Genotyping of Coxiella burnetii from domestic ruminants and human in Hungary: indication of various genotypes

Bacterial burden and molecular characterization of Coxiella burnetii in shedding pregnant and postpartum ewes from Saint Kitts

This study aimed to evaluate the bacterial burden and perform molecular characterization of Coxiella burnetii during shedding in pregnant (vaginal, mucus and feces) and postpartum (vaginal mucus, feces and milk) ewes from Saint Kitts. Positive IS1111 DNA (n=250) for C. burnetii samples from pregnant (n=87) and postpartum (n=74) Barbados Blackbelly ewes in a previous investigation were used for this study. Vaginal mucus (n=118), feces (n=100), and milk (n=32) positive IS1111 C. burnetii-DNA were analysed by real time qPCR (icd gene). For molecular characterization of C. burnetii, selected (n=10) IS1111 qPCR positive samples were sequenced for fragments of the IS1111 element and the 16 S rRNA gene. nBLAST, phylogenetic and haplotype analyses were performed. Vaginal mucus, feces and milk had estimated equal amounts of bacterial DNA (icd copies), and super spreaders were detected within the fecal samples. C. burnetii haplotypes had moderate to high diversity, were ubiquitous worldwide and similar to previously described in ruminants and ticks and humans.

Molecular detection and MST genotyping of Coxiella burnetii in ruminants and stray dogs and cats in Northern Algeria

Aiming at identifying the reservoir and contamination sources of Coxiella burnetii in Northern Algeria, we investigated the molecular presence of the bacterium in 599 samples (blood, placenta, liver, spleen, and uterus) collected from cattle, sheep, dogs and cats. Our qPCR results showed that 15/344 (4.36%) blood samples and six/255 (2.35%) organ specimens were positive for C. burnetii. In cattle, three (4%) blood and liver samples were positive. In sheep, one blood (1.19%) and 3 (8.57%) placenta samples were positive. At the Algiers dog pound, 8 (10%) and 3 (5%) blood samples were qPCR positivein dogs and cats, respectively. In addition, MST genotyping showed that MST 33 was present in cattle and sheep, MST 20 in cattle,andMST 21 in dogs and cats.

Genotyping and phylogenetic analysis of Coxiella burnetii in domestic ruminant and clinical samples in Iran: insights into Q fever epidemiology

Coxiella burnetii, a zoonotic pathogen, is the causative agent of Q fever, an endemic disease in Iran. However, there is currently a lack of available data on the genotypes of C. burnetii in the country. Here, we typed 26 C. burnetii isolates detected in milk, abortion, cotylodon, and cardiac valve samples from various geographical areas and hosts (7 cattle, 8 goats, 10 sheep, and 1 human) using Multilocus Variable Number Tandem Repeat Analysis (MLVA/VNTR) with five loci:ms24, ms27, ms28, ms33, and ms34. As IS1111 was observed to be spontaneously inserted in locus ms23 across all of our examined C. burnetii samples, five loci were employed for MLVA/VNTR genotyping. Among the 26 C. burnetii strains, 22 distinct genotypes (A-V) were identified in the discriminative loci. In silico analysis categorized Iranian C. burnetii strains into five genomic groups along with seven singletons, representing 11 exiting clonal complexes worldwide. Clusters 10 and 11 exclusively consisted of Iranian samples. These findings revealed high genotyping diversity among C. burnetii isolates in Iran. The genotypes circulating in Iran differed significantly from those found in other regions worldwide. To gain a comprehensive understanding of Q fever epidemiology in Iran, it is crucial to conduct large-scale studies that assess the distribution of C. burnetii genotypes across different geographical areas, hosts, and sources.

Role of Goats in the Epidemiology of Coxiella burnetii

Since its first description in the late 1930s, Q fever has raised many questions. Coxiella burnetii, the causative agent, is a zoonotic pathogen affecting a wide range of hosts. This airborne organism leads to an obligate, intracellular lifecycle, during which it multiplies in the mononuclear cells of the immune system and in the trophoblasts of the placenta in pregnant females. Although some issues about C. burnetii and its pathogenesis in animals remain unclear, over the years, some experimental studies on Q fever have been conducted in goats given their excretion pattern. Goats play an important role in the epidemiology and economics of C. burnetii infections, also being the focus of several epidemiological studies. Additionally, variants of the agent implicated in human long-term disease have been found circulating in goats. The purpose of this review is to summarize the latest research on C. burnetii infection and the role played by goats in the transmission of the infection to humans.

