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Clinical Microbiology Reviews Jun 2019Hypervirulent (hvKp) is an evolving pathotype that is more virulent than classical (cKp). hvKp usually infects individuals from the community, who are often healthy.... (Review)
Review
Hypervirulent (hvKp) is an evolving pathotype that is more virulent than classical (cKp). hvKp usually infects individuals from the community, who are often healthy. Infections are more common in the Asian Pacific Rim but are occurring globally. hvKp infection frequently presents at multiple sites or subsequently metastatically spreads, often requiring source control. hvKp has an increased ability to cause central nervous system infection and endophthalmitis, which require rapid recognition and site-specific treatment. The genetic factors that confer hvKp's hypervirulent phenotype are present on a large virulence plasmid and perhaps integrative conjugal elements. Increased capsule production and aerobactin production are established hvKp-specific virulence factors. Similar to cKp, hvKp strains are becoming increasingly resistant to antimicrobials via acquisition of mobile elements carrying resistance determinants, and new hvKp strains emerge when extensively drug-resistant cKp strains acquire hvKp-specific virulence determinants, resulting in nosocomial infection. Presently, clinical laboratories are unable to differentiate cKp from hvKp, but recently, several biomarkers and quantitative siderophore production have been shown to accurately predict hvKp strains, which could lead to the development of a diagnostic test for use by clinical laboratories for optimal patient care and for use in epidemiologic surveillance and research studies.
Topics: Anti-Bacterial Agents; Bacterial Typing Techniques; Humans; Klebsiella Infections; Klebsiella pneumoniae; Virulence
PubMed: 31092506
DOI: 10.1128/CMR.00001-19 -
Clinical Microbiology Reviews Dec 2022This review serves as an update to the previous review by Brown-Elliott et al. published in 2006 (B. A. Brown-Elliott, J. M. Brown, P. S. Conville, and R. J. Wallace.... (Review)
Review
This review serves as an update to the previous review by Brown-Elliott et al. published in 2006 (B. A. Brown-Elliott, J. M. Brown, P. S. Conville, and R. J. Wallace. Jr., Clin Microbiol Rev 19:259-282, 2006, https://doi.org/10.1128/CMR.19.2.259-282.2006). Included is a discussion on the taxonomic expansion of the genus, current identification methods, and the impact of new technology (including matrix-assisted laser desorption ionization-time of flight [MALDI-TOF] and whole genome sequencing) on diagnosis and treatment. Clinical manifestations, the epidemiology, and geographic distribution are briefly discussed. An additional section on actinomycotic mycetoma is added to address this often-neglected disease.
Topics: Nocardia; Bacterial Typing Techniques; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 36314911
DOI: 10.1128/cmr.00027-21 -
Clinical Microbiology Reviews Sep 2020This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the... (Review)
Review
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
Topics: Bacteria; Bacterial Infections; Bacterial Typing Techniques; Clinical Laboratory Techniques; Humans; RNA, Ribosomal, 16S
PubMed: 32907806
DOI: 10.1128/CMR.00053-19 -
Current Opinion in Infectious Diseases Aug 2021The advancement of molecular techniques such as whole-genome sequencing (WGS) has revolutionized the field of bacterial strain typing, with important implications for... (Review)
Review
PURPOSE OF REVIEW
The advancement of molecular techniques such as whole-genome sequencing (WGS) has revolutionized the field of bacterial strain typing, with important implications for epidemiological surveillance and outbreak investigations. This review summarizes state-of-the-art techniques in strain typing and examines barriers faced by clinical and public health laboratories in implementing these new methodologies.
RECENT FINDINGS
WGS-based methodologies are on track to become the new 'gold standards' in bacterial strain typing, replacing traditional methods like pulsed-field gel electrophoresis and multilocus sequence typing. These new techniques have an improved ability to identify genetic relationships among organisms of interest. Further, advances in long-read sequencing approaches will likely provide a highly discriminatory tool to perform pangenome analyses and characterize relevant accessory genome elements, including mobile genetic elements carrying antibiotic resistance determinants in real time. Barriers to widespread integration of these approaches include a lack of standardized workflows and technical training.
