Pub Date : 2026-01-28DOI: 10.1016/j.ijmmb.2026.101070
Victor O. Azuh , Samia S. Alkhalil , Oludare Temitope Osuntokun , Oluwafemi Adebayo Oyewole , Oluwafunmilayo Theresa Jimoh , Naga Raju Maddela
Background
Escherichia coli is a bacterium that lives in both human and animal intestines and it is one of the first bacteria to infiltrate the intestine. The majority of E. coli strains are benign; however, some serotypes can infect people and animals with illnesses. The genomes of E. coli and Shigella spp. are closely related phenotypically, serotypically, biochemically, clinically and molecularly.
Methods
Loop-mediated isothermal amplification (LAMP) assay was designed to accelerate E. coli detection and verify its specificity for different Shigella species and selected members of Enterobacteriaceae using specific LAMP primers designed along the E. colifliF gene region. For the E. coli sensitivity test, varying concentrations of betaine and MgSO4 were used to set up a LAMP reaction to detect 10 E. coli isolates and Enterobacteriaceae. The LAMP results interpretation was based on gel and colour change using SYBR green.
Results
Results showed that for varying combinations of betaine and MgSO4 employed, 1.5 μL betaine and 1.0 μL MgSO4 gave the best amplification. The LAMP reaction amplified all E. coli strains used and did not amplify other Enterobacteriaceae indicating sensitivity and specificity.
Conclusion
This study showed that this LAMP protocol can be used to detect E. coli among members of Enterobacteriaceae rapidly.
{"title":"Loop-mediated isothermal amplification (LAMP) assay for rapid detection and differentiation of selected Escherichia coli from other Enterobacteriaceae","authors":"Victor O. Azuh , Samia S. Alkhalil , Oludare Temitope Osuntokun , Oluwafemi Adebayo Oyewole , Oluwafunmilayo Theresa Jimoh , Naga Raju Maddela","doi":"10.1016/j.ijmmb.2026.101070","DOIUrl":"10.1016/j.ijmmb.2026.101070","url":null,"abstract":"<div><h3>Background</h3><div><em>Escherichia coli</em> is a bacterium that lives in both human and animal intestines and it is one of the first bacteria to infiltrate the intestine. The majority of <em>E. coli</em> strains are benign; however, some serotypes can infect people and animals with illnesses. The genomes of <em>E. coli</em> and <em>Shigella</em> spp. are closely related phenotypically, serotypically, biochemically, clinically and molecularly.</div></div><div><h3>Methods</h3><div>Loop-mediated isothermal amplification (LAMP) assay was designed to accelerate <em>E. coli</em> detection and verify its specificity for different <em>Shigella</em> species and selected members of Enterobacteriaceae using specific LAMP primers designed along the <em>E. coli</em> <em>fliF</em> gene region. For the <em>E. coli</em> sensitivity test, varying concentrations of betaine and MgSO<sub>4</sub> were used to set up a LAMP reaction to detect 10 <em>E. coli</em> isolates and Enterobacteriaceae. The LAMP results interpretation was based on gel and colour change using SYBR green.</div></div><div><h3>Results</h3><div>Results showed that for varying combinations of betaine and MgSO<sub>4</sub> employed, 1.5 μL betaine and 1.0 μL MgSO<sub>4</sub> gave the best amplification. The LAMP reaction amplified all <em>E. coli</em> strains used and did not amplify other Enterobacteriaceae indicating sensitivity and specificity.</div></div><div><h3>Conclusion</h3><div>This study showed that this LAMP protocol can be used to detect <em>E. coli</em> among members of Enterobacteriaceae rapidly.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"60 ","pages":"Article 101070"},"PeriodicalIF":1.3,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146090191","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 : 2026-01-27DOI: 10.1016/j.ijmmb.2026.101066
Sonya Joy , Neethu Susan Philip , Neetha Soma John
Purpose
Acute respiratory infections (ARIs) are a major global health concern, causing over 4 million deaths annually, particularly in developing countries. Traditional diagnostic methods, such as microbial culture, are slow, leading to delayed treatment and increased antimicrobial resistance (AMR). This study evaluates the BIOFIRE Pneumonia Plus panel, a multiplex PCR-based assay, for detecting bacterial and viral pathogens and AMR genes in bronchoalveolar lavage (BAL) specimens.
Methods
A method-comparison study was conducted in a tertiary care setting using identified clinical data over one year. BAL specimens were analyzed using the BIOFIRE Pneumonia Plus panel and standard culture, and their results and turnaround times were compared.
Results
Among 303 specimens, the BIOFIRE Pneumonia Plus panel detected pathogens in 70.3 % of cases, significantly outperforming standard culture (14.85 %). The most frequently identified bacteria were Pseudomonas aeruginosa (20.08 %), Klebsiella pneumoniae (17.15 %), and Haemophilus influenzae (16.31 %). The most common viruses detected were human rhinovirus/enterovirus (18.81 %) and influenza A (9.24 %). AMR genes were found in 24.09 % of cases, with CTX-M and NDM being the most prevalent. The BIOFIRE panel provided results in 2 h 35 min, compared to 56 h 46 min for standard culture.
Conclusion
The BIOFIRE Pneumonia Plus panel enables rapid and accurate pathogen detection, improving clinical decision-making and supporting antimicrobial stewardship. Despite limitations such as the detection of colonizers or non-viable microorganisms, it is a valuable tool for enhancing ARI diagnostics and guiding targeted therapy.