Q Fever—A Neglected Zoonosis

Q fever remains a neglected zoonosis in many developing countries including Pakistan. The causing agent Coxiella (C.) burnetii is resistant to environmental factors (such as drying, heat and many disinfectants), resulting in a long-lasting infection risk for both human and animals. As the infection is usually asymptomatic, it mostly remains undiagnosed in animals until and unless adverse pregnancy outcomes occur in a herd. In humans, the infection leads to severe endocarditis and vascular infection in chronic cases. Limited data are available on molecular epidemiology and evolution of this pathogen, especially in ruminants. Genomic studies will help speculating outbreak relationships in this scenario. Likewise, pathogenesis of C. burnetii needs to be explored by molecular studies. Awareness programs and ensuring pasteurization of the dairy milk before human consumption would help preventing Q fever zoonosis.

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

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.

Prevalence of Coxiella burnetii in bovine placentas in Hungary and Slovakia: Detection of a novel sequence type - Short communication

Cotyledons (n = 167) from 30 Hungarian and 5 Slovakian dairy cattle herds were analysed for Coxiella burnetii by real-time PCR targeting the IS1111 gene. Eighty (88.9%) out of the 90 cotyledons from retained placentas and 31 (40.3%) out of the 77 cotyledons from normally separated placentas tested positive. Seventeen out of the 80 positive samples (21.3%) originating from retained placentas were found to be highly loaded with C. burnetii with a cycle threshold (Ct) value lower than or equal to 27.08, ranging between 11.92 and 27.08. The rest of the positive samples from retained fetal membranes and from normally separated placentas were moderately loaded with C. burnetii DNA. Five out of the ten samples showing the strongest positivity (Ct 11.92-18.28) from retained placentas were genotyped by multispacer sequence typing based on ten loci, which revealed sequence type (ST) 61, a type that had not been detected in Hungary and Slovakia previously. Retained placenta was more likely in cows with C. burnetii PCR-positive cotyledons (odds ratio: 12.61, P = 0.0023). The high C. burnetii DNA load found in retained fetal membranes may be a potential risk factor for human infection and may also be associated with the retention of fetal membranes.

Correlating Genotyping Data of Coxiella burnetii with Genomic Groups

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.

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

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.

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

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.

Molecular prevalence of Coxiella burnetii in bulk-tank milk from bovine dairy herds: Systematic review and meta-analysis

Coxiella burnetii is an obligate intracellular zoonotic bacterium that causes Q fever. Ruminants, including cattle, are broadly known to be reservoirs for this bacterium. Since 2006, many research groups have evaluated the herd-level prevalence of C. burnetii in cattle by molecular techniques on composite milk samples. This study explored the global C. burnetii herd-level prevalence from studies done on bovine bulk-tank milk (BTM) samples using PCR-based analysis. Also, moderators were investigated to identify sources of heterogeneity. Databases (CAB Abstracts, Medline via Ovid, PubMed, Web of Science and Google Scholar) were searched for index articles on C. burnetii prevalence in BTM samples by PCR published between January-1973 and November-2018. Numerous studies (1054) were initially identified, from which seventeen original publications were included in the meta-analysis based on the pre-defined selection criteria. These studies comprised 4031 BTM samples from twelve countries. A random-effects model was used because of considerable heterogeneity (I² = 98%) to estimate the herd-level prevalence of C. burnetii as 37.0%(CI_95%25.2–49.5%). The average herd size appeared to account for a high level of the heterogeneity. No other moderators (geographic location, gross national income or notification criteria for Q fever) seemed to be determinant. This systematic evaluation demonstrated a high molecular prevalence of C. burnetii in BTM samples both in European and non-European countries, evidencing a widespread herd-level circulation of this agent in bovine dairy farms around the world. Meta-regression showed herd size as the most relevant moderator with the odds of a BTM sample testing positive doubling with every unit increase.

