Bacteremia caused by an undescribed species of Janibacter

Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs

Human cutaneous squamous cell carcinomas (SCCs) and actinic keratoses (AK) display microbial dysbiosis with an enrichment of staphylococcal species, which have been implicated in AK and SCC progression. SCCs are common in both felines and canines and are often diagnosed at late stages leading to high disease morbidity and mortality rates. Although recent studies support the involvement of the skin microbiome in AK and SCC progression in humans, there is no knowledge of this in companion animals. Here, we provide microbiome data for SCC in cats and dogs using culture-independent molecular profiling and show a significant decrease in microbial alpha diversity on SCC lesions compared to normal skin (P ≤ 0.05). Similar to human skin cancer, SCC samples had an elevated abundance of staphylococci relative to normal skin-50% (6/12) had >50% staphylococci, as did 16% (4/25) of perilesional samples. Analysis of Staphylococcus at the species level revealed an enrichment of the pathogenic species Staphylococcus felis in cat SCC samples, a higher prevalence of Staphylococcus pseudintermedius in dogs, and a higher abundance of Staphylococcus aureus compared to normal skin in both companion animals. Additionally, a comparison of previously published human SCC and perilesional samples against the present pet samples revealed that Staphylococcus was the most prevalent genera across human and companion animals for both sample types. Similarities between the microbial profile of human and cat/dog SCC lesions should facilitate future skin cancer research.

IMPORTANCE

The progression of precancerous actinic keratosis lesions (AK) to cutaneous squamous cell carcinoma (SCC) is poorly understood in humans and companion animals, despite causing a significant burden of disease. Recent studies have revealed that the microbiota may play a significant role in disease progression. Staphylococcus aureus has been found in high abundance on AK and SCC lesions, where it secretes DNA-damaging toxins, which could potentiate tumorigenesis. Currently, a suitable animal model to investigate this relationship is lacking. Thus, we examined the microbiome of cutaneous SCC in pets, revealing similarities to humans, with increased staphylococci and reduced commensals on SCC lesions and peri-lesional skin compared to normal skin. Two genera that were in abundance in SCC samples have also been found in human oral SCC lesions. These findings suggest the potential suitability of pets as a model for studying microbiome-related skin cancer progression.

Whole Genome Sequencing of First Janibacter indicus Isolate in China Revealed Three Unique Genomic Islands Compared with Saprophytic Strains

Introduction

Janibacter caused bacteriemia is one of the rare infections.

Methods

In the present study, we report the first isolation of Janibacter, a rare bacterial infection, from a bacteremia patient in China. Its 16S rDNA was amplified and designated as Janibacter YFY001, which belongs to J. indicus. In addition, its genome was sequenced through combined second- and third-generation genome sequencing methods.

Results

Based on its genome, we identified many virulence factors, such as catalase, gelatinase, FbpABC systems, and resistant genes, among others. Interestingly, three genomic islands were found in YFY001 by comparing its genome to environmental Janibacter strains.

Discussion

Our study not only provides the necessary genomic information for in-depth study of Janibacter, but also provides a novel methodology for studying future cases of rare bacterial infection.

The first case of Janibacter hoylei bacteremia in an adult

The Janibacter species are Gram positive, coryneform bacteria that belong to the Actinobacteria phylum and have been linked to bacteremia in immunocompromised children. We present the first documented adult case of Janibacter hoylei bacteremia. The patient was a 52-year-old woman with a history of recurrent Clostridioides difficile infection, sinus tachycardia and high-risk AML who had been admitted one month prior to presentation for matched unrelated donor hematopoietic stem cell transplant with reduced intensity fludarabine-melphalan. Thirty days post-transplant, the infectious disease team was consulted because blood cultures grew Janibacter hoylei, from one of two blood cultures It took nine days to identify the species. She was treated with linezolid and imipenem. Janibacter are rarely implicated in human pathology, and therein, usually identified in the context of malignancy and relative immunosuppression. J. hoylei was only previously reported from the bloodstream of a previously healthy 8-week-old infant without underlying medical conditions. Antimicrobial susceptibility testing is challenging as only in vitro susceptibility testing of Janibacter terrae has been reported. Given these challenges, it is our hope to illustrate the clinical approach to diagnosis as well as subsequent recommendations for treatment in a particularly challenging case of bacteremia in an AML patient.

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Janibacter species with evidence of genomic polymorphism isolated from resected heart valve in a patient with aortic stenosis

The authors report isolation and identification of two strains of bacteria belonging to the genus Janibacter from a human patient with aortic stenosis from a rural area of the country of Georgia. The microorganisms were isolated from aortic heart valve. Two isolates with slightly distinct colony morphologies were harvested after sub-culturing from an original agar plate. Preliminary identification of the isolates is based on amplification and sequencing of a fragment of 16SrRNA. Whole genome sequencing was performed using the Illumina MiSeq instrument. Both isolates were identified as undistinguished strains of the genus Janibacter. Characterization of whole genome sequences of each culture has revealed a 15% difference in gene profile between the cultures and confirmed that both strains belong to the genus Janibacter with the closest match to J. terrae. Genomic comparison of cultures of Janibacter obtained from human cases and from environmental sources presents a promising direction for evaluating a role of these bacteria as human pathogens.

Description of Janibacter massiliensis sp. nov., cultured from the vaginal discharge of a patient with bacterial vaginosis

Strain Marseille-P4121^T was isolated from a vaginal sample of a 45-year-old French woman with bacterial vaginosis. It is a Gram-positive, asporogenous, non-motile and aerobic bacterium. Strain Marseille-P4121^T exhibits 98.2% 16S rRNA sequence similarity with Janibacter alkaliphilus strain SCSIO 10480^T, a phylogenetically closely related species with standing in nomenclature. Its major fatty acids were identified as C_18:1ω9 (34.4%), C_16:0 (30.1%), and C_18:0 (19%). The draft genome size of strain Marseille-P4121^T is 2,452,608 bp long with a 72.5% G+C content and contains 2351 protein-coding genes and 49 RNA genes including 3 rRNA genes. We propose that strain Marseille-P4121^T (= CECT 9671^T = CSUR P4121^T) is the type strain of the new species Janibacter massiliensis sp. nov.

