Genomic analysis of Brucella isolates from animals and humans, Türkiye, 2010 to 2020.

BackgroundBrucellosis is a bacterial zoonosis causing severe illness in humans and animals and leading to economic losses in the livestock production in Türkiye and other endemic countries.AimWe aimed at investigating genomic differences of Brucella isolates from animals and humans in Türkiye.MethodsWe used whole genome sequencing (WGS) to assess the genetic diversity of Brucella isolates from 41 provinces in Türkiye and compared with isolates from other countries. We applied allele-based typing and core genome single nucleotide polymorphism (cgSNP) determination.ResultsOf the 106 Turkish Brucella isolates included, 57 were B. abortus and 49 were B. melitensis. One B. melitensis and two B. abortus isolates were identified as vaccine strains. Most (n = 55) B. abortus isolates clustered in three major branches, with no spatial discernible pattern. Of the B. melitensis isolates, 48 were assigned to the Eastern Mediterranean lineage with no discernible patterns between host species, location and sampling date. The Turkish isolates clustered with isolates from neighbouring countries such as Greece and Syria, but some also with isolates from human patients in European countries, like Germany, Norway and Sweden, suggesting that the source may be travel-related.ConclusionSeveral B. melitensis and B. abortus lineages are circulating in Türkiye. To decrease the prevalence and prevent brucellosis in animals and humans, stricter control measures are needed, particularly in areas where humans and animals have close contact. Furthermore, illegal transportation of animals across borders should be more closely controlled and regulated.

Genotype diversity of brucellosis agents isolated from humans and animals in Greece based on whole-genome sequencing.

BACKGROUND: Brucellosis is a zoonotic disease whose causative agent, Brucella spp., is endemic in many countries of the Mediterranean basin, including Greece. Although the occurrence of brucellosis must be reported to the authorities, it is believed that the disease is under-reported in Greece, and knowledge about the genomic diversity of brucellae is lacking. METHODS: Thus, 44 Brucella isolates, primarily B. melitensis, collected between 1999 and 2009 from humans and small ruminants in Greece were subjected to whole genome sequencing using short-read technology. The raw reads and assembled genomes were used for in silico genotyping based on single nucleotide substitutions and alleles. Further, specific genomic regions encoding putative virulence genes were screened for characteristic nucleotide changes, which arose in different genotype lineages. RESULTS: In silico genotyping revealed that the isolates belonged to three of the known sublineages of the East Mediterranean genotype. In addition, a novel subgenotype was identified that was basal to the other East Mediterranean sublineages, comprising two Greek strains. The majority of the isolates can be assumed to be of endemic origin, as they were clustered with strains from the Western Balkans or Turkey, whereas one strain of human origin could be associated with travel to another endemic region, e.g. Portugal. Further, nucleotide substitutions in the housekeeping gene rpoB and virulence-associated genes were detected, which were characteristic of the different subgenotypes. One of the isolates originating from an aborted bovine foetus was identified as B. abortus vaccine strain RB51. CONCLUSION: The results demonstrate the existence of several distinct persistent Brucella sp. foci in Greece. To detect these and for tracing infection chains, extensive sampling initiatives are required.

Giant cell arteritis associated with acute Q fever - A case report.

Q fever is a worldwide spread zoonotic disease, caused by the gram-negative intracellular bacillus Coxiella burnetii. Apart from its most common manifestations, Q fever has been reported to occasionally mimic autoimmune diseases. We herein present a case of acute Q fever in a 69-year-old man, manifesting as prolonged fever with pneumonitis, in whom biopsy of the temporal artery revealed giant cell arteritis. Moreover, PCR testing of the biopsy specimen was positive for Coxiella burnetii, thus further supporting the possibly infectious etiology of some cases of biopsy proven giant cell arteritis, with implications for treatment.

Expression, purification and characterization of the IcmG and IcmK proteins of the type IVB secretion system from Coxiella burnetii.

