Prevention of human exposure to livestock faecal waste in the household: a scoping study of interventions conducted in sub-Saharan Africa.

BACKGROUND: Poorly managed animal faecal waste can result in detrimental environmental and public health implications. Limiting human exposure to animal waste through Animal inclusive Water Sanitation and Hygiene (A-WASH) strategies is imperative to improve public health in livestock keeping households but has received little attention to date. A small number of A-WASH interventions have previously been identified through a systematic review by another research team, and published in 2017. To inform intervention design with the most up-to-date information, a scoping study was conducted to map the existing evidence for A-WASH in sub-Saharan Africa (SSA) emerging since the previous review. METHODS: This review followed PRISMA guidelines to identify interventions in SSA published between January 2016 to October 2022. Databases searched included PubMed, PMC Europe, CabDirect and Web of Science. Studies were eligible for inclusion if they were written in English and documented interventions limiting human contact with animal faecal material in the SSA context. Key data extracted included: the intervention itself, its target population, cost, measure of effectiveness, quantification of effect, assessment of success, acceptability and limitations. These data were synthesized into a narrative, structured around the intervention type. FINDINGS: Eight eligible articles were identified. Interventions to reduce human exposure to animal faecal matter were conducted in combination with 'standard' human-centric WASH practices. Identified interventions included the management of human-animal co-habitation, educational programs and the creation of child-safe spaces. No novel A-WASH interventions were identified in this review, beyond those identified by the review in 2017. Randomised Controlled Trials (RCTs) were used to evaluate six of the eight identified interventions, but as effect was evaluated through various measures, the ability to formally compare efficacy of interventions is lacking. CONCLUSION: This study indicates that the number of A-WASH studies in SSA is increasing and the use of RCTs suggests a strong desire to create high-quality evidence within this field. There is a need for standardisation of effect measures to enable meta-analyses to be conducted to better understand intervention effectiveness. Evaluation of scalability and sustainability of interventions is still lacking in A - WASH research.

Co-infections of respiratory pathogens and gastrointestinal parasites in smallholder pig production systems in Uganda.

A cross-sectional study was conducted to identify factors for infections of pigs with key respiratory pathogens: porcine circovirus type 2 (PCV2), porcine reproductive and respiratory syndrome virus (PPRSv), Mycoplasma hyopneumoniae (M. hyo), Actinobacillus pleuropneumoniae (App), and gastrointestinal (GI) parasites in Uganda. A structured questionnaire was used to collect data on management practices associated with infections. Ninety (90) farms and 259 pigs were sampled. Sera were screened against 4 pathogens using commercial ELISA tests. The Baerman's method was used to identify parasite species in faecal samples. Logistic regression was done to identify risk factors for infections. Results showed individual animal seroprevalence of PCV2 was 6.9% (95% CI 3.7-11.1), PRRSv 13.8% (95% CI 8.8-19.6), M. hyo 6.4% (95% CI 3.5-10.5), and App 30.4% (95% CI 24.8-36.5). The prevalence of Ascaris spp. was 12.7% (95% CI 8.6-16.8), Strongyles spp was 16.2% (95% CI 11.7-20.7), and Eimeria spp. was 56.4% (95% CI 50.3-62.4). Pigs infested with Ascaris spp. were more likely to test positive to PCV2, odds ratio (OR) 1.86 (CI 1.31-2.60; p = 0.0002). For M. hyo, infection with Strongyles spp. was a risk factor (OR 12.9, p < 0.001). Pigs that had Strongyles and Ascaris spp. Infections (ORs 3.5 and 3.4, p < 0.001 respectively) were likely to have co-infections. The model showed that use of cement, elevated floor, and limiting contacts with outside pigs were protective while using mud and helminth infestations increased risks of co-infections. This study provided evidence that improved housing and biosecurity are critical in reducing pathogen incidence in herds.

Actions and perceived impact of African swine fever control measures along the smallholder pig value chain in Uganda.

