Topological characterization of rearrangements in amorphous solids.

In amorphous materials, plasticity is localized and occurs as shear transformations. It was recently shown by Wu et al. that these shear transformations can be predicted by applying topological defect concepts developed for liquid crystals to an analysis of vibrational eigenmodes [Z. W. Wu et al., Nat. Commun. 14, 2955 (2023)10.1038/s41467-023-38547-w]. This study relates the -1 topological defects to the displacement fields expected of an Eshelby inclusion, which are characterized by an orientation and the magnitude of the eigenstrain. A corresponding orientation and magnitude can be defined for each defect using the local displacement field around each defect. These parameters characterize the plastic stress relaxation associated with the local structural rearrangement and can be extracted using the fit to either the global displacement field or the local field. Both methods provide a reasonable estimation of the molecular-dynamics-measured stress drop, confirming the localized nature of the displacements that control both long-range deformation and stress relaxation.

Enhancement and anticipation of the Ioffe-Regel crossover in amorphous/nanocrystalline composites.

Nanocomposites made of crystalline nanoinclusions embedded in an amorphous matrix are at the forefront of current research for energy harvesting applications. However, the microscopic mechanisms leading alternatively to an effectively reduced or enhanced thermal transport still escape understanding. In this work, we present a molecular dynamics simulation study of model systems, where for the first time we combine a microscopic investigation of phonon dynamics with the macroscopic thermal conductivity calculation, to shed light on thermal transport in these materials. We clearly show that crystalline nanoinclusions represent a novel scattering source for vibrational waves, modifying the nature of low energy vibrations and significantly anticipating the propagative-to-diffusive crossover (Ioffe-Regel), usually located at energies of few THz in amorphous materials. Moreover, this crossover position can be tuned by changing the elastic contrast between nanoinclusions and the matrix, and anticipated by a factor as large as 10 for a harder inclusion. While the propagative contribution to thermal transport is drastically reduced, the calculated thermal conductivity is not significantly affected in the chosen system, as the diffusive contribution dominates heat transport when all phonons are thermally populated. These findings allow finally to understand the panoply of contradictory results reported on thermal transport in nanocomposites and give clear indications to the characteristics that the parent phases should have for efficiently reducing heat transport in a nanocomposite.

Managing safety and quality through the red meat chain.

To successfully manage food safety and quality risks in meat production, a holistic approach is required. The ideal would be a fully integrated assurance system, with effective controls applied at all stages. However, the red meat industry is by nature somewhat fragmented, and a truly integrated system is not at present achievable in all but a few operations. This paper describes a variety of assurance initiatives, and explores how targeted research and development can be used to augment assurance programmes by providing underpinning knowledge, using the Australian beef and lamb industry as an example.

Quantification and prevalence of Salmonella in beef cattle presenting at slaughter.

AIMS: A survey to determine the prevalence and numbers of Salmonella in beef cattle presented for slaughter at abattoirs across Australia was conducted between September 2002 and January 2003. METHODS AND RESULTS: Automated immunomagnetic separation (AIMS) was used for detection and isolation of Salmonella enriched from cattle faeces. Salmonella were enumerated from positive samples using a combination of the Most Probable Number (MPN) technique and AIMS. A total of 310 faecal samples were tested, 155 were from lot-fed cattle and 155 from grass-fed cattle. Salmonella spp. were isolated from 21 (6.8%) of the cattle and the prevalence amongst grass-fed cattle (4.5%) was not significantly different to that found in lot-fed cattle (9%). Counts of Salmonella in positive faeces varied from <3 MPN g(-1) of faeces to 2.8 x 10(3) MPN g(-1) and 71% of positive samples had counts <10 MPN g(-1) faeces. There was no significant difference in the mean log10 number of Salmonella in faeces of cattle from each production system. CONCLUSION: Low numbers of beef cattle were found to shed Salmonella at the time of slaughter and the prevalence and the associated faecal concentrations did not vary significantly with the pre-slaughter production system (grass or lot feeding). The faecal concentration of Salmonella in the majority of faeces was low (<10 MPN g(-1)) with few high concentrations up to 3 x 10(3) MPN g(-1), suggesting there may be a low risk of carcase contamination. SIGNIFICANCE AND IMPACT OF THE STUDY: Beef cattle do not appear to be a major source of entry of Salmonella into the human food chain and the quantitative information contained in this study can be used in quantitative assessments of the associated risk of human salmonellosis.

