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Abstract Background Early detection and treatment of carbapenem-resistant Klebsiella pneumoniae (CRKP) could reduce the risk of developing life-threatening sepsis in childhood. However, little is known about sepsis caused by CRKP in children under-5 in developing countries. This study aimed to determine the epidemiology, antimicrobial resistance profile, associated risk factors and management of CRKP in children under-5 with sepsis in Ethiopia. Methods This prospective multicenter study was conducted from June 2021 to December 2023 in three tertiary hospitals in Ethiopia. Samples collection and processing, identification and antimicrobial susceptibility testing were performed according to CLSI guidelines. Sociodemographic data were collected using structured questionnaires. Data were analyzed using STATA-21 and logistic regression to determine associated risk factors. A p-value

Abstract Background Genomic structural variations (GSVs), notably copy number variations (CNVs), significantly shape genetic diversity and facilitate adaptation in cattle populations. Despite their importance, the genome-wide characterization of CNVs in indigenous Ethiopian cattle breeds—Abigar, Fellata, and Gojjam-Highland remains largely unexplored. In this study, we applied a read-depth approach to whole genome sequencing (WGS) data to conduct the first comprehensive analysis of CNVs in these populations. Results We identified 3,893 CNV regions (CNVRs) covering 19.15 Mb (0.71% of the cattle genome). These CNVRs ranged from 1.60 kb to 488.0 kb, with an average size of 4.92 kb. These CNVRs included deletions (1713), duplications (1929), and mixed events (251) showing notable differences in distribution among the breeds. Four out of five randomly selected CNVRs were successfully validated using real time polymerase chain reaction (qPCR). Further analyses identified candidate genes associated with high-altitude adaptation (GBE1 and SOD1), heat stress adaptation (HSPA13, DNAJC18, and DNAJC8) and resistance to tick infestations (BoLA and KRT33A). In addition, variance stabilizing transformation (V ST ) statistics highlighted population-specific CNVRs, emphasizing the unique genetic signatures of high-altitude adaptation in the Gojjam-Highland cattle breed. Among the detected CNVRs, 4.93% (192 out of 3,893) overlapped with 520 quantitative traits loci (QTLs) associated with six economically important trait categories suggesting that these CNVRs may significantly contribute to the genetic variation underlying these traits. Conclusions Our comprehensive analysis reveals significant CNVRs associated with key adaptive traits in Ethiopian cattle breeds highlighting their genetic diversity and resilience. These findings offer valuable insights into the genetic basis of adaptability and can inform sustainable breeding practices and conservation efforts. Future research should prioritize the functional validation of these CNVRs and their integration into breeding programs to enhance traits such as disease resistance and environmental adaptability.

Escherichia coli of different pathotypes are frequently involved in morbidity and mortality in animals and humans. The study aimed to identify E. coli pathotypes and determine antimicrobial resistance (AMR) profiles in Ethiopian smallholder livestock households. The pathotyping included 198 E. coli isolates identified from human and environmental samples collected from 98 households. AMR profiling was conducted on selected E. coli pathotypes from 89 households, along with known isolates from calf samples obtained from the same households. Morphological and biochemical tests were used to identify presumptive E. coli isolates. DNA was extracted and then singleplex PCR was used to amplify virulence genes. A disc diffusion test was applied for AMR profilings in E. coli pathotypes. Data were evaluated using chi-square tests and logistic regression. Calf (79.8 %) and human (73.7 %) samples were more likely to contain pathotypes (OR 3.2; 95 % CI: 1.7, 5.9; p = 0.001 and OR 2.3; 95 % CI: 1.2, 4.1; p = 0.008, respectively) than the environmental samples (55.6 %). ETEC (32.3 %) and STEC (15.2 %) were the most common pathotypes detected in the study samples. Out of the 176 isolates selected for AMR profiling, 85 % were resistant to at least one drug and 36 % were multi-drug resistant (MDR). The MDR isolates were found in 44 households, with 11 sharing identical pathotypes and resistance profiles among the different samples. Thus, E. coli strains were likely circulated among humans, animals, and the environment. This in turn calls for a One-health approach to improve antimicrobial usage standards and promote proper waste disposal practices.

Abstract Background Calf diarrhea is a major cause of morbidity and mortality in the livestock sector worldwide and it can be caused by multiple infectious agents. In Ethiopia, cattle are the most economically important species within the livestock sector, but at the same time the young animals suffer from high rates of morbidity and mortality due to calf diarrhea. However, studies including both screening and molecular characterization of bovine enteric pathogens are lacking. Therefore, we aimed to both detect and molecularly characterize four of the major enteric pathogens in calf diarrhea, Enterotoxigenic Escherichia coli (E. coli K99 +), Cryptosporidium spp., rotavirus A (RVA), and bovine coronavirus (BCoV) in calves from central Ethiopia. Diarrheic and non-diarrheic calves were included in the study and fecal samples were analyzed with antigen-ELISA and quantitative real-time PCR (qPCR). Positive samples were further characterized by genotyping PCRs. Results All four pathogens were detected in both diarrheic and non-diarrheic calves using qPCR and further characterization showed the presence of three Cryptosporidium species, C. andersoni, C. bovis and C. ryanae. Furthermore, genotyping of RVA-positive samples found a common bovine genotype G10P[11], as well as a more unusual G-type, G24. To our knowledge this is the first detection of the G24 RVA genotype in Ethiopia as well as in Africa. Lastly, investigation of the spike gene revealed two distinct BCoV strains, one classical BCoV strain and one bovine-like CoV strain. Conclusions Our results show that Cryptosporidium spp., E. coli K99 + , RVA and BCoV circulate in calves from central Ethiopia. Furthermore, our findings of the rare RVA G-type G24 and a bovine-like CoV demonstrates the importance of genetic characterization.

Abstract Background Early detection and proper management of maternal sepsis caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) can significantly reduce severe complications and maternal mortality. This study aimed to describe the epidemiology, antimicrobial resistance profile, and management of carbapenem-resistant K. pneumoniae among sepsis-suspected maternal cases in Ethiopia. Methods A prospective cross-sectional study was conducted in five tertiary hospitals from June 2021 to December 2023. Isolation, identification, and antimicrobial susceptibility testing of the isolates were carried out following standard microbiological procedures as stated in the CLSI guidelines. Data on socio-demographics, risk factors, and management strategies were collected with structured questionnaires. Associations between variables were determined using logistic regression analysis in STATA-21. A p-value of less than 0.05 was statistically significant. Results Of the 5613 total women suspected of having maternal sepsis, 609 (10.8%) of them were infected with K. pneumoniae. The prevalence rates of MDR, XDR, and PDR K. pneumoniae strains were 93.9%, 24.3%, and 10.9%, respectively. The resistance rates for the last-resort antibiotics; amikacin, tigecycline, carbapenem, and third-generation cephalosporin were 16.4%, 29.1%, 31.9%, and 93.0%, respectively. The combination of carbapenem with tigecycline or amikacin therapy was used to manage maternal sepsis caused by cephalosporin-and carbapenem-resistant strains. Sepsis associated risk factors, including septic abortion [AOR = 5.3; 95%CI:2.2–14.4]; extended hospitalization [AOR = 3.7; 95%CI: 1.6–19.4]; dilatation and curettage [AOR = 2.2; 95%CI:1.3–13.4]; cesarean wound infection [AOR = 4.1; 95%CI:2.0–9.2]; indwelling catheterization [AOR = 2.1;95%CI: 1.4–6.2]; ICU admission [AOR = 4.3; 95%CI:2.4–11.2]; post abortion [AOR = 9.8; 95%CI:5.7–16.3], and recurrent UTI [AOR = 3.3; 95%CI: 1.6–13.2] were significantly associated with maternal sepsis caused by K. pneumoniae. Conclusions The prevalence of maternal sepsis caused by carbapenem- resistant K. pneumoniae is high and serious attention needs to be given to combat transmission. Therefore, improving awareness, early diagnosis, IPC, integrated maternal surveillance, improved sanitation and efficient antimicrobial stewardship are crucial to combating bacterial maternal sepsis.

Mastitis is highly prevalent and causes significant economic loss in the Ethiopian dairy industry. An important aspect of monitoring dairy cow health and milk quality is understanding somatic cell count (SCC), composition and milk yield. This study aimed to evaluate milk SCC, composition, yield, and factors associated with the quality traits of Ethiopian dairy farms. A total of 3269 milk samples were collected from 1719 cows across 201 herds. The overall means and standard deviations of loge-transformed somatic cell score (SCS), fat, protein, lactose, and test day milk yield were 12.39 ± 1.61 cells/mL, 2.68 ± 1.71%, 3.17 ± 0.24%, 4.75 ± 0.36%, and 10.45 ± 5.04 litres, respectively. The results showed that 40.7% of the analysed milk samples had the SCC class ≤ 200x103 cells/mL. SCS was negatively correlated with milk yield and composition but moderately positively correlated with electrical conductivity (r = 0.41). Lactation stage, breed, parity, herd size and altitude significantly influenced most milk parameters, except fat content, which was unaffected by parity (p > 0.05). In conclusion, the highest SCS was recorded in this study. An increase in SCS negatively affects both milk yield and composition. Therefore, breed selection and herd management should focus on reducing the SCC to improve milk yield and quality.

