243 extractive question-and-answer pairs built from Microsoft Word - ANNUAL AMR REPORT_28_9_2022.docx, published by ncdc.mohfw.gov.in. The source is a 44-page publication. Source-evidenced topics include national antimicrobial resistance surveillance network, nars-net, antimicrobial resistance, priority pathogens, staphylococcus aureus, enterococcus species, escherichia coli, klebsiella species. Every answer is a verbatim span of text the source prints, and each row carries the passage it sits in, its offset in that passage, the source quote, the page and the location in the document, so any row can be checked against the original. Question types in the export: 127 factual, 77 table, 10 definition, 10 relationship, 10 summary, 8 list, 1 comparison. 39 of the 243 pairs (16.0%) ask explanatory questions; the remaining 204 are factual or table-based questions. 97.94% of rows pass the corpus quality gate.
This dataset contains 243 question-and-answer pairs derived from the 2021 Annual Antimicrobial Resistance (AMR) Report published by the National Centre for Disease Control (NCDC) in India. The data focuses on the National Antimicrobial Resistance Surveillance Network (NARS-Net) and includes information on priority pathogens, resistance trends, and surveillance methodologies. Questions cover factual, table-based, and explanatory topics, with answers sourced directly from the report. The dataset provides insights into the prevalence and resistance patterns of pathogens like Staphylococcus aureus, Enterococcus species, Escherichia coli, and Klebsiella species.
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# One-time install: pip install desidata
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import desidata
df = desidata.load("ncdc-mohfw-gov-in-a7fb99539e1e52444e3028872f2fc443")
df.head()First 10 of 243 rows
| question | answer | context | answer_start | question_type | knowledge_quality_score | source_document | source_quote | source_page | source_location | confidence | validation_status |
|---|---|---|---|---|---|---|---|---|---|---|---|
| What guidelines are used for classifying isolates as susceptible, intermediate or resistant? | Clinical & Laboratory Standards Institute (CLSI) guidelines | The WHONET software is used for the collection and analysis of the antimicrobial susceptibility (AST) data generated by the manual testing methods and the automated systems at the programme sites. The classification of the isolates as susceptible, intermediate or resistant is based on the Clinical & Laboratory Standards Institute (CLSI) guidelines. During 2021 antimicrobial susceptibility (AST) data of 96,370 priority pathogens, along with the demographic information of the patients from whom these pathogens were isolated, was reported from 35 sites in 25 states/UTs. All sentinel sites submitted the data quarterly after validation by the AMR nodal officer at the sites. | 290 | definition | 1.000 | https://ncdc.mohfw.gov.in/uploads/pdf/amr35.pdf | The classification of the isolates as susceptible, intermediate or resistant is based on the Clinical & Laboratory Standards Institute (CLSI) guidelines. | 15 | page=15,block=3 | 0.700 | valid |
| What is the name of the programme launched by the Government of India in 2013 to combat antimicrobial resistance? | National Programme on Antimicrobial Resistance (AMR) Containment | II. National AMR Surveillance Network (NARS- Net) Antimicrobial resistance (AMR) is a growing threat to public health which needs urgent attention. Government of India has already taken a series of initiatives to combat this burgeoning problem. One such initiatives is the launch “National Programme on Antimicrobial Resistance (AMR) Containment” in 2013, during the 12th five-year plan (2012-2017). This programme is being coordinated by National Centre for Disease Control (NCDC) Delhi. One of the objectives of the programme is to generate quality AMR surveillance data in order to generate evidence of AMR in the country to guide the plan of action to contain the problem. For this a network of laboratories called the National AMR Surveillance Laboratory network (NARS-Net) has been established under the programme. | 281 | definition | 1.000 | https://ncdc.mohfw.gov.in/uploads/pdf/amr35.pdf | One such initiatives is the launch “National Programme on Antimicrobial Resistance (AMR) Containment” in 2013, during the 12th five-year plan (2012-2017). | 12 | |||
