Article
Immunology
Qiaolian Yi, Meng Xiao, Xin Fan, Ge Zhang, Yang Yang, Jing-Jia Zhang, Si-Meng Duan, Jing-Wei Cheng, Ying Li, Meng-Lan Zhou, Shu-Ying Yu, Jing-Jing Huang, Xin-Fei Chen, Xin Hou, Fanrong Kong, Timothy Kudinha, Ying-Chun Xu
Summary: Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a rapid, accurate, and less labor-intensive method for identifying microorganisms, but its effectiveness in closely related yeast species has been limited. This study evaluated the performance of two commercially available MALDI-TOF systems, Autof MS 1000 and Vitek MS, in identifying yeasts within closely related species complexes. Autof MS 1000 showed good capacity for yeast identification, while Vitek MS had lower accuracy, particularly in less common species within phylogenetically closely related species complexes.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Infectious Diseases
Victoria Girard, Valerie Monnin, Delphine Giraud, Sophie Polsinelli, Marion Caille, Gary W. Procop, Marion Tuohy, Deborah Wilson, Sandra S. Richter, Katalin Kiss, Kimberly Clem, Nicholas Tolli, Laurence Bridon, Constance Bradford, Sara Blamey, Jay Li, David H. Pincus
Summary: The use of MALDI-TOF for clinical isolates has been proven to be rapid and accurate, with the VITEK MS v3.2 database showing high accuracy in identifying a wide range of isolates. The study revealed that the majority of isolates were identified to species or group level, with a small percentage of isolates identified only to the genus level. The ability of VITEK MS to identify various bacteria and fungi, including emerging and highly pathogenic species, highlights its potential as a valuable tool in clinical laboratories.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2021)
Article
Microbiology
Gyu Ri Kim, Si Hyun Kim, Eun-Young Kim, Eun Hee Park, In Yeong Hwang, Seok Hoon Jeong, Hyun Soo Kim, Young Ah Kim, Young Uh, Kyeong Seob Shin, Young Ree Kim, Namhee Ryoo, Jong Hee Shin, Jeong Hwan Shin
Summary: This study evaluated the usefulness of MALDI-TOF VITEK MS for Salmonella identification. The results showed that VITEK MS could accurately identify most Salmonella species, but had lower accuracy in identifying typhoidal Salmonella and Salmonella enterica ssp. diarizonae isolates.
Article
Multidisciplinary Sciences
Veerayuth Kittichai, Morakot Kaewthamasorn, Yudthana Samung, Rangsan Jomtarak, Kaung Myat Naing, Teerawat Tongloy, Santhad Chuwongin, Siridech Boonsang
Summary: Mosquito-borne diseases are among the top 10 causes of death in low-income countries. Controlling mosquito populations is crucial in fighting against these diseases. This study proposes an automatic screening method using deep metric learning and image retrieval to identify suitable mosquito images. The model has been tested with different data sources and shows great performance. The results can be used by public health authorities to locate mosquito vectors. Overall, the study is rated 7 out of 10 in terms of importance.
SCIENTIFIC REPORTS
(2023)
Article
Medicine, General & Internal
Ebru Evren, Julide Sedef Gocmen, Elvan Hortac Istar, Sukran Yavuzdemir, Alper Tekeli, Yasemin Yavuz, Zeynep Ceren Karahan
Summary: This study evaluated the performance of CMTA, CHROMagar Candida medium, and MALDI-TOF MS in Candida identification, and concluded that MALDI-TOF MS is the most accurate tool for clinically important Candida strains.
TURKISH JOURNAL OF MEDICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jiaming Cai, Lujuan Xing, Wangang Zhang, Lijuan Fu, Jian Zhang
Summary: This study aimed to select potential probiotic yeasts from dry-cured Xuanwei ham and investigate yeast-derived antioxidant peptides. Two potential probiotic yeasts, identified as Yamadazyma triangularis, were selected and found to exhibit tolerance under pH 2.5 and 1% bile salt and possess protease activity, auto-aggregation, antibacterial, and antioxidant activities. A peptide fraction named XHY69AP, isolated from the fermentation broth of XHY69, showed higher radical scavenging activities than glutathione. From this peptide fraction, a purified fraction named AP-D10 was obtained and seven novel peptides were identified, including Tyr-Pro-Leu-Pro, Ala-Gly-Pro-Leu, Gly-Pro-Phe-Pro, and Ala-Pro-Gly-Gly-Phe. These novel peptides were abundant in hydrophobic amino acids, especially proline residue. Among them, Tyr-Pro-Leu-Pro exhibited the highest ABTS scavenging rate. The present work highlights the discovery of new potential probiotic yeasts and novel antioxidant peptides from dry-cured Xuanwei ham.
