Microbial Systems Biology

Understanding Panaroo's outputs

Fri, 24 Nov 2023 20:00:00 +0000

This live post summarises my understandings of Panaroo’s methods and outputs in complementary to interpretations in the software’s official documentation and original paper. Please be cautious of my possible misunderstandings. Comments are welcomed.

Guidebook for processing Nanopore sequencing data

Mon, 10 Jul 2023 11:30:00 +0000

This actively developing guidebook covers bioinformatics methods for processing sequencing data from MinION flow cells.

A generalised Bayesian model for the probability of getting a false-positive PCR result

Fri, 31 Dec 2021 23:00:00 +0000

It was a disaster before the New Year that I got a positive result from my predeparture SARS-Cov-2 RT-PCR test at a commercial test centre (Site 1) and had to cancel my international flights for the reunion with my wife. I was shocked by the result as I had been self-isolating for more than 10 days before the test with limited outdoor activities (such as shopping for groceries) and I had no COVID-19 symptoms at all. After this moment of confusion and disappointment, I did a lateral-flow-device (LFD) antigen test at home and got a negative result. The second LFD test on the other day also returned a negative result. In the afternoon of the same day, I had my second PCR test at a different site (Site 2), where a professional swabbed my tonsil and nasal cavity so thoroughly that I even smelled a hint of blood. The result came quickly in the next morning and I immediately booked my third PCR test from another site (Site 3) for the same morning. All the three sites are accredited by the UK Health Security Agency (UK HSA). All my results were reported to the NHS for test and tracing.

Linux one-liners converting GFF3 to FASTA files of contigs

Wed, 25 Mar 2020 13:37:30 +0000

Despite the popularity of GFF3 format for genome annotations, to my knowledge there is no published tools for extracting DNA sequences of contigs from the GFF3 files and store them in a multi-FASTA file. EMBOSS seqret is only able to pull out the last contig from the GFF3 file, whereas other tools aim to extract the DNA sequence per feature. Therefore, I develop two Linux one-liners in this post for extract contig sequences from a GFF3 file and transfer them to a FASTA file.

Notes about ClonalFrameML

Fri, 07 Feb 2020 16:31:00 +0000

Here are my notes of the article about ClonalFrameML, a program that detects recombined regions in a multi-sequence alignment, infers phylogenetic relationships when correcting for recombination, reconstructs ancestral state, and imputes SNPs under a maximum-likelihood (ML) framework.

Comparisons between SRST2, ARIBA, and KmerResistance

Fri, 13 Dec 2019 18:25:00 +1100

SRST2¹, ARIBA², and KmerResistance (web service, code)³ are three widely used pieces of standalone software for read-based detection of target genes in bacterial genomes. Published in 2014, SRST2 is recognised as the pioneer amongst these three tools^{2, 3}. In this post, I compare methodologies underlying these tools in a concise manner to shed light on the selection of appropriate software for gene detection. Particularly, I herein presume that detecting antimicrobial resistance determinants is the only use case. Whenever unspecified, software versions referred to in this post are: SRST2 v0.2.0, ARIBA 2.14.4, and KmerResistance v2.2.

Installing environment modules on Xubuntu

Thu, 31 Oct 2019 01:25:00 +1100

In addition to Conda, [environment modules](https://en.wikipedia.org/wiki/Environment_Modules_(software)) provide users with a convenient approach to switching software environments on Linux machines. This approach is widely used on computer clusters that offer computational services to a large number of users, and the environment modules are shared by authorised users. These modules, however, are not Linux kernel modules, which are automatically launched by the OS at start-up, and they should be manually loaded to the OS by users. I learnt how to use module commands for bioinformatic analysis when I was studying at the University of Melbourne. Loading a module essentially modifies your environmental variable `$PATH`. In this post, I set up a module manager for users of my Xubuntu system.

