Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages

Measuring molecular evolution in bacteria typically requires estimation of the rate at which nucleotide changes accumulate in strains sampled at different times that share a common ancestor. This approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the ‘birthday problem’. Using large genomic datasets and comparative genomic approaches, we use isolate pairs that share recent common ancestry to estimate the rate of nucleotide change for the population. Identifying synonymous and non-synonymous nucleotide changes, both within and outside of recombined regions of the genome, we quantify clock-like diversification to estimate synonymous rates of nucleotide change for the common pathogenic bacteria Campylobacter coli (2.4 x 10⁻⁶ s/s/y) and Campylobacter jejuni (3.4 x 10⁻⁶ s/s/y). Finally, using estimated total rates of nucleotide change, we infer the number of effective lineages within the sample time frame–analogous to a shared birthday–and assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species.     

Local genes for local bacteria: Evidence of allopatry in the genomes of transatlantic Campylobacter populations

The genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distance and genetic distance, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance with past human migration, whereas in Mycobacterium tuberculosis it is the lack of recombination that causes allopatric clusters. In Campylobacter, analyses of genomic data and molecular typing have been successful in determining the reservoir host species, but not geographical origin. We investigated biogeographical variation in highly recombining genes to determine the extent of clustering between genomes from geographically distinct Campylobacter populations. Whole‐genome sequences from 294 Campylobacter isolates from North America and the UK were analysed. Isolates from within the same country shared more recently recombined DNA than isolates from different countries. Using 15 UK/American closely matched pairs of isolates that shared ancestors, we identify regions that have frequently and recently recombined to test their correlation with geographical origin. The seven genes that demonstrated the greatest clustering by geography were used in an attribution model to infer geographical origin which was tested using a further 383 UK clinical isolates to detect signatures of recent foreign travel. Patient records indicated that in 46 cases, travel abroad had occurred <2 weeks prior to sampling, and genomic analysis identified that 34 (74%) of these isolates were of a non‐UK origin. Identification of biogeographical markers in Campylobacter genomes will contribute to improved source attribution of clinical Campylobacter infection and inform intervention strategies to reduce campylobacteriosis.     

Influence of closed skill and open skill warm-ups on the performance of speed, change of direction speed, vertical jump, and reactive agility in team sport athletes

In this study, we evaluated the efficacy of two different dynamic warm-up conditions, one that was inclusive of open skills (i.e., reactive movements) and one that included only preplanned dynamic activities (i.e., closed skills) on the performance of speed, change of direction speed, vertical jump, and reactive agility in team sport athletes. Fourteen (six male, eight female) junior (mean +/- SD age, 16.3 +/- 0.7 year) basketball players participated in this study. Testing was conducted on 2 separate days using a within-subjects cross-over study design. Each athlete performed a standardized 7-minute warm-up consisting of general dynamic movements and stretching. After the general warm-up, athletes were randomly allocated into one of two groups that performed a dynamic 15-minute warm-up consisting entirely of open or closed skills. Each of the warm-up conditions consisted of five activities of 3 minute duration. At the completion of the warm-up protocol, players completed assessments of reactive agility, speed (5-, 10-, and 20-m sprints), change of direction speed (T-test), and vertical jump. No significant differences (p > 0.05) were detected among warm-up conditions for speed, vertical jump, change of direction speed, and reactive agility performances. The results of this study demonstrate that either open skill or closed skill warm-ups can be used effectively for team sport athletes without compromising performance on open skill and closed skill tasks.     

Increasing compliance to instructions in the squat jump

The purposes of this investigation were to evaluate the occurrence of a small amplitude counter-movement (SACM) in SJ (squat jump) trials of elite athletes to determine the efficacy of gross observation and the use of a portable position transducer to determine whether or not a SACM occurred. The subjects (N = 30, 20.1 +/- 3.0 years, 199.0 +/- 8.4 cm, and 87.2 +/- 9.5 kg) were a combination of high-performance (National Team) and elite athletes (Olympian) from the sports of athletics, swimming, and volleyball. All subjects performed SJ trials on a force platform, with a linear position transducer attached to a bar placed across the shoulders. Subjects performed the SJ from a depth that allowed for a 90 degrees knee angle, with the subject's instructed to maintain a 3-second isometric hold preceding the concentric action of the jump. One hundred twenty-five SJ trials were observed for a SACM and analyzed (using the force plate data and position transducer data) for a SACM. Of the 125 SJ trials, 69 trials (55.2%) were observed to have a SACM by the researchers. In the remaining 56 trials, 43 of these trials contained a force unload (>/=10% body mass) before initiation of the concentric action, indicating a SACM. Of the 119 SJ trials where a force unload was observed and detected by the force-time graph, 118 (99.2%) of these trials also showed a change in displacement using the displacement-time graph from the linear position transducer. The results of this study indicate that achieving compliance to protocol in the SJ is difficult, and that gross observation is inadequate in detecting a SACM in the SJ. From a practical perspective, these results suggest that using a force plate or a linear position transducer would allow the strength and conditioning coach to ensure compliance to instructions in the SJ.     