The prevalence and concentration of Escherichia coli O157 in faeces of cattle from different production systems at slaughter.

AIMS: To determine the prevalence and concentration of Escherichia coli O157 shed in faeces at slaughter, by beef cattle from different production systems. METHODS AND RESULTS: Faecal samples were collected from grass-fed (pasture) and lot-fed (feedlot) cattle at slaughter and tested for the presence of E. coli O157 using automated immunomagnetic separation (AIMS). Escherichia coli O157 was enumerated in positive samples using the most probable number (MPN) technique and AIMS and total E. coli were enumerated using Petrifilm. A total of 310 faecal samples were tested (155 from each group). The geometric mean count of total E. coli was 5 x 10(5) and 2.5 x 10(5) CFU g(-1) for lot- and grass-fed cattle, respectively. Escherichia coli O157 was isolated from 13% of faeces with no significant difference between grass-fed (10%) and lot-fed cattle (15%). The numbers of E. coli O157 in cattle faeces varied from undetectable (<3 MPN g(-1)) to 1.1 x 10(5) MPN g(-1). Twenty-six (67%) of 39 O157 positive faeces had <10 MPN g(-1) and three (8%) had counts between 10(3)-10(5) MPN g(-1). There was no significant difference between concentrations of E. coli O157 in the faeces of grass-fed or lot-fed cattle. CONCLUSION: The prevalence and numbers of E. coli O157 in the faeces of cattle at slaughter were not affected by the production systems evaluated in this study. SIGNIFICANCE AND IMPACT OF THE STUDY: Information on the prevalence and numbers of E. coli O157 can be used for formulating intervention strategies and in quantitative risk assessments.

In vitro studies on the colonization of bovine colonic mucosa by Shiga-toxigenic Escherichia coli (STEC).

This study investigated host-related factors that influence intestinal colonization by Shiga-toxigenic E. coli (STEC). A quantitative colonization assay was developed to comparatively measure attachment of STEC to bovine colonic tissues maintained in vitro. No differences were determined in colonization susceptibility between tissues derived from weaning calves and adult cattle, or for tissues from cattle fed grain and forage-based rations. Substrate conditions designed to represent various intra-enteric environments were tested for their effect on STEC/mucosal interaction. Under conditions corresponding to a well-fed ruminant (high volatile fatty acid and lactate concentrations, low pH), significantly less STEC colonized the mucosal surface of colonic biopsies. These results may help explain why fasted, poorly or intermittently fed cattle and pre-ruminant calves excrete STEC to a greater degree. Studies on the ecology of STEC within the ruminant gut help identify mechanisms to reduce their threat to public health.

Enumeration of Escherichia coli O157 in cattle faeces using most probable number technique and automated immunomagnetic separation.

AIMS: To determine the numbers of Escherichia coli O157 present in the faeces of naturally infected cattle. METHODS AND RESULTS: A combination of the most probable number (MPN) technique and automated immunomagnetic separation (AIMS) was used to enumerate E. coli O157 in cattle faeces from both pasture-fed and grain-fed animals. A total of 22 E. coli O157 positive faecal samples were enumerated for E. coli O157 (10 from pasture-fed and 12 from grain-fed animals). The numbers of E. coli O157 in cattle faeces varied from undetectable (<3 MPN g-1 of faeces) to 2.4 x 104 MPN g-1. There was no significant difference (P = 0.06) between the numbers of E. coli O157 in pasture-fed or grain-fed cattle faeces, although the geometric mean (antilog of the mean of log10 transformed MPN values) was higher in grain-fed (130 MPN g-1) than in pasture-fed (13 MPN g-1). CONCLUSIONS: Although the number of samples tested is small, the results indicate that E. coli O157 make up a small proportion of the total E. coli population present in cattle faeces. SIGNIFICANCE AND IMPACT OF THE STUDY: Information on the numbers of E. coli O157 present in cattle will assist in developing more robust quantitative risk assessments and formulating intervention strategies.

Horizontal transmission of Shiga toxin-producing Escherichia coli within groups of dairy calves.

To examine the dissemination of Shiga-toxigenic Escherichia coli (STEC) within cattle groups, dairy calves on two farms utilizing different calf-rearing practices were exposed to a traceable STEC strain. Test strain dissemination differed significantly between farms, with a higher prevalence being associated with group penning. Pen floors and calf hides may be the main environmental mechanisms of transmission. Dairy calf husbandry represents a control point for reducing on-farm STEC prevalence.

