Dogs are one of the most popular companion animals in the UK, with an estimated 13.5 million within UK households. Within these households, human-animal physical interactions may lead to inter-species bacterial sharing, including Escherichia coli. E. coli is an opportunistic pathogen with a broad host range and can contribute to the spread of antimicrobial resistance (AMR). This work aimed to understand the extent of E. coli co-occurrence between hosts within the same household, and between dogs and humans. E. coli was non-selectively cultured from faecal samples obtained from 24 households with at least one human (n = 31) and one dog (n = 27) sample available at the same timepoint. Up to eight presumptive E. coli colonies were selected per sample and underwent short read whole genome sequencing. In total, 217 E. coli genomes were classified into 53 known sequence types (STs) and one unknown ST. Within samples, up to four different STs were present within each human and up to three different STs within a dog. Using a five single nucleotide polymorphism (SNP) threshold, there were 20 E. coli co-occurrences between hosts, including the same and different host species. Four instances involved potential cross-species co-occurrence within the same household. A genome-wide association study using a combined unitig and gene presence and absence approach identified one gene significantly more common in human derived samples; in silico characterisation revealed this gene is likely to have a function related to Type-F conjugative transfer system pilin assembly. Overall, 48.8

Food is produced by a range of methods including extensive (organic and free range), intensive (conventional) and wild-caught production systems. Antimicrobial use varies between different food production systems, which may affect the microbial populations as well as the prevalence and diversity of antimicrobial resistance genes (ARGs) found on food at retail. In this study, shotgun metagenomics was used to investigate the microbial and ARG composition of 25 pork, 33 beef, 33 lamb, 60 chicken, 31 salmon and 41 leafy green samples collected in Norfolk, England, and labelled as extensive, wild caught or intensive. Food microbiomes consisted predominantly of spoilage-associated organisms including Pseudomonas , Lactococcus and Psychrobacter . Significant differences in bacterial diversity were found between intensive and extensive systems on chicken, and 22 differentially abundant genera were identified between production systems across beef, chicken and salmon. Genes conferring resistance to tetracyclines and beta-lactams comprised the majority of the food resistome across all commodities. Across most measures used to compare food resistomes between production methods, no significant differences were detected, except on chicken and salmon where differences in beta-diversity between production methods were detected, albeit with low effect sizes. Overall, these results suggest that differently produced foods, at least when tested at retail and in this region, may present a similar risk of antimicrobial resistance across the commodities investigated within this study. However, specific associations were identified with the microbial composition across chicken, beef and salmon, suggesting that production method may drive some variation in the microbial population structure on food products. Additional work at the farm or food processing levels is required to identify the drivers of these differences between production systems.

Klebsiella pneumoniae is a bacterium of public health importance due to its association with antimicrobial resistance (AMR) and its role as a major cause of both hospital- and community-acquired infections. While Klebsiella species have been detected in foods, our understanding of their diversity and the potential risks they pose from food is limited. This study aims to comprehensively evaluate the Klebsiella species population and their contribution to the burden of AMR, virulence, and heavy metal tolerance from diverse food samples. We generated short-read sequence data for 570 Klebsiella isolates recovered from 361 food samples, including leafy greens, pork, prawns, chicken, salmon, and shellfish. Genome analysis showed that eleven unique Klebsiella species were present across food commodities, with K. pneumoniae being the most common (28.3 %); food-derived genomes were intermingled with publicly available Klebsiella genomes isolated from human clinical infections. We detected critical AMR genes, blaCTX-M-15, blaCTX-M-27, blaSHV-70, and blaDHA-1, in K. pneumoniae (n = 8) and K. quasipneumoniae (n = 6) from prawns. Additionally, we identified 46 virulent K. pneumoniae and K. quasipneumoniae isolates from domestic and imported food, including two hypervirulent K. pneumoniae isolates from domestic pork samples. Notably, a K. planticola isolate from salmon exhibited the hypermucoviscosity phenotype. AMR and virulence genes on plasmid contigs were widespread across different Klebsiella species, while chromosome-linked genes were mostly species-specific. These results highlight that food can harbour a range of Klebsiella species with resistance and virulence genes typically found in clinical settings, underscoring the need for monitoring foodborne Klebsiella as a potential risk to human health.

