Characterization of a Novel African Swine Fever Virus p72 Genotype II from Nigeria.

African swine fever (ASF) is a high-consequence transboundary hemorrhagic fever of swine. It continues to spread across the globe causing socio-economic issues and threatening food security and biodiversity. In 2020, Nigeria reported a major ASF outbreak, killing close to half a million pigs. Based on the partial sequences of the genes B646L (p72) and E183L (p54), the virus responsible for the outbreak was identified as an African swine fever virus (ASFV) p72 genotype II. Here, we report further characterization of ASFV RV502, one of the isolates obtained during the outbreak. The whole genome sequence of this virus revealed a deletion of 6535 bp between the nucleotide positions 11,760-18,295 of the genome, and an apparent reverse complement duplication of the 5' end of the genome at the 3' end. Phylogenetically, ASFV RV502 clustered together with ASFV MAL/19/Karonga and ASFV Tanzania/Rukwa/2017/1 suggesting that the virus responsible for the 2020 outbreak in Nigeria has a South-eastern African origin.

A Retrospective Study of the Seroprevalence of Dengue Virus and Chikungunya Virus Exposures in Nigeria, 2010-2018.

Arboviruses are important public health threats in many regions of the world. Nigeria has experienced outbreaks of arboviruses over the past decades, leading to concerns of widespread endemicity, which are frequently misdiagnosed. This study aimed to determine the seroprevalence of dengue virus (DENV) (a flavivirus) and chikungunya virus (CHIKV) (an alphavirus) infections in three major population centers of Nigeria. A convenience sample of 701 sera was collected from both healthy and febrile participants between August 2010 and March 2018. Sera were tested for prior exposure to CHIKV virus and DENV using indirect IgG ELISA. Results showed that 54.1% (379/701) of participants were seropositive for anti-DENV antibodies, 41.3% (290/701) were seropositive for anti-CHIKV antibodies, and 20.1% (141/701) had previous exposure to both. The seropositivity for prior CHIKV exposure and prior exposure to DENV and CHIKV was significantly associated with age (CHIKV: OR = 2.7 (95% CI: 1.7-4.3); DENV and CHIKV: OR = 2.2 (95% CI: 1.2-4.0) for adults compared to participants under 18 years old). Overall, the high seropositivity across all age groups suggests that arboviral infections are prevalent in Nigeria and indicates that surveillance and further epidemiological studies are required to determine the true burden of these infections and the spectrum of diseases associated with these exposures.

Concurrent Resistance to Carbapenem and Colistin Among Enterobacteriaceae Recovered From Human and Animal Sources in Nigeria Is Associated With Multiple Genetic Mechanisms.

Resistance to last resort drugs such as carbapenem and colistin is a serious global health threat. This study investigated carbapenem and colistin resistance in 583 non-duplicate Enterobacteriaceae isolates utilizing phenotypic methods and whole genome sequencing (WGS). Of the 583 isolates recovered from humans, animals and the environment in Nigeria, 18.9% (110/583) were resistant to at least one carbapenem (meropenem, ertapenem, and imipenem) and 9.1% (53/583) exhibited concurrent carbapenem-colistin resistance. The minimum inhibitory concentrations of carbapenem and colistin were 2-32 µg/mL and 8 to >64 µg/mL, respectively. No carbapenem resistant isolates produced carbapenemase nor harbored any known carbapenemase producing genes. WGS supported that concurrent carbapenem-colistin resistance was mediated by novel and previously described alterations in chromosomal efflux regulatory genes, particularly mgrB (M1V) ompC (M1_V24del) ompK37 (I70M, I128M) ramR (M1V), and marR (M1V). In addition, alterations/mutations were detected in the etpA, arnT, ccrB, pmrB in colistin resistant bacteria and ompK36 in carbapenem resistant bacteria. The bacterial isolates were distributed into 37 sequence types and characterized by the presence of internationally recognized high-risk clones. The results indicate that humans and animals in Nigeria may serve as reservoirs and vehicles for the global spread of the isolates. Further studies on antimicrobial resistance in African countries are warranted.

Household and animal factors associated with sheeppox and goatpox sero-prevalence and identification of high-risk areas in selected States of northern Nigeria.