The emergence of antibiotic resistance in E. coli strains has sparked a fervent investigation of alternative therapies, such as the use of lytic bacteriophages. Phage genome sequence analysis is a novel method for learning more about proteins and other biomolecules encoded by phages, particularly phage-lytic enzymes that are crucial to the lysis of bacterial cells. Seven potential lytic E. coli phages—EH-B-A (A1), EP-M-A, EP-B-K (E2), EI-SP-GF, ET-SD-TH, and ST-TK—isolated from activated dairy farm sludges, rivers, and hospital liquid waste genomes were described in this study. The Illumina NextSeq 550 sequencer was used for sequencing phage isolates. The virus nucleotide collection (nr/nt) (taxid:10239) was used to evaluate whole-genome sequences. Phylogenetic analysis was performed using the MEGA11 software. Genome sequencing revealed that each bacteriophage contained a linear double-stranded DNA genome. Phage isolates were taxonomically identified as the Caudoviricetes class with four genera of phages, including Kagunavirus, Vequintavirus, Dhillonvirus, and Jilinvirus. Phage genome lengths varied from 24,264 to 136,204 bp, and GC contents ranged from 44 % to 55 %. In total, 33–218 CDSs (coding sequences) were predicted, with 19–77 % of CDSs encoding functional proteins. All phages lacked tRNA genes in their genomes, except for EI-SP-GF, which possessed five tRNA genes. Based on the phylogenetic tree analysis, the phage isolates were related to Enterobacteria and E. coli phage sequences in the database. Screening did not show any genes encoding for a CRISPR-like system, virulence, antibiotic resistance, or lysogeny. Because of their stringent lytic nature, these phage isolates might be used in the future to treat E. coli infections. This study might also provide some primary data for developing phage control techniques and advance our understanding of the genetic composition of E. coli phages.

Abstract Background Coagulase-negative Staphylococcus species are an emerging cause of intramammary infection, posing a significant economic and public health threat. The aim of this study was to assess the occurrence of coagulase-negative Staphylococcus species in bovine milk and dairy farms in Northwestern Ethiopia and to provide information about their antibiotic susceptibility and virulence gene profiles. Methods The cross-sectional study was conducted from February to August 2022. Coagulase-negative Staphylococcus species were isolated from 290 milk samples. Species isolation and identification were performed by plate culturing and biochemical tests and the antimicrobial susceptibility pattern of each isolate was determined by the Kirby-Bauer disc diffusion test. The single-plex PCR was used to detect the presence of virulent genes. The STATA software version 16 was used for data analysis. The prevalence, proportion of antimicrobial resistance and the number of virulent genes detected from coagulase-negative Staphylococcus species were analyzed using descriptive statistics. Results Coagulase-negative Staphylococcus species were isolated in 28.6%, (95% CI: 23.5–34.2) of the samples. Of these, the S. epidermidis, S. sciuri, S. warneri, S. haemolyticus, S. simulans, S. chromogens, S. cohnii, and S. captis species were isolated at the rates of 11, 5.2, 3.4, 3.1, 3.1, 1, 1, and 0.7% respectively. All the isolates showed a high percentage (100%) of resistance to Amoxicillin, Ampicillin, and Cefotetan and 37.5% of resistance to Oxacillin. The majority (54.2%) of coagulase-negative isolates also showed multidrug resistance. Coagulase-negative Staphylococcus species carried the icaD, pvl, mecA, hlb, sec, and hla virulent genes at the rates of 26.5%, 22.1%, 21.7%, 9.6%, 9.6% and 8.4% respectively. Conclusion The present study revealed that the majority of the isolates (54.2%) were found multidrug-resistant and carriage of one or more virulent and enterotoxin genes responsible for intramammary and food poisoning infections. Thus, urgent disease control and prevention measures are warranted to reduce the deleterious impact of coagulase-negative species. To the best of our knowledge, this is the first study in Ethiopia to detect coagulase-negative Staphylococcus species with their associated virulent and food poisoning genes from bovine milk.

Abstract Indigenous animal genetic resources play a crucial role in preserving global genetic diversity and supporting the livelihoods of millions of people. In Ethiopia, the majority of the cattle population consists of indigenous breeds. Understanding the genetic architecture of these cattle breeds is essential for effective management and conservation efforts. In this study, we sequenced DNA samples from 70 animals from seven indigenous cattle breeds, generating about two terabytes of pair-end reads with an average coverage of 14X. The sequencing data were pre-processed and mapped to the cattle reference genome (ARS-UCD1.2) with an alignment rate of 99.2%. Finally, the variant calling process produced approximately 35 million high-quality SNPs. These data provide a deeper understanding of the genetic landscape, facilitate the identification of causal mutations, and enable the exploration of evolutionary patterns to assist cattle improvement and sustainable utilization, particularly in the face of unpredictable climate changes.

Abstract Seasonal fluctuations influence foodborne illness transmission and affect patterns of microbial contamination of food. Previous investigations on the seasonality of Salmonella enterica prevalence in dairy products in Ethiopia have been minimal. However, such data are needed to inform strategic development of effective interventions to improve food safety, as seasonal differences may affect intervention strategies. This study was conducted to identify differences in the prevalence of Salmonella in milk and cheese samples between wet and dry seasons. A longitudinal study design was utilized with a random sampling occurring during both dry and wet seasons. A total of 448 milk and cottage cheese samples were collected from Oromia, Sidama, and Amhara regions. Samples were tested for Salmonella using the ISO 6579-1: 2008 method, followed by PCR confirmation. A chi-square test was conducted to assess the significance of differences in the prevalence of Salmonella in the samples between the two seasons. Results from this study showed a higher prevalence of Salmonella in all sample types during the dry season (P

Abstract Background Diarrheagenic Escherichia coli (E. coli) is a zoonotic pathogen that contaminates abattoir workers, slaughter environments, slaughter equipment, and carcasses during abattoir processing. Infection with E. coli is associated with the consumption of contaminated food and water, and it is a potential threat to the health and welfare of both humans and animals. Hence, this study aimed to detect diarrheagenic E. coli and assess its antibiogram profile in two abattoir settings, in one health lens. Methods A cross-sectional study in one health approach was conducted from December 2020 to June 2021. A total of 384 samples from abattoir workers’ hands, carcasses, knives, cattle feces, abattoir water and effluents were collected. Bacterial culture and biochemical tests were conducted to isolate E. coli, while conventional polymerase chain reaction was performed to identify virulence genes. The antibiogram of diarrheagenic E. coli was tested against nine antimicrobials using the Kirby Bauer disk diffusion method. Results A total of 115 (29.95%) E. coli were isolated from the 384 samples, and from these isolates, about 17 (14.8%) were confirmed to be diarrheagenic E. coli (DEC). Among the DEC pathotypes, nine (52.94%), five (29.4%), and three (17.65%) were Shiga toxin-producing, enterohemorrhagic, and enterotoxigenic E. coli, respectively. While 14 (82.35%) DEC isolates harbored the stx2 gene, five (29.41%) the eae gene, five (29.41%) the hlyA gene and three (17.65%) harbored the st gene. All the DEC isolates were resistant to erythromycin and vancomycin; whereas, they were susceptible to ampicillin, nalidixic acid and norfloxacin. Furthermore, 64.7% of DEC isolates showed resistance to both ceftazidime and kanamycin and 88.24% of the isolates showed multidrug resistance. Conclusion This study detected DEC isolates having different virulence genes, which showed single and multiple antimicrobial resistance. Given the existing poor hygienic and sanitary practices along the abattoir-to-table food chain, coupled with the habit of raw meat consumption, this result indicates a potential public and animal health risk from the pathogen and antimicrobial resistance.

Abstract Background Escherichia coli is a common fecal coliform, facultative aerobic, gram-negative bacterium. Pathogenic strains of such microbes have evolved to cause diarrhea, urinary tract infections, and septicemias. The emergence of antibiotic resistance urged the identification of an alternative strategy. The use of lytic bacteriophages against the control of pathogenic E. coli in clinics and different environmental setups (waste and drink water management) has become an alternative therapy to antibiotic therapy. Thus, this study aimed to isolate and characterize lytic bacteriophage from various sources in Addis Ababa, tested them against antimicrobial-resistant diarrheagenic E. coli strains and evaluated their therapeutic potential under in vitro conditions. Methods A total of 14 samples were processed against six different diarrheagenic E. coli strains. The conventional culture and plaque analysis agar overlay method was used to recover lytic bacteriophage isolates. The phage isolates were characterized to determine their lytic effect, growth characteristics, host range activity, and stability under different temperature and pH conditions. Phage isolates were identified by scanning electron microscope (SEM), and molecular techniques (PCR). Results In total, 17 phages were recovered from 84 tested plates. Of the 17 phage isolates, 11 (65%) were Myoviridae-like phages, and 6 (35%) phage isolates were Podoviridae and Siphoviridae by morphology and PCR identification. Based on the host range test, growth characteristics, and stability test 7 potent phages were selected. These phages demonstrated better growth characteristics, including short latent periods, highest burst sizes, and wider host ranges, as well as thermal stability and the ability to survive in a wide range of pH levels. Conclusions The promising effect of the phages isolated in this study against AMR pathogenic E. coli has raised the possibility of their use in the future treatment of E. coli infections.

