Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Avian chlamydiosis in chickens: from cell to population

Chlamydia gallinacea and Chlamydia psittaci are intracellular bacteria belonging to the Chlamydiaceae family and are a cause of avian chlamydiosis in poultry. C. psittaci was considered the predominant chlamydial species in poultry until C. gallinacea was discovered in 2009. C. psittaci occurs worldwide, is zoonotic and has a wide host range. C. gallinacea is widespread in chickens, and infections appear asymptomatic, but reduced weight gain has been observed in broilers. Studies about the pathogenic potential of C. gallinacea are still limited, and any zoonotic potential has yet to be determined. The aim of this study was to gain insight into the prevalence of Chlamydia in Dutch chickens and to investigate the pathogenic potential of C. gallinacea. In a prevalence study, C. gallinacea was detected in around half of the 151 layer farms, but C. psittaci was not found. Subsequent research into the pathogenic potential of Dutch C. gallinacea strains showed that C. gallinacea mainly infects the mucosa of the chickens’ gut without causing clinical signs of inflammation. Finally, it was investigated whether a previous C. gallinacea infection in chickens could protect against a C. psittaci infection. This could explain why C. psittaci was not found during the field study in layers. However, protection against C. psittaci after a previous infection with C. gallinacea was not shown. In conclusion, Chlamydia infections in Dutch chickens cannot be considered a current One Health problem, but future introductions of C. psittaci cannot be excluded

Avian chlamydiosis in chickens: from cell to population

Chlamydia gallinacea and Chlamydia psittaci are intracellular bacteria belonging to the Chlamydiaceae family and are a cause of avian chlamydiosis in poultry. C. psittaci was considered the predominant chlamydial species in poultry until C. gallinacea was discovered in 2009. C. psittaci occurs worldwide, is zoonotic and has a wide host range. C. gallinacea is widespread in chickens, and infections appear asymptomatic, but reduced weight gain has been observed in broilers. Studies about the pathogenic potential of C. gallinacea are still limited, and any zoonotic potential has yet to be determined. The aim of this study was to gain insight into the prevalence of Chlamydia in Dutch chickens and to investigate the pathogenic potential of C. gallinacea. In a prevalence study, C. gallinacea was detected in around half of the 151 layer farms, but C. psittaci was not found. Subsequent research into the pathogenic potential of Dutch C. gallinacea strains showed that C. gallinacea mainly infects the mucosa of the chickens’ gut without causing clinical signs of inflammation. Finally, it was investigated whether a previous C. gallinacea infection in chickens could protect against a C. psittaci infection. This could explain why C. psittaci was not found during the field study in layers. However, protection against C. psittaci after a previous infection with C. gallinacea was not shown. In conclusion, Chlamydia infections in Dutch chickens cannot be considered a current One Health problem, but future introductions of C. psittaci cannot be excluded

Chlamydia psittaci and C. avium in feral pigeon (Columba livia domestica) droppings in two cities in the Netherlands

BACKGROUND: Feral pigeons (Columba livia domestica) live and breed in many city centres and contact with their droppings can be a hazard for human health if the birds carry Chlamydia psittaci. OBJECTIVE: The aim of this study was to establish whether pigeon droppings in two Dutch cities (Utrecht and Haarlem) contain C. psittaci and/or C. avium, which could be a potential hazard for transmission to humans. METHODS: In May 2017 seven feral pigeon 'hot spots' with between 5 and 40+ pigeons present were identified in two cities by visual observations over two days. During the following ten days fresh droppings were collected at these hot spots and the samples were pooled per three droppings to achieve 40 - 41 samples per city. Samples were analysed for Chlamydia DNA with a broad range 23S Chlamydiaceae Real-Time PCR and positive samples were tested with a specific C. psittaci and C. avium Real-Time PCR. Positive C. psittaci samples were genotyped. RESULTS: C. psittaci and C. avium were detected in both cities. For C. psittaci the prevalences in Utrecht and Haarlem were 2.4% and 7.5%, respectively; for C. avium 36.6% and 20.0%, respectively. One sample contained both species. All C. psittaci samples belonged to genotype B. CONCLUSION: C. psittaci and C. avium are present in feral pigeon droppings in Utrecht and Haarlem. Human contact with droppings from infected pigeons or inhalation of dust from dried droppings represent a potential hazard to public health

