Causal Inference Regarding Infectious Aetiology of Chronic Conditions: A Systematic Review

Orrskog, Sofia; Medin, Emma; Tsolova, Svetla; Semenza, Jan C.

doi:10.1371/journal.pone.0068861

Cited by 12 publications

(13 citation statements)

References 128 publications

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“…C. trachomatis causes sexually transmitted infections worldwide and trachoma, a blinding disease, in developing countries (1,2). C. pneumoniae causes respiratory infections, including pneumonia, and is associated with several chronic conditions, including chronic obstructive bronchitis, asthma, and cardiovascular diseases (3,4). The genus Chlamydia also comprises well-known veterinary pathogens such as Chlamydia psittaci, C. pecorum, C. suis, and C. muridarum (5,6).…”

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confidence: 99%

Molecular Evidence of Chlamydia-Like Organisms in the Feces of Myotis daubentonii Bats

Hokynar

Vesterinen

Lilley

et al. 2017

Appl Environ Microbiol

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Chlamydia-like organisms (CLOs) are recently identified members of the Chlamydiales order. CLOs share intracellular lifestyles and biphasic developmental cycles, and they have been detected in environmental samples as well as in various hosts such as amoebae and arthropods. In this study, we screened bat feces for the presence of CLOs by molecular analysis. Using pan-Chlamydiales PCR targeting the 16S rRNA gene, Chlamydiales DNA was detected in 54% of the specimens. PCR amplification, sequencing, and phylogenetic analysis of the 16S rRNA and 23S rRNA genes were used to classify positive specimens and infer their phylogenetic relationships. Most sequences matched best with Rhabdochlamydia species or uncultured Chlamydia sequences identified in ticks. Another set of sequences matched best with sequences of the Chlamydia genus or uncultured Chlamydiales from snakes. To gain evidence of whether CLOs in bat feces are merely diet borne, we analyzed insects trapped from the same location where the bats foraged. Interestingly, the CLO sequences resembling Rhabdochlamydia spp. were detected in insect material as well, but the other set of CLO sequences was not, suggesting that this set might not originate from prey. Thus, bats represent another potential host for Chlamydiales and could harbor novel, previously unidentified members of this order. IMPORTANCE Several pathogenic viruses are known to colonize bats, and recent analyses indicate that bats are also reservoir hosts for bacterial genera. Chlamydialike organisms (CLOs) have been detected in several animal species. CLOs have high 16S rRNA sequence similarity to Chlamydiaceae and exhibit similar intracellular lifestyles and biphasic developmental cycles. Our study describes the frequent occurrence of CLO DNA in bat feces, suggesting an expanding host species spectrum for the Chlamydiales. As bats can acquire various infectious agents through their diet, prey insects were also studied. We identified CLO sequences in bats that matched best with sequences in prey insects but also CLO sequences not detected in prey insects. This suggests that a portion of CLO DNA present in bat feces is not prey borne. Furthermore, some sequences from bat droppings not originating from their diet might well represent novel, previously unidentified members of the Chlamydiales order.

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confidence: 99%

Molecular Evidence of Chlamydia-Like Organisms in the Feces of Myotis daubentonii Bats

Hokynar

Vesterinen

Lilley

et al. 2017

Appl Environ Microbiol

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“…The Cystic Fibrosis Foundation (CFF) estimates that approximately 70,000 CF patients are living worldwide and about 1,000 new CF cases are diagnosed in the United States each year (www.cff.org). Following Koch’s postulate (4), the traditional view of CF lung infections has been that specific airway pathogens are responsible for monomicrobial infections (5). CF bacterial pathogens that have been identified from patient sputum samples and commonly studied in vitro using pure culture include Pseudomonas aeruginosa, Haemophilus influenzae, Staphylococcus aureus and Burkholderia cepacia complex, including antibiotic-resistant strains such as methicillin-resistant S. aureus (MRSA) and multidrug-resistant P. aeruginosa (MDRPA) (1), as well as less common species such as Achromobacter xylosoxidans, Stenotrophomonas maltophilia and pathogenic Escherichia coli strains (6).…”

Section: Introductionmentioning

confidence: 99%

Metabolic Modeling of Cystic Fibrosis Airway Communities Predicts Mechanisms of Pathogen Dominance

