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The Genomic Characterisation and Comparison of Bacillus Cereus Strains Isolated from Indoor Air Balakrishnan N

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The Genomic Characterisation and Comparison of Bacillus Cereus Strains Isolated from Indoor Air Balakrishnan N Premkrishnan et al. Gut Pathog (2021) 13:6 https://doi.org/10.1186/s13099-021-00399-4 Gut Pathogens GENOME REPORT Open Access The genomic characterisation and comparison of Bacillus cereus strains isolated from indoor air Balakrishnan N. V. Premkrishnan1†, Cassie E. Heinle1†, Akira Uchida1, Rikky W. Purbojati1, Kavita K. Kushwaha1, Alexander Putra1, Puramadathil Sasi Santhi1, Benjamin W. Y. Khoo1, Anthony Wong1, Vineeth Kodengil Vettath1, Daniela I. Drautz‑Moses1, Ana Carolina M. Junqueira2*† and Stephan C. Schuster1*† Abstract Background: Bacillus cereus is ubiquitous in nature, found in environments such as soil, plants, air, and part of the insect and human gut microbiome. The ability to produce endospores and bioflms contribute to their pathogenicity, classifed in two types of food poisoning: diarrheal and emetic syndromes. Here we report gap‑free, whole‑genome sequences of two B. cereus strains isolated from air samples and analyse their emetic and diarrheal potential. Results: Genome assemblies of the B. cereus strains consist of one chromosome and seven plasmids each. The genome size of strain SGAir0260 is 6.30‑Mb with 6590 predicted coding sequences (CDS) and strain SGAir0263 is 6.47‑ Mb with 6811 predicted CDS. Macrosynteny analysis showed 99% collinearity between the strains isolated from air and 90.2% with the reference genome. Comparative genomics with 57 complete B. cereus genomes suggests these strains from air are closely associated with strains isolated from foodborne illnesses outbreaks. Due to virulence poten‑ tial of B. cereus and its reported involvement in nosocomial infections, antibiotic resistance analyses were performed and confrmed resistance to ampicillin and fosfomycin, with susceptibility to ciprofoxacin, tetracycline and vancomy‑ cin in both strains. Conclusion: Phylogenetic analysis combined with detection of haemolytic (hblA, hblC, and hblD) and non‑haemo‑ lytic (nheA, nheB, and nheC) enterotoxin genes in both air‑isolated strains point to the diarrheic potential of the air isolates, though not emetic. Characterization of these airborne strains and investigation of their potential disease‑ causing genes could facilitate identifcation of environmental sources of contamination leading to foodborne illnesses and nosocomial infections transported by air. Keywords: Bacillus cereus, Food poisoning, Antibiotic resistance, Enterotoxins Background Bacillus cereus is a small rod-shaped, Gram-positive, facultatively anaerobic, motile, spore-forming bacteria *Correspondence: [email protected]; [email protected] †Balakrishnan N. V. Premkrishnan and Cassie E. Heinle contributed equally [1] belonging to the Bacillus cereus sensu lato group [2] to this work of the phylum Firmicutes. Te “Bacillus cereus group” is † Ana Carolina M. Junqueira and Stephan C. Schuster contributed equally comprised of at least eight closely-related species, but to this work 1 Singapore Centre for Environmental Life Sciences Engineering, Nanyang the most studied are B. cereus, B. thuringiensis, and B. Technological University, Singapore, Singapore anthracis due to their clinical and socio-economic impor- 2 Departamento de Genética, Instituto de Biologia, Universidade Federal tance [3]. Taxonomic classifcation of these organisms do Rio de Janeiro, Rio de Janeiro, Brazil © The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creat iveco mmons .org/licen ses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/publi cdoma in/ zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Premkrishnan et al. Gut Pathog (2021) 13:6 Page 2 of 10 has long been controversial due their historical classif- commercial building in Singapore. Using an Andersen cation based on phenotypic traits [4] while DNA–DNA single-stage impactor (SKC, USA), air was impacted onto hybridization results shows that they hybridize beyond Malt Extract Agar (Sigma-Aldrich, USA) and Potato Dex- the 70% species defning limit [5] and share almost 99% trose Agar (Sigma-Aldrich, USA) at 28.3 L/min for 3 min, similarity in their 16S ribosomal RNA (rRNA) gene and incubated at 30 °C for 3 days. Resulting colonies were sequences [6]. Tis close genetic similarity has led some sub-cultured on Tryptic Soy Agar (Sigma-Aldrich, USA) authors to argue that the entire group should be consid- and the two strains were individually inoculated in lysog- ered as a single unique species with diverse strains that eny broth (LB, Becton–Dickinson, USA) at 30 °C over- difers in plasmid content or gene expression [7]. night to obtain axenic cultures. Bacillus