Genotyping of Chlamydophila psittaci by real-time PCR and high-resolution melt analysis

First detection of herpesvirus and hemosporidians in the endangered Pyrenean Capercaillie (Tetrao urogallus aquitanicus)

Pathogens affect wild bird populations worldwide, contributing to their decline. Considering the scarce health data regarding the endangered Pyrenean Capercaillie (Tetrao urogallus aquitanicus), we molecularly surveyed selected pathogens (Newcastle disease virus, Avian influenza virus, Chlamydia psittaci, avian pathogenic Escherichia coli, Campylobacter jejuni, and Salmonella spp.) in 30 Pyrenean Capercaillie feces collected in the field (Catalonia, northeastern Spain). Additionally, swab and tissue samples from eight wild Pyrenean Capercaillies of Catalonia and Andorra were molecularly tested for herpesvirus and hemosporidians (Plasmodium spp., Haemoproteus spp., and Leucocytozoon spp.). All fecal samples were negative for the pathogens tested. Nevertheless, we detected a novel herpesvirus in 50% (4/8) of the Pyrenean Capercaillies, and hemosporidian DNA in 62.5% (5/8) of the tissue samples (i.e., Haemoproteus sp. [4 of 8] and/or Leucocytozoon sp. [3 of 8]). To our knowledge, this is the first detection of herpesvirus and hemosporidians infections in Pyrenean Capercaillies. The putative novel herpesvirus belongs to the genus Iltovirus. The presence of hemosporidian parasites in this mountain bird species is of concern, and could be related to the marked increase in the average temperature in the Pyrenees as a consequence of climate change. Our findings are fundamental to improve the conservation plans for the endangered Pyrenean Capercaillie population.

Infectious agents present in monk parakeet (Myiopsitta monachus) and rose-ringed parakeet (Psittacula krameri) invasive species in the parks of Madrid and Seville, Spain

Introduction

The introduction of invasive species into an ecosystem could result in biodiversity loss and the spread of infectious agents that could cause re-emergent or emergent zoonotic diseases. Monk parakeets (Myiopsitta monachus) and rose-ringed parakeets (Psittacula krameri) are considered widespread invasive exotic species in urban habitats from the Iberian Peninsula. The aim of this study was to assess the presence of relevant infectious agents in wild parakeets captured in urban parks in Madrid and Seville (Spain).

Methods

A total of 81 cloacal samples were collected and analysed using molecular techniques.

Results

The prevalence of infectious agents varied between parakeet species: 9.5% of monk parakeets and 15% of rose-ringed parakeets were positive for enteropathogenic E. coli (EPEC), 13.3% of rose-ringed parakeets for avian influenza virus (AIV), 3.3% of rose-ringed parakeets for Newcastle disease virus (NDV), and a 23.8% of monk parakeets for Chlamydia psittaci.

Discussion

All C. psittaci-identified isolates were classified as B, E, or E/B genotypes, indicating transmission from wild urban pigeons to parakeets. These results highlight the need for monitoring parakeet populations due to the implications for human and animal health.

Multiplex Real-time PCR Assay for the Detection of all Chlamydia Species and Simultaneous Differentiation of C. psittaci and C. pneumoniae in Human Clinical Specimens

We developed and assessed the performance of a new multiplex real-time PCR assay for the detection of all Chlamydia species and simultaneous differentiation of Chlamydia psittaci and Chlamydia pneumoniae-two important human respiratory pathogens-in human clinical specimens. Next-generation sequencing was used to identify unique targets to design real-time PCR assays targeting all Chlamydia species, C. psittaci, and C. pneumoniae. To validate the assay, we used a panel of 49 culture isolates comprising seven C. psittaci genotypes, eight C. pneumoniae isolates, seven other Chlamydia species, and 22 near-neighbor bacterial and viral isolates, along with 22 specimens from external quality assessment (EQA) panels and 34 nasopharyngeal and oropharyngeal swabs and cerebrospinal fluid, stool, and sputum specimens previously identified as positive or negative for C. psittaci or C. pneumoniae. The assays were 100% specific, with limits of detection of 7.64- 9.02 fg/μL. The assay results matched with historical assay results for all specimens, except for one owing to the increased sensitivity of the new C. psittaci assay; the results of the EQA specimens were 100% accurate. This assay may improve the timely and accurate clinical diagnosis of Chlamydia infections and provide a greater understanding of the burden of disease caused by these agents.

