DOI: 10.5061/dryad.tht76hfc5
title: Data from: Genomic insights reveal zoonotic potential of <em>Morganella morganii</em> strains from diarrheal patients in Dhaka, Bangladesh

description: Morganella morganii, a Gram-negative opportunistic pathogen, is
 increasingly recognized as a cause of nosocomial and community-acquired
 infections; however, comprehensive genomic studies from Bangladesh remain
 limited. In this study, seven M. morganii isolates from diarrheal stool
 samples and three from environmental sources in Dhaka were subjected to
 whole-genome sequencing to investigate their genomic diversity,
 antimicrobial resistance (AMR) profiles, virulence factors, and
 host-pathogen protein-protein interactions (HP-PPIs). Genome sizes ranged
 from 3.75 to 4.09 Mbp, with an average GC content of ~51 %. AMR analysis
 revealed diverse array of resistance genes, including β-lactamases
 (blaCTX-M-15, blaOXA-1), aminoglycoside-modifying enzymes (aadA5,
 aph(6)-Id, aac(6’)-Ib-cr), fluoroquinolone resistance genes (qnrB4),
 sulfonamide resistance genes (sul1, sul2), and tetracycline resistance
 determinants (tet(A), tet(D)). Interolog-based predictions identified
 3,920 potential HP-PPIs, including bacterial transketolase interacting
 with human NF-κB (NFKB1), suggesting immunomodulatory capabilities.
 Importantly, phylogenomic analysis revealed clustering of clinical
 isolates with strains from animal and environmental sources, indicating
 potential zoonotic transmission of M. morganii. This study reveals key
 genomic and phenotypic features of M. morganii in Bangladesh and
 underscores the importance of surveillance and targeted control strategies
 for this emerging pathogen.
description: # Data from: Genomic insights reveal zoonotic potential of *Morganella
 morganii* strains from diarrheal patients in Dhaka, Bangladesh Dataset
 DOI: [10.5061/dryad.tht76hfc5](10.5061/dryad.tht76hfc5) ## **Overview**
 This repository contains datasets supporting the study “Genomic insights
 reveal zoonotic potential of *Morganella morganii* strains from diarrheal
 patients in Dhaka, Bangladesh." We sequenced and analyzed *M.
 morganii* isolates collected in Dhaka, Bangladesh, from clinical diarrheal
 stool samples and environmental sources. The files include isolate
 metadata, antimicrobial susceptibility testing (AST) results,
 antimicrobial resistance (AMR) gene calls, virulence gene hits, average
 nucleotide identity (ANI) results, predicted human pathogenic capacity,
 mobile genetic element outputs, predicted genomic islands, and functional
 annotation tables (eggNOG/COG categories). **Important note about
 formats:** All tabular data are provided as CSV (comma-separated values)
 to maximize accessibility and reusability.  ## **Files and variables**
 **Files included** * Supplementary_File_1__*.csv — isolate metadata, AST
 results, AMR gene lists, sequencing metrics. * Supplementary_File_2__*.csv
 — ANI (FastANI), comparative public genome metadata, PathogenFinder
 outputs. * Supplementary_File_3__*.csv — virulence gene hits and biofilm
 assay results. * Supplementary_File_4__*.csv — integrons, insertion
 sequences, genomic islands, composite transposon/IS hits,
 MobileElementFinder summary. *
 Supplementary_File_5__.csv — eggNOG-mapper functional
 annotation tables, grouped by COG functional category. 
 
 **Common identifiers used across files** * Isolate / sample identifiers
 (e.g., NGCRVN-02, NGEE-862A) are used consistently across files. * For
 gene-level outputs, contig/replicon identifiers may appear (e.g.,
 NGCRVN-02_contig_1). 
 
 **Missing data codes and conventions** * Empty cells or NA indicate not
 available or not detected (depending on context). * Gene lists in some
 tables are stored as semicolon-separated or comma-separated text within a
 single cell. * Coordinates are reported as output by the respective tools
 (typically 1-based and inclusive). 
 
 **Abbreviations** * **AMR**: antimicrobial resistance * **AST**:
 antimicrobial susceptibility testing * **ANI**: average nucleotide
 identity * **VFDB**: Virulence Factor Database * **IS**: insertion
 sequence * **GI**: genomic island * **COG**: Clusters of Orthologous
 Groups 
 
 ## **File-by-file descriptions and data dictionaries** ## **Supplementary
 File 1 tables (phenotypes, metadata, basic metrics)** #####
 **Supplementary_File_1__S1_Morganella_AST.csv** **Description:** Disc
 diffusion AST results (presence/absence) for each isolate.
 **Supplementary_File_1__S2_Morganella_AMR_Genes.csv** **Description:**
 Gene-level AMR calls per isolate, including β-lactamases,
 aminoglycoside-modifying enzymes, fluoroquinolone determinants,
 sulfonamide, and tetracycline resistance markers.
 **Supplementary_File_1__S3_Source_Date.csv** **Description:**
 Isolate-level metadata (source and collection date).
 **Supplementary_File_1__S4_Sequencing_Metrics.csv** **Description:**
 Per-sample sequencing / coverage summary metrics. 
 
 ## **Supplementary File 2 tables (ANI + comparative context)**
 **Supplementary_File_2__S1_FASTANI.csv** **Description:** Pairwise ANI
 results for the ten study isolates against the reference genome
 GCF_002968775; columns include Genome, FastANI Score (%), and Reference
 Genome. **Supplementary_File_2__S2_Publicly_Available_M_morgan.csv**
 **Description:** Metadata table for the 90 comparative public *M.
 morganii* genomes from 18 countries; fields include Assembly_Accession,
 Strain, Isolation_Source, Country, Host, and Host_Disease (where
 available). **Supplementary_File_2__S3_PathogenFinder.csv**
 **Description:** Predicted human pathogenic capacity for each genome based
 on PathogenFinder. 
 
