BackgroundCannabis powdery mildew, caused by the fungal pathogen Golovinomyces ambrosiae, poses a significant threat to licensed producers as its presence on marketable products can compromise product innocuity. While there is a focus in research for resistance genes within the Cannabis sativa germplasm, there is a lack of genetic information regarding the infecting agent, preventing validation of their effectiveness against different populations as the plant-pathogen interaction most likely follows a gene-for-gene relationship. In this paper, we assembled the first G. ambrosiae genome, providing insights into its genomic content and potential virulence determinants. The assembly was made using a hybrid approach, combining Oxford Nanopore Technologies long reads and Illumina short reads.ResultsThe resulting 155.2 Mb genome is composed of 73 contigs, 13 scaffolds and has a completeness score of 97.5%. Subsequent analysis highlighted the substantial transposable elements content of the pathogen, occupying 82.64% of its genomic composition. Prediction of protein-coding genes revealed 6995 highly confident gene models, including 169 candidate effector proteins. Among the latter, we highlighted 14 candidates sharing key characteristics of confirmed effectors in other powdery mildew pathosystems such as the presence of signal peptides, RALPH-like domains, and Y/F/WxC motifs.ConclusionsThe result of this study provides valuable resources for future identification of avirulence genes within the G. ambrosiae species, responsible of conferring resistance when encoded effectors are recognized by a cognate host's resistance genes. Those findings will lead to guided breeding strategies and, ultimately, the selection of cultivars adapted to the pathogen's virulence profile.

As part of a broader effort to survey and characterize the diversity of pectolytic bacteria affecting potato crops in Mexico, phytopathogenic strains were isolated from soft-rot symptoms on potato plants in Sinaloa. Among them, an atypical Pectobacterium-like strain, LFLA-215T, could not be confidently assigned to any known species through biochemical or molecular methods. To clarify its taxonomic position and explore its genomic and functional features, whole-genome sequencing and comparative analyses were conducted, along with biochemical, morphological and pathogenicity evaluations. The strain LFLA-215T is Gram-stain-negative, with peritrichous flagella, catalase-positive and oxidase-negative. Phylogenetic analyses based on the 16S rRNA operon, dnaJ and 923 core genes confirmed that strain LFLA-215T and three additional strains (CFBP8739, CSR2 and CSR3) are members of the genus Pectobacterium. Although genomic similarity values between LFLA-215T and other Pectobacterium species ranged from 87.73 to 93.53% (OrthoANI blast-based), 87.63-93.46% (OrthoANI USEARCH) and 34.0-52.1% (digital DNA-DNA hybridization), falling below species delineation thresholds, phylogenomic reconstructions consistently positioned all four strains within a coherent clade. This clade showed the closest relationship to 'Pectobacterium colocasium' LJ1, whereas Pectobacterium parmentieri RNS 08-42-1AT was the most distantly related. Although LFLA-215T fulfilled Koch's postulates and demonstrated pathogenicity in potato plants, its virulence on tubers was comparatively lower than that of other known Pectobacterium strains, which could be related to the size and the reduction in the total number of genes when its complete genome is reported here. Our findings support the classification of the strains LFLA-215T, CFBP8739, CSR2 and CSR3 as a novel species within the genus Pectobacterium, for which the name Pectobacterium sinaloense sp. nov. is proposed, with LFLA-215T (=NCCB 101086=CM CNRG 1201=ATCC TSD-577) designated as the type strain.

