Prevalence of multidrug-resistant Escherichia coli isolates and virulence gene expression in poultry farms in Jos, Nigeria.

Introduction: Antimicrobial resistance is increasingly becoming a global health concern. This study aimed to investigate and report MDR Escherichia coli (E. coli) prevalence, resistance, and virulence genes from poultry in Jos, Plateau State, Nigeria. Methods: The samples were analyzed using microbiological standard methods and polymerase chain reactions (PCRs). Results: A total of 179 cloacal swabs were collected from bothlocal and exotic poultry breeds, of which 99.4% (178/179) tested positive for E. coli. Among these culturally identified samples, 99.4% (177/178) were furtherconfirmed Escherichia coli with a molecular weight of 401 bp. Multidrugresistance of 45% (80/178) was observed from the confirmed isolates. PCR assays were conducted to detect genes associated with resistance to antibiotics, specifically, tetracycline (tetA gene), sulfonamide (sul1 gene), ampicillin (ampC gene), and quinolone (gyrA gene). Antimicrobial susceptibility test (AST) results revealed substantial antibiotic resistance, with 81.9% (145/177) of the isolates being resistant to tetracycline, 80.2% (142/177) to quinolone, 69.5% (123/177) to sulfonamide, and 66.1% (117/177) to ampicillin. Further analysis on 18 isolates that showed resistance to up to four different antibiotics was carried out using multiplex PCR to detect eae, hlyA, rfbE, fliC, and fstx virulence genes. The study found that 44.4% (15/18) of the isolates were positive for the eae gene, 27.7% (5/18) for stx, 22.2% (4/18) for rfbe gene, and 5.5% (1) for hlya gene, and none tested positive for fliC gene. Conclusion: These results showed high antibiotic resistance, virulent genes, and significant levels of MDR in E. coli from poultry. This study highlights the urgent need for antimicrobial stewardship practices within the poultry industry due to their profound implications for food safety and public health. This issue is particularly critical in Nigeria, where poultry farming constitutes a significant portion of smallholder farming practices.

Sequencing and Analysis of Lumpy Skin Disease Virus Whole Genomes Reveals a New Viral Subgroup in West and Central Africa.

Lumpy skin disease virus (LSDV) is a member of the capripoxvirus (CPPV) genus of the Poxviridae family. LSDV is a rapidly emerging, high-consequence pathogen of cattle, recently spreading from Africa and the Middle East into Europe and Asia. We have sequenced the whole genome of historical LSDV isolates from the Pirbright Institute virus archive, and field isolates from recent disease outbreaks in Sri Lanka, Mongolia, Nigeria and Ethiopia. These genome sequences were compared to published genomes and classified into different subgroups. Two subgroups contained vaccine or vaccine-like samples ("Neethling-like" clade 1.1 and "Kenya-like" subgroup, clade 1.2.2). One subgroup was associated with outbreaks of LSD in the Middle East/Europe (clade 1.2.1) and a previously unreported subgroup originated from cases of LSD in west and central Africa (clade 1.2.3). Isolates were also identified that contained a mix of genes from both wildtype and vaccine samples (vaccine-like recombinants, grouped in clade 2). Whole genome sequencing and analysis of LSDV strains isolated from different regions of Africa, Europe and Asia have provided new knowledge of the drivers of LSDV emergence, and will inform future disease control strategies.

Poxvirus Infections in Dairy Farms and Transhumance Cattle Herds in Nigeria.

Lumpy Skin disease (LSD) is an economically important disease in cattle caused by the LSD virus (LSDV) of the genus Capripoxvirus, while pseudocowpox (PCP) is a widely distributed zoonotic cattle disease caused by the PCP virus (PCPV) of the genus Parapoxvirus. Though both viral pox infections are reportedly present in Nigeria, similarities in their clinical presentation and limited access to laboratories often lead to misdiagnosis in the field. This study investigated suspected LSD outbreaks in organized and transhumance cattle herds in Nigeria in 2020. A total of 42 scab/skin biopsy samples were collected from 16 outbreaks of suspected LSD in five northern States of Nigeria. The samples were analyzed using a high-resolution multiplex melting (HRM) assay to differentiate poxviruses belonging to Orthopoxvirus, Capripoxvirus, and Parapoxvirus genera. LSDV was characterized using four gene segments, namely the RNA polymerase 30 kDa subunit (RPO30), G-protein-coupled receptor (GPCR), the extracellular enveloped virus (EEV) glycoprotein and CaPV homolog of the variola virus B22R. Likewise, the partial B2L gene of PCPV was also analyzed. Nineteen samples (45.2%) were positive according to the HRM assay for LSDV, and five (11.9%) were co-infected with LSDV and PCPV. The multiple sequence alignments of the GPCR, EEV, and B22R showed 100% similarity among the Nigerian LSDV samples, unlike the RPO30 phylogeny, which showed two clusters. Some of the Nigerian LSDVs clustered within LSDV SG II were with commonly circulating LSDV field isolates in Africa, the Middle East, and Europe, while the remaining Nigerian LSDVs produced a unique sub-group. The B2L sequences of Nigerian PCPVs were 100% identical and clustered within the PCPV group containing cattle/Reindeer isolates, close to PCPVs from Zambia and Botswana. The results show the diversity of Nigerian LSDV strains. This paper also reports the first documented co-infection of LSDV and PCPV in Nigeria.