Centrifugal Microfluidic Method for Enrichment and Enzymatic Extraction of Severe Acute Respiratory Syndrome Coronavirus 2 RNA

The diversification of analytical tools for diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is imperative for effective virus surveillance and transmission control worldwide. Development of robust methods for rapid, simple isolation of viral RNA permits more expedient pathogen detection by downstream real-time reverse transcriptase polymerase chain reaction (real-time RT-PCR) to minimize stalled containment and enhance treatment efforts. Here, we describe an automatable rotationally driven microfluidic platform for enrichment and enzymatic extraction of SARS-CoV-2 RNA from multiple sample types. The multiplexed, enclosed microfluidic centrifugal device (μCD) is capable of preparing amplification-ready RNA from up to six samples in under 15 min, minimizing user intervention and limiting analyst exposure to pathogens. Sample enrichment leverages Nanotrap Magnetic Virus Particles to isolate intact SARS-CoV-2 virions from nasopharyngeal and/or saliva samples, enabling the removal of complex matrices that inhibit downstream RNA amplification and detection. Subsequently, viral capsids are lysed using an enzymatic lysis cocktail for release of pathogenic nucleic acids into a PCR-compatible buffer, obviating the need for downstream purification. Early in-tube assay characterization demonstrated comparable performance between our technique and a "gold-standard" commercial RNA extraction and purification kit. RNA obtained using the fully integrated μCDs permitted reliable SARS-CoV-2 detection by real-time RT-PCR. Notably, we successfully analyzed full-process controls, positive clinical nasopharyngeal swabs suspended in viral transport media, and spiked saliva samples, showcasing the method's broad applicability with multiple sample matrices commonly encountered in clinical diagnostics.

754. A Two-step Testing Algorithm for Hospital-onset Clostridioides difficile Infection (CDI) Reduces Prescribing of C. difficile (CD) Therapy but Its Ability to Guide Treatment Decisions Remains Unclear

Background

Determining true CDI versus CD colonization through CD testing is a continuing challenge. A previously introduced decision support tool at UVA Health significantly reduced inappropriate testing without adverse outcomes. More recently, our methodology changed from nucleic acid amplification test (NAAT) alone to an initial NAAT followed by ELISA for toxin to improve specificity. The purpose of this analysis was to assess provider interpretation of test results, using targeted CD therapy as a surrogate.

Methods

This single-center, retrospective study evaluated all patients with a positive NAAT (Cepheid Xpert® C. difficile) on day 4 or later of hospitalization following 2-step algorithm implementation from Feb 2020 through Feb 2021. Toxin negative (TOX-) test results (C. DIFF QUIK CHEK COMPLETE®) were accompanied by a comment that discordance may represent colonization or CDI and to consider ID consult. The proportion of toxin positive (TOX+) versus TOX- patients receiving ≥ 1 dose of CD therapy served as the primary outcome with partial courses considered < 10 days. Clinical outcomes were also compared.

Results

Ninety patients with NAAT+ results were included, of whom 58 (64%) were TOX-. Thirty-two (100%) TOX+ (median days of therapy [IQR] = 14 [11-17]) versus 51 (88%) TOX- patients (median days of therapy [IQR] = 11 [7-14]) received CD therapy (p=0.04). Treatment decisions were guided by ID physicians for 32 (63%) TOX- patients; ID recommendations to discontinue CD therapy were followed in 2 out of 9 (22%) cases. TOX- patients received partial therapy due to patient death (n=5), presumptive colonization (n=3), and provider error (n=1). Of TOX- patients receiving partial or no treatment, there were no CDI-related adverse outcomes during the admission. CDI-related colectomy occurred in 2 (6%) and 1 (2%) TOX+ and TOX- patients, respectively. Five in-hospital deaths with CDI as a contributing factor occurred in the TOX+ group.

Conclusion

Adoption of a 2-step NAAT plus toxin testing algorithm for hospital-onset CDI reduced the frequency with which TOX- patients received CD therapy but the vast majority were still treated. Most providers considered a positive NAAT indicative of CDI, regardless of TOX status.

Disclosures

All Authors: No reported disclosures

Implementation of a Rapid Phenotypic Susceptibility Platform for Gram-Negative Bloodstream Infections with Paired Antimicrobial Stewardship Intervention: Is the Juice Worth the Squeeze?

BACKGROUND

Implementation of the Accelerate Pheno TM Gram-negative platform (RDT) paired with antimicrobial stewardship program (ASP) intervention projects to improve time to institutional-preferred antimicrobial therapy (IPT) for Gram-negative bacilli (GNB) bloodstream infections (BSI). However, few data describe the impact of discrepant RDT results from standard of care (SOC) methods on antimicrobial prescribing.

METHODS

A single-center, pre-/post-intervention study of consecutive, non-duplicate blood cultures for adult inpatients with GNB BSI following combined RDT + ASP intervention was performed. The primary outcome was time to IPT. An a priori definition of IPT was utilized to limit bias and allow for an assessment of the impact of discrepant RDT results with the SOC reference standard.

RESULTS

Five hundred fourteen patients (PRE 264; POST 250) were included. Median time to antimicrobial susceptibility testing (AST) results decreased 29.4 hours (p < 0.001) post-intervention, and median time to IPT was reduced by 21.2 hours (p <0.001). Utilization (days of therapy [DOTs]/1000 days present) of broad-spectrum agents decreased (PRE 655.2 vs. POST 585.8; p = 0.043) and narrow-spectrum beta-lactams increased (69.1 vs 141.7; p <0.001). Discrepant results occurred in 69/250 (28%) post-intervention episodes, resulting in incorrect ASP recommendations in 10/69 (14%). No differences in clinical outcomes were observed.