{"title":"Multiplex pneumonia panel for diagnosis of critically ill pneumonia patients in a tertiary care setting: A retrospective study","authors":"Sonya Joy , Neethu Susan Philip , Neetha Soma John","doi":"10.1016/j.ijmmb.2026.101066","DOIUrl":"10.1016/j.ijmmb.2026.101066","url":null,"abstract":"<div><h3>Purpose</h3><div>Acute respiratory infections (ARIs) are a major global health concern, causing over 4 million deaths annually, particularly in developing countries. Traditional diagnostic methods, such as microbial culture, are slow, leading to delayed treatment and increased antimicrobial resistance (AMR). This study evaluates the BIOFIRE Pneumonia Plus panel, a multiplex PCR-based assay, for detecting bacterial and viral pathogens and AMR genes in bronchoalveolar lavage (BAL) specimens.</div></div><div><h3>Methods</h3><div>A method-comparison study was conducted in a tertiary care setting using identified clinical data over one year. BAL specimens were analyzed using the BIOFIRE Pneumonia Plus panel and standard culture, and their results and turnaround times were compared.</div></div><div><h3>Results</h3><div>Among 303 specimens, the BIOFIRE Pneumonia Plus panel detected pathogens in 70.3 % of cases, significantly outperforming standard culture (14.85 %). The most frequently identified bacteria were <em>Pseudomonas aeruginosa</em> (20.08 %), <em>Klebsiella pneumoniae</em> (17.15 %), and <em>Haemophilus influenzae</em> (16.31 %). The most common viruses detected were human rhinovirus/enterovirus (18.81 %) and influenza A (9.24 %). AMR genes were found in 24.09 % of cases, with CTX-M and NDM being the most prevalent. The BIOFIRE panel provided results in 2 h 35 min, compared to 56 h 46 min for standard culture.</div></div><div><h3>Conclusion</h3><div>The BIOFIRE Pneumonia Plus panel enables rapid and accurate pathogen detection, improving clinical decision-making and supporting antimicrobial stewardship. Despite limitations such as the detection of colonizers or non-viable microorganisms, it is a valuable tool for enhancing ARI diagnostics and guiding targeted therapy.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"60 ","pages":"Article 101066"},"PeriodicalIF":1.3,"publicationDate":"2026-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146085598","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 : 2026-01-24DOI: 10.1016/j.ijmmb.2026.101068
Deepak Y. Patil , Rima R. Sahay , Anita M. Shete , Shubin Chenayil , Nandan Mohite , Harsha C. Palav , Juhi Khurana , Vainav Patel , Pragya D. Yadav
Background
Mpox and buffalopox are zoonotic viral infections which demonstrate distinct clinical and immune profile. This study examines the clinical presentation with genomic and immunological characteristics among three confirmed cases of Mpox Clade IIb-A.2.1 and Clade Ib infections and a buffalopox from Malappuram, Kerala, India.
Methods
Immunophenotyping via flow cytometry was used to assess T, B, Natural Killer (NK) cells, and monocytes. The viral DNA, Anti-Mpox IgG/IgM, and anti-BPXV IgG were detected using real time PCR and ELISA respectively. Genomic characterization was performed using next generation sequencing. MAFFT alignment and IQ-TREE2 with maximum likelihood method was used for phylogenetic analysis.
Results
Clinically, vesiculo-pustular lesions detected in Mpoxv infection were more severe in Clade Ib patient along with penile edema and gangrenous eschar. The face and hands were primarily affected in BPXV infection. Immunological analysis demonstrated notable differences where Mpoxv infection exhibited major increase in lymphocytes and NK cells and differential activation patterns of immune T-cell population. During BPXV infection, B-cell numbers rose with expansion of mucosal-homing B-cells. IgM and IgG responses differed among infections, where Mpoxv Clade Ib generated early but transient IgM and low IgG titer, while Clade IIb-A.2.1 and BPXV exhibited prolonged IgG response. Genomic analysis revealed deletion in diagnostic region in Clade Ib, albeit Clade IIb showed host-derived mutations. The multiple genomic alignments revealed distinct immunological responses and vaccine development capacity of orthopoxviruses.
Conclusion
The findings of the study emphasizes the need for extensive genomic surveillance and immunological research. This will help in understanding the pattern of virus evolution and host immune responses in orthopoxvirus infections.
