1
|
Reimann TM, Müdsam C, Schachtler C, Ince S, Sticht H, Herrmann C, Stürzl M, Kost B. The large GTPase AtGBPL3 links nuclear envelope formation and morphogenesis to transcriptional repression. NATURE PLANTS 2023; 9:766-784. [PMID: 37095224 DOI: 10.1038/s41477-023-01400-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Guanylate binding proteins (GBPs) are prominent regulators of immunity not known to be required for nuclear envelope formation and morphogenesis. Here we identify the Arabidopsis GBP orthologue AtGBPL3 as a lamina component with essential functions in mitotic nuclear envelope reformation, nuclear morphogenesis and transcriptional repression during interphase. AtGBPL3 is preferentially expressed in mitotically active root tips, accumulates at the nuclear envelope and interacts with centromeric chromatin as well as with lamina components transcriptionally repressing pericentromeric chromatin. Reduced expression of AtGBPL3 or associated lamina components similarly altered nuclear morphology and caused overlapping transcriptional deregulation. Investigating the dynamics of AtGBPL3-GFP and other nuclear markers during mitosis (1) revealed that AtGBPL3 accumulation on the surface of daughter nuclei precedes nuclear envelope reformation and (2) uncovered defects in this process in roots of AtGBPL3 mutants, which cause programmed cell death and impair growth. AtGBPL3 functions established by these observations are unique among dynamin-family large GTPases.
Collapse
Affiliation(s)
- Theresa Maria Reimann
- Cell Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christina Müdsam
- Cell Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christina Schachtler
- Cell Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Semra Ince
- Physical and Biophysical Chemistry, Department of Physical Chemistry 1, Ruhr-Universität Bochum (RUB), Bochum, Germany
| | - Heinrich Sticht
- Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christian Herrmann
- Physical and Biophysical Chemistry, Department of Physical Chemistry 1, Ruhr-Universität Bochum (RUB), Bochum, Germany
| | - Michael Stürzl
- Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Benedikt Kost
- Cell Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
| |
Collapse
|
2
|
Treffon J, Prior K, Dreesman J, Egelkamp R, Flieger A, Middendorf-Bauchart B, Projahn M, Richter A, Schuh E, Harmsen D, Mellmann A. Multicenter Preparedness Exercise Enables Rapid Development of Cluster-Specific PCR-Based Screening Assays from Bacterial Genomic Data. J Clin Microbiol 2023; 61:e0187322. [PMID: 36840589 PMCID: PMC10035311 DOI: 10.1128/jcm.01873-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/26/2023] [Indexed: 02/24/2023] Open
Abstract
PCR-based screening assays targeting strain-specific genetic markers allow the timely detection and specific differentiation of bacterial strains. Especially in situations where an infection cluster occurs, fast assay development is crucial for supporting targeted control measures. However, the turnaround times (TATs) for assay setup may be high due to insufficient knowledge about screening assay methods, workflows, and software tools. Here, two blind-coded and quality-controlled ring trials were performed in which five German laboratories established PCR-based screening assays from genomic data that specifically target selected bacterial clusters within two bacterial monospecies sample panels. While the first ring trial was conducted without a time limit to train the participants and assess assay feasibility, in the second ring trial, a challenging time limit of 2 weeks was set to force fast assay development as soon as genomic data were available. During both ring trials, we detected high interlaboratory variability regarding the screening assay methods and targets, the TATs for assay setup, and the number of screening assays. The participants designed between one and four assays per cluster that targeted cluster-specific unique genetic sequences, genes, or single nucleotide variants using conventional PCRs, high-resolution melting assays, or TaqMan PCRs. Assays were established within the 2-week time limit, with TATs ranging from 4 to 13 days. TaqMan probe delivery times strongly influenced TATs. In summary, we demonstrate that a specific exercise improved the preparedness to develop functional cluster-specific PCR-based screening assays from bacterial genomic data. Furthermore, the parallel development of several assays enhances assay availability.
Collapse
Affiliation(s)
- Janina Treffon
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- National Consulting Laboratory for Hemolytic Uremic Syndrome, University Hospital Münster, Münster, Germany
| | - Karola Prior
- Department of Periodontology and Operative Dentistry, University Hospital Münster, Münster, Germany
| | - Johannes Dreesman
- Department of Microbiology, Infection Protection, Hospital Hygiene, and Infection Epidemiology, Public Health Agency of Lower Saxony, Hannover, Germany
| | - Richard Egelkamp
- Department of Microbiology, Infection Protection, Hospital Hygiene, and Infection Epidemiology, Public Health Agency of Lower Saxony, Hannover, Germany
| | - Antje Flieger
- Department of Enteropathogenic Bacteria and Legionella, National Reference Center for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Barbara Middendorf-Bauchart
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- National Consulting Laboratory for Hemolytic Uremic Syndrome, University Hospital Münster, Münster, Germany
| | - Michaela Projahn
- Department of Biological Safety, National Reference Laboratory for Escherichia coli Including VTEC, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Anne Richter
- Department of Enteropathogenic Bacteria and Legionella, National Reference Center for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Elisabeth Schuh
- Department of Biological Safety, National Reference Laboratory for Escherichia coli Including VTEC, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Dag Harmsen
- Department of Periodontology and Operative Dentistry, University Hospital Münster, Münster, Germany
| | - Alexander Mellmann
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- National Consulting Laboratory for Hemolytic Uremic Syndrome, University Hospital Münster, Münster, Germany
| |
Collapse
|
3
|
Treffon J, Heppner B, Eismann J, Bothe J, Omengo B, Mellmann A. Single Nucleotide Polymorphism-Based Real-Time PCR Screening Assay for Rapid Tracking of Bacterial Infection Clusters To Complement Whole-Genome Sequencing Efforts during Outbreak Investigations. Microbiol Spectr 2022; 10:e0303622. [PMID: 36250868 PMCID: PMC9769705 DOI: 10.1128/spectrum.03036-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/16/2022] [Indexed: 01/09/2023] Open
Abstract
Infection clusters of multidrug-resistant bacteria increase mortality and entail expensive infection control measures. Whereas whole-genome sequencing (WGS) is the current gold standard to confirm infection clusters, PCR-based assays targeting cluster-specific signatures, such as single nucleotide polymorphisms (SNPs) derived from WGS data, are more suitable to initially screen for cluster isolates within large sample sizes. Here, we evaluated four software tools (SeqSphere+, RUCS, Gegenees, and Find Differential Primers) regarding their efficiency to find SNPs within WGS data sets that were specific for two bacterial monospecies infection clusters but were absent from a WGS reference data set comprising several hundred diverse genotypes of the same bacterial species. Cluster-specific SNPs were subsequently used to establish a probe-based real-time PCR screening assay for in vitro differentiation between cluster and noncluster isolates. SeqSphere+ and RUCS found 2 and 24 SNPs for clusters 1 and 14 and 24 SNPs for cluster 2, respectively. However, some signatures detected by RUCS were not cluster specific. Interestingly, all SNPs identified by SeqSphere+ were also detected by RUCS. In contrast, analyses with the remaining tools either resulted in no SNPs (with Find Differential Primers) or failed (Gegenees). Design of six cluster-specific real-time PCR assays enabled reliable cluster screening in vitro. Our evaluation revealed that SeqSphere+ and RUCS identified cluster-specific SNPs that could be used for large-scale screening in surveillance samples via real-time PCR, thereby complementing WGS efforts. This faster and simplified approach for the surveillance of bacterial clusters will improve infection control measures and will enhance protection of patients and physicians. IMPORTANCE Infection clusters of multidrug-resistant bacteria threaten medical facilities worldwide and cause immense health care costs. In recent years, whole-genome sequencing (WGS) has been increasingly applied to detect and to further control bacterial clusters. However, as WGS is still expensive and time-consuming, its exclusive application for screening and confirmation of bacterial infection clusters contributes to high costs and enhanced turnaround times, which many hospitals cannot afford. Therefore, there is need for alternative methods that can enable further surveillance of bacterial clusters that are initially detected by WGS in a faster and more cost-efficient way. Here, we established a system based on real-time PCR that enables rapid large-scale sample screening for bacterial cluster isolates within 7 days after the initial detection of an infection cluster, thereby complementing WGS efforts. This faster and simplified surveillance of bacterial clusters will improve infection control measures and will enhance protection of patients and physicians.
Collapse
Affiliation(s)
- Janina Treffon
- University Hospital Münster, Institute of Hygiene, Münster, Germany
| | - Bianca Heppner
- University Hospital Münster, Institute of Hygiene, Münster, Germany
| | | | - Julia Bothe
- inno-train Diagnostik GmbH, Kronberg, Germany
| | | | | |
Collapse
|
4
|
Madden DE, McCarthy KL, Bell SC, Olagoke O, Baird T, Neill J, Ramsay KA, Kidd TJ, Stewart AG, Subedi S, Choong K, Fraser TA, Sarovich DS, Price EP. Rapid fluoroquinolone resistance detection in Pseudomonas aeruginosa using mismatch amplification mutation assay-based real-time PCR. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background. Antimicrobial resistance (AMR) is an ever-increasing global health concern. One crucial facet in tackling the AMR epidemic is earlier and more accurate AMR diagnosis, particularly in the dangerous and highly multi-drug-resistant ESKAPE pathogen,
Pseudomonas aeruginosa
.
Objectives. We aimed to develop two SYBR Green-based mismatch amplification mutation assays (SYBR-MAMAs) targeting GyrA T83I (gyrA248) and GyrA D87N, D87Y and D87H (gyrA259). Together, these variants cause the majority of fluoroquinolone (FQ) AMR in
P. aeruginosa
.
Methods. Following assay validation, the gyrA248 and gyrA259 SYBR-MAMAs were tested on 84 Australian clinical
P. aeruginosa
isolates, 46 of which demonstrated intermediate/full ciprofloxacin resistance according to antimicrobial susceptibility testing.
Results. Our two SYBR-MAMAs correctly predicted an AMR phenotype in the majority (83%) of isolates with intermediate/full FQ resistance. All FQ-sensitive strains were predicted to have a sensitive phenotype. Whole-genome sequencing confirmed 100 % concordance with SYBR-MAMA genotypes.
Conclusions. Our GyrA SYBR-MAMAs provide a rapid and cost-effective method for same-day identification of FQ AMR in
P. aeruginosa
. An additional SYBR-MAMA targeting the GyrB S466Y/S466F variants would increase FQ AMR prediction to 91 %. Clinical implementation of our assays will permit more timely treatment alterations in cases where decreased FQ susceptibility is identified, leading to improved patient outcomes and antimicrobial stewardship.
Collapse
Affiliation(s)
- Danielle E. Madden
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Kate L. McCarthy
- University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
- Infectious Diseases Unit, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | - Scott C. Bell
- Adult Cystic Fibrosis Centre, The Prince Charles Hospital, Chermside, Queensland, Australia
- Child Health Research Centre, The University of Queensland, South Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Olusola Olagoke
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
| | - Timothy Baird
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
- Respiratory Department, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Jane Neill
- Respiratory Department, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Kay A. Ramsay
- Child Health Research Centre, The University of Queensland, South Brisbane, Queensland, Australia
| | - Timothy J. Kidd
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Adam G. Stewart
- Infectious Diseases Unit, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
- University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
| | - Shradha Subedi
- Infectious Diseases Unit, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
| | - Keat Choong
- Infectious Diseases Unit, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
| | - Tamieka A. Fraser
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Derek S. Sarovich
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Erin P. Price
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| |
Collapse
|
5
|
Anisimova EA, Fakhrutdinov NA, Mirgazov DA, Dodonova EA, Elizarova IA, Gorbunova ME, Khammadov NI, Zainullin LI, Osyanin KA. Bacillus anthracis strain differentiation based on SNP and VNTR loci. Vavilovskii Zhurnal Genet Selektsii 2022; 26:560-567. [PMID: 36313827 PMCID: PMC9556301 DOI: 10.18699/vjgb-22-68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 06/16/2023] Open
Abstract
Bacillus anthracis is the anthrax causative agent. For its epidemiology, it is important not only to identify the etiological agent but also to determine the patterns of its evolution and spread. Modern methods of molecular biology make it possible to detect a number of genetic markers suitable for indicating and differentiating the strains of B. anthracis, including the loci arranged as variable number tandem repeats (VNTRs) and SNPs, one nucleotide-sized differences in the DNA sequence of the loci being compared. The objective of the present study was to examine the effectiveness of SNP analysis and PCR amplif ication of VNTR loci combined with the high-resolution amplicon melting analysis for identif ication and differentiation of the anthrax agent strains. In the study, seven strains of B. anthracis obtained from soil samples and animal carcasses were investigated using vaccine strain STI-1 as a reference. For molecular genetic characterization of these bacteria, analysis of 12 SNPs and variability analysis of eight VNTR loci were carried out. To detect the differences between the strains, their PCR product melting points were measured in the presence of the EvaGreen (Sintol, Russia) intercalating dye. For SNP detection, a PCR assay with double TaqMan probes was applied. It was found that the studied virulent strains, except for B. anthracis No. 1 and 3, could not be attributed to any phylogenetic subgroup of the anthrax agents. The proposed method made it possible to differentiate four out of the seven investigated strains. Strains No. 5-7 had identical SNP and HRM prof iles and, as a result, formed a single cluster. Our investigation has conf irmed that the proposed method can be successfully used for preliminary analysis of an epizootic situation in the case of anthrax.
