Antimicrobial Resistance, Virulence, and Genetic Lineages of Staphylococci from Horses Destined for Human Consumption: High Detection of S. aureus Isolates of Lineage ST1640 and Those Carrying the lukPQ Gene

Antimicrobial Resistance in Equines: A Growing Threat to Horse Health and Beyond-A Comprehensive Review

The equine industry holds substantial economic importance not only in the USA but worldwide. The occurrence of various infectious bacterial diseases in horses can lead to severe health issues, economic losses, and restrictions on horse movement and trade. Effective management and control of these diseases are therefore crucial for the growth and sustainability of the equine industry. While antibiotics constitute the primary treatment strategy for any bacterial infections in horses, developing resistance to clinically important antibiotics poses significant challenges to equine health and welfare. The adverse effects of antimicrobial overuse and the escalating threat of resistance underscore the critical importance of antimicrobial stewardship within the equine industry. There is limited information on the epidemiology of antimicrobial-resistant bacterial infections in horses. In this comprehensive review, we focus on the history and types of antimicrobials used in horses and provide recommendations for combating drug-resistant bacterial infections in horses. This review also highlights the epidemiology of antimicrobial resistance (AMR) in horses, emphasizing the public health significance and transmission dynamics between horses and other animals within a One Health framework. By fostering responsible practices and innovative control measures, we can better help the equine industry combat the pressing threat of AMR and thus safeguard equine as well as public health.

Isolation and Genomic Analysis of a Case of Staphylococcus argenteus ST2250 Related to Sepsis in Italy

Staphylococcus argenteus, identified in 2006, represents a challenging case of bacterial taxonomic identification because of its high similarity to Staphylococcus aureus. In this context, neither mass spectrometry (MS) nor 16S gene analysis cannot precisely reveal the difference between the two species. In our study, the sensitivity to antibiotics of S. argenteus isolated from blood culture was tested, and the investigation of the bacterial genome was performed by Multi-Locus Sequence Typing (MLST) and Whole-Genome Next-Generation Sequencing (WG-NGS). The pathogen was identified as ST2250 and presented perfectly matched resistance genes, namely aph(3')-III, mgrA, and sepA, whereas the virulence gene detected was scn. Two plasmids were found: the pSAS plasmid, belonging to the family of Inc18, and plasmid pN315, belonging to the Rep3 group. The epidemiological distribution and the spread of S. argenteus infection are scarcely documented, particularly when associated with sepsis. Therefore, a correct taxonomy identification, antibiogram, and resistance gene analysis may help in acquiring knowledge about this bacterium and implement its detection and treatment.

Equine Gram-Negative Oral Microbiota: An Antimicrobial Resistances Watcher?

Horses are considered as reservoirs of multidrug resistant bacteria that can be spread through the environment and possibly to humans. The aim of this study was to characterize the oral Gram-negative microbiota of healthy horses and evaluate their antimicrobial susceptibility profile in a One Health approach. For this purpose, samples were collected from the gingival margin of healthy horses, free of antimicrobial therapy, cultured in selective mediums, identified, and tested for antimicrobial susceptibility. Fifty-five Gram-negative isolates were identified, with 89.5% being zoonotic and 62% affecting humans, which were also found commonly in the environment. Forty-eight isolates (96%) were MDR. The phenotypic resistance presented as higher to macrolides (81.8%), β-lactams (55.4%), and quinolones (50%), and lower to sulfonamides (27.3%), tetracyclines, and amphenicols (both with 30.9%). In total, 51.5% of the isolates presented resistance to carbapenems. In addition to being the first report on the commensal oral microbiota of horses and respective susceptibility profile, this study highlights the horse as a valuable sentinel that can control the evolution and transmission of multidrug-resistant bacteria between the "One Health triad" since it is in contact with humans, other animals, and the environment, in different geographic locations.