Comparison between human and animal isolates of Shiga toxin-producing Escherichia coli O157 from Australia.

There is very little human disease associated with enterohaemorrhagic Escherichia coli O157 in Australia even though these organisms are present in the animal population. A group of Australian isolates of E. coli O157:H7 and O157:H- from human and animal sources were tested for the presence of virulence markers and compared by XbaI DNA macrorestriction analysis using pulsed-field gel electrophoresis (PFGE). Each of 102 isolates tested contained the gene eae which encodes the E. coli attaching and effacing factor and all but one carried the enterohaemolysin gene, ehxA, found on the EHEC plasmid. The most common Shiga toxin gene carried was stx2c, either alone (16%) or in combination with stx1 (74%) or stx2 (3%). PFGE grouped the isolates based on H serotype and some clusters were source specific. Australian E. coli O157:H7 and H- isolates from human, animal and meat sources carry all the virulence markers associated with EHEC disease in humans therefore other factors must be responsible for the low rates of human infection in Australia.

Ancestral divergence, genome diversification, and phylogeographic variation in subpopulations of sorbitol-negative, beta-glucuronidase-negative enterohemorrhagic Escherichia coli O157.

The O157:H7 lineage of enterohemorrhagic Escherichia coli is a geographically disseminated complex of highly related genotypes that share common ancestry. The common clone that is found worldwide carries several markers of events in its evolution, including markers for acquisition of virulence genes and loss of physiological characteristics, such as sorbitol fermentation ability and beta-glucuronidase production. Populations of variants that are distinct with respect to motility and the sorbitol and beta-glucuronidase markers appear to have diverged at several points along the inferred evolutionary pathway. In addition to these variants, distinct subpopulations of the contemporary non-sorbitol-fermenting, beta-glucuronidase-negative O157:H7 clone were recently detected among bovine and human clinical isolates in the United States by using high-resolution genome comparison. In order to determine if these recently described subpopulations were derived from a regional or ancestral divergence event, we used octamer-based genome scanning, marker sorting, and DNA sequence analysis to examine their phylogenetic relationship to populations of non-sorbitol-fermenting, beta-glucuronidase negative O157:H7 and O157:H- strains from Australia. The inferred phylogeny is consistent with the hypothesis that subpopulations on each continent resulted from geographic spread of an ancestral divergence event and subsequent expansion of distinct subpopulations. Marker sorting and DNA sequence analyses identified sets of monophyletic markers consistent with the pattern of divergence and demonstrated that phylogeographic variation occurred through emergence of regional subclones and concentration of regional polymorphisms among distinct subpopulations. DNA sequence analysis of representative polyphyletic markers showed that genome diversity accrued through random drift and bacteriophage-mediated events.

Pre-slaughter handling of cattle and Shiga toxin-producing Escherichia coli (STEC).

AIMS: The aim of the study was to monitor the shedding and transmission of generic and Shiga toxin-producing Escherichia coli (STEC) in a consignment of cattle during lot feeding. METHODS AND RESULTS: Faecal and environmental samples were tested for total E. coli and screened with PCR specific for Shiga toxin and O157 rfb. STEC were isolated using colony hybridization and characterized by serology and genotyping. STEC prevalence initially decreased after the diet shift from pasture to grain, although there were intermittent peaks in numbers of cattle shedding STEC and E. coli O157. Water troughs and soil were intermittently contaminated. Common genotypes and serotypes were isolated from animals, water and soil in the feedlot, with additional types introduced at slaughter. CONCLUSION: STEC and E. coli O157 are endemic in cattle and intermittent peaks in shedding occur. Prevention of these peaks and/or reduction in transmission is required to reduce the risk of carcass contamination during slaughter. SIGNIFICANCE AND IMPACT OF THE STUDY: These findings contribute to the understanding of the ecology of STEC and suggest control points for reducing STEC contamination in feedlot cattle production.

Characterisation and clonal relationships of Shiga-toxigenic Escherichia coli (STEC) isolated from Australian dairy cattle.

