Modelling the impact of wastewater flows and management practices on antimicrobial resistance in dairy farms.

Dairy slurry is a major source of environmental contamination with antimicrobial resistant genes and bacteria. We developed mathematical models and conducted on-farm research to explore the impact of wastewater flows and management practices on antimicrobial resistance (AMR) in slurry. Temporal fluctuations in cephalosporin-resistant Escherichia coli were observed and attributed to farm activities, specifically the disposal of spent copper and zinc footbath into the slurry system. Our model revealed that resistance should be more frequently observed with relevant determinants encoded chromosomally rather than on plasmids, which was supported by reanalysis of sequenced genomes from the farm. Additionally, lower resistance levels were predicted in conditions with lower growth and higher death rates. The use of muck heap effluent for washing dirty channels did not explain the fluctuations in cephalosporin resistance. These results highlight farm-specific opportunities to reduce AMR pollution, beyond antibiotic use reduction, including careful disposal or recycling of waste antimicrobial metals.

Multidrug-Resistant ESBL-Producing E. coli in Clinical Samples from the UK.

Globally, cephalosporin therapy failure is a serious problem for infection control. One causative agent of cephalosporin-resistant infections is multidrug-resistant (MDR) E. coli producing extended-spectrum ß-lactamases (ESBLs) and/or plasmid-encoded AmpC (pAmpC) ß-lactamases. We evaluated the occurrence of ESBL/pAmpC genetic determinants in phenotypically MDR E. coli isolated from clinical samples of blood, faeces, ear effusion, urine and sputum from a UK hospital. Phenotypic resistance profiling for 18 antibiotics (from seven classes) showed that 32/35 isolates were MDR, with resistance to 4-16 of the tested antibiotics. Of the isolates, 97.1% showed resistance to ampicillin, 71.4% showed resistance to co-amoxiclav, cefotaxime, ceftazidime and ceftiofur, and 68.5% showed resistance to cefquinome. blaCTX-M, blaTEM and blaOXA-1 genes were detected in 23, 13 and 12 strains, respectively, and Intl1 was detected in 17 isolates. The most common subtypes among the definite sequence types were CTX-M-15 (40%) and TEM-1 (75%). No E. coli isolates carried pAmpC genes. Significant correlations were seen between CTX-M carriage and cefotaxime, ceftiofur, aztreonam, ceftazidime and cefquinome resistance; between blaCTX-M, blaTEM and blaOXA-1 carriage and ciprofloxacin resistance; and between Intl1 carriage and trimethoprim/sulfamethoxazole resistance. Thus, MDR phenotypes may be conferred by a relatively small number of genes. The level and pattern of antibiotic resistance highlight the need for better antibiotic therapy guidelines, including reduced use and improved surveillance.

Antimicrobial resistance in dairy slurry tanks: A critical point for measurement and control.

Waste from dairy production is one of the largest sources of contamination from antimicrobial resistant bacteria (ARB) and genes (ARGs) in many parts of the world. However, studies to date do not provide necessary evidence to inform antimicrobial resistance (AMR) countermeasures. We undertook a detailed, interdisciplinary, longitudinal analysis of dairy slurry waste. The slurry contained a population of ARB and ARGs, with resistances to current, historical and never-used on-farm antibiotics; resistances were associated with Gram-negative and Gram-positive bacteria and mobile elements (ISEcp1, Tn916, Tn21-family transposons). Modelling and experimental work suggested that these populations are in dynamic equilibrium, with microbial death balanced by fresh input. Consequently, storing slurry without further waste input for at least 60 days was predicted to reduce ARB spread onto land, with > 99 % reduction in cephalosporin resistant Escherichia coli. The model also indicated that for farms with low antibiotic use, further reductions are unlikely to reduce AMR further. We conclude that the slurry tank is a critical point for measurement and control of AMR, and that actions to limit the spread of AMR from dairy waste should combine responsible antibiotic use, including low total quantity, avoidance of human critical antibiotics, and choosing antibiotics with shorter half-lives, coupled with appropriate slurry storage.

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens.