Article
Microbiology
Wanitda Watthanaworawit, Tamalee Roberts, Jill Hopkins, Ian Gassiep, Robert Norton, Matthew T. Robinson, Joy Silisouk, Poda Sar, Sena Sao, Premjit Amornchai, Direk Limmathurotsakul, Vanaporn Wuthiekanun, Francois Nosten, Andrew J. H. Simpson, Paul Turner, Clare L. Ling
Summary: This study has developed a method for identifying B. pseudomallei using Vitek MS, and highlights the impact of geographical differences on strain identification using this technique.
Article
Microbiology
Yoojeong Choi, Daewon Kim, Kye Won Choe, Hyukmin Lee, Jae-Seok Kim, Jeong-Yeal Ahn, Mi-Kyung Lee
Summary: Filamentous fungi are a major cause of life-threatening infections in immuno-compromised patients. In this study, the performance of three different mass spectrometry methods for filamentous fungal identification was compared, along with the sensitivity of three different sample preparation methods.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Spectroscopy
Dickson L. Omucheni, Kenneth A. Kaduki, Wolfgang R. Mukabana
Summary: This study demonstrates the use of Raman spectroscopy for the identification and classification of three mosquito species, providing a foundation for further development of machine learning models in mosquito taxonomy.
JOURNAL OF RAMAN SPECTROSCOPY
(2023)
Article
Biotechnology & Applied Microbiology
Se-Hyung Kim, Jung-Whan Chon, Hyo-Won Jeong, Kwang-Young Song, Dong-Hyeon Kim, Dongryeoul Bae, Hyunsook Kim, Kun-Ho Seo
Summary: This study compared the accuracy of MALDI-TOF MS, VITEK 2, and 16S rRNA gene sequencing in identifying Enterococcus species. The results showed that MALDI-TOF MS correctly identified all isolates at the species level except for one, while VITEK 2 misidentified ten isolates. However, the phylogenetic trees constructed from both methods showed similar positions for all isolates. The study clearly demonstrated that MALDI-TOF MS is a reliable and rapid tool for identifying Enterococcus species with greater discriminatory power than VITEK 2.
Article
Microbiology
Romney Humphries, Shelley Campeau, Thomas E. Davis, Kristin J. Nagaro, Vincent J. LaBombardi, Simone Franklin, Lisa Heimbach, Hari P. Dwivedi
Summary: In this study, Vitek 2 AST-Gram-Negative Ceftazidime/Avibactam test results showed high agreement and accuracy compared to the CLSI BMD reference method, meeting or exceeding FDA and ISO performance criteria for routine CZA susceptibility testing.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Article
Medicine, Research & Experimental
Lucky Hartati Moehario, Enty Tjoa, Hans Putranata, Shikha Joon, Daniel Edbert, Thomas Robertus
Summary: In conclusion, there were no significant differences in the diagnostic efficiency of TDR-300B and VITEK (R) 2 for P. aeruginosa. Congruence rates and sensitivity were high for both automated systems, with VITEK (R) 2 showing slightly better performance in terms of positive predictive value and accuracy.
JOURNAL OF INTERNATIONAL MEDICAL RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Elisabeth Hodille, Clemence Prudhomme, Oana Dumitrescu, Yvonne Benito, Olivier Dauwalder, Gerard Lina
Summary: This study evaluated Nocardia identification using MALDI-TOF VITEK(R)-MS with direct deposit. The overall agreement with the reference method was 78.4%. Excluding Nocardia species not included in the VITEK(R)-MS database, the overall agreement significantly improved to 93.7%. VITEK(R)-MS rarely misidentified isolates (4/134, 3%), and among the 25 isolates that produced no result, 18 were expected due to the absence of the species in the VITEK(R)-MS database.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Infectious Diseases
Margarita Estreya Zvezdanova, Pilar Escribano, Jesus Guinea, Patricia Munoz, David Rodriguez-Temporal, Belen Rodriguez-Sanchez
Summary: The implementation of commercial kits for standardized fungal sample preparation and updated reference libraries enables the easy use of MALDI-TOF MS for routine identification of fungal species. Although further improvement in the databases is needed, this method allows for the correct identification of a significant number of fungal species at the species level.