Atypical pneumonia caused by Chlamydia psittaci during the COVID-19 pandemic

OBJECTIVES

Here, we retrospectively described the diagnosis and treatment of 32 cases diagnosed with Chlamydia psittaci pneumonia during the COVID-19 pandemic.

METHODS

Clinical information was collected from all the patients. Reverse transcription-PCR and ELISAs were conducted for the detection of COVID-19 using nasal swabs and bronchoalveolar lavage fluid (BALF) samples. Metagenomic next-generation sequencing (mNGS) was performed for the identification of causative pathogens using BALF, peripheral blood and sputum samples. End-point PCR was performed to confirm the mNGS results.

RESULTS

All 32 patients showed atypical pneumonia and had infection-like symptoms that were similar to COVID-19. Results of reverse transcription-PCR and ELISAs ruled out COVID-19 infection. mNGS identified C. psittaci as the suspected pathogen in these patients within 48 hours, which was validated by PCR, except for three blood samples. The sequence reads that covered fragments of C. psittaci genome were detected more often in BALF than in sputum or blood samples. All patients received doxycycline-based treatment regimens and showed favorable outcomes.

CONCLUSION

This retrospective study, with the highest number of C. psittaci pneumonia enrolled cases in China so far, suggests that human psittacosis may be underdiagnosed and misdiagnosed clinically, especially in the midst of the COVID-19 pandemic.

Development of a Lateral Flow Strip-Based Recombinase-Aided Amplification for Active Chlamydia psittaci Infection

Chlamydia psittaci is the causative agent of psittacosis, a worldwide zoonotic disease. A rapid, specific, and sensitive diagnostic assay would be benefit for C. psittaci infection control. In this study, an assay combining recombinase-aided amplification and a lateral flow strip (RAA-LF) for the detection of active C. psittaci infection was developed. The RAA-LF assay targeted the CPSIT_RS02830 gene of C. psittaci and could be accomplished in 15 min at a single temperature (39°C). The analytical sensitivity of the assay was as low as 1 × 100 copies/μl and no cross-reaction with some other intracellular pathogens was observed. Moreover, all feces samples from mice infected with C. psittaci at day-1 post-infection were positive in the RAA-LF assay. In conclusion, the RAA-LF assay provides a convenient, rapid, specific and sensitive method for detection of active C. psittaci infection and it is also suitable for C. psittaci detection in field.

The Application Value of Metagenomic and Whole-Genome Capture Next-Generation Sequencing in the Diagnosis and Epidemiological Analysis of Psittacosis

Background

To evaluate the value of metagenomic next-generation sequencing (mNGS) for the early diagnosis of psittacosis, and to investigate its epidemiology by whole-genome capture.

Methods

Twenty-one bronchoalveolar lavage fluid (BALF) and blood samples of 16 psittacosis patients from multiple centers during August 2019 to September 2021 were analyzed retrospectively. mNGS with normal datasets (10 M 75-bp single-end reads after sequencing) and larger datasets (30 M 150-bp paired-end reads after sequencing) as well as quantitative real-time polymerase chain reaction (qPCR) were used to detect the pathogen. Also, whole-genome capture of Chlamydophila psittaci was applied to draw the phylogenetic tree.

Results

mNGS successfully detected the pathogen in all 16 cases (100%), while qPCR was positive only in 5 out of 10 cases (50%), indicating a significantly higher sensitivity of mNGS than qPCR (p < 0.01). BALF-mNGS performed better than blood-mNGS (16/16 versus 3/5, p < 0.05). In addition, larger datasets (the read counts have tripled, and the base number was 12-fold larger compared to clinical mNGS with a normal dataset) of mNGS showed significantly increased contents of human DNA (p < 0.05) and decreased reads per million of the pathogen, suggesting no improvement. Whole-genome capture results of five samples (>60% coverage and >1 depth) were used to construct the phylogenetic tree.

Conclusion

Significant advantages of mNGS with normal datasets were demonstrated in early diagnosing psittacosis. It is the first study to use whole-genome capture to analyze C. psittaci epidemiological information.