Setting up Xubuntu in VirtualBox for bioinformatic work

Fri, 25 Oct 2019 01:47:20 +1100

Linux is a popular family of operating systems (OS) used in bioinformatics. Amongst its numerous distributions, Xubuntu is a lightweight derivative of ubuntu Linux, and aims to run on a machine with low system requirements. As a Windows user, I often need to switch to a Linux environment for program development and test. To this end, VirtualBox offers an easy-to-use but low-in-resources alternative to a dedicated physical machine or disc space (dual OS). This post records my key steps for setting up Xubuntu in VirtualBox for basic bioinformatic work.

Script gbk2tbl.py now supports Python 3

Mon, 21 Oct 2019 17:46:20 +1100

The Python script gbk2tbl.py in my GitHub repository BINF_toolkit is a popular tool for preparing input files of NCBI Sequin from GenBank files. Nonetheless, this script has only supported Python 2 since its first release in 2015, causing inconvenience to some users. Today, I got some time to make the script compatible to Python 3 with the tool 2to3 and some manual adjustments. The new script has been tested under Python 3.5.2 and pushed to my GitHub.

Popular reference databases of antimicrobial resistance genes

Thu, 03 Oct 2019 22:31:00 +1000

Reliable and up-to-date databases play a pivotal role in reference-based detection of antimicrobial resistance genes (ARGs) in bacteria. Nonetheless, these databases differ in their content and quality, making it challenging to decide an appropriate reference database for a particular research project. In order to address this challenge, this post offers a review of several ARG databases that are publicly available and widely used in bacterial genomics. Particularly, I focus on databases that are still undergoing regular maintenance, and I do not discuss any program released with these databases for sequence search or statistical analysis.

gbk2tsv.py: tabulating genomic features in GenBank files

Fri, 13 Sep 2019 16:22:00 +1000

I finally got some time this morning to write a Python script gbk2tsv.py, which converts several GenBank files into tab-delimited feature tables (plain text files with an extension “.tsv”). It can be a useful tool when we need to summarise genome annotations or acquire nucleotide and protein sequences of certain genomic features. Although the Holt Lab, where I did my PhD, has an in-house script to do a similar job, it is inappropriate for me to use or share that intellectual property for projects outside of the Holt Lab without a specific permission. Therefore, I decided to create a script from scratch after a discussion on genome annotation with Hao Luo, a PhD student at the Chalmers University of Technology, Sweden, during a lunch break of the course MESB19.

Notes of an online metagenomics course

Wed, 19 Jun 2019 16:04:20 +1000

In this post, I compile my notes of the course Metagenomics applied to surveillance of pathogens and antimicrobial resistance. This three-week course is offered by the Technical University of Denmark and is freely accessible at Coursera. As a graduate researcher working on antimicrobial resistance (AMR) in bacterial populations, I have read countless pieces of literature about bacterial population genomics, surveillance and metagenomics in the most recent four years, and I am supposed to be familiar with the content of this course. Nevertheless, the course remains quite helpful to me since it leads me to build a comprehensive knowledge framework of metagenomics from individual concepts. Here, I focus on knowledge that was once unfamiliar or ambiguous to me, and it may be new to some readers as well. More information can be found in course materials on Coursera.

To tree or not to tree: an introduction of phylogenetic networks

Sat, 15 Jun 2019 00:54:08 +1000

Phylogenetic reconstruction is of crucial importance to elucidate bacterial population structure, epidemiology and evolutionary histories. By far phylogenetic networks and trees are the most common approaches used for studying the evolutionary history of a bacterial population. However, concepts and methodology underlying phylogenetic reconstruction can be challenging to beginners. As such, I share my notes on relevant literature in this post to address these obstacles. In particular, I compare different kinds of phylogenetic networks to show their pros and cons under various conditions.

