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Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic Resistance Spreading

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Antimicrobial Agents and Resistance".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 33140

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Dr. Andrew Shelenkov

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Guest Editor

Central Research Institute of Epidemiology, Moscow, Russia
Interests: bioinformatics; NGS; ESKAPE pathogens; genomic epidemiology; antibiotic resistance; antimicrobial peptides
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Antibiotic resistance acquisition by pathogenic and opportunistic bacteria has become a major problem worldwide, which was already noticed as a global healthcare threat by the World Health Organization. The spread of multidrug-resistant bacteria, especially the ones producing extended-spectrum β-lactamases (ESBLs), represents a major challenge in clinical settings. However, the mechanisms of antibiotic resistance acquisition and spreading among different bacterial species cannot be easily revealed by traditional phenotypic analyses. Whole-genome sequencing (short- and long-read) currently attracts an increasing attention since it allows to accurately and rapidly obtain the data regarding the presence of specific antibiotic resistance genes and their locations in a bacterial genome (chromosomal or plasmid). Plasmid reconstruction using long-read sequencing data can provide essential information regarding the mechanisms of antibiotic resistance acquisition and the ways of its spreading across different species and world regions.

For this Special Issue, we therefore invite you to contribute original research and review papers describing the application of whole-genome sequencing of bacterial pathogens to revealing antimicrobial resistance genes, comparing phenotypic and genomic resistance profiles, reconstructing plasmids, performing epidemiological surveillance and elucidating the mechanisms and/or ways of antimicrobial resistance spreading and acquisition. Novel computational approaches and pipelines for performing such investigations are particularly welcome.

Dr. Andrew Shelenkov
Guest Editor

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Keywords

whole genome sequencing
pathogenic bacteria
antibiotic resistance
genomic epidemiology
bioinformatics
antimicrobial resistance prediction
plasmid assembly

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Published Papers (9 papers)

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Editorial

Jump to: Research

4 pages, 174 KiB

Open AccessEditorial

Whole-Genome Sequencing of Pathogenic Bacteria—New Insights into Antibiotic Resistance Spreading

by Andrey Shelenkov

Microorganisms 2021, 9(12), 2624; https://doi.org/10.3390/microorganisms9122624 - 19 Dec 2021

Cited by 5 | Viewed by 2861

Abstract

In recent years, the acquisition of antimicrobial resistance (AMR) by both pathogenic and opportunistic bacteria has become a major problem worldwide, which was already noticed as a global healthcare threat by the World Health Organization [...] Full article

(This article belongs to the Special Issue Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic Resistance Spreading)

Research

Jump to: Editorial

15 pages, 4106 KiB

Open AccessArticle

Complete Genome Sequence Analysis of Kribbella sp. CA-293567 and Identification of the Kribbellichelins A & B and Sandramycin Biosynthetic Gene Clusters

by Marina Sánchez-Hidalgo, María Jesús García, Ignacio González, Daniel Oves-Costales and Olga Genilloud

Microorganisms 2023, 11(2), 265; https://doi.org/10.3390/microorganisms11020265 - 19 Jan 2023

Cited by 1 | Viewed by 3120

Abstract

Minor genera actinomycetes are considered a promising source of new secondary metabolites. The strain Kribbella sp. CA-293567 produces sandramycin and kribbellichelins A & B In this work, we describe the complete genome sequencing of this strain and the in silico identification of biosynthetic gene clusters (BGCs), focusing on the pathways encoding sandramycin and kribbellichelins A–B. We also present a comparative analysis of the biosynthetic potential of 38 publicly available genomes from Kribbella strains. Full article

(This article belongs to the Special Issue Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic Resistance Spreading)

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18 pages, 2553 KiB

Open AccessArticle

Hybrid Genomic Analysis of Salmonella enterica Serovar Enteritidis SE3 Isolated from Polluted Soil in Brazil

by Danitza Xiomara Romero-Calle, Francisnei Pedrosa-Silva, Luiz Marcelo Ribeiro Tomé, Thiago J. Sousa, Leila Thaise Santana de Oliveira Santos, Vasco Ariston de Carvalho Azevedo, Bertram Brenig, Raquel Guimarães Benevides, Thiago M. Venancio, Craig Billington and Aristóteles Góes-Neto

Microorganisms 2023, 11(1), 111; https://doi.org/10.3390/microorganisms11010111 - 31 Dec 2022

