Genotypic identification of erythromycin-resistant campylobacter isolates as helicobacter species and analysis of resistance mechanism

Metagenomics assists in the diagnosis of a refractory, culture-negative pyoderma gangrenosum-like ulcer caused by Helicobacter cinaedi in a patient with primary agammaglobulinemia

Helicobacter cinaedi is known to cause various infections in immunocompromised hosts ranging from skin lesions to disseminated septicemia. Identification of H. cinaedi is difficult through conventional identification methods due to its fastidious nature. We reported a refractory and culture-negative pyoderma gangrenosum-like ulcer caused by H. cinaedi in a patient with primary agammaglobulinemia. Metagenomic next-generation sequencing (mNGS) was applied for the identification of H. cinaedi and prolonged minocycline and amoxicillin-clavulanate potassium was used to eradicate the infection. Given the difficulties in culturing this organism, it's highly possible that H cinaedi infections have been overlooked. We suggest that early consideration of H. cinaedi infection should be suspected in immunocompromised patients presenting with unexplained skin lesions as the appropriate antibiotic choice plus a prolonged treatment course is essential for the prognosis. Application of mNGS could contribute to the early identification of rare and cryptogenic pathogens.

Helicobacter cinaedi is a human-adapted lineage in the Helicobacter cinaedi/canicola/'magdeburgensis' complex

Helicobacter cinaedi is an enterohepatic Helicobacter that causes bacteremia and other diseases in humans. While H. cinaedi-like strains are isolated from animals, including dog isolates belonging to a recently proposed H. canicola, little is known about the genetic differences between H. cinaedi and these animal isolates. Here, we sequenced 43 H. cinaedi- or H. canicola-like strains isolated from humans, hamsters, rats and dogs and collected 81 genome sequences of H. cinaedi, H. canicola and other enterohepatic Helicobacter strains from public databases. Genomic comparison of these strains identified four distinct clades (clades I–IV) in H. cinaedi/canicola/‘magderbugensis’ (HCCM) complex. Among these, clade I corresponds to H. cinaedi sensu stricto and represents a human-adapted lineage in the complex. We identified several genomic features unique to clade I. They include the accumulation of antimicrobial resistance-related mutations that reflects the human association of clade I and the larger genome size and the presence of a CRISPR-Cas system and multiple toxin-antitoxin and restriction-modification systems, both of which indicate the contribution of horizontal gene transfer to the evolution of clade I. In addition, nearly all clade I strains but only a few strains belonging to one minor clade contained a highly variable genomic region encoding a type VI secretion system (T6SS), which could play important roles in gut colonization by killing competitors or inhibiting their growth. We also developed a method to systematically search for H. cinaedi sequences in large metagenome data sets based on the results of genome comparison. Using this method, we successfully identified multiple HCCM complex-containing human faecal metagenome samples and obtained the sequence information covering almost the entire genome of each strain. Importantly, all were clade I strains, supporting our conclusion that H. cinaedi sensu stricto is a human-adapted lineage in the HCCM complex.

Withdrawal of Colistin Reduces Incidence of mcr-1-Harboring IncX4-Type Plasmids but Has Limited Effects on Unrelated Antibiotic Resistance

The global dissemination of plasmid-mediated colistin resistance gene mcr and its variants have posed a great threat to public health. Therefore, the Chinese government banned the use of colistin as a feed additive in livestock in April 2017. To explore the dynamic changes of overall antibiotic resistance genes (ARGs) and phylogenetic relationship of bacteria from a single pig farm before and after the withdrawal of colistin, fecal swab samples were collected from a large-scale pig farm before (n = 32; 2 months pre-withdrawal of colistin) and after withdrawal of colistin (n = 30; 13 months post-withdrawal of colistin). Escherichia coli and Klebsiella pneumoniae were isolated. Whole-genome sequencing (Illumina, MiSeq) was performed to examine ARGs, plasmids and the genetic relationship of the isolates. The overall SNP results indicated all isolates had high genetic diversity, and the evolutionary relationship across isolates was not influenced by the ban of colistin. However, the prevalence of mcr-1.1 (5.6%, p < 0.01) was significantly lower than before the ban (86.4%). Plasmid profiling analysis showed that 17 of 20 (85.0%) observed mcr-1.1 genes reside on IncX4-type plasmids, 16 of which (94.1%) were from isolates before the ban. On the contrary, the presence of blaCTX-M gene was significantly increased (p = 0.0215) post-withdrawal of colistin. Our results showed that withdrawal of colistin reduced the incidence of mcr-1-harboring IncX4-type plasmids, but had limited influences on unrelated ARGs.

