Surveillance of Circulating
                    Bordetella pertussis
                    Strains in Europe during 1998 to 2015

ABSTRACT One reason for increased pertussis incidence is the adaptation of Bordetella pertussis to vaccine-induced immunity by modulating its genomic structure. This study, EUpert IV, includes 265 isolates collected from nine European countries during 2012 to 2015 ( n = 265) and compares the results to previous EUpert I to III studies (1998 to 2009). The analyses included genotyping, serotyping, pulsed-field gel electrophoresis (PFGE), and multilocus variable-number tandem-repeat analysis (MLVA). Genotyping results showed only small variations among the common virulence genes of B. pertussis . The frequencies of serotypes Fim2 and Fim3 varied among the four collections. Genomic analyses showed that MLVA type 27 increased to 80% between the periods of 1998 to 2001 and 2012 to 2015. Two PFGE profiles, BpSR3 (29.4%) and BpSR10 (27.2%), constituted more than 50% of the circulating isolates in the present collection. Our study indicates that the European B. pertussis population is changing and became more homogenous after the introduction of acellular pertussis vaccines.

Download Full-text

Host Range-Associated Clustering Based on Multilocus Variable-Number Tandem-Repeat Analysis, Phylotypes, and Virulence Genes of Atypical EnteropathogenicEscherichia coliStrains

Applied and Environmental Microbiology ◽

10.1128/aem.02796-18 ◽

2019 ◽

Vol 85 (6) ◽

Cited By ~ 2

Author(s):

Md Shafiullah Parvej ◽

Hiromi Nakamura ◽

Md Ashraful Alam ◽

Lili Wang ◽

Shaobo Zhang ◽

...

Keyword(s):

Spanning Tree ◽

Virulence Genes ◽

Minimum Spanning Tree ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Epidemiological Methods ◽

Content Type ◽

Repeat Analysis ◽

Group I ◽

Virulence Group

ABSTRACTAtypical enteropathogenicEscherichia coli(aEPEC) strains (36 Japanese and 50 Bangladeshi) obtained from 649 poultry fecal samples were analyzed by molecular epidemiological methods. Clermont’s phylogenetic typing showed that group A was more prevalent (58%, 50/86) than B1 (31%, 27/86). Intimin type β1, which is prevalent among human diarrheal patients, was predominant in both phylogroups B1 (81%, 22/27) and A (70%, 35/50). However, about 95% of B1-β1 strains belonged to virulence group I, and 77% of them were Japanese strains, while 17% (6/35) of A-β1 strains did. Multilocus variable-number tandem-repeat analysis (MLVA) distributed the strains into 52 distinct profiles, with Simpson’s index of diversity (D) at 73%. When the data were combined with those of 142 previous strains from different sources, the minimum spanning tree formed five zones for porcine strains, poultry strains (excluding B1-β1), strains from healthy humans, bovine and human patient strains, and the B1-β1 poultry strains. Antimicrobial resistance to nalidixic acid was most common (74%) among the isolates. Sixty-eight percent of them demonstrated resistance to ≥3 antimicrobial agents, and most of them (91%) were from Bangladesh. The strains were assigned into two groups by hierarchical clustering. Correlation matrix analysis revealed that the virulence genes were negatively associated with antimicrobial resistance. The present study suggested that poultry, particularly Japanese poultry, could be another reservoir of aEPEC (phylogroup B1, virulence group I, and intimin type β1); however, poultry strains seem to be apart from patient strains that were closer to bovine strains. Bangladeshi aEPEC may be less virulent for humans but more resistant to antibiotics.IMPORTANCEAtypical enteropathogenicEscherichia coli(aEPEC) is a diarrheagenic type ofE. coli, as it possesses the intimin gene (eae) for attachment and effacement on epithelium. Since aEPEC is ubiquitous even in developed countries, we previously used molecular epidemiological methods to discriminate aEPEC as a human pathogen. The present study assessed poultry as another source of human diarrheagenic aEPEC. Poultry could be the source of aEPEC (phylogroup B1, virulence group I, and intimin type β1) found among patient strains in Japan. However, the minimum spanning tree (MST) suggested that the strains from Japanese poultry were far from Japanese patient strains compared with the distance between bovine and patient strains. Bangladeshi avian strains seemed to be less diarrheagenic but are hazardous as a source of drug resistance genes.