A tutorial for microbial genome-scale metabolic modelling: [3] understanding the SBML format

Thu, 13 Jun 2019 16:29:20 +1000

The systems biology markup language (SBML) is a community-driven, software and platform independent standard for expressing and exchanging systems models between different simulation and analysis software. It is defined using the unified modelling language (UML) and represented using the extensible markup language (XML)¹. The SBML does not aim to produce model files that can be readily read by humans, but to provide different software with a unified medium for exchanging models. Each piece of software can then translate imported models into its own internal format¹. It is important to understand the SBML for metabolic modelling and engineering because this data language has quickly become the most popular standard of model files since its first publication in 2003¹.

A tutorial for microbial genome-scale metabolic modelling: [2] building a draft metabolic network from genome annotations of a single bacterial isolate

Mon, 03 Jun 2019 15:52:08 +1000

In my first post of this tutorial, I have demonstrated basic ways to inspect a genome-scale metabolic model (GEM). Now, let’s get our hands dirty — to reconstruct a draft metabolic network from genome annotations, which is the starting point of the protocol proposed by Thiele and Palsson for bottom-up GEM construction^{1, 2}. In this post, we will be using several bioinformatic tools to reconstruct draft metabolic networks from annotations of the fully resolved chromosomal genome of Clostridium beijerinckii str. NCIMB 8052 (KEGG organism code: cbe; PATRIC genome ID: 290402.41), a well-known butanol-producing microorganism. A GEM iCM925 of this strain has been published by Milne et al³.

A tutorial for microbial genome-scale metabolic modelling: [1] using models in MATLAB

Fri, 31 May 2019 16:51:08 +1000

This is my first post of a series of tutorials for constructing genome-scale metabolic models (GEMs) for single-cellular microbes. In this tutorial, I follow the protocol created by Heirendt et al. to demonstrate reading and visualisation of existing GEMs¹.

Bioinformatic resources for investigating clostridial metabolism

Sun, 26 May 2019 22:58:08 +1000

Solventogenic clostridia offer a promising and sustainable alternative to petroleum-based production of butanol — an important industrial chemical feedstock and fuel additive or replacement¹. They also draw our attention for their potential in reducing the emission of greenhouse gases and relieving the threat of global warming. It is of paramount importance to elucidate the metabolism of clostridia for metabolism engineering and industrial applications of gas fermentation. In addition to standard experimental approaches, bioinformatics provides us with an efficient way to identify targets (genetic or biochemical) that can be controlled to improve the product formation. In this post, I briefly summarise bioinformatic resources that are publicly accessible to date for interrogating clostridial metabolism.

A technical overview of C1 gas fermentation

Sun, 12 May 2019 15:18:00 +1000

Carbon dioxide (CO₂) and methane (CH₄) are abundant one-carbon (C1) components of greenhouse gases and their atmospheric concentrations have seen a drastic increase since the industrial revolution. Besides industrial activities, agricultural practice also causes substantial emissions of these two kinds of gases. Nowadays it is an urgent demand to reduce emissions of greenhouse gases for controlling global warming. Biological conversion of C1 gases to industrial high-value hydrocarbon-based chemicals (such as the ABE — acetone, butanol and ethanol¹) via fermentation has been proven to be an effective approach to meet the demand without completing for photosynthetic resources (e.g., food) or land². Through converting waste C1 gases into biofuels, we can reduce our reliance and demand on fossil fuels, which in turn reduces our total carbon emission. Because of this great environmental benefit, here I outline technologies that recycle waste C1 gases for industrial and environmental purposes.

Understanding SRST2 outputs

Thu, 18 Apr 2019 13:20:30 +1000

SRST2 is a widely used tool screening Illumina reads of bacterial genomes for known genes (that is, targeted gene detection). Its capability includes MLST profiling and detection of known antimicrobial resistance genes (ARGs), virulence genes, plasmids, etc. I have been using SRST2 throughout my PhD project and coded my package GeneMates on the grounds of SRST2’s outputs. Here, I explain the output formats of SRST2 in order to help users to gain a better understanding of this versatile tool. Comments and corrections from readers are welcomed since this post is based on my own understandings and experience.