 ## **Supplementary File 3 tables (virulence + biofilm)**
 **Supplementary_File_3__S1_Virulence_Genes.csv** **Description:**
 Presence/absence matrix of virulence determinants per strain, including
 locus tags, gene symbols, and functional categories.
 **Supplementary_File_3__S2_Biofilm_Results.csv** **Description:** Summary
 of microtiter plate biofilm assay results. 
 
 ## **Supplementary File 4 tables (mobilome, integrons, islands,
 transposon/IS)** **Supplementary_File_4__S1_Integron_Finder.csv**
 **Description:** IntegronFinder output summarizing integron and attC
 elements. **Supplementary_File_4__S2_ISE_Scan.csv** **Description:**
 ISEScan output for insertion sequence (IS) predictions.
 **Supplementary_File_4__S3_Genomic_Island.csv** **Description:** Predicted
 genomic island content (IslandViewer4-style output). Each row corresponds
 to a gene within a predicted genomic island; island boundaries repeat for
 all genes within the same island.
 **Supplementary_File_4__S4_Composite_Transposon_Tn_F.csv**
 **Description:** Composite transposon / insertion-sequence alignment
 summary (derived from tool output). Column names were added for clarity.
 **Supplementary_File_4__S5_Mobile_Element_Finder.csv** **Description:**
 MobileElementFinder summary per isolate. 
 
 ## **Supplementary File 5 tables (eggNOG functional annotations by COG
 category)** Files:\ \ Supplementary_File_5__D.csv,
 Supplementary_File_5__F.csv, Supplementary_File_5__H.csv,
 Supplementary_File_5__I.csv, Supplementary_File_5__J.csv,
 Supplementary_File_5__O.csv, Supplementary_File_5__Q.csv,
 Supplementary_File_5__T.csv, Supplementary_File_5__V.csv **Description:**
 eggNOG-mapper v2 annotation outputs for selected genes, grouped by COG
 functional category letter. These file summarizes the comparative
 pan-genome and COG enrichment analyses of *M. morganii* isolates,
 highlighting accessory genes unique to diarrheal strains. It includes
 functional annotations based on eggNOG-mapper v2 and statistical
 enrichment results (GeneRatio, p-values, FDR, and log₂ odds ratios),
 revealing key defense- and adaptation-related functional groups enriched
 in the diarrheal accessory genome. **COG category letters used here** * D:
 Cell cycle control, cell division, chromosome partitioning * F: Nucleotide
 transport and metabolism * H: Coenzyme transport and metabolism * I: Lipid
 transport and metabolism * J: Translation, ribosomal structure and
 biogenesis * O: Posttranslational modification, protein turnover,
 chaperones * Q: Secondary metabolites biosynthesis, transport and
 catabolism * T: Signal transduction mechanisms * V: Defense mechanisms 
 
 ## Code/software The datasets were generated using open-source
 bioinformatics tools: **Read QC, assembly & coverage.** * fastp
 v0.23.4; FastQC v0.12.0 * SPAdes v3.15.0 (de novo assembly) * minimap2
 v2.28, samtools v1.19.2 (read mapping & BAM handling) * mosdepth
 v0.3.6 (depth/coverage) **Annotation & species confirmation.** *
 Prokka v1.14.6 (genome annotation) * KmerFinder v3.2; FastANI (species/ANI
 confirmation) **AMR, virulence & mobilome profiling.** * ResFinder
 v4.7.2; CARD (database 2024‑Dec‑15); ARG‑ANNOT (database 2024‑Dec‑15) *
 VFDB (core dataset update 2024) * MobileElementFinder v1.0.3;
 PlasmidFinder v2.1.6 * ISEScan v1.7.2.3 (IS elements); IslandViewer 4
 (genomic islands) * IntegronFinder v2.0.6; TnComp_finder (transposons) *
 CRISPRCasFinder (CRISPR–Cas loci) **Phylogenomics & SNP analysis.** *
 Snippy v4.6.0 (core‑SNP calling) * IQ‑TREE v3.0.1 (maximum‑likelihood
 phylogeny) **Pan‑genome & functional enrichment.** * Roary v3.13.0
 (pan‑genome) * eggNOG‑mapper v2 (functional annotation) * clusterProfiler
 v4.12.6 (COG/KEGG enrichment) **Host–pathogen protein–protein interactions
 (HP‑PPIs).**\ Interolog‑based predictions mapped *M. morganii* proteins to
 known human interactors curated in PHISTO. Protein sets were
 redundancy‑reduced with MMseqs2 v13.45111 (easy‑cluster, min ID 0.9,
 coverage mode 1, cluster coverage 0.8). Cluster representatives were
 aligned to PHISTO bacterial proteins with BLAST+ v2.9.0‑2 using thresholds
 of query coverage ≥ 70 %, identity ≥ 30 %, e‑value ≤ 1e‑4, and bit score
 &gt; 50 (max 1 target per query). Human partner proteins were retrieved
 from UniProt. Network construction and topology (e.g., degree centrality)
 were computed in NetworkX v2.8.8, and KEGG pathway enrichment of human
 targets was performed with clusterProfiler v4.12.6. Unless otherwise
 noted, tools were run with default parameters; complete version pins and
 parameter choices are documented in the Methods. **Ethical Approval** All
 experimental protocols and samples collection were approved by the North
 South University (NSU) Institutional Review Board (IRB) /Ethical Review
 Committee (ERC) under the protocol number CTRG: NSU-RP-21-042.