Chlamydia buteonis in birds of prey presented to California wildlife rehabilitation facilities

Chlamydial infections, caused by a group of obligate, intracellular, gram-negative bacteria, have health implications for animals and humans. Due to their highly infectious nature and zoonotic potential, staff at wildlife rehabilitation centers should be educated on the clinical manifestations, prevalence, and risk factors associated with Chlamydia spp. infections in raptors. The objectives of this study were to document the prevalence of chlamydial DNA shedding and anti-chlamydial antibodies in raptors admitted to five wildlife rehabilitation centers in California over a one-year period. Chlamydial prevalence was estimated in raptors for each center and potential risk factors associated with infection were evaluated, including location, species, season, and age class. Plasma samples and conjunctiva/choana/cloaca swabs were collected for serology and qPCR from a subset of 263 birds of prey, representing 18 species. Serologic assays identified both anti-C. buteonis IgM and anti-chlamydial IgY antibodies. Chlamydial DNA and anti-chlamydial antibodies were detected in 4.18% (11/263) and 3.14% (6/191) of patients, respectively. Chamydial DNA was identified in raptors from the families Accipitridae and Strigidae while anti-C.buteonis IgM was identified in birds identified in Accipitridae, Falconidae, Strigidae, and Cathartidae. Two of the chlamydial DNA positive birds (one Swainson’s hawk (Buteo swainsoni) and one red-tailed hawk (Buteo jamaicensis)) were necropsied, and tissues were collected for culture. Sequencing of the cultured elementary bodies revealed a chlamydial DNA sequence with 99.97% average nucleotide identity to the recently described Chlamydia buteonis. Spatial clusters of seropositive raptors and raptors positive for chlamydial DNA were detected in northern California. Infections were most prevalent during the winter season. Furthermore, while the proportion of raptors testing positive for chlamydial DNA was similar across age classes, seroprevalence was highest in adults. This study questions the current knowledge on C. buteonis host range and highlights the importance of further studies to evaluate the diversity and epidemiology of Chlamydia spp. infecting raptor populations.

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.

Presence and shedding of Chlamydia psittaci in waterfowl in a rehabilitation facility and in the wild in New Zealand

AIMS

To determine the frequency of Chlamydia psittaci infection, shedding dynamics of C. psittaci, and C. psittaci genotype diversity in waterfowl temporarily resident in a rehabilitation facility and in mallards in the wild.

METHODS

Conjunctival-choanal-cloacal swabs were collected from apparently healthy captive wild mallards (Anas platyrhynchos; n = 114) and paradise shelducks (Tadorna variegata; n = 10) temporarily housed at a waterfowl breeding and rehabilitation facility (Wellington, NZ) and from wild mallards in Palmerston North (n = 50), and Southland (n = 50). DNA extracted from the swabs was analysed using quantitative PCR (qPCR) high-resolution melt curve (HRM) analysis, targeting the ompA gene of C. psittaci.

RESULTS

Of the captive waterfowl, 39/114 (34%) mallards and 6/10 (60%) paradise shelducks were positive for C. psittaci as were 24/100 (24%) wild mallards. All wild mallards and paradise shelducks carried only C. psittaci genotype C. In captive wild mallards, genotypes A and C, and a mixed infection of both genotypes were found. Captive wild mallards and paradise shelducks were found to be shedding 4 to 5 × 10⁴ and 1 × 10⁵ to 4 × 10⁵ copies of C. psittaci DNA per swab, respectively, with wild mallards shedding 4-677 DNA copies/swab.

CONCLUSIONS

Based on qPCR-HRM analysis, a high proportion of wild mallards were infected with C. psittaci but these birds were shedding only a small amount of bacterial DNA. The proportion of sampled ducks that were infected and the extent of bacterial shedding were higher in the birds in a wildlife rehabilitation facility. The major C. psittaci genotype found in the mallards and paradise shelducks was genotype C. This is the first detection of C. psittaci genotype A and co-infection of genotype A and C in ducks.

CLINICAL RELEVANCE

These results indicate that mallards are a reservoir of C. psittaci and therefore may pose a zoonotic risk to people involved in duck hunting, wildlife care and recreational duck feeding. Mallards may also pose a transmission risk to native birds, especially in captive facilities and this has conservation implications for the management of endangered native birds.

Psittacosis Outbreak among Workers at Chicken Slaughter Plants, Virginia and Georgia, USA, 2018

During August–October, 2018, an outbreak of severe respiratory illness was reported among poultry slaughter plant workers in Virginia and Georgia, USA. A multiorganizational team investigated the cause and extent of illness, determined that the illness was psittacosis, and evaluated and recommended controls for health hazards in the workplace to prevent additional cases.

