Whole-Genome Comparisons of Staphylococcus agnetis Isolates from Cattle and Chickens

Bacterial chondronecrosis with osteomyelitis lameness in broiler chickens and its implications for welfare, meat safety, and quality: a review

The exponential increase in global population continues to present an ongoing challenge for livestock producers worldwide to consistently provide a safe, high-quality, and affordable source of protein for consumers. In the last 50 years, the poultry industry has spearheaded this effort thanks to focused genetic and genomic selection for feed-efficient, high-yielding broilers. However, such intense selection for productive traits, along with conventional industry farming practices, has also presented the industry with a myriad of serious issues that negatively impacted animal health, welfare, and productivity-such as woody breast and virulent diseases commonly associated with poultry farming. Bacterial chondronecrosis with osteomyelitis (BCO) lameness is one such issue, having rapidly become a key issue affecting the poultry industry with serious impacts on broiler welfare, meat quality, production, food safety, and economic losses since its discovery in 1972. This review focuses on hallmark clinical symptoms, diagnosis, etiology, and impact of BCO lameness on key issues facing the poultry industry.

Evaluating the Impact of the PoultryStar®Bro Probiotic on the Incidence of Bacterial Chondronecrosis with Osteomyelitis Using the Aerosol Transmission Challenge Model

Bacterial chondronecrosis with osteomyelitis (BCO) lameness is a major welfare issue for broiler production worldwide affecting approximately 1.5% of broilers over 42 days old. Excessive body weight gain causes mechanical stress on long bones, leading to micro-fractures. This condition induces a bacterial infection of fractures, resulting in bone necrosis and eventual BCO lameness. Increasing gut integrity and supporting Calcium metabolism contribute to the optimal bone structure and subsequently reduce BCO lameness. Probiotics thus provide an excellent strategy for alleviating BCO due to the improvement of intestinal integrity and barrier function. Accordingly, the present study investigated the lameness reduction through the feed supplementation of a selected probiotic. Broiler chickens were assigned to three treatments, including a control litter group (FL), a PoultryStar®Bro probiotic fed group (BRO), and a control wire-flooring group (CW) designed to induce BCO lameness. The probiotic significantly decreased lameness by 46% compared to the control group (p < 0.05). The most predominant bacteria identified from the BCO lesions were Staphylococcus cohnii and Staphylococcus lentus. Moreover, significant increments of tight junction gene expression in jejunum and ileum, plus numerical improvements of body weight gain (BW; +360 g) and feed conversion ratio (FCR; -12 pts) were observed in BRO-supplemented birds.

Phylogenomic Analyses of Three Distinct Lineages Uniting Staphylococcus cohnii and Staphylococcus urealyticus from Diverse Hosts

We sequenced and assembled genomes for 17 isolates of Staphylococcus cohnii isolated from osteomyelitis lesions in young broilers from two separate experiments where we induced lameness using a hybrid wire-litter flooring system. Whole genome comparisons using three different methods support a close relationship of genomes from both S. cohnii and Staphylococcus urealyticus. The data support three different lineages, which we designated as Lineage 1, Lineage 2, and Lineage 3, uniting these two species within an evolving complex. We present evidence for horizontal transfer between lineages of genomic regions from 50-440 kbp. The transfer of a 186 kbp region from Lineage 1 to Lineage 2 appears to have generated Lineage 3. Human-associated isolates appear to be limited to Lineages 2 and 3 but Lineage 2 appears to contain a higher number of human pathogenic isolates. The chicken isolates from our lameness trials included genomically diverse isolates from both Lineage 1 and 2, and isolates from both lineages were obtained from osteomyelitis lesions of individual birds. Our results expand the diversity of Staphylococci associated with osteomyelitis in poultry and suggest a high diversity in the microbiome of day-old chicks. Our data also support a reevaluation and unification of the taxonomic classifications of S. cohnii and S. urealyticus.

