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.

Genotyping reveals the presence of a predominant genotype of Coxiella burnetii in consumer milk products.

Real-time PCR shows the widespread presence of Coxiella burnetii DNA in a broad range of commercially available milk and milk products. MLVA genotyping shows that this is the result of the presence of a predominant C. burnetii genotype in the dairy cattle population.

Genotypic diversity of Coxiella burnetii in the 2007-2010 Q fever outbreak episodes in The Netherlands.

The genotypic diversity of Coxiella burnetii in clinical samples obtained from the Dutch Q fever outbreak episodes of 2007-2010 was determined by using a 6-locus variable-number tandem repeat analysis panel. The results are consistent with the introduction of one founder genotype that is gradually diversifying over time while spreading throughout The Netherlands.

Genotypic diversity of clinical Coxiella burnetii isolates from Portugal based on MST and MLVA typing.

The temporal and spatial diversity of Coxiella burnetii genotypes associated with human and animal disease in Portugal was analysed using a 6-locus multiple-locus variable-number tandem repeat analysis (MLVA) and a 10-locus multi-spacer sequence typing (MST) panel. Fifteen cultured C. burnetii isolates from 13 Q fever patients and a stillborn goat and 6 additional PCR-positive ruminant tissue samples obtained during 2006-2011 were included in this study. Seven MLVA genotypes (types S-Y) were obtained, including 4 new MLVA types (U, V, W, and X), all corresponding to 3 MST profiles (types 4, 8, and 13) previously reported from France and Spain. MLVA types U-Y, all belonging to MST type 4, were found in acute Q fever patients from the districts of Évora, Faro, Lisbon, and Setúbal. Different MLVA types were associated with goats from Castelo Branco district (S) and chronic Q fever patients from both Castelo Branco and Lisboa districts (S and T), matching with MST types 13 and 8, respectively. In conclusion, a genotypic diversity of C. burnetii consistent with a non-outbreak situation was identified. The involvement of different genotypes in acute and chronic Q fever was found, linking one of the chronic genotypes to goats from the eastern region of the country.

Genotyping of Coxiella burnetii from domestic ruminants in northern Spain.

BACKGROUND: Information on the genotypic diversity of Coxiella burnetii isolates from infected domestic ruminants in Spain is limited. The aim of this study was to identify the C. burnetii genotypes infecting livestock in Northern Spain and compare them to other European genotypes. A commercial real-time PCR targeting the IS1111a insertion element was used to detect the presence of C. burnetii DNA in domestic ruminants from Spain. Genotypes were determined by a 6-loci Multiple Locus Variable number tandem repeat analysis (MLVA) panel and Multispacer Sequence Typing (MST). RESULTS: A total of 45 samples from 4 goat herds (placentas, N = 4), 12 dairy cattle herds (vaginal mucus, individual milk, bulk tank milk, aerosols, N = 20) and 5 sheep flocks (placenta, vaginal swabs, faeces, air samples, dust, N = 21) were included in the study. Samples from goats and sheep were obtained from herds which had suffered abortions suspected to be caused by C. burnetii, whereas cattle samples were obtained from animals with reproductive problems compatible with C. burnetii infection, or consisted of bulk tank milk (BTM) samples from a Q fever surveillance programme. C. burnetii genotypes identified in ruminants from Spain were compared to those detected in other countries. Three MLVA genotypes were found in 4 goat farms, 7 MLVA genotypes were identified in 12 cattle herds and 4 MLVA genotypes were identified in 5 sheep flocks. Clustering of the MLVA genotypes using the minimum spanning tree method showed a high degree of genetic similarity between most MLVA genotypes. Overall 11 different MLVA genotypes were obtained corresponding to 4 different MST genotypes: MST genotype 13, identified in goat, sheep and cattle from Spain; MST genotype 18, only identified in goats; and, MST genotypes 8 and 20, identified in small ruminants and cattle, respectively. All these genotypes had been previously identified in animal and human clinical samples from several European countries, but some of the MLVA genotypes are described here for the first time. CONCLUSIONS: Genotyping revealed a substantial genetic diversity among domestic ruminants from Northern Spain.

Molecular epidemiology of Coxiella burnetii from ruminants in Q fever outbreak, the Netherlands.

