The implementation and utility of clinical exome sequencing in a South African infant cohort

Genetic disorders are significant contributors to infant hospitalization and mortality globally. The early diagnosis of these conditions in infants remains a considerable challenge. Clinical exome sequencing (CES) has shown to be a successful tool for the early diagnosis of genetic conditions, however, its utility in African infant populations has not been investigated. The impact of the under-representation of African genomic data, the cost of testing, and genomic workforce shortages, need to be investigated and evidence-based implementation strategies accounting for locally available genetics expertise and diagnostic infrastructure need to be developed. We evaluated the diagnostic utility of singleton CES in a cohort of 32 ill, South African infants from two State hospitals in Johannesburg, South Africa. We analysed the data using a series of filtering approaches, including a curated virtual gene panel consisting of genes implicated in neonatal-and early childhood-onset conditions and genes with known founder and common variants in African populations. We reported a diagnostic yield of 22% and identified seven pathogenic variants in the NPHS1, COL2A1, OCRL, SHOC2, TPRV4, MTM1 and STAC3 genes. This study demonstrates the utility value of CES in the South African State healthcare setting, providing a diagnosis to patients who would otherwise not receive one and allowing for directed management. We anticipate an increase in the diagnostic yield of our workflow with further refinement of the study inclusion criteria. This study highlights important considerations for the implementation of genomic medicine in under-resourced settings and in under-represented African populations where variant interpretation remains a challenge.

Bacteriophage therapy for refractory Pseudomonas aeruginosa urinary tract infection

We describe the success of adjunctive bacteriophage therapy for refractory Pseudomonas aeruginosa urinary tract infection in the context of bilateral ureteric stents and bladder ulceration, after repeated failure of antibiotics alone. No bacteriophage-resistant bacteria arose, and the kinetics of bacteriophage and bacteria in urine suggest self-sustaining and self-limiting infection.

Comparison of blood pressure measured at the arm, ankle and calf

SUMMARY

The suitability of alternative sites for non-invasive blood pressure (NIBP) measurement was investigated in 100 awake healthy volunteers. The calf and the ankle were chosen for comparison with the arm, and the results analysed subjected to Bland-Altman analysis. Discomfort was graded using a Visual Analogue Scale. There was a poor agreement between the different sites with respect to systolic blood pressure: the agreement was closer for diastolic and mean measurements. The mean blood pressure calf measurement was on average 4 mmHg (95% limits of agreement -12 to 20), higher than the arm. The ankle was 8 mmHg higher (-8 to 24) than the arm. ANOVA demonstrated a statistically significant difference in the discomfort scores between the sites (p < 0.001). The calf demonstrated the highest discomfort score and the ankle the lowest. We suggest that the ankle should be considered in preference to the calf as an alternative site for NIBP measurement if use of an arm is undesirable or impossible.

Relationship of tibial speed of sound and lower limb length to nutrient intake in preterm infants

BACKGROUND

Metabolic bone disease of prematurity is characterised by impaired postnatal mineralisation of the rapidly growing infant skeleton.

OBJECTIVE

To longitudinally evaluate postnatal changes in tibial speed of sound (tSOS; which reflects cortical thickness and bone mineral density) and lower limb length (LLL; a measure of tibial growth) in very low birthweight preterm infants receiving contemporary neonatal care.

METHODS

tSOS and LLL were measured using a quantitative ultrasound device and an electronic neonatal knemometer, respectively, in the same limb, weekly, for a median period of four weeks (3-16 weeks) in 84 preterm infants (median gestation 26.8 weeks (range 23-35.2 weeks) and median birth weight 869.5 g (range 418-1481 g)).

RESULTS

Initial tSOS and LLL were correlated with gestation (r = 0.42, p<0.001; r = 0.76, p<0.001, respectively) and birth weight (r = 0.23, p = 0.038; r = 0.93, p<0.001, respectively). Postnatally, tSOS decreased (r = -0.15, p = 0.011) whereas LLL increased (r = 0.96, p<0.001) with age. The rate of postnatal change in LLL, but not in tSOS, was positively influenced by intake of calcium (p = 0.03), phosphorus (p = 0.01) and vitamin D (p = 0.03).

CONCLUSIONS

The postnatal decline in tSOS, which is probably due to cortical thinning secondary to endocortical bone loss, and increase in LLL provide new insight into the development of long bones in preterm infants.

