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Article ; Online: Phylogenetic diversity of

Chunchanur, Sneha K / Venugopal, Shwetha J / Ambica, R / Dakshayani, B

2020 Volume 37, Issue 3, Page(s) 438–441

Abstract: Scrub typhus has re-emerged as an important cause of acute febrile illness in India. There is a dearth of information on strain diversity of Orientia tsutsugamushi from Karnataka, India, hence the present study sought to address this issue. One hundred ... ...

Abstract	Scrub typhus has re-emerged as an important cause of acute febrile illness in India. There is a dearth of information on strain diversity of Orientia tsutsugamushi from Karnataka, India, hence the present study sought to address this issue. One hundred clinically suspected cases of scrub typhus/rickettsiosis (as per the DHR-ICMR guidelines) were included. Nested-polymerase chain reaction (PCR) for 56-kDa gene and phylogenetic analysis was performed. PCR was positive in 22 cases and phylogenetic analysis showed the presence of different strains, with predominance of clustering (57%) with Gilliam-type for the first time in Karnataka. Knowledge of genetic diversity has implications in development of diagnostics and vaccine.
MeSH term(s)	DNA, Bacterial/genetics ; Genotype ; Humans ; India ; Orientia tsutsugamushi/classification ; Orientia tsutsugamushi/genetics ; Phylogeny ; Polymerase Chain Reaction ; Scrub Typhus/classification ; Scrub Typhus/genetics ; Sequence Analysis, DNA
Chemical Substances	DNA, Bacterial
Language	English
Publishing date	2020-08-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	1038798-5
ISSN	1998-3646 ; 0255-0857
ISSN (online)	1998-3646
ISSN	0255-0857
DOI	10.4103/ijmm.IJMM_19_267
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Zs.A 2639: Show issues

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Article ; Online: Simple and low-cost nucleic acid extraction methods for detection of SARS-CoV2 in self-collected saliva and dry oral swabs.

Shwetha, J V / Chunchanur, Sneha K / Harsha, T R / Mohandas, Silpa / Shah, Pritik A / Ambica, R / Ks, Himabindhu / Sumanth, M

IJID Regions (Online)

2022 Volume 5, Page(s) 86–92

Abstract: Background: Ongoing need of alternative strategies for SARS-CoV-2 detection is undeniable. Self-collected samples without viral transport media (VTM), coupled with simple nucleic acid extraction methods for SARS-CoV-2 PCR are beneficial.: Objectives: ...

Abstract	Background: Ongoing need of alternative strategies for SARS-CoV-2 detection is undeniable. Self-collected samples without viral transport media (VTM), coupled with simple nucleic acid extraction methods for SARS-CoV-2 PCR are beneficial. Objectives: To evaluate results of SARS-CoV-2 PCR using simple nucleic acid extraction methods from self -collected saliva and oral swabs without VTM. Methods: A cross-sectional single-centre study was conducted on 125 participants (101 SARS-CoV-2 positive cases and 24 controls). PCR was performed following five simple nucleic acid extraction methods on self -collect saliva and oral swabs without VTM and results were compared with gold standard PCR. For saliva, kit-based extraction (SKE), Proteinase K and Heat extraction (SPHE), only Heat extraction (SHE) methods and for dry oral swabs, Proteinase K and Heat extraction (DPHE) and only Heat extraction (DHE) was performed. Results: SARS-CoV-2 was detected in self-collected saliva and oral swabs. 93.07% were correctly classified as positive by SKE, 69.31% by SHE, 67.33% by SPHE, 67.33% by DPHE and 55.45% by DHE. Discriminant power of SKE was significantly higher than other methods (p-value < 0.001) with good- fair agreement of alternate extraction methods against gold standard. Conclusion: Combination of self-collected saliva/ oral-swab without VTM and alternative RNA extraction methods offer a simplified, economical substitute strategy for SARS-CoV-2 detection.
Language	English
Publishing date	2022-09-18
Publishing country	England
Document type	Journal Article
ISSN	2772-7076
ISSN (online)	2772-7076
DOI	10.1016/j.ijregi.2022.09.003
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Article ; Online: Mycobacterium Species on the Cutaneous Microbiome of Very Preterm Neonates.

