Molecular screening and genetic diversity of tick-borne pathogens associated with dogs and livestock ticks in Egypt.

BACKGROUND: The Middle East and North Africa (MENA) offer optimal climatic conditions for tick reproduction and dispersal. Research on tick-borne pathogens in this region is scarce. Despite recent advances in the characterization and taxonomic explanation of various tick-borne illnesses affecting animals in Egypt, no comprehensive examination of TBP (tick-borne pathogen) statuses has been performed. Therefore, the present study aims to detect the prevalence of pathogens harbored by ticks in Egypt. METHODOLOGY/PRINCIPAL FINDINGS: A four-year PCR-based study was conducted to detect a wide range of tick-borne pathogens (TBPs) harbored by three economically important tick species in Egypt. Approximately 86.7% (902/1,040) of the investigated Hyalomma dromedarii ticks from camels were found positive with Candidatus Anaplasma camelii (18.8%), Ehrlichia ruminantium (16.5%), Rickettsia africae (12.6%), Theileria annulata (11.9%), Mycoplasma arginini (9.9%), Borrelia burgdorferi (7.7%), Spiroplasma-like endosymbiont (4.0%), Hepatozoon canis (2.4%), Coxiella burnetii (1.6%) and Leishmania infantum (1.3%). Double co-infections were recorded in 3.0% (27/902) of Hy. dromedarii ticks, triple co-infections (simultaneous infection of the tick by three pathogen species) were found in 9.6% (87/902) of Hy. dromedarii ticks, whereas multiple co-infections (simultaneous infection of the tick by ≥ four pathogen species) comprised 12% (108/902). Out of 1,435 investigated Rhipicephalus rutilus ticks collected from dogs and sheep, 816 (56.9%) ticks harbored Babesia canis vogeli (17.1%), Rickettsia conorii (16.2%), Ehrlichia canis (15.4%), H. canis (13.6%), Bo. burgdorferi (9.7%), L. infantum (8.4%), C. burnetii (7.3%) and Trypanosoma evansi (6.6%) in dogs, and 242 (16.9%) ticks harbored Theileria lestoquardi (21.6%), Theileria ovis (20.0%) and Eh. ruminantium (0.3%) in sheep. Double, triple, and multiple co-infections represented 11% (90/816), 7.6% (62/816), and 10.3% (84/816), respectively in Rh. rutilus from dogs, whereas double and triple co-infections represented 30.2% (73/242) and 2.1% (5/242), respectively in Rh. rutilus from sheep. Approximately 92.5% (1,355/1,465) of Rhipicephalus annulatus ticks of cattle carried a burden of Anaplasma marginale (21.3%), Babesia bigemina (18.2%), Babesia bovis (14.0%), Borrelia theleri (12.8%), R. africae (12.4%), Th. annulata (8.7%), Bo. burgdorferi (2.7%), and Eh. ruminantium (2.5%). Double, triple, and multiple co-infections represented 1.8% (25/1,355), 11.5% (156/1,355), and 12.9% (175/1,355), respectively. The detected pathogens' sequences had 98.76-100% similarity to the available database with genetic divergence ranged between 0.0001 to 0.0009% to closest sequences from other African, Asian, and European countries. Phylogenetic analysis revealed close similarities between the detected pathogens and other isolates mostly from African and Asian countries. CONCLUSIONS/SIGNIFICANCE: Continuous PCR-detection of pathogens transmitted by ticks is necessary to overcome the consequences of these infection to the hosts. More restrictions should be applied from the Egyptian authorities on animal importations to limit the emergence and re-emergence of tick-borne pathogens in the country. This is the first in-depth investigation of TBPs in Egypt.

Antimicrobial peptides in livestock: a review with a one health approach.

Antimicrobial peptides (AMPs), often referred to as nature's antibiotics, are ubiquitous in living organisms, spanning from bacteria to humans. Their potency, versatility, and unique mechanisms of action have garnered significant research attention. Unlike conventional antibiotics, peptides are biodegradable, adding to their appeal as potential candidates to address bacterial resistance in livestock farming-a challenge that has been under scrutiny for decades. This issue is complex and multifactorial, influenced by a variety of components. The World Health Organization (WHO) has proposed a comprehensive approach known as One Health, emphasizing the interconnectedness of human-animal-environment relationships in tackling such challenges. This review explores the application of AMPs in livestock farming and how they can mitigate the impact of this practice within the One Health framework.