Article
Infectious Diseases
Islam Sabeq, Dina Awad, Ahmed Hamad, Mohamed Nabil, Mohamed Aboubakr, Mohamed Abaza, Mohammed Fouad, Amira Hussein, Sanaa Shama, Hazem Ramadan, Shimaa Edris
Summary: The primary objective of this study was to detect Salmonella species in various sources and evaluate the resistance patterns to critically important antibiotics. The study found that Salmonella were present in food, water, and human samples, with some strains showing resistance to at least one class of antibiotics. Salmonella isolates were susceptible to certain types of antibiotics but exhibited resistance to aminoglycosides, beta-lactams, and tetracycline. The study also identified colistin resistance in Salmonella recovered from cattle minced meat and rabbit meat, which is the first report of its kind in Egypt.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Microbiology
Daniel M. Webber, Meghan A. Wallace, Carey-Ann D. Burnham
Summary: By reducing the incubation time for disk diffusion testing from 24 hours to 6 hours, the turnaround time for antimicrobial susceptibility testing can be significantly improved without additional costs or equipment requirements.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Microbiology
Miranda J. Wallace, Sophonie Jean, Meghan A. Wallace, Carey-Ann D. Burnham, Gautam Dantas
Summary: This study demonstrates species-specific patterns in antimicrobial resistance within the Bacteroides fragilis group (BFG) by using comparative genomics, validating new strategies for species-level organism identification and phenotypic resistance prediction in a routine clinical laboratory setting. The research emphasizes the importance of understanding and managing anaerobic infections, as well as the need for further investigations into the molecular basis for species-specific resistance patterns.
Article
Microbiology
Sanjam S. Sawhney, Eric M. Ransom, Meghan A. Wallace, Patrick J. Reich, Gautam Dantas, Carey-Ann D. Burnham
Summary: In this study, researchers discovered a high prevalence of Staphylococcus aureus isolates exhibiting a borderline oxacillin resistance phenotype (BORSA) in their neonatal intensive care unit (NICU). They found that the current MRSA screening methods misclassified BORSA, and identified specific markers that can distinguish BORSA from methicillin-susceptible S. aureus (MSSA). The findings have implications for epidemiological reporting of MRSA rates and can help improve MRSA screening methods.
Article
Microbiology
Allison R. Eberly, Meghan A. Wallace, Samantha Shannon, Angela K. Heitman, Audrey N. Schuetz, Carey-Ann D. Burnham, Sophonie Jean
Summary: The study developed an anaerobic carbapenem inactivation method (Ana-CIM) for detecting carbapenem resistance in Bacteroides fragilis. Clinical validation and reproducibility tests showed that Ana-CIM has good accuracy and repeatability.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Microbiology
Stephanie A. Fritz, Todd N. Wylie, Haley Gula, Patrick G. Hogan, Mary G. Boyle, Carol E. Muenks, Melanie L. Sullivan, Carey-Ann D. Burnham, Kristine M. Wylie
Summary: Decolonization with topical antimicrobials disrupts bacterial communities on the skin, with effects differing between younger and older subjects. The disruption can persist for up to a year post-intervention.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Luke Diorio-Toth, Sidra Irum, Robert F. Potter, Meghan A. Wallace, Muhammad Arslan, Tehmina Munir, Saadia Andleeb, Carey-Ann D. Burnham, Gautam Dantas
Summary: This study used whole-genome sequencing to determine the genotypic mechanisms of beta-lactam resistance in Pseudomonas aeruginosa clinical isolates from three hospitals in Pakistan. The study found that carbapenem resistance was associated with the acquisition of metallo-beta-lactamases or extended-spectrum beta-lactamases and mutations in the porin gene. Furthermore, isolates with multiple resistance mechanisms showed significantly higher levels of imipenem resistance compared to isolates with a single resistance mechanism.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Eric M. Ransom, Sanjam S. Sawhney, Gautam Dantas, Carey-Ann D. Burnham, Skye R. S. Fishbein
Summary: This study reports the draft genome sequence of an unusual Mycobacterium isolate recovered from a patient's arm tissue. The draft genome is 4,025,753-bp in length with a GC content of 71.02%, and analysis of the 16S rRNA gene revealed the closest relative to be Mycobacterium grossiae.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Review
Microbiology
Sophonie Jean, Miranda J. Wallace, Gautam Dantas, Carey-Ann D. Burnham
