In SilicoTyping and Comparative Genomic Analysis of IncFIIKPlasmids and Insights into the Evolution of Replicons, Plasmid Backbones, and Resistance Determinant Profiles

ABSTRACTIncFIIKplasmids are associated with the acquisition and dissemination of multiple-antimicrobial resistance inKlebsiella pneumoniaeand often encountered in clinical isolates of this species. Since the phylogeny and evolution of IncFIIKplasmids remain unclear, here we performed large-scalein silicotyping and comparative analysis of these plasmids in publicly available bacterial/plasmid genomes. IncFIIKplasmids are prevalent inK. pneumoniae, being found in 69% of sequenced genomes, covering 66% of sequenced STs (sequence types), but sparse in otherEnterobacteriaceae. IncFIIKreplicons have three lineages. One IncFIIKallele could be found in distinctK. pneumoniaeSTs, highlighting the lateral genetic flow of IncFIIKplasmids. A set of 77 IncFIIKplasmids with full sequences were further analyzed. A pool of 327 antibiotic resistance genes or remnants were annotated in 75.3% of these plasmids. Plasmid genome comparison reiterated that they often contain other replicons belonging to IncFIA, IncFIB, IncFIIYp, IncFIIpCRY, IncR, IncL, and IncN groups and that they share a conserved backbone featuring an F-like conjugation module that has divergent components responsible for regulation and mating pair stabilization. Further epidemiological studies of IncFIIKplasmids are required due to the sample bias ofK. pneumoniaegenomes in public databases. This study provides insights into the evolution and structures of IncFIIKplasmids.

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Whole-Genome Phylogenomic Heterogeneity of Neisseria gonorrhoeae Isolates with Decreased Cephalosporin Susceptibility Collected in Canada between 1989 and 2013

Journal of Clinical Microbiology ◽

10.1128/jcm.02589-14 ◽

2014 ◽

Vol 53 (1) ◽

pp. 191-200 ◽

Cited By ~ 78

Author(s):

Walter Demczuk ◽

Tarah Lynch ◽

Irene Martin ◽

Gary Van Domselaar ◽

Morag Graham ◽

...

Keyword(s):

Neisseria Gonorrhoeae ◽

Large Scale ◽

Epidemiological Studies ◽

23S Rrna ◽

Genome Comparison ◽

Whole Genome ◽

Content Type ◽

Genomic Epidemiology ◽

High Level ◽

Sequence Types

A large-scale, whole-genome comparison of CanadianNeisseria gonorrhoeaeisolates with high-level cephalosporin MICs was used to demonstrate a genomic epidemiology approach to investigate strain relatedness and dynamics. Although current typing methods have been very successful in tracing short-chain transmission of gonorrheal disease, investigating the temporal evolutionary relationships and geographical dissemination of highly clonal lineages requires enhanced resolution only available through whole-genome sequencing (WGS). Phylogenomic cluster analysis grouped 169 Canadian strains into 12 distinct clades. While someN. gonorrhoeaemultiantigen sequence types (NG-MAST) agreed with specific phylogenomic clades or subclades, other sequence types (ST) and closely related groups of ST were widely distributed among clades. Decreased susceptibility to extended-spectrum cephalosporins (ESC-DS) emerged among a group of diverse strains in Canada during the 1990s with a variety of nonmosaicpenAalleles, followed in 2000/2001 with thepenAmosaic X allele and then in 2007 with ST1407 strains with thepenAmosaic XXXIV allele. Five genetically distinct ESC-DS lineages were associated withpenAmosaic X, XXXV, and XXXIV alleles and nonmosaic XII and XIII alleles. ESC-DS with coresistance to azithromycin was observed in 5 strains with 23S rRNA C2599T or A2143G mutations. As the costs associated with WGS decline and analysis tools are streamlined, WGS can provide a more thorough understanding of strain dynamics, facilitate epidemiological studies to better resolve social networks, and improve surveillance to optimize treatment for gonorrheal infections.