Genomic epidemiology of Staphylococcus aureus from the Iberian Peninsula highlights the expansion of livestock associated-CC398 towards wildlife.

Staphylococcus aureus is a versatile pathobiont, exhibiting a broad host range, including humans, other mammals, and avian species. Host specificity determinants, virulence, and antimicrobial resistance genes are often shared by strains circulating at the animal-human interface. While transmission dynamics studies have shown strain exchange between humans and livestock, knowledge of the source, genetic diversification, and transmission drivers of S. aureus in wildlife lag behind. In this work, we explore a wide array of S. aureus genomes from different sources in the Iberian Peninsula to understand population structure, gene content and niche adaptation at the human-livestock-wildlife nexus. Through Bayesian inference, we address the hypothesis that S. aureus strains in wildlife originate from humanized landscapes, either from contact with humans or through interactions with livestock. Phylogenetic reconstruction applied to whole genome sequence data was completed with a dataset of 450 isolates featuring multiple clones from the 1990-2022 period and a subset of CC398 strains representing the 2008-2022 period. Phylodynamic signatures of S. aureus from the Iberian Peninsula suggest widespread circulation of most clones among humans before jumping to other hosts. The number of transitions of CC398 strains within each host category (human, livestock, wildlife) was high (88.26 %), while the posterior probability of transitions from livestock to wildlife was remarkably high (0.99). Microbial genome-wide association analysis did not evidence genome rearrangements nor biomarkers suggesting S. aureus niche adaptation to wildlife, thus supporting recent spill overs. Altogether, our findings indicate that S. aureus isolates collected in the past years from wildlife most likely represent multiple introduction events from livestock. The clonal origin of CC398 and its potential to disseminate and evolve through different animal host species are highlighted, calling for management practices at the livestock-wildlife axis to improve biosecurity and thus restrict S. aureus transmission and niche expansion along gradients of human influence.

Low-frequency transmission and persistence of antimicrobial-resistant bacteria and genes from livestock to agricultural soil and crops through compost application.

Livestock excrement is composted and applied to agricultural soils. If composts contain antimicrobial-resistant bacteria (ARB), they may spread to the soil and contaminate cultivated crops. Therefore, we investigated the degree of transmission of ARB and related antimicrobial resistance genes (ARGs) and, as well as clonal transmission of ARB from livestock to soil and crops through composting. This study was conducted at Rakuno Gakuen University farm in Hokkaido, Japan. Samples of cattle feces, solid and liquid composts, agricultural soil, and crops were collected. The abundance of Escherichia coli, coliforms, ß-lactam-resistant E. coli, and ß-lactam-resistant coliforms, as well as the copy numbers of ARG (specifically the bla gene related to ß-lactam-resistant bacteria), were assessed using qPCR through colony counts on CHROMagar ECC with or without ampicillin, respectively, 160 days after compost application. After the application of the compost to the soil, there was an initial increase in E. coli and coliform numbers, followed by a subsequent decrease over time. This trend was also observed in the copy numbers of the bla gene. In the soil, 5.0 CFU g-1 E. coli was detected on day 0 (the day post-compost application), and then, E. coli was not quantified on 60 days post-application. Through phylogenetic analysis involving single nucleotide polymorphisms (SNPs) and using whole-genome sequencing, it was discovered that clonal blaCTX-M-positive E. coli and blaTEM-positive Escherichia fergusonii were present in cattle feces, liquid compost, and soil on day 0 as well as 7 days post-application. This showed that livestock-derived ARB were transmitted from compost to soil and persisted for at least 7 days in soil. These findings indicate a potential low-level transmission of livestock-associated bacteria to agricultural soil through composts was observed at low frequency, dissemination was detected. Therefore, decreasing ARB abundance during composting is important for public health.

Tissue distribution of Coxiella burnetii and antibody responses in macropods co-grazing with livestock in Queensland, Australia.

