Beatriz Quiñones

Urban composting supports soil health but also intersects with food safety, where compost is produced near farms and communities. Here, we profiled temporal microbiome dynamics across a 6-week heat compost cycle from the urban compost piles using paired physicochemical panels and long-read metagenomics. Nutrient composition and pH shifted with compost age, coinciding with stage-structured microbial succession, including temperature-linked turnover of compost communities from mesophilic to thermotolerant taxa. Bacterial profiles included the presence of antimicrobial resistance genes and foodborne-associated genera early in the cycle, with reduced representation during the thermophilic phase. Analysis of previously unclassified long reads reveals an extensive repertoire of putative bacteriophages, including several complete genomes and candidates linked to foodborne bacteria, and their abundance is coupled to the host abundance. Together, these results support thermophilic composting as a key mitigation step for microbiological hazards in urban-adjacent systems and identify compost piles as a promising reservoir for discovering candidate lytic phages for downstream isolation and host-range testing.

The bacterial pathogen Acinetobacter baumannii is an opportunistic and nosocomial causative agent of multidrug resistant infections worldwide. The present study conducted comparative genomic analyses to identify relevant pathogenicity traits in A. baumannii strains from diverse clinical samples and geographical regions in Mexico. Pangenome analysis clustered the strains into four phylogenomic clades, comprising various international clones. Clades I and II strains, predominantly from blood and respiratory infections in the Central region, were significantly associated with the Latin American IC5 clone (P = 0.0002), whereas clade III strains, primarily from diverse samples in the Northwestern region, were significantly associated with the European IC2 clone (P = 0.0030). Virulence determinants implicated in adhesion (ompA, omp38), biofilm formation (pgaA-D, csuA/BABCDE), motility (pil, fim), regulatory systems (bfmRS, barAB, abaR/abaI), iron acquisition (bas, bau), and efflux pump-delivery systems (adeFGH) were identified among the A. baumannii strains, representing all clades and geographical regions. Analysis of intrinsic and acquired antimicrobial resistance revealed that clades I and II strains were significantly correlated with resistance to β-lactamases (blaADC-6, blaOXA-239, blaOXA-65), sulfonamides (sul2), and chloramphenicol (cmlB1) (P = 0.0001). Interestingly, clade III strains, predominantly from the agricultural Northwestern region, exhibited a significant association of broader resistance genes against aminoglycosides (aac(6’)-Ib’, aph(3’)-Ia, armA, aadA), β-lactamases (blaTEM-4, blaADC-25, blaOXA-66), sulfonamides (sul1), tetracyclines (tetA), and macrolides (mphD, msrE) (P = 0.0001). Subsequent characterization of mobile genetic elements indicated genetic plasticity and potential transfer of antimicrobial resistance. Collectively, this fundamental information would enable the improvement of epidemiological surveillance and intervention strategies for A. baumannii.

Acinetobacter baumannii is an opportunistic pathogen and a major cause of nosocomial infections worldwide. This study aimed to isolate and characterize phages with lytic activity against multidrug-resistant A. baumannii strains to enable antibacterial alternatives. Eight phages (AKO8a, PS118, B612, MCR, IDQ7, 89P13, CRL20, and CIM23) were isolated and subjected to genomic, phylogenetic, and functional analyses. Antibacterial activity was assessed in vitro against A. baumannii strain AbAK04 by measuring optical density over 17 h at multiplicities of infection (MOIs) of 0.1, 1, and 10, using a repeated-measures design with time as a crossed factor and MOI as a nested factor. Tukey’s post-hoc test identified significant bacterial growth reductions of 57–72% (p < 0.001). Specifically, phages PS118 and 89P13 reduced growth by 71% at MOI 10; CIM23, B612, and CRL20 achieved 68% reduction at MOI 1; and MCR reduced growth by 64% at MOIs 0.1 and 1. Notably, lytic phage MCR encodes a glycosyl hydrolase family 58 (GH58) enzyme, potentially contributing to its antibacterial activity. Genomic analyses confirmed absence of virulence and antibiotic resistance genes, with all phages classified as novel species within the Kagunavirus genus. These findings support the use of these phages as promising candidates for in vivo evaluation.