Infected aortic aneurysm caused by Helicobacter cinaedi: case series and systematic review of the literature

Background

Helicobacter cinaedi is rarely identified as a cause of infected aneurysms; however, the number of reported cases has been increasing over several decades, especially in Japan. We report three cases of aortic aneurysm infected by H. cinaedi that were successfully treated using meropenem plus surgical stent graft replacement or intravascular stenting. Furthermore, we performed a systematic review of the literature regarding aortic aneurysm infected by H. cinaedi.

Case presentation

We present three rare cases of infected aneurysm caused by H. cinaedi in adults. Blood and tissue cultures and 16S rRNA gene sequencing were used for diagnosis. Two patients underwent urgent surgical stent graft replacement, and the other patient underwent intravascular stenting. All three cases were treated successfully with intravenous meropenem for 4 to 6 weeks.

Conclusions

These cases suggest that although aneurysms infected by H. cinaedi are rare, clinicians should be aware of H. cinaedi as a potential causative pathogen, even in immunocompetent patients. Prolonged incubation periods for blood cultures are necessary for the accurate detection of H. cinaedi.

Molecular epidemiologic and clinical analysis of Helicobacter cinaedi bacteremia in Japan

BACKGROUND

Helicobacter cinaedi is an important pathogen that causes bloodstream infections. Owing to the challenges in its culture and identification, its clinical and bacterial characteristics remain unknown. Our study aimed to investigate the molecular epidemiology and antimicrobial susceptibility of H cinaedi.

MATERIALS AND METHODS

From 2003 to 2016, we analyzed 16 non-repetitive H cinaedi strains, isolated from blood, at the medical hospital of Tokyo Medical and Dental University. Multilocus sequence typing was performed to analyze the genetic relationship across the different isolates. The minimum inhibitory concentrations (MIC) of antibiotics were determined by the agar dilution method.

RESULTS

The median age of subjects in this study was 61 years (range, 18-84 years). The most common risk factors included the use of steroids (75.0%) and immunosuppressant drugs (37.5%). In addition, the most common symptoms of H cinaedi bacteremia included colitis (37.5%) and cellulitis (31.3%). The infection recurred in three of seven cases (42.8%) that underwent antibiotic therapy for <10 days. The strains were classified into five sequence types (ST), of which, ST 10 (43.8%) and ST 4 (31.3%) were predominant. The MIC₉₀ values of amoxicillin, gentamycin, imipenem, ciprofloxacin, and clarithromycin were 4, 0.5, 0.25, 64, and 128 mg/L, respectively.

CONCLUSIONS

Since there is no recommended guideline yet for the choice or duration of antibiotic therapy and antimicrobial break points, our results suggested, for the first time, that prolonged antibiotic therapy, except with ciprofloxacin and clarithromycin, would be required to ensure resolution of symptoms and prevention of recurrence.

Human campylobacteriosis: A public health concern of global importance

Campylobacter species are among the leading cause of bacterial foodborne and waterborne infections. In addition, Campylobacter is one of the major causative agent of bacterial gastrointestinal infections and the rise in the incidence of Campylobacter infections have been reported worldwide. Also, the emergence of some Campylobacter species as one of the main causative agent of diarrhea and the propensity of these bacteria species to resist the actions of antimicrobial agents; position them as a serious threat to the public health. This paper reviews Campylobacter pathogenicity, infections, isolation and diagnosis, their reservoirs, transmission pathways, epidemiology of Campylobacter outbreaks, prevention and treatment option, antibiotics resistance and control of antibiotics use.

First case report of thyroid abscess caused by Helicobacter cinaedi presenting with thyroid storm

Background

Helicobacter cinaedi is a microaerobic Gram-negative spiral-shaped bacterium that causes enteritis, cellulitis, and bacteremia in both immunocompromised and immunocompetent patients. While there have been increasing numbers of reported H. cinaedi infections recently, there has been no thyroid abscess case caused by H. cinaedi presenting with thyroid storm.