CONCLUSIONS

While implementation of a phenotypic RDT + ASP can improve time to IPT, close coordination with Clinical Microbiology and continued ASP follow up are needed to optimize therapy. Although uncommon, the potential for erroneous ASP recommendations to de-escalate to inactive therapy following RDT results warrants further investigation.

Acute appendicitis in four children with SARS-CoV-2 infection

We describe 4 children (11-17 years in age) at our institution with acute appendicitis in the setting of SARS-CoV-2 infection, suggesting a possible association. Providers should consider testing for this infection in patients with severe gastrointestinal symptoms, in order to take appropriate transmission based precautions, until more is understood.

Acceptability and Feasibility of Community-Based, Lay Navigator-Facilitated At-Home Self-Collection for Human Papillomavirus Testing in Underscreened Women

Objective: Women without regular health care providers or a medical home routinely fail to complete recommended cervical cancer screening. At-home self-collection of samples to test for high-risk strains of human papillomavirus (hrHPV) can improve screening rates. This study documents acceptability and feasibility of community lay navigator (LN)-facilitated at-home self-collection for underscreened women in Appalachian Virginia. Materials and Methods: This study used mixed methods in three phases. Phase I involved focus groups of LNs to ensure cultural acceptability of self-collection, and to enhance recruitment of medically underserved women. An environmental scan of community resources and climate was created in Phase II. During Phase III, underscreened women in Appalachian Virginia (the far southwest corner of Virginia) were recruited to complete hrHPV testing using LN-provided self-collection kits. Results: LN-facilitated at-home self-collection for HPV testing was deemed culturally acceptable and feasible to participants in this community-based pilot study. Self-kit training included 64 LNs, of which 35 engaged in the study and were provided 77 kits and instructions. A total of 59 self-kits were returned, of which 42 were correctly completed with valid HPV results, yielding a 16.6% hrHPV rate. Conclusions: Over a quarter of the women LNs recruited had no medical home, indicating this delivery model may have potential to reach women at increased risk of being underscreened for cervical cancer. Research is needed to identify optimal approaches to increase LN participation in outreach self-collection interventions.

Clinical Yield of a Molecular Diagnostic Panel for Enteric Pathogens in Adult Outpatients With Diarrhea and Validation of Guidelines-Based Criteria for Testing

Background

Molecular diagnostic panels for enteric pathogens offer increased sensitivity and reduced turnaround time. However, many pathogen detections do not change clinical management, and the cost is substantial.

Methods

We performed a retrospective chart review of adult outpatients with diarrhea at the University of Virginia who had samples tested by the FilmArray Gastrointestinal Panel (BioFire Diagnostics, Salt Lake City, UT) to identify the clinical yield and to validate the clinical criteria for testing recommended in the 2017 Infectious Diseases Society of America (IDSA) guidelines.

Results

We analyzed 629 tests sent from adult outpatients with diarrhea between March 23, 2015, and July 18, 2016. A pathogen was detected in 127 of 629 specimens (20.2%). The most common pathogens were enteropathogenic Escherichia coli (47, 7.5%), norovirus (24, 3.8%), enteroaggregative E. coli (14, 2.2%), Campylobacter (9, 1.4%), and Salmonella (9; 1.4%). The clinical yield of testing was low, with antimicrobial treatment clearly indicated for only 18 subjects (2.9%) and any change in clinical management indicated for 33 subjects (5.2%). Following the clinical criteria for diagnostic testing from the 2017 IDSA guidelines, which suggest diagnostic testing for patients with fever, abdominal pain, blood in stool, or an immunocompromising condition, would have reduced testing by 32.3% without significantly reducing the clinical yield (sensitivity, 97.0%; 95% confidence interval [CI], 84.2%-99.9%; negative predictive value, 99.5%; 95% CI, 97.3%-100.0%).

Conclusions

The clinical yield of molecular diagnostic testing in this population was low. Compliance with IDSA guidelines in adult outpatients with diarrhea could reduce testing by approximately one-third.

Clinical Yield of Routine Use of Molecular Testing for Adult Outpatients with Diarrhea

Background

Molecular diagnostics for enteropathogens increase yield while reducing turnaround time. However, many pathogens do not require specific therapy, and the cost is substantial.

Methods

We reviewed the use of the FilmArray GI Panel (BioFire Diagnostics, Salt Lake City, Utah) in adult outpatients at the University of Virginia and identified clinical features that could limit testing without reducing yield. We defined yield as (a) detection of a pathogen, (b) detection of a pathogen for which antimicrobial therapy is indicated, or (c) detection of a pathogen that can change management, which additionally included viral pathogens in immunocompromised patients.

Results

Between March 23, 2015 and February 25, 2016, we reviewed 452 tests from adult outpatients with diarrhea. A pathogen was detected in 88/452 (19.5%). The most common pathogens were: enteropathogenic E. coli (36; 8.0%), norovirus (17; 3.8%), Campylobacter (7, 1.5%), enteroaggregative E. coli (6, 1.3%), Giardia (6; 1.3%), and sapovirus (5; 1.1%). Based on clinical guidelines, antimicrobial treatment was clearly indicated for 19/452 subjects (4.2%). Limiting testing to patients with an additional enteric symptom (abdominal pain, nausea, vomiting, fecal urgency, tenesmus, or flatulence), a travel history, or an immunocompromising condition would reduce testing by 25.9%, with a treatable pathogen identified in 18/331 (5.4%) (sensitivity 94.7%, specificity 27.7%). Further modifying testing criteria to exclude subjects with vomiting, 18/288 (6.3%) had a treatable pathogen (sensitivity 94.7%, specificity 37.3%), and a pathogen which could change management was detected in 28/288 (9.7%) (sensitivity 96.6%, specificity 38.5%). Excluding immunocompromised subjects or those with a travel history, American College of Gastroenterology guidelines for testing were met by 293/348 (84.2%) with a documented duration of diarrhea, and a treatable pathogen was detected in 8/293 (2.7%) vs. 3/55 (5.5%) who did not meet testing guidelines.

