HAPPY NEW YEAR-2022

 Hope no more pandemic era in 2022 !!

Wish you all a strong immunity to fight against any variant of Covid-19 !!

Wish this new year bring more interesting scientific discoveries !!

Happy New Year 2022 to all my blog readers !!!!

My Scientific Achievements in 2021

BOOK

1. Upendra Thapa Shrestha and Megha Raj Banjara (2021). Instrumentation in Microbiology. A Theory book for B.Sc. Fourth-year Microbiology. First Edition, Garuda Publication, Newplaza, Kathmandu. (ISBN: 978-9937-0-9709-3).

ARTICLES

1. Upama Gaire, Upendra Thapa Shrestha, Sanjib Adhikari, Nabaraj Adhikari, Anup Bastola, Komal Raj Rijal, Prakash Ghimire, Megha Raj Banjara. Antibiotic susceptibility, biofilm production and detection of mecA gene among Staphylococcus aureus isolates from different clinical specimens. Diseases, 2021, 9: 80. https://doi.org/10.3390/diseases9040080
2. Meera Maharjan, Anil Kumar Sah, Susil Pyakurel, Sabita Thapa, Susan Maharjan, Nabaraj Adhikari, Komal Raj Rijal, Prakash Ghimire, Upendra Thapa Shrestha*. Molecular confirmation of vancomycin-resistant Staphylococcus aureus with vanA gene from a hospital in Kathmandu. International Journal of Microbiology, Hindawi, 2021, 2021, 3847347. https://doi.org/10.1155/2021/3847347.
3. Susmita Kuikel, Jyoti Acharya, Binod Dhungel, Sanjib Adhikari, Nabaraj Adhikari, Upendra Thapa Shrestha, Megha Raj Banjara. Komal Raj Rijal, Prakash Ghimire. Biofilm formation and phenotypic detection of ESBL, MBL, KPC and AmpC enzymes and their coexistence in Klebsiella spp. isolated at the National Reference Laboratory, Kathmandu, Nepal. Microbiology research, 2021, 12: 683-697. https://doi.org/10.3390/microbiolres12030049.
4. Tulsi Nayaju, Milan Kumar Upreti, Alina Ghimire, Basudha Shrestha, Basanta Maharjan, Rajesh Dhoj Joshi, Binod Lekhak, Upendra Thapa Shrestha*. Higher prevalence of extended spectrum b-lactamase producing uropathogenic Escherichia coli among patients with diabetes from a tertiary care hospital of Kathmandu, Nepal. American Journal of Tropical Medicine and Hygiene, 2021, 105(5): 1347-1355. doi:10.4269/ajtmh.21-0691
5. Sabita Thapa, Nabaraj Adhikari, Anil Kumar Shah, Ishworiya Lamichhane, Binod Dhungel, Upendra Thapa Shrestha, Bipin Adhikari, Megha Raj Banjara, Prakash Ghimire Komal Raj Rijal. Detection of NDM-1 and VIM genes in carbapenem-resistant Klebsiella pneumoniae isolates from a tertiary health care center in Kathmandu, Nepal. Chemotherapy, 2021 DOI: 10.1159/000518256.
6. Komal Raj Rijal, Megha Raj Banjara, Binod Dhungel, Samarpan Kafle, Kedar Gautam, Bindu Ghimire, Samriddh Dhungel, Nabaraj Adhikari, Upendra Thapa Shrestha, Dev Ram Sunuwar, Bipin Adhikari, Prakash Ghimire. Use of antimicrobials and antimicrobial resistance in Nepal: a nationwide survey. Scientific Reports (Nature), 2021, 11:11554. https://doi.org/10.1038/s41598-021-90812-4
7. Anu Maharjan, Binod Dhungel, Anup Bastola, Upendra Thapa Shrestha, Nabaraj Adhikari, Megha Raj Banjara, Binod Lekhak, Prakash Ghimire, Komal Raj Rijal. Antimicrobial Susceptibility Pattern of Salmonella spp. Isolated from Enteric Fever Patients in Nepal. Infect. Dis. Rep. 2021, 13, 388–400. https://doi.org/10.3390/idr13020037.
8. Rubina Gurung, Sanjib Adhikari, Nabaraj Adhikari, Sanjeep Sapkota, Jid Chani Rana, Binod Dhungel, Upendra Thapa Shrestha, Megha Raj Banjara, Prakash Ghimire, Komal Raj Rijal. Efficacy of urine dipstick test in diagnosing urinary tract infection and detection of blaCTX-M gene among ESBL-producing Escherichia coli. Diseases 2021, 9, 59. https://doi.org/10.3390/diseases9030059.
9. Ram Shanker Prasad Sah, Binod Dhungel, Binod Kumar Yadav, Nabaraj Adhikari, Upendra Thapa Shrestha, Binod Lekhak, Megha Raj Banjara, Bipin Adhikari, Prakash Ghimire, Komal Raj Rijal. Detection of TEM and CTX-M genes in Escherichia coli isolated from clinical specimens at Tertiary Care Heart Hospital, Kathmandu, Nepal. Diseases 2021, 9, 15. https://doi.org/10.3390/diseases9010015.
10. Manish Thapaliya, Sastrika Shakya, Upendra Thapa Shrestha, Astha Dangol, Kusum Shrestha. Bacteriological profie of raw chicken meat collected from Lalitpur and their antibiogram. J Microbiology and Immunology. 2021, 3(1):