Henson

Orazi

Phalak

et al. 2019

Preprint

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5Cystic fibrosis (CF) is a fatal genetic disease characterized by chronic lung infections due to aberrant 1 6 mucus production and the inability to clear invading pathogens. The traditional view that CF infections 1 7 are caused by a single pathogen has been replaced by the realization that the CF lung usually is colonized 1 8 by a complex community of bacteria, fungi and viruses. To help unravel the complex interplay between 1 9 the CF lung environment and the infecting microbial community, we developed a community metabolic 2 0 CF lung metabolomics and 16S sequencing could provide important insights into disease progression and 3 2 treatment efficacy. 3 3 Importance 3 4Cystic fibrosis (CF) is a genetic disease in which chronic airway infections and lung inflammation result 3 5 in respiratory failure. CF airway infections are usually caused by bacterial communities that are difficult 3 6 to eradicate with available antibiotics. Using species abundance data for clinically stable adult CF patients 3 7 assimilated from three published studies, we developed a metabolic model of CF airway communities to 3 8 better understand the interactions between bacterial species and between the bacterial community and the 3 9 lung environment. Our model predicted that clinically-observed CF pathogens could establish dominance 4 0 over other community members across a range of lung nutrient conditions. Heterogeneity of species 4 1 abundances across 75 patient samples could be predicted by assuming that sample-to-sample 4 2 heterogeneity was attributable to random variations in the CF nutrient environment. Our model 4 3 predictions provide new insights into the metabolic determinants of pathogen dominance in the CF lung 4 4 and could facilitate the development of improved treatment strategies. 4 5 4 6shaping community composition and behavior, and the impact of community composition on the efficacy 7 1 of antibiotic treatment regimens. 7 2In silico metabolic modeling has emerged as a powerful approach for analyzing complex microbial 7 3 communities by integrating genome-scale reconstructions of single-species metabolism within 7 4 mathematical descriptions of metabolically interacting communities (11, 12). Modeled species 7 5 interactions typically include competition for host-derived nutrients and cross-feeding of secreted 7 6 byproducts such as organic acids, alcohols and amino acids between species (13, 14). Due to challenges 7 7 in developing manually curated reconstructions of poorly studied species, including those present in the 7 8 CF lung, most in silico community models have been restricted to ~5 microbial species (15-17) and fail to 7 9adequately cover the diversity of in vivo communities. This limitation can be overcome in bacterial 8 0 communities by using semi-curated reconstructions developed through computational pipelines such as 8 1 the ModelSeed (18), AGORA (19) and other methods (20). Given the availability of suitable single-strain 8 2 metabolic reconstructions, a number of alternative methods have been develo...

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“…Chronic disease is the leading cause of death and disability in the United States [11]. In Europe, chronic conditions account for 86% of all deaths and 77% of the disease burden [12]. Chronic diseases also significantly increase health care costs related to long-term medical care.…”

Section: Introductionmentioning

confidence: 99%

“…and Chlamydia (C.) pneumoniae [12]. Association of chlamydiae other than C. pneumoniae with chronic disease is also well supported.…”

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confidence: 97%

Chronic Chlamydial Diseases: From Atherosclerosis to Urogenital Infections

Leonard

Borel

2014

Curr Clin Micro Rpt

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Chlamydiae cause a wide range of diseases in human and animal hosts. Chlamydia pneumoniae and Chlamydia trachomatis are important human pathogens with worldwide distribution that produce significant morbidity. Acute infections with C. pneumoniae cause respiratory tract infections, while chronic infection has been linked to chronic bronchitis, asthma and atherosclerosis. Ocular serovars of C. trachomatis induce trachoma, the leading cause of infectious blindness worldwide. C. trachomatis is the most common bacterial cause of sexually transmitted diseases (STDs) worldwide. Acute infections with genital serovars of C. trachomatis remain clinically silent in most women, but can progress to upper genital tract infection leading to pelvic inflammatory disease (PID), infertility and ectopic pregnancy. Chlamydiainduced, reactive arthritis can develop as a late-term condition after genital C. trachomatis or respiratory C. pneumoniae infection. In this review, we address recent information on pathogenesis, immune response, diagnosis and treatment of chronic diseases induced by C. trachomatis and C. pneumoniae. Abstract:Chlamydiae cause a wide range of diseases in human and animal hosts. Chlamydia pneumoniae and Chlamydia trachomatis are important human pathogens with worldwide distribution that produce significant morbidity. Acute infections with C. pneumoniae cause respiratory tract infections, while chronic infection has been linked to chronic bronchitis, asthma and atherosclerosis. Ocular serovars of C. trachomatis induce trachoma, the leading cause of blindness worldwide. C. trachomatis is the most common bacterial cause of sexually-transmitted diseases (STDs) worldwide. Acute infections with genital serovars of C. trachomatis remain clinically silent in most women but can progress to upper genital tract infection leading to pelvic inflammatory disease (PID), infertility and ectopic pregnancy. Chlamydia-induced, reactive arthritis can develop as a late-term condition after genital C. trachomatis or respiratory C. pneumoniae infection. In this review we address recent information on pathogenesis, immune

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Causal Inference Regarding Infectious Aetiology of Chronic Conditions: A Systematic Review

Cited by 12 publications

References 128 publications

Molecular Evidence of Chlamydia-Like Organisms in the Feces of Myotis daubentonii Bats

Molecular Evidence of Chlamydia-Like Organisms in the Feces of Myotis daubentonii Bats

Metabolic Modeling of Cystic Fibrosis Airway Communities Predicts Mechanisms of Pathogen Dominance

Chronic Chlamydial Diseases: From Atherosclerosis to Urogenital Infections

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