A total of 136 Shiga toxin-producing Escherichia coli (STEC) isolated during a longitudinal survey of three Australian dairy farms were examined to determine their virulence factors, serotype and genomic relationships. This study aimed to assess the potential of these STEC to cause disease in humans and to analyse the on-farm ecology of STEC. Virulence factors (stx, eae, ehxA) were used as determinants of potential to be enterohaemorrhagic E. coli (EHEC) and were examined using polymerase chain reaction (PCR). Among the cattle groups tested, calves, both before and during weaning, shed the most putative EHEC and were the main source of serotypes commonly associated with human disease. E. coli O157:H7 and E. coli O26:H11 represented 9.4 and 7.8% of cattle STEC isolates respectively, with other putative EHEC serotypes reported for the first time from cattle. Based on serotype and virulence factors, 20% of STEC were putative EHEC. Pulsed-field gel electrophoresis (PFGE) was used to compare the genomic profiles of STEC from dairy farms. Isolates common to cattle and the farm environment were identified. Multiple strains of STEC with high clonal turnover were detected in the faeces of cattle, and isolates appeared to be specific to individual farms. To fully assess the pre-slaughter EHEC risk factors on-farm, examination of STEC virulence is as important as determination of STEC prevalence.

A longitudinal study of Shiga-toxigenic Escherichia coli (STEC) prevalence in three Australian diary herds.

Over a 12 month period, 588 cattle faecal samples and 147 farm environmental samples from three dairy farms in southeast Queensland were examined for the presence of Shiga-toxigenic Escherichia coli (STEC). Samples were screened for Shiga toxin gene (stx) using PCR. Samples positive for stx were filtered onto hydrophobic grid membrane filters and STEC identified and isolated using colony hybridisation with a stx-specific DNA probe. Serotyping was performed to identify serogroups commonly associated with human infection or enterohaemorrhagic Escherichia coli (EHEC). Shiga-toxigenic Escherichia coli were isolated from 16.7% of cattle faecal samples and 4.1% of environmental samples. Of cattle STEC isolates, 10.2% serotyped as E. coli O26:H11 and 11.2% serotyped as E. coli O157:H7, and the E. coli O26:H11 and E. coli O157:H7 prevalences in the cattle samples were 1.7 and 1.9%, respectively. Prevalences for STEC and EHEC in dairy cattle faeces were similar to those derived in surveys within the northern and southern hemispheres. Calves at weaning were identified as the cattle group most likely to be shedding STEC, E. coli O26 or E. coli O157. In concurrence with previous studies, it appears that cattle, and in particular 1-14-week-old weanling calves, are the primary reservoir for STEC and EHEC on the dairy farm.

Dynamics of Shiga toxin-producing Escherichia coli (STEC) in feedlot cattle.

Feedlot cattle were monitored during fattening to determine changes in faecal shedding of Shiga toxin-producing Escherichia coli (STEC) and their relation to the coliform population. Faecal samples were enriched, screened for Shiga toxin genes (stx) by a polymerase chain reaction test and isolated using colony hybridization. During 117 d in the feedlot, there were differences in the numbers of coliforms shed and in the percentage of samples positive for stx. These fluctuations did not appear to be consistently related to changes in feed or time in the feedlot. The mean log coliform count for stx-positive samples (log 5.85 g-1) was similar to that for stx-negative samples (log 6.00 g-1). The STEC isolates obtained from the first 5 d in the feedlot belonged to eight serotypes. Later, one serotype (O136:H16) became the predominant STEC which appeared to be one clone as characterized by virulence determinants and pulsed-field gel electrophoresis.

Use of pulse field gel electrophoresis for the epidemiological characterisation of coagulase positive Staphylococcus isolated from meat workers and beef carcasses.

Coagulase positive staphylococci isolated at an Australian abattoir, from beef carcasses, hands, and environmental samples, were typed by the DNA macrorestriction patterns obtained following PFGE of SmaI digests. The predominant PFGE pattern of isolates collected before evisceration was different from the dominant pattern of isolates collected after evisceration. PFGE patterns for isolates from workers' hands and from concordant carcasses were indistinguishable. PFGE types among isolates collected from non-evisceration abattoir personnel and clerical staff were distinct from patterns among isolates collected from the slaughter floor personnel. Twenty-nine (85%) of the 34 isolates collected from carcasses after evisceration exhibited PFGE patterns that were 93% homologous. During evisceration the carcasses were handled extensively and it is proposed that the hands of workers at this abattoir are the primary source of staphylococcal contamination of carcasses on the slaughter floor. This paper highlights the usefulness of PFGE as an epidemiological tool for determining the source of staphylococcal contamination in the food industry.