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First meta-analysis of the PCR-based prevalence of C. burnetii in bovine milk

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Results showed a high molecular prevalence of C. burnetii in bulk-tank milk samples.

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C. burnetii is widely distributed in dairy farms in Europe and the wider world.

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Current results reinforce the need for further investigations on this zoonosis.

Molecular Detection of Rickettsia Spp. and Coxiella Burnetii in Cattle, Water Buffalo, and Rhipicephalus (Boophilus) Microplus Ticks in Luzon Island of the Philippines

Rickettsia and Coxiella burnetii are zoonotic, tick-borne pathogens that can cause febrile illnesses with or without other symptoms in humans, but may cause subclinical infections in animals. There are only a few reports on the occurrence of these pathogens in cattle and water buffalo in Southeast Asia, including the Philippines. In this study, molecular detection of Rickettsia and C. burnetii in the blood and in the Rhipicephalus (Boophilus) microplus ticks of cattle and water buffalo from five provinces in Luzon Island of the Philippines was done. A total of 620 blood samples of cattle and water buffalo and 206 tick samples were collected and subjected to DNA extraction. After successful amplification of control genes, nested PCR was performed to detect gltA of Rickettsia and com1 of C. burnetii. No samples were positive for Rickettsia, while 10 (cattle = 7, water buffaloes = 3), or 1.6% of blood, and five, or 1.8% of tick samples, were C. burnetii-positive. Sequence analysis of the positive amplicons showed 99-100% similarity to reported C. burnetii isolates. This molecular evidence on the occurrence of C. burnetii in Philippine ruminants and cattle ticks and its zoonotic nature should prompt further investigation and surveillance to facilitate its effective control.

Selective whole genome amplification and sequencing of Coxiella burnetii directly from environmental samples

Whole genome sequencing (WGS) is a widely available, inexpensive means of providing a wealth of information about an organism's diversity and evolution. However, WGS for many pathogenic bacteria remain limited because they are difficult, slow and/or dangerous to culture. To avoid culturing, metagenomic sequencing can be performed directly on samples, but the sequencing effort required to characterize low frequency organisms can be expensive. Recently developed methods for selective whole genome amplification (SWGA) can enrich target DNA to provide efficient sequencing. We amplified Coxiella burnetii (a bacterial select agent and human/livestock pathogen) from 3 three environmental samples that were overwhelmed with host DNA. The 68- to 147-fold enrichment of the bacterial sequences provided enough genome coverage for SNP analyses and phylogenetic placement. SWGA is a valuable tool for the study of difficult-to-culture organisms and has the potential to facilitate high-throughput population characterizations as well as targeted epidemiological or forensic investigations.

Molecular typing of Coxiella burnetii from sheep in Egypt

Coxiella burnetii, the etiological agent of Q fever, is a globally distributed zoonotic disease. The disease was reported serologically in different animal species and humans in Egypt but the genetic information about circulating Coxiella strains is limited. The present study aimed to genetically characterize Coxiella positive samples, identified in abortive sheep, based on a 17-loci Multiple Locus Variable number tandem repeat analysis (MLVA) panel and Multispacer Sequence Typing (MST). Four MLVA types were found among six examined samples. While all three samples examined by MST were identified as novel sequence type (ST) closely related to human heart valve isolates from France, Saudi Arabia, USA and United Kingdom. This study provides the first genetic information about circulating Coxiella strains in Egypt and improves epidemiological data of Q fever in the country.

Current perspectives on the transmission of Q fever: Highlighting the need for a systematic molecular approach for a neglected disease in Africa

Q fever is a bacterial worldwide zoonosis (except New Zealand) caused by the Gram-negative obligate intracellular bacterium Coxiella burnetii (C. burnetii). The bacterium has a large host range including arthropods, wildlife and companion animals and is frequently identified in human and livestock populations. In humans, the disease can occur as either a clinically acute or chronic aetiology, affecting mainly the lungs and liver in the acute disease, and heart valves when chronic. In livestock, Q fever is mainly asymptomatic; however, the infection can cause abortion, and the organism is shed in large quantities, where it can infect other livestock and humans. The presence of Q fever in Africa has been known for over 60 years, however while our knowledge of the transmission routes and risk of disease have been well established in many parts of the world, there is a significant paucity of knowledge across the African continent, where it remains a neglected zoonosis. Our limited knowledge of the disease across the African sub-continent have relied largely upon observational (sero) prevalence studies with limited focus on the molecular epidemiology of the disease. This review highlights the need for systematic studies to understand the routes of C. burnetii infection, and understand the disease burden and risk factors for clinical Q fever in both humans and livestock. With such knowledge gaps filled, the African continent could stand a better chance of eradicating Q fever through formulation and implementation of effective public health interventions.

