Comparison of phenotypic methods and matrix-assisted laser desorption ionisation time-of-flight mass spectrometry for the identification of aero-tolerant Actinomyces spp. isolated from soft-tissue infections

Pulmonary actinomycosis mimicking lung malignancy: About two cases

Pulmonary actinomycosis is a rare anaerobic infection with non specific clinical and radiographic presentations that delay diagnosis. Throughout literature, a significant number of misdiagnosed cases have been reported. The diagnosis is substantially based on histopathological pattern. We describe the cases of two patients evaluated and treated in pulmonary department 1 of Abderrahmane Mami hospital of Tunisia with a diagnosis of pulmonary actinomycosis. There are two men. The first patient had hypertension and chronic obstructive pulmonary disease and the second one underwent surgery for bronchiectasis. Clinical presentation was consistent with productive cough, hemoptysis, and deterioration of general status. The medical examination was non-specific. The chest X-ray revealed an apical opacity, excavated in the first case and retractable in the second one. Biology showed an inflammatory syndrome. Bronchoscopy was performed in the two cases and showed lesions mimicking lung malignancy. Diagnosis is confirmed by histopathological examinations of surgical specimens in the two cases. Both patients were received antibiotic therapy. The results were excellent with a favorable clinical course and no deaths. This study highlights the misleading patterns of actinomycosis to prompt accurate diagnosis and earlier treatment, thus improving the outcome. Given either its low culture yield or the limited use of new molecular diagnostic tools in routine clinical practice, histological examination of lung tissue specimens is crucial to get the correct diagnosis.

Screening, molecular identification, population diversity, and antibiotic susceptibility pattern of Actinomycetes species isolated from meat and meat products of slaughterhouses, restaurants, and meat stores of a developing country, Iran

Introduction

Actinomycetes can colonize surfaces of tools and equipment and can be transferred to meat and meat products during manufacture, processing, handling, and storage. Moreover, washing the meat does not eliminate the microorganisms; it only spreads them. As a result, these opportunistic pathogens can enter the human body and cause various infections. Therefore, the aim of the current study was to screen, identify, and determine the antibiotic susceptibility of Actinomycetes species from meat and meat products in the Markazi province of Iran.

Methods

A total of 60 meat and meat product samples, including minced meat, mutton, beef, chicken, hamburgers, and sausages, were collected from slaughterhouses, butchers, and restaurants in the Markazi province of Iran. The samples were analyzed using standard microbiological protocols for the isolation and characterization of Actinomycetes. PCR amplification of hsp65 and 16SrRNA genes and sequence analysis of 16SrRNA were used for genus and species identification. The minimum inhibitory concentrations (MICs) of antimicrobial agents were determined by the broth microdilution method and interpreted according to the CLSI guidelines.

Results

A total of 21 (35%) Actinomycetes isolates from 5 genera and 12 species were isolated from 60 samples. The most prevalent Actinomycetes were from the genus Mycobacterium, with six (28.6%) isolates (M. avium complex, M. terrae, M. smegmatis, and M. novocastrense), followed by the genus Rhodococcus with five (23.8%) isolates (R. equi and R. erythropolis), the genus Actinomyces with four (19.1%) isolates (A. ruminicola and A. viscosus), the genus Nocardia with four (19.1%) isolates (N. asiatica, N. seriolae, and N. niigatensis), and the genus Streptomyces with two (9.5%) isolates (S. albus). Chicken and sausage samples had the highest and lowest levels of contamination, with six and one isolates. Respectively, the results of drug susceptibility testing (DST) showed that all isolates were susceptible to Ofloxacin, Amikacin, Ciprofloxacin, and Levofloxacin, whereas all of them were resistant to Doxycycline and Rifampicin.

Discussion

The findings suggest that meat and meat products play an important role as a reservoir for the transmission of Actinomycetes to humans, thus causing life-threatening foodborne diseases such as gastrointestinal and cutaneous disorders. Therefore, it is essential to incorporate basic hygiene measures into the cycle of meat production to ensure food safety.

