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Small‐ and medium‐sized mammals play an important role in the life cycle of tick‐borne pathogens in urban habitats. Our aim was to apply the general protocol, DAMA (documentation–assessment–monitoring–action), which is an integrated proposal to build a proactive capacity to understand, anticipate, and respond to the outcomes of accelerating environmental change. Here we tested whether road‐killed carcasses in urban areas are useful sources of tissue and parasite samples to investigate these species’ contribution to the epidemiology of vector‐borne diseases. We collected 29 road‐killed and 6 carcasses with different causes of mortality (23 northern white‐breasted hedgehogs and 12 from seven other mammal species) mainly from Budapest, Hungary. We used quantitative and conventional PCRs to determine pathogens in 90 collected tissues (52 from hedgehogs; 38 from other species) and 417 ticks that were only found on hedgehogs. Tissue samples revealed a wide range of bacteria including human zoonotic pathogens identified as Anaplasma phagocytophilum ecotype I, Borrelia afzelii, B. spielmanii, Borrelia miyamotoi, Rickettsia helvetica, and Bartonella species. Among the 23 collected hedgehog carcasses, 17 (74%) were infected with A. phagocytophilum, 6 (26%) with Borrelia burgdorferi s.l., 12 (52%) with R. helvetica, and 15 (65%) with Rickettsia sp. Furthermore, we report the first detection of Rickettsia sp. infection in European moles and lesser weasel and R. helvetica in stone marten. Through sequencing B. afzelii, R. helvetica, R. monacensis and A. phagocytophilum ecotype I were identified in the ticks removed from the carcasses. We showed that road‐killed urban mammal species are exposed to multiple tick‐borne pathogens but further studies have to clarify whether they, in fact, also have a role in their maintenance and spread. Our study also demonstrates that roadkill can be used in the risk assessment of potential human infection and in the implementation of the DAMA protocol.     

Childhood violence exposure and social deprivation are linked to adolescent threat and reward neural function

BackgroundChildhood adversity is, unfortunately, highly prevalent and strongly associated with later psychopathology. Recent theories posit that two dimensions of early adversity, threat and deprivation, have distinct effects on brain development. The current study evaluated whether violence exposure (threat) and social deprivation (deprivation) were associated with adolescent amygdala and ventral striatum activation, respectively, in a prospective, well-sampled, longitudinal cohort using a pre-registered, open science approach.MethodsOne hundred and sixty-seven adolescents from the Fragile Families and Child Wellbeing Study completed functional magnetic resonance imaging (fMRI) scanning. Prospective longitudinal data from ages 3, 5 and 9 years were used to create indices of childhood violence exposure and social deprivation. We evaluated whether these dimensions were associated with adolescent brain function in response to threatening and rewarding faces.ResultsChildhood violence exposure was associated with decreased amygdala habituation (i.e. more sustained activation) and activation to angry faces in adolescence, whereas childhood social deprivation was associated with decreased ventral striatum activation to happy faces in adolescence. These associations held when adjusting for the other dimension of adversity (e.g., adjusting for social deprivation when examining associations with violence exposure), the interaction of the two dimensions of adversity, gender, internalizing psychopathology, and current life stress.ConclusionsConsistent with recent theories, different forms of early adversity were associated with region-specific differences in brain activation.     

Can EGFR mutation status be reliably determined in pre‐operative needle biopsies from adenocarcinomas of the lung?

The identification of EGFR mutations in non‐small‐cell lung cancer is important for selecting patients, who may benefit from treatment with EGFR tyrosine kinase inhibitors. The analysis is usually performed on cytological aspirates and/or histological needle biopsies, representing a small fraction of the tumour volume. The aim of the present investigation was to evaluate the diagnostic performance of this molecular test. We retrospectively included 201 patients with primary adenocarcinoma of the lung. EGFR mutation status (exon 19 deletions and exon 21 L858R point mutation) was evaluated on both pre‐operative biopsies (131 histological and 70 cytological) and on the surgical specimens, using PCR. Samples with low tumour cell fraction were assigned to laser micro‐dissection (LMD). We found nine (4.5%) patients with EGFR mutation in the lung tumour resections, but failed to identify mutation in one of the corresponding pre‐operative, cytological specimens. Several (18.4%) analyses of the pre‐operative biopsies were inconclusive, especially in case of biopsies undergoing LMD and regarding exon 21 analysis. Discrepancy of mutation status in one patient may reflect intra‐tumoural heterogeneity or technical issues. Moreover, several inconclusive results in the diagnostic biopsies reveal that attention must be paid on the suitability of pre‐operative biopsies for EGFR mutation analysis.     

Nonproportional hazards and unobserved heterogeneity in clustered survival data: When can we tell the difference?

Multivariate survival data are frequently encountered in biomedical applications in the form of clustered failures (or recurrent events data). A popular way of analyzing such data is by using shared frailty models, which assume that the proportional hazards assumption holds conditional on an unobserved cluster-specific random effect. Such models are often incorporated in more complicated joint models in survival analysis. If the random effect distribution has finite expectation, then the conditional proportional hazards assumption does not carry over to the marginal models. It has been shown that, for univariate data, this makes it impossible to distinguish between the presence of unobserved heterogeneity (eg, due to missing covariates) and marginal nonproportional hazards. We show that time-dependent covariate effects may falsely appear as evidence in favor of a frailty model also in the case of clustered failures or recurrent events data, when the cluster size or number of recurrent events is small. When true unobserved heterogeneity is present, the presence of nonproportional hazards leads to overestimating the frailty effect. We show that this phenomenon is somewhat mitigated as the cluster size grows. We carry out a simulation study to assess the behavior of test statistics and estimators for frailty models in such contexts. The gamma, inverse Gaussian, and positive stable shared frailty models are contrasted using a novel software implementation for estimating semiparametric shared frailty models. Two main questions are addressed in the contexts of clustered failures and recurrent events: whether covariates with a time-dependent effect may appear as indication of unobserved heterogeneity and whether the additional presence of unobserved heterogeneity can be detected in this case. Finally, the practical implications are illustrated in a real-world data analysis example.     

Effect of residual doxycycline concentrations on resistance selection and transfer in porcine commensal Escherichia coli

Pig feed may contain various levels of antimicrobial residues due to cross-contamination. A previous study showed that a 3% carry-over level of doxycycline (DOX) in the feed results in porcine faecal concentrations of approximately 4?mg/L.The aim of this study was to determine the effect of residual DOX concentrations (1 and 4?mg/L) in vitro on selection of DOX–resistant porcine commensal Escherichia coli and transfer of their resistance plasmids.Three different DOX–resistant porcine commensal E. coli strains and their plasmids were characterised. These strains were each brought in competition with a susceptible strain in a medium containing 0, 1 and 4?mg/L DOX. Resistant bacteria, susceptible bacteria and transconjugants were enumerated after 24?h and 48?h.The tet(A)–carrying plasmids showed genetic backbones that are also present among human E. coli isolates. Ratios of resistant to susceptible bacteria were significantly higher at 1 and 4?mg/L DOX compared with the blank control, but there was no significant difference between 1 and 4?mg/L. Plasmid transfer frequencies were affected by 1 or 4?mg/L DOX in the medium for only one of the resistance plasmids.In conclusion, DOX concentrations of 1 and 4?mg/L can select for resistant E. coli in vitro. Further research is needed to determine the effect of these concentrations in the complex environment of the porcine intestinal microbiota.