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

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

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00764-18 ◽

2018 ◽

Vol 62 (10) ◽

Cited By ~ 8

Author(s):

Dexi Bi ◽

Jiayi Zheng ◽

Jun-Jie Li ◽

Zi-Ke Sheng ◽

Xingchen Zhu ◽

...

Keyword(s):

Large Scale ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

Epidemiological Studies ◽

Genome Comparison ◽

Comparative Genomic ◽

Content Type ◽

Bacterial Plasmid ◽

Phylogeny And Evolution ◽

Sequence Types

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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Genomic Epidemiology and Molecular Resistance Mechanisms of Azithromycin-Resistant Neisseria gonorrhoeae in Canada from 1997 to 2014

Journal of Clinical Microbiology ◽

10.1128/jcm.03195-15 ◽

2016 ◽

Vol 54 (5) ◽

pp. 1304-1313 ◽

Cited By ~ 83

Author(s):

Walter Demczuk ◽

Irene Martin ◽

Shelley Peterson ◽

Amrita Bharat ◽

Gary Van Domselaar ◽

...

Keyword(s):

Neisseria Gonorrhoeae ◽

Resistance Mechanisms ◽

23S Rrna ◽

Phylogenomic Analysis ◽

Single Nucleotide ◽

Content Type ◽

E Coli ◽

Genomic Epidemiology ◽

High Level ◽

Promoter Mutations

The emergence ofNeisseria gonorrhoeaestrains with decreased susceptibility to cephalosporins and azithromycin (AZM) resistance (AZMr) represents a public health threat of untreatable gonorrhea infections. Genomic epidemiology through whole-genome sequencing was used to describe the emergence, dissemination, and spread of AZMrstrains. The genomes of 213 AZMrand 23 AZM-susceptibleN. gonorrhoeaeisolates collected in Canada from 1989 to 2014 were sequenced. Core single nucleotide polymorphism (SNP) phylogenomic analysis resolved 246 isolates into 13 lineages. High-level AZMr(MICs ≥ 256 μg/ml) was found in 5 phylogenetically diverse isolates, all of which possessed the A2059G mutation (Escherichia colinumbering) in all four 23S rRNA alleles. One isolate with high-level AZMrcollected in 2009 concurrently had decreased susceptibility to ceftriaxone (MIC = 0.125 μg/ml). An increase in the number of 23S rRNA alleles with the C2611T mutations (E. colinumbering) conferred low to moderate levels of AZMr(MICs = 2 to 4 and 8 to 32 μg/ml, respectively). Low-level AZMrwas also associated withmtrRpromoter mutations, including the −35A deletion and the presence ofNeisseria meningitidis-like sequences. Geographic and temporal phylogenetic clustering indicates that emergent AZMrstrains arise independently and can then rapidly expand clonally in a region through local sexual networks.

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Emergence and Spread of Neisseria gonorrhoeae Strains with High-Level Resistance to Azithromycin in Taiwan from 2001 to 2018

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00773-19 ◽

2019 ◽

Vol 63 (9) ◽

Cited By ~ 1

Author(s):

Yen-Hung Liu ◽

Ya-Hui Wang ◽

Chun-Hsing Liao ◽

Po-Ren Hsueh

Keyword(s):

Neisseria Gonorrhoeae ◽

23S Rrna ◽

Dilution Method ◽

Agar Dilution Method ◽

Coding Region ◽

Content Type ◽

First Choice ◽

Agar Dilution ◽

High Level ◽

Level Resistance

ABSTRACT A total of 598 Neisseria gonorrhoeae isolates obtained from patients in Taiwan from 2001 to 2018 were evaluated. The MICs of ceftriaxone (CRO) and azithromycin (AZM) against the isolates were determined by the agar dilution method. N. gonorrhoeae isolates with AZM MICs of ≥1 μg/ml were identified and characterized by the presence of AZM resistance determinants. For high-level AZM-resistant (AZM-HLR) isolates (MIC ≥ 256 μg/ml), genotyping was performed using multilocus sequence typing (MLST) and N. gonorrhoeae multiantigen sequence typing (NG-MAST). Among the N. gonorrhoeae isolates studied, 8.7% (52/598) exhibited AZM MICs of ≥1 μg/ml. Thirteen of the 52 isolates contained A2059G (23S rRNA NG-STAR type 1) or C2611T (23S rRNA NG-STAR type 2) mutations. The prevalence of the A2059G mutation was higher in AZM-HLR isolates (P < 0.001). The −35A deletion in the promoter region of the mtrR gene did not differ between AZM-HLR isolates (100%, 10/10) and the isolates with AZM MICs of 1 μg/ml to 64 μg/ml (95.2%, 40/42) (P = 1.000). The presence of mutations in the mtrR coding region was significantly different between these two groups at 90% (9/10) and 26.2% (11/42), respectively (P < 0.001). The AZM-HLR isolates, all carrying four mutated A2059G alleles, a −35A deletion, and G45D, were classified as MLST 12039/10899 and NG-MAST 1866/16497. In conclusion, Taiwan is among the countries reporting gonococci with high-level resistance to AZM so that a single dose of 1 g ceftriaxone intramuscularly as the first choice for management of N. gonorrhoeae infection should be evaluated.

