Pub Date : 2025-11-24DOI: 10.1016/j.ijmmb.2025.101031
Fengyuan He , Limin Mei , Linzi Zeng
Introduction
Pertussis is an acute respiratory disease primarily caused by Bordetella pertussis, and its incidence has shown a resurgence. Polymerase chain reaction (PCR) is a recognized molecular detection method, and various related detection methods have emerged.
Methods
This study is performed according to the PRISMA checklist. Relevant literature is adopted from the online databases. The quality of the included studies is assessed based on the REVMAN software (version 5.4). Statistical analysis is performed by STATA 14.0 and Meta-DiSc 1.4 software.
Results
The results of this meta-analysis show that four different PCR techniques—conventional PCR, real-time quantitative PCR (Q-PCR), multiplex PCR, and nested PCR—have a pooled sensitivity of 0.95 (95 % CI: 0.93–0.97), pooled specificity of 0.93 (95 % CI: 0.89–0.95), pooled positive likelihood ratio (PLR) of 12.22 (95 % CI: 8.62–17.33), pooled negative likelihood ratio (NLR) of 0.05 (95 % CI: 0.03–0.08), and pooled diagnostic odds ratio (DOR) of 244.88 (95 % CI: 133.34–449.72). Multiplex PCR has the highest pooled specificity, PLR, and DOR. Nested PCR has the highest sensitivity and the lowest NLR. PCR testing holds significant value in the early diagnosis of pertussis. Multiplex PCR, nested PCR, and Q-PCR outperform conventional PCR in diagnostic performance.
Conclusions
Each type of PCR test has its advantages and disadvantages, and clinical selection should consider factors such as testing purpose, personnel, and conditions.
{"title":"Meta-analysis of the diagnostic value of polymerase chain reaction-based nucleic acid detection methods for pertussis","authors":"Fengyuan He , Limin Mei , Linzi Zeng","doi":"10.1016/j.ijmmb.2025.101031","DOIUrl":"10.1016/j.ijmmb.2025.101031","url":null,"abstract":"<div><h3>Introduction</h3><div>Pertussis is an acute respiratory disease primarily caused by <em>Bordetella pertussis</em>, and its incidence has shown a resurgence. Polymerase chain reaction (PCR) is a recognized molecular detection method, and various related detection methods have emerged.</div></div><div><h3>Methods</h3><div>This study is performed according to the PRISMA checklist. Relevant literature is adopted from the online databases. The quality of the included studies is assessed based on the REVMAN software (version 5.4). Statistical analysis is performed by STATA 14.0 and Meta-DiSc 1.4 software.</div></div><div><h3>Results</h3><div>The results of this meta-analysis show that four different PCR techniques—conventional PCR, real-time quantitative PCR (Q-PCR), multiplex PCR, and nested PCR—have a pooled sensitivity of 0.95 (95 % CI: 0.93–0.97), pooled specificity of 0.93 (95 % CI: 0.89–0.95), pooled positive likelihood ratio (PLR) of 12.22 (95 % CI: 8.62–17.33), pooled negative likelihood ratio (NLR) of 0.05 (95 % CI: 0.03–0.08), and pooled diagnostic odds ratio (DOR) of 244.88 (95 % CI: 133.34–449.72). Multiplex PCR has the highest pooled specificity, PLR, and DOR. Nested PCR has the highest sensitivity and the lowest NLR. PCR testing holds significant value in the early diagnosis of pertussis. Multiplex PCR, nested PCR, and Q-PCR outperform conventional PCR in diagnostic performance.</div></div><div><h3>Conclusions</h3><div>Each type of PCR test has its advantages and disadvantages, and clinical selection should consider factors such as testing purpose, personnel, and conditions.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"59 ","pages":"Article 101031"},"PeriodicalIF":1.3,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145621855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Escherichia coli is a major pathogen in bloodstream infections (BSIs), with increasing concern over antimicrobial resistance (AMR) and the evolving pathogenic potential of phylogroups traditionally considered commensal. This study investigates the genetic characteristics of E. coli isolates causing BSIs in India, with a focus on phylogroups A to F.
Methods
204 E. coli bloodstream isolates received at a tertiary hospital in India were whole genome sequenced. Phylogroups, sequence types (STs), antimicrobial resistance genes (ARGs), virulence factors (VFs), and plasmid replicon types were determined. Bioinformatics analyses include MLST, ResFinder, VirulenceFinder, PlasmidFinder, and ClermonTyping for phylogroup assignment.
