Molecular detection of bacteria, placental inflammation, and neonatal sepsis risk

OBJECTIVE

To identify bacteria in umbilical cord tissue and investigate the association with placental inflammation and neonatal sepsis risk score.

STUDY DESIGN

Retrospective cohort study from 2017-2019. RNA was extracted from umbilical cord tissue and NanoString nCounter used to identify seven bacteria genera. Sepsis risk score was calculated using the Kaiser sepsis calculator. Placental histopathology was abstracted from medical records.

RESULTS

Detection of bacterial RNA in the umbilical cord (n = 96/287) was associated with high-stage maternal and fetal acute placental inflammation (maternal 35.4% vs 22.5%, p = 0.03 and fetal 34.4% vs 19.4%, p < 0.01) and maternal vascular malperfusion (36.5% vs 23.0%, p = 0.02). Detection of Ureaplasma spp. was also associated with increased sepsis risk score (1.5/1000 [0.6, 8.6] vs 0.9/1000 [0.2, 2.9], p = 0.04).

CONCLUSION

Umbilical cord bacterial pathogens are linked to fetal and maternal placental inflammation and maternal vascular malperfusion during gestation and associated with increased sepsis risk score in the neonate.

Analysis of Plasmablasts From Children With Kawasaki Disease Reveals Evidence of a Convergent Antibody Response to a Specific Protein Epitope

BACKGROUND

Kawasaki disease (KD) is a febrile illness of young childhood that can result in coronary artery aneurysms and death. Coronavirus disease 2019 (COVID-19) mitigation strategies resulted in a marked decrease in KD cases worldwide, supporting a transmissible respiratory agent as the cause. We previously reported a peptide epitope recognized by monoclonal antibodies (MAbs) derived from clonally expanded peripheral blood plasmablasts from 3 of 11 KD children, suggesting a common disease trigger in a subset of patients with KD.

METHODS

We performed amino acid substitution scans to develop modified peptides with improved recognition by KD MAbs. We prepared additional MAbs from KD peripheral blood plasmablasts and assessed MAb characteristics that were associated with binding to the modified peptides.

RESULTS

We report a modified peptide epitope that is recognized by 20 MAbs from 11 of 12 KD patients. These MAbs predominantly use heavy chain VH3-74; two-thirds of VH3-74 plasmablasts from these patients recognize the epitope. The MAbs were nonidentical between patients but share a common complementarity-determining region 3 (CDR3) motif.

CONCLUSIONS

These results demonstrate a convergent VH3-74 plasmablast response to a specific protein antigen in children with KD, supporting one predominant causative agent in the etiopathogenesis of the illness.

The Fungal Microbiome of the Upper Airway Is Associated With Future Loss of Asthma Control and Exacerbation Among Children With Asthma

BACKGROUND

Accumulating evidence suggests that the upper airway bacterial microbiota is implicated in asthma inception, severity, and exacerbation. Unlike bacterial microbiota, the role of the upper airway fungal microbiome (mycobiome) in asthma control is poorly understood.

RESEARCH QUESTION

What are the upper airway fungal colonization patterns among children with asthma and their relationship with subsequent loss of asthma control and exacerbation of asthma?

STUDY DESIGN AND METHODS

The study was coupled with the Step Up Yellow Zone Inhaled Corticosteroids to Prevent Exacerbations (ClinicalTrials.gov Identifier: NCT02066129) clinical trial. The upper airway mycobiome was investigated using Internal transcribed spacer 1 (ITS1) sequencing of nasal blow samples collected from children with asthma when asthma was well controlled (baseline, n = 194) and during early signs of loss of asthma control (yellow zone [YZ], n = 107).