Download Full-text

Potentially Human-Pathogenic Escherichia coli O26 in Norwegian Sheep Flocks

Applied and Environmental Microbiology ◽

10.1128/aem.00189-11 ◽

2011 ◽

Vol 77 (14) ◽

pp. 4949-4958 ◽

Cited By ~ 21

Author(s):

C. Sekse ◽

M. Sunde ◽

B.-A. Lindstedt ◽

P. Hopp ◽

T. Bruheim ◽

...

Keyword(s):

Escherichia Coli ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Human Pathogens ◽

Content Type ◽

Representative Sampling ◽

E Coli ◽

Pathogenic Escherichia Coli ◽

Close Relationship ◽

Large Survey

ABSTRACTA national survey ofEscherichia coliO26 in Norwegian sheep flocks was conducted, using fecal samples to determine the prevalence. In total, 491 flocks were tested, andE. coliO26 was detected in 17.9% of the flocks. One hundred forty-twoE. coliO26 isolates were examined for flagellar antigens (H typing) and four virulence genes, includingstxandeae, to identify possible Shiga toxin-producingE. coli(STEC) and enteropathogenicE. coli(EPEC). Most isolates (129 out of 142) were identified asE. coliO26:H11. They possessedeaeand may have potential as human pathogens, although only a small fraction were identified as STEC O26:H11, giving a prevalence in sheep flocks of only 0.8%. Correspondingly, the sheep flock prevalence of atypical EPEC (aEPEC) O26:H11 was surprisingly high (15.9%). The genetic relationship between theE. coliO26:H11 isolates was investigated by pulsed-field gel electrophoresis (PFGE) and multilocus variable number tandem repeat analysis (MLVA), identifying 63 distinct PFGE profiles and 22 MLVA profiles. Although the MLVA protocol was less discriminatory than PFGE and a few cases of disagreement were observed, comparison by partition mapping showed an overall good accordance between the two methods. A close relationship between a few isolates of aEPEC O26:H11 and STEC O26:H11 was identified, but all theE. coliO26:H11 isolates should be considered potentially pathogenic to humans. The present study consisted of a representative sampling of sheep flocks from all parts of Norway. This is the first large survey of sheep flocks focusing onE. coliO26 in general, including results of STEC, aEPEC, and nonpathogenic isolates.

Download Full-text

Multiple-Locus Variable-Number Tandem Repeat Analysis of Dutch Bordetella pertussis Strains Reveals Rapid Genetic Changes with Clonal Expansion during the Late 1990s

Journal of Bacteriology ◽

10.1128/jb.186.16.5496-5505.2004 ◽

2004 ◽

Vol 186 (16) ◽

pp. 5496-5505 ◽

Cited By ~ 99

Author(s):

Leo M. Schouls ◽

Han G. J. van der Heide ◽

Luc Vauterin ◽

Paul Vauterin ◽

Frits R. Mooi

Keyword(s):

The Netherlands ◽

Tandem Repeat ◽

Bordetella Pertussis ◽

Minimum Spanning Tree ◽

Whooping Cough ◽

Variable Number Tandem Repeat ◽

Clonal Expansion ◽

Variable Number ◽

Multiple Locus ◽

Repeat Analysis

ABSTRACT Bordetella pertussis, the causative agent of whooping cough, has remained endemic in The Netherlands despite extensive nationwide vaccination since 1953. In the 1990s, several epidemic periods have resulted in many cases of pertussis. We have proposed that strain variation has played a major role in the upsurges of this disease in The Netherlands. Therefore, molecular characterization of strains is important in identifying the causes of pertussis epidemiology. For this reason, we have developed a multiple-locus variable-number tandem repeat analysis (MLVA) typing system for B. pertussis. By combining the MLVA profile with the allelic profile based on multiple-antigen sequence typing, we were able to further differentiate strains. The relationships between the various genotypes were visualized by constructing a minimum spanning tree. MLVA of Dutch strains of B. pertussis revealed that the genotypes of the strains isolated in the prevaccination period were diverse and clearly distinct from the strains isolated in the 1990s. Furthermore, there was a decrease in diversity in the strains from the late 1990s, with a remarkable clonal expansion that coincided with the epidemic periods. Using this genotyping, we have been able to show that B. pertussis is much more dynamic than expected.