Clinical Aspects of Bacterial Distribution and Antibiotic Resistance in the Reproductive System of Equids

Antibiotic administration is a standard therapeutic practice for the treatment of reproductive disorders of equids. This might lead to undesirable microbial imbalance and could favour the acquisition of antibiotic resistance. Therefore, it is imperative for clinicians to understand patterns of antibiotic resistance when considering and developing treatment regimes. Continued engagement of clinicians with novel alternative approaches to treat reproductive infections would be essential in order to address this rising threat within the One Health perspective. The objectives of the present review were to present the bacterial infections in the reproductive system of equids (horses, donkeys), to upraise the literature related to the issue of antibiotic resistance of bacteria causing these infections and to discuss the topic from a clinical perspective. Initially, the review summarised the various infections of the reproductive system of equids (genital system of females, genital system of males, mammary glands) and the causal bacteria, providing relevant information about horses and donkeys. Subsequently, the clinical therapeutics of these infections were presented, taking into account the significance of antibiotic resistance of bacteria as a limiting factor in treating the infections. Finally, approaches to circumvent antibiotic resistance in clinical settings were summarized. It was concluded that awareness regarding antibiotic resistance in equine reproductive medicine would increase, as we would recognise the multifaceted problem of resistance. Actions and initiatives within the One Health approach, minimizing the potential dissemination of resistant strains to humans and to the environment, with specific applications in medicine of equids should be appropriately instituted internationally.

Staphylococcus sciuri causes disease and pathological changes in hybrid sturgeon acipenser baerii × acipenser schrencki

Hybrid sturgeon is the main species of sturgeon cultured in China, with the advantages of a fast growth rate, early sexual maturity, fertile offspring, and more stable genetic traits. In May 2021, a large number of deaths characterized by superficial hemorrhage and liver damage occurred in a sturgeon farm in Yichang, Hubei Province, which posed a significant risk to hybrid sturgeon captive breeding. We isolated a pathogenic bacterium named D-59 from the diseased sturgeon with apparent symptoms. The pathogen was identified as Staphylococcus sciuri using 16S rRNA gene phylogenetic analysis combined with biochemical identification. Regression experiments showed that D-59 exhibited clinical signs similar to those of diseased sturgeon in the farm after intraperitoneal injection into hybrid sturgeon. High-throughput sequencing of gut microbes in D-59-infected sturgeon showed that the number of gut microbial species decreased in infected sturgeon, the number of some intestinal commensal bacteria decreased, and the balance of the intestinal microorganisms was disrupted. Histopathological sections indicated many inflammatory cells, congestion, and even necrosis in the tissue of diseased sturgeon. Analysis of blood indexes revealed an increase in the proportion of mononuclear cells and a decrease in the proportion of lymphocytes in the peripheral blood of diseased sturgeon. Significantly elevated serum levels of aspartate aminotransferase and alanine aminotransferase, whereas alkaline phosphatase, total protein, albumin, and globulin were decreased in diseased sturgeon. Antimicrobial susceptibility tests demonstrated that D-59 is susceptible to florfenicol, enrofloxacin, and neomycin sulfate. This study aimed to highlight the dangers of Staphylococcus sciuri infection during hybrid sturgeon culture and to provide recommendations for diagnosis and treatment.

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial-resistant Staphylococcus aureus in cattle and horses

Staphylococcus aureus (S. aureus) was identified among the most relevant antimicrobial-resistant (AMR) bacteria in the EU for cattle and horses in previous scientific opinions. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9, and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR S. aureus can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (60-90% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1, 2 and 4 (Categories A, B and D; 1-5%, 5-10% and 10-33% probability of meeting the criteria, respectively) and the AHAW Panel was uncertain whether it meets the criteria in Sections 3 and 5 (Categories C and E, 33-90% and 60-90% probability of meeting the criteria, respectively). The animal species to be listed for AMR S. aureus according to Article 8 criteria include mainly mammals, birds, reptiles and fish.

A One Health Approach Molecular Analysis of Staphylococcus aureus Reveals Distinct Lineages in Isolates from Miranda Donkeys (Equus asinus) and Their Handlers

