Clinical Microbiology Research Articles

Retrospective analysis of antimicrobial susceptibility profiles of non- diphtheriae Corynebacterium species from a tertiary hospital and reference laboratory, 2012–2023

ABSTRACT A total of 1,925 Corynebacterium isolates were tested for antimicrobial susceptibility at the Mayo Clinic Microbiology laboratory (Rochester, Minnesota) from January 2012 to March 2023, with C. striatum (35.6%) and C. amycolatum (24.4%) identified as the predominant species. Species known to potentially carry diphtheria toxin were excluded. Common sources of isolation included skin and soft tissue (56.8%), bone and/or native joint synovial fluid (14.2%), urine (13.1%), sputum (6.1%), and blood (5.9%). For penicillin, susceptibility decreased from 47.5% (58 of 122) in 2012 to 20.6% (14 of 68) in 2023. Isolates also showed a decrease in susceptibility to erythromycin from 22.4% (26 of 116) in 2012 to 13.2% (9 of 68) in 2023. Susceptibility to trimethoprim-sulfamethoxazole averaged around 50% throughout the period. Notably, linezolid and vancomycin were universally effective in vitro against all species. The highest susceptibility rates among tested oral agents were to linezolid and doxycycline for non- C . striatum species. Daptomycin minimal inhibitory concentrations (MICs) of >256 µg/mL were observed for one C. amycolatum isolate, one C. tuberculostearicum isolate, and for seven C. striatum isolates, all from patients with prior daptomycin exposure. Daptomycin MICs of 2 µg/mL (nonsusceptible) were observed in one C. striatum isolate recovered from a daptomycin-naïve patient and in six C. jeikeium isolates, from both daptomycin-exposed and non-exposed patients. Significant variation in susceptibility profiles across different Corynebacterium species underscores the importance of performing antimicrobial susceptibility testing to guide effective treatment. Moreover, multidrug resistance observed in C. striatum poses substantial therapeutic challenges especially in patients requiring prolonged or chronic antibiotic suppression.

An antimicrobial drug recommender system using MALDI-TOF MS and dual-branch neural networks.

Timely and effective use of antimicrobial drugs can improve patient outcomes, as well as help safeguard against resistance development. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is currently routinely used in clinical diagnostics for rapid species identification. Mining additional data from said spectra in the form of antimicrobial resistance (AMR) profiles is, therefore, highly promising. Such AMR profiles could serve as a drop-in solution for drastically improving treatment efficiency, effectiveness, and costs. This study endeavors to develop the first machine learning models capable of predicting AMR profiles for the whole repertoire of species and drugs encountered in clinical microbiology. The resulting models can be interpreted as drug recommender systems for infectious diseases. We find that our dual-branch method delivers considerably higher performance compared to previous approaches. In addition, experiments show that the models can be efficiently fine-tuned to data from other clinical laboratories. MALDI-TOF-based AMR recommender systems can, hence, greatly extend the value of MALDI-TOF MS for clinical diagnostics. All code supporting this study is distributed on PyPI and is packaged at https://github.com/gdewael/maldi-nn.

Global vaccination against hepatitis E virus: position paper from the ESGVH-ESCMID.

Hepatitis E Virus (HEV) is a significant global health issue, impacting both low- and middle-income countries (LMICs) and industrialized nations. HEV genotypes 1 and 2, primarily transmitted through contaminated water, are endemic in LMICs, while genotypes 3 and 4 are zoonotically transmitted in industrialized regions. Acute HEV infection poses severe risks, particularly to pregnant women and immunocompromised individuals, while chronic HEV infection leads to serious complications in those with pre-existing liver disease and transplant recipients. The development of an HEV vaccine offers new prevention opportunities, though its availability and integration into global immunization programs remain limited. This position paper was developed by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Viral Hepatitis Study Group (ESGVH) through an extensive review of clinical data, safety profiles, efficacy, and immunogenicity of HEV vaccines. The study group focused particularly on high-risk and special populations, synthesizing global health insights and incorporating recommendations from the Strategic Advisory Group of Experts (SAGE) to formulate strategies for wider HEV vaccination use. The position paper evaluates the efficacy and safety of HEV vaccines in both general and special populations. It identifies key barriers to the integration of HEV vaccines into routine immunization programs, including infrastructure limitations, costs, and vaccine accessibility. The paper also proposes strategies to overcome these challenges and improve vaccine distribution. Furthermore, it addresses ways to enhance public awareness and international cooperation to promote HEV vaccination efforts globally. ESGVH-ESCMID recommends HEV vaccination for high-risk groups, including women of childbearing age, patients with chronic liver diseases, and immunosuppressed individuals. Prioritizing investments in vaccine logistics, integrating diagnostics, and educational outreach can enhance uptake.

