scholarly journals Clonal analysis of the serogroup B meningococci causing New Zealand's epidemic

2005 ◽  
Vol 134 (2) ◽  
pp. 377-383 ◽  
Author(s):  
K. H. DYET ◽  
D. R. MARTIN
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
16S Rrna ◽  
Meningococcal Disease ◽  
Common Ancestor ◽  
Clonal Complex ◽  
Clonal Analysis ◽  
The Other ◽  
Disease Rates ◽  
Sequence Types

An epidemic of meningococcal disease caused by serogroup B meningococci expressing the P1.7-2,4 PorA protein began in New Zealand in 1991. The PorA type has remained stable. Different porB have been found in association with the P1.7-2,4 PorA, although type 4 has been most common. The clonal origins of B:P1.7-2,4 meningococci isolated from cases during 1990 to the end of 2003 were analysed. In 1990, the year immediately preceding the recognized increase in disease rates, all three subclones (ST-41, ST-42, and ST-154) of the ST-41/44 clonal complex occurred among the five isolates of B:P1.7-2,4. The two sequence types, ST-42 and ST-154, continued to cause most disease throughout New Zealand. Isolates belonging to subclone ST-41 were mostly identified early in the epidemic and in the South Island. 16S rRNA typing indicated that isolates belonging to the subclones ST-41 and ST-154 share a common ancestor, with those typing as ST-42 more distantly related with some genetically ambiguous. It is possible that ST-41 and ST-154 may have evolved one from the other but evolution to ST-42 is more difficult to explain. It is possible that one or more of the ST types could have been introduced into New Zealand prior to the first detection of clinical cases in 1990. Genetic diversity may have occurred during carriage in the community.

scholarly journals Genetic Diversity of Campylobacter jejuni Isolates from Farm Animals and the Farm Environment

2003 ◽  
Vol 69 (12) ◽  
pp. 7409-7413 ◽  
Author(s):  
F. M. Colles ◽  
K. Jones ◽  
R. M. Harding ◽  
M. C. J. Maiden
Keyword(s):  
Genetic Diversity ◽  
Campylobacter Jejuni ◽  
Human Disease ◽  
Clonal Complex ◽  
Food Samples ◽  
Complex Model ◽  
Farm Animals ◽  
Significant Genetic Differentiation ◽  
Sequence Types ◽  
Retail Food

ABSTRACT The genetic diversity of Campylobacter jejuni isolates from farm animals and their environment was investigated by multilocus sequence typing (MLST). A total of 30 genotypes, defined by allelic profiles (assigned to sequence types [STs]), were found in 112 C. jejuni isolates originating in poultry, cattle, sheep, starlings, and slurry. All but two of these genotypes belonged to one of nine C. jejuni clonal complexes previously identified in isolates from human disease and retail food samples and one clonal complex previously associated with an environmental source. There was some evidence for the association of certain clonal complexes with particular farm animals: isolates belonging to the ST-45 complex predominated among poultry isolates but were absent among sheep isolates, while isolates belonging to the ST-61 and ST-42 complexes were predominant among sheep isolates but were absent from the poultry isolates. In contrast, ST-21 complex isolates were distributed among the different isolation sources. Comparison with MLST data from 91 human disease isolates showed small but significant genetic differentiation between the farm and human isolates; however, representatives of six clonal complexes were found in both samples. These data demonstrate that MLST and the clonal complex model can be used to identify and compare the genotypes of C. jejuni isolates from farm animals and the environment with those from retail food and human disease.

Genome typing and epidemiology of human listeriosis in New Zealand 1999-2018

2021 ◽  
Author(s):  
Lucia Rivas ◽  
Shevaun Paine ◽  
Pierre-Yves Dupont ◽  
Audrey Tiong ◽  
Beverley Horn ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
Epidemiological Data ◽  
Common Source ◽  
Snp Analysis ◽  
Whole Genome ◽  
Single Nucleotide ◽  
Low Genetic Diversity ◽  
Geographical Regions ◽  
Sequence Types

