Fatal respiratory infection due to ST308 VIM-1-producing Pseudomonas aeruginosa in a lung transplant recipient: case report and review of the literature.

BACKGROUND: Data regarding the prevalence of metallo-ß-lactamases (MBLs) among Pseudomonas aeruginosa isolates in cystic fibrosis patients are scarce. Furthermore, there is limited knowledge on the effect of MBL production on patient outcomes. Here we describe a fatal respiratory infection due to P. aeruginosa producing VIM-type MBLs in a lung transplant recipient and the results of the subsequent epidemiological investigation. CASE PRESENTATION: P. aeruginosa isolates collected in the index patient and among patients temporally or spatially linked with the index patient were analyzed in terms of antibiotic susceptibility profile and MBL production. Whole-genome sequencing and phylogenetic reconstruction were also performed for all P. aeruginosa isolates producing VIM-type MBLs. A VIM-producing P. aeruginosa strain was identified in a lung biopsy of a lung transplant recipient with cystic fibrosis. The strain was VIM-1-producer and belonged to the ST308. Despite aggressive treatment, the transplant patient succumbed to the pulmonary infection due to the ST308 strain. A VIM-producing P. aeruginosa strain was also collected from the respiratory samples of a different cystic fibrosis patient attending the same cystic fibrosis center. This isolate harbored the blaVIM-2 gene and belonged to the clone ST175. This patient did not experience an adverse outcome. CONCLUSIONS: This is the first description of a fatal infection due to P. aeruginosa producing VIM-type MBLs in a lung transplant recipient. The circulation of P. aeruginosa isolates harboring MBLs pose a substantial risk to the cystic fibrosis population due to the limited therapeutic options available and their spreading potential.

Targeted genotyping by sequencing: a new way to genome profile the cat.

Targeted GBS is a recent approach for obtaining an effective characterization for hundreds to thousands of markers. The high throughput of next-generation sequencing technologies, moreover, allows sample multiplexing. The aims of this study were to (i) define a panel of single nucleotide polymorphisms (SNPs) in the cat, (ii) use GBS for profiling 16 cats, and (iii) evaluate the performance with respect to the inference using standard approaches at different coverage thresholds, thereby providing useful information for designing similar experiments. Probes for sequencing 230 variants were designed based on the Felis_catus_8.0. 8.0 genome. The regions comprised anonymous and non-anonymous SNPs. Sixteen cat samples were analysed, some of which had already been genotyped in a large group of loci and one having been whole-genome sequenced in the 99_Lives Cat Genome Sequencing Project. The accuracy of the method was assessed by comparing the GBS results with the genotypes already available. Overall, GBS achieved good performance, with 92-96% correct assignments, depending on the coverage threshold used to define the set of trustable genotypes. Analyses confirmed that (i) the reliability of the inference of each genotype depends on the coverage at that locus and (ii) the fraction of target loci whose genotype can be inferred correctly is a function of the total coverage. GBS proves to be a valid alternative to other methods. Data suggested a depth of less than 11× is required for greater than 95% accuracy. However, sequencing depth must be adapted to the total size of the targets to ensure proper genotype inference.

Combining Genome Surveillance and Metadata To Characterize the Diversity of Staphylococcus aureus Circulating in an Italian Hospital over a 9-Year Period.

