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Bacterial Genomes and Evolution by Horizontal Gene Transfer (HGT)

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: closed (30 November 2020) | Viewed by 30966

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Special Issue Editors

Prof. Dr. Maria Tomas

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Guest Editor

Research Biomedical Institute (INIBIC), A Coruña Hospital (CHUAC), A Coruña, Spain
Interests: multi-drug resistant rathogens (MDR); Infectious treatment; antibiotics; antitumoral
Special Issues, Collections and Topics in MDPI journals

Dr. Johanna J. Kenyon

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Guest Editor

Queensland University of Technology, Brisbane, Australia
Interests: gram-negative bacterial pathogens; bacterial surface polysaccharides; bioinformatics, genomics; glycoinformatics, glycomics

Dr. Mohammad Hamidian

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Guest Editor

University of Technology Sydney, Sydney, Australia
Interests: microbiology; bacteriology; micronial genetics; medical bacteriology

Special Issue Information

Dear Colleagues,

Bacteria have highly plastic genomes that evolve rapidly via a range of different mechanisms, most importantly via horizontal gene transfer (HGT), which is critical in the context of gene acquisition and exchange between bacterial strains, species, and genera. HGT influences bacterial behavior as well as evolution, hence the importance of its study. In the last decade, advances in the whole genome-sequencing (WGS) technology have allowed for the exploration of bacterial genomes leading to the generation of detailed knowledge on mobile elements involved in horizontal genes transfer (HGT). These molecules include insertion sequences (ISs), transposons, genomic islands, plasmids, miniature inverted-repeat transposable elements (MITEs), repetitive extragenic palindromic sequences (REP), bacterial interspersed mosaic elements (BIMES), and prophages (virus). Many incorporate and carry accessory genes, including those that confer resistance to antibiotics or those that encode important virulence determinants.

The goal of this Special Issue is to provide an overview of the current scientific knowledge on these forces that shape bacterial genomes and their evolution. This may include the mechanisms for the movement of genomic features that may be involved in bacterial adaptation or persistence in different environments, an understanding of which could lead to innovative treatments and new infection control protocols. Bioinformatics tools, as well as in vitro and in vivo studies that determine the roles of these HGT mechanisms in bacterial behavior, will also be considered in this Special Issue.

Prof. Dr. Maria Tomas
Dr. Johanna J. Kenyon
Dr. Mohammad Hamidian
Guest Editors

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Keywords

bacterial evolution
horizontal gene transfer (HGT)
insertion sequences (ISs)
transposons
genomic islands
plasmids
miniature inverted-repeat transposable elements (MITEs)
repetitive extragenic palindromic sequences (REP)
bacteria interspersed mosaic elements (BIMES)
prophages (virus)
antimicrobial resistance genes
virulence genes

Published Papers (9 papers)

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Research

22 pages, 7185 KiB

Open AccessArticle

Pathogenic Determinants of the Mycobacterium kansasii Complex: An Unsuspected Role for Distributive Conjugal Transfer

by Florian Tagini, Trestan Pillonel, Claire Bertelli, Katia Jaton and Gilbert Greub

Microorganisms 2021, 9(2), 348; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9020348 - 10 Feb 2021