Salmonella poses a significant threat to food security, with frequent outbreaks reported worldwide. A large percentage of these outbreaks are associated with fresh produce intended for raw consumption. Plant microbiomes harbour diverse microbial communities, including commensal microbes such as Pseudomonas that sometimes exhibit biocontrol activity against plant pathogens. However, little is known about whether Pseudomonas strains can effectively suppress foodborne pathogens and the mechanisms they employ. In this study, we identified and characterised food derived Pseudomonas isolates capable of inhibiting Salmonella growth in vitro and in planta . The identified isolates were active against a range of Salmonella serovars, and additionally E. coli isolates derived from food. We demonstrated that dynamics of the interaction between Pseudomonas and Salmonella are environment and application dependant. To uncover the mechanisms Pseudomonas employs to suppress Salmonella , we used transcriptomics coupled with pathway analysis in the two different settings. We showed that Pseudomonas metabolism undergoes significant environment-specific changes in the presence of Salmonella , implicating different pathways responsible for the control of the pathogen in the two different settings. Our results highlight the plasticity of Pseudomonas metabolism in response to Salmonella in two distinct environments and provide evidence that Pseudomonas biocontrol activity is multifactorial and environment dependent. ### Competing Interest Statement The authors have declared no competing interest. Biotechnology and Biological Sciences Research Council, BB/X011011/1, BB/X002985/1, BB/CCG2260/1

Background: Many clinically important antimicrobial resistance (AMR) phenotypes such as fluoroquinolones and rifamycins are driven by antimicrobial resistance-conferring mutations (ARMs) in conserved chromosomal loci (e.g., gyrA , parC, rpoB ). Resistome profiling by metagenomics sequencing is often proposed as an ideal AMR surveillance tool as it is organism-agnostic, but currently, existing metagenomic AMR surveillance pipelines are only able to identify acquired AMR genes but not point mutations associated with AMR. This is a serious gap in metagenomics-based AMR surveillance, as the true extent of AMR may be underestimated. Methods: We developed MetaPointFinder (v1), a read-based method that can process both long and short metagenomic reads. The tool identifies resistance-determining regions in reads using DIAMOND (translated protein) and KMA (nucleotide), and classifies known resistant versus wild-type variants by aligning the sequences using pwalign and assessing the observed mutations based on known resistance mutations in the AMRFinderPlus database. The tool outputs ARMs per read, per gene and per antibiotic class. Results: In proof-of-concept analyses, MetaPointFinder identified known AMR-associated mutations and quantified resistant/susceptible read counts and ratios from metagenomic samples with corroborating phenotypic resistance data when available. We benchmark our tool using simulated reads from DNA and from reverse-translated protein references with read lengths of 100-5000 bp and error rates between 0 and 30%, simulating both Illumina and Nanopore error rates. We show that MetaPointFinder outperforms any available method for detection of ARMs in metagenomics data. Conclusion: MetaPointFinder complements gene-centric resistome profiling by capturing chromosomal mutation-based AMR directly from metagenomes.