Download Full-text

Prediction of Local Transmission of Mycobacterium tuberculosis Isolates of a Predominantly Beijing Lineage by Use of a Variable-Number Tandem-Repeat Typing Method Incorporating a Consensus Set of Hypervariable Loci

Journal of Clinical Microbiology ◽

10.1128/jcm.01016-17 ◽

2017 ◽

Vol 56 (1) ◽

Author(s):

Yoshiro Murase ◽

Kiyohiko Izumi ◽

Akihiro Ohkado ◽

Akio Aono ◽

Kinuyo Chikamatsu ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Tandem Repeat ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Trend Test ◽

Typing Method ◽

Content Type ◽

Tuberculosis Transmission ◽

High Prevalence ◽

Hypervariable Loci

ABSTRACT Strain genotyping based on the variable-number tandem repeat (VNTR) is widely applied for identifying the transmission of Mycobacterium tuberculosis. A consensus set of four hypervariable loci (1982, 3232, 3820, and 4120) has been proposed to improve the discrimination of Beijing lineage strains. Herein, we evaluated the utility of these four hypervariable loci for tracing local tuberculosis transmission in 981 cases over a 14-month period in Japan (2010 to 2011). We used six different VNTR systems, with or without the four hypervariable loci. Patient ages and weighted standard distances (a measure of the dispersion of genotype-clustered cases) were used as proxies for estimating local tuberculosis transmission. The highest levels of isolate discrimination were achieved with VNTR systems that incorporated the four hypervariable loci (i.e., the Japan Anti-Tuberculosis Association [JATA]18-VNTR, mycobacterial interspersed repetitive unit [MIRU]28-VNTR, and 24Beijing-VNTR). The clustering rates by JATA12-VNTR, MIRU15-VNTR, JATA15-VNTR, JATA18-VNTR, MIRU28-VNTR, and 24Beijing-VNTR systems were 52.2%, 51.0%, 39.0%, 24.1%, 23.1%, and 22.0%, respectively. As the discriminative power increased, the median weighted standard distances of the clusters tended to decrease (from 311 to 80 km, P < 0.001, Jonckheere-Terpstra trend test). Concurrently, the median ages of patients in the clusters tended to decrease (from 68 to 60 years, P < 0.001, Jonckheere-Terpstra trend test). These findings suggest that strain typing using the four hypervariable loci improves the prediction of active local tuberculosis transmission. The four-locus set can therefore contribute to the targeted control of tuberculosis in settings with high prevalence of Beijing lineage strains.

Download Full-text

Examination of Taxonomic Uncertainties Surrounding Brucella abortus bv. 7 by Phenotypic and Molecular Approaches

Applied and Environmental Microbiology ◽

10.1128/aem.03755-13 ◽

2013 ◽

Vol 80 (5) ◽

pp. 1570-1579 ◽

Cited By ~ 16

Author(s):

Bruno Garin-Bastuji ◽

Virginie Mick ◽

Gilles Le Carrou ◽

Sebastien Allix ◽

Lorraine L. Perrett ◽

...

Keyword(s):

Brucella Abortus ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Epidemiological Methods ◽

