Spectrum detection and analysis of the epidemiological characteristics of infectious pathogens in the feline respiratory tract.

Our study was designed to investigate the original spectrum of feline respiratory tract infection and to provide a scientific basis for the clinical diagnosis and treatment of feline respiratory infections and for precise prevention and control measures. A total of 400 cats with upper respiratory tract infections from animal hospitals in 12 provinces in China were examined from November 2022 to October 2023 to investigate the epidemiology of feline calicivirus (FCV), feline herpes virus type 1 (FHV-1), influenza A virus (IAV), Mycoplasma felis, Chlamydia felis, and Bordetella bronchiseptica through loop-mediated isothermal amplification (LAMP) with microfluidic chip detection. The results showed that 396 of the 400 samples tested were positive for at least one of these pathogens, with an overall detection rate of 99.00%. The detection rates were as follows: FCV, 36.00% (144/400); M. felis, 34.00% (136/400); FHV-1, 21.50% (86/400); C. felis, 15.75% (63/400); B. b, 13.00% (52/400); IAV, 4.50% (18/400). There were no statistically significant differences in the detection rates of respiratory pathogens between different sexes, ages, seasons, breeds, or regions (P > 0.05). There were 88 mixed infections, giving a total mixed infection rate of 22.00% (88/400). It is worth noting that the detection rate of FCV at different ages and of FHV-1 in different sexes showed significant differences (P < 0.05). The highest rate of FCV infection was found in animals that were 1 to 2 years old, and the rate of FHV-1 infection in male cats was higher than that in female cats. The results showed that the spectrum of feline respiratory pathogens is complex, with diverse epidemiological characteristics and mixed infections, and some differences among different respiratory pathogens were found with regard to the sex, age, and breed of the cat. Studies should be continued to provide a scientific basis for precise prevention and control of feline respiratory diseases.

Analyzing RNA-Seq data from Chlamydia with super broad transcriptomic activation: challenges, solutions, and implications for other systems.

BACKGROUND: RNA sequencing (RNA-Seq) offers profound insights into the complex transcriptomes of diverse biological systems. However, standard differential expression analysis pipelines based on DESeq2 and edgeR encounter challenges when applied to the immediate early transcriptomes of Chlamydia spp., obligate intracellular bacteria. These challenges arise from their reliance on assumptions that do not hold in scenarios characterized by extensive transcriptomic activation and limited repression. RESULTS: Standard analyses using unique chlamydial RNA-Seq reads alone identify nearly 300 upregulated and about 300 downregulated genes, significantly deviating from actual RNA-Seq read trends. By incorporating both chlamydial and host reads or adjusting for total sequencing depth, the revised normalization methods each detected over 700 upregulated genes and 30 or fewer downregulated genes, closely aligned with observed RNA-Seq data. Further validation through qRT-PCR analysis confirmed the effectiveness of these adjusted approaches in capturing the true extent of transcriptomic activation during the immediate early phase of chlamydial infection. CONCLUSIONS: This study highlights the limitations of standard RNA-Seq analysis tools in scenarios with extensive transcriptomic activation, such as in Chlamydia spp. during early infection. Our revised normalization methods, incorporating host reads or total sequencing depth, provide a more accurate representation of gene expression dynamics. These approaches may inform similar adjustments in other systems with unbalanced gene expression dynamics, enhancing the accuracy of transcriptomic analysis.

RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level.

Microbial pangenome analysis identifies present or absent genes in prokaryotic genomes. However, current tools are limited when analyzing species with higher sequence diversity or higher taxonomic orders such as genera or families. The Roary ILP Bacterial core Annotation Pipeline (RIBAP) uses an integer linear programming approach to refine gene clusters predicted by Roary for identifying core genes. RIBAP successfully handles the complexity and diversity of Chlamydia, Klebsiella, Brucella, and Enterococcus genomes, outperforming other established and recent pangenome tools for identifying all-encompassing core genes at the genus level. RIBAP is a freely available Nextflow pipeline at github.com/hoelzer-lab/ribap and zenodo.org/doi/10.5281/zenodo.10890871.

Case-control study to identify the causative agents of ophthalmia and conjunctivitis in goats in Savannakhet province of Lao PDR.