Population structure, phylogenetic signal, recombination vs. mutations

Mon, 08 Apr 2019 02:17:22 +1000

Recently, I reviewed several concepts about recombination and mutation in bacterial genomes when I was revising my manuscript of GeneMates. In this post, I summarise my understandings to two groups of terms and two measures (r/m and ρ/θ) that are relevant to these biological events, and tabulate values of these measures in six bacterial species.

A complete list of my software

Wed, 03 Apr 2019 11:22:30 +1000

This page introduces my computer code developed and published for the research community since 2015.

1. Population genomics

1.1. Detection of horizontal gene co-transfer between bacteria

GeneMates

The latest version: v0.2.2, which was released on 21 March 2020. (Documentation)

This R package implements my network approach for the detection of intra-species horizontal gene co-transfer (HGcoT) between bacteria. A manuscript is preparing for it. GeneMates takes as input bacterial whole-genome sequencing (WGS) data (in the forms of short reads and/or genome assemblies) and creates networks showing evidence of HGcoT at the allele level. This package can also be used for testing for allele-to-allele associations controlling for bacterial population structure. The following list introduces GeneMates functions that are frequently used in my experience.

Publications

Sun, 24 Mar 2019 23:02:32 +1000

1. Journal articles

Wan Y, Wong JLC, Sanchez-Garrido J, Low WW, Turton JF, et al. Genomic and molecular characterisation of a KPC-producing Klebsiella pneumoniae clinical isolate resistant to meropenem-vaborbactam, imipenem-relebactam, and ceftazidime-avibactam. BMC Genomic Data 2026;27:37. DOI: 10.1186/s12863-026-01421-x.
Doran J, Foster C, Saunders M, Chandra NL, Turton JF, et al. Two concurrent nationwide healthcare-associated outbreaks of Burkholderia cepacia complex linked to product contamination, UK and Ireland, 2010–2023. Infection Control & Hospital Epidemiology 2025;46:1006–1012. DOI: 10.1017/ice.2025.10232.
Fenske L, Jauneikaite E, Getino M, Wan Y, Goesmann A, et al. Evidence of a novel sublineage of Streptococcus agalactiae in elephants from zoo populations in Germany. Microbial Genomics 2025;11:001489. DOI: 10.1099/mgen.0.001489.
Vieira A, Wan Y, Ryan Y, Li HK, Guy RL, et al. Rapid expansion and international spread of M1_UK in the post-pandemic UK upsurge of Streptococcus pyogenes. Nature Communications 2024;15:3916. DOI: 10.1038/s41467-024-47929-7.
Wan Y, Pike R, Harley A, Mumin Z, Potterill I, et al. Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates. BMC Genomic Data 2025;26:12. DOI: 10.1186/s12863-025-01303-8.
Wan Y, Ganner M., Mumin Z., Ready D., Moore G., Potterill I., et al. Whole-genome sequencing reveals widespread presence of Staphylococcus capitis NRCS-A clone in neonatal units across the United Kingdom. Journal of Infection 2023; 87(3):210–219. DOI: 10.1016/j.jinf.2023.06.020.
Wan Y, Sabnis A, Mumin Z, Potterill I, Jauneikaite E, Brown CS, et al. IS1-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene nfsB causes nitrofurantoin heteroresistance in Escherichia coli. Microbial Genomics. 2023; 9(9):001102. DOI: 10.1099/mgen.0.001102.
