Parity and housing effects on the behavioural and hypothalamic-pituitary-adrenal axis responses of pregnant ewes.

It is common in many countries for sheep to be housed during winter from mid-gestation until lambing to protect ewes and lambs from adverse conditions and improve late gestation nutritional management. Keeping ewes indoors, however, has its own challenges as the animals may be mixed with unfamiliar conspecifics, have limited floor and feeding space, experience changes to their diet and increased handling by humans. Therefore, the objective of this study was to investigate the effect of variation in housing management (space allowance and social stability) on the behaviour and hypothalamic-pituitary-adrenal (HPA) axis responses of pregnant ewes from mid-to-late gestation (weeks 11-18 of pregnancy). Seventy-seven ewes (41 primiparous, 36 multiparous) were divided into two groups: 'Control' and 'Restricted space and mixed' (RS-Mix), where RS-Mix ewes were allocated half the amount of space (1.27 vs 2.5 m2 for RS-Mix and Control, respectively) and feedface (concentrate feeder space) allowance (36 vs 71 cm per ewe) given to the Control group and were also subjected to two social mixing events. Aggressive behaviour at the feedface and time spent standing, lying, walking, feeding and ruminating were recorded and faecal samples were collected for assessment of faecal glucocorticoid metabolite (FGM) concentrations. Higher aggression was observed in RS-Mix ewes during the first week of observation (P = 0.044), which gradually declined to the same level as Control ewes by the end of the study (P = 0.045). RS-Mix ewes were significantly less likely to be able to freely join the feedface compared to Controls (P = 0.022). No other significant treatment effects on aggressive behaviour or FGM during gestation were found. RS-Mix ewes displayed significantly higher ruminating behaviour at week 18 of gestation compared to Control ewes (P < 0.001), but no other effects were seen on general pen behaviour. However, the effect of indoor housing had a significant impact on primiparous ewes, who had lower weight gain (P = 0.015) and higher FGM concentrations (P = 0.014) compared to multiparous ewes regardless of treatment group. The data suggest that, although no sustained effects on behaviour or HPA axis responses were seen with the differences in space and feeder allowance or social stability at the levels used in this study, inexperienced (primiparous) ewes may find indoor housing more stressful; and are less able to adapt compared to multiparous ewes. These effects may influence the behaviour of the ewe at lambing time, and her offspring.

Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions.

Environmental microbiome studies rely on fast and accurate bioinformatics tools to characterize the taxonomic composition of samples based on the 16S rRNA gene. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology 2 (QIIME2) are two of the most popular tools available to perform this task. Their underlying algorithms differ in many aspects, and therefore the comparison of the pipelines provides insights into their best use and interpretation of the outcomes. Both of these bioinformatics tools are based on several specialized algorithms pipelined together, but whereas MG-RAST is a user-friendly webserver that clusters rRNA sequences based on their similarity to create Operational Taxonomic Units (OTU), QIIME2 employs DADA2 in the construction of Amplicon Sequence Variants (ASV) by applying an error model that considers the abundance of each sequence and its similarity to other sequences. Taxonomic compositions obtained from the analyses of amplicon sequences of DNA from swine intestinal gut and faecal microbiota samples using MG-RAST and QIIME2 were compared at domain-, phylum-, family- and genus-levels in terms of richness, relative abundance and diversity. We found significant differences between the microbiota profiles obtained from each pipeline. At domain level, bacteria were relatively more abundant using QIIME2 than MG-RAST; at phylum level, seven taxa were identified exclusively by QIIME2; at family level, samples processed in QIIME2 showed higher evenness and richness (assessed by Shannon and Simpson indices). The genus-level compositions obtained from each pipeline were used in partial least squares-discriminant analyses (PLS-DA) to discriminate between sample collection sites (caecum, colon and faeces). The results showed that different genera were found to be significant for the models, based on the Variable Importance in Projection, e.g. when using sequencing data processed by MG-RAST, the three most important genera were Acetitomaculum, Ruminococcus and Methanosphaera, whereas when data was processed using QIIME2, these were Candidatus Methanomethylophilus, Sphaerochaeta and Anaerorhabdus. Furthermore, the application of differential filtering procedures before the PLS-DA revealed higher accuracy when using non-restricted datasets obtained from MG-RAST, whereas datasets obtained from QIIME2 resulted in more accurate discrimination of sample collection sites after removing genera with low relative abundances (<1%) from the datasets. Our results highlight the differences in taxonomic compositions of samples obtained from the two separate pipelines, while underlining the impact on downstream analyses, such as biomarkers identification.