PRESENTATION

1. E-poster presentation entitled “Emergence of multi-drug resistant bacterial infection of lower respiratory tract among people living with HIV” at the 12th European Congress on Tropical Medicine and International Health (ECTMIH 2021) held virtually from 28th September to 1st October 2021.

FULLTEXTS ARE AVAILABLE ONLINE

Information on Omicron

 Different variants of SARS-CoV-2 and Information about latest variant; Omicron

• The SIG Variant classification scheme defines four classes of SARS-CoV-2 variants:

1.      Variant Being Monitored (VBM)

• Alpha (B.1.1.7 and Q lineages)
• Beta (B.1.351 and descendent lineages)
• Gamma (P.1 and descendent lineages)
• Epsilon (B.1.427 and B.1.429)
• Eta (B.1.525)
• Iota (B.1.526)
• Kappa (B.1.617.1)
• 1.617.3
• Mu (B.1.621, B.1.621.1)
• Zeta (P.2)
1. Variant of Interest (VOI)
2. Variant of Concern (VOC)
• Delta (B.1.617.2 and AY lineages)
• Omicron (B.1.1.529)
3. Variant of High Consequence (VOHC)

 

• To date, no variants of high consequence have been identified in the United States.
• Vaccines approved and authorized for use in the United States are effective against the predominant variant circulating in the United States and effective therapeutics are available. CDC continues to monitor all variants circulating within the United States

 

OMICRON

On 26 November 2021, WHO designated the variant B.1.1.529 a variant of concern, named Omicron, on the advice of WHO’s Technical Advisory Group on Virus Evolution (TAG-VE).  This decision was based on the evidence presented to the TAG-VE that Omicron has several mutations that may have an impact on how it behaves, for example, on how easily it spreads or the severity of illness it causes. Here is a summary of what is currently known.  

 

Current knowledge about Omicron 

Researchers in South Africa and around the world are conducting studies to better understand many aspects of Omicron and will continue to share the findings of these studies as they become available.  

Transmissibility: It is not yet clear whether Omicron is more transmissible (e.g., more easily spread from person to person) compared to other variants, including Delta. The number of people testing positive has risen in areas of South Africa affected by this variant, but epidemiologic studies are underway to understand if it is because of Omicron or other factors.  

Severity of disease: It is not yet clear whether infection with Omicron causes more severe disease compared to infections with other variants, including Delta.  Preliminary data suggests that there are increasing rates of hospitalization in South Africa, but this may be due to increasing overall numbers of people becoming infected, rather than a result of a specific infection with Omicron.  There is currently no information to suggest that symptoms associated with Omicron are different from those from other variants.  Initially reported infections were among university students—younger individuals who tend to have the more mild disease—but understanding the level of severity of the Omicron variant will take days to several weeks.  All variants of COVID-19, including the Delta variant that is dominant worldwide, can cause severe disease or death, in particular for the most vulnerable people, and thus prevention is always key. 

Effectiveness of prior SARS-CoV-2 infection 

Preliminary evidence suggests there may be an increased risk of reinfection with Omicron (i.e., people who have previously had COVID-19 could become reinfected more easily with Omicron), as compared to other variants of concern, but the information is limited. More information on this will become available in the coming days and weeks. 

