Ionization Time Of Flight Mass Spectrometry Research Articles

Identification of Enterococcus spp. from food sources by matrix-assisted laser desorption ionization-time of flight mass spectrometry and characterization of virulence factors, antibiotic resistance, and biofilm formation

The continuous detection of multi-drug-resistant enterococci in food source environments has aroused widespread concern. In this study, 198 samples from chicken products, animal feces, raw milk, and vegetables were collected in Japan and Egypt to investigate the prevalence of enterococci and virulence characterization. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was employed for species identification and taxonomic analysis of the isolates. The results showed that the rates of most virulence genes (efaA, gelE, asa1, ace, and hyl) in the Japanese isolates were slightly higher than those in the Egyptian isolates. The rate of efaA was the highest (94.9 %) among seven virulence genes detected, but the cylA gene was not detected in all isolates, which was in accordance with γ-type hemolysis phenotype. In Enterococcus faecalis, the rate of kanamycin-resistant strains was the highest (84.75 %) among the antibiotics tested. Moreover, 78 % of E. faecalis strains exhibited multi-drug resistance. Four moderately vancomycin-resistant strains were found in Egyptian isolates, but none were found in Japanese isolates. MALDI-TOF MS analysis correctly identified 98.5 % (68/69) of the Enterococcus isolates. In the principal component analysis dendrogram, strains isolated from the same region with the same virulence characteristics and similar biofilm-forming abilities were characterized by clustered distribution in different clusters. This finding highlights the potential of MALDI-TOF MS for classifying E. faecalis strains from food sources.

Genomic characterization of carbapenem and colistin-resistant Klebsiella pneumoniae isolates from humans and dogs.

Carbapenem and colistin-resistant Enterobacteriaceae, including Klebsiella pneumoniae, have become a growing global concern, posing a significant threat to public health. Currently, there is limited information about the genetic background of carbapenem and colistin-resistant K. pneumoniae isolates infecting humans and dogs in Thailand. This study aimed to characterize carbapenem and colistin-resistant genes in six resistant K. pneumoniae clinical isolates (three from humans and three from dogs) which differed in their pulse field gel electrophoresis profiles. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), antimicrobial susceptibility testing, and whole-genome sequencing were employed to identify and analyze the isolates. All six isolates were carbapenemase-producing K. pneumoniae isolates with chromosomally carried blaSHV, fosA, oqxA and oqxB genes, as well as nine to 21 virulence genes. The isolates belonged to five multilocus sequence types (STs): one isolate from a human and one from a dog belonged to ST16, with the other two human isolates being from ST340 and ST1269 and the other two dog isolates were ST147 and ST15. One human isolate and two dog isolates harbored the same blaOXA-232 gene on the ColKP3 plasmid, and one dog isolate carried the blaOXA-48 gene on the IncFII plasmid. Notably, one human isolate exhibited resistance to colistin mediated by the mcr-3.5 gene carried on the IncFII plasmid, which co-existed with resistance determinants to other antibiotics, including aminoglycosides and quinolones. In conclusion, this study provides a comprehensive characterization of both chromosome- and plasmid-mediated carbapenem and colistin resistance in a set of K. pneumoniae clinical isolates from unrelated humans and dogs in Thailand. The similarities and differences found contribute to our understanding of the potential widescale dissemination of these important resistance genes among clinical isolates from humans and animals, which in turn may contribute to outbreaks of emerging resistant clones in hospital settings.

Neonatal Sepsis Due to Multidrug-resistant Bacteria at a Tertiary Teaching Hospital in Ethiopia.

The burden of multidrug-resistant bacterial infections in low-income countries is alarming. This study aimed to identify the bacterial etiologies and antibiotic resistance patterns among neonates in Jimma, Ethiopia. An observational longitudinal study was conducted among 238 presumptive neonatal sepsis cases tested with blood and/or cerebrospinal fluid culture. The bacterial etiologies were confirmed using matrix-assisted laser desorption ionization-time of flight mass spectrometry. The antibiotic resistance patterns were determined using the automated disc diffusion method (Bio-Rad) and the results were interpreted based on the European Committee on Antimicrobial Susceptibility Testing 2021 breakpoints. Extended-spectrum β-lactamases were detected using a double disc synergy test and confirmed by Mast discs (Mast Diagnostica GmbH). A total of 152 pathogens were identified. Of these, Staphylococcus aureus (18.4%) was the predominant isolate followed by Klebsiella pneumoniae (15.1%) and Escherichia coli (10.5%). All the isolates exhibited a high rate of resistance to first- and second-line antibiotics ranging from 73.3% for gentamicin to 93.3% for ampicillin. Furthermore, 74.4% of the Gram-negative isolates were extended-spectrum β-lactamase producers and 57.1% of S. aureus strains were methicillin resistant. The case fatality rate was 10.1% and 66.7% of the deaths were attributable to infections by multidrug-resistant pathogens. The study revealed a high rate of infections with multidrug-resistant pathogens. This poses a significant challenge to the current global and national target to reduce neonatal mortality rates. To address these challenges, it is important to employ robust infection prevention practices and continuous antibiotic resistance testing to allow targeted therapy.