Epigenetics and developmental programming of welfare and production traits in farm animals.

The concept that postnatal health and development can be influenced by events that occur in utero originated from epidemiological studies in humans supported by numerous mechanistic (including epigenetic) studies in a variety of model species. Referred to as the 'developmental origins of health and disease' or 'DOHaD' hypothesis, the primary focus of large-animal studies until quite recently had been biomedical. Attention has since turned towards traits of commercial importance in farm animals. Herein we review the evidence that prenatal risk factors, including suboptimal parental nutrition, gestational stress, exposure to environmental chemicals and advanced breeding technologies, can determine traits such as postnatal growth, feed efficiency, milk yield, carcass composition, animal welfare and reproductive potential. We consider the role of epigenetic and cytoplasmic mechanisms of inheritance, and discuss implications for livestock production and future research endeavours. We conclude that although the concept is proven for several traits, issues relating to effect size, and hence commercial importance, remain. Studies have also invariably been conducted under controlled experimental conditions, frequently assessing single risk factors, thereby limiting their translational value for livestock production. We propose concerted international research efforts that consider multiple, concurrent stressors to better represent effects of contemporary animal production systems.

Why are most EU pigs tail docked? Economic and ethical analysis of four pig housing and management scenarios in the light of EU legislation and animal welfare outcomes.

To limit tail biting incidence, most pig producers in Europe tail dock their piglets. This is despite EU Council Directive 2008/120/EC banning routine tail docking and allowing it only as a last resort. The paper aims to understand what it takes to fulfil the intentions of the Directive by examining economic results of four management and housing scenarios, and by discussing their consequences for animal welfare in the light of legal and ethical considerations. The four scenarios compared are: 'Standard Docked', a conventional housing scenario with tail docking meeting the recommendations for Danish production (0.7 m2/pig); 'Standard Undocked', which is the same as 'Standard Docked' but with no tail docking, 'Efficient Undocked' and 'Enhanced Undocked', which have increased solid floor area (0.9 and 1.0 m2/pig, respectively) provision of loose manipulable materials (100 and 200 g/straw per pig per day) and no tail docking. A decision tree model based on data from Danish and Finnish pig production suggests that Standard Docked provides the highest economic gross margin with the least tail biting. Given our assumptions, Enhanced Undocked is the least economic, although Efficient Undocked is better economically and both result in a lower incidence of tail biting than Standard Undocked but higher than Standard Docked. For a pig, being bitten is worse for welfare (repeated pain, risk of infections) than being docked, but to compare welfare consequences at a farm level means considering the number of affected pigs. Because of the high levels of biting in Standard Undocked, it has on average inferior welfare to Standard Docked, whereas the comparison of Standard Docked and Enhanced (or Efficient) Undocked is more difficult. In Enhanced (or Efficient) Undocked, more pigs than in Standard Docked suffer from being tail bitten, whereas all the pigs avoid the acute pain of docking endured by the pigs in Standard Docked. We illustrate and discuss this ethical balance using numbers derived from the above-mentioned data. We discuss our results in the light of the EU Directive and its adoption and enforcement by Member States. Widespread use of tail docking seems to be accepted, mainly because the alternative steps that producers are required to take before resorting to it are not specified in detail. By tail docking, producers are acting in their own best interests. We suggest that for the practice of tail docking to be terminated in a way that benefits animal welfare, changes in the way pigs are housed and managed may first be required.

