Multilocus sequence typing identifies evidence for recombination and two distinct lineages of Corynebacterium diphtheriae

Corynebacterium ulcerans cutaneous diphtheria

We describe the case of a patient with cutaneous diphtheria caused by toxigenic Corynebacterium ulcerans who developed a right hand flexor sheath infection and symptoms of sepsis such as fever, tachycardia, and elevated C-reactive protein, after contact with domestic cats and dogs, and a fox. We summarise the epidemiology, clinical presentation, microbiology, diagnosis, therapy, and public health aspects of this disease, with emphasis on improving recognition. In many European countries, C ulcerans has become the organism commonly associated with cutaneous diphtheria, usually seen as an imported tropical disease or resulting from contact with domestic and agricultural animals. Diagnosis relies on bacterial culture and confirmation of toxin production, with management requiring appropriate antimicrobial therapy and prompt administration of antitoxin, if necessary. Early diagnosis is essential for implementation of control measures and clear guidelines are needed to assist clinicians in managing clinical diphtheria. This case was a catalyst to the redrafting of the 2014 national UK interim guidelines for the public health management of diphtheria, released as final guidelines in March, 2015.

A Case of Necrotizing Epiglottitis Due to Nontoxigenic Corynebacterium diphtheriae

Diphtheria is a rare cause of infection in highly vaccinated populations and may not be recognized by modern clinicians. Infections by nontoxigenic Corynebacterium diphtheriae are emerging. We report the first case of necrotizing epiglottitis secondary to nontoxigenic C diphtheriae. A fully vaccinated child developed fever, poor oral intake, and sore throat and was found to have necrotizing epiglottitis. Necrotizing epiglottitis predominantly occurs in the immunocompromised host. Laboratory evaluation revealed pancytopenia, and bone marrow biopsy was diagnostic for acute lymphoblastic leukemia. Clinicians should be aware of aggressive infections that identify immunocompromised patients. This case highlights the features of a reemerging pathogen, C diphtheriae.

Possible human-to-human transmission of toxigenic Corynebacterium ulcerans

Toxigenic Corynebacterium ulcerans is an emerging cause of diphtheria. In contrast to the classical diphtheria pathogen C. diphtheriae, human-to-human transmission of this primarily zoonotic pathogen has not been clearly documented. Here we report on a two-person cluster suggesting an initial zoonotic and a subsequent human-to-human transmission event.

Outbreak with clonally related isolates of Corynebacterium ulcerans in a group of water rats

Background

The zoonotic bacterium Corynebacterium ulcerans may be pathogenic both in humans and animals: toxigenic strains can cause diphtheria or diphtheria-like disease in humans via diphtheria toxin, while strains producing the dermonecrotic exotoxin phospholipase D may lead to caseous lymphadenitis primarily in wild animals. Diphtheria toxin-positive Corynebacterium ulcerans strains have been isolated mainly from cattle, dogs and cats.

Results

Here, we report a series of ten isolations of Corynebacterium ulcerans from a group of water rats (Hydromys chrysogaster) with ulcerative skin lesions, which were kept in a zoo. The isolates were clearly assigned to species level by biochemical identification systems, Fourier-transform infrared-spectroscopy, Matrix-assisted laser desorption/ionization-time of flight mass spectrometry and partial rpoB sequencing, respectively. All ten isolates turned out to represent the same sequence type, strongly indicating a cluster of infections by clonally-related isolates as could be demonstrated for the first time for this species using multilocus sequence typing. Unequivocal demonstration of high relatedness of the isolates could also be demonstrated by Fourier-transform infrared-spectroscopy. All isolates were lacking the diphtheria toxin encoding tox-gene, but were phospholipase D-positive.

Conclusions

Our results indicate that water rats represent a suitable new host species that is prone to infection and must be regarded as a reservoir for potentially zoonotic Corynebacterium ulcerans. Furthermore, the applied methods demonstrated persistent infection as well as a very close relationship between all ten isolates.

