditions (aerobic phase), while the subsequent drop of the redox potential down to -300 mV decreased the degradation rate (anaerobic phase). Formate addition decreased the overall degradation of PG by 50 and 15 % during the first and second pulse, illustrating the inhibitory effect of FO on PG degradation. The concurrent increase of Fe(III), organic carbon, and the turbidity in the column effluent after PG and FO application suggest the combined export of Fe adsorbed to fragments of detached biofilm. Neither the first-order nor the simplified Monod model was able to reconstruct the dynamic breakthrough of 50 mg l(-1) PG. The breakthrough of 1,000 mg l(-1), however, was described reasonably well with first-order kinetics. At low temperature and high water saturation, the application of first-order degradation kinetics seems therefore appropriate to describe the transport of high concentrations of PG.

From bulk to single-cell classification of the filamentous growing Streptomyces bacteria by means of Raman spectroscopy

Classification of Raman spectra recorded from single cells is commonly applied to bacteria that exhibit small sizes of approximately 1 to 2 μm. Here, we study the possibility to adopt this classification approach to filamentous bacteria of the genus Streptomyces. The hyphae can reach extensive lengths of up to 35 μm, which can correspond to a single cell identified in light microscopy. The classification of Raman bulk spectra will be demonstrated. Here, ultraviolet resonance Raman (UV RR) spectroscopy is chosen to classify six Streptomyces species by the application of a tree-like classifier. For each knot of the hierarchical classifier, estimated classification accuracies of over 94% are accomplished. In contrast to the classification of bulk spectra, the classification of single-cell spectra requires a homogenous substance distribution within the cell. Consequently, the bacterial cell chemistry can be represented by one individual spectrum. This requirement is not fulfilled when different spectra are processed from different locations within the cell. Bacteria of the investigated genus Streptomyces exhibit, besides the normal bacterial spectra, lipid-rich spectra. The occurrence of lipid enrichment depends on culture age and nutrition availability. With this study, we investigate the cell substance distribution, especially of lipid-rich fractions. The classification utilizing a tree-like classifier is also applied to the Streptomyces single-cell spectra, resulting in classification accuracies between 80 and 93% for the investigated Streptomyces species.

Cerebellar glia cells induce a correct laminar organization in chicken retinal reaggregates

We investigated the functional role of glia cells during retinogenesis using the rotation culture system. Reaggregating cells from the embryonic chick retina have the unique capacity to reassemble into laminated cellular spheres. These spheres are composed of several compartments holding the constituents of many retinal layers in a topologically correct, yet inverse orientation. However, when these spheres are cultured in the presence of conditioned media derived from monolayers of cerebellar glia cells, the reassembling retinal cells behave totally differently. The anlage of the originally reversed lamina polarity is progressively transformed within a week into a sphere with a compound and correctly laminated orientation. Conditioned media from fibroblasts, other glia cells (except Müller cells) or a set of already characterized retinogenetic factors are not able to produce this dramatic transformation. Additionally, we were able to show that only retinal cells are able to respond with a reorganization process. Reaggregating cells from the chick cerebellum also form spheroids; however, neither in the presence of cerebellar glia cell-derived conditioned medium nor their control counterparts are they able to reassemble histotypically. This indicates that cerebellar glia cells produce diffusible factors to which retinal cells can respond and that these factors can act as important determinants for the correct establishment of the retinal polarity. Since all types of laminar disorganization are of great clinical significance, the knowledge of factors which determine and sustain the normal retinal architecture are biomedically highly relevant.

On the role of Müller glia cells in histogenesis: only retinal spheroids, but not tectal, telencephalic and cerebellar spheroids develop histotypical patterns

The establishment of cell and fibre layers and the specification of different cell types are crucial processes during development of the central nervous system. Here we investigated the developmental architecture of radial glia cells in these processes using so-called spheroids that arise from dissociated chicken embryonic neural cells in rotation culture. We were able to produce retinal, tectal, and telencephalic spheroids from E6 embryos and cerebellar spheroids from E10 embryos. Cell and fibre differentiation can be observed in all types of spheroids, however, it is most abundant in retinal spheroids. Moreover, only in retinal spheroids a histotypic organization can be detected. Using immunohistochemistry and electron microscopy, we assign this -at least partially- to the capacity of Müller cells to form radial scaffolds, since we observe a congruency between these radial scaffolds and the presence of rosettes formed by photoreceptor precursors and Müller cells. Tectal, telencephalic and cerebellar spheroids do not show organized radial glia scaffolds, instead, the radial glia cells are randomly arranged and the spheroids do not show histotypical organization. The application of the specific gliotoxin 6-aminonicotinamide to growing retinal spheroids leads to a significant decrease in the number and size of the rosettes. Concomitantly, the degree of histotypical organization is also drastically reduced. This organizing capacity of Müller cells in vitro now strongly suggests the presence of a comparable function also in vivo. Moreover, since non-retinal radial glia cells are not able to re-organize an histotypic organization in vitro, Müller cells seem to be qualitatively different from other radial glia cells. In future studies we want to untangle these differences.

Müller glia stabilizes cell columns during retinal development: lateral cell migration but not neuropil growth is inhibited in mixed chick-quail retinospheroids

Radial columnar organization of cell clones is a characteristic feature of vertebrate retinae that is structurally not understood. Here we provide in vitro evidence that Müller glia processes stabilize cells within columns. Dissociated embryonic chick retinal plus pigmented cells regenerate in vitro into fully laminated stratospheroids. After reaggregating chick and quail cells, quail-derived spheroid areas are detected as isolated sectors, as shown by a quail-specific antibody. Each sector contains one or multiple cell columns. The radial borders separating chick and quail sectors are fully congruent with the extension of 3A7-labelled Müller glia processes. While cell somata do not show any lateral interspecies mixing, quail-derived neuropil extends within the inner plexiform areas far into chick sectors. After selective damage of Müller cells by the gliotoxin DL-alpha-aminoadipic acid, the columnar organization is destabilized, as evidenced by a decrease in vimentin expression and by the migration of individual neurons out of their cell column. These data demonstrate that Müller cells actively stabilize cells within their columns, while neuritic growth is not hindered.