Rapid Dynamic Surface-Enhanced Raman Spectroscopy Detection of Amoxicillin-Mediated Morphological Changes in a Pathogen for Diagnosis of Clinical Urine Samples.

The swift and stable detection of pathogens in urine samples holds significant implications for the immediate clinical diagnosis and treatment of urinary tract infections (UTIs). In this study, we propose a detection strategy utilizing a hybrid substrate composed of graphene oxide (GO) and silver nanoparticles (Ag NPs) for the detection of pathogens subjected to amoxicillin-mediated (amo-mediated) treatment. This strategy employs dynamic surface-enhanced Raman spectroscopy (D-SERS) for stable and rapid detection, capturing signal variations induced by amo-mediated changes in pathogen morphology. During the 5 min D-SERS detection time window, stable SERS signals were detected for three types of pathogens and four types of pathogens were successfully distinguished using principal component analysis (PCA). In comparison to conventional nanosubstrates, the GO/Ag NP hybrid substrate exhibits outstanding stability and enhancement effects. This approach enables the dual detection of the pathogen cell structure and metabolites, facilitating specific identification of pathogens in the urinary tract, with a detection limit for Escherichia coli reaching 1 × 104 colony-forming units (CFU)/mL, meeting the clinical microbiology laboratory diagnostic standards for UTIs (105 CFU/mL). Testing of 188 clinically collected urine samples using this strategy yielded a sensitivity (SENS) of 86.4% and a specificity (SPC) of 89.7%. This introduces a novel method for diagnosing UTIs, offering broad applications in the field of clinical pathogen detection.

Enhancing clinical microbiology for genomic surveillance of antimicrobial resistance implementation in Africa.

Surveillance is essential in the fight against antimicrobial resistance (AMR), to monitor the extent of resistance, inform prevention, control measures, and evaluate intervention progress. Traditional surveillance methods based on phenotypic antimicrobial susceptibility data offer important but limited insights into resistance mechanisms, transmission networks, and spread patterns of resistant bacterial strains. Fortunately, genomic technologies are increasingly accessible and can overcome these limitations. Genomics has the potential to advance traditional bacteriology in routine diagnosis and surveillance, it often relies on the initial isolation of bacterial strains from clinical specimens using conventional culture methods. Culture-based phenotypic characteristics are essential for making inferences about newly recognized genomic patterns. The Africa CDC Pathogen Genomics Initiative (Africa PGI) aims to enhance disease surveillance and public health partnerships through integrated, cross-continent laboratory networks equipped with the tools, human resource capacity and data infrastructure to fully leverage critical genomic sequencing technologies. For genomic surveillance of AMR, it is essential to optimize routine clinical microbiology laboratory services that are weak in many African countries. In this review, we outline shortcomings in clinical microbiology laboratories across Africa that compromise pathogen genomic epidemiology. We emphasize the necessity of investing in bacteriology and enhancing leadership capacity to fully capitalize on the advantages offered by genomic antimicrobial resistance (AMR) surveillance.

Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections.

Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) is an agnostic method for broad-based diagnosis of central nervous system (CNS) infections. Here we analyzed the 7-year performance of clinical CSF mNGS testing of 4,828 samples from June 2016 to April 2023 performed by the University of California, San Francisco (UCSF) clinical microbiology laboratory. Overall, mNGS testing detected 797 organisms from 697 (14.4%) of 4,828 samples, consisting of 363 (45.5%) DNA viruses, 211 (26.4%) RNA viruses, 132 (16.6%) bacteria, 68 (8.5%) fungi and 23 (2.9%) parasites. We also extracted clinical and laboratory metadata from a subset of the samples (n = 1,164) from 1,053 UCSF patients. Among the 220 infectious diagnoses in this subset, 48 (21.8%) were identified by mNGS alone. The sensitivity, specificity and accuracy of mNGS testing for CNS infections were 63.1%, 99.6% and 92.9%, respectively. mNGS testing exhibited higher sensitivity (63.1%) than indirect serologic testing (28.8%) and direct detection testing from both CSF (45.9%) and non-CSF (15.0%) samples (P < 0.001 for all three comparisons). When only considering diagnoses made by CSF direct detection testing, the sensitivity of mNGS testing increased to 86%. These results justify the routine use of diagnostic mNGS testing for hospitalized patients with suspected CNS infection.