The role of preoperative templating in total knee arthroplasty: comparison of three prostheses

Templating of preoperative radiographs is routinely recommended prior to knee arthroplasty. We performed this study to assess the reproducibility and accuracy of the templates for three commonly used knee implants (PFC, Kinemax, Scorpio). Six lower limb surgeons templated 10 patients for each of the three designs. The inter- and intra-observer reliability and accuracy was calculated. There was marked variation in the reliability of the templating with the tibial insert scoring better than the femoral and the Kinemax being the most reproducible of the three. In general, the intra-observer scores (kappa=0.57-0.81) were better than the inter-observer ones (kappa=0.21-0.60). The Scorpio was the most accurately templated of the three implants, with the percentage correlating with what was actually implanted ranging from 55% to 62% for the femur and 72% to 75% for the tibia, with no templated sizes more than one size different from the actual implant. The other implants ranged from 38% to 42% for the femur and 53% to 58% for the tibia with both having up to 3% more than 1 size difference from the actual implant. We believe that the use of templating in total knee arthroplasty should be interpreted with caution and we urge the development of more accurate prosthesis sizing techniques.

Living with discordance: knowledge, challenges, and prevention strategies of HIV-discordant couples in Uganda

Prevalence of HIV-discordance among couples in sub-Saharan Africa is high. Negative partners are at high risk of HIV infection but few HIV/AIDS service providers have developed effective counseling messages for HIV-discordant couples. To identify clients' explanations for discordance, challenges, and prevention strategies, 24 in-depth interviews and 4 focus group discussions were conducted with 32 female and 35 male members of HIV-discordant couples who sought HIV voluntary counseling and testing (VCT) in Uganda. In addition, counselor explanations for discordance were gathered from 62 counselor trainers during 3 interactive workshops. Misconceptions about discordance were widespread among clients and counselors. Common explanations included: the concept of a hidden infection not detectable by HIV tests, belief in immunity, the thought that gentle sex protected HIV-negative partners, and belief in protection by God. Such explanations for discordance reinforced denial of HIV risk for the negative partner within discordant couples and potentially increased transmission risk. Couples identified negotiation of sexual relations as their most formidable challenge. Prevention strategies included condom use, abstinence and separation of beds, contractual agreements for outside sexual partners, and relationship cessation. Discordant couples represent a critical risk group and improved counseling protocols that clearly explain discordance, emphasize high risk of transmission, and support risk reduction are urgently needed.

Multiplex PCR for screening of integrons in bacterial lysates

Bacterial integrons are a useful PCR amplification target in epidemiological surveys of bacterial antibiotic resistance, and a variety of primers have been published. We describe multiplex PCR methodology to test for classes 1, 2 and 3 integron-associated integrases in boiled lysates of Gram-negative bacteria. We report on performance in Acinetobacter spp. (n=50), Enterobacteriaceae (n=76), Pseudomonas aeruginosa (n=15), Bacteroidesspp. (n=69), and in undifferentiated mixed cultures derived from perineal swabs (n=50) and endotracheal aspirates (n=8). This method achieved 100% sensitivity and specificity in simple lysates made from a range of bacteria, without requiring DNA extraction, and is recommended as an efficient screening tool for surveys of integron cassettes.

Limited diversity among human isolates of Bartonella henselae

A study of 59 isolates of Bartonella henselae reveals relatively limited diversity among those of human origin (n = 28). Either of two distinct alleles of both gltA and 16S ribosomal DNA (rDNA) was found in all isolates, with a high level of congruity between 16S and gltA inheritance among proven human pathogens. Human isolates from all over Eastern Australia were most commonly 16S rDNA (Bergmans) type I, with the same gltA allele as the type strain (Houston-1). Comparable feline isolates were more commonly 16S type II, with less congruity of inheritance between 16S and gltA alleles. Previously described arbitrarily primed PCR and EagI-HhaI infrequent restriction site PCR fingerprinting techniques separated Bartonella species effectively but lacked discriminating power within B. henselae. Examination of the 16-23S intergenic spacer region revealed for several strains several point mutations as well as a repeat sequence of unknown significance which is readily detected by HaeIII restriction fragment length polymorphism analysis. The bacteriophage-associated papA gene was present in all isolates. Enterobacterial repetitive intergenic consensus PCR proved to be a useful and robust typing tool and clearly separated human isolates (including imported strains) from the majority of feline isolates. Our data are consistent with published evidence and with previous suggestions of intragenomic rearrangements in the type strain and suggest that human isolates come from a limited subset of B. henselae strains. They strengthen arguments for careful exploration of genotype-phenotype relationships and for the development of a multilocus enzyme electrophoresis and multilocus sequence typing-based approach to the phylogeny of B. henselae.