Brucellosis is a neglected zoonotic disease affecting livestock and humans that remains endemic in Ethiopia. Despite its prevalence, only a few studies have identified Brucella species circulating in livestock in the country. This study aimed to determine the Brucella species responsible for infections in livestock in the Afar region of Ethiopia and characterize the isolates using whole-genome single nucleotide polymorphism (wgSNP) analysis and in silico multi-locus sequence typing (MLST). Comparisons were made between Ethiopian Brucella and regional and global isolates to determine their phylogenetic relationships. Surveys conducted in May and October–November 2022 in six villages of the Amibara district involved the collection of vaginal swabs (n = 231) and milk samples (n = 17) from 32 sheep and 199 goats kept by 143 pastoral households reporting recent abortions in the animals. Brucella melitensis was detected in three sheep and 32 goats, i.e., 15% (35/231) of animals across 20% (29/143) of households using bacterial culture and PCR-based methods (bcsp31, AMOS, and Bruce-ladder multiplex PCR). Of the 35 positive animals, B. melitensis was isolated from 24 swabs, while the remaining 11 were culture-negative and detected only by PCR. The genomic DNA of the 24 isolates was sequenced using Illumina Novaseq 6000 and assembled using the SPAdes pipeline. Nine- and 21-locus MLST identified 23 isolates as genotype ST12, while one isolate could not be typed. The wgSNP-based phylogenetic analysis revealed that the Ethiopian isolates clustered within the African clade and were closely related to isolates from Somalia. Several virulence factors responsible for adhesion, intracellular survival, and regulatory functions were detected in all isolates. No antimicrobial resistance genes associated with resistance to drugs commonly used for treating brucellosis were detected. Since B. melitensis is prevalent in sheep and goats, vaccination with the B. melitensis Rev-1 vaccine is the recommended strategy in these pastoral systems to protect animal and human health.

Brucellosis is a common zoonotic disease affecting livestock and humans globally. The disease is endemic in Ethiopian livestock. This study was conducted to estimate Brucella seropositivity and identify its risk factors in livestock, and practices that may expose pastoralists to the disease. Data were collected from 2133 animals across 149 households (HHs) in Dubti and Amibara districts, Afar region, Ethiopia. Blood samples from livestock and household data were collected, and interviews were conducted on husbandry and dairy consumption practices. Sera were serially tested using the Rose Bengal test and indirect enzyme-linked immunosorbent assay. The overall seropositivity to anti-Brucella antibodies was 8% (95% CI, 6.6–9.2). The antibodies were found in 12.4%, 6.5%, 6%, and 3% of the goats, cattle, camels, and sheep, respectively. Among the HHs, 59.7% had at least one seropositive animal. A mixed-effects logistic regression analysis revealed species and the acquisition of new animals (in cattle and camels), and age and district (in sheep, goats, and cattle) as significant risk factors. Goats, cattle, and camels had significantly higher odds of Brucella seropositivity than sheep (p < 0.05). Seropositivity was significantly higher (p < 0.05) in adults than in young animals, in acquired than in homebred (cattle and camels), and in those with reproductive disorders than those without. Pastoralists lacked knowledge of brucellosis and its modes of transmission, while practices exposing humans and livestock to brucellosis were common. The findings underscore the need for public awareness campaigns and implementation of brucellosis control measures in pastoral systems.

Abstract Listeriosis caused by Listeria monocytogenes often poses a significant threat to vulnerable populations. Dairy products have been implicated in outbreaks of listeriosis worldwide. In Ethiopia, studies have identified Listeria spp. and L. monocytogenes in various dairy products, but the genetic diversity and phylogenetic relationships of these bacteria remain largely unknown in the low- and middle-income countries. Therefore, we conducted whole-genome sequencing on 15 L. monocytogenes and 55 L. innocua isolates obtained from different levels of the dairy supply chains across three regions in Ethiopia. Genomes were assembled and used for MLST genotyping and single nucleotide polymorphism (SNP) analysis to infer phylogenetic relationships. We identified a total of 3 L. monocytogenes (i.e., 2, 145, and 18) and 12 L. innocua (i.e., 1489, 1619, 603, 537, 1010, 3186, 492, 3007, 1087, 474, 1008, and 637) MLST sequence types among the studied isolates. Some of these sequence types showed region-specific occurrence, while others were broadly distributed across regions. Through high-quality SNP analysis, we found that among 13 L. monocytogenes identified as ST 2, 11 of them were highly similar with low genetic variation, differing by only 1 to 10 SNPs, suggesting potential selection in the dairy food supply chain. The L. innocua isolates also exhibited low intra-ST genetic variation with only 0–10 SNP differences, except for the ST 1619, which displayed a greater diversity.

Abstract Introduction Matrix metalloproteinases (MMPs) play a pathophysiological role in cancer initiation and progression. Numerous studies have examined an association between MMP-2, MMP-9, and MMP-11 expression and clinicopathological characteristics of breast cancer (BC); however, no research has been done on the MMP expression levels in BC cases from Ethiopia. Materials and methods A total of 58 formalin-fixed paraffin-embedded breast tissue samples encompassing 16 benign breast tumors and 42 BC were collected. The RNA was extracted and quantitative reverse-transcription PCR was performed. GraphPad Prism version 8.0.0 was used for statistical analysis. Results The MMP-11 expression levels were significantly higher in breast cancer cases than in benign breast tumors (P = 0.012). Additionally, BC cases with positive lymph nodes and ER-positive receptors had higher MMP-11, MMP-9, and MMP-2 expression than cases with negative lymph nodes and ER-negative, respectively. The MMP-11 and MMP-9 expressions were higher in grade III and luminal A-like tumors than in grade I-II and other subtypes, respectively. Conclusion The MMP-11 expression was higher in BC than in benign breast tumors. Additionally, MMP-11, MMP-9, and MMP-2 were higher in BC with positive lymph nodes and estrogen receptors. Our findings suggest an important impact of MMPs in BC pathophysiology, particularly MMP-11.

Cattle are central to the lives and diverse cultures of African people. It has played a crucial role in providing valuable protein for billions of households and sources of income and employment for producers and other actors in the livestock value chains. The long-term natural selection of African cattle typically signals signatures in the genome, contributes to high genetic differentiations across breeds. This has enabled them to develop unique adaptive traits to cope with inadequate feed supply, high temperatures, high internal and external parasites, and diseases. However, these unique cattle genetic resources are threatened by indiscriminate cross-breeding, breed replacements with exotic cosmopolitan breeds, and climate change pressures. Although there are no functional genomics studies, recent advancements in genotyping and sequencing technologies have identified and annotated limited functional genes and causal variants associated with unique adaptive and economical traits of African cattle populations. These genome-wide variants serve as candidates for breed improvement and support conservation efforts for endangered cattle breeds against future climate changes. Therefore, this review plans to collate comprehensive information on the identified selection footprints to support genomic studies in African cattle to confirm the validity of the results and provide a framework for further genetic association and QTL fine mapping studies.

Enteropathogenic Escherichia coli (EPEC) is a significant bacterial pathogen that causes infantile diarrhea, particularly in low- and middle-income countries. The lack of a reliable diagnostic method greatly contributes to the increased occurrence and severity of the disease. This study aimed at developing of a cost-effective, rapid, and efficient immunodiagnostic assay for detecting EPEC infection. Lipopolysaccharide (LPS) was extracted from overnight EPEC cultures and combined with alum adjuvant, and then injected into mice for three rounds of immunizations. Subsequently, sera were collected after each immunization and utilized in agglutination assays conducted on glass slides. Both the LPS and colonies of the EPEC isolate used for LPS preparation were employed in these agglutination assays. To evaluate the assay's performance, a total of 34 bacteria, which comprise pathogenic, non-diarrheic E. coli and non-E. coli pathogenic bacteria were used. The developed assay detected EPEC, which yielded positive reactions within 6 minutes on average for both purified LPS and bacterial isolates. The assay exhibited 100% sensitivity and a 95.83% specificity for the detection of EPEC local isolates. Moreover, the assay also detected a low number of bacteria forming units (104X 104 CFU/ml) in spiked fecal samples. This study conclusively confirms that the developed immunodiagnostic assay possesses multiple favorable characteristics, including user-friendliness, high sensitivity, high specificity, cost-effectiveness, and time-efficiency. Hence, this assay can be used as ideal diagnostic assay, which is highly suitable for the detection and screening of EPEC infection in both humans and cattle in one health perspective of resource-limited laboratories.