Results
Phylogroup B2 (35 %) was the most prevalent, followed by phylogroup A (32 %) and D (19 %). ST131 (B2) emerged as the dominant clone (22 %). Phylogroup A isolates, previously considered commensal and primarily associated with high AMR, now demonstrated notable acquisition of virulence factors such as fimH and iutA, indicating an emerging role as significant BSI pathogens. These isolates also showed high clonal diversity (e.g., ST167, ST410, ST617). Key resistance genes included blaCTX-M (53 %) and blaTEM (25 %), frequently associated with IncF plasmids. Multi-replicon plasmid profiles, particularly IncF variants, were significantly associated with co-carriage of both AMR and VF genes, contributing to enhanced pathogenicity.
Conclusion
This study highlights the emerging role of phylogroup A E. coli, traditionally commensal and AMR-rich as a leading cause of BSIs in India following the acquisition of virulence factors. In parallel, B2 clones like ST131 continue to drive infections through their established virulence and resistance repertoire. Such multi-replicon IncF plasmids driving AMR–VF co-selection, calls for focused surveillance and intervention in E. coli BSIs.
{"title":"Genetic plasticity of Escherichia coli causing bloodstream infections in India: A focus on phylogroups A to F","authors":"Karthik Gunasekaran , Irulappan Madhumathi , Santhosh Raj , Greesma Grace Thomas , Venkatesh Narashiman , Vishnukumar Ramesh , Subbulakshmi Rajendran , Ramprakash Rayala , Ayyanraj Neeravi , Binesh Lal , Kamini Walia , Balaji Veeraraghavan","doi":"10.1016/j.ijmmb.2025.101026","DOIUrl":"10.1016/j.ijmmb.2025.101026","url":null,"abstract":"<div><h3>Background</h3><div><em>Escherichia coli</em> is a major pathogen in bloodstream infections (BSIs), with increasing concern over antimicrobial resistance (AMR) and the evolving pathogenic potential of phylogroups traditionally considered commensal. This study investigates the genetic characteristics of <em>E. coli</em> isolates causing BSIs in India, with a focus on phylogroups A to F.</div></div><div><h3>Methods</h3><div>204 <em>E. coli</em> bloodstream isolates received at a tertiary hospital in India were whole genome sequenced. Phylogroups, sequence types (STs), antimicrobial resistance genes (ARGs), virulence factors (VFs), and plasmid replicon types were determined. Bioinformatics analyses include MLST, ResFinder, VirulenceFinder, PlasmidFinder, and ClermonTyping for phylogroup assignment.</div></div><div><h3>Results</h3><div>Phylogroup B2 (35 %) was the most prevalent, followed by phylogroup A (32 %) and D (19 %). ST131 (B2) emerged as the dominant clone (22 %). Phylogroup A isolates, previously considered commensal and primarily associated with high AMR, now demonstrated notable acquisition of virulence factors such as <em>fimH</em> and <em>iutA</em>, indicating an emerging role as significant BSI pathogens. These isolates also showed high clonal diversity (e.g., ST167, ST410, ST617). Key resistance genes included blaCTX-M (53 %) and blaTEM (25 %), frequently associated with IncF plasmids. Multi-replicon plasmid profiles, particularly IncF variants, were significantly associated with co-carriage of both AMR and VF genes, contributing to enhanced pathogenicity.</div></div><div><h3>Conclusion</h3><div>This study highlights the emerging role of phylogroup A <em>E. coli</em>, traditionally commensal and AMR-rich as a leading cause of BSIs in India following the acquisition of virulence factors. In parallel, B2 clones like ST131 continue to drive infections through their established virulence and resistance repertoire. Such multi-replicon IncF plasmids driving AMR–VF co-selection, calls for focused surveillance and intervention in <em>E. coli</em> BSIs.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"59 ","pages":"Article 101026"},"PeriodicalIF":1.3,"publicationDate":"2025-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145587295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-21DOI: 10.1016/j.ijmmb.2025.101028
Shilpi Saxena , Reena Das , Sumeeta Khurana , Saleem Amjad Mirza , Kamal Deep Joshi , Harleen Kaur
Malaria diagnosis is often difficult in cases with low parasitaemia and atypical presentations. We report a 30-year-old male with high-grade fever, chills, and vomiting. At admission, he was afebrile, pale, and had progressive splenomegaly. Despite extensive investigations, including multiple peripheral blood smears and malaria rapid diagnostic tests, results were negative. Bone marrow examination revealed rare red blood cells with Plasmodium spp., confirmed by PCR from the marrow aspirate slide. He completely recovered after treatment with Artemether-Lumefantrine and Primaquine. This case underscores the value of bone marrow microscopy and PCR in diagnosing malaria in patients with unexplained cytopenias and splenomegaly.