Staphylococcal mastitis in dairy cows

Bovine mastitis is one of the most common diseases of dairy cattle. Even though different infectious microorganisms and mechanical injury can cause mastitis, bacteria are the most common cause of mastitis in dairy cows. Staphylococci, streptococci, and coliforms are the most frequently diagnosed etiological agents of mastitis in dairy cows. Staphylococci that cause mastitis are broadly divided into Staphylococcus aureus and non-aureus staphylococci (NAS). NAS is mainly comprised of coagulase-negative Staphylococcus species (CNS) and some coagulase-positive and coagulase-variable staphylococci. Current staphylococcal mastitis control measures are ineffective, and dependence on antimicrobial drugs is not sustainable because of the low cure rate with antimicrobial treatment and the development of resistance. Non-antimicrobial effective and sustainable control tools are critically needed. This review describes the current status of S. aureus and NAS mastitis in dairy cows and flags areas of knowledge gaps.

Deoxynivalenol and fumonisin predispose broilers to bacterial chondronecrosis with osteomyelitis lameness

Bacterial chondronecrosis with osteomyelitis (BCO) lameness is the most critical animal health and welfare issue facing the broiler industry worldwide. It is estimated that 1 to 2% of bird condemnation at marketing age is caused by BCO lameness, resulting in tens of millions of dollars in annual losses. Fast-growing broilers are prone to mechanical stress that triggers bacterial translocation across epithelial barriers into the bloodstream, followed by bacterial colonization in the growth plate of long bones, and eventually, bone necrosis and lameness. Mycotoxins (MTX) are secondary metabolites produced naturally by microfungi, of which deoxynivalenol (DON), fumonisin (FUM), and zearalenone are the most prevalent in corn and soybean-meal-based diets. The presence of these mycotoxins in feed has been proven to reduce the barrier strength of the intestinal tracts and trigger immunosuppressive effects. In this study, we investigated the effects of the DON and FUM-contaminated feeds on the incidence of BCO lameness in broilers reared in both wire- and litter-floors. 720 one-day-old broiler chicks were assigned to the 2 × 2 factorial design: 2 MTX diets containing DON and FUM on wire flooring (MTX-W) and litter flooring (MTX-L), and 2 diets without MTX contamination on control wire flooring (CW) and control litter flooring (CL). Throughout the trial, the cumulative incidence of lameness per treatment was assessed by necropsying the lame birds. Birds in the MTX-W group had a higher incidence of lameness compared to those in CW (73.3% vs. 62.0%) (P < 0.05), and birds in the MTX-L group had a higher incidence of lameness compared to birds in CL (54.0% vs. 34.0%) (P < 0.05). MTX elicited net increases in BCO to a greater degree on litter (+20%) than on wire flooring (+12%). The increased incidence of BCO lameness in the MTX-W coincided with increased intestinal permeability supporting a correlation between intestinal barrier integrity and BCO lameness. To conclude, DON and FUM are predisposing factors for increasing BCO. However, no significant interaction exists between the diet and floor types in inducing lameness in broilers.

Inducing experimental bacterial chondronecrosis with osteomyelitis lameness in broiler chickens using aerosol transmission model

Lameness disease attributed to bacterial chondronecrosis with osteomyelitis in broilers affects production, animal welfare, and food safety in the poultry industry. The disease is characterized by necrotic degeneration of the rapidly growing femora and tibiae due to bacterial translocation from the respiratory or gastrointestinal tracts into the blood circulation, eventually colonizing the growth plate of the long bones. To investigate the etiology, pathogenesis, and intervention measures for BCO, developing an experimental model that reliably induces BCO lameness is of the utmost importance. In the past, we have employed a wire-flooring model and a litter-flooring model administered with a bacterial challenge to investigate strategies for mitigating BCO. However, multiple issues on labor-intensive barn setup and cleanout efforts for the wire-flooring system and concern of direct pathogenic exposure to the broilers for the litter-flooring models rendered these research models less effective. Thus, we investigated a new approach to induce experimental BCO lameness using an aerosol transmission model employing a group of birds reared on wire-flooring pens as a BCO infection source, and the disease is further disseminated through the airborne transmission to other birds reared on litter flooring in the same housing environment. The effectiveness of the aerosol transmission model in inducing BCO lameness was concluded from 4 independent experiments. The cumulative lameness generated from the BCO source group on the wire floors versus negative control treatments on the litter floors from Experiments 1, 2, 3, and 4 were 84% vs. 69.33%, P = 0.09; 54.55% vs. 60%, P = 0.56; 78% vs. 73.50%, P = 0.64; 81% vs. 74.50%, P = 0.11. Overall, the cumulative lameness generated from the wire floors was successfully transmitted to the birds on litter floors without significant statistical differences (P > 0.05). The effectiveness of the aerosol transmission model for experimentally triggering BCO lameness provides a reliable system for evaluating practical intervention strategies for BCO lameness in broilers.

