Myroides phaeus sp. nov., isolated from human saliva, and emended descriptions of the genus Myroides and the species Myroides profundi Zhang et al. 2009 and Myroides marinus Cho et al. 2011

Genomic insight into Myroides oncorhynchi sp. nov., a new member of the Myroides genus, isolated from the internal organ of rainbow trout (Oncorhynchus mykiss)

The strain M-43^T was isolated from the Oncorhynchus mykiss from a fish farm in Mugla, Turkey. Pairwise 16S rRNA gene sequence analysis was used to identify strain M-43^T. The strain was a member of the genus Myroides sharing the highest 16S rRNA gene sequence identity levels of 98.7%, 98.3%, and 98.3% with the type strains of M. profundi D25^T, M. odoratimimus subsp. odoratimimus CCUG 39352^T and M. odoratimimus subsp. xuanwuensis DSM27251^T, respectively. A polyphasic taxonomic approach including whole genome-based analyses was employed to confirm the taxonomic provenance of strain M-43^T within the genus Myroides. The overall genome relatedness indices (OGRI) for strain M-43^T compared with its most closely related type strains M. odoratimimus subsp. xuanwuensis DSM 27251^T, M. profundi D25^T, and M. odoratimimus subsp. odoratimimus ATCC BAA-634^T, were calculated as 25.3%, 25.1%, and 25% for digital DNA-DNA hybridization (dDDH), 83.3%, 83.6%, and 83.4% for average nucleotide identity (ANI) analyses, respectively. The OGRI values between strain M-43^T and its close neighbors confirmed that the strain represents a novel species in the genus Myroides. The DNA G + C content of the strain is 33.7%. The major fatty acids are iso-C_15:0 and summed feature 9 (iso-C_17:1 ω9c and/or 10-methyl C_16:0). The predominant polar lipids are phosphatidylethanolamine, an amino-lipid and five unidentified lipids. The major respiratory quinone is MK-6. Chemotaxonomic and phylogenomic analyses of this isolate confirmed that the strain represents a novel species for which the name Myroides oncorhynchi sp. nov. is proposed, with M-43^T as the type strain (JCM 34205^T = KCTC 82265^T).

Myroides fluvii sp. nov., isolated from the Han River, Republic of Korea

A Gram-stain-negative, aerobic, short rod-shaped, pale yellow-pigmented, non-motile and gentamycin-resistant bacterial strain designated CJ210^T was isolated from the Han River, Republic of Korea. Strain CJ210^T grew optimally at 30 °C and pH 7.0 in the absence of NaCl on tryptic soy agar. Flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain CJ210^T belonged to the genus Myroides within the family Flavobacteriaceae and was most closely related to Myroides odoratus KACC 14347^T (98.1 % similarity), followed by M. injenensis KCTC 23367^T (95.3 % similarity). The average nucleotide identity values between strain CJ210^T and two closely related type strains M. odoratus KACC 14347^T and M. injenensis KCTC 23367^T were 83.7 and 73.8 %, respectively. The digital DNA-DNA hybridization results between strain CJ210^T and the related type strains were 27.5 and 20.2 %, respectively. Strain CJ210^T contained menaquinone 6 (MK-6) as the predominant menaquinone. The predominant polar lipids were phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. The major fatty acids of strain CJ210^T were iso-C_15 : 0, iso-C_17 : 0 3-OH and summed feature 9 (comprising iso-C_17 : 1  ω9c and/or C_16 : 0 10-methyl). Whole genome sequencing revealed that strain CJ210^T had a genome of 3.8 Mbp with 36.5 % DNA G+C content. The genome contained several antimicrobial resistance genes including an aminoglycoside-resistant gene. On the basis of the polyphasic taxonomic study, strain CJ210^T represents a novel species in the genus Myroides, for which name Myrodies fluvii sp. nov. is proposed. The type strain is CJ210^T (=KACC 19954^T=JCM 33306^T).