Coxiella burnetii, the causative agent of Q fever, is an intracellular bacterial pathogen. Studies on Coxiella have shown that a type IVB secretion system (T4BSS) contributes to the establishment of the infection by transferring protein molecules. In this report, we focus on two core proteins of the Coxiella T4BSS, namely the IcmG/DotF protein (CBU_1626) and the IcmK/DotH protein (CBU_1628). Here we present a method for the recombinant expression of IcmG and IcmK in E. coli. IcmG was purified by Strep-Tactin affinity chromatography and size exclusion chromatography, while for the purification of IcmK an additional anion exchange chromatography step was introduced. The yields of the purified IcmG and IcmK proteins were 1.2 mg/L and 3 mg/L, respectively. The purified proteins showed predominant band on SDS-PAGE gel of 37 kDa for the IcmG and 40 kDa for the IcmK. Protein folding is confirmed by circular dichroism spectroscopy. The dynamic light scattering experiment indicated that IcmG and IcmK existed in a homogenous form. Further Blue native PAGE indicates the presences of a monomeric form for the IcmK and IcmG. Our work lays the basis for functional exploration and structural determination of IcmG and IcmK proteins of Coxiella's secretion system.

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.

Intestinal microbiota and colorectal cancer: a new aspect of research.

Colon holds a complex microbial community, which is crucial for maintaining homeostasis and regulating metabolic functions, supporting the intestinal barrier and controlling immune responses. Previous studies have supported a link between intestinal microbiota and colorectal cancer (CRC). Based on these fndings, the present review analyzed the numerous interactions that occur between microbiota and CRC, starting from the role of intestinal microbiota in colonic homoeostasis. Intestinal microbiota is a cause of CRC and involves various mechanisms such as chronic inflammation, the production of genotoxins causing DNA impairment and/or the biosynthesis of toxic compounds. Moreover, basic metabolic factors such as short-chain fatty acids (SCFAs) and bile acids are included in CRC pathogenesis. Different pathogenic pathways have been reported among different CRC regions (proximal or distal). Variations in the microbial populations are reported between the CRC from these colonic sites, possibly reflecting the bacterial dysbiosis and bioflm distribution. Bowel preparation is essential prior to colonoscopy and surgery; there is, however, minor consensus on the effects of this procedure on intestinal microbiota, notably with regard to the long-term outcomes. With regard to the therapeutic strategy in CRC, the intestinal microbiota is further involved in the modulation of the host response to chemotherapeutic agents (5-fluorouracil and irinotecan) by the interference with drug efcacy and by adverse effects and associated toxicity. In addition, the newly emerged research on CRC immunotherapy reveals an important interplay between intestinal microbiota and the immune system, which includes the possibility of targeting microbiota for the enhancement of anticancer treatment. Additional studies will further clarify the interaction between microbiota and CRC, resulting in the development of alternative therapeutic strategies by manipulating microbiota composition.

Use of MALDI-TOF mass spectrometry in the battle against bacterial infectious diseases: recent achievements and future perspectives.

INTRODUCTION: Advancements in microbial identification occur increasingly faster as more laboratories explore, refine and extend the use of mass spectrometry in the field of microbiology. Areas covered: This review covers the latest knowledge found in the literature for quick identification of various classes of bacterial pathogens known to cause human infection by the use of MALDI-TOF MS technology. Except for identification of bacterial strains, more researchers try to 'battle time' in favor of the patient. These novel approaches to identify bacteria directly from clinical samples and even determine antibiotic resistance are extensively revised and discussed. Expert commentary: Mass spectrometry is the future of bacterial identification and creates a new era in modern microbiology. Its incorporation in routine practice seems to be not too far, providing a valuable alternative, especially in terms of time, to conventional techniques. If the technology further advances, quick bacterial identification and probable identification of common antibiotic resistance might guide patient decision-making regarding bacterial infectious diseases in the near future.

Legionellosis: a Walk-through to Identification of the Source of Infection.