Shah, Pritik A / Govindarajan, Varun / Rangaiah, Ambica / Diggikar, Shivashankar / Devadas, Sahana / Chunchanur, Sneha K / Shankar, Sathyanarayan Muthur / Das, Subhadeep / Kariyappa, Mallesh

Journal of tropical pediatrics

2022 Volume 68, Issue 2

Abstract: The neonatal skin microbiome consists of all the genomes and genetic products of microorganisms harboring on an infant's skin. Host and the microbiota develop a harmonious environment resulting in symbiosis. Any disruption of this environment could lead ... ...

Abstract	The neonatal skin microbiome consists of all the genomes and genetic products of microorganisms harboring on an infant's skin. Host and the microbiota develop a harmonious environment resulting in symbiosis. Any disruption of this environment could lead to pathological disease. This study was conducted to understand the neonatal skin microbiome of very preterm neonates (under 32 weeks) admitted to the Neonatal Intensive Care Unit(NICU) at a tertiary healthcare setting before and after kangaroo mother care (KMC), using next-generation sequencing (NGS). Skin swabs were collected on two different occasions and analyzed using the NGS technique after amplification via polymerase chain reaction. The results showed relative abundance for Mycobacterium tuberculosis in 83.33% and 66.67% (p = 0.29) and Mycobacteroides abscessus in 100% and 93.33% (p = 0.30) of the very preterm neonates on the skin microbiome before and after KMC, respectively as an incidental finding. The mere presence of these bacilli as commensals or as potential pathogens is alarming due to the risk of early exposure and incidence of tuberculosis from birth. These findings, in our view, are the first findings to be established in such a setting.
MeSH term(s)	Child ; Humans ; Infant, Extremely Premature ; Infant, Newborn ; Intensive Care Units, Neonatal ; Kangaroo-Mother Care Method ; Microbiota ; Mycobacterium
Language	English
Publishing date	2022-02-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	800065-7
ISSN	1465-3664 ; 0449-3281 ; 0142-6338
ISSN (online)	1465-3664
ISSN	0449-3281 ; 0142-6338
DOI	10.1093/tropej/fmac020
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Zs.A 932: Show issues

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Article ; Online: Culture-Independent Raman Spectroscopic Identification of Bacterial Pathogens from Clinical Samples Using Deep Transfer Learning.

Singh, Saumya / Kumbhar, Dipak / Reghu, Dhanya / Venugopal, Shwetha J / Rekha, P T / Mohandas, Silpa / Rao, Shruti / Rangaiah, Ambica / Chunchanur, Sneha K / Saini, Deepak Kumar / Umapathy, Siva

Analytical chemistry

2022 Volume 94, Issue 42, Page(s) 14745–14754

Abstract: The rapid identification of bacterial pathogens in clinical samples like blood, urine, pus, and sputum is the need of the hour. Conventional bacterial identification methods like culturing and nucleic acid-based amplification have limitations like poor ... ...