Isolation and Characterization of Avian Chlamydia psittaci from Symptomatic Pet Birds in Southern Hunan, China

Chlamydia psittaci is a zoonotic pathogen with multiple hosts, especially avian, and can be transmitted to humans, causing psittacosis or ornithosis. No effective vaccines have been developed. We therefore isolate and genotype avian C. psittaci strains and investigate the pathogenicity of isolates in the southern Hunan area of China. Among 200 suspicious avian specimens, eight were positive for the C. psittaci outer membrane protein A (ompA) gene (4%), and seven were successfully cultured in human epithelial type 2 and Vero cells (87.5%). Genotyping of the ompA gene of the eight PCR-positive samples revealed that all of the cultured strains, except for the E9 strain, belonged to genotype A. Pathologic changes in the mice infected with C. psittaci via intranasal inoculation showed severe pneumonia and intense infiltration of inflammatory cells in the lung in a dose-dependent manner, and immunohistochemical staining displayed different levels of infiltration of C. psittaci inclusions in the heart, liver, spleen, kidney, and, especially, lung. Our findings demonstrate that genotype A dominates all C. psittaci genotypes in the southern Hunan area and that the C. psittaci avian isolates in this region possess dose-dependent pathogenicity.

ATYPICAL CHLAMYDIACEAE IN WILD POPULATIONS OF HAWKS ( BUTEO SPP.) IN CALIFORNIA

Chlamydiaceae bacteria infect many vertebrate hosts, and previous reports based on polymerase chain reaction (PCR) assays and serologic assays that are prone to cross-reaction among chlamydial organisms have been used to describe the prevalence of either DNA fragments or antibodies to Chlamydia spp. in wild raptorial populations. This study reports the PCR-based prevalence of Chlamydiaceae DNA that does not 100% match any avian or mammalian Chlamydiaceae in wild populations of hawks in California Buteo species. In this study, multimucosal swab samples ( n = 291) for quantitative PCR (qPCR) and plasma ( n = 78) for serology were collected from wild hawks. All available plasma samples were negative for antibodies using a C. psittaci-specific elementary body agglutination test (EBA; n = 78). For IgY antibodies all 51 available samples were negative using the indirect immunofluorescent assay. The overall prevalence of Chlamydiaceae DNA detection in wild Buteo species sampled was 1.37% (4/291) via qPCR-based analysis. Two fledgling Swainson's hawks ( Buteo swainsoni) and two juvenile red-tailed hawks ( Buteo jamaicensis) were positive by qPCR-based assay for an atypical chlamydial sequence that did not 100% match any known C. psittaci genotype. Positive swab samples from these four birds were sequenced based on the ompA gene and compared by high-resolution melt analysis with all known avian and mammalian Chlamydiaceae. The amplicon sequence did not 100% match any known avian chlamydial sequence; however, it was most similar (98.6%) to C. psittaci M56, a genotype that is typically found in muskrats and hares. Culture and full genome sequence analysis of Chlamydia spp. isolated from diseased hawks will be necessary to classify this organism and to better understand its epizootiology and potential health impact on wild Buteo populations in California.

Chlamydia pneumoniae Polioencephalomyelitis and Ganglionitis in Captive Houston Toads (Anaxyrus houstonensis)

Chlamydia pneumoniae is a ubiquitous pathogen causing disease in humans, mammals, birds, reptiles, and amphibians. Since 2012, C. pneumoniae infection has caused neurologic disease and mortality in a breeding colony of endangered Houston toads (Anaxyrus houstonensis) at the Houston Zoo. The purpose of this report is to present the histopathologic and ultrastructural characteristics of C. pneumoniae infection in Houston toads. Fourteen cases were evaluated by histopathology and 1 case was evaluated by electron microscopy. The major histopathologic finding was necrotizing and histiocytic polioencephalomyelitis and ganglionitis. Bacteria formed intracytoplasmic inclusions within neurons but frequently extended into the surrounding tissue from necrotic cells. Ultrastructural evaluation showed the bacteria formed reticulate and elementary bodies characteristic of Chlamydia spp.

Zoonotic Agents in Feral Pigeons (Columba livia) from Costa Rica: Possible Improvements to Diminish Contagion Risks

Most studies on zoonotic agents in pigeons have been conducted in the Palearctic region, but the scarcity of data is notorious in the Neotropical region, where these birds can breed all year around and are in close contact with humans. In this study, we used a combination of culture-dependent and culture-independent methods to identify infectious agents in 141 fecal samples from pigeons collected at four urban parks from Costa Rica. Of these we identified 34 positive samples for Salmonella enterica subsp. enterica serovar Braenderup (24.1%), 13 for Chlamydophila psittaci (9.2%), 9 for enteropathogenic Escherichia coli (6.4% eaeA, 0% stx-1 and 0% stx-2), and 2 for Campylobacter jejuni (1.4%). These populations of pigeons pose low risk for healthy adult humans, however, they may pose a health risk to immunocompromised patients or children. This study provides scientific data, which can be incorporated into educational programs aiming to reverse the public attitude toward pigeon feeding and to rationally justify population control efforts.

