Photobacterium damselae subspecies damselae Pneumonia in Dead, Stranded Bottlenose Dolphin, Eastern Mediterranean Sea.

Photobacterium damselae subspecies damselae, an abundant, generalist marine pathogen, has been reported in various cetaceans worldwide. We report a bottlenose dolphin in the eastern Mediterranean Sea that was found stranded and dead. The dolphin had a severe case of chronic suppurative pneumonia and splenic lymphoid depletion caused by this pathogen.

Botulinum Neurotoxin C Dual Detection through Immunological Recognition and Endopeptidase Activity Using Porous Silicon Interferometers.

Botulinum neurotoxins (BoNTs) are the most potent toxins known in nature produced by Clostridium botulinum strains, which can cause life-threatening diseases in both humans and animals. The latter is of serious environmental and economic concern, resulting in high mortality, production losses, and rejection of contaminated animal feed. The available in vivo mouse assay is inadequate for real-time and on-site assessment of outbreaks. Herein, we present a reflective-based approach for the detection of BoNT/C while estimating its activity. Two adjacent porous Si Fabry-Pérot interferometers are simultaneously utilized to quantify minute BoNT/C concentrations by a competitive immunoassay and to assess their endopeptidase activity. The reflectivity signals of each interferometer are amplified by biochemical reaction products infiltration into the scaffold or by peptide fragments detachment from the nanostructure. The optical assay is highly sensitive in compliance with the in vivo approach by presenting a detection limit of 4.24 pg mL-1. The specificity and selectivity of the designed platform are cross-validated against BoNT/B and BoNT/D, also relevant to animal health. Finally, the analytical performances of both interferometers for real-life scenarios are confirmed using actual toxins while depicting excellent compliance to complex media analysis. Overall, the presented sensing scheme offers an efficient, rapid, and label-free approach for potential biodiagnostic elucidation of botulism outbreaks.

Fungi in sands of Mediterranean Sea beaches of Israel-Potential relevance to human health and well-being.

BACKGROUND: Sand of sea harbour bacteria that may cause enteric and other infections in humans, and are controlled by regulatory measures. Data on fungi in sea sand are scarce. Thus, an international group of mycologists was formed to explore fungal flora in sand of various waterbodies. OBJECTIVES: The aim was to explore fungal sand contamination in beaches of the Israeli Mediterranean Sea Coast, regarding possible impact on human health in three aspects: (a) faecal contamination, as judged by presence of the human enteric fungi; (b) contamination by fungi, causing dermal infections; (c) and the presence of moulds, causing respiratory allergies and pose a risk for infection in immunocompromised individuals. METHODS: The study included sand screen of six urban beaches from north to south of the Israeli Mediterranean Coast. Sand samples were extracted by water, and the water wash was cultured and quantitated. The fungi were identified phenotypically, by MALDI-TOF MS system and ITS sequencing. RESULTS: The screen revealed that about 80% of the isolates were moulds and about 20% yeasts. The mould species included opportunistic pathogens and potential allergens: Aspergillus fumigatus, Fusarium and Mucorales species. Yeast isolates included Candida, Cryptococcus and Rhodotorula species. CONCLUSIONS: (a) Fungi are contaminating Israeli Mediterranean sand beaches; (b) the contaminating fungi include various yeast and mould species; (c) some of the yeasts and mould species found in sand are known opportunistic pathogens, or respiratory allergens; (d) the data could serve as basis for initiating regulatory measures to control fungal contamination of sand for the benefit of public health.

From six to zero per cent Mycobacterium avium subsp. paratuberculosis milk ELISA positivity in three years - probably induced by Mycobacterium vaccae.