{"title":"Immunological signatures and genomic adaptations in Human Mpox Clade Ib and IIb and Buffalopox Infections in India","authors":"Deepak Y. Patil , Rima R. Sahay , Anita M. Shete , Shubin Chenayil , Nandan Mohite , Harsha C. Palav , Juhi Khurana , Vainav Patel , Pragya D. Yadav","doi":"10.1016/j.ijmmb.2026.101068","DOIUrl":"10.1016/j.ijmmb.2026.101068","url":null,"abstract":"<div><h3>Background</h3><div>Mpox and buffalopox are zoonotic viral infections which demonstrate distinct clinical and immune profile. This study examines the clinical presentation with genomic and immunological characteristics among three confirmed cases of Mpox Clade IIb-A.2.1 and Clade Ib infections and a buffalopox from Malappuram, Kerala, India.</div></div><div><h3>Methods</h3><div>Immunophenotyping via flow cytometry was used to assess T, B, Natural Killer (NK) cells, and monocytes. The viral DNA, Anti-Mpox IgG/IgM, and anti-BPXV IgG were detected using real time PCR and ELISA respectively. Genomic characterization was performed using next generation sequencing. MAFFT alignment and IQ-TREE2 with maximum likelihood method was used for phylogenetic analysis.</div></div><div><h3>Results</h3><div>Clinically, vesiculo-pustular lesions detected in Mpoxv infection were more severe in Clade Ib patient along with penile edema and gangrenous eschar. The face and hands were primarily affected in BPXV infection. Immunological analysis demonstrated notable differences where Mpoxv infection exhibited major increase in lymphocytes and NK cells and differential activation patterns of immune T-cell population. During BPXV infection, B-cell numbers rose with expansion of mucosal-homing B-cells. IgM and IgG responses differed among infections, where Mpoxv Clade Ib generated early but transient IgM and low IgG titer, while Clade IIb-A.2.1 and BPXV exhibited prolonged IgG response. Genomic analysis revealed deletion in diagnostic region in Clade Ib, albeit Clade IIb showed host-derived mutations. The multiple genomic alignments revealed distinct immunological responses and vaccine development capacity of <em>orthopoxviruses</em>.</div></div><div><h3>Conclusion</h3><div>The findings of the study emphasizes the need for extensive genomic surveillance and immunological research. This will help in understanding the pattern of virus evolution and host immune responses in <em>orthopoxvirus</em> infections.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"60 ","pages":"Article 101068"},"PeriodicalIF":1.3,"publicationDate":"2026-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146051819","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}
Carbapenem resistance in Klebsiella pneumoniae (Kp) has led to increased use of colistin-based therapy in the intensive care units (ICUs). Lately however, colistin resistance among K. pneumoniae has been widely reported. This study aims to investigate the prevalence, and the potential risk factors associated with colistin resistant K. pneumoniae (ColRKp) in the intensive care unit (ICU).
Materials and methods
All ICU patients, above 18 years of age, with a culture positive blood stream infection were included. A case–control–control design was used. Patients with colistin resistant K. pneumoniae (ColRKp) blood stream infections (BSI) were defined as cases. These were compared to two control populations, Control Group A had Kp infections moderately sensitive to colistin (ColMSKp); and control group B who had other bacterial infections. 50 ColRKp isolates were subjected to whole genome sequencing (WGS).
Results
Lungs as the source of infection (13.9 % vs 6.4 %, p ≤ 0.05) and longer hospital stay (26 days vs 22 days, p ≤ 0.05) were the significant risk factors which correlated with acquisition of colistin resistance in Klebsiella pneumoniae. An increased 28-day mortality was noticed in control groups who were given colistin based upon their in vitro sensitivity, (group A, 79 % and group B, 75.8 %) compared to cases (56.9 %). From among the ColRKp isolates subjected to WGS, 72 % (n = 36) carried NDM with OXA-48 like (OXA-181/232) carbapenemases. Mutations were found in pmrA, in pmrB, pmrC and pmrABC gene. None of the isolates had insertion in mgrB gene, all isolates were negative for mcr gene variants.
Conclusions
Both NDM and OXA-48 like carbapenemases were present in ColRKp. Patients receiving colistin therapy based on their in vitro sensitivity had increased risk for developing resistance to colistin and 28-day mortality.
肺炎克雷伯菌（Kp）的碳青霉烯耐药性导致重症监护病房（icu）中以粘菌素为基础的治疗的使用增加。然而最近，肺炎克雷伯菌的粘菌素耐药性已被广泛报道。本研究旨在调查重症监护病房（ICU）耐粘菌素肺炎克雷伯菌（ColRKp）的患病率及潜在危险因素。材料与方法：所有ICU患者，年龄大于18岁，培养阳性血流感染。采用病例-对照-对照设计。耐粘菌素肺炎克雷伯菌（ColRKp）血流感染（BSI）患者定义为病例。与两个对照人群进行比较，对照组A对粘菌素（ColMSKp）中度敏感的Kp感染；对照组B有其他细菌感染。对50株ColRKp进行全基因组测序（WGS）。结果：肺部为感染源（13.9% vs 6.4%, p≤0.05）和住院时间较长（26 d vs 22 d, p≤0.05）是肺炎克雷伯菌获得粘菌素耐药的重要危险因素。根据体外敏感性给予粘菌素的对照组28天死亡率（A组为79%，B组为75.8%）高于病例（56.9%）。在WGS作用的ColRKp分离株中，72% （n=36）携带具有OXA-48样（OXA-181/232）碳青霉烯酶的NDM。pmrA、pmrB、pmrC和pmrABC基因均发生突变。所有分离株均未插入mgrB基因，mcr基因变异均为阴性。结论：ColRKp中存在NDM和OXA-48样碳青霉烯酶。根据体外敏感性接受粘菌素治疗的患者对粘菌素产生耐药性和28天死亡率的风险增加。
{"title":"Risk factors and outcome associated with the acquisition of colistin-resistant Klebsiella pneumoniae: A matched case-control-control study","authors":"Prakash Shastri , Yamuna Devi Bakthavatchalam , Vijit Jaiswal , Chand Wattal , Balaji Veeraraghavan","doi":"10.1016/j.ijmmb.2026.101052","DOIUrl":"10.1016/j.ijmmb.2026.101052","url":null,"abstract":"<div><h3>Introduction</h3><div>Carbapenem resistance in <em>Klebsiella pneumoniae</em> (Kp) has led to increased use of colistin-based therapy in the intensive care units (ICUs). Lately however, colistin resistance among <em>K. pneumoniae</em> has been widely reported. This study aims to investigate the prevalence, and the potential risk factors associated with colistin resistant <em>K. pneumoniae</em> (ColRKp) in the intensive care unit (ICU).</div></div><div><h3>Materials and methods</h3><div>All ICU patients, above 18 years of age, with a culture positive blood stream infection were included. A case–control–control design was used. Patients with colistin resistant <em>K. pneumoniae</em> (ColRKp) blood stream infections (BSI) were defined as cases. These were compared to two control populations, Control Group A had Kp infections moderately sensitive to colistin (ColMSKp); and control group B who had other bacterial infections. 