Shedding and genetic diversity of Coxiella burnetii in Polish dairy cattle

Q fever is a worldwide zoonotic disease reported in humans and many animal species including cattle. The aims of this study were to evaluate the prevalence of Coxiella (C.) burnetii shedding in Polish dairy cattle 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. The presence of C. burnetii DNA was detected using a commercial real-time PCR kit, targeting the IS1111 element. Overall, 1,439 samples from 279 herds were tested including: 897 individual milk specimens, 101 bulk tank milk samples, 409 genital tract swabs and 32 placentas. Furthermore, 30 consumer milk samples, including 10 from vending machines and 77 dairy products were also analyzed. C. burnetii shedding was confirmed in 31.54% of tested cattle herds as well as in 69.16% of consumer milk and dairy products. Among real-time PCR-positive samples, 49 specimens obtained from 49 cattle herds and 8 samples of purchased dairy products were selected for genotyping. Overall, five previously known MLVA genotypes (I, J, BG, BE, and NM) and three new ones (proposed as PL1, PL2, and PL3) were identified. Two MST sequence types were recorded: ST16 and a novel sequence (ST61). The new genotypes and sequence types need further research particularly into their pathogenicity to humans.

Genotyping of Coxiella burnetii in sheep and goat abortion samples

Background

Q fever, caused by Coxiella burnetii, is a zoonosis that presents a worldwide distribution and affects both humans and animals. The route of dispersal of the pathogen by ruminants into the environment usually involves stages of abortion and parturition, nevertheless the agent can, also, be detected in other animal samples. Therefore it is considered as important in terms of proper diagnosis, as well as, for epidemiology and surveillance purposes, to genotype the pathogen. The aim of the current study was to investigate the presence of different genotypes of the agent in animals that had suffered from abortion during a two-year survey in Greece.

Results

Sixty nine tissue samples (37 stomach contents, 11 liver samples, 21 cotyledons) were collected from 59 abortion cases in sheep (N = 45) and goats (N = 14) from 65 farms at eight different areas of Greece. Samples were screened by qPCR and positive ones were further genotyped using a 10-locus multiple loci (ms 1, 3, 7, 12, 20, 21, 22, 26, 30 and 36) variable number of tandem repeat analysis (MLVA) method.

Three genotypes were identified in sheep (A, B, C). Samples representing each of the obtained MLVA profile were further used for MST genotyping. Ten spacers (Cox 2, 5, 6, 18, 20, 22, 37, 51, 56 and 57) were amplified. A close relatedness among the identified MLVA genotypes was confirmed since they all belonged to MST group 32.

Conclusions

The current study introduces into the aspect of genotyping of C. burnetii in Greece. Further studies are needed to explore the presence of more genotypes, to associate the genotypes circulating in the animal and tick population with those causing human disease in order to further expand on the epidemiological aspects of the pathogen.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1353-y) contains supplementary material, which is available to authorized users.

Genotyping of Coxiella burnetii detected in placental tissues from aborted dairy cattle in the north of Algeria

Coxiella burnetii, is an obligate intracellular bacterium which is present throughout the world. In humans, C. burnetii is the causative agent of Q fever. In cattle, the infection is suspected to cause stillbirths, retained fetal membranes, metritis and infertility. The birth products of ruminants shed huge amounts of bacteria, and are considered a major source for human infection. The present study was designed to search for the presence of C. burnetii in placental tissues collected from aborted and normal calving dairy cows in Algeria, using molecular tools. A total of 77 placental tissue fragments were collected from dairy cows. 73 samples were collected from aborted cows and four samples were collected from natural calving cows over a period of two years from January 2013 to March 2015. The presence of C. burnetii in these samples was screened by quantitative real-time polymerase chain reaction (qPCR) targeting two different genes, IS1111 and IS30 A. The positive PCR amplicons were subsequently sequenced for Multispacer Sequence Typing determination (MST) using seven pairs of sequences (Cox2, Cox5, Cox18, Cox37, Cox56, Cox57, and Cox61). Fourteen placental tissues (19.1%) were found to be positive for C. burnetii by qPCR; 9 (12.3%) from the city of Blida and 5 (6.84%) from the city of Medea. Genotyping of the corresponding amplicons displayed 100% identity with C. burnetii MST20 genotype, confirming the circulation of this clone in dairy farms from Algeria.

