Mycobacterium tuberculosis and Mycobacterium leprae have remained, for many years, the primary species of the genus Mycobacterium of clinical and microbiological interest. The other members of the ...genus, referred to as nontuberculous mycobacteria (NTM), have long been underinvestigated. In the last decades, however, the number of reports linking various NTM species with human diseases has steadily increased and treatment difficulties have emerged. Despite the availability of whole genome sequencing technologies, limited effort has been devoted to the genetic characterization of NTM species. As a consequence, the taxonomic and phylogenetic structure of the genus remains unsettled and genomic information is lacking to support the identification of these organisms in a clinical setting. In this work, we widen the knowledge of NTMs by reconstructing and analyzing the genomes of 41 previously uncharacterized NTM species. We provide the first comprehensive characterization of the genomic diversity of NTMs and open new venues for the clinical identification of opportunistic pathogens from this genus.
Prompt identification of bloodstream pathogens is essential for optimal management of patients. Significant changes in analytical methods have improved the turnaround time for laboratory diagnosis. ...Less attention has been paid to the time elapsing from blood collection to incubation and to its potential effect on recovery of pathogens. We evaluated the performance of blood cultures collected under typical hospital conditions in relation to the length of their pre-analytical time.
We carried out a large retrospective study including 50,955 blood cultures collected, over a 30-month period, from 7,035 adult septic patients. Cultures were accepted by the laboratory only during opening time (Mon-Fri: 8am-4pm; Sat: 8am-2pm). Samples collected outside laboratory hours were stored at room temperature at clinical wards. All cultures were processed by automated culture systems. Day and time of blood collection and of culture incubation were known for all samples.
A maximum pre-analytical interval of 2 hours is recommended by guidelines. When the laboratory was open, 57% of cultures were processed within 2 h. When the laboratory was closed, 4.9% of cultures were processed within 2 h (P<0.001). Samples collected when the laboratory was closed showed pre-analytical times significantly longer than those collected when laboratory was open (median time: 13 h and 1 h, respectively, P<0.001). The prevalence of positive cultures was significantly lower for samples collected when the laboratory was closed compared to open (11% vs 13%, P<0.001). The probability of a positive result decreased of 16% when the laboratory was closed (OR:0.84; 95%CI:0.80-0.89, P<0.001). Further, each hour elapsed from blood collection to incubation resulted associated with a decrease of 0.3% (OR:0.997; 95%CI:0.994-0.999, P<0.001) in the probability of a positive result.
Delayed insertions of cultures into automated systems was associated with lower detection rates, with potentially important consequences for patients. In each hospital setting the logistic factors able to shorten pre-analytical time should be carefully investigated and specifically targeted.
Objectives To identify the source of postnatal colonization with group B Streptococcus (GBS) and to evaluate the impact of intrapartum antibiotic prophylaxis (IAP) administration in newborn infant ...transmission. Study design A prospective, longitudinal study evaluated GBS colonization in 160 mother-baby pairs. Specimens were collected from the time of delivery to 8 weeks post-partum, from rectum, vagina, and milk of mothers, and from throat and rectum of neonates. Women were grouped according to their GBS status at discharge from the hospital: culture-positive carriers (n = 83), culture-negative carriers (n = 26), and noncarriers (n = 51). Newborns were considered colonized if GBS was yielded from at least 1 site. Results A total of 35 (21.9%) neonates were colonized; 30 were born to culture-positive carriers, 2 to culture-negative carriers, and 3 to noncarriers. Infants of culture-positive carriers exposed to IAP were less likely to be colonized (15/57 vs 15/26, P = .01), or heavily colonized, (7/57 vs 9/26, P = .04). Of all newborns, those exposed to IAP and discharged GBS-free from hospital, often became colonized subsequently (12/57 vs 1/26, P = .09). Molecular typing analysis (available for 30 of 32 carrier mothers and their infants) confirmed an identical strain of GBS in all mother-baby pairs. Six of 83 culture-positive carrier mothers had a positive milk culture. Their respective neonates all were heavily colonized. Conclusions Newborns exposed to IAP and GBS-free at hospital discharge subsequently acquire GBS from their mothers. Culture-positive milk is associated with heavy neonatal colonization.
Background: Immunocompromised persons infected with Mycobacterium tuberculosis (MTB) have increased risk of tuberculosis (TB) reactivation, but their management is hampered by the occurrence of ...false-negative
results of the tuberculin skin test (TST). The T-cell interferon (IFN)-γ release blood assays T-SPOT. TB (TS.TB) Oxford Immunotec; Abingdon, UK and QuantiFERON-TB Gold In-Tube (QFT-IT) Cellestis Ltd; Carnegie, VIC, Australia
might improve diagnostic accuracy for latent TB infection (LTBI) in high-risk persons, although their performance in different
groups of immunocompromised patients is largely unknown.