This research communication reports the results of a study aimed at investigating the effects of introducing Mycobacterium vaccae on paratuberculosis carriage in a dairy herd. M. vaccae is a non-pathogenic member of the Mycobacteriaceae, with immunomodulatory and immunotherapeutic capabilities, acting by stimulating the cellular immune system, important in protection against paratuberculosis. Starting in 2014 we administered, by gavage, 1010 live M. vaccae bacteria to all new-born heifers on a dairy farm, first within 24 h of birth and again 2 weeks later. Paratuberculosis carriage was monitored yearly by milk ELISA. Faecal samples of 50% of cows, aged 3 years, born 1, 2 or 3 years before the experiment's onset, were tested by qPCR for MAP shedding and compared to 100% treated cows of the same age. Within 3 years, milk ELISA positivity was reduced from 6 to 0% and remained unchanged for the subsequent 2 years. One qPCR positive control cow was found each year for a total of 3 animals (2.46%). One positive cow (1%) was found among the treated cows. Two of the 3 positive control animals, still present on the farm at the end of 2019, tested negative whereas the positive test cow continued shedding MAP. M. vaccae shedding heifers mixing with adult cows were the probable means of the microorganism's propagation. The results of this investigation indicate that the introduction of live M. vaccae may be an inexpensive and fast alternative to current paratuberculosis control practices, justifying further exploration of the topic.

Mycobacterium gordonae infecting redclaw crayfish Cherax quadricarinatus.

The redclaw crayfish Cherax quadricarinatus (von Martens, 1868) is one of the most commonly exploited freshwater crayfish species worldwide. Redclaw crayfish are susceptible to a number of pathogens but none have been linked to widespread epizootics. Mycobacterial infections have been sporadically reported in crayfish. In the case described, histopathology and bacterial identification confirmed an opportunistic infection caused by Mycobacterium gordonae in a hatchery of C. quadricarinatus in Israel. Intranuclear inclusion bodies, recorded in cells of the tubular epithelium of the hepatopancreas by histopathology, indicate a co-infection with a viral agent, referable to C. quadricarinatus bacilliform virus (CqBV). To the best of our knowledge this is the first description of mycobacteriosis in redclaw crayfish.

Comparison of the immune responses associated with experimental bovine mastitis caused by different strains of Escherichia coli.

We studied the mammary immune response to different mammary pathogenic Escherichia coli (MPEC) strains in cows, hypothesising that the dynamics of response would differ. E. coli is a major aetiologic agent of acute clinical bovine mastitis of various degrees of severity with specific strains being associated with persistent infections. We compared challenge with three distinct pathogenic MPEC strains (VL2874, VL2732 and P4), isolated from different forms of mastitis (per-acute, persistent and acute, respectively). A secondary objective was to verify the lack of mammary pathogenicity of an environmental isolate (K71) that is used for comparison against MPEC in genomic and phenotypic studies. Twelve cows were challenged by intra-mammary infusion with one of the strains. Cellular and chemokine responses and bacterial culture follow-up were performed for 35 d. All cows challenged by any of the MPEC strains developed clinical mastitis. Differences were found in the intensity and duration of response, in somatic cell count, secreted cytokines (TNF-α, IL-6 and IL-17) and levels of milk leucocyte membrane Toll-like receptor 4 (TLR4). A sharp decrease of TLR4 on leucocytes was observed concomitantly to peak bacterial counts in milk. Intra-mammary infusion of strain K71 did not elicit inflammation and bacteria were not recovered from milk. Results suggest some differences in the mammary immune response to distinct MPEC strains that could be correlated to their previously observed pathogenic traits. This is also the first report of an E. coli strain that is non-pathogenic to the bovine mammary gland.

Comparison between point-of-care dermatophyte test medium and mycology laboratory culture for diagnosis of dermatophytosis in dogs and cats.