{"title":"Out of Sight, Should not be out of mind: A perplexing case of Malaria","authors":"Shilpi Saxena , Reena Das , Sumeeta Khurana , Saleem Amjad Mirza , Kamal Deep Joshi , Harleen Kaur","doi":"10.1016/j.ijmmb.2025.101028","DOIUrl":"10.1016/j.ijmmb.2025.101028","url":null,"abstract":"<div><div>Malaria diagnosis is often difficult in cases with low parasitaemia and atypical presentations. We report a 30-year-old male with high-grade fever, chills, and vomiting. At admission, he was afebrile, pale, and had progressive splenomegaly. Despite extensive investigations, including multiple peripheral blood smears and malaria rapid diagnostic tests, results were negative. Bone marrow examination revealed rare red blood cells with <em>Plasmodium</em> spp., confirmed by PCR from the marrow aspirate slide. He completely recovered after treatment with Artemether-Lumefantrine and Primaquine. This case underscores the value of bone marrow microscopy and PCR in diagnosing malaria in patients with unexplained cytopenias and splenomegaly.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"59 ","pages":"Article 101028"},"PeriodicalIF":1.3,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145587349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-21DOI: 10.1016/j.ijmmb.2025.101027
Mandakini Das , Biswajyoti Borkakoty , Nargis K. Bali , Neelanjana Sarmah , Aniruddha Jakharia , Rahul Hazarika , Chandrakanta Bhattacharya , Aktarul Islam Siddique , Kishore Sarma , Kimmi Sarmah , Harpreet Kaur
Purpose
Human rhinovirus (HRV), a member of the Enterovirus genus of the Picornaviridae family is a major respiratory pathogen and the leading cause of upper respiratory tract infections. Given the limited information on HRV prevalence and molecular epidemiology in Northeast India, this study investigated circulating HRV strains in the region from 2015 to 2018.
Methods
Nasopharyngeal and throat swab samples were collected and RNA was extracted for HRV detection using qRT-PCR. HRV-positive samples were subjected to bidirectional Sanger sequencing targeting the 549 bp VP4/VP2 region. Obtained sequences were aligned and analyzed phylogenetically using bioinformatics tools to determine genotype distribution and genetic diversity.
Results
Among 2642 cases, 354 (13.3 %) tested positive for HRV. HRV-C was the predominant species (48.7 %), followed by HRV-A (38.4 %) and HRV-B (7.6 %). HRV infection was significantly associated with lower respiratory symptoms such as cough (p < 0.001) and breathlessness (p < 0.026). The study identified 27 different HRV genotypes in the 39 sequenced samples, with HRV-C15 being the most common (9/39) overall and associated with disease severity (p = 0.003). Seasonality analysis indicated peak HRV circulation between August and November (48.8 %, 173/354), with the lowest detected in June–July (14.1 %). HRV-C was more frequently observed in severe acute respiratory infection (SARI) cases and demonstrated the highest heterogeneity, with an intra-species nucleotide mean p-distance of 24.0 %.
Conclusion
In conclusion, this study presents the first report on the prevalence of human rhinovirus (HRV) among influenza-like illness (ILI) cases in Dibrugarh, Assam, India. HRV-C exhibited distinct epidemiological characteristics compared to HRV-A and HRV-B strains. Molecular epidemiological analysis revealed notable nucleotide variation in the VP4/VP2 region, with HRV-C15 emerging as the predominant genotype associated with increased disease severity. Further research involving larger sample sizes and detailed clinical follow-up is essential to better understand the genotype distribution and genetic diversity of HRV strains circulating in the region.