The diagnosis and management of pulmonary actinomycosis

Pulmonary actinomycosis is a rare infection caused by the bacterial species actinomyces. This paper aims to provide a comprehensive review of pulmonary actinomycosis to improve awareness and knowledge. The literature was analysed using databases including Pubmed, Medline and Embase from 1974 to 2021. After inclusion and exclusion, a total of 142 papers were reviewed. Pulmonary actinomycosis is a rare disease occurring in approximately 1 per 3,000,000 people annually. Historically, pulmonary actinomycosis was a common infection with high mortality; however, the infection has become rarer since the widespread use of penicillins. Actinomycosis is known as "the great masquerade"; however, it can be differentiated from other diseases with acid-fast negative ray-like bacilli and sulphur granules being pathognomonic. Complications of the infection include empyema, endocarditis, pericarditis, pericardial effusion, and sepsis. The mainstay of treatment is prolonged antibiotic therapy, with adjuvant surgery in severe cases. Future research should focus on multiple areas, including the potential risk secondary to immunosuppression from newer immunotherapies, the utility of newer diagnostic techniques and ongoing surveillance post-therapy.

Paediatric pulmonary actinomycosis: A forgotten disease

Actinomycosis is a rare, indolent and invasive infection caused by Actinomyces species. Actinomycosis develops when there is disruption of the mucosal barrier, and invasion and systemic spread of the organism, which can lead to endogenous infection affecting numerous organs. It is known to spread in tissue through fascial planes and most often involves the cervicofacial (55%), abdominopelvic (20%) and thoracic (15%) soft tissue. Pulmonary actinomycosis is rare in patients under the age of five years, with the median reported age in the fifth decade. Clinical findings include chest wall mass (49%), cough (40%), pain (back, chest, shoulders) (36%), weight loss (19%), fever (19%), Draining sinuses (15%) and hemoptysis (9%). Chest x-ray findings in pulmonary actinomycosis are mostly nonspecific and can overlap with pulmonary tuberculosis, foreign body aspiration and malignancy. Endobronchial tissue aggregates may show sulphur granules, with yellow to white conglomerate areas of gram positive Actinomyces. Removal or biopsy of these large endobronchial masses must be done with care, because of the risk of bleeding and large airway obstruction. The cytology on bronchoalveolar lavage fluid may show Periodic acid-Schiff (PAS) positive stain, ZN negative and Gram-positive filamentous bacilli which is morphologically suggestive of Actinomycosis. Actinomyces spp is highly susceptible to beta lactam antibiotics, penicillin G, and amoxicillin. A minimum of 3-6 months is needed but up to 20 months of treatment may be needed. Early diagnosis and correct treatment can lead to a good prognosis with a low mortality.

Microbial Reduction of Fumonisin B1 by the New Isolate Serratia marcescens 329-2

The mycotoxin fumonisin (FB) has become a major problem in maize products in southeastern Asia. Fumonisin can affect the health of humans and many animals. Fumonisin contamination can be reduced by detoxifying microbial enzyme. Screening of 95 potent natural sources resulted in 5.3% of samples yielding a total of five bacterial isolates that were a promising solution, reducing approximately 10.0-30.0% of fumonisin B1 (FB1). Serratia marcescens, one of the dominant degrading bacteria, was identified with Gram staining, 16S rRNA gene, and MALDI-TOF/TOF MS. Cell-free extract showed the highest fumonisin reduction rates, 30.3% in solution and 37.0% in maize. Crude proteins from bacterial cells were analyzed with a label-free quantification technique. The results showed that hydrolase enzymes and transferase enzymes that can cooperate in the fumonisin degradation process were highly expressed in comparison to their levels in a control. These studies have shown that S. marcescens 329-2 is a new potential bacterium for FB1 reduction, and the production of FB1-reducing enzymes should be further explored.

Bacteremia and urogenital infection with Actinomyces urogenitalis following prolonged urinary retention

A case of bacteremia with the fastidious bacteria Actinomyces urogenitalis following lengthy urinary retention is reported in a sixty-year-old man. In 2013, the first case of bacteremia due to A. urogenitalis was presented, secondary to a tubo-ovarian abscess following transvaginal oocyte retrieval. To the best of our knowledge, this is the first male bacteremic episode involving A. urogenitalis related to a urinary tract focus. The patient had no prior urogenital medical history. Extensive susceptibility testing was done on isolates from urinary and blood cultures. The organism exhibited fluoroquinolone resistance but was susceptible to most other antibiotics used in the treatment of urinary infections. Due to its unusual growth requirements infections with A. urogenitalis are most likely an underdiagnosed entity.

