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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 -
Anaerobe Oct 2018Clostridium perfringens causes many different histotoxic and enterotoxic diseases in humans and animals as a result of its ability to produce potent protein toxins, many... (Review)
Review
Clostridium perfringens causes many different histotoxic and enterotoxic diseases in humans and animals as a result of its ability to produce potent protein toxins, many of which are extracellular. The current scheme for the classification of isolates was finalized in the 1960s and is based on their ability to produce a combination of four typing toxins - α-toxin, β-toxin, ε-toxin and ι-toxin - to divide C. perfringens strains into toxinotypes A to E. However, this scheme is now outdated since it does not take into account the discovery of other toxins that have been shown to be required for specific C. perfringens-mediated diseases. We present a long overdue revision of this toxinotyping scheme. The principles for the expansion of the typing system are described, as is a mechanism by which new toxinotypes can be proposed and subsequently approved. Based on these criteria two new toxinotypes have been established. C. perfringens type F consists of isolates that produce C. perfringens enterotoxin (CPE), but not β-toxin, ε-toxin or ι-toxin. Type F strains will include strains responsible for C. perfringens-mediated human food poisoning and antibiotic associated diarrhea. C. perfringens type G comprises isolates that produce NetB toxin and thereby cause necrotic enteritis in chickens. There are at least two candidates for future C. perfringens toxinotypes, but further experimental work is required before these toxinotypes can formally be proposed and accepted.
Topics: Animals; Bacterial Toxins; Bacterial Typing Techniques; Clostridium Infections; Clostridium perfringens; Humans
PubMed: 29866424
DOI: 10.1016/j.anaerobe.2018.04.011 -
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 -
Fertility and Sterility Jul 2017Detection of bacteria with molecular techniques has enabled the study of low biomass microbiomes in tissues and organs previously considered sterile, such as the... (Review)
Review
Detection of bacteria with molecular techniques has enabled the study of low biomass microbiomes in tissues and organs previously considered sterile, such as the endometrium. Subsequently, an abnormal endometrial microbiota has been associated with implantation failure, pregnancy loss, and other gynecological and obstetrical conditions. Further investigation of the reproductive tract microbiome will allow for a better understanding of bacterial communities' role in both physiology and pathophysiology, which in turn impacts the ability to achieve pregnancy and maintain a healthy pregnancy. Here we review the current literature that surrounds the endometrial microbiome and highlight the importance of assessing it as a future tool for improving reproductive outcomes in infertile patients.
Topics: Animals; Bacterial Typing Techniques; Embryo Implantation; Embryo Transfer; Endometrium; Evidence-Based Medicine; Female; Fertilization in Vitro; Humans; Infertility, Female; Menstrual Cycle; Microbiota; Models, Immunological; Pregnancy; Recurrence; Species Specificity; Transcriptome; Treatment Failure
PubMed: 28602480
DOI: 10.1016/j.fertnstert.2017.05.034 -
Frontiers in Cellular and Infection... 2016The empirical and pragmatic nature of diagnostic microbiology has given rise to several different schemes to subtype .coli, including biotyping, serotyping, and... (Review)
Review
The empirical and pragmatic nature of diagnostic microbiology has given rise to several different schemes to subtype .coli, including biotyping, serotyping, and pathotyping. These schemes have proved invaluable in identifying and tracking outbreaks, and for prognostication in individual cases of infection, but they are imprecise and potentially misleading due to the malleability and continuous evolution of . Whole genome sequencing can be used to accurately determine subtypes that are based on allelic variation or differences in gene content, such as serotyping and pathotyping. Whole genome sequencing also provides information about single nucleotide polymorphisms in the core genome of , which form the basis of sequence typing, and is more reliable than other systems for tracking the evolution and spread of individual strains. A typing scheme for based on genome sequences that includes elements of both the core and accessory genomes, should reduce typing anomalies and promote understanding of how different varieties of spread and cause disease. Such a scheme could also define pathotypes more precisely than current methods.