Cited by 6 | Viewed by 2725

Abstract

The Mycobacterium kansasii species comprises six subtypes that were recently classified into six closely related species; Mycobacterium kansasii (formerly M. kansasii subtype 1), Mycobacterium persicum (subtype 2), Mycobacterium pseudokansasii (subtype 3), Mycobacterium ostraviense (subtype 4), Mycobacterium innocens (subtype 5) and Mycobacterium attenuatum (subtype 6). Together with Mycobacterium gastri, they form the M. kansasii complex. M. kansasii is the most frequent and most pathogenic species of the complex. M. persicum is classically associated with diseases in immunosuppressed patients, and the other species are mostly colonizers, and are only very rarely reported in ill patients. Comparative genomics was used to assess the genetic determinants leading to the pathogenicity of members of the M. kansasii complex. The genomes of 51 isolates collected from patients with and without disease were sequenced and compared with 24 publicly available genomes. The pathogenicity of each isolate was determined based on the clinical records or public metadata. A comparative genomic analysis showed that all M. persicum, M. ostraviense, M innocens and M. gastri isolates lacked the ESX-1-associated EspACD locus that is thought to play a crucial role in the pathogenicity of M. tuberculosis and other non-tuberculous mycobacteria. Furthermore, M. kansasii was the only species exhibiting a 25-Kb-large genomic island encoding for 17 type-VII secretion system-associated proteins. Finally, a genome-wide association analysis revealed that two consecutive genes encoding a hemerythrin-like protein and a nitroreductase-like protein were significantly associated with pathogenicity. These two genes may be involved in the resistance to reactive oxygen and nitrogen species, a required mechanism for the intracellular survival of bacteria. Three non-pathogenic M. kansasii lacked these genes likely due to two distinct distributive conjugal transfers (DCTs) between M. attenuatum and M. kansasii, and one DCT between M. persicum and M. kansasii. To our knowledge, this is the first study linking DCT to reduced pathogenicity. Full article

(This article belongs to the Special Issue Bacterial Genomes and Evolution by Horizontal Gene Transfer (HGT))

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10 pages, 1522 KiB

Open AccessArticle

Mobilome Analysis of Achromobacter spp. Isolates from Chronic and Occasional Lung Infection in Cystic Fibrosis Patients

by Laura Veschetti, Angela Sandri, Cristina Patuzzo, Paola Melotti, Giovanni Malerba and Maria M. Lleò

Microorganisms 2021, 9(1), 130; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9010130 - 08 Jan 2021

Cited by 7 | Viewed by 2539

Abstract

Achromobacter spp. is an opportunistic pathogen that can cause lung infections in patients with cystic fibrosis (CF). Although a variety of mobile genetic elements (MGEs) carrying antimicrobial resistance genes have been identified in clinical isolates, little is known about the contribution of Achromobacter spp. mobilome to its pathogenicity. To provide new insights, we performed bioinformatic analyses of 54 whole genome sequences and investigated the presence of phages, insertion sequences (ISs), and integrative and conjugative elements (ICEs). Most of the detected phages were previously described in other pathogens and carried type II toxin-antitoxin systems as well as other pathogenic genes. Interestingly, the partial sequence of phage Bcep176 was found in all the analyzed Achromobacter xylosoxidans genome sequences, suggesting the integration of this phage in an ancestor strain. A wide variety of IS was also identified either inside of or in proximity to pathogenicity islands. Finally, ICEs carrying pathogenic genes were found to be widespread among our isolates and seemed to be involved in transfer events within the CF lung. These results highlight the contribution of MGEs to the pathogenicity of Achromobacter species, their potential to become antimicrobial targets, and the need for further studies to better elucidate their clinical impact. Full article

(This article belongs to the Special Issue Bacterial Genomes and Evolution by Horizontal Gene Transfer (HGT))

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11 pages, 949 KiB

Open AccessCommunication

Whole Genome Sequence-Based Prediction of Resistance Determinants in High-Level Multidrug-Resistant Campylobacter jejuni Isolates in Lithuania

by Jurgita Aksomaitiene, Aleksandr Novoslavskij, Egle Kudirkiene, Ausra Gabinaitiene and Mindaugas Malakauskas

Microorganisms 2021, 9(1), 66; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9010066 - 29 Dec 2020

