Rapid Tuberculosis Diagnostics Including Molecular First- and Second-Line Resistance Testing Based on a Novel Microfluidic DNA Extraction Cartridge.

Xpert MTB/RIF testing has improved tuberculosis (TB) diagnostics and rifampicin (Rif) resistance testing worldwide. However, it has weaknesses, such as its restriction to Rif resistance testing and the inability to use extracted DNA for further testing. Herein, a holistic diagnostic workflow, including TB detection and resistance testing toward Rif, isoniazid, and important second-line drugs (SLDs), based on a novel microfluidic DNA extraction cartridge (TB-Disk), is presented. DNA from 73 precharacterized sputum samples was extracted with TB-Disk, including 45 clinical and bacteriologically confirmed TB samples, nine TB-negative samples, and 19 sputum samples spiked with twofold dilutions of TB bacteria. The extracted DNA was subjected to further testing with FluoroType MTB (FT-MTB), GenoType MTBDRplus (GT-plus), and GenoType MTBDRsl. A total of 100% (20/20) and 72% (18/25) of smear-positive and smear-negative TB samples were identified as Mycobacterium tuberculosis complex positive. A total of 79% (33/42) of subsequently GT-plus tested samples yielded a valid result. Eight samples were identified as multidrug-resistant TB by GT-plus and further tested for resistance toward SLDs using GenoType MTBDRsl, yielding 75% (6/8) valid results. FT-MTB with cartridge-based DNA extraction (Disk-DNA) and DNA extracted with FluoroLyse yielded similar analytical sensitivities. FT-MTB with Disk-DNA was 100% specific. TB-Disk in combination with FT-MTB enables sensitive TB detection. The Disk-DNA can be further used for screening resistance toward first-line drugs and SLDs.

A non-coding RNA from the intercellular adhesion (ica) locus of Staphylococcus epidermidis controls polysaccharide intercellular adhesion (PIA)-mediated biofilm formation.

Polysaccharide intercellular adhesin (PIA)-associated biofilm formation is mediated by the intercellular adhesin (ica) locus and represents a major pathomechanism of Staphylococcus epidermidis. Here, we report on a novel long non-coding (nc)RNA, named IcaZ, which is approximately 400 nucleotides in size. icaZ is located downstream of the ica repressor gene icaR and partially overlaps with the icaR 3' UTR. icaZ exclusively exists in ica-positive S. epidermidis, but not in S. aureus or other staphylococci. Inactivation of the gene completely abolishes PIA production. IcaZ is transcribed as a primary transcript from its own promoter during early- and mid-exponential growth and its transcription is induced by low temperature, ethanol and salt stress. IcaZ targets the icaR 5' UTR and hampers icaR mRNA translation, which alleviates repression of icaADBC operon transcription and results in PIA production. Interestingly, other than in S. aureus, posttranscriptional control of icaR mRNA in S. epidermidis does not involve icaR mRNA 5'/3' UTR base pairing. This suggests major structural and functional differences in icaADBC operon regulation between the two species that also involve the recruitment of ncRNAs. Together, the IcaZ ncRNA represents an unprecedented novel species-specific player involved in the control of PIA production in NBSP S. epidermidis.

Hypervariability of biofilm formation and oxacillin resistance in a Staphylococcus epidermidis strain causing persistent severe infection in an immunocompromised patient.

We report on a leukemic patient who suffered from a persistent, generalized, and eventually fatal Staphylococcus epidermidis infection during prolonged aplasia. Over a 6-week period, we isolated a genetically and phenotypically unstable S. epidermidis strain related to an epidemic clone associated with hospital infections worldwide. Strikingly, the strain showed a remarkable degree of variability, with evidence of selection and increasing predominance of biofilm-producing and oxacillin-resistant variants over time. Thus, in the early stages of the infection, the strain was found to generate subpopulations which had spontaneously lost the biofilm-mediating ica locus along with the oxacillin resistance-conferring mecA gene. These deletion mutants were obviously outcompeted by the ica- and mecA-positive wild-type genotype, with the selection and predominance of strongly biofilm-forming and oxacillin-resistant variants in the later stages of the infection. Also, a switch from protein- to polysaccharide intercellular adhesin/poly-N-acetylglucosamine (PIA/PNAG)-mediated-biofilm production was detected among ica-positive variants in the course of the infection. The data highlight the impact of distinct S. epidermidis clonal lineages as serious nosocomial pathogens that, through the generation and selection of highly pathogenic variants, may critically determine disease progression and outcome.