Pig production in Uganda is constrained by African swine fever (ASF) which is endemic in the country. Current measures taken by the Government of Uganda in controlling ASF outbreaks include trade and livestock movement restrictions, called "quarantine." Little is known about the actions of, and impact of value chain actors in response to ASF quarantines. This study describes actions that different stakeholders in the smallholder pig value chain took, and the perceived economic impact, during ASF quarantines. Data was collected in ten focus group discussions (FGD) using participatory epidemiology tools and two key informants' (KIs) interviews with District Veterinary Officers (DVOs) of Kisoro and Moyo districts in Uganda. The results show that during ASF quarantine, pig value chain actors shifted their activities from formal places such as livestock markets, slaughter slabs, pork butcheries and pork joints to informal places such as farmers' homesteads. Farmers were perceived the most economically affected stakeholder group with forgone income due to unsold pigs, costs for implementing biosecurity measures and extra costs for feeding unsold pigs being the major perceived causes of the losses. The continued trade in pigs and pig products in informal marketplaces suggests that quarantine might not be effective for hindering activities that might spread ASF in these settings. The perceived economic losses provide an insight into the negative economic impact of the quarantine for the different stakeholders.

Molecular characterization of porcine reproductive and respiratory syndrome virus (PRRSv) identified from slaughtered pigs in northern Uganda.

BACKGROUND: A cross sectional study was conducted to detect and characterize species of porcine reproductive and respiratory syndrome virus (PRRSv) identified from slaughtered pigs in Lira district, northern Uganda. The study was conducted from March to September 2019 in three selected slaughter slabs. Pigs brought for slaughter were randomly sampled. At necropsy, lungs were extracted from the thoracic cavity and examined for pneumonic lesions. Seventy-three (73) pigs with gross lung lesions were sampled, from which one hundred and one (101) tissue samples were taken. A real-time reverse transcriptase PCR (RT-qPCR) was used to characterize PRRSv species. RESULTS: A total of 20 samples tested positive for PRRSv. The respective prevalence of PRRSv type 1 and type 2 were 24.65% (n = 18) and 2.73% (n = 2) respectively. Of the pigs sampled (n = 73), only two pigs, 2.73% (n = 2) tested positive to both species. The likelihood of PRRSv detection decreased with pig age, but increased with gross pneumonic pathology. CONCLUSIONS: This study demonstrated dual circulation of both species in northern Uganda. The association between PRRSv and lung pathology suggests that it may be an important cause of lung disease in pigs in Uganda and hence loss of production. This calls for further investigations on potential economic impacts of PRRSv on pig productivity. These findings contribute to discussions about the need of surveillance and possible vaccination strategies against PRRSv in Uganda.

The Etiology of Pneumonia From Analysis of Lung Aspirate and Pleural Fluid Samples: Findings From the Pneumonia Etiology Research for Child Health (PERCH) Study.

BACKGROUND: An improved understanding of childhood pneumonia etiology is required to inform prevention and treatment strategies. Lung aspiration is the gold standard specimen for pneumonia diagnostics. We report findings from analyses of lung and pleural aspirates collected in the Pneumonia Etiology Research for Child Health (PERCH) study. METHODS: The PERCH study enrolled children aged 1-59 months hospitalized with World Health Organization-defined severe or very severe pneumonia in 7 countries in Africa and Asia. Percutaneous transthoracic lung aspiration (LA) and pleural fluid (PF) aspiration was performed on a sample of pneumonia cases with radiological consolidation and/or PF in 4 countries. Venous blood and nasopharyngeal/oropharyngeal swabs were collected from all cases. Multiplex quantitative polymerase chain reaction (PCR) and routine microbiologic culture were applied to clinical specimens. RESULTS: Of 44 LAs performed within 3 days of admission on 622 eligible cases, 13 (30%) had a pathogen identified by either culture (5/44) or by PCR (11/29). A pathogen was identified in 12/14 (86%) PF specimens tested by either culture (9/14) or PCR (9/11). Bacterial pathogens were identified more frequently than viruses. All but 1 of the cases with a virus identified were coinfected with bacterial pathogens. Streptococcus pneumoniae (9/44 [20%]) and Staphylococcus aureus (7/14 [50%]) were the predominant pathogens identified in LA and PF, respectively. CONCLUSIONS: Bacterial pathogens predominated in this selected subgroup of PERCH participants drawn from those with radiological consolidation or PF, with S. pneumoniae and S. aureus the leading pathogens identified.