Wan Y, Myall AC, Boonyasiri A, Bolt F, Ledda A, et al. Integrated Analysis of Patient Networks and Plasmid Genomes to Investigate a Regional, Multispecies Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both bla_IMP and mcr-9 Genes. Journal of Infectious Diseases 2024;230:e159–e170. DOI: 10.1093/infdis/jiae019.
Moore G, Barry A, Carter J, Ready J, Wan Y, et al. The detection, survival and persistence of Staphylococcus capitis NRCS-A in neonatal units in England. Journal of Hospital Infection. 2023; 140: 8e14. DOI: 10.1016/j.jhin.2023.06.030.
Yuan JM, Nugent C, Wilson A, Verlander NQ, Alexander E, Fleming P, …, Wan Y, et al. Clinical outcomes of Staphylococcus capitis isolation from neonates, England, 2015–2021: a retrospective case–control study. Archives of Disease in Childhood - Fetal and Neonatal Edition. 2023; 9. DOI: 10.1136/archdischild-2023-325887.
Jones NK, Coelho J, Logan JMJ, Broughton K, Hopkins KL, …, Wan Y, et al. Soft Tissue Infection of Immunocompetent Man with Cat-Derived Globicatella Species. Emerging Infectious Diseases. 2023; 29:1684–1687. DOI: 10.3201/eid2908.221770.
Gregor R, Johnston J, Coe LSY, Evans N, Forsythe D, Jones R, …, Wan Y, et al. Building a queer- and trans-inclusive microbiology conference. mSystems. 2023 Oct 6; 0(0):e00433-23. DOI: 10.1128/msystems.00433-23.
Paranthaman K, Wilson A, Verlander N, Rooney G, Macdonald N, Nsonwu O, …, Wan Y, et al. Trends in Coagulase negative Staphylococci (CoNS), England, 2010-2021. Access Microbiology. 2023; 5(6): 000491.v3. DOI: 10.1099/acmi.0.000491.v3.
Myall A, Wiedermann M, Vasikasin P, Klamser P, Wan Y, et al. Reconstructing and predicting the spatial evolution of carbapenemase-producing Enterobacteriaceae outbreaks. International Journal of Infectious Diseases 2023; 130: S65. DOI: 10.1016/j.ijid.2023.04.163.
Harvey EJ, Ashiru-Oredope D, Hill LF, Demirjian A, Jauneikaite E, Wan Y, et al. Need for standardized vancomycin dosing for coagulase-negative staphylococci in hospitalized infants. Clinical Microbiology and Infection, 2022; 29(1): 10–12. DOI: 10.1016/j.cmi.2022.09.016.
Myall A, Peach R, Wan Y, Mookerjee S, Jauneikaite E, et al. Improved contact tracing using network analysis and spatial-temporal proximity. International Journal of Infectious Diseases 2022;116: S20. DOI: 10.1016/j.ijid.2021.12.047.
Wan Y, Mills E, Leung RCY, Vieira A, Zhi X, Croucher NJ, et al. Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom. Microbial Genomics. 2021; 7(12):000702. DOI: 10.1099/mgen.0.000702.
Wan Y, Wick R R, Zobel J, Ingle D J, Inouye M, & Holt K E. GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure. BMC Genomics, 2020; 21: 658. DOI: 10.1186/s12864-020-07019-6.
Chen Q, Wan Y, Zhang X, Lei Y, Zobel J, & Verspoor K. Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases. Journal of Data and Information Quality, 2018; 9(3): 17. DOI: 10.1145/3131611.
Chen Q, Zhang X, Wan Y, Zobel J & Verspoor K. Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions. Journal of Computational Biology, Journal of Computational Biology, 2018. DOI:10.1089/cmb.2018.0198.
Chen Q, Wan Y, Lei Y, Zobel J, & Verspoor K. Evaluation of CD-HIT for constructing non-redundant databases. 2016 IEEE International Conference on Bioinformatics and Biomedicine. 2016; 703-706. IEEE. DOI: 10.1109/BIBM.2016.7822604.
Wan Y, Gorrie C L, Jenney A, Mirceta M, & Holt K E. Draft genome sequence of a clinical isolate of Serratia marcescens, strain AH0650_Sm1. Genome Announcements, 2015; 3(5): e01007-15. DOI: 10.1128/genomeA.01007-15.