Virulence Mechanisms of Staphylococcal Animal Pathogens

Staphylococci are major causes of infections in mammals. Mammals are colonized by diverse staphylococcal species, often with moderate to strong host specificity, and colonization is a common source of infection. Staphylococcal infections of animals not only are of major importance for animal well-being but have considerable economic consequences, such as in the case of staphylococcal mastitis, which costs billions of dollars annually. Furthermore, pet animals can be temporary carriers of strains infectious to humans. Moreover, antimicrobial resistance is a great concern in livestock infections, as there is considerable antibiotic overuse, and resistant strains can be transferred to humans. With the number of working antibiotics continuously becoming smaller due to the concomitant spread of resistant strains, alternative approaches, such as anti-virulence, are increasingly being investigated to treat staphylococcal infections. For this, understanding the virulence mechanisms of animal staphylococcal pathogens is crucial. While many virulence factors have similar functions in humans as animals, there are increasingly frequent reports of host-specific virulence factors and mechanisms. Furthermore, we are only beginning to understand virulence mechanisms in animal-specific staphylococcal pathogens. This review gives an overview of animal infections caused by staphylococci and our knowledge about the virulence mechanisms involved.

Horizontal transfer of probable chicken-pathogenicity chromosomal islands between Staphylococcus aureus and Staphylococcus agnetis

Staphylococcus agnetis is an emerging pathogen in chickens but has been most commonly isolated from sub-clinical mastitis in bovines. Previous whole-genome analyses for known virulence genes failed to identify determinants for the switch from mild ductal infections in cattle to severe infections in poultry. We now report identification of a family of 15 kbp, 17-19 gene mobile genetic elements (MGEs) specific to chicken osteomyelitis and dermatitis isolates of S. agnetis. These MGEs can be present in multiple copies per genome. The MGE has been vectored on a Staphylococcus phage that separately lysogenized two S. agnetis osteomyelitis strains. The S. agnetis genome from a broiler breeder case of ulcerative dermatitis contains 2 orthologs of this MGE, not associated with a prophage. BLASTn and phylogenetic analyses show that there are closely related intact MGEs found in genomes of S. aureus. The genome from a 1980s isolate from chickens in Ireland contains 3 copies of this MGE. More recent chicken isolates descended from that genome (Poland 2009, Oklahoma 2010, and Arkansas 2018) contain 2 to 4 related copies. Many of the genes of this MGE can be identified in disparate regions of the genomes of other chicken isolates of S. aureus. BLAST searches of the NCBI databases detect no similar MGEs outside of S. aureus and S. agnetis. These MGEs encode no proteins related to those produced by Staphylococcus aureus Pathogenicity Islands, which have been associated with the transition of S. aureus from human to chicken hosts. Other than mobilization functions, most of the genes in these new MGEs annotate as hypothetical proteins. The MGEs we describe appear to represent a new family of Chromosomal Islands (CIs) shared amongst S. agnetis and S. aureus. Further work is needed to understand the role of these CIs/MGEs in pathogenesis. Analysis of horizontal transfer of genetic elements between isolates and species of Staphylococci provides clues to evolution of host-pathogen interactions as well as revealing critical determinants for animal welfare and human diseases.