Pinkeye is a highly contagious disease of goats with different aetiologies. Surveys in Lao PDR have identified eye lesions typical of pinkeye as a common condition, however, this has not been confirmed diagnostically, and the responsible pathogens have not been identified. A matched case-control study was implemented in 70 goat holdings from Savannakhet province, Lao PDR, to detect agents causing pinkeye and conduct phylogenetic analysis of the identified pathogens. Fifty eye swabs from goats with infected eyes (cases) and 50 paired samples from unaffected cohorts (controls) were collected from 25 holdings. Samples were tested using quantitative PCR assays targeting known pinkeye pathogens at the genus and species levels. The prevalence of pathogens in case and control goats was as follows: Mycoplasma conjunctivae (94% and 74% respectively, P = 0.006, OR = 5.5), Chlamydia pecorum (4%, 10%), Moraxella ovis (30%, 30%), Moraxella bovis (0%, 0%) and Moraxella bovoculi (0%, 0%). M. conjunctivae was present in a high proportion of goats in both groups revealing that Lao goats are carriers of M. conjunctivae. However, the mean log10 genome copy number/µL of DNA extract was significantly higher in case goats than control goats (P < 0.05). Thus, M. conjunctivae is likely the principal causative agent of pinkeye in Lao goats with carrier status converting to clinical infection following corneal damage or other causative factors. M. conjunctivae detected in samples from different goats and districts showed low genetic diversity. Identifying the causes of pinkeye in Lao goats will assist in designing appropriate treatment and control strategies.

Biomolecular survey on the main infectious causes of abortion in sheep in the Italian regions of Latium and Tuscany.

Background: Ruminants play an important role in economic sustenance in many developing countries. Abortion is one of the most important causes of economic losses in sheep livestock and, for this reason, it is very important to know, at an early stage, which pathogens caused abortion. Aim: The aim of the study is to obtain data about the distribution of abortifacient pathogens in the Italian regions of Latium and Tuscany, the awareness of the distribution of infectious agents causing abortion could allow the development of an appropriate vaccination and prophylaxis plan, to avoid major economic losses. Methods: 388 abortions were collected during the 2015-2018 period. Organs, tissues, and swabs were subjected to DNA extraction and then analyzed with commercial q-PCR kits for the detection of the most common abortion pathogens circulating in these geographical areas. Results: The positivity in 148 abortions was 56% for Chlamydia abortus, 14% for Coxiella burnetii, 16% for Salmonella spp, 12% for Toxoplasma gondii, and 2% for Neospora caninum. Interesting results were obtained for cases of abortions with co-infection of abortion pathogens. Conclusion: Diagnosing the cause of abortion remains a multifaceted process that may also include non-infectious factors such as deficiencies and toxicities. Further research is needed also to assess the role of low pathogen concentrations and co-infections in the abortions of sheep.

Chlamydia suis undergoes interclade recombination promoting Tet-island exchange.

BACKGROUND: The obligate intracellular bacterial family Chlamydiaceae comprises a number of different species that cause disease in various vertebrate hosts including humans. Chlamydia suis, primarily found in the gastrointestinal tract of pigs, is the only species of the Chlamydiaceae family to have naturally gained tetracycline resistance (TetR), through a genomic island (Tet-island), integrated into the middle of chromosomal invasin-like gene inv. Previous studies have hypothesised that the uptake of the Tet-island from a host outside the Chlamydiaceae family was a unique event, followed by spread among C. suis through homologous recombination. In vitro recombination studies have shown that Tet-island exchange between C. suis strains is possible. Our aim in this study was to gain a deeper understanding of the interclade recombination of the Tet-island, among currently circulating C. suis field strains compared to in vitro-generated recombinants, using published whole genome sequences of C. suis field strains (n = 35) and in vitro-generated recombinants (n = 63). RESULTS: We found that the phylogeny of inv better reflected the phylogeny of the Tet-island than that of the whole genome, supporting recombination rather than site-specific insertion as the means of transfer. There were considerable differences between the distribution of recombinations within in vitro-generated strains compared to that within the field strains. These differences are likely because in vitro-generated recombinants were selected for a tetracycline and rifamycin/rifampicin resistant background, leading to the largest peak of recombination across the Tet-island. Finally, we found that interclade recombinations across the Tet-island were more variable in length downstream of the Tet-island than upstream. CONCLUSIONS: Our study supports the hypothesis that the occurrence of TetR strains in both clades of C. suis came about through interclade recombination after a single ancestral horizontal gene transfer event.