Abstract	The rapid identification of bacterial pathogens in clinical samples like blood, urine, pus, and sputum is the need of the hour. Conventional bacterial identification methods like culturing and nucleic acid-based amplification have limitations like poor sensitivity, high cost, slow turnaround time, etc. Raman spectroscopy, a label-free and noninvasive technique, has overcome these drawbacks by providing rapid biochemical signatures from a single bacterium. Raman spectroscopy combined with chemometric methods has been used effectively to identify pathogens. However, a robust approach is needed to utilize Raman features for accurate classification while dealing with complex data sets such as spectra obtained from clinical isolates, showing high sample-to-sample heterogeneity. In this study, we have used Raman spectroscopy-based identification of pathogens from clinical isolates using a deep transfer learning approach at the single-cell level resolution. We have used the data-augmentation method to increase the volume of spectra needed for deep-learning analysis. Our ResNet model could specifically extract the spectral features of eight different pathogenic bacterial species with a 99.99% classification accuracy. The robustness of our model was validated on a set of blinded data sets, a mix of cultured and noncultured bacterial isolates of various origins and types. Our proposed ResNet model efficiently identified the pathogens from the blinded data set with high accuracy, providing a robust and rapid bacterial identification platform for clinical microbiology.
MeSH term(s)	Spectrum Analysis, Raman/methods ; Bacteria ; Machine Learning ; Nucleic Acids ; Plant Extracts
Chemical Substances	Nucleic Acids ; Plant Extracts
Language	English
Publishing date	2022-10-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c03391
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Zs.A 4033: Show issues

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Article ; Online: Virulence gene mutations as a differentiator of clinical phenotypes: insights from community-acquired uropathogenic

Yadav, Manisha / Pundir, Swati / Kumari, Rajesh / Kumar, Arvind / Venugopal, Shwetha J / Panigrahy, Rajashree / Tak, Vibhor / Chunchanur, Sneha K / Gautam, Hitender / Kapil, Arti / Das, Bimal / Sood, Seema / Salve, Harshal Ramesh / Malhotra, Sumit / Kant, Shashi / Hari, Pankaj / Chaudhuri, Susmita / Mohapatra, Sarita

Microbiology (Reading, England)

2022 Volume 168, Issue 4

Abstract: ... ...

Abstract	Uropathogenic
MeSH term(s)	Escherichia coli Infections ; Escherichia coli Proteins/genetics ; Female ; Humans ; Mutation ; Phenotype ; Pregnancy ; Urinary Tract Infections ; Uropathogenic Escherichia coli/genetics ; Virulence/genetics ; Virulence Factors/genetics
Chemical Substances	Escherichia coli Proteins ; Virulence Factors
Language	English
Publishing date	2022-05-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1180712-x
ISSN	1465-2080 ; 1350-0872
ISSN (online)	1465-2080
ISSN	1350-0872
DOI	10.1099/mic.0.001161
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Ud II Zs.140: Show issues

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Article ; Online: Antibiotic resistance of uropathogens among the community-dwelling pregnant and nonpregnant female: a step towards antibiotic stewardship.

BMC infectious diseases

2022 Volume 22, Issue 1, Page(s) 939

Abstract: Background: Indiscriminate and widespread use of antibiotics has resulted in emergence of many antibiotic-resistant organisms. Antibiotic administration during pregnancy is mostly avoided, unless there is compelling medical condition. We hypothesized ... ...