OBJECTIVES: Although a number of human Legionnaires' disease in tourists are recorded annually in Europe, there are few cases where a direct link can be made between the infected person and the source of infection (hotel or other accommodation). We present a scheme followed in order to track down and identify the source of infection in a tourist suffering from L. pneumophila sg 5 infection, who was accommodated in seven different hotels during his holidays in the island of Crete, and we comment on various difficulties and draw-backs of the process. METHOD: Water samples were collected from the seven hotels where the patient had resided and analyzed at the regional public health laboratory using cultivation and molecular tests. RESULTS: Of 103 water samples analyzed, 19 (18.4%) were positive for Legionella non-pneumophila and 8 (7.8%) were positive for L. pneumophila. A successful L. pneumophila sg 5 match was found between the clinical and environmental sample, which led us to the final identification of the liable hotel. CONCLUSION: Timely notification of the case, within the the European Legionnaires' Disease Surveillance Network (ELDSNet) of the partners involved, is crucial during a course of travel associated with Legionella case investigation. Moreover, the urinary antigen test alone cannot provide sufficient information for the source identification. However, acquiring clinical as well as environmental isolates for serogroup and SBT identification is highly important for the successful matching.

Species composition, distribution, ecological preference and host association of ticks in Cyprus.

Tick population and species depend on the effect of biotic and abiotic factors, especially vegetation, climate and host density; Cyprus, due to the mild climate, favors the appearance and spread of tick-borne infections. Our objective was to identify the tick species present in the island, to investigate their geographical distribution and their epidemiological implications. During a three-year study (2004-2006) we collected ticks from domestic and wild animals over the island of Cyprus. Data on temperature, humidity, altitude and vegetation, were also recorded. Each tick was identified by species using existing taxonomic keys. The results were mapped on a county level. During the current study 3057 ticks belonging to 11 tick species and four genera were collected from 441 (24.6%) infested animals. Rhipicephalus sanguineus was the predominant species (38.5%), followed by R. turanicus (21.3%) and R. bursa (17.8%). Most infestations occurred in May (24.0%), followed by March (13.6%) and June (12.2%). Rhipicephalus sanguineus had a positive correlation with humidity and temperature, R. bursa and Ixodes gibbosus had a positive correlation with altitude and a negative correlation with temperature. Contrary, Hyalomma excavatum had a negative correlation with altitude. Climate and the availability of hosts are among the major factors influencing ticks.

Murine typhus in elderly patients: a prospective study of 49 patients.

BACKGROUND: The characteristics of Rickettsia typhi infection in elderly patients have not been extensively described in the literature. METHODS: We conducted a prospective study on murine typhus in patients > 65 years old in two endemic areas of Greece. RESULTS: Forty-nine elderly patients were analyzed, including 30 (61.2%) males. The clinical triad of fever (100% of patients), headache (83.7%), and rash (73.5%), occurred in 63% of patients, whereas malaise (85.7%), anorexia (65.3%), and myalgia (59.2%) were also common. Frequent laboratory findings were transaminasemia (89.8%), lactate dehydrogenase elevation (65.3%), hematuria (55.1%), thrombocytopenia (53.1%), anemia (51%), leucopenia (40.8%), and mild hyponatremia (23.5%). Complications developed in 16 patients (32.7%); no deaths were recorded. CONCLUSIONS: The main clinical and laboratory characteristics of murine typhus are similar in elderly and younger adults. However, elderly patients have a more severe clinical picture, evidenced by a higher complication rate and longer duration of fever, even with appropriate treatment. To our knowledge, this is the first study to focus on murine typhus in a geriatric population.

Skin lesions and inoculation eschars at the tick bite site in spotted fever group rickettsioses: experience from a patient series in eastern crete, Greece.