Effectiveness of vaccines: WHO is working with technical partners to understand the potential impact of this variant on our existing countermeasures, including vaccines. Vaccines remain critical to reducing severe disease and death, including against the dominant circulating variant, Delta. Current vaccines remain effective against severe disease and death.   

Effectiveness of current tests: The widely used PCR tests continue to detect infection, including infection with Omicron, as we have seen with other variants as well. Studies are ongoing to determine whether there is any impact on other types of tests, including rapid antigen detection tests.  

Effectiveness of current treatments:   Corticosteroids and IL6 Receptor Blockers will still be effective for managing patients with severe COVID-19. Other treatments will be assessed to see if they are still as effective given the changes to parts of the virus in the Omicron variant.  

 Studies underway 

At the present time, WHO is coordinating with a large number of researchers around the world to better understand Omicron. Studies currently underway or underway shortly include assessments of transmissibility, the severity of infection (including symptoms), the performance of vaccines and diagnostic tests, and the effectiveness of treatments.    

WHO encourages countries to contribute to the collection and sharing of hospitalized patient data through the WHO COVID-19 Clinical Data Platform to rapidly describe clinical characteristics and patient outcomes.  

More information will emerge in the coming days and weeks. WHO’s TAG-VE will continue to monitor and evaluate the data as it becomes available and assess how mutations in Omicron alter the behaviour of the virus.  

Recommended actions for countries 

As Omicron has been designated a Variant of Concern, there are several actions WHO recommends countries to undertake, including enhancing surveillance and sequencing of cases;  sharing genome sequences on publicly available databases, such as GISAID; reporting initial cases or clusters to WHO; performing field investigations and laboratory assessments to better understand if Omicron has different transmission or disease characteristics, or impacts effectiveness of vaccines, therapeutics, diagnostics or public health and social measures.  More detail in the announcement from 26 November.  

Countries should continue to implement the effective public health measures to reduce COVID-19 circulation overall, using a risk analysis and science-based approach. They should increase some public health and medical capacities to manage an increase in cases.  WHO is providing countries with support and guidance for both readiness and response.  

In addition, it is vitally important that inequities in access to COVID-19 vaccines are urgently addressed to ensure that vulnerable groups everywhere, including health workers and older persons, receive their first and second doses, alongside equitable access to treatment and diagnostics.  

Recommended actions for people 

The most effective steps individuals can take to reduce the spread of the COVID-19 virus is to keep a physical distance of at least 1 metre from others; wear a well-fitting mask; open windows to improve ventilation; avoid poorly ventilated or crowded spaces; keep hands clean; cough or sneeze into a bent elbow o

r tissue; and get vaccinated when it’s their turn.  

WHO will continue to provide updates as more information becomes available, including following meetings of the TAG-VE. In addition, information will be available on WHO’s digital and social media platforms. 

Reference material:  

• Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern 
• Further information on TAG-VE 

 

Source: The information was directly obtained from WHO official website (https://www.who.int/news/item/28-11-2021-update-on-omicron) to spread the information to more and more people.

Molecular Confirmation of Vancomycin-Resistant Staphylococcus aureus with vanA Gene from a Hospital in Kathmandu

 Hindawi

International Journal of Microbiology

Volume 2021, Article ID 3847347, 8 pages https://doi.org/10.1155/2021/3847347

 

Molecular Confirmation of Vancomycin-Resistant Staphylococcus aureus with vanA Gene from a Hospital in Kathmandu

Meera Maharjan¹, Anil Kumar Sah², Susil Pyakurel³, Sabita Thapa¹, Susan Maharjan¹,

Nabaraj Adhikari⁴, Komal Raj Rijal⁴, Prakash Ghimire⁴ and Upendra Thapa Shrestha⁴

 

¹Department of Microbiology, Kantipur College of Medical Science, Sitapaila, Kathmandu, Nepal

²Department of Microbiology, Annapurna Neurological Institute and Allied Sciences, Maitighar, Kathmandu, Nepal

³Department of Microbiology, Shi-Gan International College of Science and Technology, Kathmandu, Nepal

⁴Central Department of Microbiology, Tribhuvan University, Kirtipur, Nepal

 

Correspondence should be addressed to Upendra Thapa Shrestha; upendrats@gmail.com

 

