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Have changes to meat and poultry food safety regulation in Australia affected the prevalence of Salmonella or of salmonellosis?

During the 1990s, there was radical change in regulation of meat and poultry hygiene in Australia, and Australian Standards were developed for each sector of the meat industry. Systems for industry/government co-regulation and company-employed meat inspection were introduced based on company HACCP programs approved and audited by the Controlling Authority. However, in the 5 years since regulatory changes took full effect, rates of salmonellosis have not decreased (surveillance and reporting systems have remained unchanged). Using statistics gathered by the National Enteric Pathogens Surveillance Scheme, an attempt was made to link Salmonella serovars isolated from meat and poultry with those causing salmonellosis. Two periods were studied, 1993/1994, before regulations were introduced, and 2000/2001, when regulations should be having an effect. For red meat, the same serovars were prominent among the top 10 isolates both before and after regulation, and there was little linkage with salmonelloses. For poultry, frequently isolated serovars differed pre- and post-regulation, however, in both periods there was some linkage between serovars isolated from poultry and those causing salmonelloses. Using published and unpublished survey data, it was concluded that there had been improvements in microbiological quality of red meat and poultry over the same timeframe as regulatory changes. That these improvements apparently have not carried through to reduced case-rates for salmonellosis may be due to numerous causes, including lack of control in the food processing, food service and home sectors. The present paper illustrates difficulties faced by governments in measuring public health outcomes of changes to food hygiene regulation.

Animals↗

[Study on national active monitoring for food borne pathogens and antimicrobial resistance in China 2001].

OBJECTIVE: To survey food borne pathogens and antimicrobial resistance in China. METHODS: A total of 4034 samples of foods (raw meats, raw milk, cooked meats, ice cream, yoghurt, aquatic product and vegetable) were examined for the presence of Escherichia coli O157:H7 Salmonella spp and Listeria monocytogens by national active foodborne pathogens surveillance system. The samples were obtained from 11 provinces in 2001. RESULTS: Approximate 5.50% of the all samples yielded 3 pathogenes, whereas Escherichia coli O157:H7 (0.82%), Salmonella servoars (3.32%) and Listeria monocytogens (1.29%). The most heavy contamination by three food borne pathogens are in raw meat (12.96%). Top seven serotype of the 137 Salmonella isolates are S. derby, S. agona, S. enteritidis, S. reading, S. anatum. S. muenster, S. typhimurium. CONCLUSION: Serotypes and antibiotic resistance patterns of Salmonella isolates are different in 11 provinces. E. coli O157:H7 strains that are isolated from raw meat and cooked meat have VT2, eae, Hly genes. Salmonella and E. coli strains of multidrug resistance were isolated and identified.

Drug Resistance, Multiple↗

Antibiotic resistance -- from pathogen to disease surveillance.

Surveillance is central to defining the epidemiology of antibiotic resistance, developing new strategies for its control, informing disease management, identifying targets for new drugs and vaccines and in turn, evaluating and refining the impact of these interventions. Current surveillance systems often fall short of this ideal. Since antibiotics are prescribed for the treatment of specific disease, surveillance that reliably links diagnosis, pathogen and antibiotic usage is likely to be more informative. By identifying diseases that are readily recognized, and are usually reliably defined microbiologically, and in turn have clear links to public-health issues, a broader ownership of surveillance data should result. The case is argued for a more disease-focused microbiological surveillance approach than exists at present. Examples are provided which reflect a cross-section of community, nosocomial, zoonotic and imported infectious disease challenges, and where new approaches are urgently required to combat the upward spiral of resistance.

Bacterial Infections↗

Communicable diseases surveillance: Highlights for 3rd quarter, 2003.

