scholarly journals A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae strains

2021 ◽  
Author(s):  
Melanie Hennart ◽  
Julien Guglielmini ◽  
Martin C.J. Maiden ◽  
Keith A. Jolley ◽  
Alexis Criscuolo ◽  
...  
Keyword(s):  
Public Health ◽  
Klebsiella Pneumoniae ◽  
Multilocus Sequence Typing ◽  
Population Biology ◽  
Basic Research ◽  
Epidemiological Surveillance ◽  
Bacterial Strains ◽  
Single Linkage ◽  
Genomic Taxonomy ◽  
Definition Of

Sublineages within microbial species can differ widely in their ecology and pathogenicity, and their precise definition is important in basic research and industrial or public health applications. Whereas the classification and naming of prokaryotes is unified at the species level and higher taxonomic ranks, universally accepted definitions of sublineages within species are largely missing, which introduces confusion in population biology and epidemiological surveillance. Here we propose a broadly applicable genomic classification and nomenclature approach for bacterial strains, using the prominent public health threat Klebsiella pneumoniae as a model. Based on a 629-gene core genome multilocus sequence typing (cgMLST) scheme, we devised a dual barcoding system that combines multilevel single linkage (MLSL) clustering and life identification numbers (LIN). Phylogenetic and clustering analyses of >7,000 genome sequences captured population structure discontinuities, which were used to guide the definition of 10 infra-specific genetic dissimilarity thresholds. The widely used 7-gene multilocus sequence typing (MLST) nomenclature was mapped onto MLSL sublineages (threshold: 190 allelic mismatches) and clonal group (threshold: 43) identifiers for backwards nomenclature compatibility. The taxonomy is publicly accessible through a community-curated platform (https://bigsdb.pasteur.fr/klebsiella), which also enables external users genomic sequences identification.

scholarly journals eBURST: Inferring Patterns of Evolutionary Descent among Clusters of Related Bacterial Genotypes from Multilocus Sequence Typing Data

2004 ◽  
Vol 186 (5) ◽  
pp. 1518-1530 ◽  
Author(s):  
Edward J. Feil ◽  
Bao C. Li ◽  
David M. Aanensen ◽  
William P. Hanage ◽  
Brian G. Spratt
Keyword(s):  
Multilocus Sequence Typing ◽  
Population Biology ◽  
Clonal Complex ◽  
Large Data ◽  
Realistic Model ◽  
Epidemiological Surveillance ◽  
Bootstrap Support ◽  
Data Sets ◽  
Data Set ◽  
Evolutionary Descent

ABSTRACT The introduction of multilocus sequence typing (MLST) for the precise characterization of isolates of bacterial pathogens has had a marked impact on both routine epidemiological surveillance and microbial population biology. In both fields, a key prerequisite for exploiting this resource is the ability to discern the relatedness and patterns of evolutionary descent among isolates with similar genotypes. Traditional clustering techniques, such as dendrograms, provide a very poor representation of recent evolutionary events, as they attempt to reconstruct relationships in the absence of a realistic model of the way in which bacterial clones emerge and diversify to form clonal complexes. An increasingly popular approach, called BURST, has been used as an alternative, but present implementations are unable to cope with very large data sets and offer crude graphical outputs. Here we present a new implementation of this algorithm, eBURST, which divides an MLST data set of any size into groups of related isolates and clonal complexes, predicts the founding (ancestral) genotype of each clonal complex, and computes the bootstrap support for the assignment. The most parsimonious patterns of descent of all isolates in each clonal complex from the predicted founder(s) are then displayed. The advantages of eBURST for exploring patterns of evolutionary descent are demonstrated with a number of examples, including the simple Spain23F-1 clonal complex of Streptococcus pneumoniae, “population snapshots” of the entire S. pneumoniae and Staphylococcus aureus MLST databases, and the more complicated clonal complexes observed for Campylobacter jejuni and Neisseria meningitidis.

scholarly journals Establishment of a Publicly Available Core Genome Multilocus Sequence Typing Scheme for Clostridium perfringens

