Journal of medical microbiology最新文献

{"title":"The effect of daily usage of Listerine Cool Mint mouthwash on the oropharyngeal microbiome: a substudy of the PReGo trial.","authors":"J G E Laumen, C Van Dijck, S S Manoharan-Basil, T de Block, S Abdellati, B B Xavier, S Malhotra-Kumar, C Kenyon","doi":"10.1099/jmm.0.001830","DOIUrl":"10.1099/jmm.0.001830","url":null,"abstract":"<p><p><b>Introduction.</b> Listerine^Ò is a bactericidal mouthwash widely used to prevent oral health problems such as dental plaque and gingivitis. However, whether it promotes or undermines a healthy oral microbiome is unclear.<b>Hypothesis/Gap Statement.</b> We hypothesized that the daily use of Listerine Cool Mint would have a significant impact on the oropharyngeal microbiome.<b>Aim.</b> We aimed to assess if daily usage of Listerine Cool Mint influenced the composition of the pharyngeal microbiome.<b>Methodology.</b> The current microbiome substudy is part of the Preventing Resistance in Gonorrhoea trial. This was a double-blind single-centre, crossover, randomized controlled trial of antibacterial versus placebo mouthwash to reduce the incidence of gonorrhoea/chlamydia/syphilis in men who have sex with men (MSM) taking HIV pre-exposure prophylaxis (PrEP). Fifty-nine MSM taking HIV PrEP were enrolled. In this crossover trial, participants received 3 months of daily Listerine followed by 3 months of placebo mouthwash or vice versa. Oropharyngeal swabs were taken at baseline and after 3 months use of each mouthwash. DNA was extracted for shotgun metagenomic sequencing (Illumina Inc.). Non-host reads were taxonomically classified with MiniKraken and Bracken. The alpha and beta diversity indices were compared between baseline and after each mouthwash use. Differentially abundant bacterial taxa were identified using ANOVA-like differential expression analysis.<b>Results.</b> <i>Streptococcus</i> was the most abundant genus in most samples (<i>n</i> = 103, 61.7 %) with a median relative abundance of 31.5% (IQR 20.6-44.8), followed by <i>Prevotella</i> [13.5% (IQR 4.8-22.6)] and <i>Veillonella</i> [10.0% (IQR 4.0-16.8)]. Compared to baseline, the composition of the oral microbiome at the genus level (beta diversity) was significantly different after 3 months of Listerine (<i>P</i> = 0.006, pseudo-<i>F</i> = 2.29) or placebo (<i>P</i> = 0.003, pseudo-<i>F</i> = 2.49, permutational multivariate analysis of variance) use. <i>Fusobacterium nucleatum</i> and <i>Streptococcus anginosus</i> were significantly more abundant after Listerine use compared to baseline.<b>Conclusion.</b> Listerine use was associated with an increased abundance of common oral opportunistic bacteria previously reported to be enriched in periodontal diseases, oesophageal and colorectal cancer, and systemic diseases. These findings suggest that the regular use of Listerine mouthwash should be carefully considered.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141249157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ciprofloxacin prophylaxis during haematopoietic cell transplantation: a role for use in patients with germ cell tumours?","authors":"Konstantinos Kavallieros, Ioannis Baltas, Giannis Konstantinou, Eirini Koutoumanou, Malick M Gibani, Mark Gilchrist, Frances Davies, Jiri Pavlu","doi":"10.1099/jmm.0.001847","DOIUrl":"10.1099/jmm.0.001847","url":null,"abstract":"<p><p><b>Introduction.</b> Fluoroquinolone prophylaxis during haematopoietic cell transplantation (HCT) can lead to antimicrobial resistance (AMR). Identifying the groups of patients that have the highest likelihood of benefiting from prophylactic antimicrobials is important for antimicrobial stewardship (AMS).<b>Hypothesis.</b> We aimed to identify groups of HCT recipients that have the highest likelihood of benefiting from prophylactic fluroquinolones.<b>Methods.</b> All admissions for HCT in a tertiary centre between January 2020 and December 2022 (<i>N</i> = 400) were retrospectively studied. Allogeneic HCT (allo-HCT) recipients had prophylaxis with ciprofloxacin during the chemotherapy-induced neutropenia, while autologous HCT (auto-HCT) recipients did not. Bacteraemias were recorded when non-contaminant bacterial pathogens were isolated in blood cultures.<b>Results.