Communicable diseases surveillance highlights for 3rd quarter, 2003 (bloodborne diseases, gastrointestinal disease, vaccine preventable diseases, vectorborne diseases, zoonoses, other bacterial infections), and surveillance outcomes from several reporting series as follows: National Notifiable Diseases Surveillance System tables, 1 July to 30 September 2003; Laboratory Serology and Virology Reporting Scheme tables, 1 July to 30 September 2003; Australian Sentinel Practices Research Network, reporting period 1 July to 30 September 2003; Gonococcal surveillance, reporting period 1 April to 30 June 2003; HIV and AIDS surveillance, reporting period 1 April to 30 June 2003, assessed as at 30 September 2003; Australian childhood immunisation coverage, 1 April to 30 June 2003 cohort, assessed as at 30 September 2003; National Enteric Pathogens Surveillance System, reporting period 1 July to 30 September 2003. These national data collections are complemented by intelligence provided by State and Territory communicable disease epidemiologists and/or data managers. This additional information has enabled the reporting of more informative highlights each quarter.

Australia↗

Emergence of carbapenemase-producing Escherichia coli in acute care hospitals in 32 European countries (the CCRE survey): a prospective, multicentre, cross-sectional, epidemiological, microbiological, and genomic surveillance study.

BACKGROUND: The emergence of carbapenem resistance in Escherichia coli is of major concern due to the high propensity of spread of this species and scarce treatment options. Herein, we examined the occurrence and spread of carbapenem-resistant E coli based on the carbapenem-resistant and/or colistin-resistant Enterobacterales (CCRE) survey performed across European countries in 2019. METHODS: We analysed epidemiological, microbiological, and whole-genome sequencing data of 548 E coli isolates from individual patients from 156 hospitals in 32 European countries over 6 months in 2019. These hospitals collected the first ten successive isolates of carbapenem-resistant or carbapenem-susceptible increased exposure (carbapenem-R/I) Klebsiella pneumoniae species complex or E coli, and carbapenem-susceptible (carbapenem-S) comparator isolates of the same species. Antimicrobial susceptibility testing was performed for 19 antimicrobial agents. Whole-genome sequencing was performed centrally using Illumina technology. Isolates from the CCRE survey were compared with those from the European Survey of Carbapenemase-Producing Enterobacteriaceae (EuSCAPE) study. FINDINGS: Of the 548 E coli isolates, 211 (38·5%) were carbapenem-resistant or susceptible, increased exposure (carbapenem-R/I), and 337 (61·5%) were carbapenem-susceptible (carbapenem-S). Five sequence types (STs) accounted for 96 (45·5%) of 211 carbapenem-R/I isolates: ST131 (27), ST410 (20), ST38 (19), ST167 (16), and ST648 (14). Carbapenemase genes were identified in 182 (86·3%) carbapenem-R/I isolates, a pronounced increase from the 2013-14 EuSCAPE study (36 of 99, 36·4%). The most common genes were blaNDM-5 (62 of 182, 34·1%) and blaOXA-48 (40 of 182, 22·0%). blaNDM-5 carriage increased substantially compared with that in EuSCAPE (two of 99, 2·02%). Phylogenetic analysis showed substantial clonal spread of globally disseminated blaNDM-5-harbouring lineages, with numerous introductions into Europe but minimal onward transmission. INTERPRETATION: High-risk STs of E coli carrying carbapenemase genes are rapidly spreading globally, although our results indicate that, in 2019, most cases in Europe were sporadic. We urge vigilant monitoring, including genomic surveillance, and strengthening of control efforts, to reduce mortality and morbidity associated with the impending rise in carbapenem-R/I E coli cases. FUNDING: European Centre for Disease Prevention and Control and the Centre for Genomic Pathogen Surveillance.

Humans↗

Diversifying selection drives the evolution of the type III secretion system pilus of Pseudomonas syringae.