50 ColRKp isolates were subjected to whole genome sequencing (WGS).</div></div><div><h3>Results</h3><div>Lungs as the source of infection (13.9 % vs 6.4 %, p ≤ 0.05) and longer hospital stay (26 days vs 22 days, p ≤ 0.05) were the significant risk factors which correlated with acquisition of colistin resistance in <em>Klebsiella pneumoniae</em>. An increased 28-day mortality was noticed in control groups who were given colistin based upon their in vitro sensitivity, (group A, 79 % and group B, 75.8 %) compared to cases (56.9 %). From among the ColRKp isolates subjected to WGS, 72 % (n = 36) carried NDM with OXA-48 like (OXA-181/232) carbapenemases. Mutations were found in pmrA, in pmrB, pmrC and pmrABC gene. None of the isolates had insertion in mgrB gene, all isolates were negative for mcr gene variants.</div></div><div><h3>Conclusions</h3><div>Both NDM and OXA-48 like carbapenemases were present in ColRKp. Patients receiving colistin therapy based on their in vitro sensitivity had increased risk for developing resistance to colistin and 28-day mortality.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"60 ","pages":"Article 101052"},"PeriodicalIF":1.3,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146043548","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}
Staphylococcus aureus is an important pathogen exhibiting antibiotic resistance and multiple virulence factors. This study analyses the antimicrobial resistance and virulence genes of Staphylococcus aureus isolates from HIV and non-HIV patients from southern India.
Methods
S. aureus strains from HIV (n = 125) and non-HIV (n = 100) patients were isolated using conventional bacterial culture techniques. Antimicrobial resistance and virulence genes were analysed using polymerase chain reaction (PCR).
Results
Methicillin resistance was detected in 88.8 % and 34 % of the S. aureus isolates from HIV and non-HIV patients, respectively, and all tested positive for the mecA gene. SCCmec type V was the most frequently detected SCCmec cassette in MRSA from both HIV (55.2%) and non-HIV patients (44.4 %). MRSA isolates from HIV patients were 98.2 % positive for the penicillin resistance gene blaZ, followed by the aminoglycoside resistance genes aacA-aphD (82 %), aac(6′)/aph(2″) (75.7 %) and aph(3″)-IIIa (51.4 %), the tetracycline resistance genes tet(K) (42.3 %) and tet(M) (13.5 %) and the erythromycin resistance genes erm(C) (55 %). Among the non-HIV-infected MRSA strains, 73.5 % were positive for blaZ, followed by aac(6’)/aph(2″) (50 %), aacA-aphD (47.1 %), aph(3”)-IIIa (23.5 %), and erm(C) (29.4 %). The seb (7.2 %), sea (5.4 %), seb and sed (2.7 %), exfoliative toxin gene eta (3.6 %) and toxic shock syndrome toxin gene tst (8.1 %) were detected among MRSA from HIV patients, and the sea (5.9 %), sec (5.9 %), eta (5.9 %) and tst (8.8 %) were found among MRSA from non-HIV patients.
Conclusions
HIV patients are at a relatively greater risk of acquiring virulent and multidrug-resistant methicillin-resistant S. aureus infections than non-HIV patients.
{"title":"Molecular profiling of virulence determinants and antimicrobial resistance in MRSA isolates from HIV-infected and non-HIV individuals","authors":"Marimuthu Ragavan Rameshkumar , Ramachandran Vignesh , Pachamuthu Balakrishnan , Narasingam Arunagirinathan","doi":"10.1016/j.ijmmb.2026.101064","DOIUrl":"10.1016/j.ijmmb.2026.101064","url":null,"abstract":"<div><h3>Background</h3><div><em>Staphylococcus aureus</em> is an important pathogen exhibiting antibiotic resistance and multiple virulence factors. This study analyses the antimicrobial resistance and virulence genes of <em>Staphylococcus aureus</em> isolates from HIV and non-HIV patients from southern India.</div></div><div><h3>Methods</h3><div><em>S. aureus</em> strains from HIV (n = 125) and non-HIV (n = 100) patients were isolated using conventional bacterial culture techniques. Antimicrobial resistance and virulence genes were analysed using polymerase chain reaction (PCR).</div></div><div><h3>Results</h3><div>Methicillin resistance was detected in 88.8 % and 34 % of the <em>S. aureus</em> isolates from HIV and non-HIV patients, respectively, and all tested positive for the <em>mecA</em> gene. SCC<em>mec</em> type V was the most frequently detected SCC<em>mec</em> cassette in MRSA from both HIV (55.2%) and non-HIV patients (44.4 %). MRSA isolates from HIV patients were 98.2 % positive for the penicillin resistance gene <em>blaZ</em>, followed by the aminoglycoside resistance genes <em>aacA-aphD</em> (82 %), <em>aac(6′)/aph(2″)</em> (75.7 %) and <em>aph(3″)-IIIa</em> (51.4 %), the tetracycline resistance genes <em>tet(K)</em> (42.3 %) and <em>tet(M)</em> (13.5 %) and the erythromycin resistance genes <em>erm(C)</em> (55 %). Among the non-HIV-infected MRSA strains, 73.5 % were positive for <em>blaZ</em>, followed by <em>aac</em><em>(6’)/aph(2″)</em> (50 %)<em>, aacA-aphD</em> (47.1 %)<em>, aph(3”)-IIIa</em> (23.5 %)<em>,</em> and <em>erm(C)</em> (29.4 %)<em>.</em> The <em>seb</em> (7.2 %), <em>sea</em> (5.4 %), <em>seb</em> and <em>sed</em> (2.7 %), exfoliative toxin gene <em>eta</em> (3.6 %) and toxic shock syndrome toxin gene <em>tst</em> (8.1 %) were detected among MRSA from HIV patients, and the <em>sea</em> (5.9 %), <em>sec</em> (5.9 %), <em>eta</em> (5.9 %) and <em>tst</em> (8.8 %) were found among MRSA from non-HIV patients.</div></div><div><h3>Conclusions</h3><div>HIV patients are at a relatively greater risk of acquiring virulent and multidrug-resistant methicillin-resistant <em>S. aureus</em> infections than non-HIV patients.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"60 ","pages":"Article 101064"},"PeriodicalIF":1.3,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146043976","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}
Urine antigen testing seems promising tool to detect tuberculosis but data is scarce for pulmonary and extrapulmonary tuberculosis in HIV negative population.