Donkeys (Equus asinus) are in decline in Europe. Occupational exposure to farm animals has been associated with increased staphylococci carriage. We aimed to isolate S. aureus and coagulase-negative staphylococci (CoNS) from donkeys and handlers and characterize the antimicrobial resistance profiles and genetic lineages of S. aureus strains. Oral and nasal swab samples were collected from 49 Miranda donkeys and 23 handlers from 15 different farms. Staphylococci species were identified by MALDI-TOF MS. The presence of antimicrobial resistance genes and virulence factors was investigated by PCR. Molecular typing was performed in S. aureus isolates. From the 49 donkey samples, 4 S. aureus (8.2%) and 21 CoNS (42.9%) were isolated. Ten handlers (43.5%) were carriers of S. aureus and 4 (17.4%) carried CoNS. The CoNS isolates showed resistance to several classes of antimicrobials encoded by the mecA, aph (3′)-IIIa, ant (4′)-Ia, tetM, tetK, lnuA, ermB, ermC, dfrA and dfrG genes. S. aureus isolates were resistant to penicillin, aminoglicosides and tetracycline harboring the blaZ, aph (3′)-IIIa, tetL, tetM and tetK genes. All S. aureus isolates from donkeys belonged to ST49 and spa-type t208 while the strains isolated from the handlers were ascribed to 3 STs and 7 spa-types. However, human isolates were from different STs than the donkey isolates. Donkeys are mainly colonized by methicillin-resistant S. sciuri. S. aureus transmission between donkeys and their handlers appears not to have occurred since the isolates belonged to different genetic lineages.

Prevalence and WGS-based characteristics of Staphylococcus aureus in the nasal mucosa and pastern of horses with equine pastern dermatitis

BACKGROUND

Many contributing factors are involved in the development of equine pastern dermatitis (EPD). Among the most frequently suspected is Staphylococcus aureus, known for its pathogenic potential in skin and soft tissue infections. We therefore investigated the association between S. aureus carriage and EPD.

RESULTS

One hundred five EPD-affected horses and 95 unaffected controls were examined for the presence of methicillin-resistant and -susceptible Staphylococcus aureus (MRSA and MSSA) on the pastern skin and in the nostrils. S. aureus isolates were cultivated from swab samples on selective MSSA and MRSA chromogenic agar and identified using MALDI-TOF MS. Isolates were analysed by Illumina whole genome sequencing for genetic relatedness (cgMLST, spa typing), and for the presence of antimicrobial resistance and virulence determinants. A markedly higher proportion of samples from EPD-affected horses proved positive for S. aureus, both from the pastern (59.0 % vs. 6.3 % in unaffected horses; P<0.001), and from the nose (59.0 % vs. 8.4 %; P<0.001). Isolates belonged to 20 sequence types (ST) with lineages ST15-t084 (spa) (18 %), ST1-t127 (13 %), and ST1-t1508 (12 %) being predominant. Eight S. aureus were MRSA ST398-t011 and ST6239-t1456, and contained the staphylococcal cassette chromosome SCCmecIVa. Antimicrobial resistance genes were almost equally frequent in pastern and in nasal samples, whereas some virulence factors such as the beta-hemolysin, ESAT-6 secretion system, and some enterotoxins were more abundant in isolates from pastern samples, possibly enhancing their pathogenic potential.

CONCLUSIONS

The markedly higher prevalence of S. aureus containing specific virulence factors in affected skin suggests their contribution in the development and course of EPD.

Nocturnal Birds of Prey as Carriers of Staphylococcus aureus and Other Staphylococci: Diversity, Antimicrobial Resistance and Clonal Lineages

Owls are nocturnal predators that inhabit urbanized and farmlands. They are in direct contact with other animals, both livestock and small wild rodents that they mostly feed on. Staphylococci can be both commensal and pathogenic bacteria that are widespread across the various ecological niches. We aimed to isolate staphylococci from owls and to characterize their antimicrobial resistance, virulence factors and genetic lineages. Swab samples were collected from the throat and cloaca of 114 owls admitted to two rehabilitation centers in Portugal. The identification of staphylococci species was performed by MALDI-TOF. Staphylococci antimicrobial resistance and virulence genes were investigated by means of the disk diffusion method and PCR. Staphylococcus aureus isolates were characterized by MLST, agr and spa-typing. Of the tested animals, 66 isolates were recovered, including 10 different species of staphylococci, of which 25 were coagulase-positive (CoPS) and 41 were coagulase-negative (CoNS). Twenty-three S. aureus were isolated, of which one mecC-MRSA was identified. The isolates were mainly resistant to penicillin, aminoglycosides, clindamycin and tetracycline. mecC-MRSA belonged to ST1245 and spa-type t843 and the remaining S. aureus were ascribed to 12 STs and 15 spa types. A high diversity of clonal lineages was identified among the S. aureus isolated from wild owls. Owls feed mainly on small rodents often exposed to waste and anthropogenic sources, which may explain the moderate prevalence of S. aureus in these animals.

