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Bacteriophages are ubiquitous organisms that can be specific to one or multiple strains of hosts, in addition to being the most abundant entities on the planet. It is estimated that they exceed ten times the total number of bacteria. They are classified as temperate, which means that phages can integrate their genome into the host genome, originating a prophage that replicates with the host cell and may confer immunity against infection by the same type of phage; and lytics, those with greater biotechnological interest and are viruses that lyse the host cell at the end of its reproductive cycle. When lysogenic, they are capable of disseminating bacterial antibiotic resistance genes through horizontal gene transfer. When professionally lytic—that is, obligately lytic and not recently descended from a temperate ancestor—they become allies in bacterial control in ecological imbalance scenarios; these viruses have a biofilm-reducing capacity. Phage therapy has also been advocated by the scientific community, given the uniqueness of issues related to the control of microorganisms and biofilm production when compared to other commonly used techniques. The advantages of using bacteriophages appear as a viable and promising alternative. This review will provide updates on the landscape of phage applications for the biocontrol of pathogens in industrial settings and healthcare. [ABSTRACT FROM AUTHOR]

Food‐borne microbial illness contributes up to one third of global disease burden. The largest category of food‐borne illness is gastroenteritis, the majority of which is caused by enteric viruses. Viruses like these are transmitted to food either by waste‐contaminated waters, or by handling and transfer during processing. An important tool for reducing or controlling food‐borne microbial risk is risk analysis. This framework has been adopted globally to manage risks associated with microbial contamination in food. Several hundred microbial risk assessments (MRAs) have been published by different national and international organisations, for different food‐hazard combinations. The use of MRAs in controlling and understanding virus risk has, to date, been limited, compared with the efforts made on bacterial pathogens. Given the large disease burden that viruses are responsible for, this disparity should be addressed. The main reasons for the relative lack of risk assessments are the difficulty in detecting and monitoring viruses compared with bacteria. This means less data on prevalence, concentration and inactivation, and allows viruses to remain silent contributors to global disease. There are also key conceptual differences between virus risk assessment and bacterial risk assessment. This project aimed to assess the current state of the art for food‐borne virus risk assessment, then to progress the field further by using the data available to produce risk rankings and risk assessments. This was done by a combination of literature reviewing and various risk assessment tools. The result was an assessment of the overall evidence base in the literature, a semi‐quantitative ranking comparison between the viruses and foods of most concern, and a survey of inactivation methods, leading to a quantitative ranking of the effectiveness of each in reducing and managing food‐borne virus risk. [ABSTRACT FROM AUTHOR]

Food‐borne microbial illness contributes up to one third of global disease burden. The largest category of food‐borne illness is gastroenteritis, the majority of which is caused by enteric viruses. Viruses like these are transmitted to food either by waste‐contaminated waters, or by handling and transfer during processing. An important tool for reducing or controlling food‐borne microbial risk is risk analysis. This framework has been adopted globally to manage risks associated with microbial contamination in food. Several hundred microbial risk assessments (MRAs) have been published by different national and international organisations, for different food‐hazard combinations. The use of MRAs in controlling and understanding virus risk has, to date, been limited, compared with the efforts made on bacterial pathogens. Given the large disease burden that viruses are responsible for, this disparity should be addressed. The main reasons for the relative lack of risk assessments are the difficulty in detecting and monitoring viruses compared with bacteria. This means less data on prevalence, concentration and inactivation, and allows viruses to remain silent contributors to global disease. There are also key conceptual differences between virus risk assessment and bacterial risk assessment. This project aimed to assess the current state of the art for food‐borne virus risk assessment, then to progress the field further by using the data available to produce risk rankings and risk assessments. This was done by a combination of literature reviewing and various risk assessment tools. The result was an assessment of the overall evidence base in the literature, a semi‐quantitative ranking comparison between the viruses and foods of most concern, and a survey of inactivation methods, leading to a quantitative ranking of the effectiveness of each in reducing and managing food‐borne virus risk. [ABSTRACT FROM AUTHOR]

In the present study, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was monitored in environmental samples from rural and vulnerable areas (a presidio, worker accommodation units, and river waters upstream and downstream of a rural community) from Minas Gerais State region, Southern Brazil, in August 2020. The sampling was performed prior to official declaration of the coronavirus disease (COVID-19) cases in those sites. SARS-CoV-2 RNA was detected in the presidio and workers accommodation units (3.0 × 104 virus genome copies (GC)/mL and 4.3 × 104 GC/mL of sewage, respectively). While SARS-CoV-2 was not detected in the river water upstream of the rural community, SARS-CoV-2 RNA was detected in downstream river waters (1.1 × 102 SARS-CoV-2 GC/mL). The results obtained in this study highlight the utility of SARS-CoV-2 monitoring in wastewater and human sewage as a non-invasive early warning tool to support health surveillance in vulnerable and remote areas, particularly in development countries. [ABSTRACT FROM AUTHOR]

Background: Resistance to colistin was an uncommon phenomenon traditionally linked to chromosome point mutations, but since the first description of a plasmid-mediated colistin-resistance in late 2015, transmissible resistance to colistin has become a Public Health concern. Despite colistin is considered as a human last resort antibiotic, it has been commonly used in swine industry to treat post-weaning diarrhoea in piglets. However, the progressively increase of colistin resistance during the last decade led to the Spanish Medicines and Healthcare Products Agency (AEMPS) to launch a strategic and voluntary plan aimed to reduce colistin consumption in pig production. Our longitudinal study (1998–2021) aimed to evaluate the trend of colistin resistance mediated through the mcr-1 mobile gene in Spanish food-producing pig population and compare it with published polymyxin sales data in veterinary medicine to assess their possible relationships. Results: The first mcr-1 positive sample was observed in 2004, as all samples from 1998 and 2002 were mcr-1 PCR-negative. We observed a progressive increase of positive samples from 2004 to 2015, when mcr-1 detection reached its maximum peak (33/50; 66%). From 2017 (27/50; 54%) to 2021 (14/81; 17%) the trend became downward, reaching percentages significantly lower than the 2015 peak (p < 0.001). The abundance of mcr-1 gene in PCR-positive samples showed a similar trend reaching the highest levels in 2015 (median: 6.6 × 104mcr-1 copies/mg of faeces), but decreased significantly from 2017 to 2019 (median 2.7 × 104, 1.2 × 103, 4.6 × 102mcr-1 copies/mg of faeces for 2017, 2018 and 2019, respectively), and stabilizing in 2021 (1.6 × 102mcr-1 copies/mg of faeces) with similar values than 2019. Conclusions: Our study showed the decreasing trend of colistin resistance associated to mcr-1 gene, after a previous increase from among 2004–2015, since the European Medicines Agency and AEMPS strategies were applied in 2016 to reduce colistin use in animals, suggesting a connection between polymyxin use and colistin resistance. Thus, these plans could have been effective in mcr-1 reduction, reaching lower levels than those detected in samples collected 17 years ago, when resistance to colistin was not yet a major concern. [ABSTRACT FROM AUTHOR]