Cited by 2 | Viewed by 2814

Abstract

In Brazil, Salmonella enterica serovar Enteritidis is a significant health threat. Salmonella enterica serovar Enteritidis SE3 was isolated from soil at the Subaé River in Santo Amaro, Brazil, a region contaminated with heavy metals and organic waste. Illumina HiSeq and Oxford Nanopore Technologies MinION sequencing were used for de novo hybrid assembly of the Salmonella SE3 genome. This approach yielded 10 contigs with 99.98% identity with S. enterica serovar Enteritidis OLF-SE2-98984-6. Twelve Salmonella pathogenic islands, multiple virulence genes, multiple antimicrobial gene resistance genes, seven phage defense systems, seven prophages and a heavy metal resistance gene were encoded in the genome. Pangenome analysis of the S. enterica clade, including Salmonella SE3, revealed an open pangenome, with a core genome of 2137 genes. Our study showed the effectiveness of a hybrid sequence assembly approach for environmental Salmonella genome analysis using HiSeq and MinION data. This approach enabled the identification of key resistance and virulence genes, and these data are important to inform the control of Salmonella and heavy metal pollution in the Santo Amaro region of Brazil. Full article

(This article belongs to the Special Issue Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic Resistance Spreading)

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15 pages, 5510 KiB

Open AccessArticle

Identification of Novel Antimicrobial Resistance Genes Using Machine Learning, Homology Modeling, and Molecular Docking

by Janak Sunuwar and Rajeev K. Azad

Microorganisms 2022, 10(11), 2102; https://doi.org/10.3390/microorganisms10112102 - 23 Oct 2022

Cited by 8 | Viewed by 3148

Abstract

Antimicrobial resistance (AMR) threatens the healthcare system worldwide with the rise of emerging drug resistant infectious agents. AMR may render the current therapeutics ineffective or diminish their efficacy, and its rapid dissemination can have unmitigated health and socioeconomic consequences. Just like with many other health problems, recent computational advances including developments in machine learning or artificial intelligence hold a prodigious promise in deciphering genetic factors underlying emergence and dissemination of AMR and in aiding development of therapeutics for more efficient AMR solutions. Current machine learning frameworks focus mainly on known AMR genes and are, therefore, prone to missing genes that have not been implicated in resistance yet, including many uncharacterized genes whose functions have not yet been elucidated. Furthermore, new resistance traits may evolve from these genes leading to the rise of superbugs, and therefore, these genes need to be characterized. To infer novel resistance genes, we used complete gene sets of several bacterial strains known to be susceptible or resistant to specific drugs and associated phenotypic information within a machine learning framework that enabled prioritizing genes potentially involved in resistance. Further, homology modeling of proteins encoded by prioritized genes and subsequent molecular docking studies indicated stable interactions between these proteins and the antimicrobials that the strains containing these proteins are known to be resistant to. Our study highlights the capability of a machine learning framework to uncover novel genes that have not yet been implicated in resistance to any antimicrobials and thus could spur further studies targeted at neutralizing AMR. Full article

(This article belongs to the Special Issue Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic Resistance Spreading)

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11 pages, 286 KiB

Open AccessArticle

Whole Genome Sequence Analysis of Multidrug Resistant Escherichia coli and Klebsiella pneumoniae Strains in Kuwait

by Ola H. Moghnia and Nourah A. Al-Sweih

Microorganisms 2022, 10(3), 507; https://doi.org/10.3390/microorganisms10030507 - 25 Feb 2022

Cited by 11 | Viewed by 4107

Abstract

The spread of carbapenem-resistant Escherichia coli and Klebsiella pneumoniae is a global concern. The management of infections caused by multidrug resistance (MDR) isolates poses substantial clinical challenges in both hospitals and communities. This study aimed to investigate the genetic characteristics and variations of MDR E. coli and K. pneumoniae isolates. Bacterial identification and antibiotic susceptibility testing against 19 antibiotics were performed by standard methods. Whole genome sequencing (WGS) was carried out on eight carbapenem-resistant isolates using an Illumina MiSeq platform. The assembled draft genomes were annotated, then sequences were blasted against antimicrobial resistance (AMR) genes database. WGS detected several resistance genes mediating the production of β-lactamases, including carbapenems and extended-spectrum β-lactamase genes as (bla_OXA-1/-48, bla_KPC-2/-29, bla_CMY-4/-6, bla_SHV-11/-12, bla_TEM-1, bla_CTX-M-15, bla_OKP-B, bla_ACT and bla_EC). Furthermore quinolone resistance including oqxA/oqxB, aac(6′)-Ib-cr5, gyrA_D87N, gyrA_S83F, gyrA_S83L, parC_S80I, parE_S458A, parE_I355T, parC_S80I, and qnrB1. In addition to aminoglycoside modifying enzymes genes (aph(6)-Id, aph(3″)-Ib, aac(3)-IIa, aac(6′)-Ib, aadA1, aadA2 and aadA5), trimethoprim-sulfamethoxazole (dfrA12/A14/A17 and sul1/sul2), tetracycline (tetA and tetB), fosfomycin (fosA and uhpT_E350Q) resistance genes, while other genes were detected conferring chloramphenicol (floR, catA2, and efflux pump cmIA5), macrolides resistance (mph(A) and erm(B), and quaternary ammonium efflux pump qacEdelta. Bleomycin and colistin resistance genes were detected as ble and pmrB_R256G, respectively. Comprehensive analysis of MDR strains provided by WGS detected variable antimicrobial resistance genes and their precise resistance mechanism. WGS is essential for control and prevention strategies to combat the growing threat of AMR and the implementation of multifaceted interventions are needed. Full article