Coxiella burnetii, the causative agent of Q fever, is a zoonotic bacteria of global public health significance. The organism has a complex, diverse, and relatively poorly understood animal reservoir but there is increasing evidence that macropods play some part in the epidemiology of Q fever in Australia. The aim of this cross-sectional survey was to estimate the animal- and tissue-level prevalence of coxiellosis amongst eastern grey (Macropus giganteus) and red (Osphranter rufus) kangaroos co-grazing with domestic cattle in a Q fever endemic area in Queensland. Serum, faeces and tissue samples from a range of organs were collected from 50 kangaroos. A total of 537 tissue samples were tested by real-time PCR, of which 99 specimens from 42 kangaroos (84% of animals, 95% confidence interval [CI], 71% to 93%) were positive for the C. burnetii IS1111 gene when tested in duplicate. Twenty of these specimens from 16 kangaroos (32%, 95% CI 20% to 47%) were also positive for the com1 or htpAB genes. Serum antibodies were present in 24 (57%, 95% CI 41% to 72%) of the PCR positive animals. There was no statistically significant difference in PCR positivity between organs and no single sample type consistently identified C. burnetii positive kangaroos. The results from this study identify a high apparent prevalence of C. burnetii amongst macropods in the study area, albeit seemingly with an inconsistent distribution within tissues and in relatively small quantities, often verging on the limits of detection. We recommend Q fever surveillance in macropods should involve a combination of serosurveys and molecular testing to increase chances of detection in a population, noting that a range of tissues would likely need to be sampled to confirm the diagnosis in a suspect positive animal.

Disposal and utilization of dead animals during breeding in livestock and poultry farming by means of synthetic microbiota.

The disposal of animal remains resulting from breeding is a significant challenge that impacts the industry's growth. To address the issues with current treatment methods, such as the large space required for corpse storage, and the high energy consumption of pyrolysis. Three strains with high protease and lipase production and one strain with high keratinase production were screened. The virulence genes were evaluated, the synthesis gene clusters of degrading enzymes were mined, secondary metabolites of each strain were analyzed, and the bacterial community with both growth rate and enzyme production ability was developed. Therefore, a microbial degradation method with mild reaction conditions and rapid liquefaction of animal residues was developed. The liquid degradation of four common farm-raised animal residues (sheep, cattle, chickens, and pigs) was tested under laboratory conditions. The results showed that the liquid degradation of animal residues was achieved within 144 h, transforming the months-long anaerobic process of traditional compost fermentation process into a mere 6 days' anaerobic process. N, P, K plant nutrients accounted for 15% of the total matrix, pH value was 5.5-6.7, heavy metal content was less than 0.2 mg L-1. Designed and improved fermentation equipment, produced a 3 m³ fermentation equipment, used in chicken, pig two types of animal residues pilot test. The emissions of greenhouse gases such as CO2 in the entire degradation process were 1.6 × 104 ppm, which was 481 times less than that of composting by 7.7 × 106. This study provides a solution for the treatment of dead livestock and poultry, which has promotional and practical value.

Zoonotic bacteria in the vicinity of animal farms as a factor disturbing the human microbiome: a review.

This review is aimed at summarizing the current state of knowledge about the relationship between environmental exposure to the bioaerosol emitted by intensive livestock farming and changes in the microbiome of people living in livestock farm vicinity. The PubMed, Scopus and Web of Science databases were searched by crossing keywords from the following 3 groups: a) "livestock," "animal farms," "animal breeding"; b) "microbiome," "resistome"; c) "livestock vicinity," "farm vicinity," "neighborhoods and health" in 2010-2022. Literature screening did not reveal any paper related to the full microbiome composition in the population studied. In the study, the authors included 7 papers (5 from the Netherlands, 1 from the USA, and 1 from China). The studies confirmed the carriage of Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), livestockassociated MRSA (LA-MRSA MC398) and multidrug-resistant S. aureus (MDRSA) in the nasal microbiome of adults and children living within 500-2000 m from a livestock farm. Clostridium difficile, including LA-ribotype RT078 carriage, was detected in the intestinal microbiome of adults living within 500-1000 m. Extended-spectrum ß-lactamase (ESBL) producing Enterobacteriaceae were confirmed in the intestinal microbiome of adults living within 500-6200 m. Knowledge on the composition of the microflora of people living in livestock farm vicinity is insufficient to conclude about changes in the microbiome caused by the environmental emission of bioaerosol. The carriage prevalence of the LA-bacteria, including both strains with antimicrobial resistance and antimicrobial resistance genes, confirms the presence of zoonotic bacteria in the human microflora in populations without occupational contact with animals. It cannot be ruled out that zoonotic bacteria, as a component of the microbiome, have a negative impact on people's health. Int J Occup Med Environ Health. 2024;37(2):138-52.

Tracing clinically-relevant antimicrobial resistances in Acinetobacter baumannii-calcoaceticus complex across diverse environments: A study spanning clinical, livestock, and wastewater treatment settings.