Collapse
Affiliation(s)
- E A Anisimova
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| | - N A Fakhrutdinov
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| | - D A Mirgazov
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| | - E A Dodonova
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| | - I A Elizarova
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| | - M E Gorbunova
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| | - N I Khammadov
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| | - L I Zainullin
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| | - K A Osyanin
- Federal Center for Toxicological, Radiation and Biological Safety, Nauchny Gorodok-2, Kazan, Russia
| |
Collapse
|
6
|
Le CT, Price EP, Sarovich DS, Nguyen TTA, Powell D, Vu-Khac H, Kurtböke Dİ, Knibb W, Chen SC, Katouli M. Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in the South Central Coast region, Vietnam. Microb Genom 2022; 8. [PMID: 35786440 PMCID: PMC9455698 DOI: 10.1099/mgen.0.000845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Between 2010 and 2015, nocardiosis outbreaks caused by Nocardia seriolae affected many permit farms throughout Vietnam, causing mass fish mortalities. To understand the biology, origin and epidemiology of these outbreaks, 20 N. seriolae strains collected from farms in four provinces in the South Central Coast region of Vietnam, along with two Taiwanese strains, were analysed using genetics and genomics. PFGE identified a single cluster amongst all Vietnamese strains that was distinct from the Taiwanese strains. Like the PFGE findings, phylogenomic and SNP genotyping analyses revealed that all Vietnamese N. seriolae strains belonged to a single, unique clade. Strains fell into two subclades that differed by 103 SNPs, with almost no diversity within clades (0–5 SNPs). There was no association between geographical origin and subclade placement, suggesting frequent N. seriolae transmission between Vietnamese mariculture facilities during the outbreaks. The Vietnamese strains shared a common ancestor with strains from Japan and China, with the closest strain, UTF1 from Japan, differing by just 220 SNPs from the Vietnamese ancestral node. Draft Vietnamese genomes range from 7.55 to 7.96 Mbp in size, have an average G+C content of 68.2 % and encode 7 602–7958 predicted genes. Several putative virulence factors were identified, including genes associated with host cell adhesion, invasion, intracellular survival, antibiotic and toxic compound resistance, and haemolysin biosynthesis. Our findings provide important new insights into the epidemiology and pathogenicity of N. seriolae and will aid future vaccine development and disease management strategies, with the ultimate goal of nocardiosis-free aquaculture.
Collapse
Affiliation(s)
- Cuong T. Le
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Institute for Aquaculture, Nha Trang University, Nha Trang, Vietnam
| | - Erin P. Price
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Derek S. Sarovich
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Thu T. A. Nguyen
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Vietnam
| | - Daniel Powell
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Hung Vu-Khac
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - D. İpek Kurtböke
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Wayne Knibb
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Shih-Chu Chen
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan, ROC
| | - Mohammad Katouli
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- *Correspondence: Mohammad Katouli,
| |
Collapse
|
7
|
Grózner D, Beko K, Kovács ÁB, Mitter A, Hrivnák V, Sawicka A, Tomczyk G, Bányai K, Jánosi S, Kreizinger Z, Gyuranecz M. Identification and detection of mutations potentially associated with decreased susceptibility to macrolides and lincomycin in Mycoplasma anserisalpingitidis isolates. Vet Microbiol 2022; 266:109362. [DOI: 10.1016/j.vetmic.2022.109362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 11/26/2022]
|
8
|
Singha H, Vorimore F, Saini S, Deshayes T, Saqib M, Tripathi BN, Laroucau K. Molecular epidemiology of Burkholderia mallei isolates from India (2015-2016): New SNP markers for strain tracing. INFECTION GENETICS AND EVOLUTION 2021; 95:105059. [PMID: 34478841 DOI: 10.1016/j.meegid.2021.105059] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022]
Abstract
Glanders, caused by a bacterium called B. mallei, is primarily an infectious horse and human disease. Although its incidence is rare in developed countries, it is nonetheless prevalent in several geographical areas of the world. There is a lack of cost-effective, rapid and specific molecular typing tools for epidemiological tracing of glanders cases. We previously reported an SNP-based typing method that categorizes global B. mallei strains into three lineages (L1 to L3), as well as additional branches, sub-branches and groups. However, further discrimination of the Indian and Pakistani isolates within the L2B2sB2 sub-branch was not possible due to the lack of sufficient epidemiological markers. In this study, 10 B. mallei strains isolated from four states in India during 2015-2016 were whole genome sequenced; SNP analysis further confirmed their position in the L2B2sB2 branch. To better track the strains, four new markers targeting Indian or Pakistani strains, and specifically targeting sub-groups within the Indian strains, were identified. The new SNP markers were tested and validated on the 10 Indian isolates included in this study as well as on 6 contemporary B. mallei Pakistani strains. These rapid and discriminating typing tools will contribute to the epidemiological monitoring of B. mallei infections, particularly in South Asia and the Middle East, endemic regions of the disease.
Collapse
Affiliation(s)
- H Singha
- ICAR-National Research Centre on Equines, Hisar, India
| | - F Vorimore
- Paris-Est University, ANSES, Laboratory for Animal Health, Bacterial Zoonosis Unit, European Union Reference Laboratory for Equine Diseases/Glanders, Maisons-Alfort, France
| | - S Saini
- ICAR-National Research Centre on Equines, Hisar, India
| | - T Deshayes
- Paris-Est University, ANSES, Laboratory for Animal Health, Bacterial Zoonosis Unit, European Union Reference Laboratory for Equine Diseases/Glanders, Maisons-Alfort, France
| | - M Saqib
- Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan
| | - B N Tripathi
- Animal Science Division, Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, India
| | - K Laroucau
- Paris-Est University, ANSES, Laboratory for Animal Health, Bacterial Zoonosis Unit, European Union Reference Laboratory for Equine Diseases/Glanders, Maisons-Alfort, France.
| |
Collapse
|
9
|
Földi D, Kreizinger Z, Bekő K, Belecz N, Bányai K, Kiss K, Biksi I, Gyuranecz M. Development of a molecular biological assay for the detection of markers related to decreased susceptibility to macrolides and lincomycin in Mycoplasma hyorhinis. Acta Vet Hung 2021; 69:110-115. [PMID: 34280127 DOI: 10.1556/004.2021.00026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/23/2021] [Indexed: 12/18/2022]
Abstract
The control of Mycoplasma hyorhinis infection relies mainly on antimicrobial therapy. However, the antibiotic susceptibility testing of the bacteria is usually not performed before applying the treatment, and thus therapeutic failures are not uncommon. In the case of M. hyorhinis, several antibiotic-resistance-related single nucleotide polymorphisms (SNPs) are known but assays for their detection have not been described yet. The aims of the present study were to investigate macrolide- and lincomycin-resistance-related SNPs in Hungarian M. hyorhinis isolates and to develop mismatch amplification mutation assays (MAMA) to detect the identified resistance markers. Minimal inhibitory concentrations (MIC) of different drugs and whole genome sequences of 37 M. hyorhinis isolates were used to find the resistance-related mutations. One MAMA assay was designed to detect the mutation of the 23S rRNA gene at nucleotide position 2058 (Escherichia coli numbering). For further evaluation, the assay was challenged with 17 additional isolates with available MIC data and 15 DNA samples from clinical specimens. The genotypes of the samples were in line with the MIC test results. The developed assay supports the practice of targeted antibiotic usage; hence it may indirectly reduce some bacterial resistance-related public health concerns.
Collapse
Affiliation(s)
- Dorottya Földi
- 1Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, H-1143, Budapest, Hungary
| | - Zsuzsa Kreizinger
- 1Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, H-1143, Budapest, Hungary
| | - Katinka Bekő
- 1Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, H-1143, Budapest, Hungary
| | - Nikolett Belecz
- 1Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, H-1143, Budapest, Hungary
| | - Krisztián Bányai
- 1Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, H-1143, Budapest, Hungary
| | | | - Imre Biksi
- 3Department of Pathology, University of Veterinary Medicine, Budapest, Hungary
| | - Miklós Gyuranecz
- 1Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, H-1143, Budapest, Hungary
| |
Collapse
|
10
|
Development of molecular assays for the rapid and cost-effective determination of fluoroquinolone, macrolide and lincosamide susceptibility of Mycoplasma synoviae isolates. PLoS One 2020; 15:e0241647. [PMID: 33125410 PMCID: PMC7598480 DOI: 10.1371/journal.pone.0241647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/13/2020] [Indexed: 11/19/2022] Open
Abstract
Mycoplasma synoviae infection occurs worldwide, leading to considerable economic losses in the chicken and turkey industry due to infectious synovitis, respiratory diseases and eggshell apex abnormalities. Control programs against M. synoviae infection are based on eradication, vaccination and medication with antimicrobial agents. Prudent use of antibiotics can be improved greatly by the determination of antibiotic susceptibility prior to the treatment. However, the conventional broth or agar microdilution is very labor-intensive and time-consuming method. Thus, there is an increasing need for rapid antimicrobial susceptibility tests in order to guide antibiotic therapy more effectively. The aim of this study was to develop mismatch amplification mutation assays (MAMAs) to detect resistance-associated mutations in M. synoviae. M. synoviae strains with previously determined minimal inhibitory concentrations (MICs) and whole genomes (n = 92) were used for target selection and assay specification. For the evaluation of the developed assays, 20 clinical samples and an additional 20 M. synoviae isolates derived from these specimens were also included in this study. MIC values of these 20 isolates were determined by broth microdilution method. Five MAMAs were designed to identify elevated MICs of fluoroquinolones, while three MAMAs were developed to detect decreased susceptibility to macrolides and lincomycin. The sensitivity of the MAMA tests varied between 102-104 template copy number/reaction depending on the assay. Clinical samples showed identical genotype calls with the M. synoviae isolates derived from the corresponding specimens in each case. Supporting the results of conventional in vitro sensitivity tests, our approach provides a feasible tool for diagnostics. Rapidity, robustness and cost-effectiveness are powerful advantages of the developed assays. Supporting prudent antibiotic usage instead of empirical treatment, the use of this method can reduce significantly the economic impact of M. synoviae in the poultry industry and decrease bacterial resistance-related public health concerns.
Collapse
|
11
|
Patrone PN, Kearsley AJ, Majikes JM, Liddle JA. Analysis and uncertainty quantification of DNA fluorescence melt data: Applications of affine transformations. Anal Biochem 2020; 607:113773. [PMID: 32526200 DOI: 10.1016/j.ab.2020.113773] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 04/22/2020] [Accepted: 05/10/2020] [Indexed: 12/17/2022]
Abstract
Fluorescence-based measurements are a standard tool for characterizing the thermodynamic properties of DNA systems. Nonetheless, experimental melt data obtained from polymerase chain-reaction (PCR) machines (for example) often leads to signals that vary significantly between datasets. In many cases, this lack of reproducibility has led to difficulties in analyzing results and computing reasonable uncertainty estimates. To address this problem, we propose a data analysis procedure based on constrained, convex optimization of affine transformations, which can determine when and how melt curves collapse onto one another. A key aspect of this approach is its ability to provide a reproducible and more objective measure of whether a collection of datasets yields a consistent "universal" signal according to an appropriate model of the raw signals. Importantly, integrating this validation step into the analysis hardens the measurement protocol by allowing one to identify experimental conditions and/or modeling assumptions that may corrupt a measurement. Moreover, this robustness facilitates extraction of thermodynamic information at no additional cost in experimental time. We illustrate and test our approach on experiments of Förster resonance energy transfer (FRET) pairs used study the thermodynamics of DNA loops.
Collapse
|
12
|
Chin KL, Sarmiento ME, Mustapha ZA, Jani J, Jamal NB, Stanis CS, Acosta A. Identification of a Mycobacterium tuberculosis-specific gene marker for diagnosis of tuberculosis using semi-nested melt-MAMA qPCR (lprM-MAMA). Tuberculosis (Edinb) 2020; 125:102003. [PMID: 33099253 DOI: 10.1016/j.tube.2020.102003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 10/23/2022]
Abstract
Tuberculosis (TB) is the deadliest of infectious diseases. TB diagnosis, based on sputum microscopy, culture, and nucleic acid amplification tests (NAATs) to identify its main causative agent, Mycobacterium tuberculosis (MTB), remains challenging. The current available NAATs, endorsed by World Health Organization (WHO), can differentiate MTB from some MTB complex (MTBC) members. Using bioinformatics, we identified a single nucleotide polymorphism (SNP) in lprM (Rv1970) gene that differentiate MTB from other MTBC members. A forward mismatch amplification mutation assay (MAMA) primer was designed for the targeted mutation and was used in a semi-nested melt-MAMA qPCR (lprM-MAMA). Using the optimized protocol, lprM-MAMA was positive with all MTB reference and clinical strains, and negative with other MTBC members, non-tuberculous mycobacteria (NTM) and other non-mycobacterial (NM) reference strains. The limit of detection (LOD) of lprM-MAMA was 76.29 fg. Xpert® MTB/RIF (Xpert)-positive sputum samples were also positive by lprM-MAMA, except for samples classified as having "very low" bacterial load by Xpert. Xpert-negative sputum samples were also negative by lprM-MAMA. In conclusion, lprM-MAMA demonstrated to be a useful tool for specific MTB diagnosis. Further evaluation with higher number of reference strains, including NTM and NM; and sputum samples are required to determine its potential for clinical application.