Aims
This prospective cross-sectional study was designed to assess the urinary lipoarabinomannan antigen (LAM) diagnostic accuracy of pulmonary and extrapulmonary tuberculosis in HIV negative population.
Materials & methods
Suspected pulmonary (PTB) and extrapulmonary tuberculosis (EPTB) patients were enrolled and samples were subjected to routine diagnostic modalities. Urine samples were subjected to LAM test using lateral flow assay of Abbott TB LAM & results were statistically evaluated to gold standard culture, microbiological reference standards (MRS).
Results
Total 224 patients of suspected tuberculosis were enrolled in the study (23.21 % PTB and 76.79 % EPTB). Microbiologically confirmed tuberculosis was detected in 44 (19.6 %), PTB (48.0 %) & EPTB (11.0 %) cases. Mycobacterium tuberculosis was detected in ZN stain (16.5 %), MGIT liquid culture (14.7 %), Gene-Xpert MTB/Rif (17.4 %), urinary LAM (22.7 %). Sensitivity, specificity, PPV and NPV of urine LAM against the gold standard test (MGIT) were 60.61 %, 83.77 %, 39.22 %, 92.49 %; and as per the MRS criteria these values were 48.0 %, 84.5 %, 47.1 %, 85.0 % respectively. Among smear positive samples sensitivity, specificity, PPV, NPV of LAM were 65.5 %, 50.0 %, 82.6 %, 28.6 % respectively.
Conclusion
Urine LAM performed better than previously reported in HIV-negative populations but remains suboptimal as a point-of-care test. This study showed higher sensitivity and PPV for pulmonary TB in MRS smear-positive cases, better specificity and NPV for extrapulmonary TB, good performance in smear-negative extrapulmonary TB, and promising utility in unconfirmed TB.
{"title":"Diagnostic accuracy of urinary lipoarabinomannan antigen detection for the diagnosis of pulmonary and extra pulmonary tuberculosis (EPTB) in HIV negative population","authors":"Kiran Bala , Rekha Rathee , Prayas Sethi , Praveen Bharti , Bhavuk Garg , Anant Mohan , Urvashi B. Singh","doi":"10.1016/j.ijmmb.2026.101053","DOIUrl":"10.1016/j.ijmmb.2026.101053","url":null,"abstract":"<div><h3>Background</h3><div>Urine antigen testing seems promising tool to detect tuberculosis but data is scarce for pulmonary and extrapulmonary tuberculosis in HIV negative population.</div></div><div><h3>Aims</h3><div>This prospective cross-sectional study was designed to assess the urinary lipoarabinomannan antigen (LAM) diagnostic accuracy of pulmonary and extrapulmonary tuberculosis in HIV negative population.</div></div><div><h3>Materials & methods</h3><div>Suspected pulmonary (PTB) and extrapulmonary tuberculosis (EPTB) patients were enrolled and samples were subjected to routine diagnostic modalities. Urine samples were subjected to LAM test using lateral flow assay of Abbott TB LAM & results were statistically evaluated to gold standard culture, microbiological reference standards (MRS).</div></div><div><h3>Results</h3><div>Total 224 patients of suspected tuberculosis were enrolled in the study (23.21 % PTB and 76.79 % EPTB). Microbiologically confirmed tuberculosis was detected in 44 (19.6 %), PTB (48.0 %) & EPTB (11.0 %) cases. <em>Mycobacterium tuberculosis</em> was detected in ZN stain (16.5 %), MGIT liquid culture (14.7 %), Gene-Xpert MTB/Rif (17.4 %), urinary LAM (22.7 %). Sensitivity, specificity, PPV and NPV of urine LAM against the gold standard test (MGIT) were 60.61 %, 83.77 %, 39.22 %, 92.49 %; and as per the MRS criteria these values were 48.0 %, 84.5 %, 47.1 %, 85.0 % respectively. Among smear positive samples sensitivity, specificity, PPV, NPV of LAM were 65.5 %, 50.0 %, 82.6 %, 28.6 % respectively.</div></div><div><h3>Conclusion</h3><div>Urine LAM performed better than previously reported in HIV-negative populations but remains suboptimal as a point-of-care test. This study showed higher sensitivity and PPV for pulmonary TB in MRS smear-positive cases, better specificity and NPV for extrapulmonary TB, good performance in smear-negative extrapulmonary TB, and promising utility in unconfirmed TB.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"60 ","pages":"Article 101053"},"PeriodicalIF":1.3,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146035753","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 : 2026-01-21DOI: 10.1016/j.ijmmb.2026.101065
Gülşah Ece Özmerdiven, Arzu İrvem
Purpose
The aim of this study is to evaluate the effectiveness of VITEK®2 and CHROMagar™ Candida Plus agar in the identification of C. auris, using MALDI-TOF MS results as the reference standard. Additionally, to assess antifungal susceptibility, the study compares the results of two widely used commercial methods in routine laboratory practice: VITEK®2 and Sensititre™ YeastOne™ (SYO).