Isolation and characterization of Chlamydia felis and its pathogenesis in cats.

Feline upper respiratory tract disease (URTD) is a common but complicated disease that occurs in domestic cats, worldwide. 396 cats in Guangxi Province, China were screened for URTD-associated pathogens from March 2022 to August 2023. Mycoplasma felis was found to be the most prevalent infectious agent with a positivity rate of 24.75 %, followed by feline calicivirus (FCV), Chlamydia felis, feline herpesvirus 1 (FHV-1) and feline influenza A virus (FeIAV) with rates of 15.91, 11.62, 5.56 and 1.52 %, respectively. In particular, C. felis and M. felis were found in 13 of 55 co-infected cats. Of the 46 C. felis-positive samples, one strain, named as GXNN36, was successfully isolated using chicken embryos and it was characterized both in vivo and in vitro. For the cat studies, both high- and low-dose challenged groups showed severe conjunctivitis, accompanied by transient fever and respiratory symptoms. C. felis replicated well in turbinate, trachea and lung tissues with high copy numbers and the infection subsequently spread to the livers, spleens, pancreas, kidneys, hearts and intestines. These findings will help our understanding of the role of C. felis in feline URTD and provide a valuable model to evaluate the efficacy of vaccines and therapeutic remedies in the future.

Serosurvey and associated risk factors for Chlamydia abortus infection in Dromedary camels in Egypt.

Chlamydia abortus (C. abortus) is a gram-negative, obligate intracellular bacterium that causes major public health problems in human and reproductive problems in animals. The information about the epidemiology of this pathogen among camels in Egypt is very rare. This study aimed to evaluate the existence of antibodies against C. abortus in camels and assess the related risk factors for infection. A total of 410 blood samples were collected from camels from three Egyptian governorates and examined using commercial ELISA kit. The overall seroprevalence rate was 6.6% and the higher C. abortus seropositivity rate was found in Giza governorate. Location, sex and infestation by ectoparasites did not influence on the seroprevalence of the disease. In addition, age, herd size, contact with small ruminants and history of abortion were identified as risk factors for C. abortus infection according to the univariate analysis. Based on multivariate analysis, age group of 4-8 years, small herd size, contact of camels with sheep and goats, and history of abortion were found to be significant risk factors for chlamydiosis transmission in camels. These factors had odds ratios of 4.23, 3.51, 2.84, and 2.5, respectively. These results suggest that camels have a role in the epidemiology of C. abortus infection. This promotes awareness and severe public health concern about infectious camel illnesses, allowing for additional diagnostic advancements and effective management techniques to be developed.

Unpredictable soil conditions can affect the prevalence of a microbial symbiosis.

The evolution of symbiotic interactions may be affected by unpredictable conditions. However, a link between prevalence of these conditions and symbiosis has not been widely demonstrated. We test for these associations using Dictyostelium discoideum social amoebae and their bacterial endosymbionts. D. discoideum commonly hosts endosymbiotic bacteria from three taxa: Paraburkholderia, Amoebophilus and Chlamydiae. Three species of facultative Paraburkholderia endosymbionts are the best studied and give hosts the ability to carry prey bacteria through the dispersal stage to new environments. Amoebophilus and Chlamydiae are obligate endosymbiont lineages with no measurable impact on host fitness. We tested whether the frequency of both single infections and coinfections of these symbionts were associated with the unpredictability of their soil environments by using symbiont presence-absence data from D. discoideum isolates from 21 locations across the eastern United States. We found that symbiosis across all infection types, symbiosis with Amoebophilus and Chlamydiae obligate endosymbionts, and symbiosis involving coinfections were not associated with any of our measures. However, unpredictable precipitation was associated with symbiosis in two species of Paraburkholderia, suggesting a link between unpredictable conditions and symbiosis.

Hijacking host cell vesicular transport: New insights into the nutrient acquisition mechanism of Chlamydia.

