Comparative genomics of Salmonella enterica serovars Derby and Mbandaka, two prevalent serovars associated with different livestock species in the UK

Background Despite the frequent isolation of Salmonella enterica sub. enterica serovars Derby and Mbandaka from livestock in the UK and USA little is known about the biological processes maintaining their prevalence. Statistics for Salmonella isolations from livestock production in the UK show that S. Derby is most commonly associated with pigs and turkeys and S. Mbandaka with cattle and chickens. Here we compare the first sequenced genomes of S. Derby and S. Mbandaka as a basis for further analysis of the potential host adaptations that contribute to their distinct host species distributions. Results Comparative functional genomics using the RAST annotation system showed that predominantly mechanisms that relate to metabolite utilisation, in vivo and ex vivo persistence and pathogenesis distinguish S. Derby from S. Mbandaka. Alignment of the genome nucleotide sequences of S. Derby D1 and D2 and S. Mbandaka M1 and M2 with Salmonella pathogenicity islands (SPI) identified unique complements of genes associated with host adaptation. We also describe a new genomic island with a putative role in pathogenesis, SPI-23. SPI-23 is present in several S. enterica serovars, including S. Agona, S. Dublin and S. Gallinarum, it is absent in its entirety from S. Mbandaka. Conclusions We discovered a new 37 Kb genomic island, SPI-23, in the chromosome sequence of S. Derby, encoding 42 ORFS, ten of which are putative TTSS effector proteins. We infer from full-genome synonymous SNP analysis that these two serovars diverged, between 182kya and 625kya coinciding with the divergence of domestic pigs. The differences between the genomes of these serovars suggest they have been exposed to different stresses including, phage, transposons and prolonged externalisation. The two serovars possess distinct complements of metabolic genes; many of which cluster into pathways for catabolism of carbon sources

Stable cycling in quasi-linkage equilibrium:fluctuating dynamics under gene conversion and selection

Genetic systems with multiple loci can have complex dynamics. For example, mean fitness need not always increase and stable cycling is possible. Here, we study the dynamics of a genetic system inspired by the molecular biology of recognition-dependent double strand breaks and repair as it happens in recombination hotspots. The model shows slow-fast dynamics in which the system converges to the quasi-linkage equilibrium (QLE) manifold. On this manifold, sustained cycling is possible as the dynamics approach a heteroclinic cycle, in which allele frequencies alternate between near extinction and near fixation. We find a closed-form approximation for the QLE manifold and use it to simplify the model. For the simplified model, we can analytically calculate the stability of the heteroclinic cycle. In the discrete-time model the cycle is always stable; in a continuous-time approximation, the cycle is always unstable. This demonstrates that complex dynamics are possible under quasi-linkage equilibrium.Comment: 35 pages, 6 figure

Bidirectional associations between fussy eating and functional constipation in preschool children

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Parental depression and child well-being: Young children's self-reports helped addressing biases in parent reports

Objectives Effects of maternal and paternal depression on child development are typically evaluated using parental reports of child problems. Yet, parental reports may be biased. Methods In a population-based cohort, parents reported lifetime depression (N = 3,178) and depressive symptoms (N = 3,131). Child emotional and behavioral problems were assessed at age 6 years by child self-report using the Berkeley Puppet Interview, by mother report using the Child Behavior Checklist (CBCL), and at age 3 years by father and mother reported CBCLs. Results Both maternal and paternal depression was associated with more child problems. Associations were of similar strength if child problems were obtained by self-reports. However, if parents reported about their own depression or depressive symptoms and about their child's problems, estimates were generally stronger for associations with the reporting parent's depression as the determinant. For instance, if mothers reported child emotional problems, associations were stronger for maternal (B = 0.27; 95% confidence interval (CI) = 0.19, 0.35) than for paternal lifetime depression (B = 0.12; 95% CI = 0.02, 0.21; P-value for difference = 0.02). Conclusion Depression of mothers and fathers affects young children's well-being. However, if parents reported about their own depression and about child problems, associations were inflated. To accurately estimate effects of parental depression, multiple-source data including young children's perspectives must be considered

Sedentary behaviors, physical activity behaviors, and body fat in 6-year-old children: The Generation R Study

Background: Childhood overweight and obesity is a major public health concern. Knowledge on modifiable risk factors is needed to design effective intervention programs. This study aimed to assess associations of children's sedentary behaviors (television viewing and computer game use) and physical activity behaviors (sports participation, outdoor play, and active transport to/from school) with three indicators of body fat, i.e., percent fat mass, body mass index (BMI) standard deviation scores, and weight status (normal weight, overweight). Methods: Cross-sectional data from 5913 6-year-old ethnically diverse children were analyzed. Children's weight and height were objectively measured and converted to BMI. Weight status was defined according to age- and sex-specific cu

Social inequalities in young children's meal skipping behaviors: The Generation R Study