Staphylococcus spp. Causatives of Infections and Carrier of blaZ, femA, and mecA Genes Associated with Resistance

Staphylococcus spp. have been associated with cases of healthcare associated infections due to their high incidence in isolates from the hospital environment and their ability to cause infections in immunocompromised patients; synthesize biofilms on medical instruments, in the case of negative coagulase species; and change in genetic material, thus making it possible to disseminate genes that code for the acquisition of resistance mechanisms against the action of antibiotics. This study evaluated the presence of blaZ, femA, and mecA chromosomal and plasmid genes of Staphylococcus spp. using the qPCR technique. The results were associated with the phenotypic expression of resistance to oxacillin and penicillin G. We found that the chromosomal femA gene was present in a greater proportion in S. intermedius when compared with the other species analyzed, while the plasmid-borne mecA gene was prevalent in the S. aureus samples. The binary logistic regression performed to verify the association among the expression of the genes analyzed and the acquisition of resistance to oxacillin and penicillin G were not significant in any of the analyses, p > 0.05.

Genomic Characterization and Antimicrobial Susceptibility of Dromedary-Associated Staphylococcaceae from the Horn of Africa

Members of the Staphylococcaceae family, particularly those of the genus Staphylococcus, encompass important human and animal pathogens. We collected and characterized Staphylococcaceae strains from apparently healthy and diseased camels (n = 84) and cattle (n = 7) in Somalia and Kenya. We phenotypically characterized the strains, including their antimicrobial inhibitory concentrations. Then, we sequenced their genomes using long-read sequencing, closed their genomes, and subsequently compared and mapped their virulence- and resistance-associated gene pools. Genome-based phylogenetics revealed 13 known Staphylococcaceae and at least two novel species. East African strains of different species encompassed novel sequence types and phylogenetically distant clades. About one-third of the strains had non-wild-type MICs. They were resistant to at least one of the following antimicrobials: tetracycline, benzylpenicillin, oxacillin, erythromycin, clindamycin, trimethoprim, gentamicin, or streptomycin, encoded by tet(K), blaZ/bla_ARL, mecA/mecA1, msrA/mphC, salA, dfrG, aacA-aphD, and str, respectively. We identified the first methicillin- and multidrug-resistant camel S. epidermidis strain of sequence type (ST) 1136 in East Africa. The pool of virulence-encoding genes was largest in the S. aureus strains, as expected, although other rather commensal strains contained distinct virulence-encoding genes. We identified toxin-antitoxin (TA) systems such as the hicA/hicB and abiEii/abiEi families, reported here for the first time for certain species of Staphylococcaceae. All strains contained at least one intact prophage sequence, mainly belonging to the Siphoviridae family. We pinpointed potential horizontal gene transfers between camel and cattle strains and also across distinct Staphylococcaceae clades and species. IMPORTANCE Camels are a high value and crucial livestock species in arid and semiarid regions of Africa and gain importance giving the impact of climate change on traditional livestock species. Our current knowledge with respect to Staphylococcaceae infecting camels is very limited compared to that for other livestock species. Better knowledge will foster the development of specific diagnostic assays, guide promising antimicrobial treatment options, and inform about potential zoonotic risks. We characterized 84 Staphylococcaceae strains isolated from camels with respect to their antimicrobial resistance and virulence traits. We detected potentially novel Staphylococcus species, resistances to different classes of antimicrobials, and the first camel multidrug-resistant S. epidermidis strain of sequence type 1136.