Microbiological and Clinical Aspects of Cervicofacial Actinomyces Infections: An Overview

Similarly to other non-spore-forming Gram-positive anaerobes, members of the Actinomyces genus are important saprophytic constituents of the normal microbiota of humans. Actinomyces infections are considered to be rare, with cervicofacial infections (also known as ‘lumpy jaw syndrome’) being the most prevalent type in the clinical practice. Actinomycoses are characterized by a slowly progressing (indolent) infection, with non-specific symptoms, and additionally, the clinical presentation of the signs/symptoms can mimic other pathologies, such as solid tumors, active Mycobacterium tuberculosis infections, nocardiosis, fungal infections, infarctions, and so on. The clinical diagnosis of actinomycosis may be difficult due to its non-specific symptoms and the fastidious, slow-growing nature of the pathogens, requiring an anaerobic atmosphere for primary isolation. Based on 111 references, the aim of this review is to summarize current advances regarding the clinical features, diagnostics, and therapy of cervicofacial Actinomyces infections and act as a paper for dentistry specialists, other physicians, and clinical microbiologists.

Actinomyces turicensis Necrotizing Soft-Tissue Infection of the Thigh in a Diabetic Male

Background: Necrotizing soft-tissue infections are a devastating infection that is rarely caused by Actinomyces spp. Case Report: A 45-year-old obese previously healthy male presented to the emergency department with diabetic ketoacidosis. The patient developed systemic signs of infections and right medial thigh pain subsequently diagnosed as a necrotizing soft-tissue infection. Successful treatment included prompt surgical intervention and initiation of broad-spectrum antimicrobial drugs. Conclusion: Actinomyces turicensis may be the pathogen causing certain necrotizing soft-tissue infections. Clinicians should consider the possibility that this organism represents a true pathogen and not colonization/contamination.

Preterm Labor Caused by Hemolysis, Elevated Liver Enzymes, Low Platelet Count (HELLP) Syndrome and Postpartum Infection Complicated with Actinomyces Species: A Case Report

Patient: Female, newborn

Final Diagnosis: Actinomyces infection

Symptoms: Premature labor

Medication: —

Clinical Procedure: —

Specialty: Infectious Disease

Identification and diversity of Actinomyces species in a clinical microbiology laboratory in the MALDI-TOF MS era

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a reliable tool for bacterial identification. This study compared the Bruker MALDI-TOF BioTyper MS (MBT) and 16S rRNA gene sequencing for the identification of Actinomyces and Actinotignum spp. The MBT identified 68/77 (88.3%) of Actinomyces isolates to the genus-level and 44/77 (57.1%) of Actinomyces isolates to the species-level using the manufacturer's identification criteria. The MBT did not yield reliable identification for only 1/77 (1.3%) and generated no identification for 8/77 (10.4%) of the isolates. No misidentifications were found. Discordance at the species level was observed for eight isolates. Overall, the MBT demonstrated good concordance with the 16S rRNA gene sequencing with the exception of the closely related species A. naeslundii, A. viscosus and A. oris. A variety of Actinomyces spp. were isolated from orocervicofacial/dental specimens, but only a limited number of species were isolated from urine or intra-abdominal specimens. This study confirms the utility of MBT in the identification of Actinomyces spp. and describes the diversity and anatomic niche of species in human clinical specimens from various body sites.

Diagnosis and Management of a Cryptoglandular Actinomycotic Fistula-in-Ano: An Update on 7 New Cases and a Review of the Literature

Purpose

Primary anal actinomycosis of cryptoglandular origin, a rare cause of anal suppurative disease, requires specific management to be cured. The aims of this retrospective study were to describe clinical, morphological, and microbiological features of this entity and to evaluate management practices for new cases observed since 2001.

Methods

This was a retrospective case series conducted at the Diaconesses-Croix Saint-Simon Hospital in Paris.