The plant pathogenic bacterium Pseudomonas syringae uses a type III secretion system to inject virulence proteins directly into the cytoplasm of its hosts. The P. syringae type III secretion apparatus is encoded, in part, by the HrpZ operon, which carries the hrpA gene encoding the pilin subunit of the pilus, various components of the structural apparatus, and the HrpZ harpin protein that is believed to produce pores in the host cell membrane. The pilus of the type III system comes into direct contact with the host cell and is, therefore, a likely target of the host's pathogen surveillance systems. We sequenced and analyzed 22 HrpZ operons from P. syringae strains spanning the diversity of the species. Selection analyses, including K(a)/K(s) tests and Tajima's D, revealed strong diversifying selection acting on the hrpA gene. This form of selection enables pathogens to maintain genetic diversity within their populations and is often driven by selection imposed by host defense systems. The HrpZ operon also revealed a single significant recombination event that dramatically changed the evolutionary relationships among P. syringae strains from 2 quite distinct phylogroups. This recombination event appears to have introduced genetic diversity into a clade of strains that may now be undergoing positive selection. The identification of diversifying selection acting on the Hrp pilus across the whole population sample and positive selection within one P. syringae lineage supports a trench warfare coevolutionary model between P. syringae and its plant hosts.

Amino Acid Sequence↗

Expression of the beta-glucan receptor, Dectin-1, on murine leukocytes in situ correlates with its function in pathogen recognition and reveals potential roles in leukocyte interactions.

Dectin-1 is a pathogen-recognition receptor on macrophages (MPhis), neutrophils, and dendritic cells (DCs). On MPhis and bone marrow-derived DCs, it has been shown to mediate the nonopsonic recognition of and response to soluble and particulate yeast beta-glucans. We have optimized the immunohistochemical detection of Dectin-1 and demonstrated its expression on neutrophils, subpopulations of MPhis in splenic red and white pulp, alveolar MPhis, Kupffer cells, and MPhis and DCs in the lamina propria of gut villi. This is consistent with its role in pathogen surveillance. A significant proportion of CD11c(+) splenic DCs expressed Dectin-1, but expression was not restricted to any one subset. Dectin-1 expression was low on resident MPhis and DCs of skin and was not detected on resident MPhis or DCs in kidney, heart, brain, or eye. The proposed, additional role of Dectin-1 as a coreceptor for T cell activation is supported by its expression on DCs in the T cell areas of the spleen and lymph nodes. Strong expression of Dectin-1 on subpopulations of MPhis and DCs in the medullary and corticomedullary regions of the thymus suggests a role distinct from pathogen recognition. Tissue localization thus revealed potential roles of Dectin-1 in leukocyte interactions during innate immune responses and T cell development.

Age Factors↗

4CMenB vaccine coverage of invasive serogroup B meningococci collected in Belgium between 2016 and 2022.

Neisseria meningitidis infections can cause life-threatening meningitis and septicemia. In Europe, serogroup B (MenB) is the leading cause of invasive meningococcal disease (IMD), particularly in young children. Genomic surveillance of circulating MenB strains through whole genome sequencing (WGS) provides a powerful tool to assess the potential impact of vaccination strategies, including the 4CMenB vaccine, which is available for infants from 2 months of age. Here, we present a retrospective WGS-based analysis of clinical MenB IMD cases (n = 311) recovered in Belgium from 2016 to 2022 by the Belgian National Reference Center. High-quality WGS data were obtained for 281 of these strains, demonstrating high genetic diversity of the antigen targets included in the 4-component meningococcal serogroup B vaccine 4CMenB (fHbp, PorA, NHBA and NadA) and at the 4CMenB Antigen Sequence Types (BAST) level. Novel antigen combinations, not yet assigned a BAST ID, were detected in 23.5% of isolates. Vaccine coverage was predicted using the Genetic Meningococcal Antigen Typing System (gMATS) and the Meningococcal Deduced Vaccine Antigen Reactivity (MenDeVAR) index. Of the 281 strains, 79.5% (lower limit-upper limit: 68.0-91.5%) were predicted to be covered by the vaccine by gMATS, and 80.7% (lower limit-upper limit: 66.5-95.4%) by MenDeVAR. No evidence of variation in vaccine coverage was found throughout the study period nor between different age groups, demonstrating the broad applicability of 4CMenB. This study highlights the benefits of a pathogen surveillance program and the need for experimental characterization of continuously evolving antigenic subvariants of Neisseria meningitidis.

Humans↗

Genotypic Analysis and Clinical Findings of Sapovirus-Associated Acute Gastroenteritis in Mie Prefecture, Japan, 2010-2022.

