Integrative and comparative genomic analyses identify clinically relevant pulmonary carcinoid groups and unveil the supra-carcinoids.

The worldwide incidence of pulmonary carcinoids is increasing, but little is known about their molecular characteristics. Through machine learning and multi-omics factor analysis, we compare and contrast the genomic profiles of 116 pulmonary carcinoids (including 35 atypical), 75 large-cell neuroendocrine carcinomas (LCNEC), and 66 small-cell lung cancers. Here we report that the integrative analyses on 257 lung neuroendocrine neoplasms stratify atypical carcinoids into two prognostic groups with a 10-year overall survival of 88% and 27%, respectively. We identify therapeutically relevant molecular groups of pulmonary carcinoids, suggesting DLL3 and the immune system as candidate therapeutic targets; we confirm the value of OTP expression levels for the prognosis and diagnosis of these diseases, and we unveil the group of supra-carcinoids. This group comprises samples with carcinoid-like morphology yet the molecular and clinical features of the deadly LCNEC, further supporting the previously proposed molecular link between the low- and high-grade lung neuroendocrine neoplasms.

Plague: Bridging gaps towards better disease control.

After centuries of epidemics and more than a hundred years since the identification of the causative bacterium, very little is known about the plague dynamics in animal reservoirs, vectors and the changing vulnerabilities for humans. The recent plague epidemic in Madagascar in 2017 highlights these gaps existing within the knowledge of the disease dynamics, the factors influencing it, the performance of diagnostic tests and the best recommended treatment. As the eradication of plague will not be possible due to the widespread existence of the bacterium in wildlife, a One Health approach, drawing on animal, human and environmental health disciplines is needed to better control this poverty-related disease. This article focused on the various aspects of the disease for which more tools and better understanding are required to better control the disease in endemic countries.

Diagnostic accuracy of the Xpert® MTB/RIF cycle threshold level to predict smear positivity: a meta-analysis.

SETTING: Xpert® MTB/RIF is the most widely used molecular assay for rapid diagnosis of tuberculosis (TB). The number of polymerase chain reaction cycles after which detectable product is generated (cycle threshold value, CT) correlates with the bacillary burden.OBJECTIVE To investigate the association between Xpert CT values and smear status through a systematic review and individual-level data meta-analysis. DESIGN: Studies on the association between CT values and smear status were included in a descriptive systematic review. Authors of studies including smear, culture and Xpert results were asked for individual-level data, and receiver operating characteristic curves were calculated. RESULTS: Of 918 citations, 10 were included in the descriptive systematic review. Fifteen data sets from studies potentially relevant for individual-level data meta-analysis provided individual-level data (7511 samples from 4447 patients); 1212 patients had positive Xpert results for at least one respiratory sample (1859 samples overall). ROC analysis revealed an area under the curve (AUC) of 0.85 (95%CI 0.82-0.87). Cut-off CT values of 27.7 and 31.8 yielded sensitivities of 85% (95%CI 83-87) and 95% (95%CI 94-96) and specificities of 67% (95%CI 66-77) and 35% (95%CI 30-41) for smear-positive samples. CONCLUSION: Xpert CT values and smear status were strongly associated. However, diagnostic accuracy at set cut-off CT values of 27.7 or 31.8 would not replace smear microscopy. How CT values compare with smear microscopy in predicting infectiousness remains to be seen.

Emergence and dissemination of a linezolid-resistant Staphylococcus capitis clone in Europe.

Objectives: We investigated the epidemiological, clinical, microbiological and genetic characteristics of linezolid-resistant (LZR) Staphylococcus capitis isolates from French ICUs, and compared them with LZR S. capitis isolates from other European countries. Methods: All LZR isolates were subjected to antimicrobial susceptibility testing (AST) and the presence of cfr and optrA genes as well as mutations in the 23S rRNA and ribosomal proteins were investigated using specific PCR with sequencing. The genetic relationship between isolates was investigated using PFGE and WGS. Epidemiological data concerning LZR S. capitis were collected retrospectively in French microbiology laboratories. Results: Twenty-one LZR isolates were studied: 9 from France, 11 from Greece and 1 from Finland. All were resistant to methicillin and aminoglycosides. In addition, this unusual AST profile was identified in S. capitis isolates from seven French hospitals, and represented up to 12% of the S. capitis isolates in one centre. A G2576T mutation in 23S rRNA was identified in all isolates; cfr and optrA genes were absent. All isolates belonged to the same clone on the basis of their PFGE profiles, whatever their geographical origin. WGS found at most 212 SNPs between core genomes of the LZR isolates. Conclusions: We identified and characterized an LZR S. capitis clone disseminated in three European countries, harbouring the same multiple resistance and a G2576T mutation in the 23S rRNA. The possible unrecognized wider distribution of this clone, belonging to a species classically regarded as a low-virulence skin colonizer, is of major concern not least because of the increasing use of oxazolidinones.