</b> Allo-HCT was performed for 43.3 % (173/400) of patients and auto-HCT was performed for 56.7 % (227/400). A bacteraemia was documented in 28.3 % (113/400) of cases. Allo-HCT recipients were more likely to have a Gram-positive bacteraemia (20.8%, 36/173, vs 10.1%, 23/227, <i>P</i> = 0.03), while a difference was not observed for Gram-negative bacteraemias (18.5%, 32/173 vs 18.1%, 41/227, <i>P</i> = 0.91). Among auto-HCT recipients not receiving ciprofloxacin prophylaxis, patients with germ cell tumours had the highest probability (<i>P</i> for trend 0.09) of recording any bacteraemia (43.5%, 10/23) followed by patients with lymphomas (32.5%, 13/40), other auto-HCT indications (22.2%, 2/9), multiple myeloma (22.1%, 29/131) and multiple sclerosis (12.5%, 3/24). The higher number of bacteraemias in patients with germ cell tumours was primarily driven by Gram-negative pathogens.<b>Conclusions.</b> Ciprofloxacin prophylaxis was associated with a reduced incidence of Gram-negative bacteraemias in allo-HCT recipients. Auto-HCT recipients due to germ cell tumours, not receiving ciprofloxacin prophylaxis, recorded the highest incidence of bacteraemias and represent a possible target group for this intervention.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11316519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141452508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antifungal activity of human antimicrobial peptides targeting apoptosis in <i>Candida auris</i>.","authors":"Siham Shaban, Mrudula Patel, Aijaz Ahmad","doi":"10.1099/jmm.0.001835","DOIUrl":"https://doi.org/10.1099/jmm.0.001835","url":null,"abstract":"<p><p><b>Introduction.</b> Innovative antifungal therapies are of crucial importance to combat the potentially life-threatening infections linked to the multidrug-resistant fungal pathogen <i>Candida auris</i>. Induction of regulated cell death, apoptosis, could provide an outline for future therapeutics. Human antimicrobial peptides (AMPs), well-known antifungal compounds, have shown the ability to induce apoptosis in pathogenic fungi.<b>Hypothesis/Gap Statement</b> <b>.</b> Although it is known that AMPs possess antifungal activity against <i>C. auris</i>, their ability to induce apoptosis requires further investigations.<b>Aim.</b> This study evaluated the effects of AMPs on the induction of apoptosis in <i>C. auris</i>.<b>Methods.</b> Human neutrophil peptide-1 (HNP-1), human β-Defensins-3 (hBD-3) and human salivary histatin 5 (His 5) were assessed against two clinical <i>C. auris</i> isolates. Apoptosis hallmarks were examined using FITC-Annexin V/PI double labelling assay and terminal deoxynucleotidyl transferase deoxynucleotidyl transferase nick-end labelling (TUNEL) to detect phosphatidylserine externalization and DNA fragmentation, respectively. Then, several intracellular triggers were studied using JC-10 staining, spectrophotometric assay and 2',7'-dichlorofluorescin diacetate staining to measure the mitochondrial membrane potential, cytochrome-c release and reactive oxygen species (ROS) production, respectively.<b>Results and conclusion.</b> FITC-Annexin V/PI staining and TUNEL analysis revealed that exposure of <i>C. auris</i> cells to HNP-1 and hBD-3 triggered both early and late apoptosis, while His 5 caused significant necrosis. Furthermore, HNP-1 and hBD-3 induced significant mitochondrial membrane depolarization, which resulted in substantial cytochrome c release. In contrast to His 5, which showed minimal mitochondrial depolarization and no cytochrome c release. At last, all peptides significantly increased ROS production, which is related to both types of cell death. Therefore, these peptides represent promising and effective antifungal agents for treating invasive infections caused by multidrug-resistant <i>C. auris.</i></p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140924052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deletion of <i>codY</i> impairs <i>Staphylococcus epidermidis</i> biofilm formation, generation of viable but non-culturable cells and stimulates cytokine production in human macrophages.","authors":"Nathalie Lopes, Renato B Pereira, Alexandra Correia, Manuel Vilanova, Nuno Cerca, Angela França","doi":"10.1099/jmm.0.001837","DOIUrl":"10.1099/jmm.0.001837","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Staphylococcus epidermidis</i> biofilms are one of the major causes of bloodstream infections related to the use of medical devices. The diagnosis of