Abstract	Background: Indiscriminate and widespread use of antibiotics has resulted in emergence of many antibiotic-resistant organisms. Antibiotic administration during pregnancy is mostly avoided, unless there is compelling medical condition. We hypothesized that the uropathogens isolated from pregnant women would be more susceptible to antibiotics compared to those isolated from nonpregnant women, thus will be helpful in formulating separate empiric guideline for pregnant women based on the resistance pattern. Methods: This was a prospective cross-sectional study conducted over a period of 2 years in which females with the clinical diagnosis of either cystitis or asymptomatic bacteriuria during pregnancy were included from the community settings. Uropathogen species and their antimicrobial resistance pattern were compared between the pregnant and nonpregnant groups. After accounting for centre-to-centre variation and adjusting for age and socio-economic status, the adjusted odds ratio for antibiotic resistance was calculated and compared between pregnant and nonpregnant women using logistic regression analysis. Results: A total of 1758 women (pregnant: 43.3%; nonpregnant: 56.6%) were screened in the study over a period of 2 years, out of which 9.3% (163/1758) were having significant bacteriuria. Escherichia coli and Klebsiella pneumoniae were the two commonest uropathogen in both the groups; their prevalence being 83.6% in pregnant women and 85.2% in nonpregnant women, respectively. Resistance against ampicillin, cefixime, cefoxitin, ceftazidime, ceftriaxone and amoxicillin-clavulanic acid were found significantly lower in the pregnant women compared to nonpregnant. After adjusting the age and socio-economic status accounting for centre-to-centre variation, the odds of resistance for cefixime, amoxicillin-clavulanic acid and co-trimoxazole were found lower and statistically significant among the pregnant women group. Conclusions: The antimicrobial resistance was significantly higher among the community-dwelling nonpregnant women compared to pregnant women in case of few antibiotics. The study highlighted the need of building local antibiogram that could help to initiate the empirical treatment and thus prevent emergence of antimicrobial resistance.
MeSH term(s)	Female ; Humans ; Pregnancy ; Bacteriuria/diagnosis ; Amoxicillin-Potassium Clavulanate Combination/therapeutic use ; Antimicrobial Stewardship ; Cefixime/therapeutic use ; Urinary Tract Infections/drug therapy ; Urinary Tract Infections/epidemiology ; Cross-Sectional Studies ; Prospective Studies ; Independent Living ; Drug Resistance, Microbial ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Escherichia coli
Chemical Substances	Amoxicillin-Potassium Clavulanate Combination (74469-00-4) ; Cefixime (97I1C92E55) ; Anti-Bacterial Agents
Language	English
Publishing date	2022-12-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2041550-3
ISSN	1471-2334 ; 1471-2334
ISSN (online)	1471-2334
ISSN	1471-2334
DOI	10.1186/s12879-022-07914-1
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Article ; Online: Outbreak of Pichia kudriavzevii fungaemia in a neonatal intensive care unit.

Nagarathnamma, T / Chunchanur, Sneha K / Rudramurthy, Shivaprakash M / Vineetha, K R / Ramamurthy, Karthik / Joseph, Jillwin / Ambica, R

Journal of medical microbiology

2017 Volume 66, Issue 12, Page(s) 1759–1764

Abstract: Purpose: Fungaemia is associated with substantial morbidity and mortality in neonates admitted to neonatal intensive care units (NICUs). We report an outbreak of fungaemia in a NICU due to rare yeast, Pichia kudriavzevii (a teleomorph of Candida krusei). ...

Abstract	Purpose: Fungaemia is associated with substantial morbidity and mortality in neonates admitted to neonatal intensive care units (NICUs). We report an outbreak of fungaemia in a NICU due to rare yeast, Pichia kudriavzevii (a teleomorph of Candida krusei). To the best of our knowledge, this is the first report of neonatal sepsis due to P. kudriavzevii. Methodology: Between August and September 2014, blood cultures from nine neonates diagnosed with late-onset sepsis in the NICU yielded yeast-like organisms. The molecular identification and typing of these isolates was performed by sequencing the D1/D2 region of 26S rDNA and fluorescent amplified fragment length polymorphism (FAFLP) respectively. Antifungal susceptibility was tested by broth microdilution as per the Clinical Laboratory Standards Institute (CLSI) guidelines. Sampling from environmental sources and the hands of healthcare workers (HCWs) in the NICU was performed. Results: Of the nine neonates, eight were preterm and six had very low birth weight (VLBW). Thrombocytopenia was present in two neonates. Sequencing identified all the isolates as P. kudriavzevii and FAFLP showed their clonal origin. Antifungal susceptibility testing revealed the susceptibility of all isolates to the antifungals tested. Treatment with voriconazole was advised. However, only seven neonates were treated successfully and discharged after improvement, whereas two were lost for follow-up. Cultures from the environment and the hands of HCWs were negative. The outbreak was controlled by the strict implementation of infection control practices. Conclusion: This study emphasizes the importance of accurate identification of the aetiological agent of sepsis and vigilant monitoring for the possibility of an outbreak in NICUs.
MeSH term(s)	Amplified Fragment Length Polymorphism Analysis ; Antifungal Agents/therapeutic use ; DNA, Fungal/isolation & purification ; Disease Outbreaks ; Drug Resistance, Multiple, Fungal ; Female ; Fungemia/epidemiology ; Fungemia/microbiology ; Humans ; Infant ; Infant, Premature/blood ; Infant, Very Low Birth Weight/blood ; Infection Control ; Intensive Care Units, Neonatal ; Male ; Microbial Sensitivity Tests ; Morbidity ; Pichia/drug effects ; Pichia/isolation & purification ; Thrombocytopenia/epidemiology ; Thrombocytopenia/microbiology ; Voriconazole/therapeutic use
Chemical Substances	Antifungal Agents ; DNA, Fungal ; Voriconazole (JFU09I87TR)
Language	English
Publishing date	2017-11-14
Publishing country	England
Document type	Journal Article
ZDB-ID	218356-0
ISSN	1473-5644 ; 0022-2615
ISSN (online)	1473-5644
ISSN	0022-2615
DOI	10.1099/jmm.0.000645
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Zs.A 634: Show issues