Antimicrobial Resistance of Coagulase-positive Staphylococcus Isolated From Healthy Crioulo Horses and Associated Risk Factors

Antimicrobial resistance (AMR) is a global concern that must be addressed from a one health perspective. Horses are companion animals and their contact with humans facilitates exchange of resistant bacteria. This study aimed to evaluate AMR of coagulase-positive Staphylococcus (CoPS), including Staphylococcus aureus, isolated from healthy Crioulo horses. Swab samples from nostrils (n = 214) and skin (n = 107) of 107 horses from Porto Alegre, South Brazil, were used for CoPS isolation. The isolates were evaluated for AMR and a multivariate logistic regression was applied to identify the risk factors associated to this outcome, using information on horses' management and installations where they were maintained. A total of 143 CoPS were isolated from 79 horses (73.8%), of which 8 (5.6%) were S. aureus. The isolates showed resistance to seven of 10 tested antimicrobials and 38.5% (55/143) of them were resistant to at least one antimicrobial. One isolate (0.7%; 1/143) was classified as multidrug-resistant. Regarding S. aureus, 62.5 % (5/8) showed AMR, but none were methicillin-resistant. The risk factors associated with CoPS' antimicrobial resistance were lower frequency of bed changing (OR = 6.40; P = .001) and nonaccumulation of bed materials (OR = 3.47; P = .002). The results point that healthy horses have antimicrobial-resistant CoPS and S. aureus in their microbiota, which may be of concern for animal and human health. Moreover, bed management was associated with AMR, which can serve as a guide for best practices to be adopted to avoid the occurrence of resistant bacteria in these animals.

Analysis of Virulence and Antimicrobial Resistance Gene Carriage in Staphylococcus aureus Infections in Equids Using Whole-Genome Sequencing

While Staphylococcus aureus is associated with significant morbidity and mortality in equids (horses, donkeys, and mules), few studies have performed whole-genome sequencing to fully categorize large collections of equine isolates. Such sequencing allows for a comprehensive analysis of the genetic lineage and relationships of isolates, as well as the virulence genes present in each, which can be important for understanding the epidemiology of strains and their range of infections. Seventy-two clinical Staphylococcus aureus isolates from equids were collected at the Texas A&M University Veterinary Medical Teaching Hospital between 2007 and 2017. Whole-genome sequencing was performed to characterize the isolates according to sequence typing, biofilm association, antimicrobial resistance, and toxin gene carriage. Of the 72 isolates, 19% were methicillin resistant, of which the majority belonged to clonal complex 8. Eighteen distinct sequence types (STs) were represented, with the most common being ST1, ST133, ST8, and ST97. Most isolates had weak or negative overall biofilm production. Toxin and antimicrobial resistance gene carriage was varied; of note, this study revealed that a large proportion of North American equine isolates carry the leucocidin PQ toxin (66% of isolates). One isolate (17-021) carried genes imparting lincosamide and high-level mupirocin resistance, a combination not previously reported in equine-derived S. aureus isolates.

IMPORTANCE This is one of the first studies to perform whole-genome sequencing (WGS) of a large collection of Staphylococcus aureus isolates, both methicillin resistant and susceptible, collected from horses. A large proportion of the isolates carry leucocidin PQ (LukPQ), making this one of the first reports of such carriage in the United States. The presence of lincosamide and high-level mupirocin resistance in a methicillin-susceptible S. aureus (MSSA) isolate highlights the importance of MSSA as a reservoir of important antimicrobial resistance genes. As microbial resistance genes on mobile genetic elements can pass between S. aureus strains and livestock-associated strains can be transferred to humans, these findings have important public health implications.

Nasal colonization and antibiotic resistance patterns of Staphylococcus species isolated from healthy horses in Tripoli, Libya

The present study investigated the colonization rates and antimicrobial susceptibility of Staphylococcus species isolated from the nostrils of healthy horses. A nonselective laboratory approach was applied, followed by confirmation using a Phoenix automated microbiological system. Among the 92 horses included in the study, 48.9% (45/92) carried Staphylococcus species of mostly the coagulase-negative staphylococci (CoNS) type yielding 70 Staphylococcus strains. Of these strains, 37.1% (26/70; 24 CoNS and 2 coagulase-positive staphylococci; CoPS) were identified as methicillin-resistant staphylococci (MRS) expressing significant resistance to important antimicrobial classes represented mainly by subspecies of CoNS. This is the first study reporting a high prevalence of various Staphylococcus species, particularly strains of CoNS expressing multidrug resistance patterns of public health concern, colonizing healthy horses in Libya.