these infections is challenging, delaying their treatment and resulting in increased morbidity and mortality rates. As such, it is urgent to characterize the mechanisms employed by this bacterium to endure antibiotic treatments and the response of the host immune system, to develop more effective therapeutic strategies. In several bacterial species, the gene <i>codY</i> was shown to encode a protein that regulates the expression of genes involved in biofilm formation and immune evasion. Additionally, in a previous study, our group generated evidence indicating that <i>codY</i> is involved in the emergence of viable but non-culturable (VBNC) cells in <i>S. epidermidis</i>.<b>Gap statement/Hypothesis.</b> As such, we hypothesized that the gene codY has have an important role in this bacterium virulence.<b>Aim.</b> This study aimed to assess, for the first time, the impact of the deletion of the gene <i>codY</i> in <i>S. epidermidis</i> virulence, namely, in antibiotic susceptibility, biofilm formation, VBNC state emergence and <i>in vitro</i> host immune system response.<b>Methodology.</b> Using an allelic replacement strategy, we constructed and then characterized an <i>S. epidermidis</i> strain lacking <i>codY,</i> in regards to biofilm and VBNC cell formation, susceptibility to antibiotics as well as their role in the interaction with human blood and plasma. Additionally, we investigate whether the <i>codY</i> gene can impact the activation of innate immune cells by evaluating the production of both pro- and anti-inflammatory cytokines by THP-1 macrophages.<b>Results.</b> We demonstrated that the deletion of the gene <i>codY</i> resulted in biofilms with less c.f.u. counts and fewer VBNC cells. Furthermore, we show that although WT and mutant cells were similarly internalized <i>in vitro</i> by human macrophages, a stronger cytokine response was elicited by the mutant in a toll-like receptor 4-dependent manner.<b>Conclusion.</b> Our results indicate that <i>codY</i> contributes to <i>S. epidermidis</i> virulence, which in turn may have an impact on our ability to manage the biofilm-associated infections caused by this bacterium.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140924015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The laboratory investigation, management, and infection prevention and control of <i>Candida auris</i>: a narrative review to inform the 2024 national guidance update in England.","authors":"Christopher R Jones, Claire Neill, Andrew M Borman, Emma L Budd, Martina Cummins, Carole Fry, Rebecca L Guy, Katie Jeffery, Elizabeth M Johnson, Rohini Manuel, Mariyam Mirfenderesky, Ginny Moore, Bharat Patel, Silke Schelenz, Karren Staniforth, Surabhi K Taori, Colin S Brown","doi":"10.1099/jmm.0.001820","DOIUrl":"10.1099/jmm.0.001820","url":null,"abstract":"<p><p>The emergent fungal pathogen <i>Candida auris</i> is increasingly recognised as an important cause of healthcare-associated infections globally. It is highly transmissible, adaptable, and persistent, resulting in an organism with significant outbreak potential that risks devastating consequences. Progress in the ability to identify <i>C. auris</i> in clinical specimens is encouraging, but laboratory diagnostic capacity and surveillance systems are lacking in many countries. Intrinsic resistance to commonly used antifungals, combined with the ability to rapidly acquire resistance to therapy, substantially restricts treatment options and novel agents are desperately needed. Despite this, outbreaks can be interrupted, and mortality avoided or minimised, through the application of rigorous infection prevention and control measures with an increasing evidence base. This review provides an update on epidemiology, the impact of the COVID-19 pandemic, risk factors, identification and typing, resistance profiles, treatment, detection of colonisation, and infection prevention and control measures for <i>C. auris</i>. This review has informed a planned 2024 update to the United Kingdom Health Security Agency (UKHSA) guidance on the laboratory investigation, management, and infection prevention and control of <i>Candida auris</i>. A multidisciplinary response is needed to control <i>C. auris</i> transmission in a healthcare setting and should emphasise outbreak preparedness and response, rapid contact tracing and isolation or cohorting of patients and staff, strict hand hygiene and other infection prevention and control measures, dedicated or single-use equipment, appropriate disinfection, and effective communication concerning patient transfers and discharge.