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Article: Presumptive diagnosis of brucella epididymoorchitis by modified cold ZN staining of testicular pus sample.

Kulkarni, R D / Chunchanur, Sneha K / Ajantha, G S / Shubhada, C / Jain, Pavitra

The Indian journal of medical research

2009 Volume 130, Issue 4, Page(s) 484–486

MeSH term(s)	Animals ; Brucella/classification ; Brucella/isolation & purification ; Brucellosis/diagnosis ; Epididymitis/diagnosis ; Epididymitis/microbiology ; Humans ; Male ; Middle Aged ; Orchitis/diagnosis ; Orchitis/microbiology ; Suppuration/microbiology ; Testis/microbiology ; Testis/pathology ; Zoonoses
Language	English
Publishing date	2009-10
Publishing country	India
Document type	Case Reports ; Letter
ZDB-ID	390883-5
ISSN	0971-5916 ; 0019-5340
ISSN	0971-5916 ; 0019-5340
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Ua VI Zs.143: Show issues

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Article ; Online: Detection and antifungal susceptibility testing of oral Candida dubliniensis from human immunodeficiency virus-infected patients.

Chunchanur, Sneha K / Nadgir, Shobha D / Halesh, L H / Patil, B S / Kausar, Yasmeen / Chandrasekhar, M R

Indian journal of pathology & microbiology

2009 Volume 52, Issue 4, Page(s) 501–504

Abstract: Context: Candida dubliniensis, an opportunistic yeast that has been implicated in oropharyngeal candidiasis (OPC) in patients infected with Human Immunodeficiency Virus (HIV) may be under-reported due to its similarity with Candida albicans. Resistance ... ...

