Pitfalls associated with the use of molecular diagnostic panels in the diagnosis of cryptococcal meningitis

Abstract We report the case of a kidney transplantation patient on chronic immunosuppressive therapy presenting with subacute meningitis. The final diagnosis of cryptococcal meningitis was delayed due to 2 false-negative cryptococcal results on a molecular diagnostic panel. Caution with such platforms in suspected cryptococcal meningitis is needed.</jats:p

Topical decolonization does not eradicate the skin microbiota of community-dwelling or hospitalized adults

Topical antimicrobials are often employed for decolonization and infection prevention and may alter the endogenous microbiota of the skin. The objective of this study was to compare the microbial communities and levels of richness and diversity in community-dwelling subjects and intensive care unit (ICU) patients before and after the use of topical decolonization protocols. We enrolled 15 adults at risk for Staphylococcus aureus infection. Community subjects (n = 8) underwent a 5-day decolonization protocol (twice daily intranasal mupirocin and daily dilute bleach-water baths), and ICU patients (n = 7) received daily chlorhexidine baths. Swab samples were collected from 5 anatomic sites immediately before and again after decolonization. A variety of culture media and incubation environments were used to recover bacteria and fungi; isolates were identified using matrix-assisted laser desorption ionization–time of flight mass spectrometry. Overall, 174 unique organisms were recovered. Unique communities of organisms were recovered from the community-dwelling and hospitalized cohorts. In the community-dwelling cohort, microbial richness and diversity did not differ significantly between collections across time points, although the number of body sites colonized with S. aureus decreased significantly over time (P = 0.004). Within the hospitalized cohort, richness and diversity decreased over time compared to those for the enrollment sampling (from enrollment to final sampling, P = 0.01 for both richness and diversity). Topical antimicrobials reduced the burden of S. aureus while preserving other components of the skin and nasal microbiota

Peregrine Falcon Survey, West Greenland, 1972

... The main purpose of the 1972 survey was to study a sample area of West Greenland to supply baseline data about peregrine falcons from which future surveys could determine the status and trends of this bird in Greenland. The main part of the study had as its goals: 1) to determine the density, distribution, and reproductive success of nesting peregrines in a sample area; 2) to band all peregrine nestlings found; 3) to determine prey species of the peregrine; 4) to make interspecific observations of peregrines and gyrfalcons; 5) to make detailed observations from a blind of a sample peregrine falcon eyrie; 6) to conduct a small-bird census in the area of the sample eyrie; 7) to make a photographic record in colour slides and movies of the investigations. ... Eight peregrine falcon eyries and 3 gyrfalcon eyries were found in the survey area. In all, 18 nestlings were found in the 8 peregrine eyries. Of the 8 eyries, 1 had no young, but showed signs of occupancy ... and was defended by an aggressive pair of falcons. Of the other 7 eyries where we found hatched young, 1 had 4 young, 4 had 3 young, and 2 had 1 young bird each. Of the total of 18 nestling peregrines, 13 were banded and 5 were fully-fledged, on the wing, and unable to be caught for banding. Of the peregrine nestlings banded, 9 were males and 4 were females. The number of nestlings (18) in the 8 peregrine eyries gave a production rate of 2.25 per eyrie, or 2.57 if an average is taken of the 7 eyries actually producing young. At 1 eyrie a young falcon was found dead (the eyrie with 4 young). We know that at least 8 of the remaining 17 young fledged successfully, but we are uncertain about the success of the others and cannot therefore make a definite statement on fledging ratio. We estimate, however, that the fledging rate of the peregrines in our survey area was at least 2.00 per producing eyrie. The maximum dimensions of our irregularly-shaped survey area were 39 x 34 miles (63 x 55 km). The estimated area of the survey was about 800 sq. mi. (2,072 sq. km), or about 700 sq. mi. (1,800 sq. km) when the surface area of fiords and lakes is excluded. The nesting density of the active, young-producing peregrine eyries (7) was about 1 pair per 100 sq. mi. (260 sq. km). ... At the 3 gyrfalcon (Falco rusticolus) eyries we found 8 nestlings or fully-fledged young, of which we were able to band 3. Peregrines and gyrfalcons (and a rare white-tailed sea eagle, Haliaetus albicilla) are the only avian predators nesting in southern West Greenland, although ravens (Corvus corax) competed for some nesting cliff sites. We collected remains of prey species and pellets at each falcon eyrie. Addled eggs (2) from 2 peregrine eyries were collected for pesticide analysis. Eggshell fragments for thickness determination were gathered at 5 peregrine eyries. ... Peregrine falcons in West Greenland appear to be in a healthy state as evidenced by a high nesting density (1/100 sq. mi.) and a high production rate (2.25/eyrie), especially in light of the unusually severe conditions in West Greenland during the winter and late spring of 1971-72. We found little interspecific competition for prey species between peregrines and gyrfalcons. The gyrfalcon is already nesting in West Greenland before the peregrines arrive from their winter migration to the south. The gyrfalcons could therefore be expected to be aggressive in defence of their nesting cliffs and thereby occupy optimal cliffs. Despite this, all the peregrines we studied occupied high, sheer, and quite optimal nesting cliffs. Gyrfalcons seemed to prefer a nesting site lower down on a cliff face than peregrines, and both falcons preferred high, sheer cliffs with a southern exposure. Ravens were relegated to lower, less desirable (more accessible) cliffs for nesting. We await pesticide analysis of the peregrine falcon eggs and prey species collected, as well as eggshell thickness determination. Before these facts are determined we can say nothing definite about the status of peregrines in Greenland. Nesting density and production, however, suggest that the status of the peregrine is better in Greenland than in other areas of the north. ..