Myroides albus sp. nov., isolated from the gut of plastic-eating larvae of the coleopteran insect Zophobas atratus

A bacterial strain, BIT-d1T, was isolated from the gut of plastic-eating larvae of the coleopteran insect Zophobas atratus. Its taxonomic position was analysed using a polyphasic approach. Cells were white-pigmented, Gram-stain-negative, non-motile, long rods without flagella. The 16S rRNA gene sequence (1401 bp) of strain BIT-d1T showed highest similarity (98.0%) to Myroides pelagicus SM1T and 96.6~92.6 % similarity to the other species of the genus Myroides . The results of phylogenetic analyses, based on the 16S rRNA gene, concatenated sequences of six housekeeping genes (gyrB, dnaK, tuf, murG, atpA and glyA) and genome sequences, placed strain BIT-d1T in a separate lineage among the genus Myroides , family Flavobacteriaceae . The major isoprenoid quinone was menaquinone-6 (MK-6) and the major fatty acids were C15 : 0 iso, C17 : 0 iso 3-OH and summed feature 9 (comprising iso-C17 : 1  ω9c and/or C16 : 0 10-methyl), which were similar to other members in the genus Myroides. In silico DNA–DNA hybridization and average nucleotide identity calculations plus physiological and biochemical tests exhibited the genotypic and phenotypic differentiation of strain BIT-d1T from the other members of the genus Myroides . Therefore, strain BIT-d1T is considered to represent a novel species within the genus Myroides , for which the name Myroides albus sp. nov is proposed. The type strain is BIT-d1T (=CGMCC 1.17043T=KCTC 72447T).

A Confirmed Catheter-Related Blood Stream Infection (CRBSI) in an Immunocompetent Patient Due to Myroides odoratimimus: Case Report and Literature Review

The genus Myroides are gram-negative bacilli which are completely aerobic, non-motile, non-fermenting and yellow-pigmented with a characteristic fruity odor. Myroides species are widely found in the environment, especially in water and soil, and are considered as low-grade opportunistic pathogens for humans. Myroides infections are most commonly seen in immunocompromised patients and only rarely occur in immunocompetent patients. We here report the first confirmed catheter-related bloodstream infection (CRBSI) due to Myroides odoratimimus in an immunocompetent patient. We also review the literature related to Myroides infections.

First report of Myroides phaeus bacteraemia identified by Polymerase chain reaction and genetic sequencing

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We report the first case of Myroides phaeus isolated from blood, causing bacteremia in an immunocompromised patient.

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The relevance of this species is that most strains are resistant to multiple drugs.

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For identification it was used MicroScan Panel in addition to PCR – genetic sequencing.

We report the first case of Myroides phaeus isolated from blood, causing bacteremia in an immunocompromised patient using the automated MicroScan Walk Away 96 system, followed by bacterial identification by amplification-sequencing of the 16S rDNA. The sequences obtained were compared with the reference sequence of the BLAST ® platform - National Library of Medicine, USA, and the isolation was identified as Myroides phaeus strain with 99.67 % identity in Blast report. In the literature we did not find previous reported cases of infections by this bacterium, however its pathogenic role is still controversial; therefore, this isolation alerts us to carry out an exhaustive surveillance of other possible acquisition routes.

Association of Myroides odoratimimus in immunocompromized piglets with post weaning multisystemic wasting syndrome

AIM

To study the association of opportunistic infection due to Myroides odoratimimus in piglets immunocompromised by porcine circovirus type 2 (PCV2) infection.

METHODS AND RESULTS

The clinical samples (n = 101) were analysed bacteriologically. The isolates were identified by their phenotypes and MALDI TOF-MS analysis as Myroides species. The phylogram constructed based on nucleotide sequences of the 16S rRNA gene showed identity (~99%) with the M. odoratimimus isolates. The minimum inhibitory concentration values for antibiotics revealed M. odoratimimus to be resistant against carbapenem, cephalosporins, aminoglycosides and fluoroquinolones. The presence of PCV2 in affected tissue samples was confirmed by amplification of the 565 bp region of ORF2 of the PCV2 genome. The topology of the phylogenetic tree grouped the PCV2 with cluster-2d.