Early experiences matter: a review of the effects of prenatal environment on offspring characteristics in poultry.

Early life experiences can be important in determining offspring phenotypes and may influence interaction with the environment and hence health, welfare, and productivity. The prenatal environment of poultry can be divided into the pre-lay environment and the egg storage/incubation environment, both of which can affect offspring outcomes. The ability to separate maternal and egg/incubation effects makes birds well suited to this type of research. There are many factors, including feeding and nutrition, environmental conditions, husbandry practices, housing system, social environment, infectious environment, and maternal health status, that can influence both the health and performance and behavior and cognition of the offspring. There are some aspects of the environments that can be changed to produce beneficial effects in the offspring, like addition of certain additives to feed or short changes in incubation temperatures, while other aspects should be avoided to reduce negative effects, such as unpredictable feeding and lighting regimens. Measures of offspring characteristics may prove to be a useful method of assessing parent stock welfare if known stressors result in predictable offspring outcomes. This has the advantage of assessing the parent environment without interfering with the animals and possibly affecting their responses and could lead to improved welfare for the animals.

Attitudes of farmers and veterinarians towards pain and the use of pain relief in pigs.

A survey of UK-based pig farmers and veterinarians was conducted, in order to investigate attitudes to pain and the use of pain relief in pigs. Survey respondents were asked to indicate which anti-inflammatory drugs they used or prescribed for pigs, how often these were administered, and the level of pain they associated with particular conditions. The survey found that veterinarians used a range of anti-inflammatory products to treat pigs with lameness. While both farmers and veterinarians gave similar pain scores overall, farmers rated gastrointestinal disease as more painful and conversely veterinarians scored lameness higher. Female and younger respondents gave higher pain scores than males and older respondents. Overall, farmers and veterinarians had a positive attitude towards pain relief in pigs with the majority agreeing that animals recovered more promptly when pain relief was administered. Most farmers agreed that the recognition and management of pain is an important part of pig husbandry, and many expressed an interest in finding out more about identifying pain in this species as well as the treatment options available. The study highlighted potential barriers to the increased application of pain relief in pigs in that almost one-third of veterinarians and two-thirds of farmers did not agree that they discussed pain management with each other, while other respondents indicated that they found it difficult to recognise pain in pigs, and did not know how to treat it appropriately.

Behavioral and physiological responses of primiparous sows to mixing with older, unfamiliar sows.

Pigs are mixed into new social groups at various stages of production, and this study investigated the response of gilts to mixing with older unfamiliar sows. Four groups of 6 gilts and 1 group of 5 gilts were housed in stable groups until the most recently bred female reached d 39 of gestation. Then, stable groups were split such that 15 gilts remained in their home pens (CON) and 14 gilts were mixed (MIX) with 3 multiparous sows for 1 wk (M1), returned to the home pen for 1 wk, and then mixed with 3 different sows for 1 wk (M2). Continuous behavioral observations of gilt location in the pen, posture, aggressive, and other social interactions were made from the start of M1 and M2 for 5 h. Five-minute scans of location, posture, and behavior as well as salivary cortisol measurements were taken before, during, and after each mix week, whereas skin lesions were counted before and after each mix. During the mixed period, MIX gilts spent more (P ≤ 0.009) time in the individual feeding stalls, ventral lying, sitting, involved in aggression, and idle and less (P < 0.001) time in the straw-bedded area, lateral lying, and performing exploratory behavior (chewing, nosing, and rooting) than CON gilts. Additionally, MIX gilts had greater (P < 0.001) salivary cortisol concentrations and accumulated more (P < 0.001) skin lesions during mixing sessions compared to CON gilts. Mixed gilts in M2 spent more (P ≤ 0.013) time in the feeding stalls and ventral lying and less (P ≤ 0.029) time standing and in the dunging passageway compared to M1. Compared to M1, gilts had lower (P < 0.001) salivary cortisol concentrations and fewer (P ≤ 0.027) lesions in front and middle regions of the body during M2. During M2, salivary cortisol concentration was positively correlated with time spent in the dunging passageway (Spearman's rank correlation [rs] = 0.650, P = 0.022) and negatively correlated with time spent in the feeding stalls (rs = -0.762, P = 0.004). Results indicated that gilts adapted their behavior during M2 by using the feeding stalls more, and they became less active, especially when interacting with the sows. Despite this adaptation in M2, lesions and salivary cortisol in M IX gilts were much greater than in CON gilts, highlighting the severity of mixing gilts with multiparous sows.