BACKGROUND: Point-of-care Dermatophyte Test Medium (PoC-DTM) is a diagnostic procedure to rule in/rule out dermatophytosis in veterinary clinics. OBJECTIVE: To evaluate the performance of PoC-DTM in the clinic compared to DTM plate culture in a mycology laboratory and to compare results obtained by general practitioners and referral clinicians. ANIMALS: Hair samples were collected from 47 cats and 54 dogs with suspected dermatophytosis and from nine healthy controls (seven cats and two dogs). METHODS: This was a multicentre blinded study. In one group (65 suspected cases, 9 healthy controls), PoC-DTM results were evaluated by clinicians in a referral clinic (SP group) who examined the colony morphology macroscopically and microscopically. In the other group (36 suspected cases) PoC-DTM results were evaluated by clinicians from general practice for colour change only, with no macroscopic or microscopic examination (GP group). All hair samples were also cultured on DTM plates in a mycology laboratory. Laboratory culture was considered the gold standard for comparison. RESULTS: Agreements between tests were 97% (two false positive; κ = 0.839) and 80.6% (five false positives and two false negatives; κ = 0.466) in the SP and GP groups, respectively. This difference between groups was significant (P = 0.024). CONCLUSION AND CLINICAL IMPORTANCE: When applying macroscopic and microscopic evaluation of the colony, PoC-DTM is accurate for diagnosing dermatophytes with only a 3% chance of error. However, when macroscopic and microscopic examination is not included there is significant (19.4%) chance for an incorrect diagnosis.

Prevalence, Risk Factors, and Transmission Dynamics of Extended-Spectrum-ß-Lactamase-Producing Enterobacteriaceae: a National Survey of Cattle Farms in Israel in 2013.

Our objectives were to study the prevalence, risk factors for carriage, and transmission dynamics of extended-spectrum-ß-lactamase (ESBL)-producing Enterobacteriaceae (ESBLPE) in a national survey of cattle. This was a point prevalence study conducted from July to October 2013 in Israel. Stool samples were collected from 1,226 cows in 123 sections on 40 farms of all production types. ESBLPE were identified in 291 samples (23.7%): 287 contained Escherichia coli and 4 contained Klebsiella pneumoniae. The number of ESBLPE-positive cows was the highest in quarantine stations and on fattening farms and was the lowest on pasture farms (P = 0.03). The number of ESBLPE-positive cows was the lowest in sections containing adult cows (age, >25 months) and highest in sections containing calves (age, <4 months) (P < 0.001). Infrastructure variables that were significant risk factors for ESBLPE carriage included crowding, a lack of manure cleaning, and a lack of a cooling (P < 0.001 for each), all of which were more common in sections containing calves. Antimicrobial prophylaxis was given almost exclusively to calves and was associated with a high number of ESBLPE carriers (P < 0.001). The 287 E. coli isolates were typed into 106 repetitive extragenic palindromic (REP)-PCR types and mostly harbored blaCTX-M-1 or blaCTX-M-9 group genes. The isolates on the six farms with ≥15 isolates of ESBLPE were of 4 to 7 different REP-PCR types, with one dominant type being harbored by about half of the isolates. Fourteen types were identified on more than one farm, with only six of the farms being adjacent to each other. The prevalence of ESBLPE carriage is high in calves in cowsheds where the use of antimicrobial prophylaxis is common. ESBLPE disseminate within cowsheds mainly by clonal spread, with limited intercowshed transmission occurring.

Alternative Traits for Genetic Evaluation of Mastitis Based on Lifetime Merit.

Genetic selection has achieved little progress in reducing mastitis incidence. Mastitis traits are problematic due to the lack of sensitivity of the data and reliance on clinical diagnosis, often missing subclinical cases, and/or on monthly somatic cell count (SCC) measurements. The current measure for mastitis is the lactation average of the somatic cells score (LSCS). We studied two datasets: (1) 148 heifers divided into non-intramammary infected, sub-clinically infected and clinical mastitis groups; (2) data from 89,601 heifers from Israeli Holsteins through the same period divided into "udder healthy" (UH) and "non-healthy" (UNH) by a threshold of SCC 120,000 cells/mL in all nine monthly milk recordings. In study 1, non-infected heifers had significantly (p < 0.05) more partum, production days and overall lifetime milk production compared to clinical and sub-clinically infected. In study 2, UH heifers (20.3%) had significantly higher (p < 0.01) lifetime milk, production days, and lactations. Subdividing datasets by sires, the same analyses detected differences in percentages of UH daughters between the sire groups. Lifetime milk production correlated (r = +0.83, p < 0.001) with udder health status. SCC threshold of less than 120,000 cells/mL during all first lactation measurements indicated healthy udder, providing a valuable insight that this dichotomous trait is advantageous for calculating lifetime net-merit index (NM$) over LSCS.