The pharmaceutical industry is currently trying to develop new bioactive compounds to inactivate both enveloped and non-enveloped viruses for therapeutic purposes. Consequently, microalgal and macroalgal bioactive compounds are being explored by pharmaceutical, as well as biotechnology and food industries. In this review, we show how compounds produced by algae include important candidates for viral control applications. We discuss their mechanisms of action and activity against enveloped and non-enveloped viruses, including those causing infections by enteric, parenteral, and respiratory routes. Indeed, algal products have potential in human and animal medicine. [ABSTRACT FROM AUTHOR]

Bacteriophages are bacterial-specific viruses and the most abundant biological form on Earth. Each bacterial species possesses one or multiple bacteriophages and the specificity of infection makes them a promising alternative for bacterial control and environmental safety, as a biotechnological tool against pathogenic bacteria, including those resistant to antibiotics. This application can be either directly into foods and food-related environments as biocontrol agents of biofilm formation. In addition, bacteriophages are used for microbial source-tracking and as fecal indicators. The present review will focus on the uses of bacteriophages like bacterial control tools, environmental safety indicators as well as on their contribution to bacterial control in human, animal, and environmental health. [ABSTRACT FROM AUTHOR]

Mangroves are ecosystems with unique characteristics due to the high salinity and amount of organic matter that house a rich biodiversity. Fungi have aroused much interest as they are an important natural source for the discovery of new bioactive compounds, with potential biotechnological and pharmacological interest. This review aims to highlight endophytic fungi isolated from mangrove plant species and the isolated bioactive compounds and their bioactivity against protozoa, bacteria and pathogenic viruses. Knowledge about this type of ecosystem is of great relevance for its preservation and as a source of new molecules for the control of pathogens that may be of importance for human, animal and environmental health. [ABSTRACT FROM AUTHOR]

Retrospective studies involving the screening of frozen stored collections of samples are commonplace when a new threat emerges, but it has been demonstrated that the freeze-thaw process can affect bacterial viability. The study of colistin-resistant bacteria in human and animal samples is an example of this issue. In this study, we compared culture-based and PCR-based methods for analyzing relative occurrence and diversity of colistin-resistant bacteria in caecal samples to determine the most appropriate method for frozen samples. Thus, 272 samples from the caecal contents of healthy pigs were tested before and after a 6-month freezing period. A selective medium was used when traditional isolation of colistin-resistant bacteria was tested, while a real-time SYBR® Green I PCR assay was applied for mcr-1 quantification. The number of samples with colistin-resistant isolates was higher in fresh samples (247/272) than in frozen ones (67/272) and showed a higher diversity of colistin-resistant genera. PCR identification of mcr colistin resistance genes evidenced that mcr-1 was the most prevalent mcr gene and mcr-2 was detected for the first time in pigs from Spanish animal production. The number of samples with mcr-1 -carrying bacteria after a freezing period decreased, while real-time quantitation of the mcr-1 gene showed similar values in frozen and fresh samples. Therefore, when frozen cecal samples need to be analyzed, molecular detection of DNA could be the best option to provide a highly representative frame of the initial population present in the sample, and culture-based methods might be a useful complement to study colistin resistance levels. [ABSTRACT FROM AUTHOR]

Zoonotic hepatitis E, mainly caused by hepatitis E virus (HEV) genotype (gt) 3, is a foodborne disease that has emerged in Europe in recent decades. The main animal reservoir for genotype 3 is domestic pigs. Pig liver and liver derivates are considered the major risk products, and studies focused on the presence of HEV in pig muscles are scarce. The objective of the present study was to evaluate the presence of HEV in different organs and tissues of 45 apparently healthy pigs from nine Spanish slaughterhouses (50% national production) that could enter into the food supply chain. Anti-HEV antibodies were evaluated in serum by an ELISA test. Ten samples from each animal were analyzed for the presence of HEV RNA by reverse transcription real-time PCR (RT-qPCR). The overall seroprevalence obtained was 73.3% (33/45). From the 450 samples analyzed, a total of 26 RT-qPCR positive samples were identified in the liver (7/45), feces (6/45), kidney (5/45), heart (4/45), serum (3/45), and diaphragm (1/45). This is the first report on detection of HEV RNA in kidney and heart samples of naturally infected pigs. HEV RNA detection was negative for rib, bacon, lean ham, and loin samples. These findings indicate that pig meat could be considered as a low risk material for foodborne HEV infection. [ABSTRACT FROM AUTHOR]

We report the characterization of 15 Listeria monocytogenes strains isolated from various food processing plants by multivirulence locus sequence typing to determine virulence types (VTs) and epidemic clones. Molecular mechanisms involved in adaptation to food processing environments and related to virulence were also studied. Phenotypic behaviors associated with various antimicrobials, biofilm formations, and invasiveness were assessed. There were 11 VTs among the 15 L. monocytogenes strains. Strains belonging to six VTs were stress survival islet 1 (SSI-1) and one strain of VT94 was SSI-2. Tn6188 was found in VT6 and VT94 strains, and bcrABC cassette genes were identified in VT21, VT60, and VT63 strains. Only one strain, in VT20, showed llxS, whereas a full-size inlA was detected in strains belonging to VT8, VT20, VT21, and VT63. VT10, VT20, VT21, VT60, and VT63 strains were the most tolerant to studied disinfectants. A VT6 strain showed the strongest biofilm formation ability in polyvinyl chloride, and strains belonging to VT10, VT11, VT20, and VT94 had moderate abilities. Antimicrobial sensitivity tests showed that all the L. monocytogenes strains were multidrug resistant. F tests revealed that only strains of VT10, VT60, and VT94 were significantly noninvasive (P < 0.05) in Caco-2 cells. Our findings illustrate how L. monocytogenes isolates exploit diverse mechanisms to adapt to adverse conditions. Consequently, detailed characterization of L. monocytogenes isolates is required for comprehensive elimination of this pathogenic bacterium in food processing environments. [ABSTRACT FROM AUTHOR]

Motivation The progress of High Throughput Sequencing (HTS) technologies and the reduction in the sequencing costs are such that Whole Genome Sequencing (WGS) could replace many traditional laboratory assays and procedures. Exploiting the volume of data produced by HTS platforms requires substantial computing skills and this is the main bottleneck in the implementation of WGS as a routine laboratory technique. The way in which the vast amount of results are presented to researchers and clinicians with no specialist knowledge of genome sequencing is also a significant issue. Results Here we present TORMES, a user-friendly pipeline for WGS analysis of bacteria from any origin generated by HTS on Illumina platforms. TORMES is designed for non-bioinformatician users, and automates the steps required for WGS analysis directly from the raw sequence data: sequence quality filtering, de novo assembly, draft genome ordering against a reference, genome annotation, multi-locus sequence typing (MLST), searching for antibiotic resistance and virulence genes, and pangenome comparisons. Once the analysis is finished, TORMES generates and interactive web-like report that can be opened in any web browser and shared and revised by researchers in a simple manner. TORMES can be run by using very simple commands and represent a quick an easy way to perform WGS analysis. Availability and implementation TORMES is free available at https://github.com/nmquijada/tormes. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