2. Conference or workshop presentations

Oral presentation (online): Integrated analysis of patient networks and plasmid genomes reveals a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both blaIMP and mcr-9 genes. 20 Sep 2023. EMBO Workshop: Plasmids as vehicles of AMR spread.
Poster [04]: Staphylococcus capitis NRCS-A clone is widespread in neonatal units across the United Kingdom. Staph GBI Conference. 22–23 Jun 2023. Galway, Ireland.
Poster [P684]: IS1-related large-scale deletion of chromosomal nfsB regions causes nitrofurantoin heteroresistance in Escherichia coli. Microbiology Society Annual Conference. 17–20 Apr 2023. Birmingham, UK.
Poster and five-min oral presentation: Staphylococcus capitis NRCS-A clone is widespread among neonatal units across the United Kingdom. 1st UKHSA Conference. 18–19 Oct. Leeds, UK.
Poster [04672]: Genomic investigation of increased Staphylococcus capitis infections in neonatal intensive care units across England. 23–26 Apr 2022. 32nd European Congress of Clinical Microbiology & Infectious Diseases (online).
Poster [03080]: Genomic and phylogenetic analyses of multidrug-resistant Pseudomonas aeruginosa isolates from a persistent nosocomial outbreak. 23–26 Apr 2022. 32nd European Congress of Clinical Microbiology & Infectious Diseases (online).
Poster [07422] (co-author): Persistence, susceptibility and environmental reservoirs of NRCS-A Staphylococcus capitis in English neonatal intensive care units. 23–26 Apr 2022. 32nd European Congress of Clinical Microbiology & Infectious Diseases (online).
Poster [P002]: Nitrofurantoin-resistant Escherichia coli in the UK: genetic basis, diversity, and undetected occurrences. Annual Conference Online 2021. 26 Apr 2021. London, UK. Microbial Society. Abstract: doi.org/10.1099/acmi.ac2021.po0086.
Oral presentation: A network approach for detecting horizontal co-transfer of antimicrobial resistance genes in bacteria. 27–28 Nov 2018. ABACBS-2018, Parkville, VIC, Australia. Australian Bioinformatics and Computational Biology Society.
Poster [POA-341]: Network analysis of bacterial genes to predict horizontal co-transfer and mobile genetic elements. Registration Award based on research summary. 8–12 Jul 2018. SMBE2018, Yokohama, Japan. Society of Molecular Biology and Evolution.
Poster: Integrative analysis of DNA methylation and gene expression in breast cancer. 11–12 Oct 2014. ABiC 2014, Parkville, VIC, Australia. Australian Bioinformatics and Computational Biology Society.
Poster: Integrative analysis of DNA methylation and gene expression in breast cancer. ABiC 2014 Conference, Parkville, VIC, Australia. 11–12 Oct 2014.
A comparison of three approaches to prokaryotic genome annotation. MESB19 course, Gothenburg, Sweden, 25–29 Aug 2019. DOI: 10.13140/RG.2.2.21120.79365.

3. Doctor of Philosophy

Thesis

Wan, Y. Detecting horizontal co-transfer of antimicrobial resistance genes in bacteria: a network approach. (The University of Melbourne, 2019).

About

Sat, 23 Mar 2019 17:40:51 +1000

Author

My name is Yu Wan¹ and I am a Chinese scientist at the University of Melbourne in Victoria, Australia. I have expertise in bioinformatics, computational biology, and microbial population genomics. My research of microbes focuses on horizontal gene transfer and mobile genetic elements.

I was born and grew up in Chongqing, China. I took an undergraduate course of automation at the Department of System Science and Engineering in the College of Electrical Engineering of Zhejiang University, Hangzhou, China, between 2004 and 2008, and got a Bachelor’s Degree in Engineering. I worked in Huawei Technology Service Co., Ltd. (Langfang, China) as a TCP/IP network engineer between 2008 and 2011, and then became a contributing editor of Global Science Magazines in its Chongqing office in 2012. I went to Australia in 2013 to take a Master course of bioinformatics and got a Master of Science Degree in 2014. Later, I joined the Holt group in 2015 to do a PhD project on horizontal transfer of antimicrobial resistance genes within Enterobacteriaceae species. I submitted my thesis in Mar 2019 and obtained my PhD degree on 11 Oct 2019.