2021 ◽  
Author(s):  
Mostafa Y. Abdel-Glil ◽  
Prasad Thomas ◽  
Jörg Linde ◽  
Keith A. Jolley ◽  
Dag Harmsen ◽  
...  
Keyword(s):  
High Resolution ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clostridium Perfringens ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Epidemiological Surveillance ◽  
Whole Genome ◽  
Bacterial Strains

Global epidemiological surveillance of bacterial pathogens is enhanced by the availability of standard tools and sharing of typing data. The use of whole-genome sequencing has opened the possibility for high-resolution characterization of bacterial strains down to the clonal and subclonal levels.

scholarly journals Hidden Host Plant Associations of Soilborne Fungal Pathogens: An Ecological Perspective

2013 ◽  
Vol 103 (6) ◽  
pp. 538-544 ◽  
Author(s):  
Glenna M. Malcolm ◽  
Gretchen A. Kuldau ◽  
Beth K. Gugino ◽  
María del Mar Jiménez-Gasco
Keyword(s):  
Host Plant ◽  
Population Biology ◽  
Fungal Pathogens ◽  
Current Knowledge ◽  
Vascular Plant ◽  
Disease Symptoms ◽  
Nonhost Plant ◽  
Plant Associations ◽  
Definition Of ◽  
Forest Plants

Much of the current knowledge on population biology and ecology of soilborne fungal pathogens has been derived from research based on populations recovered from plants displaying disease symptoms or soil associated with symptomatic plants. Many soilborne fungal pathogens are known to cause disease on a large number of crop plants, including a variety of important agronomical, horticultural, ornamental, and forest plants species. For instance, the fungus Verticillium dahliae causes disease on >400 host plants. From a phytopathological perspective, plants on which disease symptoms have not been yet observed are considered to be nonhosts for V. dahliae. This term may be misleading because it does not provide information regarding the nature of the plant–fungus association; that is, a nonhost plant may harbor the fungus as an endophyte. Yet, there are numerous instances in the literature where V. dahliae has been isolated from asymptomatic plants; thus, these plants should be considered hosts. In this article, we synthesize scattered research that indicates that V. dahliae, aside from being a successful and significant vascular plant pathogen, may have a cryptic biology on numerous asymptomatic plants as an endophyte. Thus, we suggest here that these endophytic associations among V. dahliae and asymptomatic plants are not unusual relationships in nature. We propose to embrace the broader ecology of many fungi by differentiating between “symptomatic hosts” as those plants in which the infection and colonization by a fungus results in disease, and “asymptomatic hosts” as those plants that harbor the fungus endophytically and are different than true nonhosts that should be used for plant species that do not interact with the given fungus. In fact, if we broaden our definition of “host plant” to include asymptomatic plants that harbor the fungus as an endophyte, it is likely that the host ranges for some soilborne fungal pathogens are much larger than previously envisioned. By ignoring the potential for soilborne fungal pathogens to display endophytic relationships, we leave gaps in our knowledge about the population biology and ecology, persistence, and spread of these fungi in agroecosystems.

Peri-urban water, sanitation and hygiene in Lusaka, Zambia: photovoice empowering local assessment via ecological theory

2021 ◽  
pp. 175797592199571
Author(s):  
Sikopo Nyambe ◽  
Taro Yamauchi
Keyword(s):  
Public Health ◽  
Public Policy ◽  
Health Hazard ◽  
Disease Outbreaks ◽  
Ecological Theory ◽  
Urban Slum ◽  
Health Concern ◽  
Minimal Impact ◽  
Sanitation And Hygiene ◽  
Definition Of