Novel pseudo-staphylococcal cassette chromosome mec element (ψSCCmec57395) in methicillin-resistant Staphylococcus pseudintermedius CC45.

Genetic characterization of methicillin-resistant Staphylococcus pseudintermedius (MRSP) from Thailand and Israel revealed the presence of a predominant atypical clonal lineage which was not typeable by SmaI-PFGE and SCCmec typing. All the atypical isolates (n = 34) belonged to CC45 (30 ST45 and 2 ST179 isolates, 1 ST57 isolate, and 1 ST85 isolate). The isolates originated from healthy and diseased dogs and cats, as well as from the environment of one clinic. Cfr9I-pulsed-field gel electrophoresis (Cfr9I-PFGE) and dru typing permitted the further distinction of CC45 isolates from the two different countries. Microarray analysis identified genes that confer resistance to ß-lactams (mecA; blaZ), aminoglycosides [aac(6')-Ie-aph(2')-Ia; aph(3')-III; ant(6)-Ia], macrolides and lincosamides [erm(B)], tetracyclines [tet(M)], trimethoprim [dfr(G)], streptothricin (sat4), and chloramphenicol (catpC221). Fluoroquinolone resistance was attributed to specific amino acid substitutions, i.e., Ser84Leu in GyrA and Ser80Ile and Asp84Asn in GrlA. A novel pseudo-staphylococcal cassette chromosome (ΨSCCmec57395) element was identified in MRSP strain 57395 (sequence type ST45) by whole-genome sequencing. The 12,282-bp ΨSCCmec57395 element contained a class C1 mec gene complex but no ccr genes. In addition to the methicillin resistance gene mecA, ΨSCCmec57395 also carried determinants of resistance to heavy metals, such as arsenic, cadmium, and copper. Bsu36I restriction analysis of the ΨSCCmec57395 element amplified by long-range PCR revealed the presence of ΨSCCmec57395 in the 33 additional isolates of MRSP CC45. The ΨSCCmec57395 element represents a new class of SCCmec and has been identified in MRSP of CC45, which is a predominant clonal lineage in Israel and Thailand.

Public and animal health risks associated with spillover of Brucella melitensis into dairy farms.

Brucellosis is a worldwide zoonosis with important public health, animal health and economic implications. Brucella melitensis, commonly associated with small ruminants, is an emerging bovine pathogen in dairy farms. We analysed all B. melitensis outbreaks affecting dairy farms in Israel since 2006, combining traditional and genomic epidemiology to explore the public health implications of this One Health challenge. Whole-genome sequencing was applied to bovine and related human B. melitensis isolates from dairy farm outbreaks. cgMLST-based and SNP-based typing was integrated with epidemiological and investigation data. A secondary analysis combining the bovine-human isolates with endemic human isolates from southern Israel was performed. A total of 92 isolates from dairy cows and related human cases originating from 18 epidemiological clusters were analysed. Most genomic and epi-clusters were congruent, but sequencing showed relatedness between apparently unrelated farm outbreaks. Nine secondary human infections were also genomically confirmed. The bovine-human cohort appeared intermixed with 126 endemic human isolates in southern Israel. We show a persistent and widespread circulation of B. melitensis in dairy farms in Israel with secondary occupational human infection. The genomic epidemiology also uncovered cryptic connections between outbreaks. A regional connection between bovine and endemic human brucellosis cases points to a common reservoir, most probably local small ruminant herds. Control of humans and bovine brucellosis is inseparable. Epidemiological and microbiological surveillance and implementation of control measures across the entire range of farm animals is needed to mitigate this public health challenge.

Complete genome sequence of multi-drug-resistant Salmonella enterica subsp. enterica serovar Typhimurium strain Bnaya isolated from a dairy calf in Israel.