Cited by 7 | Viewed by 2507

Abstract

Spread of antibiotic resistance via mobile genetic elements associates with transfer of genes providing resistance against multiple antibiotics. Use of various comparative genomics analysis techniques enables to find intrinsic and acquired genes associated with phenotypic antimicrobial resistance (AMR) in Campylobacter jejuni genome sequences with exceptionally high-level multidrug resistance. In this study, we used whole genome sequences of seven C. jejuni to identify isolate-specific genomic features associated with resistance and virulence determinants and their role in multidrug resistance (MDR). All isolates were phenotypically highly resistant to tetracycline, ciprofloxacin, and ceftriaxone (MIC range from 64 to ≥256 µg/mL). Besides, two C. jejuni isolates were resistant to gentamicin, and one was resistant to erythromycin. The extensive drug-resistance profiles were confirmed for the two C. jejuni isolates assigned to ST-4447 (CC179). The most occurring genetic antimicrobial-resistance determinants were tetO, beta-lactamase, and multidrug efflux pumps. In this study, mobile genetic elements (MGEs) were detected in genomic islands carrying genes that confer resistance to MDR, underline their importance for disseminating antibiotic resistance in C. jejuni. The genomic approach showed a diverse distribution of virulence markers, including both plasmids and phage sequences that serve as horizontal gene transfer tools. The study findings describe in silico prediction of AMR and virulence genetics determinants combined with phenotypic AMR detection in multidrug-resistant C. jejuni isolates from Lithuania. Full article

(This article belongs to the Special Issue Bacterial Genomes and Evolution by Horizontal Gene Transfer (HGT))

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13 pages, 802 KiB

Open AccessArticle

Plasmid Identification and Plasmid-Mediated Antimicrobial Gene Detection in Norwegian Isolates

by Abdolrahman Khezri, Ekaterina Avershina and Rafi Ahmad

Microorganisms 2021, 9(1), 52; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9010052 - 27 Dec 2020

Cited by 16 | Viewed by 5741

Abstract

Norway is known for being one of the countries with the lowest levels of antimicrobial resistance (AMR). AMR, through acquired genes located on transposons or conjugative plasmids, is the horizontal transmission of genes required for a given bacteria to withstand antibiotics. In this work, bioinformatic analysis of whole-genome sequences and hybrid assembled data from Escherichia coli, and Klebsiella pneumoniae isolates from Norwegian patients was performed. For detection of putative plasmids in isolates, the plasmid assembly mode in SPAdes was used, followed by annotation of resulting contigs using PlasmidFinder and two curated plasmid databases (Brooks and PLSDB). Furthermore, ResFinder and Comprehensive Antibiotic Resistance Database (CARD) were used for the identification of antibiotic resistance genes (ARGs). The IncFIB plasmid was detected as the most prevalent plasmid in both E. coli, and K. pneumoniae isolates. Furthermore, ARGs such as aph(3″)-Ib, aph(6)-Id, sul1, sul2, tet(D), and qnrS1 were identified as the most abundant plasmid-mediated ARGs in Norwegian E. coli and K. pneumoniae isolates, respectively. Using hybrid assembly, we were able to locate plasmids and predict ARGs more confidently. In conclusion, plasmid identification and ARG detection using whole-genome sequencing data are heavily dependent on the database of choice; therefore, it is best to use several tools and/or hybrid assembly for obtaining reliable identification results. Full article

(This article belongs to the Special Issue Bacterial Genomes and Evolution by Horizontal Gene Transfer (HGT))

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14 pages, 11135 KiB

Open AccessArticle

Integrative and Conjugative Element ICETh1 Functions as a Pangenomic DNA Capture Module in Thermus thermophilus

by Alba Blesa, Ignacio Baquedano, Sandra González-de la Fuente, Mario Mencía and José Berenguer

Microorganisms 2020, 8(12), 2051; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8122051 - 21 Dec 2020