Campylobacter infection of broiler chickens in a free-range environment

Campylobacter jejuni is the most common cause of bacterial gastroenteritis worldwide, with contaminated chicken meat considered to represent a major source of human infection. Biosecurity measures can reduce C. jejuni shedding rates of housed chickens, but the increasing popularity of free-range and organic meat raises the question of whether the welfare benefits of extensive production are compatible with food safety. The widespread assumption that the free-range environment contaminates extensively reared chickens has not been rigorously tested. A year-long survey of 64 free-range broiler flocks reared on two sites in Oxfordshire, UK, combining high-resolution genotyping with behavioural and environmental observations revealed: (i) no evidence of colonization of succeeding flocks by the C. jejuni genotypes shed by preceding flocks, (ii) a high degree of similarity between C. jejuni genotypes from both farm sites, (iii) no association of ranging behaviour with likelihood of Campylobacter shedding, and (iv) higher genetic differentiation between C. jejuni populations from chickens and wild birds on the same farm than between the chicken samples, human disease isolates from the same region and national samples of C. jejuni from chicken meat.     

Determining nitrogen requirements of Aceros and Buceros hornbills

Over 2 months, seven feeding trials were conducted at St. Catherines Island, GA, to quantify protein intake and utilization in captive mature nonreproducing Aceros (n=3 spp.) and Buceros (n=2 spp.) Hornbills were fed homogeneous isocaloric diets. A mixture of Bird of Paradise pellets, grapes, and raisins was offered to the birds as grape‐sized balls, supplemented with diced cantaloupe melon to maintain hydration. To vary the protein level (range 10.8–22.6%) within the diets, different amounts of a powdered soy protein supplement were added to the mixture. Test diets were fed for 3 consecutive days. Birds were weighed to test for differences among diets. All excreta and diet samples were collected for nitrogen (N) analysis. Feeding trials were separated by a 4‐day period, in which the bird's regular diet was fed. Data were analyzed for N balance, N equilibrium (regression of N intake vs. N excretion) and body mass. Regression analysis of N balances of the nine birds showed that the N equilibriums ranged from 0.081 to 0.595 g N/kg^0.75/d with an average of 0.387±0.298. No differences in N balances were found between Aceros and Buceros hornbills. The methodology of this study suggested a dietary crude protein (CP) requirement of 7.3±3.0% dry matter (DM) in a diet containing 4.0 kcal. However, this value was determined by extrapolation and has not been experimentally determined to be adequate. In this study, the hornbills maintained body mass on a diet containing 10.8% CP (with energy at 4.0 kcal/g DM). Zoo Biol 27:282–293, 2008. © 2008 Wiley‐Liss, Inc.     

Sub-lethal effects of off-road vehicles (ORVs) on surf clams on sandy beaches

Ecological impacts of vehicle traffic are a significant environmental management issue on many sandy shores. Impacts usually focus on lethal effects of vehicles to organisms, but sub-lethal effects which could reduce the fitness of macrofauna populations are equally possible but unknown. Consequently, we measured changes in body condition and burrowing performance of the beach clam Donax deltoides subjected to vehicle traffic on sandy shores in eastern Australia. Body mass index of clams on beaches open to traffic was 16% lower, but gonadosomatic index and relative valve thickness were not consistently linked to vehicle access to beaches. By contrast, off-road vehicles significantly impaired the burrowing performance of clams. After experimental exposure to ORV traffic (30 passes) and dislodgement from the sediment, the time taken for clams to re-bury into the sand doubled irrespective of the vehicle weight used. Because burrowing is such a critical function in the behavioural repertoire of sandy beach animals, the traffic-induced changes to organisms' performance found in this study may increase mortality by causing displacement to less favourable habitats by swash, and by intensifying the risk of predation and desiccation. When assessing the ecological impacts of vehicles on beach fauna, it is thus important to consider both lethal and sub-lethal effects.     

Multi‐locus sequence types of Campylobacter carried by flies and slugs acquired from local ruminant faeces

Aims: To assess whether flies and slugs acquire strains of Campylobacter jejuni and Campylobacter coli present in local ruminant faeces. Methods and Results: Campylobacter was cultured from flies, slugs and ruminant faeces that were collected from a single farm in Scotland over a 19‐week period. The isolates were typed using multi‐locus sequence typing (MLST) and compared with isolates from cattle and sheep faeces. Campylobacter jejuni and Camp. coli were isolated from 5·8% (n = 155, average of 75 flies per pool) and 13·3% (n = 15, average of 8·5 slugs per pool) of pooled fly and slug samples, respectively. The most common sequence type (ST) in flies was Camp. coli ST‐962 (approx. 40%) regardless of the prevalence in local cattle (2·3%) or sheep (25·0%) faeces. Two positive slug pools generated the same ST that has not been reported elsewhere. Conclusions: Despite their low carriage rate, flies are able to acquire Campylobacter STs that are locally present, although the subset carried may be biased when compared to local source. Slugs were shown to carry a previously unreported Campylobacter ST. Significance and Impact of the Study: This study has demonstrated that flies carry viable Campylobacter and may contribute to the transfer of STs within and between groups of animals on farms. Further, they may therefore present a risk to human health via their contact with ready‐to‐eat foods or surfaces.