Case presentation

A 50-year-old Japanese man presented with a 9-day history of high fever associated with palpitations, dry cough, and chronic diarrhea. The patient had a history of Basedow’s disease that had been treated with thiamazole in the past. During the current episode, the patient was diagnosed with thyroid storm and treated accordingly. The blood culture taken on admission was positive for H. cinaedi. This finding was confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOFMS). A systemic computed tomography (CT) scan revealed a thyroid abscess as the site of infection and cause of the bacteremia. The 16S rRNA gene sequencing identified the pathogen of thyroid abscess as H. cinaedi. Clinical symptoms and laboratory data normalized on admission day 7 after treatment with both effective antibiotics and antithyroid drugs.

Conclusions

The case study described a patient with a history of Basedow’s disease that presented with a thyroid abscess caused by H. cinaedi with symptoms similar to those of thyroid storm. While this bacterium has been implicated in other infections, we believe this is the first time the bacteria has been documented to have caused a thyroid abscess.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-3808-7) contains supplementary material, which is available to authorized users.

Helicobacter cinaedi bacteremia in four renal transplant patients: clinical features and an important suggestion regarding the route of infection

Helicobacter cinaedi can cause bacteremia mainly in immunocompromised patients. We present the clinical characteristics of H. cinaedi bacteremia in 4 renal transplant patients. Interestingly, all cases showed triggers of bacterial translocation: 2 cases developed after colonic perforation caused by diverticulitis, 1 case developed post cholecystectomy, and the remaining patient had chronic diarrhea. Accordingly, bacterial translocation caused by severe gastrointestinal complication could be a cause of H. cinaedi bacteremia.

Helicobacter pullorum isolated from fresh chicken meat: antibiotic resistance and genomic traits of an emerging foodborne pathogen

Meat and meat products are important sources of human intestinal infections. We report the isolation of Helicobacter pullorum strains from chicken meat. Bacteria were isolated from 4 of the 17 analyzed fresh chicken meat samples, using a membrane filter method. MIC determination revealed that the four strains showed acquired resistance to ciprofloxacin; one was also resistant to erythromycin, and another one was resistant to tetracycline. Whole-genome sequencing of the four strains and comparative genomics revealed important genetic traits within the H. pullorum species, such as 18 highly polymorphic genes (including a putative new cytotoxin gene), plasmids, prophages, and a complete type VI secretion system (T6SS). The T6SS was found in three out of the four isolates, suggesting that it may play a role in H. pullorum pathogenicity and diversity. This study suggests that the emerging pathogen H. pullorum can be transmitted to humans by chicken meat consumption/contact and constitutes an important contribution toward a better knowledge of the genetic diversity within the H. pullorum species. In addition, some genetic traits found in the four strains provide relevant clues to how this species may promote adaptation and virulence.

Clinical and bacteriological characteristics of Helicobacter cinaedi infection

Helicobacter cinaedi was first isolated from rectal cultures from homosexual men in 1984. In the 1980s to mid 1990s, the microorganism was mainly isolated from samples from homosexual men or immunocompromised patients; however, during the last two decades, H. cinaedi has been isolated from immunocompromised and from immunocompetent individuals worldwide. In Japan, the isolation of this microorganism was first reported in 2003. Since then, many cases have been reported in hospitals across the country. Despite many reports, the etiological properties and pathogenicity of H. cinaedi remain elusive; however, we are increasingly able to recognize some of the features and the clinical relevance of infection. In particular, a long incubation period is essential for detection in an automatic blood culture system and many of the recent isolates are resistant to both macrolides and quinolones. Furthermore, there is an association between infection and severe or chronic illnesses, such as meningitis or arteriosclerosis, in addition to mild diseases such as fever, abdominal pain, gastroenteritis, proctitis, diarrhea, erysipelas, cellulitis, arthritis, and bacteremia. In this review, we introduce the current knowledge and our latest findings relating to H. cinaedi.

Molecular epidemiologic analysis and antimicrobial resistance of Helicobacter cinaedi isolated from seven hospitals in Japan