Background: Carbapenem-resistant Pseudomonas aeruginosa (CRPA) poses a global health risk, yet there is insufficient knowledge about its sources and transmission routes within an integrated One Health framework. This study aimed to investigate CRPA presence and dynamics at the human-water interface inside and outside hospitals in three major cities located in different climatic zones. Methods: This cross-sectional study was conducted in Rotterdam (The Netherlands), Rome (Italy), and Jakarta (Indonesia) between March 2022 and June 2024. Samples were collected from humans, hospital environments, and various water sources. CRPA isolates underwent sequencing to determine carbapenemase gene presence and their genetic relatedness. Primary outcomes included CRPA carriage in healthy individuals and newly hospitalized patients, CRPA prevalence in hospital environments, CRPA concentrations in aquatic environments, and the frequency and transmission likelihood within epidemiological clusters. Findings: CRPA carriage was detected in 0·5% (1/194) of healthy individuals from Rotterdam, 0·0% (0/245) from Rome, and 0·8% (2/250) from Jakarta. Among patients, CRPA carriage differed significantly across cities (P<0·001), with 0·4% (2/469) in Rotterdam, 0·3% (1/363) in Rome, and 4·8% (28/584) in Jakarta. In wet hospital environments, CRPA prevalence ranged between 0·0% (Rome) and 13·4% (Jakarta). CRPA concentrations were highest in hospital wastewater and remained detectable in treated effluent of municipal wastewater treatment plants (mWWTP) and the receiving river in all cities. Carbapenemase genes were detected in 25·9% (100/386) of isolates. CRPA isolates identified in the clinical setting clustered with those from mWWTP influent or effluent (Rotterdam) or the river (Jakarta). High genetic diversity, overall and within reservoirs, was observed among isolates. Interpretation: The substantial presence of CRPA in environmental reservoirs, along with the cross-over between them, may pose a public health risk, and warrant mitigation strategies. To prevent CRPA transmission within hospitals and limit cross-sectoral transmission, robust infection prevention and control measures, alongside effective wastewater treatment, are essential.

Pseudomonas aeruginosa is an opportunistic pathogen that often colonizes the airways of people with cystic fibrosis (pwCF), and bronchiectasis causing chronic infection. When P. aeruginosa is confronted with various environmental conditions, it undergoes microevolution. To improve our understanding of the host-pathogen interactions occurring during chronic infections, we evaluated the host inflammatory responses to P. aeruginosa strains co-colonizing the lungs of pwCF. Differential inflammatory responses were elicited by several pairs of co-isolated P. aeruginosa strains in human bronchial epithelial cells. Characterization of these clinical isolates was initiated to find the factors explaining these divergent immune responses. Clonal relativeness of the co-isolated strains was confirmed by Multilocus Sequence Typing, and differential virulence patterns of the co-isolated strains was shown conserved across species using an in vivo Hydra vulgaris model. By comparing Single Nucleotide Variants (SNVs) of the co-isolated P. aeruginosa strains, the alkaline protease secretion protein F (aprF) gene was identified as a modulator of host IL-8 expression. aprF mutations led to decreased proteolytic activity in culture supernatants, leading to increased levels of flagellin and subsequent activation of TLR5 on bronchial cells. We propose a mechanism linking the dysfunction of aprF to the sequestration of the alkaline protease AprA, increasing flagellin recognition by the host through TLR5 activation promoting heightened inflammatory immune responses. In addition to aprF, we report several other P. aeruginosa candidate genes that can modulate host inflammatory responses. Understanding interaction between P. aeruginosa and lung mucosa in pwCF or bronchiectasis is essential to the development of improved therapies that will mitigate the damaging chronic inflammation, thereby improving the quality of life and survival of people with these diseases.

The bacterium Pseudomonas aeruginosa is an opportunistic pathogen responsible for several acute and chronic infections. It produces a diverse array of virulence and survival determinants, many of which are tightly regulated by three interlinked quorum sensing (QS) systems named las, rhl and pqs . RhlR, the transcriptional regulator of the rhl system, activates multiple virulence genes upon binding to its cognate autoinducer signal. Meanwhile, the pqs system relies on 4-hydroxy-2-alkylquinolines (HAQs) as signaling molecules to induce the transcriptional regulator MvfR (PqsR). MvfR then activates the transcription of the pqsABCDE operon, encoding enzymes for HAQ biosynthesis. The final gene in this operon encodes PqsE, a multifunctional protein unique to P. aeruginosa . Beyond its thioesterase activity in HAQ biosynthesis, PqsE stabilizes RhlR, facilitating its regulation of target genes, some of which are implicated in virulence. Because of its role in pathogenicity, PqsE is regarded as a promising therapeutic target for combating P. aeruginosa infections. While the role of PqsE towards the RhlR regulon is increasingly understood in prototypical P. aeruginosa strains such as PA14 and PAO1, its broader relevance as an anti-virulence target remains underexplored. Here, we confirm that PqsE is functionally relevant across a panel of twelve genetically diverse P. aeruginosa strains using metabolite quantification and phenotypic assays. Significant strain-to-strain variations further highlight the importance of studying QS regulation among diverse isolates. Moreover, this study underscores PqsE as a key QS regulator with a conserved role in coordinating virulence determinant production and social behaviors across diverse P. aeruginosa populations. IMPORTANCE Pseudomonas aeruginosa is a versatile opportunistic pathogen, naturally tolerant and readily acquiring resistance to multiple antibiotics. Consequently, the World Health Organization identified this bacterium as a high priority pathogen for researching and developing new antimicrobial strategies. P. aeruginosa utilizes quorum sensing, a cell-to-cell communication system, to regulate the expression of several of its virulence factors. Here, we confirm that the PqsE protein is conserved and that its function in quorum sensing, especially towards the RhlR regulator, is maintained across a panel of twelve genetically diverse P. aeruginosa strains. Since PqsE is conserved and unique to this bacterium, it could serve as an ideal target for anti-virulence therapies, offering new alternatives to combat antimicrobial resistance.