Sapovirus (SaV) is one of the major viruses causing acute gastroenteritis. Of the 1981 fecal specimens collected through sentinel pediatric acute gastroenteritis pathogen surveillance in Mie Prefecture, Japan (2010-2022), 236 were positive for SaV, according to PCR screening. Whole or near-whole genome sequences were determined for 158 strains by next-generation sequencing. Genotype GI.1 was the most common of the nine SaV genotypes detected, followed by GII.3 and GII.1. Phylogenetic analysis showed that SaVs of these three genotypes separated into three different clusters depending on the year of detection, suggesting continuous genetic changes in the same genotype. Coinfections involving different SaV genotypes, as well as reinfections with SaV in the same individual, were observed in this study. The main clinical manifestations were diarrhea (68.4%) and vomiting (61.6%), with an increased rate of emesis, particularly in patients over 3 years of age. In addition, 18.1% of the children had fever. This study clarified the prevalence of viral genotypes as well as clinical findings of SaV-positive gastroenteritis in children, and revealed trends by age.

Humans↗

Nanopore Sequencing for Chikungunya Virus: Principles and Application.

Nanopore sequencing is transforming viral genomics through real-time, portable, long-read analysis of RNA and DNA. Unlike traditional short-read platforms, it detects nucleotide sequences by measuring ionic current changes as nucleic acids pass through nanoscale pores, enabling direct single-molecule sequencing and base modification detection. Its simplicity, flexibility, and capacity for ultra-long reads make it ideal for resolving complex genomic regions, structural variants, and full viral genomes. These advantages have accelerated its use in pathogen surveillance and outbreak response, especially in resource-limited settings. For chikungunya virus (CHIKV), nanopore sequencing allows rapid, culture-independent recovery of complete genomes from clinical and vector samples, enabling real-time tracking of viral diversity, evolution, and spread. Experiences from Ebola, Zika, and COVID-19 have demonstrated the power of portable sequencing, now applied to CHIKV monitoring. Advances in tools such as Guppy, Dorado, Minimap2, and Medaka enhance read quality, consensus accuracy, and downstream analyses. Despite challenges in basecalling and error correction, robust quality control pipelines ensure reliable results. Ongoing improvements in chemistry, flow cell design, and machine learning will further enhance fidelity and throughput, establishing nanopore sequencing as a cornerstone of CHIKV genomic surveillance and epidemic preparedness.

Chikungunya virus↗

Ontogeny of intestinal epithelium immune functions: developmental and environmental regulation.

Intestinal mucosa integrates primary digestive functions with immune functions such as pathogen surveillance, antigen transport and induction of mucosal immunity and tolerance. Intestinal adaptive immunity is elicited in organized mucosa-associated lymphoid tissue (O-MALT) that is composed of antigen-presenting cells and lymphocytes and achieved by effector cells widely distributed in mucosa (diffuse MALT or D-MALT). Interaction between the intestinal epithelium, the O-MALT and the diffuse MALT plays a critical role in establishing an adequate immune response. In regions associated to O-MALT, lympho-epithelial cross-talks lead to acquisition of a specific epithelial phenotype that contributes to O-MALT organization and functionality. Beyond the expression of several innate immune functions, the intestinal epithelium may directly take up and present antigens due to the expression of major histocompatibility complex (MHC) and MHC-related molecules. A complex genetic program that will be outlined in the present review controls the development of immune functions of the intestinal epithelium. The effect of environmental signals on the modulation of this ontogenetic program during development and neonatal life, from bioactive components of amniotic fluid to lactation and bacterial colonization, will be discussed.

Adaptation, Physiological↗

The X-lectins: a new family with homology to the Xenopus laevis oocyte lectin XL-35.