Board invited review: The importance of the gestation period for welfare of calves: maternal stressors and difficult births.

The prenatal period is of critical importance in defining how individuals respond to their environment throughout life. Stress experienced by pregnant females has been shown to have detrimental effects on offspring biology in humans and a variety of other species. It also is becoming increasingly apparent that prenatal events can have important consequences for the behavior, health, and productivity of offspring in farmed species. Pregnant cattle may experience many potentially important stressors, for instance, relating to their social environment, housing system and physical environment, interactions with humans and husbandry procedures, and their state of health. We examined the available literature to provide a review of the implications of prenatal stress for offspring welfare in cattle. The long-term effects of dystocia on cattle offspring also are reviewed. To ensure a transparent and repeatable selection process, a systematic review approach was adopted. The research literature clearly demonstrates that prenatal stress and difficult births in beef and dairy cattle both have implications for offspring welfare and performance. Common husbandry practices, such as transport, were shown to influence offspring biology and the importance of environmental variables, including thermal stress and drought, also were highlighted. Maternal disease during pregnancy was shown to negatively impact offspring welfare. Moreover, dystocia-affected calves suffer increased mortality and morbidity, decreased transfer of passive immunity, and important physiological and behavioral changes. This review also identified considerable gaps in our knowledge and understanding of the effects of prenatal stress in cattle.

The effect of lameness prevalence on technical efficiency at the dairy farm level: an adjusted data envelopment analysis approach.

A key indicator of resource use within farming is technical efficiency, which measures the amount of physical output attainable from a given set of inputs. The social aspects, in particular the treatment of animals, have generally been ignored within these measurement schemas. In addition, animal welfare will affect the production technology under which farms operate, and some allowance for this is needed within the measurement approach. This is the first paper to apply animal welfare as a discriminating technology within a technical efficiency framework. Using results from an animal welfare monitoring study coupled with resource usage data, it presents an adjusted measure of technical efficiency applied to a sample of British dairy farms and compares differences in lameness management strategies for herds. We employ both a categorical and nondiscretionary variant of the data envelopment analysis approach to measure technical efficiencies and adjust for various degrees of lameness prevalence among these farms. This paper finds that farms with low rates of lameness (below 10% of the cattle herd) tend to have significantly higher technical efficiencies than those with lameness rates of above 10% of the herd. Farms that have levels of lameness of between 10 to 20% of the herd and higher levels of lameness (above 20% of the herd) did not differ significantly. Furthermore, low lameness farms are inefficient in terms of labor and stocking density, but this is outweighed by the gain in milk yield obtained on these farms. Consequently, we argue for a whole-farm, rather than a partial indicator, approach to assessing efficiency when noneconomic factors such as lameness are accounted for. From a policy perspective, we support programs that encourage active lameness management.

Behavior of cows during and after peak feeding time on organic and conventional dairy farms in the United Kingdom.