SUMMARY
Genomic bacterial strain typing has facilitated a paradigm shift in clinical and molecular epidemiology. The increased resolution that these new techniques provide, along with epidemiological data, will facilitate the rapid identification of transmission routes with high confidence, leading to timely and effective deployment of infection control and public health interventions in outbreak settings.
Topics: Anti-Bacterial Agents; Bacterial Typing Techniques; Disease Outbreaks; Electrophoresis, Gel, Pulsed-Field; Genome, Bacterial; Humans; Molecular Epidemiology; Multilocus Sequence Typing
PubMed: 34039880
DOI: 10.1097/QCO.0000000000000743 -
Revista Chilena de Infectologia :... Apr 2020
Topics: Bacterial Typing Techniques; Comamonas; DNA, Bacterial
PubMed: 32730480
DOI: 10.4067/s0716-10182020000200147 -
Clinical Medicine (London, England) Sep 2019Although often underappreciated, a number of bacterial zoonoses are endemic in Africa. Of these, brucellosis, leptospirosis, Q fever, and rickettsioses are responsible... (Review)
Review
Although often underappreciated, a number of bacterial zoonoses are endemic in Africa. Of these, brucellosis, leptospirosis, Q fever, and rickettsioses are responsible for a substantial proportion of febrile illness among patients seeking hospital care. In this paper, we discuss the aetiology, epidemiology, clinical presentation, diagnosis, treatment and prevention of these bacterial zoonoses. To prevent and control bacterial zoonoses, strategies targeting both animals and humans are crucial. These may lead to better outcomes than strategies based exclusively on treatment of human infections. Such strategies are referred to as the 'One Health' approach; the collaborative effort of multiple disciplines to attain optimal health for people, animals and the environment.
Topics: Africa South of the Sahara; Animals; Anti-Bacterial Agents; Bacterial Typing Techniques; Fever; Gram-Negative Bacterial Infections; Humans; One Health; Zoonoses
PubMed: 31530684
DOI: 10.7861/clinmed.2019-0180 -
Current Issues in Molecular Biology Jul 2021Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is routinely used for bacterial identification. It would be highly beneficial... (Review)
Review
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is routinely used for bacterial identification. It would be highly beneficial to also be able to use the technology as a fast way to detect clinically relevant clones of bacterial species. However, studies to this aim have often had limited success. The methods used for data acquisition, processing and data interpretation are highly diverse amongst studies on MALDI-TOF MS sub-species typing. In addition to this, feasibility may depend on the bacterial species and strains investigated, making it difficult to determine what methods may or may not work. In our paper, we have reviewed recent research on MALDI-TOF MS typing of bacterial strains. Although we found a lot of variation amongst the methods used, there were approaches shared by multiple research groups. Multiple spectra of the same isolate were often combined before further analysis for strain distinction. Many groups used a protein extraction step to increase resolution in their MALDI-TOF MS results. Peaks at a high mass range were often excluded for data interpretation. Three groups have found ways to determine feasibility of MALDI-TOF MS typing for their set of strains at an early stage of their project.
Topics: Animals; Bacteria; Bacterial Proteins; Bacterial Typing Techniques; Humans; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 34294671
DOI: 10.3390/cimb43020054 -
Microbial Genomics Aug 2021Whole-genome sequencing is becoming the standard for bacterial outbreak surveillance and infection prevention. This is accompanied by a variety of bioinformatic tools...