The Xenopus laevis oocyte cortical granule lectin (XL35) has been studied in fertilization and embryonic development. Several nucleic acid sequences that predict proteins homologous to XL35 have since been reported in frog, human, mouse, lamprey, trout, ascidian worm. These proteins also showed high degrees of amino acid sequence homology to a common fibrinogen-like motif that may involve carbohydrate binding. Although their biological functions and carbohydrate binding specificities have not been studied in detail, this new family of lectins has common characteristics. Several independent studies on this new family of lectins strongly suggest that the lectins are expressed and stored in specialized vesicles that may be released upon the infection by pathogens. In addition, some family members have been shown to bind to oligosaccharides from bacterial pathogens. Therefore, this family of lectins likely participates in pathogen surveillance as part of the innate immune system. We propose the name X-lectin family for these homologs of XL35.

Amino Acid Motifs↗

Primer design through submodular function estimation.

MOTIVATION: Multiplex PCR-based enrichment is widely used in viral genome sequencing and pathogen surveillance. However, designing large sets of primers that maximize genome coverage while minimizing primer-primer interactions remains a major computational challenge. Existing methods such as SADDLE and Olivar use heuristics to optimize a Badness score for primer dimers but lack theoretical guarantees on solution quality. RESULTS: We introduce PRISM, a new framework that formulates multiplex primer design as a constrained submodular maximization problem. Our method defines an objective that balances genome coverage and dimer risk, and applies a local search algorithm with a constant-factor approximation guarantee. Evaluations on viral genome datasets demonstrate that PRISM consistently achieves lower Badness scores compared to PrimalScheme, Olivar, and primerJinn. These results highlight the scalability and theoretical rigor of submodular optimization in primer design. AVAILABILITY: PRISM is open-source and available at https://github.com/yhhan19/PRISM-new. The experimental data, scripts, and results used in this paper are archived on Figshare at https://doi.org/10.6084/m9.figshare.32806499.

Algorithms↗

Comparative genomics reveals lineage-associated structural variation and diversification in a barley fungal pathogen.

Leaf rust, caused by Puccinia hordei, is a major barley disease worldwide. Despite repeated shifts in virulence, contrasting reproductive histories, and emerging fungicide insensitivity, the genomic basis of its diversification and adaptation remains poorly understood. In this study, we generated haplotype-resolved, chromosome-level genome assemblies for two isolates with contrasting virulence and analyzed 41 Australian isolates collected over 54 yr (1966-2020), integrating comparative and population genomics, mating-type gene phylogenies, chromosome-specific k-mer profiling, genome-wide copy-number variation (CNV) analysis, and gene-expression analysis. We identified a structurally dynamic chromosome characterized by repeat-associated rearrangements, structural variation, and lineage-associated CNV, representing the first evidence in a rust fungus of chromosome-scale structural diversification of this extent. Population analyses distinguished clonally expanded lineages from recombination-associated lineages, with mating-type gene phylogenies providing further support for lineage differentiation. More recently collected isolates showed increased duplication-associated variation, and CNV boundaries were associated with structural-variant breakpoints. We also identified lineage-associated amplification of Cyp51, with increased copy number associated with higher transcript abundance, supporting a potential role in fungicide adaptation. Overall, our findings highlight structural variation, contrasting reproductive histories, and lineage-associated CNV as important contributors to diversification in P. hordei, providing insights for future rust pathogen surveillance and management strategies.

Cyp51 gene↗

A single-nucleotide-polymorphism-based multilocus genotyping assay for subtyping lineage I isolates of Listeria monocytogenes.