Success through diversity - how Staphylococcus epidermidis establishes as a nosocomial pathogen.

Staphylococcus epidermidis normally is a commensal inhabitant of the healthy human skin and mucosa, but also a common nosocomial pathogen in immunocompromised patients. Living at the edge between commensalism and pathogenicity, S. epidermidis has developed interesting strategies to conquer the hospital environment as a novel ecological niche and to transform into a notorious pathogen. Recent progress in genome analysis and molecular epidemiology gave interesting insights into the enormous flexibility by which these bacteria generate continuously novel phenotypic and genotypic variants. Recent multilocus sequence typing studies identified S. epidermidis as a highly diverse species that evolves mainly by recombination and acquires readily mobile genetic elements. With respect to healthcare-associated isolates, a limited number of epidemic clonal lineages were found to have emerged and established in hospital settings worldwide. These isolates are characterised by the carriage of various SCCmec gene cassettes, conferring methicillin resistance, and by a striking ability to form biofilms on medical devices. Moreover, nosocomial S. epidermidis strains typically harbour multiple copies of the insertion sequence element IS256 in their genomes. Nosocomial S. epidermidis strains vary virulence- and resistance-associated gene expression in the course of an infection to a remarkably high degree. Heterogenous gene expression in S. epidermidis is achieved, on the one hand, by complex regulatory pathways. On the other hand, it is associated with genetic mechanisms that were found to be mediated by the action of the IS256 element which obviously represents an important driving force for the flexibility of the S. epidermidis genome. The data accumulated so far suggest that recombination along with the frequent acquisition of mobile genetic elements are crucial factors for the success of S. epidermidis as a nosocomial pathogen.

Identification of specific genes in Staphylococcus aureus strains associated with bovine mastitis.

Staphylococcus aureus is a common cause of bovine mastitis that is responsible for the main economic loss to the dairy industry. For identification of putative, bovine-specific molecular marker a genome comparison between bovine S. aureus strain RF122 and 52 previously sequenced S. aureus isolates associated with human infections using genome viewer, annotation tool Artemis Comparison Tool (ACT), KEGG and NCBI BLAST databases was carried out. This led to the identification of 16 unique RF122 gene sequences that may be used as molecular marker to distinguish bovine from human strains. The distribution of these genes was analyzed in a collection of bovine mastitis strains from the Netherlands and human clinical isolates by PCR and Southern blotting. Only four genes within the pathogenicity island SaPIbov3 (sab1890, sab1891, sab1892, sab1893) were present in the majority of isolates from cattle but were absent from human clinical S. aureus isolates. These results suggest that there is no gene/ORF uniformly shared by all bovine S. aureus strains that could be uniformly used as a diagnostic marker gene.

Nosocomial infections by Staphylococcus epidermidis: how a commensal bacterium turns into a pathogen.

Staphylococcus epidermidis is a commensal bacterium of the human skin. However, S. epidermidis and other coagulase-negative staphylococci (CNS) emerge also as common nosocomial pathogens infecting immunocompromized patients carrying medical devices. Antibiotic resistance and the ability of many nosocomial S. epidermidis isolates to form biofilms on inert surfaces make these infections hard to treat. Epidemiological analyses using multilocus sequence typing (MLST) and genetic studies suggest that S. epidermidis isolates in the hospital environment differ from those obtained outside of medical facilities with respect to biofilm formation, antibiotic resistance, and the presence of mobile DNA elements. Since S. epidermidis isolates exhibit high genome flexibility, they are now regarded as reservoirs for the evolution and spread of resistance traits within nosocomial bacterial communities.