The main clinical signs and symptoms caused by a rickettsial infection typically begin 6-10 days after the bite and are accompanied by nonspecific findings such as fever, headache and muscle pain. The diagnosis is mainly based on serological tests, however antibody presentation may be delayed, at least at the early stages of the disease, while seroconversion is usually detected 10-15 days after disease onset. Culture is difficult, requires optimized facilities and often proves negative. Under this scope, the presence of a characteristic inoculation eschar at the bite site may prove a useful clinical tool towards the early suspicion and diagnosis/differential diagnosis of tick-borne rickettsioses, even before the onset of rash and fever or serological confirmation. We describe herein the presence of skin lesions and/or an inoculation eschar at the tick bite site in 17 patients diagnosed, by molecular means, as suffering from spotted fever group rickettsioses. The detection of the pathogen's DNA in biopsy samples proved to be a useful means for early rickettsiae detection and identification. Moreover, the presence of an infiltrated erythema always seemed to precede the appearance of an eschar by 2-5 days and the initiation of fever by 1-10 days; these two signs might also prove useful in the context of the final diagnosis.

Minimum inhibitory concentration distribution in environmental Legionella spp. isolates.

In Greece standard tests are performed in the watering and cooling systems of hotels' units either as part of the surveillance scheme or following human infection. The purpose of this study was to establish the minimum inhibitory concentration (MIC) distributions of environmental Legionella isolates for six antimicrobials commonly used for the treatment of Legionella infections, by MIC-test methodology. Water samples were collected from 2004 to 2011 from 124 hotels from the four prefectures of Crete (Greece). Sixty-eight (68) Legionella isolates, comprising L. pneumophila serogroups 1, 2, 3, 5, 6, 8, 12, 13, 15, L. anisa, L. rubrilucens, L. maceachernii, L. quinlivanii, L. oakridgensis, and L. taurinensis, were included in the study. MIC-tests were performed on buffered charcoal yeast extract with α-ketoglutarate, L-cysteine, and ferric pyrophosphate. The MICs were read after 2 days of incubation at 36 ± 1 °C at 2.5% CO2. A large distribution in MICs was recorded for each species and each antibiotic tested. Rifampicin proved to be the most potent antibiotic regardless of the Legionella spp.; tetracycline appeared to have the least activity on our environmental isolates. The MIC-test approach is an easy, although not so cost-effective, way to determine MICs in Legionella spp. These data should be kept in mind especially since these Legionella species may cause human disease.

Attitudes and beliefs on the establishment of a national food safety authority in Cyprus. A population-based survey.

Cyprus does not have a National Food Safety Authority (NFSA), but a multi-level, fragmented system with responsibilities divided among different ministries and governmental agencies, frequently impeding efforts to effectively manage food risks by duplication and overlapping of responsibilities. A population-based survey was carried out to determine the beliefs and attitudes of interested parties concerning the establishment of a NFSA in Cyprus. Information was collected using a random stratified sampling design and a structured questionnaire. A total of 868 questionnaires were collected (704 from regular consumers, 154 from food businesses' representatives, and 10 from public services' directors or acting head officers). About 11% of food businesses' representatives and 45% of consumers reported that they did not know which public authorities are responsible for food control. Moreover, 2 out of 10 (17%) of responders from public agencies, 70% from food businesses and 91% from consumers, although not aware of ongoing efforts to establish a food safety authority in Cyprus (currently under consideration), were supportive of the idea [8 out of 10 (83%) of responders from public services, 93% from food businesses, and 89% of consumers]. Finally, 7 out of 10 (67%) from the public agencies and 84% of representatives from food businesses agreed with the separation of risk assessment from risk management activities. Public opinion in Cyprus as well as public agencies and food businesses' representatives support the establishment of a single independent national food safety authority in Cyprus based on the European paradigm including the division of risk activities.

Typing of Legionella strains isolated from environmental samples in Crete, Greece, during the period 2004-2011.

