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 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 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 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 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 New Genotypes of Coxiella burnetii Circulating in Brazil and Argentina

Pathogens ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 30 ◽  
Author(s):  
Mateus de Souza Ribeiro Mioni ◽  
Karim Sidi-Boumedine ◽  
Felipe Morales Dalanezi ◽  
Sâmea Fernandes Joaquim ◽  
Renan Denadai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
South America ◽  
Coxiella Burnetii ◽  
Tandem Repeats ◽  
Q Fever ◽  
Variable Number ◽  
Worldwide Distribution ◽  
Variable Number Tandem Repeats ◽  
Mlva Typing ◽  
Multispacer Sequence Typing

Coxiella burnetii, the zoonotic agent of Q fever, has a worldwide distribution. Despite the vast information about the circulating genotypes in Europe and North America, there is a lack of data regarding C. burnetii strains in South America. Here, we show the presence of novel multispacer sequence typing (MST) genotypes of C. burnetii in two clusters detected in Brazil and Argentina that seem to be distant in parenthood. Argentinian strains isolated from a tick belongs to a new phylogenetic branch of C. burnetii, and the Brazilians strains may be related to MST 20 and 61. Multilocus variable number tandem repeats analysis (MLVA) typing provided a deeper resolution that may be related to host clusters of bovines, caprine, ovine, and ticks. Our results corroborate with the reports of geotypes of C. burnetii. Thus, we highlight the need for more genotyping studies to understand the genetic diversity of C. burnetii in South America and to confirm the hypothesis of host-related genotypes. We also emphasize the importance of virulence studies for a better understanding of Q fever in the region, which may help in surveillance and disease prevention programs.

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 Coxiella burnetii Intratracheal Aerosol Infection Model in Mice, Guinea Pigs, and Nonhuman Primates

2019 ◽  
Vol 87 (12) ◽  
Author(s):  
A. E. Gregory ◽  
E. J. van Schaik ◽  
K. E. Russell-Lodrigue ◽  
A. P. Fratzke ◽  
J. E. Samuel
Keyword(s):  
Animal Models ◽  
Coxiella Burnetii ◽  
Guinea Pigs ◽  
Nonhuman Primates ◽  
Q Fever ◽  
Febrile Illness ◽  
Cell Vaccine ◽  
Infection Model ◽  
Atypical Pneumonia ◽  
Content Type

ABSTRACT Coxiella burnetii, the etiological agent of Q fever, is a Gram-negative bacterium transmitted to humans by inhalation of contaminated aerosols. Acute Q fever is often self-limiting, presenting as a febrile illness that can result in atypical pneumonia. In some cases, Q fever becomes chronic, leading to endocarditis that can be life threatening. The formalin-inactivated whole-cell vaccine (WCV) confers long-term protection but has significant side effects when administered to presensitized individuals. Designing new vaccines against C. burnetii remains a challenge and requires the use of clinically relevant modes of transmission in appropriate animal models. We have developed a safe and reproducible C. burnetii aerosol challenge in three different animal models to evaluate the effects of pulmonary acquired infection. Using a MicroSprayer aerosolizer, BL/6 mice and Hartley guinea pigs were infected intratracheally with C. burnetii Nine Mile phase I (NMI) and demonstrated susceptibility as determined by measuring bacterial growth in the lungs and subsequent dissemination to the spleen. Histological analysis of lung tissue showed significant pathology associated with disease, which was more severe in guinea pigs. Infection using large-particle aerosol (LPA) delivery was further confirmed in nonhuman primates, which developed fever and pneumonia. We also demonstrate that vaccinating mice and guinea pigs with WCV prior to LPA challenge is capable of eliciting protective immunity that significantly reduces splenomegaly and the bacterial burden in spleen and lung tissues. These data suggest that these models can have appreciable value in using the LPA delivery system to study pulmonary Q fever pathogenesis as well as designing vaccine countermeasures to C. burnetii aerosol transmission.

scholarly journals Outbreak of Q fever in Lohra-Rollshausen, Germany, spring 1996

1997 ◽  
Vol 2 (2) ◽  
pp. 9-11 ◽  
Author(s):  
O Lyytikaïnen ◽  
T Ziese ◽  
B Schwartländer ◽  
P Matzdorff ◽  
C Kuhnhen ◽  
...  
Keyword(s):  
Coxiella Burnetii ◽  
Q Fever ◽  
Febrile Illness ◽  
Sheep And Goats ◽  
Animal Reservoirs