BACKGROUND: Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste. There are currently ~ 2.7 million dairy cattle in the UK producing 7-8% of their own bodyweight in manure daily, and 28 million tonnes annually. To avoid pollution of UK freshwaters, manure must be stored and spread in accordance with guidelines set by DEFRA. Manures are used as fertiliser, and widely spread over crop fields, yet little is known about their microbial composition. We analysed the virome of agricultural slurry over a 5-month period using short and long-read sequencing. RESULTS: Hybrid sequencing uncovered more high-quality viral genomes than long or short-reads alone; yielding 7682 vOTUs, 174 of which were complete viral genomes. The slurry virome was highly diverse and dominated by lytic bacteriophage, the majority of which represent novel genera (~ 98%). Despite constant influx and efflux of slurry, the composition and diversity of the slurry virome was extremely stable over time, with 55% of vOTUs detected in all samples over a 5-month period. Functional annotation revealed a diverse and abundant range of auxiliary metabolic genes and novel features present in the community, including the agriculturally relevant virulence factor VapE, which was widely distributed across different phage genera that were predicted to infect several hosts. Furthermore, we identified an abundance of phage-encoded diversity-generating retroelements, which were previously thought to be rare on lytic viral genomes. Additionally, we identified a group of crAssphages, including lineages that were previously thought only to be found in the human gut. CONCLUSIONS: The cattle slurry virome is complex, diverse and dominated by novel genera, many of which are not recovered using long or short-reads alone. Phages were found to encode a wide range of AMGs that are not constrained to particular groups or predicted hosts, including virulence determinants and putative ARGs. The application of agricultural slurry to land may therefore be a driver of bacterial virulence and antimicrobial resistance in the environment. Video abstract.

Antibiotic and Metal Resistance in Escherichia coli Isolated from Pig Slaughterhouses in the United Kingdom.

Antimicrobial resistance is currently an important concern, but there are few data on the co-presence of metal and antibiotic resistance in potentially pathogenic Escherichia coli entering the food chain from pork, which may threaten human health. We have examined the phenotypic and genotypic resistances to 18 antibiotics and 3 metals (mercury, silver, and copper) of E. coli from pig slaughterhouses in the United Kingdom. The results showed resistances to oxytetracycline, streptomycin, sulphonamide, ampicillin, chloramphenicol, trimethoprim-sulfamethoxazole, ceftiofur, amoxicillin-clavulanic acid, aztreonam, and nitrofurantoin. The top three resistances were oxytetracycline (64%), streptomycin (28%), and sulphonamide (16%). Two strains were resistant to six kinds of antibiotics. Three carried the blaTEM gene. Fifteen strains (18.75%) were resistant to 25 µg/mL mercury and five (6.25%) of these to 50 µg/mL; merA and merC genes were detected in 14 strains. Thirty-five strains (43.75%) showed resistance to silver, with 19 possessing silA, silB, and silE genes. Fifty-five strains (68.75%) were resistant to 8 mM copper or above. Seven contained the pcoE gene. Some strains were multi-resistant to antibiotics, silver, and copper. The results in this study, based on strains isolated between 2007 and 2010, will aid understanding about the effects of strategies to reduce resistance and mechanisms of antimicrobial resistance (AMR).

Diversity of Lactobacillus Species of Stilton Cheese Relates to Site of Isolation.

