From genomes to genotypes: molecular epidemiological analysis of Chlamydia gallinacea reveals a high level of genetic diversity for this newly emerging chlamydial pathogen.

BACKGROUND: Chlamydia (C.) gallinacea is a recently identified bacterium that mainly infects domestic chickens. Demonstration of C. gallinacea in human atypical pneumonia suggests its zoonotic potential. Its prevalence in chickens exceeds that of C. psittaci, but genetic and genomic research on C. gallinacea is still at the beginning. In this study, we conducted whole-genome sequencing of C. gallinacea strain JX-1 isolated from an asymptomatic chicken, and comparative genomic analysis between C. gallinacea strains and related chlamydial species. RESULTS: The genome of C. gallinacea JX-1 was sequenced by single-molecule, real-time technology and is comprised of a 1,059,522-bp circular chromosome with an overall G + C content of 37.93% and sequence similarity of 99.4% to type strain 08-1274/3. In addition, a plasmid designated pJX-1, almost identical to p1274 of the type strain, except for two point mutations, was only found in field strains from chicken, but not in other hosts. In contrast to chlamydial species with notably variable polymorphic membrane protein (pmp) genes and plasticity zone (PZ), these regions were conserved in both C. gallinacea strains. There were 15 predicted pmp genes, but only B, A, E1, H, G1 and G2 were apparently intact in both strains. In comparison to chlamydial species where the PZ may be up to 50 kbp, C. gallinacea strains displayed gene content reduction in the PZ (14 kbp), with strain JX-1 having a premature STOP codon in the cytotoxin (tox) gene, while tox gene is intact in the type strain. In multilocus sequence typing (MLST), 15 C. gallinacea STs were identified among 25 strains based on cognate MLST allelic profiles of the concatenated sequences. The type strain and all Chinese strains belong to two distinct phylogenetic clades. Clade of the Chinese strains separated into 14 genetically distinct lineages, thus revealing considerable genetic diversity of C. gallinacea strains in China. CONCLUSIONS: In this first detailed comparative genomic analysis of C. gallinacea, we have provided evidence for substantial genetic diversity among C. gallinacea strains. How these genetic polymorphisms affect C. gallinacea biology and pathogenicity should be addressed in future studies that focus on phylogenetics and host adaption of this enigmatic bacterial agent.

[Research on Oil Sands Spectral Characteristics and Oil Content by Remote Sensing Estimation].

Visible and near infrared spectroscopy is a proven technology to be widely used in identification and exploration of hydrocarbon energy sources with high spectral resolution for detail diagnostic absorption characteristics of hydrocarbon groups. The most prominent regions for hydrocarbon absorption bands are 1,740-1,780, 2,300-2,340 and 2,340-2,360 nm by the reflectance of oil sands samples. These spectral ranges are dominated by various C-H overlapping overtones and combination bands. Meanwhile, there is relatively weak even or no absorption characteristics in the region from 1,700 to 1,730 nm in the spectra of oil sands samples with low bitumen content. With the increase in oil content, in the spectral range of 1,700-1,730 nm the obvious hydrocarbon absorption begins to appear. The bitumen content is the critical parameter for oil sands reserves estimation. The absorption depth was used to depict the response intensity of the absorption bands controlled by first-order overtones and combinations of the various C-H stretching and bending fundamentals. According to the Pearson and partial correlation relationships of oil content and absorption depth dominated by hydrocarbon groups in 1,740-1,780, 2,300-2,340 and 2,340-2,360 nm wavelength range, the scheme of association mode was established between the intensity of spectral response and bitumen content, and then unary linear regression(ULR) and partial least squares regression (PLSR) methods were employed to model the equation between absorption depth attributed to various C-H bond and bitumen content. There were two calibration equations in which ULR method was employed to model the relationship between absorption depth near 2,350 nm region and bitumen content and PLSR method was developed to model the relationship between absorption depth of 1,758, 2,310, 2,350 nm regions and oil content. It turned out that the calibration models had good predictive ability and high robustness and they could provide the scientific basis for rapid estimation of oil content in oil sands in future.

Engineering Probiotics for Diabetes Management: Advances, Challenges, and Future Directions in Translational Microbiology.