Collapse
Affiliation(s)
- Kai Ling Chin
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia.
| | - Maria E Sarmiento
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia
| | - Zainal Arifin Mustapha
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia
| | - Jaeyres Jani
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia
| | - Norfazirah Binti Jamal
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia
| | - Cheronie Shely Stanis
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia
| | - Armando Acosta
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia.
| |
Collapse
|
13
|
Bekő K, Kreizinger Z, Kovács ÁB, Sulyok KM, Marton S, Bányai K, Catania S, Feberwee A, Wiegel J, Dijkman R, Ter Veen C, Lysnyansky I, Gyuranecz M. Mutations potentially associated with decreased susceptibility to fluoroquinolones, macrolides and lincomycin in Mycoplasma synoviae. Vet Microbiol 2020; 248:108818. [PMID: 32891024 DOI: 10.1016/j.vetmic.2020.108818] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/01/2020] [Indexed: 11/16/2022]
Abstract
Mycoplasma synoviae is one of the economically most significant avian Mycoplasma species. It can cause great financial losses to the poultry industry by inducing respiratory diseases, infectious synovitis, or eggshell apex abnormalities. There are different approaches to control M. synoviae infection. Although antimicrobial therapy cannot replace long-term solutions, like eradication and vaccination, this strategy can be effective in the short term, as adequate antibiotic treatment can relieve economic losses through the attenuation of clinical signs and reduction of transmission. Using broth microdilution method, minimal inhibitory concentration (MIC) values to fourteen antibiotics related to eight antimicrobial groups were determined in 96 M. synoviae strains. Whole genome sequencing and sequence analysis revealed mutations potentially associated with decreased susceptibility to fluoroquinolones, macrolides and lincomycin. Molecular markers responsible for the high MICs to fluoroquinolones were found in the gyrA, gyrB, parC and parE genes. Besides, single nucleotide polymorphisms identified in genes encoding the 23S rRNA were found to be responsible for high MICs to the 50S inhibitor macrolides and lincomycin, while amino acid change in the 50S ribosomal protein L22 could be associated with decreased susceptibility to macrolides. The revealed mutations can contribute to the extension of knowledge about the genetic background of antibiotic resistance in M. synoviae. Moreover, the explored potentially resistance-related mutations may serve as targets for molecular biological assays providing data of antibiotic susceptibility prior to the laborious and time-consuming isolation of M. synoviae strains.
Collapse
Affiliation(s)
- Katinka Bekő
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária körút 21, Budapest 1143, Hungary.
| | - Zsuzsa Kreizinger
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária körút 21, Budapest 1143, Hungary.
| | - Áron B Kovács
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária körút 21, Budapest 1143, Hungary.
| | - Kinga M Sulyok
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária körút 21, Budapest 1143, Hungary.
| | - Szilvia Marton
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária körút 21, Budapest 1143, Hungary.
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária körút 21, Budapest 1143, Hungary.
| | - Salvatore Catania
- Instituto Zooprofilattico Sperimentale delle Venezie, Via San Giacomo 5, Verona 37000, Italy.
| | - Anneke Feberwee
- GD Animal Health Service, Arnsbergstraat 7, Deventer 7418 EZ, the Netherlands.
| | - Jeanine Wiegel
- GD Animal Health Service, Arnsbergstraat 7, Deventer 7418 EZ, the Netherlands.
| | - Remco Dijkman
- GD Animal Health Service, Arnsbergstraat 7, Deventer 7418 EZ, the Netherlands.
| | - Christiaan Ter Veen
- GD Animal Health Service, Arnsbergstraat 7, Deventer 7418 EZ, the Netherlands.
| | - Inna Lysnyansky
- Department of Avian Diseases, Kimron Veterinary Institute, POB 12, Beit Dagan 50250, Israel.
| | - Miklós Gyuranecz
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária körút 21, Budapest 1143, Hungary; Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Hungária körút 23-25, Budapest 1143, Hungary.
| |
Collapse
|
14
|
Felde O, Kreizinger Z, Sulyok KM, Wehmann E, Gyuranecz M. Development of molecular biological tools for the rapid determination of antibiotic susceptibility of Mycoplasma hyopneumoniae isolates. Vet Microbiol 2020; 245:108697. [PMID: 32456809 DOI: 10.1016/j.vetmic.2020.108697] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 11/17/2022]
Abstract
Mycoplasma hyopneumoniae is the etiologic agent of porcine enzootic pneumonia, a contagious respiratory disease, causing significant economic losses worldwide. Antibiotic treatment is commonly utilised in the pig industry to control M. hyopneumoniae infection. Since the conventional antibiotic susceptibility test is time-consuming, taking up to weeks' period, antibiotics are usually empirically chosen. Certain single nucleotide polymorphisms in the parC (C239A/T, G250A) and gyrA (G242C, C247 T, A260 G) genes show correlation with decreased fluoroquinolone susceptibility by the change of the target site. Furthermore, the nucleotide alteration A2059 G in the 23S rRNA sequence correlates with significantly decreased macrolide and lincosamide susceptibility of M. hyopneumoniae. Mismatch amplification mutation assays (MAMA) and high resolution melt (HRM) analysis, capable to detect the mentioned resistance markers, were developed in the present study, in order to provide susceptibility data in a considerably shorter time than the conventional methods. The results of the MAMA and HRM assays were congruent with the results of the conventional antibiotic susceptibility method of the tested M. hyopneumoniae field isolates. The sensitivity of the MAMAs was 103-104 copy numbers, while that of the HRM assay was 105-106 copy numbers. To the best of our knowledge this was the first time that MAMA and HRM assays were developed for the rapid detection of decreased fluoroquinolone, macrolide or lincosamide susceptibility in M. hyopneumoniae strains.
Collapse
Affiliation(s)
- Orsolya Felde
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Zsuzsa Kreizinger
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Kinga Maria Sulyok
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Eniko Wehmann
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Miklos Gyuranecz
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary; Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Budapest, Hungary.
| |
Collapse
|
15
|
Bekő K, Kovács ÁB, Kreizinger Z, Marton S, Bányai K, Bánáti L, Catania S, Bradbury J, Lysnyansky I, Olaogun OM, Gyuranecz M. Development of mismatch amplification mutation assay for the rapid differentiation of Mycoplasma gallisepticum K vaccine strain from field isolates. Avian Pathol 2020; 49:317-324. [PMID: 32181698 DOI: 10.1080/03079457.2020.1744523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Mycoplasma gallisepticum causes respiratory diseases and reproduction disorders in turkeys and chickens. The infection has considerable economic impact due to reduced meat and egg production. Because elimination programmes are not feasible in a large number of poultry farms, vaccination remains the only effective measure of disease control. Differentiating vaccine strains from field isolates is necessary in the control of vaccination programmes and diagnostics. The aim of this study was to develop a polymerase chain reaction based mismatch amplification mutation assay (MAMA) for the discrimination of K vaccine strain (K 5831, Vaxxinova Japan K.K.). After determining the whole genome sequence of the K strain, primers were designed to detect seven different vaccine-specific single nucleotide polymorphisms. After evaluating preliminary results, the MAMA-K-fruA test detecting a single guanine-adenine substitution within the fruA gene (G88A) was found to be the most applicable assay to distinguish the K vaccine strain from field isolates. The detected K strain-specific single nucleotide polymorphism showed genetic stability after serial passage in vitro, but this stability test should still be evaluated in vivo as well, investigating a large number of K strain re-isolates. The MAMA-K-fruA assay was tested on a total of 280 culture and field samples. The designed assay had 102 and 103 template copy number/µl sensitivity in melt-curve analysis based and agarose-gel based assays, respectively, and showed no cross reaction with other avian Mycoplasma species. The new MAMA provides a time- and cost-effective molecular tool for the control of vaccination programmes and for diagnostics.
Collapse
Affiliation(s)
- Katinka Bekő
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Áron Botond Kovács
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Zsuzsa Kreizinger
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Szilvia Marton
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - László Bánáti
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | | | - Janet Bradbury
- Institute of Veterinary Science, University of Liverpool, Neston, UK
| | - Inna Lysnyansky
- Department of Avian Diseases, Kimron Veterinary Institute, Beit Dagan, Israel
| | - Olusola Martins Olaogun
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
| | - Miklós Gyuranecz
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary.,Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Budapest, Hungary
| |
Collapse
|
16
|
Lin B, Sun J, Fraser IDC. Single-tube genotyping for small insertion/deletion mutations: simultaneous identification of wild type, mutant and heterozygous alleles. Biol Methods Protoc 2020; 5:bpaa007. [PMID: 33782652 DOI: 10.1093/biomethods/bpaa007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/17/2020] [Accepted: 03/27/2020] [Indexed: 01/01/2023] Open
Abstract
Current methods of genotyping small insertion/deletion (indel) mutations are costly, laborious, and can be unreliable. To address this, we have developed a method for small indel genotyping in a single polymerase chain reaction, with wild-type, heterozygous and mutant alleles distinguishable by band pattern in routine agarose gel electrophoresis. We demonstrate this method with multiple genes to distinguish 10 bp, 4 bp and even 1 bp deletions from the wild type. Through systematic testing of numerous primer designs, we also propose guidelines for genotyping small indel mutations. Our method provides a convenient approach to genotyping small indels derived from clustered regularly interspaced short palindromic repeats-mediated gene editing, N-ethyl-N-nitrosourea induced mutagenesis or diagnosis of naturally occurring polymorphisms/mutations.
Collapse
Affiliation(s)
- Bin Lin
- Signaling Systems Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jing Sun
- Signaling Systems Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Iain D C Fraser
- Signaling Systems Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
17
|
Lekota KE, Hassim A, van Heerden H. Genomic sequence data and single nucleotide polymorphism genotyping of Bacillus anthracis strains isolated from animal anthrax outbreaks in Northern Cape Province, South Africa. Data Brief 2019; 28:105040. [PMID: 31970271 PMCID: PMC6965700 DOI: 10.1016/j.dib.2019.105040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 10/26/2022] Open
Abstract
This report presents genomic data on sequence reads and draft genomes of Bacillus anthracis isolates from anthrax outbreaks in animals in an endemic region of South Africa as well as genotyping of the strains using canonical single nucleotide polymorphisms (canSNPs). It is derived from an article entitle "Phylogenomic structure of B. anthracis strains in the Northern Cape Province, South Africa revealed novel single nucleotide polymorphisms". Whole genome sequencing (WGS) of twenty-three B. anthracis strains isolated during 1998 and 2009 anthrax outbreaks in the Northern Cape Province (NCP), as well as a strain from Botswana (6102_6B) and one from Namibia-South Africa transfrontier conservation area (Sendlingsdrift, 6461_SP2) were obtained using both the HiSeq 2500 and MiSeq Illumina platforms. Mismatch amplification mutation assay (melt-MAMA) qPCR were used to identify the canSNP genotypes within the global population of B. anthracis. DNA sequencing data is available at NCBI Sequence Read Archive and GenBank database under accession N0. PRJNA580142 and PRJNA510736 respectively. A phylogenetic tree and CanSNP typing profiles of the isolates are presented within this article.
Collapse
Affiliation(s)
- Kgaugelo Edward Lekota
- University of Pretoria, Faculty of Veterinary Science, Department of Veterinary Tropical Diseases, Onderstepoort, 0110, South Africa.,College of Agriculture and Environmental Sciences, University of South Africa, Florida Campus, Florida, 1710, South Africa
| | - Ayesha Hassim
- University of Pretoria, Faculty of Veterinary Science, Department of Veterinary Tropical Diseases, Onderstepoort, 0110, South Africa
| | - Henriette van Heerden
- University of Pretoria, Faculty of Veterinary Science, Department of Veterinary Tropical Diseases, Onderstepoort, 0110, South Africa
| |
Collapse
|
18
|
Phylogenomic structure of Bacillus anthracis isolates in the Northern Cape Province, South Africa revealed novel single nucleotide polymorphisms. INFECTION GENETICS AND EVOLUTION 2019; 80:104146. [PMID: 31866402 DOI: 10.1016/j.meegid.2019.104146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 11/21/2022]
Abstract
Bacillus anthracis, the aetiological agent of anthrax, is regarded as a highly monomorphic pathogen that presents a low genetic diversity using standard molecular techniques. Whole genome sequencing and single nucleotide polymorphisms (SNPs) are definitive signatures for subtyping of B. anthracis. Here we employed whole genome single nucleotide polymorphism (wgSNP) analysis to investigate the genetic diversity of B. anthracis in the historically endemic region of Northern Cape Province (NCP), South Africa. Twenty-six isolates from anthrax outbreaks that occurred between 1998 and 2008/9 in NCP as well as from Namibia-South Africa Transfontier Conservation area and Botswana were compared to global B. anthracis genomes. Most NCP B. anthracis strains (n = 22) clustered in the A.Br.003/004 (A.Br.101) branch and are closely related to the Zimbabwe and Mozambique strains (A.Br.102 branch). A total of 4923 parsimony informative-SNPs accurately established the A.Br.003/004 phylogenetic relationships of the NCP isolates into two distinct sub-clades and SNP markers designated as A.Br.172 and A.Br.173 were developed. Other NCP strains (n = 2) grouped in the A.Br.001/002 (Sterne) branch while strains (n = 2) from the Namibia-South Africa Transfontier Conservation area and Botswana clustered in A.Br.005/006 (Ancient A) branch. The sequenced B. anthracis strains (A0094, A0096 and A0097) that clustered in the A.Br.064 (V770) clade were isolated from Vaalbos National Park and similar strains have not been isolated. The B. anthracis A0088 strain cluster with the NCP strains in the A.Br.003/004 (A.Br.172) SNP branch which has been isolated in NCP, South Africa. This study highlights the phylogenetic structure of NCP B. anthracis strains with distinctive SNP branches important for forensic tracing and novel SNP discovery purposes. The sequenced strains will serve as a means to further trace the dissemination of B. anthracis outbreaks in NCP, South Africa, and on the continent, as well as for forensic tracking on a global scale.