Methods
A total of 63 C. auris isolates were included in the study. VITEK®2 results were evaluated in comparison to SYO, and categorical agreement, major error (ME), and very major error (VME) rates were calculated. MIC50, MIC90 values and resistance rates determined by both methods were compared. The Eagle effect was also investigated.
Results
The VITEK®2 results (74 %) and the morphological characteristics of colonies grown on CHROMagar™ Candida Plus (100 %) were found to be consistent with MALDI-TOF MS identification. In the SYO method, the MIC values for amphotericin B, fluconazole, and voriconazole were found to be higher compared to those obtained by VITEK®2. No resistance was detected against micafungin and anidulafungin. Resistance observed in relation to caspofungin MIC values was identified as the Eagle effect. MIC50 and MIC90 values determined by VITEK®2 were lower than those obtained by SYO, except for amphotericin B, for which VITEK®2 showed a higher MIC90 value.
Conclusion
In our study, it was observed that CHROMagar™ Candida Plus can be used as a screening method for the identification of C. auris in hospitals without access to MALDI-TOF MS. Incompatibility was detected in antifungal susceptibility testing, and the rates of major error (ME) and very major error (VME) were found to be high. For caspofungin, the high dilution range in the SYO method was determined which also detected the Eagle effect.
{"title":"Candidozyma auris: Identification, antifungal susceptibility, and caspofungin-induced paradoxical growth","authors":"Gülşah Ece Özmerdiven, Arzu İrvem","doi":"10.1016/j.ijmmb.2026.101065","DOIUrl":"10.1016/j.ijmmb.2026.101065","url":null,"abstract":"<div><h3>Purpose</h3><div>The aim of this study is to evaluate the effectiveness of VITEK®2 and CHROMagar™ <em>Candida</em> Plus agar in the identification of <em>C. auris</em>, using MALDI-TOF MS results as the reference standard. Additionally, to assess antifungal susceptibility, the study compares the results of two widely used commercial methods in routine laboratory practice: VITEK®2 and Sensititre™ YeastOne™ (SYO).</div></div><div><h3>Methods</h3><div>A total of 63 <em>C. auris</em> isolates were included in the study. VITEK®2 results were evaluated in comparison to SYO, and categorical agreement, major error (ME), and very major error (VME) rates were calculated. MIC50, MIC90 values and resistance rates determined by both methods were compared. The Eagle effect was also investigated.</div></div><div><h3>Results</h3><div>The VITEK®2 results (74 %) and the morphological characteristics of colonies grown on CHROMagar™ <em>Candida</em> Plus (100 %) were found to be consistent with MALDI-TOF MS identification. In the SYO method, the MIC values for amphotericin B, fluconazole, and voriconazole were found to be higher compared to those obtained by VITEK®2. No resistance was detected against micafungin and anidulafungin. Resistance observed in relation to caspofungin MIC values was identified as the Eagle effect. MIC50 and MIC90 values determined by VITEK®2 were lower than those obtained by SYO, except for amphotericin B, for which VITEK®2 showed a higher MIC90 value.</div></div><div><h3>Conclusion</h3><div>In our study, it was observed that CHROMagar™ <em>Candida</em> Plus can be used as a screening method for the identification of <em>C. auris</em> in hospitals without access to MALDI-TOF MS. Incompatibility was detected in antifungal susceptibility testing, and the rates of major error (ME) and very major error (VME) were found to be high. For caspofungin, the high dilution range in the SYO method was determined which also detected the Eagle effect.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"60 ","pages":"Article 101065"},"PeriodicalIF":1.3,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146040574","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}
Antibiotic resistance is a growing concern in the fight against Escherichia coli, a pathogen that causes various intestinal diseases. The present study explores the antibacterial effect of lactobacillus on E. coli pathotypes.
Methods
Inpatients stool samples were collected and E. coli pathotypes were identified. The antibacterial effect of five Lactobacillus on the pathotypes was investigated by broth microdilution and well diffusion methods.
Results
The CFS of L. plantarum, L. rueteri and L. acidophilus had the greatest antibacterial effect.
Conclusion
Postbiotics have shown significant bactericidal effects against E. coli pathotypes. Their bactericidal effect can prevent the colonization of these pathotypes in hospitalized patients.