(This article belongs to the Special Issue Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic Resistance Spreading)

14 pages, 2967 KiB

Open AccessArticle

Comparison of Reference-Based Assembly and De Novo Assembly for Bacterial Plasmid Reconstruction and AMR Gene Localization in Salmonella enterica Serovar Schwarzengrund Isolates

by I-Chen Li, Gine-Ye Yu, Jing-Fang Huang, Zeng-Weng Chen and Chung-Hsi Chou

Microorganisms 2022, 10(2), 227; https://doi.org/10.3390/microorganisms10020227 - 20 Jan 2022

Cited by 3 | Viewed by 3468

Abstract

It is well established that plasmids carrying multiple antimicrobial resistance (AMR) genes can be easily transferred among bacterial isolates by horizontal gene transfer. Previous studies have shown that a combination of short- and long-read approaches is effective in reconstructing accurate plasmids. However, high-quality Illumina short reads mapped onto the long reads in the context of an AMR hybrid monitoring strategy have not yet been explored. Hence, this study aimed to improve the reconstruction of plasmids, including the localization of AMR genes, using the above-described parameters on whole-genome sequencing (WGS) results. To the best of our knowledge, this study is the first to use S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) to confirm the number and sizes of plasmids detected by in silico-based predictions in Salmonella strains. Our results showed that de novo assembly did not detect the number of bacterial plasmids more accurately than reference-based assembly did. As this new hybrid mapping strategy surpassed de novo assembly in bacterial reconstruction, it was further used to identify the presence and genomic location of AMR genes among three Salmonella enterica serovar Schwarzengrund isolates. The AMR genes identified in the bacterial chromosome among the three Salmonella enterica serovar Schwarzengrund isolates included: AAC(3)-IV, AAC(6′)-Iy, aadA2, APH(4)-Ia, cmlA1, golS, mdsA, mdsB, mdsC, mdtK, qacH, sdiA, sul2, sul3, and TEM-1 genes. Moreover, the presence of TEM-1, AAC(3)-IV, aadA2, APH(4)-Ia, cmlA1, dfrA12, floR, sul1, sul3, and tet(A) genes found within three IncFIB plasmids and one IncX1 plasmid highlight their possible transmission into the environment, which is a public health risk. In conclusion, the generated data using this new hybrid mapping strategy will contribute to the improvement of AMR monitoring and support the risk assessment of AMR dissemination. Full article

(This article belongs to the Special Issue Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic Resistance Spreading)

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17 pages, 2024 KiB

Open AccessArticle

Comparative Whole-Genome Analysis of Russian Foodborne Multidrug-Resistant Salmonella Infantis Isolates

by Anna Egorova, Yulia Mikhaylova, Stepan Saenko, Marina Tyumentseva, Aleksandr Tyumentsev, Konstantin Karbyshev, Aleksey Chernyshkov, Igor Manzeniuk, Vasiliy Akimkin and Andrey Shelenkov

Microorganisms 2022, 10(1), 89; https://doi.org/10.3390/microorganisms10010089 - 31 Dec 2021

Cited by 15 | Viewed by 2924

Abstract

Non-typhoidal Salmonella infections remain a significant public health problem worldwide. In this study, we present the first detailed genomic analysis report based on short-read (Illumina) whole-genome sequencing (WGS) of 45 multidrug-resistant (MDR) Salmonella enterica subsp. enterica serotype Infantis isolates from poultry and meat product samples obtained in Russia during 2018–2020, and long-read (MinION) WGS of five more representative isolates. We sought to determine whether foodborne S. Infantis have acquired new characteristics, traits, and dynamics in MDR growth in recent years. All sequenced isolates belonged to the sequence type ST32 and more than the half of isolates was characterized by six similar antimicrobial susceptibility profiles, most of which corresponded well with the antimicrobial resistance determinants to aminoglycosides, sulphonamides, tetracycline, and chloramphenicol revealed in silico. Some of the isolates were characterized by the presence of several types of plasmids simultaneously. Plasmid typing using WGS revealed Col440I, ColpVC, ColRNAI, IncFIB, IncFII, IncX1, IncHI2, IncHI2A, and IncN replicons. The identified virulence genes for 45 whole genomes of S. Infantis were similar and included 129 genes encoding structural components of the cell, factors responsible for successful invasion of the host, and secreted products. These data will be a valuable contribution to further comparative genomics of S. Infantis circulating in Russia, as well as to epidemiological surveillance of foodborne Salmonella isolates and investigations of Salmonella outbreaks. Full article