RESULTS

At baseline, 499 fungal genera were detected in the upper airway samples, with two commensal fungal species, Malassezia globosa and Malassezia restricta, being most dominant. The relative abundance of Malassezia species varies by age, BMI, and race. Higher relative abundance of M globosa at baseline was associated with lower risk of future YZ episodes (P = .038) and longer time to development of first YZ episode (P = .022). Higher relative abundance of M globosa at YZ episode was associated with lower risk of progression from YZ episode to severe asthma exacerbation (P = .04). The upper airway mycobiome underwent significant changes from baseline to YZ episode, and increased fungal diversity was correlated highly with increased bacterial diversity (ρ = 0.41).

INTERPRETATION

The upper airway commensal mycobiome is associated with future asthma control. This work highlights the importance of the mycobiota in asthma control and may contribute to the development of fungi-based markers to predict asthma exacerbation.

Characterization of the Eukaryotic Virome of Mice from Different Sources

Accumulating studies show that the host microbiome influences the development or progression of many diseases. The eukaryotic virome, as a key component of the microbiome, plays an important role in host health and disease in humans and animals, including research animals designed to model human disease. To date, the majority of research on the microbiome has focused on bacterial populations, while less attention has been paid to the viral component. Members of the eukaryotic virome interact with the commensal bacterial microbiome through trans-kingdom interactions, and influence host immunity and disease phenotypes as a collective microbial ecosystem. As such, differences in the virome may affect the reproducibility of animal models, and supplementation of the virome may enhance the translatability of animal models of human disease. However, there are minimal empirical data regarding differences in the virome of mice from different commercial sources. Our hypotheses were that the mice obtained from pet store sources and lab mice differ in their eukaryotic virome, and that lab mice from different sources would also have different viromes. To test this hypothesis, the ViroCap platform was used to characterize the eukaryotic virome in multiple tissues of mice from different sources including three sources of laboratory mice and two pet stores. As expected, pet store mice harbored a much greater diversity within the virome compared to lab mice. This included an ostensibly novel norovirus strain identified in one source of these mice. Viruses found in both laboratory and pet store populations included four strains of endogenous retroviruses and murine astrovirus with the latter being restricted to one source of lab mice. Considering the relatively high richness virome within different samples from healthy humans, these data suggest that mouse models from alternative sources may be more translational to the human condition. Moreover, these data demonstrate that, by characterizing the eukaryotic murine virome from different sources, novel viruses may be identified for use as field strains in biomedical research.

Metagenomic analysis of DNA viruses from posttransplant lymphoproliferative disorders

Posttransplant lymphoproliferative disorders (PTLDs), 50%-80% of which are strongly associated with Epstein-Barr virus (EBV), carry a high morbidity and mortality. Most clinical/epidemiological/tumor characteristics do not consistently associate with worse patient survival, so our aim was to identify if other viral genomic characteristics associated better with survival. We extracted DNA from stored paraffin-embedded PTLD tissues at our center, identified viral sequences by metagenomic shotgun sequencing (MSS), and analyzed the data in relation to clinical outcomes. Our study population comprised 69 PTLD tissue samples collected between 1991 and 2015 from 60 subjects. Nucleotide sequences from at least one virus were detected by MSS in 86% (59/69) of the tissues (EBV in 61%, anelloviruses 52%, gammapapillomaviruses 14%, CMV 7%, and HSV in 3%). No viruses were present in higher proportion in EBV-negative PTLD (compared to EBV-positive PTLD). In univariable analysis, death within 5 years of PTLD diagnosis was associated with anellovirus (P = 0.037) and gammapapillomavirus (P = 0.036) detection by MSS, higher tissue qPCR levels of the predominant human anellovirus species torque teno virus (TTV; P = 0.016), T cell type PTLD, liver, brain or bone marrow location. In multivariable analyses, T cell PTLD (P = 0.006) and TTV PCR level (P = 0.012) remained significant. In EBV-positive PTLD, EBNA-LP, EBNA1 and EBNA3C had significantly higher levels of nonsynonymous gene variants compared to the other EBV genes. Multiple viruses are detectable in PTLD tissues by MSS. Anellovirus positivity, not EBV positivity,was associated with worse patient survival in our series. Confirmation and extension of this work in larger multicenter studies is desirable.