MOTIVATION:Antibiotic resistance is predicted to become the leading cause of human mortality by 2050. Despite this, no other major antibiotic class has been approved for medical use since 1987. Nevertheless, phage tail proteins offer a promising alternative, given their depolymerase activity toward outer membrane polysaccharides. Several pathogenic bacteria harbor prophages, thus making these prophages' molecular target already known. RESULTS:We therefore developed a wrapper for an existing machine learning-based phage depolymerase prediction tool (Depolymerase-Predictor), called PDP-Miner, which annotates phage tail proteins ab initio, detects depolymerase activity within this candidate protein subset, and then performs post-hoc validation by annotating protein domains thereby allowing the user to investigate for protein domains indicative of depolymerase activity. This tool allowed identification of 10 high confidence phage depolymerase gene candidates across all 1294 Pseudomonas genomes available on the International Pseudomonas Consortium Database while also accurately reporting depolymerases in known phage genomes, similarly to other software like PhageDPO or DepoScope. AVAILABILITY AND IMPLEMENTATION:Source code, test datasets and documentation are freely available for download at http:///www.github.com/jeffgauthier/pdpminer. This software is free and open source under the GNU General Public License v3.0.

Background/Objectives: The global spread of carbapenem-resistant Pseudomonas aeruginosa (CRPA) warrants collaborative action. Guidance should come from integrated One Health surveillance; however, a surveillance strategy is currently unavailable due to insufficient knowledge on the sources and transmission routes of CRPA. The aim of the SAMPAN study (“A Smart Surveillance Strategy for Carbapenem-resistant Pseudomonas aeruginosa”) is to develop a globally applicable surveillance strategy. Methods: First, an international cross-sectional study will be conducted to investigate CRPA in clinical and environmental settings in Rotterdam (The Netherlands), Rome (Italy), and Jakarta (Indonesia). Screening cultures and risk factor questionnaires will be taken from healthy individuals and patients upon hospital admission. Clinical CRPA isolates will also be included. Additionally, samples will be taken twice from wet hospital environments and monthly from the hospitals’ (drinking) water system, hospital and municipal wastewater treatment plants, and receiving rivers. Whole-genome sequencing will be performed to characterize CRPA isolates and determine the genetic relatedness among the isolates from different reservoirs. Findings from the cross-sectional study, combined with expert elicitation using a Delphi method, will serve as the input for the surveillance strategy. Conclusions: The SAMPAN study will provide a broader understanding of the sources and transmission routes of CRPA. Therewith, the development of a globally applicable smart surveillance strategy will be made possible, delivering information that is needed to guide actions against the spread of CRPA.