Spontaneous ascitic fluid infection and bacteremia due to Yersinia pseudotuberculosis in a liver transplant patient.

We report herein a case of bacteremic ascitic fluid infection in a liver transplant patient caused by a strain of Yersinia pseudotuberculosis serogroup I that lost the yersiniabactin core. The patient's outcome was favorable after a combined therapy with a third-generation cephalosporin and gentamicin.

First case of cerebral abscess due to a novel Nocardia species in an immunocompromised patient.

We report the first case of cerebral abscess due to a novel species of Nocardia in a heart transplant patient and describe the antimicrobial susceptibility of this isolate. As our patient was intolerant to trimethoprim-sulfamethoxazole, we also discuss alternative therapeutic options in brain abscess due to Nocardia sp.

[Detection of extended-spectrum ß-lactamase-producing Enterobacteriaceae in rectal swabs with the Mastdiscs™ ID AmpC ßLSE detection set]. / Dépistage du portage digestif des entérobactéries productrices de ß-lactamase à spectre étendu par ensemencement direct des écouvillons rectaux à l'aide de la méthode Mastdiscs™ ID AmpC ßLSE.

OBJECTIVES: The double-disk synergy test was compared to the Mastdiscs™ ID AmpC and ESßL method for detection of ESßL production in rectal swab. METHODS: Two hundred and forty-nine rectal swabs were directly inoculated onto Mueller-Hinton plates and analyzed according to both methods. RESULTS: A total of 41 (16%) and 208 (84%) were positive and negative for ESßL, respectively. Twelve (29%) and 20 (49%) of the 41 rectal swabs positive for ESßL were detected after 24h of incubation with the double-disk synergy test and the Mastdiscs™ method, respectively (P=0.013). One hundred fifty-eight (76%) et 183 (88%) of the 208 rectal swabs were detected negative for ESßL after 24h of incubation with the double-disk synergy test and the Mastdiscs™ method, respectively (P<0.001). Finally, 79 (32%) and 46 (18%) rectal swabs respectively inoculated according to the double-disk synergy test and the Mastdiscs™ method were inconclusive after 24h of incubation. The better performance of the Mastdiscs™ method was due to an easier detection of cephalosporinase producing bacteria. CONCLUSIONS: The Mastdiscs™ method is a simple phenotypic method that detects more easily ESßL and non-ESßL producing bacteria in rectal swab.

Natural radioactive nuclides in some Tunisian thermo-mineral springs.

Radioactivity in some Tunisian thermo-mineral springs (11 hot mineral springs and one cold spring) has been determined for the first time in Tunisia using radiochemical separation procedures. The obtained results show that 238U activity concentrations vary between 1.5 and about 43 mBq/l. The measured activities of 234U and 226Ra range from 1.1 to about 82.2 mBq/l and 34-3,900 mBq/l. respectively. The radioactive disequilibria in these waters are in excess of concentration of 234U compared to that of 238U. The 226Ra/234U activity ratios are high and in the range of 9.0-691.0). U, Th and Ra activities are similar to those published for other non-polluted regions of the world. Radioactivity in the only cold mineral water from Aïn Oktor is very low, and thus health hazards due to the consumption of this water are not expected.

Study of the structure-activity relationships for the pyrazinamidase (PncA) from Mycobacterium tuberculosis.

In an attempt to investigate the molecular basis of pyrazinamide hydrolysis by the PncA protein from Mycobacterium tuberculosis, we determined the pyrazinamidase activity of nine PncA mutants bearing a single amino acid substitution. Among them, three mutants (D8G, K96T and S104R) had virtually no activity (< or =0.004 unit/mg), five (F13S, T61P, P69L, Y103S and A146V) retained a low level of activity (0.06-0.25 unit/mg) and one (T167L) exhibited a wild-type activity (1.51 units/mg). The possible structural effects of these substitutions were assessed by analysing a three-dimensional model of the PncA protein constructed on the basis of the crystal structure of the N-carbamoylsarcosine amidohydrolase (CSHase) from Arthrobacter sp., an amidohydrolase which was found by hydrophobic cluster analysis to be closely related to PncA. In the PncA model, five of the mutated residues, Asp-8, Phe-13, Lys-96, Tyr-103 and Ser-104, were located within a 6 A sphere around the cysteine residue Cys-138, which could be the counterpart of the active cysteine residue Cys-177 found in the CSHase. Among the remaining mutated residues, Thr-61, Pro-69 and Ala-146 were found to be more distant from Cys-138 but were associated with structural elements contributing to the catalytic centre, whereas Thr-167 was situated in an alpha-helix located far from the putative active site. These data suggest that the decrease in pyrazinamidase activity observed in the PncA mutant proteins is well correlated with the structural modifications the mutations can cause in the environment of the putative active cysteine Cys-138.