Collapse
|
19
|
Phylogenetic Placement of Isolates Within the Trans-Eurasian Clade A.Br.008/009 of Bacillus anthracis. Microorganisms 2019; 7:microorganisms7120689. [PMID: 31842497 PMCID: PMC6955976 DOI: 10.3390/microorganisms7120689] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/09/2019] [Indexed: 12/30/2022] Open
Abstract
The largest phylogenetic lineage known to date of the anthrax pathogen Bacillus anthracis is the wide-spread, so-called Trans-Eurasian clade systematically categorized as the A.Br.008/009 group sharing two defining canonical single-nucleotide polymorphisms (canSNP). In this study, we genome-sequenced a collection of 35 B. anthracis strains of this clade, derived from human infections, animal outbreaks or soil, mostly from European countries isolated between 1936 and 2008. The new data were subjected to comparative chromosomal analysis, together with 75 B. anthracis genomes available in public databases, and the relative placements of these isolates were determined within the global phylogeny of the A.Br.008/009 canSNP group. From this analysis, we have detected 3754 chromosomal SNPs, allowing the assignation of the new chromosomal sequences to established sub-clades, to define new sub-clades, such as two new Spanish, one Bulgarian or one German group(s), or to introduce orphan lineages. SNP-based results were compared with that of a multilocus variable number of tandem repeat analysis (MLVA). This analysis indicated that MLVA typing might provide additional information in cases when genomics yields identical genotypes or shows only minor differences. Introducing the delayed mismatch amplification assay (DMAA) PCR-analysis, we developed a cost-effective method to interrogate for a set of ten phylogenetically informative SNPs within genomes of A.Br.008/009 canSNP clade strains of B. anthracis. By this approach, additional 32 strains could be assigned to five of ten defined clades.
Collapse
|
20
|
Sariyeva G, Bazarkanova G, Maimulov R, Abdikarimov S, Kurmanov B, Abdirassilova A, Shabunin A, Sagiyev Z, Dzhaparova A, Abdel Z, Mussagaliyeva R, Morand S, Motin V, Kosoy M. Marmots and Yersinia pestis Strains in Two Plague Endemic Areas of Tien Shan Mountains. Front Vet Sci 2019; 6:207. [PMID: 31334249 PMCID: PMC6620824 DOI: 10.3389/fvets.2019.00207] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 06/11/2019] [Indexed: 11/13/2022] Open
Abstract
The main purpose of this study was to clarify the role of gray marmots (Marmota baibacina) in the long-term maintenance of highly virulent strains of Yersinia pestis in two plague endemic foci of the Tien Shan Mountains in Kyrgyzstan. We present data from regular observations of populations of M. baibacina and small rodents cohabiting with marmots in the mountainous grasslands of the Sari-Dzhas (east of Issyk-Kul Lake) and the Upper-Naryn (south of Issyk-Kul Lake) natural foci. During 2012–2017, an abundance of marmots and their ectoparasites (fleas and ticks) was significantly higher in Upper-Naryn comparing to Sari-Dzhas, although there were no differences in a number and diversity of small rodents cohabiting with marmots. The plague bacterium was detected either in marmots or in their ectoparasites collected during 4 of 6 years of observation in Sari-Dzhas and during 2 of 4 years of observation in Upper-Naryn. Plague was found in three sectors situated closely to each other in Sari-Dzhas and in 1 of 8 repeatedly surveyed sectors in Upper-Naryn. During 6 years, we isolated 9 strains of Y. pestis from marmots, two from their fleas Oropsylla silantiewi, one from an unidentified tick, and one from the gray hamster (Cricetulus migratorius). All plague strains isolated from the rodents and their ectoparasites in this study were similar to Antiqua biovar specific for marmots. The results indicate that plague can circulate continuously in the Tien Shan Mountains in populations of gray marmots and their ectoparasites with a facultative involvement of other rodent species after significant changes in rodent communities that happened in Kyrgyzstan during the previous two decades. The simultaneous field survey of two natural foci of plague, Sari-Dzhas, and Upper-Naryn, would be important for further analysis of circulation of Y. pestis strains belonging to Antiqua biovar in the Tien Shan Mountains.
Collapse
Affiliation(s)
- Gulmira Sariyeva
- Department of Natural Sciences, Issyk-Kul State University, Karakol, Kyrgyzstan
| | - Gulnara Bazarkanova
- Karakol Anti-plague Department, Republic Center of Quarantine and Dangerous Infections, Karakol, Kyrgyzstan
| | - Ravshambek Maimulov
- Karakol Anti-plague Department, Republic Center of Quarantine and Dangerous Infections, Karakol, Kyrgyzstan
| | | | - Berzhan Kurmanov
- Reference-Laboratory, Kazakh Scientific Center of Quarantine and Zoonotic Diseases, Almaty, Kazakhstan
| | - Aigul Abdirassilova
- Reference-Laboratory, Kazakh Scientific Center of Quarantine and Zoonotic Diseases, Almaty, Kazakhstan
| | - Anton Shabunin
- Department of Natural Sciences, Issyk-Kul State University, Karakol, Kyrgyzstan
| | - Zaurbek Sagiyev
- Reference-Laboratory, Kazakh Scientific Center of Quarantine and Zoonotic Diseases, Almaty, Kazakhstan
| | - Aigul Dzhaparova
- Republic Center of Quarantine and Dangerous Infections, Bishkek, Kyrgyzstan
| | - Ziyat Abdel
- Reference-Laboratory, Kazakh Scientific Center of Quarantine and Zoonotic Diseases, Almaty, Kazakhstan
| | - Raikhan Mussagaliyeva
- Reference-Laboratory, Kazakh Scientific Center of Quarantine and Zoonotic Diseases, Almaty, Kazakhstan
| | - Serge Morand
- Institute of Evolutionary Sciences, University of Montpellier, Montpellier, France
| | - Vladimir Motin
- Department of Microbiology and Immunology, Medical Branch, University of Texas, Galveston, TX, United States
| | - Michael Kosoy
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, United States
| |
Collapse
|
21
|
Development of Molecular Methods for Rapid Differentiation of Mycoplasma gallisepticum Vaccine Strains from Field Isolates. J Clin Microbiol 2019; 57:JCM.01084-18. [PMID: 30971467 DOI: 10.1128/jcm.01084-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 04/05/2019] [Indexed: 01/03/2023] Open
Abstract
Mycoplasma gallisepticum is among the most economically significant mycoplasmas causing production losses in poultry. Seven melt-curve and agarose gel-based mismatch amplification mutation assays (MAMAs) and one PCR are provided in the present study to distinguish the M. gallisepticum vaccine strains and field isolates based on mutations in the crmA, gapA, lpd, plpA, potC, glpK, and hlp2 genes. A total of 239 samples (M. gallisepticum vaccine and type strains, pure cultures, and clinical samples) originating from 16 countries and from at least eight avian species were submitted to the presented assays for validation or in blind tests. A comparison of the data from 126 samples (including sequences available at GenBank) examined by the developed assays and a recently developed multilocus sequence typing assay showed congruent typing results. The sensitivity of the melt-MAMA assays varied between 101 and 104 M. gallisepticum template copies/reaction, while that of the agarose-MAMAs ranged from 103 to 105 template copies/reaction, and no cross-reactions occurred with other Mycoplasma species colonizing birds. The presented assays are also suitable for discriminating multiple strains in a single sample. The developed assays enable the differentiation of live vaccine strains by targeting two or three markers/vaccine strain; however, considering the high variability of the species, the combined use of all assays is recommended. The suggested combination provides a reliable tool for routine diagnostics due to the sensitivity and specificity of the assays, and they can be performed directly on clinical samples and in laboratories with basic PCR equipment.
Collapse
|
22
|
Timofeev V, Bahtejeva I, Mironova R, Titareva G, Lev I, Christiany D, Borzilov A, Bogun A, Vergnaud G. Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia. PLoS One 2019; 14:e0209140. [PMID: 31116737 DOI: 10.1101/486290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/07/2019] [Indexed: 05/28/2023] Open
Abstract
This article describes Bacillus anthracis strains isolated during an outbreak of anthrax on the Yamal Peninsula in the summer of 2016 and independently in Yakutia in 2015. A common feature of these strains is their conservation in permafrost, from which they were extracted either due to the thawing of permafrost (Yamal strains) or as the result of paleontological excavations (Yakut strains). All strains isolated on the Yamal share an identical genotype belonging to lineage B.Br.001/002, pointing to a common source of infection in a territory over 250 km in length. In contrast, during the excavations in Yakutia, three genetically different strains were recovered from a single pit. One strain belongs to B.Br.001/002, and whole genome sequence analysis showed that it is most closely related to the Yamal strains in spite of the remoteness of Yamal from Yakutia. The two other strains contribute to two different branches of A.Br.008/011, one of the remarkable polytomies described so far in the B. anthracis species. The geographic distribution of the strains belonging to A.Br.008/011 is suggesting that the polytomy emerged in the thirteenth century, in combination with the constitution of a unified Mongol empire extending from China to Eastern Europe. We propose an evolutionary model for B. anthracis recent evolution in which the B lineage spread throughout Eurasia and was subsequently replaced by the A lineage except in some geographically isolated areas.
Collapse
Affiliation(s)
- Vitalii Timofeev
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Irina Bahtejeva
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Raisa Mironova
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Galina Titareva
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Igor Lev
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - David Christiany
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Alexander Borzilov
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Alexander Bogun
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| |
Collapse
|
23
|
Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia. PLoS One 2019; 14:e0209140. [PMID: 31116737 PMCID: PMC6530834 DOI: 10.1371/journal.pone.0209140] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/07/2019] [Indexed: 12/24/2022] Open
Abstract
This article describes Bacillus anthracis strains isolated during an outbreak of anthrax on the Yamal Peninsula in the summer of 2016 and independently in Yakutia in 2015. A common feature of these strains is their conservation in permafrost, from which they were extracted either due to the thawing of permafrost (Yamal strains) or as the result of paleontological excavations (Yakut strains). All strains isolated on the Yamal share an identical genotype belonging to lineage B.Br.001/002, pointing to a common source of infection in a territory over 250 km in length. In contrast, during the excavations in Yakutia, three genetically different strains were recovered from a single pit. One strain belongs to B.Br.001/002, and whole genome sequence analysis showed that it is most closely related to the Yamal strains in spite of the remoteness of Yamal from Yakutia. The two other strains contribute to two different branches of A.Br.008/011, one of the remarkable polytomies described so far in the B. anthracis species. The geographic distribution of the strains belonging to A.Br.008/011 is suggesting that the polytomy emerged in the thirteenth century, in combination with the constitution of a unified Mongol empire extending from China to Eastern Europe. We propose an evolutionary model for B. anthracis recent evolution in which the B lineage spread throughout Eurasia and was subsequently replaced by the A lineage except in some geographically isolated areas.
Collapse
|
24
|
Okutani A, Inoue S, Morikawa S. Comparative genomics and phylogenetic analysis of Bacillus anthracis strains isolated from domestic animals in Japan. INFECTION GENETICS AND EVOLUTION 2019; 71:128-139. [PMID: 30928604 DOI: 10.1016/j.meegid.2019.03.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 03/20/2019] [Accepted: 03/22/2019] [Indexed: 11/30/2022]
Abstract
Anthrax, caused by Bacillus anthracis, is a severe zoonosis with a great impact on both human and animal health. In the present study, we identified the phylogenetic relationships among 16 Japanese strains of B. anthracis, including eight bovine strains, two equine strains, five swine strains, and one former vaccine strain, using in silico canonical single nucleotide polymorphism (canSNP) and core genome SNP analyses. The results of our in silico canSNP analysis suggest that these 16 Japanese strains could be divided into four lineages: i) one equine strain in A.Br.Ames, ii) one equine and six bovine strains in A.Br.001/002, iii) five swine and one bovine strain in A.Br.Aust94, and iv) one bovine and one vaccine strain in A.Br.008/011. A comparison with non-Japanese B. anthracis strains revealed a total of 3787 SNPs identified from the whole genome sequences of the Japanese strains; these SNP data were subjected to a phylogenetic analysis using the maximum parsimony (MP) method. Our core genome SNP analysis was also able to detect differences of a few chromosomal SNPs across clonal strains from the same cases that had different storage and passage histories. Additionally, our whole genome SNP analysis clearly indicated that the Japanese swine anthrax cases of 1982 were caused by at least three independent strains; however, their phylogeny revealed no clear relationship with swine strains from other countries. The bovine strain belonging to the A.Br.008/011 lineage differed from a former Japanese vaccine strain by only 12 SNPs. Together with the phylogenic results and epidemiological circumstances, the diversity of strains reveals that the B. anthracis available in Japan probably resulted from multiple relatively recent import events, rather than reflecting the persistence of a more ancient ecologically established group.
Collapse
Affiliation(s)
- Akiko Okutani
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
| | - Satoshi Inoue
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
| | - Shigeru Morikawa
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
| |
Collapse
|
25
|
Wang CC, Chen CA, Jong YJ, Kou HS. Specific Gene Capture Combined with Restriction-Fragment Release for Directly Fluorescent Genotyping of Single-Nucleotide Polymorphisms in Diagnosing Spinal Muscular Atrophy. Anal Chem 2018; 90:11599-11606. [PMID: 30203652 DOI: 10.1021/acs.analchem.8b02996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, a fast and simple fluorescent genotyping strategy, streptavidin magnetic beads combined with biotin-coupled PCR and restriction-fragment release, was developed for determination of nucleotide variants. This method was further applied for analyzing SMN1 gene in diagnosis of spinal muscular atrophy (SMA). After biotin-coupled PCR, the streptavidin magnetic beads would capture the biotin-labeled SMN genetic fragments, and then the restriction enzyme of HPY188I could only digest and release the fluorescent end of SMN1 genetic fragment into the supernatant. Therefore, the SMN1 gene could be easily fluorescently quantified, and SMN2 would not, for diagnosis of SMA. The copy number of the SMN1 gene could be regressed using the relative fluorescent unit versus the known copy number, and the coefficient of correlation is equal to 0.9617 ( r = 0.9617). In this research, a total of 16 blind DNA samples were analyzed, including 6 wild types, 5 carriers, and 5 SMA patients. Importantly, this fast, simple, and highly efficient method is universal for detection of all nucleotides variants by replacing the specific restriction enzyme. This technique has the potency to be served as a tool for fast and accurate diagnosis of genotypes in clinical medicine.