The behavior of groups of housed, lactating dairy cattle was observed over 2 winter housing periods on 20 organic farms and 20 conventional farms in the United Kingdom. Three methods were used: (1) 6 video-clips of 10 min duration were captured of cows feeding at sections of the feed-bunk face during the peak feeding period (0 to 90 min) and continuously observed for aggressive interactions among cows; (2) the proportion of cows at the feed-bunk face was scanned every 15 min for 4.5h to include the peak feeding period (0 to 255 min); and (3) all nonfeeding behaviors were scanned every 15 min for 2.5h after the peak feeding period (120 to 255 min). The latter scans were analyzed post hoc for measures of cow comfort (freestall farms only). Management and health data were collected on each farm. On farms with open-fronted feed-bunk faces, a greater number of aggressive interactions occurred at the feed-bunk face at peak feeding time on organic farms than on conventional farms (organic = 36.3 ± 4.4; conventional = 29.1 ± 3.0). Higher proportions of cows were at the feed-bunk face at peak feeding on organic farms than on conventional farms (organic=0.58 ± 0.04; conventional=0.48 ± 0.03). Housing type (freestall versus straw pen) explained most differences in postfeeding behavior (proportion of ruminating cow in alleyways: freestalls=0.16±0.06 vs. straw-pen=0.08 ± 0.03), with few differences between organic and conventional herds. On freestall farms, the proportions of cows on organic farms lying down postfeeding was smaller than in conventional herds (organic=0.38 ± 0.09 vs. conventional=0.43 ± 0.07). Differences in behavior around peak feeding time could be associated with the reduction in food "quality" on organic farms compared with the energy requirement of the cows, with cows on organic farms being highly motivated to feed. A correlation was observed between farms that had high amounts of lying and farms that had high lameness prevalence (R(2)=55.3), suggesting a complex relationship between comfort and pain. Overall, the behavior of dairy cows on organic farms was not different from that of conventionally reared cows, and the results suggest that most behavioral welfare problems relating to housing could be alleviated by management practices.

The effect of organic status and management practices on somatic cell counts on UK dairy farms.

The numbers of organic dairy farms are increasing in the United Kingdom and in other parts of the world. On organic farms, the use of veterinary medicines is restricted. Because of this, there is concern that cow health is poorer on these farms. As udder health is primarily maintained by the use of antimicrobials, the effect of organic status on mastitis and somatic cell counts (SCC) is important to investigate. The aim of this study was therefore to determine whether the organic status and other management factors affect SCC. A group of 80 dairy farms was used in the study: 40 organic farms and 40 nonorganic farms. The farms were recruited in pairs, and each organic:nonorganic pair was matched for herd size, housing type, genetic merit for milk production and geographical location. Somatic cell count data were extracted from national databases for a standard year (2004), and analyzed using stepwise logistic regression models. The organic status of the farm did not appear in the final model, indicating no major influence of organic status on SCC. There were, however, several effects of management on SCC. Somatic cell counts were lower on farms where the udders were not cleaned or cleaned only when dirty. Somatic cell counts were also lower on farms that kept cows in larger management groups and where the majority, but not all cases of mastitis are treated with antimicrobials. It can be concluded that the control measures used on the organic farms in this study are at least as effective as those used on nonorganic farms in controlling SCC. Other management factors are influential and attention to these factors will allow farmers to reduce SCC.

Hock injury prevalence and associated risk factors on organic and nonorganic dairy farms in the United Kingdom.

The presence of hock injury was assessed in the milking herds of 80 dairy farms (40 organic, 40 nonorganic) across the United Kingdom. A wide range of information on farm management and husbandry was gathered via interview to assess the factors contributing to hock damage for all 80 farms, and a comprehensive building appraisal was conducted for 40 farms visited during the winter housing period. The prevalence of hock lesions was lower on organic compared with nonorganic farms (37.2 vs. 49.1%). Prevalence of hock damage was greater in the spring than fall (59.9 vs. 21.6%) and cows housed in free-stalls had a greater prevalence of hock lesions than those housed on straw (46.0 vs. 25.0%). Prevalence of hock damage increased with lactation number. In the analysis of fall/spring data, the age first mated, herd biosecurity, duration of summer grazing, and cow milk yield were significant factors relating to herd hock damage. Larger herds had a greater proportion of cows with hock swellings. Farms with a shorter calving interval had more cows with hock swellings. Factors relating to housing conditions that were positively associated with the prevalence of hock damage were low feed face space per cow, inferior passageway cleanliness, low total standing area per cow, and the type of bedding added to the free-stall. To assess whether free-stall versus straw-pen or organic versus nonorganic farms had different sets of risk factors, the data were reanalyzed for these types separately. For the straw-pen farms a high culling rate was associated with more hock damage. Within nonorganic farms, the length of summer grazing was significant, with longer periods meaning less hock injury. The prevalence of hock injuries on many UK farms, both organic and non-organic, exceeded levels that are deemed acceptable for cow comfort. Efforts are needed to improve housing standards to reduce the prevalence of hock injury and consequently improve cow welfare.