Non-typhoidal Salmonella enterica is a leading cause of gastrointestinal illnesses in the United States. Among the 2,600 different S. enterica serovars, Infantis has been significantly linked to human illnesses and is frequently recovered from broilers and chicken parts in the U.S. A key virulence determinant in serovar Infantis is the presence of the megaplasmid pESI, conferring multidrug resistance. To further characterize the virulence potential of this serovar, the present study identified the types of plasmids harbored by Infantis strains, recovered from surface waters adjacent to leafy greens farms in California. Sequencing analysis showed that each of the examined 12 Infantis strains had a large plasmid ranging in size from 78 kb to 125 kb. In addition, a second 4-kb plasmid was detected in two strains. Plasmid nucleotide queries did not identify the emerging megaplasmid pESI in the examined Infantis strains; however, the detected plasmids each had similarity to a plasmid sequence already cataloged in the nucleotide databases. Subsequent comparative analyses, based on gene presence or absence, divided the detected plasmids into five distinct clusters, and the phylogram revealed these Infantis plasmids were clustered based either on the plasmid conjugation system, IncI and IncF, or on the presence of plasmid phage genes. Assignment of the putative genes to functional categories revealed that the large plasmids contained genes implicated in cell cycle control and division, replication and recombination and defense mechanisms. Further analysis of the mobilome, including prophages and transposons, demonstrated the presence of genes implicated in the release of the bactericidal peptide microcin in the IncF plasmids and identified a Tn10 transposon conferring tetracycline resistance in one of the IncI1 plasmids. These findings indicated that the plasmids in the environmental S. enterica serovar Infantis strains from surface waters harbored a wide variety of genes associated with adaptation, survivability and antimicrobial resistance.

Campylobacter jejuni is a major cause of global foodborne illnesses. To develop alternative antimicrobial strategies against C. jejuni, this study designed and optimized the green synthesis of metallic nanoparticles (NPs) with intracellular components of the medicinal fungus Ganoderma sessile to provide the needed reducing and stabilizing agents. NPs were characterized by transmission electron microscopy and dynamic light scattering, and the quasi-spherical NPs had sizes of 2.9 ± 0.9 nm for the copper oxide NPs and 14.7 ± 0.6 nm for the silver NPs. Surface charge assessment revealed zeta potentials of −21.0 ± 6.5 mV and −24.4 ± 7.9 mV for the copper oxide and silver NPs, respectively. The growth inhibition of C. jejuni by the NPs occurred through attachment to the outer cell membrane and subsequent intracellular internalization and resulted in minimum inhibitory concentrations of the silver NPs at 6 µg/mL and copper oxide NPs at 10 µg/mL. On the other hand, a differential ROS production caused by silver and copper NPs was observed. In summary, this research presents the first demonstration of using green synthesis with the medicinal fungus G. sessile to produce metallic NPs that effectively inhibit C. jejuni growth, providing a sustainable and effective approach to the traditional use of antimicrobials.

Shiga toxin-producing Escherichia coli (STEC) are zoonotic enteric pathogens linked to human gastroenteritis worldwide. To aid the development of pathogen control efforts, the present study characterized the genotypic diversity and pathogenic potential of STEC recovered from sources near agricultural fields in Northwest Mexico. Samples were collected from irrigation river water and domestic animal feces in farms proximal to agricultural fields and were subjected to enrichment followed by immunomagnetic separation and plating on selective media for the recovery of the STEC isolates. Comparative genomic analyses indicated that the recovered STEC with the clinically relevant serotypes O157:H7, O8:H19, and O113:H21 had virulence genes repertoires associated with host cell adherence, iron uptake and effector protein secretion. Subsequent phenotypic characterization revealed multidrug resistance against aminoglycoside, carbapenem, cephalosporin, fluoroquinolone, penicillin, phenicol, and tetracycline, highlighting the need for improved surveillance on the use of antimicrobials. The present study indicated for the first time that river water in the agricultural Culiacan Valley in Mexico is a relevant key route of transmission for STEC O157 and non-O157 with a virulence potential. In addition, feces from domestic farm animals near surface waterways can act as potential point sources of contamination and transport of diverse STEC with clinically relevant genotypes.