The Role of hlb-Converting Bacteriophages in Staphylococcus aureus Host Adaption

As an opportunistic pathogen of humans and animals, Staphylococcus aureus asymptomatically colonizes the nasal cavity but is also a leading cause of life-threatening acute and chronic infections. The evolution of S. aureus resulting from short- and long-term adaptation to diverse hosts is tightly associated with mobile genetic elements. S. aureus strains can carry up to four temperate phages, many of which possess accessory genes encoding staphylococcal virulence factors. More than 90% of human nasal isolates of S. aureus have been shown to carry Sa3int phages, whereas invasive S. aureus isolates tend to lose these phages. Sa3int phages integrate as prophages into the bacterial hlb gene, disrupting the expression of the sphingomyelinase Hlb, an important virulence factor under specific infection conditions. Virulence factors encoded by genes carried by Sa3int phages include staphylokinase, enterotoxins, chemotaxis-inhibitory protein, and staphylococcal complement inhibitor, all of which are highly human specific and probably essential for bacterial survival in the human host. The transmission of S. aureus from humans to animals is strongly correlated with the loss of Sa3int phages, whereas phages are regained once a strain is transmitted from animals to humans. Thus, both the insertion and excision of prophages may confer a fitness advantage to this bacterium. There is also growing evidence that Sa3int phages may perform "active lysogeny," a process during which prophages are temporally excised from the chromosome without forming intact phage particles. The molecular mechanisms controlling the peculiar life cycle of Sa3int phages remain largely unclear. Nevertheless, their regulation is likely fine-tuned to ensure bacterial survival within different hosts.

S. pseudintermedius and S. aureus lineages with transmission ability circulate as causative agents of infections in pets for years

Background

Staphylococcus pseudintermedius (SP) and Staphylococcus aureus (SA) are common colonizers of companion animals, but they are also considered opportunistic pathogens, causing diseases of diverse severity. This study focused on the identification and characterization of 33 coagulase-positive staphylococci isolated from diseased pets (28 dogs and five cats) during 2009–2011 in a veterinary hospital in Spain in order to stablish the circulating lineages and their antimicrobial resistance profile.

Results

Twenty-eight isolates were identified as SP and five as SA. Nine methicillin-resistant (MR) isolates (27%) carrying the mecA gene were detected (eight MRSP and one MRSA). The 55% of SP and SA isolates were multidrug-resistant (MDR). MRSP strains were typed as ST71-agrIII-SCCmecII/III-(PFGE) A (n=5), ST68-agrIV-SCCmecV-B1/B2 (n=2), and ST258-agrII-SCCmecIV-C (n=1). SP isolates showed resistance to the following antimicrobials [percentage of resistant isolates/resistance genes]: penicillin [82/blaZ], oxacillin [29/mecA] erythromycin/clindamycin [43/erm(B)], aminoglycosides [18–46/aacA-aphD, aphA3, aadE], tetracycline [71/tet(M), tet(K)], ciprofloxacin [29], chloramphenicol [29/cat_pC221], and trimethoprim-sulfamethoxazole [50/dfrG, dfrK]. The dfrK gene was revealed as part of the radC-integrated Tn559 in two SP isolates. Virulence genes detected among SP isolates were as follow [percentage of isolates]: siet [100], se-int [100], lukS/F-I [100], sec_canine [7], and expB [7]. The single MRSA-mecA detected was typed as t011-ST398/CC398-agrI-SCCmecV and was MDR. The methicillin-susceptible SA isolates were typed as t045-ST5/CC5 (n=2), t10576-ST1660 (n=1), and t005-ST22/CC22 (n=1); the t005-ST22 feline isolate was PVL-positive and the two t045-ST45 isolates were ascribed to Immune Evasion Cluster (IEC) type F. Moreover, the t10576-ST1660 isolate, of potential equine origin, harbored the lukPQ and scneq genes. According to animal clinical history and data records, several strains seem to have been acquired from different sources of the hospital environment, while some SA strains appeared to have a human origin.

Conclusions

The frequent detection of MR and MDR isolates among clinical SP and SA strains with noticeable virulence traits is of veterinary concern, implying limited treatment options available. This is the first description of MRSA-ST398 and MRSP-ST68 in pets in Spain, as well the first report of the dfrK-carrying Tn559 in SP. This evidences that current transmissible lineages with mobilizable resistomes have been circulating as causative agents of infections among pets for years.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-020-02726-4.