Molecular and epidemiological review of toxigenic diphtheria infections in England between 2007 and 2013

Human infections caused by toxigenic corynebacteria occur sporadically across Europe. In this report, we undertook the epidemiological and molecular characterization of all toxigenic corynebacterium strains isolated in England between January 2007 and December 2013. Epidemiological aspects include case demographics, risk factors, clinical presentation, treatment, and outcome. Molecular characterization was performed using multilocus sequence typing (MLST) alongside traditional phenotypic methods. In total, there were 20 cases of toxigenic corynebacteria; 12 (60.0%) were caused by Corynebacterium ulcerans, where animal contact was the predominant risk factor. The remaining eight (40.0%) were caused by Corynebacterium diphtheriae strains; six were biovar mitis, which were associated with recent travel abroad. Adults 45 years and older were particularly affected (55.0%; 11/20), and typical symptoms included sore throat and fever. Respiratory diphtheria with the absence of a pharyngeal membrane was the most common presentation (50.0%; 10/20). None of the eight C. diphtheriae cases were fully immunized. Diphtheria antitoxin was issued in two (9.5%) cases; both survived. Two (9.5%) cases died, one due to a C. diphtheriae infection and one due to C. ulcerans. MLST demonstrated that the majority (87.5%; 7/8) of C. diphtheriae strains represented new sequence types (STs). By adapting several primer sequences, the MLST genes in C. ulcerans were also amplified, thereby providing the basis for extension of the MLST scheme, which is currently restricted to C. diphtheriae. Despite high population immunity, occasional toxigenic corynebacterium strains are identified in England and continued surveillance is required.

Multilocus sequence typing of Corynebacterium ulcerans provides evidence for zoonotic transmission and for increased prevalence of certain sequence types among toxigenic strains

Human-to-human-transmitted Corynebacterium diphtheriae was historically the main pathogen causing diphtheria and has therefore been studied extensively in the past. More recently, diphtheria caused by toxigenic Corynebacterium ulcerans is an emerging disease in several industrial countries, including the United Kingdom, the United States, France, and Germany. However, toxigenic C. ulcerans has so far been almost neglected in the development of epidemiologic tools. One of the most important tools in modern epidemiology to understand transmission pathways is sequence typing of pathogens. Here, we provide a protocol for multilocus sequence typing (MLST) to type C. ulcerans strains rapidly and relatively cost-effectively. Applying MLST to C. ulcerans for the first time, we show that related sequence types (STs) might be associated with the presence of the diphtheria toxin gene, which encodes diphtheria toxin (DT), the most important diphtheria-causing virulence factor. Interestingly, we found only two very closely related STs in the isolates derived from six dogs. Additionally, our data show that all STs derived from animals which were at least twice present in our analysis were found in humans as well. This finding is congruent with zoonotic transmission of C. ulcerans.

Toxigenic Corynebacterium ulcerans in a fatal human case and her feline contacts, France, March 2014

In March 2014, a person in their eighties who was diagnosed with extensive cellulitis due to toxigenic Corynebacterium ulcerans died from multiple organ failure. Environmental investigation also isolated C. ulcerans in biological samples from two stray cats in contact with the case. This finding provides further evidence that pets can carry toxigenic C. ulcerans and may be a source of the infection in humans.

Multilocus sequence analysis for the assessment of phylogenetic diversity and biogeography in hyphomonas bacteria from diverse marine environments

Hyphomonas, a genus of budding, prosthecate bacteria, are primarily found in the marine environment. Seven type strains, and 35 strains from our collections of Hyphomonas, isolated from the Pacific Ocean, Atlantic Ocean, Arctic Ocean, South China Sea and the Baltic Sea, were investigated in this study using multilocus sequence analysis (MLSA). The phylogenetic structure of these bacteria was evaluated using the 16S rRNA gene, and five housekeeping genes (leuA, clpA, pyrH, gatA and rpoD) as well as their concatenated sequences. Our results showed that each housekeeping gene and the concatenated gene sequence all yield a higher taxonomic resolution than the 16S rRNA gene. The 42 strains assorted into 12 groups. Each group represents an independent species, which was confirmed by virtual DNA-DNA hybridization (DDH) estimated from draft genome sequences. Hyphomonas MLSA interspecies and intraspecies boundaries ranged from 93.3% to 96.3%, similarity calculated using a combined DDH and MLSA approach. Furthermore, six novel species (groups I, II, III, IV, V and XII) of the genus Hyphomonas exist, based on sequence similarities of the MLSA and DDH values. Additionally, we propose that the leuA gene (93.0% sequence similarity across our dataset) alone could be used as a fast and practical means for identifying species within Hyphomonas. Finally, Hyphomonas' geographic distribution shows that strains from the same area tend to cluster together as discrete species. This study provides a framework for the discrimination and phylogenetic analysis of the genus Hyphomonas for the first time, and will contribute to a more thorough understanding of the biological and ecological roles of this genus.