Failure to detect Bartonella henselae infection in synovial fluid from sufferers of chronic arthritis

Bartonella henselae causes granulomatous and indolent infection in the immune competent human, and angioproliferation in the context of persistent infection and impaired immunity. This bacterium is found in up to 40% of household cats, from which humans acquire it by either a cat scratch or a bite (hence the name, cat-scratch disease). Approximately 5% of Australian and US blood donors have serological evidence of past infection, but most associated illnesses are mild or subclinical. A number of lines of evidence prompted us to consider a relationship between rheumatoid arthritis (RA) and Bartonella infection. These include epidemiological associations with household pet exposure; apparent responsiveness of some RA cases to tetracycline therapy; the granulomatous and angioproliferative nature of Bartonella lesions; the insidiousness and high seroprevalence of this infection in the community; and even reported Bartonella infection mimicking juvenile RA. In a small group of patients with chronic arthritides, we found no direct evidence of humoral antibodies to, nor of persistent infection with, Bartonella henselae in synovial fluid. While larger and more invasive studies are likely to provide more confident exclusions of this hypothesis, this suggests that persistent Bartonella infection is unlikely to play a major role in RA.

Food poisoning. Causes, remedies, and prevention

Food producers and consumers must continue to take precautions against foodborne diseases, and early diagnosis and appropriate treatment of these illnesses are essential. Food products and water can become contaminated with microorganisms and toxins that make people ill, and the very young, the elderly, and immunocompromised individuals are especially susceptible. Education of healthcare providers, food handlers, and the public is critical in reducing the incidence and spread of foodborne illness. Changes in eating habits and lifestyle and increased availability of both domestic and imported foods have made food hazards a more complex public health issue. Although most foodborne illnesses can be avoided by safe food handling procedures (see box on page 134), risk reduction is very important at every step from source to table. A concerted effort is needed to ensure continuing safety of the food supply in the United States while also assuring access to a wide variety of healthful foods. Time will tell whether consumers will accept irradiation of meats. If accepted, irradiation could rank in importance with pasteurization of milk and chlorination of water as a public health measure.

Rapid HIV testing with same-day results: a field trial in Uganda

Rapid, on-site HIV testing with same-day results may improve services and increase the number of clients who learn their serostatus in developing countries. To validate test performance under field conditions and assess the change in the proportion of clients who learn their serostatus, we conducted a field trial using the Capillus HIV-1/HIV-2 assay (Cambridge Diagnostics) at the AIDS Information Centre counselling and testing sites in Uganda. Compared to the standard 2-EIA testing algorithm, the sensitivity of Capillus was 99.6% (95% CI; 98.5%, 99.9%), the specificity was 98.8% (95% CI; 98.1%, 99.3%), the positive predictive value was 96.5% (95% CI; 94.5%, 97.8%), and the negative predictive value was 99.9% (95% CI; 99.5%, 100%). It took less than 5 min to perform a single test, and results were returned to clients in less than an hour, during which time clients were counselled. This resulted in a 27% increase in the proportion of clients who learned their serostatus and received counselling. We conclude that simple, rapid HIV tests can be performed accurately on-site within the time frame of a clinic visit, increasing the number of clients who learn their serostatus and receive post-test counselling.

The hydrophobic domains in the carboxyl-terminal signal for GPI modification and in the amino-terminal leader peptide have similar structural requirements

Proteins having a glycosyl-phosphatidylinositol (GPI) membrane anchor are synthesized with a carboxyl-terminal signal that is cleaved in the endoplasmic reticulum prior to GPI modification. The signal is characterized by a moderately hydrophobic domain downstream from the cleavage/modification site. The essential features of this domain were characterized using a truncated version of folate receptor (FR) type beta (FR-beta delta 5) in which its five carboxyl-terminal amino acid residues were deleted without affecting the efficiency of GPI modification. The amino acids at various positions in the hydrophobic domain were systematically altered and the extent of GPI modification of the recombinant proteins was determined by measuring [3H]folic acid binding at the cell surface, by Western blot analysis and from the sensitivity of the proteins to phosphatidylinositol-specific phospholipase C (PI-PLC). The results indicate that a threshold level of hydrophobicity exists at a single position below which the efficiency of GPI modification decreases with increasing hydrophilicity. Further, the hydrophobic domain is characterized by a hydrophobicity profile and not merely a minimum overall hydrophobicity. Thus, a leucine-rich core hydrophobic segment of six to eight amino acid residues is more sensitive to relatively small hydrophilic substitutions compared to its flanking regions and such mutations could be compensated by a hydrophobic substitution elsewhere within this core segment. Such a hydrophobicity profile is characteristic of the amino-terminal leader peptide. When the entire hydrophobic domain of the leader peptide of FR-beta (12 amino acid residues) was substituted with the hydrophobic domain of the GPI signal (13 amino acids), it was possible to obtain expression of FR-beta on the cell surface. In this construct, point mutations in the core hydrophobic segment and in the flanking regions within the substituting peptide produced a similar pattern of effects on the cell surface receptor expression compared to the corresponding mutations in the GPI signal of FR-beta. The results suggest that common principles may govern interactions of the hydrophobic domains of the GPI signal and the leader peptide with the endoplasmic reticulum.