The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129.

Corynebacterium diphtheriae is a Gram-positive, non-spore forming, non-motile, pleomorphic rod belonging to the genus Corynebacterium and the actinomycete group of organisms. The organism produces a potent bacteriophage-encoded protein exotoxin, diphtheria toxin (DT), which causes the symptoms of diphtheria. This potentially fatal infectious disease is controlled in many developed countries by an effective immunisation programme. However, the disease has made a dramatic return in recent years, in particular within the Eastern European region. The largest, and still on-going, outbreak since the advent of mass immunisation started within Russia and the newly independent states of the former Soviet Union in the 1990s. We have sequenced the genome of a UK clinical isolate (biotype gravis strain NCTC13129), representative of the clone responsible for this outbreak. The genome consists of a single circular chromosome of 2 488 635 bp, with no plasmids. It provides evidence that recent acquisition of pathogenicity factors goes beyond the toxin itself, and includes iron-uptake systems, adhesins and fimbrial proteins. This is in contrast to Corynebacterium's nearest sequenced pathogenic relative, Mycobacterium tuberculosis, where there is little evidence of recent horizontal DNA acquisition. The genome itself shows an unusually extreme large-scale compositional bias, being noticeably higher in G+C near the origin than at the terminus.

Massive gene decay in the leprosy bacillus.

Leprosy, a chronic human neurological disease, results from infection with the obligate intracellular pathogen Mycobacterium leprae, a close relative of the tubercle bacillus. Mycobacterium leprae has the longest doubling time of all known bacteria and has thwarted every effort at culture in the laboratory. Comparing the 3.27-megabase (Mb) genome sequence of an armadillo-derived Indian isolate of the leprosy bacillus with that of Mycobacterium tuberculosis (4.41 Mb) provides clear explanations for these properties and reveals an extreme case of reductive evolution. Less than half of the genome contains functional genes but pseudogenes, with intact counterparts in M. tuberculosis, abound. Genome downsizing and the current mosaic arrangement appear to have resulted from extensive recombination events between dispersed repetitive sequences. Gene deletion and decay have eliminated many important metabolic activities including siderophore production, part of the oxidative and most of the microaerophilic and anaerobic respiratory chains, and numerous catabolic systems and their regulatory circuits.

A re-annotation of the Saccharomyces cerevisiae genome.

Discrepancies in gene and orphan number indicated by previous analyses suggest that S. cerevisiae would benefit from a consistent re-annotation. In this analysis three new genes are identified and 46 alterations to gene coordinates are described. 370 ORFs are defined as totally spurious ORFs which should be disregarded. At least a further 193 genes could be described as very hypothetical, based on a number of criteria. It was found that disparate genes with sequence overlaps over ten amino acids (especially at the N-terminus) are rare in both S. cerevisiae and Sz. pombe. A new S. cerevisiae gene number estimate with an upper limit of 5804 is proposed, but after the removal of very hypothetical genes and pseudogenes this is reduced to 5570. Although this is likely to be closer to the true upper limit, it is still predicted to be an overestimate of gene number. A complete list of revised gene coordinates is available from the Sanger Centre (S. cerevisiae reannotation: ftp://ftp/pub/yeast/SCreannotation).