Conclusion

Testing could be reduced by 36.3% without decreasing clinical yield by limiting testing to patients with diarrhea with an additional enteric symptom and no history of vomiting, a travel history, or an immunocompromising condition. ACG guidelines did not improve testing efficiency.

Disclosures

All authors: No reported disclosures.

Clinical microbiology costs for methods of active surveillance for Klebsiella pneumoniae carbapenemase-producing Enterobacteriaceae

OBJECTIVE

To compare direct laboratory costs of different methods for perirectal screening for carbapenemase-producing Enterobacteriaceae (CPE) colonization.

DESIGN

Cost-benefit analysis.

SETTING

A university hospital and affiliated long-term acute care hospital (LTACH).

PARTICIPANTS

Inpatients from the hospital or LTACH.

METHODS

Perirectal samples were collected from inpatients at risk for exposure to CPE. In 2009, we compared the accuracy of the Centers for Disease Control and Prevention (CDC)-recommended CPE screening method with similar methods incorporating a chromogenic agar (CA). We then performed a cost projection analysis using 2012 screening results for the CA method, the CDC method, and a molecular assay with wholesale pricing based on the 2009 analysis. Comparisons of turnaround and personnel time were also performed.

RESULTS

A total of 185 (2.7%) of 6,860 samples were confirmed as CPE positive during 2012. We previously found that the CDC protocol had a lower sensitivity than the CA method and predicted that the CDC protocol would have missed 92 of the CPE-positive screening results, whereas the modified protocol using CA would have missed 26, assuming similar prevalence and performance. Turnaround time was 3 days using the CDC and CA-modified protocols compared with 1 day for molecular testing. The estimated annual total program cost and total technologist's hours would be the following: CA-modified protocol, $37,441 and 376 hours; CDC protocol, $22,818 and 482 hours; and molecular testing, $224,596 and 343 hours.

CONCLUSIONS

The CDC screening protocol appeared to be the least expensive perirectal screening method. However, expense must be weighed against a lower sensitivity and extra labor needed for additional work-up of non-CPE isolates. The molecular test has the shortest turnaround time but the greatest expense.

Association of a null allele of SPRN with variant Creutzfeldt-Jakob disease

Background:

No susceptibility genes have been identified in human prion disase, apart from the prion protein gene (PRNP). The gene SPRN, encodes Shadoo (Sho, shadow of prion protein) which has protein homology and possible functional links with the prion protein.

Methods:

A genetic screen was carried out of the open reading frame of SPRN by direct sequencing in 522 patients with prion disease, including 107 with variant Creutzfeldt–Jakob disease (vCJD), and 861 healthy controls.

Results:

A common coding variant of SPRN, two further single nucleotide polymorphisms (SNPs) and three rare insertion or deletion variants were found. A single base-pair insertion at codon 46, predicted to cause a frameshift and potentially a novel protein, was found in two patients with vCJD but not in controls (p = 0.01). Two linked SNPs, one in intron 1 and the other a missense variant at codon 7, were associated with risk of sporadic CJD (p = 0.009).

Conclusion:

These data justify the functional genetic characterisation of SPRN and support the involvement of Shadoo in prion pathobiology.

Phenotypic heterogeneity and genetic modification of P102L inherited prion disease in an international series

The largest kindred with inherited prion disease P102L, historically Gerstmann-Sträussler-Scheinker syndrome, originates from central England, with émigrés now resident in various parts of the English-speaking world. We have collected data from 84 patients in the large UK kindred and numerous small unrelated pedigrees to investigate phenotypic heterogeneity and modifying factors. This collection represents by far the largest series of P102L patients so far reported. Microsatellite and genealogical analyses of eight separate European kindreds support multiple distinct mutational events at a cytosine-phosphate diester-guanidine dinucleotide mutation hot spot. All of the smaller P102L kindreds were linked to polymorphic human prion protein gene codon 129M and were not connected by genealogy or microsatellite haplotype background to the large kindred or each other. While many present with classical Gerstmann-Sträussler-Scheinker syndrome, a slowly progressive cerebellar ataxia with later onset cognitive impairment, there is remarkable heterogeneity. A subset of patients present with prominent cognitive and psychiatric features and some have met diagnostic criteria for sporadic Creutzfeldt-Jakob disease. We show that polymorphic human prion protein gene codon 129 modifies age at onset: the earliest eight clinical onsets were all MM homozygotes and overall age at onset was 7 years earlier for MM compared with MV heterozygotes (P = 0.02). Unexpectedly, apolipoprotein E4 carriers have a delayed age of onset by 10 years (P = 0.02). We found a preponderance of female patients compared with males (54 females versus 30 males, P = 0.01), which probably relates to ascertainment bias. However, these modifiers had no impact on a semi-quantitative pathological phenotype in 10 autopsied patients. These data allow an appreciation of the range of clinical phenotype, modern imaging and molecular investigation and should inform genetic counselling of at-risk individuals, with the identification of two genetic modifiers.