Q fever is an acute (and sometimes chronic) febrile illness caused by the rickettsial organism Coxiella burnetii. The commonest animal reservoirs for C. burnetiiare cattle, sheep, and goats. Infected animals shed the organisms, which resist desiccation, i

scholarly journals Genetic Diversity of the Q Fever Agent, Coxiella burnetii, Assessed by Microarray-Based Whole-Genome Comparisons

2006 ◽  
Vol 188 (7) ◽  
pp. 2309-2324 ◽  
Author(s):  
Paul A. Beare ◽  
James E. Samuel ◽  
Dale Howe ◽  
Kimmo Virtaneva ◽  
Stephen F. Porcella ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Coxiella Burnetii ◽  
Q Fever ◽  
Point Mutations ◽  
Open Reading Frames ◽  
Cellular Functions ◽  
Genetic Changes ◽  
Large Deletions ◽  
Reference Isolate ◽  
Virulence Potential

ABSTRACT Coxiella burnetii, a gram-negative obligate intracellular bacterium, causes human Q fever and is considered a potential agent of bioterrorism. Distinct genomic groups of C. burnetii are revealed by restriction fragment-length polymorphisms (RFLP). Here we comprehensively define the genetic diversity of C. burnetii by hybridizing the genomes of 20 RFLP-grouped and four ungrouped isolates from disparate sources to a high-density custom Affymetrix GeneChip containing all open reading frames (ORFs) of the Nine Mile phase I (NMI) reference isolate. We confirmed the relatedness of RFLP-grouped isolates and showed that two ungrouped isolates represent distinct genomic groups. Isolates contained up to 20 genomic polymorphisms consisting of 1 to 18 ORFs each. These were mostly complete ORF deletions, although partial deletions, point mutations, and insertions were also identified. A total of 139 chromosomal and plasmid ORFs were polymorphic among all C. burnetii isolates, representing ca. 7% of the NMI coding capacity. Approximately 67% of all deleted ORFs were hypothetical, while 9% were annotated in NMI as nonfunctional (e.g., frameshifted). The remaining deleted ORFs were associated with diverse cellular functions. The only deletions associated with isogenic NMI variants of attenuated virulence were previously described large deletions containing genes involved in lipopolysaccharide (LPS) biosynthesis, suggesting that these polymorphisms alone are responsible for the lower virulence of these variants. Interestingly, a variant of the Australia QD isolate producing truncated LPS had no detectable deletions, indicating LPS truncation can occur via small genetic changes. Our results provide new insight into the genetic diversity and virulence potential of Coxiella species.

scholarly journals High Prevalence and New Genotype of Coxiella burnetii in Ticks Infesting Camels in Somalia

Pathogens ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 741
Author(s):  
Dimitrios Frangoulidis ◽  
Claudia Kahlhofer ◽  
Ahmed Shire Said ◽  
Abdinasir Yusuf Osman ◽  
Lidia Chitimia-Dobler ◽  
...  
Keyword(s):  
Coxiella Burnetii ◽  
One Health ◽  
Tandem Repeats ◽  
Q Fever ◽  
Epidemiological Studies ◽  
Variable Number ◽  
New Genotype ◽  
High Prevalence ◽  
Variable Number Tandem Repeats ◽  
Vntr Analysis

Coxiella burnetii is the causative agent of Q fever. It can infect animals, humans, and birds, as well as ticks, and it has a worldwide geographical distribution. To better understand the epidemiology of C. burnetii in Somalia, ticks infesting camels were collected from five different regions, including Bari, Nugaal, Mudug, Sool, and Sanaag, between January and March 2018. Collected ticks were tested for C. burnetii and Coxiella-like endosymbiont DNA by using IS1111, icd, and Com1-target PCR assays. Moreover, sequencing of the 16S-rRNA was conducted. Molecular characterization and typing were done by adaA-gene analysis and plasmid-type identification. Further typing was carried out by 14-marker Multi-Locus Variable-Number Tandem Repeats (MLVA/VNTR) analysis. The investigated ticks (n = 237) were identified as Hyalomma spp. (n = 227, 95.8%), Amblyomma spp. (n = 8, 3.4%), and Ripicephalus spp. (n = 2, 0.8%), and 59.1% (140/237) of them were positive for Coxiella spp. While Sanger sequencing and plasmid-type identification revealed a C. burnetii that harbours the QpRS-plasmid, MLVA/VNTR genotyping showed a new genotype which was initially named D21. In conclusion, this is the first report of C. burnetii in ticks in Somalia. The findings denote the possibility that C. burnetii is endemic in Somalia. Further epidemiological studies investigating samples from humans, animals, and ticks within the context of “One Health” are warranted.

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