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

Myroides species, pathogenic spectrum and clinical microbiology sight in Mexican isolates

INTRODUCTION

Myroides is a bacterial genus of opportunistic bacteria responsible for diverse infections including in the skin and soft tissues, urinary tract, cardiovascular system, and bacteremia, although the incidence of its reported infections is low, it is increasing, likely due the use of better bacterial identification methods, but also perhaps due an increase in its prevalence. In addition, their pathogenic role is limited in terms of reporting their microbial physiology, so the present work provides information in this regard in addition to the information that is available in the international literature.

OBJECTIVE

To describe the microbiological and genetic characteristics of seven different Myroides spp. clinical strains and comment on their phylum, pathogenic and resistance characteristics.

METHODS

Seven Myroides spp., strains associated with infections were included from 1/January/2012 to 1/January/20 and identified by miniaturized biochemistry and MALDI-ToF. Susceptibility tests were performed according to CLSI recommendations by broth microdilution. Whole genome sequencing was performed for each strain and bioinformatics analysis were performed.

RESULTS

Strains were identified at genus level by two methodologies. Our results revealed that likely four strains belong to the species Myroides odoratimimus, while the other two may be undescribed ones. Remarkably, all isolates harbored several genes encoding antibiotic resistance determinants for ß-lactams, aminoglycosides and glycopeptides and in concordance, presented high levels of resistance, against these antibiotics (AK and GN both 100%, ATM, CAZ and FEP 100%, e.g.); moreover, the presences of carbapenemases were evidenced by meropenem (mCIM) and imipenem (CARBA NP) degrading activity in six isolates and two strains possessed plasmids harboring mainly ribosomal RNA genes, tRNAs and genes encoding proteins with unknown functions.

CONCLUSIONS

Our study increases the knowledge about the biology of this understudied genus and highlights the potential of Myroides to emerge as a broader cause of recalcitrant opportunistic infections.

Molecular characterization of the multi-drug resistant Myroides odoratimimus isolates: a whole genome sequence-based study to confirm carbapenem resistance

The bacteria belonging to the Myroides genus are opportunistic pathogens causing community or hospital-acquired infections that result in treatment failure due to antibiotic resistance. This study aimed to investigate molecular mechanisms of antibiotic resistance, clonal relatedness, and the biofilm forming capacity of the 51 multi-drug resistant Myroides odoratimimus. All isolates were screened for blaKPC, blaOXA, blaVIM, blaIMP, blaMUS, blaTUS, blaNDM, and blaB genes by using PCR amplification. Whole genome sequencing (WGS) was applied on three randomly selected isolates for further investigation of antibiotic resistance mechanisms. Clonal relatedness was analyzed by Pulsed-field gel electrophoresis (PFGE) and the microtiter plate method was used to demonstrate biofilm formation. All isolates were positive for biofilm formation. PCR analysis resulted in a positive for only the blaMUS-1 gene. WGS identified blaMUS-1, erm(F), ere(D), tet(X), and sul2 genes in all strains tested. Moreover, the genomic analyses of three strains revealed that genomes contained a large number of virulence factors (VFs). PFGE yielded a clustering rate of 96%. High clonal relatedness, biofilm formation, and multi-drug resistance properties may lead to the predominance of these opportunistic pathogens in hospital environments and make them cause nosocomial infections.

Myroides odoratimimus: a New Threat with Persistent Infections, Multidrug Resistance, and the Potential for Hospital Outbreaks

Myroides species have recently been reported more frequently in outbreaks in clinics and intensive care units (ICUs). In this study, we aimed to investigate the epidemic potential, antibiotic resistance profile, and risk factors of M. odoratimimus isolates that are increasingly being isolated from the ICUs of our hospital. Data from patients whose Myroides spp. were isolated from their clinical specimens over a 5-year period (September 2016 to January 2022) were retrospectively analyzed. Bacterial identification was performed using a matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). The presence of antibiotic resistance genes was analyzed using polymerase chain reaction (PCR). Possible clonal associations between isolates were investigated using enterobacterial repetitive intergenic consensus (ERIC)-PCR. As a result, 66 isolates were identified as M. odoratimimus and one isolate was identified as M. odoratus. The blaMUS resistance gene was detected in all M. odoratimimus isolates, whereas sul2 was detected in ten isolates and tetX was detected in 11 isolates. No other resistance genes, such as blaTUS, were detected. Additionally, two different clonal association patterns were discovered in the 24 selected isolates through the ERIC-PCR method. The increase in the immunosuppressive patient population indicate the possibility of encountering this agent and other opportunistic pathogens more frequently in the future.