ABSTRACT

Staphylococcus aureus, a commensal on the skin and in the nasal cavity of humans, is one of the most serious cases of nosocomial infections. Moreover, methicillin-resistant S. aureus (MRSA) is a leading cause of morbidity and mortality worldwide. For the treatment of MRSA infections, vancomycin is considered as a drug of choice. However, the emergence of vancomycin resistance among MRSA isolates has been perceived as a formidable threat in therapeutic management. To estimate the rate of vancomycin-resistant S. aureus (VRSA) and to detect the vancomycin-resistant genes, namely, vanA and vanB, among the isolates, a hospital-based cross-sectional study was conducted from July to December 2018 in Annapurna Neurological Institute and Allied Science, Kathmandu, Nepal. S. aureus was isolated and identified from different clinical samples and processed for antibiotic susceptibility testing by the modified Kirby–Bauer disc diffusion method. The screening of MRSA was performed as per Clinical and Laboratory Standard Institute (CLSI) guidelines. VRSA was confirmed by the minimum inhibitory concentration (MIC) method by employing E-test strips. All the phenotypically confirmed VRSA were further processed to detect the vanA and vanB gene by using the conventional polymerase chain reaction (PCR) method. A total of 74 (20.3%) S. aureus were isolated, and the highest percentage of S. aureus was from the wound samples (36.5%). Of 74 S. aureus isolates, the highest number (89.2%) was resistant to penicillin, and on the other hand, linezolid was found to be an effective drug. Likewise, 45 (60.81%) were found to be MRSA, five (11.11%) were VRSA, and 93.2% of S. aureus isolates showed an MAR index greater than 0.2. Two VRSA isolates (40%) were positive for the vanA gene. The higher prevalence of MRSA and significant rate of VRSA in this study recommend routine surveillance for the MRSA and VRSA in hospital settings before empirical therapy.

 FULLTEXT: Download

Instrumentation in Microbiology

Our newly published book for B.Sc. Microbiology Fourth-year course on Instrumentation in Microbiology MB407 of Tribhuvan University from Garuda Publication Pvt. Ltd. The whole course is divided into 8 units with illustrated figures and annexes. In addition, a collection of TU board exam questions have been included. I hope this book will be very useful for the B.Sc students and also master level students of Microbiology, TU.

This book is available at

1. Anu book (Bhotahity)

2. Bajra Barahi Book (Bhotahity)

You can also buy a soft copy of this book (Contact at upendarts@gmail.com).

Article published in The American Journal of Tropical Medicine and Hygiene

 Am. J. Trop. Med. Hyg., 105(5), 2021, pp. 1347–1355

doi:10.4269/ajtmh.21-0691

Copyright © 2021 by The American Society of Tropical Medicine and Hygiene

 

Higher Prevalence of Extended Spectrum b-Lactamase Producing Uropathogenic Escherichia coli Among Patients with Diabetes from a Tertiary Care Hospital of Kathmandu, Nepal

 

Tulsi Nayaju^1†, Milan Kumar Upreti^1†, Alina Ghimire¹, Basudha Shrestha², Basanta Maharjan², Rajesh Dhoj Joshi², Binod Lekhak³, and Upendra Thapa Shrestha^3*

 

¹Department of Microbiology, GoldenGate International College, Kathmandu, Nepal; 

²Kathmandu Model Hospital, Kathmandu, Nepal;

³Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal

 

^*Address correspondence to Upendra Thapa Shrestha, Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Bagmati 44600, Nepal. E-mail:  upendra.thapashrestha@cdmi.tu.edu.np

 

^†These authors contributed equally to this work.

 

ABSTRACT

 