Remnant Small Bowel Length in Pediatric Short Bowel Syndrome and the Correlation with Intestinal Dysbiosis and Linear Growth

BACKGROUND

Pediatric short bowel syndrome (SBS) is a malabsorptive state placing patients at risk for malnutrition, dehydration, and bacterial overgrowth. These patients are often dependent on parenteral nutrition (PN) while intestinal adaptation is underway. The aim of this study was to characterize the effect of remnant small bowel length on the gut microbiome. Further, we sought to examine the contribution of clinical and nutritional variables to the gut microbiota and anthropometric growth.

STUDY DESIGN

Clinical data, anthropometrics, and fecal samples were collected from 14 SBS patients and 10 age- and sex-matched controls. Fecal bacterial DNA composition was analyzed using 16s ribosomal RNA gene sequencing. Statistical analysis was completed using the Mann-Whitney or Fisher's exact tests when applicable and linear mixed effect modeling.

RESULTS

Distinct microbiota changes were found among those with the least remaining small bowel (<35 cm) compared with those with longer remaining bowel and controls. Those with <35 cm small bowel displayed an increased relative abundance of Proteobacteria, while those with longer remaining small bowel had a higher proportion of Firmicutes. Further, patients with less remaining bowel required more PN (p < 0.01), with a tendency to be shorter in height (p = 0.05) and with a higher BMI (p = 0.05).

CONCLUSIONS

Remnant small bowel length appears to be a predictor of stunting with diminished linear growth, parenteral nutrition dependency, and a greater relative abundance of Proteobacteria in the gut. These findings suggest an integrated adaptive response predicted by remnant intestinal length. Further research is necessary to examine the effects of intestinal dysbiosis on clinical outcomes.

Erectile dysfunction and lower urinary tract symptoms: a consensus on the importance of co-diagnosis

Despite differences in design, many large epidemiological studies using well-powered multivariate analyses consistently provide overwhelming evidence of a link between erectile dysfunction (ED) and lower urinary tract symptoms (LUTS). Preclinical evidence suggests that several common pathophysiological mechanisms are involved in the development of both ED and LUTS. We recommend that patients seeking consultation for one condition should always be screened for the other condition. We propose that co-diagnosis would ensure that patient management accounts for all possible co-morbid and associated conditions. Medical, socio-demographic and lifestyle risk factors can help to inform diagnoses and should be taken into consideration during the initial consultation. Awareness of risk factors may alert physicians to patients at risk of ED or LUTS and so allow them to manage patients accordingly; early diagnosis of ED in patients with LUTS, for example, could help reduce the risk of subsequent cardiovascular disease. Prescribing physicians should be aware of the sexual adverse effects of many treatments currently recommended for LUTS; sexual function should be evaluated prior to commencement of treatment, and monitored throughout treatment to ensure that the choice of drug is appropriate.

Review of drug treatment for female sexual dysfunction

Female sexual dysfunction (FSD) incorporates various sexual disorders including hypoactive sexual desire disorder, sexual arousal disorder, orgasmic and sexual pain disorders. Although many strategies have been formulated for the treatment of male sexual problems, FSD remains an area that warrants further research and trial studies to identify the most efficacious treatment options. Research has highlighted numerous pharmacological interventions that have been trialled and found to exhibit positive effects. These include hormonal therapies, prostaglandins, dopaminergic agonists, phosphodiesterase type-5 (PDE-5) inhibitors and melanocortin agonists.

Management of psychosexual and relationship problems in general mental health services by psychiatry trainees

AIMS AND METHODS

All psychiatry trainees (both Basic and Higher Specialist Trainees in Adult and Old Age Psychiatry) in the Nottingham (Mid-Trent rotation) were invited to complete a questionnaire evaluating the assessment and training of psychosexual and relationship problems in the general mental health services.