The genome of the vervet (Chlorocebus aethiops sabaeus).

We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member of the Old World monkey (OWM) superfamily is uniquely valuable for genetic investigations of simian immunodeficiency virus (SIV), for which it is the most abundant natural host species, and of a wide range of health-related phenotypes assessed in Caribbean vervets (C. a. sabaeus), whose numbers have expanded dramatically since Europeans introduced small numbers of their ancestors from West Africa during the colonial era. We use the reference to characterize the genomic relationship between vervets and other primates, the intra-generic phylogeny of vervet subspecies, and genome-wide structural variations of a pedigreed C. a. sabaeus population. Through comparative analyses with human and rhesus macaque, we characterize at high resolution the unique chromosomal fission events that differentiate the vervets and their close relatives from most other catarrhine primates, in whom karyotype is highly conserved. We also provide a summary of transposable elements and contrast these with the rhesus macaque and human. Analysis of sequenced genomes representing each of the main vervet subspecies supports previously hypothesized relationships between these populations, which range across most of sub-Saharan Africa, while uncovering high levels of genetic diversity within each. Sequence-based analyses of major histocompatibility complex (MHC) polymorphisms reveal extremely low diversity in Caribbean C. a. sabaeus vervets, compared to vervets from putatively ancestral West African regions. In the C. a. sabaeus research population, we discover the first structural variations that are, in some cases, predicted to have a deleterious effect; future studies will determine the phenotypic impact of these variations.

Standardization of Laboratory Methods for the PERCH Study.

The Pneumonia Etiology Research for Child Health study was conducted across 7 diverse research sites and relied on standardized clinical and laboratory methods for the accurate and meaningful interpretation of pneumonia etiology data. Blood, respiratory specimens, and urine were collected from children aged 1-59 months hospitalized with severe or very severe pneumonia and community controls of the same age without severe pneumonia and were tested with an extensive array of laboratory diagnostic tests. A standardized testing algorithm and standard operating procedures were applied across all study sites. Site laboratories received uniform training, equipment, and reagents for core testing methods. Standardization was further assured by routine teleconferences, in-person meetings, site monitoring visits, and internal and external quality assurance testing. Targeted confirmatory testing and testing by specialized assays were done at a central reference laboratory.

Evaluation of Pneumococcal Load in Blood by Polymerase Chain Reaction for the Diagnosis of Pneumococcal Pneumonia in Young Children in the PERCH Study.

BACKGROUND.: Detection of pneumococcus by lytA polymerase chain reaction (PCR) in blood had poor diagnostic accuracy for diagnosing pneumococcal pneumonia in children in 9 African and Asian sites. We assessed the value of blood lytA quantification in diagnosing pneumococcal pneumonia. METHODS.: The Pneumonia Etiology Research for Child Health (PERCH) case-control study tested whole blood by PCR for pneumococcus in children aged 1-59 months hospitalized with signs of pneumonia and in age-frequency matched community controls. The distribution of load among PCR-positive participants was compared between microbiologically confirmed pneumococcal pneumonia (MCPP) cases, cases confirmed for nonpneumococcal pathogens, nonconfirmed cases, and controls. Receiver operating characteristic analyses determined the "optimal threshold" that distinguished MCPP cases from controls. RESULTS.: Load was available for 290 of 291 cases with pneumococcal PCR detected in blood and 273 of 273 controls. Load was higher in MCPP cases than controls (median, 4.0 × 103 vs 0.19 × 103 copies/mL), but overlapped substantially (range, 0.16-989.9 × 103 copies/mL and 0.01-551.9 × 103 copies/mL, respectively). The proportion with high load (≥2.2 log10 copies/mL) was 62.5% among MCPP cases, 4.3% among nonconfirmed cases, 9.3% among cases confirmed for a nonpneumococcal pathogen, and 3.1% among controls. Pneumococcal load in blood was not associated with respiratory tract illness in controls (P = .32). High blood pneumococcal load was associated with alveolar consolidation on chest radiograph in nonconfirmed cases, and with high (>6.9 log10 copies/mL) nasopharyngeal/oropharyngeal load and C-reactive protein ≥40 mg/L (both P < .01) in nonconfirmed cases but not controls. CONCLUSIONS.: Quantitative pneumococcal PCR in blood has limited diagnostic utility for identifying pneumococcal pneumonia in individual children, but may be informative in epidemiological studies.