Water, sanitation and hygiene (WASH) factors are responsible for 11.4% of deaths in Zambia, making WASH a key public health concern. Despite annual waterborne disease outbreaks in the nation’s peri-urban (slum) settlements being linked to poor WASH, few studies have proactively analysed and conceptualised peri-urban WASH and its maintaining factors. Our study aimed to (a) establish residents’ definition of peri-urban WASH and their WASH priorities; and (b) use ecological theory to analyse the peri-urban WASH ecosystem, highlighting maintaining factors. Our study incorporated 16 young people (aged 17–24) residing in peri-urban Lusaka, Zambia in a photovoice exercise. Participants took photographs answering the framing question, ‘What is WASH in your community?’ Then, through contextualisation and basic codifying, participants told the stories of their photographs and made posters to summarise problems and WASH priorities. Participant contextualisation and codifying further underwent theoretical thematic analysis to pinpoint causal factors alongside key players, dissecting the peri-urban WASH ecosystem via the five-tier ecological theory ranging from intrapersonal to public policy levels. Via ecological theory, peri-urban WASH was defined as: (a) poor practice (intrapersonal, interpersonal); (b) a health hazard (community norm); (c) substandard and unregulated (public policy, organisational); and (d) offering hope for change (intrapersonal, interpersonal). Linked to these themes, participant findings revealed a community level gap, with public policy level standards, regulations and implementation having minimal impact on overall peri-urban WASH and public health due to shallow community engagement and poor acknowledgement of the WASH realities of high-density locations. Rather than a top-down approach, participants recommended increased government–resident collaboration, offering residents more ownership and empowerment for intervention, implementation and defending of preferred peri-urban WASH standards.

Epidemiological surveillance and performance assessment: the two roles of health indicators during the COVID-19 pandemic

2021 ◽  
Vol 17 (2) ◽  
pp. 186-203
Author(s):  
Nathan Genicot
Keyword(s):  
Public Health ◽  
Performance Assessment ◽  
Health Indicators ◽  
Health Policies ◽  
Epidemiological Surveillance ◽  
Public Health Policies ◽  
History Of ◽  
And Performance ◽  
The One ◽  
Massive Development

AbstractThe COVID-19 pandemic has given rise to the massive development and use of health indicators. Drawing on the history of international public health and of the management of infectious disease, this paper attempts to show that the normative power acquired by metrics during the pandemic can be understood in light of two rationales: epidemiological surveillance and performance assessment. On the one hand, indicators are established to evaluate and rank countries’ responses to the outbreak; on the other, the evolution of indicators has a direct influence on the content of public health policies. Although quantitative data are an absolute necessity for coping with such disasters, it is critical to bear in mind the inherent partiality and precarity of the information provided by health indicators. Given the growing importance of normative quantitative devices during the pandemic, and assuming that their influence is unlikely to decrease in the future, they call for close scrutiny.

scholarly journals Embryoid research calls for reassessment of legal regulations

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Markus Hengstschläger ◽  
Margit Rosner
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Human Embryonic Stem Cells ◽  
Legal Status ◽  
Embryonic Stem ◽  
Basic Research ◽  
Human Embryos ◽  
Human Being ◽  
Legal Regulations ◽  
Definition Of

AbstractIt is known that in countries, in which basic research on human embryos is in fact prohibited by law, working with imported human embryonic stem cells (hESCs) can still be permitted. As long as hESCs are not capable of development into a complete human being, it might be the case that they do not fulfill all criteria of the local definition of an embryo. Recent research demonstrates that hESCs can be developed into entities, called embryoids, which increasingly could come closer to actual human embryos in future. By discussing the Austrian situation, we want to highlight that current embryoid research could affect the prevailing opinion on the legal status of work with hESCs and therefore calls for reassessment of the regulations in all countries with comparable definitions of the embryo.

scholarly journals A case of neck abscess caused by rare hypervirulent Klebsiella pneumoniae, capsular type K20 and sequence type 420

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
John Alexander McHardy ◽  
Vathshalan Selvaganeshapillai ◽  
Priya Khanna ◽  
Ashley Michael Whittington ◽  
Jane Turton ◽  
...  
Keyword(s):  
Public Health ◽  
Case Report ◽  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
East Asia ◽  
South East Asia ◽  
Neck Abscess ◽  
Global Challenge ◽  
Life Threatening ◽  
The Uk