Methods and results: Over a 1-year period, we prospectively enrolled patients in three different immunosuppressed groups, as follows: 120 liver
transplantation candidates (LTCs); 116 chronically HIV-infected persons; and 95 patients with hematologic malignancies (HMs).
TST, TS.TB, and QFT-IT were simultaneously performed, their results were compared, and intertest agreement was evaluated.
Overall, TST provided fewer positive results (10.9%) than TS.TB (18.4%; p < 0.001) and QFT-IT (15.1%; p = 0.033). Significantly
fewer HIV-infected individuals had at least one positive test (9.5%) compared with LTCs (35.8%; p < 0.001) and patients with
HMs (29.5%; p < 0.001). Diagnostic agreement between tests was moderate (κ = 0.40 to 0.65) and decreased in the HIV-infected
group when the results of the TS.TB were compared with either TST (κ = 0.16) or QFT-IT (κ = 0.19). Indeterminate blood test
results due to low positive control values were significantly more frequent with QFT-IT (7.2%) than with TS.TB (0.6%; p <
0.001).
Conclusions: Blood tests identified significantly more patients as being infected with MTB than TST, although diagnostic agreement varied
across groups. Based on these results, we recommend tailoring application of the new blood IFN-γ assays for LTBI in different
high-risk groups and advise caution in their current use in immunosuppressed patients.
Fourteen mycobacterial strains isolated from pulmonary samples of independent patients in the state of Pará (Brazil), and three strains isolated in Italy, were characterized using a polyphasic ...approach. Thorough genetic investigation, including whole-genome sequencing, demonstrated that the strains belong to the M. simiae complex, being most closely related to Mycobacterium interjectum . For 14 of the strains, evidence emerged supporting their inclusion in a previously unreported species of the genus Mycobacterium , for which the name Mycobacterium paraense sp. nov. is proposed (type strain, IEC26 ᵀ = DSM 46749 ᵀ = CCUG 66121 ᵀ). The novel species is characterized by slow growth, unpigmented or pale yellow scotochromogenic colonies, and a HPLC mycolic acid profile different from other known mycobacteria. In different genetic regions, high sequence microheterogeneity was detected.
Abstract Purpose The aim of this prospective observational study was to evaluate in patients with sepsis not requiring intensive care unit admission the relationship between the levels of endotoxin ...activity assay (EAA) early after sepsis recognition and the risk of development of organ dysfunction (OD). Methods Endotoxin activity assay levels were drawn immediately after sepsis identification (baseline) and at 6, 24, and 48 hours postbaseline in 50 patients with signs of sepsis of a duration of less than 24 hours. An EAA 0.60 units or greater was considered as highly elevated. Results Logistic regression showed independent association between EAA levels at baseline and the appearance of new OD (adjusted odd ratio, 2.41; 95% confidence interval, 1.18-4.90; P < .05). Fifteen patients (30%) who developed new OD after baseline had at least 1 EAA level 0.60 or greater. The adjusted linear regression analysis showed that across the 4 time points, EAA levels were significantly higher in patients who developed new OD (0.11; 95% confidence interval, 0.01-0.20; P < .05). Conclusions Endotoxin activity assay levels 0.60 or greater early after sepsis diagnosis in patients not requiring intensive care unit admission predict risk of development of new organ dysfunction. High EAA levels in the first 48 hours of recognition of sepsis are also predictive of risk of deterioration.
The new phylogenesis of the genus Mycobacterium Tortoli, Enrico; Fedrizzi, Tarcisio; Pecorari, Monica ...
International journal of mycobacteriology,
03/2015, Letnik:
4, Številka:
5
Journal Article
Recenzirano
Odprti dostop
Abstract Phylogenetic knowledge of the genus Mycobacterium is based on comparative analysis of their genetic sequences. The 16S rRNA has remained for many years the only target of such analyses, but ...in the last few years, other housekeeping genes have been investigated and the phylogeny based on their concatenated sequences become a standard. It is now clear that the robustness of the phylogenetic analysis is strictly related to the size of the genomic target used. Whole genome sequencing (WGS) is nowadays becoming widely accessible and comparatively cheap. It was decided, therefore, to use this approach to reconstruct the ultimate phylogeny of the genus Mycobacterium . Over 50 types of strains of the same number of species of Mycobacterium were sequenced using the Illumina HiSeq platform. The majority of the strains of which the whole sequence was already available in GenBank were excluded from this panel with the aim of maximizing the number of the species with genome available. Following assembling and annotation with proper software, the phylogenetic analysis was conducted with PhyloPhlAn and the pan-genome analysis pipeline. The phylogenetic three which emerged was characterized by a clear-cut distinction of slowly and rapidly growing species with the latter being more ancestral. The species of the Mycobacterium terrae complex occupied an intermediate position between rapid and slow growers. Most of the species revealed clearly related and occupied specific phylogenetic branches. Thanks to the WGS technology, the genus Mycobacterium is finally approaching its definitive location.
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