Journal of Medical Microbiology

Seven drug-resistant Elizabethkingia anophelis isolates were obtained from inpatients in three medical settings in Myanmar between February 2017 and January 2021. All isolates were resistant to β-lactams and colistin. Among these, four isolates were resistant to amikacin with minimum inhibitory concentration (MIC) of ≥64 µg ml-1 . Six of the seven isolates harboured genes encoding intrinsic β-lactamases, including bla B , bla CME and bla GOB , whereas one isolate harboured bla B , bla CME and an incomplete bla GOB gene...

Introduction. Prototheca is an opportunistic pathogen that can infect both humans and animals, of which Prototheca wickerhamii ( P. wickerhamii ) being the most significant pathogenic green algae. Gap statement. The incidence of human diseases caused by Prototheca has been on the rise, yet there is a significant gap in genetic research pertaining to the pathophysiological aspects of these infections. Aim. The aim of this study is to present the whole genome data from the clinical isolate InPu-22_FZ strain and to understand its genomic characteristics through comparative genomic analysis and phylogenetic tree analysis...

Introduction. The Coronavirus Disease 2019 (COVID-19) pandemic has had a significant impact on global healthcare, with high mortality and severe complications remaining a major concern. Understanding the predictors of COVID-19 severity may improve patient management and outcomes. While considerable research has focused on the pathogenesis of the virus and vaccine development, the identification of reliable demographic, clinical and laboratory predictors of severe disease remains critical. Hypothesis. Specific demographic factors, clinical signs and laboratory markers can reliably predict the severity of COVID-19...

Introduction. The human lower gastrointestinal tract microbiome is complex, dynamic and prone to disruption occurring during critical illness. Hypothesis or gap statement . The characteristics of lower gastrointestinal tract microbiome disruption and its association with clinical outcomes in patients with prolonged intensive care stay remain uncertain. Aim . To systematically review studies describing lower gastrointestinal tract molecular sequencing in patients with prolonged intensive care stay and explore associations with clinical outcomes...

Introduction. Efforts to understand the burden of antibiotic use in low- and middle-income countries such as Brazil are essential for developing strategies that are effective and appropriate in the context of endemic multidrug-resistant organisms. Aim. This study aims to determine antimicrobial-prescribing practices among patients hospitalized in intensive care units (ICUs) for adults in Brazil. Methodology. A 1-day point prevalence multicentre survey was conducted in 58 adult ICUs across the five regions of Brazil...

Background. Bacteria significantly influence human health and disease, with bacterial biosynthetic gene clusters (BGCs) being crucial in the microbiome-host and microbe-microbe interactions. Gap statement. Despite extensive research into BGCs within the human gut microbiome, their roles in the oral microbiome are less understood. Aim. This pilot study utilizes high-throughput shotgun metagenomic sequencing to examine the oral microbiota in different niches, particularly focusing on the association of BGCs with periodontitis...

Introduction. The study addresses the challenge of utilizing human gut microbiome data for the early detection of colorectal cancer (CRC). The research emphasizes the potential of using machine learning techniques to analyze complex microbiome datasets, providing a non-invasive approach to identifying CRC-related microbial markers. Hypothesis/Gap Statement. The primary hypothesis is that a robust machine learning-based analysis of 16S rRNA microbiome data can identify specific microbial features that serve as effective biomarkers for CRC detection, overcoming the limitations of classical statistical models in high-dimensional settings...

Introduction. Simethicone is an over-the-counter product that is frequently used by clinicians during endoscopic procedures to reduce foaming and improve visualization. Published studies have found simethicone residue on endoscopes after cleaning and disinfecting the devices as per the manufacturer's instructions. Some literature suggests that simethicone residue may reduce disinfection efficacy and increase the risk of patient infections. Gap Statement. However, there appears to be a lack of direct evidence in the literature to either disprove this or correlate simethicone presence with an increased microbial risk...

Introduction . Adherence is a major virulence trait in Candida glabrata that, in many strains, depends on the EPA (epithelial adhesin) genes, which confer the ability to adhere to epithelial and endothelial cells of the host. The EPA genes are generally found at subtelomeric regions, which makes them subject to subtelomeric silencing. In C. glabrata , subtelomeric silencing depends on different protein complexes, such as silent information regulator and yKu complexes, and other proteins, such as Repressor/activator protein 1 (Rap1) and Abf1...

Introduction. Reports of β-lactamase-producing Haemophilus influenzae are increasing worldwide. Aim . This study aimed to elucidate the molecular characteristics and evolution of β-lactamase-producing H. influenzae . Methodology. A total of 159 clinical isolates were characterized using multi-locus sequence typing. Antimicrobial resistance genes and integrative and conjugative element (ICE) types were identified through PCR and DNA sequencing. The genetic structure of ICE was further investigated using whole-genome sequencing...