Seroprevalence of Chlamydophila Psittaci among Employees of Two German Duck Farms

Psittacosis is a zoonotic infectious disease that is caused by Chlamydophila psittaci. To determine the occupational risk of getting the infection, we investigated the seroprevalence of C. psittaci among employees of two German duck farms and two slaughterhouses according to their level of exposure to the pathogen during the years 2010, 2007, and 2004. In summary, we found low seroprevalence (≈ 8%) throughout the study population almost irrespective of the duty of a given worker. Surprisingly, in 2010, the anti-C. psittaci-specific antibody prevalence in the group of slaughterer (38.9%) was significantly increased in comparison to the non-exposed employees (p = 0.00578). This indicates that individuals in the surrounding of slaughterhouses exposed especially to aerosols containing C. psittaci elementary bodies bear a greater occupational risk of getting infected.

Recombinant protein CPSIT_0846 induces protective immunity against Chlamydia psittaci infection in BALB/c mice

Chlamydia psittaci is an obligate intracellular bacteria that causes respiratory disease in poultry and humans. Currently, there are no licensed vaccines against chlamydial infection in humans. The transmembrane head protein CPSIT_0846 of C. psittaci is a putative member of the larger Inc protein family. In this study, we investigated immunogenicity and protective efficacy of the recombinant CPSIT_0846 protein in BALB/c mice. Mice immunized with CPSIT_0846 developed strong T-lymphocyte responses that were recalled by the immunogen CPSIT_0846 in an in vitro restimulation assay. These T cells displayed a strong Th1-biased cytokine profile with high levels of IFN-γ. At the same time, a strong humoral immune response was also detected in the immunized mice with high titers of Chlamydia psittaci-specific serum IgG antibodies. More importantly, the robust immune responses correlated well with significantly reduced chlamydial burden and inflammatory pathology in the mouse lungs upon an airway challenge infection. The above results together suggest that the CPSIT_0846 protein may be a potential vaccine candidate antigen for inducing protection against C. psittaci infection and disease in the airway.

Rapid detection and typing of pathogenic nonpneumophila Legionella spp. isolates using a multiplex real-time PCR assay

We developed a single tube multiplex real-time PCR assay that allows for the rapid detection and typing of 9 nonpneumophila Legionella spp. isolates that are clinically relevant. The multiplex assay is capable of simultaneously detecting and discriminating L. micdadei, L. bozemanii, L. dumoffii, L. longbeachae, L. feeleii, L. anisa, L. parisiensis, L. tucsonensis serogroup (sg) 1 and 3, and L. sainthelensis sg 1 and 2 isolates. Evaluation of the assay with nucleic acid from each of these species derived from both clinical and environmental isolates and typing strains demonstrated 100% sensitivity and 100% specificity when tested against 43 other Legionella spp. Typing of L. anisa, L. parisiensis, and L. tucsonensis sg 1 and 3 isolates was accomplished by developing a real-time PCR assay followed by high-resolution melt (HRM) analysis targeting the ssrA gene. Further typing of L. bozemanii, L. longbeachae, and L. feeleii isolates to the serogroup level was accomplished by developing a real-time PCR assay followed by HRM analysis targeting the mip gene. When used in conjunction with other currently available diagnostic tests, these assays may aid in rapidly identifying specific etiologies associated with Legionella outbreaks, clusters, sporadic cases, and potential environmental sources.

Development of a novel real-time PCR assay with high-resolution melt analysis to detect and differentiate OXA-48-Like β-lactamases in carbapenem-resistant Enterobacteriaceae

The rapid global spread of carbapenem-resistant Enterobacteriaceae (CRE) poses an urgent threat to public health. More than 250 class D β-lactamases (OXAs) have been described in recent years, with variations in hydrolytic activity for β-lactams. The plasmid-borne OXA-48 β-lactamase and its variants are identified only sporadically in the United States but are common in Europe. Recognition of these OXA-48-like carbapenemases is vital in order to control their dissemination. We developed a real-time PCR assay based on high-resolution melt analysis, using bla OXA-48-like-specific primers coupled with an unlabeled 3'-phosphorylated oligonucleotide probe (LunaProbe) homologous to OXA-48-like carbapenemase genes. The assay was validated using genomic DNA from 48 clinical isolates carrying a variety of carbapenemase genes, including bla KPC, bla SME, bla IMP, bla NDM-1, bla VIM, bla OXA-48, bla OXA-162, bla OXA-181, bla OXA-204, bla OXA-244, bla OXA-245, and bla OXA-232. Our assay identified the presence of bla OXA-48-like β-lactamase genes and clearly distinguished between bla OXA-48 and its variants in control strains, including between bla OXA-181 and bla OXA-232, which differ by only a single base pair in the assay target region. This approach has potential for use in epidemiological investigations and continuous surveillance to help control the spread of CRE strains producing OXA-48-like enzymes.