Results

From January 2001 to July 2016, 7 patients, 6 males and 1 female (median, 49 years), presenting with an actinomycotic abscess with a cryptoglandular anal fistula were included for study. The main symptom was an acute painful ischioanal abscess. One patient exhibited macroscopic small yellow granules (“sulfur granules”), another “watery pus” and a third subcutaneous gluteal septic metastasis. All patients were overweight (body mass index ≥ 25 kg/m²). Histological study of surgically excised tissue established the diagnosis. All the patients were managed with a combination of classical surgical treatment and prolonged antibiotic therapy. No recurrence was observed during follow-up, the median follow-up being 3 years.

Conclusion

Actinomycosis should be suspected particularly when sulfur granules are present in the pus, patients have undergone multiple surgeries or suppuration has an unusual aspect. Careful histological examination and appropriate cultures of pus are needed to achieve complete eradication of this rare, but easily curable, disease.

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.

Clinical features of actinomycosis: A retrospective, multicenter study of 28 cases of miscellaneous presentations

Actinomycosis is a rare heterogeneous anaerobic infection with misleading clinical presentations that delay diagnosis. A significant number of misdiagnosed cases have been reported in specific localizations, but studies including various forms of actinomycosis have rarely been published.We performed a multicenter retrospective chart review of laboratory-confirmed actinomycosis cases from January 2000 until January 2014. We described clinical characteristics, diagnostic procedures, differential diagnosis, and management of actinomycosis of clinical significance.Twenty-eight patients were included from 6 hospitals in France. Disease was diagnosed predominately in the abdomen/pelvis (n = 9), orocervicofacial (n = 5), cardiothoracic (n = 5), skeletal (n = 3), hematogenous (n = 3), soft tissue (n = 2), and intracranially (n = 1). Four patients (14%) were immunocompromised. In most cases (92 %), the diagnosis of actinomycosis was not suspected on admission, as clinical features were not specific. Diagnosis was obtained from either microbiology (50%, n = 14) or histopathology (42%, n = 12), or from both methods (7%, n = 2). Surgical biopsy was needed for definite diagnosis in 71% of cases (n = 20). Coinfection was found in 13 patients (46%), among which 3 patients were diagnosed from histologic criteria only. Two-thirds of patients were treated with amoxicillin. Median duration of antibiotics was 120 days (interquartile range 60-180), whereas the median follow-up time was 12 months (interquartile range 5.25-18). Two patients died.This study highlights the distinct and miscellaneous patterns of actinomycosis to prompt accurate diagnosis and earlier treatments, thus improving the outcome. Surgical biopsy should be performed when possible while raising histologist's and microbiologist's awareness of possible actinomycosis to enhance the chance of diagnosis and use specific molecular methods.

Infections Caused by Actinomyces neuii: A Case Series and Review of an Unusual Bacterium

Background. Actinomyces neuii is a Gram-positive bacillus rarely implicated in human infections. However, its occurrence is being increasingly recognized with the use of improved identification systems. Objective. To analyse A. neuii infections in Alberta, Canada, and review the literature regarding this unusual pathogen. Methods. Cases of A. neuii were identified in 2013-2014 in Alberta. Samples were cultured aerobically and anaerobically. A predominant catalase positive Gram-positive coryneform bacillus with no branching was isolated in each case. Testing was initially done with API-CORYNE® (bioMérieux) and isolates were sent to the Provincial Laboratory for Public Health for further testing. Isolates' identities were confirmed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry microbial identification system (MALDI-TOF MS MIS; bioMérieux) and/or DNA sequencing. Results. Six cases of A. neuii infection were identified. All patients had soft tissue infections; typically, incision and drainage were done followed by a course of antibiotics. Agents used included cephalexin, ertapenem, ciprofloxacin, and clindamycin. All had favourable outcomes. Conclusions. While A. neuii is infrequently recognized, it can cause a diverse array of infections. Increased use of MALDI-TOF MS MIS is leading to increased detection; thus, understanding the pathogenicity of this bacterium and its typical susceptibility profile will aid clinical decision-making.

Is the Presence of Actinomyces spp. in Blood Culture Always Significant?

The isolation ofActinomycesspp. from sterile clinical samples is traditionally regarded as significant. We reviewed the demographic characteristics, clinical risk factors, and outcomes of patients withActinomycesspp. isolated from blood cultures in our NHS Trust and found that this is not necessarily the case.

