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.

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.

Spatio-Temporal Distribution of Brucellosis in European Terrestrial and Marine Wildlife Species and Its Regional Implications.

Brucellosis is an important bacterial zoonosis of domestic and wildlife species. This disease has a significant public health concern and is characterized by reproductive failure resulting in economic losses in the livestock industry. Among thirteen known species, B. abortus, B. melitensis, B. suis, and B. canis are human pathogens. Brucellosis has been extensively investigated in humans and domestic animals. However, the situation in wildlife is still not completely reported and studied. Therefore, a systematic literature search and screening were done to clarify the situation of brucellosis in wildlife in Europe. Sixty-five articles from a total of 13,424 reports published between 1991 and 2021 were selected, applying defined inclusion criteria. Wild boars and brown hares were the most often studied terrestrial wildlife species, whereas seals and porpoises were the most often investigated marine wildlife. Poland, Croatia, and Belgium showed the highest seroprevalences of wild boars caused by B. suis biovar 2. In marine wildlife, brucellosis was mainly caused by B. ceti and B. pinnipedialis. Most samples were from carcasses. Thus, sera could not be collected. It is worrisome that B.abortus and B. melitensis were reported from both terrestrial and marine wild animals, posing a zoonotic threat to people exposed to wild animals. Currently, there is no approved vaccine available for wild animals. The main challenges are the development of specific diagnostics and their validation for use in wildlife.

Antibiotic Resistance of Legionella pneumophila in Clinical and Water Isolates-A Systematic Review.

The current systematic review investigates the antibiotic susceptibility pattern of Legionella pneumophila isolates from the 1980s to the present day, deriving data from clinical and/or water samples from studies carried out all over the world. Eighty-nine papers meeting the inclusion criteria, i.e., "Legionella pneumophila" and "resistance to antibiotics", were evaluated according to pre-defined validity criteria. Sixty articles referred to clinical isolates, and 18 articles reported water-related L. pneumophila isolates, while 11 articles included both clinical and water isolates. Several methods have been proposed as suitable for the determination of MICs, such as the E-test, broth and agar dilution, and disk diffusion methods, in vivo and in vitro, using various media. The E-test method proposed by the European Society of Clinical Microbiology and Infectious Diseases (EUCAST) seems to be the second most frequently used method overall, but it is the preferred method in the most recent publications (2000-2019) for the interpretation criteria. Erythromycin has been proved to be the preference for resistance testing over the years. However, in the last 19 years, the antibiotics ciprofloxacin (CIP), erythromycin (ERM), levofloxacin (LEV) and azithromycin (AZM) were the ones that saw an increase in their use. A decrease in the sensitivity to antibiotics was identified in approximately half of the reviewed articles.

The epidemiology of Brucellosis in Greece, 2007-2012: a 'One Health' approach.

Background: Brucellosis remains a disease that is very difficult to control and eradicate in Greece. Information exchange between the responsible authorities is crucial in order to support public health infrastructure in the sense of the 'One-Health' strategy model. Methods: The data for 2007-2012 were retrieved from the notifiable diseases system and analysed statistically for correlations between human brucellosis cases and the disease in small ruminants. Disease-related risk factors were also estimated with parallel exploitation mapping software. Results: In Greece the dominant strain for brucellosis is Brucella melitensis. The average incidence in Greece was estimated to be 1.43/100,000. The majority of human cases were males (67.60%). The age distribution of brucellosis patients differs significantly between men and women. Brucellosis in male patients was related to high risk jobs and animal contact, while brucellosis in females was related to recent consumption of dairy products. Seasonality of the disease was different in relation to the European countries an observation attributed to the traditional customs. There was a statistically significant difference in human brucellosis incidence between the eradication and vaccination zones. Conclusion: The updated information on brucellosis in Greece revealed differences in seasonality and transmission patterns. A more active cooperation between the involved public health-related sectors should be followed in order to effectively fight brucellosis as there are still foci of brucellosis in Greece.

Legionella spp. Risk Assessment in Recreational and Garden Areas of Hotels.