We studied the colonization and distribution of Listeria monocytogenes in a heavily contaminated poultry processing plant over a 1-year period. A total of 180 nonfood contact surfaces, 70 food contact surfaces, 29 personnel, and 40 food samples were analyzed. L. monocytogenes isolates were subtyped by PCR serotyping, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing. L. monocytogenes was detected in samples collected at every visit to the plant, and 43.8% (visit 4) to 65.6% (visit 7) of samples were positive, for an overall prevalence of 55.2%. The deboning area had the highest prevalence of positive samples (83.3%), and the processing area had the highest diversity of PFGE types. Ninety percent of the final products were positive for L. monocytogenes. Most of the isolates belonged to well-known persistent L. monocytogenes sequence types (ST9 and ST121). This study illustrates a well-established L. monocytogenes contamination problem in a poultry processing plant associated with a generalized failure of the food safety system as a whole. These findings reflect the potential for L. monocytogenes contamination when the food safety and quality management system is unsatisfactory, as described in the present study. It is essential to revise food safety and quality management systems to eliminate L. monocytogenes from food processing facilities, to control the entrance of sporadic sequence types, and to prevent L. monocytogenes spread within such facilities, especially in those premises with higher L. monocytogenes prevalence in the environment and final food products. [ABSTRACT FROM AUTHOR]

Although the effects of heavy metals on the behavior, including infectivity, of bacteria have been studied, little information is available about their effects on enteric viruses. We report an investigation of effects on the biosynthesis of human adenoviruses (HAdV) and hepatitis A (HAV) of waters contaminated with mineral waste following an environmental disaster in Mariana City, Minas Gerais State, Brazil. The study area was affected on November 5, 2015, by 60 million m3 of mud (containing very high concentrations of iron salts) from a mining reservoir (Fundão), reaching the Gualaxo do Norte River (sites evaluated in this study), the "Rio Doce" River and finally the Atlantic Ocean. We found substantial counts of infectious HAdV and HAV (by qPCR) in all sampled sites from Gualaxo do Norte River, indicating poor basic sanitation in this area. The effects of iron on viral infection processes were evaluated using HAdV-2 and HAV-175, as DNA and RNA enteric virus models, respectively, propagated in the laboratory and exposed to this contaminated water. Experiments in field and laboratory scales found that the numbers of plaque forming units (PFU) of HAdV and HAV were significantly higher in contaminated water with high iron concentrations than in waters with low iron concentration (< 20 µg/L of iron). These findings indicate that iron can potentiate enteric virus infectivity, posing a potential risk to human and animal health, particularly during pollution disasters such as that described here in Mariana, Brazil. [ABSTRACT FROM AUTHOR]

Clostridioides difficile infection (CDI) is currently one of the most important causes of infectious diarrhea in developed countries and the main cause in healthcare settings. Here, we characterized the gut microbiota from the feces of 57 patients with diarrhea from nosocomial and community-acquired CDI. We performed an ecological analysis by high-throughput sequencing of the V3-V4 region of 16S rRNA amplicons and evaluated the association of the various ecological profiles with CDI risk factors. Among all samples Bacteroidaceae 31.01%, Enterobacteriaceae 9.82%, Lachnospiraceae 9.33%, Tannerellaceae 6,16%, and Ruminococcaceae 5.64%, were the most abundant families. A reduced abundance of Bacteroides was associated with a poor CDI prognosis, with severe diarrhea and a high incidence of recurrence. This reduction was associated with a weakened host immune system and previous aggressive antibiotherapy. Peptostreptococcaceae family was 1.56% overall and within the family the only identified member was the genus Clostridioides , positively correlated with the presence of Akkermansia that may be predictive of the presence of a CDI. Finally, a relevant aspect that must be considered in clinical practice is the misdiagnosis of CDI, as patients with a stool sample that tests positive for C. difficile are usually diagnosed with CDI and subsequently treated as such. However, co-infection with other pathogenic agents often plays an important role in the development of diarrhea, and must be considered when prescribing antibiotic treatment. [ABSTRACT FROM AUTHOR]

The aim of the study was to evaluate the potential role of the illegal entry of food in UE in the Methicillin-resistant S. aureus (MRSA) spread. We studied the prevalence and characteristics of Staphylococcus aureus and MRSA isolated from foods of animal origin confiscated from passengers on flights from 45 non-EU countries from 2012 to 2015 by the Border Authorities at Bilbao International Airport (Spain) and Vienna International Airport (Austria), as well as foods from open markets close to EU land borders. Of 868 food samples tested (diverse meat samples including antelope, duck, guinea pig, pork, rodents, turkey, dairy products, and eggs), 136 (15.7%) were positive for S. aureus and 26 (3.0%) for MRSA. All MRSA strains were mecA-positive. The prevalence of S. aureus-positive dairy samples among food confiscated at Bilbao International Airport was 64.6%, and this airport also had the highest value (11.8%) for MRSA-positive samples. The predominant sequence type was ST5 (30.8%), followed by ST8, ST1649, ST1, and other lineages were found to a lesser extent (ST7, ST22, ST72, ST97, and ST398). Six isolates tested positive for luk-PVL genes (SCCmec IV subtypes IVc and IVe). Enterotoxin profiling revealed that 19 MRSA strains were enterotoxigenic, harboring one or more se genes. The MRSA isolates positive for luk-PVL genes were not enterotoxigenic, and none of the isolates tested positive for enterotoxin E. We found 14 resistance profiles, and more than 69% of the MRSA isolates were resistant to three or more types of antimicrobial agents. This finding reveals both the wide diversity of the antimicrobial resistance found in the strains and the capacity to resist not only to beta-lactam drugs. One MRSA strain showed unusual characteristics: it was oxacillinsusceptible, harbored SCCmec V, and was positive for sed, seg, and sej but negative for PVL virulence factors. This study shows the presence of enterotoxigenic HA-, CA-, and LA-MRSA in foods illegally entering the EU, and highlights illegal importation of food as route of enterotoxigenic MRSA spread. Uncontrolled entry of food stuffs into the EU can be a relevant neglected route of MRSA dissemination. [ABSTRACT FROM AUTHOR]

