Background The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. Results We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii. Conclusions Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.

During a stratified cross-sectional survey, 1705 pigs were sampled from 279 randomly selected households, 63 randomly selected communities and villages, from four study areas in The Gambia and Senegal during the period October 2007 to January 2008. Porcine cysticercosis prevalence detected by tongue inspection at animal level per study area ranged from 0.1% to 1.0%. Using an antigen-detection ELISA the seroprevalence of cysticercosis at both community/village and animal levels for the four selected study areas is: Western region 80.0% (95%CI: 52.4%–93.6%) and 4.8% (95%CI: 3.4%–6.5%), Bignona 86.7% (95%CI: 59.8%–96.6%) and 8.9% (95%CI: 5.0%–15.5%), Kolda 82.4% (95%CI: 46.8%–96.1%) and 13.2% (95%CI: 10.8%–16.0%), and Ziguinchor 81.3% (95%CI: 43.5%–96.1%) and 6.4% (95%CI: 4.0%–10.1%), respectively. No risk factors for cysticercosis were found significant in this study. This study proved that porcine cysticercosis is endemic and distributed widely in the study areas though its incidence might be suppressed by the generalised use of toilets and latrines in the study areas.

BackgroundQ fever is a zoonosis caused by Coxiella burnetii, a Gram negative bacterium present worldwide. Small ruminants are considered the main reservoirs for infection of humans. This study aimed to estimate the extent of C. burnetii infection among sheep and goats in part of The Gambia.Methodology/Principal FindingsThis survey was carried out from March to May 2012 at two areas in The Gambia. The first area comprised a cluster of seven rural villages situated 5–15 km west of Farafenni as well as the local abattoir. A second sampling was done at the central abattoir in Abuko (30 km from the capital, Banjul) in the Western Region. Serum samples were obtained from 490 goats and 398 sheep. In addition, 67 milk samples were obtained from lactating dams. Sera were tested with a Q fever ELISA kit. C. burnetii DNA was extracted from milk samples and then detected using a specific quantitative multiplex PCR assay, targeting the IS1111a element. A multivariable mixed logistic regression model was used to examine the relationship between seropositivity and explanatory variables. An overall seroprevalence of 21.6% was found. Goats had a significantly higher seroprevalence than sheep, respectively 24.2% and 18.5%. Seropositive animals were significantly older than seronegative animals. Animals from the villages had a significantly lower seroprevalence than animals from the central abattoir (15.1% versus 29.1%). C. burnetii DNA was detected in 2 out of 67 milk samples, whereas 8 samples gave a doubtful result.Conclusion/SignificanceA substantial C. burnetii seroprevalence in sheep and goats in The Gambia was demonstrated. People living in close proximity to small ruminants are exposed to C. burnetii. Q fever should be considered as a possible cause of acute febrile illness in humans in The Gambia. Future studies should include a simultaneous assessment of veterinary and human serology, and include aetiology of febrile illness in local clinics.

Audiological and other long-term neurological sequelae were determined in 157 cases and their controls matched for age, sex and village 6 to 12 months after an epidemic of group A meningococcal meningitis in rural West Africa. 19 cases (12.1%) and 3 controls (1.9%) had moderate or severe neurological sequelae of any type (P less than 0.001); 6 cases (3.9%) and no controls had severe or profound sensorineural hearing loss (P = 0.03). There was no difference in conductive hearing loss between cases and controls. Other cranial nerve sequelae (except visual defects) and generalized neurological and motor and co-ordination sequelae were also significantly increased in cases. Sensorineural hearing loss and other cranial nerve sequelae occurred significantly more frequently in males than in females, and co-ordination sequelae more frequently in cases aged 10 years or more than in younger cases. Sensorineural hearing loss and loss of visual acuity were found significantly more frequently in cases whose treatment was delayed for 4 d or more, compared with those who received treatment sooner.

The objective of this epidemiological study was to determine whether cysticercosis and especially neurocysticercosis is endemic in Soutou village about half a century after the 1962 outbreak. This study was carried out from September 2009 to February 2010. It involved a questionnaire administration, serology, treatment, coproscopy and neuro-imaging. Four hundred and three serum samples were collected from the village people, which covered 94% of the village population. By using a parallel combination of the antigen-detection ELISA and the enzyme-linked immunoelectrotransfer blot (EITB) a cysticercosis sero-prevalence of 11.9% (95% CI: 8.9-15.4%) was found. Cerebral CT-scans showed that 23.3% (10/43) of the seropositives were affected by neurocysticercosis. Four out of these 43 (9.3%) were tapeworm carriers. Seropositivity was significantly associated to older age groups (41-60 years old; p = 0.001 and 61-91 years old; p = 0.028) and absence of a household toilet (p = 0.001). It can be concluded that Soutou village is an active focus of Taenia solium cysticercosis about 50 years after the first reported epidemic outbreak.

Summaryobjective To determine whether epilepsy is caused by Taenia solium cysticercosis in The Gambia. methods Case-control study testing samples collected from 210 people with epilepsy and 420 matched controls by sex and age ±5 years from 69 different places around the country during the period October 2008-March 2009. All serum samples were subjected to an antigen detection ELISA (Ag-ELISA) and electro-immunotransfer blot (EITB), and the seropositives were further CT-scanned to determine the presence of cysticerci in the brain.results Although not significantly different (P = 0.668), circulating Taenia antigen was found by Ag-ELISA in 1.4% (95% CI: 0.3-4.1) of people with epilepsy and in 1.9% (95% CI: 0.8-3.7) of the controls. A non-significant (P = 0.4718) odds ratio of association 0.75 (95% CI: 0.13-3.15) between epilepsy and the presence of Taenia antigens was found. All 630 serum samples turned out seronegative by the EITB test. There were no intracranial cysts or cyst-like structures detected among the nine CT-scanned Ag-ELISA seropositives.

The objective of this study was the characterisation of the traditional milk chain in Western Region (The Gambia) and Kolda (Southern Senegal); and the analysis of milk chain actors' risk behaviours for milk-borne diseases transmission. For this purpose, cattle herds involved in milk production, milk collectors, milk vendors and small-scale milk processing units were surveyed in the two study sites. A similar general milk chain organisation was found in the two sites with some particularities in farm management, compliance with hygienic measures at different levels, treatment of milk and milk consumption patterns. This results in a variable degree of risk of consumers' exposure to milk-borne diseases. Although the quality of the milk has been improved with the development of small-scale milk processing units, serious efforts are still needed with respect to pasteurisation procedure and to change the mindset of consumers who prefer in their majority drinking raw milk, fresh or soured, without any prior treatment.

Coxiella burnetii infection is endemic among both humans and small ruminants in this area of The Gambia. Human and animal exposure to C. burnetii were related at compound level. Further research into the clinical relevance of C. burnetii infection in West Africa is needed.