Indian Journal of Medical Microbiology最新文献

Purpose

Tuberculous meningitis (TBM) is the most severe form of tuberculosis (TB). Difficulty in diagnosing the condition along with other factors, increases its potential for high morbidity and mortality. Targeted Next Generation Sequencing (tNGS) generates high quality sequence read depths, enabling the identification of low-frequency alleles linked to Drug resistance (DR). The paucibacillary nature of tuberculous meningitis is a challenge for making a definitive diagnosis.

Methods

tNGS was performed on 20 cerebrospinal fluid (CSF) samples where, MGIT has shown Positive MTB Cultures. We simultaneously performed pyrosequencing (PSQ) and phenotypic Drug susceptibility testing (pDST) for these 20 samples.

Results

Sequencing results (from tNGS and PSQ) were compared with reference standards i.e. pDST. tNGS detected MTB in 7/20 (35%) CSF samples whereas, PSQ detected MTB in 17/20 (85%).

Conclusion

Although tNGS has ability to detect minority variants along with detection of additional targets than PSQ, PSQ remains the diagnostic choice in our tertiary lab.

Bacillus cereus is rarely implicated when diarrheal cases in children are diagnosed in developing countries due to the lack of molecular methods to identify its enterotoxigenic genes. We report that out of 62 enterobacteria isolated from 70 stool samples collected from children hospitalized at the Mile 4 Hospital, Ebonyi State, Nigeria, 24 isolates were identified as B. cereus based on 16SrRNA gene sequence. The enterotoxins genes nheA and cytK2 were detected in 23 out of the 24 isolates, while hblC was detected in 19 isolates. B. cereus may be responsible for greater number of yearly incidences of acute childhood gastroenteritis in Nigeria.

Nosocomial outbreaks of Burkholderia cepacia complex, transmitted through contaminated medical surfaces or equipment have been reported. Pulsed-field Gel Electrophoresis (PFGE) is recognized as the “gold standard” for molecular subtyping, yet studies on clonal relationships in India are limited. PFGE was used to study the clonal relationships of 22 isolates of Burkholderia cenocepacia from 12 patients admitted to a critical care unit during 2 months (November and December 2021). PFGE revealed three different profiles with 15 isolates belonging to a single cluster suggesting a common source within the hospital, emphasizing the need for preventive measures to control B. cenocepacia transmission.

The Aeromonadaceae family, comprised of gram-negative bacilli, is ubiquitously distributed across the globe. Infections by Aeromonas species encompass gastroenteritis, septicaemia, skin and soft tissue infections (SSTIs), pneumonia, and peritonitis. This report delineates a case of Aeromonas hydrophila infection, manifesting as an array of pustules on the patient's lower extremities subsequent to the ingestion of marine crustaceans, specifically prawns. Prompt diagnosis and the initiation of an appropriate antibiotic regimen are imperative to mitigate the risk of further complications.

Rhino-orbital-cerebral mucormycosis (ROCM) is linked to uncontrolled diabetes, diabetic ketoacidosis, iron overload, corticosteroid therapy, and neutropenia. This study evaluated a commercial real-time PCR system's effectiveness in detecting Mucorales from nasal swabs in 50 high-risk patients. Nasal swab PCR showed 30% positivity, compared to 8% with KOH microscopy. Despite its improved sensitivity, nasal swab PCR has limitations, highlighting the importance of established sampling methods in mucormycosis diagnosis. Participants were predominantly male (64%), with diabetes (78%) and amphotericin B use (96%). Prior COVID-19 was 42%, with 30% positive for Mucorales by PCR, compared to 8% with KOH microscopy.

Purpose

In India there is evidence of antimicrobial resistance in Helicobacter pylori, a definitive pathobiont whose only known niche is human gastric mucosa. This in turn can lead to failure of treatment, persistence or chronicity of infection. This hospital based, prospective, observational study investigates the presence of antimicrobial resistance in the organism with focus on detection of A2143G and A2142G major point mutations in domain V of H. pylori 23S rRNA gene as a molecular mechanism of conferring resistance.

Methods

Endoscopic gastric biopsy samples from 52 patients presenting with dyspeptic symptoms from January 2016 to December 2016 were subjected to culture in a microaerophilic environment using Campylobacter agar with for 2–5 days. Isolates were identified using gram-staining, motility test and biochemical reactions. Modified Kirby-Bauer Disc diffusion method was used to determine antimicrobial susceptibility against Clarithromycin, Metronidazole, Amoxycillin, Levofloxacin, Tetracycline, Cotrimoxazole and Erythromycin. Additionally, detection of A2143G and A2142G point mutations conferring Clarithromycin resistance was carried out using real time PCR following extraction and quantification of bacterial DNA. Histopathological examination was carried out on all biopsy samples. Descriptive and inferential statistical analytical methods were used. Differences were considered significant for p < 0.05.

Results

Culture positivity for H. pylori by phenotypic method was found to be 36.54%. Histopathologic Examination detected H. pylori in 55.7% and PCR detected 48.08% for either the wild type or one of two mutant strains A2143G and A2142G. No sample was found positive for both mutations. Metronidazole showed the highest resistance among antibiotics (78.9%) followed by Clarithromycin (47.3%).