Helicobacter cinaedi colonizes the colons of human and animals and can cause colitis, cellulitis, and sepsis in humans, with infections in immunocompromised patients being increasingly recognized. However, methods for analyzing the molecular epidemiology of H. cinaedi are not yet established. A genotyping method involving multilocus sequence typing (MLST) was developed and used to analyze 50 H. cinaedi isolates from Japanese hospitals in addition to 6 reference strains. Pulsed-field gel electrophoresis (PFGE) results were also compared with the MLST results. Based on the genomic information from strain CCUG18818, 21 housekeeping genes were selected as candidates for MLST and were observed to have high homology (96.5 to 100%) between isolates. Following a comparison of the 21 housekeeping genes from 8 H. cinaedi isolates, 7 genes were chosen for MLST, revealing 14 sequence types (STs). The isolates from 3 hospitals belonged to the same STs, but the isolates from the other 4 hospitals belonged to different STs. Isolates belonging to ST6 were analyzed by PFGE and showed similar, but not identical, patterns between isolates. Isolates belonging to ST9, ST10, and ST11, which belonged to the same clonal complex, had the same pattern. All isolates were found to contain mutations in GyrA and the 23S rRNA gene that confer ciprofloxacin and clarithromycin resistance, respectively, in H. cinaedi. These results raise concerns about the increase in H. cinaedi isolates resistant to clarithromycin and ciprofloxacin in Japan.

Evaluation of several biochemical and molecular techniques for identification of Streptococcus pneumoniae and Streptococcus pseudopneumoniae and their detection in respiratory samples

The identification and detection of mitis group streptococci, which contain Streptococcus pneumoniae, have been hampered by the lack of sensitive and specific assays. In this study, we evaluated several biochemical and molecular assays for the identification of S. pneumoniae and Streptococcus pseudopneumoniae and their distinction from other mitis group streptococci using a collection of 54 isolates obtained by the routine culturing of 53 respiratory specimens from patients with community-acquired pneumonia. The combined results of the biochemical and molecular assays indicated the presence of 23 S. pneumoniae, 2 S. pseudopneumoniae, and 29 other mitis group streptococcal isolates. The tube bile solubility test that is considered gold standard for the identification of S. pneumoniae showed concordant results with optochin susceptibility testing (CO(2) atmosphere) and a real-time multiplex PCR assay targeting the Spn9802 fragment and the autolysin gene. Optochin susceptibility testing upon incubation in an O(2) atmosphere, bile solubility testing by oxgall disk, matrix-assisted laser desorption ionization-time of flight mass spectrometry, and sequence analysis of the tuf and rpoB genes resulted in several false-positive, false-negative, or inconclusive results. The S. pseudopneumoniae isolates could be identified only by molecular assays, and the multiplex real-time PCR assay was concluded to be most convenient for the identification of S. pneumoniae and S. pseudopneumoniae isolates. Using this method, S. pneumoniae and S. pseudopneumoniae DNA could be detected in the respiratory samples from which they were isolated and in an additional 11 samples from which only other streptococci were isolated.

First report of Atopobium vaginae bacteremia with fetal loss after chorionic villus sampling

Infectious complications after chorionic villus sampling (CVS) are rare (<0.1%) but can lead to maternal sepsis and spontaneous abortion. We report the first bacteremia with Atopobium vaginae and suggest A. vaginae to be a pathogenic microorganism that can lead to intrauterine infection and fetal death following CVS.

Prevalence of Helicobacter pullorum in conventional, organic, and free-range broilers and typing of isolates

Helicobacter pullorum represents a potential food-borne pathogen, and avian species appear to be a relevant reservoir of this organism. In this study, the prevalence of H. pullorum was investigated at 30 conventional farms where 169 ceca from 34 flocks were tested, at eight organic farms where 39 ceca from eight flocks were tested, and at seven free-range farms where 40 ceca from eight flocks were tested. All of the ceca were obtained from healthy broiler chickens. Moreover, amplified fragment length polymorphism, pulsed-field gel electrophoresis, and automated ribotyping were employed to estimate the levels of genetic variability of H. pullorum broiler isolates within and between flocks. Overall, Gram-negative, slender, curved rods, identified as H. pullorum by PCR, were isolated at 93.3% of the farms tested. The percentage of positive free-range farms (54.2%) was significantly lower than that of conventional (100%) or organic (100%) farms (P < 0.001). The level of within-flock genetic variability, calculated as the number of flocks colonized by isolates genetically different by all of the typing methods, was 34.9%. Isolates showing identical profiles by each typing method were observed in 11.6% of the flocks, but they were never detected between flocks. However, groups of isolates clustered together with an overall similarity level of ≥85%. Our results suggest that even though a high level of genetic variability is attributable to H. pullorum broiler isolates, their hierarchical genotyping produces data useful for epidemiological investigations.