Collapse
Affiliation(s)
| | - Chung-An Chen
- Institute of Applied Mechanics , National Taiwan University , Taipei , Taiwan
| | | | | |
Collapse
|
26
|
Lienemann T, Beyer W, Pelkola K, Rossow H, Rehn A, Antwerpen M, Grass G. Genotyping and phylogenetic placement of Bacillus anthracis isolates from Finland, a country with rare anthrax cases. BMC Microbiol 2018; 18:102. [PMID: 30176810 PMCID: PMC6122712 DOI: 10.1186/s12866-018-1250-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/27/2018] [Indexed: 11/24/2022] Open
Abstract
Background Anthrax, the zoonotic disease caused by the gram-positive bacterium Bacillus anthracis, is nowadays rare in northern parts of Europe including Finland and Scandinavia. Only two minor outbreaks of anthrax in 1988 and in 2004 and one sporadic infection in 2008 have been detected in animals in Finland since the 1970’s. Here, we report on two Finnish B. anthracis strains that were isolated from spleen and liver of a diseased calf related to the outbreak in 1988 (strain HKI4363/88) and from a local scrotum and testicle infection of a bull in 2008 (strain BA2968). These infections occurred in two rural Finnish regions, i.e., Ostrobothnia in western Finland and Päijänne Tavastia in southern Finland, respectively. Results The isolates were genetically characterized by PCR-based methods such as multilocus variable number of tandem repeat analysis (MLVA) and whole genome-sequence analysis (WGS). Phylogenetic comparison of the two strains HKI4363/88 and BA2968 by chromosomal single nucleotide polymorphism (SNP) analysis grouped these organisms within their relatives of the minor canonical A-branch canSNP-group A.Br.003/004 (A.Br.V770) or canonical B-branch B.Br.001/002, respectively. Strain HKI4363/88 clustered relatively closely with other members of the A.Br.003/004 lineage from Europe, South Africa, and South America. In contrast, strain BA2968 clearly constituted a new sublineage within B.Br.001/002 with its closest relative being HYO01 from South Korea. Conclusions Our results suggest that Finland harbors both unique (autochthonous) and more widely distributed, common clades of B. anthracis. We suspect that members of the common clades such as strains HKI4363/88 have been introduced only recently by anthropogenic activities involving importation of contaminated animal products. On the other hand, autochthonous strains such as isolate BA2968 probably have an older history of their introduction into Finland as evidenced by a high number of single nucleotide variant sites in their genomes. Electronic supplementary material The online version of this article (10.1186/s12866-018-1250-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Taru Lienemann
- Finnish Food Safety Authority (Evira), Veterinary Bacteriology and Pathology Research Unit, Helsinki, Finland
| | | | - Kirsti Pelkola
- Finnish Food Safety Authority (Evira), Veterinary Bacteriology and Pathology Research Unit, Helsinki, Finland
| | - Heidi Rossow
- Finnish Food Safety Authority (Evira), Risk Assessment Research Unit, Helsinki, Finland
| | | | | | - Gregor Grass
- Bundeswehr Institute of Microbiology, Munich, Germany.
| |
Collapse
|
27
|
Sahin M, Buyuk F, Baillie L, Wölfel R, Kotorashvili A, Rehn A, Antwerpen M, Grass G. The identification of novel single nucleotide polymorphisms to assist in mapping the spread of Bacillus anthracis across the Southern Caucasus. Sci Rep 2018; 8:11254. [PMID: 30050151 PMCID: PMC6062627 DOI: 10.1038/s41598-018-29738-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/17/2018] [Indexed: 11/08/2022] Open
Abstract
Anthrax is common as a zoonotic disease in the southern Caucasus area including parts of Turkey and Georgia. In this region, population genetics of the etiological agent Bacillus anthracis comprises, where known, the major canonical single nucleotide polymorphism (canSNP) groups A.Br.Aust94 and A.Br.008/009 of the pathogen's global phylogeny, respectively. Previously, isolates of B. anthracis from Turkey have been genotyped predominantly by multi locus variable number of tandem repeat analysis (MLVA) or canSNP typing. While whole genome sequencing is the future gold standard, it is currently still costly. For that reason we were interested in identifying novel SNPs which could assist in further distinguishing closely related isolates using low cost assay platforms. In this study we sequenced the genomes of seven B. anthracis strains collected from the Kars province of Eastern Anatolia in Turkey and discovered new SNPs which allowed us to assign these and other geographically related strains to three novel branches of the major A-branch canSNP-group (A.Br.) Aust94. These new branches were named Kafkas-Geo 1-3 and comprised isolates from the Kars region and the neighboring republic of Georgia suggesting a common ancestry. The novel SNPs identified in this study connect the population genetics of B. anthracis in the South Caucasus and Turkey and will likely assist efforts to map the spread of the pathogen across this region.
Collapse
Affiliation(s)
| | | | | | - Roman Wölfel
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Adam Kotorashvili
- Lugar Center for Public Health Research at the National Center for Disease Control, Tbilisi, Georgia
| | | | | | - Gregor Grass
- Bundeswehr Institute of Microbiology, Munich, Germany.
| |
Collapse
|
28
|
Fasanella A, Serrecchia L, Chiaverini A, Garofolo G, Muuka GM, Mwambazi L. Use of Canonical Single Nucleotide Polymorphism (CanSNPs) to characterize Bacillus anthracis outbreak strains in Zambia between 1990 and 2014. PeerJ 2018; 6:e5270. [PMID: 30065876 PMCID: PMC6064633 DOI: 10.7717/peerj.5270] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/29/2018] [Indexed: 11/20/2022] Open
Abstract
Anthrax caused by Bacillus anthracis is an old and neglected zoonosis that continues to raise concerns in Southern Africa. In this study, twenty (20) slides with suspected isolates of B. anthracis from anthrax cases between 1990 and 2014 and two (2) from that of a vaccine strain were analysed using MLVA with 15 VNTRs and CanSNPs test. The results from the CanSNPs indicate that all anthrax outbreaks in Zambia between 1990 and 2014 were caused by the lineage A.Br.005/006 of the clade A. This indicates a common ancestral origin of the B. anthracis circulating in the country. This data has described several environmental, wildlife, livestock and human cases that occurred in a 24 year period, from the major areas where anthrax is endemic. The molecular characterization of isolates from anthrax outbreaks in Zambia has revealed a genetic structure in agreement with previous studies from neighbouring countries. Further studies are needed to elucidate how to better manage anthrax outbreaks and define the risk maps of Zambia.
Collapse
Affiliation(s)
- Antonio Fasanella
- Anthrax Reference Institute of Italy, Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Luigina Serrecchia
- Anthrax Reference Institute of Italy, Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Alexandra Chiaverini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - Giuliano Garofolo
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - Geoffrey M Muuka
- Bacteriology Section, Ministry of Fisheries and Livestock, Veterinary Services Department, Central Veterinary Research Institute, Lusaka, Zambia
| | - Lucas Mwambazi
- Bacteriology Section, Ministry of Fisheries and Livestock, Veterinary Services Department, Central Veterinary Research Institute, Lusaka, Zambia
| |
Collapse
|
29
|
Lekota KE, Hassim A, Rogers P, Dekker EH, Last R, de Klerk-Lorist L, van Heerden H. The reporting of a Bacillus anthracis B-clade strain in South Africa after more than 20 years. BMC Res Notes 2018; 11:264. [PMID: 29716659 PMCID: PMC5930959 DOI: 10.1186/s13104-018-3366-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 04/20/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Anthrax is a disease with an age old history in Africa caused by the Gram-positive endospore forming soil bacterium Bacillus anthracis. Epizootics of wild ungulates occur annually in the enzootic region of Pafuri, Kruger National Park (KNP) in the Limpopo Province of South Africa. Rigorous routine surveillance and diagnostics in KNP, has not revealed these rare isolates since the 1990s, despite unabated annual outbreaks. In 2011 a cheetah was diagnosed as anthrax positive from a private game reserve in Limpopo Province and reported to State Veterinary Services for further investigation. Isolation, molecular diagnostics, whole genome sequencing and comparative genomics were carried out for B. anthracis KC2011. RESULTS Bacteriological and molecular diagnostics confirmed the isolate as B. anthracis. Subsequent typing and whole genome single nucleotide polymorphisms analysis indicated it clustered alongside B. anthracis SA A0091 in the B.Br.010 SNP branch. Unlike B. anthracis KrugerB strain, KC2011 strain has unique SNPs and represents a new branch in the B-clade. The isolation and genotypic characterisation of KC2011 demonstrates a gap in the reporting of anthrax outbreaks in the greater Limpopo province area. The identification of vulnerable and susceptible cheetah mortalities due to this strain has implications for conservation measures and disease control.
Collapse
Affiliation(s)
- K E Lekota
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa. .,College of Agriculture and Environmental Sciences, University of South Africa, Christiaan De Wet/Pioneer Dr., Florida, South Africa.
| | - A Hassim
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - P Rogers
- Provet Wildlife Services, Raptors Safari Junction, Main Road, Hoedspruit, South Africa
| | - E H Dekker
- State Veterinary Services, Department of Agriculture, Forestry and Fisheries, Skukuza, South Africa
| | - R Last
- Vetdiagnostix-Veterinary Pathology Services, 257 Boshoff Street, Pietermaritzburg, South Africa
| | - L de Klerk-Lorist
- State Veterinary Services, Department of Agriculture, Forestry and Fisheries, Skukuza, South Africa
| | - H van Heerden
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| |
Collapse
|
30
|
Rottmann T, Klebl F, Schneider S, Kischka D, Rüscher D, Sauer N, Stadler R. Sugar Transporter STP7 Specificity for l-Arabinose and d-Xylose Contrasts with the Typical Hexose Transporters STP8 and STP12. PLANT PHYSIOLOGY 2018; 176:2330-2350. [PMID: 29311272 PMCID: PMC5841717 DOI: 10.1104/pp.17.01493] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/29/2017] [Indexed: 05/08/2023]
Abstract
The controlled distribution of sugars between assimilate-exporting source tissues and sugar-consuming sink tissues is a key element for plant growth and development. Monosaccharide transporters of the SUGAR TRANSPORT PROTEIN (STP) family contribute to the uptake of sugars into sink cells. Here, we report on the characterization of STP7, STP8, and STP12, three previously uncharacterized members of this family in Arabidopsis (Arabidopsis thaliana). Heterologous expression in yeast (Saccharomyces cerevisiae) revealed that STP8 and STP12 catalyze the high-affinity proton-dependent uptake of glucose and also accept galactose and mannose. STP12 additionally transports xylose. STP8 and STP12 are highly expressed in reproductive organs, where their protein products might contribute to sugar uptake into the pollen tube and the embryo sac. stp8.1 and stp12.1 T-DNA insertion lines developed normally, which may point toward functional redundancy with other STPs. In contrast to all other STPs, STP7 does not transport hexoses but is specific for the pentoses l-arabinose and d-xylose. STP7-promoter-reporter gene plants showed an expression of STP7 especially in tissues with high cell wall turnover, indicating that STP7 might contribute to the uptake and recycling of cell wall sugars. Uptake analyses with radioactive l-arabinose revealed that 11 other STPs are able to transport l-arabinose with high affinity. Hence, functional redundancy might explain the missing-mutant phenotype of two stp7 T-DNA insertion lines. Together, these data complete the characterization of the STP family and present the STPs as new l-arabinose transporters for potential biotechnological applications.
Collapse
Affiliation(s)
- Theresa Rottmann
- Molecular Plant Physiology, University Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Franz Klebl
- Molecular Plant Physiology, University Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Sabine Schneider
- Molecular Plant Physiology, University Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Dominik Kischka
- Molecular Plant Physiology, University Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - David Rüscher
- Molecular Plant Physiology, University Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Norbert Sauer
- Molecular Plant Physiology, University Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Ruth Stadler
- Molecular Plant Physiology, University Erlangen-Nürnberg, 91058 Erlangen, Germany
| |
Collapse
|
31
|
Foster JT, Walker FM, Rannals BD, Hussain MH, Drees KP, Tiller RV, Hoffmaster AR, Al-Rawahi A, Keim P, Saqib M. African Lineage Brucella melitensis Isolates from Omani Livestock. Front Microbiol 2018; 8:2702. [PMID: 29379492 PMCID: PMC5775276 DOI: 10.3389/fmicb.2017.02702] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/29/2017] [Indexed: 11/13/2022] Open
Abstract
Brucellosis is a common livestock disease in the Middle East and North Africa, but remains poorly described in the region both genetically and epidemiologically. Traditionally found in goats and sheep, Brucella melitensis is increasingly recognized as infecting camels. Most studies of brucellosis in camels to date have focused on serological surveys, providing only limited understanding of the molecular epidemiology of circulating strains. We genotyped B. melitensis isolates from Omani camels using whole genome SNP assays and VNTRs to provide context for regional brucellosis cases. We identified a lineage of B. melitensis circulating in camels as well as in goats, sheep, and cattle in Oman. This lineage is genetically distinct from most genotypes from the Arabian Peninsula and from isolates from much of the rest of the Middle East. We then developed diagnostic assays that rapidly identify strains from this lineage. In analyses of genotypes from throughout the region, Omani isolates were genetically most closely related to strains from brucellosis cases in humans and livestock in North Africa. Our findings suggest an African origin for B. melitensis in Oman that has likely occurred through the trade of infected livestock. Moreover, African lineages of B. melitensis appear to be undersampled and consequently are underrepresented in genetic databases for Brucella. As we begin to more fully understand global genomic diversity of B. melitensis, finding and characterizing these unique but widespread lineages is essential. We predict that increased sampling of humans and livestock in Africa will reveal little known diversity in this important zoonotic pathogen.