Preclinical and clinical performance of the Efoora test, a rapid test for detection of human immunodeficiency virus-specific antibodies

Barriers to effective diagnostic testing for human immunodeficiency virus type 1 (HIV-1) infection can be reduced with simple, reliable, and rapid detection methods. Our objective was to determine the accuracy, sensitivity, and specificity of a new rapid, lateral-flow immunochromatographic HIV-1 antibody detection device. Preclinical studies were performed using seroconversion, cross-reaction, and interference panels, archived clinical specimens, and fresh whole blood. In a multicenter, prospective clinical trial, a four-sample matrix of capillary (fingerstick) whole-blood specimens and venous whole blood, plasma, and serum was tested for HIV-1 antibodies with the Efoora HIV rapid test (Efoora Inc., Buffalo Grove, IL) and compared with an enzyme immunoassay (EIA) (Abbott Laboratories) licensed by the Food and Drug Administration. Western blot and nucleic acid test supplemental assays were employed to adjudicate discordant samples. Preclinical testing of seroconversion panels showed that antibodies were often detected earlier by the rapid test than by a reference EIA. No significant interference or cross-reactions were observed. Testing of 4,984 archived specimens yielded a sensitivity of 99.2% and a specificity of 99.7%. A prospective multicenter clinical study with 2,954 adult volunteers demonstrated sensitivity and specificity for the Efoora HIV rapid test of 99.8% (95% confidence interval [CI], 99.3 and 99.98%) and 99.0% (95% CI, 98.5 and 99.4%), respectively. Reactive rapid HIV-1 antibody detection was confirmed in 99.6% of those with a known HIV infection (n = 939), 5.2% of those in the high-risk group (n = 1,003), and 0.1% of those in the low-risk group (n = 1,012). For 21 (0.71%) patients, there was discordance between the results of the rapid test and the confirmatory EIA/Western blot tests. We conclude that the Efoora HIV rapid test is a simple, rapid assay for detection of HIV-1 antibodies, with high sensitivity and specificity compared to a standardized HIV-1 EIA.

Methylation of human papillomavirus genomes in cells of anal epithelia of HIV-infected men

Intra-anal malignancies disproportionately affect individuals who engage in anal intercourse because of infection with human papillomaviruses (HPVs), with an increased risk attributed to infection with HIV because of a declining immunity against HPVs. Long-term persistence of HPVs suggests yet other mechanisms that determine the clinical outcome, however. Because methylation of HPV DNA represses oncogene expression in cervical samples, we investigated whether this mechanism also occurs in HIV-positive men and studied the methylation of CpG dinucleotides overlapping with the HPV-16 enhancer and promoter in 16 anal samples. Similar to cervical infections, the average methylation frequency was 12.3%, with heterogeneities between clones from different and the same samples. In low-grade anal intraepithelial neoplasia (AIN), methylation was high in CpGs overlapping the viral enhancer but rare in promoter positions, whereas methylation was high in promoter regions in high-grade AIN, especially in samples with a high load of viral genomes. The viral replication origin was never methylated. We also detected de novo methylation at methylated (me) CpA, meCpT, and meCpC dinucleotides. Our study expands the observation and mapping of HPV DNA methylation to anal infections and the HIV-positive patient population. As observed at the cervix, DNA methylation may force HPVs into latency with functional replication but repressed transcription. Escape from this repression is a prerequisite for neoplastic progression; however, methylation resumes because of chromosomal integration of HPV genomes but spares some HPV genomes in each cell that maintain the transformed phenotype. DNA methylation, taken together with virus load, may be useful to diagnose the emergence of a population of tumor cells.

The causal element for the lactase persistence/non-persistence polymorphism is located in a 1 Mb region of linkage disequilibrium in Europeans

Expression of lactase in the intestine persists into adult life in some people and not others, and this is due to a cis-acting regulatory polymorphism. Previous data indicated that a mutation leading to lactase persistence had occurred on the background of a 60 kb 11-site LCT haplotype known as A (Hollox et al. 2001). Recent studies reported a 100% correlation of lactase persistence with the presence of the T allele at a CT SNP at -14 kb from LCT, in individuals of Finnish origin, suggesting that this SNP may be causal of the lactase persistence polymorphism, and also reported a very tight association with a second SNP (GA -22 kb) (Enattah et al. 2002). Here we report the existence of a one megabase stretch of linkage disequilibrium in the region of LCT and show that the -14 kb T allele and the -22 kb A allele both occur on the background of a very extended A haplotype. In a series of Finnish individuals we found a strong correlation (40/41 people) with lactose digestion and the presence of the T allele. The T allele was present in all 36 lactase persistent individuals from the UK (phenotyped by enzyme assay) studied, 31/36 of whom were of Northern European ancestry, but not in 11 non-persistent individuals who were mainly of non-UK ancestry. However, the CT heterozygotes did not show intermediate lactase enzyme activity, unlike those previously phenotyped by determining allelic transcript expression. Furthermore the one lactase persistent homozygote identified by having equally high expression of A and B haplotype transcripts, was heterozygous for CT at the -14 kb site. SNP analysis across the 1 megabase region in this person showed no evidence of recombination on either chromosome between the -14 kb SNP and LCT. The combined data shows that although the -14 kb CT SNP is an excellent candidate for the cause of the lactase persistence polymorphism, linkage disequilibrium extends far beyond the region searched so far. In addition, the CT SNP does not, on its own, explain all the variation in expression of LCT, suggesting the possibility of genetic heterogeneity.