Genetic diversity of Coxiella burnetii in domestic ruminants in central Italy

Background

As the epidemiology of human Q Fever generally reflects the spread of Coxiella burnetii in ruminant livestock, molecular characterization of strains is essential to prevent human outbreaks. In this study we report the genetic diversity of C. burnetii in central Italy accomplished by MST and MLVA-6 on biological samples from 20 goat, sheep and cow farms.

Results

Five MST and ten MLVA profiles emerged from the analysis establishing a part of C. burnetii strain world atlas. In particular, ST32 occurred on 12 farms (60%), prevalently in goat specimens, while ST12 (25%) was detected on 4 sheep and 1 goat samples. ST8 and a variant of this genotype were described on 2 different sheep farms, whereas ST55 was observed on a goat farm. Five complete MLVA profiles different from any other published genotypes were described in this study in addition to 15 MLVA incomplete panels. Despite this, polymorphic markers Ms23, Ms24 and Ms33 enabled the identification of samples sharing the same MST profile.

Conclusions

Integration of such data in international databases can be of further help in the attempt of building a global phylogeny and epidemiology of Q fever in animals, with a “One Health” perspective.

From Q Fever to Coxiella burnetii Infection: a Paradigm Change

Coxiella burnetii is the agent of Q fever, or "query fever," a zoonosis first described in Australia in 1937. Since this first description, knowledge about this pathogen and its associated infections has increased dramatically. We review here all the progress made over the last 20 years on this topic. C. burnetii is classically a strict intracellular, Gram-negative bacterium. However, a major step in the characterization of this pathogen was achieved by the establishment of its axenic culture. C. burnetii infects a wide range of animals, from arthropods to humans. The genetic determinants of virulence are now better known, thanks to the achievement of determining the genome sequences of several strains of this species and comparative genomic analyses. Q fever can be found worldwide, but the epidemiological features of this disease vary according to the geographic area considered, including situations where it is endemic or hyperendemic, and the occurrence of large epidemic outbreaks. In recent years, a major breakthrough in the understanding of the natural history of human infection with C. burnetii was the breaking of the old dichotomy between "acute" and "chronic" Q fever. The clinical presentation of C. burnetii infection depends on both the virulence of the infecting C. burnetii strain and specific risks factors in the infected patient. Moreover, no persistent infection can exist without a focus of infection. This paradigm change should allow better diagnosis and management of primary infection and long-term complications in patients with C. burnetii infection.

Molecular epidemiology of Coxiella burnetii in French livestock reveals the existence of three main genotype clusters and suggests species-specific associations as well as regional stability

Q fever is a worldwide zoonosis caused by the bacterium Coxiella burnetii. In domestic ruminants, Q fever main clinical manifestations are abortions. Although the clinical signs may differ between ruminant species, C. burnetii's genetic diversity remains understudied in enzootic areas. Here, we focused on France, where Q fever is enzootic, with the aims to (a) identify potential associations between C. burnetii genotypes and ruminant host species; (b) assess the distribution of C. burnetii genotypes both within French farms and across France's major livestock-farming regions; and (c) suggest a subset of markers for future genotypic studies. We used DNA samples collected between 2006 and 2015 from 301 females (160 cows, 76 ewes, 65 goats) aborted of Q fever within 7 different farming regions. C. burnetii diversity was determined using a multiple-locus variable-number of tandem repeat analysis (MLVA) considering 17 markers. Using a phylogenetic approach, we identified 3 main genotypic clusters divided into 12 sub-clusters. These clusters were significantly associated with ruminant species: almost all the cattle genotypes were found in a "cattle-specific" cluster whereas small ruminants genotypes essentially grouped into the two other clusters. The clusters also proved stable over space and time, some genotypes being more specifically observed in certain farming regions. We also observed some within-farm diversity but this diversity was restricted to a same genotypic cluster. Finally, we identified 6 MLVA markers that maximized the representativeness of the diversity described. Overall, we highlighted that molecular epidemiology is a relevant approach to assess C. burnetii's genetic diversity and to reveal the existence of species-specific associations and regional stability. These results will be valuable in the field to trace genotype circulation among ruminants and from ruminants to humans. Ultimately, the potential links between genotypes and virulence traits need to be investigated to adapt control measures in livestock farms.

