Olga Sakwinska

Dynamics of Infant Gut Microbiota Are Influenced by Delivery Mode and Gestational Duration and Are Associated with Subsequent Adiposity

ABSTRACT  We found that the relatively simple microbiota of young infants shifts predictably to a more mature anaerobic microbiota during infancy and the dynamics of this shift are influenced by environmental factors. In this longitudinal study of 75 infants, we demonstrate high interindividual variability within the normal range of birth outcomes, especially in the rate of microbiota progression. Most had acquired a microbiota profile high in Bifidobacterium and Collinsella by 6 months of age, but the time point of this acquisition was later in infants delivered by caesarean section and those born after a shorter duration of gestation. Independently of the delivery mode and gestation duration, infants who acquired a profile high in Bifidobacterium and Collinsella at a later age had lower adiposity at 18 months of age. IMPORTANCE  This study shows that the acquisition of the early microbiota is strongly influenced by environmental factors such as the delivery mode and duration of gestation, even in healthy neonates. The composition of the early microbiota has been linked with long-lasting effects on health and disease. Here we show that the rate of acquisition of certain microbiota predicts adiposity at 18 months of age and so potentially the risk of later obesity. This study shows that the acquisition of the early microbiota is strongly influenced by environmental factors such as the delivery mode and duration of gestation, even in healthy neonates. The composition of the early microbiota has been linked with long-lasting effects on health and disease. Here we show that the rate of acquisition of certain microbiota predicts adiposity at 18 months of age and so potentially the risk of later obesity.

Genetic Diversity and Ecological Success of Staphylococcus aureus Strains Colonizing Humans

ABSTRACT The genetic determinants and phenotypic traits which make a Staphylococcus aureus strain a successful colonizer are largely unknown. The genetic diversity and population structure of 133 S. aureus isolates from healthy, generally risk-free adult carriers were investigated using four different typing methods: multilocus sequence typing (MLST), amplified fragment length polymorphism analysis (AFLP), double-locus sequence typing (DLST), and spa typing were compared. Carriage isolates displayed great genetic diversity which could only be revealed fully by DLST. Results of AFLP and MLST were highly concordant in the delineation of genotypic clusters of closely related isolates, roughly equivalent to clonal complexes. spa typing and DLST provided considerably less phylogenetic information. The resolution of spa typing was similar to that of AFLP and inferior to that of DLST. AFLP proved to be the most universal method, combining a phylogeny-building capacity similar to that of MLST with a much higher resolution. However, it had a lower reproducibility than sequencing-based MLST, DLST, and spa typing. We found two cases of methicillin-resistant S. aureus colonization, both of which were most likely associated with employment at a health service. Of 21 genotypic clusters detected, 2 were most prevalent: cluster 45 and cluster 30 each colonized 24% of the carrier population. The number of bacteria found in nasal samples varied significantly among the clusters, but the most prevalent clusters were not particularly numerous in the nasal samples. We did not find much evidence that genotypic clusters were associated with different carrier characteristics, such as age, sex, medical conditions, or antibiotic use. This may provide empirical support for the idea that genetic clusters in bacteria are maintained in the absence of adaptation to different niches. Alternatively, carrier characteristics other than those evaluated here or factors other than human hosts may exert selective pressure maintaining genotypic clusters.

Staphylococcus aureus Host Range and Human-Bovine Host Shift†

ABSTRACT Staphylococcus aureus is a major agent of bovine mastitis. The concomitant emergence of pig-associated methicillin-resistant S. aureus (MRSA) in human carriage and infection requires a reexamination of the host range and specificity of human- and cow-associated S. aureus strains, something which has not been systematically studied previously. The genetic relatedness of 500 S. aureus isolates from bovine mastitis cases, 57 isolates from nasal carriage of farmers, and 133 isolates from nonfarmers was determined by amplified fragment length polymorphism (AFLP) analysis and spa typing. Multilocus sequence typing (MLST) was conducted on a subset of isolates to match AFLP clusters with MLST clonal complexes (CCs). This data set allowed us to study host range and host specificity and to estimate the extent of bovine-to-human transmission. The genotype compositions of S. aureus isolates from farmers and nonfarmers were very similar, while the mastitis isolates were quite distinct. Overall, transmission was low, but specific genotypes did show increased cow-to-human transmission. Unexpectedly, more than one-third of mastitis isolates belonged to CC8, a lineage which has not been considered to be bovine mastitis associated, but it is well known from human carriage and infection (i.e., USA300). Despite the fact that we did detect some transmission of other genotypes from cows to farmers, no transmission of CC8 isolates to farmers was detected, except for one tentative case. This was despite the close genetic relatedness of mastitis CC8 strains to nonfarmer carriage strains. These results suggest that the emergence of the new bovine-adapted genotype was due to a recent host shift from humans to cows concurrent with a loss of the ability to colonize humans. More broadly, our results indicate that host specificity is a lineage-specific trait that can rapidly evolve.