Abstract Background This case report describes a neck abscess caused by a strain of Hypervirulent Klebsiella pneumoniae in a middle aged man with diabetes without a history of travel to East and South East Asia. This case report is of notable significance as Hypervirulent Klebsiella pneumoniae neck abscesses are rarely seen in the UK and are very infrequently documented in individuals who have not first travelled to the high prevalence areas of East and South East Asia. Case presentation This case report describes a 53 year old diabetic man who contracted a Hypervirulent Klebsiella pneumoniae neck abscess which led to the development of sepsis. Klebsiella pneumoniae was cultured from blood cultures and fluid aspirated from the abscess grew the pathogen with same antimicrobial susceptibility. Hypervirulence was demonstrated after the samples were analysed, at the Antimicrobial Resistance and Healthcare Associated Infections Reference Unit Public Health England Colindale, and found to contain the K20 (rmp)A and rmpA2 virulence genes. Discussion Hypervirulent Klebsiella pneumoniae is a Gram-negative, encapsulated, non-motile bacillus notable for its ability to metastatically spread and cause potentially life threatening infections in otherwise healthy adults, but especially in those with diabetes. Genes responsible for the production of hyperviscous mucoid polysaccharide capsules and siderophores, such as those isolated in this case, enable the bacteria to more efficiently evade the hosts immune system and disseminate and invade surrounding and distant tissues. Data from Public Health England shows Hypervirulent Klebsiella pneumoniae are rare in the UK. A review of current literature also showed Hypervirulent Klebsiella pneumoniae almost exclusively occur in those who have traveled to East and South East Asia. Conclusions This case reported a rare Hypervirulent Klebsiella pneumoniae neck abscess outside of, and without travel to, East and South East Asia. This raises concerns about future, potentially life threatening, Hypervirulent Klebsiella pneumoniae infections becoming more widespread without the need for endemic travel. This concern is further exacerbated by the growing global challenge of antimicrobial resistance.

scholarly journals 1564. Activity of bacteriophage against multidrug resistant Klebsiella pneumoniae

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S782-S782
Author(s):  
Sailaja Puttagunta ◽  
Maya Kahan-Haanum ◽  
Sharon Kredo-Russo ◽  
Eyal Weinstock ◽  
Efrat Khabra ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Unmet Need ◽  
Multidrug Resistant ◽  
Beta Lactamase ◽  
Bacterial Strains ◽  
Antibiotic Resistant ◽  
Extended Spectrum Beta Lactamase ◽  
Novel Approach ◽  
Infection Types

Abstract Background The prevalence of extended-spectrum beta-lactamase (ESBL) producing and carbapenem resistant (CR) Klebsiella pneumoniae (KP) has significantly risen in all geographic regions. Infections due to these bacteria are associated with high mortality across different infection types. Even with newer options, there remains an unmet need for safe and effective therapeutic options to treat infections caused by ESBL and CR KP. Phage therapy offers a novel approach with an unprecedented and orthogonal mechanism of action for treatment of diseases caused by pathogenic bacterial strains that are insufficiently addressed by available antibiotics. Phage-based therapies confer a high strain-level specificity and have a strong intrinsic safety profile. Here we describe the identification of novel phages that can effectively target antibiotic resistant KP strains. Host range of the 21 phages on 33 strain KP panel via solid culture infectivity assays. Red marks resistance to infection while sensitivity to phage is marked in green Methods KP clinical strains were isolated from human stool specimens preserved in glycerol. Selective culturing was carried, followed by testing of individual colonies for motility, indole and urease production, sequenced and analyzed by Kleborate tool to determine antibiotic resistant genes. Natural phages were isolated from plaques that developed on susceptible bacterial targets, sequenced and characterized. Results Antibiotic-resistant KP strains encoding beta lactamase genes or a carbapenemase (n=33) were isolated from healthy individuals (n=3), and patients with inflammatory bowel disease (n=26) or primary sclerosing cholangitis (n=3). Isolates sequencing revealed bla CTX-M15 and/or bla SHV encoding strains and carbapenamase KPC-2. A panel of 21 phages targeting the beta-lactamase- and carbapenemase-producing KP strains were identified. Phage sequencing revealed that all phages belong to the Caudovirales order and include 6 Siphoviridae, 14 Myoviridae, and 1 Podoviridae. In vitro lytic activity of the phages was tested on the isolated bacteria and revealed a coverage of 70% of the 33 isolated antibiotic resistant strains, >50% of which were targeted by multiple phages. Conclusion Collectively, these results demonstrate the feasibility of identifying phage with potent activity against antibiotic resistant KP strains, and may provide a novel therapeutic approach for treatment of ESBL and CR KP infections. Disclosures All Authors: No reported disclosures

scholarly journals Carios kelleyi (Acari: Ixodida: Argasidae) Infected With Rickettsial Agents Documented Infesting Housing in Kansas, United States