Coxiella burnetii Genotypes in Iberian Wildlife

To investigate if Coxiella burnetii, the causative agent of Q fever, genotypes circulating in wildlife are associated with those infecting livestock and humans, multiple-locus variable number tandem-repeat analysis (MLVA-6-marker) was carried out over C. burnetii obtained from red deer (Cervus elaphus), Eurasian wild boar (Sus scrofa), European wild rabbit (Oryctolagus cuniculus), black rat (Rattus rattus), and wood mouse (Apodemus sylvaticus). MLVA typing was performed by using six variable loci in C. burnetii: Ms23, Ms24, Ms27, Ms28, Ms33, and Ms34. The C. burnetii cooperative database from MLVABank 5.0 was employed to compare genotypes found in this study with 344 isolates of diverse origin. Twenty-two genotypes from wildlife and two genotypes from domestic goats were identified. Some MLVA genotypes identified in wildlife or in farmed game clustered with genotypes of human Q fever clinical cases, supporting the idea that humans and wildlife share C. burnetii genotypes. The major part of genotypes identified in coexisting red deer and rabbits clustered according to their host of origin, suggesting host specificity for particular C. burnetii genotypes. These findings provide important insights to understand the epidemiology of C. burnetii at the wildlife-livestock-human interface.

Coxiella burnetii in central Italy: novel genotypes are circulating in cattle and goats

Genotyping of bacteria is critical for diagnosis, treatment, and epidemiological surveillance. Coxiella burnetii, the etiological agent of Q fever, has been recognized to have a potential for bioterrorism purposes. Because few serosurveys have been conducted in Italy, there is still limited information about the distribution of this pathogen in natural conditions. In this paper, we describe the genotyping of C. burnetii strains by multispacer sequence typing (MST) detected in cattle and goat farms in the Abruzzi region of Italy. Biological samples (milk, aborted fetus) positive for C. burnetii DNA were sequenced in the spacer regions and compared with those already publicly available ( http://ifr48.timone.univ-mrs.fr/MST_Coxiella/mst/group_detail ). The MST profile of C. burnetii detected in milk samples demonstrated the presence of a new allele, whereas the C. burnetii spacer sequences from fetus and milk goat samples displayed a new allelic combination. The results suggest the circulation of novel genotypes of C. burnetii in Italy.

The contribution of genomics to the study of Q fever

Coxiella burnetii is the etiological agent of Q fever, a worldwide zoonosis that can result in large outbreaks. The birth of genomics and sequencing of C. burnetii strains has revolutionized many fields of study of this infection. Accurate genotyping methods and comparative genomic analysis have enabled description of the diversity of strains around the world and their link with pathogenicity. Genomics has also permitted the development of qPCR tools and axenic culture medium, facilitating the diagnosis of Q fever. Moreover, several pathophysiological mechanisms can now be predicted and therapeutic strategies can be determined thanks to in silico genome analysis. An extensive pan-genomic analysis will allow for a comprehensive view of the clonal diversity of C. burnetii and its link with virulence.

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Q fever is a zoonosis of worldwide distribution with the exception of New Zealand. It is caused by an intracellular bacterium, Coxiella burnetii. The disease often goes underdiagnosed because the main manifestation of its acute form is a general self-limiting flu-like syndrome. The Dutch epidemics renewed attention to this disease, which was less considered before. This review summarizes the description of C. burnetii (taxonomy, intracellular cycle, and genome) and Q fever disease (description, diagnosis, epidemiology, and pathogenesis). Finally, vaccination in humans and animals is also considered.