TEST OF SYNERGISTIC INTERACTION BETWEEN INFECTION AND INBREEDING IN DAPHNIA MAGNA

Abstract It has been proposed that parasitic infections increase selection against inbred genotypes. We tested this hypothesis experimentally using pairs of selfed and outcrossed sibling lines of the freshwater crustacean Daphnia magna, which can be maintained clonally. We studied the performance of selfed relative to outcrossed sibling clones during repeated pairwise clonal competition in the presence and absence of two species of microsporidian parasites. In 13 of the 14 pairs, the selfed clones did worse than the outcrossed ones in the control treatment, but the presence of either parasite did not result in an overall increase in this difference. Rather, it decreased the performance of the selfed relative to the outcrossed sibling in some pairs and increased it in others. Moreover, the two parasite species did not have the same effect in a given pair. This indicates that, contrary to the hypothesis that parasites generally lead to a decreased performance of inbred genotypes, their effect may depend on the genetic background of the host as well as on the parasite species, and suggests that inbreeding can lead to reduced or increased resistance to parasites. Our findings also indicate that there is variation for specific resistance to different species of parasites in the meta‐population from which the hosts for this study were obtained.

Nasopharyngeal microbiota in healthy children and pneumonia patients

ABSTRACT Our study is the first to compare the nasopharyngeal microbiota of pediatric pneumonia patients and control children by 454 pyrosequencing. A distinct microbiota was associated with different pneumonia etiologies. Viral pneumonia was associated with a high abundance of the operational taxonomic unit (OTU) corresponding to Moraxella lacunata. Patients with nonviral pneumonia showed high abundances of OTUs of three typical bacterial pathogens, Streptococcus pneumoniae complex, Haemophilus influenzae complex, and Moraxella catarrhalis. Patients classified as having no definitive etiology harbored microbiota particularly enriched in the H. influenzae complex. We did not observe a commensal taxon specifically associated with health. The microbiota of the healthy nasopharynx was more diverse and contained a wider range of less abundant taxa.

Antimicrobial Resistance of Staphylococcus aureus Strains Acquired by Pig Farmers from Pigs

ABSTRACT Carriage of animal-associated methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 398 (CC398) is common among pig farmers. This study was conducted (i) to investigate whether pig farmers are colonized with pig-specific S. aureus genotypes other than CC398 and (ii) to survey antimicrobial resistance of S. aureus isolates from pigs and pig farmers. Forty-eight S. aureus isolates from pig farmers and veterinarians and 130 isolates from pigs collected in Western Switzerland were genotyped by spa typing and amplified fragment length polymorphism (AFLP). Antimicrobial resistance profiles were determined for representative sample of the isolates. The data obtained earlier on healthy S. aureus carriers without exposure to agriculture were used for comparison. The genotype composition of S. aureus isolates from pig farmers and veterinarians was similar to isolates from pigs with predominant AFLP clusters CC398, CC9, and CC49. The resistance to tetracycline and macrolides (clarithromycin) was common among the isolates from farmers and veterinarians (52 and 21%, respectively) and similar to resistance levels in isolates from pigs (39 and 23%, respectively). This was in contrast to isolates from persons without contact with agriculture, where no (0/128) isolates were resistant to tetracycline and 3% of the isolates were resistant to clarithromycin. MRSA CC398 was isolated from pigs (n = 11) and pig farmers (n = 5). These data imply that zoonotic transmission of multidrug-resistant S. aureus from pigs to farmers is frequent, and well-known MRSA transmission merely represents the tip of the iceberg for this phenomenon. We speculate that the relatively low frequency of MRSA isolation is related to lower antimicrobial use in Switzerland compared to, for example, the Netherlands.