Clostridium perfringens causes a broad spectrum of diseases in both humans and animals and is an important cause of foodborne illness. We developed and tested a real-time (Q-)PCR assay for the species-specific detection of C. perfringens that targets the phospholipase C ( plc) gene and includes an internal amplification control (IAC), making it possible to identify false-negative results, which are common due to the high level of PCR inhibition by food compounds. The CPplc-IAC real-time PCR (RTi-PCR) assay was 100% selective, as shows with 36 Clostridium strains and 85 non- Clostridium strains, with an analytical sensitivity of 1 genome equivalent (GE) in 23% of the reactions and 10 GE in 100% of the reactions. The quantification was linear ( R = 0.9990) over a 7-log dynamic range, down to 10 GE, with a PCR efficiency E = 0.841. The applicability of this RTi-PCR assay was assessed in milk samples. The assay detected as few as 300 spores in 25 mL of artificially contaminated raw sheep milk with 78% probability and 30 spores in 25 mL with 50% probability. It also has accuracy of 83.03 to 151.18%, as shown by an evaluation of the correspondence between RTi-PCR assay results and the number of spores per milliliter determinated by standard plating. This RTi-PCR method was effective for the detection and quantification of C. perfringens in milk having an important applicability in the control of this pathogen in the dairy food industry. [ABSTRACT FROM AUTHOR]

We evaluated the capacity of the Brucella sp. eryC gene as a diagnostic marker for brucellosis by quantitative real-time PCR. eryC gene encodes the enzyme d-erythrulose-1-phosphate dehydrogenase that plays an important role in the erythritol metabolism and is related with the Brucella survival in the intracellular environment of the macrophage. The assay includes an internal amplification control (IAC) in order to avoid false negative results. It was 100% specific, with an analytical sensitivity of 1 genome equivalent (GE) in 43% of the reactions, being the quantification highly linear ( R > 0.9953) and efficient (PCR efficiency >0.8820) over a 6-log dynamic range, down to 10 GE. Finally, the applicability of this assay was evaluated with artificially contaminated biological matrices implicated in the transmission of this bacterium such as sheep raw milk and pig blood. The eryC-IAC real-time PCR assay allowed detection of as few as ten Brucella cells per 25 ml of sheep raw milk or per 1 ml of pig blood. In conclusion, we present an alternative for the detection of Brucella genus and therefore facilitate the establishment of preventive and prophylactic measures in food and farm environments. [ABSTRACT FROM AUTHOR]

Enteric pathogens from biofertilizer can accumulate in the soil, subsequently contaminating water and crops. We evaluated the survival, percolation and leaching of model enteric pathogens in clay and sandy soils after biofertilization with swine digestate: PhiX-174, mengovirus (vMC0), Salmonella enterica Typhimurium and Escherichia coli O157:H7 were used as biomarkers. The survival of vMC0 and PhiX-174 in clay soil was significantly lower than in sandy soil (ıPT90 values of 10.520 ± 0.600 vs. 21.270 ± 1.100 and 12.040 ± 0.010 vs. 43.470 ± 1.300, respectively) and PhiX-174 showed faster percolation and leaching in sandy soil than clay soil (ıPT90 values of 0.46 and 2.43, respectively). S. enterica Typhimurium was percolated and inactivated more slowly than E. coli O157:H7 (ıPT90 values of 9.340 ± 0.200 vs. 6.620 ± 0.500 and 11.900 ± 0.900 vs. 10.750 ± 0.900 in clay and sandy soils, respectively), such that E. coli O157:H7 was transferred more quickly to the deeper layers of both soils evaluated (percolation). Our findings suggest that E. coli O157:H7 may serve as a useful microbial biomarker of depth contamination and leaching in clay and sandy soil and that bacteriophage could be used as an indicator of enteric pathogen persistence. Our study contributes to development of predictive models for enteric pathogen behavior in soils, and for potential water and food contamination associated with biofertilization, useful for risk management and mitigation in swine digestate recycling. [ABSTRACT FROM AUTHOR]

The increase of foodborne viral outbreaks highlights the need for a rapid and sensitive method for the prediction of viral infectivity in food samples. This study assesses the use of propidium monoazide (PMA) coupled with real-time PCR methods (RT-qPCR or qPCR for RNA or DNA viruses, respectively) in the determination of viral infectivity in complex animal-related food matrices. Clam and Spanish fermented sausage ("chorizo") samples were spiked with infectious and heat-inactivated human adenovirus-2 (HAdV-2) and mengovirus (vMC0). PMA-qPCR/RT-qPCR discriminated infective virus particles, with significant reductions (>2.7 log10 or 99.7%). Additionally, infectious HAdV-2 and vMC0 were quantified by plaque assay (in plaque forming units, PFU), and compared with those in virus genomes copies (GCs) quantified by PMA-qPCR/RT-qPCR. A consistent correlation (R² > 0.92) was showed between PFU and GCs along serial 10-fold dilutions in both DNA and RNA virus and in both food matrices. This study shows the use of PMA coupled to qPCR/RT-qPCR as a promising alternative for prediction of viral infectivity in food samples in comparison to more expensive and time-consuming methods and for those viruses that are not able to grow under available cell culture techniques. [ABSTRACT FROM AUTHOR]

The use of propidium monoazide (PMA) coupled with real-time PCR (RT-qPCR or qPCR for RNA or DNA viruses, respectively) was assessed to discriminate infectious enteric viruses in swine raw manure, swine effluent from anaerobic biodigester (AB) and biofertilized soils. Those samples were spiked either with infectious and heat-inactivated human adenovirus-2 (HAdV-2) or mengovirus (vMC), and PMA-qPCR/RT-qPCR allowed discriminating inactivated viruses from the infective particles, with significant reductions (>99.9 %). Then, the procedure was further assayed to evaluate the presence and stability of two non-cultivable viruses (porcine adenovirus and rotavirus A) in natural samples (swine raw manure, swine effluent from AB and biofertilized soils); it demonstrated viral inactivation during the storage period at 23 °C. As a result, the combination of PMA coupled to real-time PCR can be a promising alternative for prediction of viral infectivity in comparison to more labour-intensive and costly techniques such as animal or tissue-culture infectivity methods, and for those viruses that do not have currently available cell culture techniques. [ABSTRACT FROM AUTHOR]

When analysing food samples for enteric viruses, a sample process control virus (SPCV) must be added at the commencement of the analytical procedure, to verify that the analysis has been performed correctly. Samples can on occasion arrive at the laboratory late in the working day or week. The analyst may consequently have insufficient time to commence and complete the complex procedure, and the samples must consequently be stored. To maintain the validity of the analytical result, it will be necessary to consider storage as part of the process, and the analytical procedure as commencing on sample receipt. The aim of this study was to verify that an SPCV can be recovered after sample storage, and thus indicate the effective recovery of enteric viruses. Two types of samples (fresh and frozen raspberries) and two types of storage (refrigerated and frozen) were studied using Mengovirus vMC as SPCV. SPCV recovery was not significantly different ( P > 0.5) regardless of sample type or duration of storage (up to 14 days at −20 °C). Accordingly, samples can be stored without a significant effect on the performance of the analysis. The results of this study should assist the analyst by demonstrating that they can verify that viruses can be extracted from food samples even if samples have been stored. [ABSTRACT FROM AUTHOR]

