Present case describes an apparently healthy adult who developed severe Pneumocystis jirovecii pneumonia (PJP) leading to multiple organ dysfunction syndrome. The patient presented with month-long fever, fatiguability and recent onset dyspnoea, subsequently developing acute respiratory distress syndrome (ARDS), acute kidney injury and haematological complications. Definitive diagnosis was made through microscopic examination of P.jirovecii cysts stained by Grocott Gomori Methenamine Silver (GMS) and positive PCR assay of broncho-alveolar lavage fluid. This case highlights the evolving spectrum of PJP manifestations and emphasizes the need for early diagnosis and appropriate management in apparently immunocompetent hosts.
{"title":"Fulminant Pneumocystis jirovecii pneumonia presenting as multi-organ dysfunction syndrome in an immunocompetent host","authors":"Debasish Biswal , Arupparna Sengupta , Mohit Sharma , Bijay Ranjan Mirdha , Aayush Chawla , Rohit Kumar Garg , Sadia Khan , Anubhav Pandey , Sharmila Sengupta","doi":"10.1016/j.ijmmb.2025.101037","DOIUrl":"10.1016/j.ijmmb.2025.101037","url":null,"abstract":"<div><div>Present case describes an apparently healthy adult who developed severe <em>Pneumocystis jirovecii</em> pneumonia (PJP) leading to multiple organ dysfunction syndrome. The patient presented with month-long fever, fatiguability and recent onset dyspnoea, subsequently developing acute respiratory distress syndrome (ARDS), acute kidney injury and haematological complications. Definitive diagnosis was made through microscopic examination of <em>P.jirovecii</em> cysts stained by Grocott Gomori Methenamine Silver (GMS) and positive PCR assay of broncho-alveolar lavage fluid. This case highlights the evolving spectrum of PJP manifestations and emphasizes the need for early diagnosis and appropriate management in apparently immunocompetent hosts.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"59 ","pages":"Article 101037"},"PeriodicalIF":1.3,"publicationDate":"2025-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145732941","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 : 2025-12-09DOI: 10.1016/j.ijmmb.2025.101035
Emrah Salman
Background
The primary reason for increased lab use is inappropriate or needless test requests. Our study examined the benefits of repeated antinuclear antibody (ANA) testing and the reasons for ANA test requests in accordance with reasonable test selection and inappropriate scenarios.
Methods
We examined 2.5 years of data from a Turkish tertiary hospital in this retrospective cohort analysis. ANA and other autoimmune test data and clinical information of all patients whose ANA result changed from negative to positive on repeat testing were gathered from the hospital record system.
Results
44,341 individuals had 51,959 ANA tests between February 2019 and June 2021. ANA tests were positive in 7551 (17 %) of 44,341 patients and 9303 (17.9 %) of 51,959 tests. On 14.6 % (7618 out of 51,959) of tests requested and 13.2 % (5891 out of 44,341) of patients, repeat tests were performed. Of the 5891 patients retested, 171 were initially negative but later positive. A minority (3.7 %) of initially negative ANA patients experienced a change to a titer of ≥1:100 in our 2.5-year investigation. A novel ANA associated rheumatic disease (AARD) was detected in 17 patients. The new positive ANA test had a positive predictive value of 15.1 % following an initially negative ANA test.
Conclusions
It is common to repeat ANA testing. ANA tests that yielded negative results in the beginning frequently repeat without change. Repetition had no effect on clinical prediction of AARD. Repeat ANA testing in hospital patients is ineffective rather than useful.