This manuscript reports the complete genome sequence of a Salmonella enterica subsp. enterica serovar Typhimurium strain (designated "Bnaya"), isolated from a dead dairy calf with severe diarrhea in Israel. The isolate exhibited multi-drug resistance, which is highly unusual in bovine Salmonella spp. in Israel, prompting further investigation.

What Is Hiding in the Israeli Mediterranean Seawater and Beach Sand.

OBJECTIVE: In the present study, we aimed to investigate the presence of fungi that may affect human health in sand and water on Israeli Mediterranean Sea coast beaches. METHODS: The study included screening of the sand and water of six urban beaches from north to south on the Israeli Mediterranean coast. Sand samples were extracted with water, and the water wash was cultured and quantitated. Water samples were quantitated as well. MALDI-TOF MS analysis and ITS sequencing identified the fungi. RESULTS: The study considered several parameters: 1. Presence of fecal-contamination-related fungi; 2. Presence of dermal-infection-related fungi. 3. Presence of allergy-related fungi; 4. Presence of fungi posing risk for immunocompromised individuals. The screen revealed that about 80% of the isolates were molds and about 20% yeasts. The mold species included opportunistic pathogens and potential allergens: Aspergillus fumigatus and other Aspergillus species, Fusarium, Penicillium, and Mucorales species. Yeast isolates included Candida-including the human commensals Candida albicans and Candida tropicalis-Cryptococcus, and Rhodotorula species. CONCLUSIONS: The results suggest that beaches should be monitored for fungi for safer use, better management, and the benefit of public health.

Fecal Microbiome Features Associated with Extended-Spectrum ß-Lactamase-Producing Enterobacterales Carriage in Dairy Heifers.

Extended-spectrum ß-lactamases (ESBLs) are a growing public health threat, and one key human exposure point is through livestock and the food supply. Understanding microbiome factors associated with fecal ESBL carriage can help detect and ideally assist with controlling and preventing ESBL dissemination among livestock. The objective of this study was to investigate the diversity and composition of the heifer fecal microbiota in ESBL-producing Enterobacterales (ESBL-PE) carriers and noncarriers. A total of 59 fecal samples were collected from replacement heifers between 12 and 18 months old from eight dairy farms in central Israel. Genomic DNA was extracted, and 16S rRNA amplicon sequencing was performed (Illumina short reads), focusing on a comparison between 33 ESBL-PE carriers (55.9%) and 26 (44.1%) noncarriers. Samples were analyzed and compared using QIIME2 (DADA2 pipeline and taxonomic assignment with SILVA database) and associated R packages for alpha and beta diversity and taxonomic abundances. Alpha diversity (Shannon diversity) and beta diversity (unweighted UniFrac) showed no significant difference between ESBL-PE carriers and noncarriers. Heifers from farms feeding calves with pooled colostrum had higher ESBL-PE carriage rates than heifers from farms feeding with individual mother colostrum (p < 0.001). Taxonomical abundance analysis revealed that the most common bacterial phyla were Bacteroidetes (44%) and Firmicutes (38%). There was no significant difference in taxonomic composition between ESBL-PE carriers and noncarriers at the phylum and genus levels. However, LEfSe biomarker discovery analysis identified several genera which were significantly different between carriers and noncarriers. For example, Prevotellacaea, Bacteroides, Rikenellaceae, and uncultured Bacteroidales were more abundant in ESBL carriers than noncarriers. Some aspects of microbiota composition differ between ESBL carriers and noncarriers in dairy heifers, specifically the abundance of certain genera. Feeding with pooled colostrum may play a role in that assembly. These could potentially serve as markers of ESBL-PE carriage. However, further research is needed to determine whether these observed differences have a significant impact on colonization with ESBL-PE.

The association between natural drinking water sources and the emergence of zoonotic leptospirosis among grazing beef cattle herds during a human outbreak.