This study has characterized the dominant non-starter Lactobacillus species isolated from different sites in a Stilton cheese to establish its diversity, stress-tolerance, anti-microbial activity and potential contribution to quality of cheese. Fifty-nine Lactobacillus isolates were cultured from the outer crust, blue veins and white core of the cheese and were speciated phenotypically and by 16S rDNA sequence analysis. Lactobacillus plantarum was the dominant species detected with only two isolates identified as Lactobacillus brevis. Strains were typed by pulse-field gel electrophoresis (PFGE) using the enzyme NotI to examine their genomic diversity. Cluster analysis of PFGE patterns produced five major clusters which associated isolates with their sites of isolation within the cheese. One L. plantarum isolate from each cheese site was selected and evaluated for salt, acid, relative humidity, and heat tolerance to determine whether stress conditions within the isolation site selected their phenotype. D 72°C values were 6, 13, and 17 s for strains from the crust, veins and core, respectively, suggesting strains on the crust may not have been able to survive pasteurization and therefore had been added post-pasteurization. All strains recovered from heat injury within 24-48 h at 4°C. pH values of 3, 3.5, and 4 suppressed growth but strains showed a varying ability to grow at pH 4.5 and 5; isolates from the core (which has the lowest pH) were the most acid-tolerant. All strains grew at 3.5 and 5% salt but were suppressed at 10%; those from the crust (which has a lower water activity) were the most halo-tolerant, growing at 8% salt whereas strains from the core were sensitive to this salt concentration. All 57 L. plantarum isolates were examined for antimicrobial activity and variable activity against Lactobacillus pentosus and other genera was demonstrated; plantaricin EF genes were present in 65% of strains. It was concluded that there are varied phenotypes and genotypes of Lactobacillus in a Stilton cheese according to site of isolation. Occurrence of different L. plantarum genotypes could contribute to variation in the cheese quality from batch to batch and provides criteria for selecting isolates as potential adjunct cultures.

Acid production, growth kinetics and aroma profiles of Lactobacillus flora from Stilton cheese.

The effect of Lactobacillus plantarum isolates from Stilton cheese on aroma profiles of milk fermentation was examined. Representative Lb. plantarum isolates were cultured alone and in combination with acid-producing and non-acid producing Lactococcus lactis NCIMB 9918 in UHT milk at 30 & 18 °C for 48 h & 12 weeks, respectively in presence and absence of salt, simulating cheese production and ripening. During long-term ripening, Lb. plantarum grew faster when co-cultured with non-acid producing Lc. lactis in the presence of salt. One isolate of Lb. plantarum produced the highest concentration of alcohols, organic acids and acetoin. Co-culture of Lb. plantarum with acid-producing Lc. lactis enhanced acid and alcohol production, whereas co-inoculation with non-acid producing Lc. lactis increased acetoin synthesis. Lb. plantarum is an incidental organism in cheese and its presence is unpredictable. Occurrence of different genotypes of Lb. plantarum could contribute to batch to batch variation in the cheese aroma characteristics.

Microbial community dynamics of a blue-veined raw milk cheese from the United Kingdom.

A commercial blue-veined cheese made from unpasteurized milk was examined by conventional culturing and PCR denaturing gradient gel electrophoresis analysis of the bacterial community 16S rRNA genes using 3 primer sets, V3, V4V5, and V6V8. Genomic DNA for amplification was extracted directly from raw milk, starter culture, cheese at different stages of production, fully ripened cheese, and from the cultured cells grown on various media. The outer rind was sampled separately from the inner white core and blue veins. A diverse microbiota containing Lactococcus lactis ssp. lactis, Lactobacillus plantarum, Lactobacillus curvatus, Staphylococcus gallinarum, Staphylococcus devriesei, Microbacterium sp., Sphingobacterium sp., Mycetocola sp., Brevundimonas sp., Enterococcus faecalis, Proteus sp., and Kocuria sp. was detected in the raw milk using culturing methods, but only Lactococcus lactis ssp. lactis, Lactobacillus plantarum, and Enterococcus faecalis survived to the final cheese and were detected both in the core and the rind. Using PCR denaturing gradient gel electrophoresis analysis of the cheese process samples, Staphylococcus equorum and Enterococcus durans were found in the rind of prepiercing samples but not in the core and veins; after piercing, these species were found in all parts of the cheese but survived only in the rind when the cheese was fully ripened. Brevibacterium sp., Halomonas sp., Acinetobacter sp., Alkalibacterium sp., and Corynebacterium casei were identified only by PCR denaturing gradient gel electrophoresis and not cultured from the samples. Brevibacterium sp. was initially identified in the cheese postpiercing (core and veins), Halomonas sp. was found in the matured cheese (rind), and Acinetobacter sp., Alkalibacterium sp., and Corynebacterium casei were also found in the prepiercing samples (rind) and then found through the subsequent process stages. The work suggests that in this raw milk cheese, a limited community from the milk survive to the final cheese, with salt addition and handling contributing to the final cheese consortium.