Antifungal susceptibility profile of Candida species isolated from women with vulvovaginal candidiasis

Objectives: The objective of this study was to study the occurrence of vulvovaginal candidiasis (VVC) among women with vaginitis and to determine the antifungal susceptibility testing (AFST) pattern of Candida spp. isolated. Materials and Methods: A prospective study was conducted in a tertiary care setting. The two high vaginal swabs were collected and subjected to Gram’s stain, wet mount examination, and cultured on blood agar and sabouraud dextrose agar with chloramphenicol. The cultures were incubated at 37°C for 18–24 h. The Candida spp. was identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), and AFST was performed according to the Clinical and Laboratory Standards Institute guidelines M27-A3. Statistical Analysis: The data was collected in excel sheet. The qualitative variables are presented as frequencies and percentages. The quantitative variables are presented as mean with SD and median. p value of less than 0.05 was considered statistically significant. Analysis will be done by using Epi InfoTM statistical software. Results: A total of 961 women with symptoms of vaginitis were screened. Candida spp. was isolated in 108 (11.2%) patients. The median age of affected women was 29 years, and the majority belonged to 20–30 years (60.2%). Age <40 years was the significant risk factor (P = 0.016). Vaginal discharge was the most common complaint (82.4%),followed by itching (55.6%), vulvar edema, dyspareunia, and dysuria. Candida albicans was the predominant species (46.3%),followed by Candida glabrata (36.1%), Candida krusei (6.5%), and Candida tropicalis (6.5%). Ninety-six percentages of C. albicans were sensitive to fluconazole, while only 22.4% of non-albicans Candida spp (NAC) were susceptible. C. albicans showed 8% resistance to itraconazole and 8% intermediate resistance to caspofungin, whereas C. glabrata showed resistance to fluconazole, itraconazole, and caspofungin. Conclusions: The study showed a higher incidence of NAC and higher antifungal resistance leading to treatment failure. It is, hence, crucial to send fungal cultures, speciate, and perform AFST for all symptomatic patients of vulvo-vaginal candidiasis (VVC).

Molecular characterization of non-aureus staphylococci and Mammaliicoccus from Hipposideros bats in Southwest Nigeria

Bats are not only ecologically valuable mammals but also reservoirs of zoonotic pathogens. Their vast population, ability to fly, and inhabit diverse ecological niches could play some role in the spread of antibiotic resistance. This study investigated non-aureus staphylococci and Mammaliicoccus colonization in the Hipposideros bats at Obafemi Awolowo University, Ile-Ife, Nigeria. Pharyngeal samples (n = 23) of the insectivorous bats were analyzed, and the presumptive non-aureus staphylococcal and Mammaliicoccus isolates were confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The isolates were characterized based on antibiotic susceptibility testing and whole-genome sequencing (WGS). Six bacterial genomes were assembled, and three species were identified, including Mammaliicoccus sciuri (n = 4), Staphylococcus gallinarum (n = 1), and Staphylococcus nepalensis (n = 1). All the isolates were resistant to clindamycin, while the M. sciuri and S. gallinarum isolates were also resistant to fusidic acid. WGS analysis revealed that the M. sciuri and S. gallinarum isolates were mecA-positive. In addition, the M. sciuri isolates possessed some virulence (icaA, icaB, icaC, and sspA) genes. Multi-locus sequence typing identified two new M. sciuri sequence types (STs) 233 and ST234. The identification of these new STs in a migratory mammal deserves close monitoring because previously known ST57, ST60, and ST65 sharing ack (8), ftsZ (13), glpK (14), gmk (6), and tpiA (10) alleles with ST233 and ST234 have been linked to mastitis in animals. Moreover, the broad host range of M. sciuri could facilitate the dispersal of antibiotic resistance genes. This study provides evidence of the importance of including migratory animals in monitoring the development and spread of antibiotic resistance.