Topics: Adhesins, Bacterial; Bacterial Typing Techniques; Base Sequence; DNA, Bacterial; Diarrhea; Disease Outbreaks; Enterohemorrhagic Escherichia coli; Enteropathogenic Escherichia coli; Enterotoxigenic Escherichia coli; Escherichia coli; Escherichia coli Infections; Escherichia coli Proteins; Evolution, Molecular; GTP-Binding Proteins; Genes, Bacterial; Genome, Bacterial; Humans; Molecular Typing; Phylogeny; Polymorphism, Single Nucleotide; RNA-Binding Proteins; Sequence Analysis, DNA; Serotyping; Virulence
PubMed: 27917373
DOI: 10.3389/fcimb.2016.00141 -
Infection, Genetics and Evolution :... Sep 2018Next-generation sequencing (NGS), also known as high-throughput sequencing, is changing the field of microbial genomics research. NGS allows for a more comprehensive... (Review)
Review
Next-generation sequencing (NGS), also known as high-throughput sequencing, is changing the field of microbial genomics research. NGS allows for a more comprehensive analysis of the diversity, structure and composition of microbial genes and genomes compared to the traditional automated Sanger capillary sequencing at a lower cost. NGS strategies have expanded the versatility of standard and widely used typing approaches based on nucleotide variation in several hundred DNA sequences and a few gene fragments (MLST, MLVA, rMLST and cgMLST). NGS can now accommodate variation in thousands or millions of sequences from selected amplicons to full genomes (WGS, NGMLST and HiMLST). To extract signals from high-dimensional NGS data and make valid statistical inferences, novel analytic and statistical techniques are needed. In this review, we describe standard and new approaches for microbial sequence typing at gene and genome levels and guidelines for subsequent analysis, including methods and computational frameworks. We also present several applications of these approaches to some disciplines, namely genotyping, phylogenetics and molecular epidemiology.
Topics: Alleles; Bacterial Infections; Bacterial Typing Techniques; Clone Cells; Genome, Bacterial; Gram-Negative Bacteria; Gram-Positive Bacteria; Guidelines as Topic; High-Throughput Nucleotide Sequencing; Humans; Minisatellite Repeats; Molecular Epidemiology; Multilocus Sequence Typing; Phylogeny; Polymorphism, Single Nucleotide; Sequence Analysis, DNA
PubMed: 28943406
DOI: 10.1016/j.meegid.2017.09.022 -
FEBS Letters Nov 2016An increasing body of evidence indicates the relevance of microbiota for pulmonary health and disease. Independent investigations recently demonstrated that the lung... (Review)
Review
An increasing body of evidence indicates the relevance of microbiota for pulmonary health and disease. Independent investigations recently demonstrated that the lung harbors a resident microbiota. Therefore, it is intriguing that a lung microbiota can shape pulmonary immunity and epithelial barrier functions. Here, we discuss the ways how the composition of the microbial community in the lung may influence pulmonary health and vice versa, factors that determine community composition. Prominent microbiota at other body sites such as the intestinal one may also contribute to pulmonary health and disease. However, it is difficult to discriminate between influences of lung vs. gut microbiota due to systemic mutuality between both communities. With focuses on asthma and respiratory infections, we discuss how microbiota of lung and gut can determine pulmonary immunity and barrier functions.
Topics: Bacterial Typing Techniques; Host-Pathogen Interactions; Humans; Intestines; Lung; Microbiota; Respiratory Tract Infections
PubMed: 27637588
DOI: 10.1002/1873-3468.12421 -
Proteomics. Clinical Applications Apr 2016Identification and typing of bacteria occupy a large fraction of time and work in clinical microbiology laboratories. With the certification of some MS platforms in... (Review)
Review
Identification and typing of bacteria occupy a large fraction of time and work in clinical microbiology laboratories. With the certification of some MS platforms in recent years, more applications and tests of MS-based diagnosis methods for bacteria identification and typing have been created, not only on well-accepted MALDI-TOF-MS-based fingerprint matches, but also on solving the insufficiencies of MALDI-TOF-MS-based platforms and advancing the technology to areas such as targeted MS identification and typing of bacteria, bacterial toxin identification, antibiotics susceptibility/resistance tests, and MS-based diagnostic method development on unique bacteria such as Clostridium and Mycobacteria. This review summarizes the recent development in MS platforms and applications in bacteria identification and typing of common pathogenic bacteria.
Topics: Bacterial Toxins; Bacterial Typing Techniques; Campylobacter jejuni; Clostridium; Escherichia coli; Humans; Listeria monocytogenes; Microbial Sensitivity Tests; Mycobacteriaceae; Peptide Fragments; Proteolysis; Proteomics; Salmonella; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Trypsin
PubMed: 26751976
DOI: 10.1002/prca.201500086