CONCLUSIONS

PCV2 being immunosuppressive in nature might have impaired the immunity thereby increasing the susceptibility of immunocompromised piglets to opportunistic pathogens such as M. odoratimimus leading to disease severity and high mortality. The M. odoratimimus isolates were found to be multidrug resistant and evidenced for uncertain clinical relevance and hence could act as hidden source of public health hazard.

SIGNIFICANCE AND IMPACT OF THE STUDY

Myroides odoratimimus is a rarely reported human pathogen. We reported the incidence of infection due to seemingly rare isolates of M. odoratimimus causing an outbreak of pneumonia in piglets. This appears, to the best of authors' knowledge, to be the first outbreak due to Myroides recorded in animal clinical cases described in the literature.

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Myroides spp. cellulitis and bacteremia: A case report

Myroides spp., formerly Flavobacterium spp., are gram-negative, non-motile, traditionally opportunistic pathogens that are infrequent clinical isolates. Myroides spp. have been pathogenically implicated in only 52 reported cases since the discovery of the Flavobacterium genus in the 1920s. We present a case of Myroides spp. lower extremity cellulitis and bacteremia. To our knowledge, this is the 16th case of cutaneous infection caused by Myroides spp. Etiology of this patient’s infection was felt to be related to exposure of his pre-existing lower extremity wounds to soil and water versus a dog lick in the context of relative immunosuppression from type 2 diabetes and chronic inhaled steroid use. Given the characteristic multi-drug resistance of Myroides spp., resistance to usual empiric antimicrobials given for cellulitis, and potential for fatal infection in cases of pan-resistance, it is important that clinicians remain alert to the possibility of this rare pathogen.

Whole-genome sequencing of a large collection of Myroides odoratimimus and Myroides odoratus isolates and antimicrobial susceptibility studies

The genus Myroides comprises several species of Gram-negative, non-motile, and non-fermenting bacteria, which have been regarded as non-pathogenic for decades. Multiple recent reports, however, underscore the pathogenic potential that Myroides sp. possesses for humans. These bacteria seem to be resistant to a wide range of antibiotics (including ß-lactams and aminoglycosides). Therefore, treatment options are limited. Knowledge of antimicrobial resistance, however, is based on only one meaningful comprehensive study and on data published from case reports. This lack of data motivated us to test 59 strains from our Myroides collection (43 M. odoratimimus and 16 M. odoratus) for resistance against 20 commonly used antibiotics. We also performed molecular analyses to reveal whether our bacteria harbor the genus-specific M. odoratimimus metallo-ß-lactamase (MUS-1) or the M. odoratus metallo ß-lactamase (TUS-1), and other ß-lactamases, which may provide an explanation for the extended antimicrobial resistance.

What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015

Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.

Antibiotic resistance mechanisms of Myroides sp

Bacteria of the genus Myroides (Myroides spp.) are rare opportunistic pathogens. Myroides sp. infections have been reported mainly in China. Myroides sp. is highly resistant to most available antibiotics, but the resistance mechanisms are not fully elucidated. Current strain identification methods based on biochemical traits are unable to identify strains accurately at the species level. While 16S ribosomal RNA (rRNA) gene sequencing can accurately achieve this, it fails to give information on the status and mechanisms of antibiotic resistance, because the 16S rRNA sequence contains no information on resistance genes, resistance islands or enzymes. We hypothesized that obtaining the whole genome sequence of Myroides sp., using next generation sequencing methods, would help to clarify the mechanisms of pathogenesis and antibiotic resistance, and guide antibiotic selection to treat Myroides sp. infections. As Myroides sp. can survive in hospitals and the environment, there is a risk of nosocomial infections and pandemics. For better management of Myroides sp. infections, it is imperative to apply next generation sequencing technologies to clarify the antibiotic resistance mechanisms in these bacteria.