Q fever is a zoonosis caused by the bacterium Coxiella burnetii. One of the largest reported outbreaks of Q fever in humans occurred in the Netherlands starting in 2007; epidemiologic investigations identified small ruminants as the source. To determine the genetic background of C. burnetii in domestic ruminants responsible for the human Q fever outbreak, we genotyped 126 C. burnetii-positive samples from ruminants by using a 10-loci multilocus variable-number tandem-repeat analyses panel and compared them with internationally known genotypes. One unique genotype predominated in dairy goat herds and 1 sheep herd in the human Q fever outbreak area in the south of the Netherlands. On the basis of 4 loci, this genotype is similar to a human genotype from the Netherlands. This finding strengthens the probability that this genotype of C. burnetii is responsible for the human Q fever epidemic in the Netherlands.

Identification by genotyping of a commercial antigen preparation as the source of a laboratory contamination with Coxiella burnetii and as an unexpected rich source of control DNA.

By performing genotyping, a laboratory contamination involving Q fever was traced back to the antigen preparation used in a commercially available complement fixation test. It was established that such antigen preparations contain relatively high loads of DNA/RNA, making them potential sources of contamination but also convenient preparations for control material.

Contamination of commercial PCR master mix with DNA from Coxiella burnetii.

Contamination of an in-house diagnostic real-time PCR for Q fever was traced back to a commercially obtained PCR Master Mix. It was established that this Master Mix contained DNA from Coxiella burnetii, probably as a result of the use of compounds of animal origin such as bovine serum albumin.

Interlaboratory evaluation of different extraction and real-time PCR methods for detection of Coxiella burnetii DNA in serum.

In the Netherlands, there is an ongoing and unparalleled outbreak of Q fever. Rapid and reliable methods to identify patients infected with Coxiella burnetii, the causative agent of Q fever, are urgently needed. We evaluated the performance of different DNA extraction methods and real-time PCR assays that are in use in seven diagnostic or reference laboratories in the Netherlands. A low degree of variation in the sensitivities of most of the developed real-time PCR assays was observed. However, PCR assays amplifying short DNA fragments yielded better results than those producing large DNA fragments. With regard to DNA extraction, the automated MagNA Pure Compact system and the manual QIAamp DNA mini kit consistently yielded better results than either the MagNA Pure LC system and NucliSens EasyMag (both automated) or the High Pure viral nucleic acid kit (manual). The present study shows that multiple combinations of DNA extraction kits and real-time PCR assays offer equivalent solutions to detect C. burnetii DNA in serum samples from patients suspected to have Q fever.

Environmental swabs as a tool in norovirus outbreak investigation, including outbreaks on cruise ships.

In this study, we investigated whether environmental swabs can be used to demonstrate the presence of norovirus in outbreak settings. First, a procedure was set up based on viral RNA extraction using guanidium isothiocyanate buffer and binding of nucleic acids to silica. Subsequently, environmental swabs were taken at 23 Dutch restaurants and four cruise ships involved in outbreaks of gastroenteritis. Outbreaks were selected based on clinical symptoms consistent with viral gastroenteritis and time between consumption of suspected food and onset of clinical symptoms (>12 h). Norovirus RNA was demonstrated by real-time reverse transcriptase PCR in 51 of 86 (59%) clinical specimens from 12 of 14 outbreaks (86%), in 13 of 90 (14%) food specimens from 4 of 18 outbreaks (22%), and in 48 of 119 (40%) swab specimens taken from 14 of 27 outbreaks (52%). Positive swab samples agreed with positive clinical samples in seven outbreaks, showing identical sequences. Furthermore, norovirus was detected on swabs taken from kitchen and bathroom surfaces in five outbreaks in which no clinical samples were collected and two outbreaks with negative fecal samples. The detection rate was highest for outbreaks associated with catered meals and lowest for restaurant-associated outbreaks. The use of environmental swabs may be a useful tool in addition to testing of food and clinical specimens, particularlywhen viral RNA is detected on surfaces used for food preparation.

An efficient and rapid method for recovery of norovirus from food associated with outbreaks of gastroenteritis.

Noroviruses have emerged as the most common cause of foodborne outbreaks of acute nonbacterial gastroenteritis. In this study, two methods for the extraction of viruses from deli ham were compared. Using both methods, as little as 1 to 10 reverse transcription (RT)-PCR units of inoculated norovirus and enterovirus could be detected by nested RT-PCR assays. The fastest and most efficient extraction method based on TRIzol LS Reagent was chosen to identify viruses in food items associated with three different outbreaks. Norovirus was detected using nested (real time) RT-PCR assays that target the genome region routinely used for diagnosis of human cases, thereby facilitating the comparison of sequences detected in food and clinical specimens. For one outbreak, a norovirus sequence (163/163 nucleotides) identical to those detected in clinical samples was found on salami sliced by a food handler with a recent history of gastroenteritis. For the other two outbreaks, norovirus was detected on leftovers of spareribs and ham, but fecal samples from affected persons were not available. The methods used in this study may be useful in future outbreak investigations because the extraction method is easy to perform and suitable for this particular type of food and the detection method facilitates direct comparison of patient and food data.