Campylobacter jejuni bacteremia and Helicobacter pylori in a patient with X-linked agammaglobulinemia

We describe a 15-year-old patient with X-linked agammaglobulinemia who developed malabsorption and bacteremia due to infection of Helicobacter pylori and Campylobacter jejuni. The Campylobacter bacteremia was only recognized after subculturing of blood culture bottles that failed to signal in the automated system. After 2 weeks of treatment with meropenem and erythromycin for 4 weeks, the patient developed a relapse of bacteremia 10 months later with a high level erythromycin resistant C. jejuni. Sequencing revealed an A2058C mutation in the 23 S rRNA gene associated with this resistance. Treatment with doxycycline for 4 weeks finally resulted in complete eradication. This case report illustrates the importance for physicians to use adapted culture methods and adequate prolonged therapy in patients with an immunodeficiency. A summary of published case reports and series of patients with hypogammaglobulinemia or agammaglobulinemia with Campylobacter or Helicobacter bacteremia is given.

Inaccuracy of routine susceptibility tests for detection of erythromycin resistance of Campylobacter jejuni and Campylobacter coli

In The Netherlands, both an increase in and regional differences in erythromycin resistance of Campylobacter jejuni and Campylobacter coli have been reported. To determine the accuracy of routine tests for erythromycin resistance, 48 erythromycin-resistant isolates from various laboratories that participate in the Dutch surveillance of Campylobacter infections were reinvestigated. Initial susceptibility testing for erythromycin had been performed by disk diffusion in six and MIC-based methods in two laboratories. Reinvestigation was carried out using broth microdilution as a reference standard, as well as E-test and genetic resistance testing. Of 36 C. jejuni isolates reported by the initial laboratories as erythromycin-resistant, four (11%) and five (14%) were confirmed as erythromycin-resistant using broth microdilution according to CLSI and EUCAST resistance criteria, respectively. Erythromycin resistance was found in eight of 12 (67%) C. coli isolates according to both criteria. Results of E-tests were in accordance with these results in all isolates. Resistance-associated mutations in the 23S rRNA gene (A2059G and A2058T) were found in all isolates showing high-level resistance, whereas none were found in susceptible isolates. Routine determination of the erythromycin resistance of C. jejuni and C. coli shows unacceptable interlaboratory variation. In the absence of standardized protocols and interpretive criteria for disk diffusion, and while we await the development of easily applicable and reliable methods for molecular resistance testing, the use of broth microdilution remains the best method.

Species-specific identification and differentiation of Arcobacter, Helicobacter and Campylobacter by full-spectral matrix-associated laser desorption/ionization time of flight mass spectrometry analysis

Rapid and reliable identification of Arcobacter and Helicobacter species, and their distinction from phenotypically similar Campylobacter species, has become increasingly important, since many of them are now recognized as human and/or animal pathogens. Matrix-associated laser desorption/ionization–time of flight (MALDI-TOF) MS has been shown to be a rapid and sensitive method for characterization of micro-organisms. In this study, we therefore established a reference database of selected Arcobacter, Helicobacter and Campylobacter species for MALDI-TOF MS identification. Besides the species with significance as food-borne pathogens – Arcobacter butzleri, Helicobacter pullorum, Campylobacter jejuni and Campylobacter coli – several other members of these genera were included in the reference library to determine the species specificity of the designed MALDI Biotyper reference database library. Strains that made up the reference database library were grown on Columbia agar, and yielded reproducible and unique mass spectra profiles, which were compared with the Bruker Biotyper database, version 2. The database was used to identify 144 clinical isolates using whole spectral profiles. Furthermore, reproducibility of MALDI-TOF MS results was evaluated with respect to age and/or storage of bacteria and different growth media. It was found that correct identification could be obtained even if the bacteria were stored at room temperature or at 4 °C up to 9 days before being tested. In addition, bacteria were correctly identified when grown on Campylosel agar; however, they were not when grown on modified charcoal cefoperazone deoxycholate agar. These results indicate that MALDI-TOF MS fingerprinting is a fast and reliable method for the identification of Arcobacter and Helicobacter species, and their distinction from phenotypically similar Campylobacter species, with applications in clinical diagnostics.