Survey of clinical microbiology and infectious disease testing capabilities among institutions in Africa.

Inadequate laboratory infrastructure and testing capabilities are a major impediment to addressing the infectious disease burden in Africa. Therefore, the aims of this study were to characterize the clinical microbiology/infectious disease laboratory capabilities among countries in Africa. A survey to assess the microbiological testing capabilities at hospitals, government laboratories, and free-standing public and private laboratories in African countries was developed by subject matter experts. Questions included institutional demographics and microbiology services in the broad categories of bacteriology, virology, mycology, parasitology, and rapid diagnostics/point-of-care testing. The survey was distributed using the American Society of Clinical Pathology email listserv between June and August 2022. In total, 131 unique institutions in 28 countries endorsed at least 1 type of microbiology service, with parasitology (80.9%, 106/131) and bacteriology (77.9%, 102/131) being most common, while mycology (45.0%, 59/131) and virology (45.8%, 60/131) laboratories were less prevalent. The most frequently performed bacteriology test was bacterial identification (90.2%, 92/102), followed by aerobic bacterial cultures and antimicrobial susceptibility testing (both 89.2%, 91/102). Among all clinical microbiology/infectious disease laboratories, the most commonly tested agents were HIV (90.8%, 119/131), Treponema pallidum (78.6%, 103/131), Plasmodium falciparum (76.3%, 100/131), Mycobacterium tuberculosis (76.3%, 100/131), and hepatitis C virus (74.8%, 98/131). These findings provide contemporary data regarding the availability of critical infectious disease testing capabilities among institutions in Africa. These results and future additional studies will be crucial for understanding where strategic investment in the laboratory and public health infrastructure is warranted.

Antibiotic susceptibility testing using minimum inhibitory concentration (MIC) assays

Antimicrobial resistance is due to genetic changes that allow bacteria to evade antibiotic treatment. Antimicrobial susceptibility testing is critical for the detection of antibiotic-resistant strains, the selection of effective therapeutic strategies against bacterial infections, and the evaluation of the efficacy of novel antimicrobials. Among the variety of clinical microbiology methods used for antibiotic susceptibility testing, minimum inhibitory concentration (MIC) assays have become the gold standard in clinical practice. MIC assays determine the lowest concentration of an antimicrobial agent that is required to inhibit visible bacterial growth in vitro. Here, we outline MIC assay protocols, in strict accordance with European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines that aim to assess the susceptibility of non-fastidious organisms to antimicrobial agents. The protocols described in this methods paper are intended to aid the performance of reliable and informative MIC assays for research purposes that are in line with clinical microbiology practices.

EXPRESS: Demographic, Clinical and Laboratory Characteristics of Extrapulmonary Tuberculosis: Eight-year Results of a Multicentre Retrospective Study in Turkey.

Extrapulmonary tuberculosis (EPTB) is an important public health problem due to its diverse clinical presentations, diagnostic complexities and significant impact on patient outcomes and public health. Our study aimed to understand the sociodemographic, clinical and laboratory characteristics as well as diagnostic and treatment modalities of adult patients with EPTB. This is a multicentric retrospective study that covers patients with EPTB cases followed up from January 2015 to December 2022 among TB dispensaries and Infectious Diseases and Clinical Microbiology clinics of 15 hospitals located in various regions of Turkey. The study included 64.6% women with a mean age of 44 years and a mortality rate of 3.5% within one year of diagnosis. Initial constitutional symptoms were predominantly fatigue (57%), anorexia (53.7%). The most commonly affected sites were the lymph nodes (49.1%) and pleura (9.7%). The lumbar region was particularly involved in cases with spinal TB. Diagnostic findings included acid-fast bacilli positivity in 27.5% of cases, TB PCR positivity in 41%, elevated adenosine deaminase levels in 91.2% (especially in pleural and peritoneal fluids) and mycobacterial culture positivity in 40.9%. Pathology slides showed granulomatous inflammation in 97.7%. Increased C-reactive protein levels correlated with the number of organs affected. Anti-TB treatment-related hepatotoxicity was detected in 8.9% of patients. In this study, it is important to note that the lumbar region is predominantly affected with involment in spinal region. C-reactive protein level was consistent with the number of organ involvements was one of the most critical results of this study.