Detection of methicillin-resistant coagulase-negative staphylococci and PVL/mecA genes in cefoxitin-susceptible Staphylococcus aureus (t044/ST80) from unpasteurized milk sold in stores in Djelfa, Algeria

This study was designed to determine antimicrobial resistance phenotypes and genotypes and virulence factors in Staphylococcus aureus and coagulase-negative staphylococci (CNS) in unpasteurized milk sold in Djelfa, Algeria. Eighty-two unpasteurized cow milk samples were randomly obtained from 82 retail stores in Djelfa and tested to detect staphylococci. Species were identified by biochemical tests and MALDI-TOF. Antimicrobial resistance phenotypes and genotypes were determined by disk diffusion test, PCR, and sequencing. The Staph. aureus isolates were subjected to spa typing, multilocus sequence typing, and detection of virulence genes and the scn gene by PCR and sequencing. Forty-five (54.9%) milk samples were contaminated by staphylococci and 45 isolates were recovered: 10 Staph. aureus (12.2% of total samples) and 35 CNS (42.7%). Resistance to penicillin (blaZ), tetracycline (tetL/tetK), and erythromycin (ermB/msrA/ermC) were the most common phenotypes (genotypes). Three CNS were methicillin-resistant and all were mecA-positive. The Staph. aureus isolates were ascribed to the following lineages [spa type/sequence type/associated clonal complex (number of isolates)]: t267/ST479/CC479 (n = 6), t1510/ST5651/CC45 (n = 1), t359/ST97/CC97/ (n = 1), t346/ST15/CC15 (n = 1), and t044/ST80 (n = 1). The mecA gene was detected in the cefoxitin-susceptible t044/ST80 isolate and co-harbored the lukF/lukS-PV and scn genes. The detection of mecA-PVL-positive Staph. aureus, methicillin-resistant CNS, and multidrug-resistant staphylococcal species indicates a potentially serious health issue and reveals that unpasteurized milk sold in Djelfa city could be a potential vehicle for pathogenic and antimicrobial-resistant staphylococci.

Gas Production, Digestibility and Efficacy of Stored or Fresh Plant Extracts to Reduce Methane Production on Different Substrates

Simple Summary

Medicinal plants possess the ability to mitigate methane production from ruminants. Long-term stability of these plant extracts are essential qualities to be able to replace other rumen modifiers. After one year of storage, plant secondary metabolites used in this study reduced methane production from low-quality forages, without adverse effects on feed digestibility in vitro.

Abstract

Natural compounds such as plant secondary metabolites (PSM) can be used to replace antibiotic growth promoters as rumen modifiers. In this study, the effectiveness of stored and freshly extracted Aloe vera (AV), Azadirachta indica (AZ), Moringa oleifera (MO), Jatropha curcas (JA), Tithonia diversifolia (TD) and Carica papaya (CP) crude extract and monensin on in vitro gas and methane production, organic matter digestibility (IVOMD) and volatile fatty acids (VFA) were evaluated using a total mixed ration (TMR), lucerne or Eragrostis curvula substrates. Fresh extracts were processed from the same batch of frozen (−20 °C) plant material a few days before the trial while the stored extracts were extracted and stored at 4 °C for 12 months prior to the study. Extraction was done by solubilising 50 g freeze-dried plant material in 500 mL 100% methanol. Four mL of reconstituted 50 mg crude extract per 1000 mL distilled water was added per incubation vial, which already contained 400 mg substrate and in vitro fermentation, and gas production and IVOMD evaluation were carried out using standard procedures. Results showed that storing plant extracts for 12 months did not affect the activity or stability of metabolites present in the crude extracts, as shown by the lack of differences in total gas production (TGP) and methane produced between fresh or stored extracts across the substrates. In the TMR substrate, plant extracts increased IVOMD but did not affect TGP and methane production, whereas monensin did not have any effect. Plant extracts increased IVOMD of Eragrostis substrate and supressed methane production to a greater extent than monensin (p < 0.05). It can be concluded that storing plant extracts for up to 12 months did not compromise their efficacy. In addition, the use of 50 mg/kg of AV, AZ, MO, JA, TD and CP extract to a forage-based diet will reduce methane production while improving feed digestibility.