Case Report of Myroides odoratimimus Cellulitis in Chronic Venous Stasis Dermatitis With Literature Review

Myroides spp.-induced cutaneous infections are rare, with only 17 reported cases in the literature. Myroides spp. behave like low-grade opportunistic pathogens, with symptomatic infections observed typically in severely immunocompromised patients and seldom in immunocompetent patients. In this paper, we present an immunocompetent 61-year old male with a past medical history of hypertension, hyperlipidemia, morbid obesity, and patient-reported peripheral neuropathy who presented to the transitional care clinic with bilateral lower extremity swelling and hemosiderin-pigmented dry wounds consistent with diagnosis of chronic venous stasis dermatitis with resolved secondary Myroides odoratimimus infection. Further literature review about Myroides spp. and its resistance mechanism, antibiotic susceptibility, and biofilm production are also included in this paper.

An Increasing Threat in Intensive Care Units, Evaluation of Multi-Drug-Resistant Myroides spp. Infections and Risk Factors

BACKGROUND

Myroides species are gram-negative bacilli that are commonly found in soil and water, acting as low-level opportunistic pathogens and causing a variety of infections.

AIM

The purpose of this study is to assess the risk factors for multidrug-resistant Myroides infections, their association with comorbid illnesses, patient care, and their susceptibility to antibiotics.

METHODS

This retrospective analytical study was conducted in Istanbul Başakşehir Çam and Sakura City Hospital by including patients with Myroides spp isolation in their culture samples. The total hospitalization days, first isolation days, and 30-day mortality values of the patients were analysed statistically, and the significance level was accepted as p < 0.05.

RESULTS

Myroides spp. were isolated from 228 patients' 437 culture samples. Of these cases, 210 (92.1%) were classified as having asymptomatic bacteriuria, and 18 (7.9%) as having an infection caused by Myroides spp. 174 (76.3%) of these patients were followed up in the intensive care unit, and the total hospitalization days (median = 24.50) and the first isolation day (median = 9.50) of infected patients were shorter than colonized patients (p = 0.023, p = 0.030), no difference was found between 30-day mortality (p = 0.312).

CONCLUSIONS

It was observed that Myroides infections could be seen more frequently in patients who were hospitalized for a long time, used broad-spectrum antimicrobials, had invasive procedures, and had co-factors such as diabetes and cerebrovascular disease. In addition, it was observed that the resistance rates of M. odoratus strains were higher than M. odoratimimus strains and the use of quinolone antimicrobials in the treatment of patients with M. odoratimimus infection provided more cure.

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).

Extensively Drug-Resistant Myroides odoratus in Critically Ill Patients: A Case Series and Literature Review

The bacterial genus Myroides, like other members of the Flavobacteriaceae family, consists of aerobic, non-motile, Gram-negative bacilli. Myroides spp. is considered predominantly opportunistic pathogens as, historically, most documented infections have been in immunocompromised individuals. Along with advancements in molecular assay testing, there are growing reports of clinically relevant Myroides spp. infections in immunocompetent individuals. These organisms display broad antimicrobial resistance, and while research into their mechanisms of resistance is progressing, genetic testing has revealed metallo-β-lactamases present in their genome. The sporadic identification of Myroides spp. and ongoing clarification of resistance patterns make empiric treatment difficult. This report documents two cases of extensively drug-resistant Myroides odoratus isolated from critically ill but otherwise immunocompetent patients followed by a review of available literature on Myroides spp. antibiotic sensitivities. Our findings indicate that minocycline and moxifloxacin have the highest documented in vitro activity against Myroides spp.

