Study protocol P-MAPS: microbiome as predictor of severity in acute pancreatitis-a prospective multicentre translational study

Background

Acute pancreatitis (AP) is an inflammatory disorder that causes a considerable economic health burden. While the overall mortality is low, around 20% of patients have a complicated course of disease resulting in increased morbidity and mortality. There is an emerging body of evidence that the microbiome exerts a crucial impact on the pathophysiology and course of AP. For several decades multiple clinical and laboratory parameters have been evaluated, and complex scoring systems were developed to predict the clinical course of AP upon admission. However, the majority of scoring systems are determined after several days and achieve a sensitivity around 70% for early prediction of severe AP. Thus, continued efforts are required to investigate reliable biomarkers for the early prediction of severity in order to guide early clinical management of AP patients.

Methods

We designed a multi-center, prospective clinical-translational study to test whether the orointestinal microbiome may serve as novel early predictor of the course, severity and outcome of patients with AP. We will recruit 400 AP patients and obtain buccal and rectal swabs within 72 h of admission to the hospital. Following DNA extraction, microbiome analysis will be performed using 3rd generation sequencing Oxford Nanopore Technologies (ONT) for 16S rRNA and metagenomic sequencing. Alpha- and beta-diversity will be determined and correlated to the revised Atlanta classification and additional clinical outcome parameters such as the length of hospital stay, number and type of complications, number of interventions and 30-day mortality.

Discussion

If AP patients show a distinct orointestinal microbiome dependent on the severity and course of the disease, microbiome sequencing could rapidly be implemented in the early clinical management of AP patients in the future.

Trial registration: ClinicalTrials.gov Identifier: NCT04777812

Ultrastructural Changes of the Tracheal Epithelium after Vaccination of Day-Old Chickens with the La Sota Strain of Newcastle Disease Virus

The progression of tracheal lesions induced by vaccination of day-old specific pathogen-free chicks with the La Sota strain of Newcastle disease virus (NDV) was examined by relating surface changes as observed by scanning electron microscopy with subcellular changes seen by transmission electron microscopy. NDV infection resulted in hypertrophy of goblet cells, their rupture, and the formation of excess mucus. Activation of goblet cells peaked within 4 days postvaccination. Afterward, the activation levels gradually decreased. At the level of the ciliated cells, a marked increase in the proportion of nonciliated to ciliated cells and later an almost complete deciliation of the tracheal surface were observed because a simple squamous to cuboidal epithelium replaced the original pseudostratified epithelium. Fifteen days postvaccination, all epithelial damage was restored. Because the observed vaccination-induced lesions are detrimental to epithelial integrity and function as a barrier against invading microorganisms, they might explain at the ultrastructural level the secondary complications of vaccination with the La Sota strain against NDV

Chasing notifiable avian influenza in domestic poultry: a case report of low-pathogenic avian influenza h5 viruses in two Belgian holdings

In December 2008, bird species in two geographically distant holdings were found positive for H5 viruses following the annual Avian influenza serological screening in Belgium. The virological tests performed identified in one holding a low-pathogenic avian influenza (LPAI) virus subtype H5N2, and a H5 LPAI virus was identified by real-time PCR and direct sequencing at the second holding. The first farm was an outdoor mixed holding housing ornamental birds and poultry (n = 6000) and the second a free-range geese breeding farm (n = 1500). No clinical signs or mortalities were reported. Control measures defined by Council Directive 2005/94/EC were followed, including notification to the European Commission via the Animal Disease Notification System and to the World Organization for Animal Health, and poultry were killed, while ornamental bird species were quarantined. Partial sequencing of the H5N2 virus haemagglutinin and neuraminidase N2 gene sequences revealed a close homology to some recent LPAI isolates identified from wild birds in Germany and Italy and from wild birds in Eurasia and Africa, respectively. It is noteworthy that, these two holdings were already H5 positive based on HI test results carried out during the previous serological screening; however, no virus was detected at that time. To have a better understanding of the potential 'silent' circulation of the H5N2 isolate in the field, experimental infections of chickens and turkeys were performed. The low excretion detected might in part explain viral persistence not associated with spread between gallinaceous birds in the same holding, indicating that the H5N2 LPAI isolate was not fully adapted to these two poultry species. Our results highlighted limitations to only using serological screening for the early detection of LPAI in an 'at-risk farm', suggesting that virological and serological monitoring tests be applied simultaneously as a means of testing animals in 'at-risk farms'.