Several Travel-associated Legionnaires' disease (TALD) cases occur annually in Europe. Except from the most obvious sites (cooling towers and hot water systems), infections can also be associated with recreational, water feature, and garden areas of hotels. This argument is of great interest to better comprehend the colonization and to calculate the risk to human health of these sites. From July 2000-November 2017, the public health authorities of the Island of Crete (Greece) inspected 119 hotels associated with TALD, as reported through the European Legionnaires' Disease Surveillance Network. Five hundred and eighteen samples were collected from decorative fountain ponds, showers near pools and spas, swimming pools, spa pools, garden sprinklers, drip irrigation systems (reclaimed water) and soil. Of those, 67 (12.93%), originating from 43 (35.83%) hotels, tested positive for Legionella (Legionella pneumophila serogroups 1, 2, 3, 6, 7, 8, 13, 14, 15 and non-pneumophila species (L. anisa, L. erythra, L. taurinensis, L. birminghamensis, L. rubrilucens). A Relative Risk (R.R.) > 1 (p < 0.0001) was calculated for chlorine concentrations of less than 0.2 mg/L (R.R.: 54.78), star classification (<4) (R.R.: 4.75) and absence of Water Safety Plan implementation (R.R.: 3.96). High risk (≥104 CFU/L) was estimated for pool showers (16.42%), garden sprinklers (7.46%) and pool water (5.97%).

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.

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.

Environmental investigation for the presence of Vibrio species following a case of severe gastroenteritis in a touristic island.

Global changes have caused a worldwide increase in reports of Vibrio-associated diseases with ecosystem-wide impacts on humans and marine animals. In Europe, higher prevalence of human infections followed regional climatic trends with outbreaks occurring during episodes of unusually warm weather. Similar patterns were also observed in Vibrio-associated diseases affecting marine organisms such as fish, bivalves, and corals. Following a possible human case of infection due to V. cholerae in the island of Kos (eastern Aegean, Greece), environmental samples were collected and tested for the presence of Vibrio species. Using chromogenic agar and MALDI-TOF MS, V. parahaemolyticus, V. vulnificus V. furnisii, V. alginolyticus, and V. fluvialis were isolated and/or identified. The presence of V. cholerae was established by PCR-sequencing analysis only. Following the susceptibility testing of the Vibrio isolates, only one, V. furnisii, showed intermediate resistance to ciprofloxacin. The rest of the isolates were susceptible to all antibiotics tested. The presence of Vibrio species in aquatic samples reveals potential dangers due to exposure to contaminated seawaters.

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.

Proteome studies of bacterial antibiotic resistance mechanisms.

Ever since antibiotics were used to help humanity battle infectious diseases, microorganisms straight away fought back. Antibiotic resistance mechanisms indeed provide microbes with possibilities to by-pass and survive the action of antibiotic drugs. Several methods have been employed to identify these microbial resistance mechanisms in an ongoing effort to reduce the steadily increasing number of treatment failures due to multi-drug-resistant microbes. Proteomics has evolved to an important tool for this area of research. Following rapid advances in whole genome sequencing, proteomic technologies have been widely used to investigate microbial gene expression. This review highlights the contribution of proteomics in identifying microbial drug resistance mechanisms. It summarizes different proteomic studies on bacteria resistant to different antibiotic drugs. The review further includes an overview of the methodologies used, as well as lists key proteins identified, thus providing the reader not only a summary of research already done, but also directions for future research. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

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.

Identification of a novel uncultured Rickettsia species strain (Rickettsia species strain Tselenti) in Cyprus.

In a previous study conducted in Cyprus, various spotted fever group Rickettsia species were detected and identified in ticks by molecular analysis. Among them, a partially characterized Rickettsia species was detected in Hyalomma anatolicum excavatum and Rhipicephalus turanicus ticks. We report characterization of this rickettsial strain by using polymerase chain reaction sequencing analysis of partial citrate synthase A, outer membrane protein A, outer membrane protein B, and 17-kD protein genes. We propose a provisional name Rickettsia sp. strain Tselenti for this strain until it is isolated and further characterized.

Murine typhus in Cyprus: a 9-year survey.