Acinetobacter baumannii has become a prominent nosocomial pathogen, primarily owing to its remarkable ability to rapidly acquire resistance to a wide range of antimicrobial agents and its ability to persist in diverse environments. However, there is a lack of data on the molecular epidemiology and its potential implications for public health of A. baumannii strains exhibiting clinically significant resistances that originate from non-clinical environments. Therefore, the genetic characteristics and resistance mechanisms of 80 A. baumannii-calcoaceticus (ABC) complex isolates, sourced from environments associated with poultry and pig production, municipal wastewater treatment plants (WWTPs), and clinical settings, were investigated. In total, our study classified 54 isolates into 29 previously described sequence types (STs), while 26 isolates exhibited as-yet-unassigned STs. We identified a broad range of A. baumannii STs originating from poultry and pig production environments (e.g., ST10, ST238, ST240, ST267, ST345, ST370, ST372, ST1112 according to Pasteur scheme). These STs have also been documented in clinical settings worldwide, highlighting their clinical significance. These findings also raise concerns about the potential zoonotic transmission of certain STs associated with livestock environments. Furthermore, we observed that clinical isolates exhibited the highest diversity of antimicrobial resistance genes (ARGs). In contrast to non-clinical isolates, clinical isolates typically carried a significantly higher number of ARGs, ranging from 10 to 15. They were also the exclusive carriers of biocide resistance genes and acquired carbapenemases (blaOXA-23, blaOXA-58, blaOXA-72, blaGIM-1, blaNDM-1). Additionally, we observed that clinical strains displayed an increased capacity for carrying plasmids and undergoing genetic transformation. This heightened capability could be linked to the intense selective pressures commonly found within clinical settings. Our study provides comprehensive insights into essential aspects of ABC isolates originating from livestock-associated environments and clinical settings. We explored their resistance mechanisms and potential implications for public health, providing valuable knowledge for addressing these critical issues.

Genomics to detect transmission of livestock-associated methicillin-resistant Staphylococcus aureus from UK pigs in abattoirs during slaughter.

BACKGROUND: Livestock-associated MRSA (LA-MRSA) transmission/cross-contamination can occur at abattoir through colonized pigs, increasing occupational hazards and health concerns for workers. To assess this risk we used genomics to identify LA-MRSA lineages present in batches of pigs sent to slaughter and distribution of clones. METHODS: WGS was performed on 85 LA-MRSA previously isolated from six abattoirs from 105 batches of pigs sent from 100 UK farms. spa typing and MLST were performed on all isolates. A mashtree tree was constructed to compare genomes of the LA-MRSA with 1281 global isolates from livestock and humans. A phylogenetic tree and pairwise SNP distance matrices were built from whole genomes of 109 isolates closest to those from abattoirs to compare evolutionary relationships and identify clones. RESULTS: All abattoir isolates belonged to CC398 and were mainly of spa type t011, although other spa types were present. Phylogenetic analysis confirmed the abattoir isolates were most closely related to each other and to pig LA-MRSA from across Europe, indicating a common evolutionary origin with related lineages colonizing UK pigs.Comparison of genomes using SNPs suggested between one and four clones were transferring between pigs from different batches. Transmission likely occurred on farm premises, during transportation, and/or within abattoirs through contact with contaminated surfaces in lairage or post-stunning. CONCLUSIONS: Genomics forensically identified related isolates/clones circulating in pigs at slaughter, showing contamination occurs often. Results suggest that further genomic tracking will identify hotspots, and improvements in measures such as biosecurity and disinfection will help reduce risk for workers.

An emerging zoonosis: molecular detection of multidrug-methicillin resistant Staphylococcus aureus from butchers' knives, livestock products and contact surfaces.

Methicillin-resistant Staphylococcus aureus (MRSA) transmission in livestock, community, and healthcare settings poses a significant public health concern both locally and globally. This study aimed to investigate the occurrence, molecular detection, and antibiogram of the MRSA strain in fresh beef, contact surfaces, and butchers' knives from the four major abattoirs (Karu, Gwagwalada, Deidei, and Kubwa) located in the Federal Capital Territory, Nigeria. A multi-stage sampling technique was used to collect 400 swab samples from butchers' knives (132), fresh beef (136), and contact surfaces (132). Presumptive colonies on mannitol salt agar were subjected to culture, isolation, and biotyping. The antibiogram was carried out via a Kirby-Bauer disk containing eight antibiotics. MRSA was phenotypically confirmed by oxacillin-resistant screening agar base (ORSAB) and genotypically by PCR to detect the presence of the mecA gene. Out of the 400 samples, 47.24% of fresh beef, 37% of contact surfaces, and 64.33% of butchers' knife swabs were Staphylococcus aureus positive. Thirty-two Staphylococcus aureus-positive isolates were confirmed to be MRSA, 50% fresh beef, 28.12% contact surfaces, and 21.87% butcher's knife swabs. MRSA isolates displayed multidrug-resistant traits, with a high resistance of 90.62% against cloxacillin, and a highest susceptibility of 100% to co-trimaxole. The antibiogram showed MRSA strains to be multidrug resistant. Molecular characterisation of the MRSA detected the presence of the mecA gene at a band size of 163 bp in all isolates. Strict hygiene of butchers, and working equipment in meat processing and marketing should be of top priority.

