Abstract
Objective
M. morganii is a gram-negative, non-lactose fermenting and an opportunistic pathogen frequently associated with nosocomial infections. Although first isolated in 1906 from a pediatric fecal sample, not many M. morganii isolates have been sequenced. The objective of this work is to determine the complete genome sequence of an XDR M. morganii strain (SMM01) isolated from the urine of a patient with urinary and fecal incontinence and to characterize its antimicrobial resistance profile.
Data description
Here, we report the complete genome sequence of M. morganii SMM01 generated from the hybrid assembly of Illumina HiSeq X and Nanopore MinION reads. The assembly is 100% complete with genome size of 39,30,130 bp and GC content of 51%. Genomic features include 3617 CDS, 18 rRNAs, 78 tRNAs, 4 ncRNAs and 60 pseudogenes. Antimicrobial resistance profile was characterized by the presence of genes conferring resistance to aminoglycosides, β-lactams, fluoroquinolones, chloramphenicol, and tetracyclines. Secondary metabolite biosynthetic gene clusters like NRPS, T1PKS, thiopeptide, beta-lactone, and bacteriocin were identified. The genome data described here would be the first complete genome of an Indian M. morganii isolate providing crucial information on antimicrobial resistance patterns, paving the way for further comparative genome analyses.
Keywords: M. morganii, Extensively drug resistant (XDR), Hybrid sequencing, Complete genome and antimicrobial resistance (AMR)
Objective
M. morganii is a gram-negative, facultative, non-lactose fermenting bacterium belonging to the tribe Proteae of Enterobacteriaceae family. This opportunistic pathogen was first reported in 1906 from a pediatric fecal sample [1]. M. morganii is often encountered among postoperative, immunocompromised, and intensive care unit patients [2, 3] causing catheter-associated urinary tract infections (CAUTI), sepsis and wound infections [4]. As on 24th January 2021, 98 M. morganii genomes were available in the NCBI Genbank, of which 20 were complete genomes. The objective of this study is to characterize a new, clinically isolated XDR M. morganii strain by whole genome sequencing to understand its antimicrobial resistance profile.
Here, we report a complete genome sequence of M. morganii, isolated from the urine sample of a male patient in 2018 at Sri Sathya Sai Institute of Higher Medical Sciences (SSSIHMS) Prasanthigram, India (14.1670 N 77.8091 E). The patient was admitted to the urology ward due to urinary and fecal incontinence and had a history of Road Traffic Accident (RTA), 1 year prior to the isolation of the strain. The isolate was identified as M. morganii by MALDI-TOF MS. Antibiotic Susceptibility Testing (AST) and Minimum Inhibitory Concentrations (MICs) were determined using Vitek2 as per CLSI guidelines [5].
Whole genome sequencing of M. morganii SMM01 was performed using Illumina HiSeq X (short reads technology) and Nanopore MinION (long reads technology) platforms. The reads from both the sequencing platforms were used to generate hybrid assembly using Unicycler. To the best of our knowledge, this would be the first complete genome sequence of M. morganii from India.
Data description
Upon isolation and strain purification, the isolate SMM01 was cultivated in LB broth. AST was performed using N281 card in Vitek2 and the study isolate SMM01 was found to be resistant to all the tested antibiotics except aminoglycosides (Amikacin and Gentamicin). Total genomic DNA was extracted using Macherey Nagel Nucleospin® DNA extraction kit as per manufacturer’s instructions.
Oxford Nanopore Technologies (ONT) Minion sequencing libraries were prepared using the ligation sequencing kit (SQK-LSK109) and data was collected from the FLO-MIN106 flow cell. Base-calling and demultiplexing was done using Albacore v2.0.1. MinION sequencing run produced 30,881 reads with the mean read quality score of 7.7 as assessed with NanoStat [6] (Data file 1) [7]. The passed reads were taken for adapter removal using Porechop v0.2.4 (https://github.com/rrwick/Porechop). Illumina sequencing libraries were prepared using the NEBNext Ultra II DNA library preparation kit (E7645S). The libraries were pooled after performing quantity and quality checks using Qubit2 and Agilent Bioanalyzer DNA 100 kit. Illumina HiSeq X was used to sequence the multiplexed libraries. Demultiplexing was performed using bcl2fastq v2.2 (RRID:SCR_015058). Quality of the reads was assessed with FastQC [8] and MultiQC [9] (Data file 2) [10]. The processed reads from both Illumina and Nanopore were used to generate hybrid assembly using Unicycler v0.4.8 [11] and the final assembly quality was assessed with QUAST [12] (Data file 3) [13].