Conclusion

Prevalence of antimicrobial resistance in H. pylori in North-Eastern India is substantially high with A2143G mutation being clinically most important in conferring Clarithromycin resistance. This resistance might be associated with low eradication rates despite initiation of therapy. ROC analysis of PCR proved it to be a good diagnostic tool.

During surge of COVID-19-associated mucormycosis (CAM), we identified five cases of CAM where two different species of Mucorales were isolated. All had history of diabetes mellitus and presented with clinical features suggesting rhino-orbital mucormycosis. The patients grew different species from their nasal scraping/biopsy samples, Rhizopus arrhizus, R. homothallicus (n = 2); R. homothallicus, Lictheimia corymbifera (n = 1); R. arrhizus, Mucor spp (n = 1); and L. corymbifera, Apophysomyces variabilis (n = 1). All patients underwent surgical and medical (liposomal amphotericin B) treatment. All, except one growing A. variabilis and L. corymbifera survived. Mixed infection by more than one Mucorales in CAM is unique and warrants epidemiological investigation.

Purpose

Candida albicans is the second most common cause of candidemia in Malaysia. The Clinical and Laboratory Standards Institute (CLSI) broth microdilution method is the gold standard for determining its minimum inhibitory concentration (MIC); however, it is laborious and time-consuming. This study was conducted to evaluate the usefulness of alternative methods, namely Sensititre YeastOne (SYO), VITEK 2 system, and E-test for determining the MIC of clinical C. albicans isolates.

Materials and methods

The susceptibilities of 95 C. albicans isolates were compared between SYO, VITEK 2 system, and E-test with CLSI broth microdilution method. The categorical agreement (CA), essential agreement (EA), very major errors (VME), major errors (ME) and minor errors (MiE) were calculated.

Results

Our finding showed the CA varied for SYO from 96.8% to 100%, while the EA ranged from 91.6% to 100%. The SYO method showed 1.1% of VME and ME, and up to 3.2% of MiE. Next, the CA and EA ranges for the VITEK 2 system were 97.8%–100% and 23.2%–100%, respectively. In the VITEK 2 technique, 1.1% of VME were found. For the E-test, the CA varied from 83.2% to 100% while the EA ranged from 64.2% to 98.9%. The E-test method showed 1.1% of VME and up to 16.8% of MiE.

Conclusions

In conclusion, SYO and VITEK 2 (except flucytosine) could be potential alternatives to the CLSI broth microdilution method in determining the MIC of C. albicans.

Purpose

Patients with hematologic malignancies (HM) are at high risk of invasive lung fungal infections (ILFI). To describe the main characteristics, treatment, and outcomes for five years in adult patients with HM and fungal pneumonia.

Methods

We conducted a retrospective study at Instituto Nacional de Cancerología (INCan), a referral tertiary care oncology hospital with 135 beds in Mexico City, Mexico. We included all cases of fungal pneumonia in patients with HM from January 1, 2017, to December 31, 2022. Cases were classified as proven, probable, and possible according to EORTC/MSG criteria 2021.

Results

Two hundred ten patients were included; the mean age was 40 years. The most frequent HM was acute lymphoblastic leukemia (n = 74) and acute myeloid leukemia (n = 68). One hundred forty patients (66.7%) had severe neutropenia for a median of 16 days. All patients had a CT thorax scan; in 132 (62.9%), multiple nodules were documented. Serum galactomannan (GM) was positive in 21/192 (10.9%) and bronchoalveolar lavage in 9/36 (25%). Fifty-three patients (25.2%) died in the first month. In the multivariate analysis for mortality in the first 30 days, hypoalbuminemia, shock, possible ILFI, and inappropriate antifungal treatment were statistically associated.

Conclusions

In high-risk HM patients, CT thorax scan and GM help diagnose ILFI. An appropriate antifungal improves mortality.

Purpose

Genomic surveillance of positive SARS-CoV-2 samples is important to monitor the genetic changes occurring in virus, this was enhanced after the WHO designation of XBB.1.16 as a variant under monitoring in March 2023. From 5th February till May 6, 2023 all positive SARS-CoV-2 samples were monitored for genetic changes.

Methods

A total of 1757 samples having Ct value <25 (for E and ORF gene) from different districts of Rajasthan were processed for Next Generation Sequencing (NGS). The FASTA files obtained on sequencing were used for lineage determination using Nextclade and phylogenetic tree construction.

Results and conclusions

Sequencing and lineage identification was done in 1624 samples. XBB.1.16 was the predominant lineage in 1413 (87.0%) cases while rest was other XBB (207, 12.74%) and other lineages (4, 0.2%). Of the 1413 XBB.1.16 cases, 57.47% were males and 42.53% were females. Majority (66.53%) belonged to 19–59 year age. 84.15% of XBB.1.16 cases were infected for the first time. Hospitalization was required in only 2.2% cases and death was reported in 5 (0.35%) patients. Most of the cases were symptomatic and the commonest symptoms were fever, cough and rhinorrhea. Co-morbidities were present in 414 (29.3%) cases. Enhanced genomic surveillance helped to rapidly identify the spread of XBB variant in Rajasthan. This in turn helped to take control measures to prevent spread of virus and estimate public health risks of the new variant relative to the previously circulating lineages. XBB variant was found to spread rapidly but produced milder disease.