High-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionization-time of flight mass spectrometry in conventional medical microbiology laboratories

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs and can be considered an alternative for conventional biochemical and molecular identification systems in a conventional microbiological laboratory. First, we evaluated MALDI-TOF MS using 327 clinical isolates previously cultured from patient materials and identified by conventional techniques (Vitek-II, API, and biochemical tests). Discrepancies were analyzed by molecular analysis of the 16S genes. Of 327 isolates, 95.1% were identified correctly to genus level, and 85.6% were identified to species level by MALDI-TOF MS. Second, we performed a prospective validation study, including 980 clinical isolates of bacteria and yeasts. Overall performance of MALDI-TOF MS was significantly better than conventional biochemical systems for correct species identification (92.2% and 83.1%, respectively) and produced fewer incorrect genus identifications (0.1% and 1.6%, respectively). Correct species identification by MALDI-TOF MS was observed in 97.7% of Enterobacteriaceae, 92% of nonfermentative Gram-negative bacteria, 94.3% of staphylococci, 84.8% of streptococci, 84% of a miscellaneous group (mainly Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, and Kingella [HACEK]), and 85.2% of yeasts. MALDI-TOF MS had significantly better performance than conventional methods for species identification of staphylococci and genus identification of bacteria belonging to HACEK group. Misidentifications by MALDI-TOF MS were clearly associated with an absence of sufficient spectra from suitable reference strains in the MALDI-TOF MS database. We conclude that MALDI-TOF MS can be implemented easily for routine identification of bacteria (except for pneumococci and viridans streptococci) and yeasts in a medical microbiological laboratory.

The nosocomial transmission of Helicobacter cinaedi infections in immunocompromised patients

BACKGROUND

We encountered 15 cases of Helicobacter cinaedi (H. cinaedi) infection between March and July 2008.

PATIENT, METHOD, AND RESULT

The underlying diseases were hematological malignancies in a majority of cases, many of which received chemotherapy. All patients had a fever. The fever was followed by cellulitis in three, a skin rash in six, pain in the lower limbs in three, and diarrhea in three cases. We analyzed the bacterial 23S rRNA genes. The fifteen strains were divided according to base sequence into Groups A, B, and C, respectively. All four cases in Group A were women and all ten in Group C were men, indicating that the gender of the patient corresponded precisely to the genotypes of the separated bacilli in these two groups. These findings also suggested the strong possibility of nosocomial spread.

CONCLUSION

It is highly likely that H. cinaedi infections have been overlooked due to the difficulties encountered in culturing the bacterium. The possibility of septicemia caused by H. cinaedi should be suspected especially in immunocompromised patients such as those undergoing chemotherapy, with symptoms such as fever, rash, arthritis, cellulitis, leg pain, and other systemic or local symptoms.

Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies

Bacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs are used to generate amplicons of variant regions that are informative in taxonomic assignment. One problem is that the percentage coverage and application scope of the primers used in previous studies are largely unknown. In this study, conservative fragments of available rDNA sequences were first mined and then used to search for candidate primers within the fragments by measuring the coverage rate defined as the percentage of bacterial sequences containing the target. Thirty predicted primers with a high coverage rate (>90%) were identified, which were basically located in the same conservative regions as known primers in previous reports, whereas 30% of the known primers were associated with a coverage rate of <90%. The application scope of the primers was also examined by calculating the percentages of failed detections in bacterial phyla. Primers A519–539, E969–983, E1063–1081, U515 and E517, are highly recommended because of their high coverage in almost all phyla. As expected, the three predominant phyla, Firmicutes, Gemmatimonadetes and Proteobacteria, are best covered by the predicted primers. The primers recommended in this report shall facilitate a comprehensive and reliable survey of bacterial diversity in metagenomic studies.

Identification of thermotolerant campylobacter species by fluorescence in situ hybridization

Thermotolerant Campylobacter spp. (Campylobacter jejuni, C. coli, C. lari, and C. upsaliensis) are leading causes of food-borne diarrhea in humans. In this study, the usefulness of fluorescence in situ hybridization (FISH) for the identification of Campylobacter isolates was investigated. A hierarchical FISH probe set that included six group-, genus-, and species-specific probes was developed and evaluated with 12 reference strains and 94 clinical isolates of Campylobacter, Arcobacter, and Helicobacter. FISH correctly identified all isolates to the genus level and detected all thermotolerant Campylobacter isolates. The assay showed high degrees of sensitivity for the identification of C. jejuni (90%), C. coli (97%), C. lari (81%), and C. upsaliensis (100%) to the species level.