Analysis of 114 kb of DNA sequence from fission yeast chromosome 2 immediately centromere-distal to his5.

One hundred and fourteen kilobase pairs (kb) of contiguous genomic sequence have been determined immediately distal to the his5 genetic marker located about 0.9 Mb from the centromere on the long arm of Schizosaccharomyces pombe chromosome 2. The sequence is contained in overlapping cosmid clones c16H5, c12D12, c24C6 and c19G7, of which 20 kb are identical to previously reported sequence from clone c21H7. The remaining 93 781 bp of sequence contains 10 known genes (cdc14, cdm1, cps1, gpa1, msh2, pck2, rip1, rps30-2, sad1 and ubl1), 32 open reading frames (ORFs) capable of coding for proteins of at least 100 amino acid residues in length, one 5S rRNA gene, one tRNA(Pro) gene, one lone Tf1-type long terminal repeat (LTR) and one lone Tf2-type LTR. There is a density of one protein-coding gene per 2.2 kb and 22 of the 42 ORFs (52%) incorporate one or more introns. Twenty-one of the novel ORFs show sequence similarities which suggest functions of their products, including a cyclin C, a MADS box transcription factor, mad2-like protein, telomere binding protein, topoisomerase II-associated protein, ATP-dependent DEAH box RNA helicase, G10 protein, ubiquitin-activating e1-like enzyme, nucleoporin, prolyl-tRNA synthetase, peptidylprolyl isomerase, delta-1-pyrroline-5-carboxylate dehydrogenase, protein transport protein, coatomer epsilon, TCP-1 chaperonin, beta-subunit of 6-phosphofructokinase, aminodeoxychorismate lyase, a phosphate transport protein and a thioredoxin.

Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491.

Neisseria meningitidis causes bacterial meningitis and is therefore responsible for considerable morbidity and mortality in both the developed and the developing world. Meningococci are opportunistic pathogens that colonize the nasopharynges and oropharynges of asymptomatic carriers. For reasons that are still mostly unknown, they occasionally gain access to the blood, and subsequently to the cerebrospinal fluid, to cause septicaemia and meningitis. N. meningitidis strains are divided into a number of serogroups on the basis of the immunochemistry of their capsular polysaccharides; serogroup A strains are responsible for major epidemics and pandemics of meningococcal disease, and therefore most of the morbidity and mortality associated with this disease. Here we have determined the complete genome sequence of a serogroup A strain of Neisseria meningitidis, Z2491. The sequence is 2,184,406 base pairs in length, with an overall G+C content of 51.8%, and contains 2,121 predicted coding sequences. The most notable feature of the genome is the presence of many hundreds of repetitive elements, ranging from short repeats, positioned either singly or in large multiple arrays, to insertion sequences and gene duplications of one kilobase or more. Many of these repeats appear to be involved in genome fluidity and antigenic variation in this important human pathogen.

The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences.

Campylobacter jejuni, from the delta-epsilon group of proteobacteria, is a microaerophilic, Gram-negative, flagellate, spiral bacterium-properties it shares with the related gastric pathogen Helicobacter pylori. It is the leading cause of bacterial food-borne diarrhoeal disease throughout the world. In addition, infection with C. jejuni is the most frequent antecedent to a form of neuromuscular paralysis known as Guillain-Barré syndrome. Here we report the genome sequence of C. jejuni NCTC11168. C. jejuni has a circular chromosome of 1,641,481 base pairs (30.6% G+C) which is predicted to encode 1,654 proteins and 54 stable RNA species. The genome is unusual in that there are virtually no insertion sequences or phage-associated sequences and very few repeat sequences. One of the most striking findings in the genome was the presence of hypervariable sequences. These short homopolymeric runs of nucleotides were commonly found in genes encoding the biosynthesis or modification of surface structures, or in closely linked genes of unknown function. The apparently high rate of variation of these homopolymeric tracts may be important in the survival strategy of C. jejuni.