Background: Regular meal consumption is considered an important aspect of a healthy diet. While ample evidence shows social inequalities in breakfast skipping among adolescents, little is known about social inequalities in breakfast skipping and skipping of other meals among young school-aged children. Such information is crucial in targeting interventions aimed to promote a healthy diet in children. Methods: We examined data from 4704 ethnically diverse children participating in the Generation R Study, a population-based prospective cohort study in Rotterdam, the Netherlands. Information on family socioeconomic position (SEP), ethnic background, and meal skipping behaviors was assessed by parent-reported questionnaire when the child was 6 years old. Multiple logistic regression analyses were performed to assess the associations of family SEP (educational level, household income, employment status, family composition) and ethnic backgr

FTO at rs9939609, Food Responsiveness, Emotional Control and Symptoms of ADHD in Preschool Children

The FTO minor allele at rs9939609 has been associated with body mass index (BMI: weight (kg)/height (m)2) in children from 5 years onwards, food intake, and eating behaviour. The high expression of FTO in the brain suggests that this gene may also be associated with behavioural phenotypes, such as impulsivity and control. We examined the effect of the FTO minor allele (A) at rs9939609 on eating behaviour, impulsivity and control in young children, thus before the BMI effect becomes apparent. This study was embedded in the Generation R Study, a population-based cohort from fetal life onwards. 1,718 children of European descent were genotyped for FTO at rs9939609. With logistic regression assuming an additive genetic model, we examined the association between the FTO minor allele and eating behaviour, impulsivity and control in preschool children. There was no relation between FTO at rs9939609 and child BMI at this age. The A allele at rs9939609 was associated with increased food responsiveness (OR 1.21, p = 0.03). Also, children with the A allele were less likely to have symptoms of ADHD (OR 0.74, p = 0.01) and showed more emotional control (OR 0.64, p = 0.01) compared to children without the A allele. Our findings suggest that before the association between FTO and BMI becomes apparent, the FTO minor allele at rs9939609 leads to increased food responsiveness, a decreased risk for symptoms of ADHD and better emotional control. Future studies are needed to investigate whether these findings represent one single mechanism or reflect pleiotropic effects of FTO

Prevalence of bullying and victimization among children in early elementary school: Do family and school neighbourhood socioeconomic status matter?

Background: Bullying and victimization are widespread phenomena in childhood and can have a serious impact on well-being. Children from families with a low socioeconomic background have an increased risk of this behaviour, but it is unknown whether socioeconomic status (SES) of school neighbourhoods is also related to bullying behaviour. Furthermore, as previous bullying research mainly focused on older children and adolescents, it remains unclear to what extent bullying and victimization affects the lives of younger children. The aim of this study is to examine the prevalence and socioeconomic disparities in bullying behaviour among young elementary school children. Methods. The study was part of a population-based survey in the Netherlands. Teacher reports of bullying behaviour and indicators of SES of families and schools were available for 6379 children aged 5-6 years. Results: One-third of the children were involved in bullying, most of them as bullies (17%) or bully-victims (13%), and less as pure victims (4%). All indicators of low family SES and poor school neighbourhood SES were associated with an increased risk of being a bully or bully-victim. Parental educational level was the only indicator of SES related with victimization. The influence of school neighbourhood SES on bullying attenuated to statistical non-significance once adjusted for family SES. Conclusions: Bullying and victimization are already common problems in early elementary school. Children from socioeconomically disadvantaged families, rather than children visiting schools in disadvantaged neighbourhoods, have a particularly high risk of involvement in bullying. These findings suggest the need of timely bullying preventions and interventions that should have a special focus on children of families with a low socioeconomic background. Future studies are necessary to evaluate the effectiveness of such programs

Bullying and Victimization Among Young Elementary School Children: The Role of Child Ethnicity and Ethnic School Composition

School-aged children with an ethnic minority background are relatively often involved in bullying and victimization, but the role of ethnic composition of schools in this context remains unclear. This study examined the relation between ethnic minority background, ethnic school composition, and bullying behaviour around primary school entry in the Netherlands. The study was based on a 2008/2009 school survey in Rotterdam, a Dutch city where about 50 % of children have a non-Dutch background. For 8523 children, teacher reports of bullying behaviour at age 5–6 years were available. Children with a non-Dutch background had higher odds of being a victim (adjusted OR 1.41, 95 % CI 1.11, 1.80), bully (OR 1.38, 95 % CI 1.20, 1.58) or bully-victim (OR 1.38, 95 % CI 1.19, 1.62) than children of Dutch national origin. Ethnic diversity in schools increased children’s risk of bullying behaviour (e.g. ORvictim per 0.1 increase in 0–1 diversity range = 1.06, 95 % CI 1.00, 1.13), with children of both Dutch and non-Dutch national origin relatively more often involved in bullying in ethnically diverse schools. The proportion of same-ethnic peers in school reduced the risk of bullying among children of Dutch national origin (e.g. ORvictim per 10 % more same-ethnic children = 0.90, 95 % CI 0.83, 0.98), but not among non-Dutch children. In conclusion, ethnic minority background and ethnic diversity within schools are risk factors for bullying among 5–6 year olds. Plausibly, reductions in absolute numbers of bullying events may be obtained with tailor-made interventions in ethnically diverse schools. Such interventions should preferably be offered early in the school curriculum