Clinical evaluation of the Vitek automated system with cards GNS 122 and 127 and VTK-R07.01 software for antimicrobial susceptibility testing of Pseudomonas aeruginosa

The performance of the Vitek Automated Susceptibility Testing System software version VTKR07.01 (bioMerieux Vitek, Hazelwood, MO), for testing Pseudomonas aeruginosa was evaluated by comparing results for 200 clinical isolates with those of disk diffusion and manual broth microtiter dilution testing. For cefepime, the restricted major error rate was 0.53% and the minor error rate was 12.5%. For piperacillin, the restricted major error rate was 2.15%. For ticarcillin/clavulanic acid, restricted very major and major error rates of 6.5% and 3.2%, respectively, occurred. The results of our study indicate that the Vitek system performs within acceptable limits when testing piperacillin, but remains problematic for testing cefepime and ticarcillin-clavulanic acid.

Intolerance to lactose and other dietary sugars

Intolerance of dietary carbohydrate and sugars can result from a variety of genetically determined enzyme and transporter deficiencies. This article reviews this topic and discusses in more detail the current state of our own research on lactase.

Microsatellite variation within the human RHCE gene

BACKGROUND AND OBJECTIVES

This study provides a unique method for identifying individuals carrying the Rh haplotype cDe, and supports a model for the evolution of Rh haplotypes in which cDe is the progenitor.

MATERIALS AND METHODS

DNA from 212 unrelated donors of known Rh serological phenotype was PCR amplified. The resulting products were analysed by denaturing polyacrylamide gel electrophoresis, denaturing gradient gel electrophoresis and DNA sequencing.

RESULTS

Two adjacent microsatellite repeat elements of the form (AC)n (GCAC)n were found within the human Rh blood group genes. These display copy number variation which was non-randomly distributed with respect to Rh serological phenotype, and was restricted to alleles of RHCE expressing the c antigen.

CONCLUSION

The predominantly Black African allele cDe displayed a unique set of microsatellite alleles, providing a method of identifying individuals carrying this haplotype.

Common polymorphism in a highly variable region upstream of the human lactase gene affects DNA-protein interactions

In most mammals lactase activity declines after weaning when lactose is no longer part of the diet, but in many humans lactase activity persists into adult life. The difference responsible for this phenotypic polymorphism has been shown to be cis-acting to the lactase gene. The causal sequence difference has not been found so far, but a number of polymorphic sites have been found within and near to the lactase gene. We have shown previously that in Europeans there are two polymorphic sites in a small region between 974 bp and 852 bp upstream from the start of transcription, which are detectable by denaturing gradient gel electrophoresis (DGGE). In this study, analysis of individuals from five other population groups by the same DGGE method reveals four new alleles resulting from three additional nucleotide changes within this very small region. Analysis of sequence in four primate species and comparison with the published pig sequence shows that the overall sequence of this highly variable human region is conserved in pigs as well as primates, and that it lies within a 1kb region which has been shown to control lactase downregulation in pigs. Electrophoretic mobility shift assay (EMSA) studies were carried out to determine whether common variation affected protein-DNA binding and several binding activities were found using this technique. A novel two base-pair deletion that is common in most populations tested, but is not present in Europeans, caused no change in binding activity. However, a previously published C to T transition at -958bp dramatically reduced binding activity, although the functional significance of this is not clear.

The genetically programmed down-regulation of lactase in children

BACKGROUND & AIMS

Intestinal lactase activity is high in all healthy human babies, but in adults a genetic polymorphism, which acts in cis to the lactase gene, determines high or low messenger RNA (mRNA) expression and activity (lactase persistence and nonpersistence, respectively). Our aim was to investigate the onset of expression of this polymorphism in children.

METHODS

Activities were analyzed in relation to age in normal biopsy specimens from a 20-year collection of diagnostic specimens. In a smaller set of 32 samples, aged 2-132 months, RNA was extracted for semiquantitative reverse-transcription polymerase chain reaction. Marker polymorphisms were used to determine the allelic origin of lactase mRNA transcripts.

RESULTS

Analysis of 866 children showed evidence that the lactase persistence/nonpersistence polymorphism began before 5 years of age. The 32 children tested had high lactase mRNA and activity. Six children aged 2-16 months showed equal expression of two alleles, 2 children aged 7 and 14 months showed slightly asymmetric expression, and 7 children aged 22-132 months showed very asymmetric expression, the second allele being undetectable in the 11-year-old, as previously seen in lactase-persistent heterozygote adults.

CONCLUSIONS

Genetically programmed down-regulation of the lactase gene is detectable in children from the second year of life, although the onset and extent are somewhat variable.

Lactase haplotype frequencies in Caucasians: association with the lactase persistence/non-persistence polymorphism

A genetic polymorphism is responsible for determining that some humans express lactase at high levels throughout their lives and are thus lactose tolerant, while others lose lactase expression during childhood and are lactose intolerant. We have previously shown that this polymorphism is controlled by an element or elements which act in cis to the lactase gene. We have also reported that 7 polymorphisms in the lactase gene are highly associated and lead to only 3 common haplotypes (A, B and C) in individuals of European extraction. Here we report the frequencies of these polymorphisms in Caucasians from north and south Europe and also from the Indian sub-continent, and show that the alleles differ in frequency, the B and C haplotypes being much more common in southern Europe and India. Allelic association studies with lactase persistence and non-persistence phenotypes show suggestive evidence of association of lactase persistence with certain alleles. This association was rather more clear in the analysis of small families, where haplotypes could be determined. Furthermore haplotype and RNA transcript analysis of 11 unrelated lactase persistent individuals shows that the persistence (highly expressed) allele is almost always on the A haplotype background. Non-persistence is found on a variety of haplotypes including A. Thus it appears that lactase persistence arose more recently than the DNA marker polymorphisms used here to define the main Caucasian haplotypes, possibly as a single mutation on the A haplotype background. The high frequency of the A haplotype in northern Europeans is consistent with the high frequency of lactase persistence.