Identification and Antibiotic Profiling of Wohlfahrtiimonas chitiniclastica, an Underestimated Human Pathogen

In the past 12 years, several case reports have clearly demonstrated that Wohlfahrtiimonas chitiniclastica is capable of causing sepsis and bacteremia in humans. However, since most clinicians are not familiar with this species, little is known about its pathogenicity and treatment options while it is as rare but underestimated human pathogen. Therefore, a larger strain collection is required so that methods can be identified that are most suitable to obtain rapid and reliable identification. Moreover, the antimicrobial resistance profile needs to be elucidated in order to explore possible treatment options. Over a period of 6 years, we therefore have collected a total of 14 W. chitiniclastica isolates in routine diagnostics, which now served as the basis for a comprehensive characterization with respect to identification and antibiotic profiling. We compared the accuracy and convenience of several identification techniques in which MALDI-TOF MS and sequencing of the 16S rRNA gene have proven to be suitable for identification of W. chitiniclastica. In addition, whole genome sequencing (WGS)-based digital DNA-DNA hybridization (dDDH) was used as a reference method for strain identification, and surprised with the detection of a novel W. chitiniclastica subspecies. A combination of in silico and in vitro analyses revealed a first insight into the antimicrobial resistance profile and the molecular basis of antimicrobial resistance. Based on our findings, trimethoprim/sulfamethoxazole, levofloxacin, and cephalosporins (e.g., ceftazidime) may be the best antibiotics to use in order to treat infections caused by W. chitiniclastica, while resistance to fosfomycin, amikacin and tobramycin is observed.

Assessment of the potential use of MALDI-TOF MS for the identification of bacteria associated with chilled vacuum-packaged lamb meat

The focus of this study was to compare the effectiveness of MALDI-TOF MS and partial 16S rRNA gene sequencing for the identification of bacteria isolated from VP lamb meat stored chilled at 5 °C for 21 days, at the same time gaining insights into bacterial changes over time. The identity of bacterial isolates on non-selective and selective agars was determined by both methods and results compared. Results showed that total bacterial numbers increased over the 21 days (as expected) with Staphylococcus and Pseudomonas (day 0) being replaced by Carnobacterium, Brochothrix and members of the Enterobacteriaceae family by day 21. A high level of agreement (86-100%) for bacterial isolates' identity at genus level was observed between MALDI-TOF MS and partial 16S rRNA gene-based sequencing for isolates where identification was possible. With its cheaper cost and faster turnaround time, once optimized, MALDI-TOF MS could become a useful alternative to 16S rRNA gene-sequencing for the rapid identification of red meat bacterial isolates.

A Healthcare-Associated Outbreak of Urinary Tract Infections Due to Myroides odoratimimus

Myroides spp. are low-grade opportunistic pathogens. Outbreaks due to Myroides spp. have rarely been described in the literature to date. We report a healthcare-associated outbreak of urinary tract infections (UTIs), caused by Myroides odoratimimus, in a Turkish hospital. As of March 2019 until May 2019, 6 strains of M. odoratimimus were isolated from the urine samples of patients, all of whom were hospitalized in intensive care units. After identification and antibiotic susceptibility testing using the VITEK 2 system, MALDI-TOF-MS and 16S rRNA-based sequencing methods were performed for confirmation and species-level identification. Pulsed-field gel electrophoresis (PFGE) was performed in order to investigate the clonal relatedness of the isolates. All the patients were immunocompromised and underwent urinary catheterization. None of the patients had urinary neoplasm, surgery, or calculi. VITEK 2 and MALDI-TOF-MS systems revealed that the isolates belonged to the Myroides genus; however, the aforementioned systems neglected to identify the isolates at the species level. The isolates were all successfully identified as M. odoratimimus through 16S rRNA-based sequencing. The isolates were resistant to every antibiotic tested. All isolates had an indistinguishable PFGE pattern, thus indicating cross-transmission between cases. Although M. odoratimimus is rarely isolated from human specimens, clinicians should be aware of its ability to cause UTIs and infectious outbreaks.

Molecular Epidemiology of Myroides odoratimimus in Nosocomial Catheter-Related Infection at a General Hospital in China

Purpose

Catheter-related infection (CRI) is one of the most frequent causes of hospitalizations for immunocompromised patients. A major challenge is the increased prevalence of Myroides odoratimimus. The purpose of the present study was to evaluate the clinical features and molecular characteristics of M. odoratimimus collected from a general hospital in Shanghai, China.