Chlamydia infection is an important cause of public health diseases, and no effective vaccine is currently available. Owing to its unique intracellular lifestyle, Chlamydia requires a variety of nutrients and substrates from host cells, particularly sphingomyelin, cholesterol, iron, amino acids, and the mannose-6-phosphate receptor, which are essential for inclusion development. Here, we summarize the recent advances in Chlamydia nutrient acquisition mechanism by hijacking host cell vesicular transport, which plays an important role in chlamydial growth and development. Chlamydia obtains the components necessary to complete its intracellular developmental cycle by recruiting Rab proteins (major vesicular trafficking regulators) and Rab effector proteins to the inclusion, interfering with Rab-mediated multivesicular trafficking, reorienting the nutrition of host cells, and reconstructing the intracellular niche environment. Consequently, exploring the role of vesicular transport in nutrient acquisition offers a novel perspective on new approaches for preventing and treating Chlamydia infection.

Effects of different immunomodulating liposome-based adjuvants and injection sites on immunogenicity in pigs.

Vaccine adjuvants, such as liposome-based cationic adjuvant formulations (CAFs), are able to boost immune responses and, by incorporation of distinct immunomodulators, steer immunity towards a desired direction in mice, non-human primates and humans, while less studied in pigs. Here we used commercial pigs to investigate polarizing adjuvant effects of CAFs with immunomodulators: C-type lectin receptor ligands trehalose-6,6'-dibehenate and monomycolyl glycerol, toll-like receptor 3 ligand Poly(I:C) or retinoic acid. Vaccines were formulated with a recombinant Chlamydia model protein antigen and administered via three injection routes. All adjuvants significantly increased antigen-specific IgG in serum, compared to non-adjuvanted antigen. Administering the vaccines through intramuscular and intraperitoneal routes induced significantly higher antigen-specific IgG and IgA serum antibodies, than the perirectal route. Although immunizations triggered cell-mediated immunity, no significant differences between adjuvants or injection sites were detected. Genes depicting T cell subtypes revealed only minor differences. Our findings suggest that specific signatures of the tested adjuvant immunomodulation do not translate well from mice to pigs in standard two-dose immunizations. This study provides new insights into immune responses to CAFs in pigs, and highlights that adjuvant development should ideally be carried out in the intended species of interest or in models with high predictive validity/translational value.

Chlamydia gallinacea in Brazilian backyard chicken farms.

Avian chlamydiosis is a bacterial infectious disease of birds, considered until recently caused only by Chlamydia psittaci, that now includes the newly described species C. buteonis, C. avium, and C. gallinacea, associated with several avian hosts. Since its recognition as a species in 2014 and having chickens as one of its main hosts, C. gallinacea has already been described in backyard poultry on all continents. The present study aimed to survey by molecular techniques the presence and species of Chlamydia spp. in backyard chickens from three states of the southern region of Brazil (Paraná-PR, Santa Catarina-SC, and Rio Grande do Sul-RS). DNA extracted from cloacal swab samples were tested by polymerase chain reaction (PCR) for different species of Chlamydia, namely Chlamydiaceae (23 S rRNA gene), C. psittaci (ompA gene), C. avium (enoA gene) and C. gallinacea (gidA and enoA genes). The 16 S rRNA gene was used for sequencing and phylogenetic analysis. A total of 582 backyard chicken samples were collected and grouped in 238 pools, from 134 properties in 59 municipalities. Chlamydiaceae was detected in 25.2% (60/238) of the samples, in 38.8% (52/134) of the properties and in 66.1% (39/59) of the municipalities. None of the samples yielded positive PCR results for C. psittaci or C. avium. For C. gallinacea, the overall percentage was 16.3% (39/238) according to the results of gidA and enoA genes. Sequence analysis confirmed that the samples corresponded to C. gallinacea. This is the first report of C. gallinacea in Brazil.

Novel typing scheme reveals emergence and genetic diversity of Chlamydia pecorum at the local management scale across two koala populations.