Pseudomonas aeruginosa is an opportunistic pathogen responsible for several acute and chronic infections. The production of many of its virulence factors is tightly regulated by three interlinked quorum sensing (QS) systems named las, rhl, and pqs. The pqs system relies on 4-hydroxy-2-alkylquinolines (HAQs) as signaling molecules to activate the transcriptional regulator MvfR (PqsR), which drives HAQ biosynthesis via the pqsABCDE operon. The final gene in this operon encodes PqsE, a multifunctional protein unique to P. aeruginosa. Beyond its thioesterase activity in HAQ biosynthesis, PqsE stabilizes RhlR, the transcriptional regulator of the rhl system, facilitating the regulation of virulence-related genes. Due to its pathogenic relevance, PqsE is considered a potential therapeutic target against P. aeruginosa infections. While the role of PqsE toward the RhlR regulon is increasingly understood in reference P. aeruginosa strains such as PA14 and PAO1, its broader relevance remains underexplored. In this study, pqsE and rhlR were found to be genetically conserved across a diverse panel of 12 P. aeruginosa strains. Phenotypic assays and metabolite quantification revealed that PqsE broadly influences virulence factors and multicellular behaviors, including pyocyanin production and biofilm formation. While the magnitude of PqsE-dependent phenotypes varied between strains, key functions were consistently maintained, underscoring both conservation and strain-specific modulation. Notably, PqsE proved essential for HAQ biosynthesis in most strains, challenging prior assumptions of its dispensability. This study contributes to a deeper understanding of QS regulation, highlighting that while PqsE contributes to conserved functions across P. aeruginosa strains, its impact is strain dependent.IMPORTANCEPseudomonas aeruginosa is a versatile opportunistic pathogen, naturally tolerant and readily acquiring resistance to multiple antibiotics. Consequently, the World Health Organization identified this bacterium as a high-priority pathogen for researching and developing new antimicrobial strategies. P. aeruginosa utilizes quorum sensing, a cell-to-cell communication system, to regulate the expression of several of its virulence factors. Here, we confirm that the PqsE protein is conserved, and its function in quorum sensing, especially toward the RhlR regulator, is variable across a panel of 12 P. aeruginosa strains. Since PqsE is conserved and unique to this bacterium, it has been proposed as an ideal target for antivirulence therapies, offering new alternatives to combat antimicrobial resistance. However, our results question the relevance of PqsE as an appropriate target.

The major human bacterial pathogen Pseudomonas aeruginosa causes multidrug-resistant infections in people with underlying immunodeficiencies or structural lung diseases such as cystic fibrosis (CF). We show that a few environmental isolates, driven by horizontal gene acquisition, have become dominant epidemic clones that have sequentially emerged and spread through global transmission networks over the past 200 years. These clones demonstrate varying intrinsic propensities for infecting CF or non-CF individuals (linked to specific transcriptional changes enabling survival within macrophages); have undergone multiple rounds of convergent, host-specific adaptation; and have eventually lost their ability to transmit between different patient groups. Our findings thus explain the pathogenic evolution of P. aeruginosa and highlight the importance of global surveillance and cross-infection prevention in averting the emergence of future epidemic clones.

Pseudomonas aeruginosa is one of the top priority pathogens that requires immediate attention according to the World Health Organisation (WHO). Due to the alarming shortage of novel antimicrobials, targeting quorum sensing (QS), a bacterial cell to cell signaling system controlling virulence, has emerged as a promising approach as an antibiotic adjuvant therapy. Interference with the pqs system, one of three QS systems in P. aeruginosa, results in reduction of bacterial virulence gene expression and biofilm maturation. Herein, we report a hit to lead process to fine-tune the potency of our previously reported inhibitor 1 (IC50 3.2 μM in P. aeruginosa PAO1-L), which led to the discovery of 2-(4-(3-((6-chloro-1-isopropyl-1H-benzo[d]imidazol-2-yl)amino)-2-hydroxypropoxy)phenyl)acetonitrile (6f) as a potent PqsR antagonist. Compound 6f inhibited the PqsR-controlled PpqsA-lux transcriptional reporter fusion in P. aeruginosa at low submicromolar concentrations. Moreover, 6f showed improved efficacy against P. aeruginosa CF isolates with significant inhibition of pyocyanin, 2-alkyl-4(1H)-quinolones production.

Here, we present the complete 4.77 Mb genome of Enterobacter roggenkampii 0-E assembled with Oxford Nanopore long reads. This genome harbors 19 antimicrobial resistance genes, including ramA and marA decreasing permeability to carbapenems. This genome adds novel knowledge on emerging multidrug resistance in the Enterobacter cloacae species complex.