Staphylococcus aureus is an opportunistic pathogen and a leading cause of morbidity and mortality worldwide. Genomic-based surveillance has greatly improved our ability to track the emergence and spread of high-risk clones, but the full potential of genomic data is only reached when used in conjunction with detailed metadata. Here, we demonstrate the utility of an integrated approach by leveraging a curated collection of clinical and epidemiological metadata of S. aureus in the San Matteo Hospital (Italy) through a semisupervised clustering strategy. We sequenced 226 sepsis S. aureus samples, recovered over a period of 9 years. By using existing antibiotic profiling data, we selected strains that capture the full diversity of the population. Genome analysis revealed 49 sequence types, 16 of which are novel. Comparative genomic analyses of hospital- and community-acquired infection ruled out the existence of genomic features differentiating them, while evolutionary analyses of genes and traits of interest highlighted different dynamics of acquisition and loss between antibiotic resistance and virulence genes. Finally, highly resistant clones belonging to clonal complexes (CC) 8 and 22 were found to be responsible for abundant infections and deaths, while the highly virulent CC30 was responsible for rare but deadly episodes of infections. IMPORTANCE Genome sequencing is an important tool in clinical microbiology, as it allows in-depth characterization of isolates of interest and can propel genome-based surveillance studies. Such studies can benefit from ad hoc methods of sample selection to capture the genomic diversity present in a data set. Here, we present an approach based on clustering of antibiotic resistance profiles that allows optimal sample selection for bacterial genomic surveillance. We apply the method to a 9-year collection of Staphylococcus aureus from a large hospital in northern Italy. Our method allows us to sequence the genomes of a large variety of strains of this important pathogen, which we then leverage to characterize the epidemiology in the hospital and to perform evolutionary analyses on genes and traits of interest. These analyses highlight different dynamics of acquisition and loss between antibiotic resistance and virulence genes.

[A case of mandibular chondrosarcoma]. / Su un caso di condrosarcoma mandibolare.

The Authors report a new case of chondrosarcoma of the mandible. After stressing the rarity of the tumour in the facial bones, they discuss the treatment problem. They propose a surgical approach as long as metastases are absent and recommend radio and chemotherapy just for palliation of advanced cases.

Evidences of precession and obliquity orbital forcing in oxygen-18 isotope composition of Montalbano Jonico section (Basilicata, southern Italy)

Quantitative signal processing methods have been applied to a delta(18)O profile for a land-based stratigraphic section, extending from the upper part of lower Pleistocene to the lower part of middle Pleistocene. The section is well exposed with a continuous succession of muds and muddy silts, about 400 m thick, located in the southernmost part of Bradano Trough, near Montalbano Jonico in Basilicata (south Italy). The sampled part of the section is about 240 m thick, in which a foram benthic species (Cassidulina carinata) is continuously available for oxygen isotope ratio measurements. The aim of the data treatment is to discover how much of the Earth's orbital periodic movements, precession and obliquity, which represent the dominant periodicities in paleoclimatic variations from the base of the Pleistocene until 0.735 Myr BP, are responsible for the oscillations observed in the oxygen-18 record of the Montalbano Jonico section. A time framework of the section was constructed on the basis of calcareous nannofossil biostratigraphic analyses, preliminary magnetostratigraphic results and oxygen isotope correlation with the record from DSDP s607 (isotope data collected in the NOAA World Data Center). The resulting time-scale extends from 1.15 to 0.74 Myr. Power spectrum analysis was performed on the isotope data to illuminate the most important periodicity components of the Montalbano Jonico record. The periodic components of 41,000 and 21,000 yr are present in this record; the former associated with periodic changes in the tilt of Earth's axis and the latter with periodic changes with the precession of the equinoxes, as predicted by the astronomical theory of ice ages. They are, however, not the most important components of the power spectrum, in which a lower frequency component contains most of the variance. This low-frequency component is centered at a period around 208,000 yr. This periodicity seems not to be attributable to any known astronomical or paleoclimatic phenomenon. An attempt was made to verify if this periodicity was due to the composite effect of precession and obliquity signals together at different frequencies from their forcing frequencies. In order to investigate this effect, isotope data have been parameterized in terms of a sum of simple functions of precession and obliquity signals with unknown coefficients. The coefficients are estimated from the time series with the assumption that the best coefficients are those which minimize the 'noise' i.e. the difference between the data function and the precession and obliquity functions. Cross-spectra analyses were also performed on the data and the precession signal and on the data and the obliquity signal. The power spectrum of the residual 'noise' functions and the cross-spectra demonstrate that precession and obliquity signals are not in phase with the data at their forcing frequencies and so damp. The precession and obliquity signals were then shifted towards lower frequencies at equally spaced lags, the resultant 'noise' power spectra were plotted for every combination of lags of precession and obliquity. The results of this data processing demonstrate that it is possible to have a combination of precession and obliquity cyclicities that could be responsible for the signal with 208 kyr periodicity.