The microbiological quality, shelf-life, and multidrug-resistant Salmonella contamination rates assessment in chicken giblets purchased from live poultry shops

The objective of the current study was to assess the shelf-life durations and hygienic standards of chicken giblets purchased from Egyptian live poultry outlets compared to the Egyptian Standardization Organization criteria. Salmonella prevalence and antibiotic-resistance profiles were also described. On the first day, forty-five giblet samples were randomly collected and evaluated for aerobic plate count (APC), coliform, Escherichia coli, Staphylococcus and Staphylococcus aureus, and multidrug-resistant Salmonella contamination rates using culturing methods, matrix-assisted laser desorption ionization-time of flight mass spectrometry, and the VITEK® −2 system. Four- and five-day shelf-life durations were assessed. All chicken giblets had acceptable APC levels below the 6 log cfu/g on the collection day, but 27 % were contaminated with Salmonella Enteritidis, rendering them unfit. More than 2-log CFU/gm of Escherichia coli and Staphylococcus aureus contamination was identified in 64 % and 58 % of the giblets, respectively. All targeted indices surpassed maximum authorized requirements after four and five days of chilling at 4 °C, coupled with the detection of obvious greenish discoloration and off odor. All twelve Salmonella Enteritidis were vulnerable to carbapenems, cefepime, and piperacillin/tazobactam, but 83 % were multidrug-resistant (MDR), with four demonstrating extended-spectrum beta-lactam resistance. This could be the first Egyptian report identifying such a high prevalence rate of Salmonella and MDR to key antibiotics in chicken giblets. The current study encourages Egyptian authorities to reevaluate laws governing live poultry outlets to reduce the risk of disease exposure, including the National Egyptian Food Safety Authority's direct supervision over these outlets to establish a stringent safety program.

Comparison of MALDI-TOF mass spectrometry and 16S rDNA sequencing for identification of environmental bacteria: a case study of cave mussel-associated culturable microorganisms.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is routinely used as a rapid and cost-effective method for pathogen identification in clinical settings. In comparison, its performance in other microbiological fields, such as environmental microbiology, is still being tested, although isolates of environmental microbes are essential for in-depth in vivo studies of their biology, including biotechnological applications. We investigated the applicability of MALDI-TOF MS for the identification of bacterial isolates from a highly oligotrophic environment-Dinaric Karst caves, which likely harbor specific microorganisms. We cultured bacteria from the shell surface of the endemic mussel Congeria jalzici, one of the three known cave mussels in the world that lives in the Dinaric karst underground. The bacterial isolates were obtained by swabbing the shell surface of mussels living in microhabitats with different amounts of water: 10 air-exposed mussels, 10 submerged mussels, and 10 mussels in the hygropetric zone. A collection of 87 pure culture isolates was obtained, mostly belonging to the phylum Bacillota (72%), followed by Pseudomonadota (16%), Actinomycetota (11%), and Bacteroidota (1%). We compared the results of MALDI-TOF MS identification (Bruker databases DB-5989 and version 11, v11) with the results of 16S rDNA-based phylogenetic analysis, a standard procedure for bacterial identification. Identification to the genus level based on 16S rDNA was possible for all isolates and clearly outperformed the results from MALDI-TOF MS, although the updated MALDI-TOF MS database v11 gave better results than the DB-5989 version (85% versus 62%). However, identification to the species-level by 16S rDNA sequencing was achieved for only 17% of isolates, compared with 14% and 40% for the MALDI-TOF MS databases DB-5989 and v11 database, respectively. In conclusion, our results suggest that continued enrichment of MALDI-TOF MS libraries will result with this method soon becoming a rapid, accurate, and efficient tool for assessing the diversity of culturable bacteria from different environmental niches.

Rhodococcus infection: a 10-year retrospective analysis of clinical experience and antimicrobial susceptibility profile.

Rhodococcus equi is an opportunistic pathogen known to cause pulmonary and extrapulmonary disease among immunocompromised patients. Treatment is frequently challenging due to intrinsic resistance to multiple antibiotic classes. While non-equi Rhodococcus spp. are prevalent, their clinical significance is poorly defined. There is also limited data on antibiotic susceptibility testing (AST) of Rhodococcus infection in humans. We conducted a single-center, retrospective cohort study evaluating clinical characteristics, microbiologic profile, and AST of Rhodococcus infections between June 2012 and 2022 at our tertiary academic medical center. Identification of Rhodococcus spp. was performed by Sanger 16S rRNA gene sequencing and/or matrix-assisted laser desorption ionization-time of flight mass spectrometry, and AST was performed by agar dilution. Three hundred twenty-two isolates of Rhodococcus spp. were identified from blood (50%), pulmonary (26%), and bone/joint (12%) sources. R. equi/hoagii, R. corynebacterioides, and R. erythropolis were the most frequently isolated species, with 19% of isolates identified only to genus level. One hundred ninety-nine isolates evaluated for AST demonstrated high-level resistance to amoxicillin/clavulanate, cephalosporins, and aminoglycosides. More than 95% susceptibility to imipenem, vancomycin, linezolid, rifampin, and clarithromycin was observed. Non-equi species showed a significantly more favorable AST profile relative to R. equi. Clinically significant Rhodococcus infection was rare with 10 cases diagnosed (majority due to R. equi) and managed. The majority of patients received 2- or 3-drug combination therapy for 2-6 months, with favorable clinical response. Significant differences in AST were observed between R. equi and non-equi species. Despite high antimicrobial resistance to several antibiotic classes, imipenem and vancomycin remain appropriate empiric treatment options for R. equi. Future research evaluating mechanisms underlying antimicrobial resistance is warranted.