Background Mycobacterium abscessus complex (MABC), an opportunistic nontuberculous mycobacteria, can lead to poor clinical outcomes in pulmonary infections. Conflicting data exist on person-to-person transmission of MABC within and across health care facilities. To investigate further, a comprehensive retrospective study across 5 health care institutions on the Island of Montr & eacute;al was undertaken.Methods We analyzed the genomes of 221 MABC isolates obtained from 115 individuals (2010-2018) to identify possible links. Genetic similarity, defined as <= 25 single-nucleotide polymorphisms (SNPs), was investigated through a blinded epidemiological inquiry.Results Bioinformatics analyses identified 28 sequence types, including globally observed dominant circulating clones (DCCs). Further analysis revealed 210 isolate pairs within the SNP threshold. Among these pairs, there was 1 possible laboratory contamination where isolates from different patients processed in the same laboratory differed by only 2 SNPs. There were 37 isolate pairs from patients who had provided specimens from the same hospital; however, epidemiological analysis found no evidence of health care-associated person-to-person transmission between these patients. Additionally, pangenome analysis showed higher discriminatory power than core genome analysis for examining genomic similarity.Conclusions Genomics alone is insufficient to establish MABC transmission, particularly considering the genetic similarity and wide distribution of DCCs, although pangenome analysis has the potential to add further insight. Our findings indicate that MABC infections in Montr & eacute;al are unlikely attributable to health care-associated person-to-person transmission. The study investigates Mycobacterium abscessus complex (MABC) transmission in Montr & eacute;al health care settings using genomic epidemiology analyses. Despite instances of genetic similarity between isolates from different patients, epidemiological investigation uncovered no evidence of health care-associated person-to-person transmission.

Bacteriophages (phages) are potential alternatives to chemical antimicrobials against pathogens of public health significance. Understanding the diversity and host specificity of phages is important for developing effective phage biocontrol approaches. Here, we assessed the host range, morphology, and genetic diversity of eight Salmonella enterica phages isolated from a wastewater treatment plant. The host range analysis revealed that six out of eight phages lysed more than 81% of the 43 Salmonella enterica isolates tested. The genomic sequences of all phages were determined. Whole genome sequencing data (WGS) data revealed that phage genome sizes ranged from 41 to 114 kb with GC contents be-tween 39.9 and 50.0 %. Two of the phages SB13 and SB28 represent new species Epsep-timavirus SB13 and genera Macdonaldcampvirus, respectively as designated by the In-ternational Committee for the Taxonomy of Viruses (ICTV) as per genome based taxonomic classification. One phage (SB18) belonged to the Myoviridae morphotype while the re-maining phages belonged to the Siphoviridae morphotype. The gene content analyses showed that none of the phages possessed virulence, toxin, antibiotic resistance, type I-VI toxin-antitoxin modules or lysogeny genes. Three (SB3, SB15 and SB18) out of the eight phages possessed tailspike proteins. Whole genome-based phylogeny of the eight phages with their 113 homologs revealed three clusters A, B, C and seven subclusters (A1, A2, A3, B1, B2, C1 and C2). While cluster C1 phages were predominantly isolated from animal sources, cluster B contained phages from both wastewater and animal sources. The broad host range of these phages highlights their potential use to control the presence of S. enterica in foods.

AIM: To determine the resistance profiles, genetic diversity and transmission of carbapenem-resistant Pseudomonas aeruginosa (CRPA) isolates from Indonesia. BACKGROUND: CRPA poses a significant global health threat due to high mortality and limited treatment options. Whole genome sequencing (WGS) provides a comprehensive approach to understanding the genetic determinants of resistance and transmission dynamics of CRPA. METHODS: CRPA isolates were collected from clinical and screening samples at a national reference hospital in Jakarta, Indonesia. Screening samples were collected from patients on admission and from healthy volunteers living nearby. Identification and antimicrobial susceptibility testing were performed using VITEK. WGS was performed using Oxford Nanopore and Illumina platforms, followed by hybrid assembly using NanoLite v1.1, and AMR genes were detected using the latest version of the CARD database. Genomic data were analysed to determine sequence types, carbapenemase genes and resistance determinants. RESULTS: The screening included 573 patients and 243 healthy individuals. A total of 110 CRPA isolates were analysed (71 clinical samples, 35/573 patients on admission samples and 4/243 healthy screening samples). Antimicrobial susceptibility patterns were diverse, with high rates of resistance to multiple antibiotics (Table 1-2). The carbapenemase genes IMP and VIM were not found in screening samples but were found in clinical isolates (Table 3). WGS revealed some clusters of CRPA clones, suggesting possible transmission. CONCLUSIONS: This study highlights the prevalence of CRPA in both hospital and community settings in Jakarta. WGS is critical for identifying genetic diversity and potential transmission links, highlighting its crucial role in informing effective infection control strategies.