Incidence of coagulase positive Staphylococcus on beef carcasses in three Australian abattoirs.

The contamination of beef carcasses with coagulase-positive staphylococci (CPS) was studied at three beef abattoirs (A, B and C). The incidence and the number of CPS were determined on cattle hides immediately after slaughter and on three carcass sites (brisket, flank and round) at different points during processing along the slaughter line. The incidence of CPS on cattle hides ranged from 20 to 68.6%. At abattoir A, 6.5% of the carcasses sampled before evisceration were contaminated with CPS, compared to 40% of the carcasses after evisceration. The incidence on carcasses changed little during further processing; however, after chilling for 72 h, the incidence increased to 83%. After evisceration, the brisket and flank areas were more often contaminated than the round. A similar pattern of contamination was observed at abattoir B. At abattoir C, 26.7% of the samples collected before evisceration were contaminated and this fell to 16.7% after evisceration. After chilling for 72 h, the incidence of carcass contamination with CPS increased to 46.7%. The average number of CPS on contaminated carcasses prior to and after overnight chilling was less than 50 colony-forming units (cfu)/cm2 and, after weekend chilling, increased to 64 and 112 cfu/cm2 in abattoirs A and B, respectively. Of the isolates tested, 71.4% produced staphylococcal enterotoxin and 21% could not be classified phenotypically. The hands of workers and environmental sites associated with the evisceration process were examined for CPS at abattoir A. Hands were heavily contaminated and were the likely source of CPS contamination at this abattoir.

Shiga toxin-producing Escherichia coli in sheep and pre-slaughter lambs in eastern Australia.

Sheep and lambs from 14 farms in southern Queensland and one from central New South Wales were surveyed to determine the prevalence of Shiga toxin-producing Escherichia coli (STEC). STEC, isolated from 45% of 144 sheep faeces collected on the farms and 36% of 72 lamb faeces from abattoir yards, were tested for the presence of genes encoding virulence factors. Most (64%) of the 117 STEC isolates contained Shiga toxin 1 and 2 genes, 22% contained those encoding Shiga toxin 1, and 14% contained genes encoding Shiga toxin 2. The genes encoding the E. coli attaching and effacing factor were present in 2.6% of STEC and 26% contained the enterohaemolysin gene. The isolates that contained the E. coli attaching and effacing gene were serotype O157:H. This study has shown that STEC are widely distributed in eastern Australian sheep and lambs and are shed in their faeces prior to slaughter. Thus, there is potential for contamination of carcasses and entry of STEC into the human food chain.

A PCR specific for Escherichia coli O157 based on the rfb locus encoding O157 lipopolysaccharide.

A PCR was developed for the detection of Escherichia coli O157 based on the rfbE O-antigen synthesis genes. A 479-bp PCR product was amplified specifically from E. coli O157 in cell lysates containing 200 or 2 CFU following crude DNA extraction. The PCR detected < 1 CFU of E. coli O157 per ml in raw milk following enrichment.

Isolation and identification of Burkholderia pseudomallei from soil using selective culture techniques and the polymerase chain reaction.

An environmental soil survey to detect Burkholderia pseudomallei was performed during the dry and wet seasons in Darwin, Northern Territory, Australia. Soil was sampled at regular intervals during a 15-month period at different depths from areas which were representative of the local, soil environment. Selective culture techniques using Ashdown's and Galimand and Dodin's methods and the polymerase chain reaction (PCR) using specific 16S rRNA primers were used to detect and identify the organism and determine its distribution within the soil stratum over the change in seasons. Results showed that Ashdown's method gave higher isolation rates in the dry season, and Galimand and Dodin's method gave higher isolation rates during the wet season. PCR of the soil enrichment proved to be a more sensitive method than culture and was also a useful confirmatory test in determining the identification of isolates where biochemical tests gave inconsistent results. The PCR primers were specific and able to detect 10(1) cfu g-1 soil and 10(4) cfu g-1 of soil using Ashdown's enrichment broth and Galimand and Dodin's broth, respectively. Overall the isolation of B. pseudomallei was greatest during the dry season and at the higher and lower soil depths, which is contradictory to epidemiological evidence that melioidosis occurs primarily during the wet season among patients exposed to contaminated surface soil and water.