The final complete genome assembly (Data set 1) [14] has a total length of 39,30,130 bp, GC content of 51.0% and genome coverage of 189.69x. A total of 3777 genes were predicted by NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v 4.13 [15] in the genome. These include 3617 protein-coding genes, 78 tRNAs, 18 rRNAs, 4 ncRNAs, and 60 pseudogenes. Genome completeness analysis with BUSCO v3.0.2 [16] using the “gammaproteobacteria_odb9” dataset with 452 benchmarking universal single-copy orthologs (BUSCOs) showed the presence of 100% complete BUSCOs in the hybrid assembly (data file 4) [17]. The genome was found to possess several antibiotic resistance genes, secondary metabolite gene clusters and prophages.
Given the quality control measures applied, we believe the complete genome of M. morganii strain SMM01 represents a high-quality dataset that would enhance the study of the antimicrobial resistance patterns. It may further aid in comparative genomic analyses of this emerging pathogen along with its biosynthetic and metabolic potential.
Please see Table 1 for links to Data files 1–4 and Data set 1.
Table 1.
Overview of data files/data sets
| Label | Name of data file/data set | File types (file extension) | Data repository and identifier (DOI or accession number) |
|---|---|---|---|
| Data file 1 | Basic quality statistics of MinION sequencing data | Portable Document Format file (.pdf) | 10.6084/m9.figshare.13668881 [7] |
| Data file 2 | Quality distribution of Illumina sequencing data | Portable Document Format file (.pdf) | 10.6084/m9.figshare.13668887 [10] |
| Data file 3 | Quast report of M. morganii SMM01 assembly | Portable Document Format file (.pdf) | 10.6084/m9.figshare.13668890 [13] |
| Data file 4 | Short BUSCO summary | Portable Document Format file (.pdf) | 10.6084/m9.figshare.13668893 [17] |
| Data set 1 | Genome assembly of M. morganii SMM01 | Fasta file (.fna) | https://www.ncbi.nlm.nih.gov/assembly/GCF_015698325.1 [14] |
Limitations
The complete genome sequence of M. morganii SMM01 was generated from a hybrid assembly using Illumina and ONT technologies to ensure accuracy and completeness. Further, Unicycler autocorrects read errors and polishes (using Pilon) the assembly to ensure accuracy. Annotation and further downstream specialized analyses were performed using robust and validated bioinformatics tools and webservers. Therefore, the authors are not aware of any limitations in the data.
Acknowledgements
We thank the Department of Mathematics and Computer Sciences, SSSIHL for access to the Hi-performance computing facility. We acknowledge UGC-SAP-DRS-III, DST-FIST and DBT-BIF, Govt. of India for the infrastructural support to the Department of Biosciences, SSSIHL and UGC-SRF, ICMR-SRF and NFST Fellowships from Govt. of India to BK, PPC and ML. VN is a J. C. Bose fellow of the Department of Science and Technology, Govt. of India.
Abbreviations
- NRPS
Non-ribosomal peptide synthetases
- T1PKS
Type I Polyketide synthase
- XDR
Extensively drug-resistant
- CAUTI
Catheter-associated Urinary Tract Infections
- NCBI
National Center for Biotechnology Information
- AST
Antimicrobial Sensitivity Test
- CLSI
Clinical Laboratory Standards Institute
- RTA
Road Traffic Accident
- MALDI-TOF MS
Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
- LB
Luria Bertani
- ONT
Oxford Nanopore Technologies
- BUSCO
Benchmarking Universal Single Copy Orthologs
Authors’ contributions
BEP and VN conceived and designed the experiments. PK performed strain isolation and AST. PPC and BK performed the SMM01 cultivation and DNA extraction. PPC, ML and ASKP performed the genome analysis. The manuscript was written by PPC and revised by BEP and VN. The author(s) read and approved the final manuscript.