Gauging Medical Students' Interests in Infectious Diseases.

Infectious diseases is a crucial specialty in medicine, yet applications for fellowship have declined even as the United States faces an imminent shortage of infectious disease physicians. Career interests often develop in medical school, but little is known about which interests and experiences are associated with interest in ID. Evaluate interest in ID among medical students and identify factors associated with interest and disinterest in ID careers. We developed a 26-question survey to gauge interest in infectious diseases (ID). All 16 medical schools in Texas were contacted and invited to participate. A total of 262 students across 9 medical school campuses completed the survey. Those interested in ID as a career had a significantly higher interest in public health (p<0.0001) and global (p<0.0003) health. The presence of an ID campus interest group (p<0.0015) and direct experience with the ID profession (p<0.0001) were also associated with interest. The most common reasons for lack of interest were lack of interest in pursuing internal medicine or pediatric residency, lack of compensation, and lack of procedures. Those interested in ID expressed interest in a wide variety of career pathways within ID, the most common being general inpatient and outpatient ID, as well as medical microbiology and global health/tropical medicine/travel medicine. Based on this survey, recruitment efforts for new ID fellows might include focusing on students with interests in public and global health, as well as increasing direct exposure to ID at the medical school level.

A Comparative Study of the Rate of Helicobacter pylori infection Using Three Diagnostic Techniques among Patients in Rivers State

Background: Approximately 89% of gastric cancers are attributable to H. pylori infection, however, only 1 in 5 patients survive longer than 5 years after diagnosis. Evidence has shown that screening and eradication of H. pylori in young adults would be cost-effective and could prevent 1 gastric cancer in every 4 to 6 cases. Diagnostic tests used to detect Helicobacter pylori are either invasive or noninvasive methods. These tests have varying sensitivity and specificity, having about 90% accuracy in the diagnosis of H. pylori infection in clinical practice. Aim: This study aims at detecting Helicobacter pylori using antibody-antigen, stool antigen and polymerase chain reaction (PCR) and to compare the infection rate among the different diagnostic techniques. Methodology: This was a cross-sectional study. The participants included attendants to tertiary and private hospitals in Port Harcourt metropolis for medical treatment. Blood and stool samples were collected from one hundred and eighty (180) subjects aged 1 to 60 years and above. Ethical approval for the study was obtained from the Rivers State University Teaching Hospital Ethics Committee. Convenience sampling technique was deployed. Samples were collected from subjects who consented to the study. All samples collected were analyzed in Medical Microbiology Laboratory, Rivers State Teaching Hospital and subsequently, molecular analysis was carried out. Results: The blood antibodies test (serology) method shows a greater number of positive cases (43.9%) than stool antigen method (8.3%). Also, out of the 75% stool antigen positive samples, subjected to more specific PCR, only 25% were positive. There was a significant difference (p-value of &lt;0.001) in sensitivity between antigen and serology, there was also a significant difference (p-value of &lt;0.025) between antigen and PCR result outcomes. Conclusion: The study has shown that there is a notable variation in the diagnosis of H pylori among the laboratory techniques used.

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

Myroides is a bacterial genus of opportunistic bacteria responsible for diverse infections including in the skin and soft tissues, urinary tract, cardiovascular system, and bacteremia, although the incidence of its reported infections is low, it is increasing, likely due the use of better bacterial identification methods, but also perhaps due an increase in its prevalence. In addition, their pathogenic role is limited in terms of reporting their microbial physiology, so the present work provides information in this regard in addition to the information that is available in the international literature. To describe the microbiological and genetic characteristics of seven different Myroides spp. clinical strains and comment on their phylum, pathogenic and resistance characteristics. Seven Myroides spp., strains associated with infections were included from 1/January/2012 to 1/January/20 and identified by miniaturized biochemistry and MALDI-ToF. Susceptibility tests were performed according to CLSI recommendations by broth microdilution. Whole genome sequencing was performed for each strain and bioinformatics analysis were performed. Strains were identified at genus level by two methodologies. Our results revealed that likely four strains belong to the species Myroides odoratimimus, while the other two may be undescribed ones. Remarkably, all isolates harbored several genes encoding antibiotic resistance determinants for ß-lactams, aminoglycosides and glycopeptides and in concordance, presented high levels of resistance, against these antibiotics (AK and GN both 100%, ATM, CAZ and FEP 100%, e.g.); moreover, the presences of carbapenemases were evidenced by meropenem (mCIM) and imipenem (CARBA NP) degrading activity in six isolates and two strains possessed plasmids harboring mainly ribosomal RNA genes, tRNAs and genes encoding proteins with unknown functions. Our study increases the knowledge about the biology of this understudied genus and highlights the potential of Myroides to emerge as a broader cause of recalcitrant opportunistic infections.

