scholarly journals Coxiella burnetii Shedding in Milk and Molecular Typing of Strains Infecting Dairy Cows in Greece

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 287
Author(s):  
Emmanouil Kalaitzakis ◽  
Tiziano Fancello ◽  
Xavier Simons ◽  
Ilias Chaligiannis ◽  
Sara Tomaiuolo ◽  
...  
Keyword(s):  
Dairy Cows ◽  
Coxiella Burnetii ◽  
Q Fever ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Human Infection ◽  
Animal Reservoir

Ruminants are considered the commonest animal reservoir for human infection of Coxiella burnetii, the Q fever causative agent. Considering the recently described importance of human Q fever in Greece, we aimed at providing the first comprehensive direct evidence of C. burnetii in dairy cows in Greece, including the genetic characterization of strains. The 462 examined dairy farms represented all geographical areas of Greece. One bulk tank milk sample was collected from every farm and tested for the presence of C. burnetii. Molecular genotyping of strains, performed directly on samples, revealed the existence of two separate clades characterized by single nucleotide polymorphism (SNP) genotypes of type 1 and type 2. The two clades were clearly distinguished in multiple locus variable-number tandem repeat analysis (MLVA) by two discriminative loci: MS30 and MS28. Whereas MLVA profiles of SNP-type 2 clade were closely related to strains described in other European cattle populations, the MLVA profile observed within the SNP type 1 clade highlighted a peculiar genetic signature for Greece, related to genotypes found in sheep and goats in Europe. The shedding of C. burnetii bearing this genotype might have yet undefined human epidemiological consequences. Surveillance of the genetic distribution of C. burnetii from different sources is needed to fully understand the epidemiology of Q fever in Greece.

scholarly journals Phylogeography of Human and Animal Coxiella burnetii Strains: Genetic Fingerprinting of Q Fever in Belgium

2021 ◽  
Vol 10 ◽  
Author(s):  
Sara Tomaiuolo ◽  
Samira Boarbi ◽  
Tiziano Fancello ◽  
Patrick Michel ◽  
Damien Desqueper ◽  
...  
Keyword(s):  
Coxiella Burnetii ◽  
Small Ruminant ◽  
Q Fever ◽  
Variable Number Tandem Repeat ◽  
Primary Source ◽  
Variable Number ◽  
Human Infection ◽  
Apparent Prevalence ◽  
Domestic Ruminants ◽  
Contamination Routes

Q fever is a zoonotic disease caused by the bacteria Coxiella burnetii. Domestic ruminants are the primary source for human infection, and the identification of likely contamination routes from the reservoir animals the critical point to implement control programs. This study shows that Q fever is detected in Belgium in abortion of cattle, goat and sheep at a different degree of apparent prevalence (1.93%, 9.19%, and 5.50%, respectively). In addition, and for the first time, it is detected in abortion of alpaca (Vicugna pacos), raising questions on the role of these animals as reservoirs. To determine the relationship between animal and human strains, Multiple Locus Variable-number Tandem Repeat Analysis (MLVA) (n=146), Single-Nucleotide Polymorphism (SNP) (n=92) and Whole Genome Sequencing (WGS) (n=4) methods were used to characterize samples/strains during 2009-2019. Three MLVA clusters (A, B, C) subdivided in 23 subclusters (A1-A12, B1-B8, C1-C3) and 3 SNP types (SNP1, SNP2, SNP6) were identified. The SNP2 type/MLVA cluster A was the most abundant and dispersed genotype over the entire territory, but it seemed not responsible for human cases, as it was only present in animal samples. The SNP1/MLVA B and SNP6/MLVA C clusters were mostly found in small ruminant and human samples, with the rare possibility of spillovers in cattle. SNP1/MLVA B cluster was present in all Belgian areas, while the SNP6/MLVA C cluster appeared more concentrated in the Western provinces. A broad analysis of European MLVA profiles confirmed the host-species distribution described for Belgian samples. In silico genotyping (WGS) further identified the spacer types and the genomic groups of C. burnetii Belgian strains: cattle and goat SNP2/MLVA A isolates belonged to ST61 and genomic group III, while the goat SNP1/MLVA B strain was classified as ST33 and genomic group II. In conclusion, Q fever is widespread in all Belgian domestic ruminants and in alpaca. We determined that the public health risk in Belgium is likely linked to specific genomic groups (SNP1/MLVA B and SNP6/MLVA C) mostly found in small ruminant strains. Considering the concordance between Belgian and European results, these considerations could be extended to other European countries.