目的：人鼻病毒（HRV）是小核糖核酸病毒科肠病毒属的一员，是一种主要的呼吸道病原体，是上呼吸道感染的主要原因。鉴于印度东北部HRV患病率和分子流行病学信息有限，本研究调查了2015年至2018年该地区流行的HRV菌株。方法：采集鼻咽和咽拭子标本，提取RNA，采用qRT-PCR检测HRV。hrv阳性样本针对549 bp VP4/VP2区域进行双向Sanger测序。利用生物信息学工具对获得的序列进行比对和系统发育分析，以确定基因型分布和遗传多样性。结果：2642例中，HRV阳性354例（13.3%）。HRV-C是优势种（48.7%），其次是HRV-A（38.4%）和HRV-B（7.6%）。HRV感染与咳嗽等下呼吸道症状显著相关(结论：本研究首次报道了印度阿萨姆邦迪布鲁加尔省流感样疾病（ILI）病例中人鼻病毒（HRV）的流行情况。与HRV-A和HRV-B株相比，HRV-C株具有明显的流行病学特征。分子流行病学分析显示VP2/VP4区域的核苷酸显著变异，HRV-C15成为与疾病严重程度增加相关的主要基因型。为了更好地了解该地区流行的HRV毒株的基因型分布和遗传多样性，需要开展更大样本量和详细临床随访的进一步研究。
{"title":"Molecular epidemiology of human rhinovirus from clinical cases of Dibrugarh, Assam, India","authors":"Mandakini Das , Biswajyoti Borkakoty , Nargis K. Bali , Neelanjana Sarmah , Aniruddha Jakharia , Rahul Hazarika , Chandrakanta Bhattacharya , Aktarul Islam Siddique , Kishore Sarma , Kimmi Sarmah , Harpreet Kaur","doi":"10.1016/j.ijmmb.2025.101027","DOIUrl":"10.1016/j.ijmmb.2025.101027","url":null,"abstract":"<div><h3>Purpose</h3><div>Human rhinovirus (HRV), a member of the <em>Enterovirus</em> genus of the <em>Picornaviridae</em> family is a major respiratory pathogen and the leading cause of upper respiratory tract infections. Given the limited information on HRV prevalence and molecular epidemiology in Northeast India, this study investigated circulating HRV strains in the region from 2015 to 2018.</div></div><div><h3>Methods</h3><div>Nasopharyngeal and throat swab samples were collected and RNA was extracted for HRV detection using qRT-PCR. HRV-positive samples were subjected to bidirectional Sanger sequencing targeting the 549 bp VP4/VP2 region. Obtained sequences were aligned and analyzed phylogenetically using bioinformatics tools to determine genotype distribution and genetic diversity.</div></div><div><h3>Results</h3><div>Among 2642 cases, 354 (13.3 %) tested positive for HRV. HRV-C was the predominant species (48.7 %), followed by HRV-A (38.4 %) and HRV-B (7.6 %). HRV infection was significantly associated with lower respiratory symptoms such as cough (p < 0.001) and breathlessness (p < 0.026). The study identified 27 different HRV genotypes in the 39 sequenced samples, with HRV-C15 being the most common (9/39) overall and associated with disease severity (p = 0.003). Seasonality analysis indicated peak HRV circulation between August and November (48.8 %, 173/354), with the lowest detected in June–July (14.1 %). HRV-C was more frequently observed in severe acute respiratory infection (SARI) cases and demonstrated the highest heterogeneity, with an intra-species nucleotide mean p-distance of 24.0 %.</div></div><div><h3>Conclusion</h3><div>In conclusion, this study presents the first report on the prevalence of human rhinovirus (HRV) among influenza-like illness (ILI) cases in Dibrugarh, Assam, India. HRV-C exhibited distinct epidemiological characteristics compared to HRV-A and HRV-B strains. Molecular epidemiological analysis revealed notable nucleotide variation in the VP4/VP2 region, with HRV-C15 emerging as the predominant genotype associated with increased disease severity. Further research involving larger sample sizes and detailed clinical follow-up is essential to better understand the genotype distribution and genetic diversity of HRV strains circulating in the region.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"59 ","pages":"Article 101027"},"PeriodicalIF":1.3,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145587306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-19DOI: 10.1016/j.ijmmb.2025.101024
Thripthi Ananda , Chiranjay Mukhopadhyay
Introduction
E. coli is a frequently encountered clinical pathogen, and periodic monitoring of antimicrobial resistance and virulence profiles is crucial for defining roadmaps for both infection prevention and control practices.
Objective
We aimed to compare the proportions of key phylogenetic groups, virulence associated genes (VAGs), and antimicrobial susceptibility (AST) patterns of E. coli isolated from various clinical samples and compare expression levels of key VAGs in patients with uncomplicated UTI versus those with UTI + bacteraemia in a tertiary-care hospital in South India.
Methods
Clinical E. coli isolates, confirmed using the MALDI-TOF MS, and satisfying the National Healthcare Safety Network(NHSN) criteria for infections were included. Phylogenetic grouping and VAGs detection were performed using multiplex-PCR and targeted gene expression was carried out using quantitative RT-qPCR. AST was determined using VITEK 2 system.
Results
The included 288E. coli isolates (144 from bacteraemia and non-bacteraemia cases each) predominately showed phylogroup B2 (52 %), followed by D (23 %), and most prevalent virulence genes were chuA (74.7 %), fimH(63.3 %), traT(63.2 %), and kpsMTII(54.2 %). fimH, fyuA, and hlyD were significantly associated with bacteraemia, and gene expression of these genes and the analysis demonstrated that hlyD expression was significantly higher (p = 0.012) in UTI + bacteraemia patients when compared to patients with uncomplicated UTI. Phylogroup B2 carried the highest median number of VAGs (7), followed by D (6). Highest susceptibility was towards tigecycline (99.7 %), followed by amikacin (91.7 %) and meropenem (90.0 %).