Evolution of the human RH (rhesus) blood group genes: a 50 year old prediction (partially) fulfilled

Almost exactly 50 years ago, R. A. Fisher and R. Race proposed a model for the evolution of the RH (rhesus) genes in which the less common haplotypes were derived from the commoner ones by recombination, and in which the gene order was D-C-E. No direct-evidence bearing on this model was available then, and has not been until now. Here we present evidence for non-reciprocal intergenic exchange (gene conversion) occurring once in human history to generate the common RHCE allele, Ce. We have also used new polymorphisms to construct haplotypes which suggest that intragenic recombination played a major role in the generation of the less common haplotypes, but only if RHD lies 3' of RHCE, i.e. the order is C-E-D. We provide both genetic and physical evidence supporting this arrangement.

A recombination hot spot in the Rh genes revealed by analysis of unrelated donors with the rare D-- phenotype

We have studied the arrangement of Rh (rhesus) genes in donors who are completely null for the products of one of them, RHCE. We show that five of six homozygous individuals with the so-called Rh D-- phenotype, who express no red-cell antigens of the C/c and E/e series, have rearranged RHCE genes in which internal sequences have been replaced by the corresponding sequences from RHD. Moreover, although there is heterogeneity at the 3' end, the 5' boundary of this chimerism is within the same small interval around exon 2. This interval is characterized by an exceptionally high degree of sequence homology between RHCE and RHD, a high density of dispersed repetitive elements, and the presence of an alternating purine-pyrimidine copolymer tract. We suggest that these features may explain the mechanistic basis for the origin of the rearrangement.

DNA-based rhesus typing: simultaneous determination of RHC and RHD status using the polymerase chain reaction

We describe a PCR-based method of performing RHD and C/c typing in a single reaction. The method is based on an earlier observation of a polymorphism in intron 2 of both genes which, in addition to detecting the RHD deletion responsible for most known D-negative phenotypes, is also associated with C/c serological type. Using this assay, we typed 105 unrelated individuals from at least four different population groups and compared the results to those obtained using conventional serological testing of red cells. An absolute correlation, with no exceptions, was seen. We also showed that the method has potential in the antenatal determination of RH type, as it was possible to type fetal trophoblasts recovered from the endocervical canal at 9 weeks pregnancy.

Search for linkage to schizophrenia on the X and Y chromosomes

Markers for X chromosome loci were used in linkage studies of a large group of small families (n = 126) with at least two schizophrenic members in one sibship. Based on the hypothesis that a gene for schizophrenia could be X-Y linked, with homologous loci on both X and Y, our analyses included all families regardless of the pattern of familial inheritance. Lod scores were computed with both standard X-linked and a novel X-Y model, and sib-pair analyses were performed for all markers examining the sharing of maternal alleles. Small positive lod scores were obtained for loci pericentromeric, from Xp11.4 to Xq12. Lod scores were also computed separately in families selected for evidence of maternal inheritance and absence of male to male transmission of psychosis. The lod score for linkage to the locus DXS7 reached a maximum of 1.83 at 0.08% recombination, assuming dominant inheritance on the X chromosome in these families (n = 34). Further investigation of the X-Y homologous gene hypothesis focussing on this region is warranted.

An examination of linkage of schizophrenia and schizoaffective disorder to the pseudoautosomal region (Xp22.3)

We investigated linkage between schizophrenia and the loci DXYS14, DXYS17, and MIC2 within the pseudoautosomal region in 85 families with two or more siblings suffering from schizophrenia or schizoaffective disorder. A maximum lod score of 2.44 was reached at MIC2, with a dominant model of inheritance at a recombination fraction of 0.367 in females and 0.046 in males (a F:M sex ratio > 1, i.e. opposite to that expected with a pseudoautosomal locus). Evidence consistent with linkage (P = 0.01) was also obtained with a sibling pair analysis at the MIC2 locus. These data do not support (although they do not definitively exclude) a locus within the pseudoautosomal region; they are consistent with the presence of a gene that predisposes to schizophrenia in the sex-specific regions of the X and Y chromosomes.

Male siblings with schizophrenia share alleles at the androgen receptor above chance expectation

In families that included two or more siblings with schizophrenia or schizo-affective disorder male-male pairs were found to share alleles at the androgen receptor (AR) gene (in Xq11.2-q12) above chance expectation (p < 0.003); female-female and mixed sex pairs showed no such tendency. The findings are compatible with X-Y linkage or with an X-linked contribution to liability in males.

Dementia associated with a 216 base pair insertion in the prion protein gene. Clinical and neuropathological features

We report the clinical and neuropathological findings in a patient with a 216 base pair insertion in the prion protein (PrP) gene. She died aged 57 years after a 2.5-year illness characterized by falls, axial rigidity, myoclonic jerks and progressive dementia. There was no history of affected relatives. The pathological changes consisted of the deposition in cerebellum, basal ganglia and cortex of small plaques composed of variable amounts of amyloid and degenerative material which was associated with a marked macrophage reaction. The amyloid deposits in the cerebellum and basal ganglia gave a positive immunoperoxidase staining reaction for PrP. In some places plaques bore a resemblance to senile neuritic plaques and in the hippocampus there were abundant typical neuritic plaques giving positive staining reactions for beta-amyloid protein and tau protein, but not PrP. There were few neurons bearing neurofibrillary tangles. This is the first report of the neuropathological changes associated with this particular abnormality of the PrP gene and it seems to demonstrate a transition between the pathology of prion disease and that of Alzheimer's disease. The importance of PrP gene analysis to the understanding of neurodegenerative diseases is stressed.