| What statistical method was used to analyze the linear trend for MRSA in blood over the last four years? | Chi-square for trend (Extended Mantel Haenszel) | Data of a total of 15,608 S. aureus isolates was submitted by the NARS-Net sites of which 14,695 isolates are from unique patients. AST analysis of 14,695 isolates indicated that the S. aureus isolation rate from blood is 32%, 26% from pus aspirate and 16% from OSBF. 59% resistance to methicillin is observed in S. aureus isolates from blood, and resistance to methicillin in isolates from aspirated pus and other sterile body fluids is found to be 49% and 48% respectively (Table 4). The linear trend Analysis for MRSA in blood over last 4 years was done using Chi-square for trend (Extended Mantel Haenszel) and it is found that there is significant decrease in the proportion of MRSA in blood from the year 2018 to 2021 (Chi-square value for Linear trend-18.9, p value - <0.0001). The last five-year MRSA trend in blood isolates is given below. | 563 | definition | 1.000 | https://ncdc.mohfw.gov.in/uploads/pdf/amr35.pdf | The linear trend Analysis for MRSA in blood over last 4 years was done using Chi-square for trend (Extended Mantel Haenszel) and it is found that there is significant decrease in the proportion of MRSA in blood from the year 2018 to 2021 (Chi-square value for Linear trend-18.9, p value - <0.0001). | ||||
| What type of isolates are submitted to NCDC for confirmation? | Antibiotic-resistant alert isolates of public health concern | The NRL at NCDC performed identification and susceptibility testing by strictly following the standard operating protocols (SoPs) and after confirmation results were informed to the sites. Antibiotic-resistant alert isolates of public health concern as specified under the programme were also submitted to NCDC, along with the duly filled form, for confirmation. | 189 | definition | 1.000 | https://ncdc.mohfw.gov.in/uploads/pdf/amr35.pdf | The NRL at NCDC performed identification and susceptibility testing by strictly following the standard operating protocols (SoPs) and after confirmation results were informed to the sites. Antibiotic-resistant alert isolates of public health concern as specified under the programme were also submitted to NCDC, along with the duly filled form, for confirmation. | 15 | page=15,block=3 | 0.700 | valid |
| What is WHONET software? | used for the collection and analysis of antimicrobial susceptibility data | Priority pathogens under surveillance currently include seven commonly isolated pathogens from identified specimens. The WHONET software is used for the collection and analysis of antimicrobial susceptibility data. This annual report covers the AMR data from 01 January 2021 to 31 December 2021. | 140 | definition | 0.980 | https://ncdc.mohfw.gov.in/uploads/pdf/amr35.pdf | The WHONET software is used for the collection and analysis of antimicrobial susceptibility data. | 10 | page=10,block=1 | 0.850 | valid |
| What does AMR surveillance under NARS-Net include? | standardised collection, analysis and compilation of AMR data from all the network sites | AMR surveillance under NARS-Net includes standardised collection, analysis and compilation of AMR data from all the network sites. The compiled data is used to generate the annual National AMR surveillance report which is shared with stakeholders at the National and state level and is also made available in the public domain (on NCDC website). For vancomycin resistant S. aureus and colistin resistant gram-negative bacteria, only the isolates for which identification and AST has been confirmed at the AMR-NLR at NCDC have been included in this data. This network data is also submitted annually to WHO’s Global AMR Surveillance System | 41 | definition | 0.980 | https://ncdc.mohfw.gov.in/uploads/pdf/amr35.pdf | AMR surveillance under NARS-Net includes standardised collection, analysis and compilation of AMR data from all the network sites. | 40 | page=40,block=1 | 0.700 | valid |
| What additional requirement is fulfilled by sites apart from submitting AMR data? | representative isolates were submitted by the sites to AMR NRL at NCDC | The data as per programme guidelines is to be submitted by the network sites within 15 days after each quarter: • Data from January 1 to March 31 of the current year sent by 15th April • Data from April 1 to June 30 of the current year sent by 15th July • Data from July 1 to September 30 of the current year sent by 15th October • Data from October 1 to December 31 of the previous year sent by 15th January The quarterly data submitted by the sites was screened and analyzed and the detailed feedback was provided to them for each quarter. In addition to AMR data, as per programme requirements, representative isolates were submitted by the sites to AMR NRL at NCDC as a part of the External Quality Assessment (EQA). | 598 | relationship | 0.970 | https://ncdc.mohfw.gov.in/uploads/pdf/amr35.pdf | In addition to AMR data, as per programme requirements, representative isolates were submitted by the sites to AMR NRL at NCDC as a part of the External Quality Assessment (EQA). | 15 | page=15,block=3 | 0.700 | |