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A large scale, multiple genome comparison of acidophilic Archaea (pH ≤ 5.0) extends our understanding of oxidative stress responses in polyextreme environments

10.1101/2021.11.19.469288 ◽

2021 ◽

Author(s):

Gonzalo Neira ◽

Eva Vergara ◽

Diego Nahuel Cortez ◽

David S. Holmes

Keyword(s):

Oxidative Stress ◽

Stress Responses ◽

Large Scale ◽

Genomic Analysis ◽

Low Ph ◽

Genome Comparison ◽

Comparative Genomic ◽

Acidophilic Bacteria ◽

Acidophilic Archaea ◽

Oxidative Stress Responses

Acidophilic Archaea thrive in anaerobic and aerobic low pH environments (<pH 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (·OH) and superoxide (O2·−). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic Archaea with sequenced genomes. These organisms can be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what can this tell us about the evolution of these mechanisms in acidophilic Archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic Archaea and between acidophilic Archaea and acidophilic Bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in Archaea and possible Horizontal Gene Transfer (HGT) events.

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Responses of the Human GutEscherichia coliPopulation to Pathogen and Antibiotic Disturbances

mSystems ◽

10.1128/msystems.00047-18 ◽

2018 ◽

Vol 3 (4) ◽

Cited By ~ 8

Author(s):

Taylor K. S. Richter ◽

Jane M. Michalski ◽

Luke Zanetti ◽

Sharon M. Tennant ◽

Wilbur H. Chen ◽

...

Keyword(s):

Gastrointestinal Tract ◽

Antibiotic Treatment ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

Comparative Genomic ◽

Whole Genome ◽

Human Gastrointestinal Tract ◽

Content Type ◽

E Coli ◽

Pathogen Invasion

ABSTRACTStudies ofEscherichia coliin the human gastrointestinal tract have focused on pathogens, such as diarrhea-causing enterotoxigenicE. coli(ETEC), while overlooking the resident, nonpathogenicE. colicommunity. Relatively few genomes of nonpathogenicE. colistrains are available for comparative genomic analysis, and the ecology of these strains is poorly understood. This study examined the diversity and dynamics of resident human gastrointestinalE. colicommunities in the face of the ecological challenges presented by pathogen (ETEC) challenge, as well as of antibiotic treatment. Whole-genome sequences obtained fromE. coliisolates from before, during, and after ETEC challenge were used in phylogenomic and comparative genomic analyses to examine the diversity of the residentE. colicommunities, as well as the dynamics of the challenge strain, H10407, a well-studied ETEC strain (serotype O78:H11) that produces both heat-labile and heat-stable enterotoxins. ETEC failed to become the dominantE. coliclone in two of the six challenge subjects, each of whom exhibited limited or no clinical presentation of diarrhea. TheE. colicommunities of the remaining four subjects became ETEC dominant during the challenge but reverted to their original, subject-specific populations following antibiotic treatment, suggesting resiliency of the residentE. colipopulation following major ecological disruptions. This resiliency is likely due in part to the abundance of antibiotic-resistant ST131E. colistrains in the resident populations. This report provides valuable insights into the potential interactions of members of the gastrointestinal microbiome and its responses to challenge by an external pathogen and by antibiotic exposure.IMPORTANCEResearch on human-associatedE. colitends to focus on pathogens, such as enterotoxigenicE. coli(ETEC) strains, which are a leading cause of diarrhea in developing countries. However, the severity of disease caused by these pathogens is thought to be influenced by the microbiome. The nonpathogenicE. colicommunity that resides in the human gastrointestinal tract may play a role in pathogen colonization and disease severity and may become a reservoir for virulence and antibiotic resistance genes. Our study used whole-genome sequencing ofE. colibefore, during, and after challenge with an archetype ETEC isolate, H10407, and antibiotic treatment to explore the diversity and resiliency of the residentE. colipopulation in response to the ecological disturbances caused by pathogen invasion and antibiotic treatment.

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A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH ≤ 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments

Antioxidants ◽

10.3390/antiox11010059 ◽

2021 ◽

Vol 11 (1) ◽

pp. 59

Author(s):

Gonzalo Neira ◽

Eva Vergara ◽

Diego Cortez ◽

David S. Holmes

Keyword(s):

Oxidative Stress ◽

Stress Responses ◽

Large Scale ◽

Genomic Analysis ◽

Low Ph ◽

Genome Comparison ◽

Comparative Genomic ◽

Acidophilic Bacteria ◽

Acidophilic Archaea ◽

Oxidative Stress Responses

Acidophilic archaea thrive in anaerobic and aerobic low pH environments (pH < 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (OH) and superoxide (O2−). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic archaea with sequenced genomes. These organisms are often be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what this can tell us about the evolution of these mechanisms in acidophilic archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic archaea and between acidophilic archaea and acidophilic bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in archaea and likely horizontal gene transfer (HGT) events.