This study aimed to determine the occurrence of antibiotic resistance genes for b-lactamases; bla_TEM and bla_CTX-M in uropathogenic Escherichia coli isolate from urinary tract infection (UTI) suspected diabetic and nondiabetic patients. A hospital-based cross-sectional study was conducted in Kathmandu Model Hospital, Kathmandu, in association with the Department of Microbiology, GoldenGate International College, Kathmandu, Nepal, from June to December 2018. A total of 1,267 nonduplicate midstream urine specimens were obtained and processed immediately for isolation of uropathogens. The isolates were subjected to antibiotic susceptibility testing and extended-spectrum b-lactamase (ESBL) confirmation. In addition, bla_TEM and bla_CTX-M genes were detected using specific primers. The overall prevalence of UTI was 17.2% (218/1,267), of which patients with diabetes were significantly more infected; 32.3% (31/96) as compared with nonpatients with diabetes, 15.9% (187/1,171). A total of 221 bacterial isolates were obtained from 218 culture-positive specimens in which E. coli was the most predominant; 67.9% (150/221). Forty-four percent (66/150) of the total E. coli was multidrug-resistant and 37.3% (56/150) were ESBL producers. Among 56 isolates, 92.3% (12/13) were from patients with diabetes, and 83.0% (44/53) were from nondiabetics. Furthermore, 84.9% of the screened ESBL producers were confirmed to possess either single or both of bla_TEM and bla_CTX-M genes. The bla_TEM and bla_CTX-M genes were detected in 53.6% and 87.5% of the phenotypically ESBL confirmed E. coli, respectively. Higher rates of ESBL producing uropathogenic E. coli are associated among patients with diabetes causing an alarming situation for disease management. However, second-line drugs with broad antimicrobial properties are still found to be effective drugs for multidrug-resistant strains.

Fulltext: Download

Article published in Diseases, MDPI

 

MDPI

Diseases 2021, 9, 80. https://doi.org/10.3390/diseases9040080

 

Antibiotic Susceptibility, Biofilm Production, and Detection of mecA Gene among Staphylococcus aureus Isolates from Different Clinical Specimens

Upama Gaire¹, Upendra Thapa Shrestha¹, Sanjib Adhikari¹, Nabaraj Adhikari¹, Anup Bastola², Komal Raj Rijal^1,*, Prakash Ghimire¹ and Megha Raj Banjara^1,*

¹Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu 44600, Nepal

²Sukraraj Tropical and Infectious Diseases Hospital, Teku, Kathmandu 44600, Nepal; docanup11@gmail.com

 

* Correspondence: komal.rijal@cdmi.tu.edu.np (K.R.R.); megha.banjara@cdmi.tu.edu.np (M.R.B.)

 

ABSTRACT

 The increasing incidence of methicillin-resistant and biofilm-forming S. aureus isolates in hospital settings is a gruesome concern today. The main objectives of this study were to determine the burden of S. aureus in clinical samples, assess their antibiotic susceptibility pattern and detect biofilm formation and mecA gene in them. A total of 1968 different clinical specimens were processed to isolate S. aureus following standard microbiological procedures. Antibiotic susceptibility test of the isolates was performed by Kirby–Bauer disc-diffusion method following CLSI guidelines. Biofilm was detected through tissue culture plate method. Methicillin-resistant S. aureus (MRSA) isolates were screened using cefoxitin (30 μg) discs and mecA gene was amplified by conventional polymerase chain reaction (PCR). Of 177 bacterial growth, the prevalence of S. aureus was 15.3% (n= 27). MRSA were 55.6% (15/27) and 44% (12/27) exhibited multidrug resistance (MDR). There was no significant association between methicillin resistance and MDR (p > 0.05). Both MRSA and MSSA were least sensitive to penicillin (100%, 75%) followed by erythromycin (86.6%, 66.6%). Most of the MRSA (93.4%) were susceptible to tetracycline. All S. aureus isolates were biofilm producers—19 (70%) were weak and only one (4%) was a strong biofilm producer. The strong biofilm-producing MSSA was resistant to most of the antibiotics except cefoxitin and clindamycin. None of the MSSA possessed mecA gene while 8 (53.3%) MRSA had it. More than half of S. aureus isolated were MRSA. High incidence of multidrug resistance along with capacity to form biofilm among clinical isolates of S. aureus is a matter of apprehension and prompt adoption of biosafety measures is suggested to curb their dissemination in the hospital environments.

 

Keywords: S. aureus; antibiotic susceptibility; MRSA; mecA gene; biofilm

 

Citation: Gaire, U.; Shrestha, U.T.; Adhikari, S.; Adhikari, N.; Bastola, A.; Rijal, K.R.; Ghimire, P.; Banjara, M.R. Antibiotic Susceptibility, Biofilm Production and Detection of mecA Gene among Staphylococcus aureus Isolates from Different Clinical Specimens. Diseases 2021, 9, 80. https://doi.org/10.3390/diseases9040080

 

Academic Editor: St Patrick Reid

Received: 9 October 2021

Accepted: 29 October 2021

Published: 1 November 2021

 

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

FULLTEXT: Download

Poster Presentation at 12th ECTMIH (Sept 28-Oct 1, 2021, Norway)