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First National Genomic Epidemiological Study of Neisseria gonorrhoeae Strains Spreading Across Sweden in 2016

Frontiers in Microbiology ◽

10.3389/fmicb.2021.820998 ◽

2022 ◽

Vol 12 ◽

Author(s):

Ronza Hadad ◽

Daniel Golparian ◽

Inga Velicko ◽

Anna-Karin Ohlsson ◽

Ylva Lindroth ◽

...

Keyword(s):

Neisseria Gonorrhoeae ◽

Health Agency ◽

Epidemiological Data ◽

Health Concern ◽

Dynamic Evolution ◽

Phylogenomic Analysis ◽

Whole Genome ◽

The Public ◽

Genomic Epidemiology ◽

Sequence Types

The increasing transmission and antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global health concern with worrying trends of decreasing susceptibility to also the last-line extended-spectrum cephalosporin (ESC) ceftriaxone. A dramatic increase of reported gonorrhea cases has been observed in Sweden from 2016 and onward. The aim of the present study was to comprehensively investigate the genomic epidemiology of all cultured N. gonorrhoeae isolates in Sweden during 2016, in conjunction with phenotypic AMR and clinical and epidemiological data of patients. In total, 1279 isolates were examined. Etest and whole-genome sequencing (WGS) were performed, and epidemiological data obtained from the Public Health Agency of Sweden. Overall, 51.1%, 1.7%, and 1.3% resistance to ciprofloxacin, cefixime, and azithromycin, respectively, was found. No isolates were resistant to ceftriaxone, however, 9.3% of isolates showed a decreased susceptibility to ceftriaxone and 10.5% to cefixime. In total, 44 penA alleles were found of which six were mosaic (n = 92). Using the typing schemes of MLST, NG-MAST, and NG-STAR; 133, 422, and 280 sequence types, respectively, and 93 NG-STAR clonal complexes were found. The phylogenomic analysis revealed two main lineages (A and B) with lineage A divided into two main sublineages (A1 and A2). Resistance and decreased susceptibility to ESCs and azithromycin and associated AMR determinants, such as mosaic penA and mosaic mtrD, were predominantly found in sublineage A2. Resistance to cefixime and azithromycin was more prevalent among heterosexuals and MSM, respectively, and both were predominantly spread through domestic transmission. Continuous surveillance of the spread and evolution of N. gonorrhoeae, including phenotypic AMR testing and WGS, is essential for enhanced knowledge regarding the dynamic evolution of N. gonorrhoeae and gonorrhea epidemiology.

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Emergence of Neisseria gonorrhoeae Strains Harboring a Novel Combination of Azithromycin-Attenuating Mutations

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02313-18 ◽

2019 ◽

Vol 63 (4) ◽

Author(s):

Cau D. Pham ◽

Samera Sharpe ◽

Karen Schlanger ◽

Sancta St. Cyr ◽

Justin Holderman ◽

...

Keyword(s):