Risk factors, perceptions and practices associated with Taenia solium cysticercosis and its control in the smallholder pig production systems in Uganda: a cross-sectional survey.

BACKGROUND: Prevalence studies report Taenia solium cysticercosis in pig and human populations in Uganda. However, the factors influencing occurrence in smallholder pig production systems are not well documented and little is known about farmers' perceptions of T. solium cysticercosis or farmer practices that could reduce transmission. METHODS: To determine the risk factors, perceptions and practices regarding T. solium cysticercosis, a household survey using a semi-structured questionnaire was conducted in 1185 households in the rural and urban pig production systems in Masaka, Mukono and Kamuli Districts. Logistic regression was used to measure associations of risk factors with infection. Performance scores were calculated to summarise perceptions and practices of farmers regarding taeniosis, human cysticercosis and porcine cysticercosis as well as farmer behavior related to control or breaking transmission. RESULTS: Pig breed type, farmers' knowledge about transmission, sources of water used, and pig keeping homes where family members were unable to use the latrine were all significantly associated with T. solium cysticercosis in pigs. Performance scores indicated that farmers were more aware of taeniosis (63.0%; 95% Confidence Interval 60.0-65.8) than human or porcine cysticercosis; only three farmers (0.3%, 95% CI = 0.1-0.8) had knowledge on all three conditions. More farmers reported that they dewormed pigs (94.1%) than reported deworming themselves and their family members (62.0%). Albendazole was the most commonly used drug for deworming both pigs and humans (85.0 and 81.5% respectively). Just over half (54.6%) of the farmers interviewed had clean water near the latrines for washing hands. Of these, only 41.9% used water with soap to wash hands after latrine use. CONCLUSION: Factors that significantly influenced occurrence of T. solium cysticercosis in pigs were identified. Farmers had some knowledge about the disease but did not link taeniosis, human cysticercosis, and porcine cysticercosis. Therefore, there is need to employ strategies that raise awareness and interrupt transmission.

Prevalence and risk factors for gastrointestinal parasites in small-scale pig enterprises in Central and Eastern Uganda.

In Eastern Africa, small-scale pig keeping has emerged as a popular activity to generate additional household income. Infections of pigs with gastrointestinal helminths can limit production output, increase production costs, and pose zoonotic risks. A cross-sectional, community-based study in three districts in Eastern and Central Uganda examined the prevalence of gastrointestinal helminthes and associated risk factors in 932 randomly sampled pigs. Using the combined sedimentation-flotation method, 61.4 % (58.2-64.5 %, 95 % confidence interval [CI]) tested positive for one or more gastrointestinal helminths, namely, strongyles (57.1 %, 95 % CI), Metastrongylus spp. (7.6 %, 95 % CI), Ascaris suum (5.9 %, 95 % CI), Strongyloides ransomi (4.2 %, 95 % CI), and Trichuris suis (3.4 %, 95 % CI). Coccidia oocysts were found in 40.7 % of all pigs sampled (37.5-44.0 %, 95 % CI). Significant differences across the three districts were observed for the presence of A. suum (p < 0.001), Metastrongylus spp. (p = 0.001), S. ransomi (p = 0.002), and coccidia oocysts (p = 0.05). All animals tested negative for Fasciola spp. and Balantidium coli. Thirty-five variables were included in univariable analyses with helminth infection as the outcome of interest. A causal model was generated to identify relationships among the potential predictors, and consequently, seven variables with p ≤ 0.15 were included in a multivariable analysis for helminth infection. The final regression models showed that routine management factors had a greater impact on the prevalence of infection than regular, preventive medical treatment or the level of confinement. Factors that negatively correlated with gastrointestinal infection were the routine removal of manure and litter from pig pens (p ≤ 0.05, odds ratio [OR] = 0.667) and the routine use of disinfectants (p ≤ 0.05, OR = 0.548).