Inherited prion disease with 144 base pair gene insertion. 2. Clinical and pathological features

A large family with autosomal dominant segregation of presenile dementia, and other neurological and behavioural features is described. At various times, family members have carried diagnoses of Alzheimer's disease, Huntington's disease, Parkinson's disease, myoclonic epilepsy, atypical dementia, Pick's disease, Creutzfeldt-Jakob disease and Gerstmann-Sträussler syndrome. Molecular genetic studies have enabled classification of this disease at the molecular level as one of the group of inherited prion diseases. Here we describe the phenotype of inherited prion disease (PrP 144 bp insertion).

Inherited prion disease with 144 base pair gene insertion. 1. Genealogical and molecular studies

Genealogical and molecular studies were carried out in four families in which early onset dementia is inherited as an autosomal dominant. These studies indicated that the four families derive from four siblings whose parents were born in the late 18th century in South-East England. The disease was found to be closely linked to a 144 bp insertion within the open reading frame of the prion protein (PrP) gene with a maximum LOD score of 11.02 at zero recombination. Within the general population the PrP gene is polymorphic at codon 129 (allele frequency approximately 30% valine, 70% methionine). The insertion in this family is always within a methionine-129 allele. The age at death of affected individuals whose normal allele encoded methionine at codon 129 was significantly lower than those whose normal allele encoded valine. The clinical features which were very variable and the neuropathological findings, which sometimes included spongiform encephalopathy, but which often did not, are described fully in the accompanying article (Collinge et al., 1992).

A dementing illness associated with a novel insertion in the prion protein gene

Following our previous report of an 144-bp insertion in the open reading frame of the prion protein (PrP) gene, we have now identified a larger, 216-bp, insertion in the gene. The insertion which is in frame encodes 9 extra octapeptide repeat sequences in addition to the 5 repeats normally present and represents the largest insertion so far detected in the PrP gene.

Presymptomatic detection or exclusion of prion protein gene defects in families with inherited prion diseases

The identification of defects in the prion protein (PrP) gene in families with inherited Creutzfeldt-Jakob disease or Gerstmann-Straussler syndrome allows presymptomatic diagnosis or exclusion of these disorders in subjects at risk. After counseling, PrP gene analysis was performed in three such individuals: two from families with a 144-bp insert and one with a point mutation at codon 102 in the PrP gene. The presence of a PrP gene defect was confirmed in one and excluded in two. Despite the potential problems of using PrP gene analysis in genetic prediction - specifically, uncertainty about penetrance and, generally, problems of presymptomatic testing in any inherited late-onset neurodegenerative disorder - we conclude that it has a role to play in improved genetic counseling for families with inherited prion diseases.

Evidence for a pseudo-autosomal locus for schizophrenia using the method of affected sibling pairs

A susceptibility locus for schizophrenia in the 'pseudo-autosomal' region has been proposed on the basis of the reported excess of sex-chromosome aneuploidies (e.g. XXY and XXX) among patients with schizophrenia and the finding that schizophrenic sib-pairs are more often of the same than of the opposite sex. This hypothesis has been tested in 83 sibships with two or more siblings fulfilling Research Diagnostic Criteria for schizophrenia or schizoaffective disorder. Alleles at the pseudo-autosomal telomeric locus DXYS14, which is unlinked with sex, were analysed using the method of affected sib-pairs. Affected sibs shared alleles at DXYS14 more frequently than expected by random Mendelian assortment, supporting genetic linkage between DXYS14 and schizophrenia.

Insertions in the prion protein gene in atypical dementias

A number of mutations have been demonstrated in the open reading frame (ORF) of the prion protein (PrP) gene in patients with familial Creutzfeldt-Jakob disease or Gerstmann-Sträussler syndrome. On the basis of detecting an insertion in the ORF of the PrP gene in a patient originally suspected to be suffering from familial Alzheimer-type dementia, we screened 101 individuals with atypical dementias for the known PrP gene mutations. Insertions were found in five individuals, whereas none of the other reported mutations in the PrP gene was detected in the present study. One of the five insertions was larger than that described previously, suggesting that the individuals with these mutations are unlikely to be all lineally related and that insertions in the PrP gene may not be uncommon in prion diseases.

Prion dementia without characteristic pathology

Gerstmann-Sträussler syndrome (GSS) was diagnosed in a family with presenile dementia by prion protein gene analysis. Extensive histological examination of the brain of an affected individual from this family showed no characteristic features of GSS or Creutzfeldt-Jakob disease (CJD). Thus "spongiform encephalopathy" (GSS or CJD) cannot always be excluded on neuropathological grounds in an individual dying of a dementing condition, and the true prevalence of these diseases is likely to be underestimated. Screening by prion protein gene analysis will help to determine the full clinical and neuropathological phenotype in familial cases. This observation may be relevant to the assessment of possible transmission of bovine spongiform encephalopathy to man.

Codon 129 changes in the prion protein gene in Caucasians

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A codon 129 polymorphism in the PRIP gene

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An in-frame insertion in the prion protein gene in familial Creutzfeldt-Jakob disease

In a pedigree with Creutzfeldt-Jakob disease we identified a 144-bp insertion in the open reading frame of the prion protein (PrP) gene. The insertion is in-frame and codes for 6 extra uninterrupted octapeptide repeats in addition to the 5 that are normally present in the N-terminal region of the protein. The possibility that this mutation may prove relevant to elucidating the mechanism of horizontal transmission of the spongiform encephalopathies is discussed.