Staphylococcus ratti sp. nov. Isolated from a Lab Rat

Staphylococci from the Staphylococcus intermedius-Staphylococcus hyicus species group include numerous animal pathogens and are an important reservoir of virulence and antimicrobial resistance determinants. Due to their pathogenic potential, they are possible causative agents of zoonoses in humans; therefore, it is important to address the properties of these strains. Here we used a polyphasic taxonomic approach to characterize the coagulase-negative staphylococcal strain NRL/St 03/464^T, isolated from the nostrils of a healthy laboratory rat during a microbiological screening of laboratory animals. The 16S rRNA sequence, MALDI-TOF mass spectrometry and positive urea hydrolysis and beta-glucuronidase tests clearly distinguished it from closely related Staphylococcus spp. All analyses have consistently shown that the closest relative is Staphylococcus chromogenes; however, values of digital DNA-DNA hybridization <35.3% and an average nucleotide identity <81.4% confirmed that the analyzed strain is a distinct Staphylococcus species. Whole-genome sequencing and expert annotation of the genome revealed the presence of novel variable genetic elements, including two plasmids named pSR9025A and pSR9025B, prophages, genomic islands and a composite transposon that may confer selective advantages to other bacteria and enhance their survival. Based on phenotypic, phylogenetic and genomic data obtained in this study, the strain NRL/St 03/464^T (= CCM 9025^T = LMG 31873^T = DSM 111348^T) represents a novel species with the suggested name Staphylococcus ratti sp. nov.

Embryo lethality assay as a tool for assessing virulence of isolates from bacterial chondronecrosis with osteomyelitis in broilers

We used an embryo lethality assay (ELA) to assess virulence for different isolates from cases of bacterial chondronecrosis with osteomyelitis (BCO) in broilers. Lameness is among the most significant animal welfare issues in the poultry industry. Bacterial infections are a major cause of lameness and different bacterial species have been obtained from lame broilers. Reliable lab-based assays are required to assess relative virulence of bacteria obtained from lame broilers. ELA has been used to assess lethal dosage of Enterococcus faecalis and Enterococcus cecorum. We hypothesized that ELA could substitute for more laborious and costly assessments of BCO isolate pathogenicity using live birds. We evaluated 2 different levels of bacteria injected into eggs from layer and commercial broiler embryos. Significant findings include 1) Escherichia coli from neighboring farms operated by the same integrator had very different embryo lethality, 2) isolate Staphylococcus agnetis 908 had low virulence in ELA, even though this isolate can induce more than 50% BCO lameness, 3) Enterococcus cecorum 1415 also had low pathogenicity; even though it was recovered from severe bilateral tibial dyschondroplasia, 4) human and chicken BCO isolates of S. aureus had significant pathogenicity, 5) virulence for some isolates was highly variable possibly corresponding with quality of the embryos/fertile eggs used, and 6) ELA pathogenicity was much lower for our BCO isolates than previous reports which may reflect maternal environment. Overall, ELA virulence and BCO virulence are not always concordant indicating that ELA may not be an effective measure for assessing virulence with respect to BCO.

Non-aureus Staphylococci and Bovine Udder Health: Current Understanding and Knowledge Gaps

Despite considerable efforts to control bovine mastitis and explain its causes, it remains the most costly and common disease of dairy cattle worldwide. The role and impact of non-aureus staphylococci (NAS) in udder health are not entirely understood. These Gram-positive bacteria have become the most frequently isolated group of bacteria in milk samples of dairy cows and are associated with (mild) clinical and subclinical mastitis. Different species and strains of NAS differ in their epidemiology, pathogenicity, virulence, ecology and host adaptation, and antimicrobial resistance profiles. They have distinct relationships with the microbiome composition of the udder and may also have protective effects against other mastitis pathogens. Some appear to persist on the skin and in the teat canal and udder, while others seem to be transient residents of the udder from the environment. Analyzing genotypic and phenotypic differences in individual species may also hold clues to why some appear more successful than others in colonizing the udder. Understanding species-level interactions within the microbiome and its interactions with host genetics will clarify the role of NAS in bovine mastitis and udder health.