Myroides indicus sp. nov., isolated from garden soil

A novel aerobic, non-motile, rod-shaped, catalase- and oxidase-positive bacterial strain, designated UKS3T, was isolated from garden soil, and subjected to polyphasic taxonomic analysis. Strain UKS3T formed whitish, viscous colonies on nutrient agar and was Gram-staining negative. Phylogenetic analysis, based on 16S rRNA gene sequence, showed that maximum pairwise similarity occurs with representatives of the genus Myroides. The most closely related species include Myroides marinus JS-08T (92.7 % sequence similarity), Myroides phaeus MY15T (92.7 %), Myroides odoratus DSM 2801T (91.5 %) and Myroides odoratimimus CCUG 39352T (91.4 %). Strain UKS3T contained menaquinone-6 (MK-6) as the major respiratory quinone and iso-C15 : 0 (40.2 %), anteiso-C15 : 0 (9.4 %) and iso-C17 : 0 3-OH (8.5 %) as major fatty acids. Phosphatidylethanolamine, phospholipids and three aminolipids were the major polar lipids. The DNA G+C content of strain UKS3T was 36.8 ± 2.0 mol%. On the basis of phenotypic, chemotaxonomic and molecular analysis, strain UKS3T represents a novel species of the genus Myroides, for which the name Myroides indicus sp. nov., is proposed. The type strain is UKS3T ( = DSM 28213T = NCIM 5555T ).

MYROIDES INFECTION IN A BABOON AFTER PROLONGED PIG KIDNEY GRAFT SURVIVAL

BACKGROUND

Immunosuppressed patients and experimental nonhuman primates are at risk of opportunistic infection. We report a Myroides spp infection in an immunosuppressed baboon that had received a life-supporting kidney from a genetically-engineered pig.

CASE REPORT

The baboon received a costimulation blockade-based immunosuppressive regimen as well as two anti-inflammatory agents (tocilizumab and etanercept). Although the pig kidney functioned well, approximately four months after the transplant the baboon became less active and ate and drank poorly. On day 136, it collapsed and died despite inotropic and fluid support. A blood culture drawn before death grew Myroides spp.

DISCUSSION AND CONCLUSIONS

To our knowledge, Myroides spp has not been reported as a cause of opportunistic infection in either patients with organ allotransplants or experimental animals. We summarize what is known about this rare organism, and suggest it should be considered in any immunocompromised patient or animal. In the present case, we suggest the baboon died of circulatory shock following infection through an indwelling intravenous catheter.

Microbial communities present in the lower respiratory tract of clinically healthy birds in Pakistan

Commercial poultry is an important agricultural industry worldwide. Although dense living conditions and large flocks increase meat and egg production, they also increase the risk of disease outbreaks and zoonoses. Current pathogen identification methods mostly rely on culture-dependent techniques and, therefore, are limited to a very small number of bacteria present in the environment. Next Generation Sequencing allows for culture-independent characterization of lower respiratory microbiome of birds including the identification of novel commensals and potentially emerging pathogens. In this study, we collected tracheo-bronchoalveolar lavage of 14 birds raised at 3 different farms in the Punjab province of Pakistan. To characterize the lower respiratory microbiome of these birds, we sequenced hyper-variable regions of the 16S ribosomal subunit gene. Although dominated by bacteria belonging to a small number of taxonomic classifications, the lower respiratory microbiome from each farm was far more diverse and novel than previously known. The differences in microbiome among farms suggest that inter-farm differences affect the microbiome of birds more than breed, geographic location, or management system. The presence of potential and known pathogens in genetically similar specialty breeds of chickens kept at unnaturally high densities and under variable conditions presents an extraordinary opportunity for the selection of highly pathogenic bacteria. In some instances, opportunistic respiratory pathogens were observed in apparently healthy birds. Understanding and monitoring the respiratory microbiome of such populations may allow the early detection of future disease threats.