Whole-genome sequencing is becoming the standard for bacterial outbreak surveillance and infection prevention. This is accompanied by a variety of bioinformatic tools and needs bioinformatics expertise for implementation. However, little is known about the concordance of reported outbreaks when using different bioinformatic workflows. In this multi-centre proficiency testing among 13 major Dutch healthcare-affiliated centres, bacterial whole-genome outbreak analysis was assessed. Centres who participated obtained two randomized bacterial datasets of Illumina sequences, a and a Vancomycin-resistant and were asked to apply their bioinformatic workflows. Centres reported back on antimicrobial resistance, multi-locus sequence typing (MLST), and outbreak clusters. The reported clusters were analysed using a method to compare landscapes of phylogenetic trees and calculating Kendall-Colijn distances. Furthermore, fasta files were analysed by state-of-the-art single nucleotide polymorphism (SNP) analysis to mitigate the differences introduced by each centre and determine standardized SNP cut-offs. Thirteen centres participated in this study. The reported outbreak clusters revealed discrepancies between centres, even when almost identical bioinformatic workflows were used. Due to stringent filtering, some centres failed to detect extended-spectrum beta-lactamase genes and MLST loci. Applying a standardized method to determine outbreak clusters on the reported assemblies, did not result in uniformity of outbreak-cluster composition among centres.
Topics: Bacterial Typing Techniques; Computational Biology; Decision Making; Disease Outbreaks; Genome, Bacterial; Infection Control; Klebsiella pneumoniae; Multilocus Sequence Typing; Phylogeny; Polymorphism, Single Nucleotide; Vancomycin-Resistant Enterococci; Whole Genome Sequencing
PubMed: 34356004
DOI: 10.1099/mgen.0.000612 -
International Journal of Systematic and... Sep 2021The definition of a genus has wide-ranging implications both in terms of binomial species names and also evolutionary relationships. In recent years, the definition of...
The definition of a genus has wide-ranging implications both in terms of binomial species names and also evolutionary relationships. In recent years, the definition of the genus has been debated due to the proposed split of this genus into five new genera (, , , and an emended ). Since this group of species contains many important obligate and opportunistic pathogens, it is important that any renaming of species does not cause confusion in clinical treatment as outlined by the rule (56a) of the Prokaryotic Code. In this study, we evaluated the proposed and original genus boundaries for the mycobacteria, to determine if the split into five genera was warranted. By combining multiple approaches for defining genus boundaries (16S rRNA gene similarity, amino acid identity index, average nucleotide identity, alignment fraction and percentage of conserved proteins) we show that the original genus is strongly supported over the proposed five-way split. Thus, we propose that the original genus label be reapplied to all species within this group, with the proposed five genera potentially used as sub-genus complex names.
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Mycobacterium; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 34554081
DOI: 10.1099/ijsem.0.004922 -
BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking.Nucleic Acids Research Jan 2021An increasing prevalence of hospital acquired infections and foodborne illnesses caused by pathogenic and multidrug-resistant bacteria has stimulated a pressing need for...
An increasing prevalence of hospital acquired infections and foodborne illnesses caused by pathogenic and multidrug-resistant bacteria has stimulated a pressing need for benchtop computational techniques to rapidly and accurately classify bacteria from genomic sequence data, and based on that, to trace the source of infection. BacWGSTdb (http://bacdb.org/BacWGSTdb) is a free publicly accessible database we have developed for bacterial whole-genome sequence typing and source tracking. This database incorporates extensive resources for bacterial genome sequencing data and the corresponding metadata, combined with specialized bioinformatics tools that enable the systematic characterization of the bacterial isolates recovered from infections. Here, we present BacWGSTdb 2.0, which encompasses several major updates, including (i) the integration of the core genome multi-locus sequence typing (cgMLST) approach, which is highly scalable and appropriate for typing isolates belonging to different lineages; (ii) the addition of a multiple genome analysis module that can process dozens of user uploaded sequences in a batch mode; (iii) a new source tracking module for comparing user uploaded plasmid sequences to those deposited in the public databases; (iv) the number of species encompassed in BacWGSTdb 2.0 has increased from 9 to 20, which represents bacterial pathogens of medical importance; (v) a newly designed, user-friendly interface and a set of visualization tools for providing a convenient platform for users are also included. Overall, the updated BacWGSTdb 2.0 bears great utility in continuing to provide users, including epidemiologists, clinicians and bench scientists, with a one-stop solution to bacterial genome sequence analysis.
Topics: Bacteria; Databases, Genetic; Genome, Bacterial; Internet; Multilocus Sequence Typing; User-Computer Interface; Whole Genome Sequencing
PubMed: 33010178
DOI: 10.1093/nar/gkaa821