{"title":"Antimicrobial activity of native Lactobacillus cell-free supernatant against diarrheagenic Escherichia coli isolated from hospitalized patients in northern Iran","authors":"Farzaneh Rafie Sedaghat , Ali Mojtahedi , Meysam Hasannejad-Bibalan , Tofigh Yaghubi Kalurazi , Tohid Samadpour Zahmat-dar","doi":"10.1016/j.ijmmb.2026.101063","DOIUrl":"10.1016/j.ijmmb.2026.101063","url":null,"abstract":"<div><h3>Background and aims</h3><div>Antibiotic resistance is a growing concern in the fight against <em>Escherichia coli</em>, a pathogen that causes various intestinal diseases. The present study explores the antibacterial effect of <em>lactobacillus</em> on <em>E. coli</em> pathotypes.</div></div><div><h3>Methods</h3><div>Inpatients stool samples were collected and <em>E. coli</em> pathotypes were identified. The antibacterial effect of five <em>Lactobacillus</em> on the pathotypes was investigated by broth microdilution and well diffusion methods.</div></div><div><h3>Results</h3><div>The CFS of <em>L. plantarum, L. rueteri</em> and <em>L. acidophilus</em> had the greatest antibacterial effect.</div></div><div><h3>Conclusion</h3><div>Postbiotics have shown significant bactericidal effects against <em>E. coli</em> pathotypes. Their bactericidal effect can prevent the colonization of these pathotypes in hospitalized patients.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"60 ","pages":"Article 101063"},"PeriodicalIF":1.3,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146029397","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}
Acinetobacter baumannii, a leading cause of hospital-acquired infections in critically ill patients, is increasingly resistant to carbapenems, leading WHO to designate carbapenem-resistant Acinetobacter baumannii (CRAB) as a critical priority pathogen. While the 2024 IDSA guidelines recommend sulbactam-based regimens as the cornerstone of therapy, high-dose sulbactam is effective only against isolates with MICs up to 16–32 μg/mL. This study aimed to describe the sulbactam MIC distribution and to evaluate MIC reduction and synergy when combined with β-lactam antibiotics against CRAB.
Methods
CRAB isolates from respiratory samples of ventilator-associated pneumonia patients were tested using E-tests to determine MICs of individual antibiotics. Combinations of sulbactam with ceftriaxone, cefepime, and meropenem were assessed using the E-test cross method. Synergy was evaluated by the FIC index: synergy (≤0.5), additive (>0.5–1), indifference (>1–<4), and antagonism (≥4).
Results
Thirty-five non-duplicate CRAB isolates were tested. All isolates were resistant to ceftriaxone, cefepime, and meropenem when tested individually, with MICs exceeding E-test detection limits. Hence, although sulbactam combinations significantly reduced MICs, the resulting values often remained above CLSI-defined susceptibility breakpoints.
Notably, sulbactam alone showed an MIC50 of 12 μg/mL and an MIC90 of 24 μg/mL. In combination, sulbactam MIC50/MIC90 values were reduced to 8/24 μg/mL with ceftriaxone, 6/16 μg/mL with cefepime, and 8/24 μg/mL with meropenem.
Sulbactam–cefepime showed the highest synergy (11.43 %) and additive effects (34.29 %), followed by sulbactam–ceftriaxone (2.86 % synergy; 31.43 % additive). Sulbactam–meropenem showed no synergy but 31.43 % additive effects. No antagonism was observed with any combination.
Conclusion
Combining sulbactam with β-lactams, particularly cefepime, significantly reduced sulbactam MICs. However, the β-lactam MICs themselves remained largely within not-susceptible ranges, highlighting that the observed benefit was confined primarily to sulbactam rather than the companion β-lactams. These findings supported further clinical studies of high-dose sulbactam–β-lactam combinations to optimize the pharmacodynamic efficacy of sulbactam against CRAB strains with elevated MICs.
{"title":"“In vitro evaluation of sulbactam combination therapies for Acinetobacter baumannii”","authors":"Karthick Kumar Vaitheeswaran , Seema Sood , Manish Soneja , Animesh Ray , Shivam Pandey , Arti Kapil , Naveet Wig","doi":"10.1016/j.ijmmb.2026.101051","DOIUrl":"10.1016/j.ijmmb.2026.101051","url":null,"abstract":"<div><h3>Background and objectives</h3><div><em>Acinetobacter baumannii</em>, a leading cause of hospital-acquired infections in critically ill patients, is increasingly resistant to carbapenems, leading WHO to designate carbapenem-resistant <em>Acinetobacter baumannii</em> (CRAB) as a critical priority pathogen. While the 2024 IDSA guidelines recommend sulbactam-based regimens as the cornerstone of therapy, high-dose sulbactam is effective only against isolates with MICs up to 16–32 μg/mL. This study aimed to describe the sulbactam MIC distribution and to evaluate MIC reduction and synergy when combined with β-lactam antibiotics against CRAB.</div></div><div><h3>Methods</h3><div>CRAB isolates from respiratory samples of ventilator-associated pneumonia patients were tested using E-tests to determine MICs of individual antibiotics. Combinations of sulbactam with ceftriaxone, cefepime, and meropenem were assessed using the E-test cross method. Synergy was evaluated by the FIC index: synergy (≤0.5), additive (>0.5–1), indifference (>1–<4), and antagonism (≥4).</div></div><div><h3>Results</h3><div>Thirty-five non-duplicate CRAB isolates were tested. All isolates were resistant to ceftriaxone, cefepime, and meropenem when tested individually, with MICs exceeding E-test detection limits. Hence, although sulbactam combinations significantly reduced MICs, the resulting values often remained above CLSI-defined susceptibility breakpoints.</div><div>Notably, sulbactam alone showed an MIC<sub>50</sub> of 12 μg/mL and an MIC<sub>90</sub> of 24 μg/mL. In combination, sulbactam MIC<sub>50</sub>/MIC<sub>90</sub> values were reduced to 8/24 μg/mL with ceftriaxone, 6/16 μg/mL with cefepime, and 8/24 μg/mL with meropenem.</div><div>Sulbactam–cefepime showed the highest synergy (11.43 %) and additive effects (34.29 %), followed by sulbactam–ceftriaxone (2.86 % synergy; 31.43 % additive). Sulbactam–meropenem showed no synergy but 31.43 % additive effects. No antagonism was observed with any combination.</div></div><div><h3>Conclusion</h3><div>Combining sulbactam with β-lactams, particularly cefepime, significantly reduced sulbactam MICs. However, the β-lactam MICs themselves remained largely within not-susceptible ranges, highlighting that the observed benefit was confined primarily to sulbactam rather than the companion β-lactams. These findings supported further clinical studies of high-dose sulbactam–β-lactam combinations to optimize the pharmacodynamic efficacy of sulbactam against CRAB strains with elevated MICs.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"60 ","pages":"Article 101051"},"PeriodicalIF":1.3,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145998012","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 : 2026-01-16DOI: 10.1016/j.ijmmb.2026.101050
Jaya Biswas , Kiran Bala , Neha Nityadarshini , Leander Jose , Vivek Shankar , Urvashi B. Singh
Purpose
Spinal tuberculosis, a severe form of extrapulmonary tuberculosis, poses significant diagnostic and therapeutic challenges, often leading to neurological complications and deformity. Microbiological confirmation is crucial for diagnosis and effective treatment. We aim to evaluate the microbiological profile and diagnostic yield of various methods in spinal TB cases at a tertiary care centre and to correlate with clinical features and treatment outcomes.