Current management of Staphylococcus aureus bacteremia in a Japanese university hospital.

Consultation with infectious disease specialists is associated with reduced patient mortality in the care of patients with Staphylococcus aureus bacteremia (SAB) through appropriate management of complications including infective endocarditis. This study aimed to determine the rates of confirmation of a negative blood culture, implementation of echocardiography, and administration of appropriate antibiotics in patients with SAB at a university hospital in Japan that provides general internal medicine and not an infectious disease consultation service. We conducted a retrospective cohort study at Dokkyo Medical University Hospital in Japan. Patients eligible for inclusion in the study were ≥20 years of age with ≥1 positive blood culture for S. aureus identified in a clinical microbiology laboratory. The primary outcome was the proportion of patients with confirmation of a negative blood culture, implementation of echocardiography, and administration of appropriate antimicrobial agents. A total of 109 patients with SAB were included in the analysis. Follow-up blood cultures were collected in 91 patients and negative results were documented in 88 patients. Follow-up blood culture collection was performed within 4 days of the initial blood culture collection in 49 patients. Echocardiography was performed appropriately in 40 patients. Appropriate antibiotic therapy was administered in 36 patients. Quality-of-care indicators were more commonly implemented in patients with SAB who received general internal medicine consultation than in those who did not.

An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable for Genomic Surveillance Within Clinical Diagnostic Settings.

Chronic Hepatitis B Virus (HBV) infection remains a significant public health concern, particularly in Africa, where the burden is substantial. HBV is an enveloped virus, classified into ten phylogenetically distinct genotypes (A-J). Tests to determine HBV genotypes are based on full-genome sequencing or reverse hybridization. In practice, both approaches have limitations. Whereas diagnostic sequencing, generally using the Sanger approach, tends to focus only on the S-gene and yields little or no information on intra-patient HBV genetic diversity, reverse hybridization detects only known genotype-specific mutations. To resolve these limitations, we developed an Oxford Nanopore Technology (ONT)-based HBV diagnostic sequencing protocol suitable for clinical virology that yields both complete genome sequences and extensive intra-patient HBV diversity data. Specifically, the protocol involves tiling-based PCR amplification of HBV sequences, library preparation using the ONT Rapid Barcoding Kit (Oxford nanopore Technologies, Oxford, OX4 4DQ, UK), ONT GridION sequencing, genotyping using genome detective software v1.132/1.133, a recombination analysis using jpHMM (26 October 2011 version) and RDP5.61 software, and drug resistance profiling using Geno2pheno v2.0 software. We prove the utility of our protocol by efficiently generating and characterizing high-quality near full-length HBV genomes from 148 residual diagnostic samples from HBV-infected patients in the Western Cape province of South Africa, providing valuable insights into the genetic diversity and epidemiology of HBV in this region of the world.

Rapid and accurate bacteria identification through deep-learning-based two-dimensional Raman spectroscopy

Surface-enhanced Raman spectroscopy (SERS) offers a distinctive vibrational fingerprint of the molecules and has led to widespread applications in medical diagnosis, biochemistry, and virology. With the rapid development of artificial intelligence (AI) technology, AI-enabled Raman spectroscopic techniques, as a promising avenue for biosensing applications, have significantly boosted bacteria identification. By converting spectra into images, the dataset is enriched with more detailed information, allowing AI to identify bacterial isolates with enhanced precision. However, previous studies usually suffer from a trade-off between high-resolution spectrograms for high-accuracy identification and short training time for data processing. Here, we present an efficient bacteria identification strategy that combines deep learning models with a spectrogram encoding algorithm based on wavelet packet transform and Gramian angular field techniques. In contrast to the direct analysis of raw Raman spectra, our approach utilizes wavelet packet transform techniques to compress the spectra by a factor of 1/15, while concurrently maintaining state-of-the-art accuracy by amplifying the subtle differences via Gramian angular field techniques. The results demonstrate that our approach can achieve a 99.64 % and a 90.55 % identification accuracy for two types of bacterial isolates and thirty types of bacterial isolates, respectively, while a 90 % reduction in training time compared to the conventional methods. To verify the model's stability, Gaussian noises were superimposed on the testing dataset, showing a specific generalization ability and superior performance. This algorithm has the potential for integration into on-site testing protocols and is readily updatable with new bacterial isolates. This study provides profound insights and contributes to the current understanding of spectroscopy, paving the way for accurate and rapid bacteria identification in diverse applications of environment monitoring, food safety, microbiology, and public health.