Content Type ◽

Phenotypic Profile ◽

Molecular Approaches ◽

Content Classification ◽

Species Specific ◽

Kenyan Strain

ABSTRACTBrucellataxonomy is perpetually being reshuffled, at both the species and intraspecies levels. Biovar 7 ofBrucella abortuswas suspended from theApproved Lists of Bacterial NamesBrucellaclassification in 1988, because of unpublished evidence that the reference strain 63/75 was a mixture ofB. abortusbiovars 3 and 5. To formally clarify the situation, all isolates previously identified asB. abortusbv. 7 in the AHVLA and ANSES strain collections were characterized by classical microbiological and multiple molecular approaches. Among the 14 investigated strains, including strain 63/75, only four strains, isolated in Kenya, Turkey, and Mongolia, were pure and showed a phenotypic profile in agreement with the former biovar 7, particularly agglutination with both anti-A/anti-M monospecific sera. These results were strengthened by molecular strategies. Indeed, genus- and species-specific methods allowed confirmation that the four pure strains belonged to theB. abortusspecies. The combination of most approaches excluded their affiliation with the recognized biovars (biovars 1 to 6 and 9), while some suggested that they were close to biovar 3.These assays were complemented by phylogenetic and/or epidemiological methods, such as multilocus sequence analysis (MLSA) and variable-number tandem repeat (VNTR) analysis. The results of this polyphasic investigation allow us to propose the reintroduction of biovar 7 into theBrucellaclassification, with at least three representative strains. Interestingly, the Kenyan strain, sharing the same biovar 7 phenotype, was genetically divergent from other three isolates. These discrepancies illustrate the complexity ofBrucellataxonomy. This study suggests that worldwide collections could include strains misidentified asB. abortusbv. 7, and it highlights the need to verify their real taxonomic position.

Download Full-text

Antimicrobial Resistance and Virulence Determinants in European Salmonella Genomic Island 1-Positive Salmonella enterica Isolates from Different Origins

Applied and Environmental Microbiology ◽

10.1128/aem.00425-11 ◽

2011 ◽

Vol 77 (16) ◽

pp. 5655-5664 ◽

Cited By ~ 43

Author(s):

Janine Beutlich ◽

Silke Jahn ◽

Burkhard Malorny ◽

Elisabeth Hauser ◽

Stephan Hühn ◽

...

Keyword(s):

Multidrug Resistance ◽

Antimicrobial Resistance ◽

Salmonella Enterica ◽

Genomic Island ◽

Variable Number Tandem Repeat ◽

Tetracycline Resistance ◽

Variable Number ◽

Virulence Determinants ◽

Content Type ◽

Strain Collection

ABSTRACTSalmonellagenomic island 1 (SGI1) contains a multidrug resistance region conferring the ampicillin-chloramphenicol-streptomycin-sulfamethoxazole-tetracycline resistance phenotype encoded byblaPSE-1,floR,aadA2,sul1, andtet(G). Its increasing spread via interbacterial transfer and the emergence of new variants are important public health concerns. We investigated the molecular properties of SGI1-carryingSalmonella entericaserovars selected from a European strain collection. A total of 38 strains belonging toS. entericaserovar Agona,S. entericaserovar Albany,S. entericaserovar Derby,S. entericaserovar Kentucky,S. entericaserovar Newport,S. entericaserovar Paratyphi B dT+, andS. entericaserovar Typhimurium, isolated between 2002 and 2006 in eight European countries from humans, animals, and food, were subjected to antimicrobial susceptibility testing, molecular typing methods (XbaI pulsed-field gel electrophoresis [PFGE], plasmid analysis, and multilocus variable-number tandem-repeat analysis [MLVA]), as well as detection of resistance and virulence determinants (PCR/sequencing and DNA microarray analysis). Typing experiments revealed wide heterogeneity inside the strain collection and even within serovars. PFGE analysis distinguished a total of 26 different patterns. In contrast, the characterization of the phenotypic and genotypic antimicrobial resistance revealed serovar-specific features. Apart from the classical SGI1 organization found in 61% of the strains, seven different variants were identified with antimicrobial resistance properties associated with SGI1-A (S. Derby), SGI1-C (S. Derby), SGI1-F (S. Albany), SGI1-L (S. Newport), SGI1-K (S. Kentucky), SGI1-M (S.Typhimurium), and, eventually, a novel variant similar to SGI1-C with additional gentamicin resistance encoded byaadB. Only minor serovar-specific differences among virulence patterns were detected. In conclusion, the SGI1 carriers exhibited pathogenetic backgrounds comparable to the ones published for susceptible isolates. However, because of their multidrug resistance, they may be more relevant in clinical settings.