Leptospirosis is a zoonotic bacterial disease associated with water abundance in tropical and temperate climate zones. Bacterial spread may also occur in dry and warm weather conditions when humans and animals are forced to share depleted water sources. In such settings, farm animals such as beef cattle, which may be present in large numbers in natural water sources, can play a major role in disease spread. However, the risk factors for their infection and the potential control measures to prevent the disease spread have not been adequately studied. In the face of an emerging human leptospirosis outbreak in the dry and warm Israeli 2018 summer, we tested seropositivity to Leptospira serovar Pomona in grazing beef cattle and wild boars located in proximity to the contaminated streams. Additionally, we used the natural setting of the outbreak to identify risk factors for seropositivity in beef cattle. We found high seropositivity to serovar Pomona in grazing beef cattle (233/845), and in wild boars (7/13). Seropositivity was significantly associated with beef cattle drinking from natural water sources compared to beef cattle drinking from water troughs with fresh water supply (Multivariable logistic regression; odds ratio = 18.6, 95% confidence interval = 3-116, p-value<0.01). One Health approach is necessary for mitigating zoonotic Leptospira infections, in which interactions between humans, animals, and the environment play a major role. As the global warming crisis results in severe climate changes, dry and warm weather conditions may become more common worldwide. Under such conditions, reducing inter-species interactions in contaminated natural water sources is essential for protecting public health. Our study demonstrates the role of natural water as a source for beef cattle infection and disease spread. Furthermore, we suggest using water troughs with freshwater supply for preventing future outbreaks in animals and humans in such settings.

Seroprevalence of Leptospira spp. in Horses in Israel.

Leptospirosis has been reported in both humans and animals in Israel but has not been reported in horses. In 2018, an outbreak of Leptospira spp. serogroup Pomona was reported in humans and cattle in Israel. In horses, leptospirosis may cause equine recurrent uveitis (ERU). This report describes the first identification of Leptospira serogroup Pomona as the probable cause of ERU in horses in Israel, followed by an epidemiological investigation of equine exposure in the area. Serologic exposure to Leptospira was determined by microscopic agglutination test (MAT) using eight serovars. In 2017, serovar Pomona was identified in a mare with signs of ERU. Seven of thirteen horses from that farm were seropositive for serogroup Pomona, of which three had signs of ERU. During the same time period, 14/70 horses from three other farms were positive for serogroup Pomona. In 2015, two years prior to this diagnosis, 259 horses from 21 farms were sampled and one horse tested seropositive for serovar Icterohaemorrhagiae. In 2018, one year later, 337 horses were sampled on 29 farms, with none testing seropositive. Although horses are not considered a major host of Leptospira spp., it appears that horses may be infected, and clinically affected, in the course of an outbreak in other species. The identification of leptospirosis in stabled horses may impose a significant zoonotic risk to people.

Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes.

BACKGROUND: Therapeutic and growth-promoting antibiotics are frequently used in broiler production. Indirect evidence indicates that these practices are linked to the proliferation of antimicrobial resistance (AMR), the spread of antibiotic-resistant bacteria from food animals to humans, and the environment, but there is a lack of comprehensive experimental data supporting this. We investigated the effects of growth promotor (bacitracin) and therapeutic (enrofloxacin) antibiotic administration on AMR in broilers for the duration of a production cycle, using a holistic approach that integrated both culture-dependent and culture-independent methods. We specifically focused on pathogen-harboring families (Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae). RESULTS: Antibiotic-resistant bacteria and antibiotic resistance genes were ubiquitous in chicken cloaca and litter regardless of antibiotic administration. Environment (cloaca vs. litter) and growth stage were the primary drivers of variation in the microbiomes and resistomes, with increased bacterial diversity and a general decrease in abundance of the pathogen-harboring families with age. Bacitracin-fed groups had higher levels of bacitracin resistance genes and of vancomycin-resistant Enterococcaceae (total Enterococcaceae counts were not higher). Although metagenomic analyses classified 28-76% of the Enterococcaceae as the commensal human pathogens E. faecalis and E. faecium, culture-based analysis suggested that approximately 98% of the vancomycin-resistant Enterococcaceae were avian and not human-associated, suggesting differences in the taxonomic profiles of the resistant and non-resistant strains. Enrofloxacin treatments had varying effects, but generally facilitated increased relative abundance of multidrug-resistant Enterobacteriaceae strains, which were primarily E. coli. Metagenomic approaches revealed a diverse array of Staphylococcus spp., but the opportunistic pathogen S. aureus and methicillin resistance genes were not detected in culture-based or metagenomic analyses. Camphylobacteriaceae were significantly more abundant in the cloacal samples, especially in enrofloxacin-treated chickens, where a metagenome-assembled C. jejuni genome harboring fluoroquinolone and ß-lactam resistance genes was identified. CONCLUSIONS: Within a "farm-to-fork, one health" perspective, considering the evidence that bacitracin and enrofloxacin used in poultry production can select for resistance, we recommend their use be regulated. Furthermore, we suggest routine surveillance of ESBL E. coli, vancomycin-resistant E. faecalis and E. faecium, and fluoroquinolone-resistant C. jejuni strains considering their pathogenic nature and capacity to disseminate AMR to the environment. Video Abstract.

Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles.

Farmers apply broiler chicken litter to soils to enrich organic matter and provide crops with nutrients, following varying periods of stockpiling. However, litter frequently harbors fecal-derived microbial pathogens and associated antibiotic resistance genes (ARGs), and may be a source of microbial contamination of produce. We coupled a cutting-edge Loop Genomics long-read 16S rRNA amplicon-sequencing platform with high-throughput qPCR that targeted a suite of ARGs, to assess temporal (five time points over a 60-day period) and spatial (top, middle and bottom layers) microbiome and resistome dynamics in a broiler litter stockpile. We focused on potentially pathogenic species from the Enterobacteriaceae, Enterococcaceae and Staphylococcaceae families associated with food-borne disease. Bacterial diversity was significantly lower in the middle of the stockpile, where targeted pathogens were lowest and Bacillaceae were abundant. E. coli was the most abundant Enterobacteriaceae species, and high levels of the opportunistic pathogen Enterococcus faecium were detected. Correlation analyses revealed that the latter was significantly associated with aminoglycoside (aac(6')-Ib(aka aacA4), aadA5), tetracycline (tetG), vancomycin (vanC), phenicol (floR) and MLSB (mphB) resistance genes. Staphylococcaceae were primarily non-pathogenic, but extremely low levels of the opportunistic pathogen S. aureus were detected, as was the opportunistic pathogen S. saprophyticus, which was linked to vancomycin (vanSA, vanC1), MLSB (vatE, ermB) and tetracycline (tetK) resistance genes. Collectively, we found that stockpile microbiomes and resistomes are strongly dictated by temporal fluctuations and spatial heterogeneity. Insights from this study can be exploited to improve stockpile management practice to support sustainable antimicrobial resistance mitigation policies in the future.

Globetrotting strangles: the unbridled national and international transmission of Streptococcus equi between horses.

The equine disease strangles, which is characterized by the formation of abscesses in the lymph nodes of the head and neck, is one of the most frequently diagnosed infectious diseases of horses around the world. The causal agent, Streptococcus equi subspecies equi, establishes a persistent infection in approximately 10 % of animals that recover from the acute disease. Such 'carrier' animals appear healthy and are rarely identified during routine veterinary examinations pre-purchase or transit, but can transmit S. equi to naïve animals initiating new episodes of disease. Here, we report the analysis and visualization of phylogenomic and epidemiological data for 670 isolates of S. equi recovered from 19 different countries using a new core-genome multilocus sequence typing (cgMLST) web bioresource. Genetic relationships among all 670 S. equi isolates were determined at high resolution, revealing national and international transmission events that drive this endemic disease in horse populations throughout the world. Our data argue for the recognition of the international importance of strangles by the Office International des Épizooties to highlight the health, welfare and economic cost of this disease. The Pathogenwatch cgMLST web bioresource described herein is available for tailored genomic analysis of populations of S. equi and its close relative S. equi subspecies zooepidemicus that are recovered from horses and other animals, including humans, throughout the world. This article contains data hosted by Microreact.