Molecular epidemiological analysis of the transboundary transmission of 2003 highly pathogenic avian influenza H7N7 outbreaks between the Netherlands and Belgium

The 2003 outbreak of Highly pathogenic avian influenza (HPAI) A(H7N7) in the Netherlands, Belgium and Germany resulted in significant genetic diversification that proved informative for tracing transmission events. Building on previous investigations on the Dutch outbreak, we focused on the potential transnational transmissions between the Netherlands and Belgium. Although no clear epidemiological links could be identified from the tracing data, the transmission network based on concatenated HA-NA-PB2 sequences supports at least three independent introductions from the Netherlands to Belgium and suggests one possible introduction form Belgium back to the Netherlands. Two introductions in the Belgian province of Limburg occurred from nearby farms in the Dutch province of Limburg. One introduction resulted in three secondary infected farms, while a second introduction did not cause secondary infections. The third introduction into Belgium occurred in the north of the Antwerp province, very close to the national border, and originated from the North of the Dutch province Brabant (long distance transmission, >65 km). The virus spread to two additional Belgian farms, one of which may be the source of a secondarily infected farm in the Netherlands. One infected turkey farm in the province of Antwerp (Westmalle) was geographically close to the latter introduction, but genetically clustered with the first introduction event in the Limburg province. Epidemiological tracing data could neither confirm nor exclude whether this outbreak was a result from long distance contacts within Belgium or whether this farm presented a fourth independent transboundary introduction. These multiple transnational transmissions of HPAI in spite of reinforced biosecurity measures and trade restrictions illustrate the importance of international cooperation, legislation and standardization of tools to combat transboundary diseases.

Alien invasive birds

A bird species is regarded as alien invasive if it has been introduced, intentionally or accidentally, to a location where it did not previously occur naturally, becomes capable of establishing a breeding population without further intervention by humans, spreads and becomes a pest affecting the environment, the local biodiversity, the economy and/or society, including human health. European Starling (Sturnus vulgaris), Common Myna (Acridotheres tristis) and Red-vented Bulbul (Pycnonotus cafer) have been included on the list of '100 of the World's Worst Invasive Alien Species', a subset of the Global Invasive Species Database. The 'Delivering Alien Invasive Species Inventories for Europe' project has selected Canada Goose (Branta canadensis), Ruddy Duck (Oxyura jamaicensis), Rose-ringed Parakeet (Psittacula krameri) and Sacred Ibis (Threskiornis aethiopicus) as among 100 of the worst invasive species in Europe. For each of these alien bird species, the geographic range (native and introduced range), the introduction pathway, the general impacts and the management methods are presented.

Vaccination of birds other than chickens and turkeys against avian influenza

Most avian influenza (AI) vaccination and field studies have focused on chickens and turkeys because of their high death rates and the large amounts of highly pathogenic avian influenza (HPAI) virus that they excrete into the environment when infected. Data on vaccination of other species against HPAI remain limited. An increasing number of studies have been conducted to test the efficacy of inactivated vaccines in ducks and geese since it became clear that these species are a source of HPAI H5N1. One problem is the varying susceptibility of waterfowl to H5N1 in general, and to different H5N1 clades in particular. This makes the extrapolation of protection results obtained for a particular waterfowl species against a particular viral strain very difficult. At present, the vaccine industry only produces and licenses products for chickens and turkeys. Since the market for other birds is small, it does not invest heavily in testing products in other species. Most information on vaccination in other birds comes from zoo vaccination, and consists solely of serological data. Whenever experimental challenge was performed in birds other than chickens and turkeys, vaccination using inactivated vaccines always protected against disease and mortality, provided the vaccine was sufficiently matched antigenically with the challenge virus. Inactivated vaccines induce good antibody titres in most species when applied twice and when body weight is taken into account. Until the advent of more specific waterfowl vaccines that can be used in day-old chicks, inactivated vaccines can be applied to protect not only chickens and turkeys but also ducks and other valuable and/or endangered bird species.

Prime-boost vaccination with a fowlpox vector and an inactivated avian influenza vaccine is highly immunogenic in Pekin ducks challenged with Asian H5N1 HPAI

The efficacy of different vaccination schedules was evaluated in 17-day-old Pekin ducks using an experimental inactivated whole virus vaccine based on the H5N9 A/chicken/Italy/22A/98 isolate (H5N9-It) and/or a fowlpox recombinant (vFP-H5) expressing a synthetic HA gene from an Asian H5N1 isolate (A/chicken/Indonesia/7/2003). Full protection against clinical signs and shedding was induced by the different vaccination schemes. However, the broadest antibody response and the lowest antibody increase after challenge were observed in the group of ducks whose immune system was primed with the fowlpox vectored vaccine and boosted with the inactivated vaccine, suggesting that this prime-boost strategy induced optimal immunity against H5N1 and minimal viral replication after challenge in ducks. In addition, this prime-boost vaccination scheme was shown to be immunogenic in 1-day-old ducklings.