Organizing quality assurance in a maternal-child health division

The 10-step monitoring and evaluation process is described and applied to a maternal-child health division of a 300-bed tertiary care hospital. Examples of specific important aspects of care and indicators are given. The organized plan developed for this division is examined using the Joint Commission on Accreditation of Healthcare Organization's guidelines.

Brain receptor autoradiography with [3H]-YM 09151-2: a ligand for labeling dopamine D-2 receptors

Using the technique of in vitro receptor autoradiography to slide-mounted tissue sections, we studied the suitability of [3H]-YM-09151-2 as a ligand for labeling D-2 receptors in adult F344 rat brains. Specific [3H]-YM-09151-2 binding accounted for 70-80% of the total bound ligand and reached equilibrium after a 60-90 minute incubation. Scatchard analysis revealed a Kd of 626 pM. The apparent Bmax was 23.2 fmol/tissue section. Autoradiographs demonstrated high grain densities in the striatum and olfactory tubercle. Diffuse specific binding was also observed in the cortex.

Reconstruction of the eyebrow in the pediatric burn patient

We have reviewed our experience with reconstruction of eyebrow alopecia secondary to thermal injury in the pediatric patient. Reconstruction was performed with free composite strip grafts or vascularized island pedicle flaps. The complication rates for eyebrows reconstructed with vascularized island pedicles with respect to loss of a significant portion of the flaps (30.8 percent) and malalignment of the grafts (23.1 percent) were significantly greater (p less than 0.001) than the significant tissue loss (10.6 percent) or graft malalignment (7.9 percent) observed for free composite grafts. Hair density was more predictably restored with the free composite graft technique (p = 0.0004). The patients reconstructed with composite grafts had 89.4 percent acceptable results in contrast to 38.5 percent acceptable results obtained with the island pedicle technique. Based on these findings, we reserve the use of the vascularized island pedicle technique for male patients with unilateral alopecia and heavy hair density in the remaining eyebrow and in cases where free composite grafts have failed. The remaining patients are initially treated with free composite grafts with acceptable results in the overwhelming majority of cases.

Decreased plasma fibronectin during starvation in man

This study evaluated the effect of 5 days of starvation followed by 5 days of refeeding on immunoreactive plasma and serum fibronectin and associated opsonic activity as studied by peritoneal macrophage monolayer bioassay in 12 healthy women volunteers. The temporal alteration of fibronectin was compared with the serum albumin, total iron-binding capacity, and retinol-binding protein levels. Fibronectin concentration and opsonic activity were also determined in two cachectic patients who were 61 and 78% of their ideal body weight. Prior to starvation, plasma fibronectin was 292 +/- 20 micrograms/ml and serum fibronectin was 182 +/- 16 in all subjects. After 5 days of starvation, immunoreactive fibronectin decreased (p less than 0.05) by 20-25%. This decrease was not great enough to impair opsonic activity as tested by the in vitro macrophage assay. Starvation caused no decrease in serum albumin or total iron-binding capacity, although retinol-binding protein decreased by 35%. During refeeding, subjects were randomized to a diet with (n = 6) and without (n = 6) carbohydrate. After 5 days of refeeding, fibronectin levels were normalized on the carbohydrate-containing diet, but were still low (82% of normal) on the carbohydrate-free diet. Retinol-binding protein did not fully normalize after 5 days of refeeding. In the two cachectic patients, fibronectin levels prior to total parenteral nutrition were 25 and 75% of normal. Thus, starvation can lower fibronectin levels and this protein is rapidly restored with adequate nutrition.