BackgroundShigellosis is an acute gastroenteritis infection and one of Ethiopia's most common causes of morbidity and mortality, especially in children under five. Antimicrobial resistance (AMR) has spread quickly among Shigella species due to inappropriate antibiotic use, inadequacies of diagnostic facilities, and unhygienic conditions. This study aimed to characterize Shigella sonnei (S. sonnei) using whole genome sequence (WGS) analysis in Addis Ababa, Ethiopia.MethodsThe raw reads were quality-filtered and trimmed, and a minimum length of 50bp was retained and taxonomically classified using MiniKraken version 1. The whole genome data were aligned with Antibiotic Resistance Gene (ARG) sequences of the Comprehensive Antibiotic Resistance Database (CARD) by Resistance Gene Identifier (RGI). Plasmids were analyzed using the PlasmidFinder tool version 2.1. Additionally, AMR and virulence genes were screened at the Centre for Genomic Epidemiology (CGE) web-based server.ResultsAll isolates in our investigation contained genes encoding blaEC-8 and blaZEG-1. Here, 60.7% of the isolates were phenotypically sensitive to cefoxitin among the blaEC-8 genes detected in the genotyping analysis, whereas all isolates were completely resistant to amoxicillin and erythromycin phenotypically. The study also identified genes that conferred resistance to trimethoprim (dfrA). Plasmid Col156 and Col (BS512) types were found in all isolates, while IncFII and Col (MG828) plasmids were only identified in one isolate.ConclusionThis study found that many resistant genes were present, confirming the high variety in S. sonnei strains and hence a divergence in phylogenetic relationships. Thus, combining WGS methods for AMR prediction and strain identification into active surveillance may be beneficial for monitoring the spread of AMR in S. sonnei and detecting the potential emergence of novel variations.

Optimization of fertilizer-N and -P is important to highland production of teff (Eragrostis tef) on Vertisols of central Ethiopia but may be affected by precursor crop and Vertisols type. On-farm experiments were conducted in three major teff growing districts of North Shewa (Moretina jiru, Ensaro, and Merhabete) in 2019 and 2020 with the main objectives was to determine the effect of precursor crops and Vertisols type on teff response to N and P rates. The N x P factorial combinations include 0, 60, 120, 180, and 240 kg N ha−1 and 0, 30, 60, and 90 kg P ha−1 applied each to light and heavy Vertisols with either cereal or pulse precursor crops in each district. In Merhabete, grain yield was significantly influenced by Pc x Vt x N and Pc x Vt x P but always with the lowest and highest grain yield with 0 and 240 kg N ha−1, respectively. Yield was 394 % more with 240 kg N ha−1 compared with no N and P applied. The Vt x Pc × N interaction affected teff yield in Moretina Jiru as application of 240 kg N ha−1 increased teff yield by 440 %, 30 %, 23 %, and 7 % on light Vertisols compared with 200 %, 16 %, 13 %, and 2 % on heavy Vertisols. The 4-way interaction of Vt x Pc x N x P affected grain yield in Ensaro due to the low N and P status of the soil coupled with the distinct Vertisols type in the district. In all districts, yield response to N was greater with pulse compared with cereal precursor crops and with a greater response for heavy compared with light Vertisols in Moretina Jiru and Ensaro. In Moretina Jiru, application of 170 kg−1N and soil maintenance level of 30 kg−1 of P ha−1 are recommended as an economic optimum rate (EOR). In Ensaro, the EOR for teff following cereal on light Vertisols are 166 kg N ha−1 and 65 kg P ha−1. At Ensaro, needed rates for teff following pulse on light Vertisols are 198 N ha−1 and 48 kg P ha−1. At Ensaro, needed rates for teff following cereal on heavy Vertisols are 240 N ha−1 and 90 kg P ha−1. At Ensaro, needed rates for teff following pulse on heavy Vertisols are 240 N ha−1 and 80 kg P ha−1. In Merhabete, the EOR for teff following cereal on light Vertisols are 182 kg N ha−1 and 60 kg P ha−1. In Merhabete, needed rates for teff following pulse on light Vertisols are 206 N ha−1 and 64 kg P ha−1. In Merhabete, needed rates for teff following cereal on heavy Vertisols are 240 N ha−1 and 90 kg P ha−1. In Merhabete, needed rates for teff following pulse on heavy Vertisols are 218 N ha−1 and 58 kg P ha−1. Therefore, those N and P rate are recommended for the study area, soil type and precursor crops.

The advancement of genetic engineering has revolutionized the field of immunology by allowing the utilization of intrinsic antibody structures. One of the biologics that are being produced by recombinant antibody technology is single-chain fragments variable (scFv). Genes of variable regions, the heavy and light chains that are genetically linked into a single transcript by a short flexible linker peptide, are used to generate this fragment from cellular and synthetic libraries. The specificity and affinity of these molecules are comparable to those of parental antibodies. Fusion with marker proteins and other potent molecules improves their stability, circulation half-life, activity, and efficient purification. Besides, this review comprises construction protocols, therapeutics, and diagnostic applications of scFv, as well as related challenges. Nonetheless, there are still issues with efficacy, stability, safety, intracellular administration, and production costs that need to be addressed.

Campylobacteriosis outbreaks have previously been linked to dairy foods. While the genetic diversity of Campylobacter is well understood in high-income countries, it is largely unknown in low-income countries, such as Ethiopia. This study therefore aimed to conduct the first genomic characterization of Campylobacter isolates from the Ethiopian dairy supply chain to aid in future epidemiological studies. Fourteen C. jejuni and four C. coli isolates were whole genome sequenced using an Illumina platform. Sequences were analyzed using the bioinformatics tools in the GalaxyTrakr platform to identify MLST types, and single nucleotide polymorphisms, and infer phylogenetic relationships among the studied isolates. Assembled genomes were further screened to detect antimicrobial resistance and virulence gene sequences. Among 14 C. jejuni, ST 2084 and ST 51, which belong to the clonal complexes ST-353 and ST-443, respectively, were identified. Among the 4 sequenced C. coli isolates, two isolates belonged to ST 1628 and two to ST 830 from the clonal complex ST-828. The isolates of C. jejuni ST 2084 and ST 51 carried β-lactam resistance gene blaOXA-605, a fluoroquinolone resistance-associated mutation T86I in the gryA gene, and a macrolide resistance-associated mutation A103V in 50S L22. Only ST 2084 isolates carried the tetracycline resistance gene tetO. Conversely, all four C. coli ST 830 and ST 1628 isolates carried tetO, but only ST 1628 isolates also carried blaOXA-605. Lastly, C. jejuni ST 2084 isolates carried a total of 89 virulence genes, and ST 51 isolates carried up to 88 virulence genes. Among C. coli, ST 830 isolates carried 71 genes involved in virulence, whereas two ST 1628 isolates carried up to 82 genes involved in virulence. Isolates from all identified STs have previously been isolated from human clinical cases, demonstrating a potential food safety concern. This finding warrants further monitoring of Campylobacter in dairy foods in Ethiopia to better understand and manage the risks associated with Campylobacter contamination and transmission.

PurposeDifferent biological characteristics, therapeutic responses, and disease-specific outcomes are associated with different molecular subtypes of breast cancer (BC). Although there have been different studies on BC in the Ethiopian capital city of Addis Ababa, there have been few studies in other parts of the nation, and none have evaluated biological characteristics in other locations in the context of the extensive ethnic and genetic diversity found in Ethiopia. This study was carried out to evaluate the distribution of immunohistochemistry (IHC) subtypes of BCs throughout four Ethiopian regions.MethodsA total of 227 formalin-fixed paraffin-embedded (FFPE) tissue blocks were collected from tertiary hospitals in four Ethiopian regions between 2015 and 2021. The IHC staining was performed for subtyping, ER, PR, HER2, and Ki-67 proliferation markers.ResultsThe mean age at diagnosis was 43.9 years. The percentage of ER and PR-negative tumors were 48.3% and 53.2%, respectively. The IHC subtypes showed the following distribution: 33.1% triple-negative breast cancer (TNBC), 27.6% luminal B, 25.2% luminal A, and 14.1% HER2 enriched. In multiple logistic regression analysis, grade III and HER2 positivity were associated with larger tumor size, and also originating from Jimma compared to Mekele.ConclusionPatients with ER-negative, PR-negative, and TNBC were found in 48.3%, 53.2%, and 33.1% of cases, respectively, showing that half the patients could potentially benefit from endocrine treatment. A considerably high prevalence of TNBC was reported in our study, demanding additional research that includes genetic predisposition factors. Additionally, aggressive tumors were found in a high percentage of younger age groups, which must be considered when planning personalized treatment strategies.