Chlamydia psittaci comparative genomics reveals intraspecies variations in the putative outer membrane and type III secretion system genes

Chlamydia psittaci is an obligate intracellular bacterium that can cause significant disease among a broad range of hosts. In humans, this organism may cause psittacosis, a respiratory disease that can spread to involve multiple organs, and in rare untreated cases may be fatal. There are ten known genotypes based on sequencing the major outer-membrane protein gene, ompA, of C. psittaci. Each genotype has overlapping host preferences and virulence characteristics. Recent studies have compared C. psittaci among other members of the Chlamydiaceae family and showed that this species frequently switches hosts and has undergone multiple genomic rearrangements. In this study, we sequenced five genomes of C. psittaci strains representing four genotypes, A, B, D and E. Due to the known association of the type III secretion system (T3SS) and polymorphic outer-membrane proteins (Pmps) with host tropism and virulence potential, we performed a comparative analysis of these elements among these five strains along with a representative genome from each of the remaining six genotypes previously sequenced. We found significant genetic variation in the Pmps and tbl3SS genes that may partially explain differences noted in C. psittaci host infection and disease.

Typing of Chlamydia psittaci to monitor epidemiology of psittacosis and aid disease control in the Netherlands, 2008 to 2013

Binary file ES_Abstracts_Final_ECDC.txt matches

Current and emerging Legionella diagnostics for laboratory and outbreak investigations

Legionnaires' disease (LD) is an often severe and potentially fatal form of bacterial pneumonia caused by an extensive list of Legionella species. These ubiquitous freshwater and soil inhabitants cause human respiratory disease when amplified in man-made water or cooling systems and their aerosols expose a susceptible population. Treatment of sporadic cases and rapid control of LD outbreaks benefit from swift diagnosis in concert with discriminatory bacterial typing for immediate epidemiological responses. Traditional culture and serology were instrumental in describing disease incidence early in its history; currently, diagnosis of LD relies almost solely on the urinary antigen test, which captures only the dominant species and serogroup, Legionella pneumophila serogroup 1 (Lp1). This has created a diagnostic "blind spot" for LD caused by non-Lp1 strains. This review focuses on historic, current, and emerging technologies that hold promise for increasing LD diagnostic efficiency and detection rates as part of a coherent testing regimen. The importance of cooperation between epidemiologists and laboratorians for a rapid outbreak response is also illustrated in field investigations conducted by the CDC with state and local authorities. Finally, challenges facing health care professionals, building managers, and the public health community in combating LD are highlighted, and potential solutions are discussed.

The clinical characteristics and genotype distribution of Chlamydia trachomatis infection in infants less than six months of age hospitalized with pneumonia

BACKGROUND

Chlamydia trachomatis is a common sexually-transmitted bacterial pathogen. As no routine screening is performed during pregnancy, neonates and infants are at high risk for C. trachomatis infection. The objective of this study was to investigate the morbidity, clinical characteristics and genotype distribution of C. trachomatis pneumonia in infants less than six months of age.

METHODS

Clinical manifestations and laboratory results were recorded. Respiratory sputum specimens were tested using RT-PCR targeting C. trachomatis cryptic plasmid. Simultaneously, respiratory virus antigens were detected by direct immunofluorescence and bacterial pathogens were examined by culture in all sputum samples. Positive C. trachomatis samples were further genotyped using a multiplex PCR reverse line blot assay. The relationship between genotype and pneumonia severity was explored.

RESULTS

Of 1408 infants, 101 (7.2%) were infected with C. trachomatis. Sixteen of 101 (15.8%) were assessed as severe pneumonia. These severe cases had a higher proportion of viral co-infection (37.5%) compared to mild pneumonia cases (9.4%, P<0.05).Infants with tachypnea (OR 9.2) and wheezing (OR 3.5) were more likely to be classified as severe pneumonia (P<0.05). Amongst 66 C. trachomatis specimens for which a genotyping result was available, seven genotypes were detected, and 39.4% of these specimens contained two or three genotypes. Overall, genotype E (48.5%) was the most frequent, followed by genotype F (42.4%), J (31.8%), D (12.1%), K (10.6%), G (4.5%) and H (3.0%). There were no significant correlations of particular genotypes with severity of disease, although there was a weak indication that more severe pneumonia might be associated with having certain mixed genotypes of C. trachomatis.