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141070568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diagnostic stewardship in infectious diseases: a scoping review.","authors":"Robert Shorten, Kate Pickering, Callum Goolden, Catherine Harris, Andrew Clegg, Hill J","doi":"10.1099/jmm.0.001831","DOIUrl":"10.1099/jmm.0.001831","url":null,"abstract":"<p><p><b>Introduction.</b> The term 'diagnostic stewardship' is relatively new, with a recent surge in its use within the literature. Despite its increasing popularity, a precise definition remains elusive. Various attempts have been made to define it, with some viewing it as an integral part of antimicrobial stewardship. The World Health Organization offers a broad definition, emphasizing the importance of timely, accurate diagnostics. However, inconsistencies in the use of this term still persist, necessitating further clarification.<b>Gap Statement.</b> There are currently inconsistencies in the definition of diagnostic stewardship used within the academic literature.<b>Aim.</b> This scoping review aims to categorize the use of diagnostic stewardship approaches and define this approach by identifying common characteristics and factors of its use within the literature.<b>Methodology.</b> This scoping review undertook a multi-database search from date of inception until October 2022. Any observational or experimental study where the authors define the intervention to be diagnostic stewardship from any clinical area was included. Screening of all papers was undertaken by a single reviewer with 10% verification by a second reviewer. Data extraction was undertaken by a single reviewer using a pre-piloted form. Given the wide variation in study design and intervention outcomes, a narrative synthesis approach was applied. Studies were clustered around common diagnostic stewardship interventions where appropriate.<b>Results.</b> After duplicate removal, a total of 1310 citations were identified, of which, after full-paper screening, 105 studies were included in this scoping review. The classification of an intervention as taking a diagnostic stewardship approach is a relatively recent development, with the first publication in this field dating back to 2017. The majority of research in this area has been conducted within the USA, with very few studies undertaken outside this region. Visual inspection of the citation map reveals that the current evidence base is interconnected, with frequent references to each other's work. The interventions commonly adopt a restrictive approach, utilizing hard and soft stops within the pre-analytical phase to restrict access to testing. Upon closer examination of the outcomes, it becomes evident that there is a predominant focus on reducing the number of tests rather than enhancing the current test protocol. This is further reflected in the limited number of studies that report on test performance (including protocol improvements, specificity and sensitivity).<b>Conclusion.</b> Diagnostic stewardship seems to have deviated from its intended course, morphing into a rather rudimentary instrument wielded not to enhance but to constrict the scope of testing. Despite the World Health Organization's advocacy for an ideology that promotes a more comprehensive approach to quality improvement, it may be more appropriate to con","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165918/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140900556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The emergence and circulation of human immunodeficiency virus (HIV)-1 subtype C.","authors":"Xingguang Li, Sana Tamim, Nídia S Trovão","doi":"10.1099/jmm.0.001827","DOIUrl":"https://doi.org/10.1099/jmm.0.001827","url":null,"abstract":"Introduction. Human immunodeficiency virus (HIV)-1 subtype C is the most prevalent globally and is thought to have originated in non-human primates in the Democratic Republic of Congo.Hypothesis/Gap Statement. Although the global dominance of HIV-1 subtype C is well established, a thorough understanding of its evolutionary history and transmission dynamics across various risk