Purpose: This study aimed at evaluating the performance of the Loop Mediated Isothermal Amplification (LAMP) diagnostic test, which targets the putative Fimbria protein-encoding gene (Z3276) for rapid and specific detection of locally isolated enterohemorrhagic Escherichia coli (EHEC) O157:H7. Results: A total number of 40 locally available bacteria isolates and standard strains, among them 6 entrohemorrhagic (O157:H7) and 10 entropathogenic E. coli, 7 non diarrheic E. coli strains and 13 non entrohemorrhagic shiga toxic (stx) E. coli isolates as well as 4 pathogenic non E. coli species were used to optimize and evaluate the LAMP assay. The LAMP amplified DNA samples were visualized as turbid DNA both by naked eye and gel electrophoresis followed by staining. The assay had a sensitivity of 100% (6/6), a specificity of 97.05% (33/34), and an efficiency of 97.5% (39/40). The assay was also exhibited with 100% negative predicted value and 85.7% positive predicted value. The LAMP assay was also 10-fold more sensitive than the conventional PCR assay; sensitivity was determined by serial dilution. The results of LAMP and the PCR tests showed very high agreement (k = 0.97) in the detection of the bacteria studied. Conclusion: Compared with the performance of PCR and SMAC, LAMP assay was better in terms of efficiency, rapidity and cost-effectiveness, which can be used as a point-care diagnostic test in resource-limited laboratories.

Abstract Background Ethiopia rolled out primaquine nationwide in 2018 for radical cure along with chloroquine for the treatment of uncomplicated Plasmodium vivax malaria in its bid for malaria elimination by 2030. The emergence of anti-malarial drug resistance would challenge the elimination goal. There is limited evidence on the emergence of chloroquine drug resistance. The clinical and parasitological outcomes of treatment of P. vivax with chloroquine plus radical cure using low dose 14 days primaquine were assessed in an endemic area of Ethiopia. Methods A semi-directly observed 42-days follow up in-vivo therapeutic efficacy study was conducted from October 2019 to February 2020. Plasmodium vivax mono-species infected patients (n = 102) treated with a 14 days low dose (0.25 mg/kg body weight per day) primaquine plus chloroquine (a total dose of 25 mg base/kg for 3 days) were followed for 42 days to examine clinical and parasitological outcomes. Samples collected at recruitment and days of recurrence were examined by 18 S based nested polymerase chain reaction (nPCR) and Pvmsp3α nPCR-restriction fragment length polymorphism. Asexual parasitaemia and the presence of gametocytes were assessed on the scheduled days using microscopy. Clinical symptoms, haemoglobin levels, and Hillmen urine test were also assessed. Results Of the 102 patients followed in this study, no early clinical and parasitological failure was observed. All patients had adequate clinical and parasitological responses within the 28 days of follow up. Late clinical (n = 3) and parasitological (n = 6) failures were observed only after day 28. The cumulative incidence of failure was 10.9% (95% confidence interval, 5.8–19.9%) on day 42. Among the paired recurrent samples, identical clones were detected only in two samples on day 0 and day of recurrences (day 30 and 42) using Pvmsp3α genotyping. No adverse effect was detected related to the low dose 14 days primaquine administrations. Conclusion Co-administration of CQ with PQ in the study area is well tolerated and there was no recurrence of P. vivax before 28 days of follow up. Interpretation of CQ plus PQ efficacy should be done with caution especially when the recurrent parasitaemia occurs after day 28. Therapeutic efficacy studies with appropriate design might be informative to rule out chloroquine or primaquine drug resistance and/or metabolism in the study area.

Abstract Animal sourced foods, such as dairy products, are common sources of Salmonella enterica, a foodborne pathogen of increasing global concern, particularly in developing countries. In Ethiopia, most data on the prevalence of Salmonella in dairy products is highly varied and limited to a specific region or district. Furthermore, there is no data available on the risk factors for Salmonella contamination of cow milk and cottage cheese in Ethiopia. This study was therefore conducted to determine the presence of Salmonella throughout the Ethiopian dairy value chain and to identify risk factors for contamination with Salmonella. The study was carried out in three regions of Ethiopia, including Oromia, Southern Nations, Nationalities and Peoples, and Amhara during a dry season. A total 912 samples were collected from milk producers, collectors, processors, and retailers. Samples were tested for Salmonella using the ISO 6579-1: 2008 method, followed by PCR confirmation. Concurrent with sample collection, a survey was administered to study participants to identify risk factors associated with Salmonella contamination. Salmonella contamination was highest in raw milk samples at the production (19.7%) and at milk collection (21.3%) levels. No significant difference in the prevalence of Salmonella contamination among regions was detected (p > 0.05). Regional differences were apparent for cottage cheese, with the highest prevalence being in Oromia (6.3%). Identified risk factors included the temperature of water used for cow udder washing, the practice of mixing milk lots, the type of milk container, use of refrigeration, and milk filtration. These identified factors can be leveraged to develop targeted intervention strategies aimed at reducing the prevalence of Salmonella in milk and cottage cheese in Ethiopia.

Diarrheagenic Escherichia coli (DEC) are the leading cause of infectious diarrhea and pose a significant global, regional, and national burden of disease. This study aimed to investigate the prevalence of six DEC pathotypes in children with diarrhea and determine their antibiotic resistance patterns. Samples from 107 diarrheagenic children were collected and processed for Escherichia coli (E. coli). Single-plex PCR was used to detect target virulence genes as well as characterize and categorize DEC pathotypes. Antibiotic resistance patterns were determined by the Kirby–Bauer disk diffusion method. E. coli was detected in 79 diarrheal stool samples, accounting for 73.8% of the samples collected. Additionally, 49.4% (39 out of 79) of the isolates harbored various typical virulence factors. Results revealed six pathotypes of virulence: enterotoxigenic E. coli (ETEC) (53.8%), enteropathogenic E. coli (EPEC) (12.8%), enteroaggregative E. coli (EAEC) (10.3%), Heteropathotypes (7.8%), Shiga toxin-producing E. coli (STEC), and enterohemorrhagic E. coli (EHEC) (7.7% each). The isolates exhibited high antibiotic resistance against trimethoprim/sulfamethoxazole (82.1%), amoxicillin (79.5%), ampicillin (74.4%), gentamicin (69.2%), and streptomycin (64.1%). An overall occurrence of 84.6% of multiple-drug resistance was observed in the isolates, with resistance ranging from three to four antibiotic classes. Our findings revealed a high level of pathogenic E. coli that were highly resistant to multiple categories of antibiotics among children in the Awi zone. These findings highlight the potential role of pathogenic E. coli in childhood diarrhea in tropical low-resource settings and underscore the need for continued research on the characteristics of pathogenic and antibiotic-resistant strains.

A longitudinal design with a simple random sampling method was used to collect and compare microbial hygiene levels between the dry season (January to April) and wet season (June to August). A total of 456 milk and cottage cheese samples were collected from each site along the dairy value chain from three regions. Enumeration of total aerobic mesophilic bacteria (APC), total coliforms (TCC), and Escherichia coli (EC) was performed according to standard methods. Independent t-tests were employed to assess the significant variation at (p < 0.05) between the two seasons. The cumulative result of APC of 7.61 log cfu/mL and g and TCC of 3.50 log cfu/mL in the dry season were significantly higher than the wet season of 7.15 log cfu/mL and 2.49 log cfu/mL, respectively, whereas generic E. coli count (EC) was significantly higher in the wet season (0.70 log cfu/mL and g) than that in the dry season (0.40 log cfu/mL and g). The results of hygienic indicator microbial load significantly varied with season. Hence, hygienic milk production and handling practices that comprehend seasonal influence should be implemented to improve the safety of milk.

E. coli are frequently isolated food-borne pathogens from meat, milk, and their products. Moreover, there has been a significant rise in the antimicrobial resistance patterns of E. coli O157:H7 to commonly used antibiotics. A cross-sectional study was conducted from October 2019 to July 2021 to estimate prevalence and identify associated factors of E. coli and E. coli O157:H7 and to determine antibiotic resistance pattern of E. coli O157:H7 from foods of bovine origin in Dessie and Kombolcha towns. A total of 384 samples were collected. Systematic and simple random sampling techniques were employed for sampling carcasses and milking cows, respectively. E. coli and E. coli O157:H7 were detected according to recommended bacteriological protocols. E. coli O157:H7 strains were evaluated for in vitro antimicrobial susceptibility using agar disk diffusion method. Both descriptive and inferential statistical techniques were applied to analyze the data. Overall prevalence rates of E. coli and E. coli O157:H7 were 54.7% and 6.5%, respectively. Highest prevalence rates of E. coli (79.6%) and E. coli O157:H7 (16.7%) were obtained from carcass swabs and milk tank samples, respectively. Unlike E. coli O157:H7, a statistically significant difference in the E. coli prevalence (P