Avian influenza outbreak management: action at time of confirmation, depopulation and disposal methods; the 'Belgian experience' during the H7N7 highly pathogenic avian influenza epidemic in 2003

Eradication of H5 and H7 influenza in a positive flock will include mass depopulation of birds, containment and inactivation of the virus in the carcasses and litter, and decontamination of the facility. A quick response is desired in the event of a disease outbreak. Ideally, birds should be depopulated within 24 h after detecting the virus. Mass depopulation of birds must be performed in a humane manner while minimizing human health and biosecurity risks. In the framework of the European legislation, a number of methods are authorized for the killing of poultry for processing prior to marketing. However, during emergencies such as a disease outbreak, there are fewer options. The current most commonly used procedures for large-scale emergency depopulation of birds consist of exposing poultry to CO or CO(2) gas. Both gasses have been used in Belgium during the H7N7 crisis in 2003. The gassing procedures include whole house gassing, portable panel enclosures, cage cabinets, containers and polyethylene tent method. Whole house gassing requires sealing the house to prevent gas leakage and, using specialized equipment, introducing large volumes of gas evenly over the birds. All procedures are very labour intensive, create a biosecurity risk and require a large number of personnel. There are considerable region-to-region differences in emergency depopulation techniques and disposal of carcasses and infected material. Because of the differences in bird type and species, management, housing and stocking density, it is difficult to propose a depopulation technique that will be suitable for all circumstances. Safety of the human operators is an increasing concern with all H5 and H7 strains and in particular with the highly pathogenic H5N1 strain. Researchers and commercial poultry companies in the United States recently established that non-toxic water-based foam with a certain bubble size presents a practicable, effective and humane method for mass depopulation. Foam of the right bubble size creates an occlusion in the trachea of birds, causing a rapid onset of hypoxia. The foam that blankets the broiler house induces physical hypoxia - the same cause of death as the approved method using carbon dioxide gas (CO(2)). The article illustrates the different culling and disposal methods with a focus on the methods used during the 2003 H7N7 crisis in Belgium.

Efficacy of an Inactivated and a Fowlpox-Vectored Vaccine in Muscovy Ducks Against an Asian H5N1 Highly Pathogenic Avian Influenza Viral Challenge

The efficacy of an inactivated vaccine containing the Eurasian isolate A/chicken/Italy/22A/98 H5N9 (H5N9-It) was compared with that of the fowlpox-vectored TROVACTM-AIV H5 (rFP-AIV-H5) vaccine against an H5N1 highly pathogenic avian influenza challenge. Five-week-old Muscovy ducks were vaccinated with either H5N9-It (0.5 ml) or rFP-AIV-H5 (5 log10 50% tissue culture infectious dose (TCID50)/dose), followed by a boost at 7 wk of age with the same vaccine (1.0 ml of H5N9-It or 5 log10 TCID50/dose rFP-AIV-H5), and a challenge at 9 wk of age with 10(7) egg infectious dose (lethality 50%) of A/crested eagle/ Belgium/01/2004 (H5N1). All unvaccinated challenged birds showed severe nervous signs (loss of balance, torticollis) starting 7 days postinfection (dpi). None of the vaccinated ducks showed these nervous signs. Shedding was measured in oropharyngeal and cloacal swabs, sampled from 3 to 19 dpi by titration in chicken embryo fibroblasts and by real-time reverse transcription-polymerase chain reaction. Virus shedding was significantly higher in oropharyngeal compared to cloacal swabs. Both vaccines reduced the percentage of positive swabs and the viral load in the swabs, but the reduction was higher with the H5N9-It vaccine. The inactivated vaccine induced hemagglutination inhibition (HI) titers (5.4 log2) that were boosted after the second administration (7.5 log2). rFP-AIV-H5-induced HI titers were lower (3 log2 only after the second administration), most probably because the fowlpox vector does not replicate in ducks. Altogether, these results indicate that significant protection from clinical signs and reduction in virus shedding may be achieved in ducks with conventional inactivated or fowlpox-vectored vaccine as compared with nonvaccinated challenged control birds.