{"title":"Rational test selection in immunology laboratory: Investigating the utility of repeated antinuclear antibody tests","authors":"Emrah Salman","doi":"10.1016/j.ijmmb.2025.101035","DOIUrl":"10.1016/j.ijmmb.2025.101035","url":null,"abstract":"<div><h3>Background</h3><div>The primary reason for increased lab use is inappropriate or needless test requests. Our study examined the benefits of repeated antinuclear antibody (ANA) testing and the reasons for ANA test requests in accordance with reasonable test selection and inappropriate scenarios.</div></div><div><h3>Methods</h3><div>We examined 2.5 years of data from a Turkish tertiary hospital in this retrospective cohort analysis. ANA and other autoimmune test data and clinical information of all patients whose ANA result changed from negative to positive on repeat testing were gathered from the hospital record system.</div></div><div><h3>Results</h3><div>44,341 individuals had 51,959 ANA tests between February 2019 and June 2021. ANA tests were positive in 7551 (17 %) of 44,341 patients and 9303 (17.9 %) of 51,959 tests. On 14.6 % (7618 out of 51,959) of tests requested and 13.2 % (5891 out of 44,341) of patients, repeat tests were performed. Of the 5891 patients retested, 171 were initially negative but later positive. A minority (3.7 %) of initially negative ANA patients experienced a change to a titer of ≥1:100 in our 2.5-year investigation. A novel ANA associated rheumatic disease (AARD) was detected in 17 patients. The new positive ANA test had a positive predictive value of 15.1 % following an initially negative ANA test.</div></div><div><h3>Conclusions</h3><div>It is common to repeat ANA testing. ANA tests that yielded negative results in the beginning frequently repeat without change. Repetition had no effect on clinical prediction of AARD. Repeat ANA testing in hospital patients is ineffective rather than useful.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"59 ","pages":"Article 101035"},"PeriodicalIF":1.3,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145732942","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}
Elizabethkingia meningoseptica is an emerging nosocomial pathogen with complex antimicrobial resistance. We conducted a retrospective study in intensive care units (August 2022–December 2024) involving thirteen patients (ten adults, three paediatric). Universal resistance to piperacillin/tazobactam, aminoglycosides but susceptibility to minocycline was observed. Environmental sampling revealed contamination in water outlets and sink holes. Whole genome sequencing demonstrated clonal relationships between clinical and environmental isolates, confirming nosocomial transmission. Neurological complications were significantly associated with mortality. Following targeted interventions including enhanced disinfection and thermal water flushing, no new cases occurred during three-month follow-up. This study highlights environmental surveillance and integrated infection control importance.
{"title":"Emergence and clonal transmission of Elizabethkingia meningoseptica in adult and paediatric intensive care units: An integrated clinical, microbiological, and genomic analysis","authors":"Debasish Biswal , Sharmila Sengupta , Ripenmeet Salhotra , Pankhuri Kumari , Maninder Dhaliwal , Sadia Khan , Aayush Chawla , Veena Raghunathan , Sandeep Mangla","doi":"10.1016/j.ijmmb.2025.101032","DOIUrl":"10.1016/j.ijmmb.2025.101032","url":null,"abstract":"<div><div><em>Elizabethkingia meningoseptica</em> is an emerging nosocomial pathogen with complex antimicrobial resistance. We conducted a retrospective study in intensive care units (August 2022–December 2024) involving thirteen patients (ten adults, three paediatric). Universal resistance to piperacillin/tazobactam, aminoglycosides but susceptibility to minocycline was observed. Environmental sampling revealed contamination in water outlets and sink holes. Whole genome sequencing demonstrated clonal relationships between clinical and environmental isolates, confirming nosocomial transmission. Neurological complications were significantly associated with mortality. Following targeted interventions including enhanced disinfection and thermal water flushing, no new cases occurred during three-month follow-up. This study highlights environmental surveillance and integrated infection control importance.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"59 ","pages":"Article 101032"},"PeriodicalIF":1.3,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145668261","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 : 2025-11-28DOI: 10.1016/j.ijmmb.2025.101033
G. Vithiya , V. Mangayarkarasi
We report an outbreak of Burkholderia cepacia bacteremia in a cardiothoracic surgery intensive care unit. Four cases of bloodstream infections were reported between August 16, 2024 and August 31, 2024. Microbiological surveillance of clean and sterile material from the unit revealed growth of B. cepacia from opened and sealed ultrasound gel bottles. Further cultures acquired from ultrasound gel containers from other units also grew B. cepacia and hence displaced by single use sterile gel. The outbreak was regarded terminated by the first week of September 2024 as no additional cases were described.
{"title":"Outbreak of Burkholderia cepacia bacteremia consequent to contaminated ultrasound gel-a report from a tertiary care centre in South Tamilnadu, India","authors":"G. Vithiya , V. Mangayarkarasi","doi":"10.1016/j.ijmmb.2025.101033","DOIUrl":"10.1016/j.ijmmb.2025.101033","url":null,"abstract":"<div><div>We report an outbreak of <em>Burkholderia cepacia</em> bacteremia in a cardiothoracic surgery intensive care unit. Four cases of bloodstream infections were reported between August 16, 2024 and August 31, 2024. Microbiological surveillance of clean and sterile material from the unit revealed growth of <em>B. cepacia</em> from opened and sealed ultrasound gel bottles. Further cultures acquired from ultrasound gel containers from other units also grew <em>B. cepacia</em> and hence displaced by single use sterile gel. The outbreak was regarded terminated by the first week of September 2024 as no additional cases were described.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"59 ","pages":"Article 101033"},"PeriodicalIF":1.3,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145648423","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}
Sterile pyuria poses a diagnostic challenge due to varied aetiologies. Atypical pathogens including Chlamydia trachomatis and genital mycoplasmas are considered etiological agents but are under-reported, especially in resource-limited settings. This study determined the prevalence of these atypical pathogens in sterile pyuria patients.