We investigated the pathogenicity, invasiveness, and genetic relatedness of 17 clinical Listeria monocytogenes stains isolated over a period of nine years (2006–2014). All isolates were phenotypically characterised and growth patterns were determined. The antimicrobial susceptibility of L. monocytogenes isolates was determined in E-tests. Invasion assays were performed with epithelial HeLa cells. Finally, L. monocytogenes isolates were subtyped by PFGE and MLST. All isolates had similar phenotypic characteristics (β-haemolysis and lecithinase activity), and three types of growth curve were observed. Bacterial recovery rates after invasion assays ranged from 0.09% to 7.26% (1.62 ± 0.46). MLST identified 11 sequence types (STs), and 14 PFGE profiles were obtained, indicating a high degree of genetic diversity. Genetic studies unequivocally revealed the occurrence of one outbreak of listeriosis in humans that had not previously been reported. This outbreak occurred in October 2009 and affected three patients from neighbouring towns. In conclusion, the molecular epidemiological analysis clearly revealed a cluster (three human cases, all ST1) of not previously reported listeriosis cases in northwestern Spain. Our findings indicate that molecular subtyping, in combination with epidemiological case analysis, is essential and should be implemented in routine diagnosis, to improve the tracing of the sources of outbreaks. [ABSTRACT FROM AUTHOR]

Tularemia outbreaks occurred in northwestern Spain in 1997-1998 and 2007-2008 and affected >1,000 persons. We assessed isolates involved in these outbreaks by using pulsed-field gel electrophoresis with 2 restriction enzymes and multilocus variable number tandem repeat analysis of 16 genomic loci of Francisella tularensis, the cause of this disease. Isolates were divided into 3 pulsotypes by pulsed-field gel electrophoresis and 8 allelic profiles by multilocus variable number tandem repeat analysis. Isolates obtained from the second tularemia outbreak had the same genotypes as isolates obtained from the first outbreak. Both outbreaks were caused by genotypes of genetic subclade B.Br:FTNF002-00, which is widely distributed in countries in central and western Europe. Thus, reemergence of tularemia in Spain was not caused by the reintroduction of exotic strains, but probably by persistence of local reservoirs of infection. [ABSTRACT FROM AUTHOR]

Lyophylized (L) and nonlyophylized (NL) samples of two cheeses from different batches were extracted with either methanol:water (8:2, v/v) or isopropanol:water (7:3, v/v), and the extracts were analyzed by ultraperformance liquid chromatography coupled with electrospray ionization/quadruple-time-of-flight mass spectrometry (UPLC-ESI-QToF-MS) in both positive and negative modes. Chromatographic and mass spectrometric data were further compared for different samples by paired t test and principal component analysis (PCA). Mass spectra at different elution times were manually checked and major peaks tentatively identified according to their m/ z values by search in available databases. A number of gangliosides and polyglycosilated ceramides were found to be the most abundant components. PCA showed samples could be clustered according to extraction procedure and cheese, and paired t test comparison also showed significant ( p < 0.05) differences between L and NL samples extracted with methanol:water. L and NL samples could only be distinguished in PCA when data from the whole chromatographic range were used. Results are discussed based on extraction solvent polarity and feasibility of PCA for comparison of cheese chemical composition after untargeted UPLC-MS analysis. [ABSTRACT FROM AUTHOR]

The application of plant essential oils (EOs) (hyssop and marjoram) was evaluated for inactivation of non-enveloped viruses using murine norovirus and human adenovirus as models. No significant reduction of virus titres (TCID) was observed when EOs were used at different temperatures and times. [ABSTRACT FROM AUTHOR]

We evaluated the prevalence of hepatitis E virus (HEV) in the pork production chain in Czech Republic, Italy, and Spain during 2010. A total of 337 fecal, liver, and meat samples from animals at slaughterhouses were tested for HEV by real-time quantitative PCR. Overall, HEV was higher in Italy (53%) and Spain (39%) than in Czech Republic (7.5%). HEV was detected most frequently in feces in Italy (41%) and Spain (39%) and in liver (5%) and meat (2.5%) in Czech Republic. Of 313 sausages sampled at processing and point of sale, HEV was detected only in Spain (6%). HEV sequencing confirmed only g3 HEV strains. Indicator virus (porcine adenovirus) was ubiquitous in fecal samples and absent in liver samples and was detected in 1 slaughterhouse meat sample. At point of sale, we found porcine adenovirus in sausages (1%-2%). The possible dissemination of HEV and other fecal viruses through pork production demands containment measures. [ABSTRACT FROM AUTHOR]

We evaluated the prevalence of hepatitis E virus (HEV) in the pork production chain in Czech Republic, Italy, and Spain during 2010. A total of 337 fecal, liver, and meat samples from animals at slaughterhouses were tested for HEV by real-time quantitative PCR. Overall, HEV was higher in Italy (53%) and Spain (39%) than in Czech Republic (7.5%). HEV was detected most frequently in feces in Italy (41%) and Spain (39%) and in liver (5%) and meat (2.5%) in Czech Republic. Of 313 sausages sampled at processing and point of sale, HEV was detected only in Spain (6%). HEV sequencing confirmed only g3 HEV strains. Indicator virus (porcine adenovirus) was ubiquitous in fecal samples and absent in liver samples and was detected in 1 slaughterhouse meat sample. At point of sale, we found porcine adenovirus in sausages (1%-2%). The possible dissemination of HEV and other fecal viruses through pork production demands containment measures. [ABSTRACT FROM AUTHOR]

Numerous viruses of human or animal origin can spread in the environment and infect people via water and food, mostly through ingestion and occasionally through skin contact. These viruses are released into the environment by various routes including water run-offs and aerosols. Furthermore, zoonotic viruses may infect humans exposed to contaminated surface waters. Foodstuffs of animal origin can be contaminated, and their consumption may cause human infection if the viruses are not inactivated during food processing. Molecular epidemiology and surveillance of environmental samples are necessary to elucidate the public health hazards associated with exposure to environmental viruses. Whereas monitoring of viral nucleic acids by PCR methods is relatively straightforward and well documented, detection of infectious virus particles is technically more demanding and not always possible (e.g. human norovirus or hepatitis E virus). The human pathogenic viruses that are most relevant in this context are nonenveloped and belong to the families of the C aliciviridae, A denoviridae, H epeviridae, P icornaviridae and R eoviridae. Sampling methods and strategies, first-choice detection methods and evaluation criteria are reviewed. [ABSTRACT FROM AUTHOR]