CONCLUSIONS

The prevalence of C. trachomatis in the population of young hospitalized infants with pneumonia in Shenzhen was very high. The relationship between genotype distribution and severity of pneumonia was not clear based on this study due to small sample size. Further in-depth investigation correlating genotype and disease severity based on a larger population is needed.

Detecção e classificação molecular de Chlamydophila psittaci em amostras fecais de aves assintomáticas

Chlamydophila psittaci é uma bactéria que causa doença respiratória ou sistêmica em aves e em seres humanos. Em vista do risco de transmissão para humanos, o objetivo deste estudo foi detectar a presença de Chlamydophila spp. em amostras de fezes ou suabes cloacais de aves assintomáticas. Foram colhidas 403 amostras fecais ou suabes cloacais, provenientes de aves domésticas, selvagens ou exóticas. As amostras foram submetidas à PCR em tempo real para C. psittaci, para amplificação de fragmento parcial do gene da subunidade 16S do rRNA, utilizando o SsoFastTM EvaGreen® Supermix (Bio-Rad) e análise da curva de dissociação. Para determinação do genótipo de C. psittaci, foi usada a hemi-nested PCR visando à amplificação de fragmento parcial do gene OMP-A, realizada nas amostras positivas pela PCR em tempo real, seguida de sequenciamento dos fragmentos amplificados. A PCR em tempo real revelou positividade em 17 (4,21%) amostras. A hemi-nested foi positiva em 2 amostras positivas pela PCR em tempo real. O genótipo A de C. psittaci foi identificado pelo sequenciamento de uma amostra amplificada pela hemi-nested PCR. Os resultados deste experimento demonstram que a PCR em tempo real, visando à amplificação de fragmento parcial da subunidade 16S do rRNA, seguida da análise da curva de dissociação, pode ser utilizada para detecção de DNA de Chlamydophila sp. em amostras fecais de aves assintomáticas. A classificação da espécie de Chlamydophila e do genótipo de C. psittaci deve ser realizada por meio de PCR tendo como alvo o gene ompA e sequenciamento dos fragmentos amplificados.

PCR-based diagnosis, molecular characterization and detection of atypical strains of avian Chlamydia psittaci in companion and wild birds

Chlamydiosis is one of the most important infectious diseases of birds. In this study, 253 clinical samples were taken from 27 bird species belonging to seven orders. Thirty-two (12.6%) samples were positive for Chlamydia psittaci major outer membrane gene (ompA) DNA by a nested polymerase chain reaction (PCR). Twelve nested PCR-positive specimens were typed by ompA gene-based PCR-restricted fragment length polymorphism, using CTU/CTL primers and AluI restriction enzyme. Four restriction patterns were identified, including genotype A (two specimens from an African grey parrot [Psittacus erithacus] and a lorikeet [Trichoglossus haematodus]), genotype B (two specimens from a rock dove [Columbia livia] and a canary [Serinus canaria]), a third new restriction pattern (six specimens from African grey parrots), and a fourth new restriction pattern (two specimens from a ring-necked parakeet [Psittacula krameri] and an Alexandrine parakeet [Psittacula eupatria]). The third and the fourth restriction patterns are suggested to be provisional genotypes I and J, respectively. Partial sequencing of the ompA gene of seven specimens completely correlated with the results of PCR-restricted fragment length polymorphism and confirmed the presence of genotypes A and B and the two new provisional genotypes I and J. The two new genotypes have the closest identity with C. psittaci genotype F and Chlamydia abortus, respectively. From an evolutionary perspective, both new genotypes, particularly genotype J, are intermediate between the two species, C. psittaci and C. abortus.