Conclusion
We focused on prevalent virulent genes and their expression, leading to bacteraemia, providing a comprehensive overview of an existing concern. Focusing on bacterial gene expression along with integrated surveillance of antimicrobial resistance helps in designing further research so that strategies can be planned that will later help in early risk stratification and informed clinical decision-making to prevent severe complications including secondary bacteraemia and other severe patient morbidities.
{"title":"A molecular snapshot of clinical extra-intestinal Escherichia coli strains in South India – Virulence factors, phylogrouping and resistance trends","authors":"Thripthi Ananda , Chiranjay Mukhopadhyay","doi":"10.1016/j.ijmmb.2025.101024","DOIUrl":"10.1016/j.ijmmb.2025.101024","url":null,"abstract":"<div><h3>Introduction</h3><div><em>E. coli</em> is a frequently encountered clinical pathogen, and periodic monitoring of antimicrobial resistance and virulence profiles is crucial for defining roadmaps for both infection prevention and control practices.</div></div><div><h3>Objective</h3><div>We aimed to compare the proportions of key phylogenetic groups, virulence associated genes (VAGs), and antimicrobial susceptibility (AST) patterns of <em>E. coli</em> isolated from various clinical samples and compare expression levels of key VAGs in patients with uncomplicated UTI versus those with UTI + bacteraemia in a tertiary-care hospital in South India.</div></div><div><h3>Methods</h3><div>Clinical <em>E. coli</em> isolates, confirmed using the MALDI-TOF MS, and satisfying the National Healthcare Safety Network(NHSN) criteria for infections were included. Phylogenetic grouping and VAGs detection were performed using multiplex-PCR and targeted gene expression was carried out using quantitative RT-qPCR. AST was determined using VITEK 2 system.</div></div><div><h3>Results</h3><div>The included 288<em>E. coli</em> isolates (144 from bacteraemia and non-bacteraemia cases each) predominately showed phylogroup B2 (52 %), followed by D (23 %), and most prevalent virulence genes were <em>chuA</em> (74.7 %), <em>fimH</em>(63.3 %), <em>traT</em>(63.2 %), and <em>kpsMTII</em>(54.2 %). <em>fimH, fyuA</em>, and <em>hlyD</em> were significantly associated with bacteraemia, and gene expression of these genes and the analysis demonstrated that <em>hlyD</em> expression was significantly higher (<em>p</em> = 0.012) in UTI + bacteraemia patients when compared to patients with uncomplicated UTI. Phylogroup B2 carried the highest median number of VAGs (7), followed by D (6). Highest susceptibility was towards tigecycline (99.7 %), followed by amikacin (91.7 %) and meropenem (90.0 %).</div></div><div><h3>Conclusion</h3><div>We focused on prevalent virulent genes and their expression, leading to bacteraemia, providing a comprehensive overview of an existing concern. Focusing on bacterial gene expression along with integrated surveillance of antimicrobial resistance helps in designing further research so that strategies can be planned that will later help in early risk stratification and informed clinical decision-making to prevent severe complications including secondary bacteraemia and other severe patient morbidities.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"59 ","pages":"Article 101024"},"PeriodicalIF":1.3,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145563858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
To evaluate the in-vitro activity of fosfomycin in urinary isolates of Enterococcus faecalis and look for the molecular mechanisms responsible for resistance to this antibiotic.
Methods
E. faecalis isolates recovered from urine samples were processed for the presence of genes encoding the FOS modifying enzymes, fosA, fosB, fosC, fosX and murA. DNA was extracted using QIAamp DNA Mini kit. Conventional PCR using forward and reverse primers targeting the five genes was carried out. The amplified products were electrophoresed and visualized in a gel documentation system. Antimicrobial susceptibility testing was done by disc diffusion method.
Results
A total of 274 isolates of E. faecalis isolates were part of our study out of which 57 (20.8 %) were FOS resistant. Slightly more number of FOS resistant isolates were recovered from female patients, 30 (52.6 %) and from patients in the age group of >39 yrs. Majority of the FOS resistant isolates were recovered from patients attending the OPD. Vancomycin resistance was seen in 69 (25.2 %) E. faecalis isolates. fosB was was the most common gene, present in 42 (73.7 %) isolates and murA was present in 15 (26.3 %) isolates of E. faecalis. Furthermore all the FOS resistant, vancomycin resistant isolates harboured the fosB gene (n = 26).
Conclusion
To our knowledge this study is the first to explore FOS resistance in E. faecalis isolates from this part of the country. Increased resistance to FOS as compared to what has been reported previously calls for strict implementation of infection control protocols as well as heightened surveillance studies.