Draft Genome Sequence of the Bacteriophage vB_Eco_slurp01.

Bacteriophage vB_Eco_slurp01 was isolated from porcine feces using Escherichia coli MG1655 as a host. With a genome size of 348 kb, vB_Eco_slurp01 is one of the largest bacteriophages isolated to date.

Mathematical modelling of antimicrobial resistance in agricultural waste highlights importance of gene transfer rate.

Antimicrobial resistance is of global concern. Most antimicrobial use is in agriculture; manures and slurry are especially important because they contain a mix of bacteria, including potential pathogens, antimicrobial resistance genes and antimicrobials. In many countries, manures and slurry are stored, especially over winter, before spreading onto fields as organic fertilizer. Thus, these are a potential location for gene exchange and selection for resistance. We develop and analyse a mathematical model to quantify the spread of antimicrobial resistance in stored agricultural waste. We use parameters from a slurry tank on a UK dairy farm as an exemplar. We show that the spread of resistance depends in a subtle way on the rates of gene transfer and antibiotic inflow. If the gene transfer rate is high, then its reduction controls resistance, while cutting antibiotic inflow has little impact. If the gene transfer rate is low, then reducing antibiotic inflow controls resistance. Reducing length of storage can also control spread of resistance. Bacterial growth rate, fitness costs of carrying antimicrobial resistance and proportion of resistant bacteria in animal faeces have little impact on spread of resistance. Therefore, effective treatment strategies depend critically on knowledge of gene transfer rates.

Multidrug resistant, extended spectrum ß-lactamase (ESBL)-producing Escherichia coli isolated from a dairy farm.

Escherichia coli strains were isolated from a single dairy farm as a sentinel organism for the persistence of antibiotic resistance genes in the farm environment. Selective microbiological media were used to obtain 126 E. coli isolates from slurry and faeces samples from different farm areas. Antibiotic resistance profiling for 17 antibiotics (seven antibiotic classes) showed 57.9% of the isolates were resistant to between 3 and 15 antibiotics. The highest frequency of resistance was to ampicillin (56.3%), and the lowest to imipenem (1.6%), which appeared to be an unstable phenotype and was subsequently lost. Extended spectrum ß-lactamase (ESBL) resistance was detected in 53 isolates and blaCTX-M, blaTEM and blaOXA genes were detected by PCR in 12, 4 and 2 strains, respectively. Phenotypically most isolates showing resistance to cephalosporins were AmpC rather than ESBL, a number of isolates having both activities. Phenotypic resistance patterns suggested co-acquisition of some resistance genes within subsets of the isolates. Genotyping using ERIC-PCR demonstrated these were not clonal, and therefore co-resistance may be associated with mobile genetic elements. These data show a snapshot of diverse resistance genes present in the E. coli population reservoir, including resistance to historically used antibiotics as well as cephalosporins in contemporary use.

Survival and death kinetics of Salmonella strains at low relative humidity, attached to stainless steel surfaces.

Salmonella is a major pathogen of concern for low water activity foods and understanding its persistence in dry food processing environments is important for producing safe food. The studies sought to assess the survival of 15 isolates of Salmonella on stainless steel surfaces. Additionally, the aim was to select a suitable model to describe and understand the strains' survival kinetics. Salmonella isolates were dried onto stainless steel surfaces, placed in controlled temperature (25°C) and humidity (33%) conditions and their viability assessed at times from 1h to 30days. The highest survival rate was associated with S. Typhimurium DT104, S. Muenchen, and S. Typhimurium (NCTC 12023), where, after 30days, the reduction ranged from 1.3log10 cfu/surface to 1.6log10 cfu/surface. The lowest survival was linked to a S. Typhimurium strain used in European Standard disinfectant approval tests and S. Typhimurium isolated from whey powder. For most of the strains, following an initial reduction in viability in the first hours (<72h), no further reduction was seen over the 30day period; therefore a 2-population Weibull model was fitted to model the survival kinetics. The overall survival was neither serotype nor time related. All strains had two different subpopulations, one more resistant to desiccation than the other. The results indicate the possibility of the long term survival of Salmonella on environmental surfaces (at least 30days) and suggest the most suitable model to describe and predict survival kinetics. The results also identify strains that may be used to study stress response mechanisms and potential factory control measures in future studies.

