ECOPHAGE: Combating Antimicrobial Resistance Using Bacteriophages for Eco-Sustainable Agriculture and Food Systems.

The focus of this meeting was to discuss the suitability of using bacteriophages as alternative antimicrobials in the agrifood sector. Following a One Health approach, the workshop explored the possibilities of implementing phage application strategies in the agriculture, animal husbandry, aquaculture, and food production sectors. Therefore, the meeting had gathered phage researchers, representatives of the agrifood industry, and policymakers to debate the advantages and potential shortcomings of using bacteriophages as alternatives to traditional antimicrobials and chemical pesticides. Industry delegates showed the latest objectives and demands from consumers. Representatives of regulatory agencies (European Medicines Agency (EMA) and Spanish Agency of Medicines and Health Products (AEMPS)) presented an update of new regulatory aspects that will impact and support the approval and implementation of phage application strategies across the different sectors.

A New Pipeline for Designing Phage Cocktails Based on Phage-Bacteria Infection Networks.

In recent years, the spread of antibiotic-resistant bacteria and efforts to preserve food microbiota have induced renewed interest in phage therapy. Phage cocktails, instead of a single phage, are commonly used as antibacterial agents since the hosts are unlikely to become resistant to several phages simultaneously. While the spectrum of activity might increase with cocktail complexity, excessive phages could produce side effects, such as the horizontal transfer of genes that augment the fitness of host strains, dysbiosis or high manufacturing costs. Therefore, cocktail formulation represents a compromise between achieving substantial reduction in the bacterial loads and restricting its complexity. Despite the abovementioned points, the observed bacterial load reduction does not increase significantly with the size of phage cocktails, indicating the requirement for a systematic approach to their design. In this work, the information provided by host range matrices was analyzed after building phage-bacteria infection networks (PBINs). To this end, we conducted a meta-analysis of 35 host range matrices, including recently published studies and new datasets comprising Escherichia coli strains isolated during ripening of artisanal raw milk cheese and virulent coliphages from ewes' feces. The nestedness temperature, which reflects the host range hierarchy of the phages, was determined from bipartite host range matrices using heuristic (Nestedness Temperature Calculator) and genetic (BinMatNest) algorithms. The latter optimizes matrix packing, leading to lower temperatures, i.e., it simplifies the identification of the phages with the broadest host range. The structure of infection networks suggests that generalist phages (and not specialist phages) tend to succeed in infecting less susceptible bacteria. A new metric (Φ), which considers some properties of the host range matrices (fill, temperature, and number of bacteria), is proposed as an estimator of phage cocktail size. To identify the best candidates, agglomerative hierarchical clustering using Ward's method was implemented. Finally, a cocktail was formulated for the biocontrol of cheese-isolated E. coli, reducing bacterial counts by five orders of magnitude.

Corrigendum: Diversity and Local Coadaptation of Escherichia coli and Coliphages From Small Ruminants.

[This corrects the article DOI: 10.3389/fmicb.2020.564522.].

Diversity and Local Coadaptation of Escherichia coli and Coliphages From Small Ruminants.

Bacteriophages are highly specific predators that drive bacterial diversity through coevolution while striking tradeoffs among preserving host populations for long-term exploitation and increasing their virulence, structural stability, or host range. Escherichia coli and other coliform bacteria present in the microbiota of milk and during early ripening of raw milk cheeses have been linked to the production of gas, manifested by the appearance of eyes, and the development of off-flavors; thus, they might cause early blowing and cheese spoilage. Here, we report the characterization of coliphages isolated from manure from small ruminant farms and E. coli strains isolated from goat and sheep raw milk cheese. Additionally, the virulence and host range of locally isolated and laboratory collection phages were determined by comparing the susceptibility of E. coli strains from different sources. In agreement with the high genetic diversity found within the species E. coli, clustering analysis of whole-cell protein revealed a total of 13 distinct profiles but none of the raw milk cheese isolates showed inhibition of growth by reference or water-isolated coliphages. Conversely, 10 newly isolated phages had a broad host range (i.e., able to lyse ≥50% of bacterial hosts tested), thus exhibiting utility for biocontrol and only one cheese-isolated E. coli strain was resistant to all the phages. Whereas there was a high positive correlation between bacterial susceptibility range and lysis intensity, the phages virulence decreased as range increased until reaching a plateau. These results suggest local gene-for-gene coevolution between hosts and phages with selective tradeoffs for both resistance and competitive ability of the bacteria and host-range extension and virulence of the phage populations. Hence, different phage cocktail formulations might be required when devising long-term and short-term biocontrol strategies.

Early blowing in raw goats' milk cheese: gas production capacity of Enterobacteriaceae species present during manufacturing and ripening.