Patients and Methods

From July 2015 to August 2016, a total of 22 isolates of M. odoratimimus were collected from inpatients respectively from the biliary and pancreatic surgery (6/22) and the urology department (16/22). Clonal relatedness among the isolates was assessed using pulsed-field gel electrophoresis (PFGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Moreover, the antimicrobial susceptibility tests were carried out using the Clinical and Laboratory Standards Institute (CLSI) broth microdilution method. The presence of antibiotic resistance genes was screened using the polymerase chain reaction (PCR) assay. Additionally, protein structure prediction was analyzed using PSIPRED and RaptorX.

Results

PFGE differentiated these isolates into six possibly related clones from two different departments obtained during a distinct period, indicating clonal dissemination in the two departments. We compared the dendrograms of M. odoratimimus isolates obtained by MALDI-TOF MS with those obtained by PFGE and found that the coincidence rate between them was only 68.2%. All the M. odoratimimus isolates were highly resistant to most available antibiotics, including carbapenems. Furthermore, chromosome-encoded β-lactamases MUS-1 was confirmed by PCR in 6 of 22 Myroides odoratimimus isolates. Herein, we also reported a novel variant of bla_MUS-1 in the remaining 16 isolates, which encodes MUS-3 protein at position 60 (Valine to Alanine), differing from the structure of MUS-1.

Conclusion

The opportunistic and extensively antibiotic-resistant Myroides odoratimimus has a small range of epidemics in these two different departments. Clinicians should be aware that M. odoratimimus may induce a severe nosocomial outbreak of catheter-related infections, particularly in immunocompromised patients.

A healthcare-associated outbreak of urinary tract infections due to Myroides odoratimimus

Myroides spp. are low-grade opportunistic pathogens. There were only a few outbreaks due to Myroides spp. described in the literature to date. We report a healthcare-associated outbreak of urinary tract infections caused by Myroides odoratimimus in a Turkish hospital. From March to May 2019, six strains of M. odoratimimus were isolated from the urine samples of patients hospitalized in the intensive care units (ICUs). After identification and antibiotic susceptibility testing with VITEK 2 system, MALDI-TOF-MS and 16S rRNA based sequencing methods were performed for confirmation and species level identification. Pulsed-field gel electrophoresis (PFGE) was used to investigate clonal relatedness of the isolates. All the patients were immunocompromised and underwent urinary catheterization. None of them had urinary neoplasm, surgery or calculi. VITEK 2 and MALDI-TOF-MS systems revealed that the isolates belong to the Myroides genus but lacked to identify the isolates at the species level. 16S rRNA based sequencing successfully identified all the isolates as M. odoratimimus. The isolates were resistant to all antibiotics tested. All isolates had indistinguishable PFGE pattern indicating cross-transmission between cases. Although M. odoratimimus is rarely isolated from human specimens, clinicians should be aware of its ability to cause UTIs and outbreaks.

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.

How MALDI-TOF mass spectrometry can aid the diagnosis of hard-to-identify pathogenic bacteria - the rare and the unknown

Introduction: Ten years after its introduction into clinical microbiology, MALDI-TOF mass spectrometry has become the standard routine identification tool for bacteria in most laboratories. The technology has accelerated analyses and improved the quality of results. The greatest significance has been observed for bacteria that were challenging to be identified by traditional methods. Areas covered: We searched in existing literature (Pubmed) for reports how MALDI-TOF MS has contributed to identification of rare and unknown bacteria from different groups. We describe how this has improved the diagnostics in different groups of bacteria. Reference patterns for strains which yet cannot be assigned to a known species even enable the search for related bacteria in studies as well as in routine diagnostics. MALDI-TOF MS can help to discover and investigate new species and their clinical relevance. It is a powerful tool in the elucidation of the bacterial composition of complex microbiota in culturomics studies. Expert opinion: MALDI-TOF MS has improved the diagnosis of bacterial infections. It also enables knowledge generation for prospective diagnostics. The term 'hard-to-identify' might only be rarely attributed to bacteria in the future. Novel applications are being developed, e.g. subspecies differentiation, typing, and antibiotic resistance testing which may further contribute to improved microbial diagnostics.