To overcome shortcomings in discriminating Chlamydia pecorum strains infecting the koala (Phascolarctos cinereus) at the local level, we developed a novel genotyping scheme for this pathogen to inform koala management at a fine-scale subpopulation level. We applied this scheme to two geographically distinct koala populations in New South Wales, Australia: the Liverpool Plains and the Southern Highlands to South-west Sydney (SHSWS). Our method provides greater resolution than traditional multi-locus sequence typing, and can be used to monitor strain emergence, movement, and divergence across a range of fragmented habitats. Within the Liverpool Plains population, suspected recent introduction of a novel strain was confirmed by an absence of genetic diversity at the earliest sampling events and limited diversity at recent sampling events. Across the partially fragmented agricultural landscape of the Liverpool Plains, diversity within a widespread sequence type suggests that this degree of fragmentation may hinder but not prevent spread. In the SHSWS population, our results suggest movement of a strain from the south, where diverse strains exist, into a previously Chlamydia-free area in the north, indicating the risk of expansion towards an adjacent Chlamydia-negative koala population in South-west Sydney. In the south of the SHSWS where koala subpopulations appear segregated, we found evidence of divergent strain evolution. Our tool can be used to infer the risks of strain introduction across fragmented habitats in population management, particularly through practices such as wildlife corridor constructions and translocations.

Understanding dynamics and overlapping epidemiologies of HIV, HSV-2, chlamydia, gonorrhea, and syphilis in sexual networks of men who have sex with men.

Introduction: We aimed to investigate the overlapping epidemiologies of human immunodeficiency virus (HIV), herpes simplex virus type 2 (HSV-2), chlamydia, gonorrhea, and syphilis in sexual networks of men who have sex with men (MSM), and to explore to what extent the epidemiology of one sexually transmitted infection (STI) relates to or differs from that of another STI. Methods: An individual-based Monte Carlo simulation model was employed to simulate the concurrent transmission of STIs within diverse sexual networks of MSM. The model simulated sexual partnering, birth, death, and STI transmission within each specific sexual network. The model parameters were chosen based on the current knowledge and understanding of the natural history, transmission, and epidemiology of each considered STI. Associations were measured using the Spearman's rank correlation coefficient (SRCC) and maximal information coefficient (MIC). Results: A total of 500 sexual networks were simulated by varying the mean and variance of the number of partners for both short-term and all partnerships, degree correlation, and clustering coefficient. HSV-2 had the highest current infection prevalence across the simulations, followed by HIV, chlamydia, syphilis, and gonorrhea. Threshold and saturation effects emerged in the relationship between STIs across the simulated networks, and all STIs demonstrated moderate to strong associations. The strongest current infection prevalence association was between HIV and gonorrhea, with an SRCC of 0.84 (95% CI: 0.80-0.87) and an MIC of 0.81 (95% CI: 0.74-0.88). The weakest association was between HSV-2 and syphilis, with an SRCC of 0.54 (95% CI: 0.48-0.59) and an MIC of 0.57 (95% CI, 0.49-0.65). Gonorrhea exhibited the strongest associations with the other STIs while syphilis had the weakest associations. Across the simulated networks, proportions of the population with zero, one, two, three, four, and five concurrent STI infections were 48.6, 37.7, 11.1, 2.4, 0.3, and < 0.1%, respectively. For lifetime exposure to these infections, these proportions were 13.6, 21.0, 22.9, 24.3, 13.4, and 4.8%, respectively. Conclusion: STI epidemiologies demonstrate substantial overlap and associations, alongside nuanced differences that shape a unique pattern for each STI. Gonorrhea exhibits an "intermediate STI epidemiology," reflected by the highest average correlation coefficient with other STIs.

Management of acute sexual assault presenting to a large Australian sexual health clinic in 2012-2021: a retrospective clinical audit.

Background The incidence of sexual assault continues to rise in Australia. This study aimed to describe the nature of assault, HIV/STI positivity, and its management at a sexual health clinic. Methods We performed a chart review of 516 sexual assault cases presenting to Melbourne Sexual Health Centre between 2012 and 2021, collecting data on victim demographics, details of assault, HIV/STI testing and positivity, police involvement, and offer of counselling. Results We included 516 cases: 124 males (24.0%); 384 females (74.4%); and eight transgender (1.6%) victims. The proportion of assault cases presenting to Melbourne Sexual Health Centre increased from 0.1% (37/37,070) in 2012 to 0.2% (56/36,514) in 2021 (P trend =0.006). HIV post-exposure prophylaxis was prescribed for 64.5% (80/124) of males and 12.5% (48/384) of females. Among victims, 69.4% (358/516) were tested for HIV and no one tested positive, while 71.9% (371/516) were tested for syphilis, with 1.6% (6/371) positive. Gonorrhoea and chlamydia were tested at the oropharynx (44.8% [231/516] vs 28.7% [148/516]), genitals (83.7% [432/516] vs 92.4% [477/516]) and anorectum (35.3% [182/516] vs 35.3% [182/516]). Positivity for gonorrhoea and chlamydia were: 2.6% (6/231) vs 2.0% (3/148) at oropharynx, 1.4% (6/432) vs 2.9% (14/477) at genitals, and 5.5% (10/182) vs 7.1% (13/182) at anorectum. According to clinical records, 25.2% (130/516) of victims sought police involvement, and 71.7% (370/516) were offered counselling. Conclusions Sexual assault was an uncommon presentation at Melbourne Sexual Health Centre, with diverse circumstances surrounding assault; however, clinical documentation varied, indicating a need for a standard primary care protocol for clients presenting with acute sexual assault.