Falcon Research in Greenland, 1973

... During the summer of 1972 a research team initiated the first in-depth study of the peregrine falcon (Falco peregrinus) in West Greenland. Eight eyries (nests) of this endangered species were located in an inland sample area of 700 sq. mi. Detailed observations were taken of peregrine breeding behaviour at one eyrie. Seven of the eyries produced young, containing an average of 2.57 young per successful eyrie. This high reproductive rate indicates a healthy population, but analyses of 2 addled eggs revealed high p,p'-DDE as well as polychlorinated biphenyl (PCB) residues and eggshell fragments from 9 eggs showed a 14 per cent decrease in thickness compared with 42 eggs collected in Greenland before the introduction of DDT into the environment. ... The [1973] survey area consisted of 900 sq. mi. (2,330 sq. km.), including ice-cap, lakes, fjords, and other unsuitable habitat totalling about 150 sq. mi. (388 sq. km.). We found 10 occupied peregrine falcon nesting cliffs in the survey area in 1973. ... 9 eyries produced young. Of these 9, 7 were also successful in 1972, while another was occupied throughout the season by an aggressive pair, and at the ninth a lone female mildly defended the cliff. Of the 9 producing eyries in 1973, 1 contained 4 young, 5 contained 3 young each, 2 had 2 young each, and 1 held 1 young. This gives a total of 24 young peregrines and a production rate of 2.4 young per occupied eyrie, or 2.67 young per successful eyrie. These young were counted at advanced ages varying from 2.5 weeks to just before fledging. It is believed that all or almost all fledged. We found 1 occupied eyrie per 90 sq. mi. (233 sq. km.), or 1 successful eyrie per 100 sq. mi. (260 sq. km.). All young were banded with a metal band on the left tarsus and a red plastic band on the right. ... The colour bands signify the beginning of an international peregrine colour banding system established for quick geographical identification of banding locality. During the 2 summers, 9 gyrfalcon nesting cliffs were located in the survey area. We believe that at least 6 of the 9 locations were occupied in 1972. In 1973, 8 of the 9 cliffs were checked. Young were found at 4 sites. A fifth was observed from an aircraft and appeared to be active. Lone adults were observed at 2 other locations. Seven young gyrfalcons were banded out of 10 young found. One nest site was inaccessible and the young were not banded, accounting for the difference in number located and banded. The production rate per producing pair of gyrfalcons was 2.50 young. ... Our sample survey indicates that in 1973, as in 1972, the peregrine falcon reproduced normally in West Greenland. The slightly higher production rate in 1973 can possibly be attributed to warmer temperatures during the nesting period, as the summer of 1972 was unseasonably cool. However, the 1972 data on eggshell thinning and high DDE and PCB residues reveal that this population is precariously balanced, and severe reproductive failure threatens. Analysis of the 1973 addled egg and measurement of the additional eggshell fragments will supplement the 1972 results to provide a larger data base. ..