Sheeppox and goatpox (SGP) are transboundary, highly contagious diseases affecting sheep and goats with characteristic clinical signs. SGP affect populations of small ruminants in Africa, Asia and the Middle East and, as a result, threaten farmers' livelihoods. Despite their importance, studies looking at factors that increase the risk of sheeppox-virus (SPPV) and goatpox-virus (GTPV) exposure and infection are limited. A cross-sectional study was conducted in three states of Northern Nigeria (Bauchi, Kaduna and Plateau) to determine the sero-prevalence and spatial patterns of SGP, and identify risk factors for SPPV/GTPV exposure at animal and household level. Sera samples were collected from 1,800 small ruminants from 300 households. Data on putative risk factors were collected using a standardised questionnaire. Twenty-nine small ruminants were sero-positive to SGP - apparent weighted sero-prevalence 2.0 %; 95 % C.I. 1.1-.3.0 %. Sero-positive animals came from 19 (6.3 %) households. Analysis of the questionnaire showed that a fifth (20.3 %) of farmers claimed to have experienced SGP outbreaks previously in their flocks, with 33 (1.8 %) of the individual animals sampled in this study reported to have had clinical signs. At animal level, the odds of being sero-positive were higher in older animals (>24months; OR = 8.0, p = 0.008 vs ≤24 months) and small ruminants with a history of clinical SGP (OR = 16.9, p = 0.01). Bringing new small ruminants into the household and having a history of SGP in the flock were the main factors identified at household level. Households were less likely to be sero-positive if the time between bringing animals into the household and sampling was over a year (PR = 0.31, p = 0.05), while households with a history of SGP were more likely to be sero-positive regardless of the timeframe. Important spatial heterogeneity was found. The Bayes smooth rate ranged from 0.06 to 4.10 % across local government areas (LGA), with LGA in the north-east or north-west of the study area identified as hot-spots for SGP exposure. Results from this study shed new light on the understanding of SGP epidemiology and provide key inputs to design risk-based surveillance and intervention programmes in the area.

Characterization of high level ampicillin- and aminoglycoside-resistant enterococci isolated from non-hospital sources.

PURPOSE: High level ampicillin- and aminoglycoside-resistant enterococci are being increasingly reported from non-hospital sources. This study was carried out to characterize these strains from non-hospital sources in Nigeria. METHODOLOGY: A collection of Enterococcus faecium isolated from vegetables, soil, farm animals and manure and observed to be resistant to ampicillin (n=63) and gentamicin (n=37) discs, were screened for resistance to high levels of ampicillin and aminoglycoside using E-test strips. Putative high level ampicillin- and aminoglycoside-resistant strains were screened for pbp5 and aminoglycoside modifying enzyme genes, respectively, by PCR. The C-terminal region of the amplified pbp5 gene was also sequenced. RESULTS: Five (5/63) and thirty-five (35/37) of the ampicillin- and aminoglycoside-resistant strains were identified as high level ampicillin- and aminoglycoside-resistant E. faecium strains, respectively, based on the MIC results. The amplified pbp5 gene from the high level ampicillin-resistant isolates displayed 96-99 % nucleotide sequence similarity with the reference strains and three novel insertions (500Glu→Leu, 502Asp→Arg and 614Ile→Phe) in the amino acid sequence. Aminoglycoside modifying enzyme genes aac(6')-Ie-aph(2″) (100 %), aph(2')-Ic (88.8 %), aph(3')-IIIa (90 %) and ant(4')-Ia (40 %) were detected among the high level aminoglycoside-resistant isolates. CONCLUSION: This is the first report on the characterization of high level ampicillin- and aminoglycoside-resistant Enterococcus faecium among animals and vegetables in Nigeria. The results show that non-hospital sources can constitute a reservoir for potential dissemination of these strains and genes to humans via the food chain or by direct contact.

Equine Dermatophytosis: A Survey of Its Occurrence and Species Distribution among Horses in Kaduna State, Nigeria.

This study was designed to determine the occurrence and species distribution of dermatophyte from cutaneous skin lesions of horses in Kaduna State, Nigeria. A total of 102 skin scrapings were collected from 102 horses with skin lesions. Mycological studies were carried out using conventional techniques. Dermatophytes were isolated from 18 (17.6%) of the 102 samples collected. The 18 dermatophytes were distributed into 10 different species belonging to Microsporum (n = 5) and Trichophyton (n = 5) genera. T. verrucosum (n = 4) was the most predominant species isolated followed by M. equinum (n = 3), T. vanbreuseghemii (n = 2), M. gypseum (n = 2), and M. canis (n = 2). Others include M. fulvum (n = 2), T. mentagrophytes (n = 1), T. equinum (n = 1), T. soudanense (n = 1), and M. gallinae (n = 1). The present study reveals the occurrence of dermatophytes in cutaneous skin lesions of horses in Kaduna State, Nigeria. In addition for the first time in this environment the anthropophilic dermatophyte T. soudanense was isolated from horses. These findings have great economic, veterinary, and public health significance as they relate to the cost of treatment and dissemination of zoonotic dermatophytes.