Rapid dereplication of microbial isolates using matrix-assisted laser desorption ionization time-of-flight mass spectrometry: A mini-review

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MALDI-TOF MS is applicable as high-resolution and high-throughput tool.

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The classification and characterization of cultivable microorganisms is targeted.

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Advantageous are its simple sample preparation and short measurement time.

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It accelerates the dereplication of isolates from large-scale screening campaigns.

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Applications for studying microbial diversity and future trends are discussed.

Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) has become one of the most popular methods for the rapid, cost-effective and accurate classification and characterization of cultivable microorganisms. Due to its simple sample preparation and short measurement time, MALDI-TOF MS is an excellent choice for the high-throughput study of microbial isolates from rhizospheres or plants grown under diverse environmental conditions. While clinical isolates have a higher identification rate than environmental isolates due to the focus of commercial mass spectral libraries on the former, no identification is necessary in the dereplication step of large environmental studies. The grouping of large sets of isolates according to their intact protein profiles can be performed without knowledge of their taxonomy. Thus, this method is easily applicable to environmental samples containing microorganisms from yet undescribed phylogenetic origins. The main strategies applied to achieve effective dereplication are, first, expanding existing mass spectral libraries and, second, using an additional statistical analysis step to group measured mass spectra and identify unique isolates. In this review, these aspects are addressed. It closes with a prospective view on how MALDI-TOF MS-based microbial characterisation can accelerate the exploitation of plant-associated microbiota.

From days to hours: Can MALDI-TOF MS system replace both conventional and molecular typing methods with new cut off level for Vancomycin Resistant Enterococcus faecium

Vancomycin-Resistant E. faecium (VRE) strains from clinical specimens were identified by conventional methods before. Following the phenotype-based identification, all strains were also identified using both BD Phoenix and VITEK MS bioMérieux System. Strains were typed with the Bruker MALDI-TOF MS system, pulsed field gel electrophoresis (PFGE) and 16S rRNA gene sequencing analysis and then the sensitivity compared for each. A cut off value of 850 assigned with Bruker MALDI-TOF MS system was found to give equal sensitivity to that of PFGE. Results obtained were compared with those of molecular typing. The main advantage of MALDI-TOF MS technology over the others was the much shorter analysis time which lasted only a few hours rather than days or a whole week. Also, the Bruker MALDI-TOF MS system was used for typing and compared with the gold standard method and this study is first to report the determined cut off level for typing of VRE strains.

Extensively drug-resistant Myroides odoratimimus - a case series of urinary tract infections in immunocompromised patients

Purpose

We report an outbreak of urinary tract infections (UTIs) caused by Myroides odoratimimus, which occurred in the largest clinical hospital in western Romania.

Patients and methods

From June to August 2017, four strains of M. odoratimimus were isolated from the urine samples of patients hospitalized in the urology, diabetes, and surgery departments. Hospital records of all patients whose urine cultures were positive for M. odoratimimus were reviewed retrospectively. We also reviewed the cases reported in the literature.

Results

All UTIs, except one, were hospital-acquired infections. All patients with M. odoratimimus UTIs were immunocompromised. Three patients underwent urinary catheterization with a Foley’s catheter upon admission in the emergency department and one presented for replacement of ureterostomy tubes. All Myroides isolates were resistant to almost all the tested antibiotics. Two patients were successfully treated with tigecycline and one was receiving antimicrobial treatment for another infection at the time of isolation of the microorganism.

Conclusion

Although M. odoratimimus is an uncommon pathogen, clinicians should be aware of its ability to cause UTI outbreaks, especially in the immunocompromised population. Due to its multi-drug resistance, it is important to rapidly identify Myroides spp. in order to choose the best treatment regimen.

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.