Chlamydia psittaci and C. avium in feral pigeon (Columba livia domestica) droppings in two cities in the Netherlands

Background: Feral pigeons (Columba livia domestica) live and breed in many city centres and contact with their droppings can be a hazard for human health if the birds carry Chlamydia psittaci. Objective: The aim of this study was to establish whether pigeon droppings in two Dutch cities (Utrecht and Haarlem) contain C. psittaci and/or C. avium, which could be a potential hazard for transmission to humans. Methods: In May 2017 seven feral pigeon ‘hot spots’ with between 5 and 40+ pigeons present were identified in two cities by visual observations over two days. During the following ten days fresh droppings were collected at these hot spots and the samples were pooled per three droppings to achieve 40–41 samples per city. Samples were analysed for Chlamydia DNA with a broad range 23S Chlamydiaceae Real-Time PCR and positive samples were tested with a specific C. psittaci and C. avium Real-Time PCR. Positive C. psittaci samples were genotyped. Results: C. psittaci and C. avium were detected in both cities. For C. psittaci the prevalences in Utrecht and Haarlem were 2.4% and 7.5%, respectively; for C. avium 36.6% and 20.0%, respectively. One sample contained both species. All C. psittaci samples belonged to genotype B. Conclusion: C. psittaci and C. avium are present in feral pigeon droppings in Utrecht and Haarlem. Human contact with droppings from infected pigeons or inhalation of dust from dried droppings represent a potential hazard to public health

Fatal chlamydia avium infection in captive picazuro pigeons, the Netherlands

In 2016, an outbreak of Chlamydia avium infection occurred among Picazuro pigeons (Patagioenas picazuro) living in an aviary in the Netherlands. Molecular typing revealed a unique strain of C. avium. Our findings show that C. avium infection, which usually causes subclinical infection, can cause fatal disease in pigeons.</p

Fatal Chlamydia avium Infection in Captive Picazuro Pigeons, the Netherlands

In 2016, an outbreak of Chlamydia avium infection occurred among Picazuro pigeons (Patagioenas picazuro) living in an aviary in the Netherlands. Molecular typing revealed a unique strain of C. avium. Our findings show that C. avium infection, which usually causes subclinical infection, can cause fatal disease in pigeons

Chlamydia psittaci in gezelschapsvogels : onderzoek naar de factoren die van invloed zijn op een positieve testuitslag na antibiotica behandeling

Psittacosis is a disease that can be transmitted from birds to humans and is caused by the intracellular bacterium Chlamydia psittaci. C. psittaci has been detected in more than 465 bird species and can cause clinical signs ranging from no symptoms to more severe symptoms such as conjunctivitis and pneumonia to liver failure and death. In humans, infection with C. psittaci can result in a flu-like illness and severe pneumonia, sometimes requiring hospitalisation. In the Netherlands, the disease is notifiable in humans and pet birds (except poultry). The number of human (40-70 per year) and veterinary (60-110 per year) notifications has been stable in recent years, but in 2019 there was a small increase in the number of human cases (91). The Netherlands Food and Consumer Product Safety Authority (NVWA) is responsible for the control in birds in the Netherlands, meaning the NVWA receives the notifications and carries out sampling. The owner of the birds is responsible for contacting a veterinarian to prescribe an antibiotic treatment. Two weeks after the treatment birds are retested. After treatment, birds regularly test positive with PCR, but the cause of these positive retests is unknown. In this report, existing NVWA dossiers were analysed to investigate which factors are associated with a positive retest after treatment. In total, 79 cases could be further analysed, of which 38 tested positive after the first treatment. Factors related to outdoor housing, possible outdoor contact and density appeared to be associated with a positive retest, although no strong relation was found. Additional research would be needed to confirm this relationship. In the data set, a large part of possible risk factors was missing, such as information related to treatment, housing, cleaning and disinfection. These factors could not be analysed. In addition, an improved treatment protocol for field cases was written based on existing literature. This protocol was used in one field case (autumn 2019). During this case study, it turned out that strict cleaning and disinfection is very difficult under field conditions. The analysis of the NVWA dossiers and the case study confirmed that bird husbandries are very diverse, with different types of housing and bird species. In addition, PCR results are sometimes difficult to interpret, as the presence of DNA is detected and not infectious C. psittaci bacteria, which requires a case-dependent approach. Overall, tailor-made advice is probably key in the control of psittacosis in pet birds. This report is the result of a research project within the statutory tasks of Wageningen Bioveterinary Research. This project aimed to improve the current control of psittacosis by evaluating information from available NVWA dossiers and systematically following up a number of field cases. In addition, antibiotic residues in bird feces were investigated. This information is not included in this report but will be reported to the Ministry of Agriculture, Nature and Food Quality via the usual reports