This study describes the epidemiology of listeriosis in New Zealand (NZ) between 1999 and 2018, as well as the retrospective whole genome sequencing (WGS) of 453 Listeria monocytogenes isolates corresponding to 95% of the human cases within this period. The average notified rate of listeriosis was 0.5 cases per 100,000 population and non-pregnancy associated cases were more prevalent than pregnancy-associated cases (average 19 and 5 cases per annum, respectively). Analysis of WGS data was assessed using multi-locus sequencing typing (MLST), including core-genome and whole-genome MLST (cgMLST and wgMLST) and single-nucleotide polymorphism (SNP) analysis. Thirty-nine sequence types (STs) were identified, with the most common being, ST1 (21.9%), ST4 (13.2%), ST2 (11.3%), ST120 (6.1%) and ST155 (6.4%). A total of 291 different cgMLST types were identified, with the majority (n = 243) of types observed as a single isolate, consistent with the observation that listeriosis is predominately sporadic. Amongst the 49 cgMLST types containing two or more isolates, 18 cgMLST types contained 2-4 isolates (50 isolates in total, including three outbreak-associated isolates) that shared low genetic diversity (0-2 whole-genome alleles), some of which were dispersed in time or geographical regions. SNP-analysis also produced comparable results to wgMLST. The low genetic diversity within these clusters suggests a potential common source but incomplete epidemiological data impaired retrospective epidemiological investigations. Prospective use of WGS analysis, together with thorough exposure information from cases will potentially identify future outbreaks more rapidly and possibly those that have been undetected for some time over different geographically regions.

Genetic Diversity of the Biofilm CoveringMontacuta ferruginosa (Mollusca, Bivalvia) as Evaluated by Denaturing Gradient Gel Electrophoresis Analysis and Cloning of PCR-Amplified Gene Fragments Coding for 16S rRNA†

1998 ◽  
Vol 64 (9) ◽  
pp. 3464-3472 ◽  
Author(s):  
David C. Gillan ◽  
Arjen G. C. L. Speksnijder ◽  
Gabriel Zwart ◽  
Chantal De Ridder
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
Dna Extraction ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gradient Gel Electrophoresis ◽  
Biofilm Bacteria ◽  
Sequence Types

The shell of the bivalve Montacuta ferruginosa, a symbiont living in the burrow of an echinoid, is covered with a rust-colored biofilm. This biofilm includes different morphotypes of bacteria that are encrusted with a mineral rich in ferric ion and phosphate. The aim of this research was to determine the genetic diversity and phylogenetic affiliation of the biofilm bacteria. Also, the possible roles of the microorganisms in the processes of mineral deposition within the biofilm, as well as their impact on the biology of the bivalve, were assessed by phenotypic inference. The genetic diversity was determined by denaturing gradient gel electrophoresis (DGGE) analysis of short (193-bp) 16S ribosomal DNA PCR products obtained with primers specific for the domain Bacteria. This analysis revealed a diverse consortium; 11 to 25 sequence types were detected depending on the method of DNA extraction used. Individual biofilms analyzed by using the same DNA extraction protocol did not produce identical DGGE profiles. However, different biofilms shared common bands, suggesting that similar bacteria can be found in different biofilms. The phylogenetic affiliations of the sequence types were determined by cloning and sequencing the 16S rRNA genes. Close relatives of the genera Pseudoalteromonas,Colwellia, and Oceanospirillum (members of the γ-Proteobacteria lineage), as well as Flexibacter maritimus (a member of theCytophaga-Flavobacter-Bacteroides lineage), were found in the biofilms. We inferred from the results that some of the biofilm bacteria could play a role in the mineral formation processes.

scholarly journals High Genetic Diversity in Flavobacterium psychrophilum Isolates from Healthy Rainbow Trout (Oncorhynchus mykiss) Farmed in the Same Watershed, Revealed by Two Typing Methods

2020 ◽  
Vol 87 (2) ◽  
Author(s):  
Ségolène Calvez ◽  
Nora Navarro-Gonzalez ◽  
Charlène Siekoula-Nguedia ◽  
Catherine Fournel ◽  
Eric Duchaud
Keyword(s):  
Genetic Diversity ◽  
Rainbow Trout ◽  
Oncorhynchus Mykiss ◽  
Clonal Complex ◽  
Economic Losses ◽  
High Genetic Diversity ◽  
Content Type ◽  
Flavobacterium Psychrophilum ◽  
Sequence Types ◽  
Apparently Healthy