A Universal Avian Endogenous Real-Time Reverse Transcriptase–Polymerase Chain Reaction Control and Its Application to Avian Influenza Diagnosis and Quantification

Real-time reverse transcriptase-polymerase chain reaction (RRT-PCR) is becoming an established first-line diagnostic assay as well as a precise quantification tool for avian influenza virus detection. However, there remain some limitations. First, we show that the sensitivity of RRT-PCR influenza detection can be 10- to 100-fold inhibited in oropharyngeal and cloacal swabs. Adding 0.5 U of heat-activated Taq DNA polymerase successfully reverses PCR inhibition. Second, an excellent strategy for detecting false negative samples is the coamplification of an internal control from each sample. We developed a universal avian endogenous internal control (bird beta-actin) and apply it to influenza A diagnosis. Moreover, this internal control proves useful as a normalizer control for virus quantification, because beta-actin gene expression does not change in infected vs. uninfected ducks. A combined panel of wild bird cloacal swabs, wild bird tissue samples, experimental duck swabs, and experimental duck and chicken tissue samples was used to validate the endogenous control. The application of an endogenous internal control proves an excellent strategy both for avoiding false negative diagnostic results and for standardizing virus quantification studies.

Lethality and Molecular Characterization of an HPAI H5N1 Virus Isolated from Eagles Smuggled from Thailand into Europe

On October 18, 2004, two crested hawk eagles, Spizaetus nipalensis, smuggled into Europe from Thailand were seized at Brussels International Airport. A highly pathogenic avian influenza virus, denominated A/crested eagle/Belgium/01/2004, was isolated from these birds and antigenically characterized as H5N1. Here we report on the molecular characterization of A/crested eagle/Belgium/01/2004 (H5N1). We completely sequenced all eight genome segments. The hemagglutinin (HA) and neuraminidase (NA) sequences clustered within the Z genotype and were closely related to strains circulating in Thailand during 2004, although some mutations in the HA were evident, notably a unique arginine (R) > lysine (K) replacement in the cleaving site. The HA cleavage site contained six basic amino acids, confirming its high pathogenicity (intravenous pathogenicity index = 2.94). The 20-amino acid deletion in the NA stalk region is consistent with its Thai-Viet origin. We further discuss the assembled genetic information in the light of currently known host adaptation, virulence, and antiviral resistance factors. Using infection experiments, we show that pathogenicity in chickens depends on breed, inoculation route (oculonasal vs. intramuscular), and dose. Additionally, in Muscovy ducks, pathogenicity proved to be age dependent.

Development of an M2e-Specific Enzyme-Linked Immunosorbent Assay for Differentiating Infected from Vaccinated Animals

Vaccination programs for the control of avian influenza (AI) in birds have restrictions because of some limited efficacy and the difficulty of discriminating between vaccinated and virus-infected poultry. We studied M2e, the highly conserved external domain of the influenza A M2 protein, as a potential differential diagnostic marker for influenza virus infection. The M2 protein is an integral membrane protein, scarcely present on virus particles, but abundantly expressed on virus-infected cells. M2e-specific enzyme-linked immunosorbent assays (ELISAs) for different avian influenza strains were developed by coating the peptides corresponding to the first 18 amino acids, without the first methionine, of the universal human consensus M2e sequence and the specific M2e sequence of two highly pathogenic AI (HPAI) strains, H7N7 and H5N1. Using the M2e ELISAs, M2e-specific antibodies were observed in chickens and ducks experimentally infected with H7 or H5 HPAI, respectively, that correlated well with hemagglutination inhibition (HI) antibodies. Conversely, sera from chicken and ducks inoculated with inactivated AI vaccines were positive for HI test but negative for the M2e ELISAs. Moreover, ducks inoculated with inactivated vaccine and challenged with a HPAI H5N1 seroconverted for antibodies to the M2e peptide, with significantly different levels from those measured between the vaccinated and infected groups. These results indicate the potential benefit of a simple and specific M2e ELISA in the assessment of the efficacy of vaccination as well as for diagnostic and survey applications.