In this study, the prevalence of different enteric viruses in commercial mussels was evaluated at the retail level in three European countries (Finland, Greece and Spain). A total of 153 mussel samples from different origins were analysed for human norovirus (NoV) genogroups I and II, hepatitis A virus (HAV) and hepatitis E virus (HEV). Human adenovirus (HAdV) was also tested as an indicator of human faecal contamination. A full set of controls (such as sample process control, internal amplification controls, and positive and negative controls) were implemented during the process. The use of a sample process control allowed us to calculate the efficiencies of extraction, which ranged from 79 to 0.5 %, with an average value of 10 %. Samples were positive in 41 % of cases, with HAdV being the most prevalent virus detected (36 %), but no significant correlation was found between the presence of HAdV and human NoV, HAV and HEV. The prevalences of human norovirus genogroup II, HEV and human NoV genogroup I were 16, 3 and 0.7 %, respectively, and HAV was not detected. The estimated number of PCR detectable units varied between 24 and 1.4 × 10 g of digestive tract. Interestingly, there appeared to be a significant association between the type of mussel species ( M. galloprovincialis) and the positive result of samples, although a complete overlap between country and species examined required this finding to be confirmed including samples of both species from all possible countries of origin. [ABSTRACT FROM AUTHOR]

Background: Contagious Agalactia (CA) is one of the major animal health problems in small ruminants because of its economic significance. Currently, four Mycoplasma spp. have been associated with this syndrome: M. agalactiae, M. mycoides subsp. capri, M. capricolum subsp. capricolum and M. putrefaciens. Their presence has been evaluated in several studies conducted in CA-endemic countries. However, previous Spanish studies have been focused on caprine CA, and there is a knowledge gap regarding which Mycoplasma species are present in sheep flocks from Spain, which has the second highest number of sheep amongst the 27 European Union member states. Consequently, we investigated the presence and geographic distribution of the four CA-causing mycoplasmas in Spanish dairy sheep farms. This is the first time such an investigation has been performed. Results: Three hundred thirty nine out of 922 sheep flocks were positive for M. agalactiae by real time PCR (36.8%) and 85 by microbiological identification (9.2%). Interestingly, all 597 milk samples assessed for the presence of M. mycoides subsp. capri, M. capricolum subsp. capricolum and M. putrefaciens tested negative. To evaluate the intermittent excretion of the pathogen in milk, we sampled 391 additional farms from 2 to 5 times, resulting that in 26.3% of the cases a previously positive farm tested negative in a later sampling. Conclusions: M. agalactiae was the only Mycoplasma species detected in the study area showing a high frequency of presence and wide distribution. Therefore, the establishment of a permanent surveillance network is advantageous, as well as the implementation of control and prevention measures to hinder the dissemination of M. agalactiae and to prevent the entrance of other Mycoplasma species. [ABSTRACT FROM AUTHOR]

Sample process controls (SPCs) are an essential component of methods to detect viruses in food, as they verify that the sample treatment has operated correctly. Also, the use of an SPC can allow the efficiency of extraction of the target to be estimated for each individual sample analysed. The use of murine norovirus as SPC is here described. Its efficiency of extraction from different food products was 39.47%, 24.79% and 36.29% for strawberry, lettuce and shellfish samples. An incorrectly performed sample treatment was modelled to demonstrate the effectiveness of this control. [ABSTRACT FROM AUTHOR]

When determining the effect of food processing on the infectivity of any contaminating virus, it is necessary to distinguish unambiguously between infectious and non-infectious viruses present. However, this can be difficult in the particular case of noroviruses (NoVs) because no reliable cell culture model is available. The aim of this study was to assess the use of molecular methods-RT real-time PCR (RT-qPCR) and enzymatic treatment (ET) coupled to RT-qPCR-to quantify the infectivity of NoV after application of various inactivating food-processing technologies. RT-qPCR and ET-RT-qPCR gave significantly different ( P < 0.01) results concerning the reduction in viral genome counts by all inactivation procedures and conditions used, except for HHP treatment at 600 MPa for 5 min. These findings indicate that the ET prior to RT-qPCR has an effect on the estimation of the reduction of virus genome counts, and may eliminate genomes of affected virus particles. However, no correlation was found between the results obtained by ET-RT-qPCR and those obtained by cell culture. Therefore, the effect is presumably only partial, and not adequate to allow accurate estimation of virus inactivation. Consequently, our results indicate that the quantification of virus genomes by PCR, regardless of prior ET, is not adequate for establishing virus inactivation and/or infectivity. In addition, our results also illustrate that the general effect of virus inactivation is not directly correlated to effects on the integrity of virus genome and protein capsid. Presumably, inactivation by food processing is the consequence of effects on proteins involved in adhesion and invasion stages. [ABSTRACT FROM AUTHOR]

Internal amplification controls (IACs) were constructed for incorporation into real-time nucleic acid amplification assays for bovine polyomavirus, hepatitis A virus, hepatitis E virus, human adenovirus, human norovirus genogroup I, human norovirus genogroup II, murine norovirus and porcine adenovirus. The addition of optimised amounts of IAC into the assays did not affect the limits of detection for each specific target virus. A poorly performed extraction of viral nucleic acids was simulated, and the effectiveness of IACs in identifying failed assays was demonstrated. The IACs constructed in this study can be reliably used in their specific assays to provide a robust control that can be routinely applied in the analysis of foods for viruses. [ABSTRACT FROM AUTHOR]

Synthetic multiple-target RNA and DNA oligonucleotides were constructed for use as quantification standards for nucleic acid amplification assays for human norovirus genogroup I and II, hepatitis E virus, murine norovirus, human adenovirus, porcine adenovirus and bovine polyomavirus. This approach overcomes the problems related to the difficulty of obtaining practical quantities of viral RNA and DNA from these viruses. The quantification capacity of assays using the standards was excellent in each case ( R > 0.998 and PCR efficiency > 0.89). The copy numbers of the standards were equivalent to the genome equivalents of representative viruses (murine norovirus and human adenovirus), ensuring an accurate determination of virus presence. The availability of these standards should facilitate the implementation of nucleic acid amplification-based methods for quantitative virus detection. [ABSTRACT FROM AUTHOR]

Potential ways to address the issues that relate to the techniques for analyzing food and environmental samples for the presence of enteric viruses are discussed. It is not the authors' remit to produce or recommend standard or reference methods but to address specific issues in the analytical procedures. Foods of primary importance are bivalve molluscs, particularly, oysters, clams, and mussels; salad crops such as lettuce, green onions and other greens; and soft fruits such as raspberries and strawberries. All types of water, not only drinking water but also recreational water (fresh, marine, and swimming pool), river water (irrigation water), raw and treated sewage are potential vehicles for virus transmission. Well over 100 different enteric viruses could be food or water contaminants; however, with few exceptions, most well-characterized foodborne or waterborne viral outbreaks are restricted to hepatitis A virus (HAV) and calicivirus, essentially norovirus (NoV). Target viruses for analytical methods include, in addition to NoV and HAV, hepatitis E virus (HEV), enteroviruses (e.g., poliovirus), adenovirus, rotavirus, astrovirus, and any other relevant virus likely to be transmitted by food or water. A survey of the currently available methods for detection of viruses in food and environmental matrices was conducted, gathering information on protocols for extraction of viruses from various matrices and on the various specific detection techniques for each virus type. [ABSTRACT FROM AUTHOR]