[Drug resistance in Mycobacterium tuberculosis: diagnostic methods]. / La résistance de Mycobacterium tuberculosis aux antituberculeux: méthodes diagnostiques.

The increasing frequency of multidrug-resistant strains of M. tuberculosis becomes dramatic in industrialized countries as well as in developing countries, particularly among patients infected with human immunodeficiency virus. It needs to formulate rapid strategies for diagnosing multidrug-resistant tuberculosis. For these new drug resistance, novel detection methods are developed in order to identify the resistant strains and to undertake efficacious antituberculosis therapies more rapidly. The phenotypic methods are based on the measurement of the microbial growth on nutritional supplement with antimicrobial agents; however, these proportional methods, such as the method in solid medium, the Bactec radiometric method or the MGIT method (mycobacterial growth indicator tube), are time consuming and give results in 5 to 21 days. In contrast, the genotypic tests, using knowledge of the genes involved in the resistance, reduce the time to detection of resistance from weeks to days. After amplification of the segment of the gene encoding the drug target by PCR, these methods are based on the identification of the different mutations conferring the antimicrobial resistance in M. tuberculosis. These methods are applied with success for detection of rifampicin resistance, conferring by mutations in a defined region of the rpoB gene for 99% of cases; on the contrary, results are less for other antituberculous drugs because of the insufficiency of knowledge of the molecular basis of drug resistance.

Characterization of new mutations in pyrazinamide-resistant strains of Mycobacterium tuberculosis and identification of conserved regions important for the catalytic activity of the pyrazinamidase PncA.

A new set of mutations, including transposition of the insertion sequence IS6110, was identified in the pncA gene from 19 pyrazinamide-resistant Mycobacterium tuberculosis strains. Alignment of the PncA protein from M. tuberculosis with homologous proteins from different bacterial species revealed three highly conserved regions in PncA which may play an important role in the processing of pyrazinamide.

Mycobacterium avium complex common-source or cross-infection in AIDS patients attending the same day-care facility.

To delineate the epidemiology of Mycobacterium avium complex (MAC) infection in acquired immunodeficiency syndrome patients, we studied 32 case patients with disseminated MAC infection who attended the same daycare facility during a period of 13 months. Pulsed-field gel electrophoresis analysis showed very low similarity between MAC strains, suggesting that, despite close contacts between the patients, nosocomial cross-transmission or exposure to a common source of MAC did not occur.

Use of DNA fingerprinting for primary surveillance of nosocomial tuberculosis in a large urban hospital: detection of outbreaks in homeless people and migrant workers.

SETTING: A large urban teaching hospital in the southeast of Paris. OBJECTIVE: Primary surveillance of nosocomial transmission of tuberculosis (TB) by systematic restriction fragment length polymorphism analysis (RFLP) of isolates (n = 161) recovered from smear-positive pulmonary TB patients identified from 1 March 1993 to 28 February 1994, and from all TB patients (with any form of tuberculous infection) identified from 1 March 1994 to 30 April 1995. RESULTS: Systematic RFLP analysis revealed 12 clusters of patients (n = 40) infected by strains of Mycobacterium tuberculosis showing matching RFLP patterns. None of the isolates were multidrug-resistant. Compared with non-clustered patients, clustered patients were more likely to be homeless (55% vs 19%, P < or = 0.001), or Africans living in hostels for migrant workers (20% vs 6%, P = 0.01), and had fewer previous admissions to hospital (12% vs 28%, P = 0.05). Further epidemiological investigations showed that the clustered TB cases actually resulted not from nosocomial transmission, but from transmission in the community, very likely in homeless shelters and hostels for migrant workers. CONCLUSION: No nosocomial transmission of TB was identified among the patients included during the study period. Systematic RFLP analysis using hospital-based sampling can detect the spread of TB in specific environments in the community where transmission is occurring.

Characterization of gentamicin-susceptible strains of methicillin-resistant Staphylococcus aureus involved in nosocomial spread.