cereus was frst isolated from air samples col- DNA was extracted using the Wizard genomic DNA lected from a cowshed in 1887 [8] and has been reported purifcation kit (Promega, USA) following the manufac- in soil [9], plants [10], the intestine of insects [11] and turer’s protocol and DNA quantitation was carried out animals [1], and also in clinical environments [12]. Te with NanoDrop (Termo Scientifc) and QuantiFluor ® ability to produce endospores and bioflms are crucial to dsDNA system (Promega). Libraries were prepared based allow B. cereus to endure heat and dehydration and hin- on the 20 kb SMRTbellTM Template Preparation Proto- der their removal from adhering surfaces [13, 14]. Tese col (Pacifc Biosciences) using 5 µg of purifed, sheared characteristics also contribute to their pathogenicity, DNA as input and assessed on an Agilent DNA 12,000 traditionally classifed in two types of food poisoning: chip on a 2100 Bioanalyzer (Agilent) to determine the diarrheal and emetic syndromes [15]. More recently, B. optimal cut-of for size selection. Te library was then cereus also has been identifed as an etiological agent of size-selected on a Sage Science Blue Pippin instrument, localized wound and eye infections, as well as in systemic using a dye-free 0.75% agarose cassette and 15 kb as the infections [3]. cut-of and sequenced in one SMRTcell (SGAir0260) or From 1998 to 2008, a total of 235 foodborne disease two SMRTcells (SGAir0263) on a Pacifc Biosciences RSII outbreaks (2050 illnesses in total) were reported to the single-molecule real-time (SMRT) sequencing platform Centers for Disease Control and Prevention (CDC) in the at a loading concentration of 0.2 nM. United States that were caused (881 cases) or suspected Additionally, 300 bp paired-end reads were produced to be caused (1169 cases) by B. cereus [16]. More recently, on the MiSeq platform (Illumina). Libraries preparation the Annual Communicable Diseases Surveillance report was performed according to TruSeq Nano DNA Sam- published by the Ministry of Health (Communicable Dis- ple Preparation protocol (Illumina). A total of 200 ng eases Surveillance report 2018) in Singapore documented of genomic DNA was then sheared on a Covaris E220 398 notifcations of food poisoning involving 3165 cases (Covaris) to ~ 550 bp following the manufacturer’s rec- in 2018 and B. cereus was among the top three suspects ommendation, uniquely tagged with Illumina’s TruSeq of the reported outbreaks. Several other investigations HT DNA barcodes, and pooled for sequencing. Te fn- demonstrated that B. cereus contamination can arise ished library was quantitated using QuantiFluor dsDNA after improper handling of food and raw vegetables, poor assay (Promega) and the average library size was deter- hygienic practices of food handlers, and also from pol- mined on an Agilent Tapestation 4200, followed by luted environments, including the air [17–19]. library dilution to 4 nM. Te concentration of the diluted In this article we report the complete genomes of two library was then validated by qPCR on a QuantStudio-3 B. cereus strains isolated from indoor air samples in Sin- real-time PCR system (Applied Biosystems), using the gapore, namely SGAir0260 and SGAir0263. A compara- Kapa library quantifcation kit for Illumina platforms tive analysis with 55 additional genomes of B. cereus and (Kapa Biosystems) prior to sequencing on the Illumina the identifcation of virulence genes provided a compre- MiSeq platform at a read-length of 300 bp paired-end. hensive analysis of the disease potential of SGAir strains Sequencing was perfromed at the Singapore Centre for and will be a valuable resource for investigations of food- Environmental Life Sciences Engineering (SCELSE) borne and nosocomial infections potentially caused by sequencing facility, located at Nanyang Technological strains transported by air in tropical environments, thus University (http://www.scels e.sg/Page/seque ncing -capac assisting the identifcation of sources and sinks of future ity). outbreaks. Genome assembly and annotation Methods Long reads were used for de novo genome assemblies Isolation, DNA extraction and sequencing performed after quality control using preAssembler flter Bacillus cereus strains SGAir0260 and SGAir0263 were v1 protocol, distributed with the Hierarchical Genome isolated in 2015 from indoor air samples collected in a Assembly Process version 3 (HGAP3; Pacifc Biosciences) Premkrishnan et al. Gut Pathog (2021) 13:6 Page 3 of 10 [20] with default parameters. Short reads were trimmed manually investigated at NCBI. Tese sources were clas- using Cutadapt version 1.8.1 [21] with a Phred quality sifed and added to the tree as ‘Environmental’, ‘Clinical’, score threshold of q20 (parameters “-q 20–trim-n–min- or ‘Other’. imum-length 30–match-read-wildcards”).
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