Detection of noroviruses in shellfish in the Netherlands.

Shellfish from oyster farms in the Netherlands and imported from other European countries were examined for viral contamination. A method that allows sequence matching between noroviruses from human cases and shellfish was used. The samples of shellfish (n = 42) were analyzed using a semi-nested RT-PCR that had been optimized for detection of norovirus in shellfish (SR primer sets). In addition, a different genome region was targeted using a second primer set which is routinely used for diagnosis of norovirus infection in humans (JV12Y/JV13I). To improve the detection limit for this RT-PCR a semi-nested test format was developed (NV primer sets). One of 21 oyster samples (4.8%) from Dutch farms was norovirus positive, whereas norovirus was detected in 1 out of 8 oyster samples (12.5%) and 5 out of 13 mussel samples (38.5%) collected directly after importation in the Netherlands. RNA from samples associated with an outbreak of gastro-enteritis in the Netherlands in 2001 was re-analyzed using the NV primer sets. At least one identical sequence (142/142 nt) was found in three fecal and in two oyster samples related to this outbreak. Further surveillance of norovirus by detection and typing of viruses from patients with gastroenteritis and shellfish is warranted to clarify the causes of future outbreaks.

Molecular characterization by MLVA of Coxiella burnetii strains infecting dairy cows and goats of north-eastern Italy.

Q fever is a worldwide zoonotic disease caused by Coxiella burnetii (C. burnetii), an obligate intracellular bacterium. In ruminants, shedding into the environment mainly occurs during parturition or abortion, but the bacterium is shed also in milk, vaginal mucus, stools and urine. In Italy few surveys have been conducted and reported seroprevalence values ranged between 10% and 60%, even if few human cases have been described. Genotyping of bacteria is crucial for enhancing diagnostic methods and for epidemiological surveillance. The objective of this study was to investigate genotypic differences of C. burnetii genotypes directly in 34 samples, collected during a 3-years survey among 11 dairy cattle and 11 goat farms in the north-eastern part of Italy using a 6-locus multiple loci variable number of tandem repeat analysis (MLVA) method. The samples analysed included 13 bulk tank milk (BTM), 6 individual milk, 11 vaginal swabs and 4 foetal spleens. MLVA-type 2 was determined as the most prevalent in cattle in this study. C. burnetii strains circulating in the studied cattle population are very similar to genotypes previously described, while genotypes from goats showed an important variability. Further investigation are needed to understand the reason of this pattern.

Two outbreaks of campylobacteriosis associated with the consumption of raw cows' milk.

The present paper summarises the investigation of two different outbreaks of milk-associated Campylobacter enteritis in the Netherlands. In 2005, after a school trip to a dairy farm, 22 out of a group of 34 children developed diarrhoeal illness and Campylobacterjejuni was cultured from the stool samples of 11 of the cases. The illness was found to be epidemiologically associated with drinking raw milk during the farm visit; 86% of the cases could be explained by drinking raw milk. C.jejuni was also isolated from three of 10 faecal samples from dairy cattle collected at the farm. The human isolates and C.jejuni isolates from one of these three samples of cattle faeces revealed identical restriction patterns by both pulsed-field gel electrophoresis (PFGE) and flagellin (fla) typing by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Both epidemiological and bacteriological evidence implicated contaminated raw milk as the vehicle of transmission, though C.jejuni was not isolated from the bulk tank milk or the milk filter collected during the farm investigation. In 2007, an outbreak of enteritis was notified among people who had attended a lunch at a dairy farm where bulk tank milk was served. Of the 19 persons who had consumed raw milk, 16 (84%) had become ill. Of the persons who did not drink the raw milk, none became ill. A significant association was found between tasting the raw milk and being ill (risk difference=0.84, p=0.0011). C.jejuni was cultured from four of seven cases who had submitted a stool specimen. C. jejuni was also isolated from a sample of bulk tank milk and the isolate had an identical flaA PCR-RFLP genotype to isolates obtained from patients. Also in this outbreak both the epidemiological and bacteriological findings support raw milk as the vehicle for the enteritis. These two outbreaks highlight the health risks associated with the consumption of raw milk. As long as legislation allows the sale and distribution of untreated milk these risks will continue. Therefore, consumers need to be continuously informed about the dangers inherent in consuming unpasteurised milk or products made from raw milk. Farmers need to be strongly discouraged from serving raw milk to their visitors.