Chlamydia caviae in Swiss and Dutch Guinea Pigs—Occurrence and Genetic Diversity

Chlamydia (C.) caviae is a known pathogen in guinea pigs, causing conjunctivitis, respiratory infections and abortions. Recently, a C. caviae-induced zoonotic link was identified as the etiology of severe community-acquired pneumonia in humans. Here, 784 conjunctival and rectal swabs originating from 260 guinea pigs and 110 rabbits from 64 husbandries in Switzerland, as well as 200 composite conjunctival swabs originating from 878 guinea pigs from 37 husbandries in The Netherlands were examined by real-time PCR followed by conventional PCR and sequencing. Chlamydiaceae were detected in 2.3% (18/784) and 12.5% (25/200) of all Swiss and Dutch samples, respectively. An overall C. caviae occurrence was detected in 2.7% (7/260) and 8.9% (78/878) of all Swiss and Dutch guinea pigs, respectively. OmpA genotyping of 64 C. caviae-positive samples resulted in 33 sequences sharing 100% nucleotide identity with the strains isolated from the zoonotic transmission cases in The Netherlands. However, all ompA sequences of this study were distinct from the C. caviae GPIC reference strain. C. caviae was not detected in rabbits but C. psittaci genotype A was identified in guinea pigs and rabbits, raising concerns about the importance of these animal species as novel zoonotic sources for C. psittaci

Experimental Chlamydia gallinacea infection in chickens does not protect against a subsequent experimental Chlamydia psittaci infection

Chlamydia psittaci was considered the predominant chlamydial species in poultry until Chlamydia gallinacea was discovered in 2009. C. psittaci is a zoonotic obligate intracellular bacterium reported in more than 465 bird species including poultry. In poultry, infections can result in asymptomatic disease, but also in more severe systemic illness. The zoonotic potential of C. gallinacea has yet to be proven. Infections in poultry appear to be asymptomatic and in recent prevalence studies C. gallinacea was the main chlamydial species found in chickens. The high prevalence of C. gallinacea resulted in the question if an infection with C. gallinacea might protect against an infection with C. psittaci. To investigate possible cross protection, chickens were inoculated with C. gallinacea NL_G47 and subsequently inoculated with either a different strain of C. gallinacea (NL_F725) or C. psittaci. Chickens that had not been pre-inoculated with C. gallinacea NL_G47 were used as a C. gallinacea or C. psittaci infection control. In the groups that were inoculated with C. psittaci, no difference in pharyngeal or cloacal shedding, or in tissue dissemination was observed between the control group and the pre-inoculated group. In the groups inoculated with C. gallinacea NL_F725, shedding in cloacal swabs and tissues dissemination was lower in the group pre-inoculated with C. gallinacea NL_G47. These results indicate previous exposure to C. gallinacea does not protect against an infection with C. psittaci, but might protect against a new infection of C. gallinacea