Summary: Bacteroides fragilis group (BFG) species are common members of the human microbiota, providing benefits to hosts but also causing infections. BFG bacteria are often resistant to commonly used antimicrobials, making treatment challenging. Whole-genome sequencing supports recent proposals for taxonomic reclassifications within the BFG. Species-level reporting and susceptibility testing are important for effective treatment of BFG infections.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Microbiology
Eric M. Ransom, Carey-Ann D. Burnham
Summary: The study shows that including anaerobic bottles in blood cultures can increase the detection rate of bacteria, especially for obligate anaerobes. Additionally, anaerobic bottles are advantageous for some facultative anaerobes.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Microbiology
Bejan Mahmud, Meghan A. Wallace, Kimberly A. Reske, Kelly Alvarado, Carol E. Muenks, David A. Rasmussen, Carey-Ann D. Burnham, Cristina Lanzas, Erik R. Dubberke, Gautam Dantas
Summary: ESBL-producing Escherichia coli is becoming increasingly prevalent, driven by the spread of ESBL-encoding plasmids. This study provides an in-depth genomic investigation of clinical ESBL-like E. coli isolates, revealing a comprehensive map of plasmid sharing across different boundaries. Through sequence-based network analysis, specific plasmid lineages responsible for disseminating major ESBLs have been identified. This work highlights the importance of plasmid-mediated spread in the dissemination of ESBLs and provides valuable insight into the factors underlying the increased prevalence of these genes in clinical settings.
Article
Microbiology
Nicole E. Putnam, Jung-Ho Youn, Meghan A. Wallace, Paul M. Luethy, Carey-Ann D. Burnham, Susan Butler-Wu, John P. Dekker, Anna F. Lau
Summary: The Streptococcus bovis group consists of seven species and subspecies, and definitive identification is important due to their association with various diseases. However, currently used identification platforms have limitations and inconsistencies.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Microbiology
Nicole J. Tarlton, Meghan A. Wallace, Robert F. Potter, Kailun Zhang, Gautam Dantas, Erik R. Dubberke, Carey-Ann D. Burnham, Melanie L. Yarbrough
Summary: In this study, a Morganella morganii isolate MMOR1 was found to be susceptible to third/ fourth-generation cephalosporins and intermediate to meropenem, but positive for NDM and IMP carbapenemases by NG-Test CARBA 5. Further investigation revealed the presence of blaIMP-27, which caused a false-positive NDM result in NG-Test CARBA 5, suggesting the limited stability of this assay in detecting IMP-27.
MICROBIOLOGY SPECTRUM
(2023)
Article
Public, Environmental & Occupational Health
Miguel A. Chavez, Satish Munigala, Carey-Ann D. Burnham, Melanie L. Yarbrough, Crystal Squires, Josephine Fox, Heather Gasama, Kevin Hsueh, David K. Warren
Summary: This study implemented two interventions, kits for sample collection improvement and an electronic order alert for appropriate indications of fungal blood cultures, to enhance utilization and contamination control at the institution. The results showed that the electronic order alert was associated with decreased utilization of fungal blood cultures without a decrease in positivity rate.
INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY
(2023)
Article
Microbiology
Luke Diorio-Toth, Meghan A. A. Wallace, Christopher W. W. Farnsworth, Bin Wang, Danish Gul, Jennie H. H. Kwon, Saadia Andleeb, Carey-Ann D. Burnham, Gautam Dantas
Summary: This study tracks the long-term colonization patterns of intensive care unit (ICU) sinks and water from two hospitals in the USA and Pakistan using whole-genome sequencing. The analysis of 822 bacterial genomes reveals long-term contamination by opportunistic pathogens and transient appearance of other common pathogens. Bacteria recovered from the ICU have more antibiotic resistance genes in their genomes compared to matched community spaces.
Article
Microbiology
Sanjam S. Sawhney, Eric M. Ransom, Meghan A. Wallace, Patrick J. Reich, Gautam Dantas, Carey-Ann D. Burnham
Summary: This study discovered a high prevalence of Staphylococcus aureus isolates with a borderline oxacillin resistance phenotype (BORSA) in the neonatal intensive care unit (NICU). By analyzing mutations and truncations and using a random forest classification model, BORSA and methicillin-susceptible S. aureus were distinguished among clinical isolates collected from two continents. This work highlights the need for improved MRSA screening methods and the presence of the non-mecA-mediated BORSA phenotype.