scholarly journals Molecular Detection and Characterization of Mycoplasma pneumoniae Among Patients Hospitalized With Community-Acquired Pneumonia in the United States

2015 ◽  
Vol 2 (3) ◽  
Author(s):  
Maureen H. Diaz ◽  
Alvaro J. Benitez ◽  
Kristen E. Cross ◽  
Lauri A. Hicks ◽  
Preeta Kutty ◽  
...  
Keyword(s):  
United States ◽  
Mycoplasma Pneumoniae ◽  
Variable Number Tandem Repeat ◽  
The United States ◽  
Variable Number ◽  
Community Acquired Pneumonia ◽  
Molecular Characteristics

Abstract Background.  Mycoplasma pneumoniae is a common cause of community-acquired pneumonia (CAP). The molecular characteristics of M pneumoniae detected in patients hospitalized with CAP in the United States are poorly described. Methods.  We performed molecular characterization of M pneumoniae in nasopharyngeal/oropharyngeal swabs from children and adults hospitalized with CAP in the Centers for Disease Control and Prevention Etiology of Pneumonia in the Community (EPIC) study, including P1 typing, multilocus variable-number tandem-repeat analysis (MLVA), and macrolide susceptibility genotyping. Results.  Of 216 M pneumoniae polymerase chain reaction-positive specimens, 40 (18.5%) were obtained from adults and 176 (81.5%) from children. P1 type distribution differed between adults (64% type 1 and 36% type 2) and children (84% type 1, 13% type 2, and 3% variant) (P < .05) and among sites (P < .01). Significant differences in the proportions of MLVA types 4/5/7/2 and 3/5/6/2 were also observed by age group (P < .01) and site (P < .01). A macrolide-resistant genotype was ide.jpegied in 7 (3.5%) specimens, 5 of which were from patients who had recently received macrolide therapy. No significant differences in clinical characteristics were ide.jpegied among patients with various strain types or between macrolide-resistant and -sensitive M pneumoniae infections. Conclusions.  The P1 type 1 genotype and MLVA type 4/5/7/2 predominated, but there were differences between children and adults and among sites. Macrolide resistance was rare. Differences in strain types did not appear to be associated with differences in clinical outcomes. Whole genome sequencing of M pneumoniae may help ide.jpegy better ways to characterize strains.

scholarly journals Molecular detection of Coxiella burnetii in small ruminants and genotyping of specimens collected from goats in Poland

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Agnieszka Jodełko ◽  
Monika Szymańska-Czerwińska ◽  
Jolanta Grażyna Rola ◽  
Krzysztof Niemczuk
Keyword(s):  
Coxiella Burnetii ◽  
Small Ruminant ◽  
Q Fever ◽  
Variable Number Tandem Repeat ◽  
Small Ruminants ◽  
Variable Number ◽  
Tissue Sections ◽  
Pcr Targeting ◽  
Sequence Types ◽  
Multispacer Sequence Typing

Abstract Background Coxiella burnetii is the etiological agent of Q fever, a zoonosis affecting many animal species including sheep and goats. The aims of this study were to evaluate the shedding of Coxiella burnetii in small ruminant herds and to identify the pathogen’s genotypes and sequence types (STs) using multiple-locus variable number tandem repeat analysis (MLVA) and multispacer sequence typing (MST) methods. Results Overall, 165 samples from 43 herds of goats and 9 flocks of sheep were collected including bulk tank milk (BTM), individual milk samples, vaginal swabs, tissue sections from stillborn kids, feces and placentas. These were tested by real-time PCR targeting the IS1111 element. C. burnetii infection was confirmed in 51.16% of the herds of goats and 22.2% of the flocks of sheep. Six out of nine samples originating from goats were successfully genotyped using the MLVA method. The presence was confirmed of two widely distributed MLVA genotypes (I and J) and genotype PL1 previously reported only in cattle. Only one sequence type (ST61) was identified; however, the majority of specimens represented partial STs and some of them may belong to ST61. Other partial STs could possibly be ST74. Conclusion This study confirmed the relatively common occurrence of Coxiella burnetii in small ruminant herds in Poland. Interestingly, all genotyped samples represent cattle-associated MLVA genotypes.