Respiratory infection by Corynebacterium striatum: epidemiological and clinical determinants

The increasing prevalence of advanced chronic respiratory disease, with frequent exposure to broad-spectrum antibiotics for repeated and prolonged hospitalizations, favours the emergence of nosocomial respiratory infection by Gram-positive bacteria, such as outbreaks of Corynebacterium striatum. There is little evidence about patterns of respiratory infection, transmission and adaptive ability of this pathogen. Seventy-two C. striatum isolates from 51 advanced respiratory patients, mainly chronic obstructive pulmonary disease, were studied during 38 months. Patients were 74.8 ± 8.6 years old and 81.9% were men, who had required an average of 2.2 hospitalizations and 63.5 days in the hospital in the previous year. Of 49 isolates from 42 patients we were able to identify 12 clones by multilocus sequence analysis (MLSA), nine phenotypic variants and 22 antibiotic susceptibility patterns, and we determined their clinical and epidemiological determinants. MLSA allows identification of the existence of nosocomial outbreaks by transmission of the same or different clones, the persistence of the same clone in the environment or in patient airways for months. The study showed the high variability and adaptive capacity of the isolates, the antibiotic multidrug-resistance in all of them, and their contribution to a high morbidity and mortality (41%) during the study period.

Emergence and molecular characterisation of non-toxigenic tox gene-bearing Corynebacterium diphtheriae biovar mitis in the United Kingdom, 2003–2012

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The utility of the PCR melting profile technique for typing Corynebacterium diphtheriae isolates

Selection of appropriate typing method depends on a number of factors, including the scale of the investigation, the rapidity required of the results and the financial and technical resources available. Several typing methods have been applied to Corynebacterium diphtheriae genotyping, but most are laborious and time-consuming or require expensive equipment. We report an evaluation of the utility of the PCR melting profile technique for simple and easy-to-perform genotyping of C. diphtheriae. We compared the method with ribotyping-the 'gold standard' for C. diphtheriae typing-and PFGE, MLST, AFLP, RAPD and spoligotyping.

SIGNIFICANCE AND IMPACT OF THE STUDY

Occurrence of Corynebacterium diphtheriae infections-in the form of diphtheria in endemic countries and in the form of invasive infections in countries with high antidiphtheria vaccination coverage-indicates the need for maintenance of ability to genotype this pathogen by laboratories. Application of an appropriate typing method is essential not only in outbreak investigations for understanding and predicting epidemics but also in monitoring of the evolution and spread of epidemic clones of C. diphtheriae. The PCR melting profile method presented in the study is a good alternative for C. diphtheriae typing.

A lack of genetic basis for biovar differentiation in clinically important Corynebacterium diphtheriae from whole genome sequencing

The differentiation of clinically important Corynebacterium diphtheriae into specific biovars is complex and phylogenetically unclear. Comparative genomic analyses of 17 strains indicate that the division of C. diphtheriae into different biovars does not correlate with the variation in the gene content in the relevant metabolic categories that are potentially involved in the biovar discrimination. The biochemical separation is also not supported by phylogenetic analyses, suggesting molecular methods of typing C. diphtheriae strains should be adopted much more widely.

Toxigenic Corynebacterium ulcerans in human and non-toxigenic Corynebacterium diphtheriae in cat

Corynebacterium diphtheriae and Corynebacterium ulcerans are rarely isolated from clinical samples in Belgium. A case of toxigenic C. ulcerans in a woman is described, which confirms that this pathogen is still present. During investigation of the patient's cats, only a non-toxigenic toxin-bearing C. diphtheriae strain was detected.