Materials and methods
This 4-year prospective observational study screened 640 adults admitted to Medicine wards of a tertiary care hospital for sterile pyuria, defined as urine microscopy showing >10 WBCs/HPF with no bacterial growth on culture. All sterile pyuria patients were evaluated for Chlamydia trachomatis (CT), Ureaplasma spp., Mycoplasma hominis (MH) and Mycoplasma genitalium (MG) from first void urine samples. Mycoplasma hominis and Ureaplasma spp. were detected by culture and PCR assay. Chlamydia trachomatis was detected by PCR assay. Mycoplasma genitalium was detected by Real-time PCR assay. Additional assessments for other potential causes were carried out. Patients were treated with doxycycline or azithromycin and followed for outcomes. Risk factors for infection with these atypical agents were explored.
Results
Of 640 patients screened, 100 (15.6 %) had sterile pyuria. Atypical pathogens were detected in 40 %. CT, Ureaplasma spp., and MH were detected in 19 %, 15 % and 5 % respectively. One patient tested positive for MG. Multivariate logistic regression identified multiple sexual partners (adjusted OR 12.01, 95 % CI 2.07–69.40, p = 0.005) and past pelvic surgery (adjusted OR 5.64, 95 % CI 1.43–22.24, p = 0.013) as risk factors. Twenty-five (62.5 %) of 40 patients achieved complete clinical and microbiological cure with treatment. Laboratory records revealed genitourinary tuberculosis in 2 patients.
Conclusion
This study identified 40 % prevalence of atypical pathogens in sterile pyuria patients. Unlike previous assumptions, genitourinary tuberculosis was not a common cause in our population. Our findings emphasize the necessity for comprehensive screening for CT, Ureaplasma spp., MH, and MG in sterile pyuria patients.
无菌脓尿由于病因多样,给诊断带来了挑战。包括沙眼衣原体和生殖器支原体在内的非典型病原体被认为是病原体,但报告不足,特别是在资源有限的情况下。本研究确定了无菌脓尿患者中这些非典型病原体的患病率。材料和方法这项为期4年的前瞻性观察研究筛选了一家三级医院内科病房收治的640名无菌脓尿症成年人,定义为尿液显微镜显示10个白细胞/HPF,培养物上没有细菌生长。对所有无菌脓尿患者进行首次空尿沙眼衣原体(CT)、脲原体、人支原体(MH)和生殖支原体(MG)检测。用培养法和PCR法检测人支原体和脲原体。PCR检测沙眼衣原体。采用Real-time PCR法检测生殖支原体。对其他潜在原因进行了进一步评估。患者接受强力霉素或阿奇霉素治疗并随访结果。探讨了感染这些非典型病原体的危险因素。结果640例患者中,无菌脓尿100例(15.6%)。非典型病原体检出率为40%。CT、脲原体和MH检出率分别为19%、15%和5%。一名患者MG检测呈阳性。多因素logistic回归发现多个性伴侣(校正OR 12.01, 95% CI 2.07-69.40, p = 0.005)和既往盆腔手术(校正OR 5.64, 95% CI 1.43-22.24, p = 0.013)是危险因素。经治疗,40例患者中25例(62.5%)达到临床和微生物学完全治愈。实验室记录显示2例泌尿生殖系统结核。结论无菌性脓尿患者中非典型病原体的患病率为40%。与以前的假设不同,泌尿生殖系统结核病在我们的人群中并不常见。我们的研究结果强调了对无菌脓尿患者进行CT、脲原体、MH和MG综合筛查的必要性。
{"title":"Prevalence of Chlamydia trachomatis, Ureaplasma spp., Mycoplasma hominis and Mycoplasma genitalium in patients with sterile pyuria","authors":"Anivita Aggarwal , Debasish Biswal , Jyoti Rawre , Naval Vikram , Naveet Wig , Manish Soneja , Sreenivas Vishnubhatla , Benu Dhawan","doi":"10.1016/j.ijmmb.2025.101030","DOIUrl":"10.1016/j.ijmmb.2025.101030","url":null,"abstract":"<div><h3>Introduction</h3><div>Sterile pyuria poses a diagnostic challenge due to varied aetiologies. Atypical pathogens including <em>Chlamydia trachomatis</em> and genital mycoplasmas are considered etiological agents but are under-reported, especially in resource-limited settings. This study determined the prevalence of these atypical pathogens in sterile pyuria patients.</div></div><div><h3>Materials and methods</h3><div>This 4-year prospective observational study screened 640 adults admitted to Medicine wards of a tertiary care hospital for sterile pyuria, defined as urine microscopy showing >10 WBCs/HPF with no bacterial growth on culture. All sterile pyuria patients were evaluated for <em>Chlamydia trachomatis</em> (CT), <em>Ureaplasma</em> spp., <em>Mycoplasma hominis</em> (MH) and <em>Mycoplasma genitalium</em> (MG) from first void urine samples. <em>Mycoplasma hominis</em> and <em>Ureaplasma</em> spp. were detected by culture and PCR assay. <em>Chlamydia trachomatis</em> was detected by PCR assay. <em>Mycoplasma genitalium</em> was detected by Real-time PCR assay. Additional assessments for other potential causes were carried out. Patients were treated with doxycycline or azithromycin and followed for outcomes. Risk factors for infection with these atypical agents were explored.