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Unprecedented Melioidosis Cases in Northern Australia Caused by an Asian Burkholderia pseudomallei Strain Identified by Using Large-Scale Comparative Genomics

Applied and Environmental Microbiology ◽

10.1128/aem.03013-15 ◽

2015 ◽

Vol 82 (3) ◽

pp. 954-963 ◽

Cited By ~ 31

Author(s):

Erin P. Price ◽

Derek S. Sarovich ◽

Emma J. Smith ◽

Barbara MacHunter ◽

Glenda Harrington ◽

...

Keyword(s):

Burkholderia Pseudomallei ◽

Large Scale ◽

Phylogenetic Reconstruction ◽

Genomic Analysis ◽

Comparative Genomic ◽

Antibiotic Administration ◽

Northern Australia ◽

Content Type ◽

Clone Sequence ◽

Asian Isolate

ABSTRACTMelioidosis is a disease of humans and animals that is caused by the saprophytic bacteriumBurkholderia pseudomallei. Once thought to be confined to certain locations, the known presence ofB. pseudomalleiis expanding as more regions of endemicity are uncovered. There is no vaccine for melioidosis, and even with antibiotic administration, the mortality rate is as high as 40% in some regions that are endemic for the infection. Despite high levels of recombination, phylogenetic reconstruction ofB. pseudomalleipopulations using whole-genome sequencing (WGS) has revealed surprisingly robust biogeographic separation between isolates from Australia and Asia. To date, there have been no confirmed autochthonous melioidosis cases in Australia caused by an Asian isolate; likewise, no autochthonous cases in Asia have been identified as Australian in origin. Here, we used comparative genomic analysis of 455B. pseudomalleigenomes to confirm the unprecedented presence of an Asian clone, sequence type 562 (ST-562), in Darwin, northern Australia. First observed in Darwin in 2005, the incidence of melioidosis cases attributable to ST-562 infection has steadily risen, and it is now a common strain in Darwin. Intriguingly, the Australian ST-562 appears to be geographically restricted to a single locale and is genetically less diverse than other common STs from this region, indicating a recent introduction of this clone into northern Australia. Detailed genomic and epidemiological investigations of new clinical and environmentalB. pseudomalleiisolates in the Darwin region and ST-562 isolates from Asia will be critical for understanding the origin, distribution, and dissemination of this emerging clone in northern Australia.

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First Genome Description of Providencia vermicola Isolate Bearing NDM-1 from Blood Culture

Microorganisms ◽

10.3390/microorganisms9081751 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1751

Author(s):

David Lupande-Mwenebitu ◽

Mariem Ben Khedher ◽

Sami Khabthani ◽

Lalaoui Rym ◽

Marie-France Phoba ◽

...

Keyword(s):

Complete Genome ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

University Teaching ◽

Genome Comparison ◽

Comparative Genomic ◽

Type I ◽

Type Vi Secretion System ◽

Clinical Practices ◽

Circular Chromosome

In this paper, we describe the first complete genome sequence of Providencia vermicola species, a clinical multidrug-resistant strain harboring the New Delhi Metallo-β-lactamase-1 (NDM-1) gene, isolated at the Kinshasa University Teaching Hospital, in Democratic Republic of the Congo. Whole genome sequencing of an imipenem-resistant clinical Gram-negative P. vermicola P8538 isolate was performed using MiSeq and Gridion, and then complete genome analysis, plasmid search, resistome analysis, and comparative genomics were performed. Genome assembly resulted in a circular chromosome sequence of 4,280,811-bp and 40.80% GC and a circular plasmid (pPV8538_NDM-1) of 151,684-bp and 51.93%GC, which was identified in an Escherichia coli P8540 strain isolated in the same hospital. Interestingly, comparative genomic analysis revealed multiple sequences acquisition within the P. vermicola P8538 chromosome, including three complete prophages, a siderophore biosynthesis NRPS cluster, a Type VI secretion system (T6SS), a urease gene cluster, and a complete Type-I-F CRISPR-Cas3 system. Β-lactamase genes, including blaCMY-6 and blaNDM-1, were found on the recombinant plasmid pPV8538_NDM-1, in addition to other antibiotic resistance genes such as rmtC, aac6’-Ib3, aacA4, catA1, sul1, aac6’-Ib-cr, tetA, and tetB. Genome comparison with Providencia species revealed 82.95% of average nucleotide identity (ANI), with P. stuartii species exhibiting 90.79% of proteome similarity. We report the first complete genome of P. vermicola species and for the first time the presence of the blaNDM-1 gene in this species. This work highlights the need to improve surveillance and clinical practices in DR Congo in order to reduce or prevent the spread of such resistance.