Microbial communities associated with the co-metabolism of free cyanide and thiocyanate under alkaline conditions

This study focused on the identification of free cyanide (CDO) and thiocyanate (TDO) degrading microbial communities using a culture-dependent and independent approach. Culturable microbial species were isolated from the CDOs (n = 13) and TDOs (n = 18). The CDOs were largely dominated by Bacillus sp. while the TDOs were dominated by Bacillus sp., Klebsiella oxytoca, Providencia sp. and Pseudomonas sp. However, 16S rRNA amplicon gene-sequencing revealed the complexity and diversity of the microbial communities in contrast to the organisms that were detected using culture-dependent technique. Overall, the organisms were mainly dominated by Myroides odoratimimus and Proteus sp. at 37.82 and 30.5% for CDOs, and 35.26 and 17.58% for TDOs, respectively. The co-culturing of the CDOs and TDOs resulted in biochemical changes of key metabolic enzymes, and this resulted in the complete degradation of CN- and SCN- simultaneously; a phenomenon which has not been witnessed, especially under alkaline conditions. Current ongoing studies are focused on the application of these organisms for the biodegradation of CN- and SCN- in a continuous system, under changing operational parameters, to assess their effectiveness in the biodegradation of CN- and SCN-.

Myroides odoratimimus Forms Structurally Complex and Inherently Antibiotic-Resistant Biofilm in a Wound-Like in vitro Model

Myroides odoratimimus is an aerobic, non-fermenting Gram-negative multidrug-resistant bacterium widely distributed in nature that rarely causes infections in immunocompromised patients. We recently described in a diabetic patient a case of recurrent calcaneal ulcer infection caused by a M. odoratimimus strain showing potential for biofilm formation. For the first time, we therefore evaluated the ability of M. odoratimimus to form biofilm under different pH values and glucose concentrations using an in vitro “skin-like” model, and its susceptibility to levofloxacin, meropenem, and tigecycline. The expression of some antibiotic-resistance related genes was also monitored by RT-PCR during planktonic-to-biofilm transition. Our results indicated that M. odoratimimus can produce relevant amounts of biofilm biomass, in a time-dependent manner, especially at acidic pH and regardless of glucose concentration tested. The comparative analysis of MIC and MBC values between planktonic and sessile cells showed that resistance to antibiotics increased during the planktonic-to-biofilm transition. Viable cell count indicated that none of the tested antibiotics were able to completely eradicate preformed biofilms, although meropenem and levofloxacin were the most active causing a significant, dose-independent, reduction of biofilm's viability, as also confirmed by microscopic analysis. RT-PCR showed that antibiotic-resistance related gyrA and acrB genes are over-expressed during the transition from planktonic to sessile (biofilm) lifestyle. Overall, our findings showed that M. odoratimimus can form relevant amounts of inherently antibiotic-resistant biofilm under conditions relevant to wound site, therefore suggesting a role in the pathogenesis of chronic ulcer infections.

New Subclass B1 Metallo-β-Lactamase Gene from a Clinical Pathogenic Myroides odoratus Strain

Myroides odoratus is a low-virulence opportunistic human pathogen. Infections caused by M. odoratus are not common, but reports are increasing in recent years. The biggest challenge for treatment is its resistance to most antibiotics. In 2015, we isolated a pathogenic multidrug-resistant strain of M. odoratus from a urinary tract infection (UTI) patient's urine sample. To report the experience in managing M. odoratus-related UTI and investigate the genetic mechanism of this carbapenem-resistant strain, we conducted a series of microbiological and molecular studies. The bacterial strain was identified as M. odoratus by 16S rRNA gene sequencing. The minimum inhibitory concentrations (MICs) of 17 antimicrobial agents were determined against this strain. Whole-genome sequencing was performed and screened for possible β-lactamase genes. A β-lactamase gene, bla_MOC, was identified by whole-genome sequencing, then cloned and expressed in Escherichia coli DH5α to characterize its function. Antimicrobial susceptibility testing showed that the strain had relatively low MIC to levofloxacin and sulfamethoxazole/trimethoprim (SMZ/TMP). After unsuccessful empirical therapy, the UTI was controlled by levofloxacin in combination with SMZ/TMP. Whole-genome sequencing identified a subclass B1 metallo-β-lactamase gene, bla_MOC, which conferred resistance to most β-lactams except for aztreonam and cefepime. In conclusion, a new β-lactamase gene, bla_MOC, was found in an isolate of M. odoratus. The broad antimicrobial resistance of this isolate is at least attributed partially to this gene.