scholarly journals First Complete Genome Sequence of the Dutch VeterinaryCoxiella burnetiiStrain NL3262, Originating from the Largest Global Q Fever Outbreak, and Draft Genome Sequence of Its Epidemiologically Linked Chronic Human Isolate NLhu3345937

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Runa Kuley ◽  
Hilde E. Smith ◽  
Ingmar Janse ◽  
Frank L. Harders ◽  
Frank Baas ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Coxiella Burnetii ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Q Fever ◽  
Draft Genome ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Outbreak Strain ◽  
Repeat Analysis

The largest global Q fever outbreak occurred in The Netherlands during 2007 to 2010. Goats and sheep were identified as the major sources of disease. Here, we report the first complete genome sequence ofCoxiella burnetiigoat outbreak strain NL3262 and that of an epidemiologically linked chronic human strain, both having the outbreak-relatedCbNL01multilocus variable-number tandem-repeat analysis (MLVA) genotype.

scholarly journals Correlating Genotyping Data of Coxiella burnetii with Genomic Groups

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 604
Author(s):  
Claudia M. Hemsley ◽  
Angela Essex-Lopresti ◽  
Isobel H. Norville ◽  
Richard W. Titball
Keyword(s):  
Coxiella Burnetii ◽  
Classification Scheme ◽  
Q Fever ◽  
Variable Number Tandem Repeat ◽  
Febrile Illness ◽  
Variable Number ◽  
New Classification ◽  
Genetic Lineages ◽  
Virulence Potential ◽  
Multispacer Sequence Typing

Coxiella burnetii is a zoonotic pathogen that resides in wild and domesticated animals across the globe and causes a febrile illness, Q fever, in humans. Several distinct genetic lineages or genomic groups have been shown to exist, with evidence for different virulence potential of these lineages. Multispacer Sequence Typing (MST) and Multiple-Locus Variable number tandem repeat Analysis (MLVA) are being used to genotype strains. However, it is unclear how these typing schemes correlate with each other or with the classification into different genomic groups. Here, we created extensive databases for published MLVA and MST genotypes of C. burnetii and analysed the associated metadata, revealing associations between animal host and human disease type. We established a new classification scheme that assigns both MST and MLVA genotypes to a genomic group and which revealed additional sub-lineages in two genomic groups. Finally, we report a novel, rapid genomotyping method for assigning an isolate into a genomic group based on the Cox51 spacer sequence. We conclude that by pooling and streamlining existing datasets, associations between genotype and clinical outcome or host source were identified, which in combination with our novel genomotyping method, should enable an estimation of the disease potential of new C. burnetii isolates.

scholarly journals Identification of Tick-Borne Pathogens and Genotyping of Coxiella burnetii in Rhipicephalus microplus in Yunnan Province, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Jun Jiao ◽  
Jianing Zhang ◽  
Peisheng He ◽  
Xuan OuYang ◽  
Yonghui Yu ◽  
...  
Keyword(s):  
Coxiella Burnetii ◽  
Yunnan Province ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Rhipicephalus Microplus ◽  
Nested Polymerase Chain Reaction ◽  
Phylogenetic Characterization ◽  
Pooled Dna ◽  
First Time