Members of the Pseudomonas genus are common spoilers of a range of meat, dairy and vegetable products. While we have a good understanding of the Pseudomonas species typically responsible for spoilage, we know very little about how these bacteria interact with food surfaces during spoilage. Here we assessed the spoilage capabilities of a large panel (n = 124) of Pseudomonas species food-derived isolates on meat (chicken) and leafy greens (spinach). Most isolates (71/124) were capable of spoiling both foods, but some were only capable of spoiling only chicken (21/124) or spinach (23/124), or neither (9/124). Our data also demonstrated that the type of fresh food the strain was isolated from influenced spoilage capabilities: strains isolated from meat products were equally likely to spoil both chicken and spinach; isolates from seafood products were significantly more likely to spoil chicken; and those isolated from leafy greens were significantly more likely to spoil spinach. We used fluorescence microscopy to visualise how Pseudomonas spoilage species interacted with the meat or leaf tissue and observed significant tissue destruction associated with biofilm formation. For chicken, this was associated with the formation of dense biofilm pillars that penetrated deep into the tissue. For spinach we observed biofilms on the leaf in areas of tissue degradation. Finally, we explored the correlation between potentially relevant phenotypes (in vitro biofilm, motility and secreted enzyme production) and spoilage capabilities. After controlling for the phylogenetic relationships between samples there was no evidence for association between these phenotypes and spoilage capability in either product. Overall, this study increases our understanding of processes involved in food spoilage by Pseudomonas species.

Humans and animals are ubiquitously colonized by Enterobacteriaceae, a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplasmids of up to 1.58 Mbp in length in infant and adult guts, and other microbiomes. Of 19 complete plasmid genomes, one was reconstructed from an E. coli isolate; others were linked to species of Citrobacter and Enterobacter via analysis of genome modification patterns. The detection of related plasmids in different Enterobacteriaceae, conjugation machinery, and more diverse modified motifs in certain plasmids compared to hosts suggests that these elements are self-transmissible, with a broad host range. The plasmids encode multi-drug efflux systems and potential secreted effectors. Up to 208 tRNAs are encoded and include sequence variants that may counter tRNA-centric defense mechanisms. Overall, the vast megaplasmid coding capacity may broaden host range, increase competitiveness, control invasion by other elements, and counter programmed cell death.

A diverse array of micro-organisms can be found on food, including those that are pathogenic or resistant to antimicrobial drugs. Metagenomics involves extracting and sequencing the DNA of all micro-organisms on a sample, and here, we used a combination of culture and culture-independent approaches to investigate the microbial ecology of food to assess the potential application of metagenomics for the microbial surveillance of food. We cultured common foodborne pathogens and other organisms including Escherichia coli, Klebsiella/Raoultella spp., Salmonella spp. and Vibrio spp. from five different food commodities and compared their genomes to the microbial communities obtained by metagenomic sequencing following host (food) DNA depletion. The microbial populations of retail food were found to be predominated by psychrotrophic bacteria, driven by the cool temperatures in which the food products are stored. Pathogens accounted for a small percentage of the food metagenome compared to the psychrotrophic bacteria, and cultured pathogens were inconsistently identified in the metagenome data. The microbial composition of food varied amongst different commodities, and metagenomics was able to classify the taxonomic origin of 59% of antimicrobial resistance genes (ARGs) found on food to the genus level, but it was unclear what percentage of ARGs were associated with mobile genetic elements and thus transferable to other bacteria. Metagenomics may be used to survey the ARG burden, composition and carriage on foods to which consumers are exposed. However, food metagenomics, even after depleting host DNA, inconsistently identifies pathogens without enrichment or further bait capture.

