BackgroundHuman rhinoviruses (HRVs) are a highly prevalent cause of acute respiratory infection in children. They are classified into at least three species, HRV-A, HRV-B and HRV-C, which are characterized by sequencing the 5′ untranslated region (UTR) or the VP4/VP2 region of the genome. Given the increased interest for novel HRV strain identification and their worldwide distribution, we have carried out clinical and molecular diagnosis of HRV strains in a 2-year study of children with acute respiratory infection visiting one district hospital in Shanghai.Methodology/FindingsWe cloned and sequenced a 924-nt fragment that covered part of the 5′UTR and the VP4/VP2 capsid genes. Sixty-four HRV-infected outpatients were diagnosed amongst 827 children with acute low respiratory tract infection. Two samples were co-infected with HRV-A and HRV-B or HRV-C. By comparative analysis of the VP4/VP2 sequences of the 66 HRVs, we showed a high diversity of strains in HRV-A and HRV-B species, and a prevalence of 51.5% of strains that belonged to the recently identified HRV-C species. When analyzing a fragment of the 5′ UTR, we characterized at least two subspecies of HRV-C: HRV-Cc, which clustered differently from HRV-A and HRV-B, and HRV-Ca, which resulted from previous recombination in this region with sequences related to HRV-A. The full-length sequence of one strain of each HRV-Ca and HRV-Cc subspecies was obtained for comparative analysis. We confirmed the close relationship of their structural proteins but showed apparent additional recombination events in the 2A gene and 3′UTR of the HRV-Ca strain. Double or triple infections with HRV-C and respiratory syncytial virus and/or bocavirus were diagnosed in 33.3% of the HRV-infected patients, but no correlation with severity of clinical outcome was observed.ConclusionOur study showed a high diversity of HRV strains that cause bronchitis and pneumonia in children. A predominance of HRV-C over HRV-A and HRV-B was observed, and two subspecies of HRV-C were identified, the diversity of which seemed to be related to recombination with former HRV-A strains. None of the HRV-C strains appeared to have a higher clinical impact than HRV-A or HRV-B on respiratory compromise.

Anthropogenic environments have been implicated in enrichment and exchange of antibiotic resistance genes and bacteria. Here we study the impact of confined and controlled swine farm environments on temporal changes in the gut microbiome and resistome of veterinary students with occupational exposure for 3 months. By analyzing 16S rRNA and whole metagenome shotgun sequencing data in tandem with culture-based methods, we show that farm exposure shapes the gut microbiome of students, resulting in enrichment of potentially pathogenic taxa and antimicrobial resistance genes. Comparison of students' gut microbiomes and resistomes to farm workers' and environmental samples revealed extensive sharing of resistance genes and bacteria following exposure and after three months of their visit. Notably, antibiotic resistance genes were found in similar genetic contexts in student samples and farm environmental samples. Dynamic Bayesian network modeling predicted that the observed changes partially reverse over a 4-6 month period. Our results indicate that acute changes in a human's living environment can persistently shape their gut microbiota and antibiotic resistome.

BackgroundTraumatic rib fractures can cause chest complications that need further treatment and hospitalization. We hypothesized that an increase in the number of displaced rib fractures will be accompanied by an increase in chest complications.MethodsWe retrospectively reviewed the trauma registry between January 2013 and May 2015 in a teaching hospital in northeastern Taiwan. Patients admitted with chest trauma and rib fractures without concomitant severe brain, splenic, pelvic or liver injuries were included. The demographic data, such as gender, age, the index of coexistence disease, alcohol consumption, trauma mechanisms were analyzed as potential predictors of pulmonary complications. Pulmonary complications were defined as pneumothorax, hemothorax, flail chest, pulmonary contusion, and pneumonia.ResultsIn the 29 months of the study period, a total of 3151 trauma patients were admitted to our hospital. Among them, 174 patients were enrolled for final analysis. The most common trauma mechanism was road traffic accidents (58.6%), mainly motorbike accidents (n = 70, 40.2%). Three or more displaced rib fractures had higher specificity for predicting complications, compared to three or more total rib fractures (95.5% vs 59.1%). Adjusting the severity of chest trauma using TTSS and Ribscore by multivariable logistic regression analysis, we found that three or more rib fractures or any displaced rib fracture was the most significant predictor for developing pulmonary complication (aOR: 5.49 95% CI: 1.82–16.55). Furthermore, there were 18/57 (31.6%) patients with fewer than three ribs fractures developed pulmonary complications. In these 18 patients, only five patients had delayed onset complications and four of them had at least one displaced rib fracture.DiscussionIn this retrospective cohort study, we found that the number of displaced or total rib fractures, bilateral rib fractures, and rib fractures in more than two areas were associated with the more chest complications. Furthermore, three or more rib fracture or any displacement were found to be the most sensitive risk factor for chest complications, independent of other risk factors or severity index.ConclusionThe number of displaced rib fractures could be a strong predictor for developing pulmonary complications. For patients with fewer than three rib fractures without rib displacement and initial lung or other organ injuries, outpatient management could be safe and efficient.Electronic supplementary materialThe online version of this article (doi:10.1186/s13049-017-0368-y) contains supplementary material, which is available to authorized users.