Comparison of four automated microbiology systems with 16S rRNA gene sequencing for identification of Chryseobacterium and Elizabethkingia species

Chryseobacterium and Elizabethkingia species have recently emerged as causative agents in life-threatening infections in humans. We aimed to evaluate the rates at which four common microbial identification systems identify Chryseobacterium and Elizabethkingia species in clinical microbiology laboratories. Based on the results of 16S rRNA gene sequencing, a total of 114 consecutive bacteremic isolates, including 36 (31.6%) C. indologenes, 35 (30.7%) E. anophelis, 22 (19.3%) C. gleum, 13 (11.4%) E. meningoseptica, and other species, were included in this study. The overall concordance between each method and 16S rRNA gene sequencing when identifying Chryseobacterium and Elizabethkingia species was 42.1% for API/ID32, 41.2% for Phoenix 100 ID/AST, 43.9% for VITEK 2, and 42.1% for VITEK MS. Among the 22 C. gleum isolates, only one (4.8%) was correctly identified using VITEK 2 and Phoenix 100 ID/AST, and none were accurately recognized using API/ID32 or VITEK MS. Except for two isolates that were not identified using API/ID32, all E. anophelis isolates were misidentified by all four identification systems as E. meningoseptica. Our results show that these approaches have low accuracy when identifying Chryseobacterium and Elizabethkingia species. Hence, we recommend amending the discrimination rate of and adding non-claimed pathogens to databases of microbial identification systems.

Analysis of resistance genes in pan-resistant Myroides odoratimimus clinical strain PR63039 using whole genome sequencing

To clarify the antibiotic resistance mechanisms of Myroides odoratimimus, pan-resistant M. odoratimimus strain PR63039 was isolated and its genome sequenced and analyzed. Antimicrobial susceptibility testing was conducted using the Kirby-Bauer disk diffusion method, and the Phoenix-100 Automated Microbiology System with a NMIC/ID-4 panel including aminoglycosides, β-lactams, polypeptides, quinolones, sulfonamides, chloramphenicols, and tetracyclines. Single-molecule real-time whole genome sequencing was conducted using the PacBio RSII system, and genome annotation was performed using RAST and IMG ER. To characterize the genome features, a number of databases and software programs, including GC-Profile, CG viewer, the VFDB database, ISfinder, RADB, CARD, ResFinder, and PHAST, were used. M. odoratimimus isolate PR63039 was resistant to almost all antibiotics tested, suggesting pan-drug resistance. The genome consisted of a 4,366,950-bp chromosome and a 90,798-bp plasmid (p63039), which contained a large number of resistance genes and virulence factors. The distribution of the resistance genes was distinctive, and a resistance region, designated MY63039-RR, was identified. RAST analysis indicated that 108 of the annotated genes were potentially involved in virulence, disease, and defense, all of which could be associated with resistance and pathogenicity. Prophage analysis also identified two incomplete prophages in the genome of M. odoratimimus PR63039. Multiple antibiotic-resistance genes were identified, including those associated with resistance to tetracycline (tetX), macrolides (ereB, cfrA, lasE), sulfonamides (sul2, sul3), β-lactams (bla_MUS-1, bla_TUS-1, bla_SFB-1, bla_SLB-1, bla_OXA-209, bla_OXA-347), and chloramphenicol (cat). Further, the presence of 18 antibiotic efflux pump-encoding resistance genes, including acrB, acrD, acrF, adeB, adeG, adeJ, amrB, ceoB, cmeB, mdsB, mexB, mexD, mexF, mtrD, smeE, mdtF, macB, likely accounts for the observed quinolone resistance of strain PR63039. To the best of our knowledge, this is the first report of the presence of the bla_SFB-1, bla_SLB-1, bla_OXA-209, bla_OXA-347, and tetX resistance genes in M. odoratimimus.