Molecular detection and characterization of Coxiella burnetii in aborted samples of livestock in China.

Coxiella burnetii is the causative agent of zoonotic Q fever. Animals are the natural reservoirs of C. burnetii, and domestic livestock represent the major sources of human infection. C. burnetii infection in pregnant females may causes abortion during late pregnancy, whereby massive shedding of C. burnetii with abortion products becomes aerosolized and persists in the environment. Therefore, monitoring and surveillance of this infection in livestock is important for the prevention of the C. burnetii transmission. Previous serological surveys have shown that C. burnetii infection is endemic in livestock in China. However, few data are available on the diagnosis of C. burnetii as a cause of abortion by molecular methods in livestock. To get a better understanding of the impact of C. burnetii infection on domestic livestock in China, a real-time PCR investigation was carried out on collected samples from different domestic livestock suffering abortion during 2021-2023. A total of 338 samples collected from eight herds of five livestock species were elected. The results showed that 223 (66 %) of the collected samples were positive for C. burnetii DNA using real-time PCR. For the aborted samples, 82 % (128/15) of sheep, 81 % (34/42) of goats, 44 % (15/34) of cattle, 69 % (18/26) of camels, and 50 % (17/34) of donkeys were positive for C. burnetii. Besides, 44 % (8/18) and 4 % (1/25) of asymptomatic individuals of sheep and donkey were also positive for C. burnetii. In addition, the positive samples were further confirmed by amplification and sequencing of the C. burnetii-specific isocitrate dehydrogenase (icd) gene. Phylogenetic analysis based on specific gene fragments of icd genes revealed that the obtained sequences in this study were clustered into two different groups associated with different origin of hosts and geographic regions. This is the first report confirming that C. burnetii exists in aborted samples of sheep, goats, cattle, donkeys and camels in China. Further studies are needed to fully elucidate the epidemiology of this pathogen in livestock as well as the potential risks to public health.

Multi-omics analyses reveal rumen microbes and secondary metabolites that are unique to livestock species.

Ruminant livestock, including cattle, sheep, goats, and camels, possess a distinctive digestive system with complex microbiota communities critical for feed conversion and secondary metabolite production, including greenhouse gases. Yet, there is limited knowledge regarding the diversity of rumen microbes and metabolites benefiting livestock physiology, productivity, climate impact, and defense mechanisms across ruminant species. In this study, we utilized metataxonomics and metabolomics data from four evolutionarily distinct livestock species, which had fed on diverse plant materials like grass, shrubs, and acacia trees, to uncover the unique signature microbes and secondary metabolites. We established the presence of a distinctive anaerobic fungus called Oontomyces in camels, while cattle exhibited a higher prevalence of unique microbes like Psychrobacter, Anaeromyces, Cyllamyces, and Orpinomyces. Goats hosted Cleistothelebolus, and Liebetanzomyces was unique to sheep. Furthermore, we identified a set of conserved core microbes, including Prevotella, Rickenellaceae, Cladosporium, and Pecoramyces, present in all the ruminants, irrespective of host genetics and dietary composition. This underscores their indispensable role in maintaining crucial physiological functions. Regarding secondary metabolites, camel's rumen is rich in organic acids, goat's rumen is rich in alcohols and hydrocarbons, sheep's rumen is rich in indoles, and cattle's rumen is rich in sesquiterpenes. Additionally, linalool propionate and terpinolene were uniquely found in sheep rumen, while valencene was exclusive to cattle. This may suggest the existence of species-specific microbes and metabolites that require host rumen-microbes' environment balance. These results have implications for manipulating the rumen environment to target specific microbes and secondary metabolite networks, thereby enhancing livestock productivity, resilience, reducing susceptibility to vectors, and environmentally preferred livestock husbandry.IMPORTANCERumen fermentation, which depends on feed components and rumen microbes, plays a crucial role in feed conversion and the production of various metabolites important for the physiological functions, health, and environmental smartness of ruminant livestock, in addition to providing food for humans. However, given the complexity and variation of the rumen ecosystem and feed of these various livestock species, combined with inter-individual differences between gut microbial communities, how they influence the rumen secondary metabolites remains elusive. Using metagenomics and metabolomics approaches, we show that each livestock species has a signature microbe(s) and secondary metabolites. These findings may contribute toward understanding the rumen ecosystem, microbiome and metabolite networks, which may provide a gateway to manipulating rumen ecosystem pathways toward making livestock production efficient, sustainable, and environmentally friendly.