To survive harsh winter conditions, many insects enter a state of dormancy called diapause which allows them to withstand extreme temperatures and lack of food. When diapause is induced, insects enter a state of arrested development and low metabolic rate. Because diapause and environmental conditions are closely linked, variation within and between species in diapause induction, depth, and duration is extremely common. Studies investigating the genetic underpinnings of diapause tend to focus on either different populations and/or environmental variation, which runs the risk of confounding the genetic signal either due to isolation-by-distance or variation in environmental conditions. We use the eastern spruce budworm (Choristoneura fumiferana) to circumvent these issues and investigate within-population variation in diapause. C. fumiferana usually diapauses as second instar larvae, but a small subset of individuals does not diapause and instead continues through development. This non-diapause phenotype can be selected to create a non-diapause strain. Here, we present a chromosome-level assembly of such a non-diapause strain, and compare it to an earlier published genome assembly of the diapause strain. We did not find evidence of major chromosome rearrangements, indicating that the genetic variation between strains is likely small and multi-genic. Gene expression comparisons between the strains indicate major gene expression changes, where genes associated with glycolysis and environmental signaling processing increase in expression in the diapause strain. Lastly, we found that gene expression diverges halfway through the first instar, and not before, indicating that the signal to induce diapause happens early in the first instar. ### Competing Interest Statement The authors have declared no competing interest.

Background Flight can drastically enhance dispersal capacity and is a key trait defining the potential of exotic insect species to spread and invade new habitats. The phytophagous European spongy moths (ESM, Lymantria dispar dispar) and Asian spongy moths (ASM; a multi-species group represented here by L. d. asiatica and L. d. japonica), are globally invasive species that vary in adult female flight capability-female ASM are typically flight capable, whereas female ESM are typically flightless. Genetic markers of flight capability would supply a powerful tool for flight profiling of these species at any intercepted life stage. To assess the functional complexity of spongy moth flight and to identify potential markers of flight capability, we used multiple genetic approaches aimed at capturing complementary signals of putative flight-relevant genetic divergence between ESM and ASM: reduced representation genome-wide association studies, whole genome sequence comparisons, and developmental transcriptomics. We then judged the candidacy of flight-associated genes through functional analyses aimed at addressing the proximate demands of flight and salient features of the ecological context of spongy moth flight evolution. Results Candidate gene sets were typically non-overlapping across different genetic approaches, with only nine gene annotations shared between any pair of approaches. We detected an array of flight-relevant functional themes across gene sets that collectively suggest divergence in flight capability between European and Asian spongy moth lineages has coincided with evolutionary differentiation in multiple aspects of flight development, execution, and surrounding life history. Overall, our results indicate that spongy moth flight evolution has shaped or been influenced by a large and functionally broad network of traits. Conclusions Our study identified a suite of flight-associated genes in spongy moths suited to exploration of the genetic architecture and evolution of flight, or validation for flight profiling purposes. This work illustrates how complementary genetic approaches combined with phenotypically targeted functional analyses can help to characterize genetically complex traits.

We report the draft genome sequence of Pseudomonas sp. ER28, capable of utilizing the model naphthenic acid, cyclohexane pentanoic acid, as its sole carbon source. It was recovered from oil sands process-affected water containing cyclic and acyclic naphthenic acids. The genome size is 5.7 Mbp, and the G + C content is 60%.

With the increasing occurrence and severity of cyanobacterial harmful algal blooms (cHAB) at the global scale, there is an urgent need for rapid, accurate, accessible, and cost-effective detection tools. Here, we detail the RosHAB workflow, an innovative, in-the-field applicable genomics approach for real-time, early detection of cHAB outbreaks. We present how the proposed workflow offers consistent taxonomic identification of water samples in comparison to traditional microscopic analyses in a few hours and discuss how the generated data can be used to deepen our understanding on cyanobacteria ecology and forecast HABs events. In parallel, processed water samples will be used to iteratively build the International cyanobacterial toxin database (ICYATOX; http://icyatox.ibis.ulaval.ca) containing the analysis of novel cyanobacterial genomes, including phenomics and genomics metadata. Ultimately, RosHAB will (1) improve the accuracy of on-site rapid diagnostics, (2) standardize genomic procedures in the field, (3) facilitate these genomics procedures for non-scientific personnel, and (4) identify prognostic markers for evidence-based decisions in HABs surveillance.