Background: Diabetes Mellitus (DM) is a substantial health concern worldwide, and its incidence is progressively escalating. Conventional pharmacological interventions frequently entail undesirable side effects, and while probiotics offer benefits, they are hindered by constraints such as diminished stability and effectiveness within the gastrointestinal milieu. Given these complications, the advent of bioengineered probiotics is a promising alternative for DM management. Aim of Review: The objective of this review is to provide an exhaustive synthesis of the most recent studies on the use of engineered probiotics in the management of DM. This study aimed to clarify the mechanisms through which these probiotics function, evaluate their clinical effectiveness, and enhance public awareness of their prospective advantages in the treatment of DM. Key Scientific Concepts of Review: Scholarly critiques have explored diverse methodologies of probiotic engineering, including physical alteration, bioenrichment, and genetic manipulation. These techniques augment the therapeutic potency of probiotics by ameliorating gut microbiota, fortifying the intestinal barrier, modulating metabolic pathways, and regulating immune responses. Such advancements have established engineered probiotics as a credible therapeutic strategy for DM, potentially providing enhanced results compared to conventional treatments.

Experimental infection and co-infection with Chinese strains of Ehrlichia canis and Babesia vogeli in intact and splenectomized dogs: Insights on clinical, hematologic and treatment responses.

Animal infection models are crucial for studying various aspects of Ehrlichia canis infections. To understand the pathogenesis of the first Chinese isolate of E. canis and simulate the natural progression of canine ehrlichiosis, we developed a model with 18 Beagle dogs that consisted of E. canis initial infection (days 0-17), treatment with doxycycline or rifampicin (days 18-32), recovery (days 33-66), E. canis reinfection (days 67-91), and Babesia vogeli superinfection (days 92-116). We measured body weight and rectal temperature every other day, drew blood every 4 days for routine hematology and biochemistry tests, and for quantification of E. canis and B. vogeli by quantitative PCRs. In this study, the first isolate of E. canis from China was used to experimentally infect dogs, and the infected dogs exhibited clinical signs of acute severe ehrlichiosis, including high fever, loss of appetite, dehydration, and body weight loss, confirming the similar pathogenicity of E. canis in China as compared to isolates from other regions. Infection with E. canis and B. vogeli led to reduced body weight and fever in dogs. Doxycycline treatment led to absence of E. canis DNA in infected dogs, while rifampicin treatment lowered the blood E. canis copy number up to 1.5 folds. E. canis-free infected dogs after doxycycline treatment were successfully re-infected with E. canis, indicating dogs with antibodies are still at risk of re-infection. Super-infection with B. vogeli resulted in higher fever, more severe anemia, and a reduced number of platelets. Splenectomized dogs showed significantly higher E. canis numbers during recovery and re-infection than intact dogs. The histological changes were observed in brain, lung, kidney, liver and spleen of the infected dogs. The findings in this study provide insights into clinical and hematologic responses, as well as effective treatment options, for dogs infected with the first Chinese isolate of E. canis, and may contribute to our understanding of the diagnosis and prevention of tick-borne diseases in dogs, including canine monocytic ehrlichiosis.

First molecular detection of Plasmodium relictum in Anopheles sinensis and Armigeres subalbatus.

Background: Plasmodium relictum is one of the most important avian malaria species, which is mainly seen in wild birds, with infections reported in more than 70 different species and at high prevalence. Aim: The aim of this study was to determine the molecular prevalence of Plasmodium spp. in mosquitoes collected in China. Method: A Plasmodium -specific fluorescence resonance energy transfer (FRET) polymerase chain reaction (PCR) was established in this study to analyze five species of mosquitoes (1,620 Culex pipiens pallens, 806 Aedes albopictus, 377 Armigeres subalbatus, 168 Anopheles sinensis, and 80 Culex tritaeniorhynchus) collected in hand nets from homes in 25 provinces of China. Results: Only females originated from six provinces were determined to be positive (0.6%, 10/1,809). Plasmodium species were detected in three mosquito species, such as C.pipiens pallens (0.5%, 8/1,620), A.sinensis (0.6%, 1/168), and A.subalbatus (0.3%, 1/377). Of the three mosquito species positive for P. relictum, only C. pipiens pallens is known to feed on birds and is recognized as the natural vector of P. relictum. Conclusion: This is the first time that P. relictum has been detected in A. sinensis and A. subalbatus. P. relictum, the agent of avian malaria, was present in mosquitoes in China, including mosquito species not previously thought to be the vectors.