Diversity and activities of yeasts from different parts of a Stilton cheese.

Blue cheeses are very complex food matrices presenting significant spatial differentiation between sections and the Stilton variety also has a hard brown crust making its matrix even more complex. The mycobiota communities in the three sections (blue veins, white core and outer crust) of a Stilton blue cheese were studied by employing culture-independent (TRFLP, DGGE) and culture-dependent analyses. Yeasts isolated from the cheese were studied for aroma production in a dairy model system with and without the starter Lactococcus lactis and filamentous fungus Penicillium roqueforti using SPME GC-MS. Significant qualitative and quantitative differences were observed in the yeast communities between the cheese sections with all the techniques. Yarrowia lipolytica presented strong synergistic activity with P. roqueforti enhancing the production of ketone aroma compounds, characteristic of blue cheeses. Culture techniques allowed the observation of the presence and uneven distribution of two different morphological groups of Debaryomyces hansenii in the different sections and of Trichosporon ovoides but failed to isolate Candida catenulata which dominated some parts of the cheese in the culture-independent analysis. This suggests that this species may be an important early coloniser but fails to survive into the final cheese. The study indicated that the yeast flora in the cheese sections differ including isolates that could affect their aroma profiles.

Study of the influence of yeast inoculum concentration (Yarrowia lipolytica and Kluyveromyces lactis) on blue cheese aroma development using microbiological models.

Yarrowia lipolytica and Kluyveromyces lactis occur as part of Stilton cheese microflora yet are not controlled during production. This study investigated the influence of their inoculum concentration on aroma production. Models of Y. lipolytica and K. lactis, with Penicillium roqueforti, were analysed using instrumental and sensory analysis. Different concentrations of Y. lipolytica produced important changes in the aroma profiles of microbiological models, analysed by solid-phase microextraction (SPME GC-MS). Sensory analysis with discrimination tests showed differences were detectable via human perception but did not concern the similarity to blue cheese odour. Increasing the inoculum concentration of K. lactis resulted in decreased variation between replicates. Partial least squares (PLS) regression on Flash profile data showed models inoculated with low concentrations of K. lactis exhibited blue cheese-related attributes, associated with increased ketone production. Results suggest that controlling the amount of Y. lipolytica and K. lactis during production offers potential to manipulate blue cheese aroma development.

Detection of Mycobacterium avium subsp. paratuberculosis in bulk tank milk by combined phage-PCR assay: evidence that plaque number is a good predictor of MAP.

Conventional culture and a rapid phage-PCR method were used to detect Mycobacterium avium subsp. paratuberculosis (MAP) in bulk tank milk (BTM) samples. Only two of 225 samples (0.9%) were found to contain MAP by culture whereas 50 (22%) MAP-positive samples were identified using the phage-PCR assay, including both samples that were MAP-culture positive. Results using the phage-based method for independently tested duplicate samples indicated that the assay is very reproducible (r(2)=0.897), especially when low levels of mycobacteria are present. A relationship was established between plaque number and the presence of MAP in a sample. A cut-off value was determined allowing identification of MAP-positive samples based on plaque number alone (90% sensitivity, 99% specificity; area under the curve=0.976). These results indicate that the assay is a robust method for screening BTM, providing results within 24 h.

Suicide through stress: a bacterial response to sub-lethal injury in the food environment.