目的：评价尿路分离的粪肠球菌对磷霉素的体外活性，探讨其耐药的分子机制。方法：对尿液中分离的粪肠球菌进行FOS修饰酶基因fosA、fosB、fosC、fox和murA的检测。采用QIAamp DNA Mini试剂盒提取DNA。对这5个基因分别采用正、反向引物进行常规PCR。扩增产物在凝胶记录系统中电泳和可视化。药敏试验采用纸片扩散法。结果：本研究共分离到274株粪肠球菌，其中57株（20.8%）对FOS耐药。从女性患者中分离出的FOS耐药菌株数量略多，为30株（52.6%），从bb0 ~ 39岁年龄组的患者中分离出FOS耐药菌株。大多数FOS耐药分离株是从门诊就诊的患者中恢复的。69株（25.2%）粪肠球菌对万古霉素耐药。fosB是最常见的基因，在42株（73.7%）中存在，murA在15株（26.3%）中存在。此外，所有FOS耐药、万古霉素耐药分离株均含有fosB基因（n=26）。结论：据我们所知，本研究首次探讨了该地区粪伊蚊对FOS的耐药性。与以前报告的情况相比，FOS耐药性的增加要求严格执行感染控制方案并加强监测研究。
{"title":"Molecular characterisation of fosfomycin resistant Enterococci faecalis isolated from a tertiary care medical hospital in northern India","authors":"Anjum Ara Mir, Sayim Wani, Nargis Bali, Bisma Ahad, Masooma Showkat, Aarifa Bashir","doi":"10.1016/j.ijmmb.2025.101022","DOIUrl":"10.1016/j.ijmmb.2025.101022","url":null,"abstract":"<div><h3>Purpose</h3><div>To evaluate the in-vitro activity of fosfomycin in urinary isolates of <em>Enterococcus faecalis</em> and look for the molecular mechanisms responsible for resistance to this antibiotic.</div></div><div><h3>Methods</h3><div><em>E. faecalis</em> isolates recovered from urine samples were processed for the presence of genes encoding the FOS modifying enzymes, <em>fosA, fosB, fosC, fosX</em> and <em>murA</em>. DNA was extracted using QIAamp DNA Mini kit. Conventional PCR using forward and reverse primers targeting the five genes was carried out. The amplified products were electrophoresed and visualized in a gel documentation system. Antimicrobial susceptibility testing was done by disc diffusion method.</div></div><div><h3>Results</h3><div>A total of 274 isolates of <em>E. faecalis</em> isolates were part of our study out of which 57 (20.8 %) were FOS resistant. Slightly more number of FOS resistant isolates were recovered from female patients, 30 (52.6 %) and from patients in the age group of >39 yrs. Majority of the FOS resistant isolates were recovered from patients attending the OPD. Vancomycin resistance was seen in 69 (25.2 %) <em>E. faecalis</em> isolates. <em>fosB</em> was was the most common gene, present in 42 (73.7 %) isolates and <em>murA</em> was present in 15 (26.3 %) isolates of <em>E. faecalis</em>. Furthermore all the FOS resistant, vancomycin resistant isolates harboured the <em>fosB</em> gene (n = 26).</div></div><div><h3>Conclusion</h3><div>To our knowledge this study is the first to explore FOS resistance in <em>E. faecalis</em> isolates from this part of the country. Increased resistance to FOS as compared to what has been reported previously calls for strict implementation of infection control protocols as well as heightened surveillance studies.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"59 ","pages":"Article 101022"},"PeriodicalIF":1.3,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145563836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-19DOI: 10.1016/j.ijmmb.2025.101025
Gayatree Nayak , Naveen Kumar Devanga Ragupathi , Bijayini Behera
Cefiderocol (FDC) is regarded as a reserved therapeutic option for serious CRE infections. In an earlier study, we had reported a 9.9 % FDC resistance in CRE isolates. In the present study, we are reporting the whole genome sequencing analysis findings of two FDC-resistant CRE (One E. coli and one K. pneumoniae). PBP3 insertions and mutations in the siderophore receptor cirA were the primary drivers of FDC resistance in E. coli. In K. pneumoniae, there was intact porin and a single copy of blaNDM-5, and a combination of β-lactamase and carbapenem resistance genes, including blaTEM- 1B, blaCTX-M-15,blaNDM-5 and blaOXA-181.