[Microbiological diagnosis of infections due to Chlamydia spp. and related species]

Until recently the number of completed genomes belonging to Chlamydia trachomatis was very low, despite its importance in Public Health. Now, there are currently sixty-six completed genomes of C.trachomatis sequenced in different parts of the world. This genomic revolution has helped in understanding its biology, as well as improved the sensitivity and specificity in the diagnosis, and the development of epidemiological tools, not only for in C.trachomatis, but also for related species such as C.pneumoniae and C.psittaci. The diagnosis based on cell culture, serology and microimmunofluorescence is gradually being replaced by molecular techniques based on PCR or real-time PCR. This is because these molecular tests do not have cross-reactions problems and the procedures are easily standardised between laboratories. Moreover, molecular epidemiology tools described recently, such as Multi-Locus Sequence Typing (MLST) and Variable Number Tandem Repeat (VNTR), have increased our knowledge on local and global epidemiology. This article focuses on the impact of the genomics advances achieved over the last few years as applied to the diagnosis, epidemiology and biology of the family Chlamydiaceae family and related species.

Distinctive features between community-acquired pneumonia (CAP) due to Chlamydophila psittaci and CAP due to Legionella pneumophila admitted to the intensive care unit (ICU)

The spectrum of community-acquired pneumonia (CAP) due to Chlamydophila psittaci ranges from mild, self-limited CAP, to acute respiratory failure. We performed a retrospective study of 13 consecutive patients with CAP due to C. psittaci and 51 patients with legionellosis admitted in one intensive care unit (ICU) (1993-2011). As compared to patients with legionellosis, patients with psittacosis were younger (median age 48 [38-59] vs. 60 [50-71] years, p = 0.007), less frequently smokers (38 vs. 79 %, p < 0.001), with less chronic disease (15 vs. 57 %, p = 0.02), and longer duration of symptoms before admission (median 6 [5-13] vs. 5 [3-7] days, p = 0.038). They presented with lower Simplified Acute Physiology Score II (median 28 [19-38] vs. 39 [28-46], p = 0.04) and less extensive infiltrates on chest X-rays (median 2 [1-3] vs. 3 [3-4] lobes, p = 0.007). Bird exposure was mentioned in 100 % of psittacosis cases, as compared to 5.9 % of legionellosis cases (p < 0.0001). Extrapulmonary manifestations, biological features, and mortality (15.4 vs. 21.6 %, p = 0.62) were similar in both groups. In conclusion, severe psittacosis shares many features with severe legionellosis, including extrapulmonary manifestations, biological features, and outcome. Psittacosis is an important differential diagnosis for legionellosis, especially in cases of bird exposure, younger age, and more limited disease progression over the initial few days.

Genome sequence of the zoonotic pathogen Chlamydophila psittaci

We present the first genome sequence of Chlamydophila psittaci, an intracellular pathogen of birds and a human zoonotic pathogen. A comparison with previously sequenced Chlamydophila genomes shows that, as in other chlamydiae, most of the genome diversity is restricted to the plasticity zone. The C. psittaci plasmid was also sequenced.

High-resolution DNA melting analysis in clinical research and diagnostics

Among nucleic acid analytical methods, high-resolution melting analysis is gaining more and more attention. High-resolution melting provides simple, homogeneous solutions for variant scanning and genotyping, addressing the needs of today's overburdened laboratories with rapid turnaround times and minimal cost. The flexibility of the technique has allowed it to be adopted by a wide range of disciplines for a variety of applications. In this review we examine the broad use of high-resolution melting analysis, including gene scanning, genotyping (including small amplicon, unlabeled probe and snapback primers), sequence matching and methylation analysis. Four major application arenas are examined to demonstrate the methods and approaches commonly used in particular fields. The appropriate usage of high-resolution melting analysis is discussed in the context of known constraints, such as sample quality and quantity, with a particular focus placed on proper experimental design in order to produce successful results.

Atypical pneumonia due to Chlamydophila psittaci: 3 case reports and review of literature

Chlamydophila psittaci is the causative agent of psittacosis or ornithosis. The disease is transmitted to men predominantly from birds. Most commonly noted symptoms are fever, headache and cough, but a number of other symptoms or complications may arise such as renal impairment, hepatitis or neurological symptoms. In this article 3 cases of psittacosis are presented, with a review of the literature with emphasis on laboratory diagnosis.

Rapid identification and discrimination of Brucella isolates by use of real-time PCR and high-resolution melt analysis

Definitive identification of Brucella species remains a challenge due to the high degree of genetic homology shared within the genus. We report the development of a molecular technique which utilizes real-time PCR followed by high-resolution melt (HRM) curve analysis to reliably type members of this genus. Using a panel of seven primer sets, we tested 153 Brucella spp. isolates with >99% accuracy compared to traditional techniques. This assay provides a useful diagnostic tool that can rapidly type Brucella isolates and has the potential to detect novel species. This approach may also prove helpful for clinical, epidemiological and veterinary investigations.