Outbreak of Anthrax in Livestock with Human Occupational Exposures - Minnesota, 2023.

In July 2023, the Minnesota Department of Health (MDH) was notified of possible occupational exposures to anthrax during an outbreak in animals. In consultation with the Centers for Disease Control and Prevention, MDH epidemiologists created a questionnaire that assessed exposure risks and helped determine individual illness monitoring and antibiotic post-exposure prophylaxis needs. This investigation and the resources developed for it could be useful in future scenarios where there are occupational exposures to naturally occurring anthrax.

Spatial epidemiology of human anthrax in Son La province, Vietnam, 2003-2022.

AIMS: Anthrax is reported with frequency but poorly understood in Southeast Asian countries including Vietnam. In Vietnam, anthrax surveillance is national. However, case detection, prevention, and control are implemented locally at the provincial level. Here, we describe the epidemiological characteristics, identify spatial clusters of human anthrax, and compare the variation in livestock anthrax vaccine coverage to disease incidence in humans and livestock using historical data in Son La province, Vietnam (2003-2020). METHODS AND RESULTS: Most human cases occurred between April and September. Most of the patients were male, aged 15-54 years old. The human cases were mainly reported by public district hospitals. There was a delay between disease onset and hospitalization of ~5 days. We identified spatial clusters of high-high incidence communes in the northern communes of the province using the local Moran's I statistic. The vaccine coverage sharply decreased across the study period. The province reported sporadic human anthrax outbreaks, while animal cases were only reported in 2005 and 2022. CONCLUSIONS: These results suggest underreporting for human and livestock anthrax in the province. Intersectoral information sharing is needed to aid livestock vaccination planning, which currently relies on reported livestock cases. The spatial clusters identify areas for targeted surveillance and livestock vaccination, while the seasonal case data suggest prioritizing vaccination campaigns for February or early March ahead of the April peak. A regional approach for studying the role of livestock trading between Son La and neighbouring provinces in anthrax occurrence is recommended.

Epidemiology and zoonotic potential of Livestock-associated Staphylococcus aureus isolated at Tamil Nadu, India.

BACKGROUND: Staphylococcus aureus is part of normal flora and also an opportunistic pathogen responsible for a wide range of infections in both humans and animals. Livestock-associated S. aureus (LA-SA) has gained importance in recent years due to its increased prevalence in recent years, becoming a worry in public health view. This study aimed to study the epidemiology of LA-SA strains in Madurai district, Tamil Nadu, India. METHODS: A total of 255 samples were collected from bovine and other small ruminants like goats and sheep nares (n = 129 and n = 126 respectively). Nasal swab samples were collected from study animals with sterile sample collecting cotton swabs (Hi-Media, Mumbai). Samples were transported to the lab in Cary-Blair Transport media for further analysis. The samples were tested for S. aureus using antibiotic selection and PCR-based assays. The pathogenicity of the bacteria was assessed using chicken embryo models and liver cross-sections were used for histopathology studies. RESULTS: The prevalence rate in bovine-associated samples was 42.63% but relatively low in the case of small ruminants associated samples with 28.57% only. The overall prevalence of S. aureus is found to 35.6% and MRSA 10.98% among the study samples. The antibiogram results that LA-SA isolates were susceptible to aminoglycosides and tetracyclines but resistant to ß-lactam drugs. The biofilm formation results showed that the LA-SA isolates are weak to high-capacity biofilm formers. The enterotoxigenic patterns revealed that most of the isolated strains are enterotoxigenic and possess classical enterotoxins. The survival analysis of chicken embryos suggested that the Bovine-associated strains were moderately pathogenic. CONCLUSION: The study concluded that economically important livestock animals can act as reservoirs for multi-drug resistant and pathogenic which in-turn is a concern for public health as well as livestock health.