{"title":"Whole-genome sequence analysis of cefiderocol-resistant E. coli and Klebsiella pneumoniae isolates from cefiderocol treatment-naïve patients","authors":"Gayatree Nayak , Naveen Kumar Devanga Ragupathi , Bijayini Behera","doi":"10.1016/j.ijmmb.2025.101025","DOIUrl":"10.1016/j.ijmmb.2025.101025","url":null,"abstract":"<div><div>Cefiderocol (FDC) is regarded as a reserved therapeutic option for serious CRE infections. In an earlier study, we had reported a 9.9 % FDC resistance in CRE isolates. In the present study, we are reporting the whole genome sequencing analysis findings of two FDC-resistant CRE (One <em>E. coli</em> and one <em>K. pneumoniae</em>). PBP3 insertions and mutations in the siderophore receptor <em>cirA</em> were the primary drivers of FDC resistance in <em>E. coli</em>. In <em>K. pneumoniae</em>, there was intact porin and a single copy of <em>bla</em><sub>NDM-5</sub>, and a combination of β-lactamase and carbapenem resistance genes, including <em>bla</em><sub>TEM- 1B</sub>, <em>bla</em><sub>CTX-M-15,</sub> <em>bla</em><sub>NDM-5</sub> and <em>bla</em><sub>OXA-181</sub>.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"59 ","pages":"Article 101025"},"PeriodicalIF":1.3,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145563814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-19DOI: 10.1016/j.ijmmb.2025.101023
Alisha Mahajan , Varsha Gupta , Suksham Jain
Background
Neonatal sepsis is a major cause of mortality and morbidity, representing a critical emergency that demands swift diagnosis and intervention. Recent trend shows increasing resistance to commonly used antibiotics.
Aims and objectives
To study the antimicrobial resistance pattern in blood culture positive neonatal sepsis in outborn and inborn neonates and to compare the clinical profile in neonates with proven sepsis.
Methods
Bacterial cultures of the blood samples received from neonates with suspected sepsis was performed and antimicrobial susceptibility testing of blood culture positive neonates was done. Antibiotic sensitivity tests were done as per Clinical and Laboratory Standards Institute (CLSI) 2023 guidelines.
Results
Of the 100 participants, 34 were early onset neonatal sepsis and 66 were late onset neonatal sepsis. 35 % of the delivery were vaginal whereas 65 % of the deliveries were by Caesarean section. 17 % of the total neonates delivered had to undergo neonatal resuscitation and 36 % of the neonates had birth asphyxia. The most commonly isolated organisms were Coagulase-negative Staphylococcus species (CoNS) (30 %) followed by Klebsiella pneumoniae (21 %) and Acinetobacter baumannii complex (20 %). 45.1 % were Extended Spectrum beta lactamase (ESBL) producers and 58 % were AmpC beta lactamases producers.
Case fatality rate was highest with Klebsiella pneumoniae i.e. 34.6 % followed by Acinetobacter baumannii complex i.e. 23.07 %.
Conclusion
Increase in antibiotic resistance organisms can lead to an increase in the neonatal case fatality rate (CFR), so regular surveillance is needed. Comparison between the resistance profile between inborn and outborn neonates provides an insight into the difference in the variety of organisms isolated and also the difference in resistance shown by community acquired and hospital acquired organisms.
{"title":"Antimicrobial resistance in blood culture proven sepsis in outborn and inborn neonates","authors":"Alisha Mahajan , Varsha Gupta , Suksham Jain","doi":"10.1016/j.ijmmb.2025.101023","DOIUrl":"10.1016/j.ijmmb.2025.101023","url":null,"abstract":"<div><h3>Background</h3><div>Neonatal sepsis is a major cause of mortality and morbidity, representing a critical emergency that demands swift diagnosis and intervention. Recent trend shows increasing resistance to commonly used antibiotics.</div></div><div><h3>Aims and objectives</h3><div>To study the antimicrobial resistance pattern in blood culture positive neonatal sepsis in outborn and inborn neonates and to compare the clinical profile in neonates with proven sepsis.</div></div><div><h3>Methods</h3><div>Bacterial cultures of the blood samples received from neonates with suspected sepsis was performed and antimicrobial susceptibility testing of blood culture positive neonates was done. Antibiotic sensitivity tests were done as per Clinical and Laboratory Standards Institute (CLSI) 2023 guidelines.</div></div><div><h3>Results</h3><div>Of the 100 participants, 34 were early onset neonatal sepsis and 66 were late onset neonatal sepsis. 35 % of the delivery were vaginal whereas 65 % of the deliveries were by Caesarean section. 17 % of the total neonates delivered had to undergo neonatal resuscitation and 36 % of the neonates had birth asphyxia. The most commonly isolated organisms were Coagulase-negative Staphylococcus species (CoNS) (30 %) followed by <em>Klebsiella pneumoniae</em> (21 %) and <em>Acinetobacter baumannii complex</em> (20 %). 45.1 % were Extended Spectrum beta lactamase (ESBL) producers and 58 % were AmpC beta lactamases producers.</div><div>Case fatality rate was highest with <em>Klebsiella pneumoniae</em> i.e. 34.6 % followed by <em>Acinetobacter baumannii complex</em> i.e. 23.07 %.</div></div><div><h3>Conclusion</h3><div>Increase in antibiotic resistance organisms can lead to an increase in the neonatal case fatality rate (CFR), so regular surveillance is needed. Comparison between the resistance profile between inborn and outborn neonates provides an insight into the difference in the variety of organisms isolated and also the difference in resistance shown by community acquired and hospital acquired organisms.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"59 ","pages":"Article 101023"},"PeriodicalIF":1.3,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145573097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abdominal tuberculosis (TB) poses diagnostic difficulties due to its vague symptoms and low bacterial load. Culture, the gold standard, is limited by a prolonged turnaround time of up to eight weeks. Xpert MTB/RIF Ultra (Xpert Ultra), a rapid, automated molecular test, can detect Mycobacterium tuberculosis and rifampicin resistance in under two hours. This study evaluated the diagnostic accuracy of Xpert Ultra for abdominal TB using both culture and a composite reference standard (CRS), and assessed its agreement in rifampicin resistance detection with phenotypic and genotypic drug susceptibility testing (DST).