Listeria monocytogenes is a facultative intracellular pathogen responsible for food-borne disease with high mortality rates in humans and is the leading microbiological cause of food recalls. Lineage I isolates of L. monocytogenes are a particular public health concern because they are responsible for most sporadic cases of listeriosis and the vast majority of epidemic outbreaks. Rapid, reproducible, and sensitive methods for differentiating pathogens below the species level are required for effective pathogen control programs, and the CDC PulseNet Task Force has called for the development and validation of DNA sequence-based methods for subtyping food-borne pathogens. Therefore, we developed a multilocus genotyping (MLGT) assay for L. monocytogenes lineage I isolates based on nucleotide variation identified by sequencing 23,251 bp of DNA from 22 genes distributed across seven genomic regions in 65 L. monocytogenes isolates. This single-well assay of 60 allele-specific probes captured 100% of the haplotype information contained in approximately 1.5 Mb of comparative DNA sequence and was used to reproducibly type a total of 241 lineage I isolates. The MLGT assay provided high discriminatory power (Simpson's index value, 0.91), uniquely identified isolates from the eight listeriosis outbreaks examined, and differentiated serotypes 1/2b and 4b as well as epidemic clone I (ECI), ECIa, and ECII. In addition, the assay included probes for a previously characterized truncation mutation in inlA, providing for the identification of a specific virulence-attenuated subtype. These results demonstrate that MLGT represents a significant new tool for use in pathogen surveillance, outbreak detection, risk assessment, population analyses, and epidemiological investigations. DNA sequences were deposited in the GenBank database under accession numbers DQ 812146 to DQ 812517, DQ 843664 to DQ 844598, and AY 512391 to AY 512502.

Bacterial Proteins↗

Salmonella enterica serovar London infections associated with consumption of infant formula.

Epidemiologic studies were conducted on 31 cases of Salmonella group E infection detected in 2000 through a laboratory-based pathogen surveillance in Gangwon Province, Korea. Data were collected on the environmental exposures and the patients' foods, including the brand(s) of milk consumed before the onset of diarrhea. The patients' medical records were also reviewed. All of the patients were infants under 10 months of age except one 7-year old child. Surprisingly, all of the infants were fed with infant formulas from Company A, although two infants were fed with infant formulas from both Company A and Company B. Antimicrobial susceptibility test and pulsed-field gel electrophoresis (PFGE) were performed in 25 out of 31 isolates from the patients and in 1 isolate from an opened packet of infant formula collected from the home of an infected infant. All of the 26 isolates were Salmonella enterica serovar London. They showed a single PFGE pattern, and all of the isolates were susceptible to the 18 antibiotics tested. The causative agent of the salmonella outbreaks in the Gangwon Province and its surrounding areas was Salmonella London, and the highly likely source of the infection was infant formula from Company A.

Child↗

Rational approach to limiting emergence of antimicrobial drug resistance.

Microbial resistance to the available antimicrobial agents continues to be a major problem with regard to nosocomial and community acquired pathogens. The development of resistance to commonly used antimicrobials is of particular concern when it occurs in pathogenic organisms that cause invasive disease. This has implications on morbidity and mortality of infectious diseases, and will also result in escalated costs of care due to the use of alternative antimicrobials which are often more costly. The increasing frequency of drug resistance has been attributed to combinations of microbial characteristics, selective pressure of antimicrobial use and societal factors that enhance the transmission of drug resistant organisms. The emergence of antibiotic resistant bacteria has generally correlated with the rise and fall of specific antibiotic use in clinical practice. Although the discovery of a new drug temporarily confers therapeutic superiority over bacterial pathogens, the subsequent rapid evolution of resistance limits the duration of the effectiveness of specific agents against pathogens. Surveillance and the development of drug policies that encourage judicious use of antimicrobials will help to minimise the spread of resistant infections. This paper reviews how this dual strategy may be used to control antimicrobial resistance.

Bacterial Infections↗

Antimicrobial resistance of 914 beta-hemolytic streptococci isolated from pharyngeal swabs in Spain: results of a 1-year (1996-1997) multicenter surveillance study. The Spanish Surveillance Group for Respiratory Pathogens.

A nationwide susceptibility surveillance study of beta-hemolytic streptococcal isolates from pharyngeal swabs obtained in 11 Spanish hospitals between May 1996 and April 1997 against 12 antibiotics was carried out. Of the isolates 86% (786 of 914 isolates) were group A and 8.4% (77 of 914 isolates) were group C. No resistance was found to beta-lactam antibiotics, but significant differences (P < 0.001) with respect to lack of susceptibility to macrolides were found between groups (27% for group A and 12% for group C) and between seasons (13.2% in summer and 31.7% in winter). Most of these isolates displayed the M phenotype (low-level resistance to erythromycin and susceptibility to clindamycin).

Drug Resistance, Microbial↗