Rhipicephalus microplus, a vector that can transmit many pathogens to humans and domestic animals, is widely distributed in Yunnan province, China. However, few reports on the prevalence of tick-borne pathogens (TBPs) in Rh. microplus in Yunnan are available. The aim of this study was to detect TBPs in Rh. microplus in Yunnan and to analyze the phylogenetic characterization of TBPs detected in these ticks. The adult Rh. microplus (n = 516) feeding on cattle were collected. The pooled DNA samples of these ticks were evaluated using metagenomic next-generation sequencing (mNGS) and then TBPs in individual ticks were identified using genus- or group-specific nested polymerase chain reaction (PCR) combined with DNA sequencing assay. As a result, Candidatus Rickettsia jingxinensis (24.61%, 127/516), Anaplasma marginale (13.18%, 68/516), Coxiella burnetii (3.10%, 16/516), and Coxiella-like endosymbiont (CLE) (8.33%, 43/516) were detected. The dual coinfection with Ca. R. jingxinensis and A. marginale and the triple coinfection with Ca. R. jingxinensis, A. marginale, and CLE were most frequent and detected in 3.68% (19/516) and 3.10% (16/516) of these ticks, respectively. The results provide insight into the diversity of TBPs and their coinfections in Rh. microplus in Yunnan province of China, reporting for the first time that C. burnetii had been found in Rh. microplus in China. Multilocus variable number tandem repeat analysis with 6 loci (MLVA-6) discriminated the C. burnetii detected in Rh. microplus in Yunnan into MLVA genotype 1, which is closely related to previously described genotypes found primarily in tick and human samples from different regions of the globe, indicating a potential public health threat posed by C. burnetii in Rh. microplus in Yunnan.

scholarly journals Circulation of Coxiella burnetii in a Naturally Infected Flock of Dairy Sheep: Shedding Dynamics, Environmental Contamination, and Genotype Diversity

2015 ◽  
Vol 81 (20) ◽  
pp. 7253-7260 ◽  
Author(s):  
A. Joulié ◽  
K. Laroucau ◽  
X. Bailly ◽  
M. Prigent ◽  
P. Gasqui ◽  
...  
Keyword(s):  
Coxiella Burnetii ◽  
Environmental Contamination ◽  
Q Fever ◽  
Management Strategies ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Dairy Sheep ◽  
Content Type ◽  
Ewe Lambs ◽  
Genotype Diversity

ABSTRACTQ fever is a worldwide zoonosis caused byCoxiella burnetii. Domestic ruminants are considered to be the main reservoir. Sheep, in particular, may frequently cause outbreaks in humans. Because within-flock circulation data are essential to implementing optimal management strategies, we performed a follow-up study of a naturally infected flock of dairy sheep. We aimed to (i) describeC. burnetiishedding dynamics by sampling vaginal mucus, feces, and milk, (ii) assess circulating strain diversity, and (iii) quantify barn environmental contamination. For 8 months, we sampled vaginal mucus and feces every 3 weeks from aborting and nonaborting ewes (n= 11 andn= 26, respectively); for lactating females, milk was obtained as well. We also sampled vaginal mucus from nine ewe lambs. Dust and air samples were collected every 3 and 6 weeks, respectively. All samples were screened using real-time PCR, and strongly positive samples were further analyzed using quantitative PCR. Vaginal and fecal samples with sufficient bacterial burdens were then genotyped by multiple-locus variable-number tandem-repeat analysis (MLVA) using 17 markers.C. burnetiiburdens were higher in vaginal mucus and feces than in milk, and they peaked in the first 3 weeks postabortion or postpartum. Primiparous females and aborting females tended to shedC. burnetiilonger and have higher bacterial burdens than nonaborting and multiparous females. Six genotype clusters were identified; they were independent of abortion status, and within-individual genotype diversity was observed.C. burnetiiwas also detected in air and dust samples. Further studies should determine whether the within-flock circulation dynamics observed here are generalizable.

scholarly journals Human Q Fever on the Guiana Shield and Brazil: Recent Findings and Remaining Questions

2021 ◽  
Author(s):  
Loïc Epelboin ◽  
Carole Eldin ◽  
Pauline Thill ◽  
Vincent Pommier de Santi ◽  
Philippe Abboud ◽  
...  
Keyword(s):  
South America ◽  
Geographical Distribution ◽  
Coxiella Burnetii ◽  
French Guiana ◽  
Q Fever ◽  
Guiana Shield ◽  
Animal Reservoir ◽  
The World ◽  
Unique Strain ◽  
Amazonian Region

Abstract Purpose of Review In this review, we report on the state of knowledge about human Q fever in Brazil and on the Guiana Shield, an Amazonian region located in northeastern South America. There is a contrast between French Guiana, where the incidence of this disease is the highest in the world, and other countries where this disease is practically non-existent. Recent Findings Recent findings are essentially in French Guiana where a unique strain MST17 has been identified; it is probably more virulent than those usually found with a particularly marked pulmonary tropism, a mysterious animal reservoir, a geographical distribution that raises questions. Summary Q fever is a bacterial zoonosis due to Coxiella burnetii that has been reported worldwide. On the Guiana Shield, a region mostly covered by Amazonian forest, which encompasses the Venezuelan State of Bolivar, Guyana, Suriname, French Guiana, and the Brazilian State of Amapá, the situation is very heterogeneous. While French Guiana is the region reporting the highest incidence of this disease in the world, with a single infecting clone (MST 117) and a unique epidemiological cycle, it has hardly ever been reported in other countries in the region. This absence of cases raises many questions and is probably due to massive under-diagnosis. Studies should estimate comprehensively the true burden of this disease in the region.