Molecular Detection of Rickettsia felis and Rickettsia bellii in Mosquitoes.

To add to the limited information on Rickettsia in mosquitoes in China, we carried out a PCR survey on convenience samples of 3051 mosquitoes collected with hand nets in and around domestic dwellings in 25 provinces. Five species of mosquitoes were identified: Culex pipiens pallens (n = 1620), Aedes albopictus (806), Armigeres subalbatus (377), Anopheles sinensis (168), and Culex tritaeniorhynchus (80). A Rickettsia nested-PCR targeting the variable domain of gltA showed Rickettsia felis in four mosquito species of 16 provinces Cx. pipiens pallens (1.8%, 29/1620); Ae. albopictus (1.2%, 10/806); An. sinensis (1.2%, 2/168); and Ar. subalbatus (2.1%, 8/377). Rickettsia bellii was also widespread, occurring in 12 provinces and 2 species: Cx. pipiens pallens (4.3%, 69/1620) and An. sinensis (0.6%, 1/168). R. felis and R. bellii were found in almost similar numbers in female [1.5% (27/1809) and 1.2% (21/1809), respectively] as in male mosquitoes [1.8% (22/1242) and 4.0% (49/1242), respectively]. Our results indicated that mosquitoes in China are widely infected with R. felis, the agent of human flea-borne spotted fever, and that R. bellii can also occur outside of the Americas and its usual tick hosts.

Efficient fecal-oral and possible vertical, but not respiratory, transmission of emerging Chlamydia gallinacea in broilers.

Chlamydia gallinacea is an endemic Chlamydia agent in poultry with a worldwide distribution. The aim of this study was to investigate whether C. gallinacea can be transmitted via fecal-oral, respiratory and vertical routes. After co-housing with C. gallinacea-inoculated broilers (n = 10) for 15 days, over 90.0% of SPF broilers (n = 10) became C. gallinacea-positive in their oropharyngeal and cloacal swabs. Connection of isolators with ventilation tubing resulted in transmission of infectious bronchitis virus, but not of C. gallinacea, from infected broilers in one isolator to uninfected ones in the other isolator. Chlamydia-qPCR determined that 97.6% of shells of embryonated eggs (287/294) from a breeding farm were positive for C. gallinacea. C. gallinacea positivity in egg albumen increased significantly from 7.6% (10/128) before incubating to 44.4% (8/18) of 7-day incubation, and from 5.5% (7/128) to 38.9% (7/18) in egg yolk. After incubating for 19 days, C. gallinacea DNA was detected in heart (5/55, 9.1%), liver (3/55, 5.5%), spleen (7/55, 12.7%), lung (6/55, 10.1%), kidney (8/55; 14.5%) and intestine (4/55, 7.3%) of chicken embryos. Taken together, our data indicate that C. gallinacea can be efficiently transmitted by the fecal-oral route, but not via aerosol. Additionally, vertical transmission can occur via penetration of C. gallinacea from eggshell to albumen, yolk, and the growing embryo. Our findings provide essential information for the control of C. gallinacea in poultry farms.

First description of the pathogenicity of Babesia vogeli in experimentally infected dogs.