Introduction. Rotavirus A is the most common pathogen causing diarrhoea in children less than 5 years, leading to severe complications such as dehydration, electrolyte imbalances, acidosis, myocarditis, convulsions, pneumonia, and other life-threatening conditions. Gap statement. There is an urgent need for a rapid and efficient nucleic acid detection strategy to enable early diagnosis and treatment, preventing rotavirus transmission and associated complications. Aim. This article aimed to develop a nuclear acid sequence-based amplification (NASBA)-Cas12a system for detecting rotavirus A using fluorescence intensity or lateral flow strips...

Introduction. Peri-implantitis is a plaque-associated disease that leads to implant loss and arises from bacterial biofilms on the surface of the implant. Smoking is a risk factor for peri-implantitis and impedes treatment effectiveness. Additionally, aryl hydrocarbon receptor (AHR), IL-6, and IL-22 levels are related to peri-implantitis. Aim. We aimed to investigate the effects of nicotine on inflammatory response, bacterial growth and biofilm formation. Hypothesis/Gap Statement. We hypothesized that nicotine promoted pathogenic bacterial growth and biofilm formation, thereby aggravating inflammation...

Introduction. Sepsis rates are increasing, with Gram-negative organisms representing a large proportion of bloodstream infections. Rapid antibiotic administration, alongside diagnostic investigations, is required for the effective management of these patients. Gap statement. Current diagnostics take ~48 h for a final report; therefore, rapid diagnostics are required. Aim. This study investigated a novel antibiotic sensitivity method, the scattered light integrating collector (SLIC), combined with a rapid identification method using matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) technology to determine if an accurate identification and susceptibility result can be provided within 4 h of a positive blood culture report...

Introduction. Disruptions in gut microbiota, known as dysbiosis, have been increasingly linked to pathogenic infections, with Salmonella Typhimurium being a notable contributor to these disturbances. Hypothesis. We hypothesize that the S . Typhimurium 14028 WT strain induces significant dysbiosis in the rat gut microbiota and that the dam and seqA genes play crucial roles in this process. Aim . In this study, it was aimed at investigating the dysbiotic activity of the S . Typhimurium 14028 WT strain on the rat gut microbiota and the roles of dam and seqA genes on this activity...

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Recently, bacteriophages have been considered alternatives to antibacterial treatments. Infectious diseases continue to plague the world because bacteria can adapt and develop defence mechanisms against antibiotics. The growing incidence of antibiotic-resistant bacterial infections necessitated the development of new techniques for treating bacterial infections worldwide. Clinical trials have shown efficiency against antibiotic-resistant bacteria. However, scientists in future clinical trials should scrutinize phage resistance implications, assess combination strategies with antimicrobial agents and address challenges in phage therapy delivery for effective implementation...

Introduction. Tropheryma whipplei is responsible for the classical Whipple's disease. Recently, a new Tropheryma species was described in a Belgian immunocompromised patient with pleuritis. Gap Statement. There is currently no specific molecular diagnostic test detecting other Tropheryma species than Tropheryma whipplei . Aim. To develop and validate two broad-range pan- Tropheryma genus PCRs detecting both T. whipplei and new Tropheryma species. Methodology. From shotgun sequencing data of the lung tissue biopsy of the Belgian subject, we designed two PCRs targeting the 23S rRNA and rnpB genes...

Introduction. Salmonella enterica is a significant enteric pathogen affecting human and livestock health. Pork production is a common source of Salmonella contamination, with emerging multidrug resistance (MDR) posing a global health threat. Gap statement. Salmonella contamination and antimicrobial resistance (AMR) profiles in the pig production chain are underreported. Aim. To investigate the prevalence of S. enterica in the pig production chain and characterise their AMR profiles. Methodology. We collected 485 samples from pig farms, a standard pig abattoir and retail markets in Patthalung and Songkhla provinces in southern Thailand...

Introduction. Multidrug-resistant infections present a critical public health due to scarce treatment options and high mortality. Ocimum gratissimum L. essential oil (O.geo) is a natural resource rich in eugenol known for its antimicrobial activity. Hypothesis/Gap Statement. O.geo may exert effective antimicrobial activity against polymyxin-resistant Klebsiella pneumoniae and, when combined with Polymyxin B (PMB), may exhibit a synergistic effect, enhancing treatment efficacy and reducing antimicrobial resistance...

Introduction. The European Committee on Antimicrobial Susceptibility Testing (EUCAST) specifies the agar depth (4±0.5 mm) when performing antimicrobial susceptibility testing (AST). Since the infrastructure to produce standardized agar may be lacking in settings with limited resources, we wanted to examine to what extent variation in agar depth affects the inhibition zone diameters of quality control (QC) strains and AST of clinical isolates. Methods. The inhibition zone diameters on Mueller-Hinton II agar with different depths (2-6 mm) were tested for various QC strain-antimicrobial agent combinations using Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853 and Staphylococcus aureus ATCC 29213...