Background. Bacterial pathogens contaminating retail foods can cause foodborne illness. Escherichia coli is commonly enumerated on food to assess unsafe levels of faecal contamination, but E. coli as a species is genetically variable and different types of E. coli may present more of a health risk than others. This enumeration approach provides limited insight into the types of E. coli contaminating food, whereas whole-genome sequencing (WGS) can provide insight into the genetic diversity as well as genes of concern. Current WGS studies have focused on the selection of pathogenic or antimicrobial-resistant E. coli, which has provided limited insight into the diversity and potential risk to consumers. Methods. To assess the diversity and potential risk of E. coli on food, food samples were collected from retail stores across Norfolk, UK. In this study, 126 chicken, 52 leafy green, 115 pork, 75 prawn and 33 salmon E. coli-positive samples were investigated. Up to four E. coli were isolated per sample and underwent WGS. E. coli genomes underwent in silico multi-locus sequence typing, where sequence types (STs) were investigated at the single nucleotide polymorphism (SNP) level. Furthermore, virulence genes and antimicrobial resistance (AMR) determinants were investigated. Results. From the total of 401 food samples, 1,067 E. coli genomes were isolated, sequenced and classified into 238 known STs and 54 unknown STs. Of the 145 samples in which four isolates were sequenced, 17 revealed four different STs, suggesting a high within-sample diversity. Within-sample within-ST comparisons revealed up to 845 pairwise non-recombinant SNPs. E. coli genomes contained between 0 and 14 AMR determinants. Up to four different AMR determinant combinations within a sample were identified, with 34.7% (n=139/401 samples) of all E. coli-positive samples containing three or more AMR determinants. In this dataset, 26 putative extraintestinal pathogenic E. coli (ExPEC) were identified. Discussion. A multi-isolate WGS approach identified a high diversity of STs, different AMR profiles and putative ExPEC within individual food samples which would have been missed by traditional enumeration approaches. Collecting multiple isolates and WGS is therefore necessary for ensuring thorough microbial hazard characterization for the consumer.

Vibrio is a genus of bacteria commonly found on seafood products and includes many important human pathogens. Most seafood is produced using aquaculture systems, which frequently use antimicrobial agents. Here we aimed to determine if method of seafood production was associated with Vibrio pathogenic to humans and/or antimicrobial resistant (AMR) Vibrio. Retail prawn and salmon samples that were produced using aquaculture or were wild-caught were cultured for Vibrio spp. Isolates were sequenced to identify the species and AMR genes (ARGs) present, followed by long-read sequencing of a subset of genomes to identify mobile genetic elements (MGEs). Vibrio was cultured from 136/279 of prawn and 4/157 of salmon samples, and ARG-containing Vibrio and Vibrio pathogenic to humans were associated with aquacultured prawn samples. A quarter of ARGs were found on plasmids, mostly in close vicinity to the insertion sequence type IS6/IS26. Most intrinsic chromosomal ARGs were not associated with an MGE, but most acquired chromosome ARGs were associated with a MGE, most commonly IS91. Vibrio isolates belonging to different species contained ARGs associated with similar MGEs. Vibrio has an arsenal of MGEs that can facilitate the spread of ARGs. Aquaculture practices may need to be adjusted in order to prevent the spread of AMR Vibrio and Vibrio pathogenic to humans.

Background. Nontyphoidal Salmonella (NTS) is a common cause of enterocolitis and a major cause of death in children in low- and middle-income countries (LMICs). High antimicrobial resistance (AMR) prevalence in LMICs reduces treatment options for individuals at risk of severe infections.Methods. We investigated the use of metagenomics to identify NTS and associated AMR genes in 28 faecal metagenomes from children with culture-confirmed salmonellosis in Vietnam, using accompanying NTS genomes from isolated serovars (one per metagenome). Read-based and assembly-based methods were utilised for NTS and AMR detection. Case metagenomes were compared to healthy control metagenomes (n=21) with respect to the microbiome composition, NTS relative abundances, number of unique AMR genes and antimicrobial classes to which the genes confer resistance, including classes used in Salmonella treatment.Results. Salmonellosis cases displayed significantly higher relative abundances of Enterobacteriaceae than controls. Bracken and Centrifuge analysis facilitated the identification of Salmonella enterica sequences in case metagenomes at varying relative abundances (0.00259-27.7 % of total reads), which were significantly higher than controls. MetaPhlAn4 did not detect S. enterica in any control metagenomes, though 12 case metagenomes were also negative. The isolated serovars were identified in 78.6% of the associated case metagenomes with Centrifuge, suggesting this method is the most sensitive; however, the isolated genome serovar was the most abundant in only six case metagenomes, and serovar sequences were also identified in control metagenomes. Alignment to a Salmonella reference database, followed by local assembly and realignment, predicted the isolated serovar as the most likely serovar present in 35.7% of metagenomes, whereas Salmonella in silico typing resource classification of the local assembly was concordant with the isolate genome in 28.6% of cases. Metagenome-assembled genomes produced using two tools following de novo assembly identified the isolated serovar in 17.8-21.4% of cases. The percentage of NTS AMR genes identified in each case metagenome ranged between 0.00 and 100%. There was no significant difference in the number of unique AMR genes or antimicrobial classes between cases and controls, indicating comparable resistomes between cohorts.Conclusions. This study highlights the potential of metagenomics for NTS identification in faecal samples, although overlap in S. enterica relative abundance between cohorts calls for further work to identify a diagnostic cutoff. Reliable characterisation of the organism to the serovar and AMR genotype level is affected by the complexity of the microbiome, sequencing and analysis approaches. Increased sequencing depth, for example through improved host DNA depletion, may facilitate enhanced characterisation. Detection of multiple serovars within individual samples with the Centrifuge suggests inaccurate classification or the presence of multiple serovars, making characterisation difficult.