ABSTRACT Flavobacterium psychrophilum affects salmonid health worldwide and causes economic losses. The genetic diversity of the pathogen must be considered to develop control methods. However, previous studies have reported both high and low levels of genetic diversity. The present longitudinal study aimed at assessing the genetic diversity of F. psychrophilum at a small temporal and geographic scale. Four farms located on the same watershed in France were studied. Rainbow trout (Oncorhynchus mykiss) batches were monitored, and apparently healthy individuals were sampled over 1 year. A total of 288 isolates were recovered from fish organs (gills and spleen) and eggs. Pulsed field gel electrophoresis revealed high genetic diversity. Multilocus sequence typing performed on a selection of 31 isolates provided congruent results, as follows: 18 sequence types (STs) were found, of which 13 were novel. The mean gene diversity (H = 0.8413) was much higher than that previously reported for this host species, although the sampling was restricted to a single watershed and 1 year. Seven isolates out of 31 were assigned to clonal complex ST10 (CC-ST10), which is the predominant clonal complex in the main salmonid production areas. A split decomposition tree reflected a panmictic population. This finding is important for aquaculture veterinarians in their diagnostic procedure, as the choice of adequate antibiotic treatment is conditioned by the correct identification of the causative agent. Furthermore, this study expands our knowledge on genetic diversity required for the development of an effective vaccine against F. psychrophilum. IMPORTANCE The bacterium Flavobacterium psychrophilum is a serious pathogen in many fish species, especially salmonids, that is responsible for considerable economic losses worldwide. In order to treat infections and to develop vaccines, the genetic diversity of this bacterium needs to be known. We assessed the genetic diversity of F. psychrophilum isolates from apparently healthy rainbow trout raised in several fish farms in the same watershed in France. Two different genotyping methods revealed high diversity. The majority of isolates were unrelated to clonal complex sequence type 10 (CC-ST10), the clonal complex that is predominant worldwide and associated with disease in rainbow trout. In addition, we found 13 novel sequence types. These results suggest that a diverse subpopulation of F. psychrophilum may be harbored by rainbow trout.

scholarly journals A novel haplotype of ‘Candidatus Liberibacter solanacearum’ found in Apiaceae and Polygonaceae family plants

2019 ◽  
Vol 156 (2) ◽  
pp. 413-423 ◽  
Author(s):  
Minna Haapalainen ◽  
Satu Latvala ◽  
Annika Wickström ◽  
Jinhui Wang ◽  
Minna Pirhonen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Analysis ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Northern Europe ◽  
Wild Buckwheat ◽  
The Family ◽  
Candidatus Liberibacter ◽  
Sequence Types ◽  
Eastern Finland

AbstractA previously unknown haplotype of the plant pathogen ‘Candidatus Liberibacter solanacearum’ (Lso) was found in cultivated carrots and parsnips in eastern Finland. That same haplotype was found in western Finland, over 300 km away, in the family Polygonaceae, the species Fallopia convolvulus (wild buckwheat) and Persicaria lapathifolia (pale persicaria) growing as weeds within carrot and parsnip fields. The infected plants, both apiaceous and polygonaceous, showed symptoms of foliar discolouration. This is the first report of Lso bacteria in plants of the family Polygonaceae. The finding that the polygonaceous plants infected with a previously unknown haplotype of Lso were growing among the apiaceous plants infected with Lso haplotype C suggests that these two haplotypes might be transmitted by different vectors. Phylogenetic analyses showed that the new haplotype, called haplotype H, is distinct from the previously characterized haplotypes and appears to have diverged early from their common ancestor. Multi-locus sequence analysis revealed four different sequence types (strains) within the haplotype H. These findings suggest that the haplotype H is likely to be endemic in northern Europe and that the genetic diversity within the Lso species is higher than previously assumed.

Characterization of Neisseria meningitidis isolates collected from 1974 to 2003 in Japan by multilocus sequence typing

2004 ◽  
Vol 53 (7) ◽  
pp. 657-662 ◽  
Author(s):  
Hideyuki Takahashi ◽  
Toshiro Kuroki ◽  
Yuko Watanabe ◽  
Hiroshi Tanaka ◽  
Hiroo Inouye ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Neisseria Meningitidis ◽  
Multilocus Sequence Typing ◽  
Clonal Complex ◽  
The Other ◽  
Mlst Database ◽  
Mlst Analysis ◽  
The Past ◽  
Sequence Types