RESULTS

Only 24% of trainees reported to routinely asked patients about psychosexual history, 65% felt comfortable about taking a detailed psychosexual history. 81% of trainees reported inadequacy whilst dealing with psychosexual disorders during their training in psychiatry. Only 30% reported asking patients for potential sexual side-effects when on psychotropic medication. All the trainees would refer the patient to a local psychosexual disorder clinic (if available).

CLINICAL IMPLICATIONS

Taking a sexual and relationship (both past and current) history should be an integral part of any psychiatric assessment. Training in human sexuality should be introduced in medical schools. Training in human sexuality is a core part of psychiatric training curriculum and trainees should be tested for their competency in dealing with sexual dysfunctions.

Double-blind placebo-controlled study of testosterone patch therapy on bone turnover in men with borderline hypogonadism

Clinical studies suggest there may be a threshold concentration of serum testosterone below which replacement will result in skeletal and psychological benefit. We evaluated the response to testosterone in men with borderline hypogonadism. A randomized double-blind placebo-controlled trial in 39 men over age 40 years presenting with sexual dysfunction and a borderline low testosterone level (total testosterone <10 nmol/L or free androgen index <30%). Patients were randomized to Testoderm TTS body patch (5 mg/day, n = 20) or a placebo patch (n = 19) for 6 months, followed by open-label testosterone replacement for a further 6 months in all patients. During the placebo-controlled phase of the study serum testosterone increased significantly on testosterone vs. placebo treatment (p = 0.004); this was associated with a decrease in total body fat mass (p = 0.019) and increase in haemoglobin level (p = 0.036). There were no significant changes in lean body mass, markers of bone turnover, and measures of bone mineral density (BMD). There was evidence of difference in quality of life according to the Male Erectile Dysfunction Quality of Life questionnaire (MEDQoL score, p = 0.017), mainly accounted for by deterioration in the placebo arm. When the active treatment period was combined for placebo and testosterone groups, the within-patient analysis showed a significant effect of testosterone to decrease markers of bone resorption (uNTX/Cr, p = 0.007; iFDPD/Cr, p = 0.0006) and to increase lean body mass (p = 0.001). There was little convincing evidence from this study that testosterone replacement is likely to have major benefit in men over age 40 years with borderline hypogonadism and sexual dysfunction. However, there was evidence of suppression in bone resorption and hence longer and larger studies are needed to examine its effect on BMD.

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions.

A physical map of the chicken genome

Strategies for assembling large, complex genomes have evolved to include a combination of whole-genome shotgun sequencing and hierarchal map-assisted sequencing. Whole-genome maps of all types can aid genome assemblies, generally starting with low-resolution cytogenetic maps and ending with the highest resolution of sequence. Fingerprint clone maps are based upon complete restriction enzyme digests of clones representative of the target genome, and ultimately comprise a near-contiguous path of clones across the genome. Such clone-based maps are used to validate sequence assembly order, supply long-range linking information for assembled sequences, anchor sequences to the genetic map and provide templates for closing gaps. Fingerprint maps are also a critical resource for subsequent functional genomic studies, because they provide a redundant and ordered sampling of the genome with clones. In an accompanying paper we describe the draft genome sequence of the chicken, Gallus gallus, the first species sequenced that is both a model organism and a global food source. Here we present a clone-based physical map of the chicken genome at 20-fold coverage, containing 260 contigs of overlapping clones. This map represents approximately 91% of the chicken genome and enables identification of chicken clones aligned to positions in other sequenced genomes.

Psychological difficulties within a group of patients with vulvodynia

This study reviews and reports on some of the psychological difficulties seen in a group of women with vulval pain (vulvodynia). The investigation involved 164 women (82 suffering with Vulvodynia and 82 women in a control group with general dermatology conditions) to establish the prevalence of psychological difficulties using validated questionnaires (SCL-90R and the IBQ) and reports on the possible effect these may have on sexual and relationship function and satisfaction. The level of psychological difficulties revealed significantly higher levels of psychological distress in the vulvodynia group within the domains of somatisation, obsessive-compulsive, depression, anxiety & phobic symptoms as well as with interpersonal sensitivity hostility and paranoia.