Bilateral psoas abscess caused by Janibacter terrae, an unusual condition and organism resulting in laboratory and management conundrums

Psoas abscess is commonly regarded as an unusual cause for back pains and usually associated with significant risk factors or co-morbidities. We describe the clinical presentation and findings of a young male Caucasian with bilateral psoas abscesses caused by an unusual organism, Janibacter terrae (an environmental organism) not previously described in literature and the challenges faced in managing this infection. There are very few case reports of this organism causing opportunistic infections, all reported bacteraemia mainly in patients with significant co-morbidities. This case highlights the importance of psoas abscess as a differential diagnosis in patients presenting with back pain and the potential for this organism to cause abscesses in healthy individuals which was difficult to identify using conventional laboratory methods. Management of this infection was challenging and there is limited experience with antimicrobial treatment for this organism.

First case of bacteremia caused by Janibacter hoylei

Janibacter hoylei has previously been isolated only from an air sample in the upper atmosphere and clinical significance of J. hoylei was not yet established. Herein, we report a case of bacteremia caused by J. hoylei. An 8-week-old previously healthy male infant presented to the emergency room with fever. Blood culture yielded growth of Gram-positive bacilli and this microorganism could not be identified with conventional phenotypic methods. The isolate was identified by 16S rRNA gene sequencing, and the patient was successfully treated with vancomycin. To our knowledge, this is the first report of the recovery of J. hoylei in humans. This case shows that J. hoylei can be a potential pathogen in young children.

Molecular identification of clinical "difficult-to-identify" microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2

Background

Clinical microbiology laboratories have to accurately identify clinical microbes. However, some isolates are difficult to identify by the automated biochemical text platforms, which are called “difficult-to-identify” microbes in this study. Therefore, the ability of 16S ribosomal DNA (16S rDNA) and internal transcribed spacer 2 (ITS2) sequencing to identify these “difficult-to-identify” bacteria and fungi was assessed in this study.

Methods

Samples obtained from a teaching hospital over the past three years were examined. The 16S rDNA of four standard strains, 18 clinical common isolates, and 47 “difficult-to-identify” clinical bacteria were amplified by PCR and sequenced. The ITS2 of eight standard strains and 31 “difficult-to-identify” clinical fungi were also amplified by PCR and sequenced. The sequences of 16S rDNA and ITS2 were compared to reference data available in GenBank by using the BLASTN program. These microbes were identified according to the percentage of similarity to reference sequences of strains in GenBank.

Results

The results from molecular sequencing methods correlated well with automated microbiological identification systems for common clinical isolates. Sequencing results of the standard strains were consistent with their known phenotype. Overall, 47 “difficult-to-identify” clinical bacteria were identified as 35 genera or species by sequence analysis (with 10 of these identified isolates first reported in clinical specimens in China and two first identified in the international literature). 31 “difficult-to-identify” clinical fungi tested could be identified as 15 genera or species by sequence analysis (with two of these first reported in China).

Conclusions

Our results show the importance of 16S rDNA and internal ITS2 sequencing for the molecular identification of “difficult-to-identify” bacteria and fungi. The development of this method with advantages of convenience, availability, and cost-effectiveness will make it worth extending into clinical practice in developing countries.

Adult invasive and noninvasive infections due to Streptococcus dysgalactiae subsp. equisimilis in France from 2006 to 2010

We characterized 182 Streptococcus dysgalactiae subsp. equisimilis isolates and analyzed the epidemiological data on the corresponding infections. stG6, stG485, and stG6792 were the 3 most prevalent invasive emm types among the 27 different emm types recovered. High rates of antimicrobial resistance were observed for macrolides (26.4%) and tetracycline (34.6%).

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.

The role of speciation in positive Lowenstein-Jensen culture isolates from a high tuberculosis burden country

Objective

To determine the need for routine speciation of positive Lowenstein-Jensen mycobacterial cultures in HIV-infected patients suspected of having pulmonary tuberculosis at Mulago Hospital in Kampala, Uganda.

Methods

Sputum and bronchoalveolar lavage Lowenstein-Jensen mycobacterial culture isolates from consecutive, HIV-infected patients admitted to Mulago Hospital with 2 weeks or more of cough were subjected to IS6110 PCR and rpoB genetic analysis to determine the presence of Mycobacterium tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM).

Results

Eighty (100%) mycobacterial cultures from 65 patients were confirmed to be members of MTBC. Subsequent analysis of the cultures from 54 patients by PCR and sequence analyses to identify co-infection with NTM confirmed the presence of MTBC as well as the presence of Micrococcus luteus (n = 4), Janibacter spp. (n = 1) and six cultures had organisms that could not be identified.

Conclusions

Presumptive diagnosis of tuberculosis on the basis of a positive Lowenstein-Jensen culture is sufficient in HIV-infected Ugandans suspected of having tuberculosis. Routine molecular confirmation of positive Lowenstein-Jensen cultures is unnecessary in this low resource setting.

Molecular identification of Exiguobacterium acetylicum as the aetiological agent of bacteraemia

A case of catheter-related bacteraemia caused by Exiguobacterium acetylicum is reported in an elderly patient. The availability of sequence-based methods facilitated rapid identification and expanded the spectrum of diseases attributed to coryneform bacteria and specifically to the genus Exiguobacterium.