The response of bacteria to sub-lethal injury is an important aspect of food microbiology as many inimical processes to which bacteria are subjected during processing are non-lethal. For pathogens like Salmonella and Escherichia coli, the difference in injury levels of exponential phase cells compared to their stationary phase counterparts in this regard is well recognised and evident for a variety of inimical processes. The expression of a range of stress resistance genes under the control of the sigma factor RpoS provides some explanation for the greater resistance of stationary phase cells. However in 1997 the suicide response hypothesis was put forward as an explanation for the observed response of Salmonella and E. coli to sub-lethal stresses. This hypothesis arose as an explanation for the observed protection of Salmonella and E. coli strains to heat and freeze-thaw injury by the presence of a high level of competitor organisms, a protection that had been shown to be RpoS independent. The central tenet of this theory was that under sub-lethal stress bacteria produce a burst of intracellular free radicals and it is these that lead to sub-lethal injury and/or death. Exponential phase cells because of their more active metabolism are more susceptible to this effect and suffer greater damage. This paper reviews the origins of this theory, the evidence for a free radical response and explores the potential mechanisms by which competitor cells produce a protective effect.

Demonstration of antifreeze protein activity in Antarctic lake bacteria.

Antifreeze proteins (AFPs) are a structurally diverse group of proteins that have the ability to modify ice crystal structure and inhibit recrystallization of ice. AFPs are well characterized in fish and insects, but very few bacterial species have been shown to have AFP activity to date. Thirty eight freshwater to hypersaline lakes in the Vestfold Hills and Larsemann Hills of Eastern Antarctica were sampled for AFPs during 2000. Eight hundred and sixty six bacterial isolates were cultivated. A novel AFP assay, designed for high-throughput analysis in Antarctica, demonstrated putative activity in 187 of the cultures. Subsequent analysis of the putative positive isolates showed 19 isolates with significant recrystallization inhibition (RI) activity. The 19 RI active isolates were characterized using ARDRA (amplified rDNA restriction analysis) and 16S rDNA sequencing. They belong to genera from the alpha- and gamma-Proteobacteria, with genera from the gamma-subdivision being predominant. The 19 AFP-active isolates were isolated from four physico-chemically diverse lakes. Ace Lake and Oval Lake were both meromictic with correspondingly characteristic chemically stratified water columns. Pendant Lake was a saline holomictic lake with different chemical properties to the two meromictic lakes. Triple Lake was a hypersaline lake rich in dissolved organic carbon and inorganic nutrients. The environments from which the AFP-active isolates were isolated are remarkably diverse. It will be of interest, therefore, to elucidate the evolutionary forces that have led to the acquisition of functional AFP activity in microbes of the Vestfold Hills lakes and to discover the role the antifreezes play in these organisms.

Phage amplification assay as rapid method for Salmonella detection

A aplicação de métodos rápidos é crucial para a implantação de programas de HACCP em indústrias de alimentos. Neste contexto, o método de amplificação de bacteriófagos é um instrumento de diagnóstico importante porque está baseado na interação dos bacteriófagos com suas células hospedeiras. Este método, usando o bacteriófago P22, foi aplicado para detectar Salmonella em peito de frango. Amostras de 25 g de peito de frango foram diluídas e as diluições apropriadas foram usadas no método de amplificação de bacteriófagos na detecção de Salmonella. Após 3-4 horas de incubação, foi observado uma titulação de partículas virais de, aproximadamente, 104 ufp mL-1 (unidades formadoras de placas virais), indicando a presença de células de Salmonella na carne de frango. A comprovação da presença de Salmonella neste produto foi verificada usando-se plaqueamento direto em ágar XLD e procedimento de enriquecimento convencional. As colônias suspeitas de Salmonella foram sorologicamente testadas e identificadas como pertencendo aos sorogrupos B (grupo de S. typhimurium) e D (grupo de S. enteritidis). Portanto, concluiu-se que este método pode ser aplicado, na detecção de Salmonella em alimentos, porque fornece rápido e conclusivo resultado, reduzindo o tempo de análise e o trabalho laboratorial para 3-4 horas.

Application of host-specific bacteriophages to the surface of chicken skin leads to a reduction in recovery of Campylobacter jejuni.

Retail poultry products are widely purported as the major infection vehicle for human campylobacteriosis. Numerous intervention strategies have sought to reduce Campylobacter contamination on broiler carcasses in the abattoir. This study reports the efficacy of bacteriophage in reducing the number of recoverable Campylobacter jejuni cells on artificially contaminated chicken skin.