Oral health in older patients with oropharyngeal dysphagia

BACKGROUND oropharyngeal dysphagia (OD), aspiration and poor oral health status are potential risk factors in elderly patients with aspiration pneumonia (AP). AIM to assess the oral hygiene status and the prevalence of periodontal disease and dental caries in elderly patients with OD. PATIENTS AND METHODS fifty elderly patients (79.7 ± 6.64 years) with OD associated with ageing or neurological diseases and 15 elderly patients without OD (77.01 ± 4.51 years) were enrolled in this observational-transversal study. OD and aspiration were evaluated by videofluoroscopy (VFS). Oral health was assessed by: (i) the Simplified Oral Hygiene Index (OHI-S); (ii) a complete periodontal examination, assessing the periodontal pocket depth, clinical attachment loss and bleeding on probing to study periodontal diseases (periodontitis, gingivitis); and (iii) the presence of dental caries. RESULTS 8/50 elderly patients with OD presented VFS signs of aspiration, half of them silent; 40/50, signs of penetration into laryngeal vestibule and 16/50, oropharyngeal residue. Prevalence of edentulism and caries was higher in patients with OD. Dentate older patients with OD (30/50) presented the following complications (i) poor oral hygiene in 18 patients (OHI-S 3.1-6), (ii) gingivitis in 2 and periodontitis in 28 and (iii) caries in 16. CONCLUSIONS older patients with OD presented polymorbidity and impaired health status, high prevalence of VFS signs of impaired safety of swallow and poor oral health status with high prevalence of periodontal diseases and caries. These patients are at great risk of developing AP. We recommend a policy of systematic oral health assessment in elderly patients with OD.

Response to fish kairomone in Daphnia galeata life history traits relies on shift to earlier instar at maturation

The aim of the present study was to clarify the mechanisms underlying the expression of phenotypic plasticity in Daphnia life history traits in response to fish kairomone and to explore how these mechanisms interact with genetic variation for life history traits. I studied the effect of fish kairomone on life history traits in 16 Daphnia galeata clones. Maturation occurred more often at the earlier instars in response to the fish treatment, resulting in earlier age and smaller size at maturity. The changes in age and size at maturity which occurred in the response to the fish treatment could be attributed to a large extent to this shift. In addition, fish kairomone resulted in smaller instar increments after the maturation process was initiated, but not during the juvenile period. Within groups of animals maturing at the same instar, larger size at birth resulted in larger size at maturity, but had no effect on age at maturity. However, larger size at birth brought about earlier maturity because animals which were larger at birth matured more often at the earlier instar. Fish treatment resulted in more, but smaller, offspring in the first clutch relative to the size of the mother. Genetic variation was found in all measured life history traits. Genetic variation in plasticities of life history traits was not detectable by standard methods, and was only shown when the above mechanisms of expression of life history traits were taken into account. This study illustrates the importance of a thorough understanding of the mechanisms underlying the expression of life history traits, in this case, sources and consequences of maturation in the multiple instars. Not only is this necessary to predict the long-term effect of the environment, but also to understand the response of life history traits and their plasticities to natural selection. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00442-002-0901-0

Ecological Temporal Stability of Staphylococcus aureus Nasal Carriage

ABSTRACT We described the colonization dynamics of Staphylococcus aureus in a group of 266 healthy carriers over a period of approximately 1 year. We used precise genotyping methods, i.e., amplified fragment length polymorphism (AFLP), spa typing, and double-locus sequence typing (DLST), to detect changes in strain identity. Strain change took place rather rarely: out of 89 carriers who had initially been colonized, only 7 acquired a strain different from the original one. Approximately one-third of the carriers eliminated the colonization, and a similar number became newly colonized. Some of these events probably represent detection failure rather than genuine colonization loss or acquisition. Lower bacterial counts were associated with increased probability of eliminating the colonization. We have confirmed a high mutation rate in the spa locus: 6 out of 53 strains underwent mutation in the spa locus. There was no overall change in S. aureus genotype composition.

Persistent maternal identity effects on life history traits in Daphnia.

The aim of the present study was to examine the magnitude and persistence of maternal effects in Daphnia, in particular maternal identity effects. I studied life history traits of a single clone of Daphnia galeata born to 40 different mothers belonging to three age groups. Maternal identity had large effects on offspring traits, that is, identically treated clonal females differed substantially in respect to the traits of their offspring, including size at birth, age at maturity, and number of second generation offspring. The effects of maternal identity on these traits were largely independent of maternally induced differences in offspring size, indicating that maternal effects were mediated through offspring quality. Maternal age also affected offspring traits: older mothers gave birth to larger offspring which matured earlier, were larger and more fecund, and survived better until maturity. Individuals which were larger at birth also had a better chance of survival. Contrary to expectation, I found little evidence that maternal identity or maternal age had any influence on their offsprings’ response to fish kairomones.