Innovative and rapid antimicrobial susceptibility testing systems

Antimicrobial resistance (AMR) is a major threat to human health worldwide, and the rapid detection and quantification of resistance, combined with antimicrobial stewardship, are key interventions to combat the spread and emergence of AMR. Antimicrobial susceptibility testing (AST) systems are the collective set of diagnostic processes that facilitate the phenotypic and genotypic assessment of AMR and antibiotic susceptibility. Over the past 30 years, only a few high-throughput AST methods have been developed and widely implemented. By contrast, several studies have established proof of principle for various innovative AST methods, including both molecular-based and genome-based methods, which await clinical trials and regulatory review. In this Review, we discuss the current state of AST systems in the broadest technical, translational and implementation-related scope

Genetic factors are important determinants of impaired growth after infant cardiac surgery

ObjectivesWe sought to estimate the prevalence and identify the predictors of impaired growth after infant cardiac surgery.MethodsWe performed a secondary analysis of a prospective study of the role of apolipoprotein E gene polymorphisms on neurodevelopment in young children after infant cardiac surgery. Prevalence estimates for growth velocity were derived by using anthropometric measures (weight and head circumference) obtained at birth and at 4 years of age. Genetic evaluation was also performed. Growth measure z scores were calculated by using World Health Organization Child Growth Standards. Growth velocity was evaluated by using 2 different techniques: first by clustering the children into one of 3 growth velocity subgroups based on z scores (impaired growth, difference < −0.5 standard deviation; stable growth, difference of −0.5 to 0.5 standard deviation; and improving growth, difference > 0.5 SD) and second by using continuous difference scores. Statistical analyses were conducted with a combination of proportional odds models for the ordered categories and simple linear regression for the continuous outcomes.ResultsThree hundred nineteen full-term subjects had complete anthropometric measures for weight and head circumference at birth and 4 years. The cohort was 56% male. Genetic examinations were available for 97% (309/319) of the cohort (normal, 74%; definite or suspected genetic abnormality, 26%). Frequency counts for weight categories were as follows: impaired growth, 37%; stable growth, 31%; and improving growth, 32%. Frequency counts for head circumference categories were as follows: impaired growth, 39%; stable growth, 28%; and improving growth, 33%. The presence of a definite or suspected genetic syndrome (P = .04) was found to be a predictor of impaired growth for weight but not for head circumference. When growth z scores were used as continuous outcomes, the apolipoprotein E ε2 allele was found to be predictive of lower z scores for both weight (P = .02) and head circumference (P = .03).ConclusionsImpaired growth for both weight and head circumference is common (both >30%) in this cohort of children after infant cardiac surgery. Both the apolipoprotein E ε2 allele and the presence of a definite or suspected genetic syndrome were associated with impaired weight growth velocity. The apolipoprotein E ε2 allele was also associated with impaired growth velocity for head circumference. Persistent poor growth might have long-term implications for the health and development of children with congenital heart defects

Prospective screening for postoperative deep venous thrombosis in patients undergoing infrainguinal revascularization

AbstractPurpose: The incidence of deep venous thrombosis (DVT) in patients undergoing infrainguinal bypass graft procedures has not been well documented, and the need for routine prophylaxis remains controversial. The purpose of this study was to prospectively evaluate the risk of postoperative DVT complicating infrainguinal revascularization. Methods: Seventy-four patients undergoing infrainguinal bypass graft procedures during a 12-month period were prospectively screened for DVT. Bilateral lower extremity venous duplex scan imaging was performed preoperatively and within 1 week and 6 weeks, postoperatively. Routine DVT prophylaxis was not used, with anticoagulation reserved for specific indications. Results: Of the 74 patients screened, three patients (4.1%) had DVT identified on preoperative venous duplex scan imaging and were excluded from the study. Of the remaining 71 patients enrolled, only two patients (2.8%) had postoperative DVT. Postoperative DVT was ipsilateral to the bypass graft extremity in both patients, with involvement of the peroneal vein in one patient and the femoral vein in the other. Although routine prophylaxis was not used, 18 of these patients (25%) were anticoagulated for other indications, with DVT occurring in one patient (5.6%). Of the remaining 53 patients who did not receive postoperative anticoagulation, only one patient (1.8%) had DVT. Conclusions: According to this prospective study, the risk of postoperative DVT in patients undergoing infrainguinal revascularization is low. Routine prophylaxis is not recommended, with postoperative anticoagulation reserved for specific indications. (J Vasc Surg 2000;32:669-75.