Actinomycosis: a frequently forgotten disease

Actinomycosis is a rare subacute or chronic, endogenous infection mainly by Actinomyces species, showing low virulence through fimbriae and biofilms. Cervicofacial, thoracic, abdominal, pelvic and sometimes cerebral, laryngeal, urinary and other regions can be affected. Actinomycosis mimics other diseases, often malignancy. Disease risk in immunocompromised subjects needs clarification. Diagnosis is often delayed and 'sulfur granules' are helpful but nonspecific. Culture requires immediate specimen transport and prolonged anaerobic incubation. Imaging, histology, cytology, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and molecular methods improve the diagnosis. Actinomycetes are β-lactam susceptible, occasionally resistant. Treatment includes surgery and/or long-term parenteral then oral antibiotics, but some 1-4-week regimens or oral therapy alone were curative. For prophylaxis, oral hygiene and regular intrauterine device replacement are important.

Comparison of Vitek MS and MALDI Biotyper for Identification of Actinomycetaceae of Clinical Importance

The Vitek MS in vitro diagnostic (IVD) and MALDI Biotyper IVD systems were evaluated for the identification of 158 strains of Actinomycetaceae. Correct species-level identification rates of 60.7% and 58.2% were obtained with the Vitek MS system after direct deposit and with the MALDI Biotyper system after on-plate formic acid treatment, respectively.

Actinomyces Species Isolated from Breast Infections

Actinomycosis is a chronic infection caused by Actinomyces species characterized by abscess formation, tissue fibrosis, and draining sinuses. The spectrum of infections caused by Actinomyces species ranges from classical invasive actinomycosis to a less invasive form of superficial skin and soft tissue infection. We present a review detailing all Actinomyces species isolated from breast infections in NHS Lothian between 2005 and 2013, Actinomyces species isolated from breast infections referred to the United Kingdom Anaerobe Reference Unit between 1988 and 2014, and cases describing Actinomyces breast infections published in the medical literature since 1994. Actinomyces species are fastidious organisms which can be difficult to identify and are likely to be underascertained as a cause of breast infections. Due to improved diagnostic methods, they are increasingly associated with chronic, recurrent breast infections and may play a more significant role in these infections than has previously been appreciated.

Primary Bronchopulmonary Actinomycosis Masquerading as Lung Cancer: Apropos of Two Cases and Literature Review

Actinomycosis is a rare and slowly progressive infectious disease that can affect a variety of organ systems including the lung. It is caused by filamentous Gram-positive anaerobic bacteria of the genus Actinomyces. Despite its rarity, pulmonary actinomycosis can involve lung parenchyma, bronchial structures, and chest wall. The disease can mimic lung malignancy given its nonspecific clinical and radiological presentation, thus posing a diagnostic dilemma to the attending physician. In this paper, we describe two patients with pulmonary actinomycosis mimicking bronchogenic carcinoma; the former presented with peripheral infiltrate and associated hilar/mediastinal lymphadenopathy and the latter presented with a foreign body-induced endobronchial mass. Clinical, imaging, diagnostic, and therapeutical aspects of the disease are discussed, demonstrating the paramount importance of the histological examination of lung tissue specimens in the confirmation of the infection given either its low culture yield or the limited use of new molecular diagnostic tools in routine clinical practice.

Actinomyces and related organisms in human infections

Actinomyces israelii has long been recognized as a causative agent of actinomycosis. During the past 3 decades, a large number of novel Actinomyces species have been described. Their detection and identification in clinical microbiology laboratories and recognition as pathogens in clinical settings can be challenging. With the introduction of advanced molecular methods, knowledge about their clinical relevance is gradually increasing, and the spectrum of diseases associated with Actinomyces and Actinomyces-like organisms is widening accordingly; for example, Actinomyces meyeri, Actinomyces neuii, and Actinomyces turicensis as well as Actinotignum (formerly Actinobaculum) schaalii are emerging as important causes of specific infections at various body sites. In the present review, we have gathered this information to provide a comprehensive and microbiologically consistent overview of the significance of Actinomyces and some closely related taxa in human infections.