Association of ITGA4 and ICAM-1 gene polymorphisms with the risk and clinicopathological characteristics of Crohn's disease

To assess the association between the polymorphism of integral protein α4 (ITGA4) and intercellular adhesion molecule 1 (ICAM-1) genes and the risk and clinicopathological characteristics of Crohn's disease (CD) among Chinese patients. From January 2010 to January 2021, a total of 215 CD patients and 529 gender- and age-matched healthy controls were enrolled from the Second Affiliated Hospital of Wenzhou Medical University as the study subjects. Genotypes of ITGA4 (rs6740847, rs7562325) and ICAM-1 (rs5498) were determined by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Harvey-Bradshaw Index (HBI) was applied to assess the disease activity of CD, and the patients were further divided into subgroups based on the Montreal Classification Criteria of CD. Unconditional logistic regression was employed to analyze the distribution of ITGA4 (rs6740847, rs7562325) and ICAM-1 (rs5498) polymorphisms between the patients and healthy controls and their association with the clinicopathological characteristics of the patients. The frequencies of T allele and CT+TT genotypes of ITGA4 (rs7562325) were higher in CD patients than the healthy controls (40.70% vs. 31.57%, P = 0.001; 62.79% vs. 54.36%, P = 0.042). The G variant and AG+GG genotypes of ITGA4 (rs6740847) were less common in patients with moderately to severely active CD compared with those with mildly active CD (31.18% vs. 51.72%, P = 0.002; 55.91% vs. 75.86%, P = 0.042). However, the opposite conclusion was drawn for the G allele (G) and AG+GG genotypes of ICAM-1 (rs5498) (31.45% vs. 17.24%, P = 0.027; 54.30% vs. 31.04%, P = 0.020). Compared with patients with terminal ileal or ileocolic CD, G allele and AG+GG genotypes of ITGA4 (rs6740847) were more prevalent in patients with colonic CD (55.26% vs. 29.38%, P < 0.001; 84.21% vs. 53.11%, P<0.001). The same conclusion could also be drawn for the G allele and AG+GG genotypes of ICAM-1 (rs5498) (42.11% vs. 26.84%, P = 0.008; 73.69% vs. 46.33%, P = 0.002). The frequency of homozygous GG genotype of ICAM-1 (rs5498) was lower in patients with stricturing and penetrating CD than those with non-stricturing and non-penetrating CD (0.00% vs. 12.32%, P = 0.001). The G allele and AG+GG genotypes of the ITGA4 (rs6740847) were more common in patients with perianal lesions than those without (40.28% vs. 30.77%, P = 0.049; 72.22% vs. 51.75%, P = 0.004). Variants of the ITGA4 (rs7562325) may be a risk factor for CD, whilst those of the ITGA4 (rs6740847) may be associated with the decline of disease activity and risk for colon involvement and perianal lesions. Variants of the ICAM-1 (rs5498) may increase the risk of disease activity and colonic involvement in CD patients, however, it may be a protective factor for stenosis and penetration. In addition, variants of the ITGA4 (rs6740847) and ICAM-1 (rs5498) may be associated with the early onset of CD.

Enterobacter cloacae from urinary tract infections: frequency, protein analysis, and antimicrobial resistance