Cited by 1 | Viewed by 2087

Abstract

Transjugation is an unconventional conjugation mechanism in Thermus thermophilus (Tth) that involves the active participation of both mating partners, encompassing a DNA secretion system (DSS) in the donor and an active natural competence apparatus (NCA) in the recipient cells. DSS is encoded within an integrative and conjugative element (ICETh1) in the strain Tth HB27, whereas the NCA is constitutively expressed in both mates. Previous experiments suggested the presence of multiple origins of transfer along the genome, which could generate genomic mosaicity among the progeny. Here, we designed transjugation experiments between two closely related strains of Tth with highly syntenic genomes, containing enough single nucleotide polymorphisms to allow precise parenthood analysis. Individual clones from the progeny were sequenced, revealing their origin as derivatives of our ICETh1-containing intended “donor” strain (HB27), which had acquired separate fragments from the genome of the ICETh1-free HB8 cells, which are our intended recipient. Due to the bidirectional nature of transjugation, only assays employing competence-defective HB27 derivatives as donors allowed the recovery of HB8-derived progeny. These results show a preference for a retrotransfer mechanism in transjugation in ICETh1-bearing strains, supporting an inter-strain gene-capture function for ICETh1. This function could benefit the donor-capable host by facilitating the acquisition of adaptive traits from external sources, ultimately increasing the open pangenome of Thermus, maximizing the potential repertoire of physiological and phenotypical traits related to adaptation and speciation. Full article

(This article belongs to the Special Issue Bacterial Genomes and Evolution by Horizontal Gene Transfer (HGT))

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22 pages, 2713 KiB

Open AccessArticle

Analysis of Complete Genome Sequence of Acinetobacter baumannii Strain ATCC 19606 Reveals Novel Mobile Genetic Elements and Novel Prophage

by Mohammad Hamidian, Lucia Blasco, Lauren N. Tillman, Joyce To, María Tomas and Garry S. A. Myers

Microorganisms 2020, 8(12), 1851; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8121851 - 24 Nov 2020

Cited by 13 | Viewed by 3862

Abstract

Acinetobacter baumannii isolate ATCC 19606 was recovered in the US prior to 1948. It has been used as a reference and model organism in many studies involving antibiotic resistance and pathogenesis of A. baumannii, while, until recently, a complete genome of this strain was not available. Here, we present an analysis of the complete 3.91-Mbp genome sequence, generated via a combination of short-read sequencing (Illumina) and long-read sequencing (MinION), and show it contains two small cryptic plasmids and a novel complete prophage of size 41.2 kb. We also characterised several regions of the ATCC 19606 genome, leading to the identification of a novel cadmium/mercury transposon, which was named Tn6551. ATCC 19606 is an antibiotic-sensitive strain, but a comparative analysis of all publicly available ST52 strains predicts a resistance to modern antibiotics by the accumulation of antibiotic-resistance genes via plasmids in recent isolates that belong to this sequence type. Full article

(This article belongs to the Special Issue Bacterial Genomes and Evolution by Horizontal Gene Transfer (HGT))

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13 pages, 1308 KiB

Open AccessArticle

Multidrug-Resistant Proteus mirabilis Strain with Cointegrate Plasmid

by Andrey Shelenkov, Lyudmila Petrova, Valeria Fomina, Mikhail Zamyatin, Yulia Mikhaylova and Vasiliy Akimkin

Microorganisms 2020, 8(11), 1775; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8111775 - 12 Nov 2020

Cited by 15 | Viewed by 3264

Abstract

Proteus mirabilis is a component of the normal intestinal microflora of humans and animals, but can cause urinary tract infections and even sepsis in hospital settings. In recent years, the number of multidrug-resistant P. mirabilis isolates, including the ones producing extended-spectrum β-lactamases (ESBLs), is increasing worldwide. However, the number of investigations dedicated to this species, especially, whole-genome sequencing, is much lower in comparison to the members of the ESKAPE pathogens group. This study presents a detailed analysis of clinical multidrug-resistant ESBL-producing P. mirabilis isolate using short- and long-read whole-genome sequencing, which allowed us to reveal possible horizontal gene transfer between Klebsiella pneumoniae and P. mirabilis plasmids and to locate the CRISPR-Cas system in the genome together with its probable phage targets, as well as multiple virulence genes. We believe that the data presented will contribute to the understanding of antibiotic resistance acquisition and virulence mechanisms for this important pathogen. Full article