Actinomycosis: etiology, clinical features, diagnosis, treatment, and management

Actinomycosis is a rare chronic disease caused by Actinomyces spp., anaerobic Gram-positive bacteria that normally colonize the human mouth and digestive and genital tracts. Physicians must be aware of typical clinical presentations (such as cervicofacial actinomycosis following dental focus of infection, pelvic actinomycosis in women with an intrauterine device, and pulmonary actinomycosis in smokers with poor dental hygiene), but also that actinomycosis may mimic the malignancy process in various anatomical sites. Bacterial cultures and pathology are the cornerstone of diagnosis, but particular conditions are required in order to get the correct diagnosis. Prolonged bacterial cultures in anaerobic conditions are necessary to identify the bacterium and typical microscopic findings include necrosis with yellowish sulfur granules and filamentous Gram-positive fungal-like pathogens. Patients with actinomycosis require prolonged (6- to 12-month) high doses (to facilitate the drug penetration in abscess and in infected tissues) of penicillin G or amoxicillin, but the duration of antimicrobial therapy could probably be shortened to 3 months in patients in whom optimal surgical resection of infected tissues has been performed. Preventive measures, such as reduction of alcohol abuse and improvement of dental hygiene, may limit occurrence of pulmonary, cervicofacial, and central nervous system actinomycosis. In women, intrauterine devices must be changed every 5 years in order to limit the occurrence of pelvic actinomycosis.

Evaluation of the Bruker MALDI Biotyper for identification of Gram-positive rods: development of a diagnostic algorithm for the clinical laboratory

Reported matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification rates of Gram-positive rods (GPR) are low compared to identification rates of Gram-positive cocci. In this study, three sample preparation methods were compared for MALDI-TOF MS identification of 190 well-characterized GPR strains: direct transfer, direct transfer-formic acid preparation, and ethanol-formic acid extraction. Using the interpretation criteria recommended by the manufacturer, identification rates were significantly higher for direct transfer-formic acid preparation and ethanol-formic acid extraction than for direct transfer. Reducing the species cutoff from 2.0 to 1.7 significantly increased species identification rates. In a subsequent prospective study, 215 clinical GPR isolates were analyzed by MALDI-TOF MS, and the results were compared to those for identification using conventional methods, with discrepancies being resolved by 16S rRNA and rpoB gene analysis. Using the direct transfer-formic acid preparation and a species cutoff of 1.7, congruencies on the genus and species levels of 87.4% and 79.1%, respectively, were achieved. In addition, the rate of nonidentified isolates dropped from 12.1% to 5.6% when using an extended database, i.e., the Bruker database amended by reference spectra of the 190 GPR of the retrospective study. Our data demonstrate three ways to improve GPR identification by the Bruker MALDI Biotyper, (i) optimize sample preparation using formic acid, (ii) reduce cutoff scores for species identification, and (iii) expand the database. Based on our results, we suggest an identification algorithm for the clinical laboratory combining MALDI-TOF MS with nucleic acid sequencing.

Proteomics boosts translational and clinical microbiology

The application of proteomics to translational and clinical microbiology is one of the most advanced frontiers in the management and control of infectious diseases and in the understanding of complex microbial systems within human fluids and districts. This new approach aims at providing, by dedicated bioinformatic pipelines, a thorough description of pathogen proteomes and their interactions within the context of human host ecosystems, revolutionizing the vision of infectious diseases in biomedicine and approaching new viewpoints in both diagnostic and clinical management of the patient. Indeed, in the last few years, many laboratories have matured a series of advanced proteomic applications, aiming at providing individual proteome charts of pathogens, with respect to their morph and/or cell life stages, antimicrobial or antimycotic resistance profiling, epidemiological dispersion. Herein, we aim at reviewing the current state-of-the-art on proteomic protocols designed and set-up for translational and diagnostic microbiological purposes, from axenic pathogens' characterization to microbiota ecosystems' full description. The final goal is to describe applications of the most common MALDI-TOF MS platforms to advanced diagnostic issues related to emerging infections, increasing of fastidious bacteria, and generation of patient-tailored phylotypes. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry for identification of clinically significant bacteria that are difficult to identify in clinical laboratories

AIMS

Although the revolutionary matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has been evaluated for identification of various groups of bacteria, its application in bacteria that are 'difficult-to-identify' by phenotypic tests has been less well studied. We aim to evaluate the usefulness of MALDI-TOF MS for identification of 'difficult-to-identify' bacterial isolates.