A recent study has examined the flow of antimicrobial resistance genes in food production using nearly 2,000 metagenomes, indicating a potential role for contamination in processing facilities.

Yersinia enterocolitica is an underreported cause of foodborne gastroenteritis. Little is known of the diversity of Y. enterocolitica isolated from food and which food commodities contribute to human disease. In this study, Y. enterocolitica was isolated from 37/50 raw chicken, 8/10 pork, 8/10 salmon and 1/10 leafy green samples collected at retail in the UK. Up to 10 presumptive Y. enterocolitica isolates per positive sample underwent whole genome sequencing (WGS) and were compared with publicly available genomes. In total, 207 Y. enterocolitica isolates were analyzed and belonged to 38 sequence types (STs). Up to five STs of Y. enterocolitica were isolated from individual food samples and isolates belonging to the same sample and ST differed by 0-74 single nucleotide polymorphisms (SNPs). Biotype was predicted for 205 (99 %) genomes that all belonged to biotype 1A, previously described as non-pathogenic. However, around half (51 %) of food samples contained isolates belonging to the same ST as previously isolated from UK human cases. The closest human-derived isolates shared between 17 and 7978 single nucleotide polymorphisms (SNPs) with the food isolates. Extensive food surveillance is required to determine what food sources are responsible for Y. enterocolitica infections and to re-examine the role of biotype 1A as a human pathogen.

Salmonella enterica serovar Infantis presents an ever-increasing threat to public health because of its spread throughout many countries and association with high levels of antimicrobial resistance (AMR). We analyzed whole-genome sequences of 5,284 Salmonella Infantis strains from 74 countries, isolated during 1989–2020 from a wide variety of human, animal, and food sources, to compare genetic phylogeny, AMR determinants, and plasmid presence. The global Salmonella Infantis population structure diverged into 3 clusters: a North American cluster, a European cluster, and a global cluster. The levels of AMR varied by Salmonella Infantis cluster and by isolation source; 73% of poultry isolates were multidrug resistant, compared with 35% of human isolates. This finding correlated with the presence of the pESI megaplasmid; 71% of poultry isolates contained pESI, compared with 32% of human isolates. This study provides key information for public health teams engaged in reducing the spread of this pathogen.

Campylobacter spp. are leading bacterial gastroenteritis pathogens. Infections are largely underreported, and the burden of outbreaks may be underestimated. Current strategies of testing as few as one isolate per sample can affect attribution of cases to epidemiologically important sources with high Campylobacter diversity, such as chicken meat. Multiple culture method combinations were utilized to recover and sequence Campylobacter from 45 retail chicken samples purchased across Norwich, UK, selecting up to 48 isolates per sample. Simulations based on resampling were used to assess the impact of Campylobacter sequence type (ST) diversity on outbreak detection. Campylobacter was recovered from 39 samples (87%), although only one sample was positive through all broth, temperature, and plate combinations. Three species were identified (Campylobacter jejuni, Campylobacter coli, and Campylobacter lari), and 33% of samples contained two species. Positive samples contained 1-8 STs. Simulation revealed that up to 87 isolates per sample would be required to detect 95% of the observed ST diversity, and 26 isolates would be required for the average probability of detecting a random theoretical outbreak ST to reach 95%. An optimized culture approach and selecting multiple isolates per sample are essential for more complete Campylobacter recovery to support outbreak investigation and source attribution.