The aim of this study was to identify the main Enterobacteriaceae species responsible for early gas blowing during curdling and the first week of ripening in raw goats' milk cheese. Two batches of raw goats' milk cheese were selected. One of them showed early blowing within the first 24 h of cheese ripening while the other showed no alteration. Although initial levels of Enterobacteriaceae were similar in defective and non-defective cheese, their dynamics (growth and disappearance rates of the species detected) were different. Klebsiella oxytoca and Enterobacter cloacae were the main species in the defective curd, whereas Buttiauxela spp. was predominant in normal curd. Hafnia alvei was the prevailing isolated species for both normal and defective cheese throughout the ripening process. The highest gas production was rendered by K. oxytoca and H. alvei, mainly isolated from curd and cheese. However, other species relevant in milk or curd, like Pantoea ssp. or Buttiauxela spp. were considered as low gas producers. The analysis of digitalized images of cheese showed that most of the cheese eyes were formed before the first week of ripening, although this process continued during maturation.According to the species found in the defective and non-defective cheese, their proportions at different ripening stages, their ability to produce gas and eye formation, K. oxytoca might be considered the most likely responsible for early blowing in raw goats' milk cheeses; while H. alvei increased the eyes number in the later stages of the ripening period.

Improved detection of Escherichia coli and coliform bacteria by multiplex PCR.

BACKGROUND: The presence of coliform bacteria is routinely assessed to establish the microbiological safety of water supplies and raw or processed foods. Coliforms are a group of lactose-fermenting Enterobacteriaceae, which most likely acquired the lacZ gene by horizontal transfer and therefore constitute a polyphyletic group. Among this group of bacteria is Escherichia coli, the pathogen that is most frequently associated with foodborne disease outbreaks and is often identified by ß-glucuronidase enzymatic activity or by the redundant detection of uidA by PCR. Because a significant fraction of essential E. coli genes are preserved throughout the bacterial kingdom, alternative oligonucleotide primers for specific E. coli detection are not easily identified. RESULTS: In this manuscript, two strategies were used to design oligonucleotide primers with differing levels of specificity for the simultaneous detection of total coliforms and E. coli by multiplex PCR. A consensus sequence of lacZ and the orphan gene yaiO were chosen as targets for amplification, yielding 234 bp and 115 bp PCR products, respectively. CONCLUSIONS: The assay designed in this work demonstrated superior detection ability when tested with lab collection and dairy isolated lactose-fermenting strains. While lacZ amplicons were found in a wide range of coliforms, yaiO amplification was highly specific for E. coli. Additionally, yaiO detection is non-redundant with enzymatic methods.

Salt influence on surface microorganisms and ripening of soft ewe cheese.

The effect of different brining treatments on salt uptake and diffusion during the first 30 d of ripening was determined in soft ewe cheese. Additionally, salt influence on surface microorganisms and physicochemical parameters was evaluated. Cheeses were placed into different brine solutions (14, 18 and 24°Bé) at 5 and 10 °C for 1, 2 or 3 h. Samples from rind, outer core and inner core were analysed at 0, 7, 15 and 30 d. Complete salt diffusion from rind to the inner core took about 15 d. The resulting salt gradient favoured the development of a pH gradient from the surface to the inner core. Salt concentration also had a significant effect on the growth of surface microorganisms (mesophiles, pseudomonads and halotolerants). However, mould and yeasts were not affected throughout ripening by the salt levels achieved. Brine salting by immersion for 3 h at 10 °C in 24°B brine was found to be the most suitable treatment to control pseudomonads in cheese rind, as spoilage microorganism.

Effect of high-pressure processing and thermal treatment on quality attributes and nutritional compounds of "Songold" plum purée.

UNLABELLED: The application of hydrostatic high pressure on a "Songold" plum purée was assessed in comparison with heat pasteurization. To simulate industrial conditions, one-half of the total purée was manufactured with a pretreatment of thermal blanching (TB) and the other half without it (nonthermally blanched, NTB). Changes after thermal treatment and high-pressure processing (HPP: 400, 600 MPa) and after 20 d of refrigerated storage were evaluated. HPP maintained the microbial stability of the purées until the end of the storage period. Polyphenol oxidase activity was lower in TB purées than NTB purées. No treatment was completely effective to stop the enzyme activity, although a significant reduction was reached. Thermally treated purées showed more intense color changes after processing and storage than HP-treated purées. After processing, high-pressure (HP) purées treated at 600 MPa (TB and NTB) increased the extractability of carotenoids compared with initial untreated purée. Nevertheless, at the end of the storage, the highest carotenoid content was found in the TB purée treated at 400 MPa. After processing, total polyphenol levels were similar in all purées. TB and 600 MPa processing was more effective in the maintenance of the polyphenols than the other purées. TB increased the level of antioxidants after storage, compared to NTB purées. A previous TB step is necessary to inactivate browning enzymes before HPP to maintain the levels of bioactive compounds. HPP of plum purée could be a suitable alternative to traditional thermal processing, but more studies are necessary to ensure a major inactivation of polyphenol oxidase. PRACTICAL APPLICATION: High-pressure processing is one of the most successful technologies to obtain high-quality fruit purées without appreciable losses in taste, flavor, color, and nutritive value. However, for the introduction of a new technology, some advantages compared to the traditional thermal treatment need to be emphasized. The application of this technology could be reduced due to resistance of certain enzymes to pressurization. For this reason, in some cases the application of a previous thermal blanching can be necessary at industrial level. However, this can reduce the advantages of HPP application. This paper provides interesting information about the storage stability of plum purées after high-pressure treatments and assesses the need for applying heat pretreatments.