In Greece, standard tests are performed in watering and cooling systems of hotels. A total of 1,494 water samples were collected during 2004-2011 from 124 hotels from four regions in Crete (Greece). Samples were tested for the presence of Legionella spp.; 103 isolates were identified and typed by polymerase chain reaction (PCR)-sequencing and sequence-based typing (SBT) (in case of L. pneumophila sg 1). Of those, 48 belonged to various serogroups of L. pneumophila (sg 1, 2, 3, 5, 6, 8, 12, 13, and 15), 32 were characterized as L. anisa, 17 as L. taurinensis and there was a single occurrence of L. quinlivanii, L. maceachernii, and L. oakridgensis. In the case of L. pneumophila SG1, one prevalent sequence type was revealed (ST37). The variability of Legionella spp. observed questions the existence of a single ST of the L. pneumophila sg1 species and leads towards the need for a genetic level investigation of all Legionnaires' disease cases.

Analysis of pathogen co-occurrence in host-seeking adult hard ticks from Serbia.

Past studies in Serbia have reported concurrent infections of Ixodes ricinus ticks with Borrelia burgdorferi sensu lato genospecies, Anaplasma phagocytophilum and Francisella tularensis. As a step forward, this investigation included a broader range of microorganisms and five most common and abundant tick species in Serbia. Five tick species were identified (Dermacentor marginatus, D. reticulatus, Haemaphysalis punctata, H. concinna and I. ricinus) and analyzed for the presence of seven pathogens. Anaplasma ovis, A. phagocytophilum, Babesia canis, B. burgdorferi s.l., Coxiella burnetii, Rickettsia helvetica and R. monacensis were detected. Sequencing of samples positive for F. tularensis revealed the presence of Francisella-like endosymbionts. No Bartonella spp. DNA was amplified. Concurrent infections were present in three tick species (D. reticulatus, H. concinna and I. ricinus). The rate of co-infections was highest in I. ricinus (20/27), while this tick species harbored the broadest range of co-infection combinations, with dual, triple and a quadruple infection(s) being detected.

Multi-criterion analysis of the effect of physico-chemical microbiological agents on Legionella detection in hotel water distribution systems in Crete.

Introduction: Water distribution systems in hotels have been related to outbreaks caused by Legionella spp. Certain measures, including disinfection by chlorination, maintaining increased temperatures are usually undertaken to prevent Legionella outbreaks. However, these preventive strategies are not always effective, since there are several factors (e.g., synergistic interactions with other microbes, physico-chemical factors, biofilm formation, availability of nutrients) that promote survival and proliferation of the pathogen in water pipes., Accordingly, there is a need of a holistic approach in development of preventive models for Legionella outbreaks associated with water distribution systems. Methods: Water samples were collected from hotel water systems and were tested for the presence of Legionella, E. coli, total coliforms, total mesophilic count and Pseudomonas. In each sample, temperature and chlorine were also tested. Other epidemiological factors were additionally recorded including number of rooms, stars, proximity of sampling point to the boiler, etc. Data were processed by generalized linear analysis, and modeling based on logistic regression analysis to identify independent predictive factors associated with the presence of Legionella in hotel water systems. Results: According to the generalized linear model, temperature affected (p<0.05) the presence of Legionella regardless of the species or the water supply (hot or cold). Additionally, opportunistic (P. aeruginosa) or non-opportunistic (E. coli, coliforms) pathogens were significantly associated (p<0.05) with the presence of all Legionella species. Temperature also exhibited a positive effect to all pathogens tested except for Pseudomonas according to the linear model. Multivariate analysis showed that Pseudomonas, total coliforms, HPC and temperature had a statistically significant effect on the presence of Legionella. Based on a binomial model, cold water had a positive effect on Legionella. Type of sampling and proximity of the sample to the boiler seemed to pose different effect on Legionella depending on the cfu/L. The number of hotel stars and rooms did not appear to have any effect in all tested models. Discussion: Collectively, these results indicate the need for development of individualized water safety plans tailored by the presence of other microbiological agents, and unique physico-chemical factors, which could facilitate the survival of Legionella.in hotel water systems.

Study of the whole cell lysate of two Coxiella burnetii strains using N-terminomics.