METHODS

We evaluated the performance of the Bruker MALDI-TOF MS system for a collection of 67 diverse clinically important bacterial isolates that were less commonly encountered, possessed ambiguous biochemical profiles or belonged to newly discovered species. The results were compared with 16S rRNA gene sequencing as a reference method for species identification.

RESULTS

Using 16S rRNA gene sequencing as the reference method, 30 (45%) isolates were identified correctly to species level (score ≥2.0), 20 (30%) were only identified to genus level (score ≥1.7), four (6%) were misidentified (incorrect species with score ≥2.0 or incorrect genus with score ≥1.7) and 13 (19%) showed 'no identification' (score <1.7). Aerobic Gram-positive bacteria showed the highest percentage of correct species identification, followed by aerobic Gram-negative, anaerobic Gram-positive and anaerobic Gram-negative bacteria. Sixteen isolates identified to genus level actually showed the correct species but with scores below the threshold for species identification. Most isolates which showed 'no identification' were due to the absence of the corresponding species in the Bruker database.

CONCLUSIONS

Expansion of commercial databases to include reference spectra of less commonly encountered and newly discovered species and to increase available spectra for each species is required to improve the accuracy of MALDI-TOF MS for identifying 'difficult-to-identify' bacteria.

Actinomyces urogenitalis bacteremia and tubo-ovarian abscess after an in vitro fertilization (IVF) procedure

We describe the first case of bacteremia due to Actinomyces urogenitalis. Bacteremia was secondary to a tubo-ovarian abscess following transvaginal oocyte retrieval. Identification was established by matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and confirmed by 16S rRNA gene sequencing. A. urogenitalis should be considered as a potential causative agent of infection after gynecological procedures.

Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry

During the past 5 years, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become a powerful tool for routine identification in many clinical laboratories. We analyzed our 11-year experience in routine identification of clinical isolates (40 months using MALDI-TOF MS and 91 months using conventional phenotypic identification [CPI]). Among the 286,842 clonal isolates, 284,899 isolates of 459 species were identified. The remaining 1,951 isolates were misidentified and required confirmation using a second phenotypic identification for 670 isolates and using a molecular technique for 1,273 isolates of 339 species. MALDI-TOF MS annually identified 112 species, i.e., 36 species/10,000 isolates, compared to 44 species, i.e., 19 species/10,000 isolates, for CPI. Only 50 isolates required second phenotypic identifications during the MALDI-TOF MS period (i.e., 4.5 reidentifications/10,000 isolates) compared with 620 isolates during the CPI period (i.e., 35.2/10,000 isolates). We identified 128 bacterial species rarely reported as human pathogens, including 48 using phenotypic techniques (22 using CPI and 37 using MALDI-TOF MS). Another 75 rare species were identified using molecular methods. MALDI-TOF MS reduced the time required for identification by 55-fold and 169-fold and the cost by 5-fold and 96-fold compared with CPI and gene sequencing, respectively. MALDI-TOF MS was a powerful tool not only for routine bacterial identification but also for identification of rare bacterial species implicated in human infectious diseases. The ability to rapidly identify bacterial species rarely described as pathogens in specific clinical specimens will help us to study the clinical burden resulting from the emergence of these species as human pathogens, and MALDI-TOF MS may be considered an alternative to molecular methods in clinical laboratories.

Identification of a novel 16S rRNA gene variant of Actinomyces funkei from six patients with purulent infections

Little is known about the clinical significance and laboratory diagnosis of Actinomyces funkei. In this report we describe six clinical cases where A. funkei was isolated from purulent, polymicrobial infections. Conventional identification procedures were compared with molecular methods including matrix-assisted laser desorption/ionization time-of-flight mass spectrometry technique. Analysis of the full 16S rRNA gene sequence of the six investigated strains revealed differences from the A. funkei type strain. DNA-DNA hybridization showed that the clinical strains represent a novel 16S rRNA gene variant within the species of A. funkei.