Analysis of 182 Neisseria meningitidis strains isolated over the past 30 years in Japan by serogroup typing and multilocus sequence typing (MLST) was performed. The serogroups of the 182 Japanese isolates were B (103 isolates), Y (39), W135 (1) and non-groupable (39). By MLST analysis, 65 different sequence types (ST) were identified, 42 of which were not found in the MLST database as of January 2004 and seemed to be unique to Japan. Statistical analysis of the MLST results revealed that, although the Japanese isolates seemed to be genetically divergent, they were classified into six major clonal complexes and other minor complexes. Among these isolates, well-documented ST complexes found worldwide were present, such as ST-23 complex (49 isolates), ST-44 complex (41 isolates) and ST-32 complex (8 isolates). On the other hand, a new clonal complex designated ST-2046 complex (28 isolates), which has not been identified in other countries, was also found, suggesting that this clone was indigenous to Japan. Taken together, it was speculated that meningococcal isolates in Japan comprised heterogeneous clones, which were derived both from clones identified in other countries and clones unique to Japan.

scholarly journals Characterization and Genetic Diversity of Listeria monocytogenes Isolated from Cattle Abortions in Latvia, 2013–2018

2021 ◽  
Vol 8 (9) ◽  
pp. 195
Author(s):  
Žanete Šteingolde ◽  
Irēna Meistere ◽  
Jeļena Avsejenko ◽  
Juris Ķibilds ◽  
Ieva Bergšpica ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Listeria Monocytogenes ◽  
Virulence Factors ◽  
Causative Agent ◽  
Animal Species ◽  
Clonal Complex ◽  
The Third ◽  
Wide Range ◽  
Sequence Types

Listeria monocytogenes can cause disease in humans and in a wide range of animal species, especially in farm ruminants. The aim of the study was to determine the prevalence and genetic diversity of L. monocytogenes related to 1185 cattle abortion cases in Latvia during 2013–2018. The prevalence of L. monocytogenes among cattle abortions was 16.1% (191/1185). The seasonality of L. monocytogenes abortions was observed with significantly higher occurrence (p < 0.01) in spring (March–May). In 61.0% of the cases, the affected cattle were under four years of age. L. monocytogenes abortions were observed during the third (64.6%) and second (33.3%) trimesters of gestation. Overall, 27 different sequence types (ST) were detected, and four of them, ST29 (clonal complex, CC29), ST37 (CC37), ST451 (CC11) and ST7 (CC7), covered more than half of the L. monocytogenes isolates. Key virulence factors like the prfA-dependent virulence cluster and inlA, inlB were observed in all the analyzed isolates, but lntA, inlF, inlJ, vip were associated with individual sequence types. Our results confirmed that L. monocytogenes is the most important causative agent of cattle abortions in Latvia and more than 20 different STs were observed in L. monocytogenes abortions in cattle.

scholarly journals Characterising the methylome of Legionella longbeachae serogroup 1 clinical isolates and assessing geo-temporal genetic diversity

2020 ◽  
Author(s):  
S Slow ◽  
T Anderson ◽  
DR Murdoch ◽  
S Bloomfield ◽  
D Winter ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
New Zealand ◽  
Complete Genome ◽  
Large Scale ◽  
Common Ancestor ◽  
Sequence Motifs ◽  
Plasmid Recombination ◽  
Legionnaires Disease ◽  
Temporal Genetic Diversity

AbstractLegionella longbeachae is an environmental bacterium that is commonly found in soil and composted plant material. In New Zealand (NZ) it is the most clinically significant Legionella species causing around two-thirds of all notified cases of Legionnaires’ disease. Here we report the sequencing and analysis of the geo-temporal genetic diversity of 54 L. longbeachae serogroup 1 (sg1) clinical isolates that were derived from cases from around NZ over a 22-year period, including one complete genome and its associated methylome.Our complete genome consisted of a 4.1 Mb chromosome and a 108 kb plasmid. The genome was highly methylated with two known epigenetic modifications, m4C and m6A, occurring in particular sequence motifs within the genome. Phylogenetic analysis demonstrated the 54 sg1 isolates belonged to two main clades that last shared a common ancestor between 108 BCE and 1608 CE. These isolates also showed diversity at the genome-structural level, with large-scale arrangements occurring in some regions of the chromosome and evidence of extensive chromosomal and plasmid recombination. This includes the presence of plasmids derived from recombination and horizontal gene transfer between various Legionella species, indicating there has been both intra-species and inter-species gene flow. However, because similar plasmids were found among isolates within each clade, plasmid recombination events may pre-empt the emergence of new L. longbeachae strains.Our high-quality reference genome and extensive genetic diversity data will serve as a platform for future work linking genetic, epigenetic and functional diversity in this globally important emerging environmental pathogen.Author SummaryLegionnaires’ disease is a serious, sometimes fatal pneumonia caused by bacteria of the genus Legionella. In New Zealand, the species that causes the majority of disease is Legionella longbeachae. Although the analyses of pathogenic bacterial genomes is an important tool for unravelling evolutionary relationships and identifying genes and pathways that are associated with their disease-causing ability, until recently genomic data for L. longbeachae has been sparse. Here, we conducted a large-scale genomic analysis of 54 L. longbeachae isolates that had been obtained from people hospitalised with Legionnaires’ disease between 1993 and 2015 from 8 regions around New Zealand. Based on our genome analysis the isolates could be divided into two main groups that persisted over time and last shared a common ancestor up to 1700 years ago. Analysis of the bacterial chromosome revealed areas of high modification through the addition of methyl groups and these were associated with particular DNA sequence motifs. We also found there have been large-scale rearrangements in some regions of the chromosome, producing variability between the different L. longbeacahe strains, as well as evidence of gene-flow between the various Legionella species via the exchange of plasmid DNA.