Transmission of Staphylococcus aureus from Humans to Green Monkeys in The Gambia as Revealed by Whole-Genome Sequencing.

UNLABELLED: Staphylococcus aureus is an important pathogen of humans and animals. We genome sequenced 90 S. aureus isolates from The Gambia: 46 isolates from invasive disease in humans, 13 human carriage isolates, and 31 monkey carriage isolates. We inferred multiple anthroponotic transmissions of S. aureus from humans to green monkeys (Chlorocebus sabaeus) in The Gambia over different time scales. We report a novel monkey-associated clade of S. aureus that emerged from a human-to-monkey switch estimated to have occurred 2,700 years ago. Adaptation of this lineage to the monkey host is accompanied by the loss of phage-carrying genes that are known to play an important role in human colonization. We also report recent anthroponotic transmission of the well-characterized human lineages sequence type 6 (ST6) and ST15 to monkeys, probably because of steadily increasing encroachment of humans into the monkeys' habitat. Although we have found no evidence of transmission of S. aureus from monkeys to humans, as the two species come into ever-closer contact, there might be an increased risk of additional interspecies exchanges of potential pathogens. IMPORTANCE: The population structures of Staphylococcus aureus in humans and monkeys in sub-Saharan Africa have been previously described using multilocus sequence typing (MLST). However, these data lack the power to accurately infer details regarding the origin and maintenance of new adaptive lineages. Here, we describe the use of whole-genome sequencing to detect transmission of S. aureus between humans and nonhuman primates and to document the genetic changes accompanying host adaptation. We note that human-to-monkey switches tend to be more common than the reverse and that a novel monkey-associated clade is likely to have emerged from such a switch approximately 2,700 years ago. Moreover, analysis of the accessory genome provides important clues as to the genetic changes underpinning host adaptation and, in particular, shows that human-to-monkey switches tend to be associated with the loss of genes known to confer adaptation to the human host.

High genetic diversity of Staphylococcus aureus strains colonising the nasopharynx of Gambian villagers before widespread use of pneumococcal conjugate vaccines.

BACKGROUND: With the global efforts of reducing pneumococcal disease through widespread introduction of pneumococcal vaccines, concerns have emerged on the potential increase of morbidity and mortality from S. aureus disease. Little is known however, of the carriage rates of S. aureus or of its' relationship with carriage of S. pneumoniae in rural Africa, and West Africa in particular where very high rates of carriage of S. pneumoniae have been reported. This study aims to evaluate the prevalence, antibiotic susceptibility patterns and genotypes of S. aureus isolated from the nasopharynx of healthy individuals in rural Gambia before the introduction of routine use of pneumococcal conjugate vaccines in the country. RESULTS: Overall prevalence of S. aureus nasopharyngeal carriage was 25.2%. All S. aureus isolates tested were susceptible to methicillin. Resistant was observed for sulphamethoxazole-trimethoprim (15%) and tetracycline (34.3%). We found 59 different sequence types (ST), 35 of which were novel. The most prevalent sequence types were ST 15 (28%) and ST 5 (4%). Eighty two percent (494/600) of study individuals were S. pneumoniae carriers with S. pneumoniae carriage rates decreasing with increasing age groups. S. aureus carriage among pneumococcal carriers was slightly lower than among non-pneumococcal carriers (24.3 versus 29.3%; p = 0.324). There were no associations of carriage between these two bacteria across the 4 age groups. However, analysis of pooled data children < 2 years and children 2 to < 5 years of age showed a statistically significant inverse association (24.1 and 50.0% for S. aureus carriage among S. pneumoniae carriers and non-carriers respectively; p = 0.015). CONCLUSIONS: We report that nasopharyngeal carriage of S. aureus in rural Gambia is high in all age groups, with approximately 1 out of 4 individuals being carriers in the pre-pneumococcal vaccination era. There are indications that nasopharyngeal carriage of S.aureus could be inversely related to carriage of S. pneumoniae amongst younger children in The Gambian and that S. aureus clones in The Gambia show significant genetic diversity suggesting worldwide dissemination. Findings from this study provide a useful background for impact studies evaluating the introduction of pneumococcal vaccines or other interventions targeting the control of S. aureus infections and disease.