Multicenter study to evaluate bloodstream infection by Helicobacter cinaedi in Japan

Helicobacter cinaedi has being recognized as an important human pathogen which causes bloodstream infections. Although the first case of bacteremia with this pathogen in Japan was reported in 2003, the true prevalence of H. cinaedi as a pathogen of bloodstream infections in this country is not yet known. Therefore, the aim of our study was to assess the incidence of bacteremia with H. cinaedi in Japan. We conducted a prospective, multicenter analysis in 13 hospitals during 6 months in Tokyo, Japan. Among positive blood cultures from 1 October 2003 to 31 March 2004, isolates suspected of being Helicobacter species were studied for further microbial identification. Identification of the organisms was based on their biochemical traits and the results of molecular analysis of their 16S rRNA gene sequences. A total of 16,743 blood culture samples were obtained during the study period, and 2,718 samples (17.7%) yielded positive culture results for coagulase-negative staphylococci. Among nine isolates suspected to be Helicobacter species, six isolates were finally identified as H. cinaedi. The positivity rate for H. cinaedi in blood culture was 0.06% of total blood samples and 0.22% of blood samples with any positive culture results. All patients with bacteremia with H. cinaedi were found to have no human immunodeficiency virus (HIV) infection, but many of them had complications with either malignancy, renal failure, or a history of surgical operation. Therefore, our results suggest that bacteremia with H. cinaedi is rare but can occur in compromised hosts other than those with HIV infection in Japan.

Occurrence and antibiotic susceptibility of Helicobacter pullorum from broiler chickens and commercial laying hens in Italy

In 2005, in order to investigate the occurrence of Helicobacter pullorum in poultry, the caecal contents collected from a total of 60 animals intensively reared in Italy on 15 different farms (9 farms of broiler chicken and 6 of laying hens) were examined at the slaughterhouse. A modified Steele-McDermott membrane filter method was used. Small, greyish-white colonies of Gram-negative, gently curved, slender rod bacteria were preliminarily identified as H. pullorum by a Polymerase Chain Reaction (PCR) assay based on 16S rRNA and were then subjected to an ApaLI digestion assay to distinguish H. pullorum from Helicobacter canadensis. One isolate from each farm was phenotypically characterized by biochemical methods and 1D SDS-PAGE analysis of whole cell proteins; antibiotic susceptibility was also tested. According to the PCR and PCR-RFLP results, all the animals examined were positive for H. pullorum. The 1D SDS-PAGE whole protein profile analysis showed high similarity among the 15 isolates tested. A monomodal distribution for the Minimum Inhibitory Concentrations (MICs) was found for ampicillin, chloramphenicol, gentamicin and tetracycline. For erythromycin and ciprofloxacin, a bimodal trend having a second peak at >128 micro(-1) and 32 micro(-1) was found. The isolation method used in this study seems to be highly suitable for isolating H. pullorum from chicken caecal contents. Moreover, the detection of a high number of colonies phenotypically similar to H. pullorum suggests that this microorganism, when present, colonizes the caecum at high concentration.

Bartonella quintana prosthetic valve endocarditis detected by blood culture incubation beyond 10 days

We describe the case of a 45-year-old man with mitral and aortic prosthetic valve replacement who presented with symptoms of subacute bacterial endocarditis. Bartonella quintana was grown from blood after prolonged culture. The course of the disease was complicated by splenic infarction, glomerulonephritis resulting in progressive renal insufficiency, and cerebroventricular hemorrhage. Notably, cardiac ultrasonography showed no extensive vegetations but a strand-like lesion. Culture-positive B. quintana prosthetic valve endocarditis in a formerly healthy subject represents a newly observed entity. It should be added to the differential diagnosis of prosthetic valve endocarditis, especially when it presents with features suggesting subacute bacterial endocarditis.

Recurrent bacteremia with Helicobacter cinaedi: case report and review of the literature

Background

Helicobacter cinaedi is a rare pathogen in humans, occurring mostly in immuno-compromised patients, with a high potential for recurrence. We describe a case of a patient with lymphoma hospitalized for chemotherapy.

Case presentation

At admission, the patient presented with an indolent and non-prurigenic macular rash around her implantable venous access device. Gram staining of blood cultures revealed the presence of spiral-shaped gram-negative rods that could not be grown upon subculture. Helicobacter cinaedi was identified by PCR. No other symptoms or pathology were observed in a whole body CT scan. The implantable venous access device was removed and empiric therapy by ceftriaxone and gentamicin for 2 weeks was initiated, followed by peroral clarithromycin 2 × 500 mg/day and later by levofloxacin 2 × 500 mg/day for 7 weeks. Oncologic remission was achieved 3 months later. However, the patient was re-hospitalized 2 months later for fever, shivering, reappearance of the macular non-prurigenic rash, diarrhea, cough and asthenia. Blood cultures grew H. cinaedi. Multiple investigations could not identify the source. Empiric antibiotic therapy of ceftriaxone and doxycycline was started for 2 weeks with resolution of symptoms, followed by an oral combination of amoxicillin, metronidazole and doxycycline for 2 months; doxycycline was continued for another month. Bacteremia has not recurred for a period of 19 months.