The DNA sequence of human chromosome 7

Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present more than 153 million base pairs representing 99.4% of the euchromatic sequence of chromosome 7, the first metacentric chromosome completed so far. The sequence has excellent concordance with previously established physical and genetic maps, and it exhibits an unusual amount of segmentally duplicated sequence (8.2%), with marked differences between the two arms. Our initial analyses have identified 1,150 protein-coding genes, 605 of which have been confirmed by complementary DNA sequences, and an additional 941 pseudogenes. Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame.

A physical map of the mouse genome

A physical map of a genome is an essential guide for navigation, allowing the location of any gene or other landmark in the chromosomal DNA. We have constructed a physical map of the mouse genome that contains 296 contigs of overlapping bacterial clones and 16,992 unique markers. The mouse contigs were aligned to the human genome sequence on the basis of 51,486 homology matches, thus enabling use of the conserved synteny (correspondence between chromosome blocks) of the two genomes to accelerate construction of the mouse map. The map provides a framework for assembly of whole-genome shotgun sequence data, and a tile path of clones for generation of the reference sequence. Definition of the human-mouse alignment at this level of resolution enables identification of a mouse clone that corresponds to almost any position in the human genome. The human sequence may be used to facilitate construction of other mammalian genome maps using the same strategy.

A physical map of the human Y chromosome

The non-recombining region of the human Y chromosome (NRY), which comprises 95% of the chromosome, does not undergo sexual recombination and is present only in males. An understanding of its biological functions has begun to emerge from DNA studies of individuals with partial Y chromosomes, coupled with molecular characterization of genes implicated in gonadal sex reversal, Turner syndrome, graft rejection and spermatogenic failure. But mapping strategies applied successfully elsewhere in the genome have faltered in the NRY, where there is no meiotic recombination map and intrachromosomal repetitive sequences are abundant. Here we report a high-resolution physical map of the euchromatic, centromeric and heterochromatic regions of the NRY and its construction by unusual methods, including genomic clone subtraction and dissection of sequence family variants. Of the map's 758 DNA markers, 136 have multiple locations in the NRY, reflecting its unusually repetitive sequence composition. The markers anchor 1,038 bacterial artificial chromosome clones, 199 of which form a tiling path for sequencing.

A physical map of the human genome

The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.

Deliberate self-harm and substance dependence: the management of patients seen in the general hospital

The aim of this study was to examine management decisions made at the time of assessment of an episode of deliberate self-harm seen in the general hospital and examine the extent of referral to a specialized addiction unit. Factors involved in making a clinical decision regarding the appropriate management of self-harm cases when alcohol factors were identified are reviewed. Simply referring to a specialized addiction unit was found to be an unsatisfactory method of providing a comprehensive response to the problem of substance misuse and deliberate self-harm. It is suggested that services should be developed using active posthospital discharge community follow-up. Motivational interviewing used in such a setting may increase the number of patients who will go on to accept specialist care.

Diagnosis and surgical management of obstructive ureteral calculi in cats: 11 cases (1993-1996)

OBJECTIVE

To evaluate diagnostic methods, surgical treatment, perioperative management, and renal function of cats with obstructive calcium oxalate ureteroliths.

DESIGN

Retrospective case series.

ANIMALS

11 cats that underwent surgery for removal of calcium oxalate ureteroliths.

PROCEDURE

Medical records were reviewed, and the following information was recorded: signalment; results of physical examination, clinicopathologic analyses, and abdominal imaging; surgical procedure; postoperative management; and results of ureterolith quantitative analysis.