(This article belongs to the Special Issue Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic Resistance Spreading)

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18 pages, 1060 KiB

Open AccessArticle

Hybrid Assembly Provides Improved Resolution of Plasmids, Antimicrobial Resistance Genes, and Virulence Factors in Escherichia coli and Klebsiella pneumoniae Clinical Isolates

by Abdolrahman Khezri, Ekaterina Avershina and Rafi Ahmad

Microorganisms 2021, 9(12), 2560; https://doi.org/10.3390/microorganisms9122560 - 10 Dec 2021

Cited by 25 | Viewed by 5436

Abstract

Emerging new sequencing technologies have provided researchers with a unique opportunity to study factors related to microbial pathogenicity, such as antimicrobial resistance (AMR) genes and virulence factors. However, the use of whole-genome sequence (WGS) data requires good knowledge of the bioinformatics involved, as well as the necessary techniques. In this study, a total of nine Escherichia coli and Klebsiella pneumoniae isolates from Norwegian clinical samples were sequenced using both MinION and Illumina platforms. Three out of nine samples were sequenced directly from blood culture, and one sample was sequenced from a mixed-blood culture. For genome assembly, several long-read, (Canu, Flye, Unicycler, and Miniasm), short-read (ABySS, Unicycler and SPAdes) and hybrid assemblers (Unicycler, hybridSPAdes, and MaSurCa) were tested. Assembled genomes from the best-performing assemblers (according to quality checks using QUAST and BUSCO) were subjected to downstream analyses. Flye and Unicycler assemblers performed best for the assembly of long and short reads, respectively. For hybrid assembly, Unicycler was the top-performing assembler and produced more circularized and complete genome assemblies. Hybrid assembled genomes performed substantially better in downstream analyses to predict putative plasmids, AMR genes and β-lactamase gene variants, compared to MinION and Illumina assemblies. Thus, hybrid assembly has the potential to reveal factors related to microbial pathogenicity in clinical and mixed samples. Full article

(This article belongs to the Special Issue Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic Resistance Spreading)

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13 pages, 1921 KiB

Open AccessArticle

Mobile Colistin Resistance Genetic Determinants of Non-Typhoid Salmonella enterica Isolates from Russia

by Konstantin V. Kuleshov, Anastasia S. Pavlova, Elizaveta D. Shedko, Yulia V. Mikhaylova, Gabriele Margos, Sabrina Hepner, Igor V. Chebotar, Elena V. Korneenko, Alexander T. Podkolzin and Vasiliy G. Akimkin

Microorganisms 2021, 9(12), 2515; https://doi.org/10.3390/microorganisms9122515 - 4 Dec 2021

Cited by 7 | Viewed by 3251

Abstract

Polymyxin resistance, determined by mcr genes located on plasmid DNA, currently poses a high epidemiological threat. Non-typhoid Salmonella (NTS) are one of the key pathogens causing diarrheal diseases. Here, we report the isolation and whole genome sequencing of multidrug colistin-resistant/susceptible isolates of non-typhoid Salmonella enterica serovars carrying mcr genes. Non-typhoid strains of Salmonella enterica subsp. enterica were isolated during microbiological monitoring of the environment, food, and diarrheal disease patients between 2018 and 2020 in Russia (n = 586). mcr-1 genes were detected using a previously developed qPCR assay, and whole genome sequencing of mcr positive isolates was performed by both short-read (Illumina) and long-read (Oxford Nanopore) approaches. Three colistin-resistant isolates, including two isolates of S. Enteritidis and one isolate of S. Bovismorbificans, carried the mcr-1.1 gene located on IncX4 and IncI2 conjugative plasmids, respectively. The phenotypically colistin-susceptible isolate of S. Typhimurium carried a mcr-9 gene on plasmid IncHI2. In conclusion, we present the first three cases of mcr gene-carrying NTS isolates detected in Russia with both outbreak and sporadic epidemiological backgrounds. Full article

(This article belongs to the Special Issue Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic Resistance Spreading)

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