Collapse
Affiliation(s)
- Jeffrey T Foster
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Faith M Walker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Brandy D Rannals
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - M Hammad Hussain
- Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan.,Animal Health Research Center, Ministry of Agriculture and Fisheries, Muscat, Oman
| | - Kevin P Drees
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Rebekah V Tiller
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control, Atlanta, GA, United States
| | - Alex R Hoffmaster
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control, Atlanta, GA, United States
| | | | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Muhammad Saqib
- Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan
| |
Collapse
|
32
|
Timofeev VS, Bakhteeva IV, Dyatlov IA. Genotyping of Bacillus anthracis and Closely Related Microorganisms. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418010118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
33
|
Mitchell CL, Andrianaivoarimanana V, Colman RE, Busch J, Hornstra-O’Neill H, Keim PS, Wagner DM, Rajerison M, Birdsell DN. Low cost, low tech SNP genotyping tools for resource-limited areas: Plague in Madagascar as a model. PLoS Negl Trop Dis 2017; 11:e0006077. [PMID: 29227994 PMCID: PMC5739503 DOI: 10.1371/journal.pntd.0006077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 12/21/2017] [Accepted: 10/27/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Genetic analysis of pathogenic organisms is a useful tool for linking human cases together and/or to potential environmental sources. The resulting data can also provide information on evolutionary patterns within a targeted species and phenotypic traits. However, the instruments often used to generate genotyping data, such as single nucleotide polymorphisms (SNPs), can be expensive and sometimes require advanced technologies to implement. This places many genotyping tools out of reach for laboratories that do not specialize in genetic studies and/or lack the requisite financial and technological resources. To address this issue, we developed a low cost and low tech genotyping system, termed agarose-MAMA, which combines traditional PCR and agarose gel electrophoresis to target phylogenetically informative SNPs. METHODOLOGY/PRINCIPAL FINDINGS To demonstrate the utility of this approach for generating genotype data in a resource-constrained area (Madagascar), we designed an agarose-MAMA system targeting previously characterized SNPs within Yersinia pestis, the causative agent of plague. We then used this system to genetically type pathogenic strains of Y. pestis in a Malagasy laboratory not specialized in genetic studies, the Institut Pasteur de Madagascar (IPM). We conducted rigorous assay performance validations to assess potential variation introduced by differing research facilities, reagents, and personnel and found no difference in SNP genotyping results. These agarose-MAMA PCR assays are currently employed as an investigative tool at IPM, providing Malagasy researchers a means to improve the value of their plague epidemiological investigations by linking outbreaks to potential sources through genetic characterization of isolates and to improve understanding of disease ecology that may contribute to a long-term control effort. CONCLUSIONS The success of our study demonstrates that the SNP-based genotyping capacity of laboratories in developing countries can be expanded with manageable financial cost for resource constraint laboratories. This is a practical formula that reduces resource-driven limitations to genetic research and promises to advance global collective knowledge of infectious diseases emanating from resource limited regions of the world.
Collapse
Affiliation(s)
- Cedar L. Mitchell
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | | | - Rebecca E. Colman
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Joseph Busch
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Heidie Hornstra-O’Neill
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul S. Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Minoarisoa Rajerison
- Plague Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- * E-mail: (MR); (DNB)
| | - Dawn N. Birdsell
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail: (MR); (DNB)
| |
Collapse
|
34
|
Sulyok KM, Bekő K, Kreizinger Z, Wehmann E, Jerzsele Á, Rónai Z, Turcsányi I, Makrai L, Szeredi L, Jánosi S, Nagy SÁ, Gyuranecz M. Development of molecular methods for the rapid detection of antibiotic susceptibility of Mycoplasma bovis. Vet Microbiol 2017; 213:47-57. [PMID: 29292003 DOI: 10.1016/j.vetmic.2017.11.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/12/2017] [Accepted: 11/17/2017] [Indexed: 10/18/2022]
Abstract
Determining the antibiotic susceptibility profile of Mycoplasma bovis isolates in vitro provides the basis for the appropriate choice of antibiotics in the therapy. Traditionally, the antibiotic susceptibility examination of mycoplasmas is technically demanding, time-consuming and rarely performed in diagnostic laboratories. The aim of the present study was to develop rapid molecular assays to determine mutations responsible for elevated minimal inhibitory concentrations (MICs) to fluoroquinolones, tetracyclines, aminocyclitols, macrolides, lincosamides, phenicols and pleuromutilins in M. bovis. The nine mismatch amplification mutation assays (MAMA) and seven high resolution melt (HRM) tests designed in the present study enable the simultaneous detection of these genetic markers. The sensitivity of the assays varied between 102-105 copy numbers/reaction. Cross-reactions with other mycoplasmas occurring in cattle were detected in assays targeting universal regions (e.g. 16S rRNA). Nevertheless, results of the novel method were in accordance with sequence and MICs data of the M. bovis pure cultures. Also, the tests of clinical samples containing high amount of M. bovis DNA were congruent even in the presence of other Mycoplasma spp. The presented method is highly cost-effective and can provide an antibiogram to 12 antibiotics in approximately 3-4 days when previous isolation of M. bovis is applied. In order to assure the proper identification of the genetic markers at issue, the regions examined by the MAMA and HRM tests are overlapping. In conclusion, the developed assays have potential to be used in routine diagnostics for the detection of antibiotic susceptibility in M. bovis.
Collapse
Affiliation(s)
- Kinga M Sulyok
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, 1143, Hungária körút 21, Hungary
| | - Katinka Bekő
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, 1143, Hungária körút 21, Hungary
| | - Zsuzsa Kreizinger
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, 1143, Hungária körút 21, Hungary
| | - Enikő Wehmann
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, 1143, Hungária körút 21, Hungary
| | - Ákos Jerzsele
- University of Veterinary Medicine, Budapest, István utca 2, Hungary
| | - Zsuzsanna Rónai
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, 1143, Tábornok utca 2, Hungary
| | - Ibolya Turcsányi
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, 1143, Tábornok utca 2, Hungary
| | - László Makrai
- University of Veterinary Medicine, Budapest, István utca 2, Hungary
| | - Levente Szeredi
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, 1143, Tábornok utca 2, Hungary
| | - Szilárd Jánosi
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, 1143, Tábornok utca 2, Hungary
| | - Sára Ágnes Nagy
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, 1143, Hungária körút 21, Hungary
| | - Miklós Gyuranecz
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, 1143, Hungária körút 21, Hungary.
| |
Collapse
|
35
|
Zhu L, Konsak BM, Olaogun OM, Agnew-Crumptona R, Kanci A, Marenda MS, Browning GF, Noormohammadi AH. Identification of a new genetic marker in Mycoplasma synoviae vaccine strain MS-H and development of a strategy using polymerase chain reaction and high-resolution melting curve analysis for differentiating MS-H from field strains. Vet Microbiol 2017; 210:49-55. [PMID: 29103696 DOI: 10.1016/j.vetmic.2017.08.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/28/2017] [Accepted: 08/28/2017] [Indexed: 11/25/2022]
Abstract
Mycoplasma synoviae (MS) is an economically important avian pathogen worldwide, causing subclinical respiratory tract infection and infectious synovitis in chickens and turkeys. A temperature-sensitive (ts+) live attenuated vaccine MS-H, derived from the Australian field strain 86079/7NS, is now widely used in many countries to control the disease induced by MS. Differentiation of MS-H vaccine from field strains is crucial for monitoring vaccination programs in commercial poultry. Comparison of genomic sequences of MS-H and its parent strain revealed an adenine deletion at nucleotide position 468 of the MS-H oppF-1 gene. This mutation was shown to be unique to MS-H in further comparative analyses of oppF-1 genes of MS-H re-isolates and field strains from Australia and other countries. Based on this single nucleotide, a combination of nested PCR and high-resolution melting (HRM) curve analysis was used to evaluate its potential for use in differentiation of MS-H from field strains. The mean genotype confidence percentages of 99.27 and 48.20 for MS-H and field strains, respectively, demonstrated the high discriminative power of the newly developed assay (oppF PCR-HRM). A set of 13 tracheal swab samples collected from MS-H vaccinated specific pathogen free birds and commercial chicken flocks infected with MS were tested using the oppF PCR-HRM test and results were totally consistent with those obtained using vlhA genotyping. The nested-PCR HRM method established in this study proved to be a rapid, simple and cost effective tool for discriminating the MS-H vaccine strain from Australian and international strains in pure cultures and on tracheal swabs.
Collapse
Affiliation(s)
- Ling Zhu
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary Agricultural Sciences, The University of Melbourne, Werribee, 3030, Victoria, Australia
| | - Barbara M Konsak
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary Agricultural Sciences, The University of Melbourne, Werribee, 3030, Victoria, Australia
| | - Olusola M Olaogun
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary Agricultural Sciences, The University of Melbourne, Werribee, 3030, Victoria, Australia
| | - Rebecca Agnew-Crumptona
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary Agricultural Sciences, The University of Melbourne, Werribee, 3030, Victoria, Australia
| | - Anna Kanci
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne,Parkville, 3010, Victoria, Australia
| | - Marc S Marenda
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary Agricultural Sciences, The University of Melbourne, Werribee, 3030, Victoria, Australia.
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne,Parkville, 3010, Victoria, Australia
| | - Amir H Noormohammadi
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary Agricultural Sciences, The University of Melbourne, Werribee, 3030, Victoria, Australia
| |
Collapse
|
36
|
Zhang H, Kong F, Wang X, Liang L, Schoen CD, Feng J, Wang Z. Tetra-primer ARMS PCR for rapid detection and characterisation of Plasmopara viticola phenotypes resistant to carboxylic acid amide fungicides. PEST MANAGEMENT SCIENCE 2017; 73:1655-1660. [PMID: 27990754 DOI: 10.1002/ps.4506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 12/06/2016] [Accepted: 12/10/2016] [Indexed: 05/27/2023]
Abstract
BACKGROUND The occurrence of Plasmopara viticola populations resistant to carboxylic acid amide (CAA) fungicides is becoming a serious problem in the control of grapevine downy mildew worldwide. The resistance is caused by point mutations in the PvCesA3 gene. These isolates with this mutation have been detected mainly by determining the minimum inhibitory concentration of fungicides, which is always time consuming and inefficient. RESULTS To establish a suitable method for rapid detection of the G1105S mutation in P. viticola, an efficient and simple molecular method was developed, based on tetra-primer ARMS PCR. A set of four primers were designed and optimised to distinguish the different genotypes within one step. Only 2 h was required from the sampling of symptoms to the phenotyping of fungicide resistance. Using this method, CAA-resistant P. viticola were identified for the first time in China. Also, the finding of sensitive heterozygotes indicated that the resistant allele is spreading in the population in Ziyuan. CONCLUSION This new method proved to be useful as an early warning system for resistance outbreaks of P. viticola to CAA fungicides in the field and may be helpful in decisions concerning rotation of different fungicide groups. © 2016 Society of Chemical Industry.
Collapse
Affiliation(s)
- Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Fanfang Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Xina Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Lisha Liang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
- Guilin Municipal Bureau of Forestry, Guangxi, China
| | - Cor D Schoen
- Wageningen Plant Research, Wageningen, The Netherlands
| | - Jie Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Zhongyue Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| |
Collapse
|
37
|
Kreizinger Z, Sulyok KM, Grózner D, Bekő K, Dán Á, Szabó Z, Gyuranecz M. Development of mismatch amplification mutation assays for the differentiation of MS1 vaccine strain from wild-type Mycoplasma synoviae and MS-H vaccine strains. PLoS One 2017; 12:e0175969. [PMID: 28419134 PMCID: PMC5395193 DOI: 10.1371/journal.pone.0175969] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/03/2017] [Indexed: 11/29/2022] Open
Abstract
Mycoplasma synoviae is an economically significant pathogen in the poultry industry, inducing respiratory disease and infectious synovitis in chickens and turkeys, and eggshell apex abnormality in chickens. Eradication, medication and vaccination are the options for controlling M. synoviae infection. Currently there are two commercial, live, attenuated vaccines available against M. synoviae: the temperature sensitive MS-H vaccine strain and the NAD independent MS1 vaccine strain. Differentiation of vaccine strains from field isolates is essential during vaccination and eradication programs. The present study provides melt-curve and agarose gel based mismatch amplification mutation assays (MAMA) to discriminate the MS1 vaccine strain from the MS-H vaccine strain and wild-type M. synoviae isolates. The assays are based on the A/C single nucleotide polymorphism at nt11 of a HIT family protein coding gene. The melt- and agarose-MAMAs reliably distinguish the MS1 vaccine strain genotype from the MS-H vaccine strain and wild-type M. synoviae isolate genotype from 102 template number/DNA sample. No cross-reactions with other avian Mycoplasma species were observed. The assays can be performed directly on clinical samples and they can be run simultaneously with the previously described MAMAs designed for the discrimination of the MS-H vaccine strain. The developed assays are applicable in laboratories with limited facilities and promote the rapid, simple and cost effective differentiation of the MS1 vaccine strain.