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Phylogenetic and genomic analysis reveals high genomic openness and genetic diversity of Clostridium perfringens

Microbial Genomics ◽

10.1099/mgen.0.000441 ◽

2020 ◽

Vol 6 (10) ◽

Cited By ~ 1

Author(s):

Yuqing Feng ◽

Xuezheng Fan ◽

Liangquan Zhu ◽

Xinyue Yang ◽

Yan Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Clostridium Perfringens ◽

Type Species ◽

Large Scale ◽

Bacterial Species ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

Virulence Gene ◽

Content Type ◽

Link Type

Clostridium perfringens is associated with a variety of diseases in both humans and animals. Recent advances in genomic sequencing make it timely to re-visit this important pathogen. Although the genome sequence of C. perfringens was first determined in 2002, large-scale comparative genomics with isolates of different origins is still lacking. In this study, we used whole-genome sequencing of 45 C . perfringens isolates with isolation time spanning an 80‐year period and performed comparative analysis of 173 genomes from worldwide strains. We also conducted phylogenetic lineage analysis and introduced an openness index (OI) to evaluate the openness of bacterial genomes. We classified all these genomes into five lineages and hypothesized that the origin of C. perfringens dates back to ~80 000 years ago. We showed that the pangenome of the 173 C . perfringens strains contained a total of 26 954 genes, while the core genome comprised 1020 genes, accounting for about a third of the genome of each isolate. We demonstrated that C. perfringens had the highest OI compared with 51 other bacterial species. Intact prophage sequences were found in nearly 70.0 % of C. perfringens genomes, while CRISPR sequences were found only in ~40.0 %. Plasmids were prevalent in C. perfringens isolates, and half of the virulence genes and antibiotic resistance genes (ARGs) identified in all the isolates could be found in plasmids. ARG-sharing network analysis showed that C. perfringens shared its 11 ARGs with 55 different bacterial species, and a high frequency of ARG transfer may have occurred between C. perfringens and species in the genera Streptococcus and Staphylococcus . Correlation analysis showed that the ARG number in C. perfringens strains increased with time, while the virulence gene number was relative stable. Our results, taken together with previous studies, revealed the high genome openness and genetic diversity of C. perfringens and provide a comprehensive view of the phylogeny, genomic features, virulence gene and ARG profiles of worldwide strains.

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Trust, efficacy and ethicacy when testing prisoners for COVID-19

International Journal of Prisoner Health ◽

10.1108/ijph-10-2020-0084 ◽

2021 ◽

Vol ahead-of-print (ahead-of-print) ◽

Author(s):

Steve Lambert ◽

Dean Wilkinson

Keyword(s):