Evaluation of MALDI-TOF mass spectrometry and MALDI BioTyper in comparison to 16S rDNA sequencing for the identification of bacteria isolated from Arctic sea water

MALDI-TOF Mass Spectrometry in association with the MALDI BioTyper 3.1 software has been evaluated for the identification and classification of 45 Arctic bacteria isolated from Kandalaksha Bay (White Sea, Russia). The high reliability of this method has been already demonstrated, in clinical microbiology, by a number of studies showing high attribution concordance with other credited analyses. Recently, it has been employed also in other branches of microbiology with controversial performance. The phyloproteomic results reported in this study were validated with those obtained by the "gold standard" 16S rDNA analysis. Concordance between the two methods was 100% at the genus level, while at the species level it was 48%. These percentages appeared to be quite high compared with other studies regarding environmental bacteria. However, the performance of MALDI BioTyper changed in relation to the taxonomical group analyzed, reflecting known identification problems related to certain genera. In our case, attribution concordance for Pseudomonas species was rather low (29%), confirming the problematic taxonomy of this genus, whereas that of strains from other genera was quite high (> 60%). Among the isolates tested in this study, two strains (Exiguobacterium oxidotolerans and Pseudomonas costantinii) were misidentified by MALDI BioTyper due to absence of reference spectra in the database. Accordingly, missing spectra were acquired for the database implementation.

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.

Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS

There are a number of rare and, therefore, insufficiently described bacterial pathogens which are reported to cause severe infections especially in immunocompromised patients. In most cases only few data, mostly published as case reports, are available which investigate the role of such pathogens as an infectious agent. Therefore, in order to clarify the pathogenic character of such microorganisms, it is necessary to conduct epidemiologic studies which include large numbers of these bacteria. The methods used in such a surveillance study have to meet the following criteria: the identification of the strains has to be accurate according to the valid nomenclature, they should be easy to handle (robustness), economical in routine diagnostics and they have to generate comparable results among different laboratories. Generally, there are three strategies for identifying bacterial strains in a routine setting: 1) phenotypic identification characterizing the biochemical and metabolic properties of the bacteria, 2) molecular techniques such as 16S rRNA gene sequencing and 3) mass spectrometry as a novel proteome based approach. Since mass spectrometry and molecular approaches are the most promising tools for identifying a large variety of bacterial species, these two methods are described. Advances, limitations and potential problems when using these techniques are discussed.

Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria

Identification and typing of bacteria occupy a large fraction of time and work in clinical microbiology laboratories. With the certification of some MS platforms in recent years, more applications and tests of MS‐based diagnosis methods for bacteria identification and typing have been created, not only on well‐accepted MALDI‐TOF‐MS‐based fingerprint matches, but also on solving the insufficiencies of MALDI‐TOF‐MS‐based platforms and advancing the technology to areas such as targeted MS identification and typing of bacteria, bacterial toxin identification, antibiotics susceptibility/resistance tests, and MS‐based diagnostic method development on unique bacteria such as Clostridium and Mycobacteria. This review summarizes the recent development in MS platforms and applications in bacteria identification and typing of common pathogenic bacteria.

MUS-2, a novel variant of the chromosome-encoded β-lactamase MUS-1, from Myroides odoratimimus

The aim of the present study was to investigate the molecular mechanism of carbapenem resistance of three imipenem-resistant isolates of Myroides odoratimimus recovered from two livestock farms of cows and pigeons by rectal swab in Lebanon in January 2014. Investigation of imipenem resistance of these isolates using the modified Hodge test, the EDTA test, the modified CarbaNP test and the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Ultraflex assay showed a carbapenemase activity due to the presence of a chromosome-encoded β-lactamase MUS, verified by PCR. However amplification and sequencing of this chromosomal gene showed a novel variant of it designated MUS-2 by the curators of the Lahey database of β-lactamases (http://www.lahey.org/Studies/webt.asp). Cloning of the bla_MUS-2 was performed, followed by protein expression in Escherichia coli TOP 10. Pulsed-field gel electrophoresis clearly showed that the three isolates belonged to the same clone. This study reports a novel variant of the chromosome-encoded bla_MUS-1 associated with carbapenem resistance in Myroides odoratimimus and shows that animals may represent a reservoir of bacteria harbouring several variants of resistance genes.

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.