Background Bloodstream infection due to beta-lactamase and carbapenemase-producing gram-negative bacteria poses a substantial challenge to the effectiveness of antimicrobial treatments. Therefore, this study aimed to investigate the magnitude of beta-lactamase, carbapenemase-producing gram-negative bacteria, and associated risk factors of bloodstream infections in patients at a tertiary care hospital, in Addis Ababa, Ethiopia. Methods An institutional-based cross-sectional study was conducted with convenience sampling techniques from September 2018 to March 2019. Blood cultures were analyzed from 1486 bloodstream infection suspected patients across all age groups. The blood sample was collected using two BacT/ALERT blood culture bottles for each patient. Gram stain, colony characteristics, and conventional biochemical tests were used to classify the gram-negative bacteria at the species level. Antimicrobial susceptibility testing was carried out to screen beta-lactam and carbapenem drug-resistant bacteria. The E-test was conducted for extended-spectrum-beta-lactamase and AmpC-beta-lactamase-producers. A modified and EDTA-modified carbapenem inactivation method was conducted for carbapenemase and metallo-beta-lactamases producers. Data collected using structured questionnaires and medical records were reviewed, encoded, and cleaned using EpiData V3.1. software. The cleaned data were exported and analyzed using SPSS version 24 software. Descriptive statistics and multivariate logistic registration models were used to describe and assess factors associated with acquiring drug-resistant bacteria infection. A p-value Result Among 1486 samples, 231 gram-negative bacteria were identified; of these, 195(84.4%) produce drug-hydrolyzing enzymes, and 31(13.4%) produce more than one drug-hydrolyzing enzyme. We found 54.0% and 25.7% of the gram-negative bacteria to be extended-spectrum-beta-lactamase and carbapenemase-producing, respectively. The extended-spectrum-beta-lactamase plus AmpC-beta-lactamase-producing bacteria account for 6.9%. Among the different isolates Klebsiella pneumonia 83(36.7%) was the highest drug-hydrolyzing enzyme-producing bacteria. Acinetobacter spp 25(53.2%) was the most carbapenemase producer. Extended-spectrum-beta-lactamase and carbapenemase-producing bacteria were high in this study. A significant association between age groups and extended-spectrum-beta-lactamase producer bacterial infection was seen, with a high prevalence in neonates (p = Conclusion Gram-negative bacteria were the main pathogens responsible for drug-resistant bloodstream infections. A high percentage of extended-spectrum-beta-lactamase and carbapenemase-producer bacteria were found in this study. Neonates were more susceptible to extended-spectrum-beta-lactamase and AmpC-beta-lactamase-producer bacteria. Patients in general surgery, caesarean section delivery, and intensive care unit were more susceptible to carbapenemase-producer bacteria. The suction machines, intravenous lines, and drainage tubes play an important role in the transmission of carbapenemase and metallo-beta-lactamase-producing bacteria. The hospital management and other stakeholders should work on infection prevention protocol implementation. Moreover, special attention should be given to all types of Klebsiella pneumoniae and pan-drug resistance Acinetobacter spp transmission dynamics, drug resistance genes, and virulence factors.

Background. In Ethiopia, livestock contributes 45% of agricultural GDP. Despite the economic role played by the sector, there have been little efforts to genetically improve the indigenous cattle. Morphological characterization of selected Ethiopian indigenous cattle has been made for (Bonga, Jimma, and Kerayu) cattle types. But, the selected indigenous cattle were not characterized at molecular level (genetic diversity information). Hence, this work was initiated to detect and determine the genetic diversity and population structure of selected Ethiopian indigenous cattle ecotypes using microsatellite markers. Results. Different alleles were identified (131) and thirty-three of these alleles were unique to specific ecotypes. All loci used were informative with PIC values ranging from 0.5 (TGLA126) to 0.84 (ETH10) with a mean of 0.70 per locus. The Shannon information index ranged from (I = 1.02) ILST006 to (I = 1.63) ETH10 with an average of 1.28 revealing there is genetic diversity. Moreover, analysis of molecular variance (AMOVA) revealed 84% genetic variation within a population and 13% variation among populations. The value of F-statistics (Fst) (0.129 = 13%) indicated that there was moderate genetic differentiation among ecotypes. The (UPGMA) revealed, Bonga and Jimma clustered together while Kerayu cattle were relatively distinct, Principal coordinates analysis (PCOA) and structure analysis grouped the individual into different clusters confirming the presence of ecotype admixture due to geographical origins and uncontrolled mating. Conclusion. In general, this study has successfully characterized the genetic diversity and population structure of Bonga, Jimma, and Kerayu cattle ecotypes using high polymorphic/informative microsatellite markers. According to this study, Kerayu cattle have high AR and PA when compared to Bonga and Jimma cattle populations. So, the Kerayu population is more diverse than others and it is the hotspot for genetic diversity study. The generated information is very relevant for breeder and genetic conservation.

Background. Shigella and parasitic infections are common public health problems throughout the world. Shigellosis is an acute gastroenteritis infection and one of Ethiopia’s most common causes of morbidity and mortality, especially in children under five. High resistance rates to commonly used antibiotic agents have been documented in different locations in Ethiopia. Objective. This study aimed to characterize the antimicrobial features of the Shigella species isolated from children under five years of age with acute diarrhea in Addis Ababa, Ethiopia. Methods. Using a cross-sectional study, freshly passed fecal specimens were collected for intestinal parasite and bacterial isolation. Fecal samples for bacterial identification were placed immediately in Cary–Blair media and transported to the Ethiopian Public Health Institution (EPHI) laboratory. Antimicrobial susceptibility testing (AMST) was conducted using the disk diffusion method. Data were described using descriptive statistical tools. The association of independent and dependent variables was evaluated with logistic regression. A P value ≤0.05 was considered statistically significant. Results. The prevalence of intestinal parasites was 8.2% with seven different species. Among the 534 stool-cultured specimens, 47 (8.8%) were positive for Shigella species. Antimicrobial susceptibility testing (AMST) showed that 100%, 93.6%, 80.9%, 72.3%, and 57.5% were susceptible to norfloxacin, nalidixic acid, ciprofloxacin, gentamicin, and cefoxitin, respectively. However, 100% of the isolates were resistant to amoxicillin and erythromycin. More than 50% of the isolates were resistant to three and above antibiotics, while none of them were susceptible to all the antibiotics tested. All risk factors assessed did not show a statistically significant association with Shigella infection. Conclusion. The high levels of antibiotic resistance observed among the commonly prescribed antibiotics are alarming. The emerging resistance to ciprofloxacin and nalidixic acid signals a severe public health threat in the management of shigellosis. Raising awareness about resistance and educating health professionals, policymakers, and the public can help improve the quality of patient care and rational antibiotic use.

Over time, indigenous cattle breeds have developed disease resistance, heat tolerance, and adaptability to harsh environments. Deciphering the genetic mechanisms underlying adaptive traits is crucial for their improvement and sustainable utilization. For the first time, we performed whole-genome sequencing to unveil the genomic diversity, population structure, and selection signatures of Abigar cattle living in a tropical environment. The population structure analysis revealed that Abigar cattle exhibit high nucleotide diversity and heterozygosity, with low runs of homozygosity and linkage disequilibrium, suggesting a genetic landscape less constrained by inbreeding and enriched by diversity. Using nucleotide diversity (Pi) and population differentiation (FST) selection scan methods, we identified 83 shared genes that are likely associated with tropical adaption. The functional annotation analysis revealed that some of these genes are potentially linked to heat tolerance (HOXC13, DNAJC18, and RXFP2), immune response (IRAK3, MZB1, and STING1), and oxidative stress response (SLC23A1). Given the wider spreading impacts of climate change on cattle production, understanding the genetic mechanisms of adaptation of local breeds becomes crucial to better respond to climate and environmental changes. In this context, our finding establishes a foundation for further research into the mechanisms underpinning cattle adaptation to tropical environments.

Abstract Diarrheagenic Escherichia coli are a number of pathogenic E. coli strains that cause diarrheal infection both in animal and human hosts due to their virulence factors. A cross sectional study was conducted between November, 2016 and April, 2017 to isolate and molecularly detect pathogenic E. coli from diarrheic calves to determine the pathogenic strains, antibiogram and associated risk factors in Jimma town. Purposive sampling technique was used to collect 112 fecal samples from diarrheic calves. Conventional culture and biochemical methods were conducted to isolate E. coli isolates. Molecular method was followed to identify virulence factors of pathogenic E. coli strains. Antimicrobial sensitivity patterns of the isolates were tested using the Kirby–Bauer disk diffusion method. A structured questionnaire was also used to collect information from dairy farms and socio-demographic data. The overall isolation rate of E. coli in calves was 51.8% (58/112) (95% CI 42.0–61.0). The occurrence of the bacterium differed significantly by age, colostrum feeding time, amount of milk given per time and navel treatment (P

Abstract Background In Ethiopian folk medicine, there is a claim that medicinal plants can treat urolithiasis although there is insufficient scientific evidence. The objective of this study was to evaluate the curative efficacy of Gomphocarpus fruticosus extracts in experimentally induced nephrolithiatic rats. Methods Urolithiasis was induced in male Wistar rats by feeding ethylene glycol in drinking water for 28 days. The curative effects were evaluated after oral administrations of 200 mg/kg of the extracts from 15 to 28 days. Urine samples were collected 1 day before sacrificing the rats. Blood, liver and kidney samples were gathered under anaesthetic condition at day 28. Crystals in the urine were also analyzed by light microscopy. Results G. fruticosus EtOAc extract reduced significantly the level of sodium (P