The genus Enterobacter belongs to the ESKAPE group, which includes Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. This group is characterized by the development of resistance to various antibiotics. In recent years, Enterobacter cloacae (E. cloacae) has emerged as a clinically important pathogen responsible for a wide range of healthcare-associated illnesses. Identifying Enterobacter species can be challenging due to their similar phenotypic characteristics. The emergence of multidrug-resistant E. cloacae is also a significant problem in healthcare settings. Therefore, our study aimed to identify and differentiate E. cloacae using Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) as a fast and precise proteomic analytical technique. We also tested hospital-acquired E. cloacae isolates that produce Extended-spectrum beta-lactamases (ESBL) against commonly used antibiotics for treating urinary tract infections (UTIs). We used a total of 189 E. cloacae isolates from 2300 urine samples of patients with UTIs in our investigation. We employed culturing techniques, as well as the BD Phoenix™ automated identification system (Becton, Dickinson) and Analytical Profile Index (API) system for the biochemical identification of E. cloacae isolates. We used the MALDI Biotyper (MBT) device for peptide mass fingerprinting analysis of all isolates. We utilized the single peak intensities and Principal Component Analysis (PCA) created by MBT Compass software to discriminate and cluster the E. cloacae isolates. Additionally, we evaluated the sensitivity and resistance of ESBL-E. cloacae isolates using the Kirby Bauer method. Out of the 189 E. cloacae isolates, the BD Phoenix system correctly identified 180 (95.24%) isolates, while the API system correctly identified 165 (87.30%) isolates. However, the MBT accurately identified 185 (98.95%) isolates with a score of 2.00 or higher. PCA positively discriminated the identified E. cloacae isolates into one group, and prominent peaks were noticed between 4230 mass-to-charge ratio (m/z) and 8500 m/z. The ESBL-E. cloacae isolates exhibited a higher degree of resistance to ampicillin, amoxicillin-clavulanate, cephalothin, cefuroxime, and cefoxitin. Several isolates were susceptible to carbapenems (meropenem, imipenem, and ertapenem); however, potential future resistance against carbapenems should be taken into consideration. In conclusion, MALDI-TOF MS is a powerful and precise technology that can be routinely used to recognize and differentiate various pathogens in clinical samples. Additionally, the growing antimicrobial resistance of this bacterium may pose a significant risk to human health.

Identification of environmental Actinobacteria in buildings by means of chemotaxonomy, 16S rRNA sequencing, and MALDI-TOF MS.

The manuscript addresses the challenges in identifying environmental bacteria using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) Biotyper-based protein profiling. The matter of the studies-actinobacterial strains-has been isolated mostly from building materials that originated from a confirmed moisture-damaged situation. Polyphasic taxonomy, 16S RNA gene sequencing, and MALDI-TOF mass spectrometry were applied for identification purposes. In this experimental paper, a few important facts are highlighted. First, Actinobacteria are abundant in the natural as well as built environment, and their identification on the species and genus levels is difficult and time-consuming. Second, MALDI-TOF MS is an effective tool for identifying bacterial environmental strains, and in parallel, continuous enrichment of the proteomics mass spectral databases is necessary for proper identification. Third, the chemical approach aids in the taxonomical inquiry of Actinobacteria environmental strains.

Molecular characterization of carbapenem-resistance in Gram-negative isolates obtained from clinical samples at Jimma Medical Center, Ethiopia.

In resource-constrained settings, limited antibiotic options make treating carbapenem-resistant bacterial infections difficult for healthcare providers. This study aimed to assess carbapenemase expression in Gram-negative bacteria isolated from clinical samples in Jimma, Ethiopia. A cross-sectional study was conducted to assess carbapenemase expression in Gram-negative bacteria isolated from patients attending Jimma Medical Center. Totally, 846 Gram-negative bacteria were isolated and identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Phenotypic antibiotic resistance patterns were determined using the Kirby-Bauer disk diffusion method and Etest strips. Extended-spectrum β-lactamase phenotype was determined using MAST disks, and carbapenemases were characterized using multiplex polymerase chain reactions (PCR). Among the isolates, 19% (157/846) showed phenotypic resistance to carbapenem antibiotics. PCR analysis revealed that at least one carbapenemase gene was detected in 69% (107/155) of these strains. The most frequently detected acquired genes were blaNDM in 35% (37/107), blaVIM in 24% (26/107), and blaKPC42 in 13% (14/107) of the isolates. Coexistence of two or more acquired genes was observed in 31% (33/107) of the isolates. The most common coexisting acquired genes were blaNDM + blaOXA-23, detected in 24% (8/33) of these isolates. No carbapenemase-encoding genes could be detected in 31% (48/155) of carbapenem-resistant isolates, with P. aeruginosa accounting for 85% (41/48) thereof. This study revealed high and incremental rates of carbapenem-resistant bacteria in clinical samples with various carbapenemase-encoding genes. This imposes a severe challenge to effective patient care in the context of already limited treatment options against Gram-negative bacterial infections in resource-constrained settings.