populations remains elusive. The current knowledge is insufficient to fully capture the global diversification and dissemination of this subtype.Aim. We for the first time sought to investigate the global evolutionary history and spatiotemporal dynamics of HIV-1 subtype C using a selection of maximum-likelihood-based phylodynamic approaches on a total of 1210 near full-length genomic sequences sampled from 32 countries, collected in 4 continents, with sampling dates between 1986-2019 among various risk groups were analysed.Methodology. We subsampled the HIV-1 subtype C genomic datasets based on continent and risk group traits, and performed nucleotide substitution model selection analysis, maximum likelihood (ML) phylogenetic reconstruction, phylogenetic tree topology similarity analysis, temporal signal analysis and traced the timings of viral spread both geographically and by risk group.Results. Based on the phylodynamic analyses of four datasets (full1210, locrisk626, loc562 and risk393), we inferred the time to the most recent common ancestor (TMRCA) in the 1930s and an evolutionary rate of 0.0023 substitutions per site per year. The total number of introduction events of HIV-1 subtype C between continents and between risk groups is estimated to be 71 and 115, respectively. The largest number of introductions occurred from Africa to Europe (n=32), from not-recorded to heterosexual (n=40) and from heterosexual to not-recorded (n=51) risk groups.Conclusion. Our results emphasize that HIV subtype C has mainly spread from Africa to Europe, likely through heterosexual transmission.","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"35 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141039094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dengue: A review of laboratory diagnostics in the vaccine age.","authors":"Jaimie L Frazer, Robert Norton","doi":"10.1099/jmm.0.001833","DOIUrl":"10.1099/jmm.0.001833","url":null,"abstract":"<p><p><b>Background.</b> Dengue is an important arboviral infection of considerable public health significance. It occurs in a wide global belt within a variety of tropical regions. The timely laboratory diagnosis of Dengue infection is critical to inform both clinical management and an appropriate public health response. Vaccination against Dengue virus is being introduced in some areas.<b>Discussion.</b> Appropriate diagnostic strategies will vary between laboratories depending on the available resources and skills. Diagnostic methods available include viral culture, the serological detection of Dengue-specific antibodies in using enzyme immunoassays (EIAs), microsphere immunoassays, haemagglutination inhibition or in lateral flow point of care tests. The results of antibody tests may be influenced by prior vaccination and exposure to other flaviviruses. The detection of non-structural protein 1 in serum (NS1) has improved the early diagnosis of Dengue and is available in point-of-care assays in addition to EIAs. Direct detection of viral RNA from blood by PCR is more sensitive than NS1 antigen detection but requires molecular skills and resources. An increasing variety of isothermal nucleic acid detection methods are in development. Timing of specimen collection and choice of test is critical to optimize diagnostic accuracy. Metagenomics and the direct detection by sequencing of viral RNA from blood offers the ability to rapidly type isolates for epidemiologic purposes.<b>Conclusion.</b> The impact of vaccination on immune response must be recognized as it will impact test interpretation and diagnostic algorithms.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140900510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic variations of penicillin-binding protein 1A: insights into the current status of amoxicillin-based regimens for <i>Helicobacter pylori</i> eradication in Malaysia.","authors":"Heng Kang Ng, Kek Heng Chua, Boon Pin Kee, Kee Huat Chuah, Lip Yee Por, Suat Moi Puah","doi":"10.1099/jmm.0.001832","DOIUrl":"10.1099/jmm.0.001832","url":null,"abstract":"<p><p><b>Introduction.</b> Resistance towards amoxicillin in <i>Helicobacter pylori</i> causes significant therapeutic impasse in healthcare settings worldwide. In Malaysia, the standard <i>H. pylori</i> treatment regimen includes a 14-day course of high-dose proton-pump inhibitor (rabeprazole, 20 mg) with amoxicillin (1000 mg) dual therapy.