Diagnosis of Gerstmann-Sträussler syndrome in familial dementia with prion protein gene analysis

The polymerase chain reaction was used to screen DNA samples from 12 unrelated individuals with various familial dementias and ataxias for mutation in part of the prion protein (PrP) gene, an abnormality that occurs in individuals with the spongiform encephalopathies, Gerstmann-Sträussler syndrome (GSS) and Creutzfeldt-Jakob disease. 2 members of a family in whom GSS was not previously suspected had a 0.15 kb insertion of similar size to that found in another kindred with pathologically proven spongiform encephalopathy. GSS may be more common than is currently realised; PrP gene analysis is potentially useful for diagnosis and genetic counselling in familial dementias and ataxias.

Linkage of a prion protein missense variant to Gerstmann-Sträussler syndrome

Gerstmann-Sträussler syndrome is a rare familial neurodegenerative condition that is vertically transmitted, in an apparently autosomal dominant way. It can also be horizontally transmitted to non-human primates and rodents through intracerebral inoculation of brain homogenates from patients with the disease. The exact incidence of the syndrome is unknown but is estimated to be between one and ten per hundred million. Patients initially suffer from ataxia or dementia and deteriorate until they die, in one to ten years. Protease-resistant prion protein (PrP) and PrP-immunoreactive amyloid plaques with characteristic morphology accumulate in the brains of these patients. Current diagnostic criteria for Gerstmann-Sträussler syndrome incorporate clinical and neuropathological features, as animal transmission studies can be unreliable. PrP is implicated in the pathogenesis and transmission of the condition and in scrapie, an equivalent animal disease. It was discovered by enriching scrapie-infected hamster brain fractions for infectivity. Because there is compelling evidence that the scrapie isoform of PrP is a necessary component of the infectious particle, it seemed possible that the PrP gene on the short arm of human chromosome 20 in Gerstmann-Sträussler syndrome might be abnormal. We show here that PrP codon 102 is linked to the putative gene for the syndrome in two pedigrees, providing the best evidence to date that this familial condition is inherited despite also being infectious, and that substitution of leucine for proline at PrP codon 102 may lead to the development of Gerstmann-Sträussler syndrome.

Selective decreases in MAO-B activity in post-mortem brains from schizophrenic patients with type II syndrome

The activities of the A and B forms of the enzyme monoamine oxidase (MAO, E.C. 1.4.3.4) have been assessed with the substrates 5-hydroxytryptamine and benzylamine respectively in seven areas of the brains of 39 patients with schizophrenia and 44 control subjects. Whereas previous studies have found the enzyme unchanged in brain in schizophrenia, in this study there was a modest but significant decrease in the activity of MAO-B in frontal and temporal cortices and in amygdala. This decrease could not be accounted for by neuroleptic medication, age, sex or post-mortem variables. In a series of 22 patients who had been assessed in life, the reduction in MAO-B activity was found to be associated specifically with the presence of negative symptoms (flattening of affect and paucity of speech). The findings are therefore consistent with other evidence for structural and neurochemical change in the temporal lobe that have been associated with the type II (defect state) syndrome of schizophrenia. The change in enzyme activity is unlikely to be related to a change in monoamine metabolism but may reflect a disturbance in glial function. The change in MAO-B activity in brain in this study is confined to particular areas of brain and a subgroup of patients; it is thought to be entirely unrelated to earlier reports of reductions of enzyme activity in platelets, which are probably attributable to prolonged neuroleptic medication.

Central dopaminergic mechanisms in schizophrenia

A neurochemical evaluation of the dopamine hypothesis of schizophrenia has been carried out. There was no evidence to suggest that the synthesis or inactivation of dopamine was abnormal in schizophrenia. The brain concentrations of the amine itself, its metabolities and the activities of its related enzymes were similar in controls and schizophrenics. However in vitro and in vivo evidence is presented that suggests that the illness may be associated with an increase in the numbers of dopamine D2 receptors in the brain.

Serotonergic mechanisms in brains of suicide victims

Serotonergic mechanisms have been investigated in postmortem brain samples from controls and suicide victims. The concentrations of 5-hydroxytryptamine (serotonin; 5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) were determined in occipital cortex and hippocampus and the high-affinity binding of ligands to the 5-HT1, 5-HT2 and imipramine-binding sites was assessed in frontal cortex, occipital cortex and hippocampus. The only significant difference between the two groups was a modest increase in 5-HIAA levels in the hippocampus of suicide victims. There was no evidence to suggest that those suicide victims with a clinical history of depression represented a subgroup with altered metabolite levels or binding values. The storage conditions of the samples were not related to the metabolite levels or binding values. There was, however, a significant positive correlation between [3H]imipramine binding and age in some brain regions. The results do not provide any evidence of gross alterations in 5-HT mechanisms in suicide or depression.

Tritiated etorphine and naloxone binding to opioid receptors in caudate nucleus in schizophrenia

Opioid receptor binding sites were assessed in membrane preparations of caudate nucleus from post-mortem brains of controls and of patients with schizophrenia. There was no difference between the two groups in the total specific binding of 3H-etorphine or in its 'mu' and ('delta + kappa') components. Similarly, the binding of 3H-naloxone did not differ between patients and controls. It is concluded that a previous report of reduced opioid receptors in caudate of schizophrenics is unlikely to prove a consistent finding and that the results of the present study offer no support to the claim that there is a general disturbance in opiate mechanisms in schizophrenia.