Population structure, epidemiology and antibiotic resistance patterns of Streptococcus pneumoniae serotype 5: prior to PCV-13 vaccine introduction in Eastern Gambia.

BACKGROUND: Streptococcus pneumoniae serotype 5 is among the most common serotypes causing invasive pneumococcal disease (IPD) in The Gambia. We anticipate that introduction of the 13-valent pneumococcal conjugate vaccine (PCV-13) into routine vaccination in The Gambia will reduce serotype 5 IPD. However, the emergence of new clones that have altered their genetic repertoire through capsular switching or genetic recombination after vaccination with PCV-13 poses a threat to this public health effort. In order to monitor for potential genetic changes post-PCV-13 vaccination, we established the baseline population structure, epidemiology, and antibiotic resistance patterns of serotype 5 before the introduction of PCV-13. METHODS: Fifty-five invasive S. pneumoniae serotype 5 isolates were recovered from January 2009 to August 2011 in a population-based study in the Upper River Region of The Gambia. Serotyping was done by latex agglutination and confirmed by serotype-specific Polymerase Chain Reaction (PCR). Genotyping was undertaken using Multilocus Sequence Typing (MLST). Antimicrobial sensitivity was done using disc diffusion. Contingency table analyses were conducted using Pearson's Chi(2) and Fisher's exact test. Clustering was performed using Bionumerics version 6.5. RESULTS: MLST resolved S. pneumoniae serotype 5 isolates into 3 sequence types (ST), namely ST 289(6/55), ST 3339(19/55) and ST 3404(30/55). ST 289 was identified as the major clonal complex. ST 3339, the prevalent genotype in 2009 [84.6% (11/13)], was replaced by ST 3404 [70.4% (19/27)] in 2010 as the dominant ST. Interestingly, ST 3404 showed lower resistance to tetracycline and oxacillin (P < 0.001), an empirical surrogate to penicillin in The Gambia. CONCLUSIONS: There has been an emergence of ST 3404 in The Gambia prior to the introduction of PCV-13. Our findings provide important background data for future assessment of the impact of PCV-13 into routine immunization in developing countries, such as The Gambia.

Enhancing knowledge and awareness of biosecurity practices for control of African swine fever among smallholder pig farmers in four districts along the Kenya-Uganda border.

A study was undertaken along the Kenya-Uganda border in four districts of Tororo and Busia (Uganda) and Busia and Teso (Kenya) to understand smallholder farmers' knowledge, practices and awareness of biosecurity measures. Information was collected by administering questionnaires to 645 randomly selected pig households in the study area. In addition, focus group discussions were carried out in 12 villages involving 248 people using a standardized list of questions. The outcome suggested that there was a very low level of awareness of biosecurity practices amongst smallholder farmers. We conclude that adoption of specific biosecurity practices by smallholder farmers is feasible but requires institutional support. There is a clear requirement for government authorities to sensitize farmers using approaches that allow active participation of farmers in the design, planning and implementation of biosecurity practices to enable enhanced adoption.

Serological and molecular investigation for brucellosis in swine in selected districts of Uganda.

