Metagenomic diagnosis of severe psittacosis using multiple sequencing platforms

Background

Chlamydia psittaci is an avian pathogen that can cause lethal human infections. Diagnosis of C. psittaci pneumonia is often delayed due to nonspecific clinical presentations and limited laboratory diagnostic techniques.

Results

The MinION platform established the diagnosis in the shortest time, while BGISEQ-500 generated additional in-depth sequence data that included the rapid characterization of antibiotic susceptibility. Cytopathy appeared only in cell cultures of BALF. BALF yielded a higher bacterial load than sputum or blood, and may be the most suitable clinical specimen for the genomic diagnosis of severe pneumonia.

Conclusions

This study indicated that the benefits of metagenomic sequencing include rapid etiologic diagnosis of unknown infections and the provision of additional relevant information regarding antibiotic susceptibility. The continued optimization and standardization of sampling and metagenomic analysis promise to enhance the clinical utility of genomic diagnosis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07725-9.

Occurrence of Chlamydiaceae in Raptors and Crows in Switzerland

Bacteria of the family Chlamydiaceae are globally disseminated and able to infect many bird species. So far, 11 species of Chlamydia have been detected in wild birds, and several studies found chlamydial strains classified as genetically intermediate between Chlamydia (C.) psittaci and C.abortus. Recently, a group of these intermediate strains was shown to form a separate species, i.e., C.buteonis. In the present study, 1128 samples from 341 raptors of 16 bird species and 253 corvids representing six species were examined using a stepwise diagnostic approach. Chlamydiaceae DNA was detected in 23.7% of the corvids and 5.9% of the raptors. In corvids, the most frequently detected Chlamydia species was C.psittaci of outer membrane protein A (ompA) genotype 1V, which is known to have a host preference for corvids. The most frequently detected ompA genotype in raptors was M56. Furthermore, one of the raptors harbored C.psittaci 1V, and two others carried genotype A. C.buteonis was not detected in the bird population investigated, so it remains unknown whether this species occurs in Switzerland. The infection rate of Chlamydiaceae in corvids was high compared to rates reported in other wild bird species, but neither Chlamydiaceae-positive corvids nor raptors showed overt signs of disease. Since the Chlamydiaceae of both, raptors and crows were identified as C.psittaci and all C.psittaci genotypes are considered to be zoonotic, it can be suggested that raptors and crows pose a potential hazard to the health of their handlers.

Animal sources for zoonotic transmission of psittacosis: a systematic review

Background

Human psittacosis, caused by Chlamydia (C.) psittaci, is likely underdiagnosed and underreported, since tests for C. psittaci are often not included in routine microbiological diagnostics. Source tracing traditionally focuses on psittacine pet birds, but recently other animal species have been gaining more attention as possible sources for human psittacosis. This review aims to provide an overview of all suspected animal sources of human psittacosis cases reported in the international literature. In addition, for each animal species the strength of evidence for zoonotic transmission was estimated.

Methods

A systematic literature search was conducted using four databases (Pubmed, Embase, Scopus and Proquest). Articles were included when there was mention of at least one human case of psittacosis and a possible animal source. Investigators independently extracted data from the included articles and estimated strength of evidence for zoonotic transmission, based on a self-developed scoring system taking into account number of human cases, epidemiological evidence and laboratory test results in human, animals, and the environment.

Results

Eighty articles were included, which provided information on 136 different situations of possible zoonotic transmission. The maximum score for zoonotic transmission was highest for turkeys, followed by ducks, owls, and the category ‘other poultry’. Articles reporting about zoonotic transmission from unspecified birds, psittaciformes and columbiformes provided a relatively low strength of evidence. A genotypical match between human and animal samples was reported twenty-eight times, including transmission from chickens, turkeys, guinea fowl, peafowl, pigeons, ducks, geese, songbirds, parrot-like birds and owls.

Conclusions

Strong evidence exists for zoonotic transmission from turkeys, chickens and ducks, in addition to the more traditionally reported parrot-like animal sources. Based on our scoring system, the evidence was generally stronger for poultry than for parrot-like birds. Psittaciformes should not be disregarded as an important source of human psittacosis, still clinicians and public health officials should include poultry and birds species other than parrots in medical history and source tracing.