Methods
A prospective study was conducted on samples from patients with suspected spinal TB (n = 58) from July 2023 to September 2024. All samples were processed using Ziehl-Neelsen (ZN) staining for acid-fast bacilli (AFB), culture on Lowenstein-Jensen (LJ) medium, BACTEC MGIT 960 liquid culture system, and GeneXpert MTB/RIF assay for rapid detection of MTB and rifampicin sensitivity. Relevant demographic, clinical, and radiological data were collected and analyzed. Based on susceptibility to drugs of culture isolates, treatment was started to see the outcome, and follow-ups were done with the patients.
Results
A total of 19 spinal TB cases were microbiologically confirmed, out of 58 clinically suspected spinal TB cases, with a male predominance (57.9 %) and age range of 13–72 years. The most common symptom was lower back pain (89.5 %). GeneXpert was positive in all cases, detecting rifampicin resistance in 7(36.8 %). Culture was positive in 11 cases. ZN staining was positive in 15.8 % of direct samples. Histopathology showed granulomatous inflammation in 9 (47.3 %) of cases. MRI confirmed infective spinal involvement in 17(89.5 %) patients. MDR-TB regimen was initiated in 7 patients. Overall recovery was good, except one case of neuropathy and one mortality.
Conclusions
A combination of smear microscopy, culture, and molecular diagnostics significantly improves the microbiological diagnosis of spinal TB. GeneXpert offers rapid, reliable results, especially in rifampicin resistance detection. Early and accurate microbiological confirmation, coupled with clinical-radiological correlation, is essential for effective management and improved patient outcomes.
{"title":"Unveiling the microbiological experience in exploring spinal TB cases from a tertiary care center","authors":"Jaya Biswas , Kiran Bala , Neha Nityadarshini , Leander Jose , Vivek Shankar , Urvashi B. Singh","doi":"10.1016/j.ijmmb.2026.101050","DOIUrl":"10.1016/j.ijmmb.2026.101050","url":null,"abstract":"<div><h3>Purpose</h3><div>Spinal tuberculosis, a severe form of extrapulmonary tuberculosis, poses significant diagnostic and therapeutic challenges, often leading to neurological complications and deformity. Microbiological confirmation is crucial for diagnosis and effective treatment. We aim to evaluate the microbiological profile and diagnostic yield of various methods in spinal TB cases at a tertiary care centre and to correlate with clinical features and treatment outcomes.</div></div><div><h3>Methods</h3><div>A prospective study was conducted on samples from patients with suspected spinal TB (n = 58) from July 2023 to September 2024. All samples were processed using Ziehl-Neelsen (ZN) staining for acid-fast bacilli (AFB), culture on Lowenstein-Jensen (LJ) medium, BACTEC MGIT 960 liquid culture system, and GeneXpert MTB/RIF assay for rapid detection of MTB and rifampicin sensitivity. Relevant demographic, clinical, and radiological data were collected and analyzed. Based on susceptibility to drugs of culture isolates, treatment was started to see the outcome, and follow-ups were done with the patients.</div></div><div><h3>Results</h3><div>A total of 19 spinal TB cases were microbiologically confirmed, out of 58 clinically suspected spinal TB cases, with a male predominance (57.9 %) and age range of 13–72 years. The most common symptom was lower back pain (89.5 %). GeneXpert was positive in all cases, detecting rifampicin resistance in 7(36.8 %). Culture was positive in 11 cases. ZN staining was positive in 15.8 % of direct samples. Histopathology showed granulomatous inflammation in 9 (47.3 %) of cases. MRI confirmed infective spinal involvement in 17(89.5 %) patients. MDR-TB regimen was initiated in 7 patients. Overall recovery was good, except one case of neuropathy and one mortality.</div></div><div><h3>Conclusions</h3><div>A combination of smear microscopy, culture, and molecular diagnostics significantly improves the microbiological diagnosis of spinal TB. GeneXpert offers rapid, reliable results, especially in rifampicin resistance detection. Early and accurate microbiological confirmation, coupled with clinical-radiological correlation, is essential for effective management and improved patient outcomes.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"60 ","pages":"Article 101050"},"PeriodicalIF":1.3,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145997989","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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