The etiological agent of Q fever is Coxiella burnetii , an obligate intracellular Gram-negative bacterium and the only bacterium known to date that survives and replicates within a vacuole of phagolysosomal characteristics. In humans, Q fever is characterized by a wide spectrum of clinical manifestations. Of note is that genetic diversity among C. burnetii strains has been reported. To further investigate C. burnetii's diversity, but now at the proteome level, we compared the proteomes of whole cell lysates from two reference strains, Nine Mile and Q212. Proteomes were isolated from each strain and subjected MS-driven combined fractional diagonal chromatography (COFRADIC), a peptide-centered proteomics technique, with a total of 322 proteins that were unambiguously identified. On the basis of their identified neo-N-terminal peptides that are highly likely generated upon in vivo processing by proteases, the most proteolytical sensitive proteins in these strains were identified, and a consensus cleavage pattern was obtained. Further, with the use of differential proteomics based on the here-identified N-terminal peptides, 44 proteins were found to be differentially expressed between the two C. burnetii strains, representing 13.6% of the here-identified C. burnetii proteome. Among these proteins, 10 proteins were found uniquely expressed in the NM strain including proteins with unknown functions as well as housekeeping enzymes, suggesting that strain-related proteins might be present among such uncharacterized proteins.

Investigation of rifampicin resistance mechanisms in Brucella abortus using MS-driven comparative proteomics.

Mutations in the rpoB gene have already been shown to contribute to rifampicin resistance in many bacterial strains including Brucella species. Resistance against this antibiotic easily occurs and resistant strains have already been detected in human samples. We here present the first research project that combines proteomic, genomic, and microbiological analysis to investigate rifampicin resistance in an in vitro developed rifampicin resistant strain of Brucella abortus 2308. In silico analysis of the rpoB gene was performed and several antibiotics used in the therapy of Brucellosis were used for cross resistance testing. The proteomic profiles were examined and compared using MS-driven comparative proteomics. The resistant strain contained an already described mutation in the rpoB gene, V154F. A correlation between rifampicin resistance and reduced susceptibility on trimethoprim/sulfamethoxazole was detected by E-test and supported by the proteomics results. Using 12 836 MS/MS spectra we identified 6753 peptides corresponding to 456 proteins. The resistant strain presented 39 differentially regulated proteins most of which are involved in various metabolic pathways. Results from our research suggest that rifampicin resistance in Brucella mostly involves mutations in the rpoB gene, excitation of several metabolic processes, and perhaps the use of the already existing secretion mechanisms at a more efficient level.

Spotted fever group Rickettsiae in ticks in Cyprus.

In two surveys conducted from March 1999 to March 2001 and from January 2004 to December 2006, a total of 3,950 ticks (belonging to ten different species) were collected from seven domestic and wild animals (goat, sheep, cattle, dog, fox, hare, and mouflon) from different localities throughout Cyprus. In order to establish their infection rate with Spotted Fever Rickettsiae (SFG), ticks were pooled and tested by polymerase chain reaction targeting gltA and ompA genes, followed by sequencing analysis. When tick pools tested positive, individual ticks were then tested one by one, and of the 3,950 ticks screened, rickettsial DNA was identified in 315 ticks (infection rate, 8%). Five SFG Rickettsiae were identified: Rickettsia aeschlimannii in Hyalomma marginatum marginatum, Rickettsia massiliae in Rhipicephalus turanicus and Rhipicephalus sanguineus, Rickettsia sibirica mongolotimonae in Hyalomma anatolicum excavatum, and a Rickettsia endosymbiont of Haemaphysalis sulcata (later described as Rickettsia hoogstraalii) in Haemaphysalis punctata. Two additional genes, 17 kDa and ompB, were targeted to characterize a new genotype of "Candidatus Rickettsia barbariae" genotype in R. turanicus, designated here as "Candidatus Rickettsia barbariae" Cretocypriensis. These results confirm the presence of a spectrum of SFG Rickettsiae on the island. Further studies are necessary to gain better knowledge on the epidemiology of SFG Rickettsiae in Cyprus.