Comparison of VITEK2, MALDI-TOF MS, and 16S rDNA sequencing for identification of Myroides odoratus and Myroides odoratimimus

The genus Myroides comprises the 2 medically relevant species Myroides odoratus and Myroides odoratimimus that are rare opportunistic pathogens and cause infections in immunocompromised patients. A fast identification of Myroides is of importance because these bacterial strains show multiple resistance against antibiotics and therefore limit treatment options. They are associated, for instance, with urinary tract infections, sepsis, meningitis, pneumonia, and infectious cellulitis. Since more and more Myroides spp. are being described, additional potentially pathogenic bacteria may be identified in the future demanding the need for fast and reliable identification methods at species level. However, to date, only molecular approaches meet these demands. In this study, we, therefore, attempt to define an appropriate method other than DNA fingerprinting that will permit a comparable efficacy and, possibly, a more economical strain identification. For this purpose, we compared 2 widely used automated diagnostic systems (VITEK 2 [bioMérieux, Nürtingen, Germany] and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) [Bruker Daltonics, Bremen, Germany]) and correlated the results to 16S rDNA sequencing data. In total, we analyzed 22 strains collected in the course of routine diagnostics. In this study, we demonstrate that VITEK 2 reliably identifies the genus Myroides but cannot differentiate between M. odoratimimus and M. odoratus. In contrast to this, both MALDI-TOF MS and 16S rDNA sequencing efficiently distinguish between the 2 species.

Myroides xuanwuensis sp. nov., a mineral-weathering bacterium isolated from forest soil

A Gram-reaction-negative, aerobic, non-motile, yellow-pigmented, rod-shaped bacterium, designated strain TH-19T, was isolated from a forest soil sample in Jiangsu province, China. On the basis of 16S rRNA gene sequence similarity, strain TH-19T was shown to belong to the genus Myroides , a member of the phylum Bacteroidetes , and was related to Myroides odoratimimus LMG 4029T (98.7 % similarity), Myroides profundi D25T (98.2 %) and Myroides marinus JS-08T (97.5 %). Strain TH-19T contained menaquinone-6 (MK-6) as the predominant menaquinone, and the dominant fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The DNA G+C content of strain TH-19T was 37.2 mol%. The DNA–DNA relatedness values of strain TH-19T with Myroides odoratimimus JCM 7460T, Myroides profundi D25T and Myroides marinus JS-08T were below 70 %. Based on phenotypic, genotypic and phylogenetic evidence, it is suggested that strain TH-19T represents a novel species of the genus Myroides , for which the name Myroides xuanwuensis sp. nov. is proposed. The type strain is TH-19T ( = CCTCC AB 2013145T = JCM 19200T).

Myroides guanonis sp. nov., isolated from prehistoric paintings

A novel psychrotolerant, strictly aerobic, non-motile, rod-shaped bacterial strain, designated IM13T, was isolated from a sample taken from prehistoric guano paintings in Magura Cave, northwest Bulgaria and subjected to a polyphasic taxonomic study. Strain IM13T formed yellow colonies on LB agar plates and was Gram-staining-negative, heterotrophic and alkalitolerant. It grew optimally at pH 7.5 and 30 °C in the absence of NaCl. Phylogenetic analysis of the whole 16S rRNA gene revealed that strain IM13T branched with representatives of the genus Myroides with sequence similarity of 93–94 % with other species of the genus. The novel isolate contained iso-C15 : 0 (49.1 %), iso-C17 : 1ω9c (18.2 %) and iso-C17 : 0 3-OH (14.0 %) as dominant fatty acids. The DNA G+C content of strain IM13T was 33.5 mol%. Based on phylogenetic inference and phenotypic characteristics, it was concluded that strain IM13T represents a novel species of the genus Myroides , for which the name Myroides guanonis sp. nov. is proposed. The type strain is IM13T ( = DSM 26542T = NBIMCC 8736T).