Funding
This project was supported by ICMR EMR grant (OMI/27/2020-ECD-I). The funding body played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.
Availability of data and materials
The complete genome sequence and annotation data of M. morganii SMM01 described in this data note can be freely and openly accessed on NCBI database under the accession number NZ_CP063843. The BioProject and BioSample numbers are PRJNA673656 and SAMN16619592, respectively. All the data files can be freely and openly accessed on Figshare (https://figshare.com/). The version described in this paper is NZ_CP063843.1.
Declarations
Ethics approval and consent to participate
Not applicable.
Consent for publication
Not applicable.
Competing interests
The authors declare no competing interests.
Footnotes
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Contributor Information
Pachi Pulusu Chanakya, Email: pachipulusuchanakya@sssihl.edu.in.
Balaram Khamari, Email: balaramkhamari@sssihl.edu.in.
Manmath Lama, Email: manmathlama@sssihl.edu.in.
Arun Sai Kumar Peketi, Email: arunsaikumarpeketi@sssihl.edu.in.
Prakash Kumar, Email: ammiamula@yahoo.com.
Valakunja Nagaraja, Email: vraj@iisc.ac.in.
Eswarappa Pradeep Bulagonda, Email: bepradeep@sssihl.edu.in.
References
- 1.Morgan HDR, Oxon MA. Report CII. Upon the bacteriology of the summer Diarrhoea of infants. Br Med J. 1907;2(2427):16–19. doi: 10.1136/bmj.2.2427.16-a. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.O'Hara CM, Brenner FW, Miller JM. Classification, identification, and clinical significance of Proteus, Providencia, and Morganella. Clin Microbiol Rev. 2000;13(4):534–546. doi: 10.1128/CMR.13.4.534. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Lin TY, Chan MC, Yang YS, Lee Y, Yeh KM, Lin JC, Chang FY. Clinical manifestations and prognostic factors of Morganella morganii bacteremia. Eur J Clin Microbiol Infect Dis. 2015;34(2):231–236. doi: 10.1007/s10096-014-2222-8. [DOI] [PubMed] [Google Scholar]
- 4.Liu H, Zhu J, Hu Q, Rao X. Morganella morganii, a non-negligent opportunistic pathogen. Int J Infect Dis. 2016;50:10–17. doi: 10.1016/j.ijid.2016.07.006. [DOI] [PubMed] [Google Scholar]
- 5.CLSI . Performance Standards for Antimicrobial Susceptibility Testing. CLSI Supplement M100. 30. Wayne: Clinical and Laboratory Standards Institute; 2020. [Google Scholar]
- 6.De Coster W, D'Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018;34(15):2666–2669. doi: 10.1093/bioinformatics/bty149. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Chanakya PP. Basic quality statistics of MinION sequencing data. 2021. [Google Scholar]
- 8.Andrews S, FastQC . A Quality Control tool for High Throughput Sequence Data. 2010. [Google Scholar]
- 9.Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047–3048. doi: 10.1093/bioinformatics/btw354. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Chanakya PP. Quality distribution of Illumina sequencing data. 2021. [Google Scholar]
- 11.Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017;13(6):e1005595. doi: 10.1371/journal.pcbi.1005595. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072–1075. doi: 10.1093/bioinformatics/btt086. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Chanakya PP. Quast report of M. morganii SMM01 assembly. 2021. [Google Scholar]
- 14.National Center for Biotechnology Information. Assembly: https://identifiers.org/insdc.gca: GCF_015698325.1; 2020.
- 15.Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44(14):6614–6624. doi: 10.1093/nar/gkw569. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16.Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31(19):3210–3212. doi: 10.1093/bioinformatics/btv351. [DOI] [PubMed] [Google Scholar]
- 17.Chanakya PP. Short BUSCO summary of Morganella morganii SMM01. 2021. [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The complete genome sequence and annotation data of M. morganii SMM01 described in this data note can be freely and openly accessed on NCBI database under the accession number NZ_CP063843. The BioProject and BioSample numbers are PRJNA673656 and SAMN16619592, respectively. All the data files can be freely and openly accessed on Figshare (https://figshare.com/). The version described in this paper is NZ_CP063843.1.