Epidemiological and clinical data of 193 human cases of murine typhus in Cyprus were recorded and analysed during a 9-year period (2000-2008). The incidence rate was estimated at 24.5 cases/100,000 population/year. The incidence rate varied considerably between rural, urban and semi-urban areas, with residents in rural areas accounting for 79.3% of the total cases. Most (72.5%) of the cases occurred in late summer (July and August) and early autumn (September to October) with a peak in September. Well-established persistent endemic foci with clusters of cases were identified and characterised as 'high risk' areas. Presence of or contact with rats and fleas, presence of domestic/peridomestic animals and residence in rural areas, especially locations near the 'green line' (a narrow zone patrolled by UN forces that separates the northern and southern parts of the island), increased the possibility of murine typhus infection. The results of the current study enhance the belief that murine typhus is a serious public health problem in Cyprus.

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.

Tick-borne bacteria in mouflons and their ectoparasites in Cyprus.

The Cypriot mouflon (Ovis orientalis ophion), a once almost extirpated species of wild sheep, is under strict surveillance because it can be threatened by likely transmission of pathogenic bacteria, such as Anaplasma spp., Rickettsia spp., and Coxiella burnetii, primarily from domestic ungulates. We collected 77 blood samples from Cypriot mouflons and 663 of their ectoparasites (Rhipicephalus turanicus, Rhipicephalus sanguineus, Rhipicephalus bursa, Hyalomma anatolicum excavatum, Hyalomma marginatum, Haemaphysalis punctata, Haemaphysalis sulcata, and Ixodes gibossus) and tested them by polymerase chain reaction and sequencing. Twenty-three mouflon blood samples (30%) were positive for C. burnetii, 23 (30%) for Rickettsia spp., and 8 (10%) for Anaplasma ovis. Of 109 pools of ectoparasites, 32.1% were positive for C. burnetii, 28.4% for Rickettsia spp., and 10.9% for A. ovis; 11.9% were positive for both C. burnetii and Rickettsia spp., 6.4% for both Rickettsia spp. and A. ovis, and 2.8% for all three pathogens. This is the first survey that records the presence of tick-borne pathogens, both in the Cypriot mouflon and in ticks parasitizing it.

DNA gyrase and topoisomerase IV mutations in an in vitro fluoroquinolone-resistant Coxiella burnetii strain.

The etiological agent of Q fever, Coxiella burnetii, is an obligate intracellular bacterium that multiplies within a vacuole with lysosomal characteristics. Quinolones have been used as an alternative therapy for Q fever. In this study, quinolone-resistance-determining regions of the genes coding for DNA gyrase and topoisomerase IV were analyzed by DNA sequencing from an in vitro fluoroquinolone-resistant C. burnetii strain (Q212). Sequencing and aligning of DNA gyrase encoding genes (gyrA and gyrB) and topoisomerase IV genes (parC and parE) revealed one gyrA mutation leading to the amino acid substitution Asp87Gly (Escherichia coli numbering), two gyrB mutations leading to the amino acid substitutions Ser431Pro and Met518Ile, and three parC mutations leading to the amino acid substitutions Asp69Asn, Thr80Ile, and Gly104Ser. The corresponding alignment of the C. burnetii Q212 reference strain, the in vitro developed fluoroquinolone-resistant C. burnetii Q212 strain, and E. coli resulted in the identification of several other naturally occurring mutations within and outside the quinolone-resistance-determining regions of C. burnetii providing indications of possible natural resistance to fluoroquinolones. The present study adds additional potential mutations in the DNA topoisomerases that may be involved in fluoroquinolone resistance in C. burnetii due to their previous characterization in other bacterial species.

Phylogentic analysis of Anaplasma ovis strains isolated from sheep and goats using groEL and mps4 genes.

Evidence of Anaplasma spp. in goats and sheep in Cyprus has been demonstrated by previous research. Herein, further research was performed for the identification of the exact Anaplasma spp. resulting in the identification of Anaplasma ovis strains in all samples examined. We used a bioinformatics as well as a molecular approach (study of groEl and mps4 genes) in order to verify the validity of the results. All samples depicted the presence of A. ovis regardless of the host (goat or sheep).