Occurrence and Genotyping of Coxiella burnetii in Ixodid Ticks in Oromia, Ethiopia

This study was conducted from September 2011 to March 2014 to address the occurrence and genotypes of Coxiella burnetii using molecular methods in ticks collected from domestic animals in Ethiopia. Ticks were tested for C. burnetii by quantitative real-time polymerase chain reaction (qPCR) targeting two different genes followed by multispacer sequence typing (MST). An overall prevalence of 6.4% (54/842) of C. burnetii was recorded. C. burnetii was detected in 28.6% (14/49) of Amblyomma gemma, 25% (31/124) of Rhipicephalus pulchellus, 7.1% (1/14) of Hyalomma marginatum rufipes, 3.2% (2/62) of Am. variegatum, 3.1% (4/128) of Am. cohaerens, 1.6% (1/63) of Rh. praetextatus, and 0.6% (1/153) of Rhipicephalus (Boophilus) decoloratus. Significantly higher overall frequencies of C. burnetii DNA were observed in Am. gemma and Rh. pulchellus than in other tick species (Mantel-Haenszel [MH], P < 0.0001). The overall frequency of C. burnetii was significantly higher (MH, P < 0.0001) in ticks from southeastern districts (Arero, Moyale, and Yabelo) than that from other districts. This study demonstrated the presence of C. burnetii genotype MST 18 in ticks in southeastern districts and genotype MST 20 in ticks in central districts. This study highlights the importance of ticks in the epidemiology of C. burnetii in Ethiopia.

Impact of IS1111 insertion on the MLVA genotyping of Coxiella burnetii

Q fever epidemiological investigations of the likely sources of contamination may involve Coxiella burnetii MLVA for direct and rapid typing from clinical samples. However, little information is available with regards to PCR amplification failures in C. burnetii MLVA typing. This paper focuses on difficulties encountered with MLVA loci that may impact the interpretation of MLVA data and shows that some loci may constitute hotspots for mutational events. MLVA genotyping, using 17 different loci, was used on vaginal swabs (VS) from clinically infected animals as described elsewhere (Chmielewski et al., 2009). Amplicons of interest were sequenced and identified using the BLAST software by comparison with sequences available in GenBank. All VS samples produced MLVA patterns. However, amplification failures or unexpected sizes amplicons (>to 1.5 kbp), making the interpretation of MLVA complicated, were also observed. Sequencing of these amplicons revealed the presence of IS1111 element insertion. In this C. burnetii MLVA study some difficulties encountered with genotyping are highlighted and the role of IS1111 element in genome plasticity is confirmed. Finally, the need for the selection of a set of VNTRs for an efficient MLVA scheme and the question of standardization and harmonization for comparable MLVA typing data are raised again.

Coxiella burnetii DNA detected in domestic ruminants and wildlife from Portugal

Coxiella burnetii is the etiological agent of Q fever or Coxiellosis, a zoonosis mainly affecting domestic ruminants. Information on the population structure and epidemiology of C. burnetii in animals is scarce in Portugal. Evidence of C. burnetti infection was sought in domestic, wild and captive animals based on the detection of bacterial DNA. Tissue samples from 152 domestic animals (cattle=24, goats=51, sheep=76 and swine=1), 55 wild carnivores (Egyptian mongoose=45, red fox=4, common genet=3, weasel=2 and European badger=1) and 22 zoo animals (antelopes=15, impala=1; rhinoceros=1, deer=2, zebras=2 and giraffe=1) were screened by nested-touchdown PCR. Cloacae swabs from 19 griffon vultures were also analysed. Among the domestic ruminants, goats presented the highest prevalence of infection (23.53%), followed by cattle, (20.83%) and sheep (10.53%). C. burnetii DNA was also detected in five Egyptian mongooses and two antelopes and one giraffe. Using a 6-locus multiple-locus variable-number tandem repeat analysis (MLVA-6) six complete genotypes, T, I and CM and the first reported CN, CO and CP, were identified, respectively, in small ruminants and Egyptian mongooses. Clustering analysis of genotypes exposed four distinct groups, according to detection source, enlightening an apparent association between C. burnetii genotype and host.