Abstract	Context: Candida dubliniensis, an opportunistic yeast that has been implicated in oropharyngeal candidiasis (OPC) in patients infected with Human Immunodeficiency Virus (HIV) may be under-reported due to its similarity with Candida albicans. Resistance to Fluconazole is often seen in C. dubliniensis isolates from clinical specimens. Aims: To know the prevalence of C. dubliniensis in OPC in patients infected with HIV and their antifungal susceptibility pattern. Settings and design: One hundred and thirty-two HIV seropositive individuals and 50 healthy controls were included in the study. Materials and methods: Two oral swabs were collected from the site of the lesion from 132 HIV-infected patients. Oral rinse was obtained from 50 healthy controls. Samples were inoculated on Sabouraud's dextrose agar (SDA) medium and on HiCrome Candida Differential Agar (CHROM agar) medium. Isolates were speciated by standard tests. Dark green-colored, germ tube positive isolates, which failed to grow at 420C and negative for xylose assimilation were identified as C. dubliniensis. Antifungal susceptibility test was performed by Macro broth dilution technique (National Committee for Clinical Laboratory Standards guidelines). Results and conclusions: From 132 patients, 22 (16.3%) C. dubliniensis were isolated; samples from healthy controls did not reveal their presence. Antifungal susceptibility test showed higher resistance among C. dubliniensis isolates to azoles compared to C. albicans. Five (22.7%) isolates of C. dubliniensis were resistant to Fluconazole followed by four (18.2%) to Ketoconazole. This study emphasizes the importance of identification and antifungal susceptibility testing of C. dubliniensis in HIV-infected patients.
MeSH term(s)	Antifungal Agents/pharmacology ; Azoles/pharmacology ; Candida/drug effects ; Candida/isolation & purification ; Candidiasis/epidemiology ; Candidiasis/microbiology ; Drug Resistance, Fungal ; HIV Infections/complications ; Humans ; Microbial Sensitivity Tests ; Mouth/microbiology ; Prevalence
Chemical Substances	Antifungal Agents ; Azoles
Language	English
Publishing date	2009-10
Publishing country	India
Document type	Journal Article
ZDB-ID	197621-7
ISSN	0974-5130 ; 0377-4929
ISSN (online)	0974-5130
ISSN	0377-4929
DOI	10.4103/0377-4929.56138
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Zs.B 862: Show issues

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Article: Significance of isolation and drug susceptibility testing of non-Candida albicans species causing oropharyngeal candidiasis in HIV patients.

Nadagir, Shobha D / Chunchanur, Sneha K / Halesh, L H / Yasmeen, K / Chandrasekhar, M R / Patil, B S

The Southeast Asian journal of tropical medicine and public health

2008 Volume 39, Issue 3, Page(s) 492–495

Abstract: Oropharyngeal candidiasis (OPC) continues to be a common opportunistic infection in patients infected with Human Immunodeficiency Virus (HIV) and is predictive of increasing immunosuppression. Though Candida albicans remains the predominant isolate, a ... ...

Abstract	Oropharyngeal candidiasis (OPC) continues to be a common opportunistic infection in patients infected with Human Immunodeficiency Virus (HIV) and is predictive of increasing immunosuppression. Though Candida albicans remains the predominant isolate, a rise in the frequency of isolation of non-albicans Candida (NAC) species is being observed. The levels of virulence and the sensitivities to available antifungal drugs vary among these species. Of 340 HIV seropositive patients in this study, 132 (38.8%) had oral lesions suggestive of candidiasis. Samples were collected from the lesion using sterile cotton swabs. Isolation and speciation were done by standard techniques. Antifungal drug susceptibility testing was done by macro broth dilution. The total number of Candida isolates was 135, of which, 45 (33.3%) were NAC species and 90 were C.albicans (66.6%). Of the NAC species, C. dubliniensis was the predominant pathogen (22,48.9%). Antifungal susceptibility testing showed that 14 (31.1%) of the NAC species and 11 (12.2%) of C. albicans were resistant to fluconazole (MIC > 8 microg/ml). A very high MIC of > 32 microg/ml was noted among the NAC species resistant to fluconazole.
MeSH term(s)	AIDS-Related Opportunistic Infections/microbiology ; Antifungal Agents/pharmacology ; Candida/drug effects ; Candida/isolation & purification ; Candidiasis, Oral/microbiology ; Candidiasis, Oral/virology ; Drug Resistance, Fungal ; Fluconazole/pharmacology ; HIV Infections/microbiology ; Humans ; Ketoconazole/pharmacology ; Microbial Sensitivity Tests
Chemical Substances	Antifungal Agents ; Fluconazole (8VZV102JFY) ; Ketoconazole (R9400W927I)
Language	English
Publishing date	2008-05
Publishing country	Thailand
Document type	Journal Article
ZDB-ID	800646-5
ISSN	0125-1562 ; 0038-3619
ISSN	0125-1562 ; 0038-3619
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Zs.A 844: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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