A scoping review of zoonotic parasites and pathogens associated with abattoirs in Eastern Africa and recommendations for abattoirs as disease surveillance sites.

Abattoirs are facilities where livestock are slaughtered and are an important aspect in the food production chain. There are several types of abattoirs, which differ in infrastructure and facilities, sanitation and PPE practices, and adherence to regulations. In each abattoir facility, worker exposure to animals and animal products increases their risk of infection from zoonotic pathogens. Backyard abattoirs and slaughter slabs have the highest risk of pathogen transmission because of substandard hygiene practices and minimal infrastructure. These abattoir conditions can often contribute to environmental contamination and may play a significant role in disease outbreaks within communities. To assess further the risk of disease, we conducted a scoping review of parasites and pathogens among livestock and human workers in abattoirs across 13 Eastern African countries, which are hotspots for zoonoses. Our search results (n = 104 articles) showed the presence of bacteria, viruses, fungi, and macroparasites (nematodes, cestodes, etc.) in cattle, goats, sheep, pigs, camels, and poultry. Most articles reported results from cattle, and the most frequent pathogen detected was Mycobacterium bovis, which causes bovine tuberculosis. Some articles included worker survey and questionnaires that suggested how the use of PPE along with proper worker training and safe animal handling practices could reduce disease risk. Based on these findings, we discuss ways to improve abattoir biosafety and increase biosurveillance for disease control and mitigation. Abattoirs are a 'catch all' for pathogens, and by surveying animals at abattoirs, health officials can determine which diseases are prevalent in different regions and which pathogens are most likely transmitted from wildlife to livestock. We suggest a regional approach to biosurveillance, which will improve testing and data gathering for enhanced disease risk mapping and forecasting. Next generation sequencing will be key in identifying a wide range of pathogens, rather than a targeted approach.

Multiple clonal transmissions of clinically relevant extended-spectrum beta-lactamase-producing Escherichia coli among livestock, dogs, and wildlife in Chile.

OBJECTIVES: Extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli) are a main cause of human deaths associated with antimicrobial resistance (AMR). Despite hundreds of reports of the faecal carriage of ESBL-E. coli in domestic and wild animals, the dynamics of its circulation remains poorly understood. METHODS: We used whole genome sequencing of 19 ESBL-E. coli previously isolated in the same local setting from dogs, livestock, and a wild rodent in Central Chile to assess potential cross-species transmission of ESBL-E. coli. RESULTS: Isolates harboured a large number of AMR (n = 95) and virulence (n = 45) genes, plasmids replicons (n = 24), and E. coli sequence types including top extraintestinal pathogenic E. coli ST410, ST58, ST88, and ST617. Almost identical clones (<50 single nucleotide polymorphisms difference, same antibiotic and heavy metal resistance genes, virulence genes, and plasmids) were found in faeces of dogs, cattle, or sheep from the same farm, and in a dog and a wild rodent living in proximity. CONCLUSIONS: To our knowledge, this is the first report of multiple clonal cross-species transmission of ESBL-E. coli in domestic and potentially wild animals of Latin America. Our results suggest that relatively rare spread of AMR across animal species can still occur by both clonal and plasmid dissemination. Our study highlights the need for establishing preventive measures to limit the circulation of these bacteria among animals in agricultural settings, particularly given the highly pathogenic profile of several E. coli strains detected in these animals.

Epidemiological connectivity between humans and animals across an urban landscape.

Urbanization is predicted to be a key driver of disease emergence through human exposure to novel, animal-borne pathogens. However, while we suspect that urban landscapes are primed to expose people to novel animal-borne diseases, evidence for the mechanisms by which this occurs is lacking. To address this, we studied how bacterial genes are shared between wild animals, livestock, and humans (n = 1,428) across Nairobi, Kenya-one of the world's most rapidly developing cities. Applying a multilayer network framework, we show that low biodiversity (of both natural habitat and vertebrate wildlife communities), coupled with livestock management practices and more densely populated urban environments, promotes sharing of Escherichia coli-borne bacterial mobile genetic elements between animals and humans. These results provide empirical support for hypotheses linking resource provision, the biological simplification of urban landscapes, and human and livestock demography to urban dynamics of cross-species pathogen transmission at a landscape scale. Urban areas where high densities of people and livestock live in close association with synanthropes (species such as rodents that are more competent reservoirs for zoonotic pathogens) should be prioritized for disease surveillance and control.