scholarly journals MLST Reveals a Separate and Novel Clonal Group for Acidovorax avenae Strains Causing Red Stripe in Sugarcane from Argentina

2019 ◽  
Vol 109 (3) ◽  
pp. 358-365 ◽  
Author(s):  
Paola D. Fontana ◽  
Nicolás Tomasini ◽  
Cecilia A. Fontana ◽  
Valentina Di Pauli ◽  
Pier S. Cocconcelli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Analysis ◽  
Clonal Complex ◽  
Random Amplified Polymorphic Dna ◽  
Economic Losses ◽  
Best Response ◽  
Wide Range ◽  
Dicotyledonous Plants ◽  
Sequence Types ◽  
Reference Strains

Acidovorax spp. cause a wide range of economically important diseases in monocotyledonous and dicotyledonous plants, including sugarcane, corn, rice, oat, millet, foxtail watermelon, and orchid. In Argentina, the red stripe disease of sugarcane caused by Acidovorax avenae affects 30% of the milling stems with important economic losses. To explore the genetic diversity of this bacterium associated with red stripe in Argentina, multilocus sequence typing (MLST) was applied. This study included 15 local strains isolated from four different sugarcane planting regions and selected after random amplified polymorphic DNA analysis and reference strains of A. citrulli, A. avenae, and A. oryzae to investigate their phylogenetic relationships. MLST analysis resulted in five sequence types among the sugarcane A. avenae strains which constitute a clonal complex, meaning a common and close origin. Sugarcane strains were related to A. avenae from other hosts and distant to A. citrulli. Signals of frequent recombination in several lineages of A. avenae was detected and we observed that A. oryzae is closely related to A. avenae strains. This study provides valuable data in the field of epidemiological and evolutionary investigations of novel clone of A. avenae strains causing sugarcane red stripe. The knowledge of the genetic diversity and strain-host specificity are important to select the genotypes with the best response to the red stripe disease.

Identification and proposal of a potentially new clonal complex that is a common cause of MenB disease in central and eastern Canada

2012 ◽  
Vol 58 (10) ◽  
pp. 1236-1240 ◽  
Author(s):  
Raymond S.W. Tsang ◽  
Brigitte Lefebvre ◽  
Frances B. Jamieson ◽  
Rodica Gilca ◽  
Shelley L. Deeks ◽  
...  
Keyword(s):  
Clonal Complex ◽  
Present Finding ◽  
Variable Region ◽  
The Other ◽  
Eastern Canada ◽  
Common Cause ◽  
The Third ◽  
Common Causes ◽  
Canadian Provinces ◽  
Sequence Types

This study examined serogroup B meningococci (MenB) from invasive meningococcal disease (IMD) cases in the provinces of Québec and Ontario in the last decade by multilocus sequence typing (MLST) to determine their sequence types (STs) and clonal complexes (CCs). Forty isolates from individual MenB IMD cases were found to belong to 8 related STs, with ST-336 being the founding ST and the other 7 STs being single locus variants of ST-336. Eleven isolates belonged to ST-336, 23 belonged to ST-5571, and the other 6 were represented individually by a single different ST. All but 1 of these 40 isolates have the PorA variable-region type of P1.22,14,36. Interrogation of the Neisseria MLST web site with the present finding did not put any of the 8 related STs into known CCs. Since these 8 related STs were common causes of IMD, with ST-5571 being the most frequently identified ST in Ontario and ST-336 the third most common ST identified in Québec, we propose that ST-336 and its related STs is a potentially new meningococcal clonal complex that is endemic in the Canadian provinces of Québec and Ontario, and they constitute a common cause of IMD.

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