Tuberculosis DNA vaccine encoding Ag85A is immunogenic and protective when administered by intramuscular needle injection but not by epidermal gene gun bombardment

Immunogenicity and protective efficacy of a DNA vaccine encoding Ag85A from Mycobacterium tuberculosis were compared in BALB/c and C57BL (B6 and B10) mice immunized by intramuscular (i.m.) needle injection or epidermal gene gun (gg) bombardment. In BALB/c mice, gg immunization could induce elevated antibody and cytotoxic T lymphocyte responses with plasmid doses 50-fold lower than those required for i.m. immunization. Interleukin-2 (IL-2) and gamma interferon (IFN-gamma) secretion, however, was much lower in gg-immunized than in i.m.-immunized BALB/c mice. On the other hand, C57BL mice reacted only very weakly to gg immunization, whereas elevated Ag85A-specific antibody, IL-2, and IFN-gamma responses (significantly higher than in BALB/c mice) were detected following vaccination by the i.m. route. Antibody isotypes were indicative of Th2 activation following gg injection of BALB/c and of Th1 activation following i.m. injection of C57BL mice. Finally, C57BL but not BALB/c mice were protected by i.m. Ag85A DNA immunization against intravenous M. tuberculosis challenge, as measured by reduced numbers of CFU in spleen and lungs, compared to animals vaccinated with control DNA. Gene gun immunization was not effective in either BALB/c or C57BL mice. These results indicate that i.m. DNA vaccination is the method of choice for the induction of protective Th1 type immune responses with the Ag85A tuberculosis DNA vaccine.

Identification of Melissa officinalis Subspecies by DNA Fingerprinting

The random amplified polymorphic DNA analysis (RAPD) is a method to study genetic variability within and between populations and species on the basis of the amplification of anonymous fragments from genomic DNA templates by means of polymerase chain reaction (PCR). We applied RAPD analysis in order to distinguish medicinal plant subspecies at the level of their genomes. In this study we investigated various samples of two MELISSA subspecies and showed that RAPD analysis is a fast and reliable method to distinguish subspecies on the pharmaceutical market that have been previously classified according to the distribution pattern of compounds present in the lemon balm oil.

The role of the spleen in the organ-specific metastasis of murine BW 5147 T lymphomas

Organ-specific metastasis of tumour cells may result from selective invasion and growth or from selective host cell responses. The present study demonstrates how selective interactions with the host affect the metastatic pattern of two murine T cell hybridoma lines, derived from the BW 5147 thymoma. Upon intravenous inoculation into syngeneic mice BW-14 cells preferentially colonize the kidneys, whereas BW-19 cells metastasize mainly to the spleen and the liver. The organ-specific behaviour of the two cell lines appears to be determined by a differential interaction with the spleen microenvironment. Inoculation of BW-14 cells into splenectomized mice results in increased liver colonization, indicating a negative effect of the spleen on BW-14 tumour development in the liver. Macrophages are likely to be involved in this inhibition, since inoculation of BW-14 cells into macrophage-depleted mice also leads to increased liver and spleen metastasis. In contrast, inoculation of BW-19 cells into splenectomized mice results in decreased liver metastasis, which indicates that the spleen exerts a stimulating effect on BW-19 cells. Macrophages also appear to be involved in this stimulation, since macrophage depletion causes a similar decrease in liver and spleen colonization. Hence components of the splenic microenvironment, probably macrophages, exert inhibiting or stimulating activities on BW-14 or BW-19 cells respectively, thereby determining the subsequent liver or kidney colonization.

Sexually transmitted diseases, antibodies to human immunodeficiency virus, and subsequent development of acquired immunodeficiency syndrome. Visitors of homosexual sauna clubs in Copenhagen: 1982-1983

Sera from 260 men from Denmark and elsewhere attending two Copenhagen sauna clubs for homosexual men during nine months of 1982-1983 were investigated for markers for syphilis, hepatitis A and B, and human immunodeficiency virus (HIV). Five per cent (12 men) had active syphilis, and another 35% (92) had a history of and/or serologic markers for syphilis. Ninety-four men (36%) were positive for antibodies to hepatitis A virus, ten (4%) were positive for hepatitis B surface antigen (HBsAg), and 153 (59%) were positive for antibodies to HBsAg. Antibodies to HIV were found in 45 (20%) of the 220 men investigated for this marker. Markers for hepatitis A and B and for syphilis were more frequent in the HIV antibody-positive individuals, but the association was significant only for markers for hepatitis B (relative risk = 2.0). Thus STD markers had little predictive value for seropositivity for antibodies to HIV. Among 37 men investigated more than once, a seroconversion rate of 3% per month for antibodies to HIV was found, but this estimate must be taken with reservation. The rate of seropositivity for antibodies to HIV among men from Denmark was 23%, and three (8%) of the 40 HIV-positive Danish men developed the acquired immunodeficiency syndrome (AIDS) during the four years following the initial investigation. This study shows that by 1982-1983 HIV had spread considerably in the Danish high-risk group, although there were only seven reported cases of AIDS in the country at that time.