Background: Breast cancer (BC) is the most common type of cancer in Ethiopia. The incidence of BC is also rising, but the exact figure is still poorly known. Therefore, this study was conducted to address the gap in epidemiological data on BC in southern and southwestern Ethiopia. Materials and Methods: This is a five-year (2015–2019) retrospective study. The demographic and clinicopathological data were collected from biopsy reports of different kinds of breast carcinomas in the pathology department of Jimma University Specialized Hospital and Hawassa University Specialized Referral Hospital. Histopathological grades and stages were conducted using Nottingham grading and TNM staging system, respectively. Collected data were entered and analyzed using SPSS Version-20 software. Results: The mean age of patients at diagnosis was 42.27 (SD = 13.57) years. The pathological stage of most BC patients was stage III, and most of them had tumor sizes greater than 5 cm. Most patients had moderately differentiated tumor grade, and mastectomy was the most common type of surgery at the time of diagnosis. Invasive ductal carcinoma was the most common histological type of BC, followed by invasive lobular carcinoma. Lymph node involvement was seen in 60.5% of cases. Lymph node involvement was associated with tumor size (χ2 = 8.55, p = 0.033) and type of surgery (χ2 = 39.69, p < 0.001). Conclusions: This study showed that BC patients in southern and southwestern Ethiopia displayed advanced pathological stages, relatively young age at diagnosis, and predominant invasive ductal carcinoma histological patterns.

Attributable to their major function in pathogen recognition, the use of bovine leukocyte antigens (BoLA) as disease markers in immunological traits in cattle is well established. However, limited report exists on polymorphism of the BoLA gene in zebu cattle breeds by high resolution typing methods. Thus, we used a polymerase chain reaction sequence-based typing (PCR-SBT) method to sequence exon 2 of the BoLA class II DRB3 gene from 100 animals (Boran, n = 13; Sheko, n = 20; Fogera, n = 16; Horro, n = 19), Hanwoo cattle (n = 18) and Bangladesh Red Chittagong zebu (n = 14). Out of the 59 detected alleles, 43 were already deposited under the Immuno Polymorphism Database for major histocompatibility complex (IPD-MHC) while 16 were unique to this study. Assessment of the level of genetic variability at the population and sequence levels with genetic distance in the breeds considered in this study showed that Zebu breeds had a gene diversity score greater than 0.752, nucleotide diversity score greater than 0.152, and mean number of pairwise differences higher than 14, being very comparable to those investigated for other cattle breeds. Regarding neutrality tests analyzed, we investigated that all the breeds except Hanwoo had an excess number of alleles and could be expected from a recent population expansion or genetic hitchhiking. Howbeit, the observed heterozygosity was not significantly (p < 0.05) higher than the expected heterozygosity. The Hardy Weinberg equilibrium (HWE) analysis revealed non-significant excess of heterozygote animals, indicative of plausible over-dominant selection. The pairwise FST values suggested a low genetic variation among all the breeds (FST = 0.056; p < 0.05), besides the rooting from the evolutionary or domestication history of the cattle. No detached clade was observed in the evolutionary divergence study of the BoLA-DRB3 gene, inferred from the phylogenetic tree based on the maximum likelihood model. The investigation herein indicated the clear differences in BoLA-DRB3 gene variability between African and Asian cattle breeds.

Abstract Podoconiosis, a debilitating lymphoedema of the leg, results from barefoot exposure to volcanic clay soil in genetically susceptible individuals. A previous genome-wide association study (GWAS) conducted in the Wolaita ethnic group from Ethiopia showed association between single nucleotide polymorphisms (SNPs) in the HLA class II region and podoconiosis. We aimed to conduct a second GWAS in a new sample (N = 1892) collected from the Wolaita and two other Ethiopian populations, the Amhara and the Oromo, also affected by podoconiosis. Fourteen SNPs in the HLA class II region showed significant genome-wide association (P

Diarrheagenic Escherichia coli strains are an essential cause of diarrheal infection in younger children and animals. The study was focused on understanding the associated characteristics of various DEC strains among children and calves, establishing the possible zoonotic transmission, and determining their antibiotic resistance patterns. Samples from 144 acute diarrheic children and 50 diarrheic calves were collected and processed using traditional culture methods. The molecular identification of pathotypes was completed using primer-specific polymerase chain reaction (PCR) targeting ten virulence genes (stx1, stx2, eae, aatA, lt, st, ial, hlyA bfpA, and daaE) related to six DEC pathotypes (EPEC, ETEC, EHEC, EAEC EIEC, and DAEC). The antimicrobial susceptibility testing was carried out using the Kirby-Bauer disk diffusion method. Colonies from 74 study subjects (54 diarrheic children and 20 diarrheic calves) were positive for E. coli isolates. Subsequent PCR detection discovered that 77% of children and 85% of calves’ isolates were positive for one or more virulence genes typical of particular strains. Among those ETEC [(18%), (26%)] is being the maximum predominant, and [(15%), (15%)] were positive for STEC, [(13%), (8%)] for atypical EPEC, [(6%), (7%)] for EHEC, [(6%), (5%)] for EAEC, and [(6%), (4%)] for EIEC strains in children’s and calves, respectively. Of the identified E. coli isolates, about 29% were found to be hybrid isolates. ETEC (66.7%) and STEC (58.9%) strains showed a better detection rate in contact children with diarrheic calves than children with no contacts. Most antibiotic resistances were obtained towards amoxicillin (64.9%), gentamycin (56.8%), and ampicillin (54.1%). Up to sixty-five percent of isolates were resistant to a minimum of three categories of antibiotics. This is the primary report on the wide occurrence of the six-diarrheagenic Escherichia coli strains, and ETEC was found to be the predominant pathotype among children and contact calves in Ethiopia.

Introduction. Pathogenic Escherichia coli strains cause diarrheal infection in children due to their virulence factors. A nonanalytical observational study followed by a purposive sampling technique was conducted from October 2017 to June 2018, to determine the antimicrobial susceptibility patterns and molecularly detect pathogenic Escherichia coli strains in under-five children at Wolaita Sodo town using molecular and the Kirby-Bauer disc diffusion method. Result. In the current investigation, out of 110 stool samples, Escherichia coli was isolated in 68 (61.8%) (95% CI: 52.1–70.9%). Out of 68 Escherichia coli isolates, 61.9% of Escherichia coli isolates were resistant, 9.4% were intermediately resistant, and 28.7% were susceptible. Among the antimicrobial agents, 91.2% of Escherichia coli isolates were highly sensitive to ciprofloxacin followed by norfloxacin (86.8%). Virulence genes were detected in 55.9% (38/68) (95% CI 52.1%–70.9%) of isolates. The following genes were detected: stx1 (6 (8.8%)), stx2 (4 (5.9%)), eaeA (5 (7.4%)), eaat (14 (20.5%)), and St (4 (5.9%)). Out of 68 Escherichia coli isolates, 43 (63.2%) isolates had shown multidrug resistance patterns. Furthermore, 11.8% of Escherichia coli isolates had shown resistance to eight different drugs. The multidrug resistance index value of Diarrheagenic Escherichia coli pathotypes was greater than or equal to 0.4, which indicates the high risk of resistance. Conclusion. This study demonstrated important pathogenic Escherichia coli strains and multidrug resistance in isolates containing virulence genes. Wise use of antimicrobials and improving the hygienic practices amongst parents of children reduce its occurrence. Therefore, appropriate usage of antimicrobial agents should also be highly practiced in hospitals.

Different E. coli pathotypes are common zoonotic agents. Some of these pathotypes cause recurrent and widespread calf diarrhea and contribute to significant economic losses in the livestock sector worldwide in addition to putting humans at risk. Here, we investigated the occurrence of E. coli pathotypes in diarrheic calves in Ethiopia kept under various calf management practices. One hundred fecal samples were collected from diarrheic calves in 98 different farms. E. coli was isolated in the samples from 99 of the diarrheic calves, and virulence genes were detected in 80% of the samples. The occurrence of E. coli pathotypes in the samples was 32% ETEC, 23% STEC, 18% STEC/ETEC, 3% EPEC, 2% EAEC, and 1% EHEC. No diarrheic calves were positive for the EIEC and DAEC pathotypes. The occurrence of pathotypes was positively associated with female calves (EPEC, p = 0.006), aged less than 2 weeks (STEC, p = 0.059), and calves fed colostrum via the hand method (STEC, p = 0.008 and EAEC, p = 0.003). This study revealed that several E. coli pathotypes occurred among calves affected with diarrhea. Moreover, the presence of a mixed STEC/ETEC pathotypes infection was present in the studied low-income setting. These findings indicate a considerable risk for the zoonotic transmission from calves to humans and the options to provide the better management for younger calves in order to reduce the economic loss.