Neisseria Gonorrhoeae ◽

Genetic Material ◽

23S Rrna ◽

Inhibitory Effects ◽

Antibiotic Resistant ◽

Exogenous Dna ◽

Content Type ◽

Genomic Plasticity ◽

High Level ◽

Azithromycin Resistance

ABSTRACT The nimbleness of Neisseria gonorrhoeae to evade the effect of antibiotics has perpetuated the fight against antibiotic-resistant gonorrhea for more than 80 years. The ability to develop resistance to antibiotics is attributable to its indiscriminate nature in accepting and integrating exogenous DNA into its genome. Here, we provide data demonstrating a novel combination of the 23S rRNA A2059G mutation with a mosaic-multiple transferable resistance (mosaic-mtr) locus haplotype in 14 N. gonorrhoeae isolates with high-level azithromycin MICs (≥256 μg/ml), a combination that may confer more fitness than in previously identified isolates with high-level azithromycin resistance. To our knowledge, this is the first description of N. gonorrhoeae strains harboring this novel combination of resistance determinants. These strains were isolated at two independent jurisdictions participating in the Gonococcal Isolate Surveillance Project (GISP) and in the Strengthening the U.S. Response to Resistant Gonorrhea (SURRG) project. The data suggest that the genome of N. gonorrhoeae continues to shuffle its genetic material. These findings further illuminate the genomic plasticity of N. gonorrhoeae, which allows this pathogen to develop mutations to escape the inhibitory effects of antibiotics.

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Expanding U.S. Laboratory Capacity for Neisseria gonorrhoeae Antimicrobial Susceptibility Testing and Whole-Genome Sequencing through the CDC's Antibiotic Resistance Laboratory Network

Journal of Clinical Microbiology ◽

10.1128/jcm.01461-19 ◽

2020 ◽

Vol 58 (4) ◽

Cited By ~ 2

Author(s):

Ellen N. Kersh ◽

Cau D. Pham ◽

John R. Papp ◽

Robert Myers ◽

Richard Steece ◽

...

Keyword(s):

Public Health ◽

Antibiotic Resistance ◽

Neisseria Gonorrhoeae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Antimicrobial Susceptibility ◽

Susceptibility Testing ◽

Whole Genome ◽

Content Type ◽

Laboratory Capacity

ABSTRACT U.S. gonorrhea rates are rising, and antibiotic-resistant Neisseria gonorrhoeae (AR-Ng) is an urgent public health threat. Since implementation of nucleic acid amplification tests for N. gonorrhoeae identification, the capacity for culturing N. gonorrhoeae in the United States has declined, along with the ability to perform culture-based antimicrobial susceptibility testing (AST). Yet AST is critical for detecting and monitoring AR-Ng. In 2016, the CDC established the Antibiotic Resistance Laboratory Network (AR Lab Network) to shore up the national capacity for detecting several resistance threats including N. gonorrhoeae. AR-Ng testing, a subactivity of the CDC’s AR Lab Network, is performed in a tiered network of approximately 35 local laboratories, four regional laboratories (state public health laboratories in Maryland, Tennessee, Texas, and Washington), and the CDC’s national reference laboratory. Local laboratories receive specimens from approximately 60 clinics associated with the Gonococcal Isolate Surveillance Project (GISP), enhanced GISP (eGISP), and the program Strengthening the U.S. Response to Resistant Gonorrhea (SURRG). They isolate and ship up to 20,000 isolates to regional laboratories for culture-based agar dilution AST with seven antibiotics and for whole-genome sequencing of up to 5,000 isolates. The CDC further examines concerning isolates and monitors genetic AR markers. During 2017 and 2018, the network tested 8,214 and 8,628 N. gonorrhoeae isolates, respectively, and the CDC received 531 and 646 concerning isolates and 605 and 3,159 sequences, respectively. In summary, the AR Lab Network supported the laboratory capacity for N. gonorrhoeae AST and associated genetic marker detection, expanding preexisting notification and analysis systems for resistance detection. Continued, robust AST and genomic capacity can help inform national public health monitoring and intervention.

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Molecular pathways to high-level azithromycin resistance in Neisseria gonorrhoeae

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkab084 ◽

2021 ◽

Cited By ~ 1

Author(s):

J G E Laumen ◽

S S Manoharan-Basil ◽

E Verhoeven ◽

S Abdellati ◽

I De Baetselier ◽

...

Keyword(s):