Conclusion

Although H. cinaedi is considered to be a low virulent bacteria, its potential to cause recurrent bacteremia should not be underestimated. H. cinaedi could have an endovascular source of infection and should be treated for an adequate duration with combined antibiotherapy.

Molecular basis of macrolide resistance in Campylobacter: role of efflux pumps and target mutations

BACKGROUND

Erythromycin is the drug of choice to treat human campylobacteriosis. Campylobacter isolates exhibit two different phenotypes with regard to erythromycin resistance: high-level resistant strains (HLR) and low-level resistant strains (LLR).

OBJECTIVES

To study the mechanisms of resistance of Campylobacter to erythromycin, its 6-O-methyl derivative clarithromycin and the ketolide telithromycin.

RESULTS

We observed a cross-resistance against these three molecules but in contrast, no cross-resistance to quinolones. Analyses of LLR showed no mutation on the 23S rDNA and the presence of a drug transport system, which can be inhibited by phenylalanine arginine beta-naphthylamide (PAbetaN), an efflux-pump inhibitor. In contrast, no PAbetaN-sensitive drug transport was identified in HLR but we found mutations in the rDNA, which were responsible for decreased binding of telithromycin to purified ribosomes. We further showed that the CmeB efflux pump already described in Campylobacter is not involved in the PAbetaN-sensitive transport of telithromycin.

CONCLUSIONS

Mutations in the ribosome confer high-level macrolide/ketolide resistance. Low-level resistance was mediated by an efflux mechanism which is sensitive to PAbetaN. This efflux pump was selective to macrolides/ketolide and was different from the previously described Campylobacter efflux pump.

Mycobacterium haemophilum and lymphadenitis in children

Mycobacterium haemophilum is the second most common pathogen in children with mycobacterial lymphadenitis.

Infections associated with Mycobacterium haemophilum are underdiagnosed because specific culture methods required for its recovery are not applied routinely. Using polymerase chain reaction (PCR) technology on fine needle aspirates and biopsied specimens from 89 children with cervicofacial lymphadenitis, we assessed the importance of M. haemophilum. Application of a Mycobacterium genus–specific real-time PCR in combination with amplicon sequencing and a M. haemophilum–specific PCR resulted in the recognition of M. haemophilum as the causative agent in 16 (18%) children with cervicofacial lymphadenitis. Mycobacterium avium was the most frequently found species (56%), and M. haemophilum was the second most commonly recognized pathogen. Real-time PCR results were superior to culture because only 9 (56%) of the 16 diagnosed M. haemophilum infections were positive by culture.

Pneumonia involving Aspergillus and Rhizopus spp. after a near-drowning incident with subsequent Nocardia cyriacigeorgici and N. farcinica coinfection as a late complication

Reported here is the case of a 22-year-old man who developed pneumonia with unusual pathogens after a near-drowning incident. On day 7 following admission, Rhizopus spp. and Aspergillus fumigatus were cultured from the patient's bronchoalveolar lavage fluid. One week later, sputum cultures revealed N. cyriacigeorgici as well as N. farcinica. The patient recovered fully after prolonged therapy with liposomal amphotericin B, amikacin, meropenem and cotrimoxazole.

Helicobacter pylori and extragastric diseases--other Helicobacters

Reports on Helicobacter pylori and extragastric diseases have almost doubled this year compared with last year, bearing witness to the persistent scientific interest in this branch of Helicobacter-related pathology. Data belong increasingly to the area of vascular medicine, as well as hematology, dermatology, pediatrics and other fields. Unfortunately, these studies show overall controversial results, due to the impact of several confounding factors, and to the difficulty of recruiting homogeneous patient populations. Furthermore, many studies continue to be conducted on Helicobacter species other than H. pylori, focusing on animal models of gastroenterological illnesses which may retain strong similarities with human diseases. In this paper, taxonomy, detection and characterisation of Helicobacter spp. will be reviewed, together with the most important data issued this year on other Helicobacters and animal models.