We report an outbreak of epidemic Staphylococcus aureus strains characterized by an unusual heterogeneous resistance to methicillin and resistance to tobramycin but susceptibility to gentamicin (gentamicin-susceptible methicillin-resistant S. aureus [GS-MRSA]), contrasting with gentamicin-resistant homogeneous MRSA (GR-MRSA) that have been endemic in our hospital since the 1970s. A total of 97 GS-MRSA strains, which were shown by DNA hybridization to carry the mecA and ant(4')-Ia genes, were studied. The 40 GS-MRSA strains isolated at the beginning of the outbreak (January 1992 to June 1993) were typed by using resistance patterns, phage typing, serotyping, and pulsed-field gel electrophoresis and were compared with GR-MRSA and methicillin-susceptible S. aureus (MSSA) strains isolated during the same period. Two dominant clones, A::1 and B::3, and one minor clone, C::5, were identified among the 40 GS-MRSA strains, according to pulsotypes (A to C) and their resistance patterns (1, 3, and 5), which were distinguishable from those of GR-MRSA and MSSA strains. A selection of 57 GS-MRSA strains, isolated from 1994 to 1996, were clustered in the same three clones. However, their distribution had changed in comparison with that in the 1992 to 1993 period: clone A::1 remained dominant (47 versus 42.5%), whereas clone B::3 progressively declined (5 versus 35%) and clone C::5, the most susceptible to antibiotics, spread (44 versus 2.5%). Epidemiological investigations revealed that some clones had been introduced via patients transferred from other hospitals and that cross-infection occurred within and between wards. Major changes in the use of antibiotics, especially aminoglycosides, cyclines, and macrolides, likely played a role in the emergence and spread of GS-MRSA strains.

Nonradioactive single-strand conformation polymorphism analysis for detection of fluoroquinolone resistance in mycobacteria.

A simple, rapid, and nonradioactive method for routine detection of fluoroquinolone resistance in mycobacteria is described. A single-strand conformation polymorphism (SSCP) methodology, based on the use of mini-gels and silver staining of DNA, was optimized for the analysis of denatured DNA products obtained by polymerase chain reaction (PCR) from the gyrA gene involved in fluoroquinolone resistance in mycobacteria. The method was successfully applied to fluoroquinolone-susceptible and -resistant laboratory strains of Mycobacterium smegmatis and to clinical strains of Mycobacterium tuberculosis isolated from patients who developed resistance during the course of fluoroquinolone treatment.

Nosocomial transmission of tuberculosis among mentally-handicapped patients in a long-term care facility.

SETTING: A long-term care facility at Saint-Brieuc hospital, France. OBJECTIVE: To investigate a nosocomial outbreak of culture-positive pulmonary tuberculosis in 6 (40%) of 15 mentally handicapped HIV-seronegative patients. DESIGN: The factors contributing to the outbreak were analyzed and the restriction fragment length polymorphism (RFLP) patterns of the six Mycobacterium tuberculosis strains were compared. RESULTS: RFLP analysis of the six strains demonstrated an identical banding pattern, thus confirming the spread of a unique strain. A prolonged period of contagiousness due to a delay in diagnosis of the source patient, as well as crowded living conditions in the facility, probably contributed to the outbreak. Surveillance of residents and staff in contact with the source patient resulted in the detection of five secondary cases. Because effective isolation of mentally handicapped patients in the long-term care facility turned out to be difficult, the six case-patients were transferred to the pneumology department, thus limiting the spread of tuberculosis to other residents and staff. CONCLUSIONS: The present outbreak emphasizes the difficulties of implementing control measures for preventing the nosocomial transmission of tuberculosis in long-term care facilities for mentally handicapped patients.

[Analysis of restriction fragment length polymorphism (RFLP) of Mycobacterium tuberculosis strains isolated from patients with several episodes of tuberculosis]. / Analyse du polymorphisme de longueur des fragments de restriction (RFLP) de souches de Mycobacterium tuberculosis isolées de malades ayant fait plusieurs épisodes de tuberculose.

Analysis of restriction fragment length polymorphism (RFLP), using a DNA probe directed against the insertion sequence IS6110, was applied to strains of Mycobacterium tuberculosis successively isolated from four patients. In order to determine the cause of recurrence in these patients, the RFLP patterns of the corresponding isolated were analyzed. The profils obtained from the strains isolated from each of the patients were identical, thus suggesting that a relapse, rather than an exogenous reinfection with a new strain, was the cause of recurrence. The RFLP patterns of successive isolated remained unchanged during periods of time ranging from 5 months to 7 years, and were not modified after development of rifampin resistance. These results demonstrate the stability of the polymorphism detected by the IS6110 probe. Therefore, RFLP analysis is a powerfull epidemiologic tool to distinguish relapse from exogenous reinfection.