Babesiosis is a tick-borne disease that occurs worldwide with the most recognized Babesia species that infect dogs being Babesia canis, B. vogeli, B. rossi and B. gibsoni. While B. vogeli is reported in dogs worldwide, clinical and laboratory data on infections is based on reports of naturally infected dogs. To provide reliable data on the clinical and laboratory abnormalities associated with acute and more chronic infections in healthy dogs free of other tick-borne diseases, we experimentally infected dogs with a Chinese strain of B. vogeli. All of the six infected Beagles, three of which were splenectomized, became infected with B. vogeli detected in blood smears taken the day following infection and the organism detected by FRET-qPCRs in most blood samples (77/86; 90%) collected about every 4 days until the end of the experiment on day 95. All the infected dogs showed fever, partial anorexia and malaise that was more severe in the splenectomized dogs that did not gain weight for three weeks in the period after initial infection. Regenerative anemia, thrombocytopenia and decreased white blood cell counts were seen in all dogs but were more severe in the splenectomized dogs, of which two had life threatening infections and had to be removed from the study for treatment. Following re-infection on day 66, none of the dogs showed clinical signs and copy numbers did not change significantly although all the dogs were negative by FRET-qPCR on at least some of the subsequent sampling days. Laboratory values in the non-splenectomized dogs were relatively unchanged while in the splenectomized dog there was a temporary small increase in the platelet and white blood cell counts and a temporary slight worsening of the anemia. In summary, our study shows dogs experimentally infected with a B. vogeli strain from China develop only mild clinical signs that are followed by asymptomatic infections that can last for least 95 days. In splenectomized dogs, however, severe life threatening signs may develop.

Molecular detection of colistin resistance genes (mcr-1, mcr-2 and mcr-3) in nasal/oropharyngeal and anal/cloacal swabs from pigs and poultry.

Antimicrobial resistance against colistin has emerged worldwide and is threatening the efficacy of colistin treatment of multi-resistant Gram-negative bacteria. In this study, PCRs were used to detect mcr genes (mcr-1, mcr-2, mcr-3) in 213 anal and 1,339 nasal swabs from pigs (n = 1,454) in nine provinces of China, and 1,696 cloacal and 1,647 oropharyngeal samples from poultry (n = 1,836) at live-bird markets in 24 provinces. The mcr-1 prevalences in pigs (79.2%) and geese (71.7%) were significantly higher than in chickens (31.8%), ducks (34.6%) and pigeons (13.1%). The mcr-2 prevalence in pigs was 56.3%, significantly higher than in chickens (5.5%), ducks (2.3%), geese (5.5%) and pigeons (0%). The mcr-3 prevalences in pigs (18.7%), ducks (13.8%) and geese (11.9%) were significantly higher than in chickens (5.2%) and pigeons (5.1%). In total, 173 pigs and three chickens were positive for all three mcr genes. The prevalences of the mcr were significantly higher in nasal/oropharyngeal swabs than in the anal /cloacal swabs. Phylogenetic studies identified 33 new mcr-2 variants and 12 new mcr-3 variants. This study demonstrates high prevalences of mcr in pigs and poultry in China, and indicates there is need for more thorough surveillance and control programs to prevent further selection of colistin resistance.

Chlamydia pecorum is the endemic intestinal species in cattle while C. gallinacea, C. psittaci and C. pneumoniae associate with sporadic systemic infection.

To investigate the prevalence and diversity of bovine Chlamydia spp. in cattle, whole blood from dairy and beef cattle in 11 provinces of China (n=2003) and vaginal swabs, whole blood samples, feces, milk samples from cows in a Yangzhou dairy farm (n=108) were examined using genus- and species-specific PCRs. In cattle from 11 provinces, 2.4% (48/2003) of whole-blood samples were positive for Chlamydia spp., and four Chlamydia species (C. pneumoniae, 41.7%, 20/48; C. psittaci, 22.9%, 11/48; C. gallinacea, 20.8%, 10/48; C. pecorum, 6.3%, 3/48) were identified. In a further study on a Yangzhou dairy farm, 64.8% (70/108) of the cows were positive for Chlamydia spp. C. pecorum was the intestinal endemic species (51/51, 100%), and C. gallinacea was the most frequent species in vaginal swabs (24/27, 88.9%), whole blood buffy coats (5/8, 62.5%) and milk (4/6, 66.7%). C. psittaci and C. pneumoniae were infrequently detected. DNA sequencing of the ompA gene demonstrated the presence of multiple in-herd C. pecorum serovars and single C. gallinacea and C. psittaci serovars which were identical with those of poultry from Yangzhou. This is the first report of C. gallinacea and C. pneumoniae in cattle. Further study is required to address the transmission of Chlamydia spp., in particular of C. gallinacea and C. pneumoniae from their natural hosts, and their potential pathogenic effect on health and production of cattle.