Escherichia albertii is an emerging foodborne pathogen. To better understand the pathogenesis and health risk of this pathogen, comparative genomics and phenotypic characterization were applied to assess the pathogenicity potential of E. albertii strains isolated from wild birds in a major agricultural region in California. Shiga toxin genes stx_2f were present in all avian strains. Pangenome analyses of 20 complete genomes revealed a total of 11,249 genes, of which nearly 80% were accessory genes. Both core gene-based phylogenetic and accessory gene-based relatedness analyses consistently grouped the three stx_2f-positive clinical strains with the five avian strains carrying ST7971. Among the three Stx2f-converting prophage integration sites identified, ssrA was the most common one. Besides the locus of enterocyte effacement and type three secretion system, the high pathogenicity island, OI-122, and type six secretion systems were identified. Substantial strain variation in virulence gene repertoire, Shiga toxin production, and cytotoxicity were revealed. Six avian strains exhibited significantly higher cytotoxicity than that of stx_2f-positive E. coli, and three of them exhibited a comparable level of cytotoxicity with that of enterohemorrhagic E. coli outbreak strains, suggesting that wild birds could serve as a reservoir of E. albertii strains with great potential to cause severe diseases in humans.

Citrobacter werkmanii is an emerging and opportunistic human pathogen found in developing countries and is a causative agent of wound, urinary tract, and blood infections. The present study conducted comparative genomic analyses of a C. werkmanii strain collection from diverse geographical locations and sources to identify the relevant virulence and antimicrobial resistance genes. Pangenome analyses divided the examined C. werkmanii strains into five distinct clades; the subsequent classification identified genes with functional roles in carbohydrate and general metabolism for the core genome and genes with a role in secretion, adherence, and the mobilome for the shell and cloud genomes. A maximum-likelihood phylogenetic tree with a heatmap, showing the virulence and antimicrobial genes’ presence or absence, demonstrated the presence of genes with functional roles in secretion systems, adherence, enterobactin, and siderophore among the strains belonging to the different clades. C. werkmanii strains in clade V, predominantly from clinical sources, harbored genes implicated in type II and type Vb secretion systems as well as multidrug resistance to aminoglycoside, beta-lactamase, fluoroquinolone, phenicol, trimethoprim, macrolides, sulfonamide, and tetracycline. In summary, these comparative genomic analyses have demonstrated highly pathogenic and multidrug-resistant genetic profiles in C. werkmanii strains, indicating a virulence potential for this commensal and opportunistic human pathogen.

Salmonella enterica is a leading cause of human gastrointestinal disease worldwide. Given that Salmonella is persistent in aquatic environments, this study examined the prevalence, levels and genotypic diversity of Salmonella isolates recovered from major rivers in an important agricultural region in northwestern Mexico. During a 13-month period, a total of 143 river water samples were collected and subjected to size-exclusion ultrafiltration, followed by enrichment, and selective media for Salmonella isolation and quantitation. The recovered Salmonella isolates were examined by next-generation sequencing for genome characterization. Salmonella prevalence in river water was lower in the winter months (0.65 MPN/100 mL) and significantly higher in the summer months (13.98 MPN/100 mL), and a Poisson regression model indicated a negative effect of pH and salinity and a positive effect of river water temperature (p = 0.00) on Salmonella levels. Molecular subtyping revealed Oranienburg, Anatum and Saintpaul were the most predominant Salmonella serovars. Single nucleotide polymorphism (SNP)-based phylogeny revealed that the detected 27 distinct serovars from river water clustered in two major clades. Multiple nonsynonymous SNPs were detected in stiA, sivH, and ratA, genes required for Salmonella fitness and survival, and these findings identified relevant markers to potentially develop improved methods for characterizing this pathogen.

Campylobacter species are responsible for human gastroenteritis with diverse clinical spectra, ranging from acute watery or bloody diarrhea to life-threatening autoimmune disorders. Given the importance of Campylobacter in causing human illness, this article has reviewed the transmission and attribution sources as well as methodologies for the detection and virulence characterization of campylobacteria. The recovery and detection of Campylobacter from clinical, food and environmental samples has been achieved by the combinatorial use of selective enrichment and culturing methods. Biochemical, immunological, and nucleic acid-based methodologies have enabled the detection and differentiation of closely related Campylobacter isolates in foodborne outbreak investigations and have assessed the diversity and phylogenetic relationships of these bacterial pathogens. Analyses of motility, adherence, and invasiveness in host cells have assessed the pathogenic potential of campylobacteria. Further examination of determinants conferring antimicrobial resistance in Campylobacter have supported the growing need to closely monitor antimicrobials use in clinical and agricultural sectors.