A New Case of Fournier's Gangrene Caused by Actinotignum schaalii

Actinotignum schaalii (formerly known as Actinobaculum schaalii) is an anaerobic or facultative anaerobic gram-positive bacillus that can be found commensally in the urogenital region. It can be overlooked because it grows slowly and is difficult to identify with classical microbiology laboratory techniques. Colonies become visible after 48-72 hours of incubation on blood agar in anaerobic or CO₂-rich media. While it typically causes urinary tract infection in older individuals, cases of bacteremia, vertebral osteomyelitis, endocarditis and cellulitis have been reported. Fournier's gangrene caused by A.schaalii has been reported very rarely so far. Fournier's gangrene has been defined as necrotizing fasciitis of the external genitalia, perineal and perianal region. Diabetes, immunosuppression, peripheral vascular disease, urethral anomalies, chronic alcoholism and smoking are important predisposing factors. In addition, approximately 25% of the cases have no known or identifiable etiology. The bacteria causing the infection may originate from skin, urogenital or intestinal microbiota. In this case report, a new case of Fournier's gangrene caused by A.schaalii was presented. A 65-year-old male patient admitted to the emergency department with the complaints of pain, swelling, redness in the left testis and also nausea, vomiting and chills that started three days ago. Physical examination revealed increased diameter of the scrotum, intense hyperemia of the skin and foci of necrosis. It was learned that the patient had no known chronic disease other than benign prostatic hyperplasia. The patient reported smoking of 25 packs of cigarettes per year. Routine laboratory tests revealed leukocyte= 32.41 x 109/L, neutrophil= 89.9%, procalcitonin= 1.62 ug/L, CRP= 265.07 mg/L and the patient was operated with the diagnosis of Fournier's gangrene. Gram staining of the abscess specimen obtained during the operation showed gram-positive bacilli both inside and outside the leukocytes. After 24 hours, grampositive bacilli were detected in the Gram staining of thin, transparent/gray colonies grown on 5% sheep blood and chocolate agar. The isolate was identified as A.schaalii by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) VITEK® MS (bioMérieux, France) microbial identification system. VITEK®2 ID ANC (bioMérieux, France) bacterial identification card was also used for comparison but the bacteria could be identified. As a result of the sequence analysis performed for confirmation, it was shown to be 100% homologous with Actinobaculum schaalii (GenBank accession no: FJ711193.1). For susceptibility tests, 5% sheep blood Schaedler agar was used and incubated in anaerobic environment. According to the minimal inhibitory concentration (MIC) results evaluated after 48 hours, penicillin was found to be 0.032 mg/L, clindamycin 0.125 mg/L, ciprofloxacin 0.19 mg/L, ceftazidime 4 mg/L, and amoxicillin 0.19 mg/L. The primary cause that initiated the infection in the case could not be identified, but it was thought that the presence of prostatic hyperplasia and smoking history may have contributed to the occurence or the progress of the disease. It is noteworthy that the ciprofloxacin MIC result was quite low compared to other studies. In addition, this study revealed the value of MALDI-TOF MS based methods in identification. In conclusion, it is thought that a significant proportion of A.schaalii infections may be overlooked due to the difficulty in growth and identification. Increasing the diagnostic power of clinical microbiology laboratories for poorly identified bacteria and renewing the databases of commercial identification systems are important for the early and accurate diagnosis and treatment of serious infections that may occur with such agents.

Retraction for Belkacemi et al., "Passive Filtration, Rapid Scanning Electron Microscopy, and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Treponema Culture and Identification from the Oral Cavity".

Retraction for Belkacemi et al., "Passive Filtration, Rapid Scanning Electron Microscopy, and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Treponema Culture and Identification from the Oral Cavity".

Phenotypic and genotypic detection of Beta-lactamase producing Pseudomonas aeruginosa isolated from Haryana, India

Antimicrobial resistance causes substantial risks to human health globally, and millions of people die worldwide due to multiple drug resistances. Beta-lactam drugs are common for curing infections, and resistance to these drugs cause serious threat to humans. The resistance is acquired by the gram-negative Pseudomonas aeruginosa by producing beta-lactamases such as metallo beta-lactamase (MBL), extended-spectrum beta-lactamase enzymes (ESBL), and AmpC β-lactamases. Hence, this study was intended to detect the occurrence of MBL, ESBL, and AmpC β-lactamases producing P. aeruginosa and to evaluate antibiotic sensitivity at the Pandit Bhagwat Dayal Sharma, Post Graduate Institute of Medical Sciences, Rohtak, Haryana, India. A total of 163 P. aeruginosa were isolated from the different samples of patients, such as urine, blood, sputum, pus, and pleural fluids. The P. aeruginosa was characterized morphologically, biochemically, and with matrix-assisted laser desorption ionization-time of flight mass spectrometry. Their antibiotic sensitivity was evaluated by the Kirby-Baur disc diffusion method. Antibiotic sensitivity tests of P. aeruginosa showed 163/163 were susceptible to Polymyxin-B, 78/163 and 65/163 were resistant against Ceftazidime (CAZ) and IMP antibiotics, respectively. The IMP, CAZ, and cefoxitin-resistant isolates were selected and further evaluated for ESBL, MBL, and AmpC enzyme production. In conclusion, the findings of this study indicated a significant presence of ESBL, MBL, and AmpC enzyme-producing P. aeruginosa among the patients. The ESBL prevalence was much higher in indoor patients than in outdoor patients. The total prevalence of MBL-producing strains in Imipenem-resistant P. aeruginosa (IRPA) was (46/62) 74.19%, which is an alarming signal. There was a higher prevalence of IRPA MBL-producing strains in indoor patients (36/46) 78.6% as compared to outdoor patients (10/16) 62.50%. Identification of bronchoalveolar lavage and sputum was also done using the Biofire Film Array, which revealed the resistant genes, including NDM (20 genes), CTX-M (17 genes), OXA-48-like (9 genes), VIM (5 genes), and IMP (2 genes). Antibiotics like cefotaxime and CAZ have less effect, but carbapenems and aminoglycosides are the best options for treating ESBL-producing P. aeruginosa. Drugs not recommended for treating this pathogen are penicillins and sulfonamides like co-trimoxazoles. Strict infection control measures, careful monitoring of antibiotic administration, and routine screening for ESBL-producing strains are advised before treating the patients.