Real-time plasmid transmission detection pipeline.

Plasmid-mediated spread of antimicrobial resistance is a major challenge for clinical microbiology, and monitoring of potential plasmid transmissions is essential to combat further dissemination. Whole-genome sequencing is often used to surveil nosocomial transmissions but usually limited to the detection of clonal transmissions (based on chromosomal markers). Recent advances in long-read sequencing technologies enable full reconstruction of plasmids and the detection of very similar plasmids, but so far, easy-to-use bioinformatic tools for this purpose have been missing. Here, we present an evaluation of an innovative real-time plasmid transmission detection pipeline. It is integrated into the GUI-based SeqSphere+ software, which already offers core-genome multi-locus sequence typing-based pathogen outbreak detection. It requires very limited bioinformatics knowledge, and its database, automated analyses, and alert system make it well suited for prospective clinical application.

A New Easy-to-Perform Flow Cytometry Assay for Determining Bacterial- and Viral-Infection-Induced Polymorphonuclear Neutrophil and Monocyte Membrane Marker Modulation in Febrile Patients.

We developed a flow cytometry (FC) assay enabling the rapid and accurate identification of bacterial and viral infections using whole blood samples. The streamlined flow cytometry assay is designed to be user-friendly, making it accessible even for operators with limited experience in FC techniques. The key components of the assay focus on the expression levels of specific surface markers-CD64 on polymorphonuclear neutrophils (PMN) as a marker for bacterial infection, and CD169 on monocytes (MO) for viral infection. The strong performance indicated by an area under the receiver operating characteristic (ROC) curve of 0.94 for both PMN CD64 positive predictive value (PPV) 97.96% and negative predictive value (NPV) 76.67%, and MO CD169 PPV 82.6% and NPV 86.9%, highlight the assay's robustness in differentiating between bacterial and viral infections accurately. The FC assay includes the assessment of immune system status through HLA-DR and IL-1R2 modulation in MO, providing a useful insight into the patients' immune response. The significant increase in the frequency of MO exhibiting reduced HLA-DR expression and elevated IL-1R2 levels in infected patients (compared to healthy controls) underscores the potential of these markers as indicators of infection severity. Although the overall correlation between HLA-DR and IL-1R2 expression levels was not significant across all patients, there was a trend in patients with more severe disease suggesting that these markers may have the potential to assist in stratifying patient risk. The present FC assay has the potential to become routine in the clinical microbiology laboratory community and to be helpful in guiding clinical decision making.

Clinical Practice: Estimating the Breakpoints for EUCAST Fast Antimicrobial Susceptibility Testing Using Flagged BacT/Alert Blood Culture Bottles