Microbiological changes and diversity in autochthonous non-toxigenic Corynebacterium diphtheriae isolated in France

Autochtonous toxigenic Corynebacterium diphtheriae have disappeared in mainland France, but non-toxigenic C. diphtheriae are still circulating. Using phenotypic and molecular tools, we retrospectively characterized 103 non-toxigenic C. diphtheriae collected in mainland France and highlight several changes. The proportion of C. diphtheriae belfanti increased between 1977 and 2011 and it is the most frequent biotype recovered in recent years. Resistance to ciprofloxacin has increased and most isolates with decreased sensitivity belong to the belfanti biotype. Using multilocus sequence typing, we demonstrate that French isolates are distributed in a large number of sequence types and identify three distinct lineages. C. diphtheriae mitis and gravis form lineage I while C. diphtheriae belfanti forms lineages II and III. Almost all isolates of lineage II are part of a unique clonal complex or are very close to it. Most French isolates have a dtxR sequence homologous to that of toxigenic isolates, suggesting that if lyzogenised by a corynephage, they can express diphtheria toxin.

The genus corynebacterium and other medically relevant coryneform-like bacteria

Catalase-positive Gram-positive bacilli, commonly called "diphtheroids" or "coryneform" bacteria were historically nearly always dismissed as contaminants when recovered from patients, but increasingly have been implicated as the cause of significant infections. These taxa have been underreported, and the taxa were taxonomically confusing. The mechanisms of pathogenesis, especially for newly described taxa, were rarely studied. Antibiotic susceptibility data were relatively scant. In this minireview, clinical relevance, phenotypic and genetic identification methods, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) evaluations, and antimicrobial susceptibility testing involving species in the genus Corynebacterium and other medically relevant Gram-positive rods, collectively called coryneforms, are described.

Diphtheria in Europe: current problems and new challenges

Diphtheria, caused by toxigenic strains of Corynebacterium diphtheriae, is an ancient disease with high incidence and mortality that has always been characterized by epidemic waves of occurrence. Whilst towards the beginning of the 1980s, many European countries were progressing towards the elimination of diphtheria, an epidemic re-emergence of diphtheria in the Russian Federation and the Newly Independent States of the former Soviet Union demonstrated a continuous threat of the disease into the 1990s. At present, the epidemic is under control and only sporadic cases are observed in Europe. However, the circulation of toxigenic strains is still observed in all parts of the world, posing a constant threat to the population with low levels of seroprotection. More recently, Corynebacterium ulcerans has been increasingly isolated as emerging zoonotic agent of diphtheria from companion animals such as cats or dogs, indicating the enduring threat of this thought-to-be controlled disease.

Identification and diversity of multiresistant Corynebacterium striatum clinical isolates by MALDI-TOF mass spectrometry and by a multigene sequencing approach

BACKGROUND

The genus Corynebacterium is composed of gram-positive bacteria that are widely distributed throughout the environment; these bacteria are also part of the normal microbiota of human skin and mucous membranes. Multiple studies have shown that species of this genus, including C. striatum, become pathogenic to humans under special conditions. Our aim was to determine the characteristics of clinical multiresistant strains of C. striatum that were isolated in our geographical region, to determine their diversity, and to compare them with the type strain and with related species. We studied fifty-two strains of C. striatum isolated from different hospitals from Mallorca, Spain, mainly from the Hospital Joan March in Bunyola, Mallorca. Most of the strains were isolated from sputum cultures of respiratory samples from patients with chronic obstructive pulmonary disease. To gain further insight into the genetic diversity of the strains, we analysed several housekeeping genes and other genes associated with antibiotic resistance. Strains were also characterised phenotypically by their antibiotic resistance profiles and by MALDI-TOF mass spectrometry analysis.

RESULTS

The ITS1 region, gyrA and rpoB were chosen as the appropriate genes in the C. striatum genome to study the genetic diversity of C. striatum species and to discriminate between strains. After analysing these three genes, four sequence types (ST2, ST4, ST1 and ST11) were found to be the most abundant. Splits tree analysis of the strains demonstrated that these clinical isolates did not share any alleles with the type strain of the species. Recombination was detected within all of the C. striatum isolates, and different clonal populations were detected within the samples.