Characterization of damage and biotic factors associated with the decline of Eucalyptus wandoo in southwest Western Australia

2005 ◽  
Vol 35 (11) ◽  
pp. 2589-2602 ◽  
Author(s):  
Ryan J Hooper ◽  
K Sivasithamparam
Keyword(s):  
Western Australia ◽  
Partial Harvest ◽  
Foliage Density ◽  
Density Ratios ◽  
The Relationship ◽  
Mixed Age ◽  
Eucalyptus Wandoo

Crown decline of wandoo, Eucalyptus wandoo, in southwest Western Australia has escalated over the last 10 years, so very few unaffected stands remain. To assess the canopy-damage characteristics of trees in decline a destructive, partial-harvest method was used to sample branches in natural mixed-age stands. Necrosis of common cankers was closely associated with type-1 borer damage, characterized by "longitudinal" gallery structure on declining trees only. Cankers were found to be consistently more severe on declining trees, with decay regions affecting a greater proportion of sapwood tissue. Several infestations causing type-1 borer damage that varied in age were found on declining branches, providing evidence of cyclical damage events. Type-2 borer damage characterized by "ring-barking" gallery structure caused extensive damage in canopies, but was not always associated with decline. Interactions between foliage density and canker score showed that 17.8% and 63.1% of the variability in foliage-density ratios was accounted for in declining intermediate-health and unhealthy classes, respectively. The relationship was negligible for the healthy class (9.9%), providing strong evidence that cankers are causing foliage loss in declining canopies. Evidence suggests that an interaction between type-1 borer infestations and decay-causing fungi is responsible for the decline in E. wandoo wandoo canopies.

scholarly journals The Blue Copper-Containing Nitrite Reductase fromAlcaligenes xylosoxidans: Cloning of the nirAGene and Characterization of the Recombinant Enzyme

1999 ◽  
Vol 181 (8) ◽  
pp. 2323-2329 ◽  
Author(s):  
Miguel Prudêncio ◽  
Robert R. Eady ◽  
Gary Sawers
Keyword(s):  
Amino Acid ◽  
Nitrite Reductase ◽  
Recombinant Enzyme ◽  
Leader Peptide ◽  
Resonance Spectroscopy ◽  
Gene Encoding ◽  
Blue Copper

ABSTRACT The nirA gene encoding the blue dissimilatory nitrite reductase from Alcaligenes xylosoxidans has been cloned and sequenced. To our knowledge, this is the first report of the characterization of a gene encoding a blue copper-containing nitrite reductase. The deduced amino acid sequence exhibits a high degree of similarity to other copper-containing nitrite reductases from various bacterial sources. The full-length protein included a 24-amino-acid leader peptide. The nirA gene was overexpressed inEscherichia coli and was shown to be exported to the periplasm. Purification was achieved in a single step, and analysis of the recombinant Nir enzyme revealed that cleavage of the signal peptide occurred at a position identical to that for the native enzyme isolated from A. xylosoxidans. The recombinant Nir isolated directly was blue and trimeric and, on the basis of electron paramagnetic resonance spectroscopy and metal analysis, possessed only type 1 copper centers. This type 2-depleted enzyme preparation also had a low nitrite reductase enzyme activity. Incubation of the periplasmic fraction with copper sulfate prior to purification resulted in the isolation of an enzyme with a full complement of type 1 and type 2 copper centers and a high specific activity. The kinetic properties of the recombinant enzyme were indistinguishable from those of the native nitrite reductase isolated from A. xylosoxidans. This rapid isolation procedure will greatly facilitate genetic and biochemical characterization of both wild-type and mutant derivatives of this protein.

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