Differential Protein Expression between the Motor and Sensory Fascicles in Rat Femoral Nerve Injury.

It is important to distinguish between motor and sensory fascicles of the peripheral nerves for nerve alignment in surgery. However, there are no biomarkers currently available for effective identification of motor or sensory fascicles. The objective of this study was to identify differentially expressed proteins between motor and sensory fascicles of rats in response to injury. The study was carried out using a rat femoral nerve injury model. A proteomic analysis was performed to detect differential protein expression using samples of bilateral motor and sensory branches of intact and injured rat femoral nerves through fluorescent two-dimensional difference gel electrophoresis and matrix-assisted laser desorption ionization-time of flight mass spectrometry. Chi-square tests and t-tests were performed for comparison between motor or sensory nerve groups. The data identified six proteins that were differentially expressed between motor and sensory fascicles (>1.5-fold, P < 0.05), including apolipoprotein E, neurofilament light polypepticle, TEC kinase, serine protease inhibitor A3N, peroxiredoxin-2, and TPM1. The proteomic results were consistent with the mRNA expression levels of these genes as determined by quantitative reverse transcription polymerase chain reaction. Our study suggests that these proteins may play roles in nerve regeneration and repair. Importantly, apolipoprotein E and Serpina3n may serve as specific biomarkers for distinguishing motor and sensory fascicles of the peripheral nerves for nerve alignment in surgery.

An Outbreak of Ralstonia mannitolilytica Septicaemia at a Tertiary Care Hospital: An Observational Cross-sectional Study

Introduction: Ralstonia spp. is an emerging non fermenting Gram negative bacillus implicated in cases of bloodstream infections in immunocompromised individuals. It is commonly found as an environmental contaminant in hospital settings. Several sporadic outbreaks have been reported from different parts of the world due to Ralstonia spp. This study reports a similar outbreak at a tertiary care hospital in Northern India. Aim: To determine the source of Ralstonia septicaemia in affected patients at a tertiary care centre. Materials and Methods: The present observational crosssectional study was conducted at the Department of Microbiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow, Uttar Pradesh, India from February 2020 until the end of March 2020 (two months). A total of 2,650 blood cultures were received during the study period; of these, 53 (2%) patients were found to have Ralstonia mannitolilytica infection over a two month period. All patients from various wards whose blood cultures showed growth of Ralstonia species were included in this study. The organism was identified using both biochemical tests and Matrix-Assisted Laser Desorption Ionisation-Time of Flight Mass Spectrometry (MALDI-TOF MS). Antibiotic sensitivity testing was conducted using the Kirby-Bauer disk diffusion assay. Environmental surveillance was conducted to detect the source of origin. Patients’ age, sex, duration of hospital stay, co-morbidities, and other clinical parameters were recorded. Statistical analysis was performed using Microsoft Excel. Results: There were 52 cases of septicaemia due to Ralstonia mannitolilytica, and one Ralstonia isolate was obtained from intraoperative pus. Most of the Ralstonia isolates obtained were Multidrug-Resistant (MDR), showing resistance to imipenem, meropenem, amikacin, aztreonam, and sensitivity to first-line drugs such as ceftazidime, piperacillin-tazobactam, cefoperazone-sulbactam, levofloxacin, and trimethoprimsulfamethoxazole, resulting in successful treatment. Out of 53 cases, one patient succumbed to death due to surgical complications. Environmental sampling did not yield any organisms resembling Ralstonia spp. Conclusion: The environmental source of the Ralstonia bacteraemia outbreak could not be identified in this study. All patients except one were successfully treated with antibiotics. Clinicians and microbiologists should remain vigilant in case any such case arises to prevent further outbreaks.

Identification of Autoantigens in Pediatric Gastric Juices.