Brucellosis is a notifiable zoonotic disease affecting livestock, humans, and wildlife in Uganda. Pigs can be infected with human pathogenic Brucella suis biovars 1 and 3 and can be a significant source of brucellosis for humans. Uganda has a rapidly growing pig population, and the pork consumption per capita is the highest in East Africa. The objective of this work was to determine the seroprevalence of brucellosis in Ugandan pigs. A cross-sectional serosurvey of pigs was conducted in three of the major pig-keeping districts in Uganda (Masaka (n = 381 samples), Mukono (n = 398), and Kamuli (n = 414)). In addition, pigs originating from these districts were sampled in the major pig abattoir in Kampala (n = 472). In total, 1665 serum samples were investigated by serological and molecular tests. Only three putative brucellosis-positive samples were detected serologically using indirect ELISA. These sera were found negative for Brucella antibodies by CFT; however, two had antibodies against Yersinia enterocolitica as determined by SAT. Presence of antibodies against Yersiniae was confirmed by Y. enterocolitica antibody-specific ELISA. The two Yersiniae ELISA-positive samples were brucellosis negative using real-time PCR. We tested additional 142 sera from the 1665 samples with real-time PCR. All tested negative. Under this type of production system, we expect a maximum B. suis prevalence of less than 1 % at 95 % confidence level, and therefore, the risk of acquiring brucellosis from the pigs or their products is negligible. However, pigs may harbor the zoonotic Y. enterocolitica. This is the first study to investigate the occurrence of brucellosis in pigs in Uganda and the first study to report Y. enterocolitica antibodies in swine in Uganda.

Factors associated with siman immunodeficiency virus transmission in a natural African nonhuman primate host in the wild.

UNLABELLED: African green monkeys (AGMs) are naturally infected with simian immunodeficiency virus (SIV) at high prevalence levels and do not progress to AIDS. Sexual transmission is the main transmission route in AGM, while mother-to-infant transmission (MTIT) is negligible. We investigated SIV transmission in wild AGMs to assess whether or not high SIV prevalence is due to differences in mucosal permissivity to SIV (i.e., whether the genetic bottleneck of viral transmission reported in humans and macaques is also observed in AGMs in the wild). We tested 121 sabaeus AGMs (Chlorocebus sabaeus) from the Gambia and found that 53 were SIV infected (44%). By combining serology and viral load quantitation, we identified 4 acutely infected AGMs, in which we assessed the diversity of the quasispecies by single-genome amplification (SGA) and documented that a single virus variant established the infections. We thus show that natural SIV transmission in the wild is associated with a genetic bottleneck similar to that described for mucosal human immunodeficiency virus (HIV) transmission in humans. Flow cytometry assessment of the immune cell populations did not identify major differences between infected and uninfected AGM. The expression of the SIV coreceptor CCR5 on CD4+ T cells dramatically increased in adults, being higher in infected than in uninfected infant and juvenile AGMs. Thus, the limited SIV MTIT in natural hosts appears to be due to low target cell availability in newborns and infants, which supports HIV MTIT prevention strategies aimed at limiting the target cells at mucosal sites. Combined, (i) the extremely high prevalence in sexually active AGMs, (ii) the very efficient SIV transmission in the wild, and (iii) the existence of a fraction of multiparous females that remain uninfected in spite of massive exposure to SIV identify wild AGMs as an acceptable model of exposed, uninfected individuals. IMPORTANCE: We report an extensive analysis of the natural history of SIVagm infection in its sabaeus monkey host, the African green monkey species endemic to West Africa. Virtually no study has investigated the natural history of SIV infection in the wild. The novelty of our approach is that we report for the first time that SIV infection has no discernible impact on the major immune cell populations in natural hosts, thus confirming the nonpathogenic nature of SIV infection in the wild. We also focused on the correlates of SIV transmission, and we report, also for the first time, that SIV transmission in the wild is characterized by a major genetic bottleneck, similar to that described for HIV-1 transmission in humans. Finally, we report here that the restriction of target cell availability is a major correlate of the lack of SIV transmission to the offspring in natural hosts of SIVs.

Risk factors associated with occurrence of African swine fever outbreaks in smallholder pig farms in four districts along the Uganda-Kenya border.