Analysis of genomes of bacterial isolates from lameness outbreaks in broilers

We investigated lameness outbreaks at 3 commercial broiler farms in Arkansas. We isolated several distinct bacterial species from Bacterial Chondronecrosis with Osteomyelitis (BCO) lesions from these 3 farms. The results show that BCO-lameness pathogens on particular farms can differ significantly. We characterized genomes for isolates of the 2 most prevalent species, Escherichia coli and Staphylococcus aureus. Genomes assembled for E. coli isolates from all 3 farms were quite different between farms, and most similar to genomes from different geographical locations and hosts. The E. coli phylogenomics suggests frequent host shifts for this species. Genomes for S. aureus isolates from one farm were highly related to those from chicken isolates from Europe. Highly related isolates have also been characterized from chickens in the Arkansas area for at least a decade. Phylogenomics suggest that this S. aureus has been restricted to poultry for more than 40 y. Detailed analysis of genomes from 2 neighboring clades of S. aureus human and chicken isolates, identifies the acquisition of a specific pathogenicity island in the transition from human to chicken pathogen and that pathogenesis for this clade in chickens may depend on this mobile element. Investigation of the evolution of this chicken-restricted clade from 1980 in Ireland, Poland in 2008, Oklahoma in 2010 and Arkansas in 2019, reveals the acquisition of additional virulence determinants including pathogenicity islands. Isolate-specific genome characterizations will help further our understanding of the disease mechanisms of BCO-lameness, a significant animal welfare issue.

Chondronecrosis with osteomyelitis in broilers: further defining a bacterial challenge model using standard litter flooring and protection with probiotics

This report demonstrates that high levels of lameness can be induced by a limited bacterial challenge in drinking water for birds raised on litter flooring, comparable with lameness induced by the gold standard for inducing lameness, growth on suspended wire flooring. The bacterium used in the challenge was cultured from lesions in birds induced for bacterial chondronecrosis with osteomyelitis (BCO) in the wire-flooring model so the epidemiology appears similar. The litter-flooring model could better approximate broiler operations. Furthermore, the work demonstrates that 2 commercial probiotics (GalliProTect and GalliProMax) can reduce lameness in the bacterial challenge litter-flooring model. Lameness attributable to BCO is one of the most significant animal welfare issues for broiler production. The wire-flooring and litter-flooring models afford alternatives for understanding the etiology, and epidemiology of BCO, and development of management strategies to reduce lameness. Probiotics afford a promising management strategy. The results suggest that the probiotic protection may extend beyond just intestinal health and intestinal barrier function.

A Review of Current Knowledge on Staphylococcus agnetis in Poultry

Simple Summary

This literature review provides a synthesis and evaluation of the current knowledge on Staphylococcus agnetis (S. agnetis) and its implications in poultry pathology. Recent studies revealed that S. agnetis can cause bacterial chondronecrosis with osteomyelitis (BCO), endocarditis, and septicemia in broiler chickens. Lameness constitutes one of the major health and welfare problems causing huge economic losses in the poultry industry. To date, a range of infectious and non-infectious factors have been associated with lameness in poultry. Among bacteria of the genus Staphylococcus, Staphylococcus aureus is the main species associated with locomotor problems. This contrasts with S. agnetis, which until recently had not been considered as a poultry pathogen. Previously only reported in cattle, S. agnetis has expanded its host range to chickens, and due to its unique characteristics has become recognized as a new emerging pathogen. The genotypic and phenotypic similarities between S. agnetis and other two staphylococci (S. hyicus and S. chromogenes) make this pathogen capable of escaping recognition due to misidentification. Although a significant amount of research on S. agnetis has been conducted, many facts about this novel species are still unknown and further studies are required to understand its full significance in poultry pathology.

Abstract

This review aims to summarize recent discoveries and advancements regarding the characteristics of Staphylococcus agnetis (S. agnetis) and its role in poultry pathology. S. agnetis is an emerging pathogen that was primarily associated with mastitis in dairy cattle. After a presumed host jump from cattle to poultry, it was identified as a pathological agent in broiler chickens (Gallus gallus domesticus), causing lameness induced by bacterial chondronecrosis with osteomyelitis (BCO), septicemia, and valvular endocarditis. Economic and welfare losses caused by lameness are global problems in the poultry industry, and S. agnetis has been shown to have a potential to induce high incidences of lameness in broiler chickens. S. agnetis exhibits a distinct repertoire of virulence factors found in many different staphylococci. It is closely related to S. hyicus and S. chromogenes, hence infections caused by S. agnetis may be misdiagnosed or even undiagnosed. As there are very few reports on S. agnetis in poultry, many facts about its pathogenesis, epidemiology, routes of transmission, and the potential impacts on the poultry industry remain unknown.