This study aimed to investigate the presence of autoantigens in the gastric juices of children. Gastric juice and serum samples were obtained from 53 children <15 years of age who underwent gastric endoscopy. Among these, 8, 22, and 23 participants were in the age groups 0-5, 6-10, and 11-15 years, respectively. These samples were analyzed using two-dimensional electrophoresis (2-DE), immunoblot analysis, and matrix-assisted laser desorption ionization-time of-flight mass spectrometry. Furthermore, we reviewed the histopathological findings and urease test results and compared them with the results of 2-DE and immunoblot analysis. There were no statistically significant differences in urease test positivity, grades of chronic gastritis, active gastritis, or Helicobacter pylori infiltration of the antrum and body among the three age groups. Three distinct patterns of gastric juice were observed on 2-DE. Pattern I was the most common, and pattern III was not observed below the age of 5 years. Histopathological findings were significantly different among active gastritis (p=0.037) and H. pylori infiltration (p=0.060) in the gastric body. The immunoblots showed large spots at an approximate pH of 3-4 and molecular weights of 31-45 kDa. These distinct, large positive spots were identified as gastric lipase and pepsin A and C. Three enzymes, which are normally secreted under acidic conditions were identified as autoantigens. Further investigation of the pathophysiology and function of autoantigens in the stomach is required.

Developing a novel selection method for alcoholic fermentation starters by exploring wine yeast microbiota from Greece.

The selection of native yeast for alcoholic fermentation in wine focuses on ensuring the success of the process and promoting the quality of the final product. The purpose of this study was firstly to create a large collection of new yeast isolates and categorize them based on their oenological potential. Additionally, the geographical distribution of the most dominant species, Saccharomyces cerevisiae, was further explored. Towards this direction, fourteen spontaneously fermented wines from different regions of Greece were collected for yeast typing. The yeast isolates were subjected in molecular analyses and identification at species level. RAPD (Random Amplified Polymorphic DNA) genomic fingerprinting with the oligo-nucleotide primer M13 was used, combined with Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) technique. All yeast isolates were scrutinized for their sensitivity to killer toxin, production of non-desirable metabolites such as acetic acid and H2S, β-glucosidase production and resistance to the antimicrobial agent; SO2. In parallel, S. cerevisiae isolates were typed at strain level by interdelta - PCR genomic fingerprinting. S. cerevisiae strains were examined for their fermentative capacity in laboratory scale fermentation on pasteurized grape must. Glucose and fructose consumption was monitored daily and at the final point a free sorting task was conducted to categorize the samples according to their organoleptic profile. According to our results, among the 190 isolates, S. cerevisiae was the most dominant species while some less common non-Saccharomyces species such as Trigonopsis californica, Priceomyces carsonii, Zygosaccharomyces bailii, Brettanomyces bruxellensis and Pichia manshurica were identified in minor abundancies. According to phenotypic typing, most isolates were neutral to killer toxin test and exhibited low acetic acid production. Hierarchical Cluster Analysis revealed the presence of four yeast groups based on phenotypic fingerprinting. Strain level typing reported 20 different S. cerevisiae strains from which 65% indicated fermentative capacity and led to dry wines. Sensory evaluation results clearly discriminated the produced wines and consequently, the proposed yeast categorization was confirmed. A novel approach that employs biostatistical tools for a rapid screening and classification of indigenous wine yeasts with oenological potential, allowing a more efficient preliminary selection or rejection of isolates is proposed.

Pseudomonas otitidis bacteremia in an immunocompromised patient with cellulitis: case report and literature review

BackgroundPseudomonas otitidis belongs to the genus Pseudomonas and causes various infections, including ear, skin, and soft tissue infections. P. otitidis has a unique susceptibility profile, being susceptible to penicillins and cephalosporins but resistant to carbapenems, due to the production of the metallo-β-lactamase called POM-1. This revealed genetic similarities with Pseudomonas aeruginosa, which can sometimes lead to misidentification.Case presentationWe report the case of a 70-year-old Japanese male who developed cellulitis and bacteremia during chemotherapy for multiple myeloma. He was initially treated with meropenem, but blood culture later revealed gram-negative bacilli identified as P. otitidis using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Carbapenem resistance was predicted from previous reports; therefore, we switched to dual therapy with levofloxacin and cefepime, and favorable treatment results were obtained.ConclusionThis is the first reported case of P. otitidis cellulitis and bacteremia in an immunocompromised patient. Carbapenems are typically used in immunocompromised patients and P. otitidis is often resistant to it. However, its biochemical properties are similar to those of Pseudomonas aeruginosa; therefore, its accurate identification is critical. In the present study, we rapidly identified P. otitidis using MALDI-TOF MS and switched from carbapenems to an appropriate antimicrobial therapy, resulting in a successful outcome.