We report an in-house protocol for extraction and purification of nucleic acids of enteric viruses, which gives more consistent results than representative commercial methods. The protocol uses 4 M guanidine thiocyanate, 0.5% N-lauroylsarcosine sodium salt, and 25 mM sodium citrate pH 7.0 supplemented with 0.14 M β-mercaptoethanol for lysis of virus particles. The addition of TRIzol followed by chloroform-based separation of the aqueous phase is used to purify nucleic acids from the lysate. RNA precipitation is performed using lithium chloride. This protocol was compared with QIAGEN's RNeasy Kit and bioMérieux's NucliSens method, by evaluating the ability of each to detect enteric viruses in a complex food matrix. Three different pork products, i.e., cooked ham, liver, and Spanish fermented sausage ('chorizo') were artificially contaminated with decreasing numbers of murine norovirus 1 and human adenovirus 2. The extracted and purified viral nucleic acids were detected by real-time polymerase chain reaction (PCR) assays. Whereas the two commercial extraction methods did not facilitate robust results (quantification was only possible with some viruses and/or some matrices), when coupled with the in-house protocol the linearity and the efficiency of the quantitative reverse transcription-PCR (qRT-PCR) assays were close to 1 in all the food matrices, independent of the virus. Scalability of the in-house method was evaluated by analysis of 1 and 2.5 g of spiked pig liver samples, and quantification was possible on 1 g samples contaminated with any of the two model viruses. Therefore, the in-house protocol facilitates robust qRT-PCR-based quantitative detection of viruses in pork products, and is moreover relatively cheap and simple to perform. [ABSTRACT FROM AUTHOR]

The spread and persistence of Listeria monocytogenes in smoked fish products and seafood processing factories are big concerns. Thus, the corresponding quality assurance programs must include adequate microbiological control measures. We evaluated eight different pre-PCR sample processing strategies to be coupled with a previously developed real-time PCR assay for the quantitative detection of L. monocytogenes in salmon products. The optimal pre-PCR procedure involved filtration and DNA purification with the use of a commercial kit. This strategy could detect 10 CFU of L. monocytogenes per g of smoked salmon and could quantify 1,000 CFU/g with excellent accuracy compared with the standard plate count method. Thus, this method could be a promising alternative for the quantitative detection of L. monocytogenes in smoked fish products and processing factories. This method could also detect the bacterium in raw salmon. [ABSTRACT FROM AUTHOR]

A molecular beacon-based real-time NASBA assay for detection and identification of Mycobacterium avium subsp. paratuberculosis has been developed. It targets and amplifies sequences from the dnaA gene which are specific for this bacterium. The assay includes an internal amplification control, to allow identification of inhibited reactions. The assay was tested against 18 isolates of M. avium subsp. paratuberculosis, 17 other mycobacterial strains and 25 non-mycobacterial strains, and was fully selective in that it detected all the targets but none of the non-targets. The lowest number of cells which the assay can detect with 99% probability is 150–200 cells per reaction (as determined using pure culture suspensions). Using centrifugation and nucleic acid extraction as sample treatment, the assay was able to consistently detect 103 M. avium subsp. paratuberculosis cells in 20 ml artificially contaminated drinking water. With a simple detergent and enzymatic sample pretreatment before centrifugation and nucleic acid extraction, the assay was able to consistently detect 104 M. avium subsp. paratuberculosis cells in 20 ml artificially contaminated semi-skimmed milk. The assay will be a useful addition to the range of diagnostic tools available for the study of M. avium subsp. paratuberculosis. [Copyright &y& Elsevier]

We report a duplex real-time PCR-based assay for the simultaneous quantitative detection of Listeria spp. and the food-borne pathogen Listeria monocytogenes. The targets of this single tube reaction were the 23S rDNA and hly genes of Listeria spp. and L. monocytogenes, respectively. Our assay was efficient, 100% selective (i.e., it allowed accurate simultaneous identification of 52 L. monocytogenes and 120 Listeria spp. strains through the FAM-labelled hly and the VIC-labelled 23S rDNA probes, respectively); and had a detection limit of one target molecule in 100% (23S rDNA) and 56% (hly) of the reactions. Simultaneous quantification was possible along a 5-log dynamic range, with an upper limit of 30 target molecules and R2 values >0.995 in both cases. Our results indicate that this assay based on the amplification of the 23S rDNA gene can accurately quantify any mixture of Listeria species and simultaneously unambiguously quantify L. monocytogenes. [Copyright &y& Elsevier]

A collection of 177 Francisella tularensis subsp. holarctica clinical isolates (29 from humans and 148 from animals, mainly hares and voles) was gathered from diverse tularemia outbreaks in the Castilla y León region (northwestern Spain) that occurred from the end of the 20th century to the 2020s. Along with four F. tularensis subsp. holarctica reference strains, all of these clinical isolates were tested using a broth microdilution method to determine their susceptibility to 22 antimicrobial agents, including β-lactams, aminoglycosides and one member each of the tetracycline, glycylcycline, quinolone and sulphonamide classes. Many multi-resistance profiles were found among the tested isolates, but especially among those of human origin (all but two isolates showed resistance to at least 13 of 18 antimicrobial agents). Even so, all human isolates were susceptible to gentamicin and tobramycin, while more than 96% of animal isolates were susceptible to these two aminoglycosides. Ciprofloxacin showed activity against more than 92% of animal and human isolates. However, almost 21% of human isolates were resistant to tetracycline, and more than 65% were resistant to tigecycline. Finally, a quite similar activity to other F. tularensis subsp. holarctica isolates collected 20 years earlier in Spain was observed. [ABSTRACT FROM AUTHOR]

Microbial fermentation plays an important role in the manufacturing of artisanal sausages and can have major effects on product quality and safety. We used metagenomics and culture-dependent methods to study the presence of Hepatitis E virus (HEV) and Rotavirus-A (RV-A), and fungal and bacterial communities, in artisanal Colonial salami-type dry-fermented sausages in Santa Catarina state, Brazil. Lactic acid bacteria (LAB) and yeast dominated the microbiome. Latilactobacillus sakei and Debaryomyces hansenii were ubiquitous and the most abundant species. The DNA of some foodborne pathogens was found in very low concentrations although viable cells of most of these species were undetectable by cultivation methods. The characteristics of the raw material and hygiene of the artisanal sausage manufacturing process resulted in high loads of beneficial microorganisms and the absence of HEV and RV-A viruses as determined by RT-qPCR assays. In conclusion, high LAB load in sausages was more relevant to preventing pathogen growth than the ripening time and/or physicochemical characteristics. However, the presence of Clostridium spp. and other pathogens in some samples must be taken into account for the development of future preservation methods; appropriate LAB starter cultures and health surveillance are required in the production process to prevent foodborne outbreaks. [ABSTRACT FROM AUTHOR]