Genetic diversity and variation over time of Coxiella burnetii genotypes in dairy cattle and the farm environment

The genetic diversity of Coxiella burnetii from 36 dairy cattle herds was determined by Multiple-Locus Variable number tandem repeats Analysis (MLVA), and genotypes from different sources (bulk-tank milk - BTM and surface dust) and sampling time (2009/10 and 2011/12) were compared. A total of 15 different genotypes were identified from 60 BTM and seven dust samples, including seven genotypes reported here for the first time (BN, BO, BP, BQ, BR, BS, BT). The two most prevalent genotypes (J and I), detected both in BTM and dust, accounted for 44.5% of the C. burnetii typed and have been reported infecting cattle worldwide. In 52% of herds more than one genotype was found, and mixed infection with two genotypes was observed in seven BTM samples. Comparison of C. burnetii genotypes at different samplings within each herd detected a change in genotype in 32% of herds, while a persistent genotype was identified in the remaining 68%. In addition, the genotype obtained from dust samples was always identical to that present in the BTM sample. Often persistent genotypes were among the most prevalent types. Clustering of the MLVA genotypes from this and other studies using the minimum spanning tree method separated our C. burnetii strains into two clusters, 10 genotypes clustered within genomic group (GG) III, and the remaining five types (AE, BQ, BR, BS and BT) grouped with GG II, which includes strains implicated in human outbreaks. Although presence in cattle of genotypes closely related to those identified in humans does not seem to be common event, it cannot be neglected and surveillance of genotype distribution is needed to fully understand the epidemiology of Q fever.

Identification of novel Coxiella burnetii genotypes from Ethiopian ticks

Background

Coxiella burnetii, the etiologic agent of Q fever, is a highly infectious zoonotic bacterium. Genetic information about the strains of this worldwide distributed agent circulating on the African continent is limited. The aim of the present study was the genetic characterization of C. burnetii DNA samples detected in ticks collected from Ethiopian cattle and their comparison with other genotypes found previously in other parts of the world.

Methodology/Principal Findings

A total of 296 tick samples were screened by real-time PCR targeting the IS1111 region of C. burnetii genome and from the 32 positive samples, 8 cases with sufficient C. burnetii DNA load (Amblyomma cohaerens, n = 6; A. variegatum, n = 2) were characterized by multispacer sequence typing (MST) and multiple-locus variable-number tandem repeat analysis (MLVA). One novel sequence type (ST), the proposed ST52, was identified by MST. The MLVA-6 discriminated the proposed ST52 into two newly identified MLVA genotypes: type 24 or AH was detected in both Amblyomma species while type 26 or AI was found only in A. cohaerens.

Conclusions/Significance

Both the MST and MLVA genotypes of the present work are closely related to previously described genotypes found primarily in cattle samples from different parts of the globe. This finding is congruent with the source hosts of the analyzed Ethiopian ticks, as these were also collected from cattle. The present study provides genotype information of C. burnetii from this seldom studied East-African region as well as further evidence for the presumed host-specific adaptation of this agent.

Q fever epidemic in Hungary, April to July 2013

We investigated a Q fever outbreak with human patients showing high fever, respiratory tract symptoms, headache and retrosternal pain in southern Hungary in the spring and summer of 2013. Seventy human cases were confirmed by analysing their serum and blood samples with micro-immunofluorescence test and real-time PCR. The source of infection was a merino sheep flock of 450 ewes, in which 44.6% (25/56) seropositivity was detected by enzyme-linked immunosorbent assay. Coxiella burnetii DNA was detected by real-time PCR in the milk of four of 20 individuals and in two thirds (41/65) of the manure samples. The multispacer sequence typing examination of C. burnetii DNA revealed sequence type 18 in one human sample and two manure samples from the sheep flock. The multilocus variable-number tandem repeat analysis pattern of the sheep and human strains were also almost identical, 4/5-9-3-3-0-5 (Ms23-Ms24-Ms27-Ms28-Ms33-Ms34). It is hypothesised that dried manure and maternal fluid contaminated with C. burnetii was dispersed by the wind from the sheep farm towards the local inhabitants. The manure was eliminated in June and the farm was disinfected in July. The outbreak ended at the end of July 2013.