RESULTS

Ureteroliths in the proximal portion of the ureter were removed from 5 cats (pyelotomy, 1 cat; unilateral ureterotomy, 2 cats; bilateral ureterotomies, 2 cats). Calculi in the middle and distal part of the ureter were removed by partial ureterectomy and ureteroneocystostomy (6 cats). Ten cats recovered from surgery and were discharged from the hospital. One cat died from unknown causes 4 months after surgery, and 1 cat had a nephrectomy elsewhere 5 weeks after ureterolith removal. Eight cats were evaluated 12 to 20 months after surgery. Of these, 2 cats that were markedly azotemic before surgery improved after surgery, and 2 cats developed nephroliths after surgery. Also, of 5 cats that had nephroliths that were not removed at the time of surgery, 4 still had visible nephroliths. One cat had recurrent ureteral obstruction from a ureterolith and persistent urinary tract infection. Ureteroliths or ultrasonographic evidence of ureteral obstruction were not detected in other cats.

CLINICAL IMPLICATIONS

A combination of microsurgical techniques and intensive postoperative care is necessary to minimize morbidity of cats after removal of a ureterolith. Renal function may improve or stabilize after removal of the ureteral obstruction.

Pacing-induced chronic atrial fibrillation impairs sinus node function in dogs. Electrophysiological remodeling

BACKGROUND

We assessed the effects of pacing-induced chronic atrial fibrillation (AF) on sinus node function, intra-atrial conduction, and atrial refractoriness.

METHODS AND RESULTS

In 15 mongrel dogs (20 to 30 kg), AV nodal block was produced by radiofrequency catheter ablation, and a ventricular-inhibited (VVI) pacemaker (Minix 8330, Medtronic) was implanted and programmed to pace at 80 pulses per minute. In 11 of these dogs, right atrial endocardial pacing leads were connected to a pulse generator (Itrel 7432, Medtronic) and set at a rate of 20 Hz to induce AF. Corrected sinus node recovery time, P-wave duration, 24-hour Holter ECG to assess AF duration, maximal heart rate in response to isoproterenol (10 micrograms/min), intrinsic heart rate after administration of atropine (0.04 mg/kg) and propranolol (0.1 mg/kg), and atrial effective refractory periods (ERPs) were obtained at baseline (EPS-1) and after 2 to 6 weeks (EPS-2) of VVI pacing alone (n = 4) or VVI pacing and rapid atrial pacing (n = 11). At EPS-2, corrected sinus node recovery time and P-wave duration were prolonged, maximal heart rate and intrinsic heart rate were decreased, atrial ERPs were shortened, and the duration of AF was increased significantly compared with EPS-1. These changes partially reversed toward baseline 1 week after conversion to sinus rhythm. Sinus node function and AF inducibility observed in the control dogs that underwent ventricular pacing alone (n = 4) did not change.

CONCLUSIONS

Pacing-induced chronic AF induces sinus node dysfunction, prolongs intra-atrial conduction time, shortens atrial refractoriness, and perpetuates AF, changes that reverse gradually after termination of AF.

Pilot mental health assessment and diversion scheme for an English Metropolitan Petty Sessional Division

A three-month pilot mental health assessment and diversion scheme was carried out at one of the busiest magistrates' courts outside London. In terms of demographic characteristics the sample of prisoners seen in this study was similar to those seen in diversion schemes in London and Manchester. Although 77 per cent of prisoners were found to be suffering from a psychiatric disorder, almost half were suffering from alcohol or drug dependence or misuse and the number with psychotic illnesses was small compared with the London sample. These differences may be partly due to the earlier diversion of acutely mentally ill prisoners from police custody into the health care system in Leeds. The low rate of psychiatric admission from the pilot scheme largely reflected these differences although in the cases of four patients admission was recommended by the assessing psychiatrist but not effected because of the lack of regional secure beds. Other problems identified by those involved in the scheme were the need for the provision of bail hostels specializing in the care of those with psychiatric difficulties and the need for the involvement of community psychiatric nurses within the assessment and diversion scheme.

Regular monitoring: the way to ensure flap healing. Nursing priorities following flap repair and reconstruction surgery

Surgical flap techniques are no longer confined to specialist plastic surgery units, and more nurses are being asked to manage patients following reconstructive surgery. Nursing management involves ensuring the flap's survival and healing.