Collapse
Affiliation(s)
- Zsuzsa Kreizinger
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Kinga Mária Sulyok
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Dénes Grózner
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Katinka Bekő
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Ádám Dán
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, Hungary
| | - Zoltán Szabó
- Intervet Hungária Kft., part of MSD Animal Health, Budapest, Hungary
| | - Miklós Gyuranecz
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail:
| |
Collapse
|
38
|
Origins and global context of Brucella abortus in Italy. BMC Microbiol 2017; 17:28. [PMID: 28152976 PMCID: PMC5290641 DOI: 10.1186/s12866-017-0939-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 01/24/2017] [Indexed: 11/30/2022] Open
Abstract
Background Brucellosis is a common and chronic disease of cattle and other bovids that often causes reproductive disorders. Natural infection in cattle is caused by Brucella abortus and transmission typically occurs during abortions, calving, or nursing. Brucellosis is also a major zoonotic disease due to contamination of dairy products or contact with the tissues of infected animals. Brucellosis has been eradicated from most of the developed world in the last 40 years but persists in many regions—the disease remains prevalent in portions of Africa, the Middle East, Asia, and Central and South America, as well as in the Mediterranean basin. In Italy, B. abortus has persisted in southern regions in both cattle and water buffalo. Previous attempts at analyzing the phylogenetics of B. abortus in Italy have been challenging due to limited genetic variability and unresolved global population genetic structure of this pathogen. Results We conducted genome-wide phylogenetic analyses on 11 representative strains of B. abortus from Italy, and compared these sequences to a worldwide collection of publically available genomes. Italian isolates belong to three clades that are basal to the main and global B. abortus lineage. Using six SNP-based assays designed to identify substructure within the Italian clades, we surveyed a collection of 261 isolates and found that one clade predominates throughout endemic districts in the country, while the other two clades are more geographically restricted to portions of southern Italy. Conclusions Although related strains exist worldwide, B. abortus isolates from Italy are substantially different than those found in much of the rest of Europe and North America, and are more closely related to strains from the Middle East and Asia. Our assays targeting genetic substructure within Italy allowed us to identify the major lineages quickly and inexpensively, without having to generate whole genome sequences for a large isolate collection. These findings highlight the importance of genetic studies to assess the status and the history of pathogens. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0939-0) contains supplementary material, which is available to authorized users.
Collapse
|
39
|
Dwibedi C, Birdsell D, Lärkeryd A, Myrtennäs K, Öhrman C, Nilsson E, Karlsson E, Hochhalter C, Rivera A, Maltinsky S, Bayer B, Keim P, Scholz HC, Tomaso H, Wittwer M, Beuret C, Schuerch N, Pilo P, Hernández Pérez M, Rodriguez-Lazaro D, Escudero R, Anda P, Forsman M, Wagner DM, Larsson P, Johansson A. Long-range dispersal moved Francisella tularensis into Western Europe from the East. Microb Genom 2016; 2:e000100. [PMID: 28348839 PMCID: PMC5359409 DOI: 10.1099/mgen.0.000100] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/22/2016] [Indexed: 01/31/2023] Open
Abstract
For many infections transmitting to humans from reservoirs in nature, disease dispersal patterns over space and time are largely unknown. Here, a reversed genomics approach helped us understand disease dispersal and yielded insight into evolution and biological properties of Francisella tularensis, the bacterium causing tularemia. We whole-genome sequenced 67 strains and characterized by single-nucleotide polymorphism assays 138 strains, collected from individuals infected 1947-2012 across Western Europe. We used the data for phylogenetic, population genetic and geographical network analyses. All strains (n=205) belonged to a monophyletic population of recent ancestry not found outside Western Europe. Most strains (n=195) throughout the study area were assigned to a star-like phylogenetic pattern indicating that colonization of Western Europe occurred via clonal expansion. In the East of the study area, strains were more diverse, consistent with a founder population spreading from east to west. The relationship of genetic and geographic distance within the F. tularensis population was complex and indicated multiple long-distance dispersal events. Mutation rate estimates based on year of isolation indicated null rates; in outbreak hotspots only, there was a rate of 0.4 mutations/genome/year. Patterns of nucleotide substitution showed marked AT mutational bias suggestive of genetic drift. These results demonstrate that tularemia has moved from east to west in Europe and that F. tularensis has a biology characterized by long-range geographical dispersal events and mostly slow, but variable, replication rates. The results indicate that mutation-driven evolution, a resting survival phase, genetic drift and long-distance geographical dispersal events have interacted to generate genetic diversity within this species.
Collapse
Affiliation(s)
- Chinmay Dwibedi
- Department of Clinical Microbiology and the Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Dawn Birdsell
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Adrian Lärkeryd
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Kerstin Myrtennäs
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Caroline Öhrman
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Elin Nilsson
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Edvin Karlsson
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Christian Hochhalter
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Andrew Rivera
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Sara Maltinsky
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Brittany Bayer
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
- Translational Genomics Research Institute North, Flagstaff AZ, USA
| | | | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses Friedrich-Loeffler, Institut Federal Research Institute for Animal Health, Jena, Germany
| | - Matthias Wittwer
- Biology Division, Spietz Laboratory, Federal Office for Civil Protection, Spietz, Switzerland
| | - Christian Beuret
- Biology Division, Spietz Laboratory, Federal Office for Civil Protection, Spietz, Switzerland
| | - Nadia Schuerch
- Biology Division, Spietz Laboratory, Federal Office for Civil Protection, Spietz, Switzerland
| | - Paola Pilo
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Marta Hernández Pérez
- Laboratory of Molecular Biology and Microbiology, Instituto Tecnológico Agrario de Castilla y León, Valladolid, Spain
- Departamento de Ingeniería Agrícola y Forestal, Universidad de Valladolid, Palencia, Spain
| | | | - Raquel Escudero
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro Anda
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Mats Forsman
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - David M. Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Pär Larsson
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Anders Johansson
- Department of Clinical Microbiology and the Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Correspondence Anders Johansson ()
| |
Collapse
|
40
|
Whole genome SNP analysis of bovine B. anthracis strains from Switzerland reflects strict regional separation of Simmental and Swiss Brown breeds in the past. Vet Microbiol 2016; 196:1-8. [DOI: 10.1016/j.vetmic.2016.10.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 08/11/2016] [Accepted: 10/09/2016] [Indexed: 11/20/2022]
|
41
|
Anglès d'Auriac MB. COMplementary Primer ASymmetric PCR (COMPAS-PCR) Applied to the Identification of Salmo salar, Salmo trutta and Their Hybrids. PLoS One 2016; 11:e0165468. [PMID: 27783658 PMCID: PMC5082663 DOI: 10.1371/journal.pone.0165468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/12/2016] [Indexed: 12/26/2022] Open
Abstract
Avoiding complementarity between primers when designing a PCR assay constitutes a central rule strongly anchored in the mind of the molecular scientist. 3'-complementarity will extend the primers during PCR elongation using one another as template, consequently disabling further possible involvement in traditional target amplification. However, a 5'-complementarity will leave the primers unchanged during PCR cycles, albeit sequestered to one another, therefore also suppressing target amplification. We show that 5'-complementarity between primers may be exploited in a new PCR method called COMplementary-Primer-Asymmetric (COMPAS)-PCR, using asymmetric primer concentrations to achieve target PCR amplification. Moreover, such a design may paradoxically reduce spurious non-target amplification by actively sequestering the limiting primer. The general principles were demonstrated using 5S rDNA direct repeats as target sequences to design a species-specific assay for identifying Salmo salar and Salmo trutta using almost fully complementary primers overlapping the same target sequence. Specificity was enhanced by using 3'-penultimate point mutations and the assay was further developed to enable identification of S. salar x S. trutta hybrids by High Resolution Melt analysis in a 35 min one-tube assay. This small paradigm shift, using highly complementary primers for PCR, should help develop robust assays that previously would not be considered.
Collapse
|
42
|
A Synonymous Mutation Upstream of the Gene Encoding a Weak-Link Enzyme Causes an Ultrasensitive Response in Growth Rate. J Bacteriol 2016; 198:2853-63. [PMID: 27501982 DOI: 10.1128/jb.00262-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/22/2016] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED When microbes are faced with an environmental challenge or opportunity, preexisting enzymes with promiscuous secondary activities can be recruited to provide newly important functions. Mutations that increase the efficiency of a new activity often compromise the original activity, resulting in an inefficient bifunctional enzyme. We have investigated the mechanisms by which growth of Escherichia coli can be improved when fitness is limited by such an enzyme, E383A ProA (ProA*). ProA* can serve the functions of both ProA (required for synthesis of proline) and ArgC (required for synthesis of arginine), albeit poorly. We identified four genetic changes that improve the growth rate by up to 6.2-fold. Two point mutations in the promoter of the proBA* operon increase expression of the entire operon. Massive amplification of a genomic segment around the proBA* operon also increases expression of the entire operon. Finally, a synonymous point mutation in the coding region of proB creates a new promoter for proA* This synonymous mutation increases the level of ProA* by 2-fold but increases the growth rate by 5-fold, an ultrasensitive response likely arising from competition between two substrates for the active site of the inefficient bifunctional ProA*. IMPORTANCE The high-impact synonymous mutation we discovered in proB is remarkable for two reasons. First, most polar effects documented in the literature are detrimental. This finding demonstrates that polar effect mutations can have strongly beneficial effects, especially when an organism is facing a difficult environmental challenge for which it is poorly adapted. Furthermore, the consequence of the synonymous mutation in proB is a 2-fold increase in the level of ProA* but a disproportionately large 5.1-fold increase in growth rate. While ultrasensitive responses are often found in signaling networks and genetic circuits, an ultrasensitive response to an adaptive mutation has not been previously reported.
Collapse
|
43
|
Vincent G, Stenos J, Latham J, Fenwick S, Graves S. Novel genotypes of Coxiella burnetii identified in isolates from Australian Q fever patients. Int J Med Microbiol 2016; 306:463-70. [DOI: 10.1016/j.ijmm.2016.05.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/19/2016] [Accepted: 05/24/2016] [Indexed: 11/24/2022] Open
|
44
|
Rume FI, Ahsan CR, Biswas PK, Yasmin M, Braun P, Walter MC, Antwerpen M, Grass G, Hanczaruk M. Unexpected genomic relationships between Bacillus anthracis strains from Bangladesh and Central Europe. INFECTION GENETICS AND EVOLUTION 2016; 45:66-74. [PMID: 27543395 DOI: 10.1016/j.meegid.2016.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/11/2016] [Accepted: 08/15/2016] [Indexed: 12/28/2022]
Abstract
The zoonosis anthrax caused by the bacterium Bacillus anthracis has a broad geographical distribution. Active enzootic areas are typically located away from central and northern Europe where cases of the disease occur only sporadically and in limited numbers. In contrast, a few out of the 64 districts of Bangladesh are hyper-endemic for anthrax and there the disease causes major losses in live-stock. In this study we genotyped eight strains of B. anthracis collected from the districts of Sirajganj and Tangail in 2013. All these strains belonged to canSNP group A.Br.001/002 Sterne differing only in a few of 31 tandem-repeat (MLVA)-markers. Whole genome sequences were obtained from five of these strains and compared with genomic information of B. anthracis strains originating from various geographical locations. Characteristic signatures were detected defining two "Bangladesh" clusters potentially useful for rapid molecular epidemiology. From this data high-resolution PCR assays were developed and subsequently tested on additional isolates from Bangladesh and Central Europe. Remarkably, this comparative genomic analysis focusing on SNP-discovery revealed a close genetic relationship between these strains from Bangladesh and historic strains collected between 1991 and 2008 in The Netherlands and Germany, respectively. Possible explanations for these phylogenetic relationships are discussed.
Collapse
Affiliation(s)
- Farzana Islam Rume
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh; Department of Microbiology & Public Health, Patuakhali Science and Technology University, Khanpura, Babugonj, Barisal, Bangladesh
| | | | - Paritosh Kumar Biswas
- Department of Microbiology & Veterinary Public Health, Chittagong Veterinary and Animal Sciences University, Chittagong, Bangladesh
| | - Mahmuda Yasmin
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Peter Braun
- Bundeswehr Institute of Microbiology, Munich, Germany
| | | | | | - Gregor Grass
- Bundeswehr Institute of Microbiology, Munich, Germany.
| | | |
Collapse
|
45
|
Bergqvist J, Forsman O, Larsson P, Näslund J, Lilja T, Engdahl C, Lindström A, Gylfe Å, Ahlm C, Evander M, Bucht G. Detection and isolation of Sindbis virus from mosquitoes captured during an outbreak in Sweden, 2013. Vector Borne Zoonotic Dis 2016; 15:133-40. [PMID: 25700044 DOI: 10.1089/vbz.2014.1717] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mosquito-borne alphaviruses have the potential to cause large outbreaks throughout the world. Here we investigated the causative agent of an unexpected Sindbis virus (SINV) outbreak during August-September, 2013, in a previously nonendemic region of Sweden. Mosquitoes were collected using carbon dioxide-baited CDC traps at locations close to human cases. The mosquitoes were initially screened as large pools by SINV-specific quantitative RT-PCR, and the SINV-positive mosquitoes were species determined by single-nucleotide polymorphism (SNP) analysis, followed by sequencing the barcoding region of the cytochrome oxidase I gene. The proportion of the collected mosquitoes was determined by a metabarcoding strategy. By using novel strategies for PCR screening and genetic typing, a new SINV strain, Lövånger, was isolated from a pool of 1600 mosquitoes composed of Culex, Culiseta, and Aedes mosquitoes as determined by metabarcoding. The SINV-positive mosquito Culiseta morsitans was identified by SNP analysis and sequencing. After whole-genome sequencing and phylogenetic analysis, the SINV Lövånger isolate was shown to be most closely similar to recent Finnish SINV isolates. In conclusion, within a few weeks, we were able to detect and isolate a novel SINV strain and identify the mosquito vector during a sudden SINV outbreak.
