This study characterizes xylan degradation by two major species of the human intestine.

Identification of bacterial species is a crucial bottleneck for clinical diagnosis of infectious diseases. Quick and reliable identification is a key factor to provide suitable antibiotherapies and avoid the development of multiple-drug resistance. We propose a novel nuclear magnetic resonance (NMR)-based metabolomics strategy for rapid discrimination and identification of several bacterial species that relies on untargeted metabolic profiling of supernatants from bacterial culture media. We show that six bacterial species (Gram negative: Escherichia coli, Pseudomonas aeruginosa, Proteus mirabilis; Gram positive: Enterococcus faecalis, Staphylococcus aureus, and Staphylococcus saprophyticus) can be well discriminated from multivariate statistical analysis, opening new prospects for NMR applications to microbial clinical diagnosis.

No abstract

Tuberculosis (TB) is a universal disease: it occurs all over the globe, albeit with hugely varying regional incidence. Especially in Asian and African countries, the incidence and prevalence may be extremely high. The European Journal of Clinical Microbiology and Infectious Diseases published seven papers on TB in 2013, representing 3.3 % (7/211) of its annual production. Four of the papers concerned mechanistic studies on clinical patient management, cost-effectiveness of antibiotic treatment, importance of microbiota and host genetic polymorphisms, respectively. The other three papers concerned molecular diagnostics, so, overall, hardly any attention was paid to the more classical modes of diagnosing TB. And this clearly contrasts with international needs, since classical diagnostics is still very high on the agenda in those countries where TB testing is most needed. In their 2013 Global Tuberculosis Report, the World Health Organization (WHO) claimed that culture is still the reference method for the detection of Mycobacterium tuberculosis (Mtb), with smear staining and microscopy being considered as a method of "added value". Hence, a wide array of culture systems has been developed by a large multitude of researchers and companies. Some of these are semi-automated, but most require manual intervention. Löwenstein-Jensen medium (LJ) is frequently considered the key mycobacterial growth medium when comparative studies for the verification and validation of new diagnostic tests are performed. Even the validation of liquid media in combination with semi-automated culture systems is usually performed in comparison with LJ-based cultivation as the diagnostic Gold Standard.We have set out to investigate the quality of some of the culture media proposed for the detection of Mtb in order to verify whether such media really are the appropriate Gold Standard tools for the validation of novel TB diagnostics. We performed a literature search (PubMed dd 13 August 2013) for the period between January 2008 and August 2013. In this way, 71 relevant articles were identified, of which the 19 most complete studies were selected for more detailed analysis. We collected the number of specimens tested, the culture medium used and identified, where possible, the manufacturer of the media. As such, six different producers of culture media for Mtb detection were identified. When microscopic observation of drug susceptibility (MODS) was performed, we included these data as well.Overall, the highest sensitivities and negative predictive values were shown by the BACTEC MGIT 960 System (Becton-Dickinson, Sparks, MD, USA), either when used alone or in combination with LJ. The latter combination provided the best sensitivity and also scored particularly well in the detection of non-tuberculous mycobacteria. The highest specificity and positive predictive values were shown by the LJ method itself, which obviously produced no falsepositives. So, MGIT is the top performer with regard to sensitivity, while LJ sets the current standard for spe...

Klebsiella pneumoniae is a major cause of severe healthcare-associated infections and often shows MDR phenotypes. Carbapenem resistance is frequent, and colistin represents a key molecule to treat infections caused by such isolates. Here we evaluated the antimicrobial resistance (AMR) mechanisms and the genomic epidemiology of clinical K. pneumoniae isolates from Serbia. Consecutive non-replicate K. pneumoniae clinical isolates (n = 2,298) were collected from seven hospitals located in five Serbian cities and tested for carbapenem resistance by disk diffusion. Isolates resistant to at least one carbapenem (n = 426) were further tested for colistin resistance with Etest or Vitek2. Broth microdilution (BMD) was performed to confirm the colistin resistance phenotype, and colistin-resistant isolates (N = 45, 10.6%) were characterized by Vitek2 and whole genome sequencing. Three different clonal groups (CGs) were observed: CG101 (ST101, N = 38), CG258 (ST437, N = 4; ST340, N = 1; ST258, N = 1) and CG17 (ST336, N = 1). mcr genes, encoding for acquired colistin resistance, were not observed, while all the genomes presented mutations previously associated with colistin resistance. In particular, all strains had a mutated MgrB, with MgrB C28S being the prevalent mutation and associated with ST101. Isolates belonging to ST101 harbored the carbapenemase OXA-48, which is generally encoded by an IncL/M plasmid that was no detected in our isolates. MinION sequencing was performed on a representative ST101 strain, and the obtained long reads were assembled together with the Illumina high quality reads to decipher the bla OXA-48 genetic background.