NMNI editorial report, 2016

International audienc

Soft topographic map for clustering and classification of bacteria

In this work a new method for clustering and building a topographic representation of a bacteria taxonomy is presented. The method is based on the analysis of stable parts of the genome, the so-called “housekeeping genes”. The proposed method generates topographic maps of the bacteria taxonomy, where relations among different type strains can be visually inspected and verified. Two well known DNA alignement algorithms are applied to the genomic sequences. Topographic maps are optimized to represent the similarity among the sequences according to their evolutionary distances. The experimental analysis is carried out on 147 type strains of the Gammaprotebacteria class by means of the 16S rRNA housekeeping gene. Complete sequences of the gene have been retrieved from the NCBI public database. In the experimental tests the maps show clusters of homologous type strains and present some singular cases potentially due to incorrect classification or erroneous annotations in the database

Growth on blood agar discriminates Mycobacterium avium and Mycobacterium intracellulare

Mycobacterium intracellulare and Mycobacterium avium (MAC) require specialized culture and identification procedures. To simplify the diagnosis, we inoculated reference strains, and 85 M. avium and 12 M. intracellulare clinical isolates, on egg-based and sheep blood agar. After 5 days of culture, there were significantly more colonies on sheep blood than on egg-based agar for M. avium (ratio: 250.5 ± 209) but not for M. intracellulare (ratio: 0.44 ±0.11). Using a ratio ≥20, the sensitivity of the identification of an MAC isolate as M. avium was 97.65%, the specificity was 100%, and the positive predictive value was 100%. Differential growth on egg-based and blood agar is an aid to the identification of MAC isolates

High Throughput, Multiplexed Pathogen Detection Authenticates Plague Waves in Medieval Venice, Italy

Background: Historical records suggest that multiple burial sites from the 14th-16(th) centuries in Venice, Italy, were used during the Black Death and subsequent plague epidemics.Methodology/Principal Findings: High throughput, multiplexed real-time PCR detected DNA of seven highly transmissible pathogens in 173 dental pulp specimens collected from 46 graves. Bartonella quintana DNA was identified in five (2.9%) samples, including three from the 16th century and two from the 15th century, and Yersinia pestis DNA was detected in three (1.7%) samples, including two from the 14th century and one from the 16th century. Partial glpD gene sequencing indicated that the detected Y. pestis was the Orientalis biotype.Conclusions: These data document for the first time successive plague epidemics in the medieval European city where quarantine was first instituted in the 14th century

Potential changes to French recommendations about peri-prosthetic infections based on the international consensus meeting (ICMPJI)

AbstractBackgroundDespite the large volume of studies on the prevention, diagnosis, and treatment of peri-prosthetic infections, surgical practice often rests on limited scientific evidence in this field. The vast International Consensus Meeting on Peri-prosthetic Joint Infection (ICMPJI) held in 2013 produced robust recommendations.HypothesisFrench consensus conference recommendations show no major differences with ICMPJI recommendations.Materials and methodsThe 207 recommendations developed by 300 experts at the ICMPJI were translated, and the translation was then examined by four reviewers, including 2 having participated in the consensus conference. The reviewers looked for any differences with French practices and recommendations.ResultsTwenty-three major differences or innovations were identified compared to French recommendations and standard practice. Among them, pre-operative screening for nasal or urinary micro-organisms is performed routinely in France but should be reserved according to the ICMPJI for symptomatic patients and/or patients at high risk for infection. The ICMPJI emphasizes the role for the operating room environment as a vector for infection; more specifically, the operating lamp handle and suction cannula deserve close attention. A wound discharge persisting longer than 5–7 days requires irrigation and debridement. This procedure is effective only within the first 3 post-operative months and/or the first 3 weeks after symptom onset and must include exchange of all modular implants. The ICMPJI warns against both irrigation-debridement in fungal infections (suggesting two-stage prosthesis replacement) and one-stage replacement in patients with sinus tracts. The use of spacers (articulating at the knee) is recommended in the event of two-stage prosthesis replacement.DiscussionThe ICMPJI recommendations differed in many ways with French recommendations and standard practice. They can be expected to impact practices in France, although a point worth noting is that only 1 of the 207 recommendations received unanimous agreement by the conference experts (keeping operating room traffic to a minimum)

Evidence of a Louse-Borne Outbreak Involving Typhus in Douai, 1710-1712 during the War of Spanish Succession

Background: The new field of paleomicrobiology allows past outbreaks to be identified by testing dental pulp of human remains with PCR. Methods: We identified a mass grave in Douai, France dating from the early XVIII th century. This city was besieged during the European war of Spanish succession. We tested dental pulp from 1192 teeth (including 40 from Douai) by quantitative PCR (qPCR) for R. prowazekii and B. quintana. We also used ultra-sensitive suicide PCR to detect R. prowazekii and genotyped positive samples. Results and Discussion: In the Douai remains, we identified one case of B. quintana infection (by qPCR) and R. prowazekii (by suicide PCR) in 6/21 individuals (29%). The R. prowazekii was genotype B, a genotype previously found in a Spanish isolate obtained in the first part of the XX th century. Conclusion: Louse-borne outbreaks were raging during the XVIII th century; our results support the hypothesis that typhus was imported into Europe by Spanish soldiers from America

Status of the Micromegas semi-DHCAL

The activities towards the fabrication and test of a 1 m3 semi-digital hadronic calorime- ter are reviewed. The prototype sampling planes would consist of 1 m2 Micromegas chambers with 1 cm2 granularity and embedded 2 bits readout suitable for PFA calorime- try at an ILC detector. The design of the 1 m2 chamber is presented first, followed by an overview of the basic performance of small prototypes. The basic units composing the 1 m2 chamber are 32 \times 48 cm2 boards with integrated electronics and a micro-mesh. Results of character- ization tests of such boards are shown. Micromegas as a proportional detector is well suited for semi-digital hadronic calorimetry. In order to quantify the gain in perfor- mance when using one or more thresholds, simulation studies are being carried out, some of which will be reported in this contribution

Test in a beam of large-area Micromegas chambers for sampling calorimetry

Application of Micromegas for sampling calorimetry puts specific constraints on the design and performance of this gaseous detector. In particular, uniform and linear response, low noise and stability against high ionisation density deposits are prerequisites to achieving good energy resolution. A Micromegas-based hadronic calorimeter was proposed for an application at a future linear collider experiment and three technologically advanced prototypes of 1$\times$1 m$^{2}$ were constructed. Their merits relative to the above-mentioned criteria are discussed on the basis of measurements performed at the CERN SPS test-beam facility