A cross-sectional survey was carried out to assess risk factors associated with occurrence of African swine fever (ASF) outbreaks in smallholder pig farms in four districts along Kenya-Uganda border. Information was collected by administering questionnaires to 642 randomly selected pig households in the study area. The study showed that the major risk factors that influenced ASF occurrence were purchase of pigs in the previous year (p < 0.000) and feeding of pigs with swill (p < 0.024). By employing cluster analysis, three clusters of pig production types were identified based on production characteristics that were found to differ significantly between districts. The most vulnerable cluster to ASF was households with the highest reported number of ASF outbreaks and composed of those that practiced free range at least some of the time. The majority of the households in this cluster were from Busia district in Uganda. On the other hand, the least vulnerable cluster to ASF composed of households that had the least number of pig purchases, minimal swill feeding, and less treatment for internal and external parasites. The largest proportion of households in this cluster was from Busia district Kenya. The study recommended the need to sensitize farmers to adopt proper biosecurity practices such as total confinement of pigs, treatment of swill, isolation of newly purchased pigs for at least 2 weeks, and provision of incentives for farmers to report suspected outbreaks to authorities and rapid confirmation of outbreaks.

Etiology of severe childhood pneumonia in the Gambia, West Africa, determined by conventional and molecular microbiological analyses of lung and pleural aspirate samples.

Molecular analyses of lung aspirates from Gambian children with severe pneumonia detected pathogens more frequently than did culture and showed a predominance of bacteria, principally Streptococcus pneumoniae, >75% being of serotypes covered by current pneumococcal conjugate vaccines. Multiple pathogens were detected frequently, notably Haemophilus influenzae (mostly nontypeable) together with S. pneumoniae.

First Report of the Emergence of Peste des Petits Ruminants Lineage IV Virus in Senegal.

Peste des petits ruminants (PPR) is a highly contagious viral disease and one of the deadliest affecting wild goats, sheep, and small ruminants; however, goats are generally more sensitive. The causative agent is the Peste des Petits Ruminants virus (PPRV), which is a single-stranded RNA virus of negative polarity belonging to the Paramyxoviridae family. In February 2020, an active outbreak of PPR was reported in a herd of a transhumant farmer in the village of Gainth Pathé (department of Kounguel, Kaffrine region, Senegal). Of the ten swabs collected from the goats, eight returned a positive result through a quantitative real-time PCR. The sample that yielded the strongest signal from the quantitative real-time PCR was further analyzed with a conventional PCR amplification and direct amplicon sequencing. A phylogenetic analysis showed that the sequence of the PPR virus obtained belonged to lineage IV. These results confirm those found in the countries bordering Senegal and reinforce the hypothesis of the importance of animal mobility between these neighboring countries in the control of PPRV. In perspective, following the discovery of this lineage IV in Senegal, a study on its dispersion is underway throughout the national territory. The results that will emerge from this study, associated with detailed data on animal movements and epidemiological data, will provide appropriate and effective information to improve PPR surveillance and control strategies with a view to its eradication.

Molecular Epidemiology of Peste Des Petits Ruminants Virus in West Africa: Is Lineage IV Replacing Lineage II in Burkina Faso?

This study aimed at investigating the genetic lineages of peste des petits ruminants virus (PPRV) currently circulating in Burkina Faso. As part of PPR surveillance in 2021 and 2022, suspected outbreaks in different regions were investigated. A risk map was produced to determine high-risk areas for PPR transmission. Based on alerts, samples were obtained from three regions and all sampled localities were confirmed to fall within PPR high risk areas. We collected swab samples from the eyes, mouth, and nose of sick goats. Some tissue samples were also collected from dead animals suspected to be infected by PPRV. In total, samples from 28 goats were analysed. Virus confirmation was performed with RT-PCR amplification targeting the nucleocapsid (N) gene. Partial N gene sequencing (350 bp) was carried out using the RT-PCR products of positives samples to characterise the circulating lineages. Eleven sequences, including ten new sequences, have been obtained. Our study identified the presence of the PPRV lineage IV in the three studied regions in Burkina Faso with a genetic heterogeneity recorded for the sequences analysed. Previously published data and results of this study suggest that PPRV lineage IV seems to be replacing lineage II in Burkina Faso.