Download Full-text

Phylogenetic and Variable-Number Tandem-Repeat Analyses Identify Nonpathogenic Xanthomonas arboricola Lineages Lacking the Canonical Type III Secretion System

Applied and Environmental Microbiology ◽

10.1128/aem.00835-15 ◽

2015 ◽

Vol 81 (16) ◽

pp. 5395-5410 ◽

Cited By ~ 22

Author(s):

Salwa Essakhi ◽

Sophie Cesbron ◽

Marion Fischer-Le Saux ◽

Sophie Bonneau ◽

Marie-Agnès Jacques ◽

...

Keyword(s):

Tandem Repeat ◽

Type Iii Secretion ◽

Variable Number Tandem Repeat ◽

Type Iii Secretion System ◽

Variable Number ◽

Secretion System ◽

Content Type ◽

Type Iii ◽

Xanthomonas Arboricola ◽

Canonical Type

ABSTRACTXanthomonas arboricolais conventionally known as a taxon of plant-pathogenic bacteria that includes seven pathovars. This study showed thatX. arboricolaalso encompasses nonpathogenic bacteria that cause no apparent disease symptoms on their hosts. The aim of this study was to assess theX. arboricolapopulation structure associated with walnut, including nonpathogenic strains, in order to gain a better understanding of the role of nonpathogenic xanthomonads in walnut microbiota. A multilocus sequence analysis (MLSA) was performed on a collection of 100X. arboricolastrains, including 27 nonpathogenic strains isolated from walnut. Nonpathogenic strains grouped outside clusters defined by pathovars and formed separate genetic lineages. A multilocus variable-number tandem-repeat analysis (MLVA) conducted on a collection ofX. arboricolastrains isolated from walnut showed that nonpathogenic strains clustered separately from clonal complexes containingXanthomonas arboricolapv. juglandis strains. Some nonpathogenic strains ofX. arboricoladid not contain the canonical type III secretion system (T3SS) and harbored only one to three type III effector (T3E) genes. In the nonpathogenic strains CFBP 7640 and CFBP 7653, neither T3SS genes nor any of the analyzed T3E genes were detected. This finding raises a question about the origin of nonpathogenic strains and the evolution of plant pathogenicity inX. arboricola. T3E genes that were not detected in any nonpathogenic isolates studied represent excellent candidates to be those responsible for pathogenicity inX. arboricola.

Download Full-text

Rapid and simple SNP genotyping for Bordetella pertussis epidemic strain MT27 based on a multiplexed single-base extension assay

10.21203/rs.3.rs-109399/v1 ◽

2020 ◽

Author(s):

Kazunari Kamachi ◽

Shu-Man Yao ◽

Chuen-Sheue Chiang ◽

Kentaro Koide ◽

Nao Otsuka ◽

...

Keyword(s):

Bordetella Pertussis ◽

Diversity Index ◽

Temporal Trends ◽

Variable Number Tandem Repeat ◽

Genotypic Diversity ◽

Variable Number ◽

Snp Genotyping ◽

Single Base Extension ◽

Single Base ◽

Base Extension

Abstract Multilocus variable-number tandem repeat analysis (MLVA) is widely used for genotyping of Bordetella pertussis, the causative bacteria for pertussis. However, MLVA genotyping is losing its discriminate power because prevalence of the epidemic MT27 strain (MLVA-27) is increasing worldwide. To address this, we developed a single nucleotide polymorphism (SNP) genotyping method for MT27 based on multiplexed single-base extension (SBE) assay. A total of 237 MT27 isolates collected in Japan during 1999−2018 were genotyped and classified into ten SNP genotypes (SG1 to SG10) with a Simpson’s diversity index (DI) of 0.79 (95% CI, 0.76–0.82). Temporal trends showed a marked increase in the genotypic diversity in the 2010s: Simpson’s DI was zero in 1999–2004, 0.16 in 2005–2009, 0.83 in 2010–2014, and 0.76 in 2015–2018. This indicates that the SNP genotyping is applicable to the recently circulating MT27 strain. Additionally, almost all outbreak-associated MT27 isolates were classified into the same SNP genotypes for each outbreak. Multiplexed SBE assay allows for rapid and simple genotyping, indicating that the SNP genotyping can potentially be a useful tool for subtyping the B. pertussis MT27 strain in routine surveillance and outbreak investigations.