Collapse
Affiliation(s)
- Joakim Bergqvist
- 1 Swedish Defence Research Agency, CBRN Defence and Security , Umeå, Sweden
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Vergnaud G, Girault G, Thierry S, Pourcel C, Madani N, Blouin Y. Comparison of French and Worldwide Bacillus anthracis Strains Favors a Recent, Post-Columbian Origin of the Predominant North-American Clade. PLoS One 2016; 11:e0146216. [PMID: 26901621 PMCID: PMC4763433 DOI: 10.1371/journal.pone.0146216] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 12/15/2015] [Indexed: 01/28/2023] Open
Abstract
Background Bacillus anthracis, the highly dangerous zoonotic bacterial pathogen species is currently composed of three genetic groups, called A, B and C. Group A is represented worldwide whereas group B is present essentially in Western Europe and Southern Africa. Only three strains from group C have been reported. This knowledge is derived from the genotyping of more than 2000 strains collected worldwide. Strains from both group A and group B are present in France. Previous investigations showed that the majority of sporadic French strains belong to the so-called A.Br.011/009 group A clade and define a very remarkable polytomy with six branches. Here we explore the significance of this polytomy by comparing the French B. anthracis lineages to worldwide lineages. We take advantage of whole genome sequence data previously determined for 122 French strains and 45 strains of various origins. Results A total of 6690 SNPs was identified among the available dataset and used to draw the phylogeny. The phylogeny of the French B group strains which belongs to B.Br.CNEVA indicates an expansion from the south-east part of France (the Alps) towards the south-west (Massif-Central and Pyrenees). The relatively small group A strains belonging to A.Br.001/002 results from at least two independent introductions. Strikingly, the data clearly demonstrates that the currently predominant B. anthracis lineage in North America, called WNA for Western North American, is derived from one branch of the A.Br.011/009 polytomy predominant in France. Conclusions/Significance The present work extends the range of observed substitution rate heterogeneity within B. anthracis, in agreement with its ecology and in contrast with some other pathogens. The population structure of the six branches A.Br.011/009 polytomy identified in France, diversity of branch length, and comparison with the WNA lineage, suggests that WNA is of post-Columbian and west European origin, with France as a likely source. Furthermore, it is tempting to speculate that the polytomy’s most recent common ancestor -MRCA- dates back to the Hundred Years' war between France and England started in the mid-fourteenth century. These events were associated in France with deadly epidemics and major economic and social changes.
Collapse
Affiliation(s)
- Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
- * E-mail:
| | - Guillaume Girault
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Simon Thierry
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
| | - Nora Madani
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Yann Blouin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
| |
Collapse
|
47
|
Two Distinct Yersinia pestis Populations Causing Plague among Humans in the West Nile Region of Uganda. PLoS Negl Trop Dis 2016; 10:e0004360. [PMID: 26866815 PMCID: PMC4750964 DOI: 10.1371/journal.pntd.0004360] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/14/2015] [Indexed: 01/14/2023] Open
Abstract
Background Plague is a life-threatening disease caused by the bacterium, Yersinia pestis. Since the 1990s, Africa has accounted for the majority of reported human cases. In Uganda, plague cases occur in the West Nile region, near the border with Democratic Republic of Congo. Despite the ongoing risk of contracting plague in this region, little is known about Y. pestis genotypes causing human disease. Methodology/Principal Findings During January 2004–December 2012, 1,092 suspect human plague cases were recorded in the West Nile region of Uganda. Sixty-one cases were culture-confirmed. Recovered Y. pestis isolates were analyzed using three typing methods, single nucleotide polymorphisms (SNPs), pulsed field gel electrophoresis (PFGE), and multiple variable number of tandem repeat analysis (MLVA) and subpopulations analyzed in the context of associated geographic, temporal, and clinical data for source patients. All three methods separated the 61 isolates into two distinct 1.ANT lineages, which persisted throughout the 9 year period and were associated with differences in elevation and geographic distribution. Conclusions/Significance We demonstrate that human cases of plague in the West Nile region of Uganda are caused by two distinct 1.ANT genetic subpopulations. Notably, all three typing methods used, SNPs, PFGE, and MLVA, identified the two genetic subpopulations, despite recognizing different mutation types in the Y. pestis genome. The geographic and elevation differences between the two subpopulations is suggestive of their maintenance in highly localized enzootic cycles, potentially with differing vector-host community composition. This improved understanding of Y. pestis subpopulations in the West Nile region will be useful for identifying ecologic and environmental factors associated with elevated plague risk. Plague, a severe and often fatal zoonotic disease, is caused by the bacterium Yersinia pestis. Currently, the majority of human cases have been reported from resource limited areas of Africa, where the proximity to commensal rats and other small mammals increases the likelihood for human contact with infected animals or their fleas. Over a 9 year time period, >1000 suspect cases were recorded in the West Nile region of Uganda within the districts of Arua and Zombo. Culture-confirmed cases were shown by three independent typing methods to be due to two distinct 1.ANT genetic subpopulations of Y. pestis. The two genetic subpopulations persisted throughout the 9 year time period, consistent with their ongoing maintenance in local enzootic cycles. Additionally, the two subpopulations were found to differ with respect to geographic location and elevation, with SNP Group 1 strains being found further north and at lower elevations as compared to SNP Group 2. The relative independence of the two Y. pestis subpopulations is suggestive of their maintenance in distinct foci involving enzootic cycles with differing vector-host community composition.
Collapse
|
48
|
Vogler AJ, Keim P, Wagner DM. A review of methods for subtyping Yersinia pestis: From phenotypes to whole genome sequencing. INFECTION GENETICS AND EVOLUTION 2015; 37:21-36. [PMID: 26518910 DOI: 10.1016/j.meegid.2015.10.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/23/2015] [Accepted: 10/24/2015] [Indexed: 12/28/2022]
Abstract
Numerous subtyping methods have been applied to Yersinia pestis with varying success. Here, we review the various subtyping methods that have been applied to Y. pestis and their capacity for answering questions regarding the population genetics, phylogeography, and molecular epidemiology of this important human pathogen. Methods are evaluated in terms of expense, difficulty, transferability among laboratories, discriminatory power, usefulness for different study questions, and current applicability in light of the advent of whole genome sequencing.
Collapse
Affiliation(s)
- Amy J Vogler
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA; Translational Genomics Research Institute North, Flagstaff, AZ 86001, USA.
| | - David M Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
| |
Collapse
|
49
|
Keim P, Grunow R, Vipond R, Grass G, Hoffmaster A, Birdsell DN, Klee SR, Pullan S, Antwerpen M, Bayer BN, Latham J, Wiggins K, Hepp C, Pearson T, Brooks T, Sahl J, Wagner DM. Whole Genome Analysis of Injectional Anthrax Identifies Two Disease Clusters Spanning More Than 13 Years. EBioMedicine 2015; 2:1613-8. [PMID: 26870786 PMCID: PMC4740342 DOI: 10.1016/j.ebiom.2015.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/24/2015] [Accepted: 10/02/2015] [Indexed: 12/30/2022] Open
Abstract
Background Anthrax is a rare disease in humans but elicits great public fear because of its past use as an agent of bioterrorism. Injectional anthrax has been occurring sporadically for more than ten years in heroin consumers across multiple European countries and this outbreak has been difficult to trace back to a source. Methods We took a molecular epidemiological approach in understanding this disease outbreak, including whole genome sequencing of Bacillus anthracis isolates from the anthrax victims. We also screened two large strain repositories for closely related strains to provide context to the outbreak. Findings Analyzing 60 Bacillus anthracis isolates associated with injectional anthrax cases and closely related reference strains, we identified 1071 Single Nucleotide Polymorphisms (SNPs). The synapomorphic SNPs (350) were used to reconstruct phylogenetic relationships, infer likely epidemiological sources and explore the dynamics of evolving pathogen populations. Injectional anthrax genomes separated into two tight clusters: one group was exclusively associated with the 2009–10 outbreak and located primarily in Scotland, whereas the second comprised more recent (2012–13) cases but also a single Norwegian case from 2000. Interpretation Genome-based differentiation of injectional anthrax isolates argues for at least two separate disease events spanning > 12 years. The genomic similarity of the two clusters makes it likely that they are caused by separate contamination events originating from the same geographic region and perhaps the same site of drug manufacturing or processing. Pathogen diversity within single patients challenges assumptions concerning population dynamics of infecting B. anthracis and host defensive barriers for injectional anthrax. Funding This work was supported by the United States Department of Homeland Security grant no. HSHQDC-10-C-00,139 and via a binational cooperative agreement between the United States Government and the Government of Germany. This work was supported by funds from the German Ministry of Defense (Sonderforschungsprojekt 25Z1-S-431,214). Support for sequencing was also obtained from Illumina, Inc. These sources had no role in the data generation or interpretation, and had not role in the manuscript preparation. Panel 1: Research in Context Systematic Review We searched PubMed for any article published before Jun. 17, 2015, with the terms “Bacillus anthracis” and “heroin”, or “injectional anthrax”. Other than our previously published work (Price et al., 2012), we found no other relevant studies on elucidating the global phylogenetic relationships of B. anthracis strains associated with injectional anthrax caused by recreational heroin consumption of spore-contaminated drug. There were, however, publically available genome sequences of two strains involved (Price et al., 2012, Grunow et al., 2013) and the draft genome sequence of Bacillus anthracis UR-1, isolated from a German heroin user (Ruckert et al., 2012) with only limited information on the genotyping of closely related strains (Price et al., 2012, Grunow et al., 2013). Lay Person Interpretation Injectional anthrax has been plaguing heroin drug users across Europe for more than 10 years. In order to better understand this outbreak, we assessed genomic relationships of all available injectional anthrax strains from four countries spanning a > 12 year period. Very few differences were identified using genome-based analysis, but these differentiated the isolates into two distinct clusters. This strongly supports a hypothesis of at least two separate anthrax spore contamination events perhaps during the drug production processes. Identification of two events would not have been possible from standard epidemiological analysis. These comprehensive data will be invaluable for classifying future injectional anthrax isolates and for future geographic attribution. Whole genome sequences of injectional anthrax B. anthracis isolates fall in two tight but distinct genomic clusters. The distinct genomic clusters are consistent with two or more disease events that overlap in time and space. Defining pathogen clusters will lead to better public health responses to difficult to track disease outbreaks.
Collapse
Affiliation(s)
- Paul Keim
- The Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA; The Pathogen Genomics Division, The Translational Genomics Research Institute, 3051 W. Shamrell Blvd, Suite 106, Flagstaff, AZ 86001 USA
| | | | - Richard Vipond
- Public Health England, Porton Down, Wiltshire SP4 0JG, United Kingdom; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
| | - Gregor Grass
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Alex Hoffmaster
- The Center for Disease Control and Prevention, Atlanta, GA, USA
| | - Dawn N Birdsell
- The Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA
| | | | - Steven Pullan
- Public Health England, Porton Down, Wiltshire SP4 0JG, United Kingdom; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
| | - Markus Antwerpen
- Public Health England, Porton Down, Wiltshire SP4 0JG, United Kingdom
| | - Brittany N Bayer
- The Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA
| | - Jennie Latham
- Public Health England, Porton Down, Wiltshire SP4 0JG, United Kingdom
| | - Kristin Wiggins
- The Pathogen Genomics Division, The Translational Genomics Research Institute, 3051 W. Shamrell Blvd, Suite 106, Flagstaff, AZ 86001 USA
| | - Crystal Hepp
- The Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA
| | - Talima Pearson
- The Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA
| | - Tim Brooks
- Public Health England, Porton Down, Wiltshire SP4 0JG, United Kingdom; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
| | - Jason Sahl
- The Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA; The Pathogen Genomics Division, The Translational Genomics Research Institute, 3051 W. Shamrell Blvd, Suite 106, Flagstaff, AZ 86001 USA
| | - David M Wagner
- The Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA
| |
Collapse
|
50
|
Derzelle S, Girault G, Kokotovic B, Angen Ø. Whole Genome-Sequencing and Phylogenetic Analysis of a Historical Collection of Bacillus anthracis Strains from Danish Cattle. PLoS One 2015; 10:e0134699. [PMID: 26317972 PMCID: PMC4552859 DOI: 10.1371/journal.pone.0134699] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 07/13/2015] [Indexed: 11/28/2022] Open
Abstract
Bacillus anthracis, the causative agent of anthrax, is known as one of the most genetically monomorphic species. Canonical single-nucleotide polymorphism (SNP) typing and whole-genome sequencing were used to investigate the molecular diversity of eleven B. anthracis strains isolated from cattle in Denmark between 1935 and 1988. Danish strains were assigned into five canSNP groups or lineages, i.e. A.Br.001/002 (n = 4), A.Br.Ames (n = 2), A.Br.008/011 (n = 2), A.Br.005/006 (n = 2) and A.Br.Aust94 (n = 1). The match with the A.Br.Ames lineage is of particular interest as the occurrence of such lineage in Europe is demonstrated for the first time, filling an historical gap within the phylogeography of the lineage. Comparative genome analyses of these strains with 41 isolates from other parts of the world revealed that the two Danish A.Br.008/011 strains were related to the heroin-associated strains responsible for outbreaks of injection anthrax in drug users in Europe. Eight novel diagnostic SNPs that specifically discriminate the different sub-groups of Danish strains were identified and developed into PCR-based genotyping assays.
Collapse
Affiliation(s)
- Sylviane Derzelle
- University Paris-Est, Anses, Animal Health Laboratory, Maisons-Alfort, France
| | - Guillaume Girault
- University Paris-Est, Anses, Animal Health Laboratory, Maisons-Alfort, France
| | - Branko Kokotovic
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Øystein Angen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
- * E-mail:
| |
Collapse
|