CONCLUSIONS

Our results demonstrate that the isolates were best identified using gene-based molecular methods; using these methods, the isolated strains were determined to be different from the type strain of C. striatum. The ITS1 region and the gyrA and rpoB genes were selected because of their variability and were the most useful tools for discriminating between strains. The phenotype and antibiotype characteristics of the strains did not seem suitable for typing purposes. MALDI-TOF mass spectrometry can be a useful method for identifying and discriminating between C. striatum strains.

Characterization and comparison of invasive Corynebacterium diphtheriae isolates from France and Poland

Corynebacterium diphtheriae, the agent of diphtheria, is rarely responsible for bacteremia. However, high numbers of bacteremia have been reported in countries with extensive immunization coverage. Here, we used molecular and phenotypic tools to characterize and compare 42 invasive isolates collected in France (including New Caledonia) and Poland over a 23-year period.

Canada's first case of a multidrug-resistant Corynebacterium diphtheriae strain, isolated from a skin abscess

A toxigenic Corynebacterium diphtheriae biovar mitis sequence type 136 (ST136) strain was recovered from a toe infection of an unvaccinated patient recently returned from India. The isolate was resistant to clindamycin, erythromycin (ermX positive), tetracycline, and trimethoprim-sulfamethoxazole, intermediate to ceftriaxone and cefotaxime, and had high MICs for telithromycin and chloramphenicol but was sensitive to other drugs.

Diphtheria outbreak in Norway: lessons learned

We describe an outbreak of diphtheria in Norway that occurred in 2008 and affected 3 unvaccinated family members. The epidemic caught the public health system off-guard on most levels; the diagnosis was distrusted due to its rarity, no diphtheria anti-toxin was available, and notification procedures were not rigorously followed.

Multilocus sequence types of invasive Corynebacterium diphtheriae isolated in the Rio de Janeiro urban area, Brazil

Invasive infections caused by Corynebacterium diphtheriae in vaccinated and non-vaccinated individuals have been reported increasingly. In this study we used multilocus sequence typing (MLST) to study genetic relationships between six invasive strains of this bacterium isolated solely in the urban area of Rio de Janeiro, Brazil, during a 10-year period. Of note, all the strains rendered negative results in PCR reactions for the tox gene, and four strains presented an atypical sucrose-fermenting ability. Five strains represented new sequence types. MLST results did not support the hypothesis that invasive (sucrose-positive) strains of C. diphtheriae are part of a single clonal complex. Instead, one of the main findings of the study was that such strains can be normally found in clonal complexes with strains related to non-invasive disease. Comparative analyses with C. diphtheriae isolated in different countries provided further information on the geographical circulation of some sequence types.

Analysis of multilocus sequence typing schemes for 35 different bacteria revealed that gene loci of 10 bacteria could be replaced to improve cost-effectiveness

Although multilocus sequence typing (MLST) has been widely used for bacterial typing, the contribution of the gene loci to the discriminatory power of each MLST scheme is unknown. We analyzed the discriminatory powers of 36 MLST schemes using all combinations of the 7 loci and contributions of each locus to the schemes. In 10 schemes, sequencing 6 loci can achieve the discriminatory powers of 7 loci. For the other 26 schemes, the median marginal increase in discriminatory power when 7 instead of 6 loci were used is 0.0004. Sequencing the 7 loci of 50 strains each of Pseudomonas aeruginosa and Acinetobacter baumannii revealed that the discriminatory power for P. aeruginosa was 0.9861 when either 6 (without trp) or 7 loci were used and that for A. baumannii was 0.9363 when 5, 6, or 7 loci were used. Genes that have no additional or minimal contribution to the overall discriminatory powers should be replaced.

Cutaneous diphtheria in the urban poor population of Vancouver, British Columbia, Canada: a 10-year review

Between 1998 and 2007, records from 33 patients with cutaneous diphtheria from Vancouver's inner city were reviewed. Cases were associated with injection drug use and poverty. Coinfections with Staphylococcus aureus, Streptococcus pyogenes, and Arcanobacterium haemolyticum occurred. Corynebacterium diphtheriae is endemic in Vancouver's urban core, with strains of multilocus sequence type (MLST) 76 predominating.