Introduction: Achyranthes aspera, Chenopodium murale, Satureja punctata, Rumex abyssinicus and Aloe pulcherrima are traditionally used to treat urolithiasis in Ethiopia. However, there are limited reports on toxicity studies. Objective: This study was intended to evaluate the acute and sub-acute toxicity effects of plants. Materials and Methods: The crude extracts of A. aspera and C. murale leaves, S. punctata aerial parts, R. abyssinicus rhizomes, and A. Pulcherrima gel were prepared using 70 % ethanol. In acute toxicity, 125, 500 and 2000 mg/kg were tested in a stepwise manner; whereas 2000 mg/kg administrated to female rats using gavage during sub-acute toxicity. On day 14 and 28, blood samples were collected from retro-orbital sinus; liver and kidneys of each animal were collected under anaesthesia. Data were analyzed using one-way ANOVA, Dunnett's comparison test of the Graph Pad Prism. Results: No mortality and significant weight loss for all extracts in both toxicity tests. In acute toxicity, C. murale extract significantly reduced hemoglobin and platelets (P < 0.01) compared with the control. Likewise, S. punctata (P < 0.05) and R. abyssinicus (P < 0.01) extracts revealed significant reduction in platelet count. An exposure to C. murale and R. abyssinicus extracts reduced the concentrations of platelet distribution width and platelet larger cell ratio (p < 0.05) during sub-acute toxicity test. The level of creatinine reduced due to A. aspera extract administrations(P < 0.05). Liver histopathological examinations revealed focal periportal hepatitis following sub-acute toxicity test of C. murale. Histopathological studies of liver demonstrated that R. abyssinicus, A. aspera and S. punctata extracts showed mild acute liver injury. A. pulcherrima was not associated with any toxicity. Conclusion: C. murale extract showed hematological, and histopathological toxicity profiles in rats. Furthermore, chronic toxicity studies of A. aspera, S. punctata and R. abyssinicus extracts would be beneficial to ensure safety.

Abstract Background Cattle have been identified as a major reservoir of E. coli O157:H7 for human infection; the ecology of the organism in sheep and goats is less understood. This study was carried out to determine prevalence, source of infection, antibiotic resistance and molecular characterization of Escherichia coli O157: H7 isolated from sheep and goat. Methods Systematic random sampling was carried out at Modjo export abattoir, Ethiopia, from November 2012 to April 2013 to collect 408 samples from 72 sheep and 32 goats. Samples collected were skin swabs, fecal samples, intestinal mucosal swabs and the inside and outside part of carcasses as well as carcass in contacts such as workers hands, knife, hook and carcass washing water. Then, samples were processed following standard bacteriological procedures. Non-Sorbitol fermenting colonies were tested on latex agglutination test and the positives are subjected to PCR for detection of attaching and effacing genes (eaeA) and shiga toxin producing genes (stx1 and stx2). All E. coli O157:H7 isolates were checked for their susceptibility pattern towards 15 selected antibiotics. Results E. coli O157:H7 were detected in only 20/408 samples (4.9%). Among these 20 positive samples, 70% (14/20), 25% (5/20) and 5% (1/20) were from sheep, goats and knife samples, respectively. No significant associations were found between carcasses and the assumed sources of contaminations. Of all the 20 isolates virulence genes were found in 10 (50%) of them; 3 (15%) with only the eaeA gene and 7(35%) expressing eaeA and stx2 genes. All the isolates were susceptible to Norfloxacin (NOR) (100%). Conclusions The presence of virulence genes shows E. coli O157:H7 is a potential source of human infection in Ethiopia.

BackgroundEscherichia coli O157:H7 (E. coli O157:H7) is one of the most potent zoonotic pathogens that causes mild diarrhea and leads to hemolytic uremic syndrome or death. This study was aimed to assess the prevalence and determinants of E. coli O157:H7 related to diarrhea among under-five children with acute diarrhea.MethodsA cross-sectional study design was carried out in 2018 on 378 under-five-year children recruited randomly from hospitals in Eastern Ethiopia. Stool specimens were collected and processed using enrichment, differential and selective medium. Among isolates, E. coli O157:H7 was confirmed using latex test (Oxoid, Basingstoke, Hants, England). Factors associated with E. coli O157:H7 infection were identified using binary and multivariable logistic regression. Associations were reported by odds ratio with 95% confidence interval.ResultsThe prevalence of E. coli O157:H7 related diarrhea was 15.3% (95%CI: 11.8-19.5). The E. coli O157:H7 infection was positively associated with rural residence (AOR;3.75, 95%CI:1.26-11.20), consumption of undercooked meat (AOR;3.95, 95%CI: 1.23-12.67), raw vegetables and/or fruit juice (AOR;3.37, 95%CI:1.32-8.62), presence of bloody diarrhea (AOR;4.42, 95% CI:1.78-10.94), number of under-five children in a household (AOR;7.16, 95%CI: 2.90-17.70), presence of person with diarrhea in a household (AOR;4.22, 95% CI: 1.84-12.69), owning domestic animal (AOR;3.87, 95% CI: 1.48-10.12) and uneducated mother (AOR;3.14, 95%CI: 1.05-9.42).ConclusionThe Prevalence of E. coli O157:H7 related diarrhea among under-five children is relatively high in Eastern Ethiopia. The E. coli infection was associated with sanitation and hygiene in a household. Thus, education focused on food cooking and handling, child care, and household sanitation associated with animal manure in rural resident children are helpful in.

E. coli O157:H7 is one of the most virulent foodborne pathogens. The aim of this study was to isolate E. coli O157:H7, determine virulence genes carried by the organism, and assess the antimicrobial susceptibility pattern of the isolates from beef carcass samples at Bahir Dar city. Swab samples (n = 280) were collected from the carcass of cattle slaughtered at the abattoir and processed using sorbitol MacConkey agar supplemented with cefixime telluride and confirmed with latex agglutination test. A polymerase chain reaction was performed on isolates for the detection of virulence genes stx1, stx2, hlyA, and eae. Antimicrobial susceptibility testing was performed using the disk diffusion method. Of 280 samples processed, 25 (8.9%) isolates were positive. Out of 25 isolates subjected for molecular detection, 8 (32%) and 14 (56%) isolates possessed stx1 and stx2 genes, respectively; from those, 5 (20%) isolates had both genes for the production of Shiga toxins. Compared from other virulent genes relatively higher proportion of 18 (72%) isolates carried the hlyA gene. Only 5 (2%) isolates were positive for eae. Resistance was detected in all 25 (100%) isolates and 3 (12%) against clindamycin and trimethoprim, respectively. This study result highlights the potential threat to public health. The abattoir workers need to be aware about the pathogen and should follow appropriate practices to prevent contamination of meat intended for human consumption.

Salmonella is one of the most harmful pathogens responsible for foodborne outbreaks, illnesses and deaths. The aim of this study was to evaluate the effect of potentially probiotic strains against Salmonella Typhimurium DT104 in mice. The compatibility test among the selected potential probiotic strains (Lactobacillus plantarum K132, Lactobacillus paracasei K114 and Lactococcus lactis E124) using the cross-streaking method showed the absence of antagonism. The anti-Salmonella activities of coculture of the isolated potential probiotics in the form of mixed or single culture showed a remarkable anti-Salmonella activity with 96.50 to 100% growth inhibition. The combination of strains, which showed the highest growth inhibition rates against Salmonella Typhimurium DT104, was used to test their effect on the colonization of mice by Salmonella Typhimurium DT104. White albino male mice were pretreated with the mixed potential probiotics for 7 days and infected with Salmonella Typhimurium DT104 for 1 day. A total of 3 treatments were applied, during which the negative control group was treated with phosphate-buffered saline (PBS); a positive control group (typ) was challenged with Salmonella Typhimurium DT104 alone. The treated group (pro-typ) was pretreated with mixed potential probiotic culture and then infected with Salmonella Typhimurium DT104. The survival rate of mice and counts of Salmonella in feces were recorded. The survival rate of mice on day 21 after the oral challenge with Salmonella Typhimurium DT104 was significantly p

Viral infections are causing serious problems in human population worldwide. The recent outbreak of coronavirus disease 2019 caused by SARS-CoV-2 is a perfect example how viral infection could pose a great threat to global public health and economic sectors. Therefore, the first step in combating viral pathogens is to get a timely and accurate diagnosis. Early and accurate detection of the viral presence in patient sample is crucial for appropriate treatment, control, and prevention of epidemics. Here, we summarize some of the molecular and immunological diagnostic approaches available for the detection of viral infections of humans. Molecular diagnostic techniques provide rapid viral detection in patient sample. They are also relatively inexpensive and highly sensitive and specific diagnostic methods. Immunological-based techniques have been extensively utilized for the detection and epidemiological studies of human viral infections. They can detect antiviral antibodies or viral antigens in clinical samples. There are several commercially available molecular and immunological diagnostic kits that facilitate the use of these methods in the majority of clinical laboratories worldwide. In developing countries including Ethiopia where most of viral infections are endemic, exposure to improved or new methods is highly limited as these methods are very costly to use and also require technical skills. Since researchers and clinicians in all corners of the globe are working hard, it is hoped that in the near future, they will develop good quality tests that can be accessible in low-income countries.