&amp;lt;i&amp;gt;Introduction&amp;lt;/i&amp;gt;: The escalating prevalence of multidrug resistance is a global threat to human health particularly in critically ill patients with bloodstream infections (BSIs). Delay in the administration of the appropriate antimicrobial treatment is associated with higher mortality rates and adverse consequences. This study attempted to estimate the rapid antimicrobial susceptibility testing (RAST) breakpoints directly from flagged BacT/Alert blood culture bottles in clinical practice. &amp;lt;i&amp;gt;Material &amp; Methods&amp;lt;/i&amp;gt;: A descriptive, cross-sectional study conducted at a tertiary care hospital in Delhi over a period of two months. The RAST was performed directly from the clinical samples for blood cultures received in our laboratory in parallel with the routine antimicrobial testing as per standard CLSI guidelines. Blood cultures were routinely incubated in BacT/Alert 3D. The inhibition zones were read at 4, 6, 8 and 16-20 hour of incubation as per European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. The identification of the isolates was confirmed by Vitek-2 compact system. &amp;lt;i&amp;gt;Results&amp;lt;/i&amp;gt;: In our study, the area of technical uncertainty (ATU) percentage was initially high at 4 hours but decreased significantly in later incubation periods. At 4 hours, none of the &amp;lt;i&amp;gt;S. aureus&amp;lt;/i&amp;gt; isolates showed &amp;gt;90% categorical agreement (CA) for any antimicrobial tested. However, clindamycin achieved the highest CA (100%) at 6 hours and 90% thereafter, with no very major errors (VME) or major error (ME). Cefoxitin required 8 hours to reach &amp;gt;90% CA, with no VME observed at any time point, but up to 75% ME at 8 hours. At 4 hours, most antimicrobials had high (&amp;gt;1.5%) rates of VME among &amp;lt;i&amp;gt;Enterobacteriales&amp;lt;/i&amp;gt;. By 6 hours, only Meropenem and Gentamicin had &amp;gt;90% CA, with no VME observed for other antibiotics. &amp;lt;i&amp;gt;Conclusion&amp;lt;/i&amp;gt;: The RAST method is relatively easy to implement in clinical microbiology labs, offering cost-effectiveness, simplicity, and rapid results, especially in resource-limited settings. However, reporting RAST results can be complex due to potential challenges with CA, VME, and ME, particularly in the initial hours of incubation and within the ATU.

Cefoxitin and Oxacillin Resistance Conundrums

Recently, mecA-negative Staphylococcus aureus strains with decreased susceptibility to oxacillin and cefoxitin have been sporadically reported worldwide. They are called as borderline oxacillin resistant Staphylococcus aureus (BORSA). Almost, more than 30% of such strains are often misinterpreted and reported as MRSA (methicillin resistant Staphylococcus aureus) due to the hyperproduction of beta-lactamase enzyme and other reasons which results in invitro reduced susceptibility to oxacillin as well as cefoxitin. Similar phenomenon is quite common in other staphylococci, micrococci and macrococci. In order to identify beta-lactamase hyperproducing staphylococci and other gram-positive cocci and to avoid false reporting as methicillin resistant, a one-year prospective study was conducted in Deccan college of medical sciences, Hyderabad, Telangana state, India in 2023. During one year duration, 5630 inpatient (IP) and 823 outpatient (OPD) samples accounting for total 6453 cultures were received in the microbiology laboratory. Out of this,100 cultures of different samples showing pure growth of gram-positive cocci suggestive of staphylococci, micrococci and other Gram-positive cocci were included in the present study and tested against different antibiotics panel as per CLSI guidelines (Clinical and Laboratory Standards Institute.) Inclusion of amoxiclav disc to the antibiotics test panel as per recommendation by the special phenotypic methods for the detection of antibacterial resistance in the manual of clinical microbiology was helpful to detect the beta-lactamase hyperproducers (BHP) and helped to report correct identification of the organisms and curtailed the mismanagement of more than 95% of the patients. Therefore, I do recommend to differentiate borderline from true methicillin resistant strains to streamline the antibiotic therapy and hence further avoidance of selection of the resistant strains.

Epidemiology and genetic diversity of human respiratory syncytial virus in Belgium between 2011 and 2019

BackgroundHuman respiratory syncytial virus (HRSV) is worldwide one of the leading causes of acute respiratory tract infections in young children and the elderly population. Two distinct subtypes of HRSV (A and B) and a multitude of genotypes have been described. The laboratory of Clinical and Epidemiological Virology (KU Leuven/University Hospitals Leuven) has a long-standing history of HRSV surveillance in Belgium.MethodsIn this study, the seasonal circulation of HRSV in Belgium was monitored during 8 consecutive seasons prior to the SARS-CoV-2 pandemic (2011–2012 until 2018–2019). By use of a multiplex quantitative real time PCR panel, 27,386 respiratory samples were tested for HRSV. Further subtyping and sequencing of the HRSV positive samples was performed by PCR and Sanger sequencing. The prevalence and positivity rate were estimated in 4 distinct age groups and the circulating strains of each subtype were situated in a global context and in reference to the described genotypes in literature.ResultsHRSV circulated in Belgium in a yearly re-occurring pattern during the winter months and both HRSV subtypes co-circulated simultaneously. All HRSV-B strains contained the 60 nt duplication in the HVR2 region of the G gene. Strains of subtype HRSV-A with a 72 nt duplication in the HVR2 region were first observed during the 2011–2012 season and replaced all other circulating strains from 2014 to 2015 onwards.