Improving Characterization of Understudied Human Microbiomes Using Targeted Phylogenetics.

Whole-genome bacterial sequences are required to better understand microbial functions, niche-specific bacterial metabolism, and disease states. Although genomic sequences are available for many of the human-associated bacteria from commonly tested body habitats (e.g., feces), as few as 13% of bacterium-derived reads from other sites such as the skin map to known bacterial genomes. To facilitate a better characterization of metagenomic shotgun reads from underrepresented body sites, we collected over 10,000 bacterial isolates originating from 14 human body habitats, identified novel taxonomic groups based on full-length 16S rRNA gene sequences, clustered the sequences to ensure that no individual taxonomic group was overselected for sequencing, prioritized bacteria from underrepresented body sites (such as skin and respiratory and urinary tracts), and sequenced and assembled genomes for 665 new bacterial strains. Here, we show that addition of these genomes improved read mapping rates of Human Microbiome Project (HMP) metagenomic samples by nearly 30% for the previously underrepresented phylum Fusobacteria, and 27.5% of the novel genomes generated here had high representation in at least one of the tested HMP samples, compared to 12.5% of the sequences in the public databases, indicating an enrichment of useful novel genomic sequences resulting from the prioritization procedure. As our understanding of the human microbiome continues to improve and to enter the realm of therapy developments, targeted approaches such as this to improve genomic databases will increase in importance from both an academic and a clinical perspective.IMPORTANCE The human microbiome plays a critically important role in health and disease, but current understanding of the mechanisms underlying the interactions between the varying microbiome and the different host environments is lacking. Having access to a database of fully sequenced bacterial genomes provides invaluable insights into microbial functions, but currently sequenced genomes for the human microbiome have largely come from a limited number of body sites (primarily feces), while other sites such as the skin, respiratory tract, and urinary tract are underrepresented, resulting in as little as 13% of bacterium-derived reads mapping to known bacterial genomes. Here, we sequenced and assembled 665 new bacterial genomes, prioritized from a larger database to select underrepresented body sites and bacterial taxa in the existing databases. As a result, we substantially improve mapping rates for samples from the Human Microbiome Project and provide an important contribution to human bacterial genomic databases for future studies

Descending thoracic aorta to iliofemoral artery bypass grafting: A role for primary revascularization for aortoiliac occlusive disease?

AbstractPurpose: Bypass grafts that originate from the descending thoracic aorta to the iliac or femoral arteries are well described but are not commonly used as primary procedures, and the long-term results remain unknown. A 15-year experience with 50 descending thoracic aorta to iliofemoral artery bypass grafts for aortoiliac occlusive disease is the basis of this report. Methods: From January 1983 to December 1997, patients who underwent bypass grafting procedures from the descending thoracic aorta to the iliac or femoral arteries were identified. Surgical indications, morbidity and mortality rates, primary and secondary patency rates, limb salvage rates, and survival rates were determined. Results: Fifty descending thoracic aorta to iliofemoral artery bypass grafting procedures were performed—24 (48%) for severe claudication, 22 (44%) for rest pain, and 4 (8%) for ischemic ulceration. A primary procedure was performed in 31 patients (62%) for complete occlusion (21 patients) and severe atherosclerotic disease (10 patients) of the infrarenal aorta. The indications for 19 secondary revascularizations (38%) were prior aortic or extra-anatomic graft failure in 17 cases and aortic graft infection in 2 cases. The follow-up periods ranged from 1 to 150 months (mean, 39 months). The cumulative life-table 5-year primary patency, secondary patency, limb salvage, and survival rates were 79%, 84%, 93%, and 67%, respectively. An improved patency trend was observed for patients who underwent operation for severe claudication as compared with limb-threatening ischemia (92% and 69%; P = .07). However, there was no difference between primary and secondary operations in primary patency rates (81% and 79%; P = NS) or survival rates (72% and 62%; P = NS). Conclusion: Descending thoracic aorta to iliofemoral artery bypass grafting has excellent overall long-term results. These results support its more liberal use for primary revascularization, especially for patients with severe atherosclerotic disease or complete occlusion of the infrarenal aorta. (J Vasc Surg 1999;29:249-58.