Wild and domestic bird faeces likely source of psittacosis transmission-A case-control study in Sweden, 2014-2016

Psittacosis is a zoonotic disease transmitted by birds. In Sweden, where psittacosis is notifiable, an average of eight cases per year were reported between 2002 and 2012. In 2013, an unusual increase in cases in southern Sweden was associated with exposure to wild birds. To further explore specific risk factors connected to wild birds and identify other risk factors for sporadic psittacosis, we conducted a case-control study including all domestically acquired psittacosis cases reported between December 2014 and April 2016 in Sweden. Cases were age-, sex- and geo-matched to controls randomly selected from a population register. Cases and controls completed a questionnaire investigating detailed exposures to wild and domestic birds. We compared cases to controls, calculating adjusted matched odds ratios (amOR) using conditional logistic regression. Thirty-one cases were notified: all cases lived in southern Sweden and 26 were ill during winter season. Two risk factors were independently associated with psittacosis infection: cleaning a wild bird feeder (amOR = 18.95; 95% CI: 2.11-170.03) and owning domestic birds (amOR = 5.55, 95% CI: 1.16-26.61). Our results suggest that exposure to bird faeces, for example when cleaning a wild bird feeder, was the main route of transmission. Following this study, the Public Health Agency of Sweden published recommendations on good practices when cleaning surfaces contaminated with bird faeces and recommended use of bird feeders with a design limiting faeces accumulation.

An unusual presentation of a case of human psittacosis

Background

Chlamydia psittaci is a gram-negative, obligate intracellular organism. Birds are the main reservoir, but also non-avian domestic animals and humans can be infected. In humans it mostly causes respiratory infections due to occupational exposure with varying severity. Sensitive and specific diagnostic tests are needed to define psittacosis in humans as these tests also allow rapid tracing of the animal source. However, diagnosis in humans is often based on time-consuming culture techniques and antibody detection assays as in many countries, the existing molecular diagnostic tests for psittacosis are not reimbursed by the public health insurance.

Case presentation

An 82-year old female was referred to the hospital with a non-productive cough since four weeks and since one week fever up to 39 °C, myalgia, generalized skin rash, acral edema and generalized weakness under treatment with moxifloxacin. Blood analysis showed signs of inflammation with mild eosinophilia. Chest CT showed multiple peripheral ground glass opacities with consolidation in both lungs. Pulmonary function testing only showed a mild decrease in diffusion capacity. Viral and bacterial serology were negative. As the patient kept a pet parakeet for over ten years, a nested PCR for C. psittaci was performed on a nasopharyngeal swab of the patient and on feces of the parakeet. Both returned positive for the same genotype. Genotyping was performed by a genotype-specific real-time PCR. The patient fully recovered after a ten-day course of azithromycin.

Conclusion

Due to non-specific signs during psittacosis, early detection of the infection and differentiation from hypersensitivity pneumonitis can be challenging. Culture and antibody titers for C. psittaci have a lower sensitivity than PCR-testing due to several factors. We present a case of human psittacosis (presenting as pneumonia) with diagnosis based on clinical findings confirmed by means of nested PCR. This case suggests the added value of PCR in suspect cases despite negative serology. Our current paper underlines the need for a broader implementation of PCR for early diagnosis of human psittacosis and thus early initiation of correct antibiotic treatment with reduction of morbidity and mortality.

Assessment of Chlamydia psittaci Shedding and Environmental Contamination as Potential Sources of Worker Exposure throughout the Mule Duck Breeding Process

Chlamydia psittaci is an obligate intracellular bacterium responsible for avian chlamydiosis, otherwise known as psittacosis, a zoonotic disease that may lead to severe atypical pneumonia. This study was conducted on seven mule duck flocks harboring asymptomatic birds to explore the circulation and persistence of C. psittaci during the entire breeding process and assess the potential sources of worker exposure. Cloacal swabs and air samples were taken on each occasion requiring humans to handle the birds. In parallel, environmental samples, including dust, water, and soil, were collected. Specific real-time PCR analyses revealed the presence of C. psittaci in all flocks but with three different shedding patterns involving ducks about the age of 4, 8, and 12 weeks with heavy, moderate, and low excretion levels, respectively. Air samples were only positive in flocks harboring heavy shedders. Dust in flocks with heavy or moderate shedders carried chlamydial loads strongly associated with the loads detected in avian and soil samples. Environmental contamination, significantly correlated with shedding dynamics, was considered to be the most probable source of exposure. The high prevalence of bacteriophage Chp1 in all flocks, mostly jointly present with chlamydia, suggests an important factor in C. psittaci persistence, thus creating a greater risk for humans. A survey conducted in these flocks regarding farming practices and activities showed that disinfection seems to be the most promising practice for reducing C. psittaci prevalence in ducks and that the place and the duration of action during operations seem to be potential risk factors. Strict adherence to good practices is strongly recommended.