Whole genome sequencing provides better delineation of transmission clusters in Mycobacterium tuberculosis than traditional methods. However, its ability to reveal individual transmission links ...within clusters is limited. Here, we used a 2-step approach based on Bayesian transmission reconstruction to (1) identify likely index and missing cases, (2) determine risk factors associated with transmitters, and (3) estimate when transmission happened.
We developed our transmission reconstruction method using genomic and epidemiological data from a population-based study from Valencia Region, Spain. Tuberculosis (TB) incidence during the study period was 8.4 cases per 100,000 people. While the study is ongoing, the sampling frame for this work includes notified TB cases between 1 January 2014 and 31 December 2016. We identified a total of 21 transmission clusters that fulfilled the criteria for analysis. These contained a total of 117 individuals diagnosed with active TB (109 with epidemiological data). Demographic characteristics of the study population were as follows: 80/109 (73%) individuals were Spanish-born, 76/109 (70%) individuals were men, and the mean age was 42.51 years (SD 18.46). We found that 66/109 (61%) TB patients were sputum positive at diagnosis, and 10/109 (9%) were HIV positive. We used the data to reveal individual transmission links, and to identify index cases, missing cases, likely transmitters, and associated transmission risk factors. Our Bayesian inference approach suggests that at least 60% of index cases are likely misidentified by local public health. Our data also suggest that factors associated with likely transmitters are different to those of simply being in a transmission cluster, highlighting the importance of differentiating between these 2 phenomena. Our data suggest that type 2 diabetes mellitus is a risk factor associated with being a transmitter (odds ratio 0.19 95% CI 0.02-1.10, p < 0.003). Finally, we used the most likely timing for transmission events to study when TB transmission occurred; we identified that 5/14 (35.7%) cases likely transmitted TB well before symptom onset, and these were largely sputum negative at diagnosis. Limited within-cluster diversity does not allow us to extrapolate our findings to the whole TB population in Valencia Region.
In this study, we found that index cases are often misidentified, with downstream consequences for epidemiological investigations because likely transmitters can be missed. Our findings regarding inferred transmission timing suggest that TB transmission can occur before patient symptom onset, suggesting also that TB transmits during sub-clinical disease. This result has direct implications for diagnosing TB and reducing transmission. Overall, we show that a transition to individual-based genomic epidemiology will likely close some of the knowledge gaps in TB transmission and may redirect efforts towards cost-effective contact investigations for improved TB control.
Limitations associated with linear-array probes in photoacoustic tomography are partially compensated by using advanced beamformers that exploit the temporal and spatial coherence of the recorded ...signals, such as Delay Multiply and Sum (DMAS), Minimum Variance (MV) or coherence factor (CF), among others. However, their associated signal processing leads to an overestimation of the spatial resolution, as well as alterations in the reconstructed object size. Numerical and experimental results reported here support this hypothesis. First, we show that the Rayleigh criterion (RC) is the most suitable choice to characterize the spatial resolution instead of the Point Spread Function (PSF) when considering advanced beamformers. Then, we observe that several advanced beamformers fail to properly reconstruct target sizes slightly above the spatial resolution, underestimating their size. This work sheds light on the suitability of this type of beamformers combined with linear probes for determining sizes and morphology in photoacoustic images.
Pulsed Laser Diodes (PLD) are compact and high pulse repetition rate laser sources that show a great potential for low-cost Optical Resolution Photoacoustic Microscopes (OR-PAM). Nevertheless, their ...non-uniform multimode laser beams are of low quality so that high lateral resolutions with tightly focused beams are difficult to realize at long focusing distances, as required for reflection mode OR-PAM devices of clinical application. A new strategy based on homogenizing and shaping the laser diode beam with a square-core multimode optical fiber allowed to attain competitive lateral resolutions while keeping one centimeter working distance. The theoretical expressions for the laser spot size, determining optical lateral resolution, and the depth of focus are also written for general multimode beams. An OR-PAM system was built in confocal reflection mode with a linear phased-array as the ultrasound receiver in order to test its performance, first, on a resolution test target and, afterwards, on ex vivo rabbit ears to show the system potential for subcutaneous imaging of blood vessels and hair follicles.
•Low-cost laser diode and multimode optical fiber for optoacoustic microscopy.•Laser diode beam homogenization and shaping for lateral resolution enhancement.•Reflection mode with centimeter laser working distance and linear phased-array.•Resolution tests and deep skin images of blood vessels and hair follicles ex vivo.•Lateral resolution and depth of focus general expressions for multimode beams.
Abstract Purpose The purpose of the study was to determine the independent risk factors on mortality in patients with community-acquired severe sepsis and septic shock. Methods A single-site ...prospective cohort study was carried out in a medical-surgical intensive care unit in an academic tertiary care center. One hundred twelve patients with community-acquired bloodstream infection with severe sepsis and septic shock were identified. Clinical, microbiologic, and laboratory parameters were compared between hospital survivors and hospital deaths. Results One-hundred twelve patients were included. The global mortality rate was 41.9%, 44.5% in septic shock and 34.4% in severe sepsis. One or more comorbidities were present in 66% of patients. The most commonly identified bloodstream pathogens were Escherichia coli (25%) and Staphylococcus aureus (21.4%). The proportion of patients receiving inadequate antimicrobial treatment was 8.9%. By univariate analysis, age, Acute Physiology and Chronic Health Evaluation II score, at least 3 organ dysfunctions, and albumin, but neither microbiologic characteristics nor site of infection, differed significantly between survivors and nonsurvivors. Acute Physiology and Chronic Health Evaluation II (odds ratio, 1.13; 95% confidence interval, 1.06-1.21) and albumin (odds ratio, 0.34; 95% confidence interval, 0.15-0.76) were independent risk factors associated with global mortality in logistic regression analysis. Conclusion In addition to the severity of illness, hypoalbuminemia was identified as the most important prognostic factor in community-acquired bloodstream infection with severe sepsis and septic shock.