Foodborne illnesses pose a substantial health and economic burden, presenting challenges in prevention due to the diverse microbial hazards that can enter and spread within food systems. Various factors, including natural, political and commercial drivers, influence food production and distribution. The risks of foodborne illness will continue to evolve in step with these drivers and with changes to food systems. For example, climate impacts on water availability for agriculture, changes in food sustainability targets and evolving customer preferences can all have an impact on the ecology of foodborne pathogens and the agrifood niches that can carry microorganisms. Whole-genome and metagenome sequencing, combined with microbial surveillance schemes and insights from the food system, can provide authorities and businesses with transformative information to address risks and implement new food safety interventions across the food chain. In this Review, we describe how genome-based approaches have advanced our understanding of the evolution and spread of enduring bacterial foodborne hazards as well as their role in identifying emerging foodborne hazards. Furthermore, foodborne hazards exist in complex microbial communities across the entire food chain, and consideration of these co-existing organisms is essential to understanding the entire ecology supporting pathogen persistence and transmission in an evolving food system. In this Review, Mather et al. discuss the role of genome-based approaches in deepening our understanding of both enduring and emerging bacterial foodborne pathogens in the context of evolving global food systems and environmental changes.

BackgroundExtended-spectrum cephalosporins (ESCs) are third and fourth generation cephalosporin antimicrobials used in humans and animals to treat infections due to multidrug-resistant (MDR) bacteria. Resistance to ESCs (ESC-R) in Enterobacterales is predominantly due to the production of extended-spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC β-lactamases (AmpCs). The dynamics of ESBLs and AmpCs are changing across countries and host species, the result of global transmission of ESC-R genes. Plasmids are known to play a key role in this dissemination, but the relative importance of different types of plasmids is not fully understood.MethodsIn this study, Escherichia coli with the major ESC-R genes blaCTX-M-1, blaCTX-M-15, blaCTX-M-14 (ESBLs) and blaCMY-2 (AmpC), were selected from diverse host species and other sources across Canada, France and Germany, collected between 2003 and 2017. To examine in detail the vehicles of transmission of the ESC-R genes, long- and short-read sequences were generated to obtain complete contiguous chromosome and plasmid sequences (n = 192 ESC-R E. coli). The types, gene composition and genetic relatedness of these plasmids were investigated, along with association with isolate year, source and geographical origin, and put in context with publicly available plasmid sequences.FindingsWe identified five epidemic resistance plasmid subtypes with distinct genetic properties that are associated with the global dissemination of ESC-R genes across multiple E. coli lineages and host species. The IncI1 pST3 blaCTX-M-1 plasmid subtype was found in more diverse sources than the other main plasmid subtypes, whereas IncI1 pST12 blaCMY-2 was more frequent in Canadian and German human and chicken isolates. Clonal expansion also contributed to the dissemination of the IncI1 pST12 blaCMY-2 plasmid in ST131 and ST117 E. coli harbouring this plasmid. The IncI1 pST2 blaCMY-2 subtype was predominant in isolates from humans in France, while the IncF F31:A4:B1 blaCTX-M-15 and F2:A-:B- blaCTX-M-14 plasmid subtypes were frequent in human and cattle isolates across multiple countries. Beyond their epidemic nature with respect to ESC-R genes, in our collection almost all IncI1 pST3 blaCTX-M-1 and IncF F31:A4:B1 blaCTX-M-15 epidemic plasmids also carried multiple antimicrobial resistance (AMR) genes conferring resistance to other antimicrobial classes. Finally, we found genetic signatures in the regions surrounding specific ESC-R genes, identifying the predominant mechanisms of ESC-R gene movement, and using publicly available databases, we identified these epidemic plasmids from widespread bacterial species, host species, countries and continents.InterpretationWe provide evidence that epidemic resistance plasmid subtypes contribute to the global dissemination of ESC-R genes, and in addition, some of these epidemic plasmids confer resistance to multiple other antimicrobial classes. The success of these plasmids suggests that they may have a fitness advantage over other plasmid types and subtypes. Identification and understanding of the vehicles of AMR transmission are crucial to develop and target strategies and interventions to reduce the spread of AMR.FundingThis project was supported by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR), through the Medical Research Council (MRC, MR/R000948/1), the Canadian Institutes of Health Research (CFC-150770), and the Genomics Research and Development Initiative (Government of Canada), the German Federal Ministry of Education and Research (BMBF) grant no. 01KI1709, the French Agency for food environmental and occupational health & safety (Anses), and the French National Reference Center (CNR) for antimicrobial resistance. Support was also provided by the Biotechnology and Biological Sciences Research Council (BBSRC) through the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10348 (Theme 1, Epidemiology and Evolution of Pathogens in the Food Chain).