Large Scale ◽

Current System ◽

Epidemiological Studies ◽

Careful Consideration ◽

Power Relationships ◽

England And Wales ◽

Content Type ◽

Large Scale Testing ◽

The Uk ◽

The Impact

Purpose The outbreak of the severe acute respiratory syndrome coronavirus 2 virus and subsequent COVID-19 illness has had a major impact on all levels of society internationally. The extent of the impact of COVID-19 on prison staff and prisoners in England and Wales is unknown. Testing for COVID-19 both asymptomatic and symptomatic, as well as for antibodies, to date, has been minimal. The purpose of this paper is to explore the widespread testing of COVID-19 in prisons poses philosophical and ethical questions around trust, efficacy and ethicacy. Design/methodology/approach This paper is both descriptive, providing an overview of the widespread testing of COVID-19 in prisoners in England and Wales, and conceptual in that it discusses and argues the issues associated with large-scale testing. This paper provides a discussion, using comparative studies, of the issues associated with large-scale testing of prisoners across the prison estate in England and Wales (120 prisons). The issues identified in this paper are contextualised through the lens of COVID-19, but they are equally transferrable to epidemiological studies of any pandemic. Given the prevalence of COVID-19 globally and the lack of information about its spread in prisons, at the time of writing this paper, there is a programme of asymptomatic testing of prisoners. However, there remains a paucity of data on the spread of COVID-19 in prisons because of the progress with the ongoing testing programme. Findings The authors argue that the widespread testing of prisoners requires careful consideration of the details regarding who is included in testing, how consent is gained and how tests are administered. This paper outlines and argues the importance of considering the complex nuance of power relationships within the prison system, among prisoner officers, medical staff and prisoners and the detrimental consequences. Practical implications The widespread testing of COVID-19 presents ethical and practical challenges. Careful planning is required when considering the ethics of who should be included in COVID-19 testing, how consent will be gained, who and how tests will be administered and very practical challenges around the recording and assigning of COVID-19 test kits inside the prison. The current system for the general population requires scanning of barcodes and registration using a mobile number; these facilities are not permitted inside a prison. Originality/value This paper looks at the issues associated with mass testing of prisoners for COVID-19. According to the authors’ knowledge, there has not been any research that looks at the issues of testing either in the UK or internationally. The literature available details countries’ responses to the pandemic rather and scientific papers on the development of vaccines. Therefore, this paper is an original review of some of the practicalities that need to be addressed to ensure that testing can be as successful as possible.

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Genomic Analysis of Multiresistant Staphylococcus capitis Associated with Neonatal Sepsis

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00898-18 ◽

2018 ◽

Vol 62 (11) ◽

Cited By ~ 11

Author(s):

Glen P. Carter ◽

James E. Ussher ◽

Anders Gonçalves Da Silva ◽

Sarah L. Baines ◽

Helen Heffernan ◽

...

Keyword(s):

Neonatal Sepsis ◽

Neonatal Intensive Care ◽

Genomic Analysis ◽

Bloodstream Infections ◽

Multidrug Resistant ◽

Comparative Genomic ◽

Coagulase Negative Staphylococci ◽

Content Type ◽

Staphylococcus Capitis ◽

Hospital Infection Control

ABSTRACT Coagulase-negative staphylococci (CoNS), such as Staphylococcus capitis, are major causes of bloodstream infections in neonatal intensive care units (NICUs). Recently, a distinct clone of S. capitis (designated S. capitis NRCS-A) has emerged as an important pathogen in NICUs internationally. Here, 122 S. capitis isolates from New Zealand (NZ) underwent whole-genome sequencing (WGS), and these data were supplemented with publicly available S. capitis sequence reads. Phylogenetic and comparative genomic analyses were performed, as were phenotypic assessments of antimicrobial resistance, biofilm formation, and plasmid segregational stability on representative isolates. A distinct lineage of S. capitis was identified in NZ associated with neonates and the NICU environment. Isolates from this lineage produced increased levels of biofilm, displayed higher levels of tolerance to chlorhexidine, and were multidrug resistant. Although similar to globally circulating NICU-associated S. capitis strains at a core-genome level, NZ NICU S. capitis isolates carried a novel stably maintained multidrug-resistant plasmid that was not present in non-NICU isolates. Neonatal blood culture isolates were indistinguishable from environmental S. capitis isolates found on fomites, such as stethoscopes and neonatal incubators, but were generally distinct from those isolates carried by NICU staff. This work implicates the NICU environment as a potential reservoir for neonatal sepsis caused by S. capitis and highlights the capacity of genomics-based tracking and surveillance to inform future hospital infection control practices aimed at containing the spread of this important neonatal pathogen.

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Complete Genome Resequencing of Thermus thermophilus Strain TMY by Hybrid Assembly of Long- and Short-Read Sequencing Technologies

Microbiology Resource Announcements ◽

10.1128/mra.00979-21 ◽

2021 ◽

Vol 10 (46) ◽

Author(s):

Kentaro Miyazaki ◽

Natsuko Tokito

Keyword(s):

Complete Genome ◽

Thermus Thermophilus ◽

Genomic Analysis ◽

Comparative Genomic ◽

Hybrid Assembly ◽

Genome Resequencing ◽

Short Read ◽

Content Type ◽

Sequencing Technologies ◽

Long Read

Complete genome resequencing was conducted for Thermus thermophilus strain TMY by hybrid assembly of Oxford Nanopore Technologies long-read and MGI short-read data. Errors in the previously reported genome sequence determined by PacBio technology alone were corrected, allowing for high-quality comparative genomic analysis of closely related T. thermophilus genomes.

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