</div></div><div><h3>Results</h3><div>Of 640 patients screened, 100 (15.6 %) had sterile pyuria. Atypical pathogens were detected in 40 %. CT, <em>Ureaplasma</em> spp., and MH were detected in 19 %, 15 % and 5 % respectively. One patient tested positive for MG. Multivariate logistic regression identified multiple sexual partners (adjusted OR 12.01, 95 % CI 2.07–69.40, p = 0.005) and past pelvic surgery (adjusted OR 5.64, 95 % CI 1.43–22.24, p = 0.013) as risk factors. Twenty-five (62.5 %) of 40 patients achieved complete clinical and microbiological cure with treatment. Laboratory records revealed genitourinary tuberculosis in 2 patients.</div></div><div><h3>Conclusion</h3><div>This study identified 40 % prevalence of atypical pathogens in sterile pyuria patients. Unlike previous assumptions, genitourinary tuberculosis was not a common cause in our population. Our findings emphasize the necessity for comprehensive screening for CT, <em>Ureaplasma</em> spp., MH, and MG in sterile pyuria patients.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"59 ","pages":"Article 101030"},"PeriodicalIF":1.3,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145621857","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 : 2025-11-25DOI: 10.1016/j.ijmmb.2025.101029
Aditi Gupta , Nithya S. Roy , Vibhor Tak , Manish Chaturvedy
Catheter related bloodstream infections are a common concern in hospitalized and immunocompromised patients. We report a case of CKD with an indwelling left IJV Permacath who developed fever and chills during dialysis. Investigations showed leukocytosis, elevated CRP (75 mg/L), and procalcitonin (9.1 ng/mL). Paired blood cultures grew Kocuria rhizophila, identified by MALDI-TOF, with a two-hour difference in positivity indicating CRBSI. Vancomycin led to improvement and antibiotic lock therapy was initiated. This case highlights that rare organisms such as K. rhizophila can be true pathogens in dialysis patients, and correct identification with MALDI-TOF alongside clinical correlation is crucial for appropriate management.
{"title":"Catheter-related bloodstream infection by Kocuria rhizophila in a dialysis patient","authors":"Aditi Gupta , Nithya S. Roy , Vibhor Tak , Manish Chaturvedy","doi":"10.1016/j.ijmmb.2025.101029","DOIUrl":"10.1016/j.ijmmb.2025.101029","url":null,"abstract":"<div><div>Catheter related bloodstream infections are a common concern in hospitalized and immunocompromised patients. We report a case of CKD with an indwelling left IJV Permacath who developed fever and chills during dialysis. Investigations showed leukocytosis, elevated CRP (75 mg/L), and procalcitonin (9.1 ng/mL). Paired blood cultures grew <em>Kocuria rhizophila</em>, identified by MALDI-TOF, with a two-hour difference in positivity indicating CRBSI. Vancomycin led to improvement and antibiotic lock therapy was initiated. This case highlights that rare organisms such as <em>K. rhizophila</em> can be true pathogens in dialysis patients, and correct identification with MALDI-TOF alongside clinical correlation is crucial for appropriate management.</div></div>","PeriodicalId":13284,"journal":{"name":"Indian Journal of Medical Microbiology","volume":"59 ","pages":"Article 101029"},"PeriodicalIF":1.3,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145621856","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 : 2025-11-24DOI: 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}