Background Pseudomonas species are common on food, but their contribution to the antimicrobial resistance gene (ARG) burden within food or as a source of clinical infection is unknown. Pseudomonas aeruginosa is an opportunistic pathogen responsible for a wide range of infections and is often hard to treat due to intrinsic and acquired ARGs commonly carried by this species. This study aimed to understand the potential role of Pseudomonas on food as a reservoir of ARGs and to assess the presence of potentially clinically significant Pseudomonas aeruginosa strains on food. To achieve this, we assessed the genetic relatedness (using whole genome sequencing) and virulence of food-derived isolates to those collected from humans. Results A non-specific culturing approach for Pseudomonas recovered the bacterial genus from 28 of 32 (87.5%) retail food samples, although no P. aeruginosa was identified. The Pseudomonas species recovered were not clinically relevant, contained no ARGs and are likely associated with food spoilage. A specific culture method for P. aeruginosa resulted in the recovery of P. aeruginosa from 14 of 128 (11%) retail food samples; isolates contained between four and seven ARGs each and belonged to 16 sequence types (STs), four of which have been isolated from human infections. Food P. aeruginosa isolates from these STs demonstrated high similarity to human-derived isolates, differing by 41–312 single nucleotide polymorphisms (SNPs). There were diverse P. aeruginosa collected from the same food sample with distinct STs present on some samples and isolates belonging to the same ST differing by 19–67 SNPs. The Galleria mellonella infection model showed that 15 of 16 STs isolated from food displayed virulence between a low-virulence (PAO1) and a high virulence (PA14) control. Conclusion The most frequent Pseudomonas recovered from food examined in this study carried no ARGs and are more likely to play a role in food spoilage rather than infection. P. aeruginosa isolates likely to be able to cause human infections and with multidrug resistant genotypes are present on a relatively small but still substantial proportions of retail foods examined. Given the frequency of exposure, the potential contribution of food to the burden of P. aeruginosa infections in humans should be evaluated more closely.

Despite millions of SARS-CoV-2 genomes being sequenced and shared globally, manipulating such data sets is still challenging, especially selecting sequences for focused phylogenetic analysis. We present a novel method, uvaia, which is based on partial and exact sequence similarity for quickly extracting database sequences similar to query sequences of interest. Many SARS-CoV-2 phylogenetic analyses rely on very low numbers of ambiguous sites as a measure of quality since ambiguous sites do not contribute to single nucleotide polymorphism (SNP) differences. Uvaia overcomes this limitation by using measures of sequence similarity which consider partially ambiguous sites, allowing for more ambiguous sequences to be included in the analysis if needed. Such fine-grained definition of similarity allows not only for better phylogenetic analyses, but could also lead to improved classification and biogeographical inferences. Uvaia works natively with compressed files, can use multiple cores and efficiently utilises memory, being able to analyse large data sets on a standard desktop.