Download Full-text

Epidemiology of a Salmonella enterica subsp. enterica Serovar Typhimurium Strain Associated with a Songbird Outbreak

Applied and Environmental Microbiology ◽

10.1128/aem.01408-12 ◽

2012 ◽

Vol 78 (20) ◽

pp. 7290-7298 ◽

Cited By ~ 26

Author(s):

Sonia M. Hernandez ◽

Kevin Keel ◽

Susan Sanchez ◽

Eija Trees ◽

Peter Gerner-Smidt ◽

...

Keyword(s):

United States ◽

Salmonella Enterica ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Pfge Type ◽

Eastern United States ◽

Typing Method ◽

Content Type ◽

Typhimurium Strain ◽

Serovar Typhimurium

ABSTRACTSalmonella entericasubsp.entericaserovar Typhimurium is responsible for the majority of salmonellosis cases worldwide. ThisSalmonellaserovar is also responsible for die-offs in songbird populations. In 2009, there was anS. Typhimurium epizootic reported in pine siskins in the eastern United States. At the time, there was also a human outbreak with this serovar that was associated with contaminated peanuts. As peanuts are also used in wild-bird food, it was hypothesized that the pine siskin epizootic was related to this human outbreak. A comparison of songbird and humanS. Typhimurium pulsed-field gel electrophoresis (PFGE) patterns revealed that the epizootic was attributed not to the peanut-associated strain but, rather, to a songbird strain first characterized from an American goldfinch in 1998. This sameS. Typhimurium strain (PFGE type A3) was also identified in the PulseNet USA database, accounting for 137 of 77,941 totalS. Typhimurium PFGE entries. A second molecular typing method, multiple-locus variable-number tandem-repeat analysis (MLVA), confirmed that the same strain was responsible for the pine siskin epizootic in the eastern United States but was distinct from a genetically related strain isolated from pine siskins in Minnesota. The pine siskin A3 strain was first encountered in May 2008 in an American goldfinch and later in a northern cardinal at the start of the pine siskin epizootic. MLVA also confirmed the clonal nature ofS. Typhimurium in songbirds and established that the pine siskin epizootic strain was unique to the finch family. For 2009, the distribution of PFGE type A3 in passerines and humans mirrored the highest population density of pine siskins for the East Coast.

Download Full-text

Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes

Journal of Clinical Microbiology ◽

10.1128/jcm.02344-15 ◽

2015 ◽

Vol 54 (2) ◽

pp. 333-342 ◽

Cited By ~ 130

Author(s):

Jason C. Kwong ◽

Karolina Mercoulia ◽

Takehiro Tomita ◽

Marion Easton ◽

Hua Y. Li ◽

...

Keyword(s):

Listeria Monocytogenes ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Outbreak Detection ◽

Whole Genome ◽

Genetic Population ◽

Content Type ◽

Epidemiologic Surveillance

Whole-genome sequencing (WGS) has emerged as a powerful tool for comparing bacterial isolates in outbreak detection and investigation. Here we demonstrate that WGS performed prospectively for national epidemiologic surveillance ofListeria monocytogeneshas the capacity to be superior to our current approaches using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), multilocus variable-number tandem-repeat analysis (MLVA), binary typing, and serotyping. Initially 423L. monocytogenesisolates underwent WGS, and comparisons uncovered a diverse genetic population structure derived from three distinct lineages. MLST, binary typing, and serotyping results inferredin silicofrom the WGS data were highly concordant (>99%) with laboratory typing performed in parallel. However, WGS was able to identify distinct nested clusters within groups of isolates that were otherwise indistinguishable using our current typing methods. Routine WGS was then used for prospective epidemiologic surveillance on a further 97L. monocytogenesisolates over a 12-month period, which provided a greater level of discrimination than that of conventional typing for inferring linkage to point source outbreaks. A risk-based alert system based on WGS similarity was used to inform epidemiologists required to act on the data. Our experience shows that WGS can be adopted for prospectiveL. monocytogenessurveillance and investigated for other pathogens relevant to public health.

Download Full-text