| What factors may have contributed to the significant reduction in ESBL producing E. coli isolates? | stringent internal quality control of antibiotic discs and increase in the number of sentinel sites in NARS-Net | Similar pathogen burden in respective location types was also seen in the previous year report. A significant reduction in Methicillin-resistant S. aureus (MRSA) in blood was observed this year (59%) in comparison to the previous years since 2018. Similar to the previous years, Linezolid resistance in S. aureus was found to be 0.7%. Enterococcus spp. isolated from blood cultures showed 11% resistance to Vancomycin. The linear trend analysis for ESBL producing blood isolates of E. coli showed significant decrease in the proportion of ESBL producing E. coli isolates from the year 2018 (86%) to 2021(76%). Significant reduction may be due to stringent internal quality control of antibiotic discs and increase in the number of sentinel sites in NARS-Net. Upto 33% of E. coli and upto 50% of Klebsiella spp. isolated from blood were found to be CREs. | 646 | relationship | 0.970 | https://ncdc.mohfw.gov.in/uploads/pdf/amr35.pdf | Significant reduction may be due to stringent internal quality control of antibiotic discs and increase in the number of sentinel sites in NARS-Net. | ||||
| What happens if a patient has growth of E. coli in one blood culture and in one urinary culture? | both specimen types have been included | Before starting the de-duplication process, variables containing information about the patient was checked and variables were generated if required, e.g. patient ID number, age, sex, location, department, AST in values (mm or µg/ml) etc. For analysis, only one result was considered for each patient per specimen type and per pathogen. if two blood cultures from the same patient yielded growth of E. coli, only the first has been included in the data; if the growth of E. coli was detected in one culture and of K. pneumoniae in the other, both results have been considered. If there is the growth of E. coli in one blood culture and in one urinary culture from the same patient, both specimen types have been included. From each patient, only the first isolate of a given species recovered during the investigated time interval was included, regardless of its susceptibility profile. | 681 | relationship | 0.970 | https://ncdc.mohfw.gov.in/uploads/pdf/amr35.pdf | coli in one blood culture and in one urinary culture from the same patient, both specimen types have been included. | 16 | page=16,block=3 | ||
| What happens if two blood cultures from the same patient yield growth of E. coli? | only the first has been included in the data | Before starting the de-duplication process, variables containing information about the patient was checked and variables were generated if required, e.g. patient ID number, age, sex, location, department, AST in values (mm or µg/ml) etc. For analysis, only one result was considered for each patient per specimen type and per pathogen. if two blood cultures from the same patient yielded growth of E. coli, only the first has been included in the data; if the growth of E. coli was detected in one culture and of K. pneumoniae in the other, both results have been considered. If there is the growth of E. coli in one blood culture and in one urinary culture from the same patient, both specimen types have been included. From each patient, only the first isolate of a given species recovered during the investigated time interval was included, regardless of its susceptibility profile. | 407 | relationship | 0.970 | https://ncdc.mohfw.gov.in/uploads/pdf/amr35.pdf | coli, only the first has been included in the data; if the growth of E. | 16 | page=16,block=3 | 0.700 |
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| page=12,block=1 |
| 0.700 |
| valid |
| 22 |
| page=22,block=3 |
| 0.700 |
| valid |
| valid |
| 41 |
| page=41,block=1 |
| 0.700 |
| valid |
| 0.700 |
| valid |
| valid |