Neisseria Gonorrhoeae ◽

Ribosomal Proteins ◽

Efflux Pump ◽

23S Rrna ◽

Rrna Gene ◽

23S Rrna Gene ◽

Evolution Of Resistance ◽

High Level ◽

Azithromycin Resistance ◽

Level Resistance

Abstract Background The prevalence of azithromycin resistance in Neisseria gonorrhoeae is increasing in numerous populations worldwide. Objectives To characterize the genetic pathways leading to high-level azithromycin resistance. Methods A customized morbidostat was used to subject two N. gonorrhoeae reference strains (WHO-F and WHO-X) to dynamically sustained azithromycin pressure. We tracked stepwise evolution of resistance by whole genome sequencing. Results Within 26 days, all cultures evolved high-level azithromycin resistance. Typically, the first step towards resistance was found in transitory mutations in genes rplD, rplV and rpmH (encoding the ribosomal proteins L4, L22 and L34 respectively), followed by mutations in the MtrCDE-encoded efflux pump and the 23S rRNA gene. Low- to high-level resistance was associated with mutations in the ribosomal proteins and MtrCDE efflux pump. However, high-level resistance was consistently associated with mutations in the 23S ribosomal RNA, mainly the well-known A2059G and C2611T mutations, but also at position A2058G. Conclusions This study enabled us to track previously reported mutations and identify novel mutations in ribosomal proteins (L4, L22 and L34) that may play a role in the genesis of azithromycin resistance in N. gonorrhoeae.

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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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Population Genetics and Characterization ofCampylobacter jejuniIsolates from Western Jackdaws and Game Birds in Finland

Applied and Environmental Microbiology ◽

10.1128/aem.02365-18 ◽

2018 ◽

Vol 85 (4) ◽

Cited By ~ 3

Author(s):

Sara Kovanen ◽

Mirko Rossi ◽

Mari Pohja-Mykrä ◽

Timo Nieminen ◽

Mirja Raunio-Saarnisto ◽

...

Keyword(s):

Host Specificity ◽

Campylobacter Jejuni ◽

Multilocus Sequence Typing ◽

Wild Birds ◽

Whole Genome ◽

Mallard Duck ◽

Content Type ◽

Game Birds ◽

Hygienic Measures ◽

Sequence Types

ABSTRACTPoultry are considered a major reservoir and source of human campylobacteriosis, but the roles of environmental reservoirs, including wild birds, have not been assessed in depth. In this study, we isolated and characterizedCampylobacter jejunifrom western jackdaws (n= 91, 43%), mallard ducks (n= 82, 76%), and pheasants (n= 9, 9%). Most of the western jackdaw and mallard duckC. jejuniisolates represented multilocus sequence typing (MLST) sequence types (STs) that diverged from those previously isolated from human patients and various animal species, whereas all pheasant isolates represented ST-19, a common ST among human patients and other hosts worldwide. Whole-genome MLST revealed that mallard duck ST-2314 and pheasant ST-19 isolates represented bacterial clones that were genetically highly similar to human isolates detected previously. Further analyses revealed that in addition to a divergent ClonalFrame genealogy, certain genomic characteristics of the western jackdawC. jejuniisolates, e.g., a novelcdtABCgene cluster and the type VI secretion system (T6SS), may affect their host specificity and virulence. Game birds may thus pose a risk for acquiring campylobacteriosis; therefore, hygienic measures during slaughter and meat handling warrant special attention.IMPORTANCEThe roles of environmental reservoirs, including wild birds, in the molecular epidemiology ofCampylobacter jejunihave not been assessed in depth. Our results showed that game birds may pose a risk for acquiring campylobacteriosis, because they hadC. jejunigenomotypes highly similar to human isolates detected previously. Therefore, hygienic measures during slaughter and meat handling warrant special attention. On the contrary, a unique phylogeny was revealed for the western jackdaw isolates, and certain genomic characteristics identified among these isolates are hypothesized to affect their host specificity and virulence. Comparative genomics within sequence types (STs), using whole-genome multilocus sequence typing (wgMLST), and phylogenomics are efficient methods to analyze the genomic relationships ofC. jejuniisolates.

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Whole-Genome Sequencing Confirms that Burkholderia pseudomallei Multilocus Sequence Types Common to Both Cambodia and Australia Are Due to Homoplasy

Journal of Clinical Microbiology ◽

10.1128/jcm.02574-14 ◽

2014 ◽

Vol 53 (1) ◽

pp. 323-326 ◽

Cited By ~ 28

Author(s):

Birgit De Smet ◽

Derek S. Sarovich ◽

Erin P. Price ◽

Mark Mayo ◽

Vanessa Theobald ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Analysis ◽

Burkholderia Pseudomallei ◽

Whole Genome ◽

Whole Genome Analysis ◽

Content Type ◽

Sequence Types

Burkholderia pseudomalleiisolates with shared multilocus sequence types (STs) have not been isolated from different continents. We identified two STs shared between Australia and Cambodia. Whole-genome analysis revealed substantial diversity within STs, correctly identified the Asian or Australian origin, and confirmed that these shared STs were due to homoplasy.

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