Neglected Drivers of Antibiotic Resistance: Survival of Extended-Spectrum ß-Lactamase-Producing Pathogenic Escherichia coli from Livestock Waste through Dormancy and Release of Transformable Extracellular Antibiotic Resistance Genes under Heat Treatment.

Extended-spectrum ß-lactamase (ESBL)-producing Enterobacteriaceae has caused a global pandemic with high prevalence in livestock and poultry, which could disseminate into the environment and humans. To curb this risk, heat-based harmless treatment of livestock waste was carried out. However, some risks of the bacterial persistence have not been thoroughly assessed. This study demonstrated that antibiotic-resistant bacteria (ARB) could survive at 55 °C through dormancy, and simultaneously transformable extracellular antibiotic resistance genes (eARGs) would be released. The ESBL-producing pathogenic Escherichia coli CM1 from chicken manure could enter a dormant state at 55 °C and reactivate at 37 °C. Dormant CM1 had stronger ß-lactam resistance, which was associated with high expression of ß-lactamase genes and low expression of outer membrane porin genes. Resuscitated CM1 maintained its virulence expression and multidrug resistance and even had stronger cephalosporin resistance, which might be due to the ultra-low expression of the porin genes. Besides, heat at 55 °C promoted the release of eARGs, some of which possessed a certain nuclease stability and heat persistence, and even maintained their transformability to an Acinetobacter baylyi strain. Therefore, dormant multidrug-resistant pathogens from livestock waste will still pose a direct health risk to humans, while the resuscitation of dormant ARB and the transformation of released eARGs will jointly promote the proliferation of ARGs and the spread of antibiotic resistance.

Prevalence and Load of the Campylobacter Genus in Infants and Associated Household Contacts in Rural Eastern Ethiopia: a Longitudinal Study from the Campylobacter Genomics and Environmental Enteric Dysfunction (CAGED) Project.

In our previous cross-sectional study, multiple species of Campylobacter were detected (88%) in stool samples from children (12 to 14 months of age) in rural eastern Ethiopia. This study assessed the temporal fecal carriage of Campylobacter in infants and identified putative reservoirs associated with these infections in infants from the same region. The prevalence and load of Campylobacter were determined using genus-specific real-time PCR. Stool samples from 106 infants (n = 1,073) were collected monthly from birth until 376 days of age (DOA). Human stool samples (mothers and siblings), livestock feces (cattle, chickens, goats, and sheep), and environmental samples (soil and drinking water) from the 106 households were collected twice per household (n = 1,644). Campylobacter was most prevalent in livestock feces (goats, 99%; sheep, 98%; cattle, 99%; chickens, 93%), followed by human stool samples (siblings, 91%; mothers, 83%; infants, 64%) and environmental samples (soil, 58%; drinking water, 43%). The prevalence of Campylobacter in infant stool samples significantly increased with age, from 30% at 27 DOA to 89% at 360 DOA (1% increase/day in the odds of being colonized) (P < 0.001). The Campylobacter load increased linearly (P < 0.001) with age from 2.95 logs at 25 DOA to 4.13 logs at 360 DOA. Within a household, the Campylobacter load in infant stool samples was positively correlated with the load in mother stool samples (r2 = 0.18) and soil collected inside the house (r2 = 0.36), which were in turn both correlated with Campylobacter loads in chicken and cattle feces (0.60 < r2 < 0.63) (P < 0.01). In conclusion, a high proportion of infants are infected with Campylobacter in eastern Ethiopia, and contact with the mother and contaminated soil may be associated with early infections. IMPORTANCE A high Campylobacter prevalence during early childhood has been associated with environmental enteric dysfunction (EED) and stunting, especially in low-resource settings. Our previous study demonstrated that Campylobacter was frequently found (88%) in children from eastern Ethiopia; however, little is known about potential Campylobacter reservoirs and transmission pathways leading to infection of infants by Campylobacter during early growth. In the longitudinal study presented here, Campylobacter was frequently detected in infants within the 106 surveyed households from eastern Ethiopia, and the prevalence was age dependent. Furthermore, preliminary analyses highlighted the potential role of the mother, soil, and livestock in the transmission of Campylobacter to the infant. Further work will explore the species and genetic composition of Campylobacter in infants and putative reservoirs using PCR and whole-genome and metagenomic sequencing. The findings from these studies can lead to the development of interventions to minimize the risk of transmission of Campylobacter to infants and, potentially, EED and stunting.