(This article belongs to the Special Issue Bacterial Genomes and Evolution by Horizontal Gene Transfer (HGT))

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17 pages, 2257 KiB

Open AccessArticle

Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald

by Hui-Li Zhang, Mbuya Sylvain Ntambo, Philippe C. Rott, Gongyou Chen, Li-Lan Chen, Mei-Ting Huang and San-Ji Gao

Microorganisms 2020, 8(2), 182; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8020182 - 28 Jan 2020

Cited by 16 | Viewed by 3578

Abstract

Leaf scald (caused by Xanthomonas albilineans) is an important bacterial disease affecting sugarcane in most sugarcane growing countries, including China. High genetic diversity exists among strains of X. albilineans from diverse geographic regions. To highlight the genomic features associated with X. albilineans from China, we sequenced the complete genome of a representative strain (Xa-FJ1) of this pathogen using the PacBio and Illumina platforms. The complete genome of strain Xa-FJ1 consists of a circular chromosome of 3,724,581 bp and a plasmid of 31,536 bp. Average nucleotide identity analysis revealed that Xa-FJ1 was closest to five strains from the French West Indies and the USA, particularly to the strain GPE PC73 from Guadeloupe. Comparative genomic analysis between Xa-FJ1 and GPE PC73 revealed prophage integration, homologous recombination, transposable elements, and a clustered regulatory interspaced short palindromic repeats (CRISPR) system that were linked with 16 insertions/deletions (InDels). Ten and 82 specific genes were found in Xa-FJ1 and GPE PC73, respectively, and some of these genes were subjected to phage-related proteins, zona occludens toxin, and DNA methyltransferases. Our findings highlight intra-species genetic variability of the leaf scald pathogen and provide additional genomic resources to investigate its fitness and virulence. Full article

(This article belongs to the Special Issue Bacterial Genomes and Evolution by Horizontal Gene Transfer (HGT))

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10 pages, 1570 KiB

Open AccessCommunication

Salmonella Genomic Island 1 is Broadly Disseminated within Gammaproteobacteriaceae

by Max Laurence Cummins, Mohammad Hamidian and Steven Philip Djordjevic

Microorganisms 2020, 8(2), 161; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8020161 - 23 Jan 2020

Cited by 22 | Viewed by 3611

Abstract

Salmonella genomic island 1 (SGI1) is an integrative mobilisable element that plays an important role in the capture and spread of multiple drug resistance. To date, SGI1 has been found in clinical isolates of Salmonella enterica serovars, Proteus mirabilis, Morganella morganii, Acinetobacter baumannii, Providencia stuartii, Enterobacter spp, and recently in Escherichia coli. SGI1 preferentially targets the 3´-end of trmE, a conserved gene found in the Enterobacteriaceae and among members of the Gammaproteobacteria. It is, therefore, hypothesised that SGI1 and SGI1-related elements (SGI1-REs) may have been acquired by diverse bacterial genera. Here, Bitsliced Genomic Signature Indexes (BIGSI) was used to screen the NCBI Sequence Read Archive (SRA) for putative SGI1-REs in Gammaproteobacteria. Novel SGI-REs were identified in diverse genera including Cronobacter spp, Klebsiella spp, and Vibrio spp and in two additional isolates of Escherichia coli. An extensively drug-resistant human clonal lineage of Klebsiella pneumoniae carrying an SGI1-RE in the United Kingdom and an SGI1-RE that lacks a class 1 integron were also identified. These findings provide insight into the origins of this diverse family of clinically important genomic islands and expand the knowledge of the potential host range of SGI1-REs within the Gammaproteobacteria. Full article

(This article belongs to the Special Issue Bacterial Genomes and Evolution by Horizontal Gene Transfer (HGT))

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