Methods
A prospective observational study was conducted from September 2019 to March 2021 at a tertiary care centre in North India. Adults with clinical and radiological features of abdominal TB were enrolled. Relevant abdominal samples were collected and tested using smear, culture (BACTEC MGIT 960), Xpert Ultra, histopathology, and clinical response. Rifampicin resistance was confirmed using MGIT 960 and GenoType MTBDRplus.
Results
Of 176 eligible patients, 144 were enrolled, yielding 152 abdominal samples: lymph node aspirates (52%), biopsies (42.8%), pus/aspirates (3.3%), and ascitic/omental fluids (2%). Xpert Ultra showed 84% diagnostic accuracy against CRS and 75% against culture. Rifampicin resistance detection showed 100% concordance with both phenotypic and genotypic DST.
Conclusion
Xpert Ultra offers high diagnostic accuracy and excellent concordance in rifampicin resistance detection for abdominal TB. Its speed and reliability make it a valuable diagnostic tool in high-burden settings.
{"title":"Diagnostic accuracy of Xpert MTB/RIF Ultra for abdominal tuberculosis in a tertiary care setting in North India","authors":"Anuj Pathak , Reena Raveendran , Jaswinder Kaur Oberoi , Chand Wattal , Anil Arora , Vikas Singla","doi":"10.1016/j.ijmmb.2025.101008","DOIUrl":"10.1016/j.ijmmb.2025.101008","url":null,"abstract":"<div><h3>Background</h3><div>Abdominal tuberculosis (TB) poses diagnostic difficulties due to its vague symptoms and low bacterial load. Culture, the gold standard, is limited by a prolonged turnaround time of up to eight weeks. Xpert MTB/RIF Ultra (Xpert Ultra), a rapid, automated molecular test, can detect Mycobacterium tuberculosis and rifampicin resistance in under two hours. This study evaluated the diagnostic accuracy of Xpert Ultra for abdominal TB using both culture and a composite reference standard (CRS), and assessed its agreement in rifampicin resistance detection with phenotypic and genotypic drug susceptibility testing (DST).</div></div><div><h3>Methods</h3><div>A prospective observational study was conducted from September 2019 to March 2021 at a tertiary care centre in North India. Adults with clinical and radiological features of abdominal TB were enrolled. Relevant abdominal samples were collected and tested using smear, culture (BACTEC MGIT 960), Xpert Ultra, histopathology, and clinical response. Rifampicin resistance was confirmed using MGIT 960 and GenoType MTBDRplus.</div></div><div><h3>Results</h3><div>Of 176 eligible patients, 144 were enrolled, yielding 152 abdominal samples: lymph node aspirates (52%), biopsies (42.8%), pus/aspirates (3.3%), and ascitic/omental fluids (2%). Xpert Ultra showed 84% diagnostic accuracy against CRS and 75% against culture. Rifampicin resistance detection showed 100% concordance with both phenotypic and genotypic DST.</div></div><div><h3>Conclusion</h3><div>Xpert Ultra offers high diagnostic accuracy and excellent concordance in rifampicin resistance detection for abdominal TB. Its speed and reliability make it a valuable diagnostic tool in high-burden settings.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"59 ","pages":"Article 101008"},"PeriodicalIF":1.3,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145523285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-11DOI: 10.1016/j.ijmmb.2025.101009
Shikhir Malhotra, Vibhor Tak
{"title":"Recurrent MALDI-TOF MS identification failure for Sphingomonas paucimobilis from blood cultures: A single-center observation","authors":"Shikhir Malhotra, Vibhor Tak","doi":"10.1016/j.ijmmb.2025.101009","DOIUrl":"10.1016/j.ijmmb.2025.101009","url":null,"abstract":"","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"59 ","pages":"Article 101009"},"PeriodicalIF":1.3,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145512646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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