To report a case of infectious necrotizing scleritis secondary to Aspergillus terreus after intravitreal injection therapy.
This is a case report with literature review.
A 98-year-old woman receiving ...intravitreal aflibercept injections for neovascular age-related macular degeneration in the left eye presented with severe pain, redness, and purulent discharge at the injection site. She was initially treated with topical fortified antibiotics, and clinical improvement was achieved, although microbial cultures showed negative results. Two months later, she presented with severe ocular pain and was diagnosed with anterior necrotizing scleritis. Scleral scrapings were collected for cultures, and intensive topical antibiotic therapy was reintroduced. Evaluation for autoimmune etiology and microbiological testing showed negative results. Because of the progression of the scleral necrotic area, empirical therapy with topical voriconazole was initiated, and surgical debridement was performed. Finally, the culture was positive for A. terreus. The modified therapy consisted of topical voriconazole and oral voriconazole for 3 months with an excellent clinical outcome.
To our knowledge, this is the first case of fungal necrotizing scleritis secondary to intravitreal injection. Diagnosis was delayed due to its chronic clinical course and the slow fungal growth in culture media, but the combined medical and surgical approach resulted in a satisfactory outcome.
Poor outcomes of invasive candidiasis (IC) are associated with the difficulty in establishing the microbiological diagnosis at an early stage. New scores and laboratory tests have been developed in ...order to make an early therapeutic intervention in an attempt to reduce the high mortality associated with invasive fungal infections. Candida albicans IFA IgG has been recently commercialized for germ tube antibody detection (CAGTA). This test provides a rapid and simple diagnosis of IC (84.4% sensitivity and 94.7% specificity). The aim of this study is to identify the patients who could be benefited by the use of CAGTA test in critical care setting.
A prospective, cohort, observational multicentre study was carried out in six medical/surgical Intensive care units (ICU) of tertiary-care Spanish hospitals. Candida albicans Germ Tube Antibody test was performed twice a week if predetermined risk factors were present, and serologically demonstrated candidiasis was considered if the testing serum dilution was ≥ 1:160 in at least one sample and no other microbiological evidence of invasive candidiasis was found.
Fifty-three critically ill non-neutropenic patients (37.7% post surgery) were included. Twenty-two patients (41.5%) had CAGTA-positive results, none of them with positive blood culture for Candida. Neither corrected colonization index nor antifungal treatment had influence on CAGTA results. This finding could corroborate that the CAGTA may be an important biomarker to distinguish between colonization and infection in these patients. The presence of acute renal failure at the beginning of the study was more frequent in CAGTA-negative patients. Previous surgery was statistically more frequent in CAGTA-positive patients.
This study identified previous surgery as the principal clinical factor associated with CAGTA-positive results and emphasises the utility of this promising technique, which was not influenced by high Candida colonization or antifungal treatment. Our results suggest that detection of CAGTA may be important for the diagnosis of invasive candidiasis in surgical patients admitted in ICU.
In June, 2021, WHO published the most complete catalogue to date of resistance-conferring mutations in Mycobacterium tuberculosis. Here, we aimed to assess the performance of genome-based ...antimicrobial resistance prediction using the catalogue and its potential for improving diagnostics in a real low-burden setting.
In this retrospective population-based genomic study M tuberculosis isolates were collected from 25 clinical laboratories in the low-burden setting of the Valencia Region, Spain. Culture-positive tuberculosis cases reported by regional public health authorities between Jan 1, 2014, and Dec 31, 2016, were included. The drug resistance profiles of these isolates were predicted by the genomic identification, via whole-genome sequencing (WGS), of the high-confidence resistance-causing variants included in the catalogue and compared with the phenotype. We determined the minimum inhibitory concentration (MIC) of the isolates with discordant resistance profiles using the resazurin microtitre assay.
WGS was performed on 785 M tuberculosis complex culture-positive isolates, and the WGS resistance prediction sensitivities were: 85·4% (95% CI 70·8-94·4) for isoniazid, 73·3% (44·9-92·2) for rifampicin, 50·0% (21·1-78·9) for ethambutol, and 57·1% (34·0-78·2) for pyrazinamide; all specificities were more than 99·6%. Sensitivity values were lower than previously reported, but the overall pan-susceptibility accuracy was 96·4%. Genotypic analysis revealed that four phenotypically susceptible isolates carried mutations (rpoB Leu430Pro and rpoB Ile491Phe for rifampicin and fabG1 Leu203Leu for isoniazid) known to give borderline resistance in standard phenotypic tests. Additionally, we identified three putative resistance-associated mutations (inhA Ser94Ala, katG Leu48Pro, and katG Gly273Arg for isoniazid) in samples with substantially higher MICs than those of susceptible isolates. Combining both genomic and phenotypic data, in accordance with the WHO diagnostic guidelines, we could detect two new multidrug-resistant cases. Additionally, we detected 11 (1·6%) of 706 isolates to be monoresistant to fluoroquinolone, which had been previously undetected.
We showed that the WHO catalogue enables the detection of resistant cases missed in phenotypic testing in a low-burden region, thus allowing for better patient-tailored treatment. We also identified mutations not included in the catalogue, relevant at the local level. Evidence from this study, together with future updates of the catalogue, will probably lead in the future to the partial replacement of culture testing with WGS-based drug susceptibility testing in our setting.
European Research Council and the Spanish Ministerio de Ciencia.
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