In this study, tularemia outbreaks associated with humans and several domestic and wild animals (Iberian hares, wild rabbits, voles, mice, grey shrews, sheep, dogs, foxes, wolves, ticks, and river crayfish) are reported in Spain from 2007 to 2020. Special attention was paid to the outbreaks in humans in 2007–2009 and 2014–2015, when the most important waves occurred. Moreover, positive rates of tularemia in lagomorphs were detected in 2007–2010, followed by negative results in 2011–2013, before again returning to positive rates in 2014 and in 2017 and in 2019–2020. Lagomorphs role in spreading Francisella tularensis in the epidemiological chain could not be discarded. F. tularensis is described for the first time infecting the shrew Crocidura russula worldwide, and it is also reported for the first time infecting wild rabbits (Oryctolagus cuniculus) in Spain. Serological positives higher than 0.4% were seen for sheep only from 2007–2009 and again in 2019, while serological rates greater than 1% were revealed in dogs in 2007–2008 and in wild canids in 2016. F. tularensis were detected in ticks in 2009, 2014–2015, 2017, and 2019. Lastly, negative results were achieved for river crayfish and also in environmental water samples from 2007 to 2020. [ABSTRACT FROM AUTHOR]

Colistin has a long story of safe use in animals for the treatment and prevention of certain bacterial diseases. Nevertheless, the first description of the mcr-1 gene showed that colistin resistance can spread by horizontal gene transfer and changed the landscape. This study aimed to assess the effect of colistin administration on the dispersion of resistance in the microbiota of day-old broiler chicks and how the presence of mcr-1 genes influences the spread of colistin resistance determinants. In this study, 100 one-day-old chicks were divided into four groups of 25 animals (G1, G2, G3, and G4). Animals from G3/G4 were challenged with mcr-1-carrying Salmonella (day 7), while colistin (600 mg/L) was administered daily to G2/G4 animals through drinking water (from day 8 to day 15). Two quantitative PCR assays were performed to compare the amount of Salmonella and mcr-1 that were present in the caecal samples. We observed that levels of mcr-1 were higher in G3/G4 animals, especially G4, due to the spread of mcr-1-carrying Salmonella. On day 21, Salmonella levels decreased in G4, reaching similar values as those for G3, but mcr-1 levels remained significantly higher, suggesting that colistin may accelerate the spreading process when mcr-1-carrying bacteria reach the gut. [ABSTRACT FROM AUTHOR]

Extended-spectrum beta-lactamase (ESBL) and AmpC beta-lactamase (AmpC) producing Enterobacteriaceae occur frequently in livestock animals and the subsequent stages of the meat production chain and are therefore considered a risk for human health. Strict biosecurity measures and optimal farm management should reduce or even prevent poultry flock colonization at farm level. This review summarizes and evaluates published information on the effectiveness of specific intervention measures and farm management factors aiming to reduce the occurrence and spread of ESBL/AmpC producing or commensal or pathogenic E. coli in broiler chicken farms. In this systematic literature review, a total of 643 publications were analyzed, and 14 studies with significant outcome about the effectiveness of specific measures against E. coli and ESBL/AmpC producing E. coli in broiler chicken farms were found. Different feed additives seem to have an impact on the occurrence of those microorganisms. The measures 'cleaning and disinfection' and 'competitive exclusion' showed strong effects in prevention in some studies. In summary, some intervention measures showed potential to protect against or eliminate ESBL/AmpC-producing, commensal or pathogenic E. coli at farm level. Due to the high variability in the outcome of the studies, more specific, detailed investigations are needed to assess the potential of the individual intervention measures. [ABSTRACT FROM AUTHOR]

Nocardiosis is an infectious disease caused by Nocardia species that occurs worldwide, albeit more prevalently in tropical/subtropical regions. It can appear as either acute, subacute or as a chronic infection mostly with those with a compromised/weakened immune system. Inhalation of spores and or mycelium fragments is the main transmission route for developing pulmonary nocardiosis. In contrast, cutaneous nocardiosis usually occurs via direct contact. In the subtropical region of the Sunshine Coast in Australia foaming events with thick and persistent and orange-brown color foam have been observed during summer seasons in the near shore marine environments. This study reports the existence of nocardiae in these near shore marine environments by the use of a novel isolation method which used the gas requirements of nocardiae as a selective battery. A total of 32 nocardiae were isolated with the use of this novel method and subsequently conducted molecular identification methods confirmed that the isolates belonged to the genus Nocardia. Twenty-one isolates out of the 32 were closely related to N. nova strains MGA115 and one was related to CBU 09/875, in addition when compared with human pathogenic nocardiae twenty of the isolates were found to be related to N. nova strain JCM 6044. Isolates displayed varied resistance against some of the antibiotics tested when interpretation threshold recommended the Comite de L'Antibiogramme de la Societe Francaise de Microbiologie were used. The highest level of resistance against cefotaxime (n = 27) and ceftriaxone (n = 24). Some of the isolates (n = 6) that displayed resistance to selected antibiotics also possessed potential human pathogenic characteristics such as adherence and translocation through human long epithelial cells as well as displaying phage resistance (n = 26). They might thus present a potential public health risk if frequently encountered through exposure to aerosols generated by the foam as well as direct contact through a wound. Preventative measures to control the growth of nocardiae in such environments such as the control of pollutants, might prevent potential infections that might be caused by these bacteria in humans as well as in marine animals. [ABSTRACT FROM AUTHOR]

In this study, the major mastitis pathogen prevalence in the cattle and buffalo of the world was estimated by a meta-analysis. Staphylococcus (S) species, Streptococcus (St) species, and Escherichia coli (Ec) prevalence studies reported during 1979–2019 were collected using online databases, and offline resources. A meta-analysis of these data was done with the meta package in R-Software. The Staphylococcus aureus was the major mastitis pathogen, mostly causing subclinical mastitis, Ec causing clinical mastitis and St causing subclinical and clinical mastitis. The pooled prevalence estimates of S, St, and Ec were 28%, 12%, and 11% in the world from 156, 129, and 92 studies, respectively. The S, St, and Ec prevalences were high in Latin America (51%), Oceania (25%), and Oceania (28%), respectively. Higher S, St, and Ec prevalences were observed by molecular methods, signifying high sensitivity and usefulness for future studies. Among bacterial species, S. aureus (25%) followed by coagulase-negative Staphylococcus species (20%), Escherichia coli (11%), St. agalactiae (9%), St. uberis (9%) were the important pathogens present in the milk of the world. We hypothesize that there is a urgent need to reduce mastitis pathogen prevalence by ensuring scientific farm management practices, proper feeding, therapeutic interventions to augment profits in dairying, and improving animal and human health. [ABSTRACT FROM AUTHOR]