Oportunidades perdidas en la detección temprana de la infección por VIH en pacientes con infecciones de transmisión sexual: un estudio de vida real / Missed opportunities in the early detection of HIV infection in patients with sexually transmitted infections: A real-life study

Introducción: Las enfermedades de transmisión sexual, como la cervicitis, la proctitis y la uretritis, se asocian a altas tasas de infección por VIH. Ante la sospecha de estas patologías, se debería solicitar una serología del VIH. Material y métodos: Estudio retrospectivo realizado durante 2018 en el Hospital Costa del Sol (Marbella, Málaga). Se revisaron las serologías para el VIH solicitadas en pacientes a los que se les pidió una PCR para Chlamydia trachomatis y Neisseria gonorrhoeae. Resultados: Se valoraron 1.818 pacientes, en los que se realizó serología para el VIH al 44,7%, de las cuales 14 (1,7%) resultaron positivas. El 55,3% restante fueron oportunidades perdidas de diagnóstico. Conclusiones: Las infecciones por C.trachomatis y N.gonorrhoeae están asociadas a una elevada tasa de infección oculta por el VIH. El grado de sospecha de VIH en esta población sigue siendo bajo, y resulta esencial que se refuerce ante la posibilidad de infección por estas patologías.(AU)

Introduction: Sexually transmitted diseases such as cervicitis, proctitis and urethritis are associated with high rates of HIV infection. When these pathologies are suspected, HIV serology should be requested. Material and methods: A Retrospective study was performed during 2018 at the Hospital Costa del Sol (Marbella, Málaga, Spain). HIV serologies requested in patients who were asked for PCR for Chlamydia trachomatis and Neisseria gonorrhoeae were reviewed. Results: A total of 1818 patients were evaluated, in which HIV serology was performed in 44.7%, of which 14 (1.7%) were positive. The remaining 55.3% were missed diagnostic opportunities. Conclusions: C.trachomatis and N.gonorrhoeae infections are associated with a high rate of occult HIV infection. The degree of suspicion of HIV in this population remains low and it is essential that it be reinforced in the presence of the possibility of infection by these pathologies.(AU)

Detection of a novel genotype of Chlamydia buteonis in falcons from the Emirates.

Chlamydiaceae are a family of obligate intracellular bacterial pathogens that affect both humans and animals. Recently, a new species named Chlamydia (C.) buteonis was isolated from hawks. In this study, we aimed to investigate the prevalence of Chlamydiaceae in 60 falcons that underwent a routine health check at a specialized clinic in Dubai, United Arab Emirates. Using real-time PCR, we analyzed cloacal and tracheal swabs from these birds and found that 39 of them tested positive for Chlamydiaceae. Subsequent real-time PCR assays specific for C. psittaci, C. abortus, C. avium, and C. gallinacea yielded negative results, while testing positive for C. buteonis. Analysis of ompA and MLST sequences indicated a highly conserved group of strains within this set of samples, but with sequences distinct from the C. buteonis RSHA reference strains and other C. buteonis strains isolated from hawks in the United States. Two strains were further isolated by cell culture and sequenced using whole-genome sequencing, confirming the clustering of these falcon strains within the C. buteonis species, but in a separate clade from the previously identified hawk strains. We also developed a SNP-based PCR-HRM assay to distinguish between these different genotypes. Overall, our findings suggest a high prevalence of C. buteonis in falcons in Dubai and highlight the importance of monitoring this pathogen in birds of prey.