<b>Hypothesis/Gap Statement.</b> The high eradication rate with amoxicillin-based treatment could be attributed to the primary resistance rates of amoxicillin being relatively low at 0%, however, a low rate of secondary resistance has been documented in Malaysia recently.<b>Aim.</b> This study aims to investigate the amino acid mutations and related genetic variants in PBP1A of <i>H. pylori</i>, correlating with amoxicillin resistance in the Malaysian population.<b>Methodology.</b> The full-length <i>pbp1A</i> gene was amplified via PCR from 50 genomic DNA extracted from gastric biopsy samples of <i>H. pylori</i>-positive treatment-naïve Malaysian patients. The sequences were then compared with reference <i>H. pylori</i> strain ATCC 26695 for mutation and variant detection. A phylogenetic analysis of 50 sequences along with 43 additional sequences from the NCBI database was performed. These additional sequences included both amoxicillin-resistant strains (<i>n</i>=20) and amoxicillin-sensitive strains (<i>n</i>=23).<b>Results.</b> There was a total of 21 variants of amino acids, with three of them located in or near the PBP-motif (SKN402-404). The percentages of these three variants are as follows: K403X, 2%; S405I, 2% and E406K, 16%. Based on the genetic markers identified, the resistance rate for amoxicillin in our sample remained at 0%. The phylogenetic examination suggested that <i>H. pylori</i> might exhibit unique conserved <i>pbp1A</i> sequences within the Malaysian context.<b>Conclusions.</b> Overall, the molecular analysis of PBP1A supported the therapeutic superiority of amoxicillin-based regimens. Therefore, it is crucial to continue monitoring the amoxicillin resistance background of <i>H. pylori</i> with a larger sample size to ensure the sustained effectiveness of amoxicillin-based treatments in Malaysia.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140875130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The emergence and circulation of human immunodeficiency virus (HIV)-1 subtype C.","authors":"Xingguang Li, Sana Tamim, Nídia S Trovão","doi":"10.1099/jmm.0.001827","DOIUrl":"10.1099/jmm.0.001827","url":null,"abstract":"<p><p><b>Introduction.</b> Human immunodeficiency virus (HIV)-1 subtype C is the most prevalent globally and is thought to have originated in non-human primates in the Democratic Republic of Congo.<b>Hypothesis/Gap Statement.</b> Although the global dominance of HIV-1 subtype C is well established, a thorough understanding of its evolutionary history and transmission dynamics across various risk populations remains elusive. The current knowledge is insufficient to fully capture the global diversification and dissemination of this subtype.<b>Aim.</b> We for the first time sought to investigate the global evolutionary history and spatiotemporal dynamics of HIV-1 subtype C using a selection of maximum-likelihood-based phylodynamic approaches on a total of 1210 near full-length genomic sequences sampled from 32 countries, collected in 4 continents, with sampling dates between 1986-2019 among various risk groups were analysed.<b>Methodology.</b> We subsampled the HIV-1 subtype C genomic datasets based on continent and risk group traits, and performed nucleotide substitution model selection analysis, maximum likelihood (ML) phylogenetic reconstruction, phylogenetic tree topology similarity analysis, temporal signal analysis and traced the timings of viral spread both geographically and by risk group.<b>Results.</b> Based on the phylodynamic analyses of four datasets (full1210, locrisk626, loc562 and risk393), we inferred the time to the most recent common ancestor (TMRCA) in the 1930s and an evolutionary rate of 0.0023 substitutions per site per year. The total number of introduction events of HIV-1 subtype C between continents and between risk groups is estimated to be 71 and 115, respectively. The largest number of introductions occurred from Africa to Europe (<i>n</i>=32), from not-recorded to heterosexual (<i>n</i>=40) and from heterosexual to not-recorded (<i>n</i>=51) risk groups.<b>Conclusion.</b> Our results emphasize that HIV subtype C has mainly spread from Africa to Europe, likely through heterosexual transmission.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140961207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}