2021 ◽  
Author(s):  
Robyn M Nadolny ◽  
Ashley C Kennedy ◽  
James M Rodgers ◽  
Zachary T Vincent ◽  
Hannah Cornman ◽  
...  
Keyword(s):  
Public Health ◽  
United States ◽  
Health Center ◽  
Human Disease ◽  
Multilocus Sequence Typing ◽  
The United States ◽  
Rickettsia Species ◽  
History Of ◽  
Tick Borne Disease ◽  
Blood Meals

Abstract During September–December 2018, 25 live ticks were collected on-post at Fort Leavenworth, Kansas, in a home with a history of bat occupancy. Nine ticks were sent to the Army Public Health Center Tick-Borne Disease Laboratory and were identified as Carios kelleyi (Cooley and Kohls, 1941), a species that seldom bites humans but that may search for other sources of blood meals, including humans, when bats are removed from human dwellings. The ticks were tested for numerous agents of human disease. Rickettsia lusitaniae was identified by multilocus sequence typing to be present in two ticks, marking the first detection of this Rickettsia agent in the United States and in this species of tick. Two other Rickettsia spp. were also detected, including an endosymbiont previously associated with C. kelleyi and a possible novel Rickettsia species. The potential roles of C. kelleyi and bats in peridomestic Rickettsia transmission cycles warrant further investigation.

Community of Hydrocarbon-Oxidizing Bacteria in Petroleum Products on the example of Ts-1 Aviation Fuel and AI-95 Gasoline

2021 ◽  
Vol 37 (1) ◽  
pp. 54-68
Author(s):  
E.S. Lobakova ◽  
G.A. Dolnikova ◽  
E.A. Ivanova ◽  
D.A. Sanjieva ◽  
A.A. Burova ◽  
...  
Keyword(s):  
Rhodococcus Erythropolis ◽  
Basic Research ◽  
Petroleum Products ◽  
The State ◽  
Aviation Fuel ◽  
Bacterial Strains ◽  
16S Rrna Sequence ◽  
State Assignment ◽  
Microbial Biofilms ◽  
Microbial Potential

It has been shown that the studied petroleum products (kerosene and gasoline) contain microflocules of heterogeneous microbial biofilms, the cells of which are integrated into a polymer matrix containing acidic polysaccharides. Thirteen bacterial strains were microbiologically isolated from petroleum products, and their taxonomy was identified by the 16S rRNA sequence. Kerosene was characterized by a diverse bacterial composition including the following genera: Sphingobacterium, Alcaligenes, Rhodococcus and Deinococcus, while gasoline bacterial community included only two genera: Bacillus and Paenibacillus. Representatives of the Deinococcus genera capable of growing on the hydrocarbons were isolated from fuels for the first time. The strains isolated from gasoline (Bacillus safensis Bi13 and Bacillus sp. Bi14) proved to be the most effective biodegraders of all n-alkanes, isoalkanes, cycloalkanes, alkenes and aromatic hydrocarbons, whereas the kerosene strain Rhodococcus erythropolis Bi6 effectively decomposed n-alkanes and trimethylbenzene. Both types of petroleum products contained hydrocarbon-oxidizing communities, some members of which were more active in the biodegradation of hydrocarbons, while others were capable of producing biosurfactants and had either emulsifying activity (Deinococcus sp. Bi7) or cell wall hydrophobicity (Sphingobacterium sp. Bi5 from kerosene; Bacillus pumilus Bi12 from gasoline) significantly higher than the average level. The indicated properties of the studied strains make them promising for use in bioremediation. biodegradation, petroleum products, hydrocarbon-oxidizing bacteria, bio-surfactants The work was carried out within the framework of the state assignment of the Ministry of Science and Higher Education of the Russian Federation (topic no. 10.5422.2017/8.9.). Investigation of microbial